BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly.

BackgroundThe problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the original input long reads can result in quality improvement. Previous approaches have focused on pre-processing reads and optimizing assemblers. BIGMAC takes an alternative perspective to focus on the post-processing step.ResultsUsing both the assembled contigs and original long reads as input, BIGMAC first breaks the contigs at potentially mis-assembled locations and subsequently scaffolds contigs. Our experiments on metagenomes assembled from long reads show that BIGMAC can improve assembly quality by reducing the number of mis-assemblies while maintaining or increasing N50 and N75. Moreover, BIGMAC shows the largest N75 to number of mis-assemblies ratio on all tested datasets when compared to other post-processing tools.ConclusionsBIGMAC demonstrates the effectiveness of the post-processing approach in improving the quality of metagenomic assemblies

Every-Body is Beautiful: Including Gender, Sexual Orientation, and Race in Investigations on Body Image

Although body image satisfaction has been extensively examined in straight, white women, fewer studies have covered the nuanced differences that likely exist across other demographic groups. Previously, body satisfaction, appearance-pressures from the media and family, and body respect have been shown to vary across gender, sexual orientation, and race. For instance, some studies have shown that homosexual females have higher body satisfaction compared to their homosexual male counterparts, potentially due to greater appearance-based-pressure from the media. Additionally, women of color have been shown to experience more perceived family appearance-pressure than their white counterparts. However, women of color, especially queer women of color, appear to have higher body satisfaction than their white women counterparts, supporting previous studies suggesting protective factors of high group belongingness and cultures that de-emphasize thinness in queer women of color. Interestingly, the same is not evident with queer men of color, as their body respect has shown to be significantly lower than all other demographics. This study sought to examine undergraduates’ perspectives of their bodies in personal and familial contexts, as well as how the media may influence these viewpoints. Undergraduate students in the fall of 2016 and the spring of 2017 were given an online Qualtrics questionnaire asking a series of questions related to how they viewed their body along with a set of demographic questions. The results were analyzed using a multivariate generalized linear model in SPSS, which yielded important differences across gender, race, and sexual orientation. Significant differences were observed in the variables of body image, body respect, family’s influence on body image, and the media’s influence on body image. Future studies should consider investigating whether similar trends can be observed across different age cohorts and further examine body image with the nuances of sexual orientation and gender.https://orb.binghamton.edu/research_days_posters_2021/1055/thumbnail.jp

Sexual Consent: Do you get it? How college students\u27 definitions of consent differ from their region\u27s consent policy

Although many colleges across the United States have incorporated some form of sexual consent policy into their code of conduct, these definitions vary by region and institution. Moreover, previous studies have found that although students may be aware of their university’s consent policy, it may not always be used in practice (Gronert & Raclaw, 2019; Ortiz, 2019). This study compares four samples of respondents by region (i.e. Northeast and South), assigning a regionally-typical consent policy to the sample and then analyzing the differences in sexual consent understanding and behaviors. We hypothesized that students’ internalized definitions of consent will differ both from their regionally-stated policy and from each other in significant ways. Data was collected from participants through an online national survey that asked questions regarding students’ definitions of consent and how they knew that their previous partners had given them consent. These responses were then analyzed to examine what themes exist between students’ perceptions of consent and their assigned regional policy. Implications for the utility of university consent policy upon student consensual behavior is discussed.https://orb.binghamton.edu/research_days_posters_spring2020/1013/thumbnail.jp

One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil.

We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates

Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales

Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is characterized by its ability to nodulate actinorhizal plants of the Rhamnales order, but not its original host. It represents one of the largest Frankia genomes so far sequenced (9.5 Mbp)

Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel

A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production

<p>Abstract</p> <p>Background</p> <p>Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi-billion dollar petrochemical market into one based on renewable resources. <it>Actinobacillus succinogenes </it>naturally converts sugars and CO₂into high concentrations of succinic acid as part of a mixed-acid fermentation. Efforts are ongoing to maximize carbon flux to succinate to achieve an industrial process.</p> <p>Results</p> <p>Described here is the 2.3 Mb <it>A. succinogenes </it>genome sequence with emphasis on <it>A. succinogenes</it>'s potential for genetic engineering, its metabolic attributes and capabilities, and its lack of pathogenicity. The genome sequence contains 1,690 DNA uptake signal sequence repeats and a nearly complete set of natural competence proteins, suggesting that <it>A. succinogenes </it>is capable of natural transformation. <it>A. succinogenes </it>lacks a complete tricarboxylic acid cycle as well as a glyoxylate pathway, and it appears to be able to transport and degrade about twenty different carbohydrates. The genomes of <it>A. succinogenes </it>and its closest known relative, <it>Mannheimia succiniciproducens</it>, were compared for the presence of known Pasteurellaceae virulence factors. Both species appear to lack the virulence traits of toxin production, sialic acid and choline incorporation into lipopolysaccharide, and utilization of hemoglobin and transferrin as iron sources. Perspectives are also given on the conservation of <it>A. succinogenes </it>genomic features in other sequenced Pasteurellaceae.</p> <p>Conclusions</p> <p>Both <it>A. succinogenes </it>and <it>M. succiniciproducens </it>genome sequences lack many of the virulence genes used by their pathogenic Pasteurellaceae relatives. The lack of pathogenicity of these two succinogens is an exciting prospect, because comparisons with pathogenic Pasteurellaceae could lead to a better understanding of Pasteurellaceae virulence. The fact that the <it>A. succinogenes </it>genome encodes uptake and degradation pathways for a variety of carbohydrates reflects the variety of carbohydrate substrates available in the rumen, <it>A. succinogenes</it>'s natural habitat. It also suggests that many different carbon sources can be used as feedstock for succinate production by <it>A. succinogenes</it>.</p