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Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Twenty-four ewes (eight fistulated in the rumen) were assigned to a 2 × 2 factorial design. The treatments included the pasture grazed (natural mixed swards—NMS or cultivated monophytic (Brachiaria brizantha cv. Marandu) swards—CMS) and the level of supplementation: without supplement or with a 1% supplement (dry matter (DM)/live weight). The supplement included one-third endosperm expeller (ENE) and two-thirds mesocarp expeller (ME) from Acrocomia aculeata (Jacq.) Lodd. ex Mart. In sacco rumen degradation of ENE, ME, NMS, and CMS was assessed in fistulated sheep, as were rumen fermentation variables. Average daily gain (ADG) was assessed in non-fistulated animals during a 7-week period. Potential degradability of the DM and crude protein of the expellers was not affected by the type of pasture grazed or the level of supplementation (p > 0.05), but the fractional rate of degradation (c) of DM was three times faster (p < 0.01) for ME than for ENE. The potential degradability of neutral detergent fiber was 34% higher (p < 0.0001) for ENE, with no differences in c (p > 0.1). Supplementation slowed down the c of the DM of the pastures, especially in animals grazing NMS (24% lower). Treatments affected rumen pH, concentration of volatile fatty acids, and proportion of valerate, in different ways. The use of the supplement increased ADG of sheep (six-fold in sheep grazing NMS and 40% in those grazing CMS). The use of a mixture of one-third ENE plus two-thirds ME as a protein supplement in sheep grazing either multi-species natural pastures or monophytic swards of Brachiaria brizantha cv. Marandu slows down the fractional rate of degradation of the pastures, the effect of which is more intense in animals grazing natural swards. This supplementation also increases average daily gain, more substantially with multi-species natural pastures.

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Abstract Lignocellulosic biomass is currently underutilized, but it offers promise as a resource for the generation of commercial end-products, such as biofuels, detergents, and other oleochemicals. Rhodococcus opacus PD630 is an oleaginous, Gram-positive bacterium with an exceptional ability to utilize recalcitrant aromatic lignin breakdown products to produce lipid molecules such as triacylglycerols (TAGs), which are an important biofuel precursor. Lipid carbon storage molecules accumulate only under growth-limiting low nitrogen conditions, representing a significant challenge toward using bacterial biorefineries for fuel precursor production. In this work, we screened overexpression of 27 native transcriptional regulators for their abilities to improve lipid accumulation under nitrogen-rich conditions, resulting in three strains that accumulate increased lipids, unconstrained by nitrogen availability when grown in phenol or glucose. Transcriptomic analyses revealed that the best strain (#13) enhanced FA production via activation of the β-ketoadipate pathway. Gene deletion experiments confirm that lipid accumulation in nitrogen-replete conditions requires reprogramming of phenylalanine metabolism. By generating mutants decoupling carbon storage from low nitrogen environments, we move closer toward optimizing R. opacus for efficient bioproduction on lignocellulosic biomass.

Abstract Background Intestinal epithelial cell (IEC) mitochondrial dysfunction involvement in inflammatory bowel diseases (IBD), including Crohn’s disease affecting the small intestine, is emerging in recent studies. As the interface between the self and the gut microbiota, IECs serve as hubs of bidirectional cross-talk between host and luminal microbiota. However, the role of mitochondrial-microbiota interaction in the ileum is largely unexplored. Prohibitin 1 (PHB1), a chaperone protein of the inner mitochondrial membrane required for optimal electron transport chain function, is decreased during IBD. We previously demonstrated that mice deficient in PHB1 specifically in IECs (Phb1 i∆IEC ) exhibited mitochondrial impairment, Paneth cell defects, gut microbiota dysbiosis, and spontaneous inflammation in the ileum (ileitis). Mice deficient in PHB1 in Paneth cells (epithelial secretory cells of the small intestine; Phb1 ∆PC ) also exhibited mitochondrial impairment, Paneth cell defects, and spontaneous ileitis. Here, we determined whether this phenotype is driven by Phb1 deficiency-associated ileal microbiota alterations or direct effects of loss of PHB1 in host IECs. Results Depletion of gut microbiota by broad-spectrum antibiotic treatment in Phb1 ∆PC or Phb1 i∆IEC mice revealed a necessary role of microbiota to cause ileitis. Using germ-free mice colonized with ileal microbiota from Phb1-deficient mice, we show that this microbiota could not independently induce ileitis without host mitochondrial dysfunction. The luminal microbiota phenotype of Phb1 i∆IEC mice included a loss of the short-chain fatty acid butyrate. Supplementation of butyrate in Phb1-deficient mice ameliorated Paneth cell abnormalities and ileitis. Phb1-deficient ileal enteroid models suggest deleterious epithelial-intrinsic responses to ileal microbiota that were protected by butyrate. Conclusions These results suggest a mutual and essential reinforcing interplay of gut microbiota and host IEC, including Paneth cell, mitochondrial health in influencing ileitis. Restoration of butyrate is a potential therapeutic option in Crohn’s disease patients harboring epithelial cell mitochondrial dysfunction. Video Abstract

This qualitative /quantitative investigation highlights the analysis of preservice teachers' responses to an end of semester writing prompt in a diversity course requiring them to identify an unearned privilege that they may have benefitted from. Data were analyzed using qualitative as well as quantitative methodologies. Qualitative analysis revealed a range of privileges that pre-service can rely on when they reflect on the structured nature of privilege within our society such as socio-economic status, race, education, American citizenship, gender, parental support and language. Quantitative results, which focused on descriptive statistics, revealed that Whiteness and social class were privileges that they benefitted from the most.

BACKGROUND:HIV testing and pre-exposure prophylaxis (PrEP) are effective HIV prevention strategies often underutilized by transgender people. METHODS:Recruitment occurred in two phases to identify transgender respondents in a probability sample of adults in the United States. Transgender respondents completed a self-administered paper or web-based survey designed to assess transgender population health. Sexually active respondents (HIV-negative and had sex in the 5 years prior, N = 190) and a subsample of those at risk for sexual HIV acquisition (sex with cisgender men or transgender women, n = 120) were included in analyses. RESULTS:Of the full sample of sexually active respondents, those who were transfeminine were less likely to be familiar with PrEP; most (72%) reported favorable attitudes towards PrEP. Of those at risk for HIV acquisition, 28% had never tested for HIV. Respondents of color were more likely than white respondents to meet CDC recommendations for HIV testing. Respondents who met CDC recommendations for HIV testing were more likely to report looking online for LGBT or transgender health information. Few respondents reported currently taking PrEP (3%); those who reported higher levels of non-affirmation of their gender identity were less likely to currently use PrEP. DISCUSSION:These findings may indicate some success of HIV testing outreach programs that prioritize people at higher risk for acquiring HIV, focusing on those who are vulnerable to structural marginalization. Ongoing public health efforts are needed to increase HIV testing and PrEP awareness among transgender adults, who are disproportionately impacted by HIV.

Abstract Autophagy of damaged mitochondria, called mitophagy, is an important organelle quality control process involved in the pathogenesis of inflammation, cancer, aging, and age-associated diseases. Many of these disorders are associated with altered expression of the inner mitochondrial membrane (IMM) protein Prohibitin 1. The mechanisms whereby dysfunction occurring internally at the IMM and matrix activate events at the outer mitochondrial membrane (OMM) to induce mitophagy are not fully elucidated. Using the gastrointestinal epithelium as a model system highly susceptible to autophagy inhibition, we reveal a specific role of Prohibitin-induced mitophagy in maintaining intestinal homeostasis. We demonstrate that Prohibitin 1 induces mitophagy in response to increased mitochondrial reactive oxygen species (ROS) through binding to mitophagy receptor Nix/Bnip3L and independently of Parkin. Prohibitin 1 is required for ROS-induced Nix localization to mitochondria and maintaining homeostasis of epithelial cells highly susceptible to mitochondrial dysfunction.

Hemolytic disorders, like malaria and sickle cell disease (SCD), are responsible for significant mortality and morbidity rates globally, specifically in the Americas and Africa. In both malaria and SCD, red blood cell hemolysis leads to the release of a cytotoxic heme that triggers the expression of unique inflammatory profiles, which mediate the tissue damage and pathogenesis of both diseases. MicroRNAs (miRNAs), such as miR-451a and let-7i-5p, contribute to a reduction in the pro-inflammatory responses induced by circulating free hemes. MiR-451a targets both IL-6R (pro-inflammatory) and 14-3-3ζ (anti-inflammatory), and when this miRNA is present, IL-6R is reduced and 14-3-3ζ is increased. Let-7i-5p targets and reduces TLR4, which results in anti-inflammatory signaling. These gene targets regulate inflammation via NFκB regulation and increase anti-inflammatory signaling. Additionally, they indirectly regulate the expression of key heme scavengers, such as heme-oxygenase 1 (HO-1) (coded by the HMOX1 gene) and hemopexin, to decrease circulating cytotoxic heme concentration. MiRNAs can be transported within extracellular vesicles (EVs), such as exosomes, offering insights into the mechanisms of mitigating heme-induced inflammation. We tested the hypothesis that miR-451a- or let-7i-5p-loaded artificial EVs (liposomes) will reduce heme-induced inflammation in brain vascular endothelial cells (HBEC-5i, ATCC: CRL-3245) and macrophages (THP-1, ATCC: TIB-202) in vitro. We completed arginase and nitric oxide assays to determine anti- and pro-inflammatory macrophage presence, respectively. We also assessed the gene expression of IL-6R, TLR4, 14-3-3ζ, and NFκB by RT-qPCR for both cell lines. Our findings revealed that the exposure of HBEC-5i and THP-1 to liposomes loaded with miR-451a or let-7i-5p led to a reduced mRNA expression of IL-6R, TLR4, 14-3-3ζ, and NFκB when treated with a heme. It also resulted in the increased expression of HMOX1 and hemopexin. Finally, macrophages exhibited a tendency toward adopting an anti-inflammatory differentiation phenotype. These findings suggest that miRNA-loaded liposomes can modulate heme-induced inflammation and can be used to target specific cellular pathways, mediating inflammation common to hematological conditions, like malaria and SCD.

Abstract Background Granulosa cells (GCs) are multilayered somatic cells within the follicle that provide physical support and microenvironment for the developing oocyte. In recent years, the role of Neuregulin-1 (NRG1), a member of the EGF-like factor family, has received considerable attention due to its neurodevelopmental and cardiac function. However, the exact physiological role of NRG1 in GC is mainly unknown. In order to confirm that NRG1 plays a regulatory role in rat GC functions, endogenous NRG1-knockdown studies were carried out in GCs using RNA interference methodology. Results Knockdown of NRG1 in GCs resulted in the enhanced expression and secretion of the cytokines and chemokines. In addition, the phosphorylation of PI3K/Akt/ERK1/2 was significantly low in GCs under these experimental conditions. Moreover, in vitro experimental studies suggest that tumor necrosis factor-α (TNFα) treatment causes the physical destruction of GCs by activating caspase-3/7 activity. In contrast, exogenous NRG1 co-treatment of GCs delayed the onset of TNFα-induced apoptosis and inhibited the activation of caspase-3/7 activity. Furthermore, current experimental studies suggest that gonadotropins promote differential expression of NRG1 and ErbB3 receptors in GCs of the antral follicle. Interestingly, NRG1 and ErbB3 were intensely co-localized in the mural and cumulus GCs and cumulus-oocyte complex of pre-ovulatory follicles in the estrus stage. Conclusions The present studies suggest that gonadotropins-dependent NRG1-signaling in GCs may require the balance of the cytokines and chemokines expression and secretion, ultimately which may be supporting the follicular maturation and oocyte competence for ovulation and preventing follicular atresia.

Simple Summary: Sheep producers in many countries of the world usually feed their animals with natural or improved pastures. In these situations, pastures alone usually do not cover animal needs, and supplementation is required. By-products from the oil industry are extensively used in animal feeding, and endosperm and mesocarp expellers from grugru palm may play an important role in animal feeding in the countries where it is distributed. To assess the protein value of an ingredient, the extent and rate of rumen degradation are central characteristics. However, associative effects with other components of the diet occur, and rumen degradation of individual ingredients should be assessed in the usual feeding conditions of an animal. On these grounds, the objective of this study was to provide information about rumen degradation of endosperm and mesocarp expellers from grugru palm in sheep grazing natural or cultivated monophytic pastures, and supplemented with a mixture of both expellers. The use of this mixture slows down the rate of degradation of the pastures, the effect of which is more intense in animals grazing natural swards. Supplementation with this mixture also increases the average daily gain of sheep, more substantially with multi-species natural pastures. Twenty-four ewes (eight fistulated in the rumen) were assigned to a 2 × 2 factorial design. The treatments included the pasture grazed (natural mixed swards—NMS or cultivated monophytic (Brachiaria brizantha cv. Marandu) swards—CMS) and the level of supplementation: without supplement or with a 1% supplement (dry matter (DM)/live weight). The supplement included one-third endosperm expeller (ENE) and two-thirds mesocarp expeller (ME) from Acrocomia aculeata (Jacq.) Lodd. ex Mart. In sacco rumen degradation of ENE, ME, NMS, and CMS was assessed in fistulated sheep, as were rumen fermentation variables. Average daily gain (ADG) was assessed in non-fistulated animals during a 7-week period. Potential degradability of the DM and crude protein of the expellers was not affected by the type of pasture grazed or the level of supplementation (p > 0.05), but the fractional rate of degradation (c) of DM was three times faster (p < 0.01) for ME than for ENE. The potential degradability of neutral detergent fiber was 34% higher (p < 0.0001) for ENE, with no differences in c (p > 0.1). Supplementation slowed down the c of the DM of the pastures, especially in animals grazing NMS (24% lower). Treatments affected rumen pH, concentration of volatile fatty acids, and proportion of valerate, in different ways. The use of the supplement increased ADG of sheep (six-fold in sheep grazing NMS and 40% in those grazing CMS). The use of a mixture of one-third ENE plus two-thirds ME as a protein supplement in sheep grazing either multi-species natural pastures or monophytic swards of Brachiaria brizantha cv. Marandu slows down the fractional rate of degradation of the pastures, the effect of which is more intense in animals grazing natural swards. This supplementation also increases average daily gain, more substantially with multi-species natural pastures. [ABSTRACT FROM AUTHOR]

Hemolysis is associated with many pathologies, including trauma, sepsis, hemorrhagic stroke, malaria, and genetic disorders such as sickle cell disease (SCD). When hemolysis occurs, free-heme drives vascular inflammation, resulting in oxidative tissue damage and cardiometabolic complications. A better understanding of heme clearance and detoxification is essential to preventing sustained tissue damage. Human induced pluripotent stem cell (hiPSC)-derived endothelial cells (hiPSC-ECs) provide a novel source of patient-specific cells and tissues for disease modeling, drug discovery, and regenerative therapeutics. Here we report the use of hiPSC-ECs to elucidate the role of miR-451a and let-7i-5p-loaded extracellular vesicles (EVs, such as exosomes) in the inflammatory response to free-heme as a model for heme-induced inflammation. We provide evidence of a significant correlation between miR-451a and let-7i-5p-loaded circulating exosomes in plasmodium-infected patients with reported clinical benchmarks of malaria-severity (e.g., Hemoglobin (Hb) levels, white blood cell counts). Additionally, we determined that exposure of Plasmodium falciparum (Pf) parasites to EVs, loaded with either miRNA, significantly reduces their counts in vitro. Using hiPSCs derived from individuals with wild-type Hb (HbAA) or homozygous sickle cell mutated Hb (HbSS) genotypes, we demonstrate that heme-treated hiPSC-ECs secreted inflammatory products (cytokines, chemokines and growth factors) into supporting media at concentrations that were similar to that reported in HbAA and HbSS serum. This inflammatory response was attenuated by exposure with miR-451a or let-7i-5p-loaded EVs. We also found a decrease in transcription of ICAM1 and P-Selectin, as well as the secretion of key inflammatory cytokines (e.g., CXCL10, TNF-α, and IFN-γ). Based on these findings, we propose a model in which increased levels of exosomal miR-451a and let-7i-5p in Plasmodium-infected individuals will attenuate inflammatory responses to free-heme and parasite-derived products. As a result, infected erythrocytes will less likely adhere to the endothelium, sequester in brain micro vessels, and reduce vaso-occlusive crises that exacerbate cerebral malaria.

Mammalian ovarian follicular development and maturation of an oocyte competent to be fertilized and develop into an embryo depends on tightly regulated, spatiotemporally orchestrated crosstalk among cell death, survival, and differentiation signals through extra- and intraovarian signals, as well as on a permissive ovarian follicular microenvironment. Neuregulin-1 (NRG1) is a member of the epidermal growth factor-like factor family that mediates its effects by binding to a member of the erythroblastoma (ErbB) family. Our experimental results suggest gonadotropins promote differential expression of NRG1 and erbB receptors in granulosa cells (GCs), and NRG1 in theca cells during follicular development, and promote NRG1 secretions in the follicular fluid (FF) of rat ovaries. During the estrous cycle of rat, NRG1 and erbB receptors are differentially expressed in GCs and correlate positively with serum gonadotropins and steroid hormones. Moreover, in vitro experimental studies suggest that the protein kinase C inhibitor staurosporine (STS) causes the physical destruction of GCs by the activation of caspase-3. Exogenous NRG1 treatment of GCs delayed onset of STS-induced apoptosis and inhibited cleaved caspase-3 expressions. Moreover, exogenous NRG1 treatment of GCs alters STS-induced death by maintaining the expression of ErbB2, ErbB3, pAkt, Bcl2, and BclxL proteins. Taken together, these studies demonstrate that NRG1 is gonadotropin dependent, differentially regulated in GCs and theca cells, and secreted in ovarian FF as an intracellular survival factor that may govern follicular maturation.

Toll-like receptors (TLRs) are evolutionarily conserved molecules that detect exogenous and endogenous molecular patterns and trigger both the innate and adaptive immune systems to initiate a pathogen-specific immune response and eliminate the threat. However, sustained, or prolonged activation of the immune system disrupts immunological homeostasis and leads to chronic or acute inflammatory diseases. MicroRNAs (miRNAs) can intervene in the initiation and modulation of the complex immunoregulatory networks via regulating the expression of TLRs and multiple components of TLR-signaling pathways including signaling proteins, transcription factors, and cytokines. Moreover, the aberrant expression of TLRs can induce the expression of several miRNAs which in turn regulate the expression of TLR signaling components and TLR-induced cytokines. The present review aims to highlight the emerging roles of miRNA in the regulation of TLR signaling, the interaction between the miRNAs and TLRs, and their implication in inflammatory diseases.

Background: Sickle cell anemia (SCA) is a severe monogenic disorder, caused by single nucleotide mutations in the hemoglobin (Hb) gene, that is prevalent in malaria endemic regions of the world. Sickle cell trait (SCT) individuals carry only one of the mutated alleles and were shown to be protected against malaria. However, defining the relative contribution of hematological, clinical, and environmental factors to the overall burden of malaria in individuals with hemoglobinopathies such as SCA has been challenging. Methods: We hypothesized that hematological differences, clinical presentations, and self-reported bed net usage among Plasmodium-infected and uninfected individuals may govern overall malaria burden in individuals with sickle cell disease (SCD). We conducted a cross-sectional study in Ghana from 2014 to 2019 and described clinical presentations, hematological characteristics, and bed net use based on a comprehensive questionnaire. Hematological characteristics were compared using a parametric or nonparametric ANOVA, pending if data passed D'Agostino & Pearson normality test. When comparing only two Hb genotypes hematological characteristics a Mann–Whitney U-test were used. Logistic regressions and Chi-squared tests were used to compare questionnaire responses between Hb genotypes. All statistical significance was set at p