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Can the nucleotide content of a DNA sequence predict the sequence accessibility?

Balachandran et al. | Mar 10, 2023

Can the nucleotide content of a DNA sequence predict the sequence accessibility?
Image credit: Warren Umoh

Sequence accessibility is an important factor affecting gene expression. Sequence accessibility or openness impacts the likelihood that a gene is transcribed and translated into a protein and performs functions and manifests traits. There are many potential factors that affect the accessibility of a gene. In this study, our hypothesis was that the content of nucleotides in a genetic sequence predicts its accessibility. Using a machine learning linear regression model, we studied the relationship between nucleotide content and accessibility.

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The Impact of Effective Density and Compressive Strength on the Structure of Crumpled Paper Balls

Chu et al. | Nov 19, 2020

The Impact of Effective Density and Compressive Strength on the Structure of Crumpled Paper Balls

Crumpling is the process whereby a sheet of paper undergoes deformation to yield a three-dimensional structure comprising a random network of ridges and facets with variable density. The authors hypothesized that the more times a paper sheet is crumpled, the greater its compressive strength. Their results show a relatively strong linear relationship between the number of times a paper sheet is crumpled and its compressive strength.

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Pollination Patterns by Green-Backed Firecrown Hummingbirds

Freeland et al. | May 28, 2020

Pollination Patterns by Green-Backed Firecrown Hummingbirds

The Green-backed Firecrown hummingbird is an essential pollinator in the temperate rainforests of southern South America. However, little is known about the ecology of these birds. Authors examined the foraging patterns of these birds identifying interesting differences in foraging patterns among season, age and sex.

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The Effect of Different Fructose Diets on the Lifespan of C. elegans

Chen et al. | May 10, 2020

The Effect of Different Fructose Diets on the Lifespan of <em>C. elegans</em>

High-fructose diets consumed widely in modern societies predisposes to metabolic diseases such as diabetes. Using the worm C. elegans, the authors of this study investigated the effect of fructose on the worm's survival rates. They found that worms fed 15% fructose had a lower life expectancy than those on a fructose-free diet. These results suggest that, like in humans, fructose has a negative effect on worm survival, which makes them an easy, attractive model to study the effects of fructose on health.

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Upregulation of the Ribosomal Pathway as a Potential Blood-Based Genetic Biomarker for Comorbid Major Depressive Disorder (MDD) and PTSD

Ravi et al. | Aug 22, 2018

Upregulation of the Ribosomal Pathway as a Potential  Blood-Based Genetic Biomarker for Comorbid Major Depressive Disorder (MDD) and PTSD

Major Depressive Disorder (MDD), and Post-Traumatic Stress Disorder (PTSD) are two of the fastest growing comorbid diseases in the world. Using publicly available datasets from the National Institute for Biotechnology Information (NCBI), Ravi and Lee conducted a differential gene expression analysis using 184 blood samples from either control individuals or individuals with comorbid MDD and PTSD. As a result, the authors identified 253 highly differentially-expressed genes, with enrichment for proteins in the gene ontology group 'Ribosomal Pathway'. These genes may be used as blood-based biomarkers for susceptibility to MDD or PTSD, and to tailor treatments within a personalized medicine regime.

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Assessing grass water use efficiency through smartphone imaging and ImageJ analysis

Shen et al. | Jul 27, 2022

Assessing grass water use efficiency through smartphone imaging and ImageJ analysis

Overwatering and underwatering grass are widespread issues with environmental and financial consequences. This study developed an accessible method to assess grass water use efficiency (WUE) combining smartphone imaging with open access color unmixing analysis. The method can be applied in automated irrigation systems or apps, providing grass WUE assessment for regular consumer use.

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The role of CYP46A1 and its metabolic product, 24S-hydroxycholesterol, in Neuro 2A cell death

Ni et al. | May 11, 2021

The role of CYP46A1 and its metabolic product, 24S-hydroxycholesterol, in Neuro 2A cell death

Cholesterol is a major component of neuronal cell membrane and myelin sheath. In this study, the authors either transfected Neuro 2A cells with CYP46A1 cDNA or treated the cells with 24SHC. Cells expressing CYP46A1 had significantly less viability compared to the negative control. Up to 55% reduction in cell viability was also observed in 24S-HC-treated cells. This work supports that CYP46A1 and 24S-HC could directly trigger cell death. The direct involvement of 24S-HC in cell death provides further evidence that 24S-HC can be a promising biomarker for diagnosing brain damage severity.

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