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During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, σ A , and a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA of the RNAP-promoter open complex. The structures show that σ recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between σ and template-strand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.

Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. As increasing numbers of bacteria become resistant to antibiotics, new drugs are needed to fight bacterial infections. To develop new antibacterial drugs, researchers need to understand how existing antibiotics work. There are many ways to kill bacteria, but one of the most effective is to target an enzyme called bacterial RNA polymerase. If bacterial RNA polymerase is prevented from working, bacteria cannot synthesize RNA and cannot survive. GE23077 (GE for short) is an antibiotic produced by bacteria found in soil. Although GE stops bacterial RNA polymerase from working, and thereby kills bacteria, it does not affect mammalian RNA polymerases, and so does not kill mammalian cells. Understanding how GE works could help with the development of new antibacterial drugs. Zhang et al. present results gathered from a range of techniques to show how GE inhibits bacterial RNA polymerase. These show that GE works by binding to a site on RNA polymerase that is different from the binding sites of previously characterized antibacterial drugs. The mechanism used to inhibit the RNA polymerase is also different. The newly identified binding site has several features that make it an unusually attractive target for development of antibacterial compounds. Bacteria can become resistant to an antibiotic if genetic mutations lead to changes in the site the antibiotic binds to. However, the site that GE binds to on RNA polymerase is essential for RNA polymerase to function and so cannot readily be changed without crippling the enzyme. Therefore, this type of antibiotic resistance is less likely to develop. In addition, the newly identified binding site for GE on RNA polymerase is located next to the binding site for a current antibacterial drug, rifampin. Zhang et al. therefore linked GE and rifampin to form a two-part (‘bipartite’) compound designed to bind simultaneously to the GE and the rifampin binding sites. This compound was able to inhibit drug-resistant RNA polymerases tens to thousands of times more potently than GE or rifampin alone.

Background Mitochondrial dysfunction has been implicated in sarcopenia. 31P magnetic resonance spectroscopy (MRS) enables non‐invasive measurement of adenosine triphosphate (ATP) synthesis rates to probe mitochondrial function. Here, we assessed muscle energetics in older sarcopenic and non‐sarcopenic men and compared with muscle biopsy‐derived markers of mitochondrial function. Methods Twenty Chinese men with sarcopenia (SARC, age = 73.1 ± 4.1 years) and 19 healthy aged and sex‐matched controls (CON, age = 70.3 ± 4.2 years) underwent assessment of strength, physical performance, and magnetic resonance imaging. Concentrations of phosphocreatine (PCr), ATP and inorganic phosphate (Pi) as well as muscle pH were measured at rest and during an interleaved rest–exercise protocol to probe muscle mitochondrial function. Results were compared to biopsy‐derived mitochondrial complex activity and expression to understand underlying metabolic perturbations. Results Despite matched muscle contractile power (strength/cross‐sectional area), the ATP contractile cost was higher in SARC compared with CON (low‐intensity exercise: 1.06 ± 0.59 vs. 0.57 ± 0.22, moderate: 0.93 ± 0.43 vs. 0.58 ± 0.68, high: 0.70 ± 0.57 vs. 0.43 ± 0.51 mmol L−1 min−1 bar−1 cm−2, P = 0.003, <0.0001 and <0.0001, respectively). Post‐exercise mitochondrial oxidative synthesis rates (a marker of mitochondrial function) tended to be longer in SARC but did not reach significance (17.3 ± 6.4 vs. 14.6 ± 6.5 mmol L−1 min−1, P = 0.2). However, relative increases in end‐exercise ADP in SARC (31.8 ± 9.9 vs. 24.0 ± 7.3 mmol L−1, P = 0.008) may have been a compensatory mechanism. Mitochondrial complex activity was found to be associated with exercise‐induced drops in PCr [citrate synthetase activity (CS), Spearman correlation rho = −0.42, P = 0.03] and end‐exercise ADP (complex III, rho = −0.52, P = 0.01; CS rho = −0.45, P = 0.02; SDH rho = −0.45, P = 0.03), with CS also being strongly associated with the PCr recovery rate following low intensity exercise (rho = −0.47, P = 0.02), and the cost of contraction at high intensity (rho = −0.54, P = 0.02). Interestingly, at high intensity, the fractional contribution of oxidative phosphorylation to exercise was correlated with activity in complex II (rho = 0.5, P = 0.03), CS (rho = 0.47, P = 0.02) and SDH (rho = 0.46, P = 0.03), linking increased mitochondrial complex activity with increased ability to generate energy through oxidative pathways. Conclusions This study used 31P MRS to assess ATP utilization and resynthesis in sarcopenic muscle and demonstrated abnormal increases in the energy cost during exercise and perturbed mitochondrial energetics in recovery. Associations between mitochondrial complex activity and the fractional contribution to energy requirement during exercise indicate increased ability to generate energy oxidatively in those with better mitochondrial complex activity.

Genome-wide association studies (GWAS) of Alzheimer’s disease are predominantly carried out in European ancestry individuals despite the known variation in genetic architecture and disease prevalence across global populations. We leveraged published GWAS summary statistics from European, East Asian, and African American populations, and an additional GWAS from a Caribbean Hispanic population using previously reported genotype data to perform the largest multi-ancestry GWAS meta-analysis of Alzheimer’s disease and related dementias to date. This method allowed us to identify two independent novel disease-associated loci on chromosome 3. We also leveraged diverse haplotype structures to fine-map nine loci with a posterior probability >0.8 and globally assessed the heterogeneity of known risk factors across populations. Additionally, we compared the generalizability of multi-ancestry- and single-ancestry-derived polygenic risk scores in a three-way admixed Colombian population. Our findings highlight the importance of multi-ancestry representation in uncovering and understanding putative factors that contribute to risk of Alzheimer’s disease and related dementias.

Web-based interventions for depression that are supported by coaching have generally produced larger effect-sizes, relative to standalone web-based interventions. This is likely due to the effect of coaching on adherence. We evaluated the efficacy of a manualized telephone coaching intervention (TeleCoach) aimed at improving adherence to a web-based intervention (moodManager), as well as the relationship between adherence and depressive symptom outcomes. 101 patients with MDD, recruited from primary care, were randomized to 12 weeks moodManager+TeleCoach, 12 weeks of self-directed moodManager, or 6 weeks of a waitlist control (WLC). Depressive symptom severity was measured using the PHQ-9. TeleCoach+moodManager, compared to self-directed moodManager, resulted in significantly greater numbers of login days (p = 0.01), greater time until last use (p = 0.007), greater use of lessons (p = 0.03), greater variety of interactive tools used (p = 0.02), but total instances of tool use did not reach statistical significance. (p = 0.07). TeleCoach+moodManager produced significantly lower PHQ-9 scores relative to WLC at week 6 (p = 0.04), but there were no other significant differences in PHQ-9 scores at weeks 6 or 12 (ps>0.20) across treatment arms. Baseline PHQ-9 scores were no significantly related to adherence to moodManager. TeleCoach produced significantly greater adherence to moodManager, relative to self-directed moodManager. TeleCoached moodManager produced greater reductions in depressive symptoms relative to WLC, however, there were no statistically significant differences relative to self-directed moodManager. While greater use was associated with better outcomes, most users in both TeleCoach and self-directed moodManager had dropped out of treatment by week 12. Even with telephone coaching, adherence to web-based interventions for depression remains a challenge. Methods of improving coaching models are discussed. Clinicaltrials.gov NCT00719979.

ObjectiveIn Traditional Chinese medicine (TCM), syndrome differentiation is considered to be an essential diagnostic process for tailoring Chinese herbal medicine (CHM) treatments to individual patients. We conducted a meta-epidemiological study to evaluate the potential impact of syndrome differentiation on improving effect estimates in randomized controlled trials (RCTs).Study Design and SettingSeven databases were searched to identify systematic reviews (SRs) published between 2021 and 2022 that pooled RCTs evaluating CHM treatment effects or side effects. Meta-epidemiological analyses were conducted using a two-step approach. Subgroup analyses were performed based on the disease category, outcome nature, and funding.ResultsWe included 137 SRs comprising 2,064 RCTs. The results demonstrated small and statistically nonsignificant differences in both treatment effects (ROR: 0.93, 95% confidence interval (CI): 0.86 to 1.00,  = .04 for binary outcomes; dSMD: -1.44, 95% CI: -3.95 to 1.08,  = .26 for continuous outcomes) and side effects (ROR: 1.13, 95% CI: 0.66 to 1.92,  = .66) between RCTs that incorporated syndrome differentiation and those did not. Subgroup analysis showed RCTs of gastrointestinal disease that incorporated syndrome differentiation exhibited a larger magnitude of side effects than that did not. For binary outcomes, subgroup analyses of RCTs of circulatory diseases or those reporting subjective outcomes showed that syndrome differentiation led to a statistically significantly smaller treatment effect.ConclusionIndividualizing CHM treatments through syndrome differentiation provide no significant evidence of improvement in TCM practice outcomes in RCTs. Furthermore, subgroup analyses suggest that syndrome differentiation may be associated with a smaller treatment effect among RCTs of CHM for circulatory diseases and a possible trend toward increased side effects in patients with gastrointestinal diseases.

The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres. The evolution of domestic cotton plants A phylogenetic and genomic study of plants of the cotton genus Gossypium provides insights into the role of polyploidy in the angiosperm evolution, and specifically, in the emergence of spinnable fibres in domesticated cottons. The authors show that an abrupt five- to sixfold ploidy increase about 60 million years ago, and allopolyploidy reuniting divergent genomes approximately 1–2 million years ago, conferred a roughly 30-fold duplication of ancestral flowering plant genes in the 'elite' cottons G. hirsutum and G. barbadense compared to their presumed progenitor G. raimondii . Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments 1 . Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago 2 , conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons ( Gossypium hirsutum and Gossypium barbadense ), genetic complexity equalled only by Brassica 3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii . The sequence of a G. hirsutum A t D t (in which ‘t’ indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

Patients with atherosclerotic vascular disease were randomly assigned to receive the thrombin antagonist vorapaxar or placebo. Vorapaxar reduced the rate of subsequent cardiovascular death, myocardial infarction, or stroke but increased the rate of moderate or severe bleeding. Platelets play a central role in atherothrombosis and are an important target for pharmacotherapy. In patients with acute coronary syndromes, the use of potent platelet inhibitors has been shown to reduce the rate of thrombotic events at the cost of increased bleeding. 1 – 3 In contrast, among patients with stable atherosclerosis, a reduced rate of thrombotic events with antiplatelet therapy in addition to aspirin therapy has not been established. 4 Thrombin is a serine protease that is critical in thrombosis. In addition to generating fibrin, thrombin is a potent agonist of platelets through interaction with protease-activated receptors (PARs). 5 Vorapaxar (SCH 530348, Merck) . . .

Background Dementia shows sex difference in its epidemiology. Childbirth, a distinctive experience of women, is associated with the risk for various diseases. However, its association with the risk of dementia in women has rarely been studied. Methods We harmonized and pooled baseline data from 11 population-based cohorts from 11 countries over 3 continents, including 14,792 women aged 60 years or older. We investigated the association between parity and the risk of dementia using logistic regression models that adjusted for age, educational level, hypertension, diabetes mellitus, and cohort, with additional analyses by region and dementia subtype. Results Across all cohorts, grand multiparous (5 or more childbirths) women had a 47% greater risk of dementia than primiparous (1 childbirth) women (odds ratio [OR] = 1.47, 95% confidence interval [CI] = 1.10–1.94), while nulliparous (no childbirth) women and women with 2 to 4 childbirths showed a comparable dementia risk to primiparous women. However, there were differences associated with region and dementia subtype. Compared to women with 1 to 4 childbirths, grand multiparous women showed a higher risk of dementia in Europe (OR = 2.99, 95% CI = 1.38–6.47) and Latin America (OR = 1.49, 95% CI = 1.04–2.12), while nulliparous women showed a higher dementia risk in Asia (OR = 2.15, 95% CI = 1.33–3.47). Grand multiparity was associated with 6.9-fold higher risk of vascular dementia in Europe (OR = 6.86, 95% CI = 1.81–26.08), whereas nulliparity was associated with a higher risk of Alzheimer disease (OR = 1.91, 95% CI 1.07–3.39) and non-Alzheimer non-vascular dementia (OR = 3.47, 95% CI = 1.44–8.35) in Asia. Conclusion Parity is associated with women’s risk of dementia, though this is not uniform across regions and dementia subtypes.

Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (n DM  = 178,691, n noDM  = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN ) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM. A large-scale GWAS provides insight on diabetes-dependent genetic effects on the glomerular filtration rate, a common metric to monitor kidney health in disease.