Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli.

Ring-shaped DNA sliding clamps are essential for DNA replication and genome maintenance. Clamps need to be opened and chaperoned onto DNA by clamp loader complexes (CLCs). Detailed understanding of the mechanisms by which CLCs open and place clamps around DNA remains incomplete. Here, we present a series of six structures of the Escherichia coli CLC bound to an open or closed clamp prior to and after binding to a primer-template DNA, representing the most significant intermediates in the clamp loading process. We show that the ATP-bound CLC first binds to a clamp, then constricts to hold onto it. The CLC then expands to open the clamp with a gap large enough for double-stranded DNA to enter. Upon binding to DNA, the CLC constricts slightly, allowing clamp closing around DNA. These structures provide critical high-resolution snapshots of clamp loading by the E. coli CLC, revealing how the molecular machine works.

USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication.

Mammalian DNA replication relies on various DNA helicase and nuclease activities to ensure accurate genetic duplication, but how different helicase and nuclease activities are properly directed remains unclear. Here, we identify the ubiquitin-specific protease, USP50, as a chromatin-associated protein required to promote ongoing replication, fork restart, telomere maintenance, cellular survival following hydroxyurea or pyridostatin treatment, and suppression of DNA breaks near GC-rich sequences. We find that USP50 supports proper WRN-FEN1 localisation at or near stalled replication forks. Nascent DNA in cells lacking USP50 shows increased association of the DNA2 nuclease and RECQL4 and RECQL5 helicases and replication defects in cells lacking USP50, or FEN1 are driven by these proteins. Consequently, suppression of DNA2 or RECQL4/5 improves USP50-depleted cell resistance to agents inducing replicative stress and restores telomere stability. These data define an unexpected regulatory protein that promotes the balance of helicase and nuclease use at ongoing and stalled replication forks.

Repeated pulses of volcanism drove the end-Permian terrestrial crisis in northwest China.

The Permo-Triassic mass extinction was linked to catastrophic environmental changes and large igneous province (LIP) volcanism. In addition to the widespread marine losses, the Permo-Triassic event was the most severe terrestrial ecological crisis in Earth's history and the only known mass extinction among insects, but the cause of extinction on land remains unclear. In this study, high-resolution Hg concentration records and multiple-archive S-isotope analyses of sediments from the Junggar Basin (China) provide evidence of repeated pulses of volcanic-S (acid rain) and increased Hg loading culminating in a crisis of terrestrial biota in the Junggar Basin coeval with the interval of LIP emplacement. Minor S-isotope analyses are, however, inconsistent with total ozone layer collapse. Our data suggest that LIP volcanism repeatedly stressed end-Permian terrestrial environments in the ~300 kyr preceding the marine extinction locally via S-driven acidification and deposition of Hg, and globally via pulsed addition of CO2.

Selective Dissolution of Calcium Pyrophosphate Dihydrate Crystals Using a Pyrophosphate Specific Receptor.

Pseudo-gout is caused by the deposition of highly insoluble calcium pyrophosphate dihydrate (CPPD) crystals in the joints of sufferers. This leads to inflammation and ultimately joint damage. The insolubility of CPPD is driven by the strong attraction of di-cationic calcium ions with tetra-anionic pyrophosphate ions. One of the challenges of dissolving CPPD is that a related mineral, hydroxy apatite (HA) is present in larger amounts in the form of bone and also contains strongly interacting calcium and phosphate ions. Our aim in this work was to selectively dissolve CPPD in preference to HA. To accomplish this, we used a known receptor for pyrophosphate that contains two complexed zinc ions that are ideally spaced to interact with the tetra-anion of pyrophosphate. We hypothesized that such a molecule could act as a preorganized tetra-cation that would be able to outcompete the two calcium ions present in the crystal lattice of CPPD. We demonstrate both visually and through analysis of released phosphorous that this molecule is able to preferentially dissolve CPPD over the closely related HA and thus can form the basis for a possible approach for the treatment of pseudo-gout.

Placental Mosaicism for Autosomal Trisomies: Comprehensive Follow-up of 528 Danish Cases (1983-2021): Placental mosaicism for autosomal trisomies.

BACKGROUND: Mosaicism, characterized by the presence of two or more chromosomally distinct cell lines, is detected in 2-4% of chorionic villus samples. In these cases, the aberration may be confined to the placenta or additionally present in the fetus. Fetal involvement may manifest as fetal malformations, while confined placental mosaicism poses risks such as preterm birth and low birth weight. Differentiating between true fetal mosaicism and confined placental mosaicism at the time of the chorionic villus sampling is challenging and requires follow-up by an amniocentesis and ultrasonography. OBJECTIVES: To estimate the risk of fetal involvement or adverse pregnancy outcomes for specific chromosomes after detecting mosaicism for an autosomal trisomy in a chorionic villus sample and identify high (red), intermediate (yellow) and low (green) risk chromosomes. Further, to explore possible associations with level of mosaicism and screening parameters. STUDY DESIGN: A retrospective descriptive study of all singleton pregnancies with mosaicism detected in chorionic villus samples from 1983-2021 identified in the Danish Cytogenetic Central Registry and the Danish Fetal Medicine Database. RESULTS: Of 90,973 chorionic villus samples, 528 cases had mosaicism involving an autosomal trisomy and where genetic follow-up had been performed. The overall risk of fetal involvement was 13% (69/528) with extensive variations depending on which chromosome was involved (e.g., trisomy 7: 0% (0/55) or trisomy 21: 46% (19/41)). Higher levels of mosaicism in the chorionic villus sample suggested fetal involvement as mean mosaic level was 55% in true fetal mosaics vs 28% in cases confined to the placenta (p=0.0002). In cases with confined placental mosaicism (459/528), the risk of delivering small-for-gestational-age neonates was 14% (48/341). The risk of preterm birth (before 37 weeks) was 15% (51/343). The collective risk of adverse outcome was 22% (76/343) in pregnancies that continued and where information on birth weight and gestational age at birth was available. Adverse outcomes varied substantially between chromosomes. Also, multiple-of-the-median (MoM) values of pregnancy-associated plasma protein A was predictive of these issues as it was significantly lower in cases with adverse outcome compared to cases with a normal outcome (small for gestational age: 0.23 MoM vs 0.47 MoM, p<0.0001) or preterm birth: 0.25 MoM vs 0.47 MoM, p<0.0001). After the introduction of combined first trimester screening in 2004, the detection of cases with fetal involvement seemed to increase as the risk before 2004 was 9% (16/174) compared to 15% (53/354) after 2004 (risk ratio: 1.7 (95% CI: 1.0;2.8)). The risk of adverse outcome in confined placental mosaicism pregnancies increased from 16% (22/139) before 2004 to 27% (55/204) after 2004 (risk ratio 1.7 (95% CI: 1.1;2.7)) CONCLUSIONS: Introducing combined first trimester screening increased the detection of placental mosaicism with fetal involvement and confined placental mosaicism with adverse outcome. In cases of mosaicism in chorionic villus samples, the risk of fetal involvement and adverse outcomes varied considerably between chromosomes. Importantly, adverse outcomes were seen in confined placental mosaicism for many trisomies besides trisomy 16.

Prevalence and determinants of evidence of silicosis and impaired lung function among small scale tanzanite miners and the peri-mining community in northern Tanzania.

Limited data among miners in Tanzania suggests prevalence of silicosis, obstructive lung disease and restrictive lung disease to be around 1.6%, 1.9% and 8.8% respectively. Our study aimed to determine the prevalence and factors associated with silicosis and impaired lung function among tanzanite mining community in northern Tanzania. We conducted a cross-sectional study, involving 330 miners and 330 peri-mining community members in Mererani mines. Silicosis was defined based on study participants' history of exposure to mining dust and digital chest radiological findings with reference to the 2011 ILO classification of pneumoconiosis. Impaired lung function was determined by spirometry using American Thoracic Society/European Respiratory Society recommended system 3. Association between evidence of silicosis/impaired lung function and presumed risk factors were determined using binary logistic regression analyses. The study found that 99/330 (30.0%) of miners had silicosis. Total of 65 (9.8%) participants had impaired lung function, of whom 29 (4.4%) had Chronic Obstructive Pulmonary Disease, 32 (4.8%) had restrictive lung disease and 4 (0.6%) had both obstructive and restrictive lung diseases. Unexpectedly, miners who have worked for more than 10years and those worked for 6 to 10 years had 64% (aOR 0.34, CI = 0.17-0.67, p = 0.002) and 48% (aOR 0.52, CI = 0.30-0.89, p = 0.018) lower odds of having silicosis respectively compared those worked for up to 5 years. Participants with more than 10 years of work duration had more than 3-times higher odds of impaired lung function compared to those who had worked for up to 5 years (aOR 3.11, CI = 1.53-6.34, p<0.002). We found a concerningly high prevalence of silicosis despite short durations of exposure to occupational silica dust. Immediate dust control measures including deployment of wet drilling, wearing of personal protective equipment and regular monitoring of dust exposure need to be enforced by the Occupational Safety and Health Authority-Tanzania.

Longevity of a Brain-Computer Interface for Amyotrophic Lateral Sclerosis.

The durability of communication with the use of brain-computer interfaces in persons with progressive neurodegenerative disease has not been extensively examined. We report on 7 years of independent at-home use of an implanted brain-computer interface for communication by a person with advanced amyotrophic lateral sclerosis (ALS), the inception of which was reported in 2016. The frequency of at-home use increased over time to compensate for gradual loss of control of an eye-gaze-tracking device, followed by a progressive decrease in use starting 6 years after implantation. At-home use ended when control of the brain-computer interface became unreliable. No signs of technical malfunction were found. Instead, the amplitude of neural signals declined, and computed tomographic imaging revealed progressive atrophy, which suggested that ALS-related neurodegeneration ultimately rendered the brain-computer interface ineffective after years of successful use, although alternative explanations are plausible. (Funded by the National Institute on Deafness and Other Communication Disorders and others; ClinicalTrials.gov number, NCT02224469.).

The molecular structure of an axle-less F1-ATPase.

F1Fo ATP synthase is a molecular rotary motor that can generate ATP using a transmembrane proton motive force. Isolated F1-ATPase catalytic cores can hydrolyse ATP, passing through a series of conformational states involving rotation of the central γ rotor subunit and the opening and closing of the catalytic ß subunits. Cooperativity in F1-ATPase has long thought to be conferred through the γ subunit, with three key interaction sites between the γ and ß subunits being identified. Single molecule studies have demonstrated that the F1 complexes lacking the γ axle still "rotate" and hydrolyse ATP, but with less efficiency. We solved the cryogenic electron microscopy structure of an axle-less Bacillus sp. PS3 F1-ATPase. The unexpected binding-dwell conformation of the structure in combination with the observed lack of interactions between the axle-less γ and the open ß subunit suggests that the complete γ subunit is important for coordinating efficient ATP binding of F1-ATPase.

Machine learning demonstrates the impact of proton transfer and solvent dynamics on CO2 capture in liquid ammonia.

Direct air capture of CO2 using supported amines provides a promising means to achieve the net-zero greenhouse gas emissions goal; however, many mechanistic details regarding the CO2 adsorption process in condensed phase amines remain poorly understood. This work combines machine learning potentials, enhanced sampling and grand-canonical Monte Carlo simulations to directly compute experimentally relevant quantities to elucidate the mechanism of CO2 chemisorption in liquid ammonia as a model system. Our simulations suggest that CO2 capture in the liquid occurs in a sequential fashion, with the formation of a metastable zwitterion intermediate. Furthermore, we identified the importance of solvent-mediated proton transfer and solvent dynamics, not only in the reaction pathway but also in the efficiency of CO2 chemisorption. Beyond liquid ammonia, the methodology presented here can be readily extended to simulate amines with more complex chemical structures under experimental conditions, paving the way to elucidate the structure-performance of amines for CO2 capture.

Pre-operative chemoradiotherapy followed by mastectomy and breast reconstruction-A systematic review of clinical, oncological, reconstructive and aesthetic outcomes.

BACKGROUND: Pre-operative radiotherapy (PRT) and pre-operative chemoradiotherapy (PCRT) prior to mastectomy and immediate breast reconstruction for locally advanced breast cancer have the potential to reduce radiation late-effects and expedite oncologic treatment. Recent feasibility work indicates that PCRT is safe and technically possible. Here, we present a systematic review of currently available data on clinical, oncological, reconstructive and aesthetic outcomes. METHODS: A prospectively registered search of Medline (Ovid), EMBASE (Ovid), EMCARE (Ovid) and CINAHL (EBSCO) databases was performed in August 2023. Clinical, oncological, reconstructive and aesthetic outcomes were appraised with risk of bias (ROBINS-I) and methodological quality determined (STROBE checklist) for each study. RESULTS: Twenty-two published articles (19 journal articles and 3 abstracts) were identified reporting the outcomes of 1258 patients with median follow-up between 19.0-212.4 months. Patients received neoadjuvant chemotherapy in 20 studies. Rates of locoregional recurrence and overall survival ranged between 0-21.7% and 82.0%-98.3% respectively. Rates of flap loss or necrosis ranged from 0-7.6%. Rates of revisional procedures ranged between 1.9-35.3%. Patient-reported outcomes were reported in 7 studies and were mostly 'good' or 'excellent'. CONCLUSION: PRT and PCRT preceding mastectomy and breast reconstruction produce acceptable oncological outcomes with rates of surgical complication and reconstructive outcomes within normal limits, however, the majority of available studies are of low methodological quality and at high risk of bias. A pragmatic randomised trial comparing PRT versus PMRT in the setting of breast reconstruction is now urgently required to guide surgical practice.