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Genomics in the Journals Mar 20, 2014

NEW YORK (GenomeWeb News) – In Nature, researchers from the US and Japan detailed the transcriptional dynamics and diversity they detected in Drosophila melanogaster cell lines and organ samples under various conditions.

For the analysis, the group brought together information from RNA sequencing experiments designed to look at transcription start sites, RNA splicing, exon sequences, and polyadenylation.

With samples from 29 fruit fly tissues taken at a range of developmental stages; 21 whole-animal samples tested after exposure to environmental shocks such as extreme heat, cold, or heavy metal treatment; and two-dozen cell lines, the investigators identified transcripts coinciding with new and known genes and proteins.

Among the sequences detected were those produced from neural genes that can produce variable transcripts using alternative promoter and splicing patterns. The group also characterized some of the splicing and expression shifts evidence in different Drosophila tissue type.

From the patterns identified, the authors of the study concluded that the fruit fly's transcriptome "is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites, and polyadenylation sites."

Members of the International Cancer Genome Atlas used a combination of whole-genome sequencing, whole-exome sequencing, array comparative genomic hybridization, and other approaches to characterize esophageal squamous cell carcinoma, or ESCC, an aggressive esophageal cancer.

As they reported in another Nature study, the researchers did whole-genome sequencing on matched tumor and normal pairs from 17 individuals with ESCC. To that, they added whole-exome sequencing on 71 tumor-normal sets and array CGH on samples from 123 cases.

A look at the resulting data revealed eight genes showing recurrent alterations or mutations. Half a dozen of those had been described in prior cancer studies, the study's authors noted, while two genes had not previously been implicated in cancer.

"Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt, cell cycle, and Notch pathways," they wrote, noting that "[g]enomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms."

In the early edition of the Proceedings of the National Academy of Sciences, researchers from Rutgers University and elsewhere described findings from a genome sequencing-based analysis of drug resistant bacteria from a Klebsiella pneumoniae sequence type called ST258.

Isolates from the sequence type are frequently resistant to a range of drugs, including an antibiotic called carbapenem, authors of the study noted. Such carbapenem-resistant K. pneumoniae have been linked to infections in the hospital setting that are sometimes fatal, prompting interest in understanding their origins and spread.

To begin characterizing K. pneumoniae ST258, the investigators first generated high-quality reference genomes for two isolates collected from hospitalized individuals in New Jersey. From there, they went on to re-sequence and compare the genomes of 83 more clinical isolates of ST258.

The team's phylogenetic analysis of these isolates indicated that at least two distinct clades of ST258 can contribute to hospital-acquired infections in various parts of the world, with many of the clade-specific differences appearing in parts of the K. pneumoniae genome that code for sugars that make up the outer capsule around bacterial cells.

As such, the work argues against the notion that ST258 isolates originated from a single clone. It also highlighted genetic features that may offer hints to diagnosing, treating, and vaccinating against multi-drug resistant ST258.

A PLOS One study suggests bighorn sheep originally found their way to Tiburón Island in the Gulf of California and Mexico long before being reintroduced in the mid-1970s.

Researchers from the University of California Riverside and elsewhere used a combination of carbon dating, mitochondrial DNA sequencing, and ribosomal RNA gene sequencing to characterize fossilized dung found in a cave in a mountainous region of the island.

The dung looked similar to that of modern-day big horn sheep, they explained, though there was some debate over whether the animals were native to Tiburón or introduced to the island only recently.

The team's carbon dating indicated that the dung was roughly 1,470 to 1,630 years old, while both mitochondrial and 12S rRNA gene sequences supported the notion that it came from bighorn sheep belonging to the same haplotype as bighorn sheep populations in southwest Arizona and California.

Based on their results and other available information, the study's authors speculated that bighorn sheep likely made their way to Tiburón Island during the Pleistocene era, when sea levels were especially low and exposed a land bridge linking the mainland and island. They estimated that the bighorn sheep disappeared from Tiburón sometime over the past 1,500 years.

"With extended biological baselines, such as the knowledge that the Tiburón bighorn sheep went extinct before, it is possible to refine conservation targets," first author Benjamin Wilder, a botany and plant sciences graduate student at UC Riverside, said in a statement. "Given the cultural and conservation significance of the Tiburón bighorn, actions can be taken to avoid their past fate."