Characterising hepatic B cell subsets in human chronic liver disease

B cells have been proven to have a significant role in liver fibrosis. We postulate that enrichment of B cell subsets in hepatic diseases may implicate this population in liver pathogenesis. When comparing total B cells from human immune and non-immune-mediated liver disease explants, we found an enrichment of CD20+ B cells in PBC. Furthermore, phenotypic characterization of 11 B cell subsets in matched liver and blood highlighted an enriched naïve peripheral population, and activated B cell subsets in livers. Newly identified CD19+CD24-CD38- and CD19+CD24-CD38int B cells were also augmented in livers compared to matched blood. Furthermore, CD24-CD38- B cells were elevated in PBC and formed aggregates in tissues, whereas CD24-CD38int B cells localized around bile ducts and along fibrotic tracts in PBC. CD24-CD38int B cells secreted pro-inflammatory (IL-6, IFN-γ) and immunosuppressive (IL-10) cytokines following stimulation with CpG compared to other B cell subsets, implying that CD24- B cells may play a role in liver disease pathogenesis. Our findings suggest that B cells may be influential in hepatic disease progression and pathogenesis. Elucidating their role further could provide possible therapeutic targets for prevention or treatment of chronic liver disease

PySimFrac: A Python Library for Synthetic Fracture Generation, Analysis, and Simulation

In this paper, we introduce Pysimfrac, a open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. Pysimfrac allows the user to specify one of three fracture generation techniques (Box, Gaussian, or Spectral) and perform statistical analysis including the autocorrelation, moments, and probability density functions of the fracture surfaces and aperture. This analysis and accessibility of a python library allows the user to create realistic fracture realizations and vary properties of interest. In addition, Pysimfrac includes integration examples to two different pore-scale simulators and the discrete fracture network simulator, dfnWorks. The capabilities developed in this work provides opportunity for quick and smooth adoption and implementation by the wider scientific community for accurate characterization of fluid transport in geologic media. We present Pysimfrac along with integration examples and discuss the ability to extend Pysimfrac from a single complex fracture to complex fracture networks

A novel pair of inducible expression vectors for use in Methylobacterium extorquens

Background: Due to the ever increasing use of diverse microbial taxa in basic research and industrial settings, there is a growing need for genetic tools to alter the physiology of these organisms. In particular, there is a dearth of inducible expression systems available for bacteria outside commonly used γ-proteobacteria, such as Escherichia coli or Pseudomonas species. To this end, we have sought to develop a pair of inducible expression vectors for use in the α-proteobacterium Methylobacterium extorquens, a model methylotroph. Findings: We found that the P R promoter from rhizobial phage 16-3 was active in M. extorquens and engineered the promoter to be inducible by either p-isopropyl benzoate (cumate) or anhydrotetracycline. These hybrid promoters, P R/cmtO and P R/tetO, were found to have high levels of expression in M. extorquens with a regulatory range of 10-fold and 30-fold, respectively. Compared to an existing cumate-inducible (10-fold range), high-level expression system for M. extorquens, P R/cmtO and P R/tetO have 33% of the maximal activity but were able to repress gene expression 3 and 8-fold greater, respectively. Both promoters were observed to exhibit homogeneous, titratable activation dynamics rather than on-off, switch-like behavior. The utility of these promoters was further demonstrated by complementing loss of function of ftfL - essential for growth on methanol - where we show P R/tetO is capable of not only fully complementing function but also producing a conditional null phenotype. These promoters have been incorporated into a broad-host-range backbone allowing for potential use in a variety of bacterial hosts. Conclusions: We have developed two novel expression systems for use in M. extorquens. The expression range of these vectors should allow for increased ability to explore cellular physiology in M. extorquens. Further, the P R/tetO promoter is capable of producing conditional null phenotypes, previously unattainable in M. extorquens. As both expression systems rely on the use of membrane permeable inducers, we suspect these expression vectors will be useful for ectopic gene expression in numerous proteobacteria

Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction

We would like to thank C. Dilßner and M. Neytschev (UFZ) for excellent technical assistance with CoA thioester synthesis, strain cultivation and HPLC analyses. In addition, we thank Birgit Würz (UFZ) for invaluable analytical advice and help with GC mass spectrometry. We are also indebted to L. von Wintzingerode, A. Grunwald, and J. Grabengießer (UFZ) for assistance in the cultivation and enzyme assay experiments. Many thanks to K. Eismann (UFZ) as well, for help with the proteome analysis and fruitful discussions regarding different protein extraction methods.The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2020.00691/full#supplementary-materialThe tertiary branched short-chain 2-hydroxyisobutyric acid (2-HIBA) has been associated with several metabolic diseases and lysine 2-hydroxyisobutyrylation seems to be a common eukaryotic as well as prokaryotic post-translational modification in proteins. In contrast, the underlying 2-HIBA metabolism has thus far only been detected in a few microorganisms, such as the betaproteobacterium Aquincola tertiaricarbonis L108 and the Bacillus group bacterium Kyrpidia tusciae DSM 2912. In these strains, 2-HIBA can be specifically activated to the corresponding CoA thioester by the 2-HIBA-CoA ligase (HCL) and is then isomerized to 3-hydroxybutyryl-CoA in a reversible and B12-dependent mutase reaction. Here, we demonstrate that the actinobacterial strain Actinomycetospora chiangmaiensis DSM 45062 degrades 2-HIBA and also its precursor 2-methylpropane-1,2-diol via acetone and formic acid by employing a thiamine pyrophosphate-dependent lyase. The corresponding gene is located directly upstream of hcl, which has previously been found only in operonic association with the 2-hydroxyisobutyryl-CoA mutase genes in other bacteria. Heterologous expression of the lyase gene from DSM 45062 in E. coli established a 2-hydroxyisobutyryl-CoA lyase activity in the latter. In line with this, analysis of the DSM 45062 proteome reveals a strong induction of the lyase-HCL gene cluster on 2-HIBA. Acetone is likely degraded via hydroxylation to acetol catalyzed by a MimABCD-related binuclear iron monooxygenase and formic acid appears to be oxidized to CO2 by selenium-dependent dehydrogenases. The presence of the lyase-HCL gene cluster in isoprene-degrading Rhodococcus strains and Pseudonocardia associated with tropical leafcutter ant species points to a role in degradation of biogenic short-chain ketones and highly branched organic compounds.Program Topic "Chemicals in the Environment" within the Research Program "Terrestrial Environment" of the Helmholtz Association European Union (EU) 62485

Two Unique Cases of X-linked SCID: A Diagnostic Challenge in the Era of Newborn Screening

In the era of newborn screening (NBS) for severe combined immunodeficiency (SCID) and the possibility of gene therapy (GT), it is important to link SCID phenotype to the underlying genetic disease. In western countries, X-linked interleukin 2 receptor gamma chain (IL2RG) and adenosine deaminase (ADA) deficiency SCID are two of the most common types of SCID and can be treated by GT. As a challenge, both IL2RG and ADA genes are highly polymorphic and a gene-based diagnosis may be difficult if the variant is of unknown significance or if it is located in non-coding areas of the genes that are not routinely evaluated with exon-based genetic testing (e.g., introns, promoters, and the 5\u27and 3\u27 untranslated regions). Therefore, it is important to extend evaluation to non-coding areas of a SCID gene if the exon-based sequencing is inconclusive and there is strong suspicion that a variant in that gene is the cause for disease. Functional studies are often required in these cases to confirm a pathogenic variant. We present here two unique examples of X-linked SCID with variable immune phenotypes, where IL2R gamma chain expression was detected and no pathogenic variant was identified on initial genetic testing. Pathogenic IL2RG variants were subsequently confirmed by functional assay of gamma chain signaling and maternal X-inactivation studies. We propose that such tests can facilitate confirmation of suspected cases of X-linked SCID in newborns when initial genetic testing is inconclusive. Early identification of pathogenic IL2RG variants is especially important to ensure eligibility for gene therapy

UNIQUE BENCHMARKING TOOL TO MEASURE RELATIVE CARDHOLDER CARBON FOOTPRINT COMPARED TO IN-MARKET AND GLOBAL PEERS

The present disclosure relates to a method and system for calculating Carbon (CO2) emission scores from customer purchase data and creating a score-based numerical representation to represent the carbon footprint with respect to the cardholder’s green-score benchmark. The present disclosure suggests mapping the MCCs to purchased item-level information to obtain CO2 intensity multipliers. Thereafter, the net carbon emission value is calculated based on the transaction data associated with the purchased items. Further, a visual representation of the numerical scale score is created to represent the user green score/carbon footprint

Impact on the microbial population during biological volatile fatty acid production from olive mill solid waste

This work was funded by the Spanish Ministry of Economy, Industry and Competitiveness (Ref. PID2020-116698RB-100). Dr. Antonio Serrano was funded by the Consejería de Transformación Económica, Industria, Conocimiento y Universidades (Junta de Andalucía - EMERGIA20_00114). Juan Cubero-Cardoso was funded by the Recualificación del Profesorado Universitario (Next Generation European Funds and Spanish University Ministry system).Supplementary material: Download Word document (34KB), 1-s2.0-S2352186423004054-mmc1Volatile fatty acids (VFAs) revalorisation from waste products are key in achieving industrial sustainability and circular economic goals. Hence, the objective of this work was to correlate the adaptability of the microbial community in olive mill solid waste (OMSW) anaerobic fermentation processes, to the production of VFAs under different pH conditions, i.e. under acidic (pH 4 &5), neutral (pH 6 & 7) and alkaline conditions (pH 9 & 10). At neutral conditions, anaerobic digestion exhibited minimal accumulation of VFAs, as they were primarily biotransformed to methane, where no significant changes in the microbial community were observed. At acidic conditions, a diverse profile of VFAs were present in the reactors, although the VFA production was limited to around 20 % of fed OMSW. Despite the low accumulation, the VFA profile at pH 5 was more complex than those at alkaline conditions, accounting propionic acid as the main VFA compound produced at pH 5 (60 % of the total VFAs). Acidic conditions entailed a shift in the microbial composition compared to the initial inoculum, although the reactors maintained similar diversity indices. At alkaline conditions, around 50 % of the fed OMSW was accumulated as VFAs, mainly as acetic acid. Overall, a lower diversity and higher dominance corresponded to a less diverse VFAs profile, such as the preponderance of acetic acid correlated with a microbial diversity decrease and the increased dominance of Tissirella.Spanish Ministry of Economy, Industry and Competitiveness (Ref. PID2020-116698RB-100)Junta de Andalucía - EMERGIA20_00114Recualificación del Profesorado Universitario (Next Generation European Funds and Spanish University Ministry system

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations

BSocial Analysis: http://m4m.ugr.es/BSocial.htmlEcosystem functionality depends on interactions among populations, of the same or different taxa, and these are not just the sum of pairwise interactions. Thus, know-how of the social interactions occurring in mixed-populations are of high interest, however they are commonly unknown due to the limitations posed in tagging each population. The limitations include costs/time in tediously fluorescent tagging, and the number of different fluorescent tags. Tag-free strategies exist, such as high-throughput sequencing, but ultimately both strategies require the use of expensive machinery. Our work appoints social behaviors on individual strains in mixed-populations, offering a web-tool (BSocial http://m4m.ugr.es/BSocial.html) for analyzing the community framework. Our quick and cheap approach includes the periodic monitoring of optical density (OD) from a full combinatorial testing of individual strains, where number of generations and growth rate are determined. The BSocial analyses then enable us to determine how the addition/absence of a particular species affects the net productivity of a microbial community and use this to select productive combinations, i.e., designate their social effect on a general community. Positive, neutral, or negative assignations are applied to describe the social behavior within the community by comparing fitness effects of the community against the individual strain. The usefulness of this tool for selection of optimal inoculum in biofilm-based methyl tert-butyl ether (MTBE) bioremediation was demonstrated. The studied model uses seven bacterial strains with diverse MTBE degradation/growth capacities. Full combinatorial testing of seven individual strains (triplicate tests of 127 combinations) were implemented, along with MTBE degradation as the desired function. Sole observation of highest species fitness did not render the best functional outcome, and only when strains with positive and neutral social assignations were mixed (Rhodococcus ruber EE6, Agrobacterium sp. MS2 and Paenibacillus etheri SH7), was this obtained. Furthermore, the use of positive and neutral strains in all its combinations had a significant higher degradation mean (x1.75) than exclusive negative strain combinations. Thus, social microbial processes benefit bioremediation more than negative social microbial combinations. The BSocial webtool is a great contributor to the study of social interactions in bioremediation processes, and may be used in other natural or synthetic habitat studies.JP was funded by Junta de Andalucía through the “Programa Proyectos de Excelencia” (Project reference P10-RNM-6153). The work was funded by CEIBioTic through their “II Convocatoria de Proyectos I+D+I” (project reference CEI2013-MP-31), the Spanish Ministry of Science and Technology (project reference TIN2012-38805), and the Consejeria de Innovacion, Investigacion y Ciencia, Junta de Andalucia (project reference TIC-02788)

Making of a unique birth control vaccine against hCG with additional potential of therapy of advanced stage cancers and prevention of obesity and insulin resistance

Reviewed is the work which led to the development of a unique vaccine that prevents pregnancy in sexually active women without impairment of ovulation and block of their making normally their sex steroid hormones. Being given that hCG is not expressed by non-pregnant females, immunization with the vaccine is devoid of any crossreaction with any tissue of the body. It is totally reversible and women regained fertility on decline of antibodies. A recombinant vaccine has been developed which is highly immunogenic in mice. It is undergoing extensive toxicology under GLP conditions in rodents and a primate species, the marmosets, before resumption of clinical trials. Ectopic expression of hCG or its subunits takes place in a variety of cancers, particularly at advanced stage with adverse survival and poor prognosis. Anti-hCG antibodies exercise therapeutic action against such cancers as indicated by in vitro culture and in vivo studies in nude mice. Transgenic hCG β mice put on weight and manifest insulin resistance. Immunization of these mice with the recombinant hCG β-LTB vaccine prevents obesity and insulin resistance.Fil: Talwar, G. P.. Talwar Research Foundation; IndiaFil: Rulli, Susana Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental (i); ArgentinaFil: Vyas, Hemant. Harvard Medical School; Estados UnidosFil: Purswani, Shilpi. Talwar Research Foundation; IndiaFil: Kabeer, Rafi Shiraz. Talwar Research Foundation; IndiaFil: Chopra, Prem. Sir Ganga Ram Hospital; IndiaFil: Singh, Priyanka . Talwar Research Foundation; IndiaFil: Atrey, Nishu. Talwar Research Foundation; IndiaFil: Nand, Kripa. Talwar Research Foundation; IndiaFil: Gupta, Jagdish C.. Talwar Research Foundation; Indi

Evaluation of Risk for Late Language Emergence after In Utero Antiretroviral Drug Exposure in HIV-exposed Uninfected Infants

This is not the published version.BACKGROUND Combination antiretroviral (cARV) regimens are recommended for pregnant women with HIV to prevent perinatal HIV transmission. Safety is a concern for infants who were HIV-exposed but uninfected (HEU), particularly for neurodevelopmental problems, such as language delays. METHODS We studied late language emergence (LLE) in HEU children enrolled in a US-based prospective cohort study. LLE was defined as a caregiver-reported score ≤ 10th percentile in any of 4 domains of the MacArthur-Bates Communicative Development Inventory for one-year-olds and as ≥1 standard deviation below age-specific norms for the Ages and Stages Questionnaire for two-year-olds. Logistic regression models were used to evaluate associations of in utero cARV exposure with LLE, adjusting for infant, maternal, and environmental characteristics. RESULTS 1,129 language assessments were conducted among 792 one- and two-year-olds (50% male, 62% black, and 37% Hispanic). Overall, 86% had in utero exposure to cARV and 83% to protease inhibitors. LLE was identified in 26% of one-year-olds and 23% of two-year-olds, with higher rates among boys. In adjusted models, LLE was not associated with maternal cARV or ARV drug classes in either age group. Among cARV-exposed one-year-olds, increased odds of LLE was observed for those exposed to atazanavir (aOR=1.83, 95% CI=1.10-3.04), particularly after the first trimester (aOR=3.56, p=0.001), compared to atazanavir-unexposed infants. No associations of individual ARV drugs with LLE were observed among two-year-olds. CONCLUSIONS In utero cARV exposure showed little association with LLE, except for a higher risk of language delay observed in one-year-old infants with atazanavir exposure