Biology Reviews

Research About Obesity

2009-12-18T21:41:00.000-08:00

The obesity and inflammatory marker haptoglobin attracts monocytes via interaction with chemokine (C-C motif) receptor 2 (CCR2)

Margherita Maffei , Marcella Funicello , Teresa Vottari , Olimpia Gamucci , Mario Costa , Simonetta Lisi , Alessandro Viegi , Osele Ciampi , Giuseppe Bardi , Paolo Vitti , Aldo Pinchera and Ferruccio Santini

BMC Biology 2009, 7:87doi:10.1186/1741-7007-7-87


Published:	17 December 2009

Abstract (provisional)

Background

Obesity is a chronic low inflammatory state. In the obesity condition the white adipose tissue (WAT) is massively infiltrated with monocytes/macrophages, and the nature of the signals recruiting these inflammatory cells has yet to be fully elucidated. Haptoglobin (Hp) is an inflammatory marker and its expression is induced in the WAT of obese subjects. In an effort to elucidate the biological significance of Hp presence in the WAT and of its upregulation in obesity we formulated the hypothesis that Hp may serve as a macrophage chemoattractant.

Results

We demonstrated by chemotaxis assay that Hp is able to attract chemokine (C-C motif) receptor 2 (CCR2)-transfected pre-B lymphocytes and monocytes in a dose-dependent manner. Moreover, Hp-mediated migration of monocytes is impaired by CCR2-specific inhibition or previous cell exposure to monocyte chemoattractant protein 1 (MCP1) (also known as CCR2 ligand or chemokine (C-C motif) ligand 2 (CCL2)). Downstream effects of Hp/CCR2 interaction were also investigated: flow cytometry proved that monocytes treated with Hp show reduced CCR2 expression on their surface; Hp interaction induces calcium release that is reduced upon pretreatment with CCR2 antagonist; extracellular signal-regulated kinase (ERK)1/2, a signal transducer activated by CCR2, is phosphorylated following Hp treatment and this phosphorylation is reduced when cells are pretreated with a specific CCR2 inhibitor. Consistently, blocking the ERK1/2 pathway with U0126, the selective inhibitor of the ERK upstream mitogen-activated protein (MAP)-ERK kinase (MEK), results in a dramatic reduction (by almost 100%) of the capability of Hp to induce monocyte migration.

Conclusions

Our data show that Hp is a novel monocyte chemoattractant and that its chemotactic potential is mediated, at least in part, by its interaction with CCR2.

Revolution of novel fungal genes

2009-12-18T21:38:00.000-08:00

The evolution of novel fungal genes from non-retroviral RNA viruses

Derek J. Taylor and Jeremy Bruenn

BMC Biology 2009, 7:88doi:10.1186/1741-7007-7-88


Published:	18 December 2009

Abstract (provisional)

Background

Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles.

Results

Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated Totivirus-like sequences in three fungi (Candida parapsilosis, Penicillium marneffei and Uromyces appendiculatus). The phylogenetic evidence strongly indicated that the direction of transfer was from Totivirus to fungus. However, there was evidence of transfer of Totivirus-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning.

Conclusions

Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.

Optimizing harvest of corn stover fractions based on overall sugar yields following ammonia fiber expansion pretreatment and enzymatic hydrolysis

2009-12-14T04:13:00.000-08:00

Optimizing harvest of corn stover fractions based on overall sugar yields following ammonia fiber expansion pretreatment and enzymatic hydrolysis

Rebecca J Garlock , Shishir PS Chundawat , Venkatesh Balan and Bruce E Dale

Biomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910-8596, USA

author email corresponding author email

Biotechnology for Biofuels 2009, 2:29doi:10.1186/1754-6834-2-29


Published:	24 November 2009

Abstract

Background

Corn stover composition changes considerably throughout the growing season and also varies between the various fractions of the plant. These differences can impact optimal pretreatment conditions, enzymatic digestibility and maximum achievable sugar yields in the process of converting lignocellulosics to ethanol. The goal of this project was to determine which combination of corn stover fractions provides the most benefit to the biorefinery in terms of sugar yields and to determine the preferential order in which fractions should be harvested. Ammonia fiber expansion (AFEX) pretreatment, followed by enzymatic hydrolysis, was performed on early and late harvest corn stover fractions (stem, leaf, husk and cob). Sugar yields were used to optimize scenarios for the selective harvest of corn stover assuming 70% or 30% collection of the total available stover.

Results

The optimal AFEX conditions for all stover fractions, regardless of harvest period, were: 1.5 (g NH₃g^-1biomass); 60% moisture content (dry-weight basis; dwb), 90°C and 5 min residence time. Enzymatic hydrolysis was conducted using cellulase, β-glucosidase, and xylanase at 31.3, 41.3, and 3.1 mg g^-1glucan, respectively. The optimal harvest order for selectively harvested corn stover (SHCS) was husk > leaf > stem > cob. This harvest scenario, combined with optimal AFEX pretreatment conditions, gave a theoretical ethanol yield of 2051 L ha^-1and 912 L ha^-1for 70% and 30% corn stover collection, respectively.

Conclusion

Changing the proportion of stover fractions collected had a smaller impact on theoretical ethanol yields (29 - 141 L ha^-1) compared to the effect of altering pretreatment and enzymatic hydrolysis conditions (150 - 462 L ha^-1) or harvesting less stover (852 - 1139 L ha^-1). Resources may be more effectively spent on improving sustainable harvesting, thereby increasing potential ethanol yields per hectare harvested, and optimizing biomass processing rather than focusing on the selective harvest of specific corn stover fractions.

The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass:

2009-12-14T04:04:00.000-08:00

The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: a comparative evaluation between ammonia fiber expansion and dilute acid pretreatment

Ming W Lau , Christa Gunawan and Bruce E Dale

Biotechnology for Biofuels 2009, 2:30doi:10.1186/1754-6834-2-30


Published:	4 December 2009

Abstract (provisional)

Background

Pretreatment chemistry is of central importance due to its impacts on cellulosic biomass processing and biofuels conversion. Ammonia fiber expansion (AFEX) and dilute acid are two promising pretreatments using alkaline and acidic pH that have distinctive differences in pretreatment chemistries.

Results

Comparative evaluation on these two pretreatments reveal that (i) AFEX-pretreated corn stover is significantly more fermentable with respect to cell growth and sugar consumption, (ii) both pretreatments can achieve more than 80% of total sugar yield in the enzymatic hydrolysis of washed pretreated solids, and (iii) while AFEX completely preserves plant carbohydrates, dilute acid pretreatment at 5% solids loading degrades 13% of xylose to byproducts.

Conclusions

The selection of pretreatment will determine the biomass-processing configuration, requirements for hydrolysate conditioning (if any) and fermentation strategy. Through dilute acid pretreatment, the need for hemicellulase in biomass processing is negligible. AFEX-centered cellulosic technology can alleviate fermentation costs through reducing inoculum size and practically eliminating nutrient costs during bioconversion. However, AFEX requires supplemental xylanases as well as cellulase activity. As for long-term sustainability, AFEX has greater potential to diversify products from a cellulosic biorefinery due to lower levels of inhibitor generation and lignin loss.

The Opsins

2009-12-14T03:58:00.000-08:00

The opsins

Akihisa Terakita

Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kyoto 606-8502, Japan

author email corresponding author email

Genome Biology 2005, 6:213doi:10.1186/gb-2005-6-3-213


Published:	1 March 2005

Subject areas: Neurobiology, Physiology, Cell biology, Evolution

Abstract

The photosensitive molecule rhodopsin and its relatives consist of a protein moiety - an opsin - and a non-protein moiety - the chromophore retinal. Opsins, which are G-protein-coupled receptors (GPCRs), are found in animals, and more than a thousand have been identified so far. Detailed molecular phylogenetic analyses show that the opsin family is divided into seven subfamilies, which correspond well to functional classifications within the family: the vertebrate visual (transducin-coupled) and non-visual opsin subfamily, the encephalopsin/tmt-opsin subfamily, the G_q-coupled opsin/melanopsin subfamily, the G_o-coupled opsin subfamily, the neuropsin subfamily, the peropsin subfamily and the retinal photoisomerase subfamily. The subfamilies diversified before the deuterostomes (including vertebrates) split from the protostomes (most invertebrates), suggesting that a common animal ancestor had multiple opsin genes. Opsins have a seven-transmembrane structure similar to that of other GPCRs, but are distinguished by a lysine residue that is a retinal-binding site in the seventh helix. Accumulated evidence suggests that most opsins act as pigments that activate G proteins in a light-dependent manner in both visual and non-visual systems, whereas a few serve as retinal photoisomerases, generating the chromophore used by other opsins, and some opsins have unknown functions.

Taxonomy : Classifying Life

2009-12-10T23:11:00.000-08:00

Taxonomy: Classifying Life

At least 1.7 million species of living organisms have been discovered, and the list grows longer every year (especially of insects in the tropical rain forest). How are they to be classified?

Ideally, classification should be based on homology; that is, shared characteristics that have been inherited from a common ancestor. The more recently two species have shared a common ancestor,

the more homologies they share, and
the more similar these homologies are.

Until recent decades, the study of homologies was limited to

anatomical structures and
pattern of embryonic development.

However, since the birth of molecular biology, homologies can now also be studied at the level of

Anatomical homology: an example

The figure shows the bones in the forelimbs of three mammals: human, whale, and bat (obviously not drawn to the same scale!). Although used for such different functions as throwing, swimming, and flying, the same basic structural plan is evident in them all. In each case, the bone shown in color is the radius.

Body parts are considered homologous if they have

the same basic structure
the same relationship to other body parts, and, as it turns out,
develop in a similar manner in the embryo.

It seems unlikely that a single pattern of bones represents the best possible structure to accomplish the functions to which these forelimbs are put. However, if we interpret the persistence of the basic pattern as evidence of inheritance from a common ancestor, we see that the various modifications are adaptations of the plan to the special needs of the organism. It tells us that evolution is opportunistic, working with materials that have been handed down by inheritance.

Embryonic Development

The embryonic development of all vertebrates shows remarkable similarities as you can see from these drawings (supplied by Open Court Publishing Company). The drawings in the top row are of the embryonic stage called the pharyngula. At this stage ("I") they all contain a:

notochord
dorsal hollow nerve cord
post-anal tail, and
a series of paired branchial grooves.

The branchial grooves are matched on the inside by a series of paired gill pouches. In fishes, the pouches and grooves eventually meet and form the gill slits, which allow water to pass from the pharynx over the gills and out the body.

In the other vertebrates shown here, the grooves and pouches disappear. In humans, the chief trace of their existence is the eustachian tube and auditory canal which (interrupted only by the eardrum) connect the pharynx with the outside of the head.

Recapitulation

The idea that embryonic development repeats that of one's ancestors is called recapitulation. It is often expressed as "ontogeny recapitulates phylogeny"; that is, embryonic development (ontogeny) repeats phylogeny (the genealogy of the species).

This is a distortion of the truth. It implies, for example, that early in our embryonic development we go through a fishlike stage. We do not. Rather, we pass through some (not all) of the embryonic stages that our ancestors passed through. Therefore, we find that the more distantly related two vertebrates are, the shorter the period during which they pass through similar embryonic stages (fish and human) and vice versa (fish and salamander).

We should also keep in mind that embryonic development prior to the pharyngula (stage I) may also be very different in the different groups. For example, while the pharyngulas of the human and the salamander look quite similar, their earlier development, starting with their fertilized eggs, are very different.

The idea that "ontogeny recapitulates phylogeny" was proposed over a century ago by the biologist Ernst Haeckel. He also made the drawings on which the drawings above are based. Periodically, people rediscover that in making them, he altered certain details to emphasize his theory. Though they are schematic, the story they illustrate here has stood the test of time.

Giant Pandas Research Station

2009-12-10T23:09:00.000-08:00

The San Diego Zoo has had a love affair with giant pandas ever since two of the black-and-white bears came to visit in 1987. After years of red tape and tons of application paperwork, the Zoo and China agreed on a 12-year research loan of two giant pandas, Bai Yun and Shi Shi. A brand-new exhibit area was built for our panda guests, which has since been expanded and renovated and is now called the Giant Panda Research Station. Although we currently have four giant pandas, our facility can comfortably house up to six!

Today our giant pandas enjoy deluxe accommodations with larger exhibit areas and extra vegetation and climbing structures. You'll enjoy the newer exhibit area too, with its winding, elevated viewing paths that give great panda-watching opportunities into the two main enclosures.

Next to the public panda viewing area is the building that houses the Giant Panda Team, made up of the pandas' keepers and researchers who observe and study giant panda behavior in an effort to learn all we can about these endangered bears. Be sure to stroll through the Giant Panda Discovery Center, located nearby. It includes a climb-in panda den, interactive exhibits, and even a chance to find out what pandas sound and smell like!

Fun facts

The People's Republic of China sent two giant pandas, Basi and Yuan Yuan, to the San Diego Zoo for a 200-day loan in 1987. More than two million people were able to view the pandas during their stay.
On August 21, 1999, Bai Yun gave birth to Hua Mei, the first giant panda born in North America to survive to adulthood. Millions of people around the world watched Hua Mei grow up via the Zoo's Panda Cam.
In 1979, the Zoo began working with Chinese zoos to help many of China's endangered animals, including red pandas, takins, and Manchurian cranes.
A panda narrator is at the panda's main viewing area daily to share the latest news and to answer guests' questions about the "bamboo bears."
Bamboo is grown on Zoo grounds and at several off-grounds locations to supply the pandas with their daily meals.
The San Diego Zoo has the largest number of giant pandas in the United States.

Helping giant pandas

Visiting the San Diego Zoo and the Wild Animal Park helps support our studies of wild giant panda populations. Our Applied Animal Ecology Division established its first conservation science program for wild pandas at the Foping Nature Reserve in China in 2006. Over the next three years, the program will be utilizing radiotelemetry to research several important areas to futher our understanding of natural giant panda behavior and ecology. These include: mating strategies and genetic diversity of panda populations, denning ecology, and human disturbance.

Rare Komodo Born at Singapore Zoo

2009-12-10T23:00:00.000-08:00

Singapore Zoo has successfully bred the highly-endangered Komodo dragon, officials said on Monday, reporting that the rare baby reptile was in good health.

The 40-centimeter hatchling is the first Komodo dragon born in an Asian zoo outside Indonesia, the native home of the world’s largest lizard species, a spokeswoman said.

In a press statement, assistant director of zoology Biswajit Guha said the hatching of the Komodo dragon, whose gender has not been confirmed, “is one of the most significant moments” for the zoo, one of Singapore’s top attractions.

The breeding of Komodo dragons in captivity “is fraught with difficulties due to incompatible pairings, dearth of experience in egg incubation and over-representation of males in zoos,” he said.

The reptiles are considered one of Indonesia’s national treasures. Komodos can grow up to three meters in length and weigh up to 140 kilograms. They are listed as “vulnerable” in the International Union for Conservation of Nature’s Red List of Threatened Species.

Only 3,000 of the poisonous lizards, native to Komodo and a few other islands in eastern Indonesia, remain in the wild, according to another campaign group, The Nature Conservancy, which does fieldwork in the area.

The reptiles live on a diet of large mammals, reptiles and birds, but have been known to attack humans. An Indonesian fisherman was mauled to death by a Komodo dragon in March.

Origin of Komodo Dragon

2009-12-10T22:50:00.001-08:00

Dragons may come from the land Down Under. Scientists now find that the world's largest living lizard species, the Komodo dragon, most likely evolved in Australia and dispersed westward to its current home in Indonesia.

In the past, researchers had suggested the Komodo dragon (Varanus komodoensis) developed from a smaller ancestor isolated on the Indonesian islands, evolving its large size as a response to lack of competition from other predators or as a specialist hunter of pygmy elephants known as Stegodon.

However, over the past three years, an international team of scientists unearthed numerous fossils from eastern Australia dated from 300,000 years ago to roughly 4 million years ago that they now know belong to the Komodo dragon.

"When we compared these fossils to the bones of present-day Komodo dragons, they were identical," said researcher Scott Hocknull, a vertebrate paleontologist at the Queensland Museum in Australia.

For the last 4 million years, Australia has been home to the world's largest lizards, including the 16-foot-long giant (5 meters) called Megalania, once the world's largest terrestrial lizard but which died out some 40,000 years ago.

"Now we can say Australia was also the birthplace of the three-meter (10 foot) Komodo dragon," Hocknull said.

The researchers said the ancestor of the Komodo dragon most likely evolved in Australia and spread westward, reaching the Indonesian island of Flores by 900,000 years ago. Comparisons between fossils and living Komodo dragons on Flores show that the lizard's body size has remained relatively stable since then.

Further support for this notion of dispersal from Australia comes from the island of Timor, located between Australia and Flores. Three fossil specimens from Timor represent a new, as yet unnamed species of giant monitor lizard, which was larger than the Komodo dragon, although smaller than Megalania. More specimens of this new giant lizard are needed before the species can be formally described.

"There are a lot of things we just simply don't know about this part of the world - Indonesia to Australia," Hocknull told LiveScience. "In recent years this region has thrown up remarkable discoveries - a new species of hominid, the 'Lost World' in New Guinea boasting dozens of new species having never met humans, and now an island chain of giant lizards, including the largest of them all, Megalania from Australia. However, they all went extinct, except the Komodo dragon. The big question now is why? The south-east Asian to Australian region is a hot-spot of new and exciting discoveries."

All these huge lizards were once common in Australasia for more than 3.8 million years, having evolved alongside large mammalian carnivores, such as Thylacoleo, the so-called 'marsupial lion.' The Komodo dragon is the last of these giants, but within the last 2,000 years, their populations have diminished severely, most likely due to humans, and they are now vulnerable to extinction, living now on just a few isolated islands in eastern Indonesia, between Java and Australia.

"Understanding the past history of a species is absolutely fundamental to determining its potential trajectory in the future, its responses to climate change, habitat change and extinction events," Hocknull said. "The Komodo dragon's fossil record shows that it is a resilient species - resilient to major climatic changes throughout its past, surviving extinction events which wiped out contemporary megafauna species."

One question that now pops up is why the Komodo dragon went extinct on Australia while surviving on a few isolated Indonesian isles. Hocknull noted that climate was an unlikely suspect, as "climate impacts species on islands just as much as a big continent like Australia. In Australia there is plenty of habitat which could be conducive to Komodo dragons. If you released them in Australia today they would probably do quite well."

Were humans involved? "We have no evidence for this because the youngest Komodo fossils in Australia are around 300,000 years old, well before humans arrived. So we don't know whether the Komodo dragons in Australia died out before humans arrived or after. So the jury will remain out on this question until a better fossil record is found."

Hocknull noted these islands of lizards are each, in a sense, individual experiments in evolution that shed light not only on the past of these lizards, but potentially also on the future of the world.

"It's a perfect place to see how life adapts and evolves in response to major environmental impacts, like sea level change, climatic changes, catastrophes - tsunamis and volcanic eruptions - plus each island has received modern humans at one time or another," he explained. "What were their impacts and how did species cope? This will be our Rosetta Stone when understanding how species will respond to future climate change."

The scientists will detail their findings on Sept. 30 in the journal PLoS ONE.

Biology Department on USU Indonesia

2009-12-10T22:45:00.000-08:00

Faculty of Mathematics and Natural Sciences (FMNS) was founded on September 7^th, 1955 and inaugurated by the former Vice President of Republic of Indonesia, Drs.Mohammad Hatta and former Minister of Education and Culture, Prof. Ir. Soewandi.

Due to the regional conflict, the faculty was closed in 1958 and reopened in 1962 initiated by Biology Department. Department of Pharmacy and Department of Chemistry were respectively established in 1964 and 1965 and two more departments, Physics and Mathematics, were opened in 1996.

Four departments have been accredited, i.e. Pharmacy, Biology, Chemistry and Mathematics Departments. Besides undergraduate programs, FMNS has also graduate programs in Chemistry, Biology and Pharmacy. It offers Apothecary Certification program. The Department of Pharmacy supervises the operation of the private college of pharmacy in Riau, Jambi and Palembang provinces.

To be able to compete in global labor market, the students are equipped with skills and competency. In addition to their fields of study, FMNS also provides the students with English and computer skills. The administration of FMNS encourages the department to conduct classes in English as an embryo for the international class wherein 75% of courses are conducted in English. This class has been conducted since 2002 by the Chemistry Department.

Teaching Staff

FMNS has 208 teaching staff members, with the qualification of PhD (41), Master (120) Bachelor (47), and Professors (18). To improve the quality of teaching staff, the faculty encourages and facilitates them to take Master and PhD in Indonesia as well as abroad. Currently, 52 of them are accomplishing their PhD and M.Sc studies.

Among the teaching staff earning the award are Prof.Dr Dayar Arbain who received King Bouduin Award (1993), Convocation Award (1993), and Who’s Who in The World 1999; and Prof.Dr. Edison Munaf in “Who and Who in the World”, 7^th edition (1983), 11^th Edition (1997) Marquish Publisher USA, and National Outstanding Lecturer No. III of Indonesia University Lecturer competition.

Research Activities

Each year, staff members in the FMNS successfully obtain grants from various sources. The grants come from different sources such as Minister of National Education, Minister of Research and Technology, Andalas University, Special Research Grant from Vice-President RI, UNESCO, WWF, World Bank, Kehati, ODA, IFS, JICA, etc.

Researches in Faculty of Mathematics and Natural Science include pure and applied researches and researches for development. Most of the researches are carried out in the area of biological resources, chemistry and bioactivity of medicinal plants, environmental analysis, chemistry of natural product, statistic and electronic instrument.

To promote researches and exchanges with other scientific communities, the FMNS organizes several activities such as workshop, national and international seminars. Regional Seminar and Workshop on Photochemical Survey in Natural Products of Chemistry were held in 1984 and 1987. The 1989 National Congress on Biology was organized by Biology Department. The seminar on “The Role of Chemistry in Industry and Environment” and “Workshop on Natural Products of Chemistry” has been the annual agenda of Department of Chemistry since 1998 and 2001 respectively. FMNS in collaboration with UNESCO organized “The International Seminar on Chemistry of Rainforest Plants and Their Utilization for Development” in 1992, 1996, and 2001. Since 1992, the Department of Chemistry has organized an annual national seminar on chemistry in industry and environment, under various topics/themes.

FMNS has established cooperation in education and research with several national and international institutions, i.e. The University of Western Australia, The University of Melbourne, Gifu University, Shimane University, Universite de Rennes I, Kyoto University, and Universiti Putra Malaysia. This cooperation has granted scholarships to a number of FMNS staff members to pursue some degrees at some universities abroad.

Collaborations in researches between FMNS and industries such as PT Semen Padang, PT. Indofarma, PT. Kimia Farma, BATAN, BPPT, LEMIGAS, and local government have always been nurtured. They are aimed at developing local economy and improving the applicability of FMNS research to the actual need of industries.

FMNS is provided with more than 40 laboratories and several biology research fields. At present, it has four Centers of Studies i.e. The Sumatra Natural Study Center, The Medicinal Plants Research Center, The Natural Resources Research Center, and The Chemistry of Natural Products Research Center. The Botanical Garden of Andalas University, which includes The Forest of Biological Research and Education, Arboretum, and Medicinal Plants Garden, are managed by FMNS staffs.

Scientific Journals

FMNS publishes three accredited National scientific journals, i.e. Jurnal Sains dan Teknologi Farmasi / Journal of Pharmaceutical Science and Technology, published by Pharmacy Department, Chemistry Journal of Andalas / Jurnal Kimia Andalas published by Chemistry Department; and Jumpa / Journal of Mathematics and Natural Science published by Faculty of Mathematics and Natural Sciences.

Herbarium

The Herbarium of Andalas University / ANDA, managed by the Department of Biology, has an extensive collection of plants from all over Sumatra Island especially West Sumatra, Riau, and Jambi Provinces. The number of specimens amounts to 65.000. This unit supports academic and research activities for students and staffs at FMNS as well as for other institutions.

Alumnus/Former students

Up to now, Faculty of Mathematics and Natural Sciences has 3,805 graduates and 894 Apothecaries. They occupy different kinds of job, i.e. lecturer, teacher, researcher, civil servant, entrepreneur, industrialist, and so on. Among them are Drs.Sjofiarman Tarmizi, the Marketing Director of Kimia Farma Company, Drs. Rozyan Yazid, Financial Director of BATAN, Director of Tripolyata, Drs Mulyadi, MBA, Director of Molinev, Dr. Zainal Lamid, the Head of Agricultural Technology Research Center / BPTP.

Emergence of Hepatitis C Virus Genotype 4: Phylogenetic Analysis Reveals Three Distinct Epidemiological Profiles

2009-12-10T22:22:00.000-08:00

AMC Liver Center, Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands,¹ Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands,² Cluster of Infectious Diseases, Amsterdam Health Service, Amsterdam, The Netherlands,³ Department of Internal Medicine, Academic Medical Center, University of Amsterdam, CINIMA, Amsterdam, The Netherlands,⁴ Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands⁵

Received 11 June 2009/ Returned for modification 19 August 2009/ Accepted 24 September 2009

Hepatitis C virus (HCV) genotype 4 (HCV-4) infection is consideredto be difficult to treat and has become increasingly prevalentin European countries, including The Netherlands. Using a molecularepidemiological approach, the present study investigates thegenetic diversity and evolutionary origin of HCV-4 in Amsterdam,The Netherlands. Phylogenetic analysis of the NS5B sequences(668 bp) obtained from 133 patients newly diagnosed with HCV-4infection over the period from 1999 to 2008 revealed eight distinctHCV-4 subtypes; the majority of HCV-4 isolates were of subtypes4d (57%) and 4a (37%). Three distinct monophyletic clusterswere identified, with each one having a specific epidemiologicalprofile: (i) Egyptian immigrants infected with HCV-4a (n = 46),(ii) Dutch patients with a history of injecting drug use infectedwith HCV-4d (n = 44), and (iii) Dutch human immunodeficiencyvirus (HIV)-positive men who have sex with men (MSM) infectedwith HCV-4d (n = 26). Subsequent molecular clock analyses confirmedthat the emergence of HCV-4 within these three risk groups coincidedwith (i) the parenteral antischistosomal therapy campaigns inEgypt (1920 to 1960), (ii) the popularity of injecting druguse in The Netherlands (1960 to 1990), and (iii) the rise inhigh-risk sexual behavior among MSM after the introduction ofhighly active antiretroviral therapy (1996 onwards). Our datashow that in addition to the influx of HCV-4 strains from countrieswhere HCV-4 is endemic, the local spread of HCV-4d affectinginjecting drug users and, in recent years, especially HIV-positiveMSM will further increase the relative proportion of HCV-4-infectedpatients in The Netherlands. HCV-4-specific agents are drasticallyneeded to improve treatment response rates and decrease thefuture burden of HCV-4-related disease.

Charles Darwin was Wrong !!!

2009-12-10T20:05:00.001-08:00

If a fair maiden kisses a frog which instantly changes into a handsome prince, we would call it a fairy tale. But if the frog takes 40 million years to turn into a prince, we call it evolution. Time is the evolutionist's magic wand. Fairy tales come in many forms!

We often hear that science has proved Darwin's theory of evolution. Nothing could be further from the truth. You see, people often confuse scientific fact with scientific theory. Current scientific theory regarding the evolution model does conflict with the creation model. But the facts of science do not! There are many scientists who fully accept the creation model of origins. Surprised?

Darwin's theory of evolution says that over millions of years simple life forms (one celled creatures) slowly evolved into complex life forms (fish), and that one kind of animal evolved into another kind (ape to man).The creation model, on the other hand, says that all life forms were created in six, 24 hour days. If the creation model is wrong and man actually did evolve in small graduations over a long period of time, we should find ample fossil evidence of links in intermediate stages of transition. For decades, evolutionists have searched for fossils of these links to prove the creation model wrong. Although millions of fossils have been unearthed, even evolutionists acknowledge that the links have not been found.

Darwin taught that many little changes over a long period of time will add up to big changes. Darwin predicted that the fossil record would either prove or falsify his theory. Darwin realized the difficulty the fossil record (missing links) gave his theory when he said, "Why, if species have descended from other species by fine graduation, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion, instead of the species being, as we see them, well defined?" Today, top evolutionists know that Darwin's predictions of what the fossil record would reveal have failed.

It is a well guarded fact that many evolutionists rejected Darwin's theory of evolution over 20 years ago. Stephen Jay Gould, a professor at Harvard University and one of the foremost authorities on evolution in the world said, "The extreme rarity of transitional forms (missing links) in the fossil record persists as the trade secret of paleontologists,...we view our data as so bad that we never see the very process we profess to study". Natural History, Vol. 86. Gould is still an evolutionist, he just rejects much of Darwin's theory.

Mark Ridley, another evolutionist from Oxford University said in The New Scientist magazine in June 1981 p 831, "a lot of people just do not know what evidence the theory of evolution stands upon. They think that the main evidence is the gradual descent of one species from another in the fossil record. ...In any case, no real evolutionist, whether gradualist or punctuationalist, uses the fossil record as evidence in favor of the theory of evolution as opposed to special creation." Because the fossils simply do not support many small changes between kinds over a long period of time, many evolutionists have at least been honest enough to admit this and have come up with a new theory called, "punctuated equilibrium" or the "hopeful monster theory". From the fossil record, they know that change didn't take place in small gradual steps, so they assume that the change took place in quick "quantum leaps" over long periods of time. In Darwin's theory, the changes were so slow and gradual that science cannot observe the evolution. The new theory says the change takes place so quickly it that too cannot be observed. Unobservable science? What a contradiction!

Evolutionists tell us in the new "punctuationalist" theory, that, in effect, a lizard laid an egg and out pops a baby bird. Because of the compete lack of missing links, evolutionists now accept as fact what creationists predicted from the creation model all along; namely, that no transitional fossils would be found. Evolutionists that still use Darwin or the fossil record as evidence of their theory in the '90's, are like stubborn and closed minded old country doctors who have not kept up with the latest developments of science. Then there are those who cannot even consider the possibility that there is a creator God. These scientists are so biased that they cannot not see how much better all the scientific data fits the creation model of origins as opposed to the evolution model.

Archaeopteryx, a star attraction "link" between reptile and bird has been refuted . Nature Magazine, Vol. 322, p677, "Fossil Bird Shakes evolutionary Hypotheses", reported this in 1986, "Fossil remains claimed to be of two crow-sized birds 75 million years older than Archaeopteryx have been found...a paleontologist at Texas Tech University, who found the fossils, says they have advanced avian features. ...tend to confirm what many paleontologists have long suspected, that Archaeopteryx is not on the direct line to modern birds."

Australopithecus or "Lucy", another big star to the evolutionists' stage show, has also been discarded by many evolutionists. Even the Leakey's never believed it had anything to do with the evolution of man. With good reason, they considered it simply and extinct ape. It stood three feet tall, had arms that hung down to the ankles and had a brain one third the size of humans. Adrienne Zihlman, U.C. Santa Cruze, said, "Zihlman compares the pigmy chimpanzee to 'Lucy', one of the oldest hominid fossils known, and finds the similarities striking. They are almost identical in body size, in stature and in brain size...indicates that pygmy chimps use their limbs much the same way Lucy did..." Science News, Vol. 123, Feb. 5, 1983, p89

So Good-bye Lucy! Au revoir Archaeopteryx! R.I.P. Darwin!

Although knowledgeable evolutionists buried most of Darwin's theory over 20 years ago, they still cling to a few parts like "time". Lots of time! Darwin and modern evolutionists still have faith that given long enough periods of time, frogs would evolve into handsome princes. Today they just can't explain how! With enough time the impossible becomes probable! What today's evolutionists lack for hard proof in the fossil record they make up for in blind faith in a magic wand called time. Have you ever considered that when God created the universe in six short 24 hour days, He may have been taking His time?

8 Bio-Study Tips

2009-12-10T19:54:00.000-08:00

Studying for biology can seem overwhelming, but it doesn't have to be. If you follow a few simple steps, studying for biology will be less stressful and more enjoyable. I've compiled a list of several helpful biology study tips for biology students. Whether you're in middle school, high school, or college, these tips are bound to produce results!

Bio-Study Tip 1

Always read the lecture material before the classroom lecture. I know, I know--you don't have time, but believe me, it makes an immense difference.

Bio-Study Tip 2

Biology, like most sciences, is hands-on. Most of us learn best when we are actively participating in a "topic." So make sure to pay attention in lab sessions and actually perform the experiments. Remember, you won't be graded on your lab partner's ability to perform an experiment, but your own.

Bio-Study Tip 3

Sit in the front of the class. Simple, yet effective. College students, pay close attention. You'll need recommendations one day, so make sure your professor knows you by name and you aren't 1 face in 400.

Bio-Study Tip 4

Compare notes with a friend. Since much of biology tends to be abstract, have a "note buddy." Each day after class compare notes with your buddy and fill in any gaps. Two heads are better than one!

Bio-Study Tip 5

Use the "lull" period between classes to immediately review the biology notes you have just taken.

Bio-Study Tip 6

Don't cram! As a rule, you should start studying for biology exams a minimum of two weeks prior to the exam.

Bio-Study Tip 7

This tip is very important -- stay awake in class. I've observed too many people snoozing (even snoring!) in the middle of class. Osmosis may work for water absorption, but it won't work when it comes time for biology exams.

Bio-Study Tip 8

Find some useful resources to help you when you study after class. Here are a few resources that I would suggest to help make learning biology interesting and fun:

Animal Cams
Animal Webcams give you a unique view into the lives of animals. They allow you to observe creatures in their natural or artificial environments.

Biology Homework Help
Need help with your biology homework? Find resources and information to help you answer some of your biology homework questions.

Online Dissections
Online dissections allow you to experience actual dissections without all of the mess.

Plant Biology
Learn about plant biology, plant viruses, and more. Also, discover some interesting and unusual plants

Biology Science Fair Projects
Resources and ideas for creating wining biology related science fair projects. Find information on science fair books, models, and more.

Share Your Opinions

Have your own biology study tips? Come over to the Biology Forum and share your thoughts, opinions and feelings. Until next time...

Mendel's Law of Segregartion

2009-12-10T19:40:00.000-08:00

How are traits passed from parents to offspring? The answer is by gene transmission. Genes are located on chromosomes and consist of DNA. They are passed from parents to their offspring through reproduction. The principles that govern heredity were discovered by a monk named Gregor Mendel in the 1860's. One of these principles is now called Mendel's law of segregation.

Mendel worked with pea plants and selected seven traits to study that each occurred in two different forms. For instance, one trait he studied was pod color. Some pea plants have green pods and others have yellow pods. Since pea plants are capable of self fertilization, Mendel was able to produce true-breeding plants. A true-breeding yellow-pod plant for example would only produce yellow-pod offspring. Mendel then began to experiment to find out what would happen if he cross-pollinated a true-breeding yellow pod plant with a true-breeding green pod plant. He referred to the two parental plants as the parental generation (P generation) and the resulting offspring were called the first filial or F1 generation.

When Mendel performed cross-pollination between a true-breeding yellow pod plant and a true-breeding green pod plant, he noticed that all of the resulting offspring, F1 generation, were green. He then allowed all of the green F1 plants to self-pollinate. He referred to these offspring as the F2 generation. Mendel noticed a 3:1 ratio in pod color. About 3/4 of the F2 plants had green pods and about 1/4 had yellow pods. From these experiments Mendel formulated what is now known as Mendel's law of segregation.

Mendel's law of segregation states that allele pairs separate or segregate during gamete formation, and randomly unite at fertilization. There are four main concepts involved in this idea. They are:

1. There are alternative forms for genes. This means that a gene can exist in more than one form. For example, the gene that determines pod color can either be (G) for green pod color or (g) for yellow pod color.

2. For each characteristic or trait organisms inherit two alternative forms of that gene, one from each parent. These alternative forms of a gene are called alleles. The F1 plants in Mendel's experiment each received one allele from the green pod parent plant and one allele from the yellow pod parent plant. True-breeding green pod plants have (GG) alleles for pod color, true-breeding yellow pod plants have (gg) alleles, and the resulting F1 plants have (Gg) alleles.

3. When gametes (sex cells) are produced, allele pairs separate or segregate leaving them with a single allele for each trait. This means that sex cells contain only half the compliment of genes. When gametes join during fertilization the resulting offspring contain two sets of alleles, one allele from each parent. For example, the sex cell for the green pod plant had a single (G) allele and the sex cell for the yellow pod plant had a single (g) allele. After fertilization the resulting F1 plants had two alleles (Gg).

4. When the two alleles of a pair are different, one is dominant and the other is recessive. This means that one trait is expressed or shown, while the other is hidden. For example, the F1 plants (Gg) were all green because the allele for green pod color (G) was dominant over the allele for yellow pod color (g). When the F1 plants were allowed to self-pollinate, 1/4 of the F2 generation plant pods were yellow. This trait had been masked because it is recessive. The alleles for green pod color are (GG) and (Gg). The alleles for yellow pod color are (gg).

From Mendel's law of segregation we see that the alleles for a trait separate when gametes are formed (through a type of cell division called meiosis). These allele pairs are then randomly united at fertilization. If a pair of alleles for a trait are the same they are called homozygous. If they are different they are called heterozygous. In the first example (Figure A), the F1 plants were all heterozygous for the pod color trait. Their genetic makeup or genotype was (Gg). Their phenotype or expressed physical trait was green pod color.

The F2 generation pea plants (Figure B) showed two different phenotypes (green or yellow) and three different genotypes (GG, Gg, or gg). The genotype determines the phenotype that is expressed. The F2 plants that had a genotype of either (GG) or (Gg) were green. The F2 plants that had a genotype of (gg) were yellow.

The phenotypic ratio that Mendel observed was 3:1, 3/4 green plants to 1/4 yellow plants. The genotypic ratio however was 1:2:1. The genotypes for the F2 plants were 1/4 homozygous (GG), 2/4 heterozygous (Gg), and 1/4 homozygous (gg).

New Strain of Salmonella

2009-12-10T19:30:00.000-08:00

Antibiotic resistant bacteria have become a worldwide public health issue. Researchers have identified a new strain of Salmonella typhimurium, called ST313, that has become more virulent among people living in sub-Saharan Africa regions.

The bacteria have undergone genetic changes that have allowed them to not only become resistant to commonly used antibiotics, but they are also less responsive to drugs in which they have not gained resistance. Researcher Dr. Chisomo Msefula states, "Our findings show that ST313 has acquired a block of genes that make it resistant to the common antibiotics. The genes jumped into ST313 on a mobile genetic element called a transposon, bringing with it additional genes that make the strain more deadly." The researchers hope that insight gained from this study can be used to develop new vaccines to fight against these and similar pathogens.