ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles

<p>Abstract</p> <p>Background</p> <p>Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organisms. For the common carp, an environmental model of aquacultural interest, large numbers of ESTs remained unidentified using BLAST sequence alignment. We have used the expression profiles from large-scale microarray experiments to suggest gene identities.</p> <p>Results</p> <p>Expression profiles from ~700 cDNA microarrays describing responses of 7 major tissues to multiple environmental stressors were used to define a co-expression landscape. This was based on the Pearsons correlation coefficient relating each gene with all other genes, from which a network description provided clusters of highly correlated genes as 'mountains'. We show that these contain genes with known identities and genes with unknown identities, and that the correlation constitutes evidence of identity in the latter. This procedure has suggested identities to 522 of 2701 unknown carp ESTs sequences. We also discriminate several common carp genes and gene isoforms that were not discriminated by BLAST sequence alignment alone. Precision in identification was substantially improved by use of data from multiple tissues and treatments.</p> <p>Conclusion</p> <p>The detailed analysis of co-expression landscapes is a sensitive technique for suggesting an identity for the large number of BLAST unidentified cDNAs generated in EST projects. It is capable of detecting even subtle changes in expression profiles, and thereby of distinguishing genes with a common BLAST identity into different identities. It benefits from the use of multiple treatments or contrasts, and from the large-scale microarray data.</p

Segmentação cognitiva de tradutores em formação: observação de comportamento tradutório de estudantes alemães

The project “Investigating the translation competence of apprentices in training: data collection and contrasting analysis of research results at German and Brazilian university” (PVB10375-2019) sought to contribute to studies on translation competence (PACTE, 2003, 2005, 2008). From August 2019 to July 2020, the data collected in Germany in 2018 (Leipnitz &amp; Pickbrenner, 2020) were systematized and compared with first results of the longitudinal study carried out in the Translation Course at UFPB in Brazil (Liparini Campos et al., 2015; Liparini Campos &amp; Leipnitz, 2017; Liparini Campos et al., 2017). This paper presents an analysis of the cognitive segmentation process of German students in carrying out a translation task, organized for applied research in 2018. Data collection in Leipzig was attended by 23 subjects that translated a short technical-scientific text in the abstract format. In this, 05 students translated from English into German, the same text used in the study carried out in Brazil in 2014. Translog recorded the translation process and the steps presented here correspond to: 1) analysis of the text segmentation; 2) classification of the segments in Word, Syntagma, Clause, Clausal Complex, Transentential or Non-Syntactic Segment, according to Dragsted (2004), Rodrigues (2009), and Pimentel Neto and Liparini Campos (2017); 3) analysis of the average size of the segments produced; 4) comparison with the segmentation results of Brazilian students. The initial hypothesis that suggests similar cognitive processing among German and Brazilian students in the beginning of Translation training, was confirmed. Similar behaviours were observed by the apprentices, still attached to the source text and with more expressive cognitive segmentation in categories such as Word, Syntagma and Clause. The analysis of the cognitive segmentation of Translation apprentices was revealed to the participants of the research project as a methodological possibility in the translators training.O projeto Investigando a competência tradutória de aprendizes em formação: levantamento de dados e análise contrastiva de resultados de pesquisas em universidade alemã e brasileira (PVB10375-2019) buscou contribuir com estudos sobre competência tradutória (PACTE, 2003, 2005, 2008). De agosto de 2019 a julho de 2020, foram sistematizados dados colhidos na Alemanha em 2018 (Leipnitz &amp; Pickbrenner, 2020) e comparados com resultados da primeira coleta de estudo longitudinal no Curso de Tradução da UFPB (Liparini Campos et al., 2015; Liparini Campos &amp; Leipnitz, 2017; Liparini Campos et al., 2017). Apresentam-se aqui as análises dos processos de segmentação cognitiva de estudantes alemães na realização de tarefa tradutória, organizada para a pesquisa aplicada em 2018. Participaram da coleta em Leipzig 23 sujeitos, que traduziram um texto técnico-científico curto no formato abstract. Cinco estudantes traduziram do inglês para o alemão o texto anteriormente utilizado na coleta no Brasil em 2014. O processo tradutório desses sujeitos foi registrado pelo Translog e as etapas aqui apresentadas correspondem a: 1) análise da segmentação do texto pelo registro das pausas; 2) classificação dos segmentos em Palavra, Sintagma, Oração, Complexo Oracional, Transentencial ou Não Sintático, de acordo com Dragsted (2004), Rodrigues (2009) e Pimentel Neto e Liparini Campos (2017); 3) análise do tamanho médio dos segmentos produzidos; 4) comparação com resultados da segmentação de estudantes brasileiros na primeira coleta na UFPB. A hipótese inicial de processamento cognitivo semelhante entre estudantes alemães e brasileiros em início de formação em Tradução foi confirmada. Observaram-se aprendizes com comportamentos tradutórios semelhantes, presos ao texto de partida e com segmentação cognitiva mais expressiva em categorias como Palavra, Sintagma e Oração. As análises da segmentação cognitiva de aprendizes de Tradução revelaram-se, aos participantes do projeto de pesquisa, como possibilidade metodológica na formação de tradutores

Can the fine wheat bran be a betaine source in poultry diets?

The effect of fine wheat bran (FWB) as a methyl donor source on performance, metabolism, body composition and blood traits of growing broilers was studied. Three hundred and twenty broilers from eight to 28 d of age, distributed in a randomized block design, with five treatments and eight replicates of eight animals each were used. The experimental diets were: NC, formulated with 72% of the Met+Cys requirement; Met, formulated with 85% of the Met+Cys equivalents by DL-methionine addition; Bet, formulated with 85% of the Met+Cys equivalents by anhydrous betaine addition; Fwb- , formulated with 72% of the Met+Cys requirement and 20% FWB; and Fwb+, formulated with 85% of the Met+Cys requirement and 20% FWB. Feed intake was reduced (p0.05) between the positive control diets. Supplementation of DL-methionine and anhydrous betaine showed the same (p>0.05) metabolizability of nutrients. Treatments with higher DL-methionine levels (Met and Fwb+) promoted more weight of feathers (p<0.05). Animals fed with FWB showed the lowest (p<0.05) body gains. In conclusion, FWB inclusion did not promote methyl radicals supply

Availability of betaine present in fine wheat bran in diets for growing pigs

The objective of this paper was to investigate the availability of betaine present in fine wheat bran (FWB) in diets for growing pigs. We used thirty crossbred intact males, housed individually in metabolic cages and distributed in a randomized block design, with five treatments and six replicates. Blocks consisted of two periods of 15 days. Average initial body weights were 32.00±1.30 and 44.90±1.32 kg, in the first and second periods, respectively. Treatments were modified only at the level of methionine plus cysteine (Met+Cys) required and the Met+Cys sources, consisting of a negative control (NC), formulated with 80% of Met+Cys requirements, and four positive controls (PC): PCMet - NC supplemented with 1.2 g kg−1 of DL-methionine; PCBet - NC supplemented with 0.9 g kg−1 of anhydrous betaine; PCFWB - diet formulated with FWB; and PCFWB+Met - PCFWB supplemented with 1.0 g kg−1 of DL-methionine. No differences were observed on performance-related variables or on the digestibility coefficient of dry matter. Conversely, the digestibility coefficient of crude energy was lower when pigs were fed FWB and could be associated to the higher fiber content of FWB feeds. Digestible energy of feeds was higher for FWB diets, while the metabolizable energy of FWB diets did not differ from PCMet and PCBet. Nitrogen intake and apparent absorption were lower when pigs were fed FWB, but nitrogen retention, protein utilization, and biological value of the feed protein were the same among PC treatments, indicating that nitrogen from diets was used by pigs with the same efficiency, and is supported by no differences in performance-related variables. The FWB composition showed 12 g of betaine kg−1, which is available to maintain nitrogen retention and performance

Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases

Apesar de possuir uma família de proteínas de defesa, o feijão-comum (Phaseolus vulgaris L.) pode ser atacado por insetos bruquídeos causando sérios danos aos grãos armazenados. O P. vulgaris possui duas formas ativas de inibidores de a-amilases, denominadas a-AI1 e a-AI2, que apresentam diferentes especificidades em relação às a-amilases. A a-amilase de Zabrotes subfasciatus é inibida por a-AI2 mas não por a-AI1. Em contraste, a a-amilase pancreática de porco é inibida por a-AI1 mas não é por a-AI2. O objetivo deste trabalho foi entender as bases moleculares da especificidade desses inibidores em relação às a-amilases. Para tanto, foram construídos mutantes do a-AI2, os quais foram expressados em plantas de fumo. Todos os inibidores mutantes deixaram de inibir a a-amilase de inseto sem, contudo, passar a exibir atividade contra a a-amilase de mamífero. Os modelos estruturais explicam por que a substituição de His33 do a-AI2 pela seqüência correspondente do a-AI1 (Ser-Tyr-Asn) aboliu a inibição da a-amilase de Z. subfasciatus. Dos estudos de modelagem molecular pode-se concluir que o tamanho e a complexidade da interface a-amilase-inibidor explicam por que a mutação da alça N-terminal e a quebra da atividade inibitória para a-amilase de Z. subfasciatus não levam ao ganho de atividade inibitória do mutante em relação à a-amilase de porco.Despite the presence of a family of defense proteins, Phaseolus vulgaris can be attacked by bruchid insects resulting in serious damage to stored grains. The two distinct active forms of α-amylase inhibitors, α-AI1 and α-AI2, in P. vulgaris show different specificity toward α-amylases. Zabrotes subfasciatus α-amylase is inhibited by α-AI2 but not by α-AI1. In contrast, porcine α-amylase is inhibited by α-AI1 but not by α-AI2. The objective of this work was to understand the molecular basis of the specificity of two inhibitors in P. vulgaris (α-AI1 and α-AI2) in relation to α-amylases. Mutants of α-AI2 were made and expressed in tobacco plants. The exhibited activity toward the mammalian α-amylase. The replacement of His33 of α-AI2 with the α-AI1-like sequence Ser-Tyr-Asn abolished inhibition of Z. subfasciatus α-amylase. From structural modeling, the conclusion is that the size and complexity of the amylase-inhibitor interface explain why mutation of the N-terminal loop and resultant abolition of Z. subfasciatus α-amylase inhibition are not accompanied by gain of inhibitory activity against porcine α-amylase

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio