Ribonucleolytic resection is required for repair of strand displaced nonhomologous end-joining intermediates

Nonhomologous end-joining (NHEJ) pathways repair DNA double-strand breaks (DSBs) in eukaryotes and many prokaryotes, although it is not reported to operate in the third domain of life, archaea. Here, we describe a complete NHEJ complex, consisting of DNA ligase (Lig), polymerase (Pol), phosphoesterase (PE), and Ku from a mesophillic archaeon, Methanocella paludicola (Mpa). Mpa Lig has limited DNA nick-sealing activity but is efficient in ligating nicks containing a 3′ ribonucleotide. Mpa Pol preferentially incorporates nucleoside triphosphates onto a DNA primer strand, filling DNA gaps in annealed breaks. Mpa PE sequentially removes 3′ phosphates and ribonucleotides from primer strands, leaving a ligatable terminal 3′ monoribonucleotide. These proteins, together with the DNA end-binding protein Ku, form a functional NHEJ break-repair apparatus that is highly homologous to the bacterial complex. Although the major roles of Pol and Lig in break repair have been reported, PE’s function in NHEJ has remained obscure. We establish that PE is required for ribonucleolytic resection of RNA intermediates at annealed DSBs. Polymerase-catalyzed strand-displacement synthesis on DNA gaps can result in the formation of nonligatable NHEJ intermediates. The function of PE in NHEJ repair is to detect and remove inappropriately incorporated ribonucleotides or phosphates from 3′ ends of annealed DSBs to configure the termini for ligation. Thus, PE prevents the accumulation of abortive genotoxic DNA intermediates arising from strand displacement synthesis that otherwise would be refractory to repair

Poverty and Self-Sufficiency in the Nine-County Greater Rochester Area

Poverty and Self-Sufficiency in the Nine-County Greater Rochester Area updates data from a 2013 report. Overall, it shows that poverty is rising across the region, from 13.2 percent to 14.3 percent, based on the latest available Census figures. This report aims to update key elements from both previous studies, includingpoverty data for all the counties, towns and villages in the region, relying primarily on the latest U.S. Census data, highlight the financial stress that exists in our community by differentiating between poverty and self-sufficiency; and chronicle and summarize efforts of the greater Rochester community to understand and act upon crisis

Molecular basis for DNA strand displacement by NHEJ repair polymerases

The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) resects these products to ensure that efficient ligation occurs. Here, we describe the crystal structures of these archaeal (Methanocella paludicola) NHEJ nuclease and polymerase enzymes, demonstrating their strict structural conservation with their bacterial NHEJ counterparts. Structural analysis, in conjunction with biochemical studies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the mechanisms that enable Pol and PE to displace annealed bases to facilitate their respective roles in DSB repair

Relationship of vaccine efficacy to the kinetics of DC and T-cell responses induced by PLG-based cancer vaccines

Cancer vaccines are typically formulated for bolus injection and often produce short-lived immunostimulation resulting in poor temporal control over immune cell activation and weak oncolytic activity. One means of overcoming these limitations utilizes immunologically active biomaterial constructs. We previously reported that antigen-laden, macroporous PLG scaffolds induce potent dendritic cell (DC) and cytotoxic T-lymphocyte (CTL) responses via the controlled signaling of inflammatory cytokines, antigen and toll-like receptor agonists. In this study, we describe the kinetics of these responses and illustrate their fundamental relationship to potent tumor rejection when implanted subcutaneously in a mouse B16 model of melanoma. By explanting scaffolds from mice at times ranging from 1–7 d, a seamless relationship was observed between the production of controlled CTL responses, tumor growth and long-term survival in both prophylactic and therapeutic models. Scaffolds must be implanted for > 7 d to augment CTL responses via the prolonged presentation of tumor antigen, and the benefits included a notable regression of established tumors. Host DC infiltration into the porous material persisted for 12 days (peaking at day 5 ~1.4 x 106 cells), and a sharp attenuation in DC numbers coincided with peak CD8+ CTL infiltration at day 12 (~8 x 105 cells). Importantly, these PLG systems enhanced DC numbers in the draining lymph node, resulting in increased CD8(+) CTL subsets at days 10–16 of vaccination. These results indicate that material systems can finely control innate and adaptive immune cell responses to kill typically untreatable melanoma tumors and provide critical kinetic data for the design of vaccine carriers.Engineering and Applied Science

Timing of antiretroviral therapy and adverse pregnancy outcomes : a systematic review and meta-analysis

BACKGROUND: Although life-long combination antiretroviral therapy (ART) is recommended for all HIV-infected individuals, there are limited data on pregnancy outcome with ART initiation pre-conception. We assessed the safety of ART initiated pre-conception versus post-conception on adverse pregnancy outcome. METHODS: We conducted a systematic review of studies from low-, middle-, and high-income countries. We searched Cochrane Central Register of Controlled Trials, EMBASE, LILACS, MEDLINE for randomized trials, quasi-randomized trials and prospective cohort studies conducted between 01 January 1980 to 01 June 2016). Risk ratios were pooled using a random-effects model. FINDINGS: Eleven studies were included (N=19,189 mother-infant pairs). Women initiating ART pre-conception compared to post-conception were significantly more likely to deliver preterm (pooled risk ratio[RR]=1·20, 95% confidence interval[CI] 1·01-1·14, 10 studies), very preterm (RR=1·53, 95%CI 1·22-1·92, two studies), or have low birth weight (LBW) infants (RR=1·30, 95%CI 1·04-1·62, two studies). Data on neonatal mortality was limited. We found no increase in very LBW (RR=0.18, 95% CI 0.02-1.51, one study), small for gestational age (SGA) (RR = 1·13, 95% CI 0·94-1·35, two studies), severe SGA (RR=1·09, 95%CI 0·82-1·45, one study), stillbirth (RR= RR=1·30, 95% CI 0·99-1·69, two studies) or congenital anomalies (RR= RR=1·24, 95% CI 0·61-2·49, one study). INTERPRETATION: The benefits of ART for maternal health and prevention of perinatal transmission outweigh risks, but there remain limited, poor quality data on the extent/severity of these risks. We found elevated preterm delivery and low birth weight rates associated with pre-conception ART. As pre-conception ART rapidly increases globally, it will be critical to monitor for potential adverse pregnancy outcomes

Patient-reported barriers to adherence to antiretroviral therapy : a systematic review and meta-analysis

Maintaining high levels of adherence to antiretroviral therapy (ART) is a challenge across settings and populations. Understanding the relative importance of different barriers to adherence will help inform the targeting of different interventions and future research priorities.; We searched MEDLINE via PubMed, Embase, Web of Science, and PsychINFO from 01 January 1997 to 31 March 2016 for studies reporting barriers to adherence to ART. We calculated pooled proportions of reported barriers to adherence per age group (adults, adolescents, and children). We included data from 125 studies that provided information about adherence barriers for 17,061 adults, 1,099 children, and 856 adolescents. We assessed differences according to geographical location and level of economic development. The most frequently reported individual barriers included forgetting (adults 41.4%, 95% CI 37.3%-45.4%; adolescents 63.1%, 95% CI 46.3%-80.0%; children/caregivers 29.2%, 95% CI 20.1%-38.4%), being away from home (adults 30.4%, 95% CI 25.5%-35.2%; adolescents 40.7%, 95% CI 25.7%-55.6%; children/caregivers 18.5%, 95% CI 10.3%-26.8%), and a change to daily routine (adults 28.0%, 95% CI 20.9%-35.0%; adolescents 32.4%, 95% CI 0%-75.0%; children/caregivers 26.3%, 95% CI 15.3%-37.4%). Depression was reported as a barrier to adherence by more than 15% of patients across all age categories (adults 15.5%, 95% CI 12.8%-18.3%; adolescents 25.7%, 95% CI 17.7%-33.6%; children 15.1%, 95% CI 3.9%-26.3%), while alcohol/substance misuse was commonly reported by adults (12.9%, 95% CI 9.7%-16.1%) and adolescents (28.8%, 95% CI 11.8%-45.8%). Secrecy/stigma was a commonly cited barrier to adherence, reported by more than 10% of adults and children across all regions (adults 13.6%, 95% CI 11.9%-15.3%; children/caregivers 22.3%, 95% CI 10.2%-34.5%). Among adults, feeling sick (15.9%, 95% CI 13.0%-18.8%) was a more commonly cited barrier to adherence than feeling well (9.3%, 95% CI 7.2%-11.4%). Health service-related barriers, including distance to clinic (adults 17.5%, 95% CI 13.0%-21.9%) and stock outs (adults 16.1%, 95% CI 11.7%-20.4%), were also frequently reported. Limitations of this review relate to the fact that included studies differed in approaches to assessing adherence barriers and included variable durations of follow up. Studies that report self-reported adherence will likely underestimate the frequency of non-adherence. For children, barriers were mainly reported by caregivers, which may not correspond to the most important barriers faced by children.; Patients on ART face multiple barriers to adherence, and no single intervention will be sufficient to ensure that high levels of adherence to treatment and virological suppression are sustained. For maximum efficacy, health providers should consider a more triaged approach that first identifies patients at risk of poor adherence and then seeks to establish the support that is needed to overcome the most important barriers to adherence

Factors influencing implementation of aerobic exercise after stroke: a systematic review

Objectives: This systematic review aimed to explore the perspectives of healthcare, exercise, and fitness professionals working with people post-stroke regarding the factors affecting the implementation of aerobic exercise after stroke. Data Sources: OVID SP MEDLINE, OVID SP EMBASE, and CINAHL were searched from inception to December 2018 using a combination of search terms with synonyms of stroke, aerobic exercise and barriers/facilitators. Review methods: Studies focusing on the factors affecting implementation of aerobic exercise after stroke from staff perspectives were included with no restriction on the types of study design. For inclusivity, a broad definition of aerobic exercise was used. Review authors independently extracted data from included studies using domains from the Consolidated Framework for Implementation Research, then synthesised using a framework synthesis approach. Retrospective automated screening was conducted using Rayyan software. Results: Twenty studies were included. Four reported on implementation of aerobic exercise, sixteen on general exercise interventions, all post-stroke. Factors identified as influencing implementation of aerobic exercise after stroke included professionals’ self-efficacy and knowledge about stroke, patients’ needs, communication and collaboration within and between organisations and resources such as equipment, staff and training. Conclusions: Key factors influencing the implementation of aerobic exercise after stroke included characteristics of the staff and intervention and system-level issues, some of which are modifiable. Further research should evaluate strategies which specifically target these modifiable factors to facilitate implementation in practice

Meeting Report of the Third Annual Tri-Service Microbiome Consortium Symposium

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among U.S. Department of Defense (DoD) organizations and to facilitate resource, material and information sharing among consortium members. The 2019 annual symposium was held 22–24 October 2019 at Wright-Patterson Air Force Base in Dayton, OH. Presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) human microbiomes; 2) transitioning products into Warfighter solutions; 3) environmental microbiomes; 4) engineering microbiomes; and 5) microbiome simulation and characterization. Collectively, the symposium provided an update on the scope of current DoD microbiome research efforts, highlighted innovative research being done in academia and industry that can be leveraged by the DoD, and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 3rd annual TSMC symposium

Scaffold Vaccines for Generating Robust and Tunable Antibody Responses

Traditional bolus vaccines often fail to sustain robust adaptive immune responses, typically requiring multiple booster shots for optimal efficacy. Additionally, these provide few opportunities to control the resulting subclasses of antibodies produced, which can mediate effector functions relevant to distinct disease settings. Here, it is found that three scaffold-based vaccines, fabricated from poly(lactide-co-glycolide) (PLG), mesoporous silica rods, and alginate cryogels, induce robust, long-term antibody responses to a model peptide antigen gonadotropin-releasing hormone with single-shot immunization. Compared to a bolus vaccine, PLG vaccines prolong germinal center formation and T follicular helper cell responses. Altering the presentation and release of the adjuvant (cytosine-guanosine oligodeoxynucleotide, CpG) tunes the resulting IgG subclasses. Further, PLG vaccines elicit strong humoral responses against disease-associated antigens HER2 peptide and pathogenic E. coli, protecting mice against E. coli challenge more effectively than a bolus vaccine. Scaffold-based vaccines may thus enable potent, durable and versatile humoral immune responses against disease