Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipid profile and cholesterol in meat cuts of ewe lambs fed different levels of concentrate Perfil lipídico e colesterol em cortes cárneos de borregas alimentadas com diferentes níveis de concentrado

Consumers are more interested in having healthier and better quality products. The diet offered to animals can strongly affect the composition of meat. Thus, this study aimed to evaluate the effect of different levels of concentrate on lipid profile (in natura meat) and cholesterol content (in natura and cooked meat) of ewe lambs’ meat cuts. Therefore, twenty-four lambs with a mean weight of 23.1 ± 2.1 kg were confined and fed different levels of a concentrate (20, 40, 60 and 80%) for 120 days. The diets consisted of tifton hay and concentrate based on corn and soybean meal. The muscles triceps brachii (shoulder), longissimus dorsi (loin) and semimembranosus (leg) represented the respective cuts that were analyzed. Increased levels of concentrate decreased only C18:3 (5.82 to 0.20 mg/100 g) in meat and without affecting saturated fatty acids (SFA), unsaturated (UFA), monounsaturated (MUFA), polyunsaturated (PUFA), both desirable and total levels. Levels of concentrate had no effect on UFA/ SFA (1.01), MUFA/SFA (0.97), PUFA/SFA (0.04) ratios, or the atherogenic (AI) and thrombogenic index (TI), nor on the content cholesterol in natura and cooked meat. The meat cuts had different lipid profiles, IA, IT and cholesterol content. Concentrate levels slightly alter the lipid profile and do not alter the cholesterol content, while meat cuts are different for these components.
Comparing Otoliths and Scales as Structures Used to Estimate Ages of Largemouth Bass: Consequences of Biased Age Estimates

AbstractManagement agencies often estimate the ages of Largemouth Bass Micropterus salmoides based on the examination of scales—a structure that is known to produce biased estimates—without knowing how the associated bias affects management decisions. We sought to understand the effects of this bias by comparing population metrics that were predicted using scale-derived and otolith-derived age data. We collected scales and otoliths from Largemouth Bass that were sampled during standard electrofishing surveys. The age of each fish was estimated independently by three separate readers using both scales and otoliths. We assessed the average coefficient of variation for scale-derived and otolith-derived age estimates, examined the bias of scale-derived age estimates, and estimated von Bertalanffy growth model parameters by using ages estimated from scales and otoliths. These parameter estimates were used in yield-per-recruit simulations that predicted yield and the percentage of individuals in the cohort surv.
A Probabilistic Approach for Automated Discovery of Biomarkers using Expression Data from Microarray or RNA-Seq Datasets

2 Acknowledgement . 5 List of Figures . 10 List of Tables . 13 Chapter I: Introduction and Historical Perspective . 15 I 1 Biological Complexity and Emergence . 18 I 2 Complex Diseases . 19 I 3 Organizing Principles of Biological Systems . 21 I 4 Network Biology . 23 I 5 Network Theory and Properties of Biological Networks . 24 I 6 Dynamics of Biological Networks . 32 I 6.1 Differential Expression Analysis . 33 I 7 Pathway Analysis . 35 I 7.1 Classification of Pathway Analysis . 35 I 7.2 Limitations of Pathway Analysis. 42 Chapter II: Aim of the Thesis . 45 Chapter III: Methods . 48 III – 1 Genomic and Network Data . 50 III – 1.1 Genomic Data . 50 III – 1.2 Network Data . 50 III 2 Probability of Change (Nodes and Edges) . 51
Pathology Caused by the Bacterium Edwardsiella tarda in Anabas testudineus (Bloch)

A virulent strain of Edwardsiella tarda isolated from an outbreak in an organized Clarias batrachus hatchery was used to study the infectivity pattern and pathology in Anabas testudineus. The 50% lethal dose for A. testudineus injected intraperitoneally with E. tarda was 107.8 cells. The organism produced acute disease pattern with characteristic histopathological lesions viz., hepatic necrosis and intravascular thrombus, myocardiopathy and enteritis along with mild necrosis in the spleen and kidney. E. tarda specific antigen was detected in the liver, kidney and spleen of dead fish through dot-ELISA.
Genetic Variation in Growth and Blister-Rust Resistance in a Pinus strobus x P. wallichiana Hybrid Population

Summary This experiment consists in a controlled crossing according to a factorial design performed between 7 female trees of P. strobus and 4 male trees of P. wallichiana to combine the rapid growth of former species with high resistance to Cronartium ribicola of the latter one. The hybrid families were artificially inoculated at age 2, and field planted at age 6. Blister rust resistance (BRR), tree survival (TS), total height growth, (H) annual height growth (h), diameter (D), basal area (BA), stem volume (V), stems straightness (SS) and branch thickness (BT) were the traits measured at age 17. Statistical analysis produced the results presented below. Significant (p<0.05) and highly significant (p<0.01; p<0.001) differences were found among hybrid families. Differences among female effects were highly significant (p<0.001) for all tested traits including BRR, suggesting that nuclear additive genes controlled these traits. Significant differences were found among male parents for H but no significant differences for BRR; therefore, all four male parents transmitted a similar level of resistance. The ratio σ2GCA/σ2SCA variance accounted for 8.1 for BRR, 8.5 for H, 3.5 for V, 9.3 for SS and 1.9 for BT. Similarly, the ratios of σ2GCA-F /σ2GCA-M variance due to female parents were 70.5 for BRR, 23.6 for H, 1.0 for V, 0.4 for SS and 1.0 for BT, were found. Narrow-sense heritabilities, at individual level, were low to moderately high, ranging between 0.085 for BT and 0.421 for BRR. By comparison with the mean of P. strobus parent species, the BRR heterosis was highly positive, but negative for all growth traits. If the hybrids will be used in operational planting programs, a significant genetic gain for BRR and growth traits could be achieved.
Prebiotic potential of xylanase enzyme supplemented wheat offal in broiler chickens

The recent development of antibiotics-resistant pathogens in poultry, which poses a threat to human health, has necessitated the search for an alternative to antibiotic growth promoters (AGPs) to improve the gut microflora in poultry diets. One of the alternatives to AGPs is probiotics which are beneficial organisms. The by-products of the digestion of polysaccharides for which poultry do not have enzymes to digest are called prebiotics. Prebiotics serve as food for probiotics. The application of enzymes makes this digestion possible. The prebiotic potentials of enzyme supplemented high fibre feedstuffs (HFFs) are not known. This study was conducted to assess the prebiotic potential of xylanase enzyme supplemented wheat offal on broiler chickens (in-vivo). The replacement of maize with wheat offal irrespective of levels supplemented with 100ppm xylanase enzyme caused a reduction in feed intake and an increase in weight gain and better feed conversion ratio. Birds fed diet with 20% wheat offal supplemented with a xylanase enzyme outperformed birds fed diets with 10 or 30% wheat offal supplemented with a xylanase enzyme and birds fed the control diet. The birds had normal weights of vital organs with good structural consistency. The identification of microbes (fungi and bacteria) showed that dietary levels of wheat offal (10, 20 or 30% inclusion) with supplementation of a xylanase enzyme enhanced the growth of beneficial microbes, which resulted in the inhibition or elimination of the opportunistic/pathogenic microbes. It was concluded that enzyme supplementation of high fibre feedstuffs could improve the growth performance, nutrient retention and increase concentration of beneficial microbes in the guts. The use of enzymes is therefore recommended when HFFs are required as a prebiotic source in the guts of broilers.
Occurrence of shiga toxin-producing Escherichia coli in lactating cows and in contact workers in Egypt:serotypes, virulence genes and zoonotic significance

Shiga toxin-producing Escherichia coli (STEC) are emerging food–borne zoonotic pathogens associated with haemorrhagic colitis and haemolytic uremic syndrome in humans. This study investigated the occurrence of STEC serotypes, and prevalence of STEC isolates carrying virulence genes including shiga toxins (stx1, stx2); intimin (eaeA) and enterohaemolysin (ehxA) genes in lactating cows and in contact workers. Two hundred and forty samples of milk and cows’ rectal swabs (120, each) and fifty stool swabs from in contact workers were collected from dairy farms at Sharkia Province, Egypt. These swabs were cultured on Eosin methylene blue agar. After biochemical and serological identifications, E. coli isolates were subjected to multiplex PCR. Seven enteropathogenic E. coli (EPEC) strains (O1, O2, O55, O86, O114, O119&O124); two enterohaemorrhagic E. coli (EHEC) strains (O26 &O111) and two enterotoxigenic E. coli (ETEC) strains were identified. The overall incidence of E. coli (19.1%) in milk showed a significant difference (P <0 .05) than that found in cows’ rectal swabs (63.3%) and in contact workers’ stool swabs (44%). The overall prevalence of milk STEC isolates possessing stx2 (26.1%) clarified a significant difference (P <0 .05) than that obtained in stx2 positive isolates (6.6%) from cows’ rectal swabs. Moreover, human STEC isolates carrying stx2 (22.7%) illustrated no significant difference. Of 23 isolates from milk, 3 (13%) STEC strains possessed stx1, 6(26.1%) carried stx2, 2(8.6%) harbored both stx1 and stx2 genes, and 4(17.3%) had eaeA or ehxA gene. The prevalence of STEC strains carrying stx1, stx2, stx1+stx2 and eaeA or ehxA in 76 cattle isolates was 7.8, 6.6, 5.2 and 7.8%, respectively. Out Of 22 isolates from dairy workers, 3(13.6%) STEC strains had stx1, 5(22.7%) harbored stx2, 1(4.5%) had both stx1 and stx2, 4(18.1%) carried eaeA, and 3(13.6%) possessed ehxA gene. The frequency distribution of virulence genes associated with STEC isolates was more evident in EHEC strains (O26 & O111 serogroups). This study emphasized that lactating cows are asymptomatic carriers of zoonotic STEC strains, and thus dairy workers should follow sound hygienic measures during milking and management of these animals to avoid public health hazards. Abdallah Merwad, Rasha Gharieb and Taisir Saber. Occurrence of shiga toxin-producing Escherichia coli in lactating cows and in contact workers in Egypt: serotypes, virulence genes and zoonotic significance. Life Sci J 2014;11(5):563-571] (ISSN:1097-8135). http://www.lifesciencesite. com. 86
Food habits of Peregrine Falcons in Kentucky

Poyser, London, U.K. KIMBALL, R.T. , P.G. PARKER, AND J.C. BEDNARZ. 2003. The occurrence and evolution of cooperative breeding among the diurnal raptors (Accipitridae and Falconidae). Auk 120:717-729. KORPI 'MAIn, E. , K. IAHTI, C.A. MAY, D.T. Pain, N, G.B. POWELL, P. TOLONEN, •'•O J. WETTON. 1996. Copulatory behaviour and paternity determined by DNA fingerprintings in kestrel: effects of cyclic food abundance. Anim. Behav. 51:945-955.
Ten years tracking the migrations of small landbirds: Lessons learned in the golden age of bio-logging

ABSTRACT In 2007, the first miniature light-level geolocators were deployed on small landbirds, revolutionizing the study of migration. In this paper, we review studies that have used geolocators to track small landbirds with the goal of summarizing research themes and identifying remaining important gaps in understanding. We also highlight research and opportunities using 2 recently developed tracking technologies: archival GPS tags and automated radio-telemetry systems. In our review, we found that most (54%) geolocator studies focused on quantifying natural history of migration, such as identifying migration routes, nonbreeding range, and migration timing. Studies of behavioral ecology (20%) uncovered proximate drivers of movements, including en route habitat quality; that migration routes, but not timing, may be flexible in some species; and different age and sex classes show significant differences in migration strategy. Studies of the evolution of migration (9%) have illustrated that migration is a potential barrier to hybridizing species or subspecies, and some work has correlated gene polymorphisms and methylation patterns with migration behavior. Studies of migratory connectivity (11%) have shown that a moderate level of connectivity is common, although variability across and within species exists. Studies of seasonal interactions (7%) have found mixed results: in some cases, carryover effects have been identified; in other cases, carryover effects are buffered during intervening stages of the annual cycle. Archival GPS tags provide unprecedented precision in locations of nonbreeding sites and migration routes, and will continue to improve understanding of migration across large spatial scales. Automated radio-telemetry systems are revolutionizing our knowledge of migratory stopover biology, and have led to discoveries of previously unknown stopover behaviors. Together, these tracking technologies will continue to provide insight into small migratory landbird movements and contribute important information for conservation of this rapidly declining group.
Genetic analyses reveal cryptic diversity in the native North American fire ants (Hymenoptera: Formicidae: Solenopsis)

The native North American fire ants (Solenopsis Westwood) comprise a difficult group taxonomically that has undergone multiple revisions in the past century yet remains in a state of taxonomic uncertainty. In the present study, we utilised a set of 59 microsatellite markers analysed in 238 specimens to conduct the first robust genetic analysis of the four nominal species. Our approach used a variety of methods to test operational criteria commonly employed in species delimitation, including genotypic clustering, reproductive isolation/cohesion and monophyly. We conclude from our results that the recognised North American fire ant species represent evolutionarily independent entities and, moreover, we confirm the presumed sister status of the desert fire ants, S. aurea Wheeler and S. amblychila Wheeler. However, the presence of at least two genetically divergent populations within the nominal species boundaries, including a western form of S. xyloni and a distinct population of S. aurea endemic to the Salton Trough, suggests that the current taxonomy does not fully capture the species‐level diversity in this group. Our study provides the molecular foundation for future integrated studies of the taxonomy and evolution of this scientifically and economically important group of insects.
Real-time PCR Assay for Diagnosis of Eukaryotic Peptide Chain Release Factor Subunit 1 Gene in the Stages of Giardia duodenalis

Giardiasis caused by Giardia duodenalis is a common intestinal disease. Although this parasitic infection is found in mammals including human, pets and livestock. A total of 250 samples was collected from patients that were suspected the infection with Giardia duodenalis during the period from August 2014 to October 2015. The aim of this study is to investigate the molecular identification of Giardia duodenalis in patients suffered from diarrhea depending on a Eukaryotic peptide chain release factor subunit 1 gene to Confirm its existence in both stages of Giardia dudenalis (Trophozoit and cyst) and the possibility adopting it as
Status of Antimicrobial Resistance in Bacteria Isolated From Kenyan Chickens

xv CHAPTER 1: GENERAL INTRODUCTION . 1 1.1 Background information . 1 1.2 Objectives . 2 1.2.1 Overall objective . 2 1.2.2 Specific objectives . 2 1.3 Hypothesis . 3 1.4 Justification of study . 3 CHAPTER 2: LITERATURE REVIEW . 4 2.1 Antimicrobials and antimicrobial resistance . 4 2.2 Global approaches/concerns to antimicrobial resistance . 5 2.3 Status of antimicrobial resistance in Kenya . 8 2.4 Scope of antimicrobial resistance in bacteria . 10
Effect of Dietary Fish Oil Replacement with Plant Oils on Growth Performance and Gene Expression in Juvenile Rainbow Trout (Oncorhynchus mykiss)

Abstract An eight-week feeding trial was conducted to evaluate the effects of total (100%) replacement of dietary fish oil with alternative lipid sources in juvenile rainbow trout. Six iso-nitrogenous and iso-lipidic experimental diets were formulated: CO (14%) – cod liver oil; SSO (14%) – safflower seed oil; SBO (14%) – soybean oil; LO (14%) – linseed oil; SBO (7%) + LO (7%) – a blend of soybean oil and linseed oil; and SSO (7%) + LO (7%) – a blend of safflower seed oil and linseed oil. Growth performance [specific growth rate (SGR), weight gain (WG), food conversion ratio (FCR) and survival rate (SR)], growth hormones [growth hormone (GH-I), insulin-like growth factor-I (IGF-I) and insulin-like growth factor-II (IGF-II)], immune transforming growth factor-β (TGF-β) and antioxidant [superoxide dismutase (SOD), glutathione peroxidase (GPx), glutathione reductase (GR), catalase (CAT) and glutathione S-transferase (GST)] response, and heat shock protein 70 (HSP70) mRNA levels were determined in muscle and liver. Our data indicated that final weight, weight gain, FCR and SGR showed significant difference among the six dietary treatments (P<0.05) while there were no significant differences in survival rate between the rainbow trout from supplement fed groups and control group. HSP70 mRNA level expression in muscle was higher in fish fed SSO (P<0.05) while highest level in liver was obtained from fish fed SBO compared to the other treatments (P<0.05). There were no significant differences among treatments for TGF-β mRNA expression level in muscle and liver. In conclusion, growth performance and expression levels of growth hormones, antioxidants, HSP70, except TGF-β were affected by five separate lipid sources. In addition, LO positively increased growth performance of juvenile rainbow trout by means of preventing oxidative stress and HSP70 and, enhanced expression of growth hormone related gene.
Antimicrobial peptides expressed in wheat reduce susceptibility to Fusarium head blight and powdery mildew

Badea, A. , Eudes, F. , Laroche, A. , Graf, R. , Doshi, K. , Amundsen, E. , Nilsson, D. and Puchalski, B. 2013. Antimicrobial peptides expressed in wheat reduce susceptibility to Fusarium head blight and powdery mildew. Can. J. Plant Sci. 93: 199-208. Antimicrobial peptides (AMPs) have a broad spectrum of action against bacteria, fungi and viruses, which makes them attractive for building plant defense against a diversity of pathogens. Peptides MsrA2 and 10R were cloned in three genetic constructs for tissue-specific expressions in wheat, using either Lem1, GstA1WIR1a, or Ltp6 and LTP6 signal peptide targeting the lemma/palea, leaves and spikes, epicarp and endomembrane system, respectively. The minimal cassettes for these three genetic constructs and for Pat marker construct were co-delivered in immature wheat scutella using biolistics, and green plantlets were regenerated in presence of 5 mg L-1 glufosinate. Molecular screening confirmed one regenerated plant carried and expressed all transgenes (AMP+): one copy of 10R driven by Ltp6 promoter, one copy of msrA2 driven by GstA1Wir1a and two copies of msrA2 driven by Lem1. Its offspring and T3 generation were challenged with Fusarium graminearum and Blumeria graminis in a contained environment. A reduction of 50% in Fusarium head blight susceptibility was observed in T1, and was inherited through T3 generation. The latter, also presented a 53% reduction in Fusarium damaged kernels and 62% reduction in deoxynivalenol accumulation compared with wild cv. Fielder and sister lines AMP-. MsrA2 and 10R producing T3 lines showed an average significant reduction of 59% in powdery mildew susceptibility compared with cv. Fielder. Synthetic MsrA2 and 10R peptides were effective as in vivo antifungal peptides in wheat. The expression of antimicrobial peptides in plant cells or tissues may have great potential to limit pathogen infection or growth protecting wheat against a diversity of fungal diseases.
Structural and physiological responses of the C4 grass Sorghum bicolor to nitrogen limitation

Abstract Nitrogen (N) is one of the major nutrients influencing photosynthesis and productivity of C4 plants as well as C3 plants. C4 photosynthesis operates through close coordination between mesophyll (M) and bundle sheath (BS) cells. However, how the development of structural and physiological traits in leaves of C4 plants is regulated under N limitation remains uncertain. We investigated structural and physiological responses of leaves of the NADP-ME-type C4 grass Sorghum bicolor to N limitation. Plants were grown under four levels of N supply (.05 to .6 g N per 5-L pot). Decreasing N supply resulted in decreases in net photosynthetic rate, stomatal conductance, leaf N and chlorophyll contents, and the activity ratio of phosphoenolpyruvate carboxylase to ribulose 1,5-bisphosphate carboxylase/oxygenase and increases in δ13C values and photosynthetic N use efficiency. Low-N leaves were thinner and had smaller photosynthetic cells, especially in M, resulting in lower M/BS tissue area ratio, and contained smaller and fewer chloroplasts. The BS chloroplasts in the low-N leaves accumulated abundant starch grains. The number of thylakoids per granal stack was reduced in M chloroplasts but not in BS chloroplasts. The low-N leaves had thicker cell walls, especially in the BS cells, which might be associated with less negative δ13C values, and fewer plasmodesmata in the BS cells. These data reveal structural and physiological responses of C4 plants to N limitation, most of which would be related to cellular N allocation, light use, CO2 diffusion and leakiness, and metabolite transport under N limitation.
Fish use of reef structures and adjacent sand flats: implications for selecting minimum buffer zones between new artificial reefs and existing reefs

: Artificial reefs are deployed worldwide to enhance fisheries. Placement of artificial reefs relative to nearby existing artificial and natural reefs can influence fish use of these structures, yet no quantitative guidelines exist for selecting optimal distances between new and existing reefs. Here, we documented fish abundance, biomass, species richness, community composition, and key environmental variables on 24 artificial and natural reefs with adjacent sand flats to infer minimum buffer distances around existing reefs where placement of new artificial reefs should be avoided. At each site, we surveyed 4 transects: one 30 m transect across reef structure and 3 consecutive 30 m transects of increasing distance from the reef across sand bottom. Fish abundance, biomass, and species richness were highest on reefs and progressively decreased across adjacent sand flats. Environmental variables influenced these community metrics, but patterns of fish habitat use persisted. Fish community composition shifted gradually from reefs across adjacent sand flats, with fish communities on reefs most dissimilar to communities on sand bottom farthest from the reefs. A minimum buffer of 60 m (30 m around existing reefs plus 30 m around new reefs) or 120 m (60 m plus 60 m) between reefs would encompass 77 and 97%, respectively, of fishes utilizing sand-bottom habitat around each reef. Future artificial reef deployment should maintain these minimum buffer zones between reefs to more effectively enhance fisheries by minimizing attraction of fishes from existing reefs, while also maximizing food resource availability for reef fishes and area for routine reef fish behaviors.