Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population

Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07–0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.
Temporal variation in subtidal macroalgal assemblages at Black Island, Recherche Archipelago

Temporal patterns in subtidal macroalgal diversity have not been described for much of temperate, southern Australia. To characterize temporal variation in species diversity, subtidal macroalgal assemblages were compared between austral spring and autumn collections from Black Island, Western Australia. Macroalgae (> 1 cm in length) from 0.25 m2 quadrats were harvested from the south-eastern and southern sides of the island in depths < 10 m and 1020 m in October 2002 and 2003 and April 2003 and 2004. Macroalgae were sorted, wet-weighed, and identified. A three-way analysis of variance tested for differences in total biomass, and density of thalli in the canopy with time, site, and depth. Analysis of similarity was used to test for differences in macroalgal assemblages among sampling times. Key environmental variables for the area were compiled from previous reports. A total of 254 species of macroalgae were recorded, consisting of canopy, understory, and epiphytic species. Average total biomass was not significantly different among sampling times. Density of thalli per 0.25 m2 was greater and more variable in depths < 10 m than in depths 1020 m. Macroalgal assemblages differed significantly among sampling times (Clarkes R values > 0.5, P = 0.001), and between samples collected from the same season but in different years. Each species was present, on average, in only 15% of the sampled quadrats. Chlorophyll a, seawater temperature, and salinity estimates did not vary much throughout the year with a range of 0.6 mg m-3 for chlorophyll a, 2.3 °C for seawater temperature, and 0.2 ppt for salinity. Year-round exposure to wind and wave energy from Southern Ocean gales and storms may drive the high species turnover and variability in density of thalli in depths < 10 m.
Structure and function of the UVDE repair protein

UVDE is a repair enzyme discovered for the first time in the fission yeast Schizaromyces pombe. The initial biochemical characterization of this enzyme showed that its substrate specificity includes not only UV lesions, but also abasic sites and some nucleotide mismatches. The mechanism, however, of UVDE damage recognition and DNA cleavage was not clarified. S. pombe UVDE was seen to require Mn2+ and Mg2+ for its function, but the utilization of divalent metals in its cleavage reaction was empirical and without a clear vision of the nature, the number and the exact role of the metal cofactors. UVDE homologues were found in many fungal species and in a number of bacteria such as Bacillus subtilis and Thermus thermophilus. Although the S. pombe UVDE was partially characterized, no information was available for the substrate specificity or the cofactor requirements its bacterial homologues
Tillage practices influence winter wheat grain yield prediction using seasonal precipitation

Making the best use of limited precipitation in semi-arid dryland cropping systems is important for crop production. Tillage practices may influence how this precipitation is utilized to predict winter wheat grain yield (Triticum aestivum L.). This study examined how tillage practices influence winter wheat grain yield prediction accuracy using precipitation received at three different periods of the season. Data were obtained from the period of 1972 to 2010 from a long-term tillage experiment. The study was designed as a winter wheat-fallow experiment. Each phase of the winter wheat-fallow rotation was present each year. The trial was set up as a randomized complete block design with three replications. Tillage treatments included no-till (NT), stubble mulch (SM), and moldboard plow (MP). Feed-forward neural network and multiple linear regression (ordinary least squares) were used to fit models under each tillage practice. No-till had the highest yield prediction accuracy with a root mean square error (RMSE) of 0.53 Mg ha-1 and accounted for 81% of the variability in grain yield. Stubble mulch had an RMSE of 0.55 Mg ha-1 and explained 73% of the variability in yield. Stubble mulch and NT were more accurate in yield prediction than MP which had an RMSE of 0.77 Mg ha-1 and accounted for 53% of the variability in yield. The multiple linear regression model was less accurate than the feed-forward neural network model since it had at least 0.30 Mg ha-1 more RMSE and accounted for only 5-8% of the variability in yield. Relative RMSE classified all neural network models as fair (21.6-27.3%) while linear regression models for the different tillage practices was classified as poor (33.3-43.6%), an illustration that the neural network models improve yield prediction accuracy. This study demonstrated that a large proportion of the variability in grain yield may be accounted for under NT and SM systems when using precipitation as predictors with neural networks.
Seasonal variability of satellite-derived primary production in the South China Sea from an absorption-based model

Seasonal patterns of marine net primary production (NPP) are crucial for understanding the marine ecosystem and biogeochemical cycles. Uncoupling of seasonal variations between NPP and phytoplankton chlorophyll-a over different areas has attracted much attention. In this study, following a review of previous studies, monthly climatological NPP data from 2003 to 2020, estimated using the Size-fractioned Phytoplankton Pigment Absorption (a ph)-based NPP Model (SABPM), were selected to study the seasonal variability of NPP in the South China Sea (SCS). Results showed the spatial differences of NPP seasonality and its departures from climatology in extreme El Niño-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) years. Cluster analysis for climatological monthly data identified significant differences of NPP seasonality in five typical regions. In coastal regions along the northern SCS and off eastern Vietnam, NPP exhibited the most obvious seasonal cycle with maximum (minimum) values in summer (winter), attributable mainly to river discharge and summer upwelling. In regions off northwestern Luzon and coast of southern SCS, NPP showed peaks in winter, which were related to strong mixing and upwelling. In northwestern SCS, NPP was high during May–September in phase with sea surface temperature and the primary controlling factors were found to be shallow nutricline depth and wind-driven mixing. Owing to the deep nutricline depth in the central basin, NPP exhibited little seasonal variability; only a weak signal was observed in spring in phase with photosynthetically active radiation. Local dynamics on regulating the nutrient supply and light availability contribute to these regional differences in NPP seasonality, which could also be affected by extreme climate events. The largest anomalies of the NPP seasonal cycle coincide with 2015/2016 ENSO and super IOD in 2020. During these events, enhanced (weakened) westerly winds caused fall (rise) of SLA and increase (decrease) of NPP in coastal regions along the northern SCS and that off eastern Vietnam. Overall, the a ph-based model shows a new perspective to study the spatiotemporal variations of NPP in the SCS.
Expression, function and regulation of the Him gene during Drosophila heart development

I have analysed the regulation and function of the Him gene to gain new insights into Drosophila heart development and its controlling factors. My results show that Him is important during the early specification of pericardial cells and cardioblasts. Loss of Him leads to a reduced number in both of these cell types by the end of embryogenesis. Over-expression of Him throughout the heart results in supernumerary pericardial cells. Him is expressed in all embryonic pericardial cells from embryonic stage 12 to approximately stage 15. I have identified an enhancer fragment that reproduces this expression pattern. Phylogenetic footprinting revealed three highly conserved regions within this sequence. I undertook an extensive mutational analysis of this enhancer to identify regulatory elements within it. I identified Tinman as a direct activator of Him expression. My data indicate that Him is activated in a widespread area of the dorsal mesoderm and the amnioserosa and is actively limited to the pericardial cells. A 5 bp mutation within the enhancer sequence allows for expression within the cardioblasts. Both heart cell types develop from the dorsal mesoderm and some share immediate progenitors. By stage 13, Him is pericardial cell specific and Mef2 is cardioblast specific. This is essential for normal heart development. If Him is not excluded from the cardioblasts, expression of the muscle-cell specific differentiation gene myosin is disrupted, similar to what has been described for Mef2 null mutants. If Mef2 is expressed in pericardial cells, the larval development of the pericardial cells is severely disturbed. A possible explanation for these data is that Him is part of a genetic program that prevents the premature differentiation of heart cells and its down-regulation permits the pericardial cells to undergo their correct development.
Dairy Goats, Feeding and Nutrition

Nutrition and Quality of Goat Milk Mathematical Modelling of Goat Lactation Curves Lipids of Goats Milk: Origin, Composition and Main Sources of Variation Protein Components of Goat Milk Aromatic and Nutritonal Quality of Goat Milk Energy and Protein Requirements of Goats Feed Intake Feeding Behaviour and Intake of Goats Browsing on Mediterranean Shrublands Grazing Management of Dairy Goats on Mediterranean Herbaceous Pastures Feeding Management of Dairy Goats in Intensive Systems Goat Nutrition for Fibre Production Metabolic and Nutritional diseases.
Salmonella organism transmission in hatching broiler egggs

The vertical transmission of Salmonella organism in hatching broiler eggs were investigated in selected states in South Western Nigeria. Hatching eggs obtained from five major hatcheries located within each state were used to isolate and characterize salmonella in shell, yolk and albumin of eggs. The study revealed that Salmonella gallinarum and Salmonella arizorae were isolated from hatcheries in Lagos State while some hatcheries in Oyo State respectively were positive for salmonella organism in hatcheries A & B for organism in hatcheries B while yolk & albumin were positive for salmonella organism in Lagos State (Hatchery A).
Weather-dependent survival: implications of climate change for passerine population processes

Understanding demographic processes will be essential to construct robust models of population responses to climate change. We show that survival is related to the strength of the North Atlantic Oscillation in five out of ten British resident passerine species, and explore the importance of biologically more specific variables (duration of winter frosts and snow periods; occurrence of cold, wet days; spring temperature; and summer drought). The most important variables differed between species in relation to differences in foraging strategy. In almost all cases, first-year survival was influenced by weather more than was the survival of adult birds. Particularly vulnerable species, such as the Wren Troglodytes troglodytes, may exhibit a 25% reduction in juvenile survival rates due to adverse weather within the range experienced in the last 30 years; variation in survival by 10% or more is commonplace in most species. Thus, climate influences on food availability may provide the mechanism by which populations will alter under changed climatic conditions, though the presence of density dependence may reduce the impact of this on long-term population trajectories.
The Role Of Serum Amyloid A In Inflammatory Disease - Proinflammatory Mediator Or Inert Biomarker?

Neutrophils are phagocytes of the innate immune system with prominent roles in host defense and are also believed to be important in autoimmune diseases such as rheumatoid arthritis (RA) by accumulating in inflamed joints and contribute to tissues destruction. Neutrophils differentiate in the bone-marrow and are mature cells when entering circulation with a cytoplasm packed with granules that contain toxic substances in addition to receptors that can be up-regulated to the cell surface during activation. Migration into the affected tissue is directed by mediators from the inflamed site which guides neutrophils along a chemotactic gradient and transfers the cell from restinginto a primed state. The inflammatory process triggers a systemic acute phase response characterized by the production of acute phase proteins (APP). The most prominent APP is serum amyloid A (SAA), the concentration of which can increase thousand fold in response to infection, aseptic inflammation or trauma. Patients with RA often have chronically elevated SAA in blood and joints and SAA has been implicated in the pathogenesis of RA. Recombinant SAA (rSAA) has been suggested to possess proinflammatory activities and act as a chemoattractant for neutrophils via a receptor called FPR2. A peptide (PBP10) with intracellular inhibitory activity was shown to allow discrimination between neutrophil signals mediated by FPR2 and the closely related FPR1. Next, the receptor specificity for rSAA was studied by use of PBP10 and another FPR2 specific inhibitor WRW4. rSAA affinity for FPR2 in transfected cell lines was corroborated and rSAA indeed activated primary human neutrophils. However, FPR2 was not responsible for mediating activation of primary human neutrophils by rSAA. Next, proinflammatory activity of rSAA was compared to that of endogenous SAA in circulation of RA patients. Using a sensitive marker for neutrophil activation in peripheral blood, endogenous SAA in circulation lacked proinflammatory activity and thus differed functionally from rSAA. Synovial neutrophils from patients with inflammatory arthritis and elevated SAA in joint fluid were next studied with respect to activation status. Synovial neutrophils displayed a surprisingly resting phenotype despite having transmigrated from peripheral blood to a compartment with endogenous SAA. Endogenous SAA, both in circulation and in joints, lack the proinflammatory properties present in the recombinant molecule. Key-words: neutrophils, serum amyloid A, rheumatoid arthritis ISBN: 978-91-628-8050-7
Gene cloning and sequence analysis of the cold-adapted chaperones DnaK and DnaJ from deep-sea psychrotrophic bacterium Pseudoalteromonas sp. SM9913

Pseudoalteromonas sp.SM9913 is a phychrotrophic bacterium isolated from the deep-sea sediment.The genes encoding chaperones DnaJ and DnaK of P.sp.SM9913 were cloned by normal PCR and TAIL-PCR(GenBank accession Nos DQ640312,DQ504163). The chaperones DnaJ and DnaK from the strain SM9913 contain such conserved domains as those of many other bacteria,and show some cold-adapted characteristics in their structures when compared with those from psychro-,meso-and themophilic bacteria.It is indicated that chaperones DnaJ and DnaK of P.sp.SM9913 may be adapted to low temperature in deep-sea and function well in assisting folding,assembling and translocation of proteins at low temperature.This research lays a foundation for the further study on the cold-adapted mechanism of chaperones DnaJ and DnaK of cold-adapted microorganisms.
Involvement of short RNAs in polycomb-mediated gene repression

Polycomb group proteins maintain cell identity by repressing developmental regulator genes specific for other cell types. There are two main complexes: Polycomb repressive complex 1 (PRC1) and 2 (PRC2). PRC2 methylates histone H3 lysine 27 (H3K27me3), creating a binding site for PRC1 that ubiquitinates H2AK119. Polycomb target genes are associated with stalled RNA polymerase II (RNAPII), and the initiation marker H3K4me3, known as bivalent chromatin. Our laboratory has demonstrated that short RNAs are transcribed from the promoter region of these genes in human T-cells, while the work carried out as part of the present thesis demonstrates that short RNAs are also transcribed in murine embryonic stem cells (ESCs). This indicates that they are conserved across different species and cell types. Northern blotting for RNAs ≤200 nucleotides extracted from murine ES cell deficient for PRC2 and PRC1 revealed that short RNA production is independent of Polycomb activity. When cells differentiate and Polycomb-target genes become activated, short RNAs are depleted. Given that PRC2 interacts with RNA, this loss of short RNAs might allow gene activation. Additionally, polycomb response elements (PRE) have been detected in Drosophila. These elements are necessary and sufficient for polycomb recruitment. A recently identified PRE, HOXD11.12, recruits PRC2 in human mesenchymal stem cells (MSC). It is hypothesized that PRE activity is due to the transcription of short RNAs. Blotting for RNA extracted from MSC identified short RNAs transcribed from D11.12. Moreover, these short RNAs can form the same secondary structure as the previously-identified short RNAs and are also located at a CpG island. Furthermore, RASL12 and YBX2 behave as PREs while D11.12 from active HOXD11 enhances gene expression, potentially also acting as a Trithorax response element (TRE).
Reevaluation of dietary methionine requirement by plasma methionine and ammonia concentrations in surgically modified rainbow trout, Oncorhynchus mykiss

This study was designed to re-evaluate the dietary methionine requirement by means of the plasma methionine and ammonia concentrations in surgically modified rainbow trout, Oncorhynchus mykiss. A total of 35 rainbow trout averaging 505±6.5 g (initial body weight, mean±SD) were randomly distributed into seven groups with five fish in each group. After 48 h of feed deprivation, each group of fish was fed one of seven L-amino acid based diets containing 0.5% cystine and graded levels of methionine (0.25, 0.40, 0.50, 0.60, 0.70, 0.80 or 0.95% of diet, dry matter bases) by intubation at 1% body weight on dry matter basis. Blood samples were taken at 0, 5 and 24 h after intubation. Post-prandial plasma free methionine concentrations (PPmet, 5 h after intubation) and post- absorptive plasma free methionine concentrations (PAmet, 24 h after intubation) of fish fed diets containing 0.60% or higher methionine were significantly (p<0.05) higher than those of fish fed diets containing 0.50% or lower methionine. PPmet and PAmet in fish fed diets containing 0.60% or higher methionine were not significantly different except PPmet of fish fed diet containing 0.95% methionine. Post- prandial plasma ammonia concentrations (PPA, 5 h after intubation) of fish fed diets containing 0.70% or higher methionine were significantly higher than those of fish fed diets containing 0.60% or lower methionine, and PPA of fish fed diets containing 0.25 and up to 0.60% methionine were not significantly different from each other. Broken-line model analyses on PPmet, PAmet, and PPA indicated that the dietary methionine requirement of rainbow trout was between 0.59 (1.69) and 0.67 (1.91) % of diets (% dietary protein bases) when the diets contained 0.5% cystine. (Key Words : Methionine, Rainbow trout, Requirement, Intubation, Plasma, Ammonia)
Pyrimidine Enzyme Specific Activity at Four Different Phases of Growth in Minimal and Rich Media, and Concomitant Virulence Factors Evaluation in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative rod, aerobic, non-fermenting, oxidase positive, pigment producing, and nutritionally versatile bacterium. Infections by P. aeruginosa are the most important cause of morbidity and mortality in immunocompromised patients, given virulence factor production that suppresses antibiotic therapy and promotes persistent infection. This research is the first comprehensive report of the pyrimidine biosynthetic pathway for all phases of growth in minimal and rich media coupled with the evaluation of virulence factor production of P. aeruginosa in comparison to four other bacterial species (Pseudomonas putida, Pseudomonas fluorescens, Burkholderia cepacia, and Escherichia coli wild-type strains). Cellular growth and passing genetic information to the next generation depend on the synthesis of purines and pyrimidines, the precursors of DNA and RNA. The pyrimidine biosynthetic pathway is essential and found in most organisms, with the exception of a few parasites that depend upon the pyrimidine salvage pathway for growth. Both the pyrimidine biosynthetic and salvage enzymes are targets for chemotherapeutic agents. In our laboratory, research on pyrimidine auxotrophic mutants showed the role of the pyrimidine biosynthetic pathway and its intermediates on P. aeruginosa metabolism and impaired virulence factors production. The present research shows that pyrimidine enzymes are active in all phases of growth, including the production of two forms of ATCase in the late log phase in P. aeruginosa. This finding may be explained by the displacement of the inactive PyrC' by the active PyrC or PyrC2 to form a new and larger pyrBC encoded ATCase. Pseudomonas aeruginosa wild-type appears to produce by far the most virulence factors, haemolysin, iron chelation, rhamnolipid, adherence, and three types of motility (swimming, swarming, and twitching) investigated in this study, when compared to the other four wild-type strains. Growth analysis was carried out as typically done in minimal medium but also in rich medium to simulate conditions in the blood and lung tissues of humans as P. aeruginosa infections develop.