Centromeres as universal hotspots of DNA breakage, driving RAD51-mediated recombination during quiescence.

Centromeres are essential for chromosome segregation in most animals and plants yet are among the most rapidly evolving genome elements. The mechanisms underlying this paradoxical phenomenon remain enigmatic. Here, we report that human centromeres innately harbor a striking enrichment of DNA breaks within functionally active centromere regions. Establishing a single-cell imaging strategy that enables comparative assessment of DNA breaks at repetitive regions, we show that centromeric DNA breaks are induced not only during active cellular proliferation but also de novo during quiescence. Markedly, centromere DNA breaks in quiescent cells are resolved enzymatically by the evolutionarily conserved RAD51 recombinase, which in turn safeguards the specification of functional centromeres. This study highlights the innate fragility of centromeres, which may have been co-opted over time to reinforce centromere specification while driving rapid evolution. The findings also provide insights into how fragile centromeres are likely to contribute to human disease.

DNA strand breaks at centromeres: Friend or foe?

Centromeres are large structural regions in the genomic DNA, which are essential for accurately transmitting a complete set of chromosomes to daughter cells during cell division. In humans, centromeres consist of highly repetitive α-satellite DNA sequences and unique epigenetic components, forming large proteinaceous structures required for chromosome segregation. Despite their biological importance, there is a growing body of evidence for centromere breakage across the cell cycle, including periods of quiescence. In this review, we provide an up-to-date examination of the distinct centromere environments at different stages of the cell cycle, highlighting their plausible contribution to centromere breakage. Additionally, we explore the implications of these breaks on centromere function, both in terms of negative consequences and potential positive effects.

Plasticity of ether lipids promotes ferroptosis susceptibility and evasion.

Ferroptosis-an iron-dependent, non-apoptotic cell death process-is involved in various degenerative diseases and represents a targetable susceptibility in certain cancers1. The ferroptosis-susceptible cell state can either pre-exist in cells that arise from certain lineages or be acquired during cell-state transitions2-5. However, precisely how susceptibility to ferroptosis is dynamically regulated remains poorly understood. Here we use genome-wide CRISPR-Cas9 suppressor screens to identify the oxidative organelles peroxisomes as critical contributors to ferroptosis sensitivity in human renal and ovarian carcinoma cells. Using lipidomic profiling we show that peroxisomes contribute to ferroptosis by synthesizing polyunsaturated ether phospholipids (PUFA-ePLs), which act as substrates for lipid peroxidation that, in turn, results in the induction of ferroptosis. Carcinoma cells that are initially sensitive to ferroptosis can switch to a ferroptosis-resistant state in vivo in mice, which is associated with extensive downregulation of PUFA-ePLs. We further find that the pro-ferroptotic role of PUFA-ePLs can be extended beyond neoplastic cells to other cell types, including neurons and cardiomyocytes. Together, our work reveals roles for the peroxisome-ether-phospholipid axis in driving susceptibility to and evasion from ferroptosis, highlights PUFA-ePL as a distinct functional lipid class that is dynamically regulated during cell-state transitions, and suggests multiple regulatory nodes for therapeutic interventions in diseases that involve ferroptosis.

Tocilizumab in Hospitalized Patients with Severe Covid-19 Pneumonia.

BACKGROUND: Coronavirus disease 2019 (Covid-19) is associated with immune dysregulation and hyperinflammation, including elevated interleukin-6 levels. The use of tocilizumab, a monoclonal antibody against the interleukin-6 receptor, has resulted in better outcomes in patients with severe Covid-19 pneumonia in case reports and retrospective observational cohort studies. Data are needed from randomized, placebo-controlled trials. METHODS: In this phase 3 trial, we randomly assigned patients who were hospitalized with severe Covid-19 pneumonia in a 2:1 ratio receive a single intravenous infusion of tocilizumab (at a dose of 8 mg per kilogram of body weight) or placebo. Approximately one quarter of the participants received a second dose of tocilizumab or placebo 8 to 24 hours after the first dose. The primary outcome was clinical status at day 28 on an ordinal scale ranging from 1 (discharged or ready for discharge) to 7 (death) in the modified intention-to-treat population, which included all the patients who had received at least one dose of tocilizumab or placebo. RESULTS: Of the 452 patients who underwent randomization, 438 (294 in the tocilizumab group and 144 in the placebo group) were included in the primary and secondary analyses. The median value for clinical status on the ordinal scale at day 28 was 1.0 (95% confidence interval [CI], 1.0 to 1.0) in the tocilizumab group and 2.0 (non-ICU hospitalization without supplemental oxygen) (95% CI, 1.0 to 4.0) in the placebo group (between-group difference, -1.0; 95% CI, -2.5 to 0; P = 0.31 by the van Elteren test). In the safety population, serious adverse events occurred in 103 of 295 patients (34.9%) in the tocilizumab group and in 55 of 143 patients (38.5%) in the placebo group. Mortality at day 28 was 19.7% in the tocilizumab group and 19.4% in the placebo group (weighted difference, 0.3 percentage points; 95% CI, -7.6 to 8.2; nominal P = 0.94). CONCLUSIONS: In this randomized trial involving hospitalized patients with severe Covid-19 pneumonia, the use of tocilizumab did not result in significantly better clinical status or lower mortality than placebo at 28 days. (Funded by F. Hoffmann-La Roche and the Department of Health and Human Services; COVACTA ClinicalTrials.gov number, NCT04320615.).

Experimental Open Air Burning of Vegetation Enhances Organic Matter Chemical Heterogeneity Compared to Laboratory Burns.

Wildfires produce solid residuals that have unique chemical and physical properties compared to unburned materials, which influence their cycling and fate in the natural environment. Visual burn severity assessment is used to evaluate post-fire alterations to the landscape in field-based studies, yet muffle furnace methods are commonly used in laboratory studies to assess molecular scale alterations along a temperature continuum. Here, we examined solid and leachable organic matter characteristics from chars visually characterized as low burn severity that were created either on an open air burn table or from low-temperature muffle furnace burns. We assessed how the different combustion conditions influence solid and dissolved organic matter chemistries and explored the potential influence of these results on the environmental fate and reactivity. Notably, muffle furnace chars produced less leachable carbon and nitrogen than open air chars across land cover types. Organic matter produced from muffle furnace burns was more homogeneous than open air chars. This work highlights chemical heterogeneities that exist within a single burn severity category, potentially influencing our conceptual understanding of pyrogenic organic matter cycling in the natural environment, including transport and processing in watersheds. Therefore, we suggest that open air burn studies are needed to further advance our understanding of pyrogenic organic matter's environmental reactivity and fate.

Surgical Management of Vascular Malformations of the Upper Extremity: A 12-Year Retrospective Cohort Study.

INTRODUCTION: Vascular malformations (VMs) typically appear at birth and grow commensurately with patients. They can vary broadly in vessel type and tissue involvement, and upper extremity (UE) VMs can pose unique functional and aesthetic challenges in children. Given the advent of operative and nonoperative technologies like sclerotherapy and medications, a contemporary review of the surgical management of UE VMs is warranted. METHODS: We performed a retrospective review of all patients who had surgical management of VMs from 2010 to 2021 at The Children's Hospital of Philadelphia. Demographics, lesion characteristics, treatment (including preceding nonsurgical therapies), complications, and final outcomes were recorded. Operative notes were reviewed for date of operation, depth of excision, type of closure, and current procedural terminology code. RESULTS: Sixty-seven patients with 88 procedures were studied. Average patient age was 5.8 years, with 64% White and 67% male. Venous (34%) and lymphatic (19%) malformations were most common, and anatomic locations were most frequently on the hand (33%) and forearm (25%). The average lesion diameter was 4.2 cm, although this varied by location (eg, 2.9 cm, hand; 11.1 cm, chest wall). Fifty-eight patients (87%) underwent surgical excision as their index procedure, and 9 had sclerotherapy before surgery. Thirty-nine patients (60%) had subcutaneous excisions, and the remainder required subfascial or intramuscular excisions. Nearly all excisions were closed primarily (97%). Of the 53 patients with documented follow-up, 32 patients (60%) had complete resolution of their lesion as of their final visit. Thirty of these 32 patients with no clinical evidence of residual VM had only 1 surgery for excision. CONCLUSION: Upper extremity VMs were composed of diverse conditions with varying vessel types, size, depth, and anatomic sites. Surgical excision of VMs of the UE was safe and effective. A majority of VMs were fully excised after 1 procedure and frequently closed primarily with relatively low complication rates. Future work should investigate decision-making and outcomes of all treatment options of VMs of the UE for optimal functionality and aesthetics.

Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential.

While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.

Rethinking Aerobic Respiration in the Hyporheic Zone under Variation in Carbon and Nitrogen Stoichiometry.

Hyporheic zones (HZs)─zones of groundwater-surface water mixing─are hotspots for dissolved organic matter (DOM) and nutrient cycling that can disproportionately impact aquatic ecosystem functions. However, the mechanisms affecting DOM metabolism through space and time in HZs remain poorly understood. To resolve this gap, we investigate a recently proposed theory describing trade-offs between carbon (C) and nitrogen (N) limitations as a key regulator of HZ metabolism. We propose that throughout the extent of the HZ, a single process like aerobic respiration (AR) can be limited by both DOM thermodynamics and N content due to highly variable C/N ratios over short distances (centimeter scale). To investigate this theory, we used a large flume, continuous optode measurements of dissolved oxygen (DO), and spatially and temporally resolved molecular analysis of DOM. Carbon and N limitations were inferred from changes in the elemental stoichiometric ratio. We show sequential, depth-stratified relationships of DO with DOM thermodynamics and organic N that change across centimeter scales. In the shallow HZ with low C/N, DO was associated with the thermodynamics of DOM, while deeper in the HZ with higher C/N, DO was associated with inferred biochemical reactions involving organic N. Collectively, our results suggest that there are multiple competing processes that limit AR in the HZ. Resolving this spatiotemporal variation could improve predictions from mechanistic models, either via more highly resolved grid cells or by representing AR colimitation by DOM thermodynamics and organic N.

An Evolution of the Surgical Management of Synpolydactyly: A Case Series of 21 Hands.

INTRODUCTION: Synpolydactyly is a rare congenital anomaly characterized by syndactyly and polydactyly in the central hand. Limited treatment guidelines exist for this complex condition. METHODS: A retrospective review of synpolydactyly patients was conducted at a large, tertiary pediatric referral center to describe our surgical experience and evolution of management. The Wall classification system was used to categorize cases. RESULTS: Eleven patients (21 hands) with synpolydactyly were identified. Most of the patients were White and had at least one first-degree relative who also had synpolydactyly. The Wall classification yielded the following results: 7 type 1A hands, 4 type 2B hands, 6 type 3 hands, and 4 uncategorizable hands. Each patient had an average of 2.6 surgeries and an average follow-up time of 5.2 years. The rates of postoperative angulation and flexion deformities were 24% and 38%, respectively, with many of these cases also demonstrating preoperative alignment abnormalities. These cases often required additional surgeries including osteotomies, capsulectomies, and/or soft tissue releases. The rate of web creep was 14% with 2 of these patients requiring revision surgery. Despite these findings, at the time of final follow-up, most patients had favorable functional outcomes, were able to engage in bimanual tasks, and were able to perform activities of daily living independently. CONCLUSIONS: Synpolydactyly is a rare congenital hand anomaly with a significant degree of variability in clinical presentation. The rates of angulation and flexion deformities as well as web creep are not insignificant. We have learned to prioritize correcting contractures, angulation deformities, and skin fusion, over simply trying to delete the "extra" number of bones as this may destabilize the digit(s).

Cytochrome P450 oxidoreductase contributes to phospholipid peroxidation in ferroptosis.

Ferroptosis is widely involved in degenerative diseases in various tissues including kidney, liver and brain, and is a targetable vulnerability in multiple primary and therapy-resistant cancers. Accumulation of phospholipid hydroperoxides in cellular membranes is the hallmark and rate-limiting step of ferroptosis; however, the enzymes contributing to lipid peroxidation remain poorly characterized. Using genome-wide, CRISPR-Cas9-mediated suppressor screens, we identify cytochrome P450 oxidoreductase (POR) as necessary for ferroptotic cell death in cancer cells exhibiting inherent and induced susceptibility to ferroptosis. By genetic depletion of POR in cancer cells, we reveal that POR contributes to ferroptosis across a wide range of lineages and cell states, and in response to distinct mechanisms of ferroptosis induction. Using systematic lipidomic profiling, we further map POR's activity to the lipid peroxidation step in ferroptosis. Hence, our work suggests that POR is a key mediator of ferroptosis and potential druggable target for developing antiferroptosis therapeutics.

The immune cell profile of the developing rat brain.

Little is known about the peripheral immune cell (PIC) profile of the developing brain despite growing appreciation for these cells in the mature nervous system. To address this gap, the PIC profile, defined as which cells are present, where they are located, and for how long, was examined in the developing rat using spectral flow cytometry. Select regions of the rat brain (cerebellum, hippocampus, and hypothalamus) were examined at embryonic day 20, and postnatal days 0, 7 and 16. At their peak (E20), PICs were most abundant in the cerebellum, then the hippocampus and hypothalamus. Within the PIC pool, monocytes were most prevalent in all regions and time points, and shifted from being majority classical at E20 to non-classical by PN7. T cells increased over time, and shifted from majority cytotoxic to T-helper cells by PN7. This suggests the PIC profile transitions from reactive to adaptive and surveilling in the second postnatal week. NK cells and mast cells increased temporarily, and mast cells were restricted to the hippocampus and hypothalamus, suggesting they may play a specific role in the development of those regions. Mimicking a viral infection by administration of Poly I:C increased the influx of PICs into the neonatal brain, particularly of NK cells and in the case of males only, non-classical monocytes. This work provides a map for researchers as they study immune cell contributions to healthy and pathological brain development.

Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems.

Ecological assembly processes, by influencing community composition, determine ecosystem functions of microbiomes. However, debate remains on how stochastic versus deterministic assembly processes influence ecosystem functions such as carbon and nutrient cycling. Towards a better understanding, we investigated three types of agroecosystems (the upland, paddy, and flooded) that represent a gradient of stochastic versus deterministic assembly processes. Carbon and nutrient cycling multifunctionality, characterized by nine enzymes associated with soil carbon, nitrogen, phosphorous and sulfur cycling, was evaluated and then associated with microbial assembly processes and co-occurrence patterns of vital ecological groups. Our results suggest that strong deterministic processes favour microorganisms with convergent functions (as in the upland agroecosystem), while stochasticity-dominated processes lead to divergent functions (as in the flooded agroecosystem). To benefit agroecosystems services, we speculate that it is critical for a system to maintain balance between its stochastic and deterministic assembly processes (as in the paddy agroecosystem). By doing so, the system can preserve a diverse array of functional traits and also allow for particular traits to flourish. To further confirm this speculation, it is necessary to develop a systematic knowledge beyond merely characterizing general patterns towards the associations among community assembly, composition, and ecosystem functions.

Meropenem, Cefepime, and Piperacillin Protein Binding in Patient Samples.

BACKGROUND: The mortality rate of patients with a drug-resistant bacterial infection is high, as are the associated treatment costs. To overcome these issues, optimization of the available therapeutic options is required. Beta-lactams are time-dependent antibiotics and their efficacy is determined by the amount of time the free concentration remains above the minimum inhibitory concentration. Therefore, the aim of this study was to assess the extent and variability of protein binding for meropenem, cefepime, and piperacillin. METHODS: Plasma samples for the analysis of meropenem, cefepime, and piperacillin were collected from patients admitted to a tertiary care hospital as part of the standard care. The bound and unbound drug fractions in the samples were separated by ultrafiltration. Validated liquid chromatography-tandem mass spectrometry assays were used to quantify the total and free plasma concentrations, and the protein binding was determined. RESULTS: Samples from 95 patients were analyzed. The median (range) age of patients was 56 years (17-87) and the median (range) body mass index was 25.7 kg/m (14.7-74.2). Approximately 59% of the patients were men. The median (range) unbound fraction (fu) was 62.5% (41.6-99.1) for meropenem, 61.4% (51.6-99.2) for cefepime, and 48.3% (39.4-71.3) for piperacillin. In the bivariate analysis, as the total meropenem concentration increased, the fu increased (r = 0.37, P = 0.045). A decrease in piperacillin fu was observed as the albumin concentration increased (r = -0.56, P = 0.005). CONCLUSIONS: The average fu values were lower than those reported in the literature. There was also a large variability in fu; hence, it should be considered when managing patients administered with these drugs through direct measurements of free drug concentrations.

A comparison of stochastic programming methods for portfolio level decision-making.

Several methods have been presented in the literature for the management of a pharmaceutical portfolio, i.e. selecting which clinical studies should be conducted. We compare two existing approaches that use stochastic programming techniques and formulate the problem as a mixed integer linear programme (MILP). The first approach will be referred to as the ROV (real option valuation) approach since values are assigned to drug development programmes using methods for real option valuation. The second approach will be referred to as the PS (project scheduling) approach as this approach focusses on the scheduling of clinical studies and is formulated similarly to the resource constrained project scheduling problem. The ROV approach treats the value of a drug development programme as stochastic whereas the PS approach treats the trial outcomes as the stochastic component of the programme. As a consequence, the two approaches may select different portfolios. An advantage of the PS approach is that a schedule for when trials are to be conducted is provided as part of the optimal solution. This advantage comes at a much increased computational burden, however.

Functioning Free Muscle Transfer for Brachial Plexus Injury: A Systematic Review and Pooled Analysis Comparing Functional Outcomes of Intercostal Nerve and Spinal Accessory Nerve Grafts.

BACKGROUND: The aim of this study was to compare postoperative elbow flexion outcomes in patients receiving functioning free muscle transplantation (FFMT) innervated by either intercostal nerve (ICN) or spinal accessory nerve (SAN) grafts. METHODS: A comprehensive systematic review on FFMT for brachial plexus reconstruction was conducted utilizing Medline/PubMed database. Analysis was designed to compare functional outcomes between (1) nerve graft type (ICN vs. SAN) and (2) different free muscle graft types to biceps tendon (gracilis vs. rectus femoris vs. latissimus dorsi). RESULTS: A total of 312 FFMTs innervated by ICNs (169) or the SAN (143) are featured in 10 case series. The mean patient age was 28 years. Patients had a mean injury to surgery time of 31.5 months and an average follow-up time of 39.1 months with 18 patients lost to follow-up. Muscles utilized included the gracilis (275), rectus femoris (28), and latissimus dorsi (8). After excluding those lost to follow-up or failures due to vascular compromise, the mean success rates of FFMTs innervated by ICNs and SAN were 64.1 and 65.4%, respectively. CONCLUSION: This analysis did not identify any difference in outcomes between FFMTs via ICN grafts and those innervated by SAN grafts in restoring elbow flexion in traumatic brachial plexus injury patients.

Development and Evaluation of the High-Intensity Interval Training Self-Efficacy Questionnaire.

This study involved the design and evaluation of the High-Intensity Interval Training Self-Efficacy Questionnaire (HIIT-SQ). Phase 1: Questionnaire items were developed. Phase 2: Australian adolescents (N = 389, 16.0 ± 0.4 years, 41.10% female) completed the HIIT-SQ, and factorial validity of the measurement model was explored. Phase 3: Adolescents (N = 100, age 12-14 years, 44% female) completed the HIIT-SQ twice (1 week apart) to evaluate test-retest reliability. Confirmatory factor analysis of the final six items (mean = 3.43-6.73, SD = 0.99-25.30) revealed adequate fit, χ2(21) = 21, p = .01, comparative fit index = .99, Tucker-Lewis index = .99, root mean square of approximation = .07, 90% confidence interval [.04, .11]. Factor loading estimates showed that all items were highly related to the factor (estimates range: 0.81-0.90). Intraclass coefficients and typical error values were .99 (95% confidence interval [.99, 1.00]) and .22, respectively. This study provides preliminary evidence for the validity and reliability of scores derived from the HIIT-SQ in adolescents.

High Genetic Potential for Proteolytic Decomposition in Northern Peatland Ecosystems.

Nitrogen (N) is a scarce nutrient commonly limiting primary productivity. Microbial decomposition of complex carbon (C) into small organic molecules (e.g., free amino acids) has been suggested to supplement biologically fixed N in northern peatlands. We evaluated the microbial (fungal, bacterial, and archaeal) genetic potential for organic N depolymerization in peatlands at Marcell Experimental Forest (MEF) in northern Minnesota. We used guided gene assembly to examine the abundance and diversity of protease genes and further compared them to those of N fixation (nifH) genes in shotgun metagenomic data collected across depths and in two distinct peatland environments (bogs and fens). Microbial protease genes greatly outnumbered nifH genes, with the most abundant genes (archaeal M1 and bacterial trypsin [S01]) each containing more sequences than all sequences attributed to nifH Bacterial protease gene assemblies were diverse and abundant across depth profiles, indicating a role for bacteria in releasing free amino acids from peptides through depolymerization of older organic material and contrasting with the paradigm of fungal dominance in depolymerization in forest soils. Although protease gene assemblies for fungi were much less abundant overall than those for bacteria, fungi were prevalent in surface samples and therefore may be vital in degrading large soil polymers from fresh plant inputs during the early stage of depolymerization. In total, we demonstrate that depolymerization enzymes from a diverse suite of microorganisms, including understudied bacterial and archaeal lineages, are prevalent within northern peatlands and likely to influence C and N cycling.IMPORTANCE Nitrogen (N) is a common limitation on primary productivity, and its source remains unresolved in northern peatlands that are vulnerable to environmental change. Decomposition of complex organic matter into free amino acids has been proposed as an important N source, but the genetic potential of microorganisms mediating this process has not been examined. Such information can inform possible responses of northern peatlands to environmental change. We show high genetic potential for microbial production of free amino acids across a range of microbial guilds in northern peatlands. In particular, the abundance and diversity of bacterial genes encoding proteolytic activity suggest a predominant role for bacteria in regulating productivity and contrasts with a paradigm of fungal dominance of organic N decomposition. Our results expand our current understanding of coupled carbon and nitrogen cycles in northern peatlands and indicate that understudied bacterial and archaeal lineages may be central in this ecosystem's response to environmental change.

Spirocyclic Acetal-Modified Dextran as a Flexible pH-Sensitive Solubility-Switching Material.

Bioresponsive polymers can enable the development of more effective drug delivery vehicles and medical materials. Acetal-modified polysaccharides allow pH-triggered solubility switching in a versatile and effective manner, but prior work has been limited to a combination of acyclic alkoxyisopropyl and cyclic isopropylidene acetals. We describe here the preparation and characterization of spirocyclic acetal-modified dextran (SpAc-Dex), which comprises dextran decorated with cyclopentyl, cyclohexyl, or cycloheptyl acetals (SpAc5-, SpAc6-, and SpAc7-Dex, respectively). A library of materials with varying acyclic and cyclic acetal contents was synthesized, and organic-soluble materials were formed into microparticles and assessed for degradability and cytocompatibility. At high levels of modification, SpAc5-Dex degraded most quickly and SpAc7-Dex degraded most slowly. SpAc6-Dex features lower degrees of substitution but spans a wide range of degradability. These materials were found to be noncytotoxic and may find future use in biomedical applications.