Highlights of the BMC-series: February 2016

Rethinking reporting guidelines • Mathematical model of planarian stem cells • Lack of competition influences sperm size in peeper frogs • Predicting how DNA state influences gene expression • Compression of metagenomic data • Alcohol risks vary based on community wealth status • Measuring the potential for pandemic spread through airports

From the BMC Series Blog: Rethinking reporting guidelines

The BMC series is collaborating with the EQUATOR Network and Penelope Research to improve reporting guidelines, in order to promote transparency and reproducibility in published studies. We are currently testing a software wizard to help authors identify the necessary reporting requirements; in early trials, the wizard was highly accurate and reliable and could prove useful as a general tool to help authors and publishers improve reporting standards.

 

Systems Biology: Mathematical model of planarian stem cells

A mathematical model of feedback control in planarian flatworm stem cells makes testable predictions about the dynamics of the animal’s size, cell mortality and stem cell signaling systems under different conditions of food availability and after events such as wounding.

 

Evolutionary Biology: Lack of competition influences sperm size in peeper frogs

A lack of sperm competition between male spring peeper frogs found in Ontario prospectively results in relaxed selection for sperm phenotype. This could be observed in the highly variably morphology and frequency of abnormalities in samples collected from individual frogs. As an increased proportion of abnormal sperm can negatively impact fertilization, these results may reflect challenges in reproductive fitness for isolated spring peeper frogs.

 

Biophysics: Predicting how DNA state influences gene expression

The supercoiled state of DNA can impede RNA Polymerase access and lower transcription initiation rate. Bohrer and Roberts used mathematical modeling to explore the dynamics of supercoil buildup and transcriptional bursts in geographically related genes. The association between expression levels of neighboring genes and the supercoiled state of their chromosomal location demonstrates an intriguing aspect of gene regulation occurring at a structural level.

 

Image of the month:

Attribution: Schuna et al (2016)

The Pennington Pedal DeskTM is equipped with digital tracking capability, so users can continually monitor their usage and progress as they work toward increasing physical activity during the workday. Schuna Jr. et. al., BMC Research Notes, 2016 9:74.

 

Bioinformatics: Compression of metagenomic data

Sequenced metagenomic samples usually comprise reads from a large number of different bacterial communities. This results in large file sizes typically ranging between 1GB to 10GB which presents challenges in analyzing, transferring and storing the data. In BMC Bioinformatics, Kim and co-workers have described the first architecture for reference-based, lossless compression of metagenomic data. The proposed methodology also enables running different components in parallel and it provides the user with taxonomic and assembly information generated during execution of the compression pipeline.

 

Public Health: Alcohol risks vary based on community wealth status

In an English survey, alcohol use was associated with adverse health effects such as smoking, excess weight, and poor exercise habits, particularly in economically deprived communities. Taking these identified correlations into account, tailored approaches to healthcare and public health communications for different socioeconomic groups may be effective in dealing with alcohol usage and its related effects.

 

Infectious Diseases: Measuring the potential for pandemic spread through airports

Our ability to travel around the world and the increase in flights has resulted in the increased risk and rate of pandemics spreading from one country to another, but the location of the start of the outbreak has an effect on its ability to become a pandemic.

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