Evidence for direct contact between the RPA3 subunit of the human replication protein A and single-stranded DNA

Replication Protein A is a single-stranded (ss) DNA-binding protein that is highly conserved in eukaryotes and plays essential roles in many aspects of nucleic acid metabolism, including replication, recombination, DNA repair and telomere maintenance. It is a heterotrimeric complex consisting of three subunits: RPA1, RPA2 and RPA3. It possesses four DNA-binding domains (DBD), DBD-A, DBD-B and DBD-C in RPA1 and DBD-D in RPA2, and it binds ssDNA via a multistep pathway. Unlike the RPA1 and RPA2 subunits, no ssDNA-RPA3 interaction has as yet been observed although RPA3 contains a structural motif found in the other DBDs. We show here using 4-thiothymine residues as photoaffinity probe that RPA3 interacts directly with ssDNA on the 3′-side on a 31 nt ssDNA

A serological assay to detect SARS-CoV-2 seroconversion in humans

Development of an enzyme-linked immunosorbent assay to detect antibodies to the SARS-CoV-2 spike protein in human sera and plasma. Here, we describe a serological enzyme-linked immunosorbent assay for the screening and identification of human SARS-CoV-2 seroconverters. This assay does not require the handling of infectious virus, can be adjusted to detect different antibody types in serum and plasma and is amenable to scaling. Serological assays are of critical importance to help define previous exposure to SARS-CoV-2 in populations, identify highly reactive human donors for convalescent plasma therapy and investigate correlates of protection.Peer reviewe

Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: Differentiation of subpopulations

Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei’s genetic distance between populations increased significantly with altitude (R2 = 0.71) and geographic distance (R2 = 0.78). On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei’s gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst) was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R2 = 0.63). Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D’2IS exceeded D’2ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool

Levering proteomic analysis of Pseudomonas fluorescens mediated resistance responses in tomato during pathogenicity of Fusarium oxysporum f. sp. oxysporum

The tomato, one of the world’s most extensively cultivated and consumed vegetable crops is negatively impacted by various pathogens. This study aimed to observe the differentially expressed proteins in tomato samples in plant–pathogen-biocontrol interactions. The fungal pathogen associated with wilted plants were isolated and identified based on its morphological and molecular characteristics. Fourteen strains of Pseudomonas fluorescens from agricultural soils were identified and described using biochemical assays, molecular analyses, and screening for antagonistic ability against the Fusarium wilt pathogen. Results demonstrated that the potential of P. fluorescens (TPf12) positively influenced the expression of antagonism against tomato wilt disease. A total of 14 proteins expressed differently were revealed in the 2D-PAGE-MS investigation. Proteins such as nucleoside diphosphate kinase, phenylalanine ammonia-lyase, protein kinase family protein, Ser/Thr protein kinase-like are unchanged in FOL pathogen interaction, but up-regulated in FOL + TPf12 treated roots, and lipid transfer-like protein, and phenylalanine ammonia-lyase were down-regulated in FOL infested roots and upregulated in FOL + TPf12 treated tomato roots. Phenylalanine ammonia-lyase protein expression is commonly found in TPf12 bioenriched roots, and FOL + TPf12 treated roots, indicating its role in response to the application of TPf12 in tomato. A GC–MS analysis was performed to detect the bioactive metabolites synthesized by TPf12. Molecular docking investigations were conducted using the maestro’s GLIDE docking module of the Schrodinger Software program. Among the secondary metabolites, Cyclohexanepropanoic acid, 2-oxo-, methyl ester (CAS), and 3-o-(4-o-Beta-D-Galactopyranosyl-Beta-D-Galactopyraosyl)-2-Acetylamino-2-Deoxy-D-Galactose were shown to be top-ranked with a least docking score against each differently expressed proteins. The profiled molecules expressed differently due to plant-pathogen-biocontrol interactions may be directly or incidentally involved in the wilt disease resistance of tomato plants

High-Performance Computing for SKA Transient Search: Use of FPGA based Accelerators -- a brief review

This paper presents the High-Performance computing efforts with FPGA for the accelerated pulsar/transient search for the SKA. Case studies are presented from within SKA and pathfinder telescopes highlighting future opportunities. It reviews the scenario that has shifted from offline processing of the radio telescope data to digitizing several hundreds/thousands of antenna outputs over huge bandwidths, forming several 100s of beams, and processing the data in the SKA real-time pulsar search pipelines. A brief account of the different architectures of the accelerators, primarily the new generation Field Programmable Gate Array-based accelerators, showing their critical roles to achieve high-performance computing and in handling the enormous data volume problems of the SKA is presented here. It also presents the power-performance efficiency of this emerging technology and presents potential future scenarios.Comment: Accepted for JoAA, SKA Special issue on SKA (2022

Azimuthal correlations for inclusive 2-jet, 3-jet, and 4-jet events in pp collisions at root s=13 TeV

Azimuthal correlations between the two jets with the largest transverse momenta p(T) in inclusive 2-, 3-, and 4-jet events are presented for several regions of the leading jet p(T) up to 4 TeV. For 3- and 4-jet scenarios, measurements of the minimum azimuthal angles between any two of the three or four leading p(T) jets are also presented. The analysis is based on data from proton-proton collisions collected by the CMS Collaboration at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1). Calculations based on leading-order matrix elements supplemented with parton showering and hadronization do not fully describe the data, so next-to-leading-order calculations matched with parton shower and hadronization models are needed to better describe the measured distributions. Furthermore, we show that azimuthal jet correlations are sensitive to details of the parton showering, hadronization, and multiparton interactions. Anext-to-leading-order calculation matched with parton showers in the MC@NLO method, as implemented in HERWIG 7, gives a better overall description of the measurements than the powheg method.Peer reviewe

Population differentiation of Southern Indian male lineages correlates with agricultural expansions predating the caste system

Christina J. Adler, Alan Cooper, Clio S.I. Der Sarkissian and Wolfgang Haak are contributors to the Genographic ConsortiumPrevious studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed, <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna(caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.GaneshPrasad ArunKumar, David F. Soria-Hernanz, Valampuri John Kavitha, Varatharajan Santhakumari Arun, Adhikarla Syama, Kumaran Samy Ashokan, Kavandanpatti Thangaraj Gandhirajan, Koothapuli Vijayakumar, Muthuswamy Narayanan, Mariakuttikan Jayalakshmi, Janet S. Ziegle, Ajay K. Royyuru, Laxmi Parida, R. Spencer Wells, Colin Renfrew, Theodore G. Schurr, Chris Tyler Smith, Daniel E. Platt, Ramasamy Pitchappan, The Genographic Consortiu

Nurses' perceptions of aids and obstacles to the provision of optimal end of life care in ICU

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