Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis

The uterine lining (endometrium) exhibits a pro-inflammatory phenotype in women with endometriosis, resulting in pain, infertility, and poor pregnancy outcomes. The full complement of cell types contributing to this phenotype has yet to be identified, as most studies have focused on bulk tissue or select cell populations. Herein, through integrating whole-tissue deconvolution and single-cell RNAseq, we comprehensively characterized immune and nonimmune cell types in the endometrium of women with or without disease and their dynamic changes across the menstrual cycle. We designed metrics to evaluate specificity of deconvolution signatures that resulted in single-cell identification of 13 novel signatures for immune cell subtypes in healthy endometrium. Guided by statistical metrics, we identified contributions of endometrial epithelial, endothelial, plasmacytoid dendritic cells, classical dendritic cells, monocytes, macrophages, and granulocytes to the endometrial pro-inflammatory phenotype, underscoring roles for nonimmune as well as immune cells to the dysfunctionality of this tissue.

Plexins Promote Hedgehog Signaling Through Their Cytoplasmic GAP Activity

Hedgehog signaling controls tissue patterning during embryonic and postnatal development and continues to play important roles throughout life. Characterizing the full complement of Hedgehog pathway components is essential to understanding its wide-ranging functions. Previous work has identified Neuropilins, established Semaphorin receptors, as positive regulators of Hedgehog signaling. Neuropilins require Plexin co-receptors to mediate Semaphorin signaling, but a role for Plexins in Hedgehog signaling has not yet been explored. Here, we provide evidence that multiple Plexins promote Hedgehog signaling in NIH/3T3 fibroblasts and that Plexin loss-of-function in these cells results in significantly reduced Hedgehog pathway activity. Catalytic activity of the Plexin GTPase activating protein (GAP) domain is required for Hedgehog signal promotion, and constitutive activation of the GAP domain further amplifies Hedgehog signaling. Additionally, we demonstrate that Plexins promote Hedgehog signaling at the level of GLI transcription factors and that this promotion requires intact primary cilia. Finally, we find that Plexin loss-of-function significantly reduces the response to Hedgehoga pathway activation in the mouse dentate gyrus. Together, these data identify Plexins as novel components of the Hedgehog pathway and provide insight into their mechanism of action.

4D Seismic Detectability in a Brazilian Pre-Salt Carbonate Field

This paper is dedicated to a pre-salt carbonate field located within the Santos Basin, Brazil, comprising thick Aptian reservoirs interspersed with igneous rocks. One of the main challenges for reservoir management is the surface constraint on the gas, as all of the produced gas will have to be reinjected and can be miscible with the in-situ hydrocarbons. The recovery mechanism selected is mainly WAG (water alternating gas) injection, with both producers and injectors equipped with intelligent completions using Inflow Control Valves (ICVs). A 4D seismic monitoring survey is planned to delineate gas and water fronts in reservoir flow units about 10m thick, providing critical information to help piloting a planned 6-month WAG cycle for improved recovery. Seismic imaging is challenging in this case and 4D signal is expected to be weak (±2% dIp/Ip). We propose here, a methodology, based on a 1-D Gassmann fluid substitution model at wells (only limited reservoir fluid PVT data available) to rapidly answer the following pertinent questions as posed by the asset team in charge of the field: From a phenomenological stand-point and neglecting some possible processing, imaging and acquisition challenges, will 4D data (post 4D inversion) detect a gas streak from an injector to a producer? What is the 4D seismic detection limit based on reservoir thickness? What kind of seismic acquisition will assure this detectability? Under the assumptions made in this work, this methodology shows that a permanent system of acquisition seems to be a fit-for-purpose technology for detectability. Further work is however recommended using full complement of a 3D static and dynamic simulation model coupled with a complete fluid PVT model in order to assess more complex 3D dynamic interactions between the injectors and producers.

Species and Metabolic Pathways Involved in Bioremediation of Vietnamese Soil From Bien Hoa Airbase Contaminated With Herbicides

Four bacterial strains were isolated from enrichment cultures inoculated with soil from Bien Hoa military base in Vietnam contaminated with the herbicides 2,4-dichlorophenoxyacetate (2,4-D) and 2,4,5-trichlorophenoxyacetate (2,4,5-T). They were classified as Pseudomonas aeruginosa BT1 2.2, Sphingomonas histidinilytica BT1 5.2, Bordetella petrii BT1 9.2, and Achromobacter xylosoxidans BT1 10.2. All four were able to degrade 2,4-D and 2,4,5-T, but only the last three species used them as the sole sources of carbon and energy. Mass balance analyses suggest that between 33 and 46% of the carbon in the herbicides is incorporated into dry weight (DW). We obtained insight into their degradation pathways by the genomic analysis of these strains. A tfdCDEF gene cluster was found in A. xylosoxidans BT1 10.2 with amino acid sequences of their gene products showing high identity to those in B. petrii DSM12804. Bordetella petrii BT1 9.2 has a full complement of the tfdABCDEF genes. Surprisingly, the gene organization along with the amino acid sequences of the gene products are virtually identical to those of Cupriavidus pinatubonensis JMP134, referred to as type I tfd genes, and different from those of A. xylosoxidans BT1 10.2 and B. petrii DSM12804. We hypothesize that some of the genetic potential to degrade the herbicides has been recruited in recent mating events between these species and other members of the proteobacteria. This is the first report showing that B. petrii BT1 9.2 emerges as a key player in the degradation of 2,4-D.

Examination of the Catalytic Role of the Axial Cystine Ligand in the Co-Type Nitrile Hydratase from Pseudonocardia thermophila JCM 3095

The strictly conserved αSer162 residue in the Co-type nitrile hydratase from Pseudonocardia thermophila JCM 3095 (PtNHase), which forms a hydrogen bond to the axial αCys108-S atom, was mutated into an Ala residue. The αSer162Ala yielded two different protein species: one was the apoform (αSerA) that exhibited no observable activity, and the second (αSerB) contained its full complement of cobalt ions and was active with a kcat value of 63 ± 3 s−1 towards acrylonitrile at pH 7.5. The X-ray crystal structure of αSerA was determined at 1.85 Å resolution and contained no detectable cobalt per α2β2 heterotetramer. The axial αCys108 ligand itself was also mutated into Ser, Met, and His ligands. All three of these αCys108 mutant enzymes contained only half of the cobalt complement of wild-type PtNHase, but were able to hydrate acrylonitrile with kcat values of 120 ± 6, 29 ± 3, and 14 ± 1 s−1 for the αCys108His, Ser, and Met mutant enzymes, respectively. As all three of these mutant enzymes are catalytically competent, these data provide the first experimental evidence that transient disulfide bond formation is not catalytically essential for NHases.

Management of the Index COVID -19 Obstetric Patient at the University of Benin Teaching Hospital

Introduction: The novel coronavirus (COVID-19) was first identified in Wuhan City, Hubei province of China, November 2019. As at September 2020, over 28 million infections have been identified with almost a million deaths worldwide causing an alarming pandemic. Clinical presentations in pregnant patients with COVID-19 could be atypical with normal temperature (56%) and leukocytosis. This is further masked by the features of pregnancy. We present the management of a COVID-19 parturient in our obstetric unit. Case Report: A 32 year old unbooked G₃P₁⁺1 lady at 32 weeks who presented via referral from a private facility with a history of elevated blood pressure and ++ of protein in urine. Also, complaints of cough and difficulty with breathing. On examination she was noted to be anxious, afebrile, not pale, anicteric, acyanosed, not dehydrated. Had bilateral pedal oedema. Tachypnic with a respiratory rate of 28 cycles per min with basal crepitations. Pulse rate was 96bpm full and regular. Blood pressure was 180/100 mmHg. Heart sounds S₁S₂only.An impression of Chronic hypertension with superimposed pre-eclampsia at 32 wks GA in a primipara with one previous CS with pulmonary edema. Keep in view COVID-19. She was managed with oxygen, antihypertensives, steroids, while observing strict infection control protocol. She had an emergency caesarean section under subarachnoid block and was delivered of a live female neonate. A confirmatory positive result for covid-19 was obtained 24hrs later. Neonate was however negative. None of the staff became positive also. Conclusion: The management of suspected cases of COVID-19 infection should be same as cases already confirmed. As the epidemic persists, numbers will continue to rise andhence our index of suspicion should be heightened. Pregnant women will also present with symptoms masked by the features of a sick parturient. Full complement of PPE must be worn by all staff attending to both confirmed and suspicious cases of COVID-19 infection and strict adherence to stated protocols must be observed.

The expression of essential selenoproteins during zebrafish development requires SECIS binding protein 2-like

The dietary requirement for selenium is based on its incorporation into selenoproteins, which contain the amino acid selenocysteine (Sec). The Sec insertion sequence (SECIS) is an RNA structure found in the 3' UTR of all selenoprotein mRNAs, and it is required to convert in-frame UGA codons from termination to Sec-incorporating codons. There are two proteins that bind to SECIS elements, but only one, SECIS binding protein 2 (Sbp2), has been shown to be required for Sec incorporation. The Sbp2 paralogue, SECIS binding protein 2-like (Secisbp2l) is conserved in all vertebrates and shares many features with Sbp2, but its function is unknown. Here we set out to determine the relative roles of Sbp2 and Secisbp2l by introducing CRISPR mutations in both genes in zebrafish. By monitoring selenoprotein synthesis with 75Se labeling during embryogenesis, we found that sbp2-/- embryos still make a select subset of selenoproteins but secisbp2l-/- embryos retain the full complement. Abrogation of both genes completely prevents selenoprotein synthesis and juveniles die at 14 days post fertilization. Embryos lacking Sbp2 are sensitive to oxidative stress and express the stress marker Vtg1. We propose a model where Secisbp2l is required to promote essential selenoprotein synthesis during stress.

Discovery of a novel glucuronan lyase system in Trichoderma parareesei

Glucuronan lyases (EC 4.2.2.14) catalyze depolymerization of linear β-(1, 4)-polyglucuronic acid (glucuronan). Only a few glucuronan lyases have been characterized until now, most of them originating from bacteria. Here we report the discovery, recombinant production, and functional characterization of the full complement of six glucuronan specific polysaccharide lyases in the necrotic mycoparasite Trichoderma parareesei . The enzymes belong to four different polysaccharide lyase families and have different reaction optima and glucuronan degradation profiles. Four of them showed endo-lytic action and two, TpPL8A and TpPL38A, displayed exo-lytic action. NMR revealed that the monomeric end-product from TpPL8A and TpPL38A underwent spontaneous rearrangements to tautomeric forms. Proteomic analysis of the secretomes from T. parareesei growing on pure glucuronan and lyophilized A. bisporus fruiting bodies, respectively, showed secretion of five of the glucuronan lyases and HPAEC-PAD analysis confirmed the presence of glucuronic acid in the A. bisporus fruiting bodies. By systematic genome annotation of more than 100 fungal genomes and subsequent phylogenetic analysis of the putative glucuronan lyases, we show that glucuronan lyases occur in several ecological and taxonomic groups in the fungal kingdom. Our findings suggest that a diverse repertoire of glucuronan lyases is a common trait among Hypocreales spp. with mycoparasitic and entomopathogenic lifestyles. IMPORTANCE This paper reports the discovery of a set of six complementary glucuronan lyase enzymes in the mycoparasite Tricoderma parareseei . Apart from the novelty of the discovery of these enzymes in T. parareesei, the key importance of the study is the finding that the majority of these lyases are induced when T. parareseei is inoculated on Basidiomycete cell walls that contain glucuronan. The study also reveals putative glucuronan lyase encoding genes in a wealth of other fungi that furthermore points at fungal cell wall glucuronan being a target C-source for many types of fungi. In a technical context, the findings may lead to controlled production of glucuronan oligomers for advanced pharmaceutical applications and pave the way for development of new fungal biocontrol agents.

Understanding the influence of combustion on atmospheric CO₂ over Europe by using satellite observations of CO₂ and reactive trace gases

We assess how nitrogen oxides (NOx = NO + NO2), carbon monoxide (CO) and formaldehyde (HCHO) can be used as proxies to determine the combustion contribution to atmospheric carbon dioxide (CO2) using satellite observations. We focus our analysis on 2018 when there is a full complement of column data from the TROPOspheric Monitoring Instrument (NO2, CO, and HCHO) and the Orbiting Carbon Observatory-2 (CO2). We use the nested GEOS-Chem atmospheric chemistry model to relate high-resolution emission inventories over Europe to these atmospheric data, taking into account scene-dependent averaging kernels. We find that that NO2 and CO are the better candidates to identify incomplete combustion and fingerprints of different combustion sectors, but both have their own challenges associated with properly describing their atmospheric chemistry. The secondary source of HCHO from oxidation of biogenic volatile organic compounds, particularly over southern European countries, compromises its use as a proxy for combustion emissions. We find a weak positive correlation between the CO : CO2 inventory ratio and observed column enhancements of ΔCO : ΔCO2 (R < 0.2), suggesting some consistency and linearity in CO chemistry and transport. However, we find a stronger negative correlation between the NOx : CO2 inventory ratio and observed column enhancements of ΔNO2 :ΔCO2 (R < 0.50), driven by non-linear photochemistry. Both of these observed ratios are described well by the GEOS-Chem atmospheric chemistry transport model, providing confidence of the quality of the emission inventory and that the model is a useful tool for interpreting these tracer-tracer ratios. Our results also provide some confidence in our ability to develop a robust method to infer combustion CO2 emission estimates using satellite observations of reactive trace gases that have up until now mostly been used to study surface air quality.