Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermophilic Enterococcus faecium QU 50 enabled open repeated batch fermentation for L-lactic acid production from mixed sugars without carbon catabolite repression

Enterococcus faecium QU 50, a novel thermophilic L-lactic acid (LA) producing strain, was used in this study to ferment sugar mixtures into LA. Under the optimal fermentation conditions (50 °C, pH 6.5), strain QU 50 could ferment both mixed glucose/xylose sugars with relaxed CCR and mixed cellobiose/xylose sugars simultaneously without CCR to produce homo L-LA. The activity of enzymes related to xylose metabolism was also investigated. In the cells grown in a medium containing cellobiose/xylose, the activity of xylose isomerase and xylulose kinase, was 3.22 and 1.91 times higher, respectively, as compared to that of cells grown in a glucose/xylose medium. Strain QU 50 produced 70.8 g L−1 of L-LA with a yield of 1.04 g g−1 and a productivity of 2.95 g L−1 h−1 from simulated energy cane hydrolysate in batch fermentation. Immobilisation of strain QU 50 improved the operational stability of open repeated fermentation (three cycles), resulting in 61.1–64.3 g L−1 of L-LA with a yield of 1.01–1.02 g g−1 and a productivity of 3.22–3.82 g L−1 h−1. Thus, an efficient and cost-effective fermentation system was successfully established for L-LA production from sugar mixtures.
Sleep deprivation and its impact on circadian rhythms and glucose metabolism

Located in the hypothalamic suprachiasmatic nucleus (SCN), the master clock generates rhythms of behavioural and metabolic processes in mammals. For example, daily rhythms of sleep-wake, fasting-feeding, plasma glucose concentration, glucose tolerance and insulin sensitivity are regulated by the SCN clock. Light is the primary synchronizer of SCN pacemaker though many light-independent factors such as behavioural arousal and metabolic cues also have phase and period resetting properties. The aim of thesis was to study different aspects of the interactions between behavioural arousal, circadian rhythms and glucose metabolism. In the first part, we extended the study of brain control of glucose metabolism by investigating the central action of gastrin-releasing peptide (GRP), a neuropeptide synthesized in the SCN, on glucose metabolism. Our result indicates that central GRP induces long-lasting hyperglycemia. We also showed that acute sleep deprivation leads to impaired glucose tolerance. In the second part, we demonstrated that behavioural arousal induced by sleep deprivation or caffeine treatment enhances photic-entrainment of the SCN clock in the diurnal Sudanian grass rat, Arvicanthis ansorgei. These circadian responses in a diurnal species are opposite to the earlier findings in nocturnal rodents and may have biomedical applications.
Effects of β-Hydroxy-β-Methylbutyrate Supplementation on IL-4, IL-10 and TGF-β1 during Resistance Exercise in Athletes

A The aim of this study was to investigate the effect of β-Hydroxy-β-methylbutyrate (HMB) supplementation on anti-inflammatory cytokines including IL-4, IL-10 and TGF-β during an acute bout of resistance exercise (RE) in young resistance trained men. Ten resistance-trained men in a randomized, double-blind, placebo-controlled and crossover study, were administered a 7-day HMB supplementation (3×1 g.d-1 of HMB) and placebo (3×1 g.d-1 of Maltodextrin) with a 7 days washout period. After supplementation periods, subjects performed three sets of bench press, lat pull down, leg extension, leg curl, biceps curl, triceps curl and shoulder press to failure with 85% of one repetition to maximum (1RM). Blood samples were obtained before(Pre), immediately post(IP) and 1 hour-post RE (1h P) to assess serum concentrations of IL-4, IL-10 and TGF-β1. The data were analyzed using 2 (treatment: HMB and PL) × 3 (time points: Pre, IP and 1hP) repeated measures analysis of variance (ANOVA) followed by the Bonferroni post hoc test with a significant level of p<0.05. Serum IL-4 was significantly higher at IP resistance exercise in HMB compared to placebo. Circulating IL-4 and TGF-β1 were significantly raised at IP compared to Pre in both HMB and placebo treatments. No significant differences between treatments were observed for IL-10 and TGF-β1at any time points. In conclusion, HMB supplementation increased the circulating level of IL-4 during RE in resistance-trained men, which may attenuate inflammation and facilitate adaptation to RE.
Trichoderma virens 106 inoculation stimulates defence enzyme activities and enhances phenolic levels in tomato plants leading to lowered Rhizoctonia solani infection

ABSTRACT Interaction of tomato roots with Trichoderma virens TRS106 provided protection against Rhizoctonia solani-induced disease. In tomato, plants inoculated with R. solani disease symptoms were observed on the roots as brown, necrotic lesions. These symptoms were limited on plants treated with TRS106 and inoculated with R. solani. It was shown that TRS106 did not directly inhibit Rhizoctonia growth in in vitro test. The tested Trichoderma isolate stimulated systemic defence responses in tomato plants, by activating defence enzymes including guaiacol peroxidase (GPX), syringaldazine peroxidase (SPX) and phenylalanine ammonia lyase (PAL). Simultaneously, it enhanced accumulation of phenolics and hydrogen peroxide (H2O2) accompanied by decrease in lipid peroxidation in the leaves. HPLC analysis indicated remarkable increases in the concentrations of 22 phenolics in the leaves of Trichoderma-treated tomato, both uninoculated and inoculated with R. solani. Some of the phenolics were present in a free form, the others were accumulated in a bound form as glycosylated conjugates belonging to phenylpropanoids, hydroxybenzoic and cinnamic acid derivatives and flavonoids. Several of the detected phenolics: ferulic and salicylic acids, pyrocatechol and hesperetin were strongly toxic to R. solani in plate tests. The systemic mobilisation of phenolic metabolism might be an element of tomato defence response positively involved in biocontrol of R. solani by TRS106. Based on the results, T. virens TRS106 may have potential to develop a new biofungicide for integrated management of R. solani-induced disease.
Characterizing Migratory Signaling Pathways Of Transplantable Retinal Progenitor Cells And Photoreceptor Precursor Cells Toward Restoration Of Degenerative Retina ' A Systems Biology Approach

units, relative measurements where the expression level of a gene is normalized to its expression in a reference condition/sample, discrete values assigned based on a pre-defined threshold intensity or as vectors in a three-dimensional space where genes and biological conditions are used to form a matrix in the vector space [282]. Gene expression data for all genes under an experimental condition – sample expression profile – or for a gene across different experimental conditions – gene expression profile – is then analyzed to obtain meaningful biological information.
Latitudinal‐diversity gradients can be shaped by biotic processes: new insights from an eco‐evolutionary model

The processes involved in shaping latitudinal-diversity gradients (LDGs) have been a longstanding source of debate and research. Climatic, historical and evolutionary factors have all been shown to contribute to the formation of LDGs. However, metaanalyses have shown that different clades have LDG slopes that may vary in more than one order of magnitude. Such large variation cannot be explained solely by climatic or historical factors (e.g. difference in surface area between temperate and tropical zones) given that all clades within a geographic region are subject to the same conditions. Therefore, biotic processes intrinsic to each taxonomic group could be relevant in explaining rate differences in diversity decline across latitudinal gradients among groups. In this study, we developed a model simulating multiple competing species subjected (or not) to a demographic Allee effect. We simulated the range expansion of these species across an environmental gradient to show how these two overlooked factors (competition and Allee effects) are capable of modulating LDGs. Allee effects resulted in a steeper LDG given a higher probability of local extinction and lower colonization capacity compared to species without Allee effects. Likewise, stronger competition also led to a steeper decline in species diversity compared to scenarios with weaker species antagonistic interactions. This pattern occurred mostly due to the strength of priority effects, wherein scenarios with strong competition, species that dispersed earlier in the landscape were able to secure many patches whereas late-arriving species were progressively precluded from expanding their ranges. Overall, our results suggest that the effect of biotic processes in shaping macroecological patterns could be more important than it is currently appreciated.
The Role of αSAP97 and βSAP97 at the Glutamatergic Synapse

iii Acknowledgements . v Table of contents . vii List of figures. xiii List of tables. xv List of abbreviations . xvii Chapter 1: Introduction . 1 1.1 Overview . 1 1.2 The excitatory glutamatergic synapse . 2 1.3 The presynaptic active zone . 2 1.4 The postsynaptic density . 5 1.4. 1 Shank and Homer provide the core scaffold of the PSD . 6 1.4. 2 The PSD95 MAGUK proteins stabilise the Shank/Homer complex . 8 1.5 Postsynaptic glutamate receptors . 9 1.6 Glutamate receptor incorporation into synapses . 10 1.6. 1 Receptor recycling: endocytosis and exocytosis . 11 1.6. 2 Lateral diffusion of receptors into synapses . 14 1.7 AMPA receptor scaffolding at synapses . 17 1.7. 1 Synaptic scaffolding proteins . 18 1.7. 2 Synaptic gating mechanisms . 21 1.8 N-terminal isoforms of synapse-associated protein-97 . 22 1.8. 1 SAP97 is alternatively spliced . 22 1.8. 2 SAP97 protein structure . 23 1.8. 3 SAP97 expression patterns . 23 1.9 α and βSAP97 isoforms scaffold synaptic and extrasynaptic receptors . 24
Genomic Data from an Endangered Amphibian Reveal Unforeseen Consequences of Fragmentation by Roads

Roads fragment landscapes and can cause the loss of metapopulation dynamics in threatened species, but as relatively new landscape features, few studies have had the statistical power to genetically examine road effects. We used DNA sequence data from thousands of nuclear loci to characterize the population structure of New York-endangered Eastern tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. We uncovered highly genetically structured populations over an extremely small spatial scale (approximately 40 km2) in an increasingly human-modified landscape. Geographic distance and the presence of roads between ponds are both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors are responsible for the observed patterns of genetic variation. Our study demonstrates the value of genomic approaches in molecular ecology, as these patterns did not emerge in an earlier study of the same system using microsatellite loci. Ponds supported small effective population sizes, and pond surface area showed a strong positive correlation with salamander population size. When combined with the high degree of structuring in this heavily modified landscape, our study indicates that these endangered amphibians require management at the individual pond, or pond cluster, level. Particular efforts should be made to preserve large vernal pools, which harbor the greatest genetic diversity, and their surrounding upland habitat. Contiguous upland landscapes between ponds that facilitate natural metapopulation connectivity and demographic rescue from future local extirpations should also be protected.
Eco Friendly Management of Arecanut Root Grub (Leucopholis lepidophora Blanchard) in Hilly Tracts of Uttar Kannada, Karnataka

Amongst the several factors attributed for lower productivity of Arecanut, damage by root grubs is substantially important in Malnad belt of Uttar Kannada district. The root grubs cause damage to the arecanut tree by directly feeding on roots resulting in symptoms like yellowing of leaves, stem tapering at the crown region, reduced inter-node length, nut fall and ultimately leads to reduced vigour, yield and death of plant. To manage this insect, usually insecticides are recommended but farmers of this district are reluctant to use chemical pesticides due to the deleterious effects on soil health, fauna and flora. Indigenous technical knowledge followed by the farmers were documented in 15 villages of three taluks viz., Sirsi, Siddapur and Yellapur and based on scientific validation, an on farm trial was conducted to evaluate the feasibility and economic viability of aqueous extract of soap nut and neem oil 5% mixture and entomopathodenic fungi, Metarrihizium anisopliae 2 X 10 8 conidia/g @ 20 g per palm tree against root grubs in arecanut during 2009–12 at farmers'fields. The results revealed that the recommended practice i.e. drenching with chlorpyrifos 20 EC @ 10 ml/l of water (3-4l of solution per palm tree) recorded highest grub mortality of 86.83 per cent as against 64.88 per cent in aqueous extract of soap nut and neem oil 5% mixture treated palms. Appearance of new healthy green frond and improvement in the growth of the palms are the visual indicators. Neem oil and soap nut extract was the best alternative to chemical insecticides, locally available and is ecofriendly.
A survey for sex determination systems in East African Lake Malawi cichlids

African cichlids are at an early stage in the evolution of sex chromosomes. Their sex chromosomes have not become distinct from the rest of their autosomal chromosomes, and no morphologically distinct sex chromosomes have been identified (Kornfield, 1984). These fishes therefore provide a unique model for understanding the early stages of sex chromosome evolution. It is further speculated that evolution of sex chromosomes may have an effect on cichlid speciation as well. Lake Malawi formed in East African ∼700,000 years ago and contains a diverse flock of endemic cichlid fish (Danley at al., 2001). Within this flock the genus Metriaclima contains ∼70 species. Genotyping of families from seven species of Metriaclima identified a male heterogametic (XX: XY) sex determiner on linkage group 7. The genotypes of three other Metriaclima species identified a female heterogametic (WZ: ZZ) sex determiner on linkage group 5. One species, Metriaclima pyrsonotus , was segregating both the male (XY) and the female (WX) heterogametic sex determination systems. Two outgroup species, Aulonocara baenschi and Pseudotropheus 'dakarti', segregate for the male heterogametic system on linkage group 7. Thus at least two distinct genetic sex determination systems are present within the Lake Malawi species flock. The male heterogametic (XX: XY) sex determiner localized to a 10 cM region on linkage group 7. Within this region, comparative mapping identified four candidate genes for sex determination. The female heterogametic (WZ: ZZ) sex determiner localized to a 7.6 cM region on linkage group 5. These sex-determining loci in haplochromine cichlids are on different chromosomes than the sex-determining loci identified in tilapia, which are on chromosomes one and three.
Combining Ability of Channel Catfish, Ictalurus punctatus, Females and Blue Catfish, I. furcatus, Males for Early Growth, Growth Variation, Disease Resistance, and Carcass Yield of their Progeny

ii Dedication . iv Acknowledgments . v List of Tables . viii List of Illustrations . x List of Abbreviations . xiv Chapter 1 General Introduction and Literature Review Introduction . 1 Current Status of the Catfish Industry . 2 Quantitative Genetics and Its Application to Catfish Production . 2 Combining Ability: Concepts and Principles . 11 References . 15 Chapter 2 General and Specific Combining Ability for Early Performance Traits of Channel Catfish (Ictalurus punctatus) Female x Blue Catfish (I. furcatus) Male F1 Hybrid
Effects of Some Environmental Factors on Milking Time Milk Yield in Red Holstein Cows

The purpose of this study is to investigate the environmental factors on the milking time milk yield of Red Holstein cows. For this aim, 172,826 morning milk yield (MMY) and 172,771 evening milk yield (EMY) data collected between 2001 and 2010 from a dairy farm in Aydin Province, Turkey were used. The THI is over 72 from June to August in the region. The effects of calving month, calving year, parity, lactation month and milking month on MMY and EMY were found to be statistically significant. For every month, year and parity, the MMY means were higher than those of the EMY. The peak daily milk yield was determined on the 46th day of lactation (31.7±0.013 kg). For parity, the highest milk yield means were detected for the third parity: 13.69±0.023 kg for MMY and 11.70±0.021 kg for EMY. In conclusion, taking precautions to protect the cows from heat stress especially for the cows calved in summer and keeping the milking interval equal for whole year would help increasing the milk yield.
Landuse impacts on soil organic carbon fractions in different rainfall areas of a subtropical dryland

ABSTRACT Landuse can alter soil organic carbon (SOC) fractions by affecting carbon inflows and outflows. This study evaluated changes in SOC fractions in response to different landuses under variable rainfalls. We compared cropland, grassland and forest soils in high rainfall (Islamabad ~1142 mm) and low rainfall (Chakwal ~667 mm) areas of Pothwar dryland, Pakistan. Forest soils in both rainfall areas had highest SOC (11.32 g kg−1), particulate organic carbon (POC, 1.70 g kg−1), mineral-associated organic carbon (MOC, 7.17 g kg−1) and aggregate-associated organic carbon (AOC, 7.86 g kg−1). However, in rangeland and cropland soils, these varied with rainfall. Under high rainfall, SOC and MOC were 12% and 17% higher in rangeland than in cropland while POC and AOC were equal. Under low rainfall, SOC and MOC were higher in rangeland than in cropland by 7.21 and 1.79 g kg−1 at 0–15 cm and equal at 15–30 cm depth. POC and AOC were higher in rangeland than in cropland, in both depths. Averagely, SOC, POC, MOC and AOC were 26%, 68%, 76% and 30% higher in high rainfall than in low rainfall soils. Sensitivity of SOC fractions to landuses observed under different rainfalls could provide useful information for soil management in subtropical drylands.
Biochemical Basis of Fresh Ham Color Development

Commercial hams display variation in color uniformity across the cut surface, especially the semimembranosus (SM) muscle. This variation in fresh ham color, or two-toning, persists through further processing and contributes to production of a less desirable end product. In an attempt to understand the underlying source of this color variation, we evaluated the differences in muscle fiber-type composition and glycolytic metabolism in the SM muscle of fresh hams differing in color uniformity. Fifty-eight fresh SM muscles, ranging in color, were selected at 24 h postmortem and each partitioned into four distinct regions and three color classes based on color uniformity in the caudal region. The L* (lightness) values were greatest and a* (redness) values lowest in the most caudal portions of the muscle. The caudal portion also exhibited the lowest ultimate pH (P < 0.0001), lowest myoglobin (P < 0.05), greatest glycolytic potential (GP) (P < 0.0001) and the lowest myosin heavy chain type I isoform (P < 0.0001) abundance of all regions in “normal” colored hams. After segregating based on L* values, the caudal region had identical pH, GP, LDH, and MyHC-I, despite significant differences in L* (P < 0.0001). These data show the most caudal aspects of the SM are indeed more prone to adverse postmortem metabolism and suggest that inherent differences in muscles of the ham may make some areas of the ham more vulnerable to temperature abuse during harvesting.
The role of microRNAs in mammary tumorigenesis

THE ROLE OF MICRORNAS IN MAMMARY TUMORIGENESIS Erinne Barnett Advisor: University of Guelph Dr. Roger Moorehead MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate the expression of mRNA targets, and are aberrantly expressed in several cancers, including breast cancer. Using a transgenic mouse model of mammary tumorigenesis (MTB-IGFIR), a miRNA array was previously performed in our lab to study the expression level of various miRNAs in mammary tumours compared to wild-type mammary tissue. Next, the expression of a number of the differentially expressed miRNAs was confirmed and manipulated in a tumour cell line (RM11A) generated from a MTB-IGFIR mammary tumour. Synthetic miRNA precursors and inhibitors were then used to overexpress and knockdown, respectively, the levels of five miRNAs: miR-31, miR-183, miR-200c, miR210, and miR-378. Upon optimization of miRNA overexpression and downregulation in RM11A cells, this study tested the effects of these miRNAs on cellular growth, survival, or invasiveness in vitro. Compared to negative controls, overexpression of all five miRNAs was associated with a significant decrease in cellular invasion, while only the overexpression of miR-31 had a significant effect on proliferation. No significant effects were found on cell survival. Our results implicate these five miRNAs in different aspects of mammary tumorigenesis, as well as having a tissue specific role in RM11A cells.
Use of cast antlers to assess antler size variation in red deer populations: effects of mast seeding, climate and population features in Mediterranean environments

R.P. received support from Marie Curie Actions (FP7‐PEOPLE‐2013‐IOF‐627450). M.P. acknowledges the financial support of the Spanish Ministry of Education (FPU13/00567) and thanks the ‘Consejo Social of the Polytechnic University of Madrid’ for providing funds during the stay at Laval University.
The Effect of Plant Growth Promoting Rhizobacteria (PGPR) on Germination and Seedling Growth of Sorghum bicolor L. Moench

Germination is the first important step of the plant growth in the land. The germination and growth of sorghum in marginal land can be optimized by inoculating with PGPR (inoculants), hydrogel and CMC (carriers). The aim of the research was to evaluate the response of germination and seedling growth of sorghum using PGPR inoculation with hydrogel and CMC as carriers (in vitro) and pots containing sterile sand (in vivo). The experiment used PGPR (Azospirillum lipoferum 1103D, Azotobacter chroococcum 4103D, and Bacillus sp. 3D), and hydrogels as the reserve water, as well as carboxymethyl cellulose (CMC) as the adhesive media. The results showed that the combination of PGPR-mix (Azospirillum, Azotobacter, Bacillus) with hydrogels as bio-organic fertilizer and CMC as carriers has promoted the growth of the roots, shoots and vigour index of in vitro sorghum germination, as well as increased the root length, shoot length and total dry weight of sorghum seedlings in pots containing sterile sand. The best result of in vitro experiment (root length = 8.67 cm; shoot length = 12.6 cm; and vigor index = 2127.00) was obtained by sorghum seed inoculated with single PGPR inoculant (A. lipoferum) with carrier of CMC. The root length, shoot length and total dry weight of the highest sorghum seedlings were obtained by PGPR-mix inoculants without carriers (46.5 cm, 12 cm, and 0.477 g), PGPR-mix with carrier of CMC (48.67 cm, 15.67 cm, and 0.431 g), and PGPR-mix with carrier of hydrogel (48.67 cm, 15 cm, and 0.430 g).