Reverse genetics for herbicide-resistance detection A new molecular tool developed by Australian and Japanese researchers is expected to help farmers address what has become one of the major threats to conventional agricultural practices – herbicide resistance. New South Wales Department of Primary Industries molecular biologist, Dr. Mui-Keng Tan, and a team of researchers led by Dr. Guang-Xi Wang from Kyoto University, Japan, investigated “eco-tilling” technique and found that it offers a quick, cheap and reliable means of detecting early signs of herbicide resistance in weeds. Unlike the traditional molecular approach, eco-tilling uses reverse genetics. Genes are not fully sequenced; instead, mutations in single molecules that make up genes are identified purely on the basis of their position in the genome. Dr. Tan said new mutations can be detected and known ones can be screened for a fraction of the cost of alternative genetic methods. This makes it a powerful, low-cost and high-throughput alternative to full sequencing. Dr. Tan’s research focused on herbicide resistance in two of the most significant weeds affecting Australian cropping systems – wild oats and rye grass – and to together with Dr. Wang she also examined weeds in rice fields in Japan. She said that every weed-herbicide system is specific, and the eco-tilling technique can be applied on any particular system. Source: www.sciencedaily.com Grapevine genome decoded A group of researchers from France and Italy have deciphered the complete genome sequence for the pinot noir grapevine Vitis vitifera. The draft sequence of the grapevine genome is the first one produced for a fruit crop and fourth for a flowering plant after rice, Arabidopsis and poplar. The French-Italian Public Consortium for Grapevine Genome Characterization, which collectively conducted the study, discovered a large number of gene families related to wine characteristics, like those coding for terpenes and tannins, compounds responsible for the wine’s aroma and taste. Multiple copies of the genes coding for enzymes necessary for the biosynthesis of resveratrol were also found. Resveratrol is an antioxidant found in red wine and known for its anticancer, antiviral, anti-inflammatory and neuroprotective properties. The large number of gene families was attributed to man’s selection and hybridization during thousands of years. The findings will pave the way for genetic manipulations to improve the flavour and pathogen resistance of a crop that generates some US$200 billion a year in revenue.  Source: www.isaaa.org Estrogen can switch on breast cancer gene A team of researchers from Australia has found that the female sex hormone estrogen can turn on a gene linked to breast cancer. The cancer biology team from the University of Queensland’s Diamantina Institute for Cancer, Immunology and Metabolic Medicine in Brisbane says the finding helps explain the link between breast cancer, the gene known as MYB, and high levels of estrogen. “What is important in breast cancer is the ability of estrogen to turn on MYB rather than there being a mutation in the gene itself,” said the research team leader Dr. Tom Gonda. The gene MYB is found in about 70 per cent of all breast cancers and is one of several dozen genes called oncogenes that promote cancer growth. Researchers in Melbourne, Adelaide, and the United States worked with the University of Queensland team. Source: www.sciencedaily.com New complexity found in human genome Geneticists from University of Toronto, Canada, have found that the human nervous system plays an important role in regulating genetic activity. Led by Professor Benjamin Blencowe, they were searching for mechanisms that could account for the genetic differences between simple and more complex life forms. The researchers found that increased functional and cellular complexity can be largely explained by how genes and gene products are regulated. The researchers found a step in gene expression – alternative splicing – is more highly regulated in a cell and tissue-specific manner than previously thought and much of that additional regulation occurs in the nervous system. The step allows a single gene to specify multiple protein products by processing the RNA transcripts made from genes that are translated to make protein. Source: www.sciencedaily.com Scientists discover ‘tall gene’ Dr. Timothy Frayling and colleagues at Peninsula Medical School in Exeter, the United Kingdom, have discovered the first genetic link to height. Their study shows that a single letter change in the DNA sequence of a gene called HMGA2 can boost a person’s height by around 1 cm. Although height is thought to be 90 per cent down to genetics, scientists have previously had difficulty in identifying the hundreds of genes thought to be involved, in the absence of new technology that allows the entire genome of thousands of people to be analysed. In the hunt for the gene, the researchers began by scanning the entire genome of 5,000 people to identify single letter changes linked to height differences. This led to the discovery of a tiny variation in the HMGA2 gene. Next, they looked for the same variation in another 29,000 people, confirming that the gene variant is linked to height. The researchers found that people who carry two copies of the ‘tall’ version of the gene are an average of 1 cm taller than people who carry two copies of the ‘short’ version, while those who carry one of each are somewhere in the middle. Source: www.bionews.org.uk Genetics of loneliness People who experience chronically high levels of loneliness show gene-expression patterns that differ markedly from those of people who don’t feel lonely, according to a new molecular analysis led by Dr. Steven Cole at University of California Los Angeles (UCLA) School of Medicine in the United States. The findings suggest that feelings of social isolation are linked to alterations in immune system activity, which result in increased inflammatory signalling within the body. This is the first study to show an alteration in genome-wide transcriptional activity linked to a social epidemiological risk factor. It thus provides a genetic framework for understanding why social factors are linked to an increased risk of diseases where inflammation is thought to be a factor, such as heart disease, infection and cancer. In their study, Dr. Cole and colleagues at UCLA and the University of Chicago used DNA microarrays to survey the activity of all known human genes in white blood cells from 14 individuals. Six participants scored in the top 15 per cent of the UCLA Loneliness Scale (a widely used measure of loneliness that was developed in the 1970s), the others scored in the bottom 15 per cent. The researchers found 209 transcripts were differentially expressed between the two groups, with 78 being overexpressed and 131 underexpressed. Genes overexpressed in highly lonely individuals included many involved in immune system activation and inflammation. However, several key gene sets were underexpressed, including those involved in antiviral responses and antibody production. Bioinformatics analyses identified some of the biological signalling pathways that shaped these differences in gene expression, including reduced activity of the anti-inflammatory glucocorticoid pathway and the pro-inflammatory NF-ê B/Rel pathway. The changes in immune cell gene expression were specifically linked to the subjective experience of social distance. “The changes were even independent of the objective size of a person’s social network. What counts, at the level of gene expression, is not how many people you know; it is how many you feel really close to over time,” he added. Source: www.eurekalert.com The genes involved in rheumatoid arthritis identified The results from screening of the human genome for the genetic causes of rheumatoid arthritis both confirm previous hypotheses and turn the spotlight on entirely new genes. An international team of researchers from Sweden, the United States and Singapore – led by Prof. Lars Klareskog and Prof. Lars Alfredsson at the Swedish Medical University Karolinska Institutet – compared the genomes of over 15,000 rheumatics with those of 1,850 controls. Their analysis shows that the DNA of these two groups are at a variance at three sites, two genes previously linked to the disease and a previously unexamined gene complex known as TRAF-C5. The scientists have also used the same material to examine the significance of a specific area of the genome. They found that yet another gene, STAT 4, could be linked to the disease. The previously studied genes and the newly discovered TRAF-C5 and STAT4 genes are each important in its own way for the function of the body’s immune cells. Source: www.sciencedaily.com Gene for glaucoma found A group of scientists has discovered two common single nucleotide polymorphisms (SNPs) in the sequence of the human genome that appear to account for 99 per cent of cases of exfoliative glaucoma (XFG). The scientists from deCODE Genetics and the National University Hospital in Rekjavik, both in Iceland, and from the Uppsala University in Sweden reported that the SNPs are located in the lysyl oxidase-like 1 gene (LOX1) on Chromosome 15. This finding offers hope for more efficient diagnosis and treatment of XFG. The team began its work with an analysis of over 300,000 SNPs using DNA scanning chips. By comparing patients and control subjects, the scientists were able to determine the sites linked with the disease. Dr. Kari Stefansson, CEO of deCODE, and his colleagues discovered two risk variants in the LOX1 gene that are strongly linked to XFG; these SNPs confer increased risk of 26-fold and 8-fold compared with the low-risk versions of the same markers. Over 16,000 patients and controls took part in the study. The LOX1 protein encoded by the gene is produced in many tissues of the body, including the eye, and is involved in cross-linking elastin fibres. The effect of the genetic variants seems to be to lower the production rate of this protein. In XFG, microfibullar deposits build on the surfaces on the front of the eye, increasing fluid pressure that gradually damages the optic nerve, leading to a progressive loss of vision. According to Dr. Stefansson, the risk conferred by these variants is such that it accounts for virtually all cases of XFG, meaning that if the impact of these variants could be neutralized the disease could be eliminated. Source: www.bionews.org.uk