Elevated rates of horizontal gene transfer in the industrialized human microbiome

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.Peer reviewe

Current Status of a Model System: The Gene Gp-9 and Its Association with Social Organization in Fire Ants

The Gp-9 gene in fire ants represents an important model system for studying the evolution of social organization in insects as well as a rich source of information relevant to other major evolutionary topics. An important feature of this system is that polymorphism in social organization is completely associated with allelic variation at Gp-9, such that single-queen colonies (monogyne form) include only inhabitants bearing B-like alleles while multiple-queen colonies (polygyne form) additionally include inhabitants bearing b-like alleles. A recent study of this system by Leal and Ishida (2008) made two major claims, the validity and significance of which we examine here. After reviewing existing literature, analyzing the methods and results of Leal and Ishida (2008), and generating new data from one of their study sites, we conclude that their claim that polygyny can occur in Solenopsis invicta in the U.S.A. in the absence of expression of the b-like allele Gp-9b is unfounded. Moreover, we argue that available information on insect OBPs (the family of proteins to which GP-9 belongs), on the evolutionary/population genetics of Gp-9, and on pheromonal/behavioral control of fire ant colony queen number fails to support their view that GP-9 plays no role in the chemosensory-mediated communication that underpins regulation of social organization. Our analyses lead us to conclude that there are no new reasons to question the existing consensus view of the Gp-9 system outlined in Gotzek and Ross (2007)

Resilience Among Urban African American Male Adolescents: A Study of the Protective Effects of Sociopolitical Control on Their Mental Health

Resilience refers to the notion that some people succeed in the face of adversity. In a risk-protective model of resilience, a protective factor interacts with a risk factor to mitigate the occurrence of a negative outcome. This study tested longitudinally the protective effects of sociopolitical control on the link between helplessness and mental health. The study included 172 urban, male, African American adolescents, who were interviewed twice, 6 months apart. Sociopolitical control was defined as the beliefs about one's capabilities and efficacy in social and political systems. Two mental health outcomes were examined—psychological symptoms and self-esteem. Regression analyses to predict psychological symptoms and self-esteem over time were conducted. High levels of sociopolitical control were found to limit the negative consequences of helplessness on mental health. The results suggest that sociopolitical control may help to protect youths from the negative consequences of feelings of helplessness. Implications for prevention strategies are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44052/1/10464_2004_Article_416735.pd

The global abundance of tree palms

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

A randomized controlled efficacy trial of behavioral activation for concurrent stimulant use and sexual risk for HIV acquisition among MSM: project IMPACT study protocol.

BackgroundIn the United States, problematic stimulant use is a prevalent and difficult to treat problem among men who have sex with men (MSM), as well as a major driver of HIV transmission through the large number of sexual partners and concomitant condomless anal sex (CAS). Evidence-based behavioral studies that address problematic stimulant use in MSM at risk for HIV infection are also lacking. In this paper, we describe the design of a behavioral intervention trial to reduce sexual risk behavior and stimulant use in HIV-uninfected MSM.MethodsThis study, funded by the National Institute on Drug Abuse (NIDA), is a randomized controlled trial (RCT) testing an integrated HIV risk reduction and behavioral activation counseling intervention (IMPACT) for HIV-uninfected, stimulant using MSM in Boston, MA, and Miami, FL. Participants are randomized (2:2:1) to either (1) the IMPACT intervention; (2) a relaxation condition, an active therapy time- and intensity-matched control; or (3) a standard of care risk reduction counseling comparison. At enrollment, all participants receive an HIV test and pre- and post-test counseling. The primary outcome is the difference in the rate of change in the number of self-reported condomless anal sex acts without the protection of consistent Pre-Exposure Prophylaxis (PrEP) use, as well as reductions in stimulant use during the prior 4-months. Major assessments are conducted at baseline, 4-, 8-, and 12-month follow-up visits.DiscussionEffective and sustainable behavioral interventions are sorely needed to reduce HIV acquisition in stimulant using MSM at risk for HIV infection. In this study, we will evaluate the evidence of efficacy of the IMPACT intervention to reduce HIV acquisition in HIV-uninfected, stimulant-using MSM. If found effective, the intervention tested here holds promise for being readily integrated into real-world clinical settings.Trial registrationClinicalTrials.gov number NCT03175159 , registered June 5, 2017

A randomized controlled efficacy trial of behavioral activation for concurrent stimulant use and sexual risk for HIV acquisition among MSM: project IMPACT study protocol

Abstract Background In the United States, problematic stimulant use is a prevalent and difficult to treat problem among men who have sex with men (MSM), as well as a major driver of HIV transmission through the large number of sexual partners and concomitant condomless anal sex (CAS). Evidence-based behavioral studies that address problematic stimulant use in MSM at risk for HIV infection are also lacking. In this paper, we describe the design of a behavioral intervention trial to reduce sexual risk behavior and stimulant use in HIV-uninfected MSM. Methods This study, funded by the National Institute on Drug Abuse (NIDA), is a randomized controlled trial (RCT) testing an integrated HIV risk reduction and behavioral activation counseling intervention (IMPACT) for HIV-uninfected, stimulant using MSM in Boston, MA, and Miami, FL. Participants are randomized (2:2:1) to either (1) the IMPACT intervention; (2) a relaxation condition, an active therapy time- and intensity-matched control; or (3) a standard of care risk reduction counseling comparison. At enrollment, all participants receive an HIV test and pre- and post-test counseling. The primary outcome is the difference in the rate of change in the number of self-reported condomless anal sex acts without the protection of consistent Pre-Exposure Prophylaxis (PrEP) use, as well as reductions in stimulant use during the prior 4-months. Major assessments are conducted at baseline, 4-, 8-, and 12-month follow-up visits. Discussion Effective and sustainable behavioral interventions are sorely needed to reduce HIV acquisition in stimulant using MSM at risk for HIV infection. In this study, we will evaluate the evidence of efficacy of the IMPACT intervention to reduce HIV acquisition in HIV-uninfected, stimulant-using MSM. If found effective, the intervention tested here holds promise for being readily integrated into real-world clinical settings. Trial registration ClinicalTrials.gov number NCT03175159, registered June 5, 2017