XRCC1 is a molecular scaffold protein that assembles multi-protein complexes involved in DNA single-strand break repair. Here we show that biallelic mutations in the human XRCC1 gene are associated ...with ocular motor apraxia, axonal neuropathy, and progressive cerebellar ataxia. Cells from a patient with mutations in XRCC1 exhibited not only reduced rates of single-strand break repair but also elevated levels of protein ADP-ribosylation. This latter phenotype is recapitulated in a related syndrome caused by mutations in the XRCC1 partner protein PNKP and implicates hyperactivation of poly(ADP-ribose) polymerase/s as a cause of cerebellar ataxia. Indeed, remarkably, genetic deletion of Parp1 rescued normal cerebellar ADP-ribose levels and reduced the loss of cerebellar neurons and ataxia in Xrcc1-defective mice, identifying a molecular mechanism by which endogenous single-strand breaks trigger neuropathology. Collectively, these data establish the importance of XRCC1 protein complexes for normal neurological function and identify PARP1 as a therapeutic target in DNA strand break repair-defective disease.
Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) ...Consortium, we apply a reproducible, cloud-based pipeline to integrate multiple short- and linked-read sequencing datasets and provide benchmark calls for human genomes. We generate benchmark calls for one previously analyzed GIAB sample, as well as six genomes from the Personal Genome Project. These new genomes have broad, open consent, making this a 'first of its kind' resource that is available to the community for multiple downstream applications. We produce 17% more benchmark single nucleotide variations, 176% more indels and 12% larger benchmark regions than previously published GIAB benchmarks. We demonstrate that this benchmark reliably identifies errors in existing callsets and highlight challenges in interpreting performance metrics when using benchmarks that are not perfect or comprehensive. Finally, we identify strengths and weaknesses of callsets by stratifying performance according to variant type and genome context.
Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing ...a very small sample of the human population. There is a need for reference genomes from multiple human populations to avoid potential biases.
Here, we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are > 99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. Forty of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. Eleven genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~ 1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes.
The Ash1 genome is presented as a reference for any genetic studies involving Ashkenazi Jewish individuals.
The secondary injury cascade that is activated following traumatic brain injury (TBI) induces responses from multiple physiological systems, including the immune system. These responses are not ...limited to the area of brain injury; they can also alter peripheral organs such as the intestinal tract. Gut microbiota play a role in the regulation of immune cell populations and microglia activation, and microbiome dysbiosis is implicated in immune dysregulation and behavioral abnormalities. However, changes to the gut microbiome induced after acute TBI remains largely unexplored. In this study, we have investigated the impact of TBI on bacterial dysbiosis. To test the hypothesis that TBI results in changes in microbiome composition, we performed controlled cortical impact (CCI) or sham injury in male 9-weeks old C57BL/6J mice. Fresh stool pellets were collected at baseline and at 24 h post-CCI. 16S rRNA based microbiome analysis was performed to identify differential abundance in bacteria at the genus and species level. In all baseline vs. 24 h post-CCI samples, we evaluated species-level differential abundances via clustered and annotated operational taxonomic units (OTU). At a high-level view, we observed significant changes in two genera after TBI,
, and
. At the species-level, we found significant decreases in three species (
, and
, and significant increases in two additional species (
, and
. These results pinpoint critical changes in the genus-level and species-level microbiome composition in injured mice compared to baseline; highlighting a previously unreported acute dysbiosis in the microbiome after TBI.
IMPORTANCE: Competency-based assessments of surgical resident performance require metrics of entrustable autonomy. OBJECTIVES: To designate entrustable professional activities (EPAs) in global ...performance and in specific operations, and to identify differences in perceived capability, autonomy, and expectations between surgical faculty and residents. DESIGN, SETTING, AND PARTICIPANTS: This survey study was conducted from August 9, 2016, through August 24, 2016, in the Department of Surgery at the UCLA David Geffen School of Medicine. The survey instrument consisted of 5-point Likert scales for assessing perceptions of entrustability for 5 global and 5 operative EPAs. Faculty members were surveyed regarding resident capabilities and expected capabilities by postgraduate year. Residents were surveyed regarding their own capabilities, actual autonomy entrusted in the last EPA performed, and expected capabilities. MAIN OUTCOMES AND MEASURES: Differences in mean ratings were assessed across 7 comparison domains. RESULTS: Among 78 total faculty members, 31 (40%) participated in the survey. Among 49 residents, 39 (80%) participated in the survey. Residents generally rated their global EPA performance higher than the faculty did (mean, 3.7 vs 2.8; P < .01), but operative EPA performance ratings were equivalent (mean, 2.7 vs 2.4; P < .12). Faculty members perceived senior residents as underperforming expectations in operative EPAs. Most faculty members (80%) expected residents not to be independently capable of performing complex operations by graduation. Faculty members perceived residents in postgraduate years 4 and 5 to have greater operative capability than the level of autonomy entrusted to those residents (95% CI, 3.3-3.5 vs 1.9-2.2). CONCLUSIONS AND RELEVANCE: Global and operative EPAs are practical for developing competency-based curricula. Graduated autonomy should be granted to improve the operative experience for residents.
Abstract Introduction The evidence for adrenaline in out-of-hospital cardiac arrest (OHCA) resuscitation is inconclusive. We systematically reviewed the efficacy of adrenaline for adult OHCA. Methods ...We searched in MEDLINE, EMBASE, and Cochrane Library from inception to July 2013 for randomized controlled trials (RCTs) evaluating standard dose adrenaline (SDA) to placebo, high dose adrenaline (HDA), or vasopressin (alone or combination) in adult OHCA patients. Meta-analyses were performed using random effects modeling. Subgroup analyses were performed stratified by cardiac rhythm and by number of drug doses. The primary outcome was survival to discharge and the secondary outcomes were return of spontaneous circulation (ROSC), survival to admission, and neurological outcome. Results Fourteen RCTs ( n = 12,246) met inclusion criteria: one compared SDA to placebo ( n = 534), six compared SDA to HDA ( n = 6174), six compared SDA to an adrenaline/vasopressin combination ( n = 5202), and one compared SDA to vasopressin alone ( n = 336). There was no survival to discharge or neurological outcome differences in any comparison group, including subgroup analyses. SDA showed improved ROSC (RR 2.80, 95%CI 1.78–4.41, p < 0.001) and survival to admission (RR 1.95, 95%CI 1.34–2.84, p < 0.001) compared to placebo. SDA showed decreased ROSC (RR 0.85, 95%CI 0.75–0.97, p = 0.02; I2 = 48%) and survival to admission (RR 0.87, 95%CI 0.76–1.00, p = 0.049; I2 = 34%) compared to HDA. There were no differences in outcomes between SDA and vasopressin alone or in combination with adrenaline. Conclusions There was no benefit of adrenaline in survival to discharge or neurological outcomes. There were improved rates of survival to admission and ROSC with SDA over placebo and HDA over SDA.
Microgravity is known to impact bone health, similar to mechanical unloading on Earth. In the absence of countermeasures, bone formation and mineral deposition are strongly inhibited in Space. There ...is an unmet need to identify nutritional countermeasures. Curcumin and carnosic acid are phytonutrients with anticancer, anti-inflammatory, and antioxidative effects and may exhibit osteogenic properties. Zinc is a trace element essential for bone formation. We hypothesized that these nutraceuticals could counteract the microgravity-induced inhibition of osteogenic differentiation and function. To test this hypothesis, we cultured 7F2 murine osteoblasts in simulated microgravity (SMG) in a Random Positioning Machine in the presence and absence of curcumin, carnosic acid, and zinc and evaluated cell proliferation, function, and differentiation. SMG enhanced cell proliferation in osteogenic medium. The nutraceuticals partially reversed the inhibitory effects of SMG on alkaline phosphatase (ALP) activity and did not alter the SMG-induced reduction in the expression of osteogenic marker genes in osteogenic medium, while they promoted osteoblast proliferation and ALP activity in the absence of traditional osteogenic media. We further observed a synergistic effect of the intermix of the phytonutrients on ALP activity. Intermixes of phytonutrients may serve as convenient and effective nutritional countermeasures against bone loss in space.
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