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Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using white Coconversion

Thu, 01/05/2017 - 6:09pm

Adoption of a streamlined version of the bacterial clustered regular interspersed short palindromic repeat (CRISPR)/Cas9 defense system has accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, directed by a simplified, CRISPR-like single-guide RNA, catalyzes a double-stranded DNA break at a specific genomic site; subsequent repair by end joining can introduce mutagenic insertions or deletions, while repair by homologous recombination using an exogenous DNA template can incorporate new sequences at the target locus. However, the efficiency of Cas9-directed mutagenesis is low in Drosophila melanogaster Here, we describe a strategy that reduces the time and effort required to identify flies with targeted genomic changes. The strategy uses editing of the white gene, evidenced by altered eye color, to predict successful editing of an unrelated gene-of-interest. The red eyes of wild-type flies are readily distinguished from white-eyed (end-joining-mediated loss of White function) or brown-eyed (recombination-mediated conversion to the whitecoffee allele) mutant flies. When single injected G0 flies produce individual G1 broods, flies carrying edits at a gene-of-interest were readily found in broods in which all G1 offspring carried white mutations. Thus, visual assessment of eye color substitutes for wholesale PCR screening of large numbers of G1 offspring. We find that end-joining-mediated mutations often show signatures of microhomology-mediated repair and that recombination-based mutations frequently involve donor plasmid integration at the target locus. Finally, we show that gap repair induced by two guide RNAs more reliably converts the intervening target sequence, whereas the use of Lig4169 mutants to suppress end joining does not improve recombination efficacy.

Prevention of sexual transmission of Ebola in Liberia through a national semen testing and counselling programme for survivors: an analysis of Ebola virus RNA results and behavioural data

Thu, 01/05/2017 - 6:09pm

BACKGROUND: Ebola virus has been detected in semen of Ebola virus disease survivors after recovery. Liberia's Men's Health Screening Program (MHSP) offers Ebola virus disease survivors semen testing for Ebola virus. We present preliminary results and behavioural outcomes from the first national semen testing programme for Ebola virus.

METHODS: The MHSP operates out of three locations in Liberia: Redemption Hospital in Montserrado County, Phebe Hospital in Bong County, and Tellewoyan Hospital in Lofa County. Men aged 15 years and older who had an Ebola treatment unit discharge certificate are eligible for inclusion. Participants' semen samples were tested for Ebola virus RNA by real-time RT-PCR and participants received counselling on safe sexual practices. Participants graduated after receiving two consecutive negative semen tests. Counsellors collected information on sociodemographics and sexual behaviours using questionnaires administered at enrolment, follow up, and graduation visits. Because the programme is ongoing, data analysis was restricted to data obtained from July 7, 2015, to May 6, 2016.

FINDINGS: As of May 6, 2016, 466 Ebola virus disease survivors had enrolled in the programme; real-time RT-PCR results were available from 429 participants. 38 participants (9%) produced at least one semen specimen that tested positive for Ebola virus RNA. Of these, 24 (63%) provided semen specimens that tested positive 12 months or longer after Ebola virus disease recovery. The longest interval between discharge from an Ebola treatment unit and collection of a positive semen sample was 565 days. Among participants who enrolled and provided specimens more than 90 days since their Ebola treatment unit discharge, men older than 40 years were more likely to have a semen sample test positive than were men aged 40 years or younger (p=0.0004). 84 (74%) of 113 participants who reported not using a condom at enrolment reported using condoms at their first follow-up visit (p < 0.0001). 176 (46%) of 385 participants who reported being sexually active at enrolment reported abstinence at their follow-up visit (p < 0.0001).

INTERPRETATION: Duration of detection of Ebola virus RNA by real-time RT-PCR varies by individual and might be associated with age. By combining behavioural counselling and laboratory testing, the Men's Health Screening Program helps male Ebola virus disease survivors understand their individual risk and take appropriate measures to protect their sexual partners.

FUNDING: World Health Organization and the US Centers for Disease Control and Prevention.

RNA polymerase II depletion promotes transcription of alternative mRNA species

Thu, 01/05/2017 - 6:09pm

BACKGROUND: Cells respond to numerous internal and external stresses, such as heat, cold, oxidative stress, DNA damage, and osmotic pressure changes. In most cases, the primary response to stress is transcriptional induction of genes that assist the cells in tolerating the stress and facilitate the repair of the cellular damage. However, when the transcription machinery itself is stressed, responding by such standard mechanisms may not be possible.

RESULTS: In this study, we demonstrate that depletion or inactivation of RNA polymerase II (RNAPII) changes the preferred polyadenylation site usage for several transcripts, and leads to increased transcription of a specific subset of genes. Surprisingly, depletion of RNA polymerase I (RNAPI) also promotes altered polyadenylation site usage, while depletion of RNA polymerase III (RNAPIII) does not appear to have an impact.

CONCLUSIONS: Our results demonstrate that stressing the transcription machinery by depleting either RNAPI or RNAPII leads to a novel transcriptional response that results in induction of specific mRNAs and altered polyadenylation of many of the induced transcripts.

The pesticidal Cry6Aa toxin from Bacillus thuringiensis is structurally similar to HlyE-family alpha pore-forming toxins

Thu, 01/05/2017 - 6:09pm

BACKGROUND: The Cry6 family of proteins from Bacillus thuringiensis represents a group of powerful toxins with great potential for use in the control of coleopteran insects and of nematode parasites of importance to agriculture. These proteins are unrelated to other insecticidal toxins at the level of their primary sequences and the structure and function of these proteins has been poorly studied to date. This has inhibited our understanding of these toxins and their mode of action, along with our ability to manipulate the proteins to alter their activity to our advantage. To increase our understanding of their mode of action and to facilitate further development of these proteins we have determined the structure of Cry6Aa in protoxin and trypsin-activated forms and demonstrated a pore-forming mechanism of action.

RESULTS: The two forms of the toxin were resolved to 2.7 A and 2.0 A respectively and showed very similar structures. Cry6Aa shows structural homology to a known class of pore-forming toxins including hemolysin E from Escherichia coli and two Bacillus cereus proteins: the hemolytic toxin HblB and the NheA component of the non-hemolytic toxin (pfam05791). Cry6Aa also shows atypical features compared to other members of this family, including internal repeat sequences and small loop regions within major alpha helices. Trypsin processing was found to result in the loss of some internal sequences while the C-terminal region remains disulfide-linked to the main core of the toxin. Based on the structural similarity of Cry6Aa to other toxins, the mechanism of action of the toxin was probed and its ability to form pores in vivo in Caenorhabditis elegans was demonstrated. A non-toxic mutant was also produced, consistent with the proposed pore-forming mode of action.

CONCLUSIONS: Cry6 proteins are members of the alpha helical pore-forming toxins - a structural class not previously recognized among the Cry toxins of B. thuringiensis and representing a new paradigm for nematocidal and insecticidal proteins. Elucidation of both the structure and the pore-forming mechanism of action of Cry6Aa now opens the way to more detailed analysis of toxin specificity and the development of new toxin variants with novel activities.

The E-Coach technology-assisted care transition system: a pragmatic randomized trial

Thu, 01/05/2017 - 6:09pm

Care transitions from the hospital to home remain a vulnerable time for many patients, especially for those with heart failure (CHF) and chronic obstructive pulmonary disease (COPD). Despite regular use in chronic disease management, it remains unclear how technology can best support patients during their transition from the hospital. We sought to evaluate the impact of a technology-supported care transition support program on hospitalizations, days out of the community and mortality. Using a pragmatic randomized trial, we enrolled patients (511 enrolled, 478 analyzed) hospitalized with CHF/COPD to "E-Coach," an intervention with condition-specific customization and in-hospital and post-discharge support by a care transition nurse (CTN), interactive voice response post-discharge calls, and CTN follow-up versus usual post-discharge care (UC). The primary outcome was 30-day rehospitalization. Secondary outcomes included (1) rehospitalization and death and (2) days in the hospital and out of the community. E-Coach and UC groups were similar at baseline except for gender imbalance (p = 0.02). After adjustment for gender, our primary outcome, 30-day rehospitalization rates did not differ between the E-Coach and UC groups (15.0 vs. 16.3 %, adjusted hazard ratio [95 % confidence interval]: 0.94 [0.60, 1.49]). However, in the COPD subgroup, E-Coach was associated with significantly fewer days in the hospital (0.5 vs. 1.6, p = 0.03). E-Coach, an IVR-augmented care transition intervention did not reduce rehospitalization. The positive impact on our secondary outcome (days in hospital) among COPD patients, but not in CHF, may suggest that E-Coach may be more beneficial among patients with COPD.NIH trial registry number: NCT01135381Trial Protocol: 10.1016/j.cct.2012.08.007.

The weight loss blogosphere: an online survey of weight loss bloggers

Thu, 01/05/2017 - 6:08pm

Blogging is a form of online journaling that has been increasingly used to document an attempt in weight loss. Despite the prevalence of weight loss bloggers, few studies have examined this population. We examined characteristics of weight loss bloggers and their blogs, including blogging habits, reasons for blogging, like and dislikes of blogging, and associations between blogging activity and weight loss. Participants (N = 194, 92.3 % female, mean age = 35) were recruited from Twitter and Facebook to complete an online survey. Participants reported an average weight loss of 42.3 pounds since starting to blog about their weight loss attempt. Blogging duration significantly predicted greater weight loss during blogging (beta = -3.65, t(185) = -2.97, p = .003). Findings suggest that bloggers are generally successful with their weight loss attempt. Future research should explore what determines weight loss success/failure in bloggers and whether individuals desiring to lose weight would benefit from blogging.

Human iPSC-Derived Neuronal Model of Tau-A152T Frontotemporal Dementia Reveals Tau-Mediated Mechanisms of Neuronal Vulnerability

Thu, 01/05/2017 - 6:08pm

Frontotemporal dementia (FTD) and other tauopathies characterized by focal brain neurodegeneration and pathological accumulation of proteins are commonly associated with tau mutations. However, the mechanism of neuronal loss is not fully understood. To identify molecular events associated with tauopathy, we studied induced pluripotent stem cell (iPSC)-derived neurons from individuals carrying the tau-A152T variant. We highlight the potential of in-depth phenotyping of human neuronal cell models for pre-clinical studies and identification of modulators of endogenous tau toxicity. Through a panel of biochemical and cellular assays, A152T neurons showed accumulation, redistribution, and decreased solubility of tau. Upregulation of tau was coupled to enhanced stress-inducible markers and cell vulnerability to proteotoxic, excitotoxic, and mitochondrial stressors, which was rescued upon CRISPR/Cas9-mediated targeting of tau or by pharmacological activation of autophagy. Our findings unmask tau-mediated perturbations of specific pathways associated with neuronal vulnerability, revealing potential early disease biomarkers and therapeutic targets for FTD and other tauopathies.

MMP-9 and MMP-2 Contribute to Neuronal Cell Death in iPSC Models of Frontotemporal Dementia with MAPT Mutations

Thu, 01/05/2017 - 6:08pm

How mutations in the microtubule-associated protein tau (MAPT) gene cause frontotemporal dementia (FTD) remains poorly understood. We generated and characterized multiple induced pluripotent stem cell (iPSC) lines from patients with MAPT IVS10+16 and tau-A152T mutations and a control subject. In cortical neurons differentiated from these and other published iPSC lines, we found that MAPT mutations do not affect neuronal differentiation but increase the 4R/3R tau ratio. Patient neurons had significantly higher levels of MMP-9 and MMP-2 and were more sensitive to stress-induced cell death. Inhibitors of MMP-9/MMP-2 protected patient neurons from stress-induced cell death and recombinant MMP-9/MMP-2 were sufficient to decrease neuronal survival. In tau-A152T neurons, inhibition of the ERK pathway decreased MMP-9 expression. Moreover, ectopic expression of 4R but not 3R tau-A152T in HEK293 cells increased MMP-9 expression and ERK phosphorylation. These findings provide insights into the molecular pathogenesis of FTD and suggest a potential therapeutic target for FTD with MAPT mutations.

Dynamics of Nucleosome Positioning Maturation following Genomic Replication

Thu, 01/05/2017 - 6:08pm

Chromatin is thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture occurring during genomic replication. Here, we measure a key aspect of chromatin structure dynamics during replication-how rapidly nucleosome positions are established on the newly replicated daughter genomes. By isolating newly synthesized DNA marked with 5-ethynyl-2'-deoxyuridine (EdU), we characterize nucleosome positions on both daughter genomes of S. cerevisiae during chromatin maturation. We find that nucleosomes rapidly adopt their mid-log positions at highly transcribed genes, which is consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in hir1Delta mutants reveal a role for HIR in nucleosome spacing. We also characterized nucleosome positions on the leading and lagging strands, uncovering differences in chromatin maturation dynamics at hundreds of genes. Our data define the maturation dynamics of newly replicated chromatin and support a role for transcription in sculpting the chromatin template.

The impact of deliberate reflection with WISE-MDTM modules on critical thinking of nurse practitioner students: A prospective, randomized controlled pilot study

Thu, 01/05/2017 - 2:40pm

Objective: Nurse practitioner (NP) students at our graduate school of nursing use WISE-MDTM simulation modules in the curriculum. This prospective randomized controlled pilot study was undertaken to evaluate critical-thinking outcomes associated with adding metacognitive deliberate-reflection guidance to the learning strategy with WISE-MDTM simulation modules.

Methods: Of 33 NP students randomly assigned to intervention and control groups, 16 completed the study. The intervention group received WISE-MDTM learning modules with specific guidance or deliberate reflection. Controls used the modules with instructions for periodic free-thought reflections. Students’ tape-recorded reflections were categorized according to author-developed critical-thinking categories. Data were analyzed using NVIVOTM. Students’ feedback was collected by post-intervention anonymous survey.

Results: Critical thinking outcomes (student responses to exercises after free-thinking or deliberate-reflection guidance) did not differ between groups. However, the intervention group demonstrated a higher level of critical thought after deliberate-reflection guidance. Post-intervention quantitative and qualitative feedback from both groups endorsed the value of the WISE-MDTM modules for NP education.

Conclusions: Despite no difference in unprompted outcomes between groups, the intervention group often verbalized more thoughtful clinical decision-making. We speculate that the deliberate-reflection guidance intervention utilized with students throughout only two modules was insufficient for them to internalize the critical-thinking process. We propose using free-thought reflections with one or two WISE-MDTM modules to identify struggling students’ clinical decision-making process. These students’ remediation plan could include recording their deliberate-reflection process while viewing WISE-MDTM modules. Students would be guided to verbalize and record their critical-thinking processes for faculty review until students sufficiently integrate the process into their clinical decision-making.

The Effects of Interleukin-10 on Skeletal Muscle Insulin Resistance and Myogenesis

Wed, 01/04/2017 - 5:25pm

Skeletal muscle insulin resistance is a major characteristic of obesity and type 2 diabetes. Although obesity-mediated inflammation is causally associated with insulin resistance, the underlying mechanism is unclear. Our lab and others have shown that a chronic low-grade inflammation takes place in skeletal muscles during diet-induced obesity, as evidenced by increased macrophage markers and pro-inflammatory cytokine levels. Interleukin (IL)-10 is a Th2-type cytokine that inhibits the synthesis and activity of pro-inflammatory cytokines and counteracts the Toll-like receptor-mediated inflammation. Our lab has previously demonstrated the preventive role of IL-10 against insulin resistance. Here, I have analyzed the effects of IL-10 on the skeletal muscle glucose metabolism and myogenesis in three different insulin resistant states (high fat diet-induced, leptin-deficiency-induced and aging-induced). The first model involved long-term (16 weeks) high-fat diet (HFD) feeding that resulted in markedly obese and hyperglycemic mice, representative of obese type 2 diabetic subjects. In mice overexpressing IL-10 specifically in the skeletal muscle (MIL10), we observed improved whole-body and skeletal muscle insulin sensitivity as compared to wild-types after long-term high fat diet feeding. The improved insulin sensitivity in the skeletal muscle was due to increased Akt signaling and decreased muscle inflammation. Leptin is an important adipocyte-derived hormone that is elevated in obesity, and it regulates numerous physiological functions including the energy balance and inflammation. Thus, my second model examined the effects of muscle-specific overexpression of IL-10 on glucose metabolism in the hyperphagic, leptin-deficient ob/ob mice. We detected improved whole-body insulin sensitivity compared to the control mice. My third model examined the effects of increased IL-10 expression using MIL10 mice during aging-induced insulin resistance. In 18-month old MIL10 mice, we found enhanced whole-body and skeletal muscle insulin sensitivity due to improved insulin signaling and decreased muscle inflammation as compared to wild-type mice. Last, to test whether direct signaling of IL-10 on skeletal muscle is responsible for the beneficial effects of IL-10 on muscle glucose metabolism, I generated mice lacking IL-10 receptor 1 type chain selectively in skeletal muscle (M-IL10R-/-). We observed more prominent muscle inflammation and whole-body insulin resistance in HFD-fed M-IL10R-/- mice as compared to wild-type mice. Interestingly, when studying insulin resistance in the IL-10 transgenic mouse models, we identified a consistent increased lean mass phenotype, and conversely decreased lean mass in the HFD-fed M-IL10R-/- mice. Quantitative RT-PCR on HFD-fed MIL10 group muscles to measure myogenesis-related gene expression identified a correlation between lean mass and both IL-10 and MyoD mRNA expression levels. In support of this, I showed that IL-10 caused an increase in in vitro cultured myoblast proliferation rates. Together, these results highlight the potential benefits of IL-10 expression not only in muscle glucose metabolism but also in maintaining muscle mass during insulin resistant states. Overall, these results demonstrate that selective expression of IL-10 in skeletal muscle suppresses inflammation, improves glucose metabolism and muscle growth in obese and aging mice, and further establishes that these effects are at least partially mediated by direct activation of IL-10 signaling in skeletal muscle.