Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of a Fermented Yeast Product on the Gastrointestinal Tract Microbial Diversity of Weaned Pigs Challenged With Salmonella Enterica Typhimurium Dt104

Gastrointestinal tract (GIT) microorganisms play important roles in animal health, including providing energy and vitamins, improving the host immune response and preventing pathogenic microorganisms from colonizing. Prebiotic feed supplementation offers an alternative to antimicrobial growth promoters by stimulating key populations of the GIT bacteria that can ferment these non-digestible compounds, producing various short chain fatty acids used by the animal. The objective of this study was to quantify the effects of a proprietary Saccharomyces cerevisiae fermentation product (XPC, Diamond V Mills, Inc., Cedar Rapids, IA) inclusion in nursery diets on the microbial diversity and growth performance of pigs before, during and after an oral challenge with Salmonella. Pigs (n= 40) were weaned at 21 d of age, blocked by body weight (BW) and assigned in a 2×2 factorial arrangement consisting of diet (control or 0.2% XPC) and inoculation (broth or Salmonella). Diet had no effect on pig growth performance prior to inoculation; however, consumption of XPC altered the composition of the gastrointestinal microbial community resulting in increased growth performance prior to inoculation. After Salmonella infection, XPC altered the composition of the gastrointestinal microbial community resulting in increased (P < 0.05) populations of Bacteroidetes and Lactobacillus. Infection with Salmonella and treatment of the piglets with ceftiofur-HCl resulted in alterations to the species richness and abundance of key members of the GIT community. The addition of XPC to the diets of weaning pigs results in greater compensatory gains after infection with Salmonella and an increase in beneficial bacteria within the GIT.
Engineering bacteria for biofuel production

This thesis addresses the need for environmentally and socially responsible sources of energy. Biofuels, made from organic matter, have recently become a viable alternative to petroleum-based fossil fuel. Sugar and starch make up the majority of feedstock used in biofuel production as it is easily digested. However, the use of these feedstocks is problematic as they consume resources with negative implications. By using a bacterium able to utilise five and six carbon sugars, such as the thermophile Geobacillus thermoglucosidans, organic lignocellulosic waste material can be used as a feedstock. The aim of this project was to investigate and utilise key genetic regulators of fermentation in G. thermoglucosidans and to construct genetic engineering tools that enable strain development for second generation biofuel production. We have focused on the redox-sensing transcriptional regulator Rex, widespread in Grampositive bacteria, which controls the major fermentation pathways in response to changes in cellular NAD+/NADH ratio. Following the identification of several members of the Rex regulon via bioinformatics analysis, ChIP-seq and qRT-PCR experiments were performed to locate genome-wide binding sites and controlled genes in G. thermoglucosidans. Initial electromobility shift assay experiments were performed to demonstrate the potential for use of Rex from Clostridium thermocellum as an orthogonal regulator. To further this research, novel in vivo synthetic regulatory switches were designed and tested with the aim of controlling gene expression in response to changes in cellular redox state. In addition, new tools for the efficient genetic engineering of G. thermoglucosidans were produced and optimised, including an E. coli-G. thermoglucosidans conjugation method for plasmid transfer and gene disruption.
Simple Models for Describing Ruminant Herbivory

The use of quantitative independent variables in experiments allows the use of regres- sion to explore the functional relationship between treatments applied and measured responses. It provides the opportunity to not only understand the magnitude and impor- tance of the response but also ascertain its nature. The simplest approach is to fit a poly -nomial. While it is often possible to obtain a very good fit using this approach, it offers in the way of providing insight into the response. At best, you can determine if the response is nonlinear and if so, if it is complex or not. The model parameters are empirical and gen - erally cannot be interpreted as having any biological, chemical, or physical meaning—at least not directly. There are situations, however, when such a meaning can be inferred from a model fit using simple regression. In general, this is true when the relationship is truly linear or when a nonlinear model can be considered to be “intrinsically” linear; that is, it can be linearized by transforming the data in a way that can be fit using simple linear regression. A series of forage quality examples are used to illustrate these concepts in this article.
Adsorption of Textile Dye by Activated Carbon Made from Rice Straw and Oil Palm Midrib

Synthetic dye wastewater from textile industries is characterized by strong color, high temperature, variable pH and high chemical oxygen demand (COD). The strong color of wastewater affects aesthetic and water transparency of water bodies. The metabolites could be toxic to aquatic biota and posing a potential hazard to human health. Eventually, it will cause severe environmental problems. One of method that has advantages in term of simplicity to remove synthetic dyes is adsorption. Environmentally benign and low-cost materials to make adsorbent are biomass-based materials. Two different biomaterial wastes of rice straw and oil palm midrib were used in this study to develop activated carbon adsorbents. These adsorbents were applied for the removal of Naphtol AS-G dye in aqueous solution. The effects of solution pH, adsorbents masses and contact time on dye adsorption were evaluated based on batch experiments. Removal of dye can be achieved within 60 minutes at a wide pH range starting from 4 to 8. At lower pH, synthetic dye removal was decreasing probably due to protonation of adsorbent’s active sites. The adsorption isotherms based on Langmuir and Freundlich models were analyzed. The isotherms analysis indicated that the adsorption by rice straw and oil palm can be represented by Langmuir and Freundlich isotherm model, respectively. Adsorption isotherms of Naphtol AS-G onto activated carbon are favorable with high adsorption capacity for both biomaterials. The mechanisms of color removal by activated carbon involved chemical and physical adsorption, in accordance with both the Langmuir and Freundlich models. The calculated maximum dye adsorption capacities onto rice straw and oil palm midrib activated carbon were 55.86 and 69.44 mg/g, respectively. Adsorption using biomass-based activated carbon offers a good technique for textile wastewater treatment as it could remove up to 95% of the color intensity besides reducing other pollutants such as COD, nitrate and phosphate.
Reproductive ecology and establishment of naturally colonized tilapine cichlid, Sarotherodon galilaeus (Pisces: Actinopterigii: Perciformes) from a man-made lake, Southern Benin, West Africa: implications for sustainable fisheries and aquacultural valorization

Some aspects of the reproductive ecology of Sarotherodon galilaeus, a freshwater tilapine cichlid, were examined to evaluate the establishment of the species in the man-made lake of Ahozon (South-Benin). S. galilaeus individuals were sampled monthly during wet, flood and dry seasons from August/2014 to July/2015. This species dominated Lake Ahozon and made 85.21% of the fish community. Among the 5,550 individuals sampled, 33.55% were juveniles, 12.25% were sub-adults and 54.20% were adults. S. galilaeus showed a sex-ratio of (0.60:1) and low batch fecundities (42-1,149 oocytes). Sizes at sexual maturity (L50) in Lake Ahozon were 131 mm and 106 mm for males and females, respectively, and the species spawned all seasons. The favorable water quality and the life-history strategy between “r” and “k” selection of S. galilaeus, accounted for its rapid establishment in Lake Ahozon. A sustainable fisheries/aquaculture exploitation of S. galilaeus in Lake Ahozon requires a holistic management scheme.
Change of Feeding Strategy Prior to Migration: A Comparative Diet Analysis in the Lesser Kestrel (Falco Naumanni)

Assessing the variation in diet composition of a species, over different years and between periods, offers insights to comprehend its ecological niche as well as to define different feeding strategies. We studied the diet of the Lesser Kestrel (Falco naumanni) by analysing 1040 regurgitated pellets collected in the city of Ioannina (northwestern Greece). We compared diet composition between the breeding period (data from years 2010–2015) and the pre-migration period (data from 2013–2015) at the study site. A total of 8920 prey items were identified and classified into 13 different prey families. The Lesser Kestrel shows a consistent pattern of diet composition throughout years, displaying significant differences between breeding and pre-migration periods. The diet is rather diverse during the breeding season (Levins' diet breadth, B = 4.12) and is composed mainly of Orthoptera and Coleoptera, while during pre-migration, the species shows a more narrow diet breadth (B = 1.98) and feeds more often and on larger amounts of Orthoptera. These results indicate a specialised feeding strategy during pre-migration. In addition, the examination of the Orthoptera consumption during this period indicates a peak in the abundance of grasshoppers (Acrididae) in the second half of August. We suggest that at this time birds exploit high elevation open grasslands around the roosting site where grasshopper abundance is high. Thus, such areas are of high conservation importance as Lesser Kestrels depend on this localised abundance of Orthoptera in order to fuel up before their trans-Saharan migration.
Occurrence of Leishmania chagasi, Trypanosoma cruzi, Babesia canis vogeli, Anaplasma platys, and Ehrlichia canis in canine blood donors

The transfusion of blood components is common in a veterinary clinic; however, the safety of this therapeutic measure cannot always be guaranteed. Studies show a high risk of haemoparasite transmission during blood transfusion in canines. These parasites include Leishmania chagasi, Anaplasma platys, and Ehrlichia canis, which are endemic to the city of Cuiaba. This study aimed to evaluate the occurrence of L. chagasi, Trypanosoma cruzi, Babesia (canis) vogeli, A. platys, and E. canis in canine blood donor candidates, and identify possible factors associated with the infection of these agents. Sixty-six canines were evaluated using serologic and molecular tests, for the presence of the Leishmania species. While one canine sample showed a positive result for L. chagasi with indirect fluorescent antibody test, with titer of 1:40, and seven canine samples were positive using DPP, all other samples were negative when using PCR and ELISA. All canines were negative for T. cruzi when using PCR. The B. (c.) vogeli infection was identified in one canine and A. platys was identified in six canines. E. canis was identified in 17 canines, with a prevalence of 25.7%. There were no significant factors associated with the infection of the pathogens investigated. Given the observation of infection, even in the absence of clinical symptoms, emphasis must be placed on the need for the use of more sensitive and specific diagnostic methods for the screening of donor canines.
Dynamics of the cerebral microvasculature during the course of memory consolidation in the rat : physiological and altered conditions induced by hypertension and hypergravity

While the cerebral microvasculature is known to adapt its activity according to the metabolic demand of surrounding neurons, the functional contribution of vascular networks to memory consolidation, the process by which memory traces acquire stability over time, remains elusive. By using an associative olfactory memory task in rats coupled to biochemical and imaging techniques, we investigated the dynamics of vascular changes during memory consolidation which requires a transitory interaction between the hippocampus and distributed cortical regions that ultimately support storage of enduring memories. We found that remote memory formation was associated, upon encoding, with a hypoxic signal that triggered transitory angiogenesis in specific cortical regions which support memory storage and retrieval only weeks later. Manipulating early cortical angiogenesis (ECA) by selectively blocking or stimulating the angiopoietin-2 signaling pathway impaired or improved remote memory retrieval, respectively. Enhancing ECA in spontaneously hypertensive rats, which exhibit reduced angiopoietin- 2 expression when cognitively challenged and are unable to properly stabilize and/or retrieve remotely acquired information, was efficient in rescuing the observed memory deficit, thus confirming the functional importance of ECA as a prerequisite for the formation of remote memories. Hypergravity, known to impair vascular functions, failed to alter the organization of recent and remote memory. Altogether, our findings identify ECA as a crucial neurobiological process underlying the formation and stabilization of remote memory. They highlight the importance of vascular plasticity in modulating cognitive functions and suggest that the early structural changes within vascular networks constitute a permissive mechanism for the regulation of neuronal plasticity within cortical networks which support the formation and storage of enduring memories.
Effects of the Depuration Process on Microbiological Quality and Nutritional Composition of Mediterranean Mussel (Mytilus galloprovincialis Lamarck, 1819)

ABSTRACT In this study, the effects of the depuration period on Mediterranean mussel (Mytilus galloprovincialis L., 1819), collected from Bandırma Harbor Area by the Sea of Marmara, were investigated. Distinctive changes were found to exist in the percentage of moisture, protein, fat, and ash content. The process of depuration was determined to have an effect on the number of total aerobic mesophilic/psychrophilic bacteria. Salmonella spp. , Listeria monocytogenes, Vibrio parahaemolyticus, Vibrio cholera, Escherichia coli, and Staphylococcus aureus could not be identified during the study. The substances of aluminum, iron, zinc, copper, manganese, nickel, cadmium, chromium, lead, and potassium were determined to decrease in the Mediterranean mussel from the baseline to the end of the depuration. It was found that the process of depuration has a positive effect on alanine, phenylalanine, lysine, tyrosine, valine, leucine, and isoleucine; a negative effect on aspartic acid, glutamic acid, threonine, proline, and arginine and no effect on methionine, histidine, glycine, and serine. The total saturated fatty acids, total monounsaturated fatty acids, and total polyunsaturated fatty acids at the end of depuration were found to be 29.29%, 12.51%, and 45.57%, respectively, and the change in the amount of polyunsaturated fatty acids was found to be significant (p < 0.05).
Effect of leaf decomposition stage and water temperature on fragmentation activity of a shredder invertebrate species in lotic ecosystems

The attractiveness of a given leaf detritus to invertebrates depends on the chemical composition, physical structure, stage of microbial colonization and decomposition level. In addition to the leaf detritus quality, water temperature also affects organic matter cycling in aquatic environments. In this context, the objectives of this study were: i) to increase knowledge about the role of invertebrate shredders on fragmenting senescent, conditioned senescent and green leaves of Richeria grandis Vahl. (Phyllanthaceae) under gradual temperature rise and check leaf mass loss; ii) to verify the preference of Phylloicus sp. (Trichoptera) for leaves for larval case production. The experiment I consisted of three treatments with different water temperatures: 20°C, 24°C and 28°C. In the experiment II, we added 10 discs of green leaves of R. grandis and two shredder invertebrates (Phylloicus sp.) to each aquarium. Leaf mass loss in the presence or absence of fragmentation was not significantly influenced by differences in the intraspecific quality of the detritus or temperature. Intraspecific quality of resources mixed with green leaves can lead to increased contact of phenolic content on senescent leaves, leading to a similarity in food exploitation by invertebrates. However, the production of larval cases by Phylloicus sp. seems to be dependent on the resistance presented by the resource rather than the phenolic content, thus leading the shredders to use significantly more senescent detritus, regardless temperature.
Diet of the Mohave Ground Squirrel (Xerospermophilus mohavensis) in Relation to Season and Rainfall

Abstract. The Mohave ground squirrel (Xerospermophilus mohavensis) is endemic to the western Mojave Desert of California. It is listed as threatened under the California Endangered Species Act, yet there is little published information on its habitat requirements. We studied the diet of Mohave ground squirrels at 4 sites in desert scrub habitat in Inyo County, California, primarily by microhistological analysis of 754 samples of fecal pellets collected from live-trapped animals. Over all sites and seasons, shrub foliage was the largest component of the diet (39.8% relative density) and mainly derived from several taxa of Chenopodiaceae: winterfat (Krascheninnikovia lanata), spiny hopsage (Grayia spinosa), and saltbushes (Atriplex spp.). Forb leaves were next in importance (34.1% relative density), especially from Fabaceae (Astragalus and Lupinus), Polemoniaceae (Gilia and Linanthus), and Asteraceae. Flowers, pollen, and seeds were also major components (20.3% relative density). Leaves composed nearly all of the diet in spring, whereas pollen, flowers, and seeds made up about a third of the diet in summer. Following dry winters when annual forbs were limited, Mohave ground squirrels depended primarily on foliage from perennial shrubs and forbs. Following wet winters when spring annuals were abundant and most plant species flowered and set seed prolifically, squirrels consumed a high proportion of leaves plus flowers, pollen, and seeds of annual forbs. Mohave ground squirrels reproduced only after winter rainfall >80 mm that resulted in a standing crop of herbaceous annuals ≥100 kg · ha-1. Mohave ground squirrels consumed very little of the nonnative annual plant biomass present on our study sites (Erodium, Salsola, Bromus, and Schismus contributed <3% overall to the diet). Conservation implications include the following: (1) priority should be given to protecting habitats supporting preferred perennial forage plants, including winterfat and spiny hopsage; (2) habitats with an understory dominated by native annual forbs have higher value than those dominated by nonnative plants, especially annual grasses; and (3) if climate change results in lower and less regular winter precipitation, suitable habitat for Mohave ground squirrels may be reduced and fragmented in the drier portions of the geographic range.
Exposure of Food Safety Knowledge and Inadequate Practices among Food Vendors at Rawalpindi; the Fourth Largest City of Pakistan

Street food vending trade has earned a significant place all over the world. Rawalpindi city has huge food industry with large market places dedicated only for food items, often coined with food streets which require investigation of food safety knowledge and handling practices among vendors. For this purpose 223 vendors from six clusters of Rawalpindi were selected. 37% of the vendors were from the age bracket of 26-35 years Mojority of them showed the unprofessional attitude towards food preparation and maintenance – about 61% did not cover their food at all and the remaining had the insufficient covering arrangements. Thereby, more than 80% of the stalls were exposed to flies (P=0.000) regardless of the type of cart (P=0.000). 75% vendors used the tap water for their food preparation, amongst which majority (60%) was of those vending either on mobile carts or stalls near to footpath (P = 0.000). Almost 98% handled the food with bare hands. However, 80% vendors agreed that food could be contaminated with the microbes, insects, dust particles, food coloring, and spices used in the preparation of food. Malpractices during the preparation of food and unhygienic conditions may cause foodborne outbreaks.
Nucleotide-binding Oligomerization Domain Containing 2 Characterization and Function during Mycobacterium tuberculosis Infection of Human Macrophages

ii Dedication . v Acknowledgments. vi Vita. viii List of Figures . xvii CHAPTER 1 : Introduction . 1 1.1 The immune system . 1 1.2 Innate immunity . 1 1.2. 1 PKC isoforms . 3 1.2. 2 iNOS and NO production . 5 1.3 Adaptive immunity. 6 1.4 Pulmonary innate immunity . 8 1.5 Alveolar macrophage . 9 1.6 Macrophage activation . 9 1.7 Macrophage receptors . 11
Effect of Castration Methods on Gene Expression of Androgen Receptor Gene in Skeletal Muscles of Awassi Sheep

The effect of castration on skeletal muscle development in awassi sheep were studied at the gene expressed for androgen receptor. The result showed that live weigh for epididymectomy rams was heavier than control and orchidectomy rams, respectively. There was significant difference (p < .05). By using the (2^ΔCT) with reference gene method, the findings documented that there was higher up-regulated in mRNA expression for androgen receptor in splenius muscles cells for epididymectomy rams compare with interact rams. In contrast, there was down-regulated for mRNA expression for androgen receptor cells for orchidectomy rams. In conclusion the continuous producing of testes hormones lead to growth of skeletal muscles of wether's significant increase the growth of skeletal muscles of wethers by epididymectomy companied with other rams.
SEASONAL VARIATION OF FATTY ACID AND AMINO ACID COMPOSITIONS IN THE MUSCLE TISSUE OF ZANDER (SANDER LUCIOPERCA LINNAEUS, 1758) AND THE EVALUATION OF IMPORTANT INDEXES RELATED TO HUMAN HEALTH

In this study, the seasonal fatty acid and amino acid amounts in the muscles of the zander from Beysehir Lake, Turkey, and their important indices for human health were evaluated. It was found that aspartic acid, glutamic acid and lysine levels in zander were dominant among the amino acids. The ratio of essential amino acids (EAA) to non-essential amino acids (NEAA) was between 0.69 and 0.78. In all seasons, the polyunsaturated fatty acid (PUFA, 89.85-109.11 mg/100g) amount in zanders was higher than saturated fatty acids (SFA, 55.08-81.89 mg/100g) and monounsaturated fatty acids (MUFA, 29.16-78.89 mg/100g). It was determined that EPA, DHA and omega-3 rates were high. The fatty acid quality indices (AI, TI, FLQ, w6/w3, h/H) were found at proper levels for human health. Summing up the results, it was found that seasons influenced both the compositions of amino acids and fatty acids of zander.