Miracle-dz/UniFAR-FTUs huggingface dataset:
Speed and Stamina in Three Fish

1. Measurements of the maximum speed sustained during bursts of swimming of up to 20 sec. duration by dace, trout and goldfish of various lengths are reported. 2. The ability to sustain periods of swimming appears to be related differently to length in different species. In the dace it is proportional to L 1.09, in the trout and goldfish to L 0.65 2. The ability to sustain periods of swimming appears to be related differently to length in different species. In the dace it is proportional to L 1.09, in the trout and goldfish to L 0.65. 3. The dependence of this relationship upon various factors is considered. It is concluded that allometric increase of muscle and the influence of an increasing Reynolds number, possibly combined with other, physiological, factors could adequately account for the variation observed. 4. The precise form of the speed/duration relationship differs in different species. These variations are also probably accountable for by a combination of different muscle percentages and fineness ratios together with other, physiological, factors. 5. The ability to maintain speed diminishes rapidly with increasing time interval in all the species measured. The maintained speed falls from about 10 L /sec. , maintainable for only 1 sec. of swimming, down to 5 L /sec. for 10 sec. and further to a cruising speed of about 4 L /sec. by 20 sec. The nature of this time/speed relationship is considered to be determined by the ability of the muscle to utilize stores of raw material and by the rates at which these can be supplied to, and waste products removed from, the muscle. 6. A diagram showing the relationship between velocity of water flow and the maximum distance which various hypothetical fish could traverse in such currents is constructed; and possible applications of this information are briefly considered.
Efficacy of fresh fruit from Cucumis myriocarpus as Nemarioc-AL phytonematicide on suppression of root-knot nematodes in tomato plant production

ABSTRACT Experimental System: Fermented dried fruit of wild cucumber (Cucumis myriocarpus Naude.) Had been successfully used as Nemarioc-AL phytonematicide in managing plant-parasitic nematodes in various cropping systems. However, the specialised oven-drying equipment are inaccessible to most resource-poor smallholder farmers in marginalised communities. Procedures: The objective of this study was to determine the efficacy of fermented crudes extracts of C. myriocarpus fruit when used in fresh form as Nemarioc-AL phytonematicide on management of population densities of root-knot (Meloidogyne species) nematodes and growth of tomato (Solanum lycorpersicum L.) plants. Seedlings at five leaf-stage were transplanted into pots containing 2700 ml steam-pasteurised river sand and Hygromix at 3:1 (v/v) ratio. Each seedling was inoculated with approximately 3000 eggs and second-stage juveniles (J2) at transplanting. The phytonematicide was applied at 0%, 2%, 4%, 8%, 16%, 32% and 64%, arranged in a randomised complete block design, with five replications and validated in time. Results: At 56 days after treatment, nematode variables and phytonematicide concentrations exhibited negative quadratic relations, with coeffients of determination (COD) ranging from 93% to 97%. Similarly, plant variables and phytonematicide concentrations exhibited positive quadratic relations, with COD from 96% to 98%. Conclusions: In conclusion, when prepared from fresh fruit of C. myriocarpus, Nemarioc-AL phytonematicide was suitable for use in managing nematode population densities of Meloidogyne species in tomato production.
The evolutionary history and dynamics of the cellulose synthase superfamily

The plant cell wall is central to the success of the embryophyte radiation. The high tensile strength of the cell wall supports complex branching architectures adapted to a varying and highly competitive environment. The cell wall has also played an integral role during the evolution of multicellularity by bonding cells together, controlling cell differentiation, acting as an energy store and mediating chemical signals. Polysaccharides are the dominant component of the plant cell wall and the genes involved in their biosynthesis are a major focus of cell wall research. The work presented in this thesis aims to reconstruct the evolutionary history and selection dynamics of the embryophyte cellulose synthase (CesA) and cellulose synthase-like (Csl) superfamily. The commercially significant Poaceae (grasses) have received considerable attention. The commercially significant Poaceae (grasses) have received considerable attention from the plant cell wall research community, not least because they are unique in containing a high abundance of (1,3;1,4)-β-glucan. Chapter 2 reconstructs the molecular phylogeny and evolutionary dynamics of the CesA superfamily in the Poaceae. Bayesian and likelihood-based models yielded a well-resolved gene tree for the superfamily and revealed heterogeneous selection pressures among amino acid sites. To provide a functional context to these findings, an energetically refined homology model of HvCslF6 was constructed — this is an important enzyme implicated in the biosynthesis of (1,3;1,4)-β-glucan — that was used to map amino-acid residues under selection onto a three-dimensional structure.
Transmission and control of Fish-borne Zoonotic Trematodes in aquaculture

Fish-borne Zoonotic Trematodes (FZTs) affect the health of millions of humans worldwide. For persistence, the life cycle of FZTs depends on aquatic snails, fish, and definitive hosts like humans, pigs or chickens. Definitive hosts can become infected by eating raw or undercooked fish. Integrated Agriculture Aquaculture (IAA) systems improve the livelihood of small scale farmers, but may enhance transmission of FZTs because all types of hosts and all transmission routes can be present on a single farm. This thesiscombines experiments, statistical analyses and mathematical modelling to gain insight into transmission mechanisms of FZTs to fish in aquaculture and to use this insight to compare and discuss control measures against FZTs. Currently, medication of humans is the main strategy to control FZTs. Modelling indicated that this does not lead to elimination of FZTs because both humans and definitive hosts other than humans will maintain the life cycle of FZTs independently. Treatment of (a part of) these host types may eliminate FZTs, e.g. treating all humans and 54% of definitive hosts other than humans. Aquaculture may provide opportunities for control of FZTs by adapting management measures. Experiments showed that smaller fish get more often and more heavily infected with FZTs than larger fish; common carp (Cyprinus carpio) of more than 50 g rarely acquire new infections. Once carp are infected, FZTs persist for at least 27 weeks, implying that harvestable fish still contain FZTs and, therefore, are a risk to human health. In most IAA systems, fish are kept FZT free until 0.5 g before being stocked into a fish pond where they are very likely to be exposed to FZTs. Stocking fish at more than 25 g, or at more than 14 g in combination with treating all humans with anthelmintics, may lead to elimination of FZTs. Also, control of snails by either decreasing density or increasing mortality of snails may lead to elimination of FZTs in aquaculture. Farmers and policy makers should evaluate which combination of control measures is attractive to them.
Evaluation of Pheromone Dispensers for Use in Gypsy Moth Detection (Lepidoptera: Lymantriidae)2

Seven controlled-release dispenser formulations containing 500 μg of gypsy moth pheromone (+)-disparlure, were compared in laboratory and field tests. Pheromone release rates, residual pheromone contents, and male moth captures in traps baited with the dispensers were compared following pre-aging of the dispensers in a greenhouse at 35 °C for 0, 4, 12, and 16 wk. The laminate dispenser, now used in USDA detection traps, became less attractive over time as its pheromone release rate and content dropped below the threshold values previously reported as necessary for effective attraction. A polyvinyl chloride coated twine dispenser produced high male moth captures and gave release rates and residual contents above these thresholds (30 ng/h release rate and 100 μg content) at all aging periods. The tube-A dispenser was the most effective of the new commercially prepared formulations, followed by the membrane and tube-B whose male moth captures and release rates tended to increase with aging time. The capsule .
Iron acquisition in Listeria monocytogenes

Jackie McCluskey: Iron Acquisition in Listeria m onocytogenes This investigation was designed to study iron acquisition mechanisms of Listeria monocytogenes. Molecular biology techniques were employed. A listerial genomic library in E. coli and a library of listerial transposon mutants was constructed and screened. The assay used to screen both libraries was based on the ability of a ferrous iron chelator, ferrozine, to produce a red colour when complexed with ferrous iron. After screening approximately 10,000 clones from the genomic library and 12,000 mutants from the transposon library of mutants, 11 apparently ferric reductase-negative transposon mutants were identified. Subsequent analysis of these mutants showed them to be ferric reductase-positive. The reason for this reversal of phenotype is not known and was not investigated further. To identify genes which were involved in the growth of L. monocytogenes in low-iron environments, the library of listerial transposon mutants was screened in low-iron medium. From the 5,500 screened, two mutants were identified which showed reduced ability to grow in both low-ferric and low-ferrous iron medium. In the high-iron medium, the growth of the mutants was similar to that of the wild type. Mutant 9E was phenotypically similar to the wild type except for the inability to grow in low-iron medium. Mutant 7D had two additional difference; increased haemolytic activity and decreased motility when observed using phase microscopy. Sequencing of the flanking chromosomal DNA led to the identity of the genes which had been disrupted; flaA in mutant 7D and argC in mutant 9E. Sequence analysis upstream from the flaA gene identified a new gene, cheV, in L. monocytogenes. The relationship of these mutations to the observed phenotypes was discussed. The ability of both mutants to grow in vivo was similar to that of the parental wild type.
Tick fauna of the autochthonous Zackel sheep in South Serbia region.

: Sheep production is an example of a sustainable production fully integrated within the local rural development. One of the main threats on the outdoor breeding of sheep is parasitism. Ticks are nuisances and vectors of several diseases agents. The distribution of ticks appears to be changing, with spread to previously unaffected areas. Tick and tick-borne disease control is one of the major components of animal health program protecting livestock in the developing countries, which reflects impact on the livelihood of resource-poor farming communities. Taking into consideration the negative impact on the health status of the livestock, also the direct and indirect economic losses, it is necessary to examine the tolerance and resistance of certain species against diseases. It is one of the most important elements of the strategy of selection and screening for resistant animals. The aim of this study was to determine the tick species persisting in 45 tested autochthonous Zackel sheep flocks, and examine their seasonal occurrence from March 2010 to January 2011, in the region of South Serbia. The result showed that Ixodes, Dermacentor, Ripicephalus and Haemaphysalis were the most abundant ticks found, affecting 50.40% tested sheep. The result of this study is a survey of tick species from autochthonous Zackel sheep in Serbia and implication of possible preventions measures for diseases caused and transmitted by ticks.
Effect of Foliar Applications of Zingiber officinale Extracts on Origanum majorana

ABSTRACT The effect of foliar application of the hydroalcohol extract of Zingiber officinale (5 and 10 mg.L–1) on the chemical constituents of Origanum majorana plants was studied. Foliar application of Z. officinale extract increased total soluble sugar and decreased the essential oil (EO) percent, oil yield, and percent nitrogen. The main constituents of the plant EO were quantitatively altered. Apigenin was identified and quantified in O. majorana using high-performance liquid chromatography. The total flavonoid content concentration was 99.5 and 165.5 mg.g–1 of quercetin equivalent, for the plants treated with Z. officinale extracts at 5 and 10 mg.L–1, respectively. The total phenol content decreased to 48.6 mg.g–1 and 46.4 mg.g–1 of gallic acid equivalent (GAE) compared to control (69.7 mg.g–1 GAE). The apigenin concentration increased (3.83 mg.g–1) with the foliar treatment of 10 mg.L–1 of Z. officinale extracts compared to control (2.40 mg.g–1).
IDENTIFICATION AND CHARACTERIZATION OF REGULATORY MIRNAS AND MRNAS IN THE LONGITUDINAL HUMAN HOST RESPONSE TO VAGINAL MICROBIOTA

Title of Dissertation: IDENTIFICATION AND CHARACTERIZATION OF REGULATORY MIRNAS AND MRNAS IN THE LONGITUDINAL HUMAN HOST RESPONSE TO VAGINAL MICROBIOTA. Steven Smith, Doctor of Philosophy, 2017 Dissertation directed by: Dr. Jacques Ravel, School of Medicine, University of Maryland, Baltimore. The human vagina and the bacterial communities that reside therein exist in a finely balanced mutualistic association. Dysbiotic states of the vaginal microbiota, including bacterial vaginosis (BV), are characterized by a paucity of Lactobacillus spp. , the presence of a wide array of strict and facultative anaerobes, and a pH >4.5. Symptoms such as odor and discharge can accompany these microbial dysbiotic states, however, epidemiologically, vaginal dysbioses have been associated with increased susceptibility to STIs, including chlamydia. The mechanisms by which vaginal microbiota protect or increase the risk to infections remain unknown. This thesis aimed to identify the molecular factors that control host cellular responses to Lactobacillus spp. -dominated and dysbiotic microbiota. Chapter 2 characterized the in vivo host microRNA (miRNA) response to different types of vaginal microbiota to gain insight into host functions that play a role in vaginal homeostasis. Leveraging daily collected vaginal samples in conjunction with a machine learning approach, eight miRNAs were discovered to be differently controlled by vaginal microbiota. Of these, expression of miR-193b, known to regulate host cell proliferation, was increased by Lactobacillus spp. -dominated microbiota. In vitro, vaginal epithelial cells exposed to Lactobacillus spp. culture supernatants exhibited reduced epithelial cell proliferation, high miRNA-193b expression and decreased abundance of cyclin D1. More importantly, epithelial cell proliferation was identified as a requirement for efficient Chlamydia trachomatis infection. Chapter 3 characterized the in vitro transcriptome of epithelial cells exposed to Lactobacillus spp. relative to Gardnerella vaginalis, a surrogate for dysbiotic vaginal microbiota. Immune response and cell cycle pathways were found to be among the most modulated by Lactobacillus spp. Longitudinal gene expression suggested a role of histone deacetylases (HDAC) as an intermediary between immune stimulation and cell proliferation. Additionally, the epidermal growth factor receptor (EGFR), required for C. trachomatis infection, was decreased when epithelial cells were exposed to Lactobacillus spp. These findings contribute to the fundamental understanding of the vaginal microbiota’s role in cellular homeostasis as a requirement for resistance to STI agents such as C. trachomatis, and ultimately will lead to improved preventive strategies against STIs through the modulation of vaginal microbiota composition and function. IDENTIFICATION AND CHARACTERIZATION OF REGULATORY MIRNAS AND MRNAS IN THE LONGITUDINAL HUMAN HOST RESPONSE TO VAGINAL MICROBIOTA.
Comparative phylogenetic and transcriptional analysis of the Bacillus cereus sensu lato enterotoxin genes nhe, hbl and cytK

B. cereus sensu lato was found to comprise seven genomospecies. Enterotoxin genes are distributed irregularly among them. Hbl, cytK and plcR evolved through frequent horizontal gene transfer, while nhe developed strictly vertical. Transcription of nhe and hbl is strain-specific, media-dependent and controlled by several regulators via exceptionally long 5' untranslated regions.
The Impact of Different Dietary Forms (Mash, Crumble and Pellets) on Some Growth Traits and Carcass Characteristics of Broilers

| This study was conducted to investigate the effect of different physical forms of diet (mash, crumble, and pellets) on some growth traits and carcass characteristics of broilers. Chicks (n=300, Ross 308) were distributed in a factorial arrangement with 3 treatments and 2 replicates (50 birds/replicates). The weight gain (WG), feed intake (FI), feed conversion ratio (FCR), and mortality rate were measured during the experimental periods (1-42 d). Some carcass traits were recorded at the end of the experiment (42 days) including weight of carcass, thigh, breast, and abdominal fat. Results revealed that WG and FI were significantly (P<0.05) improved and FCR was significantly (P<0.05) lower in broiler fed crumble and pellet diet than mash during the three periods (22-32 d, 33-42 d and 1-42 d). The significant (P<0.05) improvement was also found in carcass weight, thigh and breast. The superiority of broiler fed crumble and pellet was extended to include each of Performance Index (PI), European Production Efficiency Factors (EPEF) and European Broiler Index (EBI). The mortality rate was not significantly differed across all three diet forms. The results of the present study give an impression that crumble and pellet form of feed is better than mash for the productive performance of commercial broiler during the age of 21 to 42 days.
Virulence genes in Escherichia coli strains isolated from urine of elderly patients

Abstract Urinary tract infections (UTIs) are one of the most frequent infections in elderly people. The majority of infections is caused by uropathogenic E. coli. These strains contain a broad spectrum of virulence factors and are able to overcome defense barriers and colonize host organism. Population of elderly individuals has been growing globally and for that reason it is possible to expect a rise of UTIs among them. The aim of this study was to determine the phylogenetic group (A, B1, B2 and D) of urinary strains of E. coli isolated from elderly patients and evaluate the presence of 14 virulence genes (hly, cnf1, cdt, sat, afa, sfa, pap, aer, upaH, cah, pic, neuC, kpsMT II and traT) in these strains. We have carried out a phylogenetic analysis and virulence genes identification of 75 urinary E. coli isolates. Among our 75 E. coli strains, phylogenetic group B2 (64%) was the most dominant followed by groups D (16%), B1 (10.7%) and A (9.3%). The genes kpsMT II (65.3%), traT (61.3%), upaH (58.6%) and aer (52.0%) were found to be the most prevalent. We identified from 5 to 10 virulence genes in 44% strains belonging to B2 phylogroup. E. coli urinary strains examined in this study belonged mainly to phylogenetic group B2. We have also found that the majority of examined virulence genes, which are crucial for the establishment and maintenance of infection, were present in these strains.
Stimulation de la survie et de la régénération des cellules ganglionnaires de la rétine par inactivation de la GTPase Rho après lésion du nerf optique du rat adulte

Rho family GTPases (Rho, Rac and Cdc42) are key moiecules in intracellular signaling pathways controlling axonal growth during development. Reacting to attractive or repulsive guidance cues, they control axonal elongation, tuming or retraction, and guide the axon towards its target. Whereas Rac and Cdc42 activation are mostly associated with attractive signais, Rho is activated mainly by repulsive eues, and its activation tends to stop growth. Rho could be a key component in the absence of axonal regeneration following a central nervous system (CNS) lesion, which is mainly attributed to the presence of growth inhibitory molecules, known to activate Rho. To determine how Rho is involved in CNS regeneration inhibition, we used the optic nerve lesion model. We studied the effects of Rho antagonists on the survival and regeneration of retinal ganglion celis (RGCs), the neurons whose axons make up the optic nerve. We inactivated Rho with intraocular injections of ceil permeable C3, a modified version of Rho antagonist C3. C3 ADP-ribosylates Rho on amino acid Asparagine 41 and prevents its activation. The modified version has an additional transport sequence that facilitates its entry into ceils. Rho inactivation with a single injection of ceil permeable C3 performed immediately afier optic nerve lesion doubled the survival and quadrupled axonal regeneration of RGC afier 2 weeks, compared to controls. We then showed that both survival and regeneration could be enhanced with repeated injections. Survival at 2 weeks increased from 13.2% to 20.1% with multiple injections. Regeneration more than doubled with repeated injections, and close to 4.5% of surviving RGCs regenerated an axon past the lesion site, with almost haif of those reaching 500 p.m. We tested different injection schedules, which allowed us to determine that the therapeutic window during which
Evaluation of Pseudomonas fluorescens isolates for the management of Fusarium oxysporum f.sp. lycopersici and Rhizoctonia solani causing wilt complex in tomato.

Twenty-five isolates of Pseudomonas fluorescens were isolated from healthy plants of tomato on Kings’B medium, for exploring their bio-efficacy potential against Fusarium oxysporum f.sp. lycopersici and Rhizoctonia solani, responsible for wilt complex disease. Out of all, six isolates (I-7, I-15, I-18, I-23, I-24 and I-25) significantly inhibited the growth of both fungal pathogens under laboratory conditions. Under green house conditions, bacterization of tomato seeds with these six isolates of P. fluorescens in pathogen infested soil significantly reduced the incidence of disease caused by F. oxysporum f.sp. lycopersici and R. solani, with maximum (12.50 and 10.41%) by isolate I-23, and simultaneously increased the plant growth parameters. Application of isolate I-23 also resulted in maximum per cent germination, shoot length and root length of 80.00 and 77.50 per cent and 54 and 38 cm and 16.27 and 11.97 cm, respectively as compared to their untreated control.