Biology subjects

Gould, M.

Publications and source records attributed to Gould, M..

4 recordsLinked to original sources

bioRxiv2024

Expanding and enriching the LncRNA gene landscape using the GeneCaRNA database

The GeneCaRNA human gene database is a member of the GeneCards Suite. It presents [~]280,000 human non-coding RNA genes, identified algorithmically from [~]690,000 RNAcentrals transcripts. This expands by [~]tenfold the ncRNA gene count relative to other sources. GeneCaRNA thus contains [~]120,000 long non-coding RNAs (LncRNAs, >200 bases long), including [~]100,000 novel genes. The latter have sparse functional information, a vast terra incognita for future research. LncRNA genes are uniformly represented on all nuclear chromosomes, with 10 genes on mitochondrial DNA. Data obtained from MalaCards, another GeneCards Suite member, finds 1,547 genes associated with 1 to 50 diseases. [~]15% of the associations portray experimental evidence, with cancers tending to be multigenic. Preliminary text mining within GeneCaRNA discovers interactions of LncRNA transcripts with target gene products, with 25% being ncRNAs and 75% proteins. GeneCaRNA has a biological pathways section, which at present shows 131 pathways for 38 LncRNA genes, a basis for future expansion. Finally, our GeneHancer database provides regulatory elements for [~]110,000 LncRNA genes, offering pointers for co-regulated genes and genetic linkages from enhancers to diseases. We anticipate that the broad vista provided by GeneCaRNA will serve as an essential guide for further LncRNA research in disease decipherment.

bioinformatics↗

bioRxiv2021

Sulfite preservatives effects on the mouth microbiome: changes in viability, diversity and composition of microbiota

Processed foods make up about 70 percent of the American diet. Sulfites and other food preservatives are added to these foods largely to limit bacterial contamination. The mouth microbiota and its associated enzymes are the first to encounter food and therefore likely to be the most affected. Eight saliva samples from ten individuals were exposed to two sulfite preservatives, sodium sulfite and sodium bisulfite. One sample set was evaluated for bacteria composition utilizing 16s rRNA sequencing, and the number of viable cells in all sample sets was determined utilizing ATP assays at 10 and 40-minute exposure times. All untreated samples were analyzed for baseline lysozyme activity, and possible correlations between the number of viable cells and lysozyme activity. Sequencing results indicated significant increases in alpha diversity with sodium bisulfite exposure and changes in relative abundance of 3 amplicon sequence variants (ASV). Sodium sulfite treated samples showed a significant decrease in the Firmicutes/Bacteroidetes ratio, a marginally significant change in alpha diversity, and a significant change in the relative abundance for Proteobacteria, Firmicutes, Bacteroidetes, and for 6 ASVs. Beta diversity didnt show any separation between groups, however, all but one sample set was observed to be moving in the same direction under sodium sulfite treatment in a principal component analysis. ATP assays indicated a significant and consistent average decrease in activity ranging from 24 - 46% at both exposure times with both sulfites. Average initial rates of lysozyme activity between all individuals ranged from +/- 76% compared to individual variations of +/- 10 - 34%. No consistent, significant correlation was found between ATP and lysozyme activity in any sample sets. ConclusionsSulfite preservatives, at concentrations regarded as safe by the FDA, alter the relative abundance and richness of the microbiota found in saliva, and decrease the number of viable cells, within 10 minutes of exposure.

microbiology↗

bioRxiv2020

Critical role for cold shock protein YB-1 in cytokinesis

High levels of the cold shock protein Y-box-binding protein-1, YB-1, are tightly correlated with increased cell proliferation and cancer progression. However, the precise mechanism by which YB-1 regulates proliferation is unknown. Here, we found that YB-1 depletion in several cell lines resulted in cytokinesis failure, multinucleation and an increase in G1 transit time. Rescue experiments indicated that YB-1 was required for completion of cytokinesis. Using confocal imaging of cells undergoing cytokinesis both in vitro and in zebrafish embryos, we found that YB-1 was critical for microtubule organization during cytokinesis. Using mass spectrometry we identified multiple novel phosphorylation sites on YB-1. We show that phosphorylation of YB-1 at multiple serine residues was essential for its function during cytokinesis. Using atomistic modelling we show how multiple phosphorylations alter YB-1 conformation, allowing it to interact with protein partners. Our results establish phosphorylated YB-1 as a critical regulator of cytokinesis, defining for the first time precisely how YB-1 regulates cell division. SUMMARYY-box-binding protein-1, YB-1, is essential for cell division, but it is not clear how it functions. Using live imaging and confocal microscopy we show that YB-1 functions only in the last step of division, specifically being required to initiate cytokinesis.

cell biology↗

bioRxiv2020

Polynomial Phylogenetic Analysis of Tree Shapes

AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic trees are a central tool in evolutionary biology. They demonstrate evolutionary patterns among species, genes, and with modern sequencing technologies, patterns of ancestry among sets of individuals. Phylogenetic trees usually consist of tree shapes, branch lengths and partial labels. Comparing tree shapes is a challenging aspect of comparing phylogenetic trees as there are few tools to describe tree shapes in a quantitative, accurate, comprehensive and easy-to-interpret way. Current methods to compare tree shapes are often based on scalar indices reflecting tree imbalance, and on frequencies of small subtrees. In this paper, we present tree comparisons and applications based on a polynomial that fully characterizes trees. Polynomials are important tools to describe discrete structures and have been used to study various objects including graphs and knots. There are also polynomials that describe rooted trees. We use tree-defining polynomials to compare tree shapes randomly generated by simulations and tree shapes reconstructed from data. Moreover, we show that the comparisons can be used to estimate parameters and to select the best-fit model that generates specific tree shapes.

systems biology↗