The primary structure of three hemoglobin chains from the indigo snake (Drymarchon corais erebennus, Serpentes): First evidence for αD chains and two β chain types in snakes

The hemoglobin of the indigo snake (Drymarchon corais erebennus, Colubrinae) consists of two components, HbA and HbD, in the ratio of 1:1. They differ in both their alpha and beta chains. The amino acid sequences of both alpha chains (alpha(A) and alpha(D)) and one beta chain (betaI) were determined. The presence of an alpha(D)chain in a snake hemoglobin is described for the first time. A comparison of all snake beta chain sequences revealed the existence of two paralogous beta chain types in snakes as well, which are designated as betaI and betaII type. For the discussion of the physiological properties of Drymarchon hemoglobin, the sequences were compared with those of the human alpha and beta chains and those of the closely related water snake Liophis miliaris where functional data are available. Among the heme contacts, the substitution alpha(D)58(E7)His-->Gln is unusual but most likely without any effect. The residues responsible for the main part of the Bohr effect are the same as in mammalian hemoglobins. In each of the three globin chains only two residues at positions involved in the alpha1/beta2 interface contacts, most important for the stability and the properties of the hemoglobin molecule, are substituted with regard to human hemoglobin. On the contrary, nine, eleven, and six alpha1/beta1 contact residues are replaced in the alpha(A), alpha(D), betaI chains, respectively

Growth analysis in the potato crop under different irrigation levels

Conduziu-se um experimento na Fazenda São Manoel, localizada em São Manuel, SP, pertencente à Faculdade de Ciências Agronômicas da Universidade Estadual Paulista, com o objetivo de avaliar os efeitos de diferentes lâminas de irrigação no crescimento da cultura da batata (Solanum tuberosum ssp. tuberosum), cultivar Aracy. O ensaio foi instalado em um Latossolo Vermelho-Escuro, textura arenosa, sob uma cobertura de plástico. O delineamento experimental utilizado foi o de blocos ao acaso, com cinco tratamentos, cinco coletas de plantas para fins de análise de crescimento, e quatro repetições. Os tratamentos consistiam em irrigar a batata quando a tensão da água no solo atingia 15, 35, 55, 75 e 1.500 kPa. O aumento nas lâminas de irrigação induz incremento no índice de área foliar, na duração da área foliar, na taxa de crescimento relativo e na taxa assimilatória líquida. _________________________________________________________________________________________ ABSTRACT: An experiment was carried out at Fazenda São Manoel, pertaining to the Faculdade de Ciências Agronômicas of the Universidade Estadual Paulista, São Manuel, SP, Brazil, to evaluate irrigation levels in the potato (Solanum tuberosum ssp. tuberosum) growth, cv. Aracy. This work was installed in a sandy Dark-Red Latosol, under a plastic cover. The experimental design was an entirely randomized block composed by irrigation in the potato plots when the soil water potential has reached 15, 35, 55, 75 and 1,500 kPa, and five plant sampling time with four replicates. It was found that higher irrigation levels led to increase of the leaf area index, leaf area duration, relative growth rate and net assimilation rate

Growth of pea plants (Pisum sativum L.) subjected to different soil water potentials : physiological indexes

A ervilha é cultivada no Brasil Central, durante o inverno seco, exigindo para o pleno êxito da cultura o uso da irrigação. Assim, o presente trabalho se propõe a avaliar os efeitos do potencial da água no solo nos índices fisiológicos da análise quantitativa de crescimento de plantas de ervilha (Pisum sativum L.). O experimento foi montado em casa de vegetação, em solos de textura argilosa, com delineamento experimental inteiramente casualizado, com quatro tratamentos decorrentes de potenciais mínimos da água no solo (-33, -100, -200 e -1500 kPa) em três repetições, cada qual contendo duas plantas de ervilha, cultivar Caprice. Os resultados obtidos evidenciaram que a redução do potencial água no solo, induziu o decréscimo na área foliar, sem interferir no comportamento da razão de massa foliar, razão de área foliar, taxa assimilatória líquida e taxa de crescimento relativo. _________________________________________________________________________________________ ABSTRACT: Peas are cultivated in the central region of Brazil, during the dry winter, demanding for the complete success the use of irrigation. Therefore, the present work has the aim of evaluating soil water potential effects on the indexes of physiological growth analysis of peas (Pisum sativum L.). The experiment was carried out in a greenhouse using soils of clayey texture, in a fully randomized design, with four treatments, based on minimum soil water potentials (-33, -100, -200 and -1500 kPa) in three replicates, each one containing two pea plants Caprice cultivar. The results obtained indicate that the reduction of soil water potential induced the decrease of leaf area, but did not interfer on the behaviour of leaf weight ratio, leaf area ratio, net assimilation rate and relative growth rate

Landscape of mutations in early stage primary cutaneous melanoma: An InterMEL study

It is unclear why some melanomas aggressively metastasize while others remain indolent. Available studies employing multi-omic profiling of melanomas are based on large primary or metastatic tumors. We examine the genomic landscape of early-stage melanomas diagnosed prior to the modern era of immunological treatments. Untreated cases with Stage II/III cutaneous melanoma were identified from institutions throughout the United States, Australia and Spain. FFPE tumor sections were profiled for mutation, methylation and microRNAs. Preliminary results from mutation profiling and clinical pathologic correlates show the distribution of four driver mutation sub-types: 31% BRAF; 18% NRAS; 21% NF1; 26% Triple Wild Type. BRAF mutant tumors had younger age at diagnosis, more associated nevi, more tumor infiltrating lymphocytes, and fewer thick tumors although at generally more advanced stage. NF1 mutant tumors were frequent on the head/neck in older patients with severe solar elastosis, thicker tumors but in earlier stages. Triple Wild Type tumors were predominantly male, frequently on the leg, with more perineural invasion. Mutations in TERT, TP53, CDKN2A and ARID2 were observed often, with TP53 mutations occurring particularly frequently in the NF1 sub-type. The InterMEL study will provide the most extensive multi-omic profiling of early-stage melanoma to date. Initial results demonstrate a nuanced understanding of the mutational and clinicopathological landscape of these early-stage tumors

InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma

INTRODUCTION: We are conducting a multicenter study to identify classifiers predictive of disease-specific survival in patients with primary melanomas. Here we delineate the unique aspects, challenges, and best practices for optimizing a study of generally small-sized pigmented tumor samples including primary melanomas of at least 1.05mm from AJTCC TNM stage IIA-IIID patients. We also evaluated tissue-derived predictors of extracted nucleic acids' quality and success in downstream testing. This ongoing study will target 1,000 melanomas within the international InterMEL consortium. METHODS: Following a pre-established protocol, participating centers ship formalin-fixed paraffin embedded (FFPE) tissue sections to Memorial Sloan Kettering Cancer Center for the centralized handling, dermatopathology review and histology-guided coextraction of RNA and DNA. Samples are distributed for evaluation of somatic mutations using next gen sequencing (NGS) with the MSK-IMPACTTM assay, methylation-profiling (Infinium MethylationEPIC arrays), and miRNA expression (Nanostring nCounter Human v3 miRNA Expression Assay). RESULTS: Sufficient material was obtained for screening of miRNA expression in 683/685 (99%) eligible melanomas, methylation in 467 (68%), and somatic mutations in 560 (82%). In 446/685 (65%) cases, aliquots of RNA/DNA were sufficient for testing with all three platforms. Among samples evaluated by the time of this analysis, the mean NGS coverage was 249x, 59 (18.6%) samples had coverage below 100x, and 41/414 (10%) failed methylation QC due to low intensity probes or insufficient Meta-Mixed Interquartile (BMIQ)- and single sample (ss)- Noob normalizations. Six of 683 RNAs (1%) failed Nanostring QC due to the low proportion of probes above the minimum threshold. Age of the FFPE tissue blocks (p<0.001) and time elapsed from sectioning to co-extraction (p = 0.002) were associated with methylation screening failures. Melanin reduced the ability to amplify fragments of 200bp or greater (absent/lightly pigmented vs heavily pigmented, p<0.003). Conversely, heavily pigmented tumors rendered greater amounts of RNA (p<0.001), and of RNA above 200 nucleotides (p<0.001). CONCLUSION: Our experience with many archival tissues demonstrates that with careful management of tissue processing and quality control it is possible to conduct multi-omic studies in a complex multi-institutional setting for investigations involving minute quantities of FFPE tumors, as in studies of early-stage melanoma. The study describes, for the first time, the optimal strategy for obtaining archival and limited tumor tissue, the characteristics of the nucleic acids co-extracted from a unique cell lysate, and success rate in downstream applications. In addition, our findings provide an estimate of the anticipated attrition that will guide other large multicenter research and consortia

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