High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

BACKGROUND: Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns. RESULTS: High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg) and Root Mean Square Deviation (RMSD) have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles. CONCLUSION: Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE), shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here

Determinants of private well water testing in Maine

Objectives: Describe sociodemographic characteristics associated with ever testing well water using data from the 2014-2017 Maine Behavioral Risk Factor Surveillance System (BRFSS) (n= 12,152).https://knowledgeconnection.mainehealth.org/lambrew-retreat-2021/1005/thumbnail.jp

Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome

BACKGROUND: Transcription is the first step in cellular information processing. It is regulated by cis-acting elements such as promoters and operators in the DNA, and trans-acting elements such as transcription factors and sigma factors. Identification of cis-acting regulatory elements on a genomic scale requires computational analysis. RESULTS: We have used oligonucleotide profiling to predict regulatory regions in a bacterial genome. The method has been applied to the Escherichia coli K12 genome and the results analyzed. The information content of the putative regulatory oligonucleotides so predicted is validated through intra-genomic analyses, correlations with experimental data and inter-genome comparisons. Based on the results we have proposed a model for the bacterial promoter. The results show that the method is capable of identifying, in the E.coli genome, cis-acting elements such as TATAAT (sigma70 binding site), CCCTAT (1 base relative of sigma32 binding site), CTATNN (LexA binding site), AGGA-containing hexanucleotides (Shine Dalgarno consensus) and CTAG-containing hexanucleotides (core binding sites for Trp and Met repressors). CONCLUSION: The method adopted is simple yet effective in predicting upstream regulatory elements in bacteria. It does not need any prior experimental data except the sequence itself. This method should be applicable to most known genomes. Profiling, as applied to the E.coli genome, picks up known cis-acting and regulatory elements. Based on the profile results, we propose a model for the bacterial promoter that is extensible even to eukaryotes. The model is that the core promoter lies within a plateau of bent AT-rich DNA. This bent DNA acts as a homing segment for the sigma factor to recognize the promoter. The model thus suggests an important role for local landscapes in prokaryotic and eukaryotic gene regulation

Early fate of exogenous promoters in E. coli

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones

Wildfire Predictions: Determining Reliable Models using Fused Dataset

Wildfires are a major environmental hazard that causes fatalities greater than structural fire and other disasters Computerized models have increased the possibilities of predictions that enhanced the firefighting capabilities in U S While predictive models are faster and accurate it is still important to identify the right model for the data type analyzed The paper aims at understanding the reliability of three predictive methods using fused dataset Performances of these methods Support Vector Machine K-Nearest Neighbors and decision tree models are evaluated using binary and multiclass classifications that predict wildfire occurrence and its severity Data extracted from meteorological database and U S fire database are utilized to understand the accuracy of these models that enhances the discussion on using right model for dataset based on their size The findings of the paper include SVM as the best optimum models for binary and multiclass classifications on the selected fused datase

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease with a complex spectrum of cellular and molecular characteristics including several dramatic changes in the populations of peripheral leukocytes. These changes include general leukopenia, activation of B and T cells, and maturation of granulocytes. The manifestation of SLE in peripheral blood is central to the disease but is incompletely understood. A technique for rigorously characterizing changes in mixed populations of cells, microarray expression deconvolution, has been applied to several areas of biology but not to SLE or to blood. Here we demonstrate that microarray expression deconvolution accurately quantifies the constituents of real blood samples and mixtures of immune-derived cell lines. We characterize a broad spectrum of peripheral leukocyte cell types and states in SLE to uncover novel patterns including: specific activation of NK and T helper lymphocytes, relationships of these patterns to each other, and correlations to clinical variables and measures. The expansion and activation of monocytes, NK cells, and T helper cells in SLE at least partly underlie this disease's prominent interferon signature. These and other patterns of leukocyte dynamics uncovered here correlate with disease severity and treatment, suggest potential new treatments, and extend our understanding of lupus pathology as a complex autoimmune disease involving many arms of the immune system

Evidence of a Double-Lid Movement in Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations

Pseudomonas aeruginosa lipase is a 29-kDa protein that, following the determination of its crystal structure, was postulated to have a lid that stretched between residues 125 and 148. In this paper, using molecular dynamics simulations, we propose that there exists, in addition to the above-mentioned lid, a novel second lid in this lipase. We further show that the second lid, covering residues 210–222, acts as a triggering lid for the movement of the first. We also investigate the role of hydrophobicity in the movement of the lids and show that two residues, Phe214 and Ala217, play important roles in lid movement. To our knowledge, this is the first time that a double-lid movement of the type described in our manuscript has been presented to the scientific community. This work also elucidates the interplay of hydrophobic interactions in the dynamics, and hence the function, of an enzyme

Plasma concentrations of per- and polyfluoroalkyl substances and body composition from mid-childhood to early adolescence

BACKGROUND • Per- and polyfluoroalkyl substances (PFAS) may alter body composition by lowering anabolic hormones and increasing inflammation. Prior studies have found positive, inverse, and null associations of PFAS concentrations with adiposity among children and adolescents. Few studies have examined associations of PFAS concentrations with changes in body composition longitudinally. No study has examined the association of PFAS plasma concentrations with lean mass.https://knowledgeconnection.mainehealth.org/lambrew-retreat-2021/1038/thumbnail.jp

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms

Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology

Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive evolutionary forces. Teasing apart these forces is an important step toward functional analyses of the different components of CRNs, designing regulatory perturbation experiments, and constructing synthetic networks. Although tests of neutrality and selection based on molecular sequence data exist, no such tests are currently available based on CRNs. In this work, we present a unique genotype model of CRNs that is grounded in a genomic context and demonstrate its use in identifying portions of the CRN with properties explainable by neutral evolutionary forces at the system, subsystem, and operon levels.We leverage our model against experimentally derived data from Escherichia coli. The results of this analysis show statistically significant and substantial neutral trends in properties previously identified as adaptive in originﾗdegree distribution, clustering coefficient, and motifsﾗ within the E. coli CRN. Our model captures the tightly coupled genomeﾖ interactome of an organism and enables analyses of how evolutionary events acting at the genome level, such as mutation, and at the population level, such as genetic drift, give rise to neutral patterns that we can quantify in CRNs