The ataxia telangiectasia-mutated (ATM) and Rad3-related kinase (ATR) is a central component of the cell cycle checkpoint machinery required to induce cell cycle arrest in response to DNA damage. ...Accumulating evidence suggests a role for ATR in signaling DNA damage during S-phase. Here we show that ATR is recruited to nuclear foci induced by replication fork stalling in a manner that is dependent on the single stranded binding protein replication protein A (RPA). ATR associates with chromatin in asynchronous cell cultures, and we use a variety of approaches to examine the association of ATR with chromatin in the absence of agents that cause genotoxic stress. Under our experimental conditions, ATR exhibits a decreased affinity for chromatin in quiescent cells and cells synchronized at mitosis but an increased affinity for chromatin as cells re-enter the cell cycle. Using centrifugal elutriation to obtain cells enriched at various stages of the cell cycle, we show that ATR associates with chromatin in a cell cycle-dependent manner, specifically during S-phase. Cell cycle association of ATR with chromatin mirrors that of RPA in addition to claspin, a cell cycle checkpoint protein previously shown to be a component of the replication machinery. Furthermore, association of ATR with chromatin occurs in the absence of detectable DNA damage and cell cycle checkpoint activation. These data are consistent with a model whereby ATR is recruited to chromatin during the unperturbed cell cycle and points to a role of ATR in monitoring genome integrity during normal S-phase progression.
The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ...ex situ population was established from which captive‐bred individuals were released into free‐living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400–480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993–2008) with restriction site‐associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free‐living population. However, further genetic rescue with captive‐bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.
Resumen
La paloma rosada (Nesoenas mayeri) es una especie endémica de Mauricio que se ha recuperado impresionantemente después de un grave cuello de botella poblacional a principios de la década de 1970 que duró hasta inicios de la década de 1990. Antes de este cuello de botella se había establecido una población ex situ de la cual se liberaban individuos reproducidos en cautiverio a las subpoblaciones en libertad para incrementar la variación genética y el tamaño poblacional. Este rescate de conservación derivó en una recuperación rápida de la población (400‐480 individuos) y la especie cambió positivamente de categoría dos veces en la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza (UICN). Analizamos los impactos del cuello de botella y el rescate genético sobre la variación genética neutral durante y después de la recuperación poblacional (de 1993 a 2008) mediante secuenciación RAD, análisis de microsatélites y análisis genéticos cuantitativos de los datos del libro genealógico de 1112 aves ubicadas en zoológicos de Europa y los Estados Unidos. Usamos simulaciones por computadora para estudiar los cambios pronosticados en la variación genética y en la viabilidad poblacional del pasado hacia el futuro. La variación genética declinó rápidamente, a pesar de la recuperación poblacional, y el tamaño efectivo de la población fue aproximadamente un orden de magnitud más pequeño que el tamaño del censo. La especie contó con una carga genética elevada de casi 15 equivalentes letales para la longevidad. Nuestras simulaciones pronostican que la endogamia continua probablemente resultará en un incremento en la expresión de mutaciones deletéreas (es decir, una carga realizada elevada) y en una depresión endogámica severa. Sin acciones continuas para la conservación, es probable que la paloma rosada esté extinta en vida libre dentro de cien años. El rescate de conservación de la paloma rosada ha sido fundamental en la recuperación de la población silvestre; sin embargo, se requiere de un rescate genético adicional con las aves de reproducción en cautiverio de los zoológicos para recuperar la variación perdida, reducir la expresión de la variación deletérea dañina y prevenir la extinción. El uso de la genómica y los datos modelados puede orientar las valoraciones de la UICN sobre la viabilidad y el riesgo de extinción de las especies, además de que ayuda en la evaluación de la dependencia que tienen las poblaciones de la conservación.
Latent tuberculosis infection (LTBI) is characterised by the presence of immune responses to previously acquired Mycobacterium tuberculosis infection without clinical evidence of active tuberculosis ...(TB). Here we report evidence-based guidelines from the World Health Organization for a public health approach to the management of LTBI in high risk individuals in countries with high or middle upper income and TB incidence of <100 per 100 000 per year. The guidelines strongly recommend systematic testing and treatment of LTBI in people living with HIV, adult and child contacts of pulmonary TB cases, patients initiating anti-tumour necrosis factor treatment, patients receiving dialysis, patients preparing for organ or haematological transplantation, and patients with silicosis. In prisoners, healthcare workers, immigrants from high TB burden countries, homeless persons and illicit drug users, systematic testing and treatment of LTBI is conditionally recommended, according to TB epidemiology and resource availability. Either commercial interferon-gamma release assays or Mantoux tuberculin skin testing could be used to test for LTBI. Chest radiography should be performed before LTBI treatment to rule out active TB disease. Recommended treatment regimens for LTBI include: 6 or 9 month isoniazid; 12 week rifapentine plus isoniazid; 3-4 month isoniazid plus rifampicin; or 3-4 month rifampicin alone.
Effective management of freshwater fish habitat is essential to supporting healthy aquatic ecosystems and sustainable fisheries. In Canada, recent changes to the Fisheries Act enhanced the protection ...of fish habitat, but application of those provisions relies on sound scientific evidence. We employed collaborative research prioritization methods to identify scientific research questions that, if addressed, would significantly advance the management of freshwater fish habitat in Canada. This list was generated by a diverse group of freshwater fish experts, including substantial contributions from practitioners who administer provisions of the Fisheries Act. The research questions generated in this study identify priority topics for future research, while highlighting issues that could be addressed with different funding models. As a result, this study should support evidence-based management of Canada’s aquatic resources by identifying scientific knowledge gaps faced by practitioners, and suggesting mechanisms to address them. Given the important contribution of Canadian freshwater systems to global ecosystem values, and the similar scientific challenges facing fish habitat managers in other jurisdictions, this study is likely to have broad applicability.
A key aspect of contemporary fish habitat management is the need to account for losses and gains associated with development and offsetting measures while protecting high quality features. We propose ...an ecological accounting framework for aquatic ecosystems using habitat equivalents scaled to aquatic productivity, and using fish-to-habitat associations by life stage, based on local fish community needs. The framework uses both landscape-scale and site-level evaluations of pre- and post-project habitat changes to assign and track habitat parcels, using ecological baselines and fish-habitat target setting. Concepts of natural capital reserves and productivity-based ecotypes are used for trading losses and gains between impacts from development projects and offsets, including restoration actions, while maintaining ecologically important areas intact. Traditional accounting terms such as deposits, withdrawals, and transfers are defined using scaled habitat-equivalents as the currency. Other key features of the framework include setting a service area that is ecologically meaningful, and conducting habitat transactions guided by habitat conservation, protection, and restoration (
habitat CPR
) principles. The nearshore area of the Toronto and Region is used as a case study to illustrate the eco-accounting framework and how habitat banking could be incorporated along with planned restoration to remediate this degraded but continually developed area. The framework represents significant advances in managing cumulative habitat effects in an integrated way, moving away from a focus on only project- or site-level assessments. We feel this approach could be adapted to other ecosystem types in addition to the lake, nearshore area example provided here.
Nearly 5000 chamber measurements of CH4 flux were collated from 21 sites across the United Kingdom, covering a range of soil and vegetation types, to derive a parsimonious model that explains as much ...of the variability as possible, with the least input requirements. Mean fluxes ranged from −0.3 to 27.4 nmol CH4 m−2 s−1, with small emissions or low rates of net uptake in mineral soils (site means of −0.3 to 0.7 nmol m−2 s−1) and much larger emissions from organic soils (site means of −0.3 to 27.4 nmol m−2 s−1). Less than half of the observed variability in instantaneous fluxes could be explained by independent variables measured. The reasons for this include measurement error, stochastic processes and, probably most importantly, poor correspondence between the independent variables measured and the actual variables influencing the processes underlying methane production, transport and oxidation. When temporal variation was accounted for, and the fluxes averaged at larger spatial scales, simple models explained up to ca. 75% of the variance in CH4 fluxes. Soil carbon, peat depth, soil moisture and pH together provided the best sub‐set of explanatory variables. However, where plant species composition data were available, this provided the highest explanatory power. Linear and nonlinear models generally fitted the data equally well, with the exception that soil moisture required a power transformation. To estimate the impact of changes in peatland water table on CH4 emissions in the United Kingdom, an emission factor of +0.4 g CH4 m−2 yr−1 per cm increase in water table height was derived from the data.
The effect of a liberal transfusion strategy as compared with a restrictive strategy on outcomes in critically ill patients with traumatic brain injury is unclear.BACKGROUNDThe effect of a liberal ...transfusion strategy as compared with a restrictive strategy on outcomes in critically ill patients with traumatic brain injury is unclear.We randomly assigned adults with moderate or severe traumatic brain injury and anemia to receive transfusion of red cells according to a liberal strategy (transfusions initiated at a hemoglobin level of ≤10 g per deciliter) or a restrictive strategy (transfusions initiated at ≤7 g per deciliter). The primary outcome was an unfavorable outcome as assessed by the score on the Glasgow Outcome Scale-Extended at 6 months, which we categorized with the use of a sliding dichotomy that was based on the prognosis of each patient at baseline. Secondary outcomes included mortality, functional independence, quality of life, and depression at 6 months.METHODSWe randomly assigned adults with moderate or severe traumatic brain injury and anemia to receive transfusion of red cells according to a liberal strategy (transfusions initiated at a hemoglobin level of ≤10 g per deciliter) or a restrictive strategy (transfusions initiated at ≤7 g per deciliter). The primary outcome was an unfavorable outcome as assessed by the score on the Glasgow Outcome Scale-Extended at 6 months, which we categorized with the use of a sliding dichotomy that was based on the prognosis of each patient at baseline. Secondary outcomes included mortality, functional independence, quality of life, and depression at 6 months.A total of 742 patients underwent randomization, with 371 assigned to each group. The analysis of the primary outcome included 722 patients. The median hemoglobin level in the intensive care unit was 10.8 g per deciliter in the group assigned to the liberal strategy and 8.8 g per deciliter in the group assigned to the restrictive strategy. An unfavorable outcome occurred in 249 of 364 patients (68.4%) in the liberal-strategy group and in 263 of 358 (73.5%) in the restrictive-strategy group (adjusted absolute difference, restrictive strategy vs. liberal strategy, 5.4 percentage points; 95% confidence interval, -2.9 to 13.7). Among survivors, a liberal strategy was associated with higher scores on some but not all the scales assessing functional independence and quality of life. No association was observed between the transfusion strategy and mortality or depression. Venous thromboembolic events occurred in 8.4% of the patients in each group, and acute respiratory distress syndrome occurred in 3.3% and 0.8% of patients in the liberal-strategy and restrictive-strategy groups, respectively.RESULTSA total of 742 patients underwent randomization, with 371 assigned to each group. The analysis of the primary outcome included 722 patients. The median hemoglobin level in the intensive care unit was 10.8 g per deciliter in the group assigned to the liberal strategy and 8.8 g per deciliter in the group assigned to the restrictive strategy. An unfavorable outcome occurred in 249 of 364 patients (68.4%) in the liberal-strategy group and in 263 of 358 (73.5%) in the restrictive-strategy group (adjusted absolute difference, restrictive strategy vs. liberal strategy, 5.4 percentage points; 95% confidence interval, -2.9 to 13.7). Among survivors, a liberal strategy was associated with higher scores on some but not all the scales assessing functional independence and quality of life. No association was observed between the transfusion strategy and mortality or depression. Venous thromboembolic events occurred in 8.4% of the patients in each group, and acute respiratory distress syndrome occurred in 3.3% and 0.8% of patients in the liberal-strategy and restrictive-strategy groups, respectively.In critically ill patients with traumatic brain injury and anemia, a liberal transfusion strategy did not reduce the risk of an unfavorable neurologic outcome at 6 months. (Funded by the Canadian Institutes of Health Research and others; HEMOTION ClinicalTrials.gov number, NCT03260478.).CONCLUSIONSIn critically ill patients with traumatic brain injury and anemia, a liberal transfusion strategy did not reduce the risk of an unfavorable neurologic outcome at 6 months. (Funded by the Canadian Institutes of Health Research and others; HEMOTION ClinicalTrials.gov number, NCT03260478.).
Current neurointensive care guidelines recommend intracranial pressure (ICP) and cerebral perfusion pressure (CPP) centered management for moderate-severe traumatic brain injury (TBI) because of ...their demonstrated associations with patient outcome. Cerebrovascular reactivity metrics, such as the pressure reactivity index (PRx), pulse amplitude index (PAx), and RAC index, have also demonstrated significant prognostic capabilities with regard to outcome. However, critical thresholds for cerebrovascular reactivity indices have only been identified in two studies conducted at the same center. In this study, we aim to determine the critical thresholds of these metrics by leveraging a unique multi-center database. The study included a total of 354 patients from the CAnadian High-Resolution TBI (CAHR-TBI) Research Collaborative. Based on 6-month Glasgow Outcome Scores, patients were dichotomized into alive versus dead and favorable versus unfavorable. Chi-square values were then computed for incrementally increasing values of each physiological parameter of interest against outcome. The values that generated the greatest chi-squares for each parameter were considered to be the thresholds with the greatest outcome discriminatory capacity. To confirm that the identified thresholds provide prognostic utility, univariate and multivariable logistical regression analyses were performed adjusting for the International Mission for Prognosis and Analysis of Clinical Trials (IMPACT) variables. Through the chi-square analysis, a lower limit CPP threshold of 60 mm Hg and ICP thresholds of 18 mm Hg and 22 mm Hg were identified for both survival and favorable outcome predictions. For the cerebrovascular reactivity metrics, different thresholds were identified for the two outcome dichotomizations. For survival prediction, thresholds of 0.35, 0.25, and 0 were identified for PRx, PAx, and RAC, respectively. For favorable outcome prediction, thresholds of 0.325, 0.20, and 0.05 were found. Univariate logistical regression analysis demonstrated that the time spent above/below thresholds were associated with outcome. Further, multivariable logistical regression analysis found that percent time above/below the identified thresholds added additional variance to the IMPACT core model for predicting both survival and favorable outcome. In this study, we were able to validate the results of the previous two works as well as to reaffirm the ICP and CPP guidelines from the Brain Trauma Foundation (BTF) and the Seattle International Severe Traumatic Brain Injury Consensus Conference (SIBICC).
We evaluated associations between antepartum weight change and adverse pregnancy outcomes and between antiretroviral therapy (ART) regimens and week-50 postpartum body mass index in IMPAACT 2010.
...Women with HIV-1 in 9 countries were randomized 1:1:1 at 14-28 weeks gestational age (GA) to start dolutegravir(DTG)+emtricitabine(FTC)/tenofovir alafenamide fumarate(TAF) versus DTG+FTC/tenofovir disoproxil fumarate(TDF) versus efavirenz (EFV)/FTC/TDF. Insufficient antepartum weight gain was defined using IOM guidelines. Cox-proportional hazards regression models were used to evaluate the association between antepartum weight change and adverse pregnancy outcomes: stillbirth (≥20 weeks GA), preterm delivery (<37 weeks GA), small for gestational age (SGA<10th percentile), and a composite of these endpoints.
643 participants were randomized: 217 in DTG+FTC/TAF, 215 in DTG+FTC/TDF, and 211 in EFV/FTC/TDF arms. Baseline medians were: GA 21.9 weeks, HIV RNA 903 copies/mL, CD4 count 466 cells/uL. Insufficient weight gain was least frequent with DTG+FTC/TAF (15.0%) versus DTG+FTC/TDF (23.6%) and EFV/FTC/TDF (30.4%). Women in the DTG+FTC/TAF arm had the lowest rate of composite adverse pregnancy outcome. Low antepartum weight gain was associated with higher hazard of composite adverse pregnancy outcome (HR 1.44, 95%CI 1.04, 2.00) and SGA (HR 1.48, 95%CI 0.99, 2.22). More women in the DTG+FTC/TAF arm had body mass index ≥25 kg/m2 at 50 weeks postpartum (54.7%) versus the DTG+FTC/TDF (45.2%) and EFV/FTC/TDF (34.2%) arms.
Antepartum weight gain on DTG regimens was protective against adverse pregnancy outcomes traditionally associated with insufficient weight gain, supportive of guidelines recommending DTG-based ART for women starting ART during pregnancy. Interventions to mitigate postpartum weight gain are needed.
Near-infrared spectroscopy regional cerebral oxygen saturation (rSO
) has gained interest as a raw parameter and as a basis for measuring cerebrovascular reactivity (CVR) due to its noninvasive ...nature and high spatial resolution. However, the prognostic utility of these parameters has not yet been determined. This study aimed to identify threshold values of rSO
and rSO
-based CVR at which outcomes worsened following traumatic brain injury (TBI).
A retrospective multi-institutional cohort study was performed. The cohort included TBI patients treated in four adult intensive care units (ICU). The cerebral oxygen indices, COx (using rSO
and cerebral perfusion pressure) as well as COx_a (using rSO
and arterial blood pressure) were calculated for each patient. Grand mean thresholds along with exposure-based thresholds were determined utilizing sequential chi-squared analysis and univariate logistic regression, respectively.
In the cohort of 129 patients, there was no identifiable threshold for raw rSO
at which outcomes were found to worsen. For both COx and COx_a, an optimal grand mean threshold value of 0.2 was identified for both survival and favorable outcomes, while percent time above - 0.05 was uniformly found to have the best discriminative value.
In this multi-institutional cohort study, raw rSO
was found to contain no significant prognostic information. However, rSO
-based indices of CVR, COx and COx_a, were found to have a uniform grand mean threshold of 0.2 and exposure-based threshold of - 0.05, above which clinical outcomes markedly worsened. This study lays the groundwork to transition to less invasive means of continuously measuring CVR.
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