Miltoncontact

A Leaf print method, Plant Stomata Catalogue and the Plant Stomata Encyclopedia

2025-02-01T12:12:00.003+00:00

Leaf print of a garden fern showing a single stoma (stomata)

A brief note on some useful links for anyone interested in looking at or researching plant epidermis and in particular Stomata.

Stomata are the special pores on the leaves of plants, through which water and gas exchange occurs. They can be visualised by making prints of the leaf surface on a microscope slide and viewing under a microscope.

Recently Brown and Ratford developed a method using UV Crystal Resin, as used by jewellery crafters,

which is very simple and effective. I have written my experience and guidance with practical methods in the Quekett Bulletin ISSN 1350-9128, October 2024 edition (appeared January 2025), pp 11-15. The paper is freely accessible to all from the Internet Archive here:

Chris Thomas Leaf Epidermis and stomata prints method using UV Crystal Resin Quekett Bulletin 87 Sept 24.

I have also begun an open source catalogue of plant stomata images, to which anyone can contribute, on Wikimedia Commons here:

Category:Leaf epidermis and stomata prints

Paul Adanick brough a very useful site to my attention which aims to bring all references/literature relating plant stomata together, managed by Professor Willem Van Cotthem. You can find the site here:

Plant Stomata Encyclopedia

I hope that this information is of use to you if you are interested in microscopy as an amateur, professional, school or research institution, and want to give looking at stomata a go!

The Woodcut initials of Matthew Parker's Bishops Bible 1572

2024-11-29T12:47:00.005+00:00

Why is there an image of the God Poseidon illustrating the letter T in a copy of a 16th century bible!? I can only assume that the printer, Richard Jugge, based in the prining centre of London at St Pauls Graveyard, wanted an eye catching woodcut intial at the start of a chapter. It obviously had not caused any offence to the Archbishop Matthew Parker, who commissioned the 1568 first edition of this bible and ensured this 1572 edition was also printed.

I became interested in this Bible , when it was (re)discovered in the collection of the Norris Museum, St Ives, Cambridgeshire, where I am a volunteer. I've spent several years collecting and collating data which I hope to continue to report on, as well as giving talks on the dangerous nature of Bibles, olitics and Art in the tumultuous years of the Tudors and the reformation.

The 1572, second edition of the Bishops Bible has 1311 woodcut initials throughout its 1442 pages. What is surprising is the variety of different types for each represented letter of the alphabet. The most frequently used initials are A, 14 types – 433 occurrences, I, 15 types – 133 occurrences, T 15 types – 276 occurrences.

All the letters, bar three, are Roman initials, in contrast to the black letter font of most of the bible text. The three exceptions are where the initial forms part of a design incorporating a coat of arms, one large O and two different large T, listed as loosely historiated in figure 1.

The remaining woodcut initials comprise an almost equal balance of 57 floriated (having a floral pattern) and 58 inhabited designs (where there are animal or mythical or human figures included). Including the three coat of arms designs, there are 16 historiated initials, showing recognisable scenes from mythology, including the controversial G with Leda and the swan, and two that are a variation of Eve and the serpent.

I have prepared and uploaded a full catalogue of the 132 woodcut initials from the 1572 Bishops Bible, which can be found in the Internet Archive at https://archive.org/details/bishops-bible-capitals-sized-ordered-b/page/6/mode/2up or by searching there for "The 132 Woodcut initials of the Bishops Bible 1572".

More articles on the subject will follow.

Empirical sedimentation times for pollen

2024-03-21T00:03:00.027+00:00

Summary

When preparing pollen preparations from plants for microscopy, it is often useful to concentrate collected pollen, by centrifugation or by allowing it to settle into a pellet (sedimentation) when centrifugation is not an option.

The following empirical experiments were conducted to find a more rational basis for sedimentation times when centrifugation is not possible that I had evolved when preparing pollen for microscopy.

My conclusions from the data shown below are:

For pollen suspended in water or alcohol (iso-propanol), allow 1 minute of sedimentation for every 1 mm liquid height of the pollen suspension.
If there is still a turbid supernatant from the first sedimentation of fresh pollen from flowers after the alloted sedimentation time, this can be discarded. If in doubt, collect the supernatant and leave to stand overnight, then check any sediment from the supernatant for presence of pollen.
Pollen suspended in a 20% dilution of honey in water sediments at least 6 times more slowly. convection movements can have an effect in larger vessels. Therefore allow to sediment in a location at constant temperature overnight. Higher dilutions of honey than 1in 5 will speed up sedimentation.

Method

Preparation of pollen

Flower pollen was collected from ripe anthers of Lily, Magnolia and Alstroemeria by rinsing in a 30 ml sample tube filled with iso-propanol. The pollens were allowed to settle overnight and most of the supernatant removed. The lily pollen was resuspended and allowed to settle several times in isopropanol till the supernatant was only faintly coloured. The abundant pellet was then resuspended in 10 ml ispropanol. The supernatants over the magnolia and alstroemeria pollen pellets pipetted off and the pellets resuspended in 1 ml iso-propanol.

Honey pollen was collected from 50 g spring honey dissolved with 200 ml tap water. The pollen was allowed to sediment out overnight in a jar. Most of the supernatant was carefully siphoned off, leaving about 25 ml liquid. The sediment at the base of the jar was resuspended the remaining liquid and was trasferred to a 30 ml sample tube and allowed to settle overnight. Most of the supernatant above the pellet was carefully removed and the pellet resuspended in 1 ml iso-propanol.

1 ml of each of the flower pollens and the honey sediment was transferred to separate 1.5 ml eppendorf (centrifugation) tubes and centrifuged for 30 s at 7000 RPM (maximum relative centrifugal force 2680 x g) in a microfuge. The supernatant was carefully pipetted off and the pellets resuspended in 1 ml deionised water. The tubes were again centrifuged at 7000 rpm for 30 seconds, the supernatants pipetted off, and the pellets resuspended in 1 ml fresh deionised water.

Microscopy of samples

Approximately 50 µl to 100 µl of each pollen suspension was applied to the centre of a microscope slide, on a hot plate at hand hot, and spread to a disk of approximately 15 mm diameter and allowed to dry. A drop of molten pollen glycerine jelly with dilute basic fuchsin dye (Brunel glycerine pollen jelly) was added to the centre of each dried disk and a coverslip carefully lowered onto the drop. The slides were left for 15 mintes on the hot plate to allow the glycerine jelly to spread under the slip and hydrate and stain the pollen.

Samples were then viewed under the microscope, first with a 10 x objective NA 0.17 and then with a 40 x objective, NA 0.65, to check that pollen was present and, in the case of honey, that several different pollen species were present.

Pollen grains were photographed under the 40 x objective using a chinese 5 MPx inspection camera with eyepiece adapter and Toupview software on the PC. 20 µm scale bars were included.

Images with the 40 x objective were taken as a sequence of 30 to 50 steps, focussing from the top of a grain to the equator of the grain. The images were then used to create a photostack using the freeware Picolay.

Pollen sedimentation from suspension in 1 ml water

To record sedimentation of pollen from suspensions in water, in 1.5 ml eppendorf tubes, the remaining pollen preparations in water were made up to 1 ml in their tubes. Each tube was shaken thoroughly and then suspended in a jar, with a black card as background, and a lamp shining from one side, and a video recoding started immediately using a smartphone on a stand.

Recording was stopped after 20 minutes and the procedure repeated with the next sample.

The four separate videos were combined using Corel VideoStudio plus.

Pollen sedimentation from suspension in 1 ml 20% honey in water solution

The supernatants were pipetted off the pollen pellets that had sedimented in water in the previous experiment. The pellets were resuspended 1 ml of a 20% honey in water solution (5 g honey mixed with 20 ml deionised water). The suspension was then photographed at time 0 and at 10 minute intervals for up to an hour.

Pollen sedimentation from the top of a 25 ml water or diluted honey column

Three separate experiments were set up, where a lilly pollen suspension was applied on top of either a water or a diluted 1:5 honey water mix, to see how the lily pollen behaved passing through a liquid column:

The pellet from a hydrated lily pollen was mixed with 1 ml vegetable oil and then layered on top of 25 ml of deionised water in a 30 ml tube.
1 ml of lily pollen in water was slightly warmed and gently pipetted on top of a cooled column of 25 ml deionised water in a 30 ml tube.
1 ml of lily pollen in water was layered on top of 25 ml of 1:5 honey - water mix.

Each column was then videod over time, 20 minutes for 1 and 2, 1 hour for 3. The three videos were combined for comparison into one video.

Pollen sedimentation from alcohol check

For some pollens or samples rinsed in alcohol, there is still visible turbid material throughout the supernatant after an hour's settling. Examples include pollen collected from wind-borne material, some honeys, some pollens collected from flowers). To determine whether this is pollen or pollen rich, the following procedure was used.

Nine pendulous catkins from Silver Birch were rinsed in approximately 25 ml iso-propanol. Any large particulate material was removed with a seeker. The resultant cloudy solution was allowed to stand for 1 hour. The still turbid supernatant was carefully pipetted off to within 1 ml of the pellet. The pellet was transferred to a 1.5 ml tube. The supernatant was centrifuged in 1.5 ml tubes at 7000 rpm for 1 minute, the now clear supernatants removed, and the remaining pellets resuspended and combined in 1 ml isopropanol in one tube.

The tubes with 1 ml of the original resuspended pellet, and the 1 ml resuspended pellet obtained from centrifuging the supernatant, were centrifuged again at 7000 rpm for 1 minute. The clear supernatants were pipeeted off and discarded and the pellets resuspended in 1 ml deionised water and again centrifuged at 700 x g for 1 minute. The clear supernatants were pipetted off and discarded and the remaining pellets resuspended in 400 µl deionised water.

100 µl of each resuspended pellet was spread in a 12 mm disk on the centre of a microscope slide on a hot plate (hand hot) and allowed to dry and then mounted in glycerine pollen jelly and used for microscopy as described above.

Results

Pollen samples used

Four different pollen samples used for main experiments: Lily, Magnolia, Altroemeria and Spring Honey. Photostacks. 40 x objective. Scale bars 20 µm.

Microscopy of the original pollen samples used in these experiments showed a wide varety of shapes, sizes and surface structure. The samples from flowers were uniform in type, from large (Lily and Altroemeria, 100 µm long axis) to medium (Magnolia, 40 µm long axis). The honey pollen was predominantly rape (round, 4 sutures and pores, 20 µm diameter) with a scatter of larger and different pollen species. pollen textures varied from netted (Lily) to spiky (daisy type).

Sedimentation in 1 ml water

The video recording shows that all the pollens had completely sedimented out of the suspension in water after 20 minutes. Some pollen grains adhered to the side of the tubes. The height of the water 1 ml water column was 25 mm.

Sedimentation in 1 ml 20% honey in water

Sedimentation observed at 20 minute intervals up to an hour using pollen suspended in 1.5 ml 20% honey in water as the solution.

Both with the lily pollen and pollen from spring honey, a substantial pellet had formed by 1 hour. With the lily suspension, there was still unsedimented material visible, suggesting that a longer time was required for complete settling into a pellet.

Sedimentation though a column of 25 ml water or 20% honey in water

Where pollen had been layered in oil on top of water, there was a slow release of pollen grains, which sedimented at a fairly constant rate through the water column. However, some particles travelled 10 mm in 10 to 30 seconds, whilst the slower ones migrated at 10 mm in up to 90 seconds. The total water column height was 75 mm, which the fastest particles could cover in under 2 minutes, whereas the slowest ones required more than 11 minutes, beyond recording time.

Where the attempt had been made to layer pollen in warm water on top of a cold water column, there was an uneven flow with an initial bulk of pollen dragging water with it as it descended. The column was practically clear of pollen by 10 minutes recording.

Pollen layered on top of 20% honey solution also flowed down unevenly into the honey solution. whilst a substantial amount of pollen has pelleted after two and a half minutes, vortices set up in the solution still kept pollen grains in suspension, often flowing back up through the column.

Contents of pellets and turbid supernatants from Silver Birch pollen in alcohol.

Top left, pollen clearly visible in the pellet from the alcohol sedimentation (10x objective, 100 µm scale bar). Top right, the material centrifuged down from the turbid alcohol supernatant. This comprises plant and other non-pollen debris (10x objective, 100 µm scale bar). The bottom image shows the distinctive stained Silver Birch pollen from the pellet in detail, using a 40 x objective (20 µm scale bar).

After one hour settling in isopropanol, all the Silver Birch pollen was in the pellet. The turbid material in the supernatant did not contain any of the pollen. Both the pollen pellet and supernatant contained other debris.

Conclusions & discussion

Pollen grains vary in their size, shape, density and surface structure. This makes it difficult to calculate their theoretical sedimentation rate in water or other solutions. If you have access to a centrifuge, the g forces that can be generated easily pellet biological particles. Practical experience with a variety of pollens collected over the past year has demonstrated that 30 seconds in a microcentrifuge giving about 700 x g in a 1.5 ml microcentrifuge tube is sufficient not only to pellet pollen but any other debris in a pollen suspension, giving a clear supernatant.

However, I've obserrved that if I leave pollen suspensions in water or alcohol to stand for any length of time in 1.5 ml tubes, sedimentation into a pellet becomes visible within minutes. Simillarly, when purifying pollen from honey, I and others have found that leaving a larger volume (100s of ml) of a 20% solution of honey overnight will give a good pollen sediment for microscopy.

If you don't have a centrifuge, simply allowing pollen to settle out will work.

The experiments illustrated here show that allowing a 1 ml suspension of pollen, in water or alcohol in a 1.5 ml microcentrifuge tube, to stand for 20 minutes is more than sufficient to pellet pollen from a variety of sources. With a liquid column height of 25 mm in the 1.5 ml tube, a good approximation is to allow 1 minute per 1 mm water or alcohol height.

Sedimentation from pollen in 20% honey in water is at least 3 times slower in 1.5 ml tubes. Whilst most pollen may have sedimented after 1 hour in the 20% honey, leaving for at least several hours would be best. presumably this could be shortened with pollen in more dilute honey solutions.

The attempts to determine a sedimentation rate through water or 20% honey were only partially successful.

Where the pollen grains emerged gradually from oil over a 75 mm column of water, the results were most reliable. The lily pollen grains, with a hydrated length of 100 µm along the longest axis were visible as small specks, which seemed to travel fairly uniformly downwards. However particle speeds varied from 0.1 mm per second to 1 mm per second. The higher speeds tended to be brighter specks, which might suggest aggregates of several grains. With the other two tries, pollen in water suspension applied either to the top of a water column, or 20% honey column, the density due to high pollen concentration led to non laminar flow and turbulence. Still, practically all the pollen had sedimented in water after 10 minutes, whilst in 20% honey, it took an hour and there were still visible particles in suspension.

Trying to determine whether all pollen has sedimented from a 25 ml suspension of pollen from flowers in alcohol or water can be complicated by a turbid supernatant. The trial of sedimenting a suspention of Silver Birch pollen in alcohol showed that after standing for 1 hour, the pellet constained the pollen (and other debris from or attached to the wind blown catkins), with no significant amount of pollen in the supernatant, which contained undefined debris.

From these experiments, the following are recommended:

For pollen suspended in water or alcohol (iso-propanol), allow 1 minute of sedimentation for every 1 mm liquid height of the pollen suspension.
If there is still a turbid supernatant from the first sedimentation of fresh pollen from flowers after the alloted sedimentation time, this can be discarded. If in doubt, collect the supernatant and leave to stand overnight, then check any sediment from the supernatant for presence of pollen.
Pollen suspended in a 20% dilution of honey in water sediments at least 6 times more slowly. convection movements can have an effect in larger vessels. Therefore allow to sediment in a location at constant temperature overnight. Higher dilutions of honey than 1in 5 will speed up sedimentation.

Hayfever - Airborne allergens under the microscope

2023-07-02T22:10:00.002+01:00

A day of sneezing and irritated eyes again, now that it has rained in Milton. Here is what I found in the air and put under the microscope - masses of pollen grains, fungal spores and even starch grains! The sample is from a comparable day last week, when I rinsed a roughly 30cm x 30cm (1 square foot) piece of fine netting that had been on the washing line for 18 hours!

The various types are shown with numbered examples on the following figures, using the labelling:

Pollen grains from flowering plants stained red and can vary a lot in shape and size
Pollen grains from grass - are stained red, plain ovals with a single pore, and can vary in size
Fungal spores - generally brown, beige or grey, ranging from lage paddle shapes to small ovals
Fragments of fungal hyphae - look like broken brown twigs
Starch grains - variable sizes, transparent, circular to oval with a hint of a central marking

From the first picture above you can get an idea of the abundance of pollen and fungal spores in 1/600 of the collected material. The spiky pink pollen comes from a plant in the daisy family.

For us hayfever sufferers, our problem is compounded by the fact that all these very small particles stick quite readily to our hair, faces and clothes. Our symptoms can be triggered if even if just a few become loose when we move indoors or go to bed, hence the advice to wash hair and change outer clothes frequently if you do suffer badly from hayfever. Thank heavens that many of our cars have pollen filters!

I calculated that overall my total sample from a small piece of netting contains about

7,200 pollen grains
42,000 fungal spores
600 starch grains

Hayfever is when our own immune system becomes sensitive to airborne dust, pollen, spores, hair, for example, treating them as a threat and trying to protect us. Unfortunately, our eyes and noses are the areas most likely to be exposed and react. What's more, each one of us develops our own typical allerge to one or more of the many different particles in the air.

I can manage with taking hayfever tablets daily during the main hayfever season, and eyedrops when it is particularly bad on the eyes. I only need to avoid going out on particularly bad days. Many others suffer much more seriously and find their lives dramatically impaired. In those cases it is worth seeing if your doctor or health system offer both a service to identify your specific allergens and a possible corresponding desensitisation program. two useful lins in the UK are:

NHS Hayfever page https://www.nhs.uk/conditions/hay-fever/
AllergyUK https://www.allergyuk.org/types-of-allergies/hayfever/
A page from the US NIH on desensitisation https://www.ncbi.nlm.nih.gov/books/NBK279487/

There is also another side to being able to capture and identify pollens and spores - in forensics, when trying to match a person or vehicle to a crime location. Here, the fact that pollen and spores are so pernicious and will be very specific to locations helps, as illustrated in a fantastc book by Patricial Wiltshire 'Traces' - https://www.amazon.co.uk/Traces-forensic-scientist-criminal-investigator/dp/1788700635/ref=tmm_pap_swatch_0?_encoding=UTF8&qid=1688324266&sr=8-1

Airborne particles. I hadn't really realised how abundant they are! My sympathy if you are a hayfever sufferer.

For your interest, below are some more images from the airborne pollen sample.

The caplet shaped pollens are from the same family as Cow Parsley.

The largest pollen grain (1) is similar to Hazel pollen. The grass pollen (2, bottom) has a visible single pore.

The large pollen grain (1) is very characteristic for pines, the two black circles within it are trapped air bubbles. The starch grain (5) is on the large side. Starch in airborne dust most likely comes from decayed plants and very small grains can come from some pollens. The fungal fragments (4) would also have come from dried decaying plants and soil.

Reviving UK-DE trade - Some notes on a March 2023 Trade mission

2023-03-22T19:53:00.006+00:00

Tower Bridge London at night

Executive Summary

Six German companies specialising in innovative building transformations, modernisations and restoration attended 2 days of talks and bilateral information exchanges in London on 20-21 March before continuing with site visits in the following days. Key messages from both UK and DE side were 1. Shared interests in working and collaboration between companies in the sector. 2. The difficulties in finding skilled craftspersons and apprentices. 3. Cross-border hurdles impacting on collaborations and the need to find suitable solutions to ameliorate them. 4. Deep frustration at the lack of political action in the UK

The trade mission was a German BMWK Ministry (https://www.bmwk.de/Navigation/EN/Home/home.html) event organised and enabled by Europartnerships (https://www.europartnerships.co.uk/). It was held at both the German Embassy, London and the Institute of Practitioners in Advertising (IPA), both at Belgrave Square.

Day 1. Talks in a secure environment

Hearing that I was the sole person allowed to bring in a laptop for the day's event at the German Embassy, with special dispensation from the Chancellor, I was only mildly disappointed to find out that it was not the German Chancellor, but the almost equally eminent embassy's Chancellor. I am unable for obvious reasons to reveal the other stringent security restrictions and precautions we had to undergo before we could reach our meeting room, but we were in the hands of the extremely professional and courteous and friendly staff throughout.

We were warmly greeted and had a good outline of the current situation re post Brexit trade and UK politics by the Deputy head of Economics Mariko Higuchi (https://uk.diplo.de/uk-en/01/embassy). The directors of the six german companies were then provided with advice on a wide variety of relevant topics. These ranged from basic cultural differences, via the new tax issues arising through crossborder trade, to the impact of visas, BIM and onsite Health and Safety on doing business in the UK. Key message to emerge, life is simpler if you have partners in both countries.

Compliments to the speakers, Marc Lehnfeld (Director GTAI www.gtai.com), Sven Riemann (Marketing AHK www.ahk-london.co.uk) - a long standing and witty contributor at past events, Martin Werhahn (Tax Services AHK www.ahk-london.co.uk), and Robert Hunt (associate Konduit Ltd www.konduit.uk), who proved himself to be one of the rare breed of 0.5% of british in the UK who could definitely speak German.

Though retired, my role for Europartnerships over the years has been to come in as meeting's chair for the two days, to ensure the fair timing of talks takes us agreeably through to breaks and mealtimes, without bias and on time.

Six different personalilities, skills and businesses

We (the delegates) made our way to the Motel One, Tower Hill, afterwards to meet up at 4:30 to go through the six comapny presentations in a relaxed manner. This is a crucial and really helpful stage for me. It gives me a chance to get to know not only their businesses and objectives, but the different personalities, something cemented in The Dean Swift pub, close to Tower Bridge later that evening. It helps with supporting them on the following day.

I'll try to give some single line summaries of the six different companies and their services:

Felix Graf of Felix Graf GmbH: A family business with a a strong link with its community and employees, that has grown to specialise in the interior fittings for the hotel and catering industry. www.felixgraf.de
Lars Krauss of Greengineers: Consultants and specialist planning services to provide tailored sustainable solutions that meet their client's needs. www.greengineers.de/english
Jörn Brennscheidt of Hokon. Making impossible stairways possible! www.hokon.de
Thomas Schubert of Ingeneurbüro für Kirchenbau, Glocken und Denkmalpflege. Rebuilding and recovering churches, community buildings and creating welcoming communal places. www.ibkirchenbau.de/about-us
Christian Schulte of Mühlenhof Restaurierungen GmbH. Sympathetic and authentic restaurations of historic windows, doors, floors, panelling and furniture in collaboration with architects and art historians. www.muehlenhof-restaurierungen.de/en
Peter Spor of Tischlerei Spor GmbH & Co KG. A traditional joinery and carpentry company whose expertise include dry wall construction and the repair and build of solid wooden floors. www.tischlerei-spor.de/english/fields-of-activity

Most of the companies already have international experience and are english speakers, with several having completed projects in the UK prior to Brexit.

Day 2. Presentations and key issues.

Day 2 was held at the Institue of Practitioners in Advertising (IPA https://ipa.co.uk/), almost opposite to the German Embassy, on the other side of Belgrave Square, a long standing and friendly venue for Europartnerships.

Over 70 UK architects and other companies in the construction and restoration sector had expressed an interest and a substantial number filled the larger conference room upstairs at the IPA. This time it was the turn of Markus Knauf (Head of the Economics Department at the German Embassy https://uk.diplo.de/uk-en/01/embassy) and Mark Dodsworth, director of Europartnerships (https://www.europartnerships.co.uk/) to welcome the guests, as well as thanking Petra Riemenschneider and team at Europartnerships for their herculean efforts in organising the event.

For once, technology was on our side as the first of the mornings talks, by Marie-Theres Sobik of Thyssen (www.thyssenkrupp-materials.co.uk) on "The vocational training system in Germany" was given remotely using Teams. A training system that had a century of experience behind it, contrasting with the mixed and changing approaches in the UK. Circumstances had prevented Marie-Theres from being able to attend and her physical presence was sorely missed by me and the Europartnerships team. Like Sven mentioned above, she had been a stalwart and bright, constructive presence at many previous events in the past. Afterwards, Michael Schienke of Vorbild Architecture (https://vorbild.co.uk/) and Sven Riemann (AHK www.ahk-london.co.uk) reversed yesterday's role and enlightened the british audience on cultural differences across the channel, revealing that in Germany too, there was a diversity of regional prides, traditions and ways of doing things.

Our six german companies then had their turn in the spotlight. Gradually, the audience came alive with shared experiences and questions not only to the companies, but also about how to overcome some of the hurdles presented since Brexit. After all, the UK had fallen out of the list of top 10 trading partners with Germany. Here, the presentations given to us at the embassy proved invaluable; problems with taxation through the transfer of goods several times back and forth across the UK-EU borders could be overcome to some degree with professional assistance and sometimes even at a final null cost calculation. Building partnerships with one member in the EU and the other in the UK was a good route to take, each familiar with their own ideosyncratic bureaucracies, regulations and regional issues and helping solve the border transitions of goods and services.

What I understood was, that the greatest regret was the loss of access to the Erasmus program, with some UK delegates speaking of the way it had helped their careers. In turn, the German companies had young staff who would leap at the chance to gain experience in the UK. A representative from one of the UK bodies in the industry implored the German Embassy to seek more routes to collaboration in the training of up and coming craftspeople in the construction and in the restoration sectors. Apparently there were promising comments from the government - but at present little action.

We ended the day with a buffet lunch and many individual discussions between attendees and the german company representatives, followed by the longer one-to-ones from pre-arranged appointments.

My personal feeling at the end of the day was, that there were opportunities and an interest in longer term collaboration between the two countries in innovative building transformations, modernisation and restoration, despite the hurdles raised by Brexit.

From the german companies' point of view, it was an insight into the opportunities that might exist, possible partners to contact when back home, as well as a better knowledge of the potential barriers. Ultimately, it would be their judgement whether it would be worth their time and investment in trying to enter the UK market.

Creamed Honey crystal microscopy using LOCA - Method

2023-03-19T00:11:00.066+00:00

Crystals of creamed honey (sourece Honigmanufaktur Meerbusch). 40x objective, industrial microscope camera, transmitted light, crossed polarisation filters and quarter wave plate.

I returned from a family vsit to Germany with a small jar of creamed honey, made by Honigmanufaktur Meerbusch (www.honigmanufaktur-meerbusch.de). Coming to the bottom of the jar, of this very smooth, cream like honey, I looked for the best way to visualise and measure the honey crystals. Through experimentation, a simple method for producing a thin layer of honey crystals and mounting in LOCA was developed. Samples were best observed between crossed polarisation filters with a quarter wave plate.

Method

I tried several methods to get a thin layer of the sugar crystals.

Taking a small drop on a slide, covering with a cover slip and pressing hard. Not very successful,
Small drop of honey on a slide mixed with some oil then pressed with a cover slip. Partially successful, giving areas with some thinner layers. see figures 1 & 2
Small drop of honey mixed with isopropanol - too viscous too smear.
Making a thin streak of honey across the width of a slide and trying to spread it as you would a blood smear, pulling a thin film behind another angled slide. Honey too viscous to be spread.
Making a thin streak and using an angled other slide to smear it thinly. Unsuccessful - the smear was of a viscous thin layer solution wihout many crystals until the place where the dragging slide was pulled off, There a slip of thick crystals remained.
The final approach was a modification of method 5. Making a thin streak and using an angled other slide to smear it thinly at first and then reducing the pressure over a 2 cm stretch of the slide. SUCCESS! there was an area of the smear that was thick enough to leave crystals yet thin enough to have them at almost a single layer. A drop of LOCA was placed on the thin area, a cover slip added and pressed. The slide was set by exposure to a hand held UV torch for 60 seconds and then cleaned according to the method published by Gordon Brown, 2020, creating a permanent slide.

Slides were photographed using a Reichert Zetopan microscope witha 40x objective and a Chinese 5 megapixel objective camera and the software ToupView. Lighting techniques used were standard brightfield, use of crossed polarisation filters without and then with a quarter wave filter. A series of images at different focus through the sample were taken and combined in a focus stack using Picolay.

Results

Method 2. The sample of honey mixed with sunflower oil had areas that were thin enough to see defined crystals. There were planar, needle and fragmentary types. However the sample was still fairly thick.

Figure 1. Creamed honey crystals. Method 2. Mixed with sunflower oil, 40x objective, between crossed polarisation filters. Field of view 250 µm.

Figure 2. Creamed honey crystals. Method 2. Mixed with sunflower oil, 40x objective, between crossed polarisation filters plus quarter wave plate. Field of view 250 µm.

Method 6. Sample spread as a smear of increasing thickness on slide and mounted in LOCA. More parts of the slide could be found where the layer of crystals was thin enough to resolve individual crystals.

The crystals in this cream honey are extrememly thin and show little contrast in transmitted light (figure 3). Greater contrast of the crystals against background is achieved using polarisation. Their thinness is also reflected in the fact that they appear in pale colourless shades between crossed polars (figure 4). The planar like crystals have 120 degree angles reflecting molecular sugar. There are also small needle like crystals.

Whilst the contrast is less with the inclusion of a half wave plate (figure 5), it does reveal crystals missed under just crossed polars. making this the preferred method for photography.

The images reveal that most of the crystals are smaller than 20 µm in diameter. The result is consistent with the cream like nature of this honey.

Figure 3. Method 6, sample spread and mounted in LOCA. 40 x objective. Normal transmitted light.

Figure 4. Creamed honey crystals. Method 6, sample spread and mounted in LOCA. 40 x objective, between crossed polarisation filters.

Figure 5. Creamed honey crystals. Method 6, sample spread and mounted in LOCA. 40 x objective, between crossed polarisation filters plus quarter wave plate.

Discussion

Honey is liquid in the beehive, where it is kept at about 35 degrees C by the bees themselves. When stored at home after purchasing, honey will begin to crystallise from the bottom of the jar upwards if the room temperture is cooler than 35 degrees C. The rate of crystallisation is dependent on the fructose/glucose ratio; more fructose, the slower crystalisation occurs.

Particle size has an impact of the mouth feel of foods. Larger grains feel coarse and the food 'grainy', whilst particles smaller than 20 µm impart a creamy texture in chocolate, for example.

Honey with coarse crystals can be liquified again by warming if desired.

On the other hand, a smooth, cream honey can be deliberately created. Liquid honey is seeded with 10% of its volume of existing cream honey or large honey crystals that have been blended into sufficiently small particles. The added crystals are stirred into the liquid honey and the mixture left to stand for a week or more by which time the honey becomes saturated with small crystals and is turned into a cream honey.

Useful references and links

Important temperatures for beekeeping: https://sheffieldbeekeepers.org.uk/important-temperatures-beekeeping/
Fact sheet on honey crystalisation: https://www.qsi-q3.com/fact-sheet-crystallization/
Paper on factors affecting honey crystallisation https://www.researchgate.net/profile/Reshma-Krishnan-3/publication/351418323_Honey_crystallization_Mechanism_evaluation_and_application/links/6099889c299bf1ad8d90881f/Honey-crystallization-Mechanism-evaluation-and-application.pdf
Creamed honey Wikipedia https://en.wikipedia.org/wiki/Creamed_honey
Creamed honey -theory and Dyce method https://www.bobsbeekeeping.com.au/image/bee-resources/Creamed-Honey.pdf
Particle size and grittiness mouth- feel https://www.jstage.jst.go.jp/article/jhej1987/46/12/46_12_1151/_pdf
Using LOCA for making permanent slides. Gordon Brown, 2020, 'Living the Vida LOCA', Quekett Bulletin No. 78, pp 18-23. PDF reprints available on request from Gordon Brown, contact detail accessible here https://www.quekett.org/about/contact/gordon-brown

Feathers under the microscope

2023-03-13T17:13:00.011+00:00

The unexpected finding for me personally, on identifying feathers under the microscope, was that it was the downy feathers or down parts of feathers that can be key to identification.

A fellow microscopist and I in Milton had missed being able to attend an Iceni meeting in Norfolk a couple of weekends ago on the topic of feathers. So later in the day, we got together to have a go ourselves. In addition to some feathers we had, we were able to borrow some from my neighbours here in Hall End.

Selection of feathers

That doesn't mean that the flight feathers are uninteresting. A closer look at the rigid part of the pheasant feather reveals the hooking mechanism on the barbules. These are the fine filaments that create the interlocking between the regular rows of barbs radiating from the main feather stem.

Pheasant feather at 40x, 100x and 400x magnification, showing hooks and notches on barbules

Downy barbs can not only be found on (surprise surprise) down, but also on the bases of other feathers on a bird. Looked at closely, the barbs have fine filamentous barbules with distinctive nodes that can be seen at higher magnification. Below are some of the examples that we discovered.

Pheasant down at 40x, 100x and 400x magnification

Macaw down at 40x, 100x and 400x magnification

Goldfinch down at 40x, 100x and 400x magnification

Possible swan down at 40x, 100x and 400x magnification

Unknown down, possily pigeon at 40x, 100x and 400x magnification

Just to add a bit of colour, I had a go at making a stitched image of a peacock's feather, using the software Image View (which is very like Toupe View). Normally I would take separate pictures and use Hugin to stitch them together. Image View allows you to do the stitching automatically by moving the sample in rows or columns. The second attampt sort of worked, as shown below.

Eye of a peacock feather scanned with Imave View at about 40 magnification, equivalent to about 8 images stitched together.

All in all, it was a very enjoyable exercise and occupied a Sunday afternoon plus a bit extra for picture editing.

Useful identification guides for feathers under the microscope:

Microscopy of Feathers: Carla J. Dove & Sandra L. Koch, 2011. A Practical Guide for Forensic Feather Identification. THE MICROSCOPE • Vol 59:2, pp 51-71.

PDF from https://www.researchgate.net/publication/289232335_Microscopy_of_feathers_A_practical_guide_for_forensic_feather_identification

Tim G. Brom, 1986. Microscopic identification of feathers and feather fragments of Palearctic birds. Bijdragen tot de Dierkunde, 56 (2): 181-204

PDF from https://brill.com/view/journals/btd/56/2/article-p181_1.xml?language=en

A better gluten free bread loaf crumb using aquafaba foam

2022-07-18T20:29:00.002+01:00

Wheat free/gluten free bread loaf with a better crumb using aquafaba foam

Once an ardent bread baker, you can imagine my disappointment, nay, despair at having to bake wheat free bread. Crumbly, developing a grainy texture if left for any period of time. I therefore made it my objective to find a better solution. The solution first and my recipe second.

Solution: My elements for palatable gluten free bread are:

Creating a stiff peaked aquafaba foam and folding it into the bread dough.
Slicing and freezing a freshly baked loaf once it has cooled to room temperature. Take however many slices you need out of the freezer and heat them before using and eating.

Recipe for gluten free bread using aquafaba foam

Adapted from recipe on Doves Farm Freee White bread flour recipe.

Ingredients

Ingredients clockwise from top: Yeast in water with some sugar, olive oil, all other dry ingredients plus most of sugar, lemon juice, aquafaba

300g Doves Farm Freee White Bread Flour blend: rice, tapioca, potato, thickener: xanthan gum
75g Buckwheat flour
75g Chickpea aqua faba at room temperature (you can use egg white from 2 eggs)
5ml lemon juice
27ml Olive oil
36g Sugar
6g Dried east: yeast, emulsifier sorbitan monostearate, vitamin C
6g Salt
0.75 tsp/1.5g Psyllium husk
250ml Water

Method

Mix a teaspoon of sugar, water and yeast and leave at least 5 mins to activate at no more than 33 degC
In new large bowl, add lemon juice to aqua faba and using hand mixer, mix until stiff peaks achieved

Aquafaba and lemon juice mixed to stiff peaks

Add flours, salt and Psyllium husk to a bowl
Add remaining bulk of sugar, yeast and water and mix
Add oil to flour mix and mix

Right: Dry ingredients mixed with oil and yeast in water

Add the aquafaba stiff foam to flour mix and fold under with a large spoon until completely even

Aquafaba foam added to mixed dough

Aquafaba foam folded evenly into dough with spoon

Preheat oven to 200 degC
Line a 2lb loaf tin with non stick paper
Pour and spoon the thick-batter like mix into the tin

Pour and spoon the thick batter mix into the lined bread tin

Cover gently and leave to rise till doubled in size

bread mix in tin at start of rise.

Mix covered with a sheet of paper

bread dough doubled in size

OPTIONAL: gently spray surface with milk
Bake at 200 degC till internal temperature over 90 degC, about 45 minutes

Check internal temperature over 90 degrees C

Remove from tin and allow to cool before slicing and freezing any bread not used immediately.

Loaf cooling on wire rack

A bit of science

Why whip the aquafaba?

We know that with normal wheat bread, it is the gluten that provides the structure that hold the bubbles created as the yeast ferments any natural sugars in the dough. The gluten forms long chains of gluten molecules.

Aquafaba (or egg white) contain proteins that can also be usedd to create a bubble structure by whipping them.

During whipping, the natural structure of these proteins is broken open (denatured) and the protein molecules form chains that can coat air bubbles.

Room temperature and a bit of acidity from lemon juice or tatrate make the proteins easier to denature and foam during whipping.

Folding the foam into the dough mimics the effect of the gluten in wheat bread sufficiantly to hold the dough and the bubbles created during yeast fermentation.

Why check if the internal temperature is 90 degC or above after baking?

The bread dough contains a significant amount of water and during baking, only the crust loses sufficient water to be dry enough to brown. The interior of the loaf will only heat up to the boiling point of water at 100 degC unless you bake it to a charred crisp.

If the dough reaches a temperature of 90 degC or above, all the starch grains that make flour gritty will have been dissolved into the dough, making it smooth and all the proteins will have been completely denatured, fixing the bubbles in the bread permanently.

Whilst you can check if the bread has baked by tapping it to see if it sounds hollow, I simply prefer the certaintly of knowing absolutely that the bread has been baked all the way through.

As the bread cools to room temperature, the dissolved starch will also create a jelly, just like a thick gravy that has been allowed to cool and set. The bread is easier to slice and ready to eat.

Why freeze gluten free bread and reheat slices to eat?

If you leave your gluten free bread out over time, it can acquire that irritating gritty texture. As the bread stands, water begins to migrate towards the crust and small starch crystals begin to form (see https://onlinelibrary.wiley.com/doi/abs/10.1002/star.200400330). Many gluten free recipes have a higher water content than the equivalent gluten wheat based ones to combat this.

By slicing and freezing the bread you slow down this crystallisation dramatically.

By heating the slices, you then melt any gritty crystals that are present and recreate a better bread texture.

Blog Reset - from Business to Personal

2022-07-18T17:22:00.001+01:00

I finally closed Milton Contact Ltd in March, leaving just a legacy website www.miltoncontact.com.

I have retired and this blog will reflect my personal interest and activities, which range from microscopy to museum volunteering to getting to grips with gluten free cooking!

GB-DE Rail sectors on track in London this week

2021-11-26T17:04:00.001+00:00

Trains ready at Kings Cross (2020)

This time, a trip to London was quite an adventure, in this Covid era! I was off to Belgrave Square to spend two days chairing an event between a delegation of German companies in the rail sector, with a combined annual turnover of over a billion pounds, and GB representatives of key organisations, companies, and government departments.

The event had been planned and implemented by Europartnerships, on behalf of the BMWi, the German Federal Ministry for Economic Affairs and Energy and the ministry's program "Mittelstand Global", which supports exporting German SMEs.

Day one, Hendrik, Stefan, Johann, Stuart, Robert, Yannik and Thomas, representing the seven participation companies (see links at bottom of article), were the audience to a range of presentations. Although their companies already had global business presences, including the GB, Covid and Brexit meant that it was important to get up to speed with the current situation vis a vis GB-DE trade.

Some of the points that struck me personally follow.

Topics covered were:

The excellent support available by their own BMWi through export development initiatives and portal IXPOS. One of the reasons for the success of German businesses abroad is the integrated assistance provided to SMEs, from theri local regions upwards to the federal level.
Different distrubution channels and important cultural factors (how to understand us Brits), presented by the German Chamber of Commerce in the United Kingdom - AHK. (Do accept the invitation to go to the pub after meetings!). Perhaps the most worrying part of the presentation is that our (UK) importance for the German market (the 4th largest gloal economy), in terms of imports has rapidly declined down from 5th to 11th place and still sinking.
The UKs decline in trade with Germany was also repeated in figures shown by the GTAI (Germany Trade and Invest) and was coupled with uncertainty about the GB reorientation post brexit. That said, the UK was still the 5th largest economy, expected to have strong growth in the coming years, and therefore a major partner to seek out.
The Department for Transport gave us an update on Rail in the UK, showing that in terms of passenger miles, the UK was outperforming our neighbours - and that this was coupled with an exemplary safety record, including only 10 fatalities on the whole network in 2020-21. HS2 and the planned investment in the eastern parts of the North were in progress and a major organisatory change, in the formation of Great British Railways, was imminent.
The Department for International Trade gave a very positive presentation on the opportunities and support for companies based in the UK. This was complemented by a useful list of project opportunities and places to look out for forthcoming contracts, as well as contacts for our German delegates to get in touch with at the DIT.
With the UK being the birthplace of the rail sector, it is no surprise that one of the key membership organisations, the RIA (Rail Industry Association) has a 145 year history, a substantive membership of relevant companies in the sector, of which more than 60% are SMEs. As influencers of policy and public affairs, they also provide a comprehensive program of events and support, as well as encouraging innovation and providing trade missions overseas themselves.
I suppose we all anticipated an opportunity for a nap during the presentation on Tax law peculiarities in the UK, by the speaker from Blick Rothenberg. Instead, the consequences of Brexit had us gripped by their impact on the import and export of goods across the new border with Great Britain. Theoretically The EU–UK Trade and Cooperation Agreement (TCA) allows for more than 99% of trade between us to go on without tariffs, if the goods are made more than 70% in the EU. Unfortunately, the sticking point for complex items is that the supplier has to do considerable checks to assess the percentage of non-EU items in multi component items or complex equipment and confirm it is below the 30% level to comply. More fundamentally, all your accompanying paperwork has to be in order, otherwise your goods get stuck in the Customs quagmire. Audience tip: if importing goods from EU to UK, get your UK recipient to sort out the paperwork and carriage. I was already aware of the risk of double taxation, by both the sender and recipient country from another as goods transferred across borders. This was another detailed presentation and emphasised the importance of getting the right advice to avoid pitfalls in trade.
The talk by Entreprenör covered the assistance in setting up a copany in the UK (much simpler than in Germany but with public transparancy re accounts and personell information held at Companies House. One of the new hazards to look out for was that an audit may be required based on the size of the worldwide group.
Day 1 ended with a very informative talk on Transport for London (TFL) and Cross Rail, which shone a light on the recovery after the initial covid Epidemic.

Millstone phallus comes to Godmanchester Museum

2021-08-01T12:39:00.004+01:00

Godmanchester Millstone with Phallus held by Curator Kate Hadley (courtesy of Godmanchester Museum)

I left the preparations for the reinstated annual Hall End BBQ for a quick dash up the A14 for a very important date. Godmanchester Museum was celebrating its re-opening with a major event, the display of the new exhibit, part of a Roman millstone emblazoned with a phallus (Saturday 31st July 2021). This is a very rare item indeed - only four are known of amongst the tens of thousands of Roman millstone fragments found to date in Britain.

My small involvement with this stone began with a phone call taken by my wife Jane, from the Godmanchester Museum's curator Kate Hadley, who wanted the stone photographed.

"Kate called, saying that she was holding a p....s you might be interested in!" was the message. How could I resist! Kate and I spent an afternoon in June trying to get the best lighting and positioning of the stone to reveal its true magnificence.

By the time I arrived, a crowd had already gathered for the Godmanchester Museum opening and David Stokes, Chairman of the museum, began the proceedings at 2:30 pm.

David Stokes, Chairman of the Godmanchester Museum, opening proceedings

Interested crowd at the opening of the Godmanchester Museum

He was followed by Claire Hardy, Director of the Norris Museum, who had generously brought along their rare example of another Roman millstone fragment with a phallus, from the Norris collection, (partner to another fragment held at the Norris showing engraved curves).

Claire Hardy, Director of the Norris Museum, and their phallus millstone

Godmanchester Mayor Councillor Clifford Thomas and Philip Saunders, Chairman of the Huntingdonshire Local History Society

The Godmanchester millstone fragment had been found in a posthole at Offord Hill house, during the excavations prior to the new A14 build. Archaeologist Ruth Shaffrey, realised its significance when when was conducting a routine catalogueing of the finds. She had been researching Roman millstones and was a specialist in ancient worked stone. It was thanks to Quentin Carrol, Historic Environment Assistant Director and Archaeologist, Cambridgeshire County Council, that the remarkable millstone was made available to its nearest hometown museum.

Ruth Shaffrey, Archaeological Worked Stone Specialist, with the Godmanchester millstone phallus (courtesy of Godmanchester Museum)

It was great to hear from Ruth about the origins and possible significance of the millstone. This is what I recall from her talk.

During Roman times, millstones were made using stone excavated from the Millstone grit from the Peak District/Yorkshire. The Godmanchester and Norris millstones were of a medium size and probably animal driven, whilst larger ones could be water powered.

In a typical Roman bakery, the counter would be in the central part of the room, the millstone at one end of the room and the ovens at the other. Customers would therefore have quite likely seen the magnificent carved stones displayed in action.

The millstone had obviously broken at some time and was later used as a quernstone for hand grinding of grain in its own right. It was also used as a sharpening tool for blades. It finally ended up in a filled-in post hole, where it was finally discovered in the A14 dig.

Millstones with carvings upon them are rare and would most likely have been commissioned by a wealthy baker or merchant. Whilst the use of a phallus might seem unusual to the modern eye, it was a familiar emblem in Roman times and used both in domestic and other settings, including as jewellery and even being worn by children (https://imperiumromanum.pl/en/curiosities/phallus-symbol-in-roman-and-greek-world/). It is thought that it was a lucky symbol as well as the usual possible links to fertility that we would associate it with.

Much like anvils, millstones were themselves seen as important objects, imbued with symbolism, as they were closely linked to grain, harvests and the production of food. To have an object like a millstone, that is already highly symbolic, and then to have it engraved with another important symbol was therefore unusual, hence their rarity.

Ruth also revealed that our region was regarded as one of the granaries of Britain and that more millstones and fragments had been discovered here than in the rest of the UK.

After a walk around the exhibition afterwards and purchase of one of the magnificent postcards of the millstone, I left Ruth to enjoy her specially made Roman vegetarian meal. It had been prepared by local Godmanchester Roman cookery expert, Sosia Juncina. It was back to Milton for our own annual BBQ and street party!

Lewis Woolnough - a life under the microscope (Obituary)

2021-05-26T16:47:00.001+01:00

Memories by Chris Thomas. 06 May 2021

I always knew it was Lewis, as soon as I heard his “Hello Chris” on the phone. A quiet yet warm voice that shone with light of his positive yet reserved nature.

Of course I had met and occasionally chatted to him at meetings of the Quekett Microscopical Club, but it was really when he approached me about re-issuing his book ‘Understanding and Using the Stereomicroscope’ that I came to know him better.

Lewis was above all an open, positive but self deprecating person. Yet in his quiet way, it soon became apparent that appeared ever so slightly unhappy with the way an old first version of his book had been produced and presented. For those of us who got to know Lewis well, this was so uncharacteristic of his usual unflappable outlook, that the small hints of dissatisfaction spoke volumes about his feelings on the matter. I might therefore have had some initial reservations on embarking on the project of producing the book in a way that he wanted.

Such fears were soon dispelled as I found that here was someone with a deep shared interest in helping and instructing others. What really struck a chord with me was his constructive and cooperative approach to transferring his knowledge to an audience starting out in microscopy. No didactic lecturing, here was a friend who would take you through right from the beginning to proficiency in using the stereomicroscope.

I really enjoyed debating certain points with him, as he or I would try to persuade the other to our viewpoint, each of us microscopy experts in our own right. There was a steely core of certainty about what his objectives were underlying that calm smiling exterior, combined with a flexibility of mind that allowed compromise where it would ultimately benefit the book. We worked well as a team and I looked forward to his company, despite our different personalities.

We were able to combine his text and quirky black and white illustrations with many colour photos, include colour coded sections for easy reference and even introduce stereoscopic images. The result was the new first edition, published in 2010 by the Quekett Microscopical Club – which was recognised as a useful handbook, not only for novices but also those already familiar with stereomicroscopy. It is now out of print.

Milton Contact Ltd published the second edition of his book with added material in 2018.

The second edition of Understanding and Using the Stereomicroscope

Digital printing also allowed smaller print runs, in the hundreds rather than thousands. When a batch was close to running out, we simply ordered another small print run to tide him over. There are several retailers still selling the book, Brunel Microscopes and Northern Bee Books being examples. The Quekett also purchased copies use at special events and for the Arkwright Scholarship course on microscopy that it runs annually. Individuals also ordered copies directly from Lewis, with many copies going abroad.

Such was the feeling of success from the relationship that I was inspired to write and publish ‘Understanding and using the light microscope’ with Lewis’ assistance, input and co-authorship. We had great fun hiring a photographic studio for an afternoon, roping in my student daughter for age and gender balance. We produced nine instructional videos accompanying the book. Lewis was such an excellent teacher that we basically agreed a topic for each video, an outline of the content and then just let the camera roll as all three of us turned these into real life lessons on using the light microscope. We did have to do several takes on certain parts sometimes but it went remarkably smoothly, with great fun had all round.

Other fond memories I have are of meeting Lewis and Janet in their home, having a lunch or a tea in the kitchen overlooking their large garden. Lewis and I would then ensconce ourselves in the study to pore over microscopes, samples and generally talk of things microscopical. At the end of the day, Lewis would always safely wave me out onto the road from his drive as a large hedge on the right obscured the view and I feared for my safety.

Whilst I could always find my way to Lewis, I invariably had trouble finding the route to the nearby Village Hall in Bradfield St George, where Lewis was involved in the organisation of the annual East of England Microscopy meeting in Autumn. I must have found at least three different routes to get there and exit over the years, seemingly finally coming to the venue almost by chance!

Lewis was also the turn to person when it came to meeting the relatives of other microscopists and helping them find good homes for their microscopes, slides and occasional hazardous stains and solvents!

Lewis was also there with constructive advice and support when I contemplated and finally joined the new Quekett Committee.

From our occasional conversations this year, I learnt almost as an aside of Lewis’ illness, and hearing of his hospitalisation and passing away, I felt the loss of a decade’s long companion and like minded person in microscopy, as well as the an author.

But Lewis is still there within me, the shared memories, laughter, debates and interests. I’m pleased that I can tread in his footsteps by taking on the first part of the Quekett’s Arkwright Scholarship course, aiming to continue his aim of making microscopy education fun, interesting and interactive.

The searchable Cambridge Open Studios 2019 guide

2021-03-01T16:54:00.002+00:00

A searchable version of the Cambridge Open Studios guide for 2019 is now available to view as an eBook on the internet archive, or to search directly on this page in the window below. (For a full leafable version, click on the link below the book)

COVID-19 deaths per 100,000 population increase with freedom and level of democracy by February 2021

2021-02-08T01:24:00.003+00:00

SUMMARY

There appears to be a trend towards a greater number of deaths from COVID-19 per 100,000 population with increasing freedom and level of democracy. The results below were obtained by plotting COVID-19 deaths per 100,000 population against four different categories of freedom and democracy for 171 countries, where possible.

The COVID-19 data used was published by Johns Hopkin University of Medicine at https://coronavirus.jhu.edu/data/mortality on the 5th February 2021.

Four indices of freedom or democracy for the same countries were obtained from the Wikipedia ‘ List of freedom indices’ available at https://en.wikipedia.org/wiki/List_of_freedom_indices. They covered data gathered from 2018 to 2020 and were:

Freedom in the World
Index of Economic Freedom
Press Freedom Index
Democracy Index

RESULTS

All four indices appeared to show a positive correlation between COVID-19 deaths per 100,000 population and increasing freedom or democracy. Some of the differences appear to be significant.

The data is skewed and not normally distributed. Data can also cover quite a range from low to high values of COVID-19 deaths per 100,000 population for each freedom or democracy category within in each chart

THE CHARTS

The charts below show both a distribution of each countries value for a given freedom or democracy index as blue dots, and the data described in the form of boxplots.

Figure 1. Deaths per 100K population for countries identified as free, Partly free and Not free.

Figure 2. Deaths per 100K population for countries identified with Economic freedom, categories Free, Mostly free, Moderately free, Moderately unfree and Repressed.

Figure 3. Deaths per 100K population for countries identified with press Freedom categories Good, Satisfactory. Some problems, Difficult and Very serious.

Figure 4. Deaths per 100K population for countries identified withcategories of Democracy: Full deomocracy, Flawed democracy, Hybrid regime and Authoritarian regime.

THE TABLES

The data for the box plots is summarised in the charts below. The red boxes in the tables of percentage differences between any two sets of data within an analysis suggest the data is significant.

Table 1. Data used for figure 1 on Freedom in the World

Table 2. Data used for figure 2 on Economic freedmom

Table 3. Data used for figure 3 on Press Freedom

Table 4. Data used for figure 4 on Democracy index

The full spreadsheets with all the raw data and calculation are available from the author on request.

CONCLUSIONS

I simply visualise the correlation between increase in COVID-19 deaths per 100,000 population with increases in freedom and democracy. It requires a more detailed analysis of the way different countries experienced and tackled their epidemics, to identify which factors might be responsible for these trends.

Areas to consider could include:

Acceptable balance of increase risk of deaths per 100,000 population against temporary maintenance or loss of freedoms
Ability to take action in the face of a growing epidemic.
Impact of differing political and economic viewpoints on speed of decision making process.
Local factors that impact on public willingness to accept decisions relating to the epidemic.

Chris Thomas, 08 February 2021

Ann Hales-Tooke, née Petre 1926 - 2020: My inspiration to become a publisher

2020-11-16T18:28:00.005+00:00

There are some special people in your life who change your future direction in a totally unexpected way. Ann Hales-Tooke, née Petre, was the person who set me onto the path to publishing back in 2005.

Her son Hugh called me to let me know that she had passed away peacefully in her sleep on the 6th November 2020.

Before I go into my personal story, here is an insight to her life.

Ann Petre was born in 1926 at Langley Hall Farm, Norfolk, coming from a family that included aviation pioneers and WWI heroes, and lived through some of the most tumultuous decades of the 20th Century. An independently minded and active person, she followed a varied path in life, rich in experiences.

Ann gained an Oxford degree in Modern Greats in 1947, took on various administrative jobs and work in an agricultural firm near Cambridge, leading to her marriage and to her raising three sons there. Interest in early child development and freelance writing led to her involvement with the movement to liberalise the care of children in hospital. She wrote two books on the subject and became a Governor of the United Cambridge Hospitals in 1970. In 1977, after gaining a P.G.C.E. (Postgraduate Certificate in Education), she worked in primary and special schools specialising in the teaching of sign language. For this she was awarded a Research Associateship in 1984, at the Institute of Education. She trained as a psychodynamic counsellor with the Cambridgeshire Consultancy in Counselling. She gained BACP (British Association for Counselling and Psychotherapy) accreditation and taught counselling for a number of years for the university.

Ann also exhibited as an accomplished artist at the Tavistock Foundation and with the Cambridge Open Studios for the fourteen years.

Le Trepied Dolmen

All this was unbeknown to me when she first approached me as a fellow member of Cambridge Open Studios in 2005.

Ann had recently travelled to many Bronze Age sites to make paintings of ancient sacred places. She asked for my help in photographing the paintings so that she could make cards for her art sales at Cambridge Open Studios and the important Christmas market.

It was while we were meeting to go over the images in readiness to have them printed that Ann uttered a question that was to change the direction of my work.

"Chris, I've been writing my memoirs since my 50s. I'd like to get them published next year in time for my 80th Birthday. Can you help?"

Not knowing much about publishing but good at research, I went away to find out how she could achieve her ambition.

I returned with the news that she would probably have to find a book agent who would then target the main publishing houses. The likelihood of success was small as she would be competing against thousands of others, of which only a very small number would be successful.

However, since desktop self publishing was now possible, and she was comfortable using Word, I suggested she could produce and publish the book herself.

"I can't do this on my own - could you help me?" was Ann's fateful reply.

A networking colleague, Julie Buck, put me in touch with an Irish publisher, based in Spain, who helped authors self publish. David Cronin of Moyhill Publishing was happy to help, letting us do the layout of the book and cover and dealing with the book registration, publishing and finding a suitable printer.

Completing the final version of the illustrated manuscript and the cover was an exciting period for both Ann and me. The printed books came a bit later than Ann's birthday, arriving in July 2006, but we were both happy with the end result that was "Journey into Solitude".

It was at this point that Ann also revealed her experience of promoting herself - presumably gained from Cambridge Open Studios. She planned a big book launch and signing session and began busily corresponding with friends and family to ensure a full house. As her book included an element of her journey in faith, its loss and then regaining faith, Ann also successfully place her book in the SPCK bookshop in Cambridge. As I would tell future authors, "producing the book is the easy part, selling you have to work at".

I was proud to be at the bustling launch party that went well, including food and readings by Ann.

Journey into Solitude was simply an interesting project for me at the time. That is, until it prompted others to come and ask for my publishing services. Gaining confidence, and with David Cronin's good will, I took on the full role of publisher for local authors. Now that I'm semi retired, it is my main activity with over 50 books published. All because of Ann's fateful question "I can't do this on my own - could you help me?"

The success of "Journey into Solitude" inspired Ann to venture into historical fiction.

At the time, she lived in Priory Road, close to the ruins of the Cellarer's Chequer, part of the Barnwell Priory which was dissolved by King Henry VIII in 1539.

Ann made the priory the focus of a story of a murder at Stourbridge Fair in 1534, the suicide of the Manager of a Homeless project hounded in 1990, the loss of a new-born baby and the painful end of Margaret Clifton, local visionary and artist. The story lines touched on the question, "does the Evil that men do live after them, but the Good redeem itself in many ways?"

Ann's son, Hugh Hales-Tooke, reprised his role as cover photographer. His beautiful photo, taken with infrared film had graced 'Journey into Solitude'. For 'The Lost Priory', 83 year old Ann was game to be photographed by Hugh as the ghostly figure outside the Cellarer's Chequer.

Barnwell Priory was closely associated with the ancient Stourbridge Fair, outside Cambridge. Ann invited us (my wife Jane and I) to attend a revival event outside the Leper's Chapel, as she had a stand there.

It was another example of her sense of fun and willingness to go out and meet people to share her art and, of course, her books.

Our final collaboration came at the end of 2016, when Ann tackled the history of the Petre family prior to and during the first World War, in her book "The Family That Flew".

1914 was a key year for Ann's family, the Tor Bryan Petres. There were seven offspring. Four sons fighting - three sons flying and the fourth, an aviation pioneer, already dead. The book vividly protrays the tragedy and sacrifice, fortitude and hopefulness in the face of loss, through photographs, letters and memories.

The story begins in the Victorian era with the family influenced by the deep spirituality of Ann's grandmother, Elise Sibeth. It portrays the excitement of aviation in the Edwardian years and something of the sadness and horrors of WWI.

The seven siblings, Ann's aunts and uncles, mirrored their times. The eldest, Mary, the family ‘carer’, was imprisoned by Edwardian mores. They all shared a passion for flight that led to the untimely deaths of Edward and Jack. Henry went on to found the Royal Australian Air Force. Sybil, the youngest, enjoyed more freedom as an ambulance driver and considerable artist.

The book was also the story of Tor Bryan, Ingatestone, a unique Arts and Crafts House, built in 1850 by Ann's grandfather and destroyed by developers a hundred years later. In Ann's mind, the demise of the house mirrored the lives, and deaths, of its occupants.

At 90, Ann had thrown herself fully into the project and the burden of bringing the story to paper would occasionally weigh heavily upon her mind. Illness too interrupted her progress. Then she would recover, regroup and progress. Despite the minor hurdles, we started working together in August and managed to get the final draft of the book to the printers by the beginning of January 2017.

Extract from the press release: "The Author, Ann Petre, (married name Ann Hales-Tooke), aged 90, is launching ‘The Family That Flew’, to an expected audience of 50 guests, at St Andrews Church Hall, Chesterton, on Saturday 21st January, 2017, at 2:30pm."

Yet again, Ann, with the help of friends, organised a launch party with tea and cakes, book signings and readings. Her children and grandchildren were involved and it was a memorable day! The photos below reflect how I will remember her.

All throughout the time between books, we stayed in sporadic contact and I was happy to help with other matters as they arose. As the first author I ever worked with, a fellow artist, and the initiator of my change in direction, Ann has always had a special place in my heart that went beyond the purely transactional.

Ann, thinking about you passing does make me melancholy and regret losing a friend. But this is balanced by the positive memories of our working together over the 15 years, the shared cups of tea and biscuits - and your smile when all the hard work was done or a hurdle overcome.

It has been a privelege to be a part of your life, Ann. Thank you.

Chris Thomas 16.11.2020

The 1967 Be-Ro Home Recipes Cookery Book

2020-08-24T12:46:00.024+01:00

Sitting on our small bookshelf in the kitchen is the most used and referred to cookery book of our home, 'Be-Ro Home Recipes: For Self Raising and Plain Flour'. It was bought by Jane who sent off for the book whilst still at primary school in the late sixties. Her 1967 edition cost a princely shilling and sixpence in old money. It is the first book she goes to when wanting to look up cake and biscuit recipes. It is the book that Jane first refers me to when I am looking for a recipe to do with flour and pastry. First produced in 1925, the book had already gone through multiple print runs and editions, and was entering its 31st million by 1967.

The 1967 Be-Ro Home Recipes Cook Book

That should have placed it in the list of top one hundred best selling books, on a par with Gone with the Wind, Nineteen Eighty Four and The Great Gatsby! https://en.wikipedia.org/wiki/List_of_best-selling_books#List_of_best-selling_regularly_updated_books.

Much to my delight and surprise, Be-Ro products and, more importantly, the Be-Ro book , still exist and you can order a copy of the 41st edition here from https://www.be-ro.co.uk/ at a mere £2.99. Naturally, I had to get Jane a copy!

Our 1967 book is now suffering from the wear and tear of such loving attention for more than half a century and I resolved to ensure that we had a digital copy we could use. Using my photographic and computer skills, I prepared a readable PDF version.

This little DL shaped book with 84 pages packed with information and recipies is a historic gem that deserves to be shared. The layout and images may appear dated but ingredients and instructions are clear and as relevant and tasty today as then. As a former scientist, my only gripe is that I have to get used to imperial measures. Fortunately, my kitchen scales can switch from grams and kilograms to pounds and ounces! The new 41st edition is both metric and imperial and also has useful conversion charts for temperatures and weights.

With the permission of Premier Foods, the parent company of Be-Ro, I have made the 1967 book available to all by uploading it to the Internet Archive - free to read and access for non-commercial use. you can find it here:

https://archive.org/details/be-ro-Home-Recipes-1967/mode/2up

My favorite recipe is Cheese Scones on page 7 in the 1967 edition and page 9 in the most recent 41st edition. My only change - I use butter instead of margerine.

Last chance to capture Comet Neowise

2020-07-23T15:58:00.001+01:00

Jupiter (top centre) and Saturn (top right)

Half past midnight, I stuck my head out of the front door and checked. Had the cloud cover broken for the promised hour? There were gaps where the stars glinted through, so I put on a jacket, grabbed the tripod and camera and wandered down Fen Road.

Beyond the last street lights, I entered the dark tunnel of trees and hedges, came out into the open at the level crossing and continued down the winding road till I reached the small bridge over the creek.

There was a clear view across the fields. To the South, Jupiter and Saturn were visible between the broken clouds and I took my first photographs of them to settle in. As the cloud cleared and I zoomed in with my 55-300 mm lens, I could see Jupiter sporting two moons to one side.

Saturn and Jupiter with two moons close by

Facing North and aiming for between the Big Dipper and the trees on the horizon, I started hunting for, and found, Comet Neowise. It was invisible to my naked eye but it could be seen even with the 55 mm lens.

First sight of Comet Neowise

Zooming in was a problem. I had to find a distant light, zoom in and refocus, then go back to where I thought the comet was. I could only find it my taking several pictures as I scanned the horizon.

Zooming in on Comet Neowise

The core of the comet definitely had a green tinge, hinting at the cyanogen gas being emitted and ionised by the sun's solar radiation.

After an hour, I suddenly noticed the cold, packed up and mady my way home. A lone figure loomed out of the darkness, followed by jogging little green lights that turned out to be the luminous collar of his dog. We chatted and then went our separate ways in the silent village night.

As I made myslef a cup of hot chocolate, I could see the clouds scurrying in again and counted myself lucky to have had this last window to see the comet before it disappeared on its 4000 to 6600 year journey out and back again through the solar system. https://en.wikipedia.org/wiki/C/2020_F3_(NEOWISE).

Daily COVID-19 charts of USA, UK and selected EU countries

2020-05-17T23:02:00.420+01:00

UPDATED 28-06-2021

This post is charting the progress after the first coronavirus peak in Europe.

The toughest rules to try and contain the Coronavirus epidemic in the UK are now being relaxed. A faster spreading variant of the virus from India, named delta, has been spreading in parts of the UK, however, the vaccine appears to give protection. The hope is that this time, it might still be possible to relax rules fully in June. Travel from the UK to some countries is possible again, with the NHS app providing a Covid Vaccination Passport.

Cumulative global cases to date pass the 180 million mark at 180,817,269. Cumulative global deaths due to COVID-19 to date: 3,923,238.

The first two charts are key to showing whether countries have managed to gain control over the COVID-19 epidemic. What we all want to see is that the number of new cases per day is decreasing. The day to day data varies quite a bit. To even out the curve to see the underlying trend, I plot the average of the values for the 7 days including the most recent day.

Figure 1. shows the USA data which appeared to have passed its fifth peak, declined to less than 10,000 new cases per day and continues to be decreasing further. The USA is compared to the daily cases for Russia, France, the UK, Italy, Germany and Belgium, which all have passed their most recent peaks. The UK was later in reaching its peak of daily cases, at roughly the same time at the US then declined to be lower even than Belgium. However in the past weeks, daily new cases have been rising again in the UK, predominantly in unvaccinated younger people. At present, UK deaths do not appear to be following suit.

There is a new concern about the so-called delta variant of SARS CoV 2 B.1.617.2, which appears to be more transmissable and has become the dominant strain in UK. The current vaccines do seem to be effective against the strain after two jabs.

Figure 1. Following a long decline after the first coronavirus peak, there has been a second peak and and then a third peak. The USA and the EU countries are now past their most recent peak.

The current strategy is to identify hot spots and damp them down by reinforcing the total lockdowns, track and trace, and concentrated vaccinations until the coronavirus levels decline.

Figures 3 appears to suggest that the increase in the number of global cases is slowing down. The reassuring feature is that the death rate has decreased from a peak of 7% in April 2020 to 2.2% at the most recent date, or 2.3% of the cases infected 28 days ago.

Figure 3. Global cumulative cases of COVID 19 and deaths by Covid over time.

The cumulative figures below reflect the rise, slowdown and new rise and slowdown in cases seen in many countries. Most remarkable is the UK curve, which showed the impact of the hard lockdown and vaccination in reducing the rise in daily cases. However, the new delta strain which has become dominant in the UK is resulting in a new rapid increase in daily cases, which fortunately does not seem to be matched by an increase in hospital cases.

Figure 4. Cumulative cases of Covid-19 for the USA and selected European countries.

Figure 5. Cumulative COVID-19 cases in the UK and selected European countries.

For information on COVID-19 gleaned during the first COVID-19 peak -see post "State of Covid-19, caused by the SARS-CoV2 virus, on 16th May 2020" available here http://www.miltoncontact-blog.com/2020/02/should-i-worry-about-covid-19-wuhan.html.

USA figures are from their CDC (Centre for Disease Control), occasionally from the Worldometer when not.

UK figures from UK Department of Health and Social Care and Public Health England, Global and other EU data from WHO situation reports.

What could I find out with a Wuhan COVID-19 coronavirus sequence?

2020-02-05T13:05:00.001+00:00

When I heard on the news that the sequence of the new Wuhan COVID-19 coronavirus had been made public, the nerd in me was awoken. It triggered memories of when I used to work with plant viruses two decades ago. Would I still be able to find out more about the virus using some of the methods I would have used back then? Would I be able to understand how the up-to-date and vastly more experienced teams in animal and human virology might approach the problem? Could I explain it to others who don’t work with viruses?

If you are simply looking for general information on the current COVID-19 epidemic, have a look at my earlier post here http://www.miltoncontact-blog.com/2020/02/should-i-worry-about-wuhan-2019-ncov.html. This includes up to date charts and tables on the progress of the epidemic using data from the WHO situation reports.

For my adventure with the Covid-19 sequence, read on.

Finding the Wuhan COVID-19 sequence

One of the great early benefits of the internet was the setting up of DNA databases accessible to all scientists, via The European Molecular Biology Laboratory (EMBL), a molecular biology research institution supported by 27 member states - https://www.embl.org/. This database is currently held by the EBI, the European Bioinformatics Institute, whose centre is based in Hinxton, just outside of Cambridge.

My first step was to see if I could find and download the 2019 nCoV (COVID-19) sequence, using the European Nucleotide Sequence Browser that I found at https://www.ebi.ac.uk/ena/browser/home. In the last week of January, I found a sequence of "A novel coronavirus associated with a respiratory disease in Wuhan of Hubei province, China" provided by F. Wu and a further 18 co-workers. It had been submitted on 05-JAN-2020 by the Shanghai Public Health Clinical Center & School of Public Health, Fudan University, Shanghai, China and entered into the database on 13-JAN-2020. Its entry number on the EBI database is MN908947.

Note that if you search now, you will pick up a different set of 7 later sequences under the accession number MN988668: The first two are from "RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak"; Emerg Microbes Infect :0(2019) by Chen Land others, submitted 23-JAN-2020, State Key Laboratory of Virology, Wuhan University, Bayi Road, Wuchang District, Wuhan, Hubei 430072, P.R. China. These cover the first two sequences.

There are 5 further sequences from US laboratories from isolates of the virus from US patients in Arizona, California and Illinois, also from around the end of January.

Update 24 February 2020: 24 different COVID-19 sequences were available, from the US, Japan, China and Italy

The virus sequence is given as 29,881 nucleotides

Are there differences between the eight COVID-19 sequences?

I downloaded all the sequences and combined them into a merged file using the software SeqVerter, part of a downloaded freeware called GenStudio Pro. I then uploaded the merged file to Clustal Omega, an EBI program that compares multiple sequences online. After a cup of tea and a scone (with jam), the result appeared on the screen.

They were all 100% identical – the three Chinese and the 5 five different US isolates.

Short section showing sequence identity over the eight available 2019 nCoV (COVID-19) sequences

From a disease point of view, this was ‘good’ news. It showed that from the beginning of the outbreak in China to the first cases in the US, the virus had not mutated into a different strain.

From an old virologist’s point of view, this was quite an unusual result. Why? Well, virus RNA is replicated with a far higher error rate than DNA. The rate is 1 in 10,000 nucleotides. The virus RNA is almost 30,000 nucleotides long. So every time the virus reproduces, I would expect two to three differences to be introduced. When you get millions of virus particles made during an infection, the sequences are actually a spread of mutations that average out around a consensus sequence. An RNA virus is thus not a species as such, but technically a quasispecies. This hold true for another coronavirus disease, MERS (Middle East Respiratory Syndrom), as explained in Mandary et a; (2019) “Impact of RNA Virus Evolution on Quasispecies Formation and Virulence” https://www.researchgate.net/publication/335938867_Impact_of_RNA_Virus_Evolution_on_Quasispecies_Formation_and_Virulence.

I would expect it to be true for the COVID-19.

Diseases like polio, for example, took advantage of these spread of mutations. After infecting a body and causing mild symptoms, a few viruses were able to break through the blood brain barrier and cause the more severe paralysis. This spread of mutations is also what might make it possible for a virus to jump species and infect a host it does not normally reproduce in.

When I did sequencing more than 20 years ago, we had to clone virus fragments and then sequence each clone. We would have seen the different sequence mutations and would have had to sequence a number of clones to get the average quasispecies sequence.

Modern virus sequencing gets around the individual cloning by using NGS, next generation sequencing https://bitesizebio.com/21193/a-beginners-guide-to-next-generation-sequencing-ngs-technology/. The viral RNA, with its whole population of different sequences is extracted, amplified and sequenced. The sequence obtained is the most average sequence, the quasi-species sequence (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708773/pdf/1471-2164-14-444.pdf).

Update 24 February 2020: A news report stated that there were now sufficient sequences of COVID-19 for researchers to determine how the disease might be migrating into different countries.

I therefore had a go myself, generating a first phylogenetic tree. Here are the results I obtained with Clustal with unedited sequences straight from the EBA.

I do not claim that these results are definitive linkages of relationship or origin at this point.

24 February 2019: Phylogenetic tree showing possible relationships using unedited COVID-19 sequences from the EBA.

Tentative questions from my data. Are there really two major families of the virus? Are the Japanese and the Italian strains closely related?

A more comprehensive chart created by researchers can be found at the global flu initiative GISAID at https://www.gisaid.org/.

What is the closest relative to the COVID-19?

The beauty of having a public sequence database is that you can take a new sequence, like COVID-19, and use it to see if you find similar sequences amongst the millions already there. I did this online at EBI, using the nucleotide similarity search, Fasta. It was limited to finding 50 related sequences.

I had the results displayed as a “Phylogenetic tree cladogram”, a branching pattern showing the degree of similarity between the different sequences.

My first phylogenetic tree using 2019 nCoV (Wuhan Seafood Market, COVID-19) against the EBI nucleotide database

The tree showed that the closest similarity of the COVID-19 (Wuhan Seafood Market) coronavirus was to Bat SARS-like viruses, and more distantly to other SARS viruses. Those simply called SARS are human isolates. There was a SARS epidemic, which also originated in China, back in 2002, which was finally brought under control in 2004. SARS stands for Severe Acute Respiratory Syndrome. It killed almost one in ten of people infected.

It is interesting how many patent sequences were also picked up. Presumably from companies and organisations that wanted to provide detection and possibly treatment products against SARS.

I wanted a different display to put the COVID-19 in a wider context. I therefore downloaded a number of species specific Coronavirus sequences that I found by searching the European Nucleotide Sequence Browser for coronavirus. I also removed all the patent sequences from the original set found. The new set of data was uploaded for analysis.

The new phylogenetic tree is shown below. I’ve left the accession numbers in to make to make it easier for future work. I also stretched the tree horizontally from the original, to make the branching clearer and coloured different groups for interpretation.

My second phylogenetic tree from using the results from the first search, minus the patent sequences, plus 15 other coronaviruses from different animals

The different human SARS (simply called SARS) sequences in dark red divide into two groups. One has similarities to Civet SARS (in orange), the other has links that reach to Bat SARS strains (orange). The Wuhan COVID-19, marked in bold red, is more closely related to the Bat SARS. The MERS, Middle Eastern Respiratory Syndrome (dark red), was first identified in Saudi Arabia in 2012. It seems to be more lethal than SARS, with about 36% of individuals diagnosed with the disease dying from it. However, it does not seem to spread easily and there have been around 2000 cases recorded in the period 2012 to 2017. My and the professional advice is – keep away from sick camels.

The remaining animal coronaviruses marked in black cover a range from pig to human to rat. The human coronavirus OC43 is one of a number of viruses that cause the common cold.

Using the COVID-19 sequence to find a vaccine

Companies and organisations around the world, including the US and Porton Down in the UK, are now racing to develop a vaccine. One company in the news recently hoping to get to human trials in the Summer.

Where would I begin?

A search for antigenic regions in SARS on Google, after the last SARS outbreak, will find a number of publications. Researchers use blood serum from people who are ill with, or have just recovered from SARS and see if their sera cross react with any of the virus’s proteins (are they antigenic). If they do, they probably contain useful antibodies.

A paper I particularly liked studied the SARS spike protein. The spike protein sits on the outside of the virus capsule. It interacts with the human cells during infection and plays a part in the absorption of the virus into the cell. The spike protein has two domains (stretches), S1 and S2. S1 is not very antigenic, but S2 is. Hong Zhang et al (2004) used a strain of the human SARS called BJ01 (accession no. AY278488). They created 12 different overlapping fragments of the S2 domain of the spike protein. They labelled them F1 to F13. They looked at which of these fragments were bound by antibodies in sera from 15 different SARS patients. (published as “Identification of an Antigenic Determinant on the S2 Domain of the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Capable of Inducing Neutralizing Antibodies” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC421668/).

The fragments F3 and F9 in SARS turned out to be antigenic, i.e., the patients’ sera reacted with them. Proteins are made up of chains of amino-acids. F3 stretched from the amino acid Arginine at position 797 in the spike protein to amino acid Proline at position 844. F9 stretched from amino-acid Leucine at position 1045 to Aspartic acid at 1109.

Using a single letter code for each amino acid, the sequences of F3 and F9 are:

F3=RSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLP

F9=LHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCD

First I compared how similar the human SARS BJ01, a Bat SARS, a MERS and a human coronavirus spike proteins were to that of COVID-19 (labelled 2019 nCoV). I did this in pairs using the alignment program in GenStudioPro. The results are shown in the figure below. You can get a good first impression how well sequences match by looking for how much of the aligned protein sequences is coloured darkly, indicating a 100% match.

Pairs of alignments between COVID-19 (2019 nCoV) and human SARS BJ01, a Bat SAR, a MERS and human coronavirus OC43. The locations of the antigenic fragments F3 and F9 from human SARS BJ01 are marked in red bars. The dark colours in the aligned sequences show a 100% match.

Just from the colour patterns alone, you can see that the spike protein of COVID-19 is very similar to both the human and the bat SARS sequences. There is much less matching between 2019 nCoV and the MERS or human coronavirus OC43.

I then looked more closely at the similarities between the F3 and F9 antigenic fragments from human coronavirus OC43 and a variety of sequences. I always included the F3 or F9 fragment, the human coronavirus OC43 sequence from which it was derived, and the COVID-19 sequence.

Looking at similarities to the F3 antigen from human SARS BJ01 with COVID-19 (2019 nCoV) and Bat SARS, a MERS and human coronavirus OC43. Differences just in the COVID-19 (2019 nCoV) are highlighted in red. Differences in the other sequences are highlighted in orange.

Looking at similarities to the F9 antigen from human SARS BJ01 with COVID-19 (2019 nCoV) and Bat SARS, a MERS and human coronavirus OC43. Differences just in the COVID-10 (2019 nCoV) are highlighted in red. Differences in the other sequences are highlighted in orange.

COVID-19 shows three differences in amino acids from F3, marked in red and a further three differences from Bat SARS marked in orange. Compared to F9, COVID-19 shows 9 differences marked in red, as well as a further three differences from Bat SARS.

The question I might try to answer in experimental trials would be, if I changed the F3 and the F9 sequences to match those of COVID-19, would these changes give me antigens that could generate antibodies, and therefore help create potential vaccines against the current COVID-19 outbreak?

Other approaches

The answer to my question might actually be no. Remember earlier on we learnt that an RNA virus like COVID-19 is likely to be a quasispecies. It is not one definite sequence but a population of viruses with an average around the published sequence. The altered F3 and F9 based vaccines would only affect those viruses in the population with exactly these changes. Those with a different mutation might slip through.

Vaccines made with live attenuated viruses are often the most effective and can be made by using such a mixed population found in a quasispecies virus. The other strategy could well be to create an attenuated version of the COVID-19. By being weakened in some functions so it did not cause disease, it might still being able to induce the same antibodies against the native and more dangerous virus and so create an effective vaccine. The availability of the consensus viral sequence and existing information on related SARS viruses might make this work easier.

Conclusion

I hope this gives an insight on what can be done if you have available sequences for a new disease like COVID-19. But do remember, I am just an outsider, 20 years behind the times, who used to work with plant viruses, which are very different to animal and human viruses.
It is reassuring to know, as the disease continues its growth and spread, that vastly more experienced research teams in public labs and private companies are racing to generate an effective vaccine.
They are likely to do so at a pace that I would have found unbelievable when I was working in my field.

State of Covid-19, caused by the SARS-CoV2 virus, on 16th May 2020

2020-02-03T01:08:00.002+00:00

Photo: CDC/C.S. Goldsmith - https://www.cdc.gov/sars/lab/images.html

Updated 16 May 2020 15:30
data as of 15 May April 2020

COVID-19 still affects many people in Europe and the US. The disease could be with us for the next few months and possibly into next year.

Most of the hardest hit European countries and the USA are seeing the results of their varied lockdowns.
The number of new COVID-19 cases per day appears to have reached its peak in many of them, begun to decline in some such as France and Germany and recently, the USA
At last, the number of new cases in the UK begins to show a decline.
Russia is a latecomer to infection and is just reaching its peak.
The controls are being loosened slightly in some countries. Everyone is on the alert for any negative impact of lesser restrictions.
Most countries are ramping up testing for track and trace as a tool of combating the progress of the disease, possibly with the help of apps.
Several preliminary trials of potential vaccines are being tested globally.
Testing/screening

PCR is still the most accurate method of testing for coronavirus infection, but takes time and expertise.
There is a new fast single step DNA test awaiting approval, which uses CRISPR technology. It might even be possible to conduct this one at home.
Faster antigen based tests against the virus are being evaluated to identify COVID-19 infection in greater numbers.
Screens for virus specific antibodies are also being evaluated to identify those who have recovered and to see if they have a longer lasting immunity.

This article covers:

What is the COVID-19 coronavirus? Symptoms and risks.
The spread of COVID-19 in Charts
Will I be infected?
How can I protect myself?
What nations and the international community can do
So, should I be concerned?

What is the COVID-19 coronavirus? Symptoms and risks.

COVID-19, is the disease caused by SARS CoV 2, formerly known as the Wuhan 2019 nCoV by the WHO (World Health Organisation). This is a new coronavirus that began in the Chinese city of Wuhan and originated in bats.

Symptoms can include fever, sore throat, dry cough, fatigue and breathing difficulties. A recent report suggests digestive problems can by symptomatic in nearly half of admitted patients. There are lots of different coronaviruses infecting humans and animals. Some of the colds you had in the past were probably caused by a human coronavirus.

This COVID-19 appears to be mild in most cases. However, those with pre-existing health problems and the elderly are more likely to be severely affected. In severe cases it can cause a viral pneumonia and cause death. See below for more information.

Further results show that men and persons from black, Asian and other minority groups (BAME) are more likely to be adversely affected by COVID-19. Social (poverty and and differences in family groupings) appear to be important here.

COVID-19 is different from flu and the common cold in that it affects the lower respiratory tract rather than the upper. A recent publication suggest that digestive issues often arise before the other symptoms. See the comparison of symptoms below. The colours indicate likelihood from red = most likely to white = not likely:

Table 1. Comparison of symptoms between COVID-19, Flu and the common cold. Collated from various medical sources. Includes recent article on gastric problems in the American Journal of Gastroenterology.

COVID-19 seems to be at least as infectious as flu, with an average rate of one person infecting between 2 to 4 people, with suggestions tending towards the higher figure. One person with Rubella infects 5 to 7 people and one with measles, 12 - 18 people.

If you are fit and healthy, the COVID-19 disease is much less likely to be severe. You are at much greater risk if you have a compromised immune system or are affected by other illnesses. As with many diseases, the over 60s are more vulnerable.

Current estimates are that the death rate from COVID-19 from global figures has risen from 5%, or 1 in 20 on average to 6.9%. However, it is higher for figures given by some countries. For example, Italy has a mortality figure of about 13%, the UK also has a figure of 13%. This may be the result of insufficient testing, such as only testing admissions to hospital.

For comparison, Measles kills 1 in 500, a previous coronavirus – SARS - killed almost 1 in 10. Seasonal flu usually has a death rate one tenth that of COVID-19.

Detailed figures on mortality rates for COVID-19 are now available based on 44,672 cases from the Chinese Centre for Disease Control and Prevention (figure 2). Age is an important factor. How healthy you are also has a significant effect.

Figure 2. Mortality rate with age for COVID-19 based on on 44,672 cases from the Chinese Centre for Disease Control and Prevention. I have deliberately set the vertical axis to 100% to avoid over-emphasising the figures.

Figure 3. The effect of pre-existing conditions on deaths by COVID-19. I have deliberately set the vertical axis to 100% to avoid over-emphasising the figures.

A preliminary Chinese study (https://www.medrxiv.org/content/10.1101/2020.03.11.20031096v2) looking at ABO blood groups in COVID-19 patients suggested that blood group A was associated with a slightly higher risk for acquiring COVID-19 (about 1.2 x above average) compared with non-A blood groups, whereas blood group O was associated with a slightly lower lower risk (0.67 x of average) for the infection compared with non-O blood groups. The results still need to be validated by others.

The spread of COVID-19 in Charts

By the 15 May:

Europe is still the centre of the pandemic but the US has overtaken all countries in number of COVID-19 cases
The rest of the world is still showing a linear increase at about 70,000 new cases per day. However some countries appear to have passed the peak
215 countries and territories have cases of COVID-19 recorded now. For all daily data from the WHO, see https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

I have limited my monitoring to countries with historic high cases of COVID-19 (China, Iran, South Korea) as well as Japan, Australia, and European countries with more than 1,000 cases. Of the countries I am monitoring:

Eight countries have 1000 -2,000 cases: Bosnia and Herzegovinia, Bulgaria, Estonia, Iceland, Lithuania, North Macedonia, Slovenia, Slovakia.
Twelve countries have more than 2000 - 11000 cases: Armenia, Australia, Croatia, Czechia, Denmark, Finland, Greece, Hungary, Luxembourg, Norway, Republic of Moldova, Serbia.
Eleven countries have 10,000 to 50,000 COVID-19 cases - Austria, Ireland, Japan, The Netherlands, Poland, Portugal, Romania, South Korea, Sweden, Switzerland, Ukraine.
Ten countries have more than 50,000 cases of COVID-19: Belgium, China, France, Germany, Iran, Italy, Russia, Spain, the United Kingdom, the USA.

I use the data from the WHO Situation Reports, which reflect figures that lag about 12-24 hours behind the final figures on any date. They are at least consistent and allow trends to be observed over time. US figures have been obtained from the CDC or the Worldometer when CDC unavailable at Weekends, and UK figures from Public Health England. (UK counts now include the results from the expanded testing from the beginning of May.)

By the morning of 15 May, 2020, more than 4,338,658 total cases of COVID-19 had been reported worldwide.

Figure 4 below shows that after the leveling off of cases in China by the 16th February, cases in the rest of the world began, and still are, increasing (figures 4 and 5) but the rate of increase is linear, not exponential (figure 4 & 5,) at a rate of half a million cases per week. The number of deaths to date globally is 297,119 (figure 4 and 5). There is still a daily increase.

The top scoring locations are USA and a number of European countries, who account for most of all cases (figures 6,7, 8 and 9). Cases in the USA exceed those of other countries more five and a half times.

Some European countries and the USA have now implemented measures to relax their strict lock-down measures. The number of new cases in European countries is beginning to slow down, judging by data from the past few weeks (figures 6 and 7).

Figure 4. Total counts of global accumulated COVID-19 cases and recorded deaths over time

Figure 5. Same data as figure 4 but as a logarithmic plot (base 2) of global cases of COVID-19 and global deaths. Horizontal lines for values increasing 2 fold.

I have introduced two new charts which show the number of new cases per day (figures 6 and 7). Daily figures do vary a lot, so I have used an average of the previous 7 days for each day which smooths the curve. The climb to a peak, leveling off and decline is seen much more easily.

It looks as if Spain and Italy have reached the peak and are on the decline. Germany and France also appear to be past their peak. The UK at last shows a similar trend though the sign of decline in new cases is only just appearing. USA values are so high, they merit their own graph (figure 6) but appear to have reached a peak at 32,000 new cases per day are declining slowly.

Figure 06. The number of new COVID-19 cases in the USA per day, Seven day average.

The dates of the peaks of new cases per day are interesting: Italy 26th March; Spain 31st March; Germany, France and Iran by the 2nd-4th April, USA 10-14th April; the UK 13th - 16th April. Among lower scoring countries, Austria and Switzerland peaked at almost the same time. Belgium and The Netherlands show a similar pattern of reaching a peak at about the same time and then plateauing off without a significant decline for more than a fortnight afterwards.

Figure 07. The number of new COVID-19 cases in countries other than the USA per day, Seven day average. Note the 10 fold differences in scales in these two figures.

The following graphs show the cumulative number of COVID-19 cases over time for selected countries. USA has had five and half times as many cases than any other country so is shown separately in some of the charts. Russia is showing a late rapid increase in cases but has reached its peak.

Figure 8.Ten countries have more than 50,000 total cases of COVID-19: Belgium, China, France, Germany, Iran, Italy, Russia, Spain, the United Kingdom, the USA. The graphs is also shown without the US as the values in the US are more than five times higher than any other country.

Figure 9. The same data as figure 8 but using a logarithmic plot (base 2 ). Horizontal lines for values increasing 2 fold. Ten countries have more than 50,000 cases of COVID-19: Belgium, China, France, Germany, Iran, Italy, Russia, Spain, the United Kingdom, the USA.

Most countries with 10,000 plus cases out of their exponential growth phase as seen in figures 8 and 9, showing a slow down in the number of new cases over the past few weeks (figures 10 & 11).

Figure 10.Eleven countries have 10,000 to 50,000 COVID-19 cases to date - Austria, Ireland, Japan, The Netherlands, Poland, Portugal, South Korea, Romania, Sweden, Switzerland., Ukraine.

Figure 11.Logarithmic plot, base 2. Eleven countries have 10,000 to 50,000 COVID-19 cases to date - Austria, Ireland, Japan, The Netherlands, Poland, Portugal, South Korea, Romania, Sweden, Switzerland., Ukraine.

Taking the UK as an example, the rate of increase of new cases is slowing down. Figure 12 below shows that the time taken for a ten fold increase in cases in the UK has come down from ten-fold every 7 days to two-fold every 46 days and declining. Hopefully the rate will continue to slow down.

Figure 12. Graph showing the change in the rate at which new cases arise in the UK. The rate of increase in COVID-19 cases, based on the last 7 days, is about two fold every 46 days and declining.

Table 3. Showing data for countries with more than 10,000 cases of COVID-19

Public Health England map and charts of COVID-19 across the UK

https://www.arcgis.com/apps/opsdashboard/index.html?fbclid=IwAR3Fztr_XCIHs0MvsNv7D9QJNIfVwsz_rkQJ_ef2KehtIujYd_I4R1GtCxA#/f94c3c90da5b4e9f9a0b19484dd4bb14

COVID 19 Symptom tracker for the UK https://covid.joinzoe.com/data
Note that this suggests more than twice as many cases as given by figures from tests done so far.

Will I be infected?

Information was that you have to be within 2 meters of someone. The consensus is that the main route of infection to avoid is - touching surfaces contaminated by the virus and then touching your mouth or eyes. Even when you do, this does not mean that you will always become ill (see 'How can I protect myself' below) as you have to receive a certain dose of virus for successful infection.

The virus is possibly shed into the air by an infected person.
The virus can even be spread by people who are not displaying obvious symptoms like fever or a cough.
The highest shedding of virus occurs just before the onset of symptoms and then declines.
Your risk of infection is dramatically reduced the further away you are from ill people.

The virus can survive for up to a couple of days on surfaces outside of the body (Source https://www.nejm.org/doi/full/10.1056/NEJMc2004973).

Aerosol: 3+ hours
Copper: 8 hours
Cardboard: 24 hours
Stainless Steel: 3 days
Plastic: 3 days

However, it is possible that a significant percentage of the population will be infected eventually.

What does the virus COVID-19 do?

The COVID-19 coronavirus infects the cells lining the airways of the body, the epithelial cells. In severe cases it seems to progress to the lungs, causing pneumonia.

The virus has a complex protein capsule that contains the virus genes. The virus genes are on a single strand of RNA – not DNA. This strand is 29903 bases (units) long. Numerrous isolates of the virus have been sequenced and their sequences made publically available for all scientists - see https://www.ebi.ac.uk/ena/browser/text-search?query=Wuhan%202019%20nCoV.

On contact with one of your epithelial cells, the cell is triggered to take up the virus. Inside the cell, the virus hijacks your cell’s own functions to make copies of its single RNA strand. The genes encoded on the virus RNA are translated into a range of virus proteins by the cell. New virus particles are then assembled within the cell. They are then either exported by the cell or released when the cell dies. Neighbouring cells are then infected. If the conditions are right, the virus begins to spread along your airways.

COVID-19 can be symptomless in some people for between 5 to 12 days. If they appear, the symptoms you may get range from fever, sore throat, dry cough, fatigue and breathing difficulties. A recent paper in the American Journal of Gastroenterology suggests that digestive problems may be an early indicator of COVID-19 in nearly 49% of cases, in advance of other symptoms.

They are in part due to the virus affecting/killing cells but also due to your body going into overdrive to try to fight the virus infection (often described as a cytokine storm). How ill you are is a balance between virus multiplication and how fast and effectively your body defence works. There is more information below in the next section on how you can protect yourself.

How can I protect myself?

Your choices NOW affect how many cases the NHS has to deal with in 14 days.

There is no vaccine for COVD-19 yet – but with the full sequence of the virus available, work is in progress to provide a vaccine in the next months. Therefore isolation and quarantine remain the most effective means to prevent the spread of the disease. Things you can do are:

Keeping healthy by eating and sleeping well, exercising*
Avoiding locations and people with the illness
Hand-washing
Use hand sanitisers
Good personal hygiene generally
Use the new tracking and trace app when it is on general release

Note, the use of even the best masks is more likely to protect others from you when you are ill, rather than protecting you from others. Here is some advice on the best materias to make your own https://smartairfilters.com/en/blog/best-materials-make-diy-face-mask-virus/?fbclid=IwAR2rsvWhc7uPA0qQvFwCNjraA3IAHwfRsHBOB8p6CpB4N5ZoRfIuPRjbl-o

*Keeping healthy is a great prophylactic as it means that your immune system is in best condition. Our bodies are actually geared to be alert to any foreign invaders and illnesses and the incoming virus does not have it all its own way.

Get the COVID Symptom Tracker app

You can join in with research on the progress of COVID 19 in the UK by downloading the COVID Symprom tracker app from https://covid.joinzoe.com/

Disinfecting smooth surfaces:

You can use:

70% or stronger alcohol to wipe surfaces (preferred - effective and leaves no residue)
Thin bleach or diluted thick bleach
Soapy water.

Remember to wear rubber gloves. Wipe with paper towels you can throw away. AND WASH YOUR HANDS AFTERWARDS.

Clothing/ cloth articles

Wash in washing machine with your usual detergent.
WASH YOUR HANDS AFTER placing possibly contaminated clothes into washing machine.

Possible UV inactivation of CoV SARS 2

Hospitals and laboratories often use special flow cabinets with UV lights to sterilise surfaces. From the publications I looked at, RNA viruses in aerosols are quite resistant to UV exposure, requiring times of half an hour or more with shortwave UV (about 254 nm). For those wanting to pursue this further, the following may be of interest.

Inactivation of bacteria, viruses and other pathogens by UV-C irradiation in the Leica cryostat product family: https://www.bio-strategy.com/site/bio-strategy/files/Supplier_Subs/Leica_CM_UVC_Certificate_Bacteria.pdf
A Genomic Model for Predicting the Ultraviolet Susceptibility of Viruses, 2009 https://iuvanews.com/stories/pdf/archives/110201KowalskiEtAl_Article.pdf
Effect of Ultraviolet Germicidal Irradiation on Viral Aerosols, 2007 https://pubs.acs.org/doi/abs/10.1021/es070056u

Your body - your best defender!

If a cell in your body is overcome by an infection and dies, this triggers other chemical signals which alert a variety of white blood cells. Some, called macrophages, come to absorb the invading foreign viruses and take the information back to T-cells. The T-cells in turn use this information to help create killer T-cells and antibodies. There are also memory cells that will remember the antibodies required to fight any future infections by the same strain of virus.

Some of my neutrophils from a cold,
photographed at over 1000x magnification
using anoptral contrast

In the meantime, a whole army of another type of white cell, neutrophils, invade the infected area and gobble up all the debris of damaged cells and the viruses they come across. When you have pus from a spot, or your runny nose produces the thick white stuff, or you cough up thick phlegm - that is mostly made up of these short lived neutrophils that have gorged themselves on what is infecting you.

Incoming coronaviruses also trigger the production of interferons within the cell and initiate other yet unknown responses. These seem to slow down virus action. In turn, viruses continually evolve to overcome the cell’s defences. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593566/).

In chemotherapy and radiotherapy, these immune systems are weakened, hence you become more susceptible to infections taking over. So take extra care.

What nations and the international community can do

Countries and the World Health Organisation have plans and structures in place to trigger action when diseases are spreading. The WHO had expressed its opinion that this was still a controllable pandemic and that a shift from containment to mitigation would be wrong and dangerous.

UK Response

PM Boris Johnson acknowledged that this was "the worst public health crisis for a generation".

The UK is trying containment by restrictions on movement and will be introducing track and trace in the near future.
The UK is ramping up testing for all critical care workers (hospitals, care homes, emergency services, including police, teachers etc.).
Individuals with a fever or cough must self isolate for seven days. Families with one infected person need to self isolate for 14 days to ensure everyone is in the clear.
Schools and non-critical businesses have been closed from the weekend of 21st March, exceptions are for critical care workers and essential functions to keep the country running.
People over 70 and those with pre-existing health conditions have been told to self isolate for the foreseeable future.
Travel locally and abroad is strongly discouraged
The NHS has survived the current peak and people with symptoms are no longer required to call NHS 111. They are instead directly to look for information on the NHS website and 111 online.

Latest Documents from the UK Government accessible here:

https://www.gov.uk/government/latest?topical_events%5B%5D=coronavirus-covid-19-uk-government-response

The plan

The aim is to slow down the rate of infection so that the peak in hospital cases is lower and spread, so that the NHS can cope.

Even after the virus has been brought under some degree of control, the virus and some degree of control measures are with us for the foreseeable future - possibly more than one year.

The number of tests for infection is to be dramatically increased to determine which key workers are affected and which individuals can work in critical posts. The UK is still lagging behind in testing compared to a number of other developed countries.

In the near future, testing to see who has been infected and recovered will be possible. This will most likely be by using mass produced antibody kits, similar to pregnancy tests. Knowing someone has recovered and is resistant to the virus will give reassurance that they can return to work without being at risk to themselves and others.

Ultimately, the country needs to gain a significant proportion of the population that is resistant to the virus. This "herd immunity" (see below) can be obtained both by recovery from being infected and from vaccination.

Vaccines are being developed and tests have begun both in animal and small scale human studies. It could take a year or more before a vaccine is generally available.

Herd Immunity and Vaccination

Herd immunity by recovery is a real effect with a number of diseases. Governments around the world expect that a significant percentage of the population will be infected over the coming year. The hope is that recovered individuals will be immune.

Note of caution, immunity to existing corona-viruses, such as those causing the common cold, disappears quickly. We do not yet know if we gain immunity after infection with the SARS CoV2 and how long the immunity will last.

Natural herd immunity occurs when a significant proportion of the population has been infected and survived. The survivors are resistant to the illness and, if their numbers are high enough, it becomes more and more difficult for the disease to find uninfected persons. The progress of an epidemic slows or can even peter out if herd immunity is high enough.

With the current estimate of an average rate of one person infecting between 2 to 4 people for COVID-19, this could mean that 50% to 80% of the population would have to go through infection to achieve full herd immunity against COVID-19 (based on figures in https://en.wikipedia.org/wiki/Herd_immunity#Mechanism).

However, it could be that the UK is hoping that a lower figure of herd immunity may reduce the level of general infection in the population, if not achieving outright cessation of the epidemic.

In the meantime, vaccine development, testing and then mass production will be undertaken as fast as possible to provide our protection in future years. The first safety trials of some vaccines have already started. Earliest prospects for a possible vaccine in low numbers suggested for end of year. Realistically we might have to wait till 2021.

Other countries' responses

As Europe was the new focus of the pandemic, the US and other countries stopped people from European countries (including the UK and Ireland) entering.

Within Europe, France, Germany, The UK and Spain had joined Italy and also introduced more control measures, promoting self isolation, banning public gatherings and restricting movement within and between countries. Now the controls are being relaxed gradually. The aim is to allow more and more freedom but to a level that we do not have another sudden flash of cases and allows the health systems cope at a reasonable level.

The USA had implemented more testing and stringent control measures to try and limit the escalating crisis in its states. However, there is very strong pressure to relax controls and get the economy going again and different states are opening up to varying degrees, often contradicting the recommended scientific tests. The balance between scientific modelling and advice and political decision making is beginning to lean towards the latter. So far this has worked OK as new cases continue to decline.

The differing responses of countries to the coronavirus epidemic have in effect been a global experiment whose results will reveal best strategies for future epidemics. The same is now true for the rate of relaxation of controls in different countries - it is the next global experiment.

The general global practice with new diseases prior to COVID-19

Every year, new strains of influenza arise naturally by mutation as the virus adapts to us changing humans. Rather than letting a large proportion of the world’s population become ill (letting many people die) with the survivors therefore gaining resistance to the newest strain, we humans are proactive. Up and coming new strains of viruses are identified and vaccines produced so that by the time the disease arrives in your part of the world, you are protected in advance and do not get ill, or only have mild symptoms

With totally new viruses, like the COVID-19 coronavirus, there is no immediate vaccine defence. It is therefore vital that a country keeps tabs on new illnesses that arise. They need to have plans in place to deal with the isolation of infected people. They also need to provide care whilst patients go through the illness, to mitigate symptoms until they get well.

Until we have a vaccine, severe cases may be helped by giving them antibodies from people who have recovered from the disease. This method was used against diphtheria in the early 1900's in Alaska, though the antibody serum was actually derived from horses. I do not know if this is currently being pursued. Cloned antibodies might be an alternative solution.

Update 08/03/2020 re using antibodies from people who have recovered: first reports in news that Germany and USA looking to use plasma from recovered patient for serious cases.

Update 20/04/2020: Plasma treatment (using antibodies from people who have recovered) being trialed in the UK, including Addenbrookes, Cambridge.

In this interconnected world, nations also have a responsibility to alert the WHO early about upcoming diseases. This time round, full marks for the Chinese response, because we were made aware of the issue earlier than in the past. The world was able to start monitoring for carriers of the illness and put in place travel restrictions.

Despite the WHO advice to act quickly and decisively, most countries underestimated the speed at which the COVID-19 spread in the population and held back from mass testing and tracing whilst numbers were still low. Now, outbreaks such as those in the USA and most of western Europe are now challenging us with a significant number of deaths and stretched healthcare systems.

Information, documents and guidance from the WHO, the UK and US.

The UK and WHO have the following information on responses to epidemics and the teams and mechanisms in place. They can be found in public documents such as:

Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf
WHO Technical guidance on all matters relating to detection and control of COVID-19 https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance
PHE Infectious Diseases Strategy 2020 – 2025 https://www.gov.uk/government/publications/phe-infectious-diseases-strategy
Communicable Disease Outbreak Management: Operational guidance https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/343723/12_8_2014_CD_Outbreak_Guidance_REandCT_2__2_.pdf
WHO Document on Managing Epidemics https://www.who.int/emergencies/diseases/managing-epidemics-interactive.pdf
UK Coronavirus information https://www.gov.uk/guidance/coronavirus-covid-19-information-for-the-public
UK most recent documents https://www.gov.uk/government/latest?topical_events%5B%5D=coronavirus-covid-19-uk-government-response
US coronavirus information https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Fcases-in-us.html

So, should I be concerned?

Yes. COVID-19 is still affecting many people in Europe and the US. The disease could be with us for the next few months and possibly into the coming years.

The hard containment measures have slowed down the number of new infections in a number of countries. Relaxation of restrictions is gradually being introduced but with an eye being kept on the effect on virus reproduction in the population.

Look out for public advice from the authorities dealing with the outbreak. The following advice is practical not just in this instance but to minimise your risk of getting ill from any disease that is circulating:

Keep healthy by eating and sleeping well and exercising
Avoiding locations and people with the illness
Regular hand-washing
Use of hand sanitisers where there might be a risk in public
Note, the use of masks is best for protecting others from you when you are ill rather than protecting you from others.

If you have returned from a region seriously affected by COVID-19, or met an individual who has subsequently succumbed to the illness, and begin to experience chest and cough symptoms, stay at home and look online at NHS 111 in the UK https://111.nhs.uk/covid-19. This ensures that you get the right response and treatment and do not accidentally spread the disease further, endangering people in public places, doctors surgeries or hospital reception.

I have also been looking at some of the more technical aspects of the virus genome sequence in the article "What could I find out with a Wuhan COVID-19 coronavirus sequence?" here http://www.miltoncontact-blog.com/2020/02/what-could-i-find-out-with-wuhan-2019.html

Preventing spread and getting a good bounce with a mixed rye-wheat bread

2020-01-28T01:33:00.000+00:00

Mixed rye-wheat sourdough load with a good bounce

This ever happened to you? I had a break in baking my sourdough loaves over Christmas. The next loaves I set up in the new year all seemed to have a more plastic dough. it spread more during the final rise. When slashed and in the oven, it hardly rose, coming out of the oven like a slightly thicker discus. I tried again. Same result.

I checked through my method line by line. There was one small difference. I'd kept the last rise in a large but closed container to stop the dough drying out too much over the usual three to four hour rise. Before Christmas, I'd covered the floured dough ball with a tea towel.

The third time, I kept the last rise under a tea towel. The dough rose and spread less. The outer surface had formed a slightly drier skin, which resisted the expansion, leading to a more domed loaf. I cut a cross with a sharp knife as previously, to an inch depth and almost to the base the dough was on.

This time, the large bounce occurred within the first 10 minutes of baking and continued slightly till the end of the bake.

Covering the floured dough with a tea towel prevented the dough from drying out too much. The the less flexible thin skin formed on the surface maintained the loaf's shape and also, I suspect, put the gas bubbles formed in the dough under a slight pressure. After slashing and placing in the oven, the heat caused the rapid controlled expansion which was helped by the cuts exposing the interior, still very moist and flexible, dough

A STEM Afternoon With Polarised Light and Microscope

2018-03-15T22:22:00.001+00:00

Polar Bear Fur at 100x magnification between crossed polarisation filters

Thirty year 3 primary school students, arranged in a horseshoe jostled each other as they held out 3D cinema glasses, with the arms of the frame pointing at the white desktop screen behind me. They turned the frames, gasped as the polarising lenses suddenly blocked out the light from the screen and then exploded into different directions in the library to get closer to other screens themselves. Soon, some of the more inquisitive also tried out viewing at the live projection screen, the windows, lights and white paper, discovering that the blanking out could only happen at the desktop screens (as these have their own primary polarising filters). Some students collaborated and found that you could also get the darkening effect on lights if you used two sets of glasses/two sets of filters

They were reluctantly dragged back to be still again in a wide circle around the screen. Glasses held at extinction, I slowly lowered an A6 sized rectangle of clear acetate sheet in front of the screen. the hubbub rose again and then got excited when I stuck a piece of Sellotape to the sheet and revealed a range of polarisation colours. From then on the class teacher and I were the focus of a constant stream of students coming back for more and more Sellotape for their own abstract hidden artworks.

This remarkably simple demonstration, of creating colour effects that could only be seen using polarisation filters, filled a good part of 15 minutes. It brought home to me that what seems like a simple everyday technique for many amateur microscopists (and geologists) still had the capability to bring a sense of discovery and wonder to those who saw it for the first time.

You could also tell that the school/teachers had a very positive and supportive nature in working with their young students as the latter were unafraid and open to trying things out and asking questions when they did not understand. Their enthusiasm only had to be curbed when it got too exuberant. Not everyone understood my explanations of polarisation, but they seemed to have come away having learned a new insight or experience of unexpected things you can do with objects they normally take for granted.

The two sessions of 30 students each took over 90 minutes, including talk, demonstration and the practicals. They were topped and tailed by the preparation and packing time in the library. As I was setting up over half an hour, there was a steady flow of students - to the workstations, and to the books. But this was not a reverent or even dull silent area. It was a place to talk about what books a reader might want to go to next after returning the last one, a discussion of preferences.

I found myself pulled in on a conversation as I saw Peter Bunzl's Clockheart and Moonlocket. I'd been drawn into the series after spending my birthday at Leicester Space Centre last November, when there was a simultaneous exhibition of Steampunk. Cogheart struck my eye as a memento to take home and enjoy with my new rocket adorned mug. The paperback versions of the Magyk series was also on the table, with its lovely black and white illustrations.

After the rush of the sessions, the library emptied and I began to pack, the cheery librarian returned, and now it was the turn of parents and children to come and visit in ones and twos. The microscope stayed on the table, slides and filters were brought out again as the curious came to peer and delight in what they saw, adult and child alike. The head louse slide was a common denominator for us parents!

Head louse, composite stacked images of 2D panorama

I found myself chatting to a German parent about the books I enjoyed as a child - from Ottfried Preussler to Michael Ende and Cornelia Funke, and recommending animal and vet related books by James Herriot, Gerald Durrell and, on a more fantastical side, the Redwall series.

After Stephen Hawking's death yesterday I also recommended the children series he'd written with daughter Lucy, as I'd enjoyed reading 'George's Secret Key to the Universe' in one go last night in his memory. I found it a much easier and yet scientifically informative read than the highly lauded but seldom finished 'A Brief History of Time'. It had hard facts as a part of the fiction (something done so well by the adult exponent of the hard SciFi genre, Hal Clement, with 'A Mission of Gravity').

The son of the last parent to arrive had been in one of the earlier sessions. His voice carried over as he explained to his amazed mum why a 3D cinema glasses lens could darken a PC screen "It works because there is already a filter on the computer screen!" Subconsciously turning to look at me after he had said it, I gave him a thumbs up across the room.

I left at 5 pm, having extended the STEM activity for a couple of hours, from a hectic full class session to a more calmly paced one to two with a number of parents and children. Tired but positive.

Going from from Micro to Macrophotography with Melolin

2018-01-15T12:25:00.003+00:00

Multiple layers Melolin dressing taken though the microscope

Recently, I've had a play with macro-photography. I'm comfortable photographing through the microscope, creating panoramas and stacks but wanted to try capturing subjects more in the centimeter size range and ended up reading around and just experimenting.

I was trying to capture almost a whole specimen on a microscope slide. Initially I tried using my camera with its usual lens but with a lot of extension tubes (66 mm). The sample was also between tow polarisation filters for colour effects. This worked reasonably well, especially when I took a range of images at different focus and combined them. However, when you look more closely at the image (Full screen), you could see a softening of the image around the edges.

Melolin membrane using 50 mm lens with 66 mm extension tubes

This bugged me, so the next day I thought, why not simply use a low power microscope objective as the lens for the camera? Cutting some card and and using blue-tac I finally bodged the arrangement below. Note that the camera is also mounted on a Newer two way rail which I am quite impressed with!

Using a low power microscope objective on the camera

Taking another stack of photos at focus through the slide, I generated a much more satisfactory image as shown below.

Melolin membrane between crossed polars, with low power objective attached to camera.

Trying the same method on a different slide with several layers of melolin membrane on top of each other gave this beautiful coloured image, created by the interference of the polarised light passing through the different filters.

Multiple layers of melolin membranes between crossed polars, taken with low power objective on camera

Of course, the final question is, what is Melolin membrane? The membrane is used in Melolin dressings. Melolin is a trademark of Smith & Nephew http://www.smith-nephew.com/uk/products/wound_management/product-search/melolin/.

As you can see from the image of the single layer, the membrane has numerous very small pores. It is made of poly(ethylene terephthalate) and can be applied to lightly leaking sutures, abrasions or wounds without sticking to them. Dressings can be provided with absorbant pads over the filter, so that the exudate passes through the filter and is absorbed on the pad.

There is a simple beauty in a practical everyday object, that makes even more sense when you know how it works.

An HBN 'Out and About' to Webtec, St Ives

2017-11-13T21:50:00.002+00:00

HBN does a series of interesting visits to local companies in Huntingdonshire (our 'Out and About'), so it was with some curiosity that I took a lift with Nick Smith of EAM Consulting to this month's visit, mulling over the company name. I knew it was likely to be manufacturing, but obviously, judging by the name, internet related.

I couldn't have been more wrong! As Managing Director Martin Cuthbert soon explained after welcoming the select group of visitors, Webtec's name came from pre-web days, Web was an abbreviated version of Webster. The tec was, and still is, technology, specifically monitoring equipment for hydraulic systems.

Oversimplified, hydraulics is the use of liquids in pipes. Because liquids are by and large very difficult to compress, if you push plunger in at one end of a pipe, the pressure and movement will be transferred to the other end. As Martin wryly commented, whenever he travels down the building site that is the A14, he cannot help but notice the hydraulics in use in diggers, lifters, drilling rigs and a myriad of other machinery. Hydraulics also allow you to transfer energy at very high pressures, which can be used to drive specialised turbines or exert great force.

Working with hydraulic systems means that things can occasionally leak or systems go wrong. Webtec helps in providing measuring equipment that can help detect either the optimum performance of a machine or the first signs that a service might be in order. The company uses state of the art computerised machinery to make components from blocks of aerospace grade aluminium and steel. We could see how a component gradually developed from a simple block of metal to a high precision milled unit.

We learnt a very useful tip when checking for leaks in hydraulic systems, don't try to find the leaks with your hand. The liquid can be ejected at such high pressure from a pin-prick hole, that it is injected under your skin. This has to be treated quickly as it can cause you further damage and poisoning.

Webtec's products are exported globally, mirroring the UK in that 50 percent of exports go to the EU. Which naturally raised the question of Brexit. As with many other companies international exporters, the key frustration was the current uncertainty. This was coupled with pragmatically putting contingencies in place, to allow border free trading, a rapid response and the good customer relationships that clients will still be expecting within the EU.

The other fascinating story was the transition from an autocratic family-head led firm to a modern business. Martin is one of the two brothers who took over the company from their father, who had bought it from the American firm he was originally working for. Together, the brothers instigated a program of change, with devolved and shared responsibilities amongst the workforce.

One of the biggest problems for engineering firms is getting youngsters to join the business. Webtec has proactively built up a relationship with the regional colleges. Staff are challenged by going out to get involved in STEM activities. They often get insights from the way the students bring new and unexpected solutions to the challenges they are given. The company in turn offers apprenticeships which look to find the best and maintain the continuing growth and development of the business.

I particularly liked the fact that Webtecc viewed the unusual requests or problems in hydraulics as challenges - ones that opened up new and unforeseen opportunities. When asked how Webtec survived in a competitive world, where big players had hoovered up a lot of the smaller companies, Martin's response was: flexibility, a genuine interest in your customer's issues and helping them find the best solution.

A good HBN 'Out and About'.

The CETC Annual Garden Party

2017-09-01T01:40:00.000+01:00

Cambridge MP Daniel Zeichner Keynote Speaker at CETC Garden Party

The torrential rain cleared and a rainbow heralded the CETC (Cambridge Enterprise and Technology Club) Annual Garden Party. Around fifty members and guests wound their way through Wolfson College to reach its Lee Hall. Armed with drinks we chatted in groups and admired the Betty Wu Lee Garden through the opened veranda doors.

CETC Chair, Dr Andrea Lorenz, wearing a shimmering red chinese jacket patterned with golden dragons, gave a welcome speech. Peppered with witty comments and reminiscences, she spoke of the past year's successful meetings and the ambitious 2017/18 program. Above all, she thanked the attending visitors and guests and invited them to take part in a competition to suggest future speakers and topics. The winner would win a flight over London in a four-seater plane - or the equivalent for those of a more nervous disposition.

Cambridge MP Daniel Zeichner, was our invited keynote speaker and he reflected on the vibrancy of business, science and technology interacting and collaborating in Cambridge, due in no small part to networking and events such as the CETC talks.

The food and the venue were excellent and the place was still buzzing with conversation at its close.