Relationship between Syracuse University Employees’ Perceptions, Behaviors, Environment, and Fruit and Vegetable Intake

Objective: To determine how employees’ perceptions of the availability and price of fruits and vegetables within the work and surrounding environment correspond to the actual availability and price of fruits and vegetables and influence employees’ fruit and vegetable intakes. Design: This study is a cross-sectional design comparing a survey of employees’ perceptions and behaviors and an environmental audit assessing the healthfulness of dining facilities on campus. Setting: Syracuse University and the surrounding eating environment. Participants: 130 Syracuse University employees. Methods: Employees were invited to complete the Work Campus Environment & Behavior Perceptions Survey. The survey consisted of 28 Likert scale questions to assess employee’s perceptions of the healthfulness of the work environment and their related behaviors (choosing healthy foods, exercise, etc). The survey assessed fruit and vegetable intake, perceived weight category (under, over) and weight intention (lose, maintain). Employees self-reported weight and height, and body mass index (BMI) was calculated. The environmental audits assessed the dining options both on and off campus, including convenience stores, dining halls, sit-down, fast food, and delivery restaurants. The audits were conducted by trained undergraduate research assistants to evaluate the healthfulness of the dining facility based on specific criteria, such as the availability of fruits and vegetables, whole grains, and less healthful choices. The healthfulness of the foods and the supportiveness of the environment sub-scores were generated for each dining facility. Non-parametric, t-test, and ANOVA statistics were used to compare the results. Results: The average fruit and vegetable intake among employees was 1.17 ± 1.0 and 2.04 ± 1.3, respectively. BMI was not related to fruit and vegetable intake, but it did affect weight intention. Only 3% of employees believed that the university encourages healthy eating, while 56% believe there is healthy food where they usually eat on campus. However, those with the highest fruit /vegetable intake perceived limited supports for healthy eating on campus. Dining halls had the highest average sub-scores for healthfulness of food (37.56 ± 12.0) and supportiveness of environment (25.33 ± 5.9). Delivery restaurants had the lowest sub-scores for both categories. Conclusion: While this study uncovered important information regarding how perceptions, behaviors, and the work environment can affect fruit and vegetable intake, further research should incorporate worksite interventions and compare results to other campuses

The antibody loci of the domestic goat (Capra hircus)

The domestic goat (Capra hircus) is an important ruminant species both as a source of antibody-based reagents for research and biomedical applications and as an economically important animal for agriculture, particularly for developing nations that maintain most of the global goat population. Characterization of the loci encoding the goat immune repertoire would be highly beneficial for both vaccine and immune reagent development. However, in goat and other species whose reference genomes were generated using short-read sequencing technologies, the immune loci are poorly assembled as a result of their repetitive nature. Our recent construction of a long-read goat genome assembly (ARS1) has facilitated characterization of all three antibody loci with high confidence and comparative analysis to cattle. We observed broad similarity of goat and cattle antibody-encoding loci but with notable differences that likely influence formation of the functional antibody repertoire. The goat heavy-chain locus is restricted to only four functional and nearly identical IGHV genes, in contrast to the ten observed in cattle. Repertoire analysis indicates that light-chain usage is more balanced in goats, with greater representation of kappa light chains (~ 20-30%) compared to that in cattle (~ 5%). The present study represents the first characterization of the goat antibody loci and will help inform future investigations of their antibody responses to disease and vaccination

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation.

Natural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is in part created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high-quality draft genome assemblies for cattle and goat; re-annotated sheep, pig, and horse genome assemblies; and the published human, rat, and mouse lemur NKC. The major NKC genes are largely in the equivalent positions in all eight species, with significant independent expansions and deletions between species, allowing us to propose a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ, and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between the NKC genes concentrated in the predicted extracellular ligand-binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting that this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination

Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia

<p>Abstract</p> <p>Background</p> <p>Genome analysis of three <it>Frankia sp. </it>strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of <it>Frankia </it>strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN) has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN) differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS) from 9 IS families.</p> <p>Results</p> <p>Insertion sequences in the <it>Frankia </it>genomes were analyzed using BLAST searches, PHYML phylogenies and the IRF (Inverted Repeat Finder) algorithms. To identify putative or decaying IS elements, a PSI-TBLASTN search was performed on all three genomes, identifying 36%, 39% and 12% additional putative transposase ORFs than originally annotated in strains CcI3, EAN and ACN, respectively. The distribution of transposase ORFs in each strain was then analysed using a sliding window, revealing significant clustering of elements in regions of the EAN and CcI3 genomes. Lastly the three genomes were aligned with the MAUVE multiple genome alignment tool, revealing several Large Chromosome Rearrangement (LCR) events; many of which correlate to transposase clusters.</p> <p>Conclusion</p> <p>Analysis of transposase ORFs in <it>Frankia </it>sp. revealed low inter-strain diversity of transposases, suggesting that the majority of transposase proliferation occurred without recent horizontal transfer of novel mobile elements from outside the genus. Exceptions to this include representatives from the IS3 family in strain EAN and seven IS4 transposases in all three strains that have a lower G+C content, suggesting recent horizontal transfer. The clustering of transposase ORFs near LCRs revealed a tendency for IS elements to be associated with regions of chromosome instability in the three strains. The results of this study suggest that IS elements may help drive chromosome differences in different <it>Frankia </it>sp. strains as they have adapted to a variety of hosts and environments.</p

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses

Copy number variation in dairy cattle using next-generation sequencing.

Gene copy number variants (CNV) have been shown to be associated with several production traits in dairy cattle; however, the detection and validation of CNVs in crossbred cattle is currently lacking. In order to provide a basis for future association studies, we sought to identify CNV regions (CNVRs) within the Girolando composite breed resulting from a mating of the Holstein (taurine) and Gir (indicine) breeds. A read depth method was performed using CNVnator software on NGS data from two Girolando, two Gir and ten Holstein bulls. The individual CNVs were merged into CNVRs based on genomic regions overlapping by at least 1 bp. In total, we identified a composite of 1,286 CNVRs (520 deletions, 255 duplications, 511 mixed) on the genomes of all samples. We observed 34 CNVRs (nine deletions, 25 mixed) in common (overlapping > 50%) only between Girolando and Holstein and 181 CNVRs (20 deletions, 21 duplications,140 mixed) only in Girolando and Gir, suggesting parent-of-origin inheritance from Holstein and Gir cattle, respectively. One of these Holstein-specific CNVRs intersected with the interleukin 6 family cytokine (LIF) gene which is linked to fat production and fertility traits in Holstein. Genes related to disease resistance (e.g. the CD4 gene) also coincided with CNVRs present only in Gir and Girolando cattle suggesting an indicine origin for the CNV. These results showed evidence of specific CNVRs shared by Girolando and purebred breeds which may be targeted for future selective breeding.PAG 2018. P0490. Na publicação: Adhemar Zerlotini, Marcos Vinicius B. da Silva

RAPTR-SV: A Hybrid Method for the Detection of Structural Variants

Identification of Structural Variants (SV) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation. Simulations using RAPTR-SV and other, similar algorithms for SV detection revealed that RAPTR-SV had superior sensitivity and precision, as it recovered 66.4% of simulated tandem duplications with a precision of 99.2%. When compared to calls made by Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified two-fold more duplications than Delly, while making approximately 85% fewer duplication predictions. RAPTR-SV is written in Java and uses new features in the collections framework in the latest release of the Java version 8 language specifications. A compiled version of the software, instructions for usage and test results files are available on the GitHub repository page: https://github.com/njdbickhart/RAPTR-SV

Characterization of the domestic goat γδ T cell receptor gene loci and gene usage

Goats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCRγ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied slightly as a result of duplications and differences occurred in mutations resulting in pseudogenes. WC1+ γδ T cells in cattle have been shown to use TCRγ genes from only one of the six available cassettes. The structure of that Cγ gene product is unique and may be necessary to interact with WC1 for signal transduction following antigen ligation. Using RT-PCR and PacBio sequencing, we observed the same restriction for goat WC1+ γδ T cells. In contrast, caprine WC1+ and WC1− γδ T cell populations had a diverse TCRδ gene usage although the propensity for particular gene usage differed between the two cell populations. Noncanonical recombination signal sequences (RSS) largely correlated with restricted expression of TCRγ and δ genes. Finally, caprine γδ T cells were found to incorporate multiple TRD diversity gene sequences in a single transcript, an unusual feature among mammals but also previously observed in cattle

Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha.

Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors

An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome

BACKGROUND: The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome. FINDINGS: Short-read Illumina (55× coverage), long-read Pacific Biosciences (75× coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50× coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. CONCLUSIONS: The ARS-UI_Ramb_v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep