High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0.

MOTIVATION: Gene regulatory networks define regulatory relationships between transcription factors and target genes within a biological system, and reconstructing them is essential for understanding cellular growth and function. Methods for inferring and reconstructing networks from genomics data have evolved rapidly over the last decade in response to advances in sequencing technology and machine learning. The scale of data collection has increased dramatically; the largest genome-wide gene expression datasets have grown from thousands of measurements to millions of single cells, and new technologies are on the horizon to increase to tens of millions of cells and above. RESULTS: In this work, we present the Inferelator 3.0, which has been significantly updated to integrate data from distinct cell types to learn context-specific regulatory networks and aggregate them into a shared regulatory network, while retaining the functionality of the previous versions. The Inferelator is able to integrate the largest single-cell datasets and learn cell-type-specific gene regulatory networks. Compared to other network inference methods, the Inferelator learns new and informative Saccharomyces cerevisiae networks from single-cell gene expression data, measured by recovery of a known gold standard. We demonstrate its scaling capabilities by learning networks for multiple distinct neuronal and glial cell types in the developing Mus musculus brain at E18 from a large (1.3 million) single-cell gene expression dataset with paired single-cell chromatin accessibility data. AVAILABILITY AND IMPLEMENTATION: The inferelator software is available on GitHub (https://github.com/flatironinstitute/inferelator) under the MIT license and has been released as python packages with associated documentation (https://inferelator.readthedocs.io/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression.

Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant Cuphea palustris harbors two distinct TEs: C. palustris FatB1 (CpFatB1) (C8 specificity, lower activity) and CpFatB2 (C14 specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Notably, chimera 4 exhibited an increased C8 fatty acid production in correlation with improved microbial expression. This chimera led us to identify CpFatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and in silico docking with ACP, we identified a "positive patch" within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from CpFatB1 into CpFatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Thus, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control.IMPORTANCE Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Similarly, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing.

Perspectives on HIV pre-exposure prophylaxis (PrEP) implementation in Mississippi among Black women and clinical staff: Recommendations for clinical trauma-informed programs.

Intimate partner violence (IPV) can constraint Black women's ability to prioritize and access Human Immunodeficiency Virus (HIV) pre-exposure prophylaxis (PrEP) services. Recent research has called for the development of trauma-informed PrEP implementation programs to improve the delivery of PrEP to Black cisgender women; however, many PrEP-prescribing settings do not reflect this recommendation. The current study sought to identify key components to develop a trauma-informed PrEP implementation program for Black cisgender women and clinical staff. We conducted focus groups with PrEP-eligible Black cisgender women (February-June 2019), and semi-structured interviews with clinical staff offering HIV prevention and treatment services (October-November 2020) in community healthcare clinics in Mississippi. Seven themes were identified as needed to facilitate integration of trauma-informed approaches into existing PrEP programs, including defining intimate partner violence (IPV), appropriate IPV screening and response, HIV prevention in abusive relationships, staff training needs, and creating supportive clinic environments. PrEP-eligible Black women and clinical staff generally agreed on how to best operationalize IPV screening and response, the importance of trauma-informed staff training, and the need for Black women-specific informational campaigns. However, Black women highlighted the need for providers to discuss HIV prevention in controlling relationships, and to respond to IPV disclosure. HIV pre-exposure prophylaxis has yet to achieve the potential impact observed in trials. Ultimately, realizing the HIV prevention potential of PrEP in the US necessitates centering the perspectives of Black cisgender women and staff to better integrate trauma-informed approaches.

Community Interventions for Childhood Asthma ED Visits and Hospitalizations: A Systematic Review.

A systematic review of interventions in community environments found significant reductions in childhood asthma exacerbations leading to emergency department visits and hospitalizations. BACKGROUND AND OBJECTIVES: Structural and social determinants of childhood asthma inequities manifest within geographic communities that are often segregated. Childhood asthma disproportionately affects Black, Hispanic, and low-income populations. Community interventions have the potential to improve inequities in emergency healthcare. This systematic review was conducted to assess the effectiveness of childhood asthma community interventions and provide a conceptual model to inform implementation of future community interventions. METHODS: Publications from PubMed, ScienceDirect, CINAHL, Cochrane Library, Web of Science, and hand searched references were examined from 2010 to 2021. Community intervention studies among children with asthma were included. Main outcomes were emergency department visits and hospitalizations. Community interventions exclusively focusing on schools or hospitals were excluded. Two reviewers independently assessed eligibility for final inclusion. Emergency healthcare findings were extracted in addition to co-benefits (eg, fewer missed school days and caregiver workdays). RESULTS: Out of 1856 records, 26 publications met the inclusion criteria. Community interventions were categorized by care coordination (n = 8), policy and environmental changes (eg, smoke-free legislature, traffic reduction models, and green housing) (n = 8), home-based (n = 6), and community-based health services (n = 4). Selected studies indicated that community interventions significantly reduced childhood asthma emergency department visits and hospitalizations through increased caregiver self-efficacy, home environmental trigger reduction, and increased access to healthcare. Because of heterogeneity among studies, we were unable to conduct a meta-analysis. CONCLUSIONS: Findings show significant associations between community interventions and the reduction of emergency healthcare, suggesting a protective effect for severe cases of childhood asthma.

Levels of Apolipoprotein A1, B100 and Lipoprotein (a) in Controlled and Uncontrolled Diabetic Patients and in Non-Diabetic Healthy People.

INTRODUCTION: Diabetes Mellitus (DM) is always a multifactorial metabolic disorder having a wide range of abnormalities in carbohydrate, lipid and protein metabolism. Dyslipidemia is a natural process of DM causing abnormal variations of different lipoproteins and it is one of the significant risk factors for Cardiovascular Disorder (CVD). There is a need to closely evaluate newer approaches in case of DM because even if dyslipidemia is treated, there is always a risk of CVDs in DM patients because of the hyperglycemia itself. So, lipid abnormalities should be assessed aggressively and treated as part of diabetes care. Apolipoprotein B100 (Apo B100), Apolipoprotein A1 (Apo A1) and Lipoprotein (a) {Lp(a)} are newer markers which are always welcome and necessary as many of the reported cases with normal conventional lipid profile have developed cardiac events. AIM: Study the correlation between glycemic control and the levels of Apo A1, Apo B100 and Lp(a). MATERIALS AND METHODS: Total 56 patients of (DM) diagnosed on the basis of American Diabetic Association guidelines were recruited, out of which 28 were identified as uncontrolled-diabetic patients and remaining 28 as controlled-diabetics on the basis of Glycosylated HbA1c (HbA1c). The control group consisted of normal healthy 28 individuals. Apo B100, Apo A1 and Lp(a) along with traditional lipid profile, Fasting Blood Sugar (FBS) and HbA1c were estimated in all the subjects. RESULTS: Apo B100/Apo A1 ratio and Lp(a) levels showed highly significant difference (p-value <0.001) between uncontrolled diabetics, controlled diabetics and healthy Controls. Apo B100/Apo A1 ratio and Lp(a) showed significant positive correlations with HbA1c (r= 0.494, p <0.0001) and with each other. CONCLUSION: Apo B100/Apo A1 ratio and Lp(a) show a highly significant positive relationship with glucose tolerance of the patients as reflected in the HbA1c values. If proper glycemic control is maintained, the levels of Apo B100/Apo A1 ratio and Lp(a) can be controlled as reflected by the lower levels of these parameters observed in controlled diabetics in comparison to uncontrolled diabetics.

Study of Glycated Haemoglobin (HbA1c) In Non-Diabetic Subjects with Subclinical Hypothyroidism.

INTRODUCTION: India has the higher prevalence of prediabetes, diabetes and hypothyroidism. Subclinical Hypothyroidism (SH) is more prevalent in the females than in the males. Studies have shown the elevated HbA1c in the non-diabetic hypothyroid patients. SH is defined by normal serum triiodothyronine (T3), thyroxine (T4) levels and serum Thyroid Stimulating Hormone (TSH) level falling between 4.2 to 10 mU/L. AIM: To study the HbA1c level in the non-diabetic SH patients and to compare the HbA1c level with the controls. MATERIALS AND METHODS: This case-control study was conducted on 200 subjects. A total of 100 subjects of the SH without diabetes were selected on the basis of the serum TSH (> 4.2 to < 10 mU/L), Fasting Blood Sugar (FBS) (< 110 mg/dl) level and another 100 age and sex matched normal healthy individuals were selected as the control. The HbA1c levels were measured using Immunoturbidimetry method in the Cobas Integra 400 plus. An independent t-test is applied to find out the statistically significant difference in the level of HbA1c in the case and the control groups. RESULTS: Subjects with the non-diabetic SH had a significant higher level (5.70±0.35 %) of the HbA1c than the controls (5.26±0.17 %) (p<0.0001). There was no significant difference between the cases and the controls for the age, sex, FBS, vitamin D3, Haemoglobin (Hb), serum T3 and serum T4 levels. CONCLUSION: Our data suggest that the non-diabetic subjects with SH show misleadingly high levels of the HbA1c. Therefore, the effect of altered levels of the serum TSH on the HbA1c must be considered when interpreting the HbA1c for the diagnosis of diabetes in the SH patients.