Time Series Data Mining Algorithms for Identifying Short RNA in Arabidopsis thaliana

The class of molecules called short RNAs (sRNAs) are known to play a key role in gene regulation. Th are typically sequences of nucleotides between 21-25 nucleotides in length. They are known to play a key role in gene regulation. The identification, clustering and classification of sRNA has recently become the focus of much research activity. The basic problem involves detecting regions of interest on the chromosome where the pattern of candidate matches is somehow unusual. Currently, there are no published algorithms for detecting regions of interest, and the unpublished methods that we are aware of involve bespoke rule based systems designed for a specific organism. Work in this very new field has understandably focused on the outcomes rather than the methods used to obtain the results. In this paper we propose two generic approaches that place the specific biological problem in the wider context of time series data mining problems. Both methods are based on treating the occurrences on a chromosome, or “hit count” data, as a time series, then running a sliding window along a chromosome and measuring unusualness. This formulation means we can treat finding unusual areas of candidate RNA activity as a variety of time series anomaly detection problem. The first set of approaches is model based. We specify a null hypothesis distribution for not being a sRNA, then estimate the p-values along the chromosome. The second approach is instance based. We identify some typical shapes from known sRNA, then use dynamic time warping and fourier trans-form based distance to measure how closely the candidate series matches. We demonstrate that these methods can find known sRNA on Arabidopsis thaliana chromosomes and illustrate the benefits of the added information provided by these algorithms

Genome Update. Let the consumer beware: Streptomyces genome sequence quality.

A genome sequence assembly represents a model of a genome. This article explores some tools and methods for assessing the quality of an assembly, using publicly available data for Streptomyces species as the example. There is great variability in quality of assemblies deposited in GenBank. Only in a small minority of these assemblies are the raw data available, enabling full appraisal of the assembly quality

Some (bacilli) like it hot: genomics of Geobacillus species.

n/aBiotechnology and Biological Sciences Research Council (BBSRC). Grant Numbers: BB/H016120/1, BB/I024631/1, BB/I025956/1, BB/K003240/2, BB/L012499/

Variations in Plumage Wear in Three Closely Related Tidal Marsh Sparrow Species

Tidal marsh sparrow species like Saltmarsh Sparrows (Ammospiza caudacuta), Nelson’s Sparrows (Ammospiza nelsoni) and Seaside Sparrows (Ammospiza maritima) are particularly vulnerable to the environmental stressors related to climate change and human activity like sea-level rise, warming temperatures, and increased coastal development, as they nest in the grasses of tidal marsh ecosystems where the principal mode of nest mortality is flooding. With increased sea-level rise, these species may not be equipped to adapt to changing tidal cycles, and thus have reduced fitness and population sizes. Saltmarsh Sparrows are experiencing sharp declines in population, so it is more vital than ever to investigate patterns in breeding behaviors, plumage wear, and latitudinal differences to develop feasible conservation strategies. My study investigates the differences in plumage wear and severity across conspecifics in Saltmarsh, Nelson’s, and Seaside Sparrows and identifies significant relationships between the date of capture, latitude, and severity of feather wear observed. I observed a decrease in plumage wear and broken feather percentage with latitude but an increase in these metrics in relation to date. Conversely, fault bars and severity displayed an increase with latitude but a decrease with date. Lastly, my findings demonstrate high amounts of feather wear in Seaside Sparrows compared to Saltmarsh and Nelson’s Sparrows

Silicon Valley Startup Companies: A Question of Culture

In recent years, Silicon Valley has become virtually synonymous with startup companies. These companies are defined by their famous startup culture. An interesting and unanticipated outcome of this research was the finding that the discourse of Silicon Valley startups is framed centrally in terms of culture. I use discourse analysis to understand the way people create and perpetuate structures of power, gender, and culture. By studying the way people in startup companies talk about their expectations and experiences, this analysis hopes to gain a deeper understanding into the normalized cultural discourses surrounding startup organizations, as well as the way individuals negotiate their subjective realities within this sphere

Recently published Streptomyces genome sequences

This is the final version of the article. Available from Wiley via the DOI in this record.ntroductionMany readers of this journal will need no introduction tothe bacterial genusStreptomyces, which includes severalhundred species, many of which produce biotechnolo-gically useful secondary metabolites. The last 2 yearshave seen numerous publications describingStrepto-mycesgenome sequences (Table 1), mostly as shortgenome announcements restricted to just 500 wordsand therefore allowing little description and analysis. Ouraim in this current manuscript is to survey these recentpublications and to dig a little deeper where appro-priate. The genusStreptomyces is now one of the mosthighly sequenced, with 19 finished genomic sequences(Table 2) and a further 125 draft assemblies available inthe GenBank database as of 3rd of May 2014; by the timethis is published, no doubt there will be more. The reasonsgiven for sequencing this latest crop ofStreptomycesinclude production of industrially important enzymes, deg-radation of lignin, antibiotic production, rapidJames Harrison was supported by a PhD studentship from the Biotechnology and Biological Sciences Research Council

PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data

© 2008 MacLean et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants.

Published onlineWe report here the annotated draft genome sequences of strains Xanthomonas arboricola pv. celebensis NCPPB 1832 and NCPPB 1630 (NCPPB, National Collection of Plant Pathogenic Bacteria), both isolated from Musa species in New Zealand. This will allow the comparison of genomes between phylogenetically distant xanthomonads that have independently converged with the ability to colonize banana plants.Biotechnology and Biological Sciences Research Council (BBSRC) provided funding to James Harrison. James Harrison was supported by a Ph.D. studentship from the Biotechnology and Biological Sciences Research Council (BBSRC). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication