Thursday, May 31, 2012

Tomato is tomato because of two whole genome triplications

Tomato Genome Update - 2

Analysis of the recently sequence tomato genome in comparison to potato and grape genome reveal that massive genome duplication events shaped the evolution of these plants. Ancestors of tomato genome underwent whole genome triplication twice, one very early in a common eudicot ancestor shared with rosid and the second more recent triplication in the ancestor of tomato and potato followed by widespread gene loss. This recent  triplication has occurred around  71 million years ago well before divergence of tomato and potato which took place approximately

How many genes in Tomato ?

Tomato Genome Update-1:

  • The genome size of tomato is ca. 900 MB (Approximate values: Human genome is 3000 MB, rice genome is 370 MB, Arabidopsis genome  is 130 MB, E.coli genome is 4.5 MB)
  • Total number of protein coding genes: 34,727 (8615 groups common between rice, Arabidopsis, grape, tomato and potato; 1727 groups are common between

Breaking Discovery: Tomato genome sequenced

The genome of tomato (Solanum lycopersicum),  a major crop plant and a model system for fruit development,  is sequenced by an International Consortium of Scientists. The genome of   domesticated tomato and  its closest wild relative, Solanumpimpinellifolium were sequenced.  The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis,

Transfer PCR: a new method for one step transfer of gene from one plasmid vector to another

A new method called Transfer PCR (TPCR) which  combines PCR amplification of a gene present in a vector / plasmid and subsequent integration of the PCR product into the recipient vector without intermediate product purification and without the need of any commercial kit has been discovered by Researchers from Hebrew University of Jerusalem,and  Weizmann Institute of Science,  Israel.

For DNA cloning, the donor and the recipient plasmids are present in the same reaction tube together with the other reaction components, including primers, reaction buffer and dNTPs. The two primers include sequences, which are complimentary to the target gene at the 3′ end and sequences corresponding to the integration site in the recipient vector at the 5′ end.

{Image courtesy: Journal of Structural Biology)

The transcription factor IIE α subunit (ΤFIIEα, ∼1300 bp) gene is  in

Wednesday, May 30, 2012

tssRNA , a new type of transcription start site associated small RNA in bacteria

Researchers from Spain have identified a  new class of small RNA (~45 bases long)  in gram positive and negative bacteria. These tssRNAs are associated with RNA polymerase pausing some 45 bases downstream of the transcription start site and show global changes in expression during the growth cycle.  They are related to eukaryotic tiRNAs in their localization (transcription start sites, TSS) but not in their biogenesis. tssRNAs are generated at the same positions

Tuesday, May 29, 2012

BREAKTHROUGH DISCOVERY: Tet-assisted bisulfite sequencing (TAB-Seq), a new method for mapping methylation to single base resolution of entire genome


Tet-assisted bisulfite sequencing (TAB-Seq), a new method for mapping methylation to single base resolution of entire genome

DNA methylation regulating gene expression is a known fact but study of this 5-hydroxylmethylcytosines (5hmC) has been hampered by the lack of a method to map it at single-base resolution on a genome-wide scale. Affinity purification-based methods (which are used currently) cannot precisely locate 5hmC nor accurately determine its relative abundance at each modified site.  For the first time a revolutionary  genome-wide approach  named “ Tet-assisted bisulfite sequencing (TAB-Seq)” has been devised by Scientists from University of Chicago, Ludwig Institute for Cancer Research, University of California, San Diego and Emory University.  This method,  when combined with traditional bisulfite sequencing can be used for

Ferroptosis, a new type of cell death with potential applications

Ferroptosis, a new type of cell death,  is the iron dependent form of nonaptotic cell death triggered by  the oncogenic  RAS-selective lethal small molecule erastin (Nonapoptotic forms of cell death may facilitate the selective elimination of some tumor cells or be activated in specific pathological states). Ferroptosis is dependent upon intracellular iron, but not other metals, and is morphologically, biochemically, and genetically distinct from

What is Cancer Genome Atlas ?

Cancer genome atlas is a very important project aiming to map all genomic variations associated with different cancers and create a comprehensive atlas. This was initiated by The National Cancer Institute (USA)and the National Human Genome Research Institute (USA) and is being carried out by a network of more than 100 researchers at many

Saturday, May 26, 2012

Segmental genome duplication responsible for our brain power

Genome duplication is the trigger for evolution. Complex multicellular organisms have evolved from simple unicellular organisms by genome duplication and other genome rearrangements. Genome duplication can be of two types: whole genome duplication in which a diploid organism becomes a tetraploid and provide whole set of additional genes i.e for every old gene a new copy is provided. This type of change is considered to be responsible for major changes in organisms including speciation. The second type of duplication is called segmental duplication or copy number variation.  Here only a part of the genome gets duplicated and provide additional copies of only those genes in the duplicated regions. This type of  variation is considered to be responsible for differences among closely related organisms for example between monkeys and humans. Immediately after sequencing genomes of chimp and other primates Scientists were expecting to find a segmental duplication of  genomic regions possessing genes associated with  the brain i.e neural system but were not successful.

Recently  two  groups of Scientists led by Evan Eichler and Franck Polleux have found a part of the missing clue.  They identified segmental duplication that led to

Friday, May 25, 2012

BREAKING DISCOVERY: Radiation treatment converts a normal breast cancer cells to breast cancer stem cells which are more tumorigenic

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.

Thursday, May 24, 2012

Global Research Council (GRC) formed to coordinate scientific collaborations

The Global Research Council (GRC) (a voluntary organization), has been formed recently  to share best practice and encourage common principles for research collaborations in  different countries. Leaders of about 50 national research-funding agencies met at the headquarters of the US National Science Foundation (NSF) in Arlington, Virginia, to discuss the GRC’s agenda: issues such as peer review, data sharing, research integrity, open access, career development and ethical conduct in research on humans.  The GRC’s first meeting produced a set of short, uncontroversial statements

Saturday, May 19, 2012

Light switch for gene expression with potential use in therapeutics

Scientists from  North Carolina State University have identified light-activated molecules to turn gene expression on and off. Triplex-forming oligonucleotides (TFOs) are commonly used molecules that can prevent gene transcription by binding to double-stranded DNA

A light-activated “cage” was attached to a Triplex-forming oligonucleotides. In the absence of light, transcription activity is 100 percent. When exposed to ultraviolet (UV) light, the cage is

Friday, May 18, 2012

DNA sequencing found to be better than flow cytometry in predicting cancer relapse

In a recent study Scientists at  University of Washington, University of New Mexico Health Sciences Center, University of Virginia,  University of California and  Fred Hutchinson Cancer Research Center have found that  high-throughput sequencing could improve the diagnosis and post-treatment monitoring of leukemia. The sequencing-based method is more sensitive than flow cytometry and cheaper  and faster than the quantitative real-time PCR. They used high throughput sequencing (HTS)  to the diagnosis of T-lineage acute lymphoblastic leukemia/lymphoma. 43 paired patient samples were used for assessing

Germline low-methylated regions are more prone for structural mutation than methylated regions

The human genome contains many loci with high incidence of structural mutations, including insertions and deletions of chromosomal segments. This excessive mutability has accelerated evolution and contributed to human disease but has yet to be explained. 

Segments of DNA repeated in low-copy numbers (LCRs) have been previously implicated in promoting structural mutability in specific disease-associated loci. Lack of methylation (hypo-methylation) of genomic DNA has been previously associated with high structural mutability in gibbons and in human cancer cells, but the association with structural mutability in the human germline has not been explored. 

A recent study carried out by Scientists from

Tuesday, May 15, 2012

SOMETHING UNUSUAL: RecA of Dinococcus radiodurans binds to double standed DNA first

The D. radiodurans RecA protein (361 amino acids, Mr 38,013) is 57% identical (72% similar) to the E. coli RecA protein (352 amino acids, Mr 37,842). In vitro, the protein promotes all of the key recombino genic activities of RecA-class recombinases. It forms filaments on DNA, hydrolyses ATP and dATP in a DNA-dependent fashion and promotes DNA-strand exchange. However, the D. radiodurans RecA protein has one distinct function. The DNA strand-exchange reactions of the E. coli RecA protein, and all other homologues examined to date, are ordered so that the single-stranded DNA is generally bound first, before the double-stranded DNA is bound.

Development of a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state.

Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification.  A new method  using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state has been developed by a group of Scientists from Cornell University.

This device evaluates the fluorescence from labeled epigenetic modifications