Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Human Gut Microbiota Metabolite Profile in Autism Spectrum Disorder

CHARACTERIZATION OF THE HUMAN GUT MICROBIOTA METABOLITE PROFILE IN AUTISM SPECTRUM DISORDER Erin Elizabeth Bolte University of Guelph, 2015 Advisor: Dr. Emma Allen-Vercoe The human gut microbiota is an ecosystem of microbes existing in symbiosis with the human host. If the microbiota is disrupted, dysbiosis (imbalance) of the component microbes could contribute to the etiology of some diseases. One ailment connected to gut dysbiosis is Autism Spectrum Disorder (ASD). A subgroup of ASD individuals suffers from gut abnormalities, dysbiosis, and abnormal levels of gut-microbial metabolites. To investigate the connection between these factors, fecal samples from ASD participants and neurotypical controls were analyzed via proton nuclear magnetic resonance, revealing a subgroup of ASD samples with abnormal levels of many metabolites. Fecal water samples from this subgroup of ASD participants also induced increased interleukin-8 secretion from human colonocytes (Caco-2 cells) in vitro. The data suggest that the interaction between the gut microbiota and the human host is pivotal in understanding the underlying mechanism behind the functioning of the gut microbiota and host symptomology in ASD.
Evaluation of new non-scented CMS lines and their maintainer lines of rice (Oryza sativa L.) for their agronomical and floral traits.

Eighteen CMS lines and their isogonic maintainers were evaluated for agronomical traits viz., days to 50% flowering, plant height (cm), number of panicles per plant, number of spikelets per panicle, spikelet fertility (%),panicle exertion (%),scent and floral traits viz., pollen fertility (%), stigma length (mm), style length (mm), angle between stigma lobes (q), anther length (mm), anther breadth (mm), filament length (mm) and out crossing rate of CMS lines (%) with standard check cms line IR 58025A. Generally A lines took more number of days to 50 per cent flowering than the corresponding B lines. All the CMS lines were shorter than their corresponding maintainers. Number of panicles were more in B line than in A lines. More number of spikelets per panicle was observed in KCMS 17A, KCMS 16A and KCMS 21A. Maximum out crossing rate was noticed in KCMS 11A, KCMS 16A, CRMS 31A and KCMS 12A. Most of the CMS lines showed 100 per cent pollen sterility and less than 3.4 per cent spikelet fertility. All the CMS lines were non-scented in nature. Genotype KCMS 11A and IR 68888A were promising for panicle exsertion, the CMS lines IR 70369A, CRMS 32A, KCMS 17A, KCMS 12A, KCMS 22A and KCMS 25A had long stigma. The style length of RTN 10A and CRMS 32A were high, while KCMS 25A and CRMS 32A exhibited greater angle between stigma lobes. The maintainer lines KCMS 10B, IR 70369, RTN 10B, IR 68888B excelled in anther length, anther breadth and filament length. Two CMS lines viz., KCMS 11A, KCMS 16A and CRMS 31A were identified as promising ones as they showed high out crossing rate, low pollen fertility and low spikelet fertility and are suitable for hybrids development.
Effects of dietary betaine supplementation on back fat thickness and serum IGF-1 in late finishing pigs

This study was performed in finishing pigs to investigate the effects of betaine HCl on carcass fat deposition and lipid metabolism in relation to growth hormone (GH) and insulin-like growth factor 1 (IGF-1) alterations. Sixty cross-bred finishing pigs (30 gilts and 30 barrows) with an average initial body weight of 74.0±1.8 kg were randomly allocated into two groups, each with six replicate pens. Each group was fed either 0% or 0.125% betaine HCl supplementation for 41 days. Results showed that the betaine HCl supplementation had no effect on growth performance (P>0.05). In the betaine-supplemented group, Lenden-speck-quotient index, average back fat thickness, serum triglycerides concentrations and fatty acid synthase (FAS) activities were lower than those in the untreated control group (P 0.05), but serum IGF-1 concentrations were higher in the betaine group (P<0.01). In conclusion, betaine reduced lipogenesis by reducing the FAS activity and increased serum IGF-1, leading to improvement in carcass characteristics.
Processing Methods of Soybean Meal 2. Effect of Autoclaving and Quebracho Tannin Treated-Soybean Meal on Gas Production and Rumen Fermentation in vitro

The present study was conducted to evaluate the effect of soybean meal (SBM) treated by heating (autoclaving) o r quebracho tannins (condensed tannins, Q T) a t t hree levels (1 , 2 or 3 % of D M) in comparison with gelatin as a low degradable protein source on gas production, rumen fermentation, energy content and organic matter digestibility (OMD) in vitro. A gas production technique was performed using rumen fluid collected from fistulated sheep. Cumulative gas production was recorded at 3, 6, 9, 12, 24, 48 and 7 2 h of incubation. Kinetics of gas production was fitted t o a n exponential model described a s y = a 3 + b (1-exp ). Ammonia-N (NH -N) and volatile fatty acids (VFA) concentrations were determined at 0, 1, -ct 3 and 6 h of incubation. The results showed t QT and aut oclaving SBM reduced t he asymptote of gas production. The soluble fraction (a) was significantly (P<0.05) decreased when SBM was treated by autoclaving o r Q T at three levels (1, 2 or 3% of DM). The gas production from t he insoluble fraction (b) was significantly (P<0.05) decreased when SBM was treated by autoclaving or QT. The value of (b) for gelatin on average was significantly (P<0.05) low when compared with untreated or treated SBM by heating (autoclaving) o r w ith QT at t he three levels. However, the gas production rate constant f or th e insoluble fraction (c) was lowered by the QT, indicating the possibility of reduced microbial cellulolysis. The 3 concentrations of NH -N and VFA were decreased (P<0.05) when SBM treated with heating (autoclaving) or Q T. The O rganic m atter dig estibility, metabolizable energy , net energy and microbial protein were decreased by both t reatments. The present study concluded that the treatment of SBM decreased the gas production and hence, decreased the gas production from soluble, insoluble fractions of SBM. These results suggest to s pray 1% quebracho t annins on SBM or feeding with t anninferous plant species that protect protein from degradation in the rumen due to the presence o f small amounts o f QT in the plant species. Key word: Soybean meal, autoclaving, co ndensed tannins, ga s p roduction, ru men fermentation, in vitro
Advancing molecular crustacean chronobiology through the characterisation of the circadian clock in two malacostracan species, Euphausia superba and Parhyale hawaiensis

The ability to entrain to environmental cycles and therefore anticipate and prepare for the changes they predictably bring is the preserve of the endogenous biological clock, most widely studied at the circadian level. Despite a rich history of research into the behavioural and physiological rhythms shown by many crustacean species, the underlying molecular system driving such traits is not well understood. The aim of this research was to develop our understanding of crustacean clocks through the study of two species, one of major ecological importance and the other a powerful model organism. The Antarctic krill Euphausia superba is a keystone species in the Southern Ocean ecosystem, and evidence suggests that the clock may influence both daily and seasonal rhythms. Using a variety of approaches, including the creation of a de novo assembled head transcriptome, a full suite of clock-related genes have now been cloned and characterised. Unlike many species Euphausia superba possesses orthologs of every canonical core clock gene, and cell culture assays indicate that the central feedback loop has the capacity for complete transcriptional inhibition via two separate pathways, raising the possibility that the krill clock may be an ancestral type or employ multiple oscillators to control rhythms of differing periods. In contrast to the relatively intractable krill, the amphipod Parhyale hawaiensis has simple maintenance requirements and an extensive genetic toolkit with the potential to enable sophisticated dissection of the molecular clock. With the aim of laying the groundwork for future research the clock genes of this species have also been identified, along with the development of a locomotor activity assay. Parhyale hawaiensis shows evidence of bimodal patterns of activity under the control of a molecular clock that combines mammalian-like characteristics with some unique features worthy of further investigation.
Free amino acid content in muscle tissue of bighead carp and wels catfish

wels the The present research was aimed at a comparative analysis of free amino acid (FAA) levels in the muscle tissue of herbivorous and predatory fish. The FAA concentration in the muscle tissue samples from bighead carp and wels catfish was determined by ion-exchange chromatography. The bighead carp muscle tissue, as compared to that of wels catfish, showed significantly higher concentrations of arginine, histidine, methionine, phenyloalanine, alanine, asparagine, serine, glycine, and taurine, but significantly lower levels of isoleucine, leucine, threonine, valine, glutamine, cystationine, β-alanine, ethanoloamine, as well as aspartic, glutamic, cysteic, α- and γ-aminobutyric acids. The muscle tissues of bighead carp and wels catfish did not differ significantly in the levels of cystine, lysine, tryptophan, tyrosine, α-aminoadipic acid, cytrulline, ornithine and 1-methyl-histidine. Proline was detected only in the wels catfish muscle. The results obtained have shown differences in free amino acid concentration in muscle tissue of examined fish. A differentiated natural diet induces changes in free amino acid content in fish tissues. Knowledge of levels of free amino acids which are precursors for biogenic amines facilitates setting the safety criteria for fish and fishery products from species other than those mentioned in the Commission Regulation No 2073/2005.
Stripes, jewels and spines: further investigations into the evolution of defensive strategies in a chemically defended gecko radiation (Strophurus, Diplodactylidae)

The geckos in the genus Strophurus (Diplodactylidae) are one of only two squamate lineages with specialized caudal defensive glands. Many species in this genus also have distinctive caudal ornamentation combined with bright and/or contrasting colour pattern elements on the iris, tail and especially the lining of the mouth that are hypothesized to be adaptations for specialized (e.g. deimatic) defensive functions. We present the first multilocus, phylogenetic analysis of the biogeography and evolution of all recognized taxa of Strophurus. Contrary to previous phenotypic and ecological assessments, our phylogenetic analyses delineate four divergent lineages. Three lineages are relatively small (snout‐vent length [SVL] 40–60 mm), species‐poor (<5 recognized taxa), cryptically coloured (either striped or spotted) and lack precloacal pores (a secondary sexual trait) and putative deimatic elements. In contrast, the remaining lineage is comparatively species rich (at least 14 taxa), attains a larger body size (SVL 60–90 mm), possesses precloacal pores and shows extensive variation in caudal ornamentation and often bright and/or contrasting eye, tail and mouth colouration. The three less diverse lineages have smaller distributions and tend to be associated with spinifex (e.g. Triodia) hummock grasses or rocks, whereas the fourth lineage is much more widespread (including multiple biomes) and consistently reported to utilize more exposed diurnal microhabitats on shrubs and trees. Biogeographical analyses also indicate that – in contrast to many other Australian radiations – the arid biome is the ancestral area of occupation for Strophurus, with multiple inferred shifts into surrounding sclerophyll and monsoon biomes. This study emphasizes that – independent of caudal defensive glands – it appears to be a shift in microhabitat use that correlates with the accumulation of bright and contrasting colouration elements, secondary sexual characters and the widest geographic distribution.
STUDY THE POSSIBILITY OF SYMBIOTIC ICE CREAM PRODUCTION USING SUGAR BEET FIBER AND BIFIDOBACTERIUM BIFIDUM BB-12

Sugar Beet waste is obtained from sugar industry and usually is used for animal feeding. However it is a rich source of dietary fibers that, in addition to its abundance, is cheap. In this study, the effect of adding fiber obtained from beet waste at levels of 0, 0.7, 1.5 and 2% on the rheological, physicochemical features and the viability of Bifidobacterium bifidum BB-12 in ice cream during 60 days at -18°C was investigated. All the mixes showed pseudo plastic flow behavior and the apparent viscosity decreased with increasing shear rate. Increasing the amount of sugar beet fiber led to increasing consistency coefficient and apparent viscosity values while decreasing flow behavior index of ice cream mixes. Ice cream melting resistance improved by increasing the amount of sugar beet fiber . Increasing fiber content in ice cream had no significant effect on the viability of Bifidobacterium bifidum BB-12 cells obtained from the freezing process, but at the end of the storage period, the number of live organisms in samples containing higher amount of sugar beet fiber was more. Sensory evaluation of the samples also revealed that the application of sugar beet fiber up to 0.7% in ice cream is acceptable.
Phenotyping approaches to evaluate nitrogen-use efficiency related traits of diverse wheat varieties under field conditions*

Abstract. Nitrogen (N) is a key mineral element required for crop growth, yield and quality. Nitrogen-use efficiency (NUE) in crop plants is low despite significant research efforts. Excessive use of N fertiliser results in significant economic cost and contributes to environmental pollution. Therefore, it is crucial to develop crop varieties with improved NUE, and this requires efficient phenotyping approaches to screen genotypes under defined N conditions. To address this, 15 wheat (Triticum aestivum L.) varieties, grown under three N levels, were phenotyped for NUE-related traits under field conditions. Significant genotypic differences were observed in varieties having low to high responsiveness to N applications. The results suggest that basal low N can be used to screen wheat varieties that are less responsive to N, whereas N supply from 80 to 160 kg N ha–1 could be used to screen high N-responsive varieties. Normalised difference vegetation index (NDVI) measured by using Crop Circle, and SPAD units measured by SPAD meter at heading stage, were well correlated with shoot dry biomass, grain yield, and shoot and grain N concentration, and could potentially be used as tools to phenotype different wheat varieties under varying N treatments. The data also demonstrated that NDVI and SPAD could be used to differentiate wheat varieties phenotypically for NUE-related traits. The prospect of utilising efficient, non-destructive phenotyping to study NUE in crops is also discussed.
Yield and weight distribution of two potato cultivars grown from seed potatoes of different physiological ages

ABSTRACT After seed potatoes (Solanum tuberosum L.) are harvested, they may be stored in sheds, in low temperature coolers or left un-lifted in the ground. This research describes the response of tuber yield and distribution (formed by the weight grade of each potato) of ‘Bondi’ and ‘Fraser’ crops planted from seed potatoes at different physiological ages generated from different combinations of these storage regimes applied in the Early and Late phases of storage. De-sprouting half of the potatoes prior to planting was used to accelerate the rate of physiological ageing, synchronise the planting material and increase the range of treatments. Total yield and number of potatoes produced were unaffected by any of the storage treatments and reflected a constant pattern of canopy development, radiation use efficiency and harvest index. The largest tubers were attained by higher rates of tuber growth which was inversely related to the number of stems per plant.
Comparative action of hurain and trypsin on native and denatured proteins.

Hurain, the proteolytic enzyme of the sap of the jabillo tree (Hura crePitans), has been reported to be activated by Fe++ and inhibited by Ni++, Zn++, Cd++1 and Clions2; its activity is also diminished in the presence of trypsin inhibitors from soy bean, black bean, Ascaris lumbricoides3 and egg white4• A comparison between the activity of trypsin and hurain on synthetic substrates has been published5• In the present paper, some experiments on the action of these enzymes on native and urea denatured proteins are reported.
FIRST REPORT OF ASPERGILLUS MINISCLEROTIGENES AS A POSTHARVEST PATHOGEN OF SOYBEAN SEEDS FROM PAKISTAN

In August 2014, seeds of Glycine max in storage rooms at Lahore, Pakistan, were found to be colonized by an unknown fungus. For pathogen isolation, seeds were incubated on moist blotters, developing a green mass of fungal spores. Spores were transferred to Czapek Dox agar medium and incubated at 25±2°C. After 7 days of incubation colonies were velvety, green and floccose, consisting of white vegetative mycelium and acquired the diameter of 3-4 cm. Globose dark brown sclerotia were produced, smaller than A. flavus. Radiate conidial heads were observed that were mostly biseriate however uniseriate heads were also present. Conidiophores were hyaline, coarsely roughened and 0.9-1.2 mm in length. Vesicles were subglobose to globose, 25-40 μm in diameter, while metulae were 8-12 μm and phialides 5-8 μm long. Conidia were pale or olive green, 3.5-5 μm in diameter. Pathogen was identified as Aspergillus minisclerotigenes (FCBP1353) (Pildain et al., 2008) and differentiated from A. flavus and A. parvisclerotigenus by studying aflatoxin profiles (B1, B2, G1, and G2) using thin-layer chromatography. Amplification of DNA fragment of 650 bp was done using the universal primers ITS1/ITS4 (Batista et al., 2008) and total genomic DNA as a template (White et al., 1990). BLAST analysis of this strain (GenBank accession No. KJ564033) showed 99% similarity to different strains (JX292091, JF412776, KF841549, JF412775). Phylogenetic analysis of identified pathogen and closely related species of A. flavus group by the Maximum Likelihood Hood tree method and profiling of DNA bands examined in the members of Aspergillus section Flavi amplified by three different Inter Simple Sequence Repeat (ISSR) primers clearly confirmed the pathogen identity. Surface sterilized healthy seeds were soaked in spore suspension (104 spores ml-1) from a one week old pathogen culture for 30 s, dried and transferred onto moist blotting paper in Petri plates. Control seeds were treated with sterilized distilled water. After 7 days incubation at 25°C, 90% of seeds were colonized and re-isolation of the same pathogen confirmed the Koch's postulates. To our knowledge, this is the first report of A. minisclerotigenes seed rot from Pakistan.
Influence of pH, Temperature, and Biofungicides on Clubroot of Canola

INFLUENCE OF pH, TEMPERATURE, AND BIOFUNGICIDES ON CLUBROOT OF CANOLA Hema Kasinathan Advisors: University of Guelph, 2012 Dr. Mary Ruth McDonald Dr. Bruce D. Gossen Management of clubroot caused by the soil-borne biotrophic plant protist Plasmodiophora brassicae on canola and other Brassica crops is an important challenge to producers. Studies on the interaction of pH and temperature on root hair infection (RHI) and clubroot symptom development in canola roots revealed that high levels of clubroot can occur under optimum temperature, moisture and spore load, even at alkaline pH of 7.5. Clubroot was suppressed at all temperatures at pH 8.0, but not totally eliminated. The occurrence of maximum levels of root hair infection and clubroot development (RHI = 61%, Clubroot incidence (CI) & Disease severity index (DSI) = 100%) at temperatures of 20° and 25°C and pH of 5.0 to 6.5 was confirmed. The efficacy of biofungicides against P. brassicae was influenced by pathogen load, host, growth media and its properties. Drench application of Serenade and Prestop were moderately effective in reducing clubroot levels in canola (Brassica napus L. and B. rapa L.) and to a lesser extent in Shanghai pak choy (B. rapa L. ssp. Chinensis (Rupr.) var. communis Tsen and Lee). The mean clubroot incidence and severity caused by Pathotype 3 was found to be slightly higher than that of Pathotype 6. Clubroot level increased with increase in soil bulk density.
Novel Polyaromatic Hydrocarbon (PAH) degraders from oil contaminated soil samples

Manuscript History: Background: Polycyclic aromatic hydrocarbons (PAHs) are generally a hazardous class of organic compounds. They may be produced as a result of combustion or pyrolysis of fossil fuels or other organic matter. Microbial degradation is majorly responsible for ecological recovery of PAHs from sites contaminated with it. The present study was conducted to isolate microbial strains capable of degrading naphthalene with the aid of biosurfactant production. Methods: Oil contaminated soil samples collected from Oil and Natural Gas Corporation (ONGC), Karaikal, Tamil Nadu, India were enriched, serially diluted and spread plated in Bushnell Haas (BH) medium with naphthalene as a carbon source. The isolates grown from the enriched samples were further screened for naphthalene degraders and for biosurfactant production by appropriate protocols. Results: A total of 13 naphthalene degrading strains extended among 9 genera namely Morganella, Actionomyces, Pseudomonas, Stenotrophomonas, Bacillus, Corynebacterium, Actinomadura, Serratia and Staphylococcus were isolated from the samples. This is the first report which describes new strains capable of degrading naphthalene. These include species of Actinomadura, Morganella, Stenotrophomonas and Serratia. Morganella morganii subspecies morganii was found to be the best PAH degrader. Strains from the genera Serratia and Stenotrophomonas were identified as the best biosurfactant producers. Conclusion: The isolates obtained were screened for their ability to utilize naphthalene as a sole source of carbon and energy with the aid of biosurfactant production. This confirms high degradative ability and ubiquity associated with these isolates as it concerns biodegradation of both soil and water environments polluted with petroleum and its many products. Further studies in this direction can reveal interesting options in bioremediation of PAH.
Influence of Exogenous ABA on Hordeum vulgare seedling Damage under Cd Stress

Effect of exogenous ABA on Hordeum vulgare seedling damage under Cd stress was studied by present indoor cultivation experiments,including the cellular membrane permeability(CMP),malondialdehyde(MDA) content,superoxide dismutase(SOD) and peroxidase(POD) activities.The results showed that the cellular membrane permeability(CMP) and malondialdehyde(MDA) content of H.vulgare seedling leaves increased significantly,difference between CK was very distinct when the seedlings were under T2 heavy metal Cd stress;superoxide dismutase(SOD) and peroxidase(POD) activities increased first and decreased later,their activities might be lost when the seedlings were under T3 heavy metal Cd stress.At the mean time,after using exogenous abscise acid on the treatment of T2 heavy metal Cd,SOD and POD activities in the leaf of H.vulgare seedling increased,CMP and MDA content decreased significantly.Therefore,use of exogenous abscise could alleviate the injury of H.vulgare seedling under heavy metal stress.