Archive for the ‘Biotechnology’ Category

First of all a very happy new year to everyone!

For the past several days I was preoccupied with a good many assignments that kept me away from posting articles on the blog. But the burden of many of them have been shed, and I hope I would be able to resume my activities on this blog.

Today’s post is a short one and talks about the website I created one year back. The site is aimed at biotechnology and molecular biology scholars in particular, and biology students in general, and as the introduction to the website on the homepage states “A dedicated resource serving the molecular biology and biotechnology research fraternity”.

This website is the outcome of a little bit of HTML and CSS I learnt during my free time (a luxurious item). Yeah, I know, it is not good looking, and looks could kill. But, I feel, it is a useful collection of links/online resources important for any biotechnology and biology scholar. It has been divided into sections like Arabidopsis, Databases, Caenorhabditis, Tutorials, Protocols, Humans, Microarrays, etc. A toolbar has also been provided. You can download the toolbar here.

Yesterday, a new section on IMMUNOLOGY was added. Click here. The section has links to many useful online utilities associated with immunology, like immunobiology databases, immunoinformatics, etc. The URL is http://biophilessurf.info/immuno.html

I hope you would like the site, and more importantly find it useful.

Any comments, suggestions, ideas, and, of course, criticism, is always welcome.

And no, the blog would not talk of this website again and again. Only on occasions when important updates are available or a new section is added.


Read Full Post »

Drosophila melanogaster, the fly extensively studied by TH Morgan, and a powerful model organism highly suited for the study of animal biology and evolution, is known from Africa, Asia, the Americas and the Pacific Islands. The different fly species range from cosmopolitan (D. melanogaster and D. simulans) to the ones inhabiting a single island only (D. sechellia). Their feeding habits are also diverse ranging from generalists to specialist (D. sechellia) feeding on the fruit of a single plant species.

The genome sequences of two fly species, D. melanogaster and D. pseudoobscura are already known, and 9 more species were sequenced (D. yakuba, D. erecta, D. ananassae, D. willistoni, D. virilis, D. mojavensis, D. grimshawi, D. sechellia and D. persimilis). In the first of large-scale genome comparison studies published in the November 8 issue of Nature, scientists at the Broad Institute of MIT and Harvard, the Computer Science and Artificial Intelligence Laboratory (CSAIL) at MIT, and many collaborating institutions, sequenced the genomes of above mentioned 9 species, and then analyzed and compared the genome sequences of the already-sequenced and the newly-sequenced fly species.

This analysis is highly beneficial in understanding the species evolution in a broader perspective and in unlocking the secrets hidden in the genome sequences and functions associated with them. This would also help better understand our own genome. Manolis Kellis, associate member of the Broad Institute, assistant professor in MIT’s CSAIL, and one of the consortium’s project leaders, said, “Having the sequences of many closely related species allows us to study the evolutionary forces that have shaped the fruit fly’s family tree, and to discover the working parts of the fly genome in a systematic way.”

The study revealed that 77% of the approximately 13,700 protein-coding genes in D. melanogaster are shared with all of the other 11 species. The genes required for interactions with the environment and in reproduction display adaptive evolution, as they provided some survival advantage. The researchers also studied the conserved (unchanged) parts of the fly genome and play crucial and similar roles in the fly biology. The investigations further led to the the discovery of 1,193 new sequences that encode proteins. In addition, new RNA genes, microRNA genes and new DNA sequences involved in gene expression regulation were identified. A total of more than 9,000 ncRNA (non coding RNA) genes were annotated from recognized ncRNA classes: The number of ncRNA genes per family is relatively low.

The genome structure is found to be well conserved across the 12 sequenced species. Total protein-coding sequence ranges from 38.9 Mb in D. melanogaster to 65.4 Mb in D. willistoni. Intronic DNA is also largely conserved, ranging from 19.6 Mb in D. simulans to 24.0 Mb in D. pseudoobscura. The analysis of transposable elements revealed that D. grimshawi has the lowest transposable element/repeat content, and D. ananassae and D. willistoni have the highest levels of transposable element/repeat content. The comparative analysis of the 12 fly genomes also led to the discovery of hitherto undocumented transposable element lineage, the P instability factor (PIF) superfamily of DNA transposons. The synteny relationships across the species were also investigated. 112 syntenic blocks were identified between D. melanogaster and D. sechellia (with an average of 122 genes per block), 1,406 syntenic blocks were identified between D. melanogaster and D. grimshawi (with an average of 8 genes per block). The similarity across the genomes is recapitulated at the level of individual genes.

The study also undertook a comparison of cis-regulatory elements, which provided insights into gene regulatory mechanisms operating in Drosophila species.

The landmark study thus: showed genome conservation across the 12 species, identified new RNA genes, demonstrated that multigene families are found in all the species examined, revealed the variations among protein-coding genes, and identified many protein-coding genes that defy the traditional rules of translation.

Read the full paper here.


Read Full Post »

Transgenic plants expressing Bt gene have been widely used for pest control for the past several years. However, due to certain limitations associated with using this technology scientists have been looking for alternatives, and they found one in RNAi. The researchers at the Chinese Academy of Sciences, Shanghai, and at Monsanto and Devgen, a Belgian company have shown for the first time that RNAi could be used as an efficient means of pest control. In two independent studies, when scientists fed the insect larvae with the plant material expressing dsRNA for the insect genes, it was found that it triggered the RNAi pathway in insect larvae and blocked the expression those genes.

In the first study, cotton bollworm (Helicoverpa armigera) was the target. dsRNA for a cotton bollworm cytochrome P450 gene, CYP6AE14, was made to express in the plants. This plant material was then fed to the insect larvae, and it was found that the levels of the cytochrome P450 transcript in the larval midgut decreased and larval growth retarded. This cytochrome P450 gene permits Helicoverpa armigera to tolerate inhibitory concentrations of the cotton metabolite, gossypol, and survive. In the absence of this gene, the insect showed decline in its growth. The abstract is here.

In another study, scientists made corn plants that silenced a gene essential for energy production in corn rootworms. Read the abstract here.

Many research workers are optimistic about this technology. Read the full story here.

via: Technology Review


Read Full Post »

Green fluorescent protein (GFP) is a naturally occurring fluorescent protein found in jellyfish, Aequorea victoria, and corals mostly. The protein by virtue of its green fluorescence confers the characteristic bioluminescence property upon these organisms. The protein consists of 238 amino acids, and the side chains of critically placed serine, tyrosine and glycine react with one another to form fluorescent chromophore. Thus the protein does not have any other small molecule interacting with it to produce fluorescence, rather the protein itself is capable enough to fluoresce. GFP has been used in several biotechnological applications like localization of cells within a tissue, as marker gene in transgenics, or subcellular localization of proteins. The reader is referred to a detailed review on GFP here.

Until now GFPs were known from jellyfish or corals only. However, in a recent publication in Biological Bulletin, Dimitri Deheyn and his colleagues have demonstrated for the first time the presence of green fluorescent proteins (GFPs) in amphioxus (a primitive chordate), a fish-like animal. This is an important finding from the evolutionary point of view and suggests that the property of fluorescence may be prevalent across several animal kingdoms and not restricted to corals or jellyfish only. Or is the protein also found in terrestrial animals? Why fluorescence is present in amphioxus? Deheyn hypothesizes that the protein “might be used as a form of “sunscreen,” protecting the animal by absorbing harmful ultraviolet light and shielding it away as fluorescent light.” It has also been suggested that GFPs may act as antioxidant proteins, protecting cells from temperature fluctuations or other environmental changes.

The amino acid sequence comparison of the amphioxus and jellyfish GFPs would shed light on how amphioxus GFP produces fluorescence. Are the amino acid residues forming the chromophore same in the two GFPs? Read the full story here.

via: ScienceDaily


Read Full Post »

The Ri (root-inducing) plasmid of Agrobacterium rhizogenes carries agropine genes. When A. rhizogenes infects a plant, a portion of the Ri plasmid DNA enters the host plant cell and causes the production of hairy roots at the site of action. A foreign gene could be inserted into modified Ri plasmid and the recombinant DNA (plasmid) could be introduced into plants in much the same way as with the Ti plasmid of A. tumefaciens. The recombinant Ri plasmid would induce the production of hairy roots after the infection of the host plant. Scientists are now trying to use these hairy roots as potential drug factories. In a new study, scientists have successfully maintained a transgenic hairy root culture alive for 4-and-a-half years, and they hope that this could be a great source of continuous drug production. Read the full story here.

via: ScientificBlogging


Read Full Post »

Newts and salamanders have long been known for their capability to renew damaged body parts. Scientists have now identified a protein playing the significant role in this process of regeneration. Researchers working at the University College London (UCL) identified that a protein called nAG is important for the production of blastema cells, which regrow the missing body part. The protein is secreted by nerve and skin cells, and proposed to hold importance for regenerative medicine. The scientists of the research group which discovered this key protein said that the results of the study “may hold promise for future efforts to promote limb regeneration in mammals”. Read the full story here.

via: Reuters


Read Full Post »

Scientists have created genetically modified mouse which manifests remarkable physical behaviour. It can run 6 kms at a speed of of 20 metres per minute for five hours, eats 60% more than normal mouse, does not put on weight, enjoys an active sex life to an old age, and lives longer. The mouse produces very little lactic acid, which causes muscle cramps, a feature associated with endurance athletes. All in all a very strong mouse. The phosphonenolpyruvate carboxykinase (PEPCK-C) is an enzyme of gluconeogenesis pathway. The formation of glucose from nonhexose precursors is gluconeogenesis. The enzyme PEPCK-C catalyzes the conversion of oxaloacetate to phosphoenolpyruvate using GTP as the phosphate donor. The transgenic mice carrying the gene for PEPCK-C, under the control of skeletal actin gene promoter, were created. The transformed mice showed a highly increased production of this enzyme. This led to the enhancement of physical and behavioral characters of the mice. Professor Hanson, who led the team of researchers responsible for the creation of the “mighty mouse”, said, “They are metabolically similar to Lance Armstrong biking up the Pyrenees. They utilise mainly fatty acids for energy and produce very little lactic acid. They are not eating or drinking and yet they can run for four or five hours. They are 10 times more active than ordinary mice in their home cage. They also live longer – up to three years of age – and are reproductively active for almost three years. In short, they are remarkable animals.”On the possibilities of trying the same in humans he said, “We humans have exactly the same gene. But this is not something that you’d do to a human. It’s completely wrong. We do not think that this mouse model is an appropriate model for human gene therapy. It is currently not possible to introduce genes into the skeletal muscles of humans and it would not be ethical to even try.” Read the full story here.

via: The Independent


Read Full Post »

Older Posts »