Exploring the removal of Spo11 and topoisomerases from DNA breaks in S. cerevisiae by human Tyrosyl DNA Phosphodiesterase 2.

Meiotic recombination is initiated by DNA double-strand breaks (DSBs) created by Spo11, a type-II topoisomerase-like protein that becomes covalently linked to DSB ends. Whilst Spo11 oligos-the products of nucleolytic removal by Mre11-have been detected in several organisms, the lifetime of the covalent Spo11-DSB precursor has not been determined and may be subject to alternative processing. Here, we explore the activity of human Tyrosyl DNA Phosphodiesterase, TDP2-a protein known to repair DNA ends arising from abortive topoisomerase activity-on Spo11 DSBs isolated from S. cerevisiae cells. We demonstrate that TDP2 can remove Spo11 peptides from ssDNA oligos and dsDNA ends even in the presence of competitor genomic DNA. Interestingly, TDP2-processed DSB ends are refractory to resection by Exo1, suggesting that ssDNA generated by Mre11 may be essential in vivo to facilitate HR at Spo11 DSBs even if TDP2 were active. Moreover, although TDP2 can remove Spo11 peptides in vitro, TDP2 expression in meiotic cells was unable to remove Spo11 in vivo-contrasting its ability to aid repair of topoisomerase-induced DNA lesions. These results suggest that Spo11-DNA, but not topoisomerase-DNA cleavage complexes, are inaccessible to the TDP2 enzyme, perhaps due to occlusion by higher-order protein complexes at sites of meiotic recombination.

Adherence to antiretroviral therapy among people living with HIV attending medication-assisted treatment clinics in Dar es Salaam, Tanzania: a cross-sectional study.

Introduction: the prevalence of human immunodeficiency virus (HIV) among people who inject drugs (PWIDs) in Tanzania is estimated at 35%, significantly surpassing the 4.6% HIV prevalence of the general population. People who inject drugs living with HIV have been reported to exhibit lower adherence to antiretroviral therapy (ART), leading to increased rates of mortality, morbidity, and HIV transmission. This study assessed adherence to ART and associated factors among PWIDs in Dar es Salaam. Methods: this cross-sectional study involved 277 PWIDs living with HIV who attended MAT clinics in Dar es Salaam from May to July 2022. Antiretroviral therapy adherence was assessed using a validated one-month self-recall medication adherence scale, and associated factors were obtained through a structured questionnaire. Statistical analyses included chi-square tests, Fisher exact tests, and log-binomial regression. Data were analyzed using STATA version 15, with a p-value of <0.05 considered statistically significant. Results: this study found that 83% of the study participants had a high level of adherence to ART. Additionally, the results revealed that PWIDS who consume alcohol were less likely to have high adherence to ART (aPR 0.820). On the other hand, higher odds of ART adherence were observed among participants who had family support (aPR 1.028) and those who had adequate knowledge of ART benefits (aPR 1.285). Conclusion: the government and development partners should implement novel interventions such as alcohol reduction programs, ART education, and expanded HIV community outreach services. These interventions have the potential to improve ART adherence and reduce HIV transmission among PWIDs.

Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference.

During meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, in S. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we provide evidence that DSB clustering is abolished when meiotic prophase timing is extended via deletion of the NDT80 transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, when Tel1 is absent but Ndt80 is present and thus cells are able to rapidly exit meiotic prophase, genome-wide maps of Spo11-DSB formation are skewed towards pericentromeric regions and regions that load pro-DSB factors early-revealing regions of preferential priming-but this effect is abolished when NDT80 is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering-a phenomenon that is exacerbated in tel1Δ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.

Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri.

Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.

Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis.

DNA double-strand break (DSB) repair by homologous recombination (HR) uses a DNA template with similar sequence to restore genetic identity. Allelic DNA repair templates can be found on the sister chromatid or homologous chromosome. During meiotic recombination, DSBs preferentially repair from the homologous chromosome, with a proportion of HR events generating crossovers. Nevertheless, regions of similar DNA sequence exist throughout the genome, providing potential DNA repair templates. When DSB repair occurs at these non-allelic loci (termed ectopic recombination), chromosomal duplications, deletions and rearrangements can arise. Here, we characterize in detail ectopic recombination arising between a dispersed pair of inverted repeats in wild-type Saccharomyces cerevisiae at both a local and a chromosomal scale-the latter identified via gross chromosomal acentric and dicentric chromosome rearrangements. Mutation of the DNA damage checkpoint clamp loader Rad24 and the RecQ helicase Sgs1 causes an increase in ectopic recombination. Unexpectedly, additional mutation of the RecA orthologues Rad51 and Dmc1 alters-but does not abolish-the type of ectopic recombinants generated, revealing a novel class of inverted chromosomal rearrangement driven by the single-strand annealing pathway. These data provide important insights into the role of key DNA repair proteins in regulating DNA repair pathway and template choice during meiosis.

Concerted cutting by Spo11 illuminates meiotic DNA break mechanics.

Genetic recombination arises during meiosis through the repair of DNA double-strand breaks (DSBs) that are created by Spo11, a topoisomerase-like protein1,2. Spo11 DSBs form preferentially in nucleosome-depleted regions termed hotspots3,4, yet how Spo11 engages with its DNA substrate to catalyse DNA cleavage is poorly understood. Although most recombination events are initiated by a single Spo11 cut, here we show in Saccharomyces cerevisiae that hyperlocalized, concerted Spo11 DSBs separated by 33 to more than 100 base pairs also form, which we term 'double cuts'. Notably, the lengths of double cuts vary with a periodicity of 10.5 base pairs, which is conserved in yeast and mice. This finding suggests a model in which the orientation of adjacent Spo11 molecules is fixed relative to the DNA helix-a proposal supported by the in vitro DNA-binding properties of the Spo11 core complex. Deep sequencing of meiotic progeny identifies recombination scars that are consistent with repair initiated from gaps generated by adjacent Spo11 DSBs. Collectively, these results revise our present understanding of the mechanics of Spo11-DSB formation and expand on the original concepts of gap repair during meiosis to include DNA gaps that are generated by Spo11 itself.

Finding Purpose in the Conservation of Biodiversity by the Commingling of Science and Ethics.

Averting the biodiversity crisis requires closing a gap between how humans tend to behave, individually and collectively, and how we ought to behave-"ought to" in the sense of behaviors required to avert the biodiversity crisis. Closing that gap requires synthesizing insight from ethics with insights from social and behavioral sciences. This article contributes to that synthesis, which presents in several provocative hypotheses: (i) Lessening the biodiversity crisis requires promoting pro-conservation behavior among humans. Doing so requires better scientific understanding of how one's sense of purpose in life affects conservation-relevant behaviors. Psychology and virtue-focused ethics indicate that behavior is importantly influenced by one's purpose. However, conservation psychology has neglected inquiries on (a) the influence of one's purpose (both the content and strength of one's purpose) on conservation-related behaviors and (b) how to foster pro-conservation purposes; (ii) lessening the biodiversity crisis requires governance-the regulation of behavior by governments, markets or other organization through various means, including laws, norms, and power-to explicitly take conservation as one of its fundamental purposes and to do so across scales of human behaviors, from local communities to nations and corporations; (iii) lessening the biodiversity crisis requires intervention via governance to nudge human behavior in line with the purpose of conservation without undue infringement on other basic values. Aligning human behavior with conservation is inhibited by the underlying purpose of conservation being underspecified. Adequate specification of conservation's purpose will require additional interdisciplinary research involving insights from ethics, social and behavioral sciences, and conservation biology.

A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome.

DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes-and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage-distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

Regulatory control of DNA end resection by Sae2 phosphorylation.

DNA end resection plays a critical function in DNA double-strand break repair pathway choice. Resected DNA ends are refractory to end-joining mechanisms and are instead channeled to homology-directed repair. Using biochemical, genetic, and imaging methods, we show that phosphorylation of Saccharomyces cerevisiae Sae2 controls its capacity to promote the Mre11-Rad50-Xrs2 (MRX) nuclease to initiate resection of blocked DNA ends by at least two distinct mechanisms. First, DNA damage and cell cycle-dependent phosphorylation leads to Sae2 tetramerization. Second, and independently, phosphorylation of the conserved C-terminal domain of Sae2 is a prerequisite for its physical interaction with Rad50, which is also crucial to promote the MRX endonuclease. The lack of this interaction explains the phenotype of rad50S mutants defective in the processing of Spo11-bound DNA ends during meiotic recombination. Our results define how phosphorylation controls the initiation of DNA end resection and therefore the choice between the key DNA double-strand break repair mechanisms.

The evolution of offensive realism.

Offensive realism, a theory of international relations, holds that states are disposed to competition and conflict because they are self-interested, power maximizing, and fearful of other states. Moreover, it argues that states are obliged to behave this way because doing so favors survival in the international system. Debate continues as to whether modern states actually do, or should, behave in this way, but we are struck by a different question. In this article, we ask whether the three core assumptions about behavior in offensive realism-self-help, power maximization, and outgroup fear-have any basis in scientific knowledge about human behavioral evolution. We find that these precise traits are not only evolutionarily adaptive but also empirically common across the animal kingdom, especially in primate and human societies. Based on these findings, we hypothesize that states behave as offensive realists predict not just because of anarchy in the modern international system but also because of the legacy of our evolution. In short, offensive realism may really be describing the nature of the human species more than the nature of the international system. If our hypothesis is correct, then evolutionary theory offers the following: (1) a novel ultimate cause of offensive realist behavior; (2) an extension of offensive realism to any domain in which humans compete for power; and (3) an explanation for why individual leaders themselves, and not just states, seek power. However, a key insight from evolution is that the primacy of self-help, power maximization, and outgroup fear does not necessarily condemn individuals or groups to competition and conflict; rather, these traits can in themselves give rise to cooperation and alliances.

Reduced Anticoagulant Effect of Dabigatran in a Patient Receiving Concomitant Phenytoin.

Dabigatran, a direct thrombin inhibitor, is an oral anticoagulant indicated for the prevention of stroke in patients with atrial fibrillation (AF) and for the treatment and prevention of deep vein thrombosis and pulmonary embolism. Dabigatran, as well as the other new anticoagulants-rivaroxaban, apixaban, and edoxaban-are substrates for P-glycoprotein (P-gp). Although the U.S. labeling for rivaroxaban and apixaban states to avoid concomitant use with phenytoin, a known P-gp inducer, the U.S. labeling for dabigatran and edoxaban are less clear. We describe the first case report, to our knowledge, documenting a drug interaction between phenytoin and dabigatran by using laboratory measurements of dabigatran serum concentrations. A 45-year-old African-American man was admitted to the inpatient cardiology service following defibrillations from his implantable cardioverter defibrillator. The patient was evaluated and received appropriate antitachycardia pacing for atrial tachyarrhythmias for an episode of ventricular tachycardia (VT), and antiarrhythmic therapy with sotalol was initiated to reduce both his AF and VT burden. On review of the patient's medications for potential interactions, it was discovered that the patient was taking both dabigatran and phenytoin. To determine the magnitude of this drug interaction prior to making a change in his anticoagulation regimen, a dabigatran serum concentration was measured. This concentration was undetectable, indicating that phenytoin had a significant influence on dabigatran's metabolism and that this patient was at high risk for stroke. Clinicians should be aware of this interaction between phenytoin and dabigatran as well as with all other new oral anticoagulants. In patients taking phenytoin who require an anticoagulant, only warfarin should be prescribed to minimize the risk of stroke. In addition, the prescribing information for dabigatran should be updated to include other medications that result in a significant reduction in dabigatran serum concentrations, such as phenytoin.

Cardiac rehabilitation in African Americans: evidence for poorer outcomes compared with whites, especially in women and diabetic participants.

BACKGROUND: Cardiac rehabilitation (CR) improves coronary artery disease risk factors and mortality. Outcomes after CR in African Americans (AAs) compared with whites have not been studied extensively. METHODS: A total of 1,096 patients (169 AAs, 927 whites) were enrolled in a 36-session CR program for ischemic heart disease or postcardiac surgery. The program consisted of exercise, lifestyle modification, and pharmacotherapy. RESULTS: After CR, quality of life, blood pressure, and low-density lipoprotein cholesterol improved significantly in both AAs and whites, although to a lesser degree in AAs. Whites also had significant improvements in weight and triglyceride concentrations. Overall, mean peak exercise capacity, measured in metabolic equivalents (METs), improved by only 1.6 (95% CI 1.3-1.8) in AAs compared with 2.4 (2.3-2.6) in CCs (P< .001 for AAs vs CCs). African American women had the least improvement in METs, but changes were still significant (1.1 [CI 0.9-1.4]). The subgroup with the least improvement in METs was AA diabetic patients (1.4 (CI 1.1-1.7]). CONCLUSION: African Americans derive a significant benefit from CR, but not to the same degree as whites, based on changes in risk factors and in exercise capacity. Within both ethnic groups, both women and diabetic patients appeared to have markedly less improvement.

Effect of early enrollment on outcomes in cardiac rehabilitation.

Outpatient cardiac rehabilitation (CR) is most beneficial when delivered 1 to 3 weeks after the index cardiac event. The effects of delayed enrollment on subsequent outcomes are unclear. A total of 1,241 patients were enrolled in CR after recent (<1 year) treatment of cardiac events or postcardiac surgery. Risk factors and metabolic equivalent levels (METs) during aerobic exercise were calculated before and after CR. The mean CR delay time was 34 days (maximum of 327). Delay time >30 days was associated with older age, female gender, nonwhite race, being unemployed, and increased length of hospital stay before CR after index cardiac event (p <0.05 vs 0 to 15 and 16 to 30 days for all comparisons). Patients with delay time >30 days had significant improvements in all CR metrics, but peak METs and weight improvements were lesser in magnitude compared with patients with CR delay times 0 to 15 and 16 to 30 days. After multivariate adjustment, delay time >30 days remained an independent predictor of decreased MET improvement compared with delay time 0 to 15 days (ß = -0.59, p <0.001). In conclusion, time to enrollment in CR varies substantially and is independently linked to demographics and length of index hospital stay. Delayed enrollment in CR is directly related to patient outcomes. Although all patients showed improvements in key metrics regardless of delay time, CR was of greatest benefit, particularly for weight and exercise capacity, when initiated within 15 days of the index event.

Effects of cardiac rehabilitation in diabetic patients: both cardiac and noncardiac factors determine improvement in exercise capacity.

BACKGROUND: Diabetic patients have a worse prognosis than nondiabetic patients after myocardial infarction. Although exercise improves risk factors, exercise capacity, and mortality, it is still unclear if these benefits are the same as in nondiabetics. Furthermore, although exercise tolerance is predicted by systolic and diastolic dysfunction in nondiabetics, its role as a predictor of exercise capacity in diabetics remains unclear. HYPOTHESIS: Diabetics and nondiabetics see a similar improvement in their cardiac risk factors and exercise parameters from exercise-based cardiac rehabilitation (CR). METHODS: A series of 370 diabetics and 942 nondiabetics entered a 36-session outpatient CR program after interventions for coronary heart disease or after bypass or cardiac valve surgery. The program consisted of physical exercise, lifestyle modification, and pharmacotherapy. RESULTS: Quality of life, weight, blood pressure, and lipid profiles improved significantly in both groups during the 12-week program. Baseline metabolic equivalents (METs) were lower in diabetics vs nondiabetics at the start of CR (2.4 vs 2.7, P < 0.001). Although both groups increased their exercise capacity, diabetics had less improvement (change in METs 1.7 vs 2.6, P < 0.001). Significant predictors for improvement after CR included age, sex, and weight, as well as both systolic and diastolic function. After adjustment for these, diabetes remained a significant predictor of reduced improvement in exercise capacity. CONCLUSIONS: Diabetics saw a significant benefit in quality of life, weight, exercise tolerance, and cardiac risk factors, but to a lesser extent when compared with nondiabetics. The mechanisms for poorer improvement in diabetics following CR also include noncardiac factors and require further study.

Comparison of usefulness of secondary prevention of coronary disease in patients <80 versus ≥80 years of age.

The population older than 80 years is increasing but data on prevention of coronary disease in this age group are sparse. The present study compared the improvement in quality of life, lipid profile, blood pressure, weight, and physical performance after cardiac rehabilitation in patients <80 versus ≥80 years of age. A total of 1,112 patients, of whom 79 were older than 80 years, entered a 36-session outpatient cardiac rehabilitation program after interventions for coronary heart disease. The program consisted of physical exercise, lifestyle modification, and pharmacotherapy. Quality of life improved by 1.3 (95% confidence interval [CI] 0.6 to 2.0) in octogenarians and 1.8 (95% CI 1.5 to 2.1) in younger patients (p = 0.21), whereas weight decreased by 1.7 lbs (95% CI -2.9 to -0.4) and 3.1 lbs (95% CI -3.6 to -2.5, p = 0.04), respectively. In hypertensive patients, systolic blood pressure decreased from 155 ± 11 to 133 ± 20 mm Hg in octogenarians versus 155 ± 13 to 130 ± 20 mm Hg in younger patients, reducing the prevalence of hypertension to approximately 10% in both groups. Low-density lipoprotein cholesterol decreased by 16 mg/dl (95% CI -27 to -5) versus 19 mg/dl (95% CI -22 to -16), increasing the percentage of patients at recommended goals from 32% to 46% in the elderly (p = 0.04) and from 18% to 30% in younger patients (p <0.001). Metabolic equivalent levels increased by 1.0 (95% CI 0.7 to 1.3) in octogenarians versus 2.4 (95% CI 2.2 to 2.5) in younger patients (p <0.001). In conclusion, patients ≥80 years of age in an active secondary prevention program derive a significant benefit in well being, risk factors, and exercise capacity and should not be denied such treatment because of age.

The evolution of error: error management, cognitive constraints, and adaptive decision-making biases.

Counterintuitively, biases in behavior or cognition can improve decision making. Under conditions of uncertainty and asymmetric costs of 'false-positive' and 'false-negative' errors, biases can lead to mistakes in one direction but - in so doing - steer us away from more costly mistakes in the other direction. For example, we sometimes think sticks are snakes (which is harmless), but rarely that snakes are sticks (which can be deadly). We suggest that 'error management' biases: (i) have been independently identified by multiple interdisciplinary studies, suggesting the phenomenon is robust across domains, disciplines, and methodologies; (ii) represent a general feature of life, with common sources of variation; and (iii) offer an explanation, in error management theory (EMT), for the evolution of cognitive biases as the best way to manage errors under cognitive and evolutionary constraints.

Dead certain: confidence and conservatism predict aggression in simulated international crisis decision-making.

Evolutionary psychologists have suggested that confidence and conservatism promoted aggression in our ancestral past, and that this may have been an adaptive strategy given the prevailing costs and benefits of conflict. However, in modern environments, where the costs and benefits of conflict can be very different owing to the involvement of mass armies, sophisticated technology, and remote leadership, evolved tendencies toward high levels of confidence and conservatism may continue to be a contributory cause of aggression despite leading to greater costs and fewer benefits. The purpose of this paper is to test whether confidence and conservatism are indeed associated with greater levels of aggression-in an explicitly political domain. We present the results of an experiment examining people's levels of aggression in response to hypothetical international crises (a hostage crisis, a counter-insurgency campaign, and a coup). Levels of aggression (which range from concession to negotiation to military attack) were significantly predicted by subjects' (1) confidence that their chosen policy would succeed, (2) score on a liberal-conservative scale, (3) political party affiliation, and (4) preference for the use of military force in real-world U.S. policy toward Iraq and Iran. We discuss the possible adaptive and maladaptive implications of confidence and conservatism for the prospects of war and peace in the modern world.

Providing a Spanish interpreter using low-cost videoconferencing in a community health centre: a pilot study using tablet computers.

BACKGROUND: The advent of more mobile, more reliable, and more affordable videoconferencing technology finally makes it realistic to offer remote foreign language interpretation in the office setting. Still, such technologies deserve proof of acceptability to clinicians and patients before there is widespread acceptance and routine use. OBJECTIVE: We sought to examine: (1) the audio and video technical fidelity of iPad/Facetime(TM) software, (2) the acceptability of videoconferencing to patients and clinicians. METHODS: The convenience sample included Spanish-speaking adult patients at a community health care medicine clinic in 2011. Videoconferencing was conducted using two iPads(TM) connecting patient/physician located in the clinic examination room, and the interpreter in a remote/separate office in the same building. A five-item survey was used to solicit opinions on overall quality of the videoconferencing device, audio/video integrity/fidelity, perception of encounter duration, and attitude toward future use. RESULTS: Twenty-five patients, 18 clinicians and 5 interpreters participated in the project. Most patients (24/25) rated overall quality of videoconferencing as good/excellent with only 1 'fair' rating. Eleven patients rated the amount of time as no longer than in-person, and nine reported it as shorter than inperson. Most patients, 94.0% (24/25), favoured using videoconferencing during future visits. For the 18 clinicians, the results were similar. CONCLUSIONS: Based on our experience at a singlesite community health centre, the videoconferencing technology appeared to be flawless, and both patients and clinicians were satisfied. Expansion of videoconferencing to other off-site healthcare professionals should be considered in the search for more cost-effective healthcare.