Impact of analytic provenance in genome analysis

Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical analysis of choices made during the sequence assembly and gene annotation stages. These choices have a direct impact on the biologically relevant products of a genomic analysis - for instance identification of common and differentiating regions among genomes in a comparison, or identification of enriched gene functional categories in a specific strain. Here, we examine the outcomes of different assembly and analysis steps in typical workflows in a comparison among strains of Vibrio vulnificus

Early Short Course Corticosteroids in Hospitalized Patients with COVID-19

BACKGROUND: There is no proven antiviral or immunomodulatory therapy for COVID-19. The disease progression associated with the pro-inflammatory host response prompted us to examine the role of early corticosteroid therapy in patients with moderate to severe COVID-19. METHODS: We conducted a single pre-test, single post-test quasi-experiment in a multi-center health system in Michigan from March 12 to March 27, 2020. Adult patients with confirmed moderate to severe COVID were included. A protocol was implemented on March 20, 2020 using early, short-course, methylprednisolone 0.5 to 1 mg/kg/day divided in 2 intravenous doses for 3 days. Outcomes of standard of care (SOC) and early corticosteroid groups were evaluated, with a primary composite endpoint of escalation of care from ward to ICU, new requirement for mechanical ventilation, and mortality. All patients had at least 14 days of follow-up. RESULTS: We analyzed 213 eligible subjects, 81 (38%) and 132 (62%) in SOC and early corticosteroid groups, respectively.The composite endpoint occurred at a significantly lower rate in the early corticosteroid group (34.9% vs. 54.3%, p=0.005). This treatment effect was observed within each individual component of the composite endpoint. Significant reduction in median hospital length of stay was also observed in the early corticosteroid group (8 vs. 5 days, p \u3c 0.001). Multivariate regression analysis demonstrated an independent reduction in the composite endpoint at 14-days controlling for other factors (aOR: 0.41; 95% CI [0.22 - 0.77]). CONCLUSION: An early short course of methylprednisolone in patients with moderate to severe COVID-19 reduced escalation of care and improved clinical outcomes

Maternal Methadone Destabilizes Neonatal Breathing and Desensitizes Neonates to Opioid-Induced Respiratory Frequency Depression

16 pagesPregnant women and developing infants are understudied populations in the opioid crisis, despite the rise in opioid use during pregnancy. Maternal opioid use results in diverse negative outcomes for the fetus/newborn, including death; however, the effects of perinatal (maternal and neonatal) opioids on developing respiratory circuitry are not well understood. Given the profound depressive effects of opioids on central respiratory networks controlling breathing, we tested the hypothesis that perinatal opioid exposure impairs respiratory neural circuitry, creating breathing instability. Our data demonstrate maternal opioids increase apneas and destabilize neonatal breathing. Maternal opioids also blunted opioid-induced respiratory frequency depression acutely in neonates; a unique finding since adult respiratory circuity does not desensitize to opioids. This desensitization normalized rapidly between postnatal days 1 and 2 (P1 and P2), the same age quantal slowing emerged in respiratory rhythm. These data suggest significant reorganization of respiratory rhythm generating circuits at P1–2, the same time as the preBötzinger Complex (key site of respiratory rhythm generation) becomes the dominant respiratory rhythm generator. Thus, these studies provide critical insight relevant to the normal developmental trajectory of respiratory circuits and suggest changes to mutual coupling between respiratory oscillators, while also highlighting how maternal opioids alter these developing circuits. In conclusion, the results presented demonstrate neurorespiratory disruption by maternal opioids and blunted opioid-induced respiratory frequency depression with neonatal opioids, which will be important for understanding and treating the increasing population of neonates exposed to gestational opioids.Supported by the University of Oregon (AHu)

Effect of HSV-1 Infection on the Exercise-induced Mobilization of T-cell Subsets

Acute exercise mobilizes highly-differentiated memory and senescent T-cells into the blood compartment, which could have important implications for post-exercise immune surveillance. This response differs in individuals with latent cytomegalovirus (CMV) infection (a herpesvirus), but it is unknown if other latent herpesviruses, such as herpes simplex virus type 1 (HSV-1), also influence this exercise-induced immune response. As HSV-1 infects 50% of the US population, this could have implications for many athletes. PURPOSE: To examine the effects of an acute bout of exercise on the frequency and relative proportion of naïve, memory, and senescent T-cells in the peripheral blood in HSV-1 infected and non-infected participants. METHODS: Eleven HSV-1-infected and twelve non-infected men (mean±SD: Age: 28±5 yrs; VO2max: 40.64±10.15 ml/kg/min) cycled at 85% of their estimated maximum power for 30 min. Blood samples were collected before and immediately after exercise, and mononuclear cells were isolated using density gradient centrifugation. Cells were labeled with monoclonal antibodies to identify naïve (CD28+CD57-KLRG1- or CD45RA+CCR7+), memory (CD28+CD57-KLRG1+, CD45RA+CCR7-, CD45RA-CCR7+, or CD45RA-CCR7-), and senescent (CD28-CD57+KLRG1+) subsets of CD3+CD4+ and CD3+CD8+ T-cells using four-color flow cytometry. HSV-1 serostatus was determined by an ELISA test. Main effects for exercise and serostatus, and exercise x serostatus interaction effects, were detected using maximum likelihood linear mixed models. RESULTS: A main effect for exercise was found on proportions of naïve (-8.82±8.49%), memory (+35.04±26.48%), and senescent (+64.12±56.12%) CD4+ T-cells, as well as on naïve (-21.02±11.56%) and senescent (+53.89±53.26%) CD8+ T-cells (p\u3c0.05). There were main effects for serostatus on proportions of memory CD4+ and CD8+ T-cells, with decreased levels in HSV-1+ subjects in all memory phenotypes examined (p\u3c0.05). Interaction effects between HSV-1 serostatus and exercise were found. HSV-1+ subjects had lower naïve cell counts, and a greater increase in the proportion of senescent cells, post-exercise (p\u3c0.05) than HSV-1-non-infected subjects. CONCLUSIONS: HSV-1 infection led to a decrease of memory T-cell subsets found in peripheral blood. It also influenced the relative response of naïve and senescent T-cells to acute exercise, although this effect was not nearly as great as that seen with other herpesviruses (i.e. CMV). This indicates that individuals with and without latent HSV-1 infection may have a different lymphocyte mobilization in response to exercise

Heterotic Moduli Stabilization with Fractional Chern-Simons Invariants

We show that fractional flux from Wilson lines can stabilize the moduli of heterotic string compactifications on Calabi-Yau threefolds. We observe that the Wilson lines used in GUT symmetry breaking naturally induce a fractional flux. When combined with a hidden-sector gaugino condensate, this generates a potential for the complex structure moduli, Kahler moduli, and dilaton. This potential has a supersymmetric AdS minimum at moderately weak coupling and large volume. Notably, the necessary ingredients for this construction are often present in realistic models. We explore the type IIA dual phenomenon, which involves Wilson lines in D6-branes wrapping a three-cycle in a Calabi-Yau, and comment on the nature of the fractional instantons which change the Chern-Simons invariant.Comment: 43 pages. v2: references adde

Wnt3a deficiency irreversibly impairs hematopoietic stem cell self-renewal and leads to defects in progenitor cell differentiation

Canonical Wnt signaling has been implicated in various aspects of hematopoiesis. Its role is controversial due to different outcomes between various inducible Wnt-signaling loss-of-function models and also compared with gain-of-function systems. We therefore studied a mouse deficient for a Wnt gene that seemed to play a nonredundant role in hematopoiesis. Mice lacking Wnt3a die prenatally around embryonic day (E) 12.5, allowing fetal hematopoiesis to be studied using in vitro assays and transplantation into irradiated recipient mice. Here we show that Wnt3a deficiency leads to a reduction in the numbers of hematopoietic stem cells (HSCs) and progenitor cells in the fetal liver (FL) and to severely reduced reconstitution capacity as measured in secondary transplantation assays. This deficiency is irreversible and cannot be restored by transplantation into Wnt3a competent mice. The impaired long-term repopulation capacity of Wnt3a-/- HSCs could not be explained by altered cell cycle or survival of primitive progenitors. Moreover, Wnt3a deficiency affected myeloid but not B-lymphoid development at the progenitor level, and affected immature thymocyte differentiation. Our results show that Wnt3a signaling not only provides proliferative stimuli, such as for immature thymocytes, but also regulates cell fate decisions of HSC during hematopoiesis

Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates

Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number one cause of seafood-related deaths in the US. Many V. vulnificus isolates have been studied, and it has been shown that two genetically distinct subtypes, distinguished by 16S rDNA and other gene polymorphisms, are associated predominantly with either environmental or clinical isolation. While local genetic differences between the subtypes have been probed, only the genomes of clinical isolates have so far been completely sequenced. In order to better understand V. vulnificus as an agent of disease and to identify the molecular components of its virulence mechanisms, we have completed whole genome shotgun sequencing of three diverse environmental genotypes using a pyrosequencing approach. V. vulnificus strain JY1305 was sequenced to a depth of 33×, and strains E64MW and JY1701 were sequenced to lesser depth, covering approximately 99.9% of each genome. We have performed a comparative analysis of these sequences against the previously published sequences of three V. vulnificus clinical isolates. We find that the genome of V. vulnificus is dynamic, with 1.27% of genes in the C-genotype genomes not found in the E- genotype genomes. We identified key genes that differentiate between the genomes of the clinical and environmental genotypes. 167 genes were found to be specifically associated with environmental genotypes and 278 genes with clinical genotypes. Genes specific to the clinical strains include components of sialic acid catabolism, mannitol fermentation, and a component of a Type IV secretory pathway VirB4, as well as several other genes with potential significance for human virulence. Genes specific to environmental strains included several that may have implications for the balance between self-preservation under stress and nutritional competence