Photospheric and Subphotospheric Dynamics of Emerging Magnetic Flux

Magnetic fields emerging from the Sun's interior carry information about physical processes of magnetic field generation and transport in the convection zone. Soon after appearance on the solar surface the magnetic flux gets concentrated in sunspot regions and causes numerous active phenomena on the Sun. This paper discusses some properties of the emerging magnetic flux observed on the solar surface and in the interior. A statistical analysis of variations of the tilt angle of bipolar magnetic regions during the emergence shows that the systematic tilt with respect to the equator (the Joy's law) is most likely established below the surface. However, no evidence of the dependence of the tilt angle on the amount of emerging magnetic flux, predicted by the rising magnetic flux rope theories, is found. Analysis of surface plasma flows in a large emerging active region reveals strong localized upflows and downflows at the initial phase of emergence but finds no evidence for large-scale flows indicating future appearance a large-scale magnetic structure. Local helioseismology provides important tools for mapping perturbations of the wave speed and mass flows below the surface. Initial results from SOHO/MDI and GONG reveal strong diverging flows during the flux emergence, and also localized converging flows around stable sunspots. The wave speed images obtained during the process of formation of a large active region, NOAA 10488, indicate that the magnetic flux gets concentrated in strong field structures just below the surface. Further studies of magnetic flux emergence require systematic helioseismic observations from the ground and space, and realistic MHD simulations of the subsurface dynamics.Comment: 21 pages, 15 figures, to appear in Space Science Review

Advances in Global and Local Helioseismology: an Introductory Review

Helioseismology studies the structure and dynamics of the Sun's interior by observing oscillations on the surface. These studies provide information about the physical processes that control the evolution and magnetic activity of the Sun. In recent years, helioseismology has made substantial progress towards the understanding of the physics of solar oscillations and the physical processes inside the Sun, thanks to observational, theoretical and modeling efforts. In addition to the global seismology of the Sun based on measurements of global oscillation modes, a new field of local helioseismology, which studies oscillation travel times and local frequency shifts, has been developed. It is capable of providing 3D images of the subsurface structures and flows. The basic principles, recent advances and perspectives of global and local helioseismology are reviewed in this article.Comment: 86 pages, 46 figures; "Pulsation of the Sun and Stars", Lecture Notes in Physics, Vol. 832, Rozelot, Jean-Pierre; Neiner, Coralie (Eds.), 201

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

Semi-automated assembly of high-quality diploid human reference genomes

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Phylogeny and Classification of Cercomonadida (Protozoa, Cercozoa): Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov.

Cercomonads (=Cercomonadida) are biflagellate gliding bacterivorous protozoa, abundant and diverse in soil and freshwater. We establish 56 new species based on 165 cultures, differential interference contrast microscopy, and 18S and ITS2 rDNA sequencing, and a new genus Cavernomonas studied by scanning electron microscopy. We fundamentally revise the phylogeny and classification of cercomonad Cercozoa. We describe 40 Cercomonas species (35novel), six Eocercomonas (five novel), two Cavernomonas, and 18 Paracercomonas species (14 novel). We obtained additional cercomonad clade A (Cercomonas, Eocercomonas, Cavernomonas) sequences from multiple environmental DNA libraries. The most commonly cultivated genotypes are not the commonest in environmental DNA, suggesting that cercomonad ecology is far more complex than implied by laboratory cultures. Cercomonads have never been isolated from saline environments, although some species can grow in semi-saline media in the laboratory, and environmental DNA libraries regularly detect them in coastal marine sediments. The first ultrastructural study of an anaerobic cercozoan, Paracercomonas anaerobica sp. nov., a highly divergent cercomonad, shows much simpler ciliary roots than in clade A cercomonads, a ciliary hub-lattice and axosome, and mitochondria with tubular cristae, consistent with it being only facultatively anaerobic. We also describe Agitata tremulans gen. et sp. nov., previously misidentified as Cercobodo(=Dimastigamoeba) agilis Moroff. (C) 2009 Elsevier GmbH. All rights reserve

Chikungunya and dengue fever among hospitalized febrile patients in Northern Tanzania

10.4269/ajtmh.2012.11-0393American Journal of Tropical Medicine and Hygiene861171-177AJTH