Gut microbiota composition in himalayan and andean populations and its relationship with diet, lifestyle and adaptation to the high-altitude environment

Human populations living at high altitude evolved a number of biological adjustments to cope with a challenging environment characterised especially by reduced oxygen availability and limited nutritional resources. This condition may also affect their gut microbiota composition. Here, we explored the impact of exposure to such selective pressures on human gut microbiota by considering different ethnic groups living at variable degrees of altitude: the high-altitude Sherpa and low-altitude Tamang populations from Nepal, the high-altitude Aymara population from Bolivia, as well as a low-altitude cohort of European ancestry, used as control. We thus observed microbial profiles common to the Sherpa and Aymara, but absent in the low-altitude cohorts, which may contribute to the achievement of adaptation to high-altitude lifestyle and nutritional conditions. The collected evidences suggest that microbial signatures associated to these rural populations may enhance metabolic functions able to supply essential compounds useful for the host to cope with high altitude-related physiological changes and energy demand. Therefore, these results add another valuable piece of the puzzle to the understanding of the beneficial effects of symbiosis between microbes and their human host even from an evolutionary perspective

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

Faecal sludge management in Kathmandu valley : current situation and outlook

Kathmandu valley faces numerous environmental problems due to the rapid urban growth andunplanned settlement. One of the serious problems is the river and water pollution in the valleydue to disposal of untreated wastewater from households. Much effort is needed to improve theenvironmental sanitation situation. Experiences show that sewerage and large-scale wastewatertreatment systems are not the appropriate solution curbing pollution because often they are tooexpensive and require high operational costs. Therefore other alternative appropriate approachesneed to be explored. One of the alternatives would be to provide onsite excreta managementsystems such as use of septic tanks. However, these systems should be complemented by faecalsludge management (FSM). Currently, there is a lack of proper FSM system in the KathmanduValley. Thus this study aimed to explore and document the existing state of art practise andproblems in order to help to improve the situation and support for future planning of FSM.The study found that the issue of FSM has not been addressed at the policy level. There are nopolicies, standards and strategies developed so far. Some relevant legislation in relation toexcreta management such as the National Building Code and by laws of the municipalitymandates the need to construct septic tanks in each house. However, the enforcement of thecodes and by laws is very weak. Similarly, there are conflicting roles and responsibilitiesbetween stakeholders for water supply and sanitation management for Kathmandu Valley. Afew stakeholders are currently involved in FSM of the Kathmandu Valley such as theKathmandu Municipality (KMC), Private Operators collecting faecal sludge (FS), Manual PitEmptier and Private Households with septic tanks. Kathmandu Municipality has been playing alead role in FSM in the Kathmandu Valley.The characteristics of faecal sludge of the Kathmandu Valley show an average TS content of 27g/L out of which 65% of is volatile solids indicating that FS were only partially stabilised in theseptic tanks. The study estimated that around 65,000 to 130,000 m3 of FS is generated annuallyout of the share of mechanical emptying is around 60%. Currently, it is estimated that around10,000 m3 of FS is collected mechanically by different private operators and KMC. However,only 60% of this collected sludge is emptied in the treatment plant. Private sector collects about80% of the FS and the remaining is collected by KMC. The economic analysis of the FScollection service providers shows that private sector is profiting from the FSM collectionbusiness whereas the public sector like KMC is in loss. This indicates poor operational andfinancial management system within the public sectors. The difference between the estimatedannual FS generation and the current mechanical emptying rate shows that there is morebusiness opportunity in future.To improve the FSM situation in the Valley; the study foresees the need to bring coordinationbetween the different stakeholders involved in water supply and sanitation. An Urban NationalSanitation Policy should be developed and must address the issue of FSM as an integralcomponent of sanitation. The study also recommends the need for improvement in the overallsystem of faecal FSM from the point of generation to disposal and treatment practices.Mandatory provisions for septic tank construction backed up by standard designs could improvethe use of septic tanks at household level. Similarly, it is recommended that treatment andmanagement of overall FSM can be improved by strengthening the private sector to operate andmanage small-scale treatment plants under the supervision of local municipalities, authoritiesand civil groups

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species

The ATLAS experiment at the CERN Large Hadron Collider: a description of the detector configuration for Run 3

The ATLAS detector is installed in its experimental cavern at Point 1 of the CERN Large Hadron Collider. During Run 2 of the LHC, a luminosity of ℒ = 2 × 1034 cm-2 s-1 was routinely achieved at the start of fills, twice the design luminosity. For Run 3, accelerator improvements, notably luminosity levelling, allow sustained running at an instantaneous luminosity of ℒ = 2 × 1034 cm-2 s-1, with an average of up to 60 interactions per bunch crossing. The ATLAS detector has been upgraded to recover Run 1 single-lepton trigger thresholds while operating comfortably under Run 3 sustained pileup conditions. A fourth pixel layer 3.3 cm from the beam axis was added before Run 2 to improve vertex reconstruction and b-tagging performance. New Liquid Argon Calorimeter digital trigger electronics, with corresponding upgrades to the Trigger and Data Acquisition system, take advantage of a factor of 10 finer granularity to improve triggering on electrons, photons, taus, and hadronic signatures through increased pileup rejection. The inner muon endcap wheels were replaced by New Small Wheels with Micromegas and small-strip Thin Gap Chamber detectors, providing both precision tracking and Level-1 Muon trigger functionality. Trigger coverage of the inner barrel muon layer near one endcap region was augmented with modules integrating new thin-gap resistive plate chambers and smaller-diameter drift-tube chambers. Tile Calorimeter scintillation counters were added to improve electron energy resolution and background rejection. Upgrades to Minimum Bias Trigger Scintillators and Forward Detectors improve luminosity monitoring and enable total proton-proton cross section, diffractive physics, and heavy ion measurements. These upgrades are all compatible with operation in the much harsher environment anticipated after the High-Luminosity upgrade of the LHC and are the first steps towards preparing ATLAS for the High-Luminosity upgrade of the LHC. This paper describes the Run 3 configuration of the ATLAS detector