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Deciphering correlation and causation in risk factors for heart disease with Mendelian randomization

Singh et al. | Feb 08, 2023

Deciphering correlation and causation in risk factors for heart disease with Mendelian randomization
Image credit: Robina Weermeijer

Here, seeking to identify the risk of coronary artery disease (CAD), a major cause of cardiovascular disease, the authors used Mendelian randomization. With this method they identified several traits such as blood pressure readings, LDL cholesterol and BMI as significant risk factors. While other traits were not found to be significant risk factors.

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Genomic Signature Analysis for the Strategic Bioremediation of Polycyclic Aromatic Hydrocarbons in Mangrove Ecosystems in the Gulf of Tonkin

Dao et al. | Jun 27, 2021

Genomic Signature Analysis for the Strategic Bioremediation of Polycyclic Aromatic Hydrocarbons in Mangrove Ecosystems in the Gulf of Tonkin

Engineered bacteria that degrade oil are currently being considered as a safe option for the treatment of oil spills. For this approach to be successful, the bacteria must effectively express oil-degrading genes they uptake as part of an external genoming vehicle called a "plasmid". Using a computational approach, the authors investigate plasmid-bacterium compatibility to find pairs that ensure high levels of gene expression.

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Comparing Virulence of Three T4 Bacteriophage Strains on Ampicillin-Resistant and Sensitive E. coli Bacteria

Hudanich et al. | Dec 09, 2020

Comparing Virulence of Three T4 Bacteriophage Strains on Ampicillin-Resistant and Sensitive <em>E. coli</em> Bacteria

In this study, the authors investigate an alternative way to kill bacteria other than the use of antibiotics, which is useful when considering antibiotic-resistance bacteria. They use bacteriophages, which are are viruses that can infect bacteria, and measure cell lysis. They make some important findings that these bacteriophage can lyse both antibiotic-resistant and non-resistant bacteria.

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Contrasting role of ASCC3 and ALKBH3 in determining genomic alterations in Glioblastoma Multiforme

Sriram et al. | Sep 27, 2022

Contrasting role of <i>ASCC3</i> and <i>ALKBH3</i> in determining genomic alterations in Glioblastoma Multiforme

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.

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