Serial Analysis of Gene Expression (SAGE) in the Skeletal Muscle of Pig

Skeletal muscle growth represents one of the main economic traits in pig production. To gain a better understanding of expressions profile in pig muscle, serial analysis of gene expression (SAGE) was performed in Longissimus dorsi of two pigs at 3 and 9 months of age. A total of 53,120 long tags were obtained and sequenced from the four muscle SAGE libraries, representing 17,902 different tags, or putative transcripts, 0.64% (+0.09) of which had a relative expression level higher than 1‰. Overall, a total of 218 tags were highly expressed and 31 had a frequency higher than 3‰. Functional characterisation of the expression profiles was performed using Kyoto Encyclopedia of Genes and Genomes metabolic maps and 139 pathways were identified for swine skeletal muscle. Focal adhesion, Mitogen-Activated Protein Kinase signalling, oxidative phosphorylation, ribosomal proteins, regulation of actin cytoskeleton and insulin signalling pathways showed an abundance of genes greater than 1.5% of all the expressed transcripts. A comparison with human SAGE library indicated no statistical differences for the frequency of genes involved in these metabolic pathways

Investigation of rumen metagenome in Italian Simmental and Italian Holstein cows using a whole-genome shotgun sequencing technique

The study aimed at investigating the rumen microbiome composition and functional activity in mid lactating cows of Italian Holstein (IH) and Italian Simmental (IS) breeds. Eight IH and eight IS pluriparous cows with days in milking (DIM) ranging from 90 to 180 were selected and rumen contents were sampled with oesophageal tube. Rumen metagenome was analysed using a whole shotgun sequencing. Data were analysed for taxonomic classification and microbial genes. The relative abundance of Archaea, the Archaea to Bacteria ratio and the Archaea to Eukarya ratio were higher (p < .05) in IS than IH cows. The comparison between IH and IS underlined differences for the abundances of Bacteria, being Bactroidaceae, Bacteroides, Prevotellaceae and Prevotella lower (p < .05) in IS than in IH cows. The IS cows showed higher abundances of Euryarchaeota (p < .05), Methanosphera (p < .01) and Methanothermobacter (p < .05) than IH cows. The annotation of sequences to KEGG revealed that 170 genes were differentially abundant between IS and IH cows and among these, 20% were involved in protein biosynthesis, 8.8% in one-carbon metabolism, as methyl coenzyme M reductase associated protein and of six isoforms of methyl coenzyme M reductase. The present results suggest a genetic link between breed and microbiome, although this interaction can be influenced by several biological factors. Considering that there are still a low number of whole genome shotgun sequencing analysis of rumen communities, these data can provide further information to scientific community

Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs

Background: Dietary intervention studies are required to deeper understand the variability of gut microbial ecosystem in healthy dogs under different feeding conditions and to improve diet formulations. The aim of the study was to investigate in dogs the influence of a raw based diet supplemented with vegetable foods on faecal microbiome in comparison with extruded food. Methods: Eight healthy adult Boxer dogs were recruited and randomly divided in two experimental blocks of 4 individuals. Dogs were regularly fed a commercial extruded diet (RD) and starting from the beginning of the trial, one group received the raw based diet (MD) and the other group continued to be fed with the RD diet (CD) for a fortnight. After 14 days, the two groups were inverted, the CD group shifted to the MD and the MD shifted to the CD, for the next 14 days. Faeces were collected at the beginning of the study (T0), after 14 days (T14) before the change of diet and at the end of experimental period (T28) for DNA extraction and analysis of metagenome by sequencing 16SrRNA V3 and V4 regions, short chain fatty acids (SCFA), lactate and faecal score. Results: A decreased proportion of Lactobacillus, Paralactobacillus (P < 0.01) and Prevotella (P < 0.05) genera was observed in the MD group while Shannon biodiversity Index significantly increased (3.31 +/- 0.15) in comparison to the RD group (2.92 +/- 0.31; P < 0.05). The MD diet significantly (P < 0.05) decreased the Faecal Score and increased the lactic acid concentration in the feces in comparison to the RD treatment (P < 0.01). Faecal acetate was negatively correlated with Escherichia/Shigella and Megamonas (P < 0.01), whilst butyrate was positively correlated with Blautia and Peptococcus (P < 0.05). Positive correlations were found between lactate and Megamonas (P < 0.05), Escherichia/Shigella (P < 0.01) and Lactococcus (P < 0.01). Conclusion: These results suggest that the diet composition modifies faecal microbial composition and end products of fermentation. The administration of MD diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to RD diet

Evaluation of gene expression profiles of pig skeletal muscle in response to energy content of the diets using human microarrays

The aim of the research was to compare gene transcription profiles of Musculus longissimus dorsi (MLD) between pigs fed diets with high (HED) or low (LED) energy contents. Two groups of 4 Casertana pigs were reared from 3 to 12 months of age in the same environmental conditions and fed HED or LED. In the HED, the ave rage daily gain and back fat thickness were significantly (P<0.05) higher than in LED pigs. Differential expression of genes in MLD of pigs fed diets with different energy density was assessed by a human high-density complementary DNA (cDNA) muscle microarray consisting of 4670 probes and further confirmed by quantitative real time RT-PCR analysis. Seven of the genes up-regulated in MLD of HED pigs were invo l ved in the glycolytic and ox i d a t i ve metabolism (phosphoglycerate mutase 2, glyc e ra l d e hyde-3-phosphate dehydrogenase, NADH dehydrogenase ubiquinone1 beta 9, muscle pyruvate kinase, enolase 3, muscle creatine kinase, isocitrate dehydrogenase 3 (NAD+) gamma) and four in the contractile apparatus (tropomyosin 1 alpha, troponin C2, fast, fast skeletal myosin light chain 2, troponin T3, skeletal, fast). Instead, HED diet reduced the level of expression of muscle proteins associated with slow fibre type (troponin T1, skeletal, slow, supervillin, myosin binding protein C, slow type, titin, myosin, heavy polypeptide 7, beta, calponin homology-associated smooth muscle) and signal transduction (SH3-binding domain protein 5-like, hypothetical protein FLJ21438, protein kinase cAMP-dependent, catalytic, rho guanine nucleotide exchange factor 15). The down-regulation of CTSB was also observed for HED group. From the results it can be assumed that high energy content of the diet influence physiological processes in the muscle tissue by switching slow fibres into fast reacting fibres and thus enhancing meat quality

Analisis Intangible Factors Yang Mempengaruhi Penentuan Harga Produk Karya Seni

This research aims to develop a new quantitative method to determine painting pricing based on 10 intangible factors, i.e. curator, amount of exhibition, painter\u27s year of birth, painting\u27s years of made, auction record,estimation price, exhibition place, painting media, painting size, and previous sales record. The selling price data are obtained from six auction houses. Kano Model and Linear Regression Model are used to examine the relationbetween pricing and each variable. Based on the model development scheme, there are 6 alternative models that can be obtained. Each model then was evaluated by cross-validation procedure using 21 data. Based on the value of R2for each model, the Kano Model with variable previous sales is the best model with R2 of 70

Meniscal ossicles as micro-CT imaging biomarker in a rodent model of antigen-induced arthritis: A synchrotron-based x-ray pilot study

It is increasingly recognized that early detection of bone erosion plays an important role in the overall evaluation of rheumatoid arthritis and in the choice of the correct treatment approach. Since an appropriate use of imaging biomarkers in preclinical settings offers the prospect of smaller and optimized sample size, in the present study we define an anatomical imaging biomarker that could be objectively measured from micro-CT imaging data as an indicator of bone erosion in arthritis process. The well-characterized antigen-induced arthritis (AIA) model in rats was used. The animals were divided into 2 groups: arthritic disease control and arthritic having been administrated with the tumor necrosis factor alpha-blocking agent (Humira). Rats were sacrificed in the acute phase of AIA; peripheral blood and synovial tissue were collected for assessment of arthritis. Ex vivo micro-CT tomography of knee joints was performed at the Elettra synchrotron light source (Trieste, Italy). Overall, results from this study suggest that use of high-resolution micro-CT analysis coupled with meniscal ossicles bone parameters quantification provide a powerful combination to enhance data interpretation and assessment of disease-modifying drugs in an animal model of arthritis

DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa

There is a strong need to find new, good biomarkers of head and neck squamous cell carcinoma (HNSCC) because of the bad prognoses and high mortality rates. The aim of this study was to identify the potential biomarkers in HNSCC that have differences in their DNA methylome and potentially premalignant oral lesions, in comparison to healthy oral mucosa. In this study, 32 oral samples were tested: nine healthy oral mucosae, 13 HNSCC, and 10 oral lesions for DNA methylation by the Infinium MethylationEPIC BeadChip. Our findings showed that a panel of genes significantly hypermethylated in their promoters or specific sites in HNSCC samples in comparison to healthy oral samples, which are mainly oncogenes, receptor, and transcription factor genes, or genes included in cell cycle, transformation, apoptosis, and autophagy. A group of hypomethylated genes in HNSCC, in comparison to healthy oral mucosa, are mainly involved in the host immune response and transcriptional regulation. The results also showed significant differences in gene methylation between HNSCC and potentially premalignant oral lesions, as well as differently methylated genes that discriminate between oral lesions and healthy mucosa. The given methylation panels point to novel potential biomarkers for early diagnostics of HNSCC, as well as potentially premalignant oral lesions

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

An online tool for fetal fraction prediction based on direct size distribution analysis of maternal cell-free DNA

The discovery of circulating fetal DNA in the plasma of pregnant women has greatly promoted advances in noninvasive prenatal testing. Screening performance is enhanced with higher fetal fraction and analysis of samples whose fetal DNA fraction is lower than 4% are unreliable. Although current approaches to fetal fraction measurement are accurate, most of them are expensive and time consuming. Here we present a simple and cost-effective solution that provides a quick and reasonably accurate fetal fraction by directly evaluating the size distribution of circulating DNA fragments in the extracted maternal cell-free DNA. The presented approach could be useful in the presequencing stage of noninvasive prenatal testing to evaluate whether the sample is suitable for the test or a repeat blood draw is recommended