Structural basis of a transcription pre-initiation complex on a divergent promoter.

Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.

Archaic chaperone-usher pili self-secrete into superelastic zigzag springs.

Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria1-3. Archaic chaperone-usher pathway pili, the most diverse and widespread chaperone-usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens1,4,5. However, their architecture and assembly-secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii-a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed for the first time, to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.

Toxoplasma gondii rhoptry discharge factor 3 is essential for invasion and microtubule-associated vesicle biogenesis.

Rhoptries are specialized secretory organelles conserved across the Apicomplexa phylum, essential for host cell invasion and critical for subverting of host cellular and immune functions. They contain proteins and membranous materials injected directly into the host cells, participating in parasitophorous vacuole formation. Toxoplasma gondii tachyzoites harbor 8 to 12 rhoptries, 2 of which are docked to an apical vesicle (AV), a central element associated with a rhoptry secretory apparatus prior to injection into the host cell. This parasite is also equipped with 5 to 6 microtubule-associated vesicles, presumably serving as AV replenishment for iterative rhoptry discharge. Here, we characterized a rhoptry protein, rhoptry discharge factor 3 (RDF3), crucial for rhoptry discharge and invasion. RDF3 enters the secretory pathway, localizing near the AV and associated with the rhoptry bulb. Upon invasion, RDF3 dynamically delocalizes, suggesting a critical role at the time of rhoptry discharge. Cryo-electron tomography analysis of RDF3-depleted parasites reveals irregularity in microtubule-associated vesicles morphology, presumably impacting on their preparedness to function as an AV. Our findings suggest that RDF3 is priming the microtubule-associated vesicles for rhoptry discharge by a mechanism distinct from the rhoptry secretory apparatus contribution.

Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors.

The process by which bacterial cells build their intricate flagellar motility apparatuses has long fascinated scientists. Our understanding of this process comes mainly from studies of purified flagella from two species, Escherichia coli and Salmonella enterica. Here, we used electron cryo-tomography (cryo-ET) to image the assembly of the flagellar motor in situ in diverse Proteobacteria: Hylemonella gracilis, Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Shewanella oneidensis. Our results reveal the in situ structures of flagellar intermediates, beginning with the earliest flagellar type III secretion system core complex (fT3SScc) and MS-ring. In high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, we discovered novel cytoplasmic rings that interact with the cytoplasmic torque ring formed by FliG. These rings, associated with the MS-ring, assemble very early and persist until the stators are recruited into their periplasmic ring; in their absence the stator ring does not assemble. By imaging mutants in Helicobacter pylori, we found that the fT3SScc proteins FliO and FliQ are required for the assembly of these novel cytoplasmic rings. Our results show that rather than a simple accretion of components, flagellar motor assembly is a dynamic process in which accessory components interact transiently to assist in building the complex nanomachine.

An apical membrane complex for triggering rhoptry exocytosis and invasion in Toxoplasma.

Apicomplexan parasites possess secretory organelles called rhoptries that undergo regulated exocytosis upon contact with the host. This process is essential for the parasitic lifestyle of these pathogens and relies on an exocytic machinery sharing structural features and molecular components with free-living ciliates. However, how the parasites coordinate exocytosis with host interaction is unknown. Here, we performed a Tetrahymena-based transcriptomic screen to uncover novel exocytic factors in Ciliata and conserved in Apicomplexa. We identified membrane-bound proteins, named CRMPs, forming part of a large complex essential for rhoptry secretion and invasion in Toxoplasma. Using cutting-edge imaging tools, including expansion microscopy and cryo-electron tomography, we show that, unlike previously described rhoptry exocytic factors, TgCRMPs are not required for the assembly of the rhoptry secretion machinery and only transiently associate with the exocytic site-prior to the invasion. CRMPs and their partners contain putative host cell-binding domains, and CRMPa shares similarities with GPCR proteins. Collectively our data imply that the CRMP complex acts as a host-molecular sensor to ensure that rhoptry exocytosis occurs when the parasite contacts the host cell.

High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering.

Cryoelectron tomography directly visualizes heterogeneous macromolecular structures in their native and complex cellular environments. However, existing computer-assisted structure sorting approaches are low throughput or inherently limited due to their dependency on available templates and manual labels. Here, we introduce a high-throughput template-and-label-free deep learning approach, Deep Iterative Subtomogram Clustering Approach (DISCA), that automatically detects subsets of homogeneous structures by learning and modeling 3D structural features and their distributions. Evaluation on five experimental cryo-ET datasets shows that an unsupervised deep learning based method can detect diverse structures with a wide range of molecular sizes. This unsupervised detection paves the way for systematic unbiased recognition of macromolecular complexes in situ.

Diagnostic meta-analysis of the efficacy of ultrasonography for diagnosing carpal tunnel syndrome: A comparison between Asian and non-Asian populations.

BACKGROUND: Ultrasonography is used to diagnose carpal tunnel syndrome (CTS) according to various criteria. This diagnostic meta-analysis aimed to evaluate the efficacy of ultrasonography for diagnosing CTS, focusing on the cross-sectional area (CSA) of the median nerve (MN) at the inlet of the carpal tunnel and regional variations in diagnostic thresholds between Asian and non-Asian populations. METHODS: A comprehensive literature search was conducted using PubMed, Embase, and the Cochrane Library. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2). Patient demographic data, diagnostic "gold standards", CSA cutoff values, and diagnostic results were extracted. Meta-analysis was performed to determine the sensitivity, specificity, and optimal CSA cutoff values. RESULTS: For the 25 included studies, a combined sensitivity of 88% and specificity of 84% for CSA measurements at the carpal tunnel inlet were obtained. The Asian group had a sensitivity of 84% and specificity of 86%, while the non-Asian group had a sensitivity of 91% and specificity of 82%. The mean CSA in the Asian group was significantly lower than that in the non-Asian group (12.93 mm2 and 14.77 mm2, respectively; p = 0.042). For the Asian group, the summary receiver operating characteristic curve had an area under the curve (AUC) of 0.92 with an optimal cutoff of 10.5 mm2; for the non-Asian group, an AUC of 0.94 was obtained with a cutoff of 11.5 mm2. CONCLUSION: Ultrasonography is a reliable diagnostic method for CTS, with distinct optimal cutoff values observed between Asian and non-Asian populations. Therefore, population-specific diagnostic criteria for CTS are recommended.

Nanoscale details of mitochondrial constriction revealed by cryoelectron tomography.

Mitochondria adapt to changing cellular environments, stress stimuli, and metabolic demands through dramatic morphological remodeling of their shape, and thus function. Such mitochondrial dynamics is often dependent on cytoskeletal filament interactions. However, the precise organization of these filamentous assemblies remains speculative. Here, we apply cryogenic electron tomography to directly image the nanoscale architecture of the cytoskeletal-membrane interactions involved in mitochondrial dynamics in response to damage. We induced mitochondrial damage via membrane depolarization, a cellular stress associated with mitochondrial fragmentation and mitophagy. We find that, in response to acute membrane depolarization, mammalian mitochondria predominantly organize into tubular morphology that abundantly displays constrictions. We observe long bundles of both unbranched actin and septin filaments enriched at these constrictions. We also observed septin-microtubule interactions at these sites and elsewhere, suggesting that these two filaments guide each other in the cytosolic space. Together, our results provide empirical parameters for the architecture of mitochondrial constriction factors to validate/refine existing models and inform the development of new ones.

A hydrophilic polyimidazolium antibiotic targeting the membranes of Gram-negative bacteria.

OBJECTIVES: The rise of MDR Gram-negative bacteria (GNB), especially those resistant to last-resort drugs such as carbapenems and colistin, is a global health risk and calls for increased efforts to discover new antimicrobial compounds. We previously reported that polyimidazolium (PIM) compounds exhibited significant antimicrobial activity and minimal mammalian cytotoxicity. However, their mechanism of action is relatively unknown. We examined the efficacy and mechanism of action of a hydrophilic PIM (PIM5) against colistin- and meropenem-resistant clinical isolates. METHODS: MIC and time-kill testing was performed for drug-resistant Escherichia coli and Klebsiella pneumoniae clinical isolates. N-phenyl-1-naphthylamine and propidium iodide dyes were employed to determine membrane permeabilization. Spontaneous resistant mutants and single deletion mutants were generated to understand potential resistance mechanisms to the drug. RESULTS: PIM5 had the same effectiveness against colistin- and meropenem-resistant strains as susceptible strains of GNB. PIM5 exhibited a rapid bactericidal effect independent of bacterial growth phase and was especially effective in water. The polymer disrupts both the outer and cytoplasmic membranes. PIM5 binds and intercalates into bacterial genomic DNA upon entry of cells. GNB do not develop high resistance to PIM5. However, the susceptibility and uptake of the polymer is moderately affected by mutations in the two-component histidine kinase sensor BaeS. PIM5 has negligible cytotoxicity on human cells at bacterial-killing concentrations, comparable to the commercial antibiotics polymyxin B and colistin. CONCLUSIONS: PIM5 is a potent broad-spectrum antibiotic targeting GNB resistant to last-resort antibiotics.

Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient.

The bacterial flagellum is an amazing nanomachine. Understanding how such complex structures arose is crucial to our understanding of cellular evolution. We and others recently reported that in several Gammaproteobacterial species, a relic subcomplex comprising the decorated P and L rings persists in the outer membrane after flagellum disassembly. Imaging nine additional species with cryo-electron tomography, here, we show that this subcomplex persists after flagellum disassembly in other phyla as well. Bioinformatic analyses fail to show evidence of any recent horizontal transfers of the P- and L-ring genes, suggesting that this subcomplex and its persistence is an ancient and conserved feature of the flagellar motor. We hypothesize that one function of the P and L rings is to seal the outer membrane after motor disassembly.

Discovery of a Novel Inner Membrane-Associated Bacterial Structure Related to the Flagellar Type III Secretion System.

The bacterial flagellar type III secretion system (fT3SS) is a suite of membrane-embedded and cytoplasmic proteins responsible for building the flagellar motility machinery. Homologous nonflagellar (NF-T3SS) proteins form the injectisome machinery that bacteria use to deliver effector proteins into eukaryotic cells, and other family members were recently reported to be involved in the formation of membrane nanotubes. Here, we describe a novel, evolutionarily widespread, hat-shaped structure embedded in the inner membranes of bacteria, of yet-unidentified function, that is present in species containing fT3SS. Mutant analysis suggests a relationship between this novel structure and the fT3SS, but not the NF-T3SS. While the function of this novel structure remains unknown, we hypothesize that either some of the fT3SS proteins assemble within the hat-like structure, perhaps including the fT3SS core complex, or that fT3SS components regulate other proteins that form part of this novel structure. IMPORTANCE The type III secretion system (T3SS) is a fascinating suite of proteins involved in building diverse macromolecular systems, including the bacterial flagellar motility machine, the injectisome machinery that bacteria use to inject effector proteins into host cells, and probably membrane nanotubes which connect bacterial cells. Here, we accidentally discovered a novel inner membrane-associated complex related to the flagellar T3SS. Examining our lab database, which is comprised of more than 40,000 cryo-tomograms of dozens of species, we discovered that this novel structure is both ubiquitous and ancient, being present in highly divergent classes of bacteria. Discovering a novel, widespread structure related to what are among the best-studied molecular machines in bacteria will open new venues for research aiming at understanding the function and evolution of T3SS proteins.

Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography.

MOTIVATION: Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning-based subtomogram classification has played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset. RESULTS: To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labeling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. This strategy enforces the model to be aware of the inductive bias during classification and subtomogram selection, which satisfies the discriminativeness principle in AL literature. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Such query strategy encourages to match the data distribution between the labeled and unlabeled subtomogram samples, which essentially encodes the representativeness criterion into the subtomogram selection process. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources. AVAILABILITY AND IMPLEMENTATION: https://github.com/xulabs/aitom. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Functional Outcomes and Physical Performance of Knee Osteoarthritis Patients After Ultrasound-Guided Genicular Nerve Radiofrequency Ablation.

OBJECTIVE: To elucidate the effectiveness of ultrasound-guided genicular nerve radiofrequency ablation in alleviating pain as well as its effects on functional outcomes, quality of life and physical performance in knee osteoarthritis patients. DESIGN: Prospective observational study. SETTING: Patients were recruited within one community hospital. SUBJECTS: Patients with knee osteoarthritis. METHODS: The subjects underwent ultrasound-guided radiofrequency ablation of genicular nerves after showing a positive response to a diagnostic block. Outcome assessments were performed at baseline and at 2 and 12 weeks posttreatments using the 36-item Short Form Health Survey (SF-36), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and a physical performance evaluation including balance tests, quadriceps muscle strength test, two-minute walking test and knee joint proprioception test. RESULTS: Thirteen out of 38 patients were eligible for genicular nerve radiofrequency ablation. There were significant improvements from baseline to posttreatment in the numeric rating scale score, physical health domain score of SF-36, and pain and stiffness domain scores of the WOMAC. Regarding physical performance, the step test result significantly improved over the 12 weeks of follow-up. On the other hand, no significant deteriorations in the single leg stance test, isokinetic quadriceps muscle strength test, knee joint proprioception test or two-minute walking test results were observed after radiofrequency ablation of genicular nerves. CONCLUSIONS: Radiofrequency ablation of genicular nerves may significantly alleviate pain and improve functional outcomes in knee osteoarthritis patients. More importantly, static balance control and quadriceps muscle strength were preserved and there was a change of proprioception in the good direction.

The successful rehabilitation of a 75-year-old female with debilitating long COVID: A case report.

A 75-year-old previously healthy female became severely ill, functionally dependent, and required long-term home oxygen therapy, after recovery from coronavirus disease 2019 (COVID-19) with acute respiratory failure and extensive pulmonary fibrosis. After two months of respiratory muscle training and a comprehensive cardiopulmonary rehabilitation program, her dyspnea, physical performance, pulmonary function parameters, and activities of daily living rapidly improved. This Case highlights the importance of a timely active rehabilitation program for COVID-19 survivors experiencing the long-term effects of coronavirus (long COVID).

Short FtsZ filaments can drive asymmetric cell envelope constriction at the onset of bacterial cytokinesis.

FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ filaments and their role in division continue to be debated. Here, we apply electron cryotomography to image the native structure of intact dividing cells and show that constriction in a variety of Gram-negative bacterial cells, including Proteus mirabilis and Caulobacter crescentus, initiates asymmetrically, accompanied by asymmetric peptidoglycan incorporation and short FtsZ-like filament formation. These results show that a complete ring of FtsZ is not required for constriction and lead us to propose a model for FtsZ-driven division in which short dynamic FtsZ filaments can drive initial peptidoglycan synthesis and envelope constriction at the onset of cytokinesis, later increasing in length and number to encircle the division plane and complete constriction.

Influence of temperature on sonographic images of the median nerve for the diagnosis of carpal tunnel syndrome: a case control study.

BACKGROUND: In addition to nerve conduction studies (NCSs), ultrasonography has been widely used as an alternative tool for diagnosing carpal tunnel syndrome (CTS). Although the results of NCSs are influenced by local skin temperature, few studies have explored the effects of skin temperature on ultrasonography of the median nerve. Since swelling and intraneural blood flow of the median nerve might be influenced by local temperature changes, the aim of this study was to evaluate the cross-sectional area (CSA) and intraneural blood flow of the median nerve under three skin temperatures (30 °C, 32 °C, 34 °C). METHODS: Fifty patients with CTS and 50 healthy volunteers were consecutively recruited from a community hospital. Each participant received physical examinations and NCSs and underwent ultrasonography, including power Doppler, to evaluate intraneural vascularity. RESULTS: The CSA of the median nerve in the CTS patients was significantly larger than that in the healthy controls at all three temperatures. However, significant differences in the power Doppler signals of the median nerve between the two studied groups were observed only at 30 and 32 °C, not at 34 °C. CONCLUSION: The significant difference in the intraneural vascularity of the median nerve between the patients with CTS and the healthy subjects was lost at higher temperatures (34 °C). Therefore, the results of power Doppler ultrasonography in diagnosing CTS should be cautiously interpreted in patients with a high skin temperature or those who reside in warm environments.

Improved Dynamics of Thoracic Cage and Exercise Capacity after Nuss Repair for Pectus Excavatum.

BACKGROUND: Pectus excavatum (PE) reduces the dynamics of the thoracic cage, with a negative impact on exercise capacity. We aimed to evaluate the effects of Nuss repair for PE on the dynamics of the thoracic cage and exercise capacity in adults. METHODS: This was a prospective observational study of 46 adults (mean age, 26.2 years) who underwent PE correction using the Nuss procedure between September 2016 and August 2017. Cirtometry was used to obtain measures of thoracic cage circumference at two levels (axillary level [AL] and xyphoid level [XL]), at the end points of inspiration and expiration. Circumference measures were obtained before surgery and at 1, 3, and 6 months after surgery. Exercise capacity was also evaluated using the 6-minute walk test (6MWT). The association between the 6MWT data and cirtometry measures was evaluated using Pearson's correlation. RESULTS: The circumference at maximum inspiration increased from baseline to 3 months after surgery (p < 0.01), at both the AL (84.5 ± 4.9 vs. 88.5 ± 5.1 cm) and XL (80.1 ± 4.8 vs. 83.7 ± 5.1 cm). The 6MWT also significantly improved from baseline to 3 months after surgical correction (544.7 ± 64.1 vs. 637.3 ± 59.4 m, p < 0.01), with this improvement being correlated to the increase in thoracic circumference on maximal inspiration at both the AL and XL (0.8424 and 0.7951, respectively). CONCLUSION: Improved dynamics of the thoracic cage were achieved after Nuss repair for PE in adults. This increase in thoracic circumference at maximum inspiration was associated with an improvement in exercise capacity at 3 months after surgery.

Polar delivery of Legionella type IV secretion system substrates is essential for virulence.

A recurrent emerging theme is the targeting of proteins to subcellular microdomains within bacterial cells, particularly to the poles. In most cases, it has been assumed that this localization is critical to the protein's function. Legionella pneumophila uses a type IVB secretion system (T4BSS) to export a large number of protein substrates into the cytoplasm of host cells. Here we show that the Legionella export apparatus is localized to the bacterial poles, as is consistent with many T4SS substrates being retained on the phagosomal membrane adjacent to the poles of the bacterium. More significantly, we were able to demonstrate that polar secretion of substrates is critically required for Legionella's alteration of the host endocytic pathway, an activity required for this pathogen's virulence.

In vivo structures of an intact type VI secretion system revealed by electron cryotomography.

The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like structure anchored in the bacterial cell envelope via a cytoplasmic baseplate and a periplasmic membrane complex. Rapid contraction of the sheath in the bacteriophage tail-like structure propels an inner tube/spike complex through the target cell envelope to deliver effectors. While structures of purified contracted sheath and purified membrane complex have been solved, because sheaths contract upon cell lysis and purification, no structure is available for the extended sheath. Structural information about the baseplate is also lacking. Here, we use electron cryotomography to directly visualize intact T6SS structures inside Myxococcus xanthus cells. Using sub-tomogram averaging, we resolve the structure of the extended sheath and membrane-associated components including the baseplate. Moreover, we identify novel extracellular bacteriophage tail fiber-like antennae. These results provide new structural insights into how the extended sheath prevents premature disassembly and how this sophisticated machine may recognize targets.

In situ structure of the Legionella Dot/Icm type IV secretion system by electron cryotomography.

Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron cryotomography (ECT), we report the in situ structure of the Dot/Icm type IVB secretion system (T4BSS) utilized by the human pathogen Legionella pneumophila This is the first structure of a type IVB secretion system, and also the first structure of any T4SS in situ While the Dot/Icm system shares almost no sequence similarity with type IVA secretion systems (T4ASSs), its overall structure is seen here to be remarkably similar to previously reported T4ASS structures (those encoded by the R388 plasmid in Escherichia coli and the cag pathogenicity island in Helicobacter pylori). This structural similarity suggests shared aspects of mechanism. However, compared to the negative-stain reconstruction of the purified T4ASS from the R388 plasmid, the L. pneumophila Dot/Icm system is approximately twice as long and wide and exhibits several additional large densities, reflecting type-specific elaborations and potentially better structural preservation in situ.