Genetic elements of microbes: a comprehensive and integrated genomic database application

The increasing abundance of genomic data has led to the creation of several databases containing the sequence data, metadata about the sequences and information about the organisms. These data are useful in many areas of biological research. Of the many available databases, few contain a significant amount of genome-associated data. In an effort to create a comprehensive microbial genomes database, the Genetic Elements of Microbes (GEM) database application was created. A K-mer analysis tool was also created and added the GEM application to provide an analysis of sequence composition and potential Lateral Gene Transfer (LGT) identification. The GEM application was designed to be convenient to maintain and extend. The K-mer analysis tool\u27s ability to identify islands and to identify LGT events was tested with comparisons to published works. The GEM database application provides another source of genomic sequence and genome-associated data for the scientific community. The K-mer analysis addition provides an easy-to-customize tool to identify regions of dissimilarity and identify potential LGT events. The GEM application interface is publicly accessible at http://bucatini.bioinformatics.rit.edu/~amb4541/cgi-bin/GEMSearch.cgi. The standalone K-mer analysis interface is available at http://bucatini.bioinformatics.rit.edu/~amb4541/cgi-bin/KmerAnalysis.cgi

Nationalistic Stereotyping in Automotive Advertising: The Use and Viewer Response on the Internet

This research is focused on the usage of nationalistic stereotypes in television commercials in the automotive industry. We specifically analyzed one case in which nationalistic stereotypes were used in an automotive advertisement in the USA, using netnographic and document analysis methods. Our main objectives were to first uncover how an automotive advertisement is now using these stereotypes to boost brand awareness, and secondly, to analyze how the public reacts and experiences advertisements that use these stereotypes. By applying Hall's Encoding/Decoding Theory and Brewer’s In-Group Bias Theory, we uncovered that advertisers are now using nationalistic stereotypes to provoke and create controversy that cuts through the clutter and creates buzz. As opposed to the previous tactics in implementing these nationalistic stereotypes in this industry where the ad addressed an entire nation to promote one country of manufacturing over another, this advertisement stereotyped a specific kind of American based on distinct values and ideologies in order to directly target their audience. It was also observed that the responses to the same commercial could be found on two ideological extremes, depending on political orientation. Another interesting finding of our research is the propensity for viewers’ to manufacture their response and comments within the social platform where a discussion is taking place. Our research seeks to make consumers aware of advertisers using nationalistic stereotypes in this way, so that viewers do not perpetuate stereotypes they’ve seen in commercials, but make decisions based on experiences of their own. Simultaneously, this research can serve to educate advertisers on what type of responses and reactions the public can have towards their usage of nationalistic stereotypes

Computational Processing of Omics Data: Implications for Analysis

<p>In this work, I present four studies across the range of 'omics data types - a Genome- Wide Association Study for gene-by-sex interaction of obesity traits, computational models for transcription start site classification, an assessment of reference-based mapping methods for RNA-Seq data from non-model organisms, and a statistical model for open-platform proteomics data alignment.</p><p>Obesity is an increasingly prevalent and severe health concern with a substantial heritable component, and marked sex differences. We sought to determine if the effect of genetic variants also differed by sex by performing a genome-wide association study modeling the effect of genotype-by-sex interaction on obesity phenotypes. Genotype data from individuals in the Framingham Heart Study Offspring cohort were analyzed across five exams. Although no variants showed genome-wide significant gene-by-sex interaction in any individual exam, four polymorphisms displayed a consistent BMI association (P-values .00186 to .00010) across all five exams. These variants were clustered downstream of LYPLAL1, which encodes a lipase/esterase expressed in adipose tissue, a locus previously identified as having sex-specific effects on central obesity. Primary effects in males were in the opposite direction as females and were replicated in Framingham Generation 3. Our data support a sex-influenced association between genetic variation at the LYPLAL1 locus and obesity-related traits.</p><p>The application of deep sequencing to map 5' capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: focused promot- ers with transcription start sites (TSSs) that occur in a narrowly defined genomic span and dispersed promoters with TSSs that are spread over a larger window. Pre- vious studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, and our collaborators recently inves- tigated the relationship with chromatin features. It was found that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Here, we present computational models supporting the stronger contribution of chro- matin features to the definition of dispersed promoters compared to focused start sites. Specifically, dispersed promoters display enrichment for well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone vari- ants (H2A.Z) and marks (H3K4 methylation), as well as insulator binding (such as CTCF), independent of the expression levels of affected genes.</p><p>The application of next-generation sequencing technology to gene expression quantification analysis, namely, RNA-Sequencing, has transformed the way in which gene expression studies are conducted and analyzed. These advances are of partic- ular interest to researchers studying non-model organisms, as the need for knowl- edge of sequence information is overcome. De novo assembly methods have gained widespread acceptance in the RNA-Seq community for non-model organisms with no true reference genome or transcriptome. While such methods have tremendous utility, computational complexity is still a significant challenge for organisms with large and complex genomes. Here we present a comparison of four reference-based mapping methods for non-human primate data. We explore mapping efficacy, correlation between computed expression values, and utility for differential expression analyses. We show that reference-based mapping methods indeed have utility in RNA-Seq analysis of mammalian data with no true reference, and that the details of mapping methods should be carefully considered when doing so. We find that shorter seed sequences, allowance of mismatches, and allowance of gapped alignments, in addition to splice junction gaps result in more sensitive alignments of non-human primate RNA-Seq data.</p><p>Open-platform proteomics experiments seek to quantify and identify the proteins present in biological samples. Much like differential gene expression analyses, it is often of interest to determine how protein abundance differs in various physiological conditions. Label free LC-MS/MS enables the rapid measurement of thousands of proteins, providing a wealth of peptide intensity information for differential analysis. However, the processing of raw proteomics data poses significant challenges that must be overcome prior to analysis. We specifically address the matching of peptide measurements across samples - an essential pre-processing step in every proteomics experiment. Presented here is a novel method for open-platform proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion data. Our results suggest that the inclusion of additional data results in higher numbers of more confident matches, without increasing the number of mismatches. We also show that the incorporation of product ion data can improve results dramatically. Based on these results, we argue that the incorporation of ion mobility drift times and product ion information are worthy pursuits. In addition, alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods. The addition of drift times and/or high energy to alignment methods and accurate mass and time (AMT) tag databases can greatly improve experimenters ability to identify measured peptides, reducing analysis costs and potentially the need to run additional experiments.</p>Dissertatio

Parents’ Pandemic NICU Experience in the United States: A Qualitative Study

Background Prior to the COVID-19 pandemic, parents of infants in the Neonatal Intensive Care Unit (NICU) frequently reported high levels of stress, uncertainty, and decreased parenting confidence. Early research has demonstrated that parents have had less access to their infants in the hospital due to restrictions on parental presence secondary to the pandemic. It is unknown how parents have perceived their experiences in the NICU since the beginning of the COVID-19 pandemic. The purpose of this study was to describe the lived experience of parents who had an infant in the NICU in the context of the COVID-19 pandemic to inform healthcare providers and policy makers for future development of policies and care planning. Methods The study design was a qualitative description of the impact of the COVID-19 pandemic on parents’ experiences of having an infant in the NICU. Free-text responses to open-ended questions were collected as part of a multi-method study of parents’ experiences of the NICU during the first six months of the pandemic. Participants from the United States were recruited using social media platforms between the months of May and July of 2020. Data were analyzed using a reflexive thematic approach. Findings Free-text responses came from 169 parents from 38 different states in the United States. Three broad themes emerged from the analysis: (1) parents’ NICU experiences during the COVID-19 pandemic were emotionally isolating and overwhelming, (2) policy changes restricting parental presence created disruptions to the family unit and limited family-centered care, and (3) interactions with NICU providers intensified or alleviated emotional distress felt by parents. A unifying theme of experiences of emotional distress attributed to COVID-19 circumstances ran through all three themes. Conclusions Parents of infants in the NICU during the first six months of the COVID-19 pandemic experienced emotional struggles, feelings of isolation, lack of family-centered care, and deep disappointment with system-level decisions. Moving forward, parents need to be considered essential partners in the development of policies concerning care of and access to their infants. Background The COVID-19 pandemic created unprecedented conditions for administrators and clinicians working in Neonatal Intensive Care Units (NICU) and greatly affected parents of infants requiring hospitalization. Prior to the COVID-19 pandemic, parents of infants admitted to a NICU reported high levels of stress, anxiety, uncertainty, and decreased parenting confidence when compared to parents of healthy full-term infants [1,2,3,4,5,6]. Approximately 28–40% of mothers of infants admitted to a NICU were diagnosed with a new mental illness, such as depression or perinatal post-traumatic stress disorder [7]. Fathers of infants requiring NICU hospitalization also reported significant stress and need for reassurance and support [8, 9]

Social Buffering of Pesticides in Bumblebees: Agent-Based Modeling of the Effects of Colony Size and Neonicotinoid Exposure on Behavior Within Nests

Neonicotinoids are a globally prevalent class of pesticides that can negatively affect bees and the pollination services they provide. While there is evidence suggesting that colony size may play an important role in mitigating neonicotinoid exposure in bees, mechanisms underlying these effects are not well understood. Here, a recently developed agent-based computational model is used to investigate how the effects of sub-lethal neonicotinoid exposure on intranest behavior of bumblebees (Bombus impatiens) are modulated by colony size. Simulations from the model, parameterized using empirical data on bumblebee workers exposed to imidacloprid (a common neonicotinoid pesticide), suggest that colony size has significant effects on neonicotinoid-sensitivity within bumblebee nests. Specifically, differences are reduced between treated and untreated workers in larger colonies for several key aspects of behavior within nests. Our results suggest that changes in both number of workers and nest architecture may contribute to making larger colonies less sensitive to pesticide exposure

Gene by Sex Interaction for Measures of Obesity in the Framingham Heart Study

Obesity is an increasingly prevalent and severe health concern with a substantial heritable component and marked sex differences. We sought to determine if the effect of genetic variants also differed by sex by performing a genome-wide association study modeling the effect of genotype-by-sex interaction on obesity phenotypes. Genotype data from individuals in the Framingham Heart Study Offspring cohort were analyzed across five exams. Although no variants showed genome-wide significant gene-by-sex interaction in any individual exam, four polymorphisms displayed a consistent BMI association (P-values .00186 to .00010) across all five exams. These variants were clustered downstream of LYPLAL1, which encodes a lipase/esterase expressed in adipose tissue, a locus previously identified as having sex-specific effects on central obesity. Primary effects in males were in the opposite direction from females and were replicated in Framingham Generation 3. Our data support a sex-influenced association between genetic variation at the LYPLAL1 locus and obesity-related traits

The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis

Background: The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups—A and B—corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. Methods: We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. Findings: We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. Interpretation: A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital. Funding: Wellcome Trust.Peer Reviewe

Analysis of blood type for SARS-CoV-2 and correlation for disease acquisition in various sociodemographic groups including women of childbearing age.

BACKGROUND: Multiple studies have occurred to determine if a patient\u27s blood type, Rhesus factor (Rh), and sociodemographic attributes contribute to contracting SARS-CoV-2. True association remains unknown. METHODS: Inclusion criteria included in-patients who were tested for SARS-CoV-2 with blood type assessed. Study endpoints combined ABO, Rh and all-cause inpatient mortality (ACIM) with testing positivity. Pregnancy status was one of several secondary endpoints evaluated. A logistic regression analysis was used to estimate association. RESULTS: Of the 27,662 patients who met inclusion criteria, Type A blood was associated with increased positivity [1.01 (1.0-1.21), P = .03]. Type B [1.10 (0.99-1.23), P = .08] and AB [0.98 (0.81-1.19), P = .84] showed no association. When evaluating ACIM, type A [1.18 (0.91-1.52), P = .22], B [1.13 (0.82- 1.56), P = .480], and AB [1.06 (0.62-1.81), P = .839] were not associated with increased mortality. The female subgroup was less likely to test positive [0.88 (0.82-0.986), P = .002]. Black patients demonstrated a higher likelihood of positivity when compared to White [1.96 (1.79-2.14), P \u3c .001]. Non-pregnant women exhibited a 2.5 times greater likelihood of testing positive [2.49 (2.04-3.04), P \u3c .001]. CONCLUSIONS: This study confirms results of previous research which showed SARS-Co-V-2 positivity related to blood type. It also confirms more recent research demonstrating inequities related to acquisition of SARS-CoV-2 for certain sociodemographic groups. Larger studies are warranted to confirm and further explore novel pregnancy findings

Genome-Wide Association Study of Lp-PLA2 Activity and Mass in the Framingham Heart Study

Lipoprotein-associated phospholipase A2 (Lp-PLA2) is an emerging risk factor and therapeutic target for cardiovascular disease. The activity and mass of this enzyme are heritable traits, but major genetic determinants have not been explored in a systematic, genome-wide fashion. We carried out a genome-wide association study of Lp-PLA2 activity and mass in 6,668 Caucasian subjects from the population-based Framingham Heart Study. Clinical data and genotypes from the Affymetrix 550K SNP array were obtained from the open-access Framingham SHARe project. Each polymorphism that passed quality control was tested for associations with Lp-PLA2 activity and mass using linear mixed models implemented in the R statistical package, accounting for familial correlations, and controlling for age, sex, smoking, lipid-lowering-medication use, and cohort. For Lp-PLA2 activity, polymorphisms at four independent loci reached genome-wide significance, including the APOE/APOC1 region on chromosome 19 (p = 6×10−24); CELSR2/PSRC1 on chromosome 1 (p = 3×10−15); SCARB1 on chromosome 12 (p = 1×10−8) and ZNF259/BUD13 in the APOA5/APOA1 gene region on chromosome 11 (p = 4×10−8). All of these remained significant after accounting for associations with LDL cholesterol, HDL cholesterol, or triglycerides. For Lp-PLA2 mass, 12 SNPs achieved genome-wide significance, all clustering in a region on chromosome 6p12.3 near the PLA2G7 gene. Our analyses demonstrate that genetic polymorphisms may contribute to inter-individual variation in Lp-PLA2 activity and mass