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.

Van der Woude syndrome is a common birth defect caused by mutations in the gene Irf6. In this project, students used microarray expression analysis from wild-type and Irf6-deficient mice in order to identify gene networks or pathways differentially regulated due to the Irf6 mutation. They found NF-κB pathway to be activated in deficient mice.

Alzheimer's disease (AD) involves the reduction of cholinergic activity due to a decrease in neuronal levels of nAChR α7. In this work, Sanyal and Cuellar-Ortiz explore the role of the nAChR α7 in learning and memory retention, using Drosophila melanogaster as a model organism. The performance of mutant flies (PΔEY6) was analyzed in locomotive and olfactory-memory retention tests in comparison to wild type (WT) flies and an Alzheimer's disease model Arc-42 (Aβ-42). Their results suggest that the lack of the D. melanogaster-nAChR causes learning, memory, and locomotion impairments, similar to those observed in Alzheimer's models Arc-42.

In this study, the authors analyze gene expression datasets to determine if there is a core set of genes dysregulated during nonalcoholic steatohepatitis.

Smartphones are not only becoming an inseparable part of our daily lives, but also a low-cost, powerful optical imaging tool for more and more scientific research applications. In this work, smartphones were used as a low-cost, high-speed, photographic alternative to expensive equipment, such as those typically found in scientific research labs, to accurately perform motion tracking and analysis of fast-moving objects. By analyzing consecutive images, the speed and flight trajectory of water droplets in the air were obtained, thereby enabling us to estimate the area of the water droplets landing on the ground.

Major depressive disorder (MDD) is a prevalent mood disorder. The direct causes and biological mechanisms of depression still elude understanding, though genetic factors have been implicated. This study looked to identify the mechanism behind the aberrant response to the dexamethasone suppression test (DST) displayed by MDD patients, in which they display a lack of cortisol suppression. Analysis revealed several pro-inflammatory genes that were significant and differentially expressed between affected and non-affected groups in response to the DST. Looking at ways to decrease the inflammatory response could have implications for treatment and may explain why some people treated for depression still display symptoms or may lead researchers to different classes of drugs for treatment.

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.

Here, seeking to identify a possible explanation for the more frequent diagnosis of autism spectrum disorder (ASD) in males than females, they sought to investigate a potential sex bias in the expression of ASD-associated genes. Based on their analysis, they identified 17 ASD-associated candidate genes that showed stronger collective sex-dependent expression.

Glioblastoma Multiforme (GBM) is the most malignant brain tumor with the highest fraction of genome alterations (FGA), manifesting poor disease-free status (DFS) and overall survival (OS). We explored The Cancer Genome Atlas (TCGA) and cBioportal public dataset- Firehose legacy GBM to study DNA repair genes Activating Signal Cointegrator 1 Complex Subunit 3 (ASCC3) and Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 3 (ALKBH3). To test our hypothesis that these genes have correlations with FGA and can better determine prognosis and survival, we sorted the dataset to arrive at 254 patients. Analyzing using RStudio, both ASCC3 and ALKBH3 demonstrated hypomethylation in 82.3% and 61.8% of patients, respectively. Interestingly, low mRNA expression was observed in both these genes. We further conducted correlation tests between both methylation and mRNA expression of these genes with FGA. ASCC3 was found to be negatively correlated, while ALKBH3 was found to be positively correlated, potentially indicating contrasting dysregulation of these two genes. Prognostic analysis showed the following: ASCC3 hypomethylation is significant with DFS and high ASCC3 mRNA expression to be significant with OS, demonstrating ASCC3’s potential as disease prediction marker.

Modern day fossil fuels are prone to polluting our environment, which can provide major habitat loss to many animals in our ecosystems. Algae-based biofuels have become an increasingly popular alternative to fossil fuels because of their sustainability, effectiveness, and environmentally-friendly nature. To encourage algae growth and solidify its role as an emerging biofuel, we tested basic (in terms of pH) solutions on pond water to determine which solution is most efficient in inducing the growth of algae.