Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative assessment of native, crossbred and exotic pigs during different seasons (winter, spring and summer) based on rhythmic changes in the levels of serum cortisol, lactate dehydrogenase levels and PBMC HSP70 mRNA expression pattern

ABSTRACT The present study was conducted to ascertain the adaptive capability of pigs to different seasons based on changes in serum cortisol and lactate dehydrogenase (LDH) levels, and peripheral blood mononuclear cell (PBMC) heat shock protein 70 (HSP70) mRNA expression. Based on average THI, the seasons were classified as winter (November–February), spring (March–June), and summer (July–October). Hormone cortisol was found to be influenced by season (p < 0.01), age (p < 0.05), and genetics of the animal (p < 0.05). However, level of LDH was not influenced by either of these factors. HSP70 mRNA expression was higher in almost all age groups in crossbred and exotic pigs during summer in comparison to other seasons. Lower HSP70 gene expression was observed in almost all age groups of native pigs in comparison to crossbred and exotic during summer. In conclusion, native pigs were acclimatized for thermal stress in comparison to crossbred and exotic breeds of pigs. Also, the expression pattern of HSP70 gene is breed-specific, most likely due to variations in thermal tolerance and adaptation to different environmental conditions. Both serum cortisol and HSP70 gene may act as reliable biological markers for assessing the adaptive capabilities of pigs to different seasons.
Molecular characterization of anti-platelet aggregating proteins in salivary gland extracts of Hyalomma anatolicum ticks

Tick saliva is a cocktail of potent anti-haemostatic, anti-inflammatory and immunomodulatory molecules that help the ticks to obtain a blood meal from their vertebrate hosts. Thrombin is considered as an activator for stimulation of blood platelets at different receptor sites and thrombin induced platelet aggregation depends on the interaction among thrombin exosites and the receptors on platelet membrane. Thus, the present study was planned to isolate and characterize the salivary anti-platelet aggregating proteins from Hyalomma anatolicum ticks. A hundred pairs of salivary glands were dissected out and extract was prepared by fractionation of proteins by gel filtration chromatography. The fractions so obtained were tested for thrombin induced platelet aggregation and platelet-collagen adhesion inhibition activities. Proteins in fraction nos. 28, 29, 30, 31, 32, 42, 58, 111 and 112 were found to inhibit platelet aggregation. These proteins also showed significant inhibitory effects on platelet adhesion to collagen when compared to agonist thrombin. This indirectly indicates inhibition of glycoprotein 1b (GP1b), glycoprotein VI (GPVI) and integrin a2b1 receptors of platelets as these proteins are involved in aggregation of platelets for formation of platelet plug. On electrophoretic separation of fractions by SDS-PAGE, the proteins/peptides present in initial fractions were having approximate molecular weight in the range of 6.5 to 113.4kDa. However, in the fraction no. 112 only single prominent protein band of approximate 65.4kDa was present and is expected to inhibit platelet aggregation possibly through inhibition of platelet receptors such as proteins platelet activating receptors-1 and 4 playing direct role in platelet aggregation. In conclusion, there are possibilities of exploring these anti-platelet aggregating proteins/peptides for therapeutics against cardio-vascular disorders as well as for raising anti-tick vaccine.
Resource use efficiency as a function of species richness and stand composition in upper montane conifer forests of the Sierra Nevada

Questions: I. Does resource use efficiency increase with increased species richness in conifer forests? 2. Do patterns found in resource use support niche differentiation/ complementarity between species, or is any increase indicative of a selection effect? Location: All data were collected from upper montane (22002600 m a.s.1) conifer forests of the Desolation Wilderness in the central California Sierra Nevada, USA. Methods: We established 281 plots of varying levels of conifer richness throughout the wilderness area. Within each plot we used hemispherical photos to measure canopy closure and LAI, total soil carbon and nitrogen from the A-horizon, and stand basal area. We used linear regression and ANOVA to analyse the relationship between stand species richness and resource availability. Results: We found no correlation of either soil nitrogen or carbon with stand biomass. Nor did soil nitrogen and carbon levels change with species richness. Canopy closure increased with species richness but also varied significantly between pure stands of different species. Pure Pinus monticola stands had the lowest canopy closure, Tsuga mertensiana stands the highest. Composition explained more canopy cover variation than did species richness. We found evidence supporting both the sampling effect and niche differentiation models at different stages of stand development. Conclusions: During initial stages of stand development, the interaction between the shade-intolerant Pinus species and shade-tolerant Abies magnifica and T. mertensiana followed the niche differentiation model, but switched to the sampling effect model during the competitive-exclusion stage. In contrast, interaction between A. magnifica and T. mertensiana followed the niche differentiation model.
Investigating the structure & function of ViCin1, a novel repeat protein from the apple scab fungus Venturia inaequalis

v Acknowledgements . vii Table of contents . ix List of tables. xiii List of figures . xv Abbreviations . xix Chapter 1: general introduction . 1 1.1 Venturia inaequalis . 1 1.1.1 Life cycle of V. inaequalis.2 1.1.2 Cellophane: an in vitro model for in planta growth . 5 1.2 Plant-pathogen interactions . 7 1.3 The extracellular surface of fungi . 9 1.3.1 ITRs . 10 1.3. 2 Fungal genes with ITRs . 10 1.3. 2.1 STRPs of U. maydis . 11 1.3. 2.2 STRPs of M. graminicola . 14 1.3. 2.3 STRPs of Aspergillus spp. 15 1.3. 2.4 STRPs of Trichoderma spp. & Glomus intraradices.17 1.3. 2.5 STRPs of yeasts . 19 1.3. 2.6 STRPs of oomycete phytopathogens . 22 1.3. 3 The ever-changing fungal cell surface: the role of ITR variability . 24 1.3. 3.1 The effect of sequence variability on protein function . 25 1.4 The V. inaequalis-Malus interaction . 27 1.4. 1 STRPs of V. inaequalis: ViCin1 & ViCin3 . 28 1.5 Research aim . 31 Chapter 2: restriction of ViCin1 to the Venturia genus.33 2.
Gamification of farmer-participatory priority setting in plant breeding: Design and validation of “AgroDuos”

ABSTRACT Participatory methods to characterize farmers’ needs and preferences play an important role in plant breeding to ensure that new varieties fulfill the needs and expectations of end users. Different farmer-participatory methods for priority setting exist, each one responding differently to trade-offs between various requirements, such as replicability, simplicity, or granularity of the results. All available methods, however, require training, academic skill, and staff time of specially qualified professionals. Breeding and variety replacement may be accelerated by empowering non-academic organizations, such as NGOs and farmer organizations, to carry out farmer-participatory priority setting. But for this use context, currently no suitable method is available. A new method is needed that demands relatively low skill levels from enumerators and respondents, engages farmers without the need for extrinsic incentives, and gives statistically robust results. To achieve these objectives, we followed principles of “gamification” in the design of AgroDuos, a choice experiment that resembles a card game and that involves pairwise ranking of variety traits. We tested the method in a pilot with 39 farmers in Honduras to define their trait priorities for common bean (Phaseolus vulgaris L.). To validate our results, we independently carried out conjoint analysis, an established method for priority setting in plant breeding. We found that AgroDuos produced valid and useful results while enabling rapid, easy, and engaging data collection. Challenges persist concerning local adaptation and data analysis by non-specialist staff, which may be resolved in the future by providing templates and online support.
Molecular characterisation of Trichoderma species using SRAP markers

Abstract Trichoderma are commonly used as bio control agents in various agro ecosystems. They are known to produce a variety of compounds that induce resistance responses in plants. Among different species of Trichoderma, T. harzianum, T. viride, T. koningii and T. hamatum are commercially used as bio control agents. In the present study, four commercially important species of Trichoderma isolated from coffee ecosystem were screened with sequence related amplified polymorphism (SRAP) markers. Among 48 SRAP primer pairs tested, 29 primers were polymorphic and generated 316 distinct scorable fragments. Out of 347 amplified fragments, 177 fragments were found polymorphic with an average of 6.10 fragments per primer combination. The average polymorphism information content (PIC) and resolving power (Rp) of the 29 polymorphic SRAP primer pair were 0.42 and 14.62, respectively. The UPGMA dendrogram clearly divided Trichoderma species into two broad clusters. The highest homology (83.0%) was observed between T. viride and T. Harzianum and the lowest homology (74.0%) was observed between T. Harzianum and T. konangii. Further, among 29 polymorphic SRAP markers screened, four primer pairs (ME1-EM3, ME1-EM20, ME1-EM22 and ME2-EM4) produced unique fragments specific to each species. These markers can be useful in easy and rapid identification of the species.
Influence of γ-glutamyltransferase and alkaline phosphatase activity on in vitro fertilisation of bovine frozen/thawed semen

Abstract The aim of this work was to evaluate whether the residual amount of γ-glutamyl-transferase (GGT) and alkaline phosphatase (ALP) in bovine sperm after freezing/thawing is correlated with fertility parameters, including blastocyst rates after in vitro fertilisation (IVF). The enzyme activities were determined in both spermatozoa and supernatant after centrifugation. While ALP was only correlated with sperm viability, GGT activity was correlated with sperm motility (rs = .4; p < .05) both in sperm and supernatant. Interestingly, GGT activity was also correlated with cleavage (rs = .5; p < .05 and .8; p < .01, for sperm and supernatant respectively) and blastocyst (rs = .6 and .9, for sperm and supernatant respectively; p < .01) rates obtained after IVF. These results suggest that GGT could play an important role in the protection of sperm against oxidative stress and could be considered a reliable marker to assess frozen/thawed sperm quality in bovine.
Dynamical Architectures for Controlling Feeding in Aplysia californica

by KENDRICK M. SHAW For behaviors such as swallowing, walking, and swimming, the nervous system must reliably generate sequences of motor behavior. Two competing models have been proposed for how this task is accomplished chain reflex theory and central pattern generator theory. Chain reflex theory posits that the nervous system contains a sequence of reflexes, so that the action of one reflex creates the sensory input required to trigger the next. In contrast, central pattern generator theory posits that the nervous system is capable, in the absence of sensory input, of generating motor patterns that closely resemble the motor patterns during behavior. When modeling these behaviors with systems of differential equations, these two ideas correspond to a collection of stable nodes, in the case of the chain reflex theory, and a stable limit cycle, in the case of central pattern generator theory. Many systems can exhibit motor patterns in the absence of sensory input, violating the predictions of chain reflex theory, but those patterns are very distorted compared to in vivo behaviors, violating the assumptions of central pattern generator theory. This dissertation explores a third hypothesis, known as a stable heteroclinic channel, where a trajectory slows dramatically
Influence of Glutamine and Vitamin E on the Performance and the Immune Responses of

This study aimed at evaluating the influence of Glutamine (Gln) and Vitamin E (VE) supplementation on the performance and immune response of broilers. A completely randomizes experimental design with a 2 x 3 (VE x Gln) factorial arrangement was used. VE was supplemented at 10 and 500 mg/kg feed, with or without Gln (1%) addition, and two periods of supplementation in the starter diets (1-7 and 1-14 days of age), with five replicates of 50 birds each. The analyzed parameters were: live performance (weight gain, feed intake, and feed conversion ratio); relative weights of the spleen, bursa, and thymus; antibody titers (with sheep red blood cells suspension – SRBC) and cutaneous basophilic hypersensivity (CBH). Data were submitted to the analysis of variance, and means were compared using the test of Tukey. Treatments did not influence (P>0.05) live performance parameters or antibody titers. VE reduced (P=0.01) CBH, with the level of 10 mg VE/kg allowing higher cell proliferation as compared to 500 mg VE/kg. As to lymphoid organs, only the spleen was affected (P=0.035) by Gln, which resulted in higher spleen relative weight when fed during the first week of age. Results showed that 10 mg VE/kg with Gln (1-7 days) promoted better immune responses.
Purification of Porphobilinogen Deaminase and the Sequencing and Expression of thehemC Gene of Rhodobacter Capsulatus.

Rhodobacter capsulatus uses the common tetrapyrrole pathway to synthesize heme, bacteriochlorophyll, siroheme and vitamin B-12. As part of our studies on the regulation of this pathway, the product of the hemC gene, porphobilinogen deaminase was purified approximately 200-fold. The molecular weight, isoelectric point, pH optimum and K„ of the enzyme were all similar to other porphobilinogen deaminases. The stoichiometry of the enzyme was found not to be the expected four porphobilinogens used per one uroporphyrin formed. Rather a 9:1 ratio was typically seen. Further study of this atypical ratio uncovered evidence of possible in vivo regulation of porphobilinogen deaminase dependant on the cellular redox state. The protein was isolated from a two-dimensional gel and the sequence of the first twenty amino acids from the N-terminus was determined. This protein sequence matched a putative amino acid sequence 110 bp upstream of the R. capsulatus hemE gene. The putative hemC locus was subcloned from the plasmid pCAP154 which contains the R. capsulatus hemE gene with 1.2 Kb of upstream DNA. The sequence of the upstream DNA was determined by dideoxy sequencing of both strands. A single open reading frame of 951 bp was found which could code for a 317 amino acid protein of 34,082 Da. The putative protein has 49% identity with the E. coli porphobilinogen deaminase and 44% identity with the B. subtilis enzyme. When a plasmid carrying the R. capsulatus hemC was inserted into E. coli and R. capsulatus, a four-fold and ten-fold increase in porphobilinogen deaminase activity was seen respectively.
Investigation of Ticks and Tick-Borne Pathogens in Deciduous Forests of Eastern Central Alabama

ii Acknowledgments. iii List of Tables . viii List of Figures . ix List of Abbreviations . x Chapter 1 Overview of tick biology and role in pathogen transmission . 1 1.1 Tick morphology and systematics . 2 1.2 Life cycle . 4 1.3 Tick ecology and behavior. 6 1.3. 1 Nidicolous and non-nidicolous ticks . 6 1.3. 2 Effects of climate on ticks . 8 1.3. 3 Diapause. 12 1.3. 4 Tick-host interactions. 13 1.4 Important tick-borne pathogens, vectors, and associated diseases of the Southeast . 15 1.4. 1 Biology of pathogen transmission by ixodid ticks . 16 1.4. 2 Ixodes scapularis and associated pathogens and illnesses . 19 1.4. 3 Amblyomma americanum and associated pathogens and illnesses . 22
Re-Evaluation of the Effect of Daily and Within-Day Mixed Feeding Schedules of Varying Dietary Protein Content on the Growth Performance of Nile Tilapia Fry Using Constant Ingredient Composition

Feed is the main cost to aquaculture production, management practices, and feeding strategies are aimed at optimizing feed intake and efficiency. Knowledge about feeding protocols and behavior habits may be of an interest for optimization of aquaculture production, reducing aquaculture waste output and to achieve sustainability. This study investigated trends based on daily feeding schedules. Two growth trials were conducted to investigate the effect of day to day mixed feeding schedules on the growth performance of Nile tilapia. Three experimental isocaloric diets of low (A; 20%), regular feeding (RF; 30%) and high (B; 40%) protein levels were prepared. In the first trial, fish were continuously fed a normal protein diet (RF-30%), alternate feeding of a 1-day diet A; followed by a 1-day diet B (1A/1B) and alternate feeding of 2-day diet A; followed by a 2-day diet B (2A/2B) and a 3-day diet A followed by a 3-day diet B (3A/3B) were tested. In the second trial, three times a day feeding schedules were continuously examined by feeding tilapia with diet (RF), alternate feeding of diet A in the morning followed by diet B in the afternoon (A am/B pm) and alternate feeding of diet B in the morning followed by diet A in the afternoon (B am/A pm). In the first trial, the best specific growth rate (SGR) was observed for fry maintained on the RF diet followed by (2A/2B). In the second trial, the mixed feeding schedule (A am/B pm) showed the best SGR and feed conversion ratio (FCR) followed by a RF diet. The overall ranking of daily mixed feeding schedules was the highest for RF diet with the mixed feeding schedule of (3A/3B). In addition, day to day mixed feeding schedules showed that fish utilize high protein diet more efficiently during an afternoon phase rather than a morning phase. The results from this study show that, the daily feeding schedule achieved better growth performance, nutrients retention and feed utilization of Nile tilapia rather than alternate feeding schedules between days for Nile tilapia.
The study of antioxidants in grapevine seeds

Grapevine seeds contain a large amount of antioxidant components, and are therefore recommended in the prevention and treatment of many diseases. For this research, we studied the antioxidant properties of grapevine seeds from the Marlen variety, as evidence suggests that these types have higher resistance against fungal diseases. Through high-performance liquid chromatography with UV/VIS detection, a total of 10 antioxidant components were selected for further investigation, specifically: catechin, epicatechin, rutin, quercitrin, quercetin, caftaric acid, caffeic acid, p-coumaric acid, ferulic acid, and gallic acid. The antioxidant activity was determinated spectrophotometrically through the adoption of three fundamentally different methods (the DPPH assay, the ABTS method, and the FRAP method). Using the Folin-Ciocalteu method, it was possible to determine the content of all the polyphenolic compounds. The results of the assessment antioxidant activity and the content of polyphenolic compounds were recalculated to gallic acid equivalents (GAE). The values of the antioxidant activity as determinated by the DPPH test were 6643 (±154) mg of GAE; 1984 (±88) mg of GAE when using the FRAP method; and 812 (±31) mg of GAE when the ABTS method was utilised. The content of the total polyphenolic compounds came to 6982 (±221) mg of GAE. The most abundant antioxidant was catechin, with a content of 115 mg.L -1 , whilst the least represented compound was ferulic acid (0.139 mg.L -1 ). Overall, this study showed a high antioxidant potential of grapevine seeds.
Diurnal Periodicity of the Expression of Genes Involved in Monolignol Biosynthesis in Differentiating Xylem of Cryptomeria japonica

The cell wall in wood is mainly composed of three components: cellulose, hemicellulose and lignin. According to electron microscopy observations of the innermost surface of cell walls in the tracheids of Cryptomeria japonica , cellulose microfibrils are deposited during the day and a matrix containing hemicellulose is deposited at night. This indicates that the deposition of cell wall components exhibits diurnal periodicity. To gain new insights into the diurnal periodicity of lignin deposition not revealed by microscopic observations, we examined diurnal fluctuations in the expression of genes involved in monolignol biosynthesis in C. japonica saplings grown in the field and in growth chambers under a 12 h light/dark cycle. In the field experiment, two gene expression peaks were observed daily, at dusk and dawn. In the growth chamber experiment, two daily peaks were observed 0 h and 6 - 9 h after the light switched on.
Comparative Evaluation of Three Commercial Systems for Nucleic Acid Extraction from Urine Specimens

A nucleic acid extraction system that can handle small numbers of specimens with a short test turnaround time and short hands-on time is desirable for emergent testing. We performed a comparative validation on three systems: the MagNA Pure compact system (Compact), the NucliSens miniMAG extraction instrument (miniMAG), and the BioRobot EZ1 system (EZ1). A total of 75 urine specimens submitted for polyomavirus BK virus detection were used. The human -actin gene was detected on 75 (100%), 75 (100%), and 72 (96%) nucleic acid extracts prepared by the miniMAG, EZ1, and Compact, respectively. The miniMAG produced the highest quantity of nucleic acids and the best precision among the three systems. The agreement rate was 100% for BKV detection on nucleic acid extracts prepared by the three extraction systems. When a full panel of specimens was run, the hands-on time and test turnaround time were 105.7 and 121.1 min for miniMAG, 6.1 and 22.6 min for EZ1, and 7.4 and 33.7 min for Compact, respectively. The EZ1 and Compact systems processed automatic nucleic acid extraction properly, providing a good solution to the need for sporadic but emergent specimen detection. The miniMAG yielded the highest quantity of nucleic acids, suggesting that this system would be the best for specimens containing a low number of microorganisms of interest.
Identification of Mutations that Extend the Fission Yeast Schizosaccharomyces pombe Chronological Lifespan by a Novel Parallel Selection Approach

By BO-RUEI CHEN A chronological lifespan (CLS) assay was developed to study eukaryotic cell aging using the fission yeast Schizosaccharomyces pombe. This assay measures how long cells remain viable in a non-dividing state, allows a continuous decline in viability without detectable re-growth until all cells in the culture are dead, and recapitulates the evolutionarily conserved features of lifespan shortening by over nutrition and lifespan extension as well as increased stress resistance by caloric restriction. Genome-wide studies in the evolutionarily distant yeast Saccharomyces cerevisiae have uncovered several longevity pathways that are conserved in other eukaryotes. The current approaches rely on analysis of individual ORF deletion mutants from a large, pre-defined library or microarray analysis of the barcodes associated with these deletions. The creation of this barcoded, ORF deletion strain set was a major effort that is difficult to extend to other model systems. Therefore, we constructed a barcode-tagged random insertion mutant library in S. pombe that allowed for the parallel selection of mutants with extended chronological lifespan. Mutants selected from this library can be analyzed by