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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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The Effect of the Stomatal Index on the Net Rate of Photosynthesis in the Leaves of Spinacia oleracea, Vinca minor, Rhododendron spp, Epipremnum aureum, and Hedera spp

Segev et al. | Nov 15, 2015

The Effect of the Stomatal Index on the Net Rate of Photosynthesis in the Leaves of <i>Spinacia oleracea</i>, <i>Vinca minor</i>, <i>Rhododendron spp</i>, <i>Epipremnum aureum</i>, and <i>Hedera spp</i>

The density of stomata, or stomatal index, in plant leaves is correlated with the plant's rate of photosynthesis, and affected by the plant's climate. In this paper, authors measure the stomatal index of five plant species to derive their rates of photosynthesis. These results could help track changes in plants' photosynthetic rates with changing climate.

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Expression of Anti-Neurodegeneration Genes in Mutant Caenorhabditis elegans Using CRISPR-Cas9 Improves Behavior Associated With Alzheimer’s Disease

Mishra et al. | Sep 14, 2019

Expression of Anti-Neurodegeneration Genes in Mutant <em>Caenorhabditis elegans</em> Using CRISPR-Cas9 Improves Behavior Associated With Alzheimer’s Disease

Alzheimer's disease is one of the leading causes of death in the United States and is characterized by neurodegeneration. Mishra et al. wanted to understand the role of two transport proteins, LRP1 and AQP4, in the neurodegeneration of Alzheimer's disease. They used a model organism for Alzheimer's disease, the nematode C. elegans, and genetic engineering to look at whether they would see a decrease in neurodegeneration if they increased the amount of these two transport proteins. They found that the best improvements were caused by increased expression of both transport proteins, with smaller improvements when just one of the proteins is overly expressed. Their work has important implications for how we understand neurodegeneration in Alzheimer's disease and what we can do to slow or prevent the progression of the disease.

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Characterization of Drought Tolerance in Arabidopsis Mutant fry1-6

Kim et al. | Jan 07, 2019

Characterization of Drought Tolerance in Arabidopsis Mutant  fry1-6

In a world where water shortage is becoming an increasing concern, and where population increase seems inevitable, food shortage is an overwhelming concern for many. In this paper, the authors aim to characterize a drought-resistant strain of A. thaliana, investigating the cause for its water resistance. These and similar studies help us learn how plants could be engineered to improve their ability to flourish in a changing climate.

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Investigating KNOX Gene Expression in Aquilegia Petal Spur Development

Hossain et al. | Feb 03, 2014

Investigating KNOX Gene Expression in Aquilegia Petal Spur Development

Plants, and all other multi-cellular organisms, develop through the coordinated action of many sets of genes. The authors here investigate the genes, in a class named KNOX, potentially responsible for organizing a certain part of Aquilegia (columbine) flowers called petal spurs. Through the technique Reverse Transcription-Polymerase Chain Reaction (RT-PCR), they find that certain KNOX genes are expressed non-uniformly in petal spurs, suggesting that they may be involved, perhaps in a cell-specific manner. This research will help guide future efforts toward understanding how many beautiful flowers develop their unique shapes.

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Pancreatic Adenocarcinoma: An Analysis of Drug Therapy Options through Interaction Maps and Graph Theory

Gupta et al. | Feb 04, 2014

Pancreatic Adenocarcinoma: An Analysis of Drug Therapy Options through Interaction Maps and Graph Theory

Cancer is often caused by improper function of a few proteins, and sometimes it takes only a few proteins to malfunction to cause drastic changes in cells. Here the authors look at the genes that were mutated in patients with a type of pancreatic cancer to identify proteins that are important in causing cancer. They also determined which proteins currently lack effective treatment, and suggest that certain proteins (named KRAS, CDKN2A, and RBBP8) are the most important candidates for developing drugs to treat pancreatic cancer.

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Friend or foe: Using DNA barcoding to identify arthropods found at home

Wang et al. | Mar 14, 2022

Friend or foe: Using DNA barcoding to identify arthropods found at home

Here the authors used morphological characters and DNA barcoding to identify arthropods found within a residential house. With this method they identified their species and compared them against pests lists provided by the US government. They found that none of their identified species were considered to be pests providing evidence against the misconception that arthropods found at home are harmful to humans. They suggest that these methods could be used at larger scales to better understand and aid in mapping ecosystems.

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Ribosome distribution affects stalling in amino-acid starved cancer cells

Deng et al. | Jan 07, 2022

Ribosome distribution affects stalling in amino-acid starved cancer cells

In this article, the authors analyzed ribosome profiling data from amino acid-starved pancreatic cancer cells to explore whether the pattern of ribosome distribution along transcripts under normal conditions can predict the degree of ribosome stalling under stress. The authors found that ribosomes in amino acid-deprived cells stalled more along elongation-limited transcripts. By contrast, they observed no relationship between read density near start and stop and disparities between mRNA sequencing reads and ribosome profiling reads. This research identifies an important relationship between read distribution and propensity for ribosomes to stall, although more work is needed to fully understand the patterns of ribosome distribution along transcripts in ribosome profiling data.

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Expressional correlations between SERPINA6 and pancreatic ductal adenocarcinoma-linked genes

Selver et al. | Oct 06, 2021

Expressional correlations between <em>SERPINA6</em> and pancreatic ductal adenocarcinoma-linked genes

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer, with early diagnosis and treatment challenges. When any of the genes KRAS, SMAD4, TP53, and BRCA2 are heavily mutated, they correlate with PDAC progression. Cellular stress, partly regulated by the gene SERPINA6, also correlates with PDAC progression. When SERPINA6 is highly expressed, corticosteroid-binding globulin inhibits the effect of the stress hormone cortisol. In this study, the authors explored whether there is an inverse correlation between the expression of SERPINA6 and PDAC-linked genes.

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DyGS: A Dynamic Gene Searching Algorithm for Cancer Detection

Wang et al. | Jun 05, 2018

DyGS: A Dynamic Gene Searching Algorithm for Cancer Detection

Wang and Gong developed a novel dynamic gene-searching algorithm called Dynamic Gene Search (DyGS) to create a gene panel for each of the 12 cancers with the highest annual incidence and death rate. The 12 gene panels the DyGS algorithm selected used only 3.5% of the original gene mutation pool, while covering every patient sample. About 40% of each gene panel is druggable, which indicates that the DyGS-generated gene panels can be used for early cancer detection as well as therapeutic targets in treatment methods.

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