Biology News Net - Bioinformatics

Giraffes more speciose than expected

Thu, 08 Sep 2016 19:41:13 -0500

Scientists from the Senckenberg and the Giraffe Conservation Foundation have analysed the genetic relationships of all major populations of giraffe in the wild. The large study on the genetic makeup of giraffe, published today in Current Biology, shows that there are four distinct giraffe species. Until now, only one giraffe species had been recognized. The unexpected results are based on analyses using several nuclear marker genes of more than 100 animals. The new insights are set to improve protection efforts of these endangered animals in Africa.

Artificial intelligence expedites breast cancer risk prediction

Mon, 29 Aug 2016 18:12:50 -0500

Researchers at Houston Methodist have developed an artificial intelligence (AI) software that reliably interprets mammograms, assisting doctors with a quick and accurate prediction of breast cancer risk. According to a new study published in Cancer (early online Aug. 29), the computer software intuitively translates patient charts into diagnostic information at 30 times human speed and with 99 percent accuracy.

Warbler genomes look to be 99.97 percent alike

Tue, 23 Aug 2016 18:09:19 -0500

This is an illustration of warbler. For decades, conservationists have considered blue-winged warblers to be a threat to golden-winged warblers, a species being considered for federal Endangered Species protection. Blue-winged warbler populations have declined 66 percent since 1968, according to the North American Breeding Bird Survey.

Genomics solutions to the riddle of the tobacco hornworm sphinx moth

Mon, 15 Aug 2016 18:29:45 -0500

Manduca sexta caterpillars can grow up to 10 cm long making them ideal for laboratory experiments to investigate their biochemistry and physiology. "Whooo ... are ... you?" asked the hookah-smoking caterpillar of Alice, in Wonderland. Asking the question of the caterpillar instead, an international team of scientists have published their findings from the sequencing, annotation, and exploration of the genome of the tobacco hornworm moth. The project involved 114 scientists from 50 research institutions worldwide, including from the SIB Swiss Institute of Bioinformatics and the University of Geneva (UNIGE). This remarkable moth and strikingly beautiful and very large caterpillar are known by the Latin name, Manduca sexta, but also as the tobacco hornworm, Carolina sphinx moth, goliath worm, or 'Le sphinx du tabac'. The giant caterpillars are a favourite childhood pet, but they are considered serious agricultural pests as they feed voraciously on tobacco, potato, tomato, and pepper plants. The large size of the caterpillars means that this moth has become one of the most important model species for studying insect physiology, biochemistry, and molecular biology, and sequencing its genome opens many new research avenues.

Every grain of rice: Ancient rice DNA data provides new view of domestication history

Wed, 27 Jul 2016 17:24:16 -0500

This is a comparison of ancient rice remains and modern rice. Rice, or Oryza sativa as its scientifically known, feeds more than a third of the globe. Yet the majority of rice crops that supply 90 percent of the world come from just two domesticated varieties, japonica and indica.

Quantitating the complete human proteome

Mon, 25 Jul 2016 18:09:06 -0500

This is an illustration of SRM peaks and a human face. Reporting in the journal Cell, Senior Research Scientist Dr. Ulrike Kusebauch, of Institute for Systems Biology (ISB), describes the results of a collaboration between scientists at ISB, ETH Zurich and a number of other contributing institutes to develop the Human SRMAtlas, a compendium of proteomic assays for any human protein. The Human SRMAtlas is a compendium of highly specific mass spectrometry assays for the targeted identification and reproducible quantification of any protein in the predicted human proteome, including assays for many spliced variants, non-synonymous mutations and post-translational modifications. Using the technique called selected reaction monitoring, assays were developed with the use of 166,174 well-characterized, chemically synthesized proteotypic peptides. The SRMAtlas resource is freely publicly available at http://www.srmatlas.org and will equally benefit focused, hypothesis-driven and large proteome-scale studies. We expect this resource will significantly advance protein-based experimental biology to understand disease transitions and wellness trajectories because any human protein can now, in principle, be identified and quantified in any sample.

Genome of 6,000-year-old barley grains sequenced for first time

Mon, 18 Jul 2016 18:59:16 -0500

Right: Photograph during excavation exhibiting excellent dry preservation of plant remains
Left: A well-preserved, desiccated barley grain found at Yoram Cave An international team of researchers has succeeded for the first time in sequencing the genome of Chalcolithic barley grains. This is the oldest plant genome to be reconstructed to date. The 6,000-year-old seeds were retrieved from Yoram Cave in the southern cliff of Masada fortress in the Judean Desert in Israel, close to the Dead Sea. Genetically, the prehistoric barley is very similar to present-day barley grown in the Southern Levant, supporting the existing hypothesis of barley domestication having occurred in the Upper Jordan Valley.

How do you turn a mosquito's genes on and off?

Mon, 11 Jul 2016 17:01:30 -0500

A microscope image shows a four-segment section of the nervous system of an Aedes aegypti mosquito embryo. The dark purple indicates areas where a gene called "short gastrulation " is being... Scientists are using machine learning to identify important sequences of DNA within the mosquito genome that regulate how the insect's cells develop and behave.

A 'big data' approach to developing cancer drugs

Fri, 08 Jul 2016 18:38:05 -0500

There are thousands of scientific papers dedicated to a particular type of tumor, a particular gene, a type of specific molecular lesion or the effect of a particular drug. However, there are very few examples of publications that integrate these four concepts (type of tumor, gene alteration and drug) in a significant amount of samples. An article published in Cell, in collaboration with the group of Dr. Manel Esteller, Director of the Epigenetics and Cancer Biology Program at the Bellvitge Biomedical Research Institute (IDIBELL), ICREA researcher and Professor of Genetics at the University of Barcelona, provides us with this important source of information.

New technique sorts drivers from passengers in cancer genomics, implicates GON4L

Wed, 29 Jun 2016 16:50:44 -0500

Tumor DNA is cluttered with genomic alterations, the vast majority of which have little or no functional or clinical relevance. This means that even when cancer researchers discover an alteration in a tumor or a line of cancer cells, the alteration may or may not be relevant to the progression of the disease - chances are good (and history has shown) that many alterations that are correlated with cancer are not causative of cancer; many alterations are "passengers" rather than "drivers". A University of Colorado Cancer Center study published in the journal Cancer Research demonstrates a novel method for sorting passenger from driver alterations, and uses this method to pinpoint a new driver and potential therapeutic target in cancer progression, GON4L.