Supporting Vermont Families in Packing Healthy Lunches for Children in Childcare

Introduction. Partnering with Hunger Free Vermont, an organization that works to end hunger and malnutrition across the state, we investigated the nutritional value of the packed meals parents provide for their children in early childcare. The USDA\u27s My Plate resource was used as a measure to assess variety, dividing foods into five groups: grains, dairy, vegetables, fruits, and protein. The results will help Hunger Free Vermont design nutrition education materials for childcare centers to provide to the families they serve. Methods. Online surveys were distributed, asking parents to report the foods they recently provided for their children in packed lunches, to rate how \u27healthy\u27 they thought those lunches were, and to note any barriers they experience to packing healthy foods. Results. Survey results showed that the average number of sweets packed by parents who had low confidence in their ability to pack healthy meals was significantly higher than the average number packed by parents with high confidence (p \u3c 0.05). Additionally, the total number of cited barriers was significantly higher in parents who had low confidence in their ability to pack healthy meals (p \u3c 0.01). Conclusions. Many parents cited time constraints and ‘picky’ children as barriers to providing healthy meals, with concerns about the expense of healthy items and lack of childcare for shopping or food-prep time following close behind. In the future, education materials that address children’s unhealthy food preferences or further investigations into barriers to providing healthy lunches may facilitate development of resources for Vermont families.https://scholarworks.uvm.edu/comphp_gallery/1259/thumbnail.jp

Perturbing HIV-1 Ribosomal Frameshifting Frequency Reveals a cis Preference for Gag-Pol Incorporation into Assembling Virions

HIV-1 virion production is driven by Gag and Gag-Pol (GP) proteins, with Gag forming the bulk of the capsid and driving budding, while GP binds Gag to deliver the essential virion enzymes protease, reverse transcriptase, and integrase. Virion GP levels are traditionally thought to reflect the relative abundances of GP and Gag in cells (;1:20), dictated by the frequency of a 21 programmed ribosomal frameshifting (PRF) event occurring in gag-pol mRNAs. Here, we exploited a panel of PRF mutant viruses to show that mechanisms in addition to PRF regulate GP incorporation into virions. First, we show that GP is enriched ;3-fold in virions relative to cells, with viral infectivity being better maintained at subphysiological levels of GP than when GP levels are too high. Second, we report that GP is more efficiently incorporated into virions when Gag and GP are synthesized in cis (i.e., from the same gag-pol mRNA) than in trans, suggesting that Gag/GP translation and assembly are spatially coupled processes. Third, we show that, surprisingly, virions exhibit a strong upper limit to trans-delivered GP incorporation; an adaptation that appears to allow the virus to temper defects to GP/Gag cleavage that may negatively impact reverse transcription. Taking these results together, we propose a "weighted Goldilocks"scenario for HIV-1 GP incorporation, wherein combined mechanisms of GP enrichment and exclusion buffer virion infectivity over a broad range of local GP concentrations. These results provide new insights into the HIV-1 virion assembly pathway relevant to the anticipated efficacy of PRF-targeted antiviral strategies.National Institutes of Health R01AI110221, P01CA022332, R35GM118131, T32GM00834

Redox‐controlled preservation of organic matter during “OAE 3” within the Western Interior Seaway

During the Cretaceous, widespread black shale deposition occurred during a series of Oceanic Anoxic Events (OAEs). Multiple processes are known to control the deposition of marine black shales, including changes in primary productivity, organic matter preservation, and dilution. OAEs offer an opportunity to evaluate the relative roles of these forcing factors. The youngest of these events—the Coniacian to Santonian OAE 3—resulted in a prolonged organic carbon burial event in shallow and restricted marine environments including the Western Interior Seaway. New high‐resolution isotope, organic, and trace metal records from the latest Turonian to early Santonian Niobrara Formation are used to characterize the amount and composition of organic matter preserved, as well as the geochemical conditions under which it accumulated. Redox sensitive metals (Mo, Mn, and Re) indicate a gradual drawdown of oxygen leading into the abrupt onset of organic carbon‐rich (up to 8%) deposition. High Hydrogen Indices (HI) and organic carbon to total nitrogen ratios (C:N) demonstrate that the elemental composition of preserved marine organic matter is distinct under different redox conditions. Local changes in δ13C indicate that redox‐controlled early diagenesis can also significantly alter δ13Corg records. These results demonstrate that the development of anoxia is of primary importance in triggering the prolonged carbon burial in the Niobrara Formation. Sea level reconstructions, δ18O results, and Mo/total organic carbon ratios suggest that stratification and enhanced bottom water restriction caused the drawdown of bottom water oxygen. Increased nutrients from benthic regeneration and/or continental runoff may have sustained primary productivity.Key PointsBottom water redox changes triggered carbon burial within the WIS during OAE 3Anoxia developed due to O2 drawdown in a stratified water columnRedox‐controlled changes in OM preservation altered primary δ13Corg signalsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/112294/1/palo20210.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/112294/2/palo20210-sup-0001-SupportingInfo.pd

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

Computational methods to identify functional genomic elements using genetic information have been very successful in determining gene structure and in identifying a handful of cis-regulatory elements. But the vast majority of regulatory elements have yet to be discovered, and it has become increasingly apparent that their discovery will not come from using genetic information alone. Recently, high-throughput technologies have enabled the creation of information-rich epigenetic maps, most notably for histone modifications. However, tools that search for functional elements using this epigenetic information have been lacking. Here, we describe an unsupervised learning method called ChromaSig to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known patterns associated with transcriptional promoters and enhancers. Interestingly, we observe that the distinct chromatin signatures found at enhancers mark distinct functional classes of enhancers in terms of transcription factor and coactivator binding. In addition, we identify three clusters of novel chromatin signatures that contain evolutionarily conserved sequences and potential cis-regulatory elements. Applying ChromaSig to a panel of 21 chromatin marks mapped genomewide by ChIP-Seq reveals 16 classes of genomic elements marked by distinct chromatin signatures. Interestingly, four classes containing enrichment for repressive histone modifications appear to be locally heterochromatic sites and are enriched in quickly evolving regions of the genome. The utility of this approach in uncovering novel, functionally significant genomic elements will aid future efforts of genome annotation via chromatin modifications

The Complete Genome of Teredinibacter turnerae T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms)

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels

The Complete Genome of \u3cem\u3eTeredinibacter turnerae\u3c/em\u3e T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms)

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host\u27s nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (\u3e100). However, unlike S. degradans, which degrades a broad spectrum (\u3e10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels

Decision-making: initiating insulin therapy for adults with diabetes

<b>AIM:</b> This paper is a report of a study to describe nurses' perceptions of decision-making and the evidence base for the initiation of insulin therapy. <b>BACKGROUND:</b> Several theoretical perspectives and professional's attributes underpin decision-making to commence insulin therapy. The management of type 2 diabetes is moving from secondary to primary care and this affects how clinical decisions are made, by whom and the evidence base for these decisions. <b>METHOD:</b> A postal survey was conducted with a stratified sample of 3478 Diabetes Specialist Nurses and Practice Nurses with a special interest in diabetes across the four countries of the United Kingdom. A total of 1310 valid responses were returned, giving a response rate of 37.7%. The questionnaire was designed for the study and pilot-tested before use. Responses were given using Likert-type scales. Data were collected during 2005 and 2006, and one reminder was sent. <b>RESULTS:</b> People with diabetes are seen as having little influence in decision-making. Consultant physicians appear to be influential in most decisions, and the nursing groups held varying perceptions of who made clinical decisions. Nurses' identified different responsibilities for those working solely in secondary care from those working in both community and secondary care. Practice nurses were not as involved as anticipated. <b>CONCLUSION:</b> Nurses working with people with diabetes need to encourage them to become more active partners in care. Clinical guidelines can assist in decision-making where nurses are least experienced in initiating insulin therapy

Flexible mapping of homology onto structure with Homolmapper

<p>Abstract</p> <p>Background</p> <p>Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine.</p> <p>Results</p> <p>We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs.</p> <p>Conclusion</p> <p>Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at <url>http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm</url>.</p

Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Comprehensive genome-wide analysis of the epigenetic and transcription status of the TLR4-induced transcriptional program in macrophages suggests that Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early- (I/E) and late-response genes results from a sequential process in which signal-independent factors initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. Promoters of I/E genes are distinguished from those of late genes by encoding a distinct set of signal-dependent transcription factor elements, including TATA boxes, which lead to preferential binding of TBP and basal enrichment for RNA polymerase II immediately downstream of transcriptional start sites. Global nuclear run-on (GRO) sequencing and total RNA sequencing further indicates that TLR4 signaling markedly increases the overall rates of both transcriptional initiation and the efficiency of transcriptional elongation of nearly all I/E genes, while RNA splicing is largely unaffected. Collectively, these findings reveal broadly utilized mechanisms underlying temporally distinct patterns of TLR4-dependent gene activation required for homeostasis and effective immune responses

Quality Measures for the Diagnosis and Non-Operative Management of Carpal Tunnel Syndrome in Occupational Settings

Introduction: Providing higher quality medical care to workers with occupationally associated carpal tunnel syndrome (CTS) may reduce disability, facilitate return to work, and lower the associated costs. Although many workers’ compensation systems have adopted treatment guidelines to reduce the overuse of unnecessary care, limited attention has been paid to ensuring that the care workers do receive is high quality. Further, guidelines are not designed to enable objective assessments of quality of care. This study sought to develop quality measures for the diagnostic evaluation and non-operative management of CTS, including managing occupational activities and functional limitations. Methods: Using a variation of the well-established RAND/UCLA Appropriateness Method, we developed draft quality measures using guidelines and literature reviews. Next, in a two-round modified-Delphi process, a multidisciplinary panel of 11 U.S. experts in CTS rated the measures on validity and feasibility. Results: Of 40 draft measures, experts rated 31 (78%) valid and feasible. Nine measures pertained to diagnostic evaluation, such as assessing symptoms, signs, and risk factors. Eleven pertain to non-operative treatments, such as the use of splints, steroid injections, and medications. Eleven others address assessing the association between symptoms and work, managing occupational activities, and accommodating functional limitations. Conclusions: These measures will complement existing treatment guidelines by enabling providers, payers, policymakers, and researchers to assess quality of care for CTS in an objective, structured manner. Given the characteristics of previous measures developed with these methods, greater adherence to these measures will probably lead to improved patient outcomes at a population level