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The Meiotic Recombination Activator PRDM9 Trimethylates Both H3K36 and H3K4 at Recombination Hotspots In Vivo. - PLoS genetics
In many mammals, including humans and mice, the zinc finger histone methyltransferase PRDM9 performs the first step in meiotic recombination by specifying the locations of hotspots, the sites of genetic recombination. PRDM9 binds to DNA at hotspots through its zinc finger domain and activates recombination by trimethylating histone H3K4 on adjacent nucleosomes through its PR/SET domain. Recently, the isolated PR/SET domain of PRDM9 was shown capable of also trimethylating H3K36 in vitro, raising the question of whether this reaction occurs in vivo during meiosis, and if so, what its function might be. Here, we show that full-length PRDM9 does trimethylate H3K36 in vivo in mouse spermatocytes. Levels of H3K4me3 and H3K36me3 are highly correlated at hotspots, but mutually exclusive elsewhere. In vitro, we find that although PRDM9 trimethylates H3K36 much more slowly than it does H3K4, PRDM9 is capable of placing both marks on the same histone molecules. In accord with these results, we also show that PRDM9 can trimethylate both K4 and K36 on the same nucleosomes in vivo, but the ratio of K4me3/K36me3 is much higher for the pair of nucleosomes adjacent to the PRDM9 binding site compared to the next pair further away. Importantly, H3K4me3/H3K36me3-double-positive nucleosomes occur only in regions of recombination: hotspots and the pseudoautosomal (PAR) region of the sex chromosomes. These double-positive nucleosomes are dramatically reduced when PRDM9 is absent, showing that this signature is PRDM9-dependent at hotspots; the residual double-positive nucleosomes most likely come from the PRDM9-independent PAR. These results, together with the fact that PRDM9 is the only known mammalian histone methyltransferase with both H3K4 and H3K36 trimethylation activity, suggest that trimethylation of H3K36 plays an important role in the recombination process. Given the known requirement of H3K36me3 for double strand break repair by homologous recombination in somatic cells, we suggest that it may play the same role in meiosis.
Literal grid map models for animal navigation: Assumptions and predictions. - Journal of theoretical biology
Many animals can navigate from unfamiliar locations to a familiar target location with no outward route information or direct sensory contact with the target or any familiar landmarks. Several models have been proposed to explain this phenomenon, one possibility being a literal interpretation of a grid map. In this paper we systematically compare four such models, which we label: Correct Bicoordinate navigation, both Target and Release site based, Approximate Bicoordinate navigation, and Directional navigation. Predictions of spatial patterns of initial orientation errors and efficiencies depend on a combination of assumptions about the navigation mechanism and the geometry of the environmental coordinate fields used as model inputs. When coordinates axes are orthogonal at the target the predictions from the Correct Bicoordinate (Target based) model and Approximate Bicoordinate model are identical. However, if the coordinate axes are non-orthogonal different regional patterns of initial orientation errors and efficiencies can be expected from these two models. Field anomalies produce high magnitudes of orientation errors close to the target, while region-wide nonlinearity leads to orientation errors increasing with distance from the target. In general, initial orientation error patterns are more useful for distinguishing between different assumption combinations than efficiencies. We discuss how consideration of model predictions may be helpful in the design of experiments.Copyright Â© 2016 Elsevier Ltd. All rights reserved.
Race Making in a Penal Institution. - AJS; American journal of sociology
This article provides a ground-level investigation into the lives of penal inmates, linking the literature on race making and penal management to provide an understanding of racial formation processes in a modern penal institution. Drawing on 135 days of ethnographic data collected as an inmate in a Southern California county jail system, the author argues that inmates are subjected to two mutually constitutive racial projects--one institutional and the other microinteractional. Operating in symbiosis within a narrative of risk management, these racial projects increase (rather than decrease) incidents of intraracial violence and the potential for interracial violence. These findings have implications for understanding the process of racialization and evaluating the effectiveness of penal management strategies.
A Self-Assembled Metallomacrocycle Singlet Oxygen Sensitizer for Photodynamic Therapy. - Chemistry (Weinheim an der Bergstrasse, Germany)
Although metal-ion-directed self-assembly has been widely used to construct a vast number of macrocycles and cages, it is only recently that the biological properties of these systems have begun to be explored. However, up until now, none of these studies have involved intrinsically photoexcitable self-assembled structures. Herein we report the first metallomacrocycle that functions as an intracellular singlet oxygen sensitizer. Not only does this Ru2 Re2 system possess potent photocytotoxicity at light fluences below those used for current medically employed systems, it offers an entirely new paradigm for the construction of sensitizers for photodynamic therapy.Â© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
ERK and AKT phosphorylation status in lung cancer and emphysema using nanocapillary isoelectric focusing. - BMJ open respiratory research
Emphysema is an independent risk factor for the development of lung cancer in smokers. Activation of oncogenic signalling proteins AKT and ERK by phosphorylation has an established role in the development of lung cancer and has also been implicated in the pathogenesis of emphysema. The aim of this study was to compare the protein level and phosphorylation status of AKT and ERK in paired lung cancer and emphysema tissue using a highly sensitive phosphoprotein analysis approach.An antibody-based, nanocapillary isoelectric focusing (cIEF) assay was used to determine the relative quantities and phosphorylation status of AKT and ERK in tumour and matched lung tissue from patients, with or without evidence of emphysema, undergoing curative resection for non-small cell lung cancer.20 patients with adenocarcinoma (n=9) or squamous cell carcinoma (n=11) of the lung were included (mean age 67.3â€…years (SD 7.5, range 47-80â€…years)), 12 were men and all were current (n=10) or former smokers (n=10). Paired macroscopically normal lung tissue was either histologically normal (n=7) or showed emphysema (n=13). Total and phosphorylated AKT levels were fourfold (p=0.0001) and fivefold (p=0.001) higher in tumour compared with matched lung, respectively. There was no correlation with tumour histology, stage or differentiation; however, total AKT signal in tumour was significantly correlated with fluorodeoxyglucose avidity on positron emission tomography-CT scan (r=0.53, p=0.035). Total ERK was not differentially expressed, but doubly phosphorylated (activated) ERK was threefold higher in emphysema (23.5%, SD 9.2) than either matched tumour (8.8%, SD 8.6) or normal lung tissue (8.3%, SD 9.0) and correlated with the histological severity of emphysema (p=0.005).cIEF offers opportunities for quantifying subtle shifts in the phosphorylation status of oncoproteins in nanogram amounts of lung tissue. ERK activation is a feature of emphysema.
Prognostic utility of plasma lactate measured between 24 and 48Â h after initiation of early goal-directed therapy in the management of sepsis, severe sepsis, and septic shock. - Journal of intensive care
Based on the proven efficacy of lactate in predicting mortality and morbidity in sepsis when measured early in the resuscitative protocol, our group hypothesized that this utility extends later in the course of care. This study sought to investigate the prognostic potential of plasma lactate clearance measured 24-48 h after the initiation of treatment for nonsurgical patients with sepsis, severe sepsis, and septic shock.Plasma lactate values, measured 24-48 h after the initiation of treatment, were collected in nonsurgical septic, severe septic, and septic shock patients. The primary outcome was 30-day mortality, while secondary outcomes included requirements for vasopressors and boluses of intravenous fluids. Analysis of these three outcomes was performed while controlling for clinical severity as measured by Sequential Organ Failure Assessment (SOFA), renal dysfunction, and hepatic dysfunction. Lactate clearance was defined as the percent change in plasma lactate levels measured after 24-48 h of treatment from the plasma lactate level at initial presentation.Two hundred twenty-nine nonsurgical patients were divided into two groups, clearers (above median lactate clearance [31.6 %]) and nonclearers (below median lactate clearance [31.6 %]). The adjusted odds ratio of mortality in clearers compared to nonclearers was 0.39 (CI 0.20-0.76) (p = 0.006). For vasopressor requirement, the adjusted odds ratio was 0.41 (CI 0.21-0.79) in clearers compared to nonclearers (p = 0.008). For intravenous fluid bolus requirement, the adjusted odds ratio was 0.81 (CI 0.48-1.39) in clearers compared to nonclearers (p = 0.45).Lower plasma lactate clearance 24-48 h after the initiation of treatment is associated with higher 30-day mortality and requirements for vasopressors in nonsurgical septic patients and may be a useful noninvasive measurement for guiding late-sepsis treatment. Further investigation looking at mechanisms and therapeutic targets to improve lactate clearance in late sepsis may improve patient mortality and outcomes.
Stereotypic behaviour in standard non-enriched cages is an alternative to depression-like responses in C57BL/6 mice. - Behavioural brain research
Depressive-like forms of waking inactivity have been recently observed in laboratory primates and horses. We tested the hypotheses that being awake but motionless within the home-cage is a depression-like symptom in mice, and that in impoverished housing, it represents an alternative response to stereotypic behaviour. We raised C57BL/6 ('C57') and DBA/2 ('DBA') females to adulthood in non-enriched (n=62 mice) or enriched (n=60 mice) cages, observing home-cage behaviour during the active (dark) phases. We predicted that being still but awake would be reduced by environmental enrichment; more pronounced in C57s, as the strain most prone to learned helplessness; negatively related to stereotypic behaviour; and positively related to immobility in Forced Swim Tests (FST). Compared to enriched mice, non-enriched subjects did spend more time spent being inactive but awake, especially if they displayed relatively little stereotypic behaviour. C57 mice also spent more time awake but motionless than DBAs. Furthermore, even after statistically controlling for housing type and strain, this behaviour very strongly tended to predict increased immobility in the FST, while high levels of stereotypic behaviours in contrast predicted low immobility in the FST. Being awake but motionless is thus a reaction to non-enriched housing that seems to be an alternative to stereotypic behaviour, and could reflect depression-like states.Copyright Â© 2016 Elsevier B.V. All rights reserved.
Mixed-strain housing for female C57BL/6, DBA/2, and BALB/c mice: validating a split-plot design that promotes refinement and reduction. - BMC medical research methodology
Inefficient experimental designs are common in animal-based biomedical research, wasting resources and potentially leading to unreplicable results. Here we illustrate the intrinsic statistical power of split-plot designs, wherein three or more sub-units (e.g. individual subjects) differing in a variable of interest (e.g. genotype) share an experimental unit (e.g. a cage or litter) to which a treatment is applied (e.g. a drug, diet, or cage manipulation). We also empirically validate one example of such a design, mixing different mouse strains -- C57BL/6, DBA/2, and BALB/c -- within cages varying in degree of enrichment. As well as boosting statistical power, no other manipulations are needed for individual identification if co-housed strains are differentially pigmented, so also sparing mice from stressful marking procedures.The validation involved housing 240 females from weaning to 5 months of age in single- or mixed- strain trios, in cages allocated to enriched or standard treatments. Mice were screened for a range of 26 commonly-measured behavioural, physiological and haematological variables.Living in mixed-strain trios did not compromise mouse welfare (assessed via corticosterone metabolite output, stereotypic behaviour, signs of aggression, and other variables). It also did not alter the direction or magnitude of any strain- or enrichment-typical difference across the 26 measured variables, or increase variance in the data: indeed variance was significantly decreased by mixed- strain housing. Furthermore, using Monte Carlo simulations to quantify the statistical power benefits of this approach over a conventional design demonstrated that for our effect sizes, the split- plot design would require significantly fewer mice (under half in most cases) to achieve a power of 80%.Mixed-strain housing allows several strains to be tested at once, and potentially refines traditional marking practices for research mice. Furthermore, it dramatically illustrates the enhanced statistical power of split-plot designs, allowing many fewer animals to be used. More powerful designs can also increase the chances of replicable findings, and increase the ability of small-scale studies to yield significant results. Using mixed-strain housing for female C57BL/6, DBA/2 and BALB/c mice is therefore an effective, efficient way to promote both refinement and the reduction of animal-use in research.
TIMP2â€¢IGFBP7 biomarker panel accurately predicts acute kidney injury in high-risk surgical patients. - The journal of trauma and acute care surgery
Acute kidney injury (AKI) is an important complication in surgical patients. Existing biomarkers and clinical prediction models underestimate the risk for developing AKI. We recently reported data from two trials of 728 and 408 critically ill adult patients in whom urinary TIMP2â€¢IGFBP7 (NephroCheck, Astute Medical) was used to identify patients at risk of developing AKI. Here we report a preplanned analysis of surgical patients from both trials to assess whether urinary tissue inhibitor of metalloproteinase 2 (TIMP-2) and insulin-like growth factor-binding protein 7 (IGFBP7) accurately identify surgical patients at risk of developing AKI.We enrolled adult surgical patients at risk for AKI who were admitted to one of 39 intensive care units across Europe and North America. The primary end point was moderate-severe AKI (equivalent to KDIGO [Kidney Disease Improving Global Outcomes] stages 2-3) within 12 hours of enrollment. Biomarker performance was assessed using the area under the receiver operating characteristic curve, integrated discrimination improvement, and category-free net reclassification improvement.A total of 375 patients were included in the final analysis of whom 35 (9%) developed moderate-severe AKI within 12 hours. The area under the receiver operating characteristic curve for [TIMP-2]â€¢[IGFBP7] alone was 0.84 (95% confidence interval, 0.76-0.90; p < 0.0001). Biomarker performance was robust in sensitivity analysis across predefined subgroups (urgency and type of surgery).For postoperative surgical intensive care unit patients, a single urinary TIMP2â€¢IGFBP7 test accurately identified patients at risk for developing AKI within the ensuing 12 hours and its inclusion in clinical risk prediction models significantly enhances their performance.Prognostic study, level I.
Protein Z: A putative novel biomarker for early detection of ovarian cancer. - International journal of cancer
Ovarian cancer (OC) has the highest mortality of all gynaecological cancers. Early diagnosis offers an approach to achieving better outcomes. We conducted a blinded-evaluation of prospectively collected preclinical serum from participants in the multimodal group of the United Kingdom Collaborative Trial of Ovarian Cancer Screening. Using isobaric tags (iTRAQ) we identified 90 proteins differentially expressed between OC cases and controls. A second targeted mass spectrometry analysis of twenty of these candidates identified Protein Z as a potential early detection biomarker for OC. This was further validated by ELISA analysis in 482 serial serum samples, from 80 individuals, 49 OC cases and 31 controls, spanning up to 7 years prior to diagnosis. Protein Z was significantly down-regulated up to 2 years pre-diagnosis (pâ€‰=â€‰0.000000411) in 8 of 19 Type I patients whilst in 5 Type II individuals, it was significantly up-regulated up to 4 years before diagnosis (pâ€‰=â€‰0.01). ROC curve analysis for CA-125 and CA-125 combined with Protein Z showed a statistically significant (p= 0.00033) increase in the AUC from 77 to 81% for Type I and a statistically significant (p= 0.00003) increase in the AUC from 76 to 82% for Type II. Protein Z is a novel independent early detection biomarker for Type I and Type II ovarian cancer; which can discriminate between both types. Protein Z also adds to CA-125 and potentially the Risk of Ovarian Cancer algorithm in the detection of both subtypes.Â© 2016 The Authors International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.
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