Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes?

The evolution of genome size as well as structure and organization of genomes belongs among the key questions of genome biology. Here we show, based on a comparative analysis of 30 genomes, that there is generally a tight correlation between the number of genes per chromosome and the length of the respective chromosome in eukaryotic genomes. The surprising exceptions to this pattern are placental mammalian genomes. We identify the number and, more importantly, the uneven distribution of gene deserts among chromosomes, i.e., long (>500 kb) stretches of DNA that do not encode for genes, as the main contributing factor for the observed anomaly of eutherian genomes. Gene-rich placental mammalian chromosomes have smaller proportions of gene deserts and vice versa. We show that the uneven distribution of gene deserts is a derived character state of eutherians. The functional and evolutionary significance of this particular feature of eutherian genomes remains to be explained

Socioeconomic factors and health status disparities associated with difficulty in ADLs and IADLs among long-lived populations in Brazil: a cross-sectional study

© 2021 The Authors. Published by Sage. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://journals.sagepub.com/doi/full/10.1177/00469580211007264Objective: To evaluate the association between socioeconomic factors, health status, and Functional Capacity (FC) in the oldest senior citizens in a metropolis and a poor rural region of Brazil. Method: Cross-sectional study of 417 seniors aged ≥80 years, data collected through Brazil’s Health, Well-being and Aging survey. FC assessed by self-reporting of difficulties in Activities of Daily Living (ADLs) and Instrumental Activities of Daily Living (IADLs). Chi-square tests and multiple logistic regression analyses were performed using “R” statistical software. Results: Socioeconomic and demographic inequalities in Brazil can influence FC in seniors aged 80 years and older. Comparatively, urban long-lived people had a higher prevalence of difficulties for ADLs and rural ones showed more difficulties for IADLs. Among urban oldest seniors, female gender and lower-income were correlated with difficulties for IADLs. Among rural oldest seniors, female gender, stroke, joint disease, and inadequate weight independently were correlated with difficulties for ADLs, while the number of chronic diseases was associated with difficulties for IADLs. Conclusion: Financial constraints may favor the development of functional limitations among older seniors in large urban centers. In poor rural areas, inadequate nutritional status and chronic diseases may increase their susceptibility to functional decline

Performance of the First Short Model 150-mm-Aperture Nb3Sn Quadrupole MQXFS for the High-Luminosity LHC Upgrade

The U.S. LHC Accelerator Research Program (LARP) and CERN combined their efforts in developing Nb Sn magnets for the high-luminosity LHC upgrade. The ultimate goal of this collaboration is to fabricate large aperture Nb Sn quadrupoles for the LHC interaction regions. These magnets will replace the present 70-mm-Aperture NbTi quadrupole triplets for expected increase of the LHC peak luminosity up to 5 × 10 cm s or more. Over the past decade, LARP successfully fabricated and tested short and long models of 90 and 120-mm-Aperture Nb Sn quadrupoles. Recently, the first short model of 150-mm-diameter quadrupole MQXFS was built with coils fabricated both by LARP and CERN. The magnet performance was tested at Fermilab's vertical magnet test facility. This paper reports the test results, including the quench training at 1.9 K, ramp rate and temperature dependence, as well as protection heater studies. 3 3 3 34 -2 -

Progress on HL-LHC Nb3Sn Magnets

The high-luminosity Large Hadron Collider (HL-LHC) project aims at allowing to increase the collisions in the LHC by a factor of ten in the decade 2025-2035. One essential element is the superconducting magnet around the interaction region points, where the large aperture magnets will be installed to allow to further reduce the beam size in the interaction point. The core of this upgrade is the Nb Sn triplet, made up of 150-mm aperture quadrupoles in the range of 7-8 m. The project is being shared between the European Organization for Nuclear Research and the US Accelerator Upgrade Program, based on the same design, and on the two strand technologies. The project is ending the short model phase, and entering the prototype construction. We will report on the main results of the short model program, including the quench performance and field quality. A second important element is the 11 T dipole that replaces a standard dipole making space for additional collimators. The magnet is also ending the model development and entering the prototype phase. A critical point in the design of this magnet is the large current density, allowing increase of the field from 8 to 11 T with the same coil cross section as in the LHC dipoles. This is also the first two-in-one Nb Sn magnet developed so far. We will report the main results on the test and the critical aspects. 3

Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis

<p>Abstract</p> <p>Background</p> <p>The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments. The use of mutual information to identify distinctive residues responsible for functional variants makes this approach highly suitable for analyzing large sets of sequences. To support mutual information analysis, we developed the AVANA software, which utilizes sequence annotations to select sets for comparison, according to user-specified criteria. The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the mutation history of these components.</p> <p>Results</p> <p>We compared over 3,000 PB2 protein sequences of human-transmissible and avian isolates, to produce a catalogue of sites involved in adaptation to human-to-human transmission. This analysis identified 17 characteristic sites, five of which have been present in human-transmissible strains since the 1918 Spanish flu pandemic. Sixteen of these sites are located in functional domains, suggesting they may play functional roles in host-range specificity. The catalogue of characteristic sites was used to derive sequence signatures from historical isolates. These signatures, arranged in chronological order, reveal an evolutionary timeline for the adaptation of the PB2 protein to human hosts.</p> <p>Conclusion</p> <p>By providing the most complete elucidation to date of the functional components participating in PB2 protein adaptation to humans, this study demonstrates that mutual information is a powerful tool for comparative characterization of sequence sets. In addition to confirming previously reported findings, several novel characteristic sites within PB2 are reported. Sequence signatures generated using the characteristic sites catalogue characterize concisely the adaptation characteristics of individual isolates. Evolutionary timelines derived from signatures of early human influenza isolates suggest that characteristic variants emerged rapidly, and remained remarkably stable through subsequent pandemics. In addition, the signatures of human-infecting H5N1 isolates suggest that this avian subtype has low pandemic potential at present, although it presents more human adaptation components than most avian subtypes.</p

Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene

Mutations in PROP1 are a common genetic cause of multiple pituitary hormone deficiency (MPHD). We used a comparative genomics approach to predict the transcriptional regulatory domains of Prop1 and tested them in cell culture and mice. A BAC transgene containing Prop1 completely rescues the Prop1 mutant phenotype, demonstrating that the regulatory elements necessary for proper PROP1 transcription are contained within the BAC. We generated DNA sequences from the PROP1 genes in lemur, pig, and five different primate species. Comparison of these with available human and mouse PROP1 sequences identified three putative regulatory sequences that are highly conserved. These are located in the PROP1 promoter proximal region, within the first intron of PROP1, and downstream of PROP1. Each of the conserved elements elicited orientation-specific enhancer activity in the context of the Drosophila alcohol dehydrogenase minimal promoter in both heterologous and pituitary-derived cells lines. The intronic element is sufficient to confer dorsal expansion of the pituitary expression domain of a transgene, suggesting that this element is important for the normal spatial expression of endogenous Prop1 during pituitary development. This study illustrates the usefulness of a comparative genomics approach in the identification of regulatory elements that may be the site of mutations responsible for some cases of MPHD