Dynamics of early establishment of SARS-CoV-2 VOC Omicron lineages in Minas Gerais, Brazil

Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Brazil. In this study, we examined the effects of the Omicron introduction in Minas Gerais (MG), the second-most populous state of Brazil. A total of 430 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples from November 2021 to June 2022 from Belo Horizonte (BH) city were sequenced. These newly sequenced genomes comprise 72% of all previously available SARS-CoV-2 genomes for the city. Evolutionary analysis of novel viral genomes reveals that a great diversity of Omicron sublineages have circulated in BH, a pattern in-keeping with observations across Brazil more generally. Bayesian phylogeographic reconstructions indicate that this diversity is a product of a large number of international and national importations. As observed previously, São Paulo state is shown as a significant hub for viral spread throughout the country, contributing to around 70% of all viral Omicron introductions detected in MG

Isolation and functional characterization of a cotton ubiquitination-related promoter and 5'UTR that drives high levels of expression in root and flower tissues

<p>Abstract</p> <p>Background</p> <p>Cotton (<it>Gossypium </it>spp.) is an important crop worldwide that provides raw material to 40% of the textile fiber industry. Important traits have been studied aiming the development of genetically modified crops including resistance to insect and diseases, and tolerance to drought, cold and herbicide. Therefore, the characterization of promoters and regulatory regions is also important to achieve high gene expression and/or a specific expression pattern. Commonly, genes involved in ubiquitination pathways are highly and differentially expressed. In this study, we analyzed the expression of a cotton ubiquitin-conjugating enzyme (E2) family member with no previous characterization.</p> <p>Results</p> <p>Nucleotide analysis revealed high identity with cotton <it>E2 </it>homologues. Multiple alignment showed a premature stop codon, which prevents the encoding of the conserved cysteine residue at the <it>E2 </it>active site, and an intron that is spliced in <it>E2 </it>homologues, but not in <it>GhGDRP85</it>. The <it>GhGDRP85 </it>gene is highly expressed in different organs of cotton plants, and has high transcript levels in roots. Its promoter (uceApro2) and the 5'UTR compose a regulatory region named uceA1.7, and were isolated from cotton and studied in <it>Arabidopsis thaliana</it>. uceA1.7 shows strong expression levels, equaling or surpassing the expression levels of CaMV35S. The uceA1.7 regulatory sequence drives GUS expression 7-fold higher in flowers, 2-fold in roots and at similar levels in leaves and stems. GUS expression levels are decreased 7- to 15-fold when its 5'UTR is absent in uceApro2.</p> <p>Conclusions</p> <p>uceA1.7 is a strong constitutive regulatory sequence composed of a promoter (uceApro2) and its 5'UTR that will be useful in genetic transformation of dicots, having high potential to drive high levels of transgene expression in crops, particularly for traits desirable in flower and root tissues.</p

Classical and Quantum Solitons in the Symmetric Space Sine-Gordon Theories

We construct the soliton solutions in the symmetric space sine-Gordon theories. The latter are a series of integrable field theories in 1+1-dimensions which are associated to a symmetric space F/G, and are related via the Pohlmeyer reduction to theories of strings moving on symmetric spaces. We show that the solitons are kinks that carry an internal moduli space that can be identified with a particular co-adjoint orbit of the unbroken subgroup H of G. Classically the solitons come in a continuous spectrum which encompasses the perturbative fluctuations of the theory as the kink charge becomes small. We show that the solitons can be quantized by allowing the collective coordinates to be time-dependent to yield a form of quantum mechanics on the co-adjoint orbit. The quantum states correspond to symmetric tensor representations of the symmetry group H and have the interpretation of a fuzzy geometric version of the co-adjoint orbit. The quantized finite tower of soliton states includes the perturbative modes at the base.Comment: 53 pages, additional comments and small errors corrected, final journal versio

Consórcios de caupi e milho em cultivo orgânico para produção de grãos e espigas verdes.

No período de outono-inverno-primavera de 2007, foi conduzido um estudo em Seropédica, Região Metropolitana do estado do Rio de Janeiro (Baixada Fluminense), com o objetivo de avaliar diferentes tipos de consórcio entre caupi (cv. Mauá) e milho (cv. AG-1051), em sistema orgânico de produção. O experimento foi instalado em área de Argissolo Vermelho-Amarelo no delineamento de blocos ao acaso, com quatro repetições. Os tratamentos constaram de diferentes épocas ou intervalos de tempo de semeadura do caupi em relação à do milho, a saber: (E1) 21 dias antes do milho; (E2) 14 dias antes do milho; (E3) 7 dias antes do milho; e (E4) no mesmo dia do milho. Tratamentos correspondentes aos cultivos solteiros do caupi e do milho foram incluídos, ambos semeados na data do tratamento E4. O cultivo consorciado com o caupi não interferiu na produtividade do milho em espigas verdes e também em termos de comprimento e diâmetro basal dessas espigas, independentemente do intervalo entre semeaduras. Com referência ao caupi, a produtividade em grãos verdes no cultivo solteiro foi superior à dos consórcios com o milho. Os valores obtidos para os Índices de Equivalência de Área (IEA), foram todos acima de 1,0, indicando que os consórcios foram eficientes quanto ao desempenho agronômico/biológico. Considerando, ainda a produtividade de cada cultura participante do consórcio, a semeadura do caupi antecipada de 21 dias em relação à do milho afigura-se mais adequada ao manejo orgânico adotado e às condições edafoclimáticas da região

Genotype by environment interaction in Nelore cattle from five Brazilian states

Records from 75,941 Nelore cattle were used to determine the importance of genotype by environment interaction (GEI) in five Brazilian states. (Co)variance components were estimated by single-trait analysis (with yearling weight, W450, considered to be the same trait in all states) and multiple-trait analysis (with the record from each state considered to be a different trait). The direct heritability estimates for yearling weight were 0.51, 0.39, 0.44, 0.37 and 0.41 in the states of Goiás, Mato Grosso, São Paulo, Mato Grosso do Sul and Minas Gerais, respectively. The across-state genetic correlation estimates between Goiás and Mato Grosso, Goiás and Minas Gerais, São Paulo and Minas Gerais, and Mato Grosso do Sul and Minas Gerais ranged from 0.67 to 0.75. These estimates indicate that GEIs are biologically important. No interactions were observed between Goiás and São Paulo, Goiás and Mato Grosso do Sul, Mato Grosso and São Paulo, Mato Grosso and Mato Grosso do Sul, Mato Grosso and Minas Gerais, or São Paulo and Mato Grosso do Sul (0.82 to 0.97). Comparison of single and multiple-trait analyses showed that selection based on the former was less efficient in the presence of GEI, with substantial losses (up to 10%) during selection

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies

Antimalarial chemotherapy, globally reliant on artemisinin-based combination therapies (ACTs), is threatened by the spread of drug resistance in Plasmodium falciparum parasites. Here we use zinc-finger nucleases to genetically modify the multidrug resistance-1 transporter PfMDR1 at amino acids 86 and 184, and demonstrate that the widely prevalent N86Y mutation augments resistance to the ACT partner drug amodiaquine and the former first-line agent chloroquine. In contrast, N86Y increases parasite susceptibility to the partner drugs lumefantrine and mefloquine, and the active artemisinin metabolite dihydroartemisinin. The PfMDR1 N86 plus Y184F isoform moderately reduces piperaquine potency in strains expressing an Asian/African variant of the chloroquine resistance transporter PfCRT. Mutations in both digestive vacuole-resident transporters are thought to differentially regulate ACT drug interactions with host haem, a product of parasite-mediated haemoglobin degradation. Global mapping of these mutations illustrates where the different ACTs could be selectively deployed to optimize treatment based on regional differences in PfMDR1 haplotypes.This work was funded in part by the National Institutes of Health (R01 AI50234, AI124678 and AI109023) and a Burroughs Wellcome Fund Investigator in Pathogenesis of Infectious Diseases award to D.A.F. This research also received funding from the Portuguese Fundacao para a Ciencia e Tecnologia (FCT), cofunded by Programa Operacional Regional do Norte (ON.2-O Novo Norte); from the Quadro de Referencia Estrategico Nacional (QREN) through the Fundo Europeu de Desenvolvimento Regional (FEDER) and from the Projeto Estrategico - LA 26 - 2013-2014 (PEst-C/SAU/LA0026/2013). M.I.V. is the recipient of a postdoctoral fellowship from FCT/Ministerio da Ciencia e Ensino Superior, Portugal-MCES (SFRH/BPD/76614/2011). A.M.L. was supported by an Australian National Health and Medical Research Council (NHMRC) Overseas Biomedical Fellowship (585519). R.E.M. was supported by an NHMRC RD Wright Biomedical Fellowship (1053082). A.C.U. was supported by an Irving scholarship from Columbia University. We thank Dr Andrea Ecker for her help with plasmid design and Pedro Ferreira for his expert help with Fig. 6.info:eu-repo/semantics/publishedVersio