Coevolved Multidrug-Resistant HIV-1 Protease and Reverse Transcriptase Influences Integrase Drug Susceptibility and Replication Fitness

Integrase strand transfer inhibitors (InSTIs) are recommended agents in first-line combination antiretroviral therapy (cART). We examined the evolution of drug resistance mutations throughout HIV-1 pol and the effects on InSTI susceptibility and viral fitness. We performed single-genome sequencing of full-length HIV-1 pol in a highly treatment-experienced patient, and determined drug susceptibility of patient-derived HIV-1 genomes using a phenotypic assay encompassing full-length pol gene. We show the genetic linkage of multiple InSTI-resistant haplotypes containing major resistance mutations at Y143, Q148 and N155 to protease inhibitor (PI) and reverse transcriptase inhibitor (RTI) resistance mutations. Phenotypic analysis of viruses expressing patient-derived IN genes with eight different InSTI-resistant haplotypes alone or in combination with coevolved protease (PR) and RT genes exhibited similar levels of InSTI susceptibility, except for three haplotypes that showed up to 3-fold increases in InSTI susceptibility (p ≤ 0.032). The replicative fitness of most viruses expressing patient-derived IN only significantly decreased, ranging from 8% to 56% (p ≤ 0.01). Interestingly, the addition of coevolved PR + RT significantly increased the replicative fitness of some haplotypes by up to 73% (p ≤ 0.024). Coevolved PR + RT contributes to the susceptibility and viral fitness of patient-derived IN viruses. Maintaining patients on failing cART promotes the selection of fitter resistant strains, and thereby limits future therapy options

An optimized strategy to measure protein stability highlights differences between cold and hot unfolded states

Macromolecular crowding ought to stabilize folded forms of proteins, through an excluded volume effect. This explanation has been questioned and observed effects attributed to weak interactions with other cell components. Here we show conclusively that protein stability is affected by volume exclusion and that the effect is more pronounced when the crowder's size is closer to that of the protein under study. Accurate evaluation of the volume exclusion effect is made possible by the choice of yeast frataxin, a protein that undergoes cold denaturation above zero degrees, because the unfolded form at low temperature is more expanded than the corresponding one at high temperature. To achieve optimum sensitivity to changes in stability we introduce an empirical parameter derived from the stability curve. The large effect of PEG 20 on cold denaturation can be explained by a change in water activity, according to Privalov's interpretation of cold denaturation

Catastrophic chromosomal restructuring during genome elimination in plants.

Genome instability is associated with mitotic errors and cancer. This phenomenon can lead to deleterious rearrangements, but also genetic novelty, and many questions regarding its genesis, fate and evolutionary role remain unanswered. Here, we describe extreme chromosomal restructuring during genome elimination, a process resulting from hybridization of Arabidopsis plants expressing different centromere histones H3. Shattered chromosomes are formed from the genome of the haploid inducer, consistent with genomic catastrophes affecting a single, laggard chromosome compartmentalized within a micronucleus. Analysis of breakpoint junctions implicates breaks followed by repair through non-homologous end joining (NHEJ) or stalled fork repair. Furthermore, mutation of required NHEJ factor DNA Ligase 4 results in enhanced haploid recovery. Lastly, heritability and stability of a rearranged chromosome suggest a potential for enduring genomic novelty. These findings provide a tractable, natural system towards investigating the causes and mechanisms of complex genomic rearrangements similar to those associated with several human disorders

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.

Common Variable Immunodeficiency Disorders (CVIDs) are the most prevalent cause of primary antibody failure. CVIDs are highly variable and a genetic causes have been identified in <5% of patients. Here, we performed whole genome sequencing (WGS) of 34 CVID patients (94% sporadic) and combined them with transcriptomic profiling (RNA-sequencing of B cells) from three patients and three healthy controls. We identified variants in CVID disease genes TNFRSF13B, TNFRSF13C, LRBA and NLRP12 and enrichment of variants in known and novel disease pathways. The pathways identified include B-cell receptor signalling, non-homologous end-joining, regulation of apoptosis, T cell regulation and ICOS signalling. Our data confirm the polygenic nature of CVID and suggest individual-specific aetiologies in many cases. Together our data show that WGS in combination with RNA-sequencing allows for a better understanding of CVIDs and the identification of novel disease associated pathways

Informal carers' health-related quality of life and patient experience in primary care: evidence from 195,364 carers in England responding to a national survey.

BACKGROUND: We aim to describe the health-related quality of life of informal carers and their experiences of primary care. METHODS: Responses from the 2011-12 English General Practice Patient Survey, including 195,364 informal carers, were analysed using mixed effect logistic regressions controlling for age, gender, ethnicity and social deprivation to describe carer health-related quality of life (mobility, self-care, usual activities, pain, and anxiety/depression, measured using EQ-5D) and primary care experience (access, continuity and communication). RESULTS: Informal carers reported poorer health-related quality of life than non-carers of similar age, gender, ethnicity and social deprivation. Increasing caring commitment was associated with worse EQ-5D scores, with carers of 50+ hours a week scoring 0.05 points lower than non-carers (95 % CI 0.05 to 0.04), equivalent to 18 fewer days of full health annually. Considering each domain of EQ-5D separately, carers of 50+ hours/week were more likely to report pain OR = 1.53 (1.50-1.57), p < 0.0001, and anxiety/depression OR = 1.69 (1.66-1.73), p < 0.0001, than non-carers. Younger carers scored lower on EQ-5D than non-carer peers but the converse was true among over-85s. In the most deprived areas carers reported the equivalent of 37 fewer days of full health annually than carers in the most affluent areas. On average, carers reported poorer patient experiences in all areas of primary care than non-carers (odds ratios 0.84-0.97), with this difference being most marked in the domain of access. CONCLUSIONS: Informal carers experience a double disadvantage of poorer health-related quality of life and poorer patient experience in primary care. We find no evidence for health benefits of caregiving. We recommend physicians identify and treat carer health problems, including pain and anxiety/depression, particularly among young, deprived and high time-commitment carers. Improving patient experience for carers, including access to primary care, should be a priority.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s12875-015-0277-

Simple study designs in ecology produce inaccurate estimates of biodiversity responses

Monitoring the impacts of anthropogenic threats and interventions to mitigate these threats is key to understanding how to best conserve biodiversity. Ecologists use many different study designs to monitor such impacts. Simpler designs lacking controls (e.g. Before-After (BA) and After) or pre-impact data (e.g. Control-Impact (CI)) are considered to be less robust than more complex designs (e.g. Before-After Control-Impact (BACI) or Randomised Controlled Trials (RCTs)). However, we lack quantitative estimates of how much less accurate simpler study designs are in ecology. Understanding this could help prioritise research and weight studies by their design’s accuracy in meta-analysis and evidence assessment. 2. We compared how accurately five study designs estimated the true effect of a simulated environmental impact that caused a step-change response in a population’s density. We derived empirical estimates of several simulation parameters from 47 ecological datasets to ensure our simulations were realistic. We measured design performance by determining the percentage of simulations where: (i) the true effect fell within the 95% Confidence Intervals of effect size estimates, and (ii) each design correctly estimated the true effect’s direction and magnitude. We also considered how sample size affected their performance. 3. We demonstrated that BACI designs performed: 1.3-1.8 times better than RCTs; 2.9-4.2 times vs BA; 3.2-4.6 times vs CI; and 7.1-10.1 times vs After designs (depending on sample size), when correctly estimating true effect’s direction and magnitude to within ±30%. Although BACI designs suffered from low power at small sample sizes, they outperformed other designs for almost all performance measures. Increasing sample size improved BACI design accuracy but only increased the precision of simpler designs around biased estimates. 4. Synthesis and applications. We suggest that more investment in more robust designs is needed in ecology since inferences from simpler designs, even with large sample sizes may be misleading. Facilitating this requires longer-term funding and stronger research-practice partnerships. We also propose ‘accuracy weights’ and demonstrate how they can weight studies in three recent meta-analyses by accounting for study design and sample size. We hope these help decision-makers and meta-analysts better account for study design when assessing evidence

Longitudinal Atomic Beam Spin Echo Experiments: A possible way to study Parity Violation in Hydrogen

We discuss the propagation of hydrogen atoms in static electric and magnetic fields in a longitudinal atomic beam spin echo (lABSE) apparatus. Depending on the choice of the external fields the atoms may acquire both dynamical and geometrical quantum mechanical phases. As an example of the former, we show first in-beam spin rotation measurements on atomic hydrogen, which are in excellent agreement with theory. Additional calculations of the behaviour of the metastable 2S states of hydrogen reveal that the geometrical phases may exhibit the signature of parity-(P-)violation. This invites for possible future lABSE experiments, focusing on P-violating geometrical phases in the lightest of all atoms.Comment: 6 pages, 4 figure

Down-regulation of GP130 signaling sensitizes bladder cancer to cisplatin by impairing Ku70 DNA repair signaling and promoting apoptosis

Chemoresistance is one of the barriers for the development of bladder cancer treatments. Previously, we showed that glycoprotein-130 (GP130) is overexpressed in chemoresistant bladder cancer cells and that knocking down GP130 expression reduced cell viability. In our current work, we showed that down-regulation of GP130 sensitized bladder cancer cells to cisplatin-based chemotherapy by activating DNA repair signaling. We performed immunohistochemistry and demonstrated a positive correlation between the levels of Ku70, an initiator of canonical non-homologous end joining repair (c-NHEJ) and suppressor of apoptosis, and GP130 in human bladder cancer specimens. GP130 knockdown by SC144, a small molecule inhibitor, in combination with cisplatin, increased the number of DNA lesions, specifically DNA double-stranded breaks, with a subsequent increase in apoptosis and reduced cell viability. Furthermore, GP130 inhibition attenuated Ku70 expression in bladder and breast cancer cells as well as in transformed kidney cells. In addition, we fabricated a novel polymer-lipid hybrid delivery system to facilitate GP130 siRNA delivery that had a similar efficiency when compared with Lipofectamine, but induced less toxicity

Vision and Foraging in Cormorants: More like Herons than Hawks?

Background Great cormorants (Phalacrocorax carbo L.) show the highest known foraging yield for a marine predator and they are often perceived to be in conflict with human economic interests. They are generally regarded as visually-guided, pursuit-dive foragers, so it would be expected that cormorants have excellent vision much like aerial predators, such as hawks which detect and pursue prey from a distance. Indeed cormorant eyes appear to show some specific adaptations to the amphibious life style. They are reported to have a highly pliable lens and powerful intraocular muscles which are thought to accommodate for the loss of corneal refractive power that accompanies immersion and ensures a well focussed image on the retina. However, nothing is known of the visual performance of these birds and how this might influence their prey capture technique. Methodology/Principal Findings We measured the aquatic visual acuity of great cormorants under a range of viewing conditions (illuminance, target contrast, viewing distance) and found it to be unexpectedly poor. Cormorant visual acuity under a range of viewing conditions is in fact comparable to unaided humans under water, and very inferior to that of aerial predators. We present a prey detectability model based upon the known acuity of cormorants at different illuminances, target contrasts and viewing distances. This shows that cormorants are able to detect individual prey only at close range (less than 1 m). Conclusions/Significance We conclude that cormorants are not the aquatic equivalent of hawks. Their efficient hunting involves the use of specialised foraging techniques which employ brief short-distance pursuit and/or rapid neck extension to capture prey that is visually detected or flushed only at short range. This technique appears to be driven proximately by the cormorant's limited visual capacities, and is analogous to the foraging techniques employed by herons

What do hospital decision-makers in Ontario, Canada, have to say about the fairness of priority setting in their institutions?

BACKGROUND: Priority setting, also known as rationing or resource allocation, occurs at all levels of every health care system. Daniels and Sabin have proposed a framework for priority setting in health care institutions called 'accountability for reasonableness', which links priority setting to theories of democratic deliberation. Fairness is a key goal of priority setting. According to 'accountability for reasonableness', health care institutions engaged in priority setting have a claim to fairness if they satisfy four conditions of relevance, publicity, appeals/revision, and enforcement. This is the first study which has surveyed the views of hospital decision makers throughout an entire health system about the fairness of priority setting in their institutions. The purpose of this study is to elicit hospital decision-makers' self-report of the fairness of priority setting in their hospitals using an explicit conceptual framework, 'accountability for reasonableness'. METHODS: 160 Ontario hospital Chief Executive Officers, or their designates, were asked to complete a survey questionnaire concerning priority setting in their publicly funded institutions. Eight-six Ontario hospitals completed this survey, for a response rate of 54%. Six close-ended rating scale questions (e.g. Overall, how fair is priority setting at your hospital?), and 3 open-ended questions (e.g. What do you see as the goal(s) of priority setting in your hospital?) were used. RESULTS: Overall, 60.7% of respondents indicated their hospitals' priority setting was fair. With respect to the 'accountability for reasonableness' conditions, respondents indicated their hospitals performed best for the relevance (75.0%) condition, followed by appeals/revision (56.6%), publicity (56.0%), and enforcement (39.5%). CONCLUSIONS: For the first time hospital Chief Executive Officers within an entire health system were surveyed about the fairness of priority setting practices in their institutions using the conceptual framework 'accountability for reasonableness'. Although many hospital CEOs felt that their priority setting was fair, ample room for improvement was noted, especially for the enforcement condition