Miracle-dz/UniFAR-FTUs huggingface dataset:
Sensitivity of Guadalupe Bass Swim‐up Fry to Hyperoxia

AbstractHatchery-reared fingerling Guadalupe Bass Micropterus treculii are stocked into central Texas rivers to restore threatened populations and combat hybridization with Smallmouth Bass M. dolomieu. Fry survival in hatchery rearing ponds has declined by more than 50% in recent years, and pilot investigations indicated that exposure to high dissolved oxygen (DO) concentrations (>20 mg/L; hyperoxia) during tempering might have contributed to fry mortality. To test this hypothesis, Guadalupe Bass swim-up fry (11 d posthatch; 8.45 ± 0.25 mm TL [mean ± SD]) were exposed to normbaric DO concentrations ranging from 7.9 to 33.3 mg/L at 18°C, mimicking the hatchery tempering protocols followed during 2014 and 2015. After a 30-min exposure to the DO treatment (flow rate = 18 L/h), jars were flushed with nonoxygenated water for 1 min to rapidly lower the DO, mimicking the release of fry into ponds after tempering. Jars were then supplied with freshwater at a rate of 36 L/h and were monitored for 72 h. One control.
Thelytokous parthenogenesis in the exotic dacetine ant Strumigenys rogeri (Hymenoptera: Formicidae) in Taiwan

Only recently has it become clear that several species of eusocial hymenopterans regularly reproduce by thelytokous parthenogenesis, that is, the production of diploid female offspring by unmated females. This phenomenon suggests that parthenogenetic reproduction might be advantageous to organisms under certain environmental conditions. Here the occurrence of asexual reproduction is reported for the first time in the dacetine ant, Strumigenys rogeri, at least for the focal populations in Taiwan. Virgin queens of S. rogeri maintained with several workers produced both workers and young queens from unfertilized eggs under laboratory conditions in as short as 39 days, whereas workers were strictly sterile as no spermatheca was discovered after dissection. Combined with additional evidence (i.e. absence of males in field colonies), queen thelytoky is confirmed. Such a reproductive mode and short development time may jointly help explain the success of this tramp ant species in Taiwan and elsewhere.
Effects of silage additives on intake, live-weight gain and carcass traits of growing and finishing dairy bulls fed pre-wilted grass silage and barley grain-based ration

SUMMARY The effects of silage additives on performance of dairy bulls were determined in a feeding trial using 45 Nordic Red and 45 Holstein bulls. Both breeds were allotted randomly to three treatments: (1) timothy silage (TS) without additives + barley (CON); (2) TS with sodium benzoate, potassium sorbate and sodium nitrate-based additive + barley (SALT); and (3) TS with a mixture of mostly formic acid and propionic acid-based additive + barley (ACID). The bulls were fed total mixed rations ad libitum. During the experimental period of 259 days, the average dry matter intake was 10·1 kg/d and there was no difference among the treatments. The average live-weight gain (LWG) and carcass gain was 1363 and 741 g/d, respectively. There were no treatment differences in the carcass gain but LWG of the CON bulls was 5% higher compared with the SALT and ACID bulls. Carcass conformation score of the SALT and ACID bulls was 6% higher compared with the CON bulls. The experiment demonstrated that there was only a slight benefit from silage additives in animal performance when silage dry matter was 350–400 g/kg and silage was ensiled in round bales.
ANTIOXIDANT PROPERTIES OF HORSERADISH (ARMORACIA RUSTICANA) – PILOT STUDIES

The aim of the study was to evaluate the antioxidant properties of horseradish extracts (Armoraciarusticana). The study’s material consisted of wild, horseradish samples coming from three different regions ofPoland (Mazowsze, Wielkopolska and Podlasie). Antioxidant activity was investigated using DPPH• free radical,and the final result was converted into the equivalent of the antioxidant activity of vitamin C. Studies haveshown that one of the samples had significantly higher antioxidant activity than the other two, whose antioxidantpotential was similar from a statistical point of view. It was calculated that 1 g dry substance of horseradishsamples had an antioxidant activity corresponding to 4.31 – 8.78 mg of vitamin C.
Physiological and biochemical responses of Festuca sinensis seedlings to temperature and soil moisture stress.

The interaction effects between temperature and soil moisture on Festuca sinensis Keng ex E.B. Alexeev were analysed to determine how F. sinensis responds to these environmental conditions. A pot experiment was conducted in a greenhouse under simulated growth conditions with four soil moisture contents (80, 65, 50 and 35% relative saturation moisture content) and three temperature conditions (15, 20 and 25°C). Physiological (relative water content and root activity) and biochemical parameters (chlorophyll, peroxidase (POD), malondialdehyde (MDA), soluble protein, soluble sugar and free proline) were evaluated at the seedling stage. Results showed that with a decrease in soil water content, the POD activities, MDA content, soluble protein content, soluble sugar content and free proline content of plants under the 15°C and 20°C treatments initially decreased and then increased, whereas they increased with a decrease of soil water content at 25°C. The relative water contents of plants under the three temperature treatments decreased with a decreasing soil moisture content, but then increased temperature significantly reduced the relative water content of the seedlings under low soil water content. The chlorophyll contents of plants under the 25°C treatment decreased with a decrease of soil moisture content, but those of plants under the 15°C and 20°C treatments initially increased and then decreased. The root activities of plants under the 15°C and 20°C treatments increased with a decreasing soil moisture content; however, those of plants under the 25°C treatment initially increased and then decreased. Thus, results indicated that changes of temperature and soil moisture content had significant and complicated effects on the physiological-biochemical characteristics of F. sinensis; the conditions of 20°C and 65% RSMC had positive effects on F. sinensis seedling growth and the appropriate drought stress could promote the growth of seedling roots under the three different temperature conditions. In conclusion, F. sinensis seedlings could adapt to certain changes in the ecological environment by regulating their physiological and biochemical reactions.
Studies on the Chloramphenicol Halogenase CmlS

ii Co-Authorship Statement.iii Acknowledgements . iv List of Figures.ix List of Tables.xiv List of Abbreviations.xv Chapter 1 Introduction . 1 1.1 Halogenated Natural Products. 1 1.2 Enzymatic Halogenation . 3 1.2.1 Haloperoxidases . 3 1.2.1.1 Heme-Dependent Haloperoxidases . 3 1.2.1.2 Vanadium-Dependent Haloperoxidases. 4 1.2.2 Perhydrolases . 5 1.2. 3 Non-Heme Iron Halogenases . 6 1.2. 4 Nucleophilic Halogenases . 7 1.3 Flavin-Dependent Halogenases. 9 Chapter 2 The Crystal Structure of CmlS . 17 2.1 Introduction . 17 2.1.1 Chloramphenicol and its Dichloroacetyl Moiety . 17 2.1.2 CmlS, A Flavin-Dependent Halogenase . 20 2.2 Experimental Procedures and Methods. 21 2.2.1 Materials. 21 2.2.2 Cloning of the Halogenase Gene cmlS . 22 2.2. 3 Expression and Purification of CmlS. 22 2.2. 4 Crystallization of CmlS. 24 2.2. 5 The Structure of CmlS . 25 2.2. 5.1 The Overall Structure of CmlS . 25 2.2. 5.2 ESI-Mass Spectrometry of CmlS . 26 2.2. 5.3 Generation, Expression and Purification of CmlS Mutants . 27 2.2. 5.4 Chemical Denaturation of CmlS . 29
The mitonuclear compatibility species concept

ABSTRACT The avian world is packaged into genetic assemblages that we call species. Although ornithologists can, with a few important exceptions, agree on the boundaries among avian gene pools that delimit species, the evolutionary process that created this structured subdivision of Aves remains uncertain and contentious. Moreover, although avian species are recognizable and diagnosable, many bear signatures of recent, often substantial, exchange of nuclear (N) genetic material. As a result, there is debate regarding the process that gives rise to and maintains the genetic structure of avian populations. I propose that a key missing consideration in discussions of speciation is the necessity of coadaptation between N and mitochondrial (mt) genes to enable core energy production via oxidative phosphorylation. Because mt genomes are non-recombining and subject to high mutation rates, they evolve rapidly. Consequently, N and mt coadaptation persists only through perpetual coevolution between mt and N genes. Mitonuclear coevolution leads to rapid divergences in coadapted mitonuclear gene sets whenever there is a disruption in gene flow among populations. As a result, once populations diverge in coadapted mitonuclear genotypes, the reduced fitness of offspring due to mitonuclear incompatibilities prohibits exchange of mt and N-mt genes and effectively isolates individuals with shared coadapted N and mt genotypes. Given these considerations, I propose that avian species can be objectively diagnosed by uniquely coadapted mt and N genotypes that are incompatible with the coadapted mt and N genotype of any other population. According to this mitonuclear compatibility species concept, mitochondrial genotype is the best current method for diagnosing species.
Expression of innate immune genes, proteins and microRNAs in lung tissue and leukocytes of pigs infected with influenza virus

Body: This study aimed at providing a better understanding of the involvement of innate immune factors including microRNA (miRNA) in the local and systemic host response to influenza virus infection. Twenty pigs were challenged by influenza A virus subtype H1N2. Expression of miRNA, mRNA and proteins were quantified at different time points after challenge (24h, 72h, and 14days post infection (pi)). Gene expression was quantified using 48.48 Dynamic Arrays (Fluidigm Corporation, CA, USA) combining 48 samples with 48 primer sets for 2304 individual and simultaneous qPCR reactions. Several groups of genes were significantly regulated according to time point and infection status: Pattern recognition receptors (TLR2, TLR3, TLR7, RIG1, MDA5), IFN and IFN induced genes (IFNB, IFNG, IRF7, STAT1, ISG15 and OASL), cytokines (IL1B, IL1RN, IL6, IL7, IL10, IL12A, TNF, CCL2, CCL3 and CXCL10), and several acute phase proteins. Likewise, the following miRNAs were differentially expressed in one or more time groups compared to the control pigs: miR-15a, miR-21, miR-146, miR-206, miR-223 and miR-451. At day one pi lung tissue protein levels of IL-6, IL-12 and IFN-α were significantly increased compared to the control group, and haptoglobin and C-reactive protein were at significantly increased at day three pi. MiRNA are small non coding RNA molecules, that regulate gene expression in a wide range of organisms. Cellular miRNAs might be involved in influenza infection, both by targeting immune related host transcripts but also by targeting viral gene products. Our results suggest that in addition to a wide range of immune factors, miRNAs are involved in fine tuning of an efficient innate immune response to influenza infection.
Prospection et première caractérisation moléculaire de l'exocortis (Citrus exocortis viroid, CEVd) dans la région du Gharb

Les viroides sont des agents transmissible mecaniquement et par greffage, et dissemines a longue distance par le materiel vegetal. Des prospections ont ete menees, durant Juillet 2013, dans la region du Gharb a la recherche des viroides des agrumes. Un total de 53 echantillons a ete collecte et utilise pour l’inoculation du cedratier ‘Etrog’ avant d’etre teste par RT-PCR pour la detection de l’exocotris ( Citrus exocortis viroid , CEVd). Les resultats obtenus ont montre que le CEVd a ete tres repandu dans la region avec un pourcentage d’infection de 84.9% des echantillons analyses. Apres le sequencage genomique, une etude de la diversite genetique a ete realisee sur trois isolats locaux representatifs du CEVd. La comparaison entre les sequences nucleotidiques marocaines du CEVd a montre une diversite genetique inferieure a 3%. Mots-cles: Agrumes, Citrus exocortis viroid , RT-PCR, sequencage, Gharb. Abstract Viroids are graft- and mechanically transmissible agents, disseminated through budding. A field survey was conducted, during July 2013, for citrus viroids in the Gharb region. A total of 53 samples was collected and used for inoculation of ‘Etrog’ citron before being tested by RT-PCR for the detection of exocotris ( Citrus exocortis viroid , CEVd). The obtained results showed that CEVd was widespread in the region with an infection rate of 84.9% in the analyzed samples. After genomic sequencing, a study of the genetic diversity was conducted on three representative local isolates of CEVd. The comparison between the nucleotide sequences of moroccan CEVd isolates revealed a genetic diversity less than 3%. Key words: Citrus, Citrus exocortis viroid , RT-PCR, sequencing, Gharb.
Phytobiotics in poultry and swine nutrition – a review

Abstract The trend in the use of phytobiotics in animal feed has been increased during last two decades. Investigations showed that excessive use of in-feed antibiotics will intensify the potential risks of increasing resistance in human pathogens. Bacterial resistance and antibiotic residues in animal products led to raising the concern in using antibiotics as growth promoters and finally resulted in the ban on using in-feed antibiotics in most of the developed countries. As an alternative, phytobiotics were recommended by researchers and nutritionists. Plenty of studies have been done using phytobiotics in poultry and swine nutrition so far. They have mostly shown the antimicrobial, antioxidant, anti-inflammatory and growth promoting effects of phytobiotics. Antioxidative function of phytobiotics can positively affect the stability of animal feed and increase animal’s products quality and storage time. Generally, the available documents indicate the positive effects of phytobiotics on poultry and swine performance. Due to the contradictions in published results, further research and investigations are still necessary to elucidate various nutritional aspects of phytobiotics. In the following context, the authors try to provide an overview of the recently published results on application of phytobiotics and possible mode of actions as an alternative for in-feed antibiotics in poultry and swine nutrition.
Bathymetric Analysis of St. Croix Ridge, U.S. Virgin Islands

BACKGROUND The St. Croix Ridge lies within the U.S. Virgin Islands in the Caribbean Sea. The areas of interest are located along the ridge, approximately 18 km southeast from the most eastern tip of St. Croix (Fig. 1a). A 70 km long, S-shaped submarine canyon – which will be referred to as “S-Shaped Canyon” – runs through the shallow (500 m depth) portion of the ridge and spills into the deep ocean at a depth of 3350 m (Fig. 1b), where it converges with a 36 km long “Straight Canyon. ” The canyons range in depth from 500 to 3,500 m. Deep corals often inhabit ridge systems and canyons (Armstrong et al., 2014) and can be found at depths up to 4,000 m near the equator (Roberts et al., 2006). Submarine canyons have steep topographic features that are associated with coral habitat (Baker et al., 2012). The purpose of this study is to identify high potential areas for deep coral habitat. ABSTRACT In early 2015, seafloor to the southeast of St. Croix, U.S. Virgin Islands was mapped using multibeam sonar data collected by a Kongsberg EM302 system on the NOAA Ship Okeanos Explorer. Bathymetry and backscatter data were post-processed with CARIS HIPS and SIPS 9.0 software to examine two submarine canyons which range in depth from 500 to 3,500 m. Both canyons cut through shallow ridges and converge in the deep ocean, and are approximately 36 and 70 km in length. Hard substrate is necessary for deep coral settlement, and hardground canyon walls are often sites for deep coral habitat. Bathymetric surfaces overlain with backscatter intensity imagery are used to identify areas of highest potential for deep coral habitat. Pinpointing these sites is essential to designating potential Marine Protected Areas and protecting the biodiversity of this region.
Plant community patterns in Moroccan temporary ponds along latitudinal and anthropogenic disturbance gradients

Background: Temporary ponds, an abundant habitat in the Maghreb region and notably in Morocco, have a high conservation value. However, they are mainly known from the north of the country. Aims: The aim of this work was to characterise the vegetation of Moroccan temporary ponds along a combined gradient of latitude and anthropogenic pressure. Methods: Eighty-five ponds distributed along a north–south gradient of 750 km were sampled. For each pond, all vegetation was surveyed (flooded and dry parts) and the local abiotic characteristics were measured during two successive hydrological cycles. The prevailing anthropogenic pressures were also identified and were attributed an impact score. Results: Eighty-one characteristic pond species (including 17 rare species) were recorded, with several new distribution data in the southern part of the latitudinal gradient. Plant communities were related to climatic and anthropogenic factors, but mostly to local factors, such as maximum water depth and soil pH. The northern ponds (wettest macroclimate) were rich in characteristic species and rare species, while the southern (driest macroclimate) ponds were more species poor. Conclusions: In addition to the direct impact of increasing human activity, a further reduction of the floristic richness of temporary ponds is expected due to climatic changes. This is particularly the case for characteristic species which have a high conservation value.
Mosquito (Diptera: Culicidae) fauna in Alappuzha and Kottayam district of the Kerala state, south India

The study was conducted to look at the mosquito fauna in different sites of Alappuzha and Kottayam districts, Kerala state to generate information on the diversity of mosquitoes. A total of 44 species of mosquitoes belonging to 21 subgenera and 11 genera were recorded in Alappuzha district and 21 species of mosquitoes belonging to 14 subgenera and 9 genera were recorded in Kottayam districts. The genus Aedes, Anopheles, Mansonia, Heizmannia, Culex, Ficalbia, Uranotaenia, Tripteroides, Armigeres, Coquillettidia, and Mimomyia were recorded in Alappuzha district. Aedes, Anopheles, Armigeres, Culex, Heizmannia, Tripteroides, Toxorhynchites and Uranotaenia were recorded in Kottayam district. Species common to both districts were Aedes aegypti (Linnaeus), Aedes albopictus (Skuse), Aedes vittatus (Bigot), Armigeres subalbatus (Coquillett), Culex fuscanus (Wiedemann), Culex quinquefasciatus (Say), Culex tritaeniorhynchus (Giles), Heizmannia greenii (Theobald), Heizmannia indica (Theobald) and Toxorhynchites affinis (Edwards). Paddy field, mud pools, fallow fields, man-made artificial containers were the common breeding area in Alappuzha district and in Kottayam district tree holes, coconut shells, artificial containers and leaf axils were the main breeding habitats.
Use of enzymes and inoculants to manipulate the feeding value of liquid fed DDGS for young pigs

Use of enzymes and inoculants to manipulate the feeding value of liquid fed DDGS for young pigs Melissa Wiseman Advisor: University of Guelph, 2016 Professor C.F. M. de Lange Corn distiller’s dried grains with solubles (DDGS) is an alternative nutrient and energy source in swine diets. It has been suggested as a functional ingredient in weanling pig diets via decreasing digesta viscosity, and inhibition of enteric pathogen growth due to high insoluble fiber content. DDGS feeding value may be enhanced through fiber hydrolysis promotion, probiotic growth (e.g. Lactobacilli), production of organic acids (particularly lactic acid), and prebiotic formation (e.g. arabinoxylan oligosaccharides) in liquid feed. Micro-scale fermentations were initially conducted to establish effective conditions for manipulating DDGS feeding value. Three studies were then performed to determine the effects of (1) including untreated DDGS in a conventional diet, (2) steeping DDGS with enzymes (xylanase and βglucanase) for inclusion in liquid feed, and (3) partially fermenting DDGS with a silage inoculant and enzymes for inclusion in liquid feed on growth performance and gut function of weanling pigs. In micro-scale fermentations partially fermented DDGS was produced via incubation at 40°C (16% dry matter) between 1 and 7 days with silage inoculant and enzymes, yielding >100 mM lactic acid, pH <4.5, and acetic acid <40 mM. However, in macro-scale fermentations, variability in acetic acid and lactic acid concentrations was observed. Liquid feeding partially fermented DDGS improved average daily gain in piglets weaned at low body weight (5.8 ± 0.6 kg) in week 7 post-weaning compared to pigs fed unfermented DDGS (P<0.05). Intestinal weights and digesta organic acid profiles were influenced by dietary treatments throughout the nursery period (P<0.10). Liquid feeding partially fermented DDGS reduced Chao 1 alpha-diversity measures in the ileal mucosa and feces of pigs on day 42 postweaning (P<0.05) and resulted in the establishment of an abundant ileal mucosa Lactobacillus proportion. Liquid feeding partially fermented DDGS with silage inoculants and enzymes was shown to positively impact growth of pigs under challenge and result in probiotic colonization of the ileal mucosa. Efforts must be taken to improve consistency in fermentation conditions, identify relevant quality markers, and elucidate optimal DDGS inclusion levels and inclusion timing in order to establish a viable feeding program for practical application.
The Epoxyeicosatrienoic Acid Pathway Enhances Hepatic Insulin Signaling and Is Repressed In High Fat Diet Induced Hepatic Insulin Resistance

Hepatic insulin resistance is a hallmark of type 2 diabetes. I conducted quantitative proteomic profiling of liver tissue in a high fat diet (HFD) mouse model of hepatic insulin resistance. The epoxyeicosatrienoic acid (EET) pathway emerged as a candidate for functional validation, as its repression coincided with hepatic insulin resistance. I showed that EETs enhance insulin signaling in hepatocytes at the level of its central protein kinase, Akt. These results imply that HFD may contribute to hepatic insulin resistance by repressing the synthesis of positive modulators of insulin signaling.