Miracle-dz/UniFAR-FTUs huggingface dataset:
Average daily gain rates determine eye muscle area and rump fat depth of beef heifers

Abstract In cow-calf beef production systems, the growth and development of replacement heifers deserve special attention because they affect the age at puberty and the onset of reproductive activity. Therefore, the objective of this study was to test if changes in average daily gain (ADG) have an effect on eye muscle area, rump fat depth and back-fat thickness in developing beef heifers. These traits of 42 beef heifers were measured over time. The results of the current study allow inferring that heifers older than 385 days and with high rates of ADG (above 0.950 kg per day) have the greatest impact on longissimus muscle area growth (above 57 cm2). On the other hand, it is observed that younger heifers (less than 230 days old) do not exceed 48 cm2 of the longissimus muscle area, even with ADGs around 1.25 kg. A positive relationship between the rate of ADG and rump fat depth was also evidenced, observing that rump fat depth deposition is influenced by the rate of ADG. The results of the current study show a linear trajectory of rump fat depth, indicating that for every 0.10 kg of ADG during a period exceeding 56 days, an increase of 1.09 mm of rump fat depth occurs. In conclusion, this study illustrates a simple way on how ADG and age affect the body composition traits in beef heifers and shows that changes in average daily gain affect muscle and fat tissue growth, as determined by longissimus muscle area and rump fat depth in growing beef heifers.
A case report on Protein Losing Enteropathy and its therapeutic management in a dog

A male German shepherd dog of age 2½years was presented at Teaching Veterinary Clinical Complex (TVCC) College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati with a complaint of anorexia, vomiting, pronounced muscle wasting, lethargy and profuse watery diarrhoea. Based on the clinical examinations and haemato-biochemical profile it was diagnosed as Protein losing enteropathy (PLE). The serum albumin concentration was recorded to be 1.7g/dl which is much lower than the normal range. The therapeutic management was rendered with plasma expander, metronidazole, amino acid and multi-vitamin supplement. Prednisolone was administered at tapering dosage in schedule occasions till the animal becomes stable. Feeding of low fat feed along with high protein diet for about 60 days has lead to a remarkable response in gaining body weight.
The Impact of Aging and Ovariectomy on Cardiac Contractile Function in Isolated Ventricular Myocytes

Fares E, Howlett SE. Impact of ovariectomy on cardiac contractile function in aged murine ventricular myocytes. J Mol Cell Cardiol, 2010. Fares E, Pyle WG, Chen RP, Howlett SE. Long-term ovariectomy modifies intracellular calcium homeostasis in cardiomyocytes from aging female mice. J Mol Cell Cardiol, 2011. Fares E, Parks RJ, MacDonald JK, Egar JM, Howlett SE. Ovariectomy increases the size of calcium sparks and enhances SR calcium release in ventricular myocytes from sexually-mature female mice. J Mol Cell Cardiol, 2011. Parks RJ, Fares E, MacDonald JK, Ernst MC, Sinal CJ, Rockwood KJ, Howlett SE. Deficit accumulation in aging mice: Frailty in an animal model of aging. Can J Ger, 2011. Fares E, Howlett SE. Contractile function declines in cardiomyocytes from male, but not female mice in extreme old age. J Mol Cell Cardiol, 2012.
ROSE: a deep learning based framework for predicting ribosome stalling

We present a deep learning based framework, called ROSE, to accurately predict ribosome stalling events in translation elongation from coding sequences based on high-throughput ribosome profiling data. Our validation results demonstrate the superior performance of ROSE over conventional prediction models. ROSE provides an effective index to estimate the likelihood of translational pausing at codon resolution and understand diverse putative regulatory factors of ribosome stalling. Also, the ribosome stalling landscape computed by ROSE can recover the functional interplay between ribosome stalling and cotranslational events in protein biogenesis, including protein targeting by the signal recognition particle (SRP) and protein secondary structure formation.
Comparative transcriptomics of albino and warningly‐coloured caterpillars

Colouration is perhaps one of the most prominent adaptations for survival and reproduction of most taxa. Colouration is of particular importance for aposematic species, which rely on their colouring and patterning to act as a warning signal against predators. Most research has focused on the evolution of warning colouration by natural selection. However, little information is available for colour mutants of aposematic species, particularly at the genomic level. Here I compare the transcriptomes of albino mutant caterpillars of the wood tiger moth (Arctia plantaginis) to those of their full-sibs having their distinctive orange-black warning colouration. The results showed >300 differentially expressed genes transcriptome-wide. Genes involved in the immune system, structural constituents of cuticle, and peptidase activity were mostly down-regulated in the albino larvae. Surprisingly, higher expression was observed in core melanin genes from albino larvae, suggesting that melanin synthesis may be disrupted in terminal ends of the pathway during its final conversion. I further identified 25 novel genes uniquely expressed in the albino larvae. Functional annotation showed that these genes are involved in nucleotide biosynthesis, copper ion transmembrane transport, and nucleic acid binding. Taken together, these results suggest that caterpillar albinism may not be due to a depletion of melanin precursor genes. In contrast, the albino condition may result from the combination of faulty melanin conversion late in its synthesis and structural deficiencies in the cuticle preventing its deposition.
The diazotrophic community in oat rhizosphere: effects of legume intercropping and crop growth stage

In this study, the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil in three cropping systems and at two oat growth stages were investigated using real-time PCR and Illumina MiSeq sequencing. The nifH gene abundance in oat-soybean intercropping (OSO) and oat-mungbean intercropping (OMO) was significantly greater than that in sole oat (O), but the nifH gene abundance significantly decreased at the later stage in all the treatments. Alpha diversity indices in OSO and OMO were higher at the heading stage, but lower at the maturity stage than that in O. Bradyrhizobium and Skermanella were the dominant genera identified in all samples, with an average proportion of 35.8% and 12.4%, respectively. The proportion of dominant genera showed significant differences and varied with cropping system and growth stage. Principal component analysis showed that growth stage had a stronger effect than intercropping on the diazotrophic community structure. However, Mantel test and redundancy analysis showed there was no environmental factor significantly correlated to the diazotrophic community structure. Our results demonstrate that intercropping had a weaker effect than growth stage on the abundance, diversity and structure of the diazotrophic community in oat rhizosphere soil.
Effect of Confidence Interval Construction on Judgment Accuracy

Three experiments (N = 550) examined the effect of an interval construction elicitation method used in several expert elicitation studies on judgment accuracy. Participants made judgments about topics that were either searchable or unsearchable online using one of two order variations of the interval construction procedure. One group of participants provided their best judgment (one step) prior to constructing an interval (i.e., lower bound, upper bound, and a confidence rating that the correct value fell in the range provided), whereas another group of participants provided their best judgment last, after the three-step confidence interval was constructed. Theoverall effect of this elicitation method was not significant in 8 out of 9 univariate tests. Moreover, the calibration of confidence intervals also was not affected by elicitation order. The findings warrant skepticism regarding the benefit of prior confidence interval construction forimproving judgment accuracy.
Cellular localisation and function of neuronal SK potassium channels.

In the central nervous system, small conductance calcium-activated potassium channels (SK) are important for the generation of the afterhyperpolarisation that follows single or trains of action potentials. Three SK channels have been cloned (SKI, SK2 and SK3), which are selectively blocked by the venom toxin apamin and present distinct pharmacological properties. The principal aim of this work is to investigate the subcellular distribution of SK2 and SK3 channels in neurones. For this purpose, antibodies directed against specific regions of SK2 and SK3 subunits were raised, purified and characterised. Immunohistochemistry on rat brain sections showed that the SK2 protein is localised in somatic and dendritic structures in various brain regions. SK3 immunoreactivity is mainly associated with fibers, but also with neuronal somata and dendrites. Intense SK3 expression was detected in the substantia nigra pars compacta, the locus coeruleus and the dorsal raphe. In these brain regions, the distribution of the channel was analysed in relation to monoamine- containing neurones, at two different developmental stages. In this work, I also report the characterization of a new SK2 variant, SK2-860, which differs from the SK2 subunit by having an extended amino terminus. Heterologous expression of this variant in primary neurones indicates that the majority of the protein is located in clusters distributed throughout the cytoplasm. Western blot analysis with the SK2 antibody and with a specific antibody for the new variant showed that SK2-860 subunit is expressed in the rat central nervous system. The distribution pattern of the SK2-860 in the rat brain largely overlaps the one observed for SK2. Finally, in the last part of this work, the molecular determinants responsible for the difference in apamin sensitivity among the different members of the SK channel family were investigated. The study showed that the extracellular loop that connects transmembrane segments S3 and S4 of SK channel a subunits significantly contributes to apamin sensitivity of SK2 channels.
Convergence dans l'évolution de la spécialisation d'hôte chez des tiques : modèle tiques-oiseaux de mer à distribution mondiale

Les interactions intimes et repetees entre hotes et parasites peuvent engendrer la specialisation d’un parasite a son hote, grâce a des adaptations comportementales, morphologiques et/ou genetiques, combinees avec un flux de genes limite. C’est un processus clef car il participe a l’evolution de la biodiversite parasitaire et peut ainsi permettre de mieux comprendre l’emergence d’organismes pathogenes. Encore peu etudie, une specialisation d’hotes a neanmoins ete demontre lors de precedentes etudes chez deux especes de tiques nidicoles : chez Ixodes uriae une tique dure, parasite des oiseaux marins coloniaux en zone arctique, et dans un complexe de tiques molles Ornithodoros capensis sensu lato, parasitant aussi de nombreuses especes d’oiseaux marins, mais cette fois-ci en zones temperees et tropicales. Ces deux especes sont vectrices d’une grande diversite d’agents pathogenes incluant des virus, des bacteries et des protozoaires. Cependant, les facteurs impliques dans le phenomene de specialisation d’hote restent inconnus. Dans ce cadre, le but de ma these etait donc de determiner 1) si l’evolution des divergences en fonction des hotes est toujours accompagnee par les memes changements phenotypiques et 2) si ces changements pourraient permettre d’identifier les facteurs de selection sous-jacents. Dans ce contexte, des campagnes d’echantillonnage de tiques ont ete menees durant la periode de reproduction des hotes oiseaux dans les differentes zones de leur repartition et nous avons realise des analyses morphometriques, basees sur l’utilisation de landmarks et de contours sur chaque individu tique et des analyses phylogenetiques et genetiques des populations sur les memes individus. L’ensemble de ces resultats suggere la presence de convergences morphologiques au sein de ces systemes et souligne un role de la selection dans ce processus de divergence. En effet, les caracteristiques ecologiques des hotes mais aussi le micro-habitat exercent des pressions selectives importantes dans ces deux systemes pouvant etre a l’origine de la divergence observee entre les populations. De plus, les caracteristiques biologiques de chaque espece de tiques, telle que la capacite de dispersion, entrent egalement en jeu et peuvent fortement modifier l’epidemiologie des agents infectieux dont elles sont vectrices.Mots cles : Argasidae, ecologie de la transmission, evolution convergente, interactions hote-parasite, Ixodidae, oiseaux marins.
Comparison of Different Media for Germ Tube Production by Candida albicans: A Retrospective Study

The incidence and prevalence of invasive fungal infections have increased in the last decade, especially due to large population of immunocompromised patients and/or those hospitalized with serious underlying diseases. Indeed, Candida spp. are the fourth most common cause of hospital-acquired systemic infections in India with crude mortality rates of up to 30%. In healthy individuals this colonization generally remains benign. C. albicans can cause two major types of infections in human’s superficial infections, such as oral or vaginal candidiasis, and lifethreatening systemic infections. Indeed, HIV is a major risk factor for developing oral candidiasis (Ruhnke, 2006). Systemic candidiasis is associated with a high crude mortality rate, even with first line antifungal therapy. Both neutropenia and damage of the gastrointestinal mucosa are risk factors for the development of systemic (disseminated) candidiasis. Further risk factors include central venous catheters, which allow direct access of the fungus to the bloodstream, the application of broad-spectrum antibacterials, which enable fungal overgrowth, and trauma or gastrointestinal surgery, which disrupts mucosal barriers (Sachin et al., 2012).
Evaluation of the impact of azo dyes on the metabolism of stabilized fecal communities and in vitro cell culture

EVALUATION OF THE IMPACT OF AZO DYES ON THE METABOLISM OF STABILIZED FECAL COMMUNITIES AND IN VITRO CELL CULTURE Ives Ivusic Polic Advisor: University of Guelph Dr. Gisèle LaPointe The human gut microbiota is a complex and dynamic ecosystem of microbes existing in symbiosis with the host and can be altered by diet. Azo dyes are present in a large portion of our diet. To investigate the impact of azo dyes on gut microbial metabolites, a stabilized fecal slurry was subjected to Tartrazine exposure and metabolites were analyzed via 1-dimensional proton nuclear magnetic resonance. Results revealed that Tartrazine had a negative effect on 10 out of 13 profiled metabolites. Tartrazine had a negative impact on the transepithelial resistance of in vitro cultured Caco2 epithelial cells and increased the secretion of TNFα. Data from Guelph Health Family Studies suggested that children up to 6 years of age tend to consume 1.2 meals daily containing azo dye. This study suggests that dyes present in food interact with gut microbiota; the resulting metabolites may cause inflammation, leading to effects on human health.
The Effect of Juvenile Abalone Haliotis midae (Linnaeus, 1758) Weaning Diet on Gut-Bacterial Formation

ABSTRACT Previous research has shown that gut-bacterial populations in farmed abalone are shaped by ontogeny, their macroalgal diet substrates, bacteria present in the environment, and other environmental factors. It has been suggested that weaning postsettlement diatom-fed abalone onto artificial feed may alter the natural succession of bacterial establishment in their guts. The gut-bacterial composition of Haliotis midae (5–9 mm) weaned onto either a commercial formulated feed (Abfeed-S34), fresh kelp (Ecklonia maxima), or a commercial formulated feed containing kelp (E. maxima) (Abfeed-S34K) was compared. The gut microbiota of postsettlement diatom-fed abalone was dominated by Planctomycetes. Weaning to kelp or formulated feed resulted in a significant difference in the gut-bacterial communities, with the Firmicutes becoming dominant in the kelp-fed treatment and the Proteobacteria dominating in the two formulated feed treatments (analysis of similarities: R = 0.77, P = 0.02). The gut microbiota of kelp-fed abalone displayed a relatively low diversity compared with that of abalone fed formulated feeds and was dominated by fermentative Clostridia bacteria. There was no difference in gut-bacterial communities of the abalone fed commercial formulated feed with or without kelp inclusion. The dominance of the Clostridia in the kelp-fed abalone guts is explained by the large volume of fermentable polysaccharides present in macroalgae, whereas the energy-rich formulated feeds appeared to reduce the selectivity of the gut environment resulting in a relatively higher bacterial diversity.
Enhancing composition and persistence of mixed pasture swards in southern New South Wales through alternative spatial configurations and improved legume performance

Abstract. This study examined whether the productivity and persistence of mixed pastures that included subterranean clover (Trifolium subterraneum L.), lucerne (Medicago sativa L.), and/or phalaris (Phalaris aquatica L.) were improved if species were spatially separated rather than being sown together in each drill row. The study also compared the productivity and persistence of subterranean clover with alternative annual legume species biserrula (Biserrula pelecinus L.) and strand medic (Medicago littoralis Rhode ex Loisel). Twelve pasture treatments were sown in replicated field experiments at five locations across the medium-rainfall region of south-western New South Wales in 2012 and monitored for 3 years. Pastures that included lucerne, phalaris and subterranean clover were generally more productive than pastures with only one or two of those species, regardless of sowing configuration. Averaged across sites, subterranean clover regeneration in year 3 was 29% higher and total cumulative biomass 13% higher where subterranean clover was sown in a 1 : 1 configuration with lucerne than where the species were mixed together in every drill row. There were fewer consistent benefits of alternative spatial configurations on swards containing phalaris with subterranean clover or with lucerne. Results of the present study appeared to be highly site-specific, or season-dependent, and therefore alternative spatial configurations cannot be recommended as a universal strategy at this time. More research is required to understand the factors driving the responses to alternative spatial configurations observed in the present study. Neither biserrula nor strand medic was superior to subterranean clover in a 3-year pasture phase with lucerne, despite abundant rhizobia compatible with all species at all sites. The density of subterranean clover in year 3 was 29% and 41% higher than of biserrula and strand medic, respectively. A narrow choice of adapted cultivars as well as excessive levels of hard seed for the legumes used in phased pastures with lucerne are suggested as contributing to the inferior performance of the alternative legumes species tested in the study.
Breaking a Disjunct Distribution: A Review of the Southern Hemisphere Genera Cylorygmus and Relictorygmus gen. nov. (Hydrophilidae: Cylominae)

Abstract. The southern hemisphere water scavenger beetle genus Cylorygmus Orchymont, 1933 (Coleoptera: Hydrophilidae: Cylominae) is revised. Three species are recognized, one in Chile and two in South Africa. The morphological differences indicate that the African species are not congeneric with the Chilean one. Relictorygmus gen. nov. is established for the African R. trevornoahi sp. nov. (type species) and R. repentinus (Hebauer, 2002), both known from few localities in the Western Cape province of the Republic of South Africa. The genus Cylorygmus with the only species C. lineatopunctatus Orchymont, 1933 is endemic to a small region in central Chile. Its larva is described in detail based on specimens collected in association with adults. Both genera and all species are diagnosed, described and illustrated, and an identification key for adults is provided. Our study demonstrates that the trans-Atlantic disjunct distribution of Cylorygmus was based on inaccurate taxonomic treatment and did not reflect the real evolutionary history of these beetles.
It’s not all about the creeks: protection of multiple habitats will improve biodiversity conservation in a eucalypt forest

Abstract. Understanding patterns in the distribution and abundance of wildlife across the landscape can aid in identifying the relative importance of habitats for biodiversity conservation. We aimed to identify whether riparian habitats were more important than other areas in the landscape to small terrestrial vertebrates. The study site was surveyed using 450 pit traps distributed across riparian, midslope and ridge top habitat. Riparian sites had the greatest abundance of small vertebrates of the three habitats. During some months of the year, there was a significant difference in the composition of the faunal assemblage between habitats. Unsurprisingly, riparian habitats were particularly important for frog species and it was these species that accounted for the greater abundance in this habitat. Riparian habitat was less important for other taxonomic groups and the more floristically rich midslope and ridge habitats, which had a greater abundance of leaf litter, fallen logs and rock cover, were favoured by mammal and reptile species. The conservation of riparian sites, without the protection of other habitats, overlooks a substantial proportion of the biodiversity in the landscape. This study may help inform management decisions in the Upper Warren region and other similar forested landscapes, regarding the location and timing of fauna monitoring and the frequency of fuel reduction burns.