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OBJECTIVE: Metformin is the most common treatment for type 2 diabetes (T2D). However, there have been no pharmacogenomic studies for T2D in which a population of color was used in the discovery analysis. This study sought to identify genomic variants associated with metformin response in African American patients with diabetes. RESEARCH DESIGN AND METHODS: Patients in the discovery set were adult, African American participants from the Diabetes Multi-omic Investigation of Drug Response (DIAMOND), a cohort study of patients with T2D from a health system serving southeast Michigan. DIAMOND participants had genome-wide genotype data and longitudinal electronic records of laboratory results and medication fills. The genome-wide discovery analysis identified polymorphisms correlated to changes in glycated hemoglobin (HbA1c) levels among individuals on metformin monotherapy. Lead associations were assessed for replication in an independent cohort of African American participants from Kaiser Permanente Northern California (KPNC) and in European American participants from DIAMOND. RESULTS: The discovery set consisted of 447 African American participants, whereas the replication sets included 353 African American KPNC participants and 466 European American DIAMOND participants. The primary analysis identified a variant, rs143276236, in the gene ARFGEF3, which met the threshold for genome-wide significance, replicated in KPNC African Americans, and was still significant in the meta-analysis (P = 1.17 × 10−9). None of the significant discovery variants replicated in European Americans DIAMOND participants. CONCLUSIONS: We identified a novel and biologically plausible genetic variant associated with a change in HbA1c levels among African American patients on metformin monotherapy. These results highlight the importance of diversity in pharmacogenomic studies. [ABSTRACT FROM AUTHOR]

Genome-wide significant loci for metformin response in type 2 diabetes reported elsewhere have not been replicated in the Diabetes Prevention Program (DPP). To assess pharmacogenetic interactions in prediabetes, we conducted a genome-wide association study (GWAS) in the DPP. Cox proportional hazards models tested associations with diabetes incidence in the metformin (MET; n = 876) and placebo (PBO; n = 887) arms. Multiple linear regression assessed association with 1-year change in metformin-related quantitative traits, adjusted for baseline trait, age, sex, and 10 ancestry principal components. We tested for gene-by-treatment interaction. No significant associations emerged for diabetes incidence. We identified four genome-wide significant variants after correcting for correlated traits (P < 9 × 10−9). In the MET arm, rs144322333 near ENOSF1 (minor allele frequency [MAF]AFR = 0.07; MAFEUR = 0.002) was associated with an increase in percentage of glycated hemoglobin (per minor allele, β = 0.39 [95% CI 0.28, 0.50]; P = 2.8 × 10−12). rs145591055 near OMSR (MAF = 0.10 in American Indians) was associated with weight loss (kilograms) (per G allele, β = −7.55 [95% CI −9.88, −5.22]; P = 3.2 × 10−10) in the MET arm. Neither variant was significant in PBO; gene-by-treatment interaction was significant for both variants [P(G×T) < 1.0 × 10−4]. Replication in individuals with diabetes did not yield significant findings. A GWAS for metformin response in prediabetes revealed novel ethnic-specific associations that require further investigation but may have implications for tailored therapy. [ABSTRACT FROM AUTHOR]

Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes. [ABSTRACT FROM AUTHOR]

Background: Mitochondria support critical cellular functions, such as energy production through oxidative phosphorylation, regulation of reactive oxygen species, apoptosis, and calcium homeostasis. Objective: Given the heightened level of cellular activity in patients with asthma, we sought to determine whether mitochondrial DNA (mtDNA) copy number measured in peripheral blood differed between individuals with and without asthma. Methods: Whole genome sequence data was generated as part of the Trans-Omics for Precision Medicine (TOPMed) Program on participants from the Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-ethnicity (SAPPHIRE) and the Study of African Americans, Asthma, Genes, & Environment II (SAGE II). We restricted our analysis to individuals who self-identified as African American (3,651 asthma cases and 1,344 controls). Mitochondrial copy number was estimated using the sequencing read depth ratio for the mitochondrial and nuclear genomes. Respiratory complex expression was assessed using RNA-sequencing. Results: Average mitochondrial copy number was significantly higher among individuals with asthma when compared with controls (SAPPHIRE: 218.60 vs. 200.47, P<0.001; SAGE II: 235.99 vs. 223.07, P<0.001). Asthma status was significantly associated with mitochondrial copy number after accounting for potential explanatory variables, such as participant age, sex, leukocyte counts, and mitochondrial haplogroup. Despite the consistent relationship between asthma status and mitochondrial copy number, the latter was not associated with time-to-exacerbation or patient-reported asthma control. Mitochondrial respiratory complex gene expression was disproportionately lower in individuals with asthma when compared with individuals without asthma and other protein-encoding genes. Conclusions: We observed a robust association between asthma and higher mitochondrial copy number. Asthma having an effect on mitochondria function was also supported by lower respiratory complex gene expression in this group. [ABSTRACT FROM AUTHOR]

Lithium-sulfur batteries show great promise among future battery technologies, but their cycle life is mainly restricted by the shuttling effect of soluble lithium polysulfides (LiPSs). The catalytic conversion of LiPSs appears to be a fundamental way of suppressing this. The highly conductive metal nitrides show great potentials as high-performance catalysts, but the presence of a thin surface oxidation layer, which is normal for nanomaterials, restrains the surface electron transfer and catalytic activity. In this study, we demonstrate that the doping of the oxidation layer is an ideal solution to reviving and enhancing the catalytic activity of nitrides. As a proof of concept, sulfur-doping of a titanium nitride (TiN) oxidation layer is presented here, and the Ti S bonds formed are responsible for transmitting electrons from the conductive TiN matrix thus guaranteeing a high catalytic activity. Interfacing of Ti S with Ti O bonds at the atomic level helps realize strong trapping and fast conversion of LiPSs simultaneously. As a result, the specific capacity, rate performance, and cyclic stability are all greatly improved by the interlayer composed of sulfur-doped TiN and graphenes, which indicates a practical avenue for building high performance lithium-sulfur batteries. Image 1 • Sulfur doping of inert surface layer revives catalysis of TiN towards polysulfides. • Ti S interfacing with Ti O bonds results in fast conversion of polysulfide. • Using sulfur-doped TiN in the interlayer prolongs the cycling life of Li S batteries. [ABSTRACT FROM AUTHOR]

The shuttling of dissolved polysulfide intermediates and their sluggish reaction kinetics largely reduce the cycle life and sulfur utilization of lithium–sulfur (Li–S) batteries. In this study, low-cost bacterial cellulose was used as the precursor for interconnected carbon networks and a supporting framework for impregnated molybdate ions. After freeze-drying and solid-state thermal reactions, necklace-like molybdenum carbide embedded in interconnected N-doped carbon nanofibers (MoC@N-CNF) was obtained to be used as a high sulfur loading host. On the one hand, the interconnected conductive carbon network enables fast electron and ion transport, and on the other hand, the embedded sulfiphilic MoC efficiently immobilizes polysulfides and catalytically promotes their redox conversion. Therefore, the as-prepared electrode coupled with the lithium polysulfide catholyte exhibits good cycling stability with a low capacity decay of 0.084% per cycle at 1C for 350 cycles and a high rate capability of 799 mA h g−1 at 2C. Moreover, a high areal capacity of 12.3 mA h cm−2 with an areal sulfur loading of 10 mg cm−2 at 0.1C is also achieved. [ABSTRACT FROM AUTHOR]

Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences.

Bacterial biofilms are ubiquitous in natural environments and play an essential role in bacteria's environmental adaptability. Quorum sensing (QS), as the main signaling mechanism bacteria used for cell-to-cell communication, plays a key role in bacterial biofilm formation. However, little is known about the role of QS circuit in the N-transformation type strain, Paracoccus denitrificans , especially for the regulatory protein PdeR. In this study, we found the overexpression of pdeR promoted bacterial aggregation and biofilm formation. Through RNA-seq analysis, we demonstrated that PdeR is a global regulator which could regulate 656 genes expression, involved in multiple metabolic pathways. Combined with transcriptome as well as biochemical experiments, we found the overexpressed pdeR mainly promoted the intracellular degradation of amino acids and fatty acids, as well as siderophore biosynthesis and transportation, thus providing cells enough energy and iron for biofilm development. These results revealed the underlying mechanism for PdeR in biofilm formation of P. denitrificans , adding to our understanding of QS regulation in biofilm development., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wang, Gao, Xiao and Zhuang.)

The practical use of lithium-sulfur (Li-S) batteries is limited by serious self-discharge, fast capacity loss, and severe lithium anode erosion due to the shuttling of lithium polysulfides (LiPSs). Herein, we developed a highly efficient ion and electron conductive interlayer composed of Ti 2 (SO 4 ) 3 /carbon composite layer-coated Li 1.3 Al 0.3 Ti 1.7 (PO 4 ) 3 (CLATP) and graphene to effectively block the diffusion of polysulfide anions but allow rapid Li ion transfer, therefore significantly inhibiting the self-discharge and boosting the cyclic stability of Li-S batteries. The Ti 2 (SO 4 ) 3 /carbon thin protective layer endows an optimized adsorption ability toward LiPSs and avoids the side reactions between LATP and LiPSs. The high electronic conductivity of graphene and high ionic conductivity of CLATP ensures the hybrid interlayer rapid electron and fast Li ion transport. As a result, the Li-S battery with the hybrid interlayer shows a high discharge capacity of 671 mAh g -1 after 500 cycles with an extremely low capacity fading of 0.022% per cycle at 1 C. Moreover, the battery shows no self-discharge even after rest for 12 days. This work opens up a new way for the design of functional separators to significantly improve the electrochemical performance of Li-S batteries.

Introduction: Global shortages in the supply of SARS-CoV-2 vaccines have resulted in campaigns to first inoculate individuals at highest risk for death from COVID-19. Here, we develop a predictive model of COVID-19-related death using longitudinal clinical data from patients in metropolitan Detroit., Methods: All individuals included in the analysis had a laboratory-confirmed SARS-CoV-2 infection. Thirty-six pre-existing conditions with a false discovery rate p<0.05 were combined with other demographic variables to develop a parsimonious prediction model using least absolute shrinkage and selection operator regression. The model was then prospectively validated in a separate set of individuals with confirmed COVID-19., Results: The study population consisted of 15 502 individuals with laboratory-confirmed SARS-CoV-2. The main prediction model was developed using data from 11 635 individuals with 709 reported deaths (case fatality ratio 6.1%). The final prediction model consisted of 14 variables with 11 comorbidities. This model was then prospectively assessed among the remaining 3867 individuals (185 deaths; case fatality ratio 4.8%). When compared with using an age threshold of 65 years, the 14-variable model detected 6% more of the individuals who would die from COVID-19. However, below age 45 years and its risk equivalent, there was no benefit to using the prediction model over age alone., Discussion: Using a prediction model, such as the one described here, may help identify individuals who would most benefit from COVID-19 inoculation, and thereby may produce more dramatic initial drops in deaths through targeted vaccination., Competing Interests: Competing interests: DEL reports serving as a consultant for Amgen, Janssen, Ortho Diagnostics, DCRI (Novartis), Cytokinetics and Martin Pharmaceuticals and having participated in the running clinical trials for Amgen, Bayer, and Janssen; these activities are unrelated to the subject matter of the current manuscript. LKW reports owning stock in companies which produce SARS-CoV-2 vaccines; there was no transactional relationship related to this manuscript. None of the other authors report any competing interests., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Rationale: The 17q12-21.1 locus is one of the most highly replicated genetic associations with asthma. Individuals of African descent have lower linkage disequilibrium in this region, which could facilitate identifying causal variants. Objectives: To identify functional variants at 17q12-21.1 associated with early-onset asthma among African American individuals. Methods: We evaluated African American participants from SAPPHIRE (Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity) ( n  = 1,940), SAGE II (Study of African Americans, Asthma, Genes and Environment) ( n  = 885), and GCPD-A (Study of the Genetic Causes of Complex Pediatric Disorders-Asthma) ( n  = 2,805). Associations with asthma onset at ages under 5 years were meta-analyzed across cohorts. The lead signal was reevaluated considering haplotypes informed by genetic ancestry (i.e., African vs. European). Both an expression-quantitative trait locus analysis and a phenome-wide association study were performed on the lead variant. Measurements and Main Results: The meta-analyzed results from SAPPHIRE, SAGE II, and the GCPD-A identified rs11078928 as the top association for early-onset asthma. A haplotype analysis suggested that the asthma association partitioned most closely with the rs11078928 genotype. Genetic ancestry did not appear to influence the effect of this variant. In the expression-quantitative trait locus analysis, rs11078928 was related to alternative splicing of GSDMB (gasdermin-B) transcripts. The phenome-wide association study of rs11078928 suggested that this variant was predominantly associated with asthma and asthma-associated symptoms. Conclusions: A splice-acceptor polymorphism appears to be a causal variant for asthma at the 17q12-21.1 locus. This variant appears to have the same magnitude of effect in individuals of African and European descent.

Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV 1 ), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV 1 on chromosome 12 in 867 African American children with asthma ( P = 1.26 × 10 -8 , β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV 1 Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with KITLG (KIT ligand, also known as SCF ), and their minor alleles were associated with increased expression of the KITLG gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure ( P = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV 1 , possibly mediated through KITLG , in African American children with asthma. This is the first study that has identified a genetic association between lung function and KITLG , which has established a role in orchestrating allergic inflammation in asthma., (Copyright © 2020 by the Genetics Society of America.)

Large-scale implementation of electrochemical water splitting for hydrogen evolution requires cheap and efficient catalysts to replace expensive platinum. However, catalysts that work well at high current densities with ultrafast intrinsic activities is still the central challenge for hydrogen evolution. An ideal case is to use single atoms on monolayer two-dimensional (2D) materials, which simplifies the system and in turn benefits the mechanism study, but is a grand challenge to synthesize. Here, we report a universal cold hydrogen plasma reduction method for synthesizing different single atoms sitting on 2D monolayers. In the case of molybdenum disulfide, we design and identify a type of active site, i . e ., unsaturated Mo single atoms on cogenetic monolayer molybdenum disulfide. The catalyst shows exceptional intrinsic activity with a Tafel slope of 36.4 mV dec -1 in 0.5 M H 2 SO 4 and superior performance at a high current density of 400 mA cm -2 with an overpotential of ∼260 mV, based on single flake microcell measurements. Theoretical studies indicate that coordinately unsaturated Mo single atoms sitting on molybdenum disulfide increase the bond strength between adsorbed hydrogen atoms and the substrates through hybridization, leading to fast hydrogen adsorption/desorption kinetics and superior hydrogen evolution activity. This work shines fresh light on preparing highly efficient electrocatalysts for water splitting and other electrochemical processes, as well as provides a general method to synthesize single atoms on two-dimensional monolayers.

Objective: As compensation transitions from a fee-for-service to pay-for-performance healthcare model, providers must prioritize patient-centered experiences. Here, the authors' primary aim was to identify predictors of patient dissatisfaction at 1 and 2 years after lumbar surgery., Methods: The Michigan Spine Surgery Improvement Collaborative (MSSIC) was queried for all lumbar operations at the 1- and 2-year follow-ups. Predictors of patients' postoperative contentment were identified per the North American Spine Surgery (NASS) Patient Satisfaction Index, wherein satisfied patients were assigned a score of 1 ("the treatment met my expectations") or 2 ("I did not improve as much as I had hoped, but I would undergo the same treatment for the same outcome") and unsatisfied patients were assigned a score of 3 ("I did not improve as much as I had hoped, and I would not undergo the same treatment for the same outcome") or 4 ("I am the same or worse than before treatment"). Multivariable Poisson generalized estimating equation models were used to report adjusted risk ratios (RRadj)., Results: Among 5390 patients with a 1-year follow-up, 22% reported dissatisfaction postoperatively. Dissatisfaction was predicted by higher body mass index (RRadj =1.07, p < 0.001), African American race compared to white (RRadj = 1.51, p < 0.001), education level less than high school graduation compared to a high school diploma or equivalent (RRadj = 1.25, p = 0.008), smoking (RRadj = 1.34, p < 0.001), daily preoperative opioid use > 6 months (RRadj = 1.22, p < 0.001), depression (RRadj = 1.31, p < 0.001), symptom duration > 1 year (RRadj = 1.32, p < 0.001), previous spine surgery (RRadj = 1.32, p < 0.001), and higher baseline numeric rating scale (NRS)-back pain score (RRadj = 1.04, p = 0.002). Conversely, an education level higher than high school graduation, independent ambulation (RRadj = 0.90, p = 0.039), higher baseline NRS-leg pain score (RRadj = 0.97, p = 0.013), and fusion surgery (RRadj = 0.88, p = 0.014) decreased dissatisfaction.Among 2776 patients with a 2-year follow-up, 22% reported dissatisfaction postoperatively. Dissatisfaction was predicted by a non-white race, current smoking (RRadj = 1.26, p = 0.004), depression (RRadj = 1.34, p < 0.001), symptom duration > 1 year (RRadj = 1.47, p < 0.001), previous spine surgery (RRadj = 1.28, p < 0.001), and higher baseline NRS-back pain score (RRadj = 1.06, p = 0.003). Conversely, at least some college education (RRadj = 0.87, p = 0.035) decreased the risk of dissatisfaction., Conclusions: Both comorbid conditions and socioeconomic circumstances must be considered in counseling patients on postoperative expectations. After race, symptom duration was the strongest predictor of dissatisfaction; thus, patient-centered measures must be prioritized. These findings should serve as a tool for surgeons to identify at-risk populations that may need more attention regarding effective communication and additional preoperative counseling to address potential barriers unique to their situation.

Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light on potential causal variants and genes at known and newly identified loci. Several of the novel genes encode proteins with predicted or established drug targets, including KCNK2 and CDK12. Our study highlights the utility of multiethnic and integrative genomics approaches to extend existing knowledge of the genetics of lung function and clinical relevance of implicated loci.

Mitochondrial genomes (mitogenomes) are remarkably diverse in genome size and organization, but the origins of dynamic mitogenome architectures are still poorly understood. For instance, the mutational burden hypothesis postulates that the drastic difference between large plant mitogenomes and streamlined animal mitogenomes can be driven by their different mutation rates. However, inconsistent trends between mitogenome sizes and mutation rates have been documented in several lineages. These conflicting results highlight the need of systematic and sophisticated investigations on the evolution and diversity of mitogenome architecture. This study took advantage of the strikingly variable mitogenome size among different yeast species and also among intraspecific strains, examined sequence dynamics of introns, GC-clusters, tandem repeats, mononucleotide repeats (homopolymers) and evaluated their contributions to genome size variation. The contributions of these sequence features to mitogenomic variation are dependent on the timescale, over which extant genomes evolved from their last common ancestor, perhaps due to a combination of different turnover rates of mobile sequences, variable insertion spaces, and functional constraints. We observed a positive correlation between mitogenome size and the level of genetic drift, suggesting that mitogenome expansion in yeast is likely driven by multiple types of sequence insertions in a primarily nonadaptive manner. Although these cannot be explained directly by the mutational burden hypothesis, our results support an important role of genetic drift in the evolution of yeast mitogenomes., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Human telomeres are associated with ATM and the protein complex consisting of MRE11, RAD50 and NBS1 (MRN), which are central to maintaining genomic stability. Here we show that when targeted to telomeres, wild-type RAD50 downregulates telomeric association of TRF1, a negative regulator of telomere maintenance. TRF1 binding to telomeres is upregulated in cells deficient in NBS1 or under ATM inhibition. The TRF1 association with telomeres induced by ATM inhibition is abrogated in cells lacking MRE11 or NBS1, suggesting that MRN and ATM function in the same pathway controlling TRF1 binding to telomeres. The ability of TRF1 to interact with telomeric DNA in vitro is impaired by ATM-mediated phosphorylation. We propose that MRN is required for TRF1 phosphorylation by ATM and that such phosphorylation results in the release of TRF1 from telomeres, promoting telomerase access to the ends of telomeres.