Future Genomics

Super-Mendelian inheritance mediated by CRISPR–Cas9

2019-01-29T21:50:00.000-08:00

A gene drive biases the transmission of one of the two copies of a gene such that it is inherited more frequently than by random segregation. Highly efficient gene drive systems have recently been developed in insects, which leverage the sequence-targeted DNA cleavage activity of CRISPR–Cas9 and endogenous homology-directed repair mechanisms to convert heterozygous genotypes to homozygosity. If implemented in laboratory rodents, similar systems would enable the rapid assembly of currently impractical genotypes that involve multiple homozygous genes (for example, to model multigenic human diseases). However, such a system has not yet been demonstrated in mammals. Here an active genetic element that encodes a guide RNA, which is embedded in the mouse tyrosinase (Tyr) gene, is used to evaluate whether targeted gene conversion can occur when CRISPR–Cas9 is active in the early embryo or in the developing germline. Although Cas9 efficiently induces double-stranded DNA breaks in the early embryo and male germline, these breaks are not corrected by homology-directed repair. By contrast, Cas9 expression limited to the female germline induces double-stranded breaks that are corrected by homology-directed repair, which copies the active genetic element from the donor to the receiver chromosome and increases its rate of inheritance in the next generation. These results demonstrate the feasibility of CRISPR–Cas9-mediated systems that bias inheritance of desired alleles in mice and that have the potential to transform the use of rodent models in basic and biomedical research.

http://www.nature.com/articles/s41586-019-0875-2

Plants fight fungi using kiwellin proteins

2019-01-20T21:56:00.004-08:00

Fungal pathogens of plants often secrete proteins that aid growth and reproduction in the host. These are termed effector proteins, and some are deregulated metabolic enzymes that manipulate key metabolic pathways in plants. A new protein has been identified in maize which blocks the enzymatic activity of a fungal effector enzyme, thereby thwarting the effector’s ability to influence maize metabolism in a way that limits the plant’s defence response.

For more details: https://www.nature.com/articles/d41586-019-00092-2

INTRONS HELP TO OVERCOME STARVATION

2019-01-20T21:46:00.004-08:00

Introns are ubiquitous features of all eukaryotic cells. Introns need to be removed from nascent messenger RNA through the process of splicing to produce functional proteins.Physical presence of introns in the genome promotes cell survival under starvation conditions. A systematic deletion set of all known introns in budding yeast genes indicates that, in most cases, cells with an intron deletion are impaired when nutrients are depleted. This effect of introns on growth is not linked to the expression of the host gene, and was reproduced even when translation of the host mRNA was blocked. Transcriptomic and genetic analyses indicate that introns promote resistance to starvation by enhancing the repression of ribosomal protein genes that are downstream of the nutrient-sensing TORC1 and PKA pathways.

www.nature.com/articles/s41586-018-0859-7?fbclid=IwAR3GQJDf7E_qBhZ6zKLjnhLipzubL7pxfsXbyJhaAz42MYyPTfYyJe08vJQ

Bacteria Live in Brain Cells

2018-11-13T23:10:00.001-08:00

BACTERIA IN BRAIN

Images of human brain slices reveal bacteria, shown here to the left of a blood vessel—tantalizing but preliminary evidence of a “brain microbiome.”
https://www.sciencemag.org/news/2018/11/do-gut-bacteria-make-second-home-our-brains

Cross-talk between alternate polyadenylation and miRNA

2018-11-13T23:07:00.001-08:00

3′ UTRs play important roles in the gene regulation network via their influence on mRNA stability, translational efficiency, and subcellular localization. For a given gene, 3′ UTRs of different lengths generated by alternative polyadenylation (APA) may result in functional differences in regulation. The mechanistic details of how length changes of 3′ UTRs alter gene function remain unclear. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3′ UTRs were bound with more polysomes in six cell lines but not in NIH3T3 cells, suggesting that changing 3′ UTRs to shorter isoforms may lead to a higher gene translational efficiency. By interfering with the expression of TNRC6A and analyzing AGO2-PAR-CLIP data, we revealed that the APA effect on translational efficiency was mainly regulated by miRNAs, and this regulation was cell cycle dependent. The discrepancy between NIH3T3 and other cell lines was due to contact inhibition of NIH3T3. Thus, the crosstalk between APA and miRNAs may be needed for the regulation of protein translational efficiency.

For Details visit: https://genome.cshlp.org/content/28/11/1656.full.pdf+html

Cancer Moonshot initiative on Cancer Genomics

2016-06-30T23:22:00.002-07:00

You are aware that cancer is the second most deadly disease killing thousands of people daily. As cancer is a complex disease application of high throughput genomics methods opens up new avenues for understanding and treating the disease. Cancer genomics programme is moving to the next level because of the initiatives made by Cancer Moonshot Programme (Click here to read more about Cancer Moon Shot Programme). As part of the US-Cancer Moonshot and the US-President’s Precision Medicine Initiative, Foundation Medicine is more than doubling the total number of patients represented within the NCI's Genomic Data Commons (GDC), bringing its total to over 32,000 patients accumulated in just over a month. At its launch in early June, the GDC already shared more than five petabytes of raw unprocessed genomic data from large research projects on nearly thirty tumor types from more than 14,000 patients, along with associated clinical data (e.g. clinical diagnosis, treatment history, survival data), creating a foundational system for broad sharing and analysis of cancer genomic data, which is critical for advancing the field of precision medicine and improving the care of cancer patients.

Why I want to discuss about climate change now ?:

2016-05-31T00:39:00.002-07:00

There is a real possibility of Donald Trump becoming US president. He does not believe in climate change. Read his views below:

"Well, first of all, I’m not a believer in global warming. And I’m not a believer in man-made global warming. It could be warming, and it’s going to start to cool at some point. And you know, in the early, in the 1920s, people talked about global cooling. I don’t know if you know that or not. They thought the Earth was cooling. Now, it’s global warming. And actually, we’ve had times where the weather wasn’t working out, so they changed it to extreme weather, and they have all different names, you know, so that it fits the bill. But the problem we have, and if you look at our energy costs, and all of the things that we’re doing to solve a problem that I don’t think in any major fashion exists. I mean, Obama thinks it’s the number one problem of the world today. And I think it’s very low on the list. So I am not a believer, and I will, unless somebody can prove something to me, I believe there’s weather. I believe there’s change, and I believe it goes up and it goes down, and it goes up again. And it changes depending on years and centuries, but I am not a believer, and we have much bigger problems. You know, I talk about global warming. You know, to me, the worst global warming, and I mentioned this to you once before, is nuclear warming. That’s our global warming. That’s what I see, because we have incompetent people, and we have these rogue nations, and not even rogue nations anymore. You know, we had a case where Vladimir Putin about three months ago threw out the nuke word. And I never thought I’d hear that from a Russia. But he said they’d better, essentially, they’d better be careful, because you know, we are a nuclear nation. That was a hell of a statement for him to make. And that’s a statement that’s made because of a lack of respect."

If this is the belief of the future US president what happens to the Paris Agreement. He might scrap the agreement. If he becomes US president the world may be in trouble. I will post soon Scientific evidences available on current climate change

The 100,000 Genomes Project by UK

2015-07-03T04:19:00.001-07:00

The project will sequence 100,000 genomes from around 70,000 people. Participants are NHS patients with a rare disease, plus their families, and patients with cancer.

The aim is to create a new genomic medicine service for the NHS – transforming the way people are cared for. Patients may be offered a diagnosis where there wasn’t one before. In time, there is the potential of new and more effective treatments.

The project will also enable new medical research. Combining genomic sequence data with medical records is a ground-breaking resource. Researchers will study how best to use genomics in healthcare and how best to interpret the data to help patients. The causes, diagnosis and treatment of disease will also be investigated. We also aim to kick-start a UK genomics industry. This is currently the largest national sequencing project of its kind in the world.

Find out more about 100,000 genome project

What is the US plan for next 5 years in Plant Genomics ?

2015-07-03T04:12:00.001-07:00

NATIONAL PLANT GENOME INITIATIVE FIVE-YEAR PLAN: 2014–2018

Major objectives:

Objective 1: Develop a new generation of databases and tools to enable every step in the innovation chain from basic discovery to translation into practical application and widespread use.

Objective 2: Create a network of plant germplasm resources to meet the Nation’s research and breeding needs for the 21st century

Objective 3: Build tools to advance our understanding of plant biology and translate this knowledge into precision plant breeding for the development of sustainable systems for food, bioenergy, and industrial feedstock production

Objective 4: Empower the workforce to use a new generation of tools and resources

Objective 5: Build public-private partnerships to advance the translation of basic discoveries into practical application and support innovation in the practice of agriculture

Objective 6: Strengthen international partnerships to bring the benefits of new discoveries to all

Read the complete document for deatls

Next generation sequencing enables revisiting the concept of Non-collinear transcripts in higher Eukaryotas

2014-10-01T01:39:00.000-07:00

An interesting class of transcripts called non-collinear transcripts was found recently when genomes were sequenced with NGS methods. They are chimeric RNAs that contain sequences from multiple non-collinear positions in the genome (some of them are mapped to different chromosomes are faraway positions in the same chromosome). Though genome rearrangements are said to behind their emergence no clear mechanism is known in eukaryotes.

Structural studies of RNAs in several species have revealed that the sequences that are ultimately joined together on the same mature transcript can be encoded in separately transcribed RNAs with multiple distinct genomic origins. Individual RNAs can be transcribed on separate chromosomes or on the same chromosome but with a different the genomic order from that found in the mature RNA or on the same chromosome but transcribed from different strands, or on the same chromosome but from different alleles. Similar phenomenon was known in lower organisms and the origin was due transplicing. For examples and more details read the following papers.

Implications of chimeric non-collinear transcripts

Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants

Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Transcription-Mediated Chimeric RNAs in Prostate Cancer: Time to Revisit Old Hypothesis?

Why overexpressed proteins are toxic to E.coli ?

2013-08-30T23:57:00.002-07:00

A majority of E. coli proteins when overexpressed inhibit its growth, but the reasons behind overexpression toxicity of proteins remain unknown. Understanding the mechanism of overexpression toxicity is important from evolutionary, biotechnological and possibly clinical perspectives. Here we study sequence and functional features of cytosolic proteins of E. coli associated with overexpression toxicity to understand its mechanism. We find that number of positively charged residues is significantly higher in proteins showing
overexpression toxicity. Very long proteins also show high overexpression toxicity. Among the functional classes, transcription factors and regulatory proteins are enriched in toxic proteins, while catalytic proteins are depleted. Overexpression toxicity could be predicted with reasonable accuracy using these few properties. The importance of charged residues in overexpression toxicity indicates that nonspecific electrostatic interactions resulting from protein overexpression cause toxicity of these proteins and suggests ways to improve the expression level of native and foreign proteins in E. coli for basic research and biotechnology. These results might also be applicable to other bacterial species.

To Read the original paper published in Plos One Click here

Breaking Discovery: Eighteen species of bacteria found in troposphere (between 8-15 km above the earth)

2013-02-14T01:34:00.000-08:00

Microbes are said to be in every part of earth including the hottest (under sea volcanoes) and coldest (Polar regions) places of earth. What is being studied in Microbiology is those microbes which can be cultured. They constitute less than 1% of the total microbes in the earth. Can you believe the news that microbes exist even in troposphere which is eight kilometres above the earth. A recent study conducted by Scientists from School of Biology, School of Earth and Atmospheric Sciences, School of Civil and Environmental Engineering, School of Chemical and Biomolecular Engineering of Georgia Institute of Technology at Atlanta, USA and Chemistry and Dynamics Branch/Science Directorate, National
Aeronautics and Space Administration Langley Research Center, Hampton, USA revealed the composition and prevalence of microorganisms in the middle-to-upper troposphere (8–15 km altitude) and their role in aerosol-cloud-precipitation. They studied the microbiome of low- and high-altitude air masses sampled onboard the National Aeronautics and Space Administration DC-8 platform in the Caribbean Sea. The samples were collected in cloudy and cloud-free air masses before, during, and after two major tropical hurricanes, Earl and Karl.

Quantitative PCR and microscopy revealed that viable bacterial cells represented on average around 20% of the total particles in the 0.25- to 1-μm diameter range and were at least an order of magnitude more abundant than fungal cells, suggesting that bacteria represent an important and underestimated fraction of micrometer-sized atmospheric aerosols. The samples from the two hurricanes were characterized by significantly different bacterial communities, revealing that hurricanes aerosolize a large amount of new cells. Seventeen bacterial taxa, including taxa that are known to use C1–C4 carbon compounds present in the atmosphere, were found in all samples, indicating that these organisms possess traits that allow survival in the troposphere. Further studies are needed to find the role of these microbes on the hydrological cycle, clouds, and climate.

[Click Here to Read the Original Paper published in Proceedings of National Academy of Sciences, USA]

A fruit company has made Nonbrowning apple by genetic engineering ( gene silensing)

2013-01-17T01:05:00.005-08:00

Apples turn brown when the fruit’s phenolic compounds react with oxygen. This oxidation process is driven by polyphenol oxidase (PPO), an enzyme. When an apple’s cells are ruptured – for example, by bruising, biting or cutting – the browning reaction begins when PPO found in one part of the cell is able to react with phenolic compounds found elsewhere in the cell.

Recent mapping of apple’s genome revealed that PPO is genetically encoded in a diverse, multi-gene family. Apples have at least eight PPO genes, in three main PPO gene families. To breed a truly nonbrowning apple, all of the active PPO genes must be silenced. Arctic® apples have been genetically engineered to produce little or no PPO enzyme, so cell disruption doesn’t lead to browning.

The top 10 causes of death

2012-12-19T22:28:00.001-08:00

Low-income countries	Deaths in millions	% of deaths
Lower respiratory infections	1.05	11.3%
Diarrhoeal diseases	0.76	8.2%
HIV/AIDS	0.72	7.8%
Ischaemic heart disease	0.57	6.1%
Malaria	0.48	5.2%
Stroke and other cerebrovascular disease	0.45	4.9%
Tuberculosis	0.40	4.3%
Prematurity and low birth weight	0.30	3.2%
Birth asphyxia and birth trauma	0.27	2.9%
Neonatal infections	0.24	2.6%

Middle-income countries	Deaths in millions	% of deaths
Ischaemic heart disease	5.27	13.7%
Stroke and other cerebrovascular disease	4.91	12.8%
Chronic obstructive pulmonary disease	2.79	7.2%
Lower respiratory infections	2.07	5.4%
Diarrhoeal diseases	1.68	4.4%
HIV/AIDS	1.03	2.7%
Road traffic accidents	0.94	2.4%
Tuberculosis	0.93	2.4%
Diabetes mellitus	0.87	2.3%
Hypertensive heart disease	0.83	2.2%

High-income countries	Deaths in millions	% of deaths
Ischaemic heart disease	1.42	15.6%
Stroke and other cerebrovascular disease	0.79	8.7%
Trachea, bronchus, lung cancers	0.54	5.9%
Alzheimer and other dementias	0.37	4.1%
Lower respiratory infections	0.35	3.8%
Chronic obstructive pulmonary disease	0.32	3.5%
Colon and rectum cancers	0.30	3.3%
Diabetes mellitus	0.24	2.6%
Hypertensive heart disease	0.21	2.3%
Breast cancer	0.17	1.9%

World	Deaths in millions	% of deaths
Ischaemic heart disease	7.25	12.8%
Stroke and other cerebrovascular disease	6.15	10.8%
Lower respiratory infections	3.46	6.1%
Chronic obstructive pulmonary disease	3.28	5.8%
Diarrhoeal diseases	2.46	4.3%
HIV/AIDS	1.78	3.1%
Trachea, bronchus, lung cancers	1.39	2.4%
Tuberculosis	1.34	2.4%
Diabetes mellitus	1.26	2.2%
Road traffic accidents	1.21	2.1%

Indian Express article on GM CROP REPORT

2012-11-04T21:30:00.001-08:00

The SC must reject the biased interim report of the committee on GE crops

While hearing two writ petitions opposing genetic engineering technology in agriculture, the Supreme Court constituted a technical expert committee with six members and seven terms of reference. It asked the committee to hear interested parties and submit an interim report on open-field trials of GE crops, whether to ban them or not and what protocol should be imposed by the court if they are to be continued.

The committee submitted a confidential interim report on October 7, which soon became public and was widely covered in the media. However, the report very seriously impacts the prospects of GE crop technology in India, and was probably leaked only so that wide publicity would make it difficult for the court to reject it.

The only agricultural scientist on the technical expert committee dissociated himself, leaving five members who are biologists, but not biotechnologists, much less agricultural biotechnologists. The staunch opposition of these five to GE crop technology is well known, so it wasn’t surprising that they produced a heavily biased report. But the recommendation to ban all open-field trials of GE crops for 10 years, including the ongoing trials, surpassed even the wildest dreams of the petitioners and activists. If this recommendation is accepted, it will push Indian agricultural development back by at least two decades, surpassing the damage caused by the moratorium on Bt brinjal.

The committee overshot its mandate, digressing into a range of far-reaching issues. Fourteen of the 31 people who appeared before the committee are supporters of this technology and provided information on some of these issues, but they were sidelined. The committee was indifferent to the voluminous peer-reviewed literature of some 15 years that answered their questions. Only some of these issues are addressed here.

The fact that India is a signatory to the Convention on Biodiversity (CBD), which is dedicated to sustainable development, does not place any additional burden to hinder GE technology, since the US, Canada, China, Argentina, Brazil, etc are also signatories to the CBD and leading GE-crop adopters. The Cartagena Protocol on Biosafety (CPB) is about transboundary movement of GE crops. No provision of either CBD or CPB is meant to prevent new agricultural technologies. The precautionary principle is about moving cautiously, not an excuse to hinder technological development. The impact of a GE crop on biodiversity should be assessed on a case-by-case basis as it depends on the possibilities of gene flow to other varieties of the same crop — there has been no evidence of this in the 15 years that they have been grown, in some 30 countries.

Their efficacy, safety and the socio-economic benefits to farmers and consumers have been amply demonstrated. About 350 million people in North America have been consuming GE crop foods for over 15 years without any proven adverse effects. Bt cotton transformed India into a cotton-exporting country. But the committee was not impressed by any of this.

It wants to impose on GE crops chemical toxicology tests such as the Ames test used to determine the potential to cause cancer and the micronucleus test to determine genetic damage. It recommends that 39 tests be conducted on all GE crops, irrespective of need or relevance. This surpasses even the 31 tests (most of which are unwarranted) insisted on by the “scientific” face of Indian anti-tech activism. Biosafety tests have to be chosen for each crop, depending on the science-based need for them. A history of safe use of a crop minimises toxicology tests, and allergenicity tests are warranted only if the non-GE variety of the crop was allergenic. The technical expert committee insists on long-term and integration feeding studies, dismissing the international norm that 90-day rat feeding tests, equal to testing for 24.5 years on humans, are more than adequate, and that no new data would emerge out of longer testing. Development of a GE crop costs about US$ 140 million and takes 12 to 15 years to commercialisation. Unwarranted tests enhance these costs. All biosafety parameters stipulated for a particular GE crop have to be satisfied when the application for commercial release is considered, and insisting on any particular sequence for them is unreasonable.

The Indian biosafety regulatory system incorporated the best global practices and is very stringent. However, it is nobody’s contention that it is perfect. The Biotechnology Regulatory Authority of India (BRAI) bill meant to remedy any shortcomings is now before Parliament. Since it would take some five years before the BRAI is operationalised, the existing system should be allowed to function. If any changes are made, they cannot be applied retrospectively.

The constitution of the technical expert committee and the terms of reference seem to have been accepted by all parties. If this committee is biased and if its interim report affects the modernisation of Indian agriculture, the blame also rests on the respondents and their counsel who meekly allowed such a situation. Scientists, industry and the government should now plead before the Supreme Court that it not accept this flawed interim report.

ANSWERS TO SCIENCE POLICY QUESTIONS BY US PRESIDENTIAL CANDIDATES -1

2012-10-20T10:54:00.002-07:00

Question -1: Innovation and the Economy. Science and technology have been responsible for over half of the growth of the U.S. economy since WWII, when the federal government first prioritized peacetime science mobilization. But several recent reports question America’s continued leadership in these vital areas. What policies will best ensure that America remains a world leader in innovation?

Answer

Barack Obama:

I believe that in order to be globally competitive in the 21st century and to create an American economy that is built to last, we must create an environment where invention, innovation, and industry can flourish. We can work together to create an economy built on American manufacturing, American energy, and skills for American workers.

I am committed to doubling funding for key research agencies to support scientists and entrepreneurs, so that we can preserve America’s place as the world leader in innovation, and strengthen U.S. leadership in the 21st century’s high-tech knowledge-based economy. To prepare American children for a future in which they can be the highly skilled American workers and innovators of tomorrow, I have set the goal of preparing 100,000 science and math teachers over the next decade. These teachers will meet the urgent need to train one million additional science, technology, engineering and math (STEM) graduates over the next decade.

Mitt Romney:

Innovation is the key to economic growth and job creation, and increasingly important to American competitiveness in the global economy. Three-quarters of all U.S. economic growth, and three-quarters of the U.S. productivity advantage over other OECD nations, is directly attributable to innovation, and wages in innovation-intensive industries have grown more than twice as fast as other wages in recent decades.

My plan for a stronger middle class will rebuild the American economy on the principles of free enterprise, hard work, and innovation. The promotion of innovation will begin on Day One, with efforts to simplify the corporate tax code, reform job retraining programs, reduce regulatory burdens, and protect American intellectual property around the world.

A Growth Agenda

Over the course of my campaign, I have laid out a detailed economic plan that seeks to strengthen the American economy by empowering entrepreneurs and workers and rewarding innovation. This plan emphasizes critical structural adjustments to promote growth rather than short-term fixes.

Human Capital. We must reform America’s legal immigration system to attract and retain the best and the brightest, and equip more Americans with the skills to succeed. I will raise visa caps for highly skilled foreign workers, offer permanent residence to foreign students graduating with advanced degrees in relevant fields, and restructure government retraining programs to empower individual workers and welcome private sector participation.
Taxes. We must pursue fundamental tax reform that simplifies the tax code, broadens the tax base, and lowers tax rates. I will lower the corporate tax rate to 25 percent, strengthen and make permanent the R&D tax credit, and transition to a territorial tax system. I will cut individual income tax rates across the board, and maintain today’s low tax rates on investment. And I will ensure that these changes are made permanent, so that investors and entrepreneurs are not confronted with a constantly shifting set of rules.
Regulation. We must reduce the power of unaccountable regulators by requiring that all major regulations receive congressional approval and by imposing a regulatory cap that prevents the addition of new regulatory costs. In a Romney Administration, agencies will have to limit the costs they are imposing on society and recognize that their job is to streamline and reduce burdens, not to add new ones.
Trade. We must open new markets for American businesses and workers. I will create a Reagan Economic Zone encompassing nations committed to the principles of free enterprise. At the same time, I will confront nations like China that steal intellectual property from American innovators while closing off American access to their markets.
Education. America’s K-12 education system lags behind other developed nations, and while our higher education system remains the envy of the world its costs are spiraling out of control. We must pursue genuine education reform that puts the interests of parents and students ahead of special interests and provides a chance for every child. I will take the unprecedented step of tying federal funds directly to dramatic reforms that expand parental choice, invest in innovation, and reward teachers for their results instead of their tenure. I will also ensure that students have diverse and affordable options for higher education to give them the skills they need to succeed after graduation.
Basic Research.President Obama’s misguided attempts to play the role of venture capitalist, pick winners and losers, and spend tens of billions of dollars on politically-prioritized investments have been a disaster for the American taxpayer. Yet at the same time, we must never forget that the United States has moved forward in astonishing ways thanks to national investment in basic research and advanced technology. As president, I will focus government resources on research programs that advance the development of knowledge, and on technologies with widespread application and potential to serve as the foundation for private sector innovation and commercialization.

A Foundation for Innovation

The private sector is far more effective at pursuing and applying innovation than government could ever be. However, there are key areas in which government policy must strengthen the ability of the private sector to innovate effectively.

Six French Science Academies Dismiss Study Finding GM Corn Harmed Rats

2012-10-20T10:39:00.000-07:00

Translation of French science academies critique of controversial Séralini GM corn study— Document Transcript

1. The French science academies’ statement on problems with the Séralini et al. study of health impacts of GM corn and Roundup herbicide on rat health, translated (via U.S.embassy in Paris). Related Dot Earth post.Given the media coverage around this issue and its impact on the public opinion, the Academies decided to jointly publish a review covering several aspects: scientific,societal, and ethical, and including recommendations.- Science aspects: the Academies would like to point several severe flaws of the article: Statistics and methodology: in the case of the Seralini 2-year study, a significantly higher number of animals should have been used as recommended by guidelines, of in the specific case of a total number of 200, a lower number of groups would have allowed to answer specific questions, such as (1) can the studied GMO have a toxic or tumorigenic impact on its own? (2) can Roundup have a toxic or tumorigenic impact on its own? (3) is there a specific impact of the combination of the 2 products? The use of small size groups of 10 animals cannot answer the specific questions. There is no significant difference between the groups, according to the results presented. Saying that animals fed with GM corn present more tumors than those receiving conventional corn has no statistical value. This finding on its own should have suspended the analysis of the contents of this article, which cannot establish any toxicity. Tumorigenesis: the words “cancer” and “cancerogenesis” do not appear in Seralini’s article, but the word “tumor” that is used is confusing because everyone thinks of cancer and this is the word that the media have taken over. The analysis of longevity rather than mortality is not satisfactory due to the statistical methodology. Considering any death occurring after the average survival as “natural” is not acceptable. The choice of the strain of Sprague-Dawley is particularly unfortunate with regard to tumorigenesis. This rat strain has a high rate of spontaneous tumors, which shows that there is a specific genetic predisposition field in these rats and also that the statistical analysis must focus on a high number of rats (which has not been done in Séralini’s experiments). Other: feed composition is not detailed, there is no dose/effect relation, the presentation of methods and results is very short.- Societal impact of the article: The orchestration of the reputation of a scientist or of a team is a serious misconduct when it helps to spread to the general public fears not based on any established conclusion. Consumers not having sufficient information, this results in increased fears of GMOs spread by 1
2. “catastrophic” media. This is particularly serious for people who consume large quantities of GMOs, as in South Africa. This is also very harmful to other countries where both use and research on GMOs may be questioned.- Ethical aspects: Orchestrated media coverage around work without strong conclusion poses a major ethical problem: that of the authors who have seen fit to organize a high scale communication campaign around these works, a process which appears to be motivated more by ideology than by the quality or relevance of the data obtained, and that of the journal that has agreed to publish data that appear very fragile on many aspects, if only statistics. The conditions of distribution to the press, which was unable to be informed in advance and therefore which had not no opportunity to comment with full knowledge of the facts, are not acceptable. Assuming that Séralini was convinced of the quality of his work and the accuracy of his conclusions, his duty was to warn as early as 2011 the highest health authorities of the country to draw their attention to the very serious danger of Roundup and the NK603 GMO for the population. Withholding this information is a serious professional misconduct on his part and on all those who were aware of the results. As for the conflicts of interest of which G.E. Seralini continuously accuses all scientists of all kinds, one can wonder about the absence of such conflicts of interest for himself and those around him given their environmental commitment and financial support they received from retailers groups advertising the absence of GMOs in the food products they sell to customers.- Questions about the publication of the article in Food and Chemical Toxicology On can wonder how such a scientifically weak article could be accepted. Failures unanimously identified in the work design are such that it is quite surprising that the peer review of a scientific journal of good reputation has accepted its publication. In any event, in science, publication by itself does not establish the proof of a scientific fact. It is the opinion of the scientific community, peers, after publication, independent confirmation of the results and integrating them in a wider data that all support one another, which will allow to pass from experiment to science facts. 2
3. - Conclusions and recommendations: It appears that the media and political hype caused by the disclosure of the results of Séralini is not based on results as indisputable as they should have been compared to the consequences of media coverage they lead to. Two responsibilities are clear. First, that of the journal that should have never accepted this article, and this is serious because the expertise of the article by journals serves as initial assessment by peers. Second, that of Séralini for having orchestrated an advance media exposure based on questionable results not bringing any start of proof. In terms of health, it is necessary firstly to reassure the population and confirm statements already given on the low quality of the article. The issues raised need to be studied by reputable researchers, not suspected of conflict of interest, and funded under public control. Broadcast media have widely reported shocking images that could only strike the viewers. They contributed to fuel totally irrational fears since the results presented are not valid science. To limit such abuse, the six Academies recommend the establishment within the Chairman of the Supreme Audiovisual Council (CSA) a "High Level Committee on Science and Technology." The mission of the High Committee would draw the attention of the Chairperson of the CSA on the media coverage of scientific work questioning knowledge shared by the vast majority of the scientific community without officials in television or radios be previously sure of their validity, while the dissemination of which could be later be "false news" will and unduly influenced deeply the French, sometimes irreversibly.

BREAKING DISCOVERY: INDEPENDENT STUDIES CONFIRM EXISTENCE OF CANCER STEM CELLS

2012-08-03T04:32:00.003-07:00

Why cancer treatment fails ? – This question is raised by family members of cancer patients around the world and Doctors and Researchers were unable to answer. Many recent studies have shown that one of the main reason for failures in cancer treatment could be lack of precision in targeting the right cells. But what are right cells ?. This was not difficult to answer as most researchers believed that they are the cancer stem cells but were difficult to identify as there were no proper methods available to identify them. If these cells can be identified and distinguished from other cells, treatment strategies could be more focused.

Four recent studies found a way to identify the cancer stem cells. If this is found in other cancers also, then it will change totally the parameters used for evaluating success of chemotherapy and method of treating cancers.

Finding of study -1: [from our earlier post]

Breast cancers are thought to be organized hierarchically with a small number of breast cancer stem cells (BCSCs) able to regrow a tumor while their progeny lack this ability. Recently, several groups reported enrichment for BCSCs when breast cancers were subjected to classic anticancer treatment. However, the underlying mechanisms leading to this enrichment are incompletely understood.

Using non-BCSCs sorted from patient samples, we found that ionizing radiation reprogrammed differentiated breast cancer cells into induced BCSCs (iBCSCs). iBCSCs showed increased mammosphere formation, increased tumorigenicity, and expressed the same stemness-related genes as BCSCs from nonirradiated samples. Reprogramming occurred in a polyploid subpopulation of cells, coincided with re-expression of the transcription factors Oct4, sex determining region Y-box 2, Nanog, and Klf4, and could be partially prevented by Notch inhibition. We conclude that radiation may induce a BCSC phenotype in differentiated breast cancer cells and that this mechanism contributes to increased BCSC numbers seen after classic anticancer treatment.

Findings of Study-2:

This studey tested a genetic marker that labels healthy adult neural stem cells (but not their differentiated descendents) on tumors and checked weather the marker also labels cancer stem cells in brain cancer. When they did so, they found that all tumours contained at least a few labelled cells — presumably stem cells. Tumours also contained many unlabelled cells2. The unlabelled cells could be killed with standard chemotherapy, but the tumours quickly returned. Further experiments showed that the unlabelled cells originated from labelled predecessors. When chemotherapy was paired with a genetic trick to suppress the labelled cells the tumours shrank back into “residual vestiges” that did not resemble glioblastoma.

[Stem cells stained red]

Findings of study-3

This study followed their earlier results which showed that a genetic marker that labels healthy gut stem cells also labels stem cells in benign intestinal tumours, which are precursors of cancer. In the present study a transgenic mice carrying a gene for a drug-inducible marker was used. This marker , when activated, causes labelled cells to make molecules that fluoresce one of four colours. This experiment yielded single-colour tumours consisting of several cell types, suggesting that each tumour arose from a single stem cell.

Finding of study -4:

This study was on skin cancer cells where individual cancer cells were labeled without targeting stemm cells specifically. The cells showed two distinct patterns of division: they either produced a handful of cells before petering out, or went on to produce many cells. Once again, the results pointed to a distinct subset of cells as the engine of tumour growth. What’s more, as tumours became more aggressive, they were more likely to produce new stem cells — which can divide indefinitely — and less likely to produce differentiated cells, which can divide only a limited number of times.

So, what is the future ?. These studies show that there are special cells called cancer stem cells which are responsible for tumor growth and not killing them specifically could be the reason for failure in cancer treatment using chemotherapy. We can expect targeted methods to kill them in the near future. Wish better success rate in cancer treatment soon.

Read Original article concerning this post:

Driessens, G., Beck, B., Caauwe, A., Simons, B. D. & Blanpain, C.

Defining the mode of tumour growth by clonal analysis Nature http://dx.doi.org/10.1038/nature11344 (2012).

Chann Lagadec, Erina Vlashi, Lorenza Della Donna, Carmen Dekmezian, Frank Pajonk Radiation-Induced Reprogramming of Breast Cancer Cells STEM CELLS Volume 30, Issue 5, pages 833–844, May 2012 (2012)

Chen, J. et al. A restricted cell population propagates glioblastoma growth after chemotherapy

Nature http://dx.doi.org/10.1038/nature11287 (2012).

Schepers, A. G. et al. Lineage Tracing Reveals Lgr5+ Stem Cell Activity in Mouse Intestinal Adenomas Sciencehttp://dx.doi.org/10.1126/science.1224676 (2012).

Aged termites carry out suicide missions on behalf of their nest mates.

2012-07-27T02:27:00.001-07:00

Biologists led by biochemist Robert Hanus of the Academy of Sciences of the Czech Republic in Prague found something strange with termites in a forest in French Guiana. The strange thing is presence of unique spots of blue on the backs of the insects in one nest [see figure below]. When touched with forceps the termites having these spots exploded. Further study of these blue spots showed that they contain explosive crystals. These spots (crystals) were found only on the backs of the oldest termites in the colony. Their study concluded that the aged termites carry out suicide missions on behalf of their nest mates.

After their initial observation, the team carried out field studies of Neocapritermes taracua termites and discovered that those with the blue spots also exploded during encounters with other species of termites or larger predators. The researchers report online today in Science that the secretions released during the explosion killed or paralyzed opponents from a competing termite species. However, if the scientists removed the blue crystal from the termites, their secretions were no longer toxic.

These blue termites always had shorter, worn-down mandibles than others from the same species, indicating that they were older. Analysis of the crystals showed that they contained a novel protein that is unusually rich with copper, suggesting that it's an oxygen binding-protein. Rather than being toxic itself, it likely is an enzyme that converts a nontoxic protein into something toxic. It has been suggested that s when the termites explode, the contents of the back pouch actually interact with secretions from the salivary gland and the mixture becomes toxic. It's the first time two interacting chemicals have been shown responsible for a defense mechanism in termites.

[READ THE ORIGINAL ARTICLE PUBLISHED IN SCIENCE]

Rare Genomics Institute - giving free genomic solutions to people affected by rare diseases

2012-07-26T04:13:00.000-07:00

An estimated 250 million people worldwide suffer from rare diseases. However, because each individual disease affects such a small number of people, little funding is used to study these conditions. Consequently, these patients are left with neither hope of a cure nor understanding of the disease. Each day is a living struggle for them to find a social identity in a world where they feel socially neglected and lost. Because most rare diseases are genetic in nature, it is believed that genome sequencing has the power to help these patients in a way that conventional diagnostics cannot. However, most families affected with rare diseases are under financial strain, making access to such technologies difficult. To address this need, an institute called Rare Genomics Institute has been established.

Rare genomics Institute (RGI) is a non-profit organization that gives families afflicted by rare genetic disorders access to genome sequencing and expert analysis.It act as a hub to help families raise funds and connect them to scientists who can help them. RGI has recruited a number of researchers and clinicians from top research institutions around the world. Through RGI, patients can gain access to world-class genomic sequencing and interpretation services at a much lower cost compared to commercially-equivalent solutions. RGI also provide a fundraising platform to help patients raise funds. Visit RARE GENOMICS INSTITUTE website

Questions on Science Policies for US Presidential Candidates

2012-07-21T01:00:00.000-07:00

ScienceDebate [ Science Debate is a nonprofit organization dedicated to elevating science and engineering policy issues in the national dialogue of the United States] has asked the Obama and Romney campaigns to address the following questions on Science policies by mid-August. It would be interesting to give these questions to our leaders.

1. Innovation and economics: Science and technology have fueled more than half of U.S. economic growth since World War II, but studies suggest that may be changing. What policies will best ensure America remains a world leader in innovation?

2. Climate change: What is your position on cap-and-trade, carbon taxes and other policies to address global warming? What steps can we take to improve our ability to tackle challenges like climate change that cross national boundaries?

3. Research and the future: Many other countries are making big investments in scientific research, but since the next U.S. Congress will inevitably have to curb spending, how would you prioritize research projects in your budget proposals?

4. Pandemics and biosecurity: In an era of constant and rapid international travel, what steps should the U.S. take to protect its population from emerging diseases, global pandemics and/or deliberate biological attacks?

5. Education: Why do you think U.S. students have fallen behind in science, math, technology and engineering over the last three decades? What role should the federal government play to better prepare students for the global economy?

6. Energy: What policies would you support to meet America's high demand for energy while ensuring an economically and environmentally sustainable future?

7. Food: America has the world's most diverse and productive agricultural sector, but many Americans are increasingly worried about potential dangers like hormones, antibiotics, pesticides and animal diseases. What steps would you take to ensure the health, safety and productivity of America's food supply?

8. Freshwater: Less than 1 percent of Earth's H2O is liquid freshwater, and much of that is now threatened by overconsumption, evaporation and pollution. What steps, if any, should the U.S. take to secure clean, abundant freshwater for all Americans?

9. Internet: The Internet plays a central role in both our economy and our society. What steps, if any, should the federal government take to manage the Web and ensure its robust social, scientific and economic role?

10. Oceans: Most global fisheries are in decline, key habitats like coral risks are at risk and ocean pollution is rampant. How can the U.S. use domestic and foreign policy to protect the oceans' environmental and economic vitality?

11. Science in public policy: How will you ensure that policy and regulatory decisions are fully informed by the best available scientific and technical information, and that the public is able to evaluate the basis of these policy decisions?

12. Space: The U.S. is in a major discussion over our national goals in space. What should America's space exploration and utilization goals be in the 21st century, and what steps should the government take to help achieve them?

13. Natural resources: Supply shortages of natural resources affect economic growth, quality of life and national security. What steps should the federal government take to ensure the quality and availability of critical natural resources?

14. Vaccines and public health: Vaccination campaigns against preventable diseases rely on high participation to be effective, but vaccination rates have fallen sharply in some communities. What actions would you support to enforce vaccinations in the interest of public health, and when should exemptions be allowed?

Aged people get more cancers than young ones due to use of Non-homologous end joining instead of homologous recombination for repairing double strand breaks

2012-07-20T03:55:00.001-07:00

Double stranded breaks are the most dangerous form of DNA damage occurring in the genome. Double strand breaks are caused by internal agents like reactive oxygen species and many external agents like radiation. Replication errors also cause double strand breaks. Living organisms have two methods for correcting this error: Homologous recombination(HR) found both in bacteria and eukaryotes and non-homologous end joining (NHEJ) found mostly in eukaryotes. HR is a method which corrects the double strand breaks by using the homologous chromosome as the reference (this is the reason for diploid nature of most eukaryotes). Except for gene conversion, it does not cause mutation to the genes in which the double strand break has occurred (usually broken ends have damaged bases which are removed and correct bases are added by HR using the homologous chromosome as the template). But NHEJ just joins the broken ends without replacing the damaged bases (as it does not have a template to refer) leading to mutation of the genes in which double strand breaks occurred.

It was not clear when HR is used and when NHEJ is used for repairing double stranded DNA breaks. Use of either of these methods has great implication on the health of the organisms. In a recent research work published in PNAS it has been shown that in humans HR declines sharply with increasing replicative age, with an up to 38-fold decrease in efficiency in presenescent cells relative to young cells. This decline is not explained by a reduction of the number of cells in S/G2/M stage as presenescent cells are actively dividing. Results of this study using normal human fibroblasts with a chromosomally integrated HR cassette showed that in aging cells, the precise HR pathway becomes repressed giving way to a more error-prone NHEJ pathway. These changes in the processing of DSBs may contribute to age-related genomic instability and a higher incidence of cancer with age.

[Click here to Read the Full paper]

BT Cotton increased yield by 24 % and profit by 50 %

2012-07-20T03:17:00.000-07:00

Bt cotton, the genetically engineered cotton plant, contains genes from Bacillus thuringiensis that make
the plant resistant to the cotton bollworm complex. This inbuilt insect resistance was predicted to reduce the pesticide usage. Most short term analyses showed that farmers are benefited because of reduced pesticide usage and increased yield. But environmentalists never agreed with these analyses.
In a recent study involving 6 years data on BT cotton cultivation in India, two German Researchers have found that Bt has caused a 24% increase in cotton yield per acre through reduced pest damage and a 50% gain in cotton profit among smallholders. These benefits were found to be stable and increased over time.

[Click here to Read the Full paper published in PNAS]

ARSENIC DNA DISCOVERY IS FLAWED: NO DNA WITH ARSENIC IN PLACE OF PHOSPHATE

2012-07-10T02:12:00.000-07:00

Last year NASA made a sensational claim about discovery of DNA in which the phosphorous is replaced by arsenic. The bacterial strain GFAJ-1 was isolated from the arsenic-rich sediments of California’s Mono Lake by its ability to grow in the artificial Mono Lake medium without phosphate but with high concentrations of arsenate. It was claimed that GFAJ-1 grew in -P medium only when arsenate was provided, and significant amounts of arsenate were detected in subcellular fractions. This was interpreted as “ growth due to use of arsenate in place of phosphate”. Wolfe-Simon et al. further reported that arsenic was incorporated into the DNA backbone of GFAJ-1 in place of phosphorus, with an estimated 4% replacement of P by As based on the As:P ratio measured in DNA samples embedded in agarose gel slices.

Read the original paper by clicking here

This discovery claim by NASA Scientists was sensational as
it changes the basic rules of life and prompted many to think that life is much more diverse than we know before so we can expect life forms with different basic components in different planets. But many Scientists were skeptical about this and predicted possible phosphate contamination in the media used. Two recent studies have found that media contamination may have contributed attributed to the bacterial growth and not arsenic replacement of phosphorous .

In recent paper published ahead of print in Science journal Erb et al (2012) have shown that , although the bacterium is able to grow under high-arsenate and low-phosphate conditions, it needs to be supplied with some amount of phosphate in order to grow at all. They found no evidence of arsenic substitution for phosphorus in the bacterium's metabolism. Phosphorus remained essential for the organisms to grow, they conclude, although that particular strain of bacterium is able to grow at much lower phosphate concentrations than other arsenate-resistant strains. In another independent study published simultaneously, Reaves et al (2012) have shown that arsenic does not contribute to the bacteria's growth and the faulty findings is attributed to trace contamination with phosphorous that let the bacteria grow.

HIGGS BOSON (God Particle) discovered last week may be an impostor

2012-07-09T22:34:00.000-07:00

Last week CERN scientists announced proof of the existence of the Higgs boson that gives us mass and holds the Universe together. Now a group of Scientists have reinterpreted the data and conclude that the particle identified as Higgs Boson may be an impostor.

Click the link below for the full article about this

http://arxiv.org/pdf/1207.1093v1.pdf