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

Extremely low gestational age and very low birthweight for gestational age are risk factors for autism spectrum disorder in a large cohort study of 10-year-old children born at 23-27 weeks’ gestation

No prospective cohort study of high-risk children has used rigorous exposure assessment and optimal diagnostic procedures to examine the perinatal antecedents of autism spectrum disorder (ASD), separately among those with and without cognitive impairment

Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance.

Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus, an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought. To test the first hypotheses, we analyzed relationships between water quality parameters and maturity/distribution pattern of Delta Smelt. Salinity better explained the distribution pattern of Delta Smelt at subadult and adult stages compared with water temperature or turbidity. Although there are some freshwater locations where mature Delta Smelt can frequently be found during the spawning season, Delta Smelt at the final maturation stage (Stage 5: hydration) and post spawners appeared to be widespread in the area where salinity was below 1.0 during the spawning season. Therefore, Delta Smelt could theoretically spawn in any freshwater locations, with more specific spawning requirements in the wild (e.g., substrate type and depth) still unknown. Delta Smelt, which experienced dry and critically dry conditions (the 2013 and 2014 year-classes), showed smaller oocytes, and lower clutch size and gonadosomatic index compared with the fish caught in a wet year (2011 year-class) at the late vitellogenic stage (Stage 4 Late), suggesting reproductive performance was negatively affected by environmental conditions during the drought

The United States National Cancer Institute’s Coordinated Research Effort on Tobacco Use as a Major Cause of Morbidity and Mortality among People with HIV

The use of antiretroviral therapy for people with HIV (PWH) has improved life expectancy. However, PWH now lose more life-years to tobacco use than to HIV infection. Unfortunately, PWH smoke at higher rates and have more difficulty maintaining abstinence than the general population, compounding their risk for chronic disease. In this Commentary, we describe a United States National Cancer Institute-led initiative to address the relative lack of research focused on developing, testing, and implementing smoking cessation interventions for PWH. This initiative supports seven clinical trials designed to systematically test and/or develop and test adaptations of evidence-based smoking cessation interventions for PWH (eg, combination of behavioral and pharmacological). We summarize each project, including setting/recruitment sites, inclusion/exclusion criteria, interventions being tested, and outcomes. This initiative provides critical opportunities for collaboration and data harmonization across projects. The knowledge gained will inform strategies to assist PWH to promote and maintain abstinence, and ensure that these efforts are adaptable and scalable, thereby addressing one of the major threats to the health of PWH. Reducing smoking behavior may be particularly important during the COVID-19 pandemic given that smokers who become infected with SARS-CoV-2 may be at risk for more severe disease.ImplicationsThis Commentary describes a National Cancer Institute-led initiative to advance the science and practice of treating tobacco use among PWH, which is now responsible for more life years lost than HIV. We describe the scope of the problem, the objectives of the initiative, and a summary of the seven funded studies. Harmonization of data across projects will provide information related to treatment mediators and moderators that was not previously possible. Stakeholders interested in tobacco cessation, including researchers, clinicians and public health officials, should be aware of this initiative and the evidence-base it will generate to advance tobacco treatment among this high-risk population

Make greenhouse-gas accounting reliable - build interoperable systems Comment

Global integrated reporting is essential if the planet is to achieve net-zero emissions

Altered juvenile fish communities associated with invasive <i>Halophila stipulacea</i> seagrass habitats in the U.S. Virgin Islands

<div><p>Caribbean seagrass habitats provide food and protection for reef-associated juvenile fish. The invasive seagrass <i>Halophila stipulacea</i> is rapidly altering these seascapes. Since its arrival in the Caribbean in 2002, <i>H</i>. <i>stipulacea</i> has colonized and displaced native seagrasses, but the function of this invasive seagrass as a juvenile fish habitat remains unknown. To compare diversity, community structure, and abundance of juvenile fish between <i>H</i>. <i>stipulacea</i> and native seagrass beds, fish traps were deployed in four nearshore bays around St. Thomas, U.S. Virgin Islands. Traps were deployed in Frenchman, Lindbergh, and Sprat Bays for 24 h intervals in patches of bare sand, patches of <i>H</i>. <i>stipulacea</i> and patches of the native Caribbean seagrasses <i>Thalassia testudinum</i> and S<i>yringodium filiforme</i>. Traps were then deployed in Brewers Bay for 12 h intervals in stands of <i>H</i>. <i>stipulacea</i> and <i>S</i>. <i>filiforme</i>. Relative and total abundances of juvenile fish, identified at least to family, were compared across treatment habitats for each trap deployment period. The catch from <i>H</i>. <i>stipulacea</i>, compared to native seagrasses, comprised a greater abundance of nocturnal carnivores <i>Lutjanus synagris</i> (family Lutjanidae) and <i>Haemulon flavolineatum</i> (family Haemulidae). Additionally, the herbivore species <i>Sparisoma aurofrenatum</i> (family Labridae) and <i>Acanthurus bahianus</i> (family Acanthuridae) and the diurnal carnivore species <i>Pseudopeneus maculatus</i> (family Mullidae) were relatively scarce in <i>H</i>. <i>stipulacea</i>. The catch from sand was much smaller, compared to vegetated habitats, and comprised only <i>L</i>. <i>synagris</i>, <i>H</i>. <i>flavolineatum</i>, and <i>H</i>. <i>aurolineatum</i>. These results provide evidence of reduced family diversity and altered juvenile fish assemblages in <i>H</i>. <i>stipulacea</i>, driven by an abundance of some nocturnal carnivores and scarcity of herbivores and diurnal carnivores. The findings from the present work underpin the need for further investigation and mitigation of this invasion, particularly where <i>H</i>. <i>stipulacea</i> is driving seascape-alterations of key juvenile fish habitats.</p></div

Mean juvenile fish abundance in 12 h trap deployments.

<p>(A) Mean abundance of the total catch (<b>±</b> SEM), separated by treatment habitat and soak type. The contribution of each family to the mean abundance is indicated by stacked colored bars. For each guild, a legend with colors corresponding to each family and plots of the mean abundance (<b>± SEM)</b> across seagrass habitats are given for (B) nocturnal carnivores, (C) diurnal carnivores, and (D) herbivores.</p

NMDS of juvenile fish family relative abundance during 12 h deployments.

<p>Points represent individual traps, and 95% confidence ellipses indicate sampling distributions for each seagrass. Data were pooled across soak types.</p