Identification of mechanisms involved in mastitis response by means of gene network building.

Mastitis, an inflammation of the mammary gland, is the most prevalent and costly production disease in dairy herds worldwide. It is caused generally by bacteria and accounts for a significant decrease in milk production and quality. One promising approach to reduce problems caused by mastitis, in addition to sanitary care, is the selection of animals resistant to disease and the incorporation of this trait into the herds. Therefore, studies to better understand the mechanisms involved in animal response to this disease are essential to the proposition of new advances in area. In this context, the aim of this study was to identify groups of genes involved in cow response to mastitis infection, through gene network building from microarray data. Gene expression data from the GeneChipâ Bovine Genome Array (Affymetrix) hybridization with milk somatic cells samples from Holstein-Zebu crossbreed dairy cows, obtained before (B) and 24 hrs after (A) artificial infection with Staphylococcus agalactiae, were analyzed using a network building methodology based on gene co-expression. We used WGCNA (Weighted Gene Co-expression Analysis), a systems biology method for describing the correlation patterns among genes across microarray samples, that can be used for finding clusters (modules) of highly correlated genes to identify modules of co-expressed genes, which may correspond to functionally related genes. By comparing two networks (between contrasting data sets), conserved and non-conserved modules can be identified. This strategy, named differential network analysis, aims to identify genes groups that are both differentially expressed and differentially connected, and changes in connectivity may correspond to large-scale rewiring, in response to environmental changes and/or physiologic perturbations. Two microarray data sets, B (n=5) and A (n=5), were preprocessed using affy and gcrma R/Bioconductor packages. A filter was applied, which resulted in the use of only those transcripts present in all samples. Gene co-expression networks were identified separately for each group (B and A), by the R/WGCNA package. Gene networks were compared between the two groups, and non-conserved modules were uncovered from a correlation test of the connectivity values. Our analysis identified a total of 17 modules of co-expressed genes, three of them, designed by the colors grey (n=35), blue (n=37) and turquoise (n=192), non-conserved between the groups. Using Blast2GO for enrichment analysis, we find the molecular function Protein Binding overrepresented in all three modules. However, in despite of the same molecular function, each one of the modules showed distinct characteristcs. Genes of grey module (BTG3, CD3E, MBD1, CHIC2, PLXNA3, MOCS3, NEIL1, VPS45, BCL2) were related to apoptosis and antigen recognition. Genes of turquoise module were enriched in inflammation mediators, including known mastitis marker genes (FGL1, GJA1, F2RL1, PTPRF, S100A2, TGFB2). The blue one uncovered genes involved in cell division and inflammatory response (CD97, MAD2L1, ZFP106, CDKN2C, LOC514364, NOP14, PCBD1, LOC100139798, AP1S1, EDN1, IL1B, ANXA11). Our study identified some mechanisms (represented by gene modules) that have changed in cows in early response to mastitis infection. Further analysis are being carried out, based on these results, to advance the understanding of animals response to the disease, which can lead to identify the candidate genes that could be used in breeding programs.X-MEETING 2011

Identificação de mecanismos envolvidos na resposta de bovinos ao carrapato Rhipicephalus microplus.

O objetivo desse trabalho foi identificar grupos de genes envolvidos na resposta de bovinos à infestação artificial com o carrapato Rhipicephalus microplus, por meio da construção de redes gênicas. Dados de um experimento com microarranjos, provenientes da hibridização de amostras de pele de fêmeas cruzadas Senepol x Nelore, Angus x Nelore e Nelore, obtidas antes (A) e (D) após a infestação artificial com o carrapato, foram analisados por meio de uma metodologia de construção de redes baseada em co-expressão gênica (WGCNA). Os dados foram pré-processados usando os pacotes affy e gcrma do R/Bioconductor e as redes de co-expressão identificadas separadamente para cada grupo (A e D), pelo pacote R/WGCNA. As redes foram comparadas e os módulos não conservados entre os dois grupos foram identificados a partir de um teste de correlação dos valores de conectividade. Nossa análise identificou 8 módulos de genes co-expressos, sendo um deles (6) não conservado entre os grupos. O modulo 6 (n=85 genes) mostrou-se enriquecido para o processo biológico Proteólise, sugerindo o envolvimento desse processo e dos genes identificados (ADAMTS4, CASP4, C3, CFB, PRSS22 e SPCS3) na resposta dos animais à infestação

Identificação de mecanismos envolvidos na resposta de bovinos ao carrapato Rhipicephalus microplus.

O objetivo desse trabalho foi identificar grupos de genes envolvidos na resposta de bovinos à infestação artificial com o carrapato Rhipicephalus microplus, por meio da construção de redes gênicas. Dados de um experimento com microarranjos, provenientes da hibridização de amostras de pele de fêmeas cruzadas Senepol x Nelore, Angus x Nelore e Nelore, obtidas antes (A) e (D) após a infestação artificial com o carrapato, foram analisados por meio de uma metodologia de construção de redes baseada em co-expressão gênica (WGCNA). Os dados foram pré-processados usando os pacotes affy e gcrma do R/Bioconductor e as redes de co-expressão identificadas separadamente para cada grupo (A e D), pelo pacote R/WGCNA. As redes foram comparadas e os módulos não conservados entre os dois grupos foram identificados a partir de um teste de correlação dos valores de conectividade. Nossa análise identificou 8 módulos de genes co-expressos, sendo um deles (6) não conservado entre os grupos. O modulo 6 (n=85 genes) mostrou-se enrique ido para o processo biológico Proteólise, sugerindo o envolvimento desse processo e dos genes identificados (ADAMTS4, CASP4, C3, CFB, PRSS22 e SPCS3) na resposta dos animais à infestação

A gene expression atlas of Vellozia nivea, a desiccation-tolerant species from the Brazilian campos rupestres.

Velloziaceae are an angiosperm family that contains the most desiccation-tolerant species (approximately 200 out of 270 species). More than 80% of the Velloziaceae species occur in South America, where the greatest morphological diversity is also found. The genus Vellozia comprises both desiccation-tolerant and non-desiccation-tolerant species, offering an excellent model for studying the evolution of desiccation- and drought-tolerance traits on plant genomes. To date, only limited genomic or transcript sequences are available for Velloziaceaespecies. Here we present a Vellozia nivea gene expression atlas across different plant organs and tissues, including flower, developing seeds, root, leaf, stem and seedling. Vellozia nivea is a desiccation-tolerant species, endemic to the Brazilian campos rupestres (rupestrian grasslands) and highly adapted to their extreme conditions. A total of 180.67 Gb of raw data were generated, and of these, 152.79 Gb were subjected to downstream analysis after quality control (QC). Vellozia niveade novotranscriptome assembly was performed with the Trinity bioinformatics tool, resulting in 684.615 contigs. After filtering contaminated sequence contigs from bacteria and fungi and removal of contigs with less than 10 sequence reads associated with the initial assembly, the transcriptome resulted in 195.512 remaining sequences. A GO enrichment analysis was performed on tissue‐specific transcripts. The Vellozia nivea transcriptome should be a useful resource for genome annotation and gene function discovery studies.PE1028

Update on Streptococcus suis research and prevention in the era of antimicrobial restriction: 4th International Workshop on S. suis

Streptococcus suis is a swine pathogen and a zoonotic agent afflicting people in close contact with infected pigs or pork meat. Sporadic cases of human infections have been reported worldwide. In addition, S. suis outbreaks emerged in Asia, making this bacterium a primary health concern in this part of the globe. In pigs, S. suis disease results in decreased performance and increased mortality, which have a significant economic impact on swine production worldwide. Facing the new regulations in preventive use of antimicrobials in livestock and lack of effective vaccines, control of S. suis infections is worrisome. Increasing and sharing of knowledge on this pathogen is of utmost importance. As such, the pathogenesis and epidemiology of the infection, antimicrobial resistance, progress on diagnosis, prevention, and control were among the topics discussed during the 4th International Workshop on Streptococcus suis (held in Montreal, Canada, June 2019). This review gathers together recent findings on this important pathogen from lectures performed by lead researchers from several countries including Australia, Canada, France, Germany, Japan, Spain, Thailand, The Netherlands, UK, and USA. Finally, policies and recommendations for the manufacture, quality control, and use of inactivated autogenous vaccines are addressed to advance this important field in veterinary medicine

Coronary artery disease, left ventricular hypertrophy and diastolic dysfunction are associated with stroke in patients affected by persistent non-valvular atrial fibrillation: a case-control study

Persistent non-valvular atrial fibrillation (NVAF) is associated with an increased risk of cardiovascular events such as stroke, and its rate is expected to rise because of the ageing population. The absolute rate of stroke depends on age and comorbidity. Risk stratification for stroke in patients with NVAF derives from populations enrolled in randomized clinical trials. However, participants in clinical trials are often not representative of the general population. Many stroke risk stratification scores have been used, but they do not include transthoracic echocardiogram (TTE), pulsate wave Doppler (PWD) and tissue Doppler imaging (TDI), simple and non- invasive diagnostic tools. The role of TTE, PWD and TDI findings has not been previously determined. Our study goal was to determine the association between TTE and PWD findings and stroke prevalence in a population of NVAF prone outpatients

Meditation on the Soles of the Feet Practice Provides Some Control of Aggression for Individuals with Alzheimer’s Disease

Alzheimer’s disease is a progressive neurodegenerative condition that affects cognition, mental and physical health, and functionality of older people. As the disease progresses from the mild to moderate stage, there is a concomitant increase in several behavioral variables, chiefly agitation, anger, and aggression. Currently, there are no evidence-based treatments for these behaviors in this population. Three individuals with moderate Alzheimer’s disease were taught an informal mindfulness practice, meditation on the Soles of the Feet (SoF), as a self-management strategy within a multiple-baseline design across participants. All three were able to learn and use the SoF practice to manage their verbal and physical aggression. Their use of the SoF practice was correlated with decreased perceived psychological stress for their spouses and caregivers, as well as for the participants, but to a much smaller degree. In terms of social validity, the participants, their spouses, and caregivers rated the SoF practice as acceptable, effective, with no unintended effects, and indicated that they would recommend the practice to others. However, they also rated SoF as effortful for the participants because it involves the participants remembering to use the practice with rising anger, a requirement particularly challenging for those with memory problems. The SoF practice may enable individuals in the early stages of dementia to manage their anger and aggression. The data were derived from an internally valid experimental design, suggestive of initial proof-of-concept, but needs to be replicated before any clinical implications can be imputed from this study

Constraining primordial non-Gaussianity with cosmological weak lensing: shear and flexion

We examine the cosmological constraining power of future large-scale weak lensing surveys on the model of \emph{Euclid}, with particular reference to primordial non-Gaussianity. Our analysis considers several different estimators of the projected matter power spectrum, based on both shear and flexion, for which we review the covariances and Fisher matrices. The bounds provided by cosmic shear alone for the local bispectrum shape, marginalized over $\sigma_8$, are at the level of $\Delta f_\mathrm{NL} \sim 100$. We consider three additional bispectrum shapes, for which the cosmic shear constraints range from $\Delta f_\mathrm{NL}\sim 340$ (equilateral shape) up to $\Delta f_\mathrm{NL}\sim 500$ (orthogonal shape). The competitiveness of cosmic flexion constraints against cosmic shear ones depends on the galaxy intrinsic flexion noise, that is still virtually unconstrained. Adopting the very high value that has been occasionally used in the literature results in the flexion contribution being basically negligible with respect to the shear one, and for realistic configurations the former does not improve significantly the constraining power of the latter. Since the flexion noise decreases with decreasing scale, by extending the analysis up to $\ell_\mathrm{max} = 20,000$ cosmic flexion, while being still subdominant, improves the shear constraints by $\sim 10$ when added. However on such small scales the highly non-linear clustering of matter and the impact of baryonic physics make any error estimation uncertain. By considering lower, and possibly more realistic, values of the flexion intrinsic shape noise results in flexion constraining power being a factor of $\sim 2$ better than that of shear, and the bounds on $\sigma_8$ and $f_\mathrm{NL}$ being improved by a factor of $\sim 3$ upon their combination. (abridged)Comment: 30 pages, 4 figures, 4 tables. To appear on JCA

Cardiac biomarkers of prognostic importance in chronic obstructive pulmonary disease

Background: Ischemic heart disease is common in COPD and associated with worse prognosis. This study aimed to investigate the presence and prognostic impact of biomarkers of myocardial injury and ischemia among individuals with COPD and normal lung function, respectively. Methods: In 2002–04, all individuals with airway obstruction (FEV1/VC < 0.70, n = 993) were identified from population-based cohorts, together with age and sex-matched non-obstructive referents. At re-examination in 2005, spirometry, Minnesota-coded ECG and analyses of high-sensitivity cardiac troponin I (hs-cTnI) were performed in individuals with COPD (n = 601) and those with normal lung function (n = 755). Deaths were recorded until December 31st, 2010. Results: Hs-cTnI concentrations were above the risk stratification threshold of ≥5 ng/L in 31.1 and 24.9% of those with COPD and normal lung function, respectively. Ischemic ECG abnormalities were present in 14.8 and 13.4%, while 7.7 and 6.6% had both elevated hs-cTnI concentrations and ischemic ECG abnormalities. The 5-year cumulative mortality was higher in those with COPD than those with normal lung function (13.6% vs. 7.7%, p < 0.001). Among individuals with COPD, elevated hs-cTnI both independently and in combination with ischemic ECG abnormalities were associated with an increased risk for death (adjusted hazard ratio [HR]; 95% confidence interval [CI] 2.72; 1.46–5.07 and 4.54; 2.25–9.13, respectively). Similar associations were observed also among individuals with COPD without reported ischemic heart disease. Conclusions: In this study, elevated hs-cTnI concentrations in combination with myocardial ischemia on the electrocardiogram were associated with a more than four-fold increased risk for death in a population-based COPD-cohort, independent of disease severity

Electron paramagnetic resonance and other properties of hydrogenases isolated from Desulfovibrio vulgaris (strain Hildenborough) and Megasphaera elsdenii

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65872/1/j.1432-1033.1983.tb07727.x.pd