Monthly Archives: February 2015

Lac Operon, Human Genome Project and DNA Fingerprinting - AIIMS AIPMT State CET Botany Video Lecture
AIIMS AIPMT State CET Botany Video Lectures and Study Material developed by highly experienced and dedicated faculty team of Rao IIT Academy. Visit http://www.raoiit.com or email ...

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Lac Operon, Human Genome Project and DNA Fingerprinting - AIIMS AIPMT State CET Botany Video Lecture - Video

Second Conference Presentation about Rope Worms. Funis Vermis. Genome Project
Second Conference Presentation about Rope Worms. Funis Vermis. Please support the rope worm genome project: http://www.youcaring.com/other/rope-worm-genome-project/293911.

By: Alex Volinsky

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Second Conference Presentation about Rope Worms. Funis Vermis. Genome Project - Video

iCLiKVAL debut presentation, Genome Informatics 2014, Cambridge, UK
iCLiKVAL stands for "Interactive Crowdsourced Literature Key-Value Annotation Library." Presented by Todd D. Taylor on September 22, 2014 at Churchill College, Cambridge, UK. iCLiKVAL (http://iclik ...

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iCLiKVAL debut presentation, Genome Informatics 2014, Cambridge, UK - Video

Within the framework of the JGI Mycorrhizal Genomics Initiative, we are sequencing a phylogenetically and ecologically diverse suite of mycorrhizal fungi (Basidiomycota and Ascomycota), which include the major clades of symbiotic species associating with trees and woody shrubs. Analyses of these genomes will provide insight into the diversity of mechanisms for the mycorrhizal symbiosis, including ericoid-, orchid- and ectomycorrhizal associations.

The Boletus edulis species complex includes ectomycorrhizal fungi producing edible mushrooms highly prized worldwide. B. edulis cultivation is a challenge targeted by many agro-food biotech companies involved in mushroom crop production. Unfortunately, a major problem up to now is that only a few ECM fungal species can be induced to fruit in co-culture in interaction with their hosts (ie., in tree nursery). Deciphering fruit body production by using molecular genetics and a better understanding of the developmental processes underlying fruiting in this charismatic edible model would undoubtly help in mushroom production/cultivation. Population genomics of B. edulis populations will also provide informations on fruiting in natural conditions.

Boletus edulis sensu lato (penny bun mushroom, cep, cpe de Bordeaux, porcino, Steinpilz) is a complex of at least five species of mycorrhizal fungi which grow primarily with hosts in Fagaceae, Pinaceae, and Betulaceae. However, high number of taxa - including several varieties, subspecies and/or species sensu stricto - have been described in this species complex. Like other boletes (Boletineae), it occurs in a wide variety of habitats throughout the Northern Hemisphere and has been accidentally introduced into South Africa and New Zealand. The fungus grows in deciduous and coniferous forests and tree plantations, forming symbiotic ectomycorrhizal associations (middle/late stage the fruiting succession). The fungus produces spore-bearing fruit bodies above ground in Summer and Autumn.

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Home - Boletus edulis v1.0

Toronto scientists uncovered how viral remnants helped shape control of our genes.

If genes were lights on a string of DNA, the genome would appear as an endless flicker, as thousands of genes come on and off at any given time. Tim Hughes, a Professor at the University of Toronto's Donnelly Centre, is set on figuring out the rules behind this tightly orchestrated light-show, because when it fails, disease can occur.

Genes are switched on or off by proteins called transcription factors. These proteins bind to precise sites on the DNA that serve as guideposts, telling transcription factors that their target genes are nearby.

In their latest paper, published in Nature Biotechnology, Hughes and his team did the first systematic study of the largest group of human transcription factors, called C2H2-ZF.

Despite their important roles in development and disease, these proteins have been largely unexplored because they posed a formidable challenge for researchers.

C2H2-ZF transcription factors count over 700 proteins -- around three per cent of all human genes! To make matters more complicated, most human C2H2-ZF proteins are very different from those in other organisms, like those in mice. This means that scientists could not apply insights gained from animal studies to human C2H2-ZFs.

Hughes' team found something remarkable: the reason C2H2-ZFs are so abundant and diverse -- which makes them difficult to study -- is that many of them evolved to defend our ancestral genome from damage caused by the notorious "selfish DNA."

Selfish DNA are bits of parasitic DNA whose only purpose is to multiply, a kind of virus for our genome. They seize a cell's resources to make copies of themselves, which they insert randomly across the genome -- causing harmful mutations along the way.

Almost half the human genome is made of selfish DNA, which probably came from ancient retro-viruses which, similar to modern counterparts, inserted their DNA into the host's genome. When this happens in an egg or sperm, the viral DNA gets passed on to the next generation, and the selfish DNA is then known as endogenous retro-elements (EREs).

Evolutionary biologists believe that selfish DNA was instrumental in making genomes bigger, giving natural selection additional DNA material to tinker with.

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Genome's tale of 'conquer and enslave'

In 2001, scientists first mapped the human genome, what MIT's Manolis Kellis, senior author of a groundbreaking study released this week in Nature, recently referred to as "the 'book of life' that encodes a human being." But the story doesn't end with what's written in our DNA.

Over the last several years, research has suggested that what you eat, how (or if) you exercise, and the quality of the air you breathe can all have an effect on the way your genes function. Some scientists go so far as to say that these changes can persist into the next generation. But if we learn to harness these changes, careful tweaking of genetic expression could hold promise for a new kind of cancer treatments.

It's the science of epigenetics, or the ways that our lives can affect the workings of our cells, turning some genes on and off without changing the underlying DNA structure.

A team of international researchers has just reached a major milestone, publishing the most comprehensive maps yet of the epigenome, the collection of tiny changes along the strands of the double helix and its outer structure that can alter how genes work in very big ways.

"All our cells have a copy of the same book, but they're reading different chapters, bookmarking different pages, and highlighting different paragraphs and words," Kellis continued in his remarks accompanying the release of a special issue of Nature comprising two dozen genomics studies. "The human epigenome is this collection of marks placed on the genome in each cell type, in the form of chemical modifications on the DNA itself, and on the packaging that holds DNA together."

Working with other scientists from all over the world as part of the Roadmap Epigenomics program, Kellis mapped epigenomes from 111 types of tissues and cells -- brain, heart, liver, blood -- elucidating the different ways the same sequence of DNA can be interpreted in each.

To do this, the consortium carried out 2,800 experiments on enough genetic material to cover the entire human genome 3,000 times. Kellis and his team then developed computational methods to drill down the massive dataset into meaningful bits, which allowed them to identify so-called control regions, or switches, in each of the cell types that turn genes on or off.

"Knowing where the switches are gives us a reference for studying the molecular basis of human disease, by revealing the control regions that harbor genetic variants associated with different disorders," Kellis said.

For instance, in a second study Kellis authored in Nature, he found that Alzheimer's disease is associated with changes in the regulatory regions that control the expression of immune system genes.

The researchers found more than 50 other examples in which the genes associated with human traits -- from height to multiple sclerosis -- overlapped with control switches. Some of that overlap occurred in cell types that scientists didn't previously think were involved.

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Mapping your other genome