Impact of housing system on intestinal microbiota of laying hens - A systematic review.

Studies on the housing system's impact on laying hens' intestinal microbiota were retrieved from the Web of Science, PubMed, and Scopus (between 2017 and 2022). Inclusion criteria were studies that discussed measurable effects related to the topic written in English, Portuguese, and Spanish. Of 3281 articles in the identification stage, 12 studies were used in the systematic review. Asia developed most research relating to the subject. Most studies compared the intestinal microbiota of laying hens from conventional cages versus Cage-Free or Free-Range. However, no study has evaluated the intestinal microbiota of laying hens maintained in an organic system. Greengene and Silva were the most used reference in the studies. According to the results observed in the studies included in the systematic review, there is greater alpha diversity in the alternative system and a high dissimilarity between the conventional and alternative systems. Exposure to environmental factors such as soil, vegetation, natural lighting, access to pastures, and ingesting fibrous foods can lead to changes in the intestinal microbiota. A brief outline of published scientific evidence demonstrates that the housing system can change the gut microbiome of hens. This study summarises the relationship between the housing system and the intestinal microbiome of laying hens and provides a roadmap for future research regarding the gut microbiome of hens.

Influence of cold-water immersion on lower limb muscle oxygen consumption, as measured by near-infrared spectroscopy.

CONTEXT: Cold-water immersion (CWI) is reported to reduce tissue metabolism post immersion, yet there is a lack of physiologic data regarding muscle metabolic response to its application. Near-infrared Spectroscopy (NIRS) is a non-invasive optical technique that can inform upon muscle haemodynamics and tissue metabolism. OBJECTIVE: The purpose of our study was to investigate the effects of CWI at two different water temperatures (10°C and 15°C) upon NIRS calculated measurements of muscle oxygen consumption (mVO2). DESIGN: A randomised, crossover design. SETTING: University Sports Rehabilitation Centre. PARTICIPANTS: Eleven long-distance runners (age; 23.4 ± 3.4 years, mean adipose tissue thickness; 6.7 ± 2.7 mm) (NCAA Division 2), adult males. MAIN OUTCOME MEASURE(S): mVO2 was calculated pre and post immersion at both 10°C and 15°C. Changes in tissue oxyhaemoglobin (O2Hb), deoxyhaemoglobin (HHb), total haemoglobin (tHb), haemoglobin difference (Hbdiff) and tissue saturation index (TSI %) were measured during both 20 minute immersion temperatures. RESULTS: There was a significant decrease in mVO2 following both the 10°C and 15°C immersion (P = 0.001). During the 20 min immersion at both temperatures there was a significant main effect of time for O2Hb (P = 0.001)), HHb (P = 0.009) tHb (P = 0.001), and Hbdiff (P = 0.020), in which they decreased over the course of the 20 min immersion. Post-hoc pairwise comparisons showed these changes occurred within the final 5 minutes of immersion for tHb and O2Hb. CONCLUSIONS: Our results demonstrated that a 20 min CWI at 10°C and 15°C led to a significant reduction in mVO2. The reduction in mVO2 was greater following 10°C immersion. The reduction in mVO2 suggests a decrease in muscle metabolic activity i.e. O2 utilisation following CWI. Calculating mVO2 via the NIRS-occlusion technique may offer further insight into muscle metabolic responses, beyond what is attainable from observing the NIRS primary signals.

Reinforcement amid genetic diversity in the Candida albicans biofilm regulatory network.

Biofilms of the fungal pathogen Candida albicans include abundant long filaments called hyphae. These cells express hypha-associated genes, which specify diverse virulence functions including surface adhesins that ensure biofilm integrity. Biofilm formation, virulence, and hypha-associated gene expression all depend upon the transcription factor Efg1. This transcription factor has been characterized extensively in the C. albicans type strain SC5314 and derivatives, but only recently has its function been explored in other clinical isolates. Here we define a principal set of Efg1-responsive genes whose expression is significantly altered by an efg1Δ/Δ mutation across 17 clinical isolates. This principal gene set includes 68 direct Efg1 targets, whose 5' regions are bound by Efg1 in five clinical isolates, and 42 indirect Efg1 targets, whose 5' regions are not detectably bound by Efg1. Three direct Efg1 target genes encode transcription factors-BRG1, UME6, and WOR3 -whose increased expression in an efg1Δ/Δ mutant restores expression of multiple indirect and direct principal targets, as well as biofilm formation ability. Although BRG1 and UME6 are well known positive regulators of hypha-associated genes and biofilm formation, WOR3 is best known as an antagonist of Efg1 in the sexual mating pathway. We confirm the positive role of WOR3 in biofilm formation with the finding that a wor3Δ/Δ mutation impairs biofilm formation in vitro and in an in vivo biofilm model. Positive control of Efg1 direct target genes by other Efg1 direct target genes-BRG1, UME6, and WOR3 -may buffer principal Efg1-responsive gene expression against the impact of genetic variation in the C. albicans species.

Collaboration between Antagonistic Cell Type Regulators Governs Natural Variation in the Candida albicans Biofilm and Hyphal Gene Expression Network.

Candida albicans is among the most significant human fungal pathogens. However, the vast majority of C. albicans studies have focused on a single clinical isolate and its marked derivatives. We investigated natural variation among clinical C. albicans isolates in gene regulatory control of biofilm formation, a process crucial to virulence. The transcription factor Efg1 is required for biofilm-associated gene expression and biofilm formation. Previously, we found extensive variation in Efg1-responsive gene expression among 5 diverse clinical isolates. However, chromatin immunoprecipitation sequencing analysis showed that Efg1 binding to genomic loci was uniform among the isolates. Functional dissection of strain differences identified three transcription factors, Brg1, Tec1, and Wor1, for which small changes in expression levels reshaped the Efg1 regulatory network. Brg1 and Tec1 are known biofilm activators, and their role in Efg1 network variation may be expected. However, Wor1 is a known repressor of EFG1 expression and an inhibitor of biofilm formation. In contrast, we found that a modest increase in WOR1 RNA levels, reflecting the expression differences between C. albicans strains, could augment biofilm formation and expression of biofilm-related genes. The analysis of natural variation here reveals a novel function for a well-characterized gene and illustrates that strain diversity offers a unique resource for elucidation of network interactions. IMPORTANCE Clinical isolates of all pathogens vary in the strength of traits linked to disease. In this study, we focused on variation in a pathogenicity trait of the fungal pathogen Candida albicans, biofilm formation. This trait is under the control of the cell type regulator Efg1. Expression of Efg1 is known from previous studies to be repressed by a second cell type regulator, Wor1. However, we found that natural variation in biofilm formation and biofilm-related gene expression was driven by collaboration between Efg1 and Wor1. Our findings show that analysis of natural isolates can reveal unexpected features of gene function, even for well-studied genes.

False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5' UTR annotations.

Hyperconserved genomic sequences have great promise for understanding core biological processes. It has been recently proposed that scores of hyperconserved 5' untranslated regions (UTRs), also known as transcript leaders (hTLs), encode internal ribosome entry sites (IRESes) that drive cap-independent translation, in part, via interactions with ribosome expansion segments. However, the direct functional significance of such interactions has not yet been definitively demonstrated. We provide evidence that the putative IRESes previously reported in Hox gene hTLs are rarely included in transcript leaders. Instead, these regions function independently as transcriptional promoters. In addition, we find the proposed RNA structure of the putative Hoxa9 IRES is not conserved. Instead, sequences previously shown to be essential for putative IRES activity encode a hyperconserved transcription factor binding site (E-box) that contributes to its promoter activity and is bound by several transcription factors, including USF1 and USF2. Similar E-box sequences enhance the promoter activities of other putative Hoxa gene IRESes. Moreover, we provide evidence that the vast majority of hTLs with putative IRES activity overlap transcriptional promoters, enhancers, and 3' splice sites that are most likely responsible for their reported IRES activities. These results argue strongly against recently reported widespread IRES-like activities from hTLs and contradict proposed interactions between ribosomal expansion segment ES9S and putative IRESes. Furthermore, our work underscores the importance of accurate transcript annotations, controls in bicistronic reporter assays, and the power of synthesizing publicly available data from multiple sources.

Multiplexed Analysis of Human uORF Regulatory Functions During the ISR Using PoLib-Seq.

Protein synthesis is a highly regulated essential process. As such, it is subjected to substantial regulation in response to stress. One hallmark of the Integrated Stress Response (ISR) is the immediate shutdown of most translation through phosphorylation of the alpha subunit of translation initiation factor eIF2 and activation of eIF4E binding proteins. While these posttranslational modifications largely inhibit cap-dependent translation, many mRNA resist this inhibition by alternative translation mechanisms involving cis-regulatory sequences and structures in 5' transcript leaders, including upstream Open Reading Frames (uORFs), Internal Ribosome Entry Sites (IRESes), and Cap-Independent Translation Elements (CITEs). Studies of uORF and IRES activity are often performed on a gene-by-gene basis; however, high-throughput methods have recently emerged. Here, we describe a protocol for Polysome Library Sequencing (PoLib-Seq; Fig. 1), a multiplexed assay of reporter gene translation that can be used during the ISR. A designer library of reporter RNAs are transfected into tissue-culture cells, and their translation is assayed via sucrose gradient fractionation followed by high-throughput sequencing. As an example, we include PoLib-seq results simultaneously assaying translation of wildtype and uORF mutant human ATF4 reporter RNAs, recapitulating the known function of uORF1 in resisting translational inhibition during the ISR.

High-Throughput Quantitation of Yeast uORF Regulatory Impacts Using FACS-uORF.

Eukaryotic upstream Open Reading Frames (uORFs) are short translated regions found in many transcript leaders (Barbosa et al. PLoS Genet 9:e1003529, 2013; Zhang et al. Trends Biochem Sci 44:782-794, 2019). Modern transcript annotations and ribosome profiling studies have found thousands of AUG-initiated uORFs, and many more uORFs initiated by near-cognate codons (CUG, GUG, UUG, etc.). Their translation generally decreases the expression of the main encoded protein by preventing ribosomes from reaching the main ORF of each gene, and by inducing nonsense mediated decay (NMD) through premature termination. Under many cellular stresses, uORF containing transcripts are de-repressed due to decreased translation initiation (Young et al. J Biol Chem 291:16927-16935, 2016). Traditional experimental evaluation of uORFs involves comparing expression from matched uORF-containing and start-codon mutated transcript leader reporter plasmids. This tedious process has precluded analysis of large numbers of uORFs. We recently used FACS-uORF to simultaneously assay thousands of yeast uORFs in order to evaluate the impact of codon usage on their functions (Lin et al. Nucleic Acids Res 2:1-10, 2019). Here, we provide a step-by-step protocol for this assay.

Origin and population structure of Brazilian hair sheep breeds.

Brazilian hair sheep constitute a genetic diversity hotspot. These animals are found in the harsh environments of the Brazilian Northwest (semi-arid) region. Genotypes (50K SNP chip) from seven Brazilian sheep breeds (five hair and two coarse wool types) and 87 worldwide breeds were used to test for population structure, admixture and genetic diversity. Moreover, phylogenetic trees evaluating migration events between genetic groups were built. Brazilian Somali, a fat-tailed breed, had a close relationship with East African breeds and clustered distinctly from other Brazilian breeds. Brazilian Blackbelly and Barbados Blackbelly had a close relationship. The Morada Nova breed did not show close relationships with European or African breeds, revealing a single migration event from an Algerian hair breed. Brazilian Fat-tail and Morada Nova share a common ancestor, but the former showed introgressions from Brazilian Somali and Afrikaner breeds, explaining the fat-tail phenotype. The Santa Inês breed received a substantial contribution from Brazilian Bergamasca and showed an admixed origin with recent introgressions from other breeds, mainly from Suffolk. Furthermore, Brazilian Somali and Brazilian Fat-tail are the most endangered sheep genetic resources in Brazil and should be the focus for ex situ conservation programs. In conclusion, Brazilian hair sheep show an African origin and are characterized by diverse genetic composition, reinforcing the need for conservation of these genetic resources, and at the same time, this highly diverse group has variability that can be used in breeding programs.

Physiological and hematological parameters of sheep reared in the tropics and subtropics / [Parâmetros fisiológicos e hematológicos de ovinos criados nos trópicos e nos subtrópicos]

This study aimed to determine the physiological and hematological parameters of sheep in Brazil. Therefore, 5,081 observations were used from previous experiments with animals from different Brazilian regions with the time of day, gender, breed, age, physiological characteristics, hematological and climatic variables. The animals were classified according to their stress level, and only data of non-stressed animals were used to calculate the reference values. Respiratory rate was the parameter that most differed from the normal range, with values ​​above the limits usually reported for the species, being higher in commercial wool sheep. For hematological variables, differences were observed between the present results and the previously reported values in the literature. A higher number of red blood cells (RBC), lower hemoglobin and mean corpuscular hemoglobin concentration (MCHC) were observed in young animals. A higher number of RBC and MCHC were noted in sheep crossed with local breeds. Considering that physiological and hematological parameters are indicators of the animal's pathological or physiological state, for a correct interpretation of the results, the use of reference values based on animals with similar racial characteristics and subjected to similar environmental conditions is recommended.(AU)

O objetivo deste estudo foi determinar parâmetros fisiológicos e hematológicos de ovinos no Brasil. Portanto, foram utilizadas 5.081 observações de experimentos anteriores com animais de diversas regiões do Brasil, com diferentes horário, sexo, raça, idade, características fisiológicas, variáveis ​​hematológicas e climáticas. Os animais foram classificados de acordo com o nível de estresse, e apenas os dados dos animais não estressados ​​foram utilizados para o cálculo dos valores de referência. A frequência respiratória foi o parâmetro que mais diferiu em relação à normalidade, com valores acima dos limites usualmente relatados para a espécie, sendo maior em ovinos de lã comercial. Para as variáveis ​​hematológicas, também foram verificadas diferenças entre os resultados observados e os valores previamente relatados na literatura. Maior número de hemácias, menor hemoglobina e concentração de hemoglobina corpuscular média (CHbCM) foram observados em animais jovens e maior número de hemácias e CHbCM em ovinos cruzados com raças locais. Considerando que os parâmetros fisiológicos e hematológicos são indicadores do estado patológico ou fisiológico do animal, para uma correta interpretação dos resultados recomenda-se a utilização de valores de referência baseados em animais com características raciais semelhantes e submetidos a condições ambientais também semelhantes.(AU)

Spatial distribution of Brazilian bovine taurine breeds associated with climatic, physical and socioeconomic variables / [Distribuição espacial de raças taurinas bovinas brasileiras associada a variáveis climáticas, físicas e socioeconômicas]

The objective of this study was to evaluate the spatial distribution of purebred Bos taurus taurus bovine breeds raised in Brazil in association with climatic, physical and socioeconomic variables. The breeds Aberdeen Angus, Ayrshire, Braford, Brangus, Charolais, Devon, Flemish, Hereford, Pinzgauer, Shorthorn and Simental were classified according to their aptitude (milk, meat or dual-purpose). They were spatialized according to their aptitude using state and municipal information. The milk breeds were found in the states of Rio Grande do Sul and Santa Catarina, while the dual-purpose breeds were found in Minas Gerais and Rio Grande do Sul states and the beef breeds were concentrated in the southern region. Only the Aberdeen Angus meat breed showed higher dispersion in other regions. Meat and dual-purpose breeds tended to be raised in regions with lower maximum temperature, average temperature, thermal amplitude and temperature-humidity index. Dual-purpose breeds were found in municipalities with high humidity and altitude, but with a low gross domestic product, little technical guidance received from cooperatives and the government, low control of diseases and parasites, as well as low use of pasture rotation systems. The spatial distribution of Brazilian bovine taurine breeds, regardless of aptitude, was related to climatic, physical and socioeconomic factors.(AU)

O objetivo deste estudo foi avaliar a distribuição espacial de raças bovinas puras Bos taurus taurus criadas no Brasil, associadas a variáveis climáticas, físicas e socioeconômicas. As raças Aberdeen Angus, Ayrshire, Braford, Brangus, Charolês, Devon, Flamenga, Hereford, Pinzgauer, Shorthorn e Simental foram classificadas de acordo com sua aptidão (leite, carne ou duplo-propósito). Elas foram espacializadas de acordo com sua aptidão a partir de informações estaduais e municipais. As raças leiteiras foram encontradas nos estados do Rio Grande do Sul e de Santa Catarina, enquanto as raças de duplo-propósito foram encontradas nos estados de Minas Gerais e Rio Grande do Sul, e as raças de carne concentraram-se na região Sul. Apenas a raça de carne Aberdeen Angus apresentou maior dispersão nas demais regiões. As raças de carne e de duplo-propósito tendem a ser criadas em regiões com menores temperatura máxima, temperatura média, amplitude térmica e índice de temperatura e umidade. As raças de duplo-propósito foram encontradas em municípios com alta umidade e altitude, mas com baixo produto interno bruto, pouca orientação técnica recebida de cooperativas e do governo, baixo controle de doenças e de parasitas e baixo uso de sistema de rotação de pastagens. A distribuição espacial das raças taurinas bovinas brasileiras, independentemente da aptidão, foi relacionada a fatores climáticos, físicos e socioeconômicos.(AU)

Variations in the Course of the Carotid Arteries in Patients with Retropharyngeal Parathyroid Adenomas.

The carotid arteries, classically described as taking a relatively straight course through the neck, deviate medially in a minority of patients. At the extreme, the internal carotid arteries may "kiss" in the midline, coming extremely close to the pharyngeal wall. In this clinical report, we describe 5 patients with primary hyperparathyroidism, all with ectopic retropharyngeal parathyroid adenomas but all with varying carotid artery anatomy. We describe these variations using a previously developed clinical grading system that highlights 1) the relationship between carotid artery location and risk of injury during pharyngeal procedures and 2) the importance of universal, objective criteria to classify carotid anatomy. Radiologists should be familiar with variations in carotid anatomy and communicate them to the operative team.

Effect of housing system during pregnancy on reproductive parameters of sows / [Efeito do sistema de alojamento durante a gestação sobre os parâmetros reprodutivos de porcas]

The aim of this study was to evaluate the reproductive performance of sows in individual stalls (Stall) or group-housed into groups on days 3 to 5 (Pen5) or 38 to 42 (Pen42) after breeding. The reproductive data was collected from the operating system of the farm establishing the average of the weekly performances of the sows that gave birth, for four years, except for the Pen5 system, which was evaluated for three years. Statistical analyses were performed using SAS®, using MIXED (for quantitative traits), NPAR1WAY (for categorical traits) and LOGISTIC (binomial traits) procedures, using sows as a repeated measure. Sows in Stall system had piglets with higher birth weight them sows in the group-housed system (P<0.05), however the piglets born alive, total piglets weaned, average litter weight, and duration of farrowing were lower in this system than in the group-housed (P<0.0001). There was no difference between Pen5 and Stall systems for gestation period and mummified piglets. The Pen42 system had a higher percentage of mummified piglets and a shorter gestation period, when compared Pen5 and Stall systems (P<0.0001), and similar results to the Pen5 system for duration of farrowing, piglets born alive, stillbirths, total piglets weaned, average litter weight and birth weight (P<0.0001).(AU)

O objetivo deste estudo foi avaliar a performance reprodutiva de matrizes suínas alojadas individualmente (Individual) ou em grupos, nos dias 3 a 5 (Grupo 5) ou 38 a 42 (Grupo 42) após a inseminação. Os dados reprodutivos foram coletados do sistema operacional da granja, estabelecendo-se a média dos desempenhos semanais das matrizes que pariram por semana, durante quatro anos, exceto para o sistema Grupo 5, que foi avaliado por três anos. A análise estatística foi realizada com SAS®, usando-se os procedimentos MIXED (para variáveis quantitativas), NPAR1WAY (para variáveis categóricas) e LOGISTIC (para variáveis binomiais), tendo a matriz como uma medida repetida. As matrizes no sistema Individual tiveram leitões com maior média de peso ao nascer do que as matrizes nos sistemas de alojamento em grupo (P<0,05), porém os leitões nascidos vivos, o total de leitões nascidos, o peso médio da leitegada e a duração do parto foram menores no sistema Individual do que nos sistemas de alojamento em grupo (P<0,0001). Não houve diferença entre os sistemas Grupo 5 e Individual para o tempo de duração da gestação e o número de leitões mumificados. O sistema Grupo 42 apresentou maior porcentagem de leitões mumificados e menor período de gestação, quando comparado aos sistemas Grupo 5 e Individual (P<0,0001), e resultados semelhantes ao sistema Grupo 5 para duração do parto, leitões nascidos vivos, natimortos, total de leitões desmamados, peso médio da leitegada e peso ao nascer (P<0,0001).(AU)

Different methods of assessing udder temperature through thermography and their relation with rectal temperature.

Infrared thermography of the lateral side portion of the udder was taken from 38 lactating cows in a 6-day experiment. Thermograms were analyzed using specific software with the use of eight different methods. The experiment was aimed at correlating the different methods with each other and with rectal temperature (RT), in order to suggest a method to assess udder side temperature, and also at creating regression equations to enable RT calculation through the use of thermographic data. All methods of analyzing thermograms were highly correlated; correlations between thermograms and RT were significant (P < 0.01) and above 0.840. The highest correlation was between RT and the maximum temperature obtained using a horizontal rectangle placed within the lateral (side) portion of the udder (maximum temperature in a horizontal rectangle (MHR), 0.897). With the exception of the average temperature of a horizontal rectangle, linear regression coefficients were significant (P < 0.05) and coefficients of determination were higher than 75.51%. We suggest the use of MHR to evaluate udder side temperature. The ease of accessing the side of the udder, the welfare advantages of non-invasive observations, and the high correlation with RT suggest the use of thermograms in the lateral portion of the udder to assess animals' temperature.

Genomics and climate change.

Climate change is predicted to change the nature and distribution of global farming systems, and strategies will be needed to adapt and optimise global food-producing systems. If genomic technologies are to be useful in this scenario, there is a need for the careful definition of phenotypes and routine sample collection, as well as large-scale genotyping of animal populations. Genomic tools will greatly enhance the characterisation of available germplasm and exploration of local genetic resources, while faster and cheaper DNA sequencing is leading to an increased understanding of the underlying genetic basis of traits. The use of genomic tools to increase animal resilience, reduce methane emissions from cattle and sheep, improve disease resistance, decrease environmental impact, reduce competition for land and water and, finally, increase production may be the most feasible path for the future of livestock production. In this review, the authors discuss various genomic strategies in the light of climate change, focusing on the selection of resistant/tolerant animals, landscape genomics, metagenomics and gene editing.

L'un des effets anticipés du changement climatique sera la modification de la nature et de la distribution des systèmes d'élevage dans le monde, raison pour laquelle des stratégies seront nécessaires pour adapter et optimiser les systèmes mondiaux de production alimentaire. Si l'on veut que les technologies de la génomique soient utiles dans ce scénario, il faudra procéder avec soin à la définition des phénotypes et à la collecte de routine des échantillons, et réaliser le génotypage à grande échelle des populations animales. Les outils génomiques permettront d'améliorer nettement la caractérisation du germoplasme disponible et d'effectuer une exploration plus approfondie des ressources génétiques locales, tandis que le séquençage ADN devenu plus rapide et meilleur marché se traduira par une meilleure compréhension de la base génétique sousjacente des caractères. Le recours à des outils génomiques pour augmenter la résilience animale, réduire les émissions de méthane du cheptel bovin et ovin, améliorer la résistance aux maladies, diminuer l'impact environnemental, réduire la concurrence pour les terres et les ressources hydrographiques et, enfin, accroître la production pourrait être la voie à suivre la plus réaliste pour l'avenir de la production animale. Les auteurs examinent plusieurs stratégies génomiques à la lumière du changement climatique, en se concentrant sur la sélection des animaux résistants/tolérants, sur la génomique du paysage, sur la métagénomique et sur l'édition génomique.

Según apuntan las predicciones, el cambio climático va a modificar la naturaleza y la distribución de los sistemas agropecuarios del mundo y por doquier en el planeta harán falta estrategias destinadas a adaptar y optimizar los sistemas de producción de alimentos. Para que las herramientas de la genómica sean útiles, en caso de que efectivamente se cumplan estos augurios, es indispensable disponer de detalladas caracterizaciones fenotípicas, muestreos sistemáticos y tipificaciones génicas a gran escala de las poblaciones animales. Las herramientas de la genómica mejorarán mucho la caracterización del germoplasma existente y el estudio de los recursos genéticos locales, a la vez que la secuenciación de ADN, cada vez más rápida y barata, nos aporta ya un conocimiento más profundo de la base genética de los rasgos fenotípicos. Quizá el camino más practicable para el porvenir de la producción ganadera sea el que pasa por utilizar las herramientas de la genómica para conferir más resiliencia a los animales, reducir las emisiones de metano del ganado vacuno y ovino, mejorar la resistencia a enfermedades, atenuar el impacto ambiental, reducir la competencia por los suelos y el agua y, por último, incrementar la producción. Los autores examinan una serie de estrategias genómicas desde la óptica del cambio climático, centrándose en la selección de animales resistentes o tolerantes, la genómica de paisajes, la metagenómica y la edición génica.

Productive characteristics in dairy buffalo (Bubalus bubalis) in the Eastern Amazon / Características produtivas em búfalos leiteiros (Bubalus bubalis) na Amazônia

The objective of this study was to determine factors affecting phenotypic characteristics related to milk production and reproductive efficiency of dairy buffalo. Phenotypic records of 2,459 Murrah, Mediterranean and crossbred buffaloes from the Embrapa Eastern Amazônia herd, from 1969 to 2013 were used. Traits included: total milk production during lactation (TMP), milk production corrected for 305 days (P305); cow weight at calving (CW), fat milk percentage (F), age at first calving (AFC), calving interval (CI), calf birth weight (BW), as well as lactation (LP) and service periods (SP). Most traits were affected by genetic group as well as year and season or interaction between them. Genetic group affected F, CI, SP and CW. Very young and older cows showed poorer production traits. There was interaction between season and year for F, CI and CW. Correlations traits were generally medium to low. The principal component analysis showed that higher fat milk percentage was associated with higher percentage of Murrah breed, longer lactation period and older cows. Phenotypic characteristics in buffaloes reared in the Brazilian Amazon were significantly affected by genetic and management factors. This information can be used to help build sustainable production systems for the region and guide farmer decisions.(AU)

O objetivo deste estudo foi determinar os fatores que afetam as características fenotípicas relacionadas à produção de leite e a eficiência reprodutiva de búfalas leiteiras. Foram utilizados os registros fenotípicos de 2.459 búfalas das raças Murrah, Mediterrâneo e seus cruzamentos do rebanho da Embrapa Amazônia Oriental, de 1969 a 2013. As características incluídas foram: produção total de leite durante a lactação (PTL), produção de leite corrigida para 305 dias (P305), peso da búfala ao parto (PV), percentual de gordura do leite (G), idade ao primeiro parto (IPP), intervalo entre partos (IP), peso do bezerro ao nascimento (PN), assim como os períodos de lactação (PL) e de serviço (PS). A maioria das características foi afetada pelo grupo genético, bem como pelo ano e pela estação ou pela interação entre eles. O grupo genético afetou o G, IP, PS e PV. Búfalas muito jovens e mais velhas mostraram características de produção mais baixas. Houve interação entre estação e o ano para G, IP e PV. As correlações entre as características foram geralmente de médias a baixas. A análise de componentes principais mostrou que a maior porcentagem de gordura no leite foi associada com a maior porcentagem de sangue Murrah, com o maior período de lactação e com búfalas mais velhas. As características fenotípicas das búfalas criadas na Amazônia brasileira foram significativamente afetadas por fatores genéticos e de manejo. Essas informações podem ser usadas para ajudar a construir sistemas de produção sustentáveis para a região e orientar as decisões dos produtores.(AU)

Dynamics of genomic architecture during composite breed development in cattle.

Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non-uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality.

Metabolic adaptation is linked to the ability of the opportunistic pathogen Candida albicans to colonize and cause infection in diverse host tissues. One way that C. albicans controls its metabolism is through the glucose repression pathway, where expression of alternative carbon source utilization genes is repressed in the presence of its preferred carbon source, glucose. Here we carry out genetic and gene expression studies that identify transcription factors Mig1 and Mig2 as mediators of glucose repression in C. albicans. The well-studied Mig1/2 orthologs ScMig1/2 mediate glucose repression in the yeast Saccharomyces cerevisiae; our data argue that C. albicans Mig1/2 function similarly as repressors of alternative carbon source utilization genes. However, Mig1/2 functions have several distinctive features in C. albicans. First, Mig1 and Mig2 have more co-equal roles in gene regulation than their S. cerevisiae orthologs. Second, Mig1 is regulated at the level of protein accumulation, more akin to ScMig2 than ScMig1. Third, Mig1 and Mig2 are together required for a unique aspect of C. albicans biology, the expression of several pathogenicity traits. Such Mig1/2-dependent traits include the abilities to form hyphae and biofilm, tolerance of cell wall inhibitors, and ability to damage macrophage-like cells and human endothelial cells. Finally, Mig1 is required for a puzzling feature of C. albicans biology that is not shared with S. cerevisiae: the essentiality of the Snf1 protein kinase, a central eukaryotic carbon metabolism regulator. Our results integrate Mig1 and Mig2 into the C. albicans glucose repression pathway and illuminate connections among carbon control, pathogenicity, and Snf1 essentiality.

Genetic evaluation of milking buffaloes (Bubalus bubalis): bull ranking / Avaliação genética de búfalas leiteiras (Bubalus bubalis): classificação de touros

The objective of this study was to evaluate genetic aspects related to production and reproductive efficiency of Murrah and Mediterranean buffaloes and their crosses. A ranking of bulls from Embrapa Eastern Amazonia was also composed to guide assisted mating. Birth records of 2,322 Murrah, Mediterranean, and crossbred buffaloes from the Embrapa Eastern Amazon herd, from 1953 to 2013, as well as information on production and reproductive traits were used. Genetic analyzes were performed in the WOMBAT software using the animal model with two-trait analysis. While heritability (h2) for total milk production (TMP) and fat milk percentage (F) were generally high, for reproductive traits h2 tended to be low. Genetic correlations for TMP with the other traits were low and negative, except for TMP with calving interval (CI) and service period (SP) in the Mediterranean breed and with age at first calving (AFC) and SP in crossbred, which were positive and high. Bull 1001 had high predicted transmitting ability (PTA) for TMP, so it should transmit a greater volume of milk to his offspring, although it had a lower PTA for F. There was sufficient variability within the herd to work with genetic management for both production and reproductive efficiency.(AU)

O objetivo deste estudo foi avaliar os aspectos genéticos relacionados à produção e à eficiência reprodutiva de búfalas das raças Murrah, Mediterrâneo e suas cruzas. Uma classificação de touros da Embrapa Amazônia Oriental também foi composta para orientar os cruzamentos assistidos. Foram utilizados 2.322 registros de nascimento de búfalas das raças Murrah, Mediterrâneo e cruzadas do rebanho da Embrapa Amazônia Oriental, de 1953 a 2013, bem como características produtivas e reprodutivas. As análises genéticas foram realizadas pelo software Wombat, utilizando-se o modelo animal com análise de duas características. Enquanto a herdabilidade (h 2 ) para a produção total de leite (PTL) e para a porcentagem de gordura (G) foi alta, para as características reprodutivas a h 2 tendeu a ser baixa. As correlações genéticas da PTL com as demais características foram baixas e negativas, exceto para a PTL com intervalo entre partos (IP) e período de serviço (PS) na raça Mediterrâneo e com idade ao primeiro parto (IPP) e PS nas cruzadas, que foram positivas e altas. O touro 1001 apresentou alta capacidade de transmissão predita (CTP) para a PTL, então deve transmitir um maior volume de leite para seus descendentes, embora com um menor conteúdo transmissível de CTP para G. Portanto, existe variabilidade suficiente dentro do rebanho para trabalhar com o manejo genético para a produção e a eficiência reprodutiva.(AU)

Impacts of uORF codon identity and position on translation regulation.

Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5' mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a minority of uORFs encode conserved functional peptides, the coding regions of most uORFs are not conserved. Thus, the importance of uORF coding sequences on their regulatory functions remains largely unknown. We investigated the impact of an uORF coding region on gene regulation by assaying the functions of thousands of variants in the yeast YAP1 uORF. Varying uORF codons resulted in a wide range of functions, including repressing and enhancing expression of the downstream ORF. The presence of rare codons resulted in the most inhibitory YAP1 uORF variants. Inhibitory functions of such uORFs were abrogated by overexpression of complementary tRNA. Finally, regression analysis of our results indicated that both codon identity and position impact uORF function. Our results support a model in which a uORF coding sequence impacts its regulatory functions by altering the speed of uORF translation.

Circuit diversification in a biofilm regulatory network.

Genotype-phenotype relationships can vary extensively among members of a species. One cause of this variation is circuit diversification, the alteration of gene regulatory relationships among members of a species. Circuit diversification is thought to be a starting point for the circuit divergence or rewiring that occurs during speciation. How widespread is circuit diversification? Here we address this question with the fungal pathogen Candida albicans, which forms biofilms rich in distinctive hyphal cells as a prelude to infection. Our understanding of the biofilm/hyphal regulatory network comes primarily from studies of one clinical isolate, strain SC5314, and its marked derivatives. We used CRISPR-based methods to create mutations of four key biofilm transcription factor genes-BCR1, UME6, BRG1, and EFG1 -in SC5314 and four additional clinical isolates. Phenotypic analysis revealed that mutations in BCR1 or UME6 have variable impact across strains, while mutations in BRG1 or EFG1 had uniformly severe impact. Gene expression, sampled with Nanostring probes and examined comprehensively for EFG1 via RNA-Seq, indicates that regulatory relationships are highly variable among isolates. Our results suggest that genotype-phenotype relationships vary in this strain panel in part because of differences in control of BRG1 by BCR1, a hypothesis that is supported through engineered constitutive expression of BRG1. Overall, the data show that circuit diversification is the rule, not the exception, in this biofilm/hyphal regulatory network.