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Genomics in the Journals: Jun 30, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – University of Notre Dame researchers used microarrays to track gene expression in Anopheles gambiae mosquitoes over time, looking at how transcriptional profiles coincide with daily behavioral cycles in the malaria parasite-spreading pests. By testing tissue collected every few hours from mosquitoes exposed to specific light and dark conditions, the team found 1,293 genes exhibiting rhythmic expression shifts in the mosquito head and another 600 genes in the body. Those involved in the study, published in the early, online version of the Proceedings of the National Academy of Sciences, say it "highlights the fundamental roles that both the circadian clock and light play in the physiology of this important insect vector and suggests targets for intervention."

In the journal Cancer Discovery, an international research team describes how it used exome sequence and copy number data to unravel the order in which mutations cropped up in eight primary cutaneous squamous cell carcinoma skin cancers — an approach that they subsequently validated using data on 10 serous ovarian adenocarcinoma samples assessed through The Cancer Genome Atlas. The strategy brings together mutation and copy number data to not only catalog genetic glitches in tumors, but also to sort out which mutations preceded copy number changes and vice versa in each.

"We trace the mutational evolution of individual tumors, using a novel, sequence-based assessment strategy and, in doing so, provide a patient-centric complement to more traditional 'mutation-by-stage' approaches," senior author Raymond Cho, a dermatology researcher at the University of California at San Francisco, and co-authors wrote. "Our results illuminate key aspects of timing in cancer evolution without requiring large sample series, for which precursor lesions are often inaccessible."

An international group led by researchers at the University of Copenhagen and BGI-Shenzhen outline findings from their sequencing and analysis of the genome of Acromyrmex echinatior, a leaf-cutter ant from Panama, in Genome Research. The team used the Illumina HiSeq 2000 to sequence the 313 million base ant genome to an average of 123 times coverage. By folding in transcriptome sequence data, they identified 17,278 predicted protein-coding genes. Through comparisons with sequences from other ants and insects, they then narrowed in on genes suspected of contributing to everything from sex determination and reproduction to metabolism and social structure in the fungus-farming ants.

Earlier this year, another research team reported that it had sequenced the genome of the Atta cephalotes leaf-cutter ant species.

A group of researchers from Australia, the US, Norway, and Germany used sequencing and computational analyses to find a key bacterial species in the gut of the Tammar wallaby, a marsupial animal with a macropodid digestive system that relies on microbes to help break down plant biomass. Macropodid digestion is similar to that found in ruminant animals, they explained in Science online, though it produces a fraction of the methane per energy unit. Using 'reverse metagenomics,' the researchers characterized the wallaby's gut microbial community using 16S rRNA sequencing before narrowing in on a dominant bacterial species, dubbed "Wallaby Group 1" from the Succinivibrionaceae family. They then isolated and cultured WG-1 and did genome analyses to learn more about the bug's metabolic capabilities — information that may they say may eventually help curb methane output by ruminant animals as well.

"Our findings with the Tammar wallaby were a bit of a surprise, but we think they provide an important clue for how rumen fermentation might be directed away from methane formation," senior author Mark Morrison, an animal sciences researcher affiliated with Ohio State University and CSIRO Livestock Industries in Queensland, said in a statement.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.