Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the F Antigen-Specific papA Alleles of Extraintestinal Pathogenic Escherichia coli Using a Novel Multiplex PCR-Based Assay

Polymorphisms in PapA, the major structural subunit and antigenic determinant of P ﬁmbriae of extrain- testinal pathogenic Escherichia coli , are of considerable epidemiological, phylogenetic, and immunotherapeutic importance. However, to date, no method other than DNA sequencing has been generally available for their detection. In the present study, we developed and rigorously validated a novel PCR-based assay for the 11 recognized variants of papA and then used the new assay to assess the prevalence, phylogenetic distribution, and bacteriological associations of the papA alleles among 75 E. coli isolates from patients with urosepsis. In comparison with conventional F serotyping, the assay was extremely sensitive and speciﬁc, evidence that papA sequences are highly conserved within each of the traditionally recognized F serotypes despite the diversity observed among F types. In certain strains, the assay detected serologically occult copies of papA , of which some were shown to represent false-negative serological results and others were shown to represent the presence of nonfunctional pap fragments. Among the urosepsis isolates, the assay revealed considerable segregation of papA alleles according to O:K:H serotype, consistent with vertical transmission within clones, but with exceptions which strongly suggested horizontal transfer of papA alleles between lineages. Sequencing of papA from two strains that were papA positive by probe and PCR but F negative in the new PCR assay led to the discovery of two novel papA variants, one of which was actually more prevalent among the urosepsis isolates than were several of the known papA alleles. These ﬁndings provide novel insights into the papA alleles of extraintestinal pathogenic E. coli and indicate that the F PCR assay represents a versatile new molecular tool for epidemiological and phylogenetic investigations which should make rapid, speciﬁc detection of papA alleles available to any laboratory with PCR capability.
Investigation of Anthocyanidins and Anthocyanins for Targeting α-Glucosidase in Diabetes Mellitus

Anthocyanidins are bioactive compounds found mostly in colored plants and fruits. Consumption of anthocyanidin-rich foods has been shown to reduce the risk of diabetes. However, limited information is available regarding the inhibitory effect and interactions of anthocyanidins on α-glucosidase, the key enzyme that controls diabetes through degrading carbohydrate. Therefore, we used computational docking analysis to investigate the degree and type of inhibition by α-glucosidase, and the structural interactions of enzyme-selected anthocyanidins. The results suggested that anthocyanidins exhibit half maximal inhibitory concentration of 4∼55 μM; the strongest and weakest α-glucosidase inhibitors were delphinidin and malvidin, respectively. Indeed, delphinidin inhibits α-glucosidase in a mixed type, close to non-competitive manner with an inhibitory constant of 78 nM. Addition of a glycoside (glucoside or galactoside) at C3 on the C ring of delphinidin significantly decreased inhibitory activity, and addition of glycosides at C3 on the C ring and C5 on the A ring of delphinidin prevented all inhibitory activity. Molecular docking and free binding energy accurately confirmed the mode of inhibition determined by enzyme kinetics. These data will inform the use of alternative sources of anthocyanidins in functional foods and dietary supplements for prevention of diabetes. The results provide useful information for evaluating possible molecular models using anthocyanins/anthocyanidins as templates and α-glucosidase as the key enzyme in management of diabetes.
The function of mitochondrial dynamics, content and localization during adult hippocampal neurogenesis

In the present study, the role of mitochondria in the generation of new neurons in the hippocampus of adult mice was investigated. This question was approached via live cell labeling of newborn neurons generated from stem cells and their genetic manipulation. It was demonstrated that mitochondrial biogenesis, dynamics and transport represent a basic cell biological mechanism for the maturation and synaptic integration of adult newborn neurons in the hippocampus.
Direct Somatic Embryogenesis of Selected Commercial Coffea Arabica L. Varieties in Kenya

xii TABLE OF CONTENTS . iv LIST OF TABLES . vii LIST OF FIGURES . viii LIST OF PLATES . ix LIST OF APPENDICE . x LIST OF ABBREVIATIONS AND ACRONYMS . xi CHAPTER ONE .
Transcriptomic Imputation of Bipolar Disorder and Bipolar subtypes reveals 29 novel associated genes

Bipolar disorder is a complex neuropsychiatric disorder presenting with episodic mood disturbances. In this study we use a transcriptomic imputation approach to identify novel genes and pathways associated with bipolar disorder, as well as three diagnostically and genetically distinct subtypes. Transcriptomic imputation approaches leverage well-curated and publicly available eQTL reference panels to create gene-expression prediction models, which may then be applied to “impute” genetically regulated gene expression (GREX) in large GWAS datasets. By testing for association between phenotype and GREX, rather than genotype, we hope to identify more biologically interpretable associations, and thus elucidate more of the genetic architecture of bipolar disorder. We applied GREX prediction models for 13 brain regions (derived from CommonMind Consortium and GTEx eQTL reference panels) to 21,488 bipolar cases and 54,303 matched controls, constituting the largest transcriptomic imputation study of bipolar disorder (BPD) to date. Additionally, we analyzed three specific BPD subtypes, including 14,938 individuals with subtype 1 (BD-I), 3,543 individuals with subtype 2 (BD-II), and 1,500 individuals with schizoaffective subtype (SAB). We identified 125 gene-tissue associations with BPD, of which 53 represent independent associations after FINEMAP analysis. 29/53 associations were novel; i.e., did not lie within 1Mb of a locus identified in the recent PGC-BD GWAS. We identified 37 independent BD-I gene-tissue associations (10 novel), 2 BD-II associations, and 2 SAB associations. Our BPD, BD-I and BD-II associations were significantly more likely to be differentially expressed in post-mortem brain tissue of BPD, BD-I and BD-II cases than we might expect by chance. Together with our pathway analysis, our results support long-standing hypotheses about bipolar disorder risk, including a role for oxidative stress and mitochondrial dysfunction, the post-synaptic density, and an enrichment of circadian rhythm and clock genes within our results.
Genetic and Pathogenic Characterization of Bacterial Wilt Pathogen, Ralstonia pseudosolanacearum (Ralstonia solanacearum Phylotype I), on Roses in Korea

The purpose of this study was to analyze the genetic and pathogenic characteristics of Ralstonia pseudosolanacearum in roses in Korea, and to examine the similarities and differences between Korean isolates and the first-reported European strains. Between 2017 and 2019, seventeen isolates from rose plants were identified as R. pseudosolanacearum using Ralstonia-specific primers. All 17 isolates were identified as race 1 using race-specific primers, and were confirmed as biovar 3 due to their ability to utilize carbon sources. Multiplex PCR using phylotype discriminating specific primers identified the 17 isolates as phylotype I. Sequevar comparison with reference sequevars using the sequences of the egl, mutS, and fliC genes, and only the egl gene, revealed that the strains evaluated in this study corresponded to sequevar I-33. The pathogenicity in roses differed depending on the rose cultivars. The different methods used for the genetic characterization of R. pseudosolanacearum indicate that the 17 rose bacterial wilt isolates had the same genetic characteristics. The lack of genetic variation in these isolates indicates their recent introduction from other countries (likely European countries). Therefore, appropriate quarantine and control measures should be taken in order to avoid further increases in the pathogenicity and/or secondary host range of R. pseudosolanacearum through genetic mutation.
Efeitos dos processamentos do milho comum e soja integral no desempenho de leitões desmamados aos 28 dias de idade

One hundred and sixty commercial hybrid pigs weaned at 28 days of age and 7.7 initial bodyweight were used in two experiments to determine the effect of processing corn and whole soybean. In the first experiment treatments were: A- Common corn (CC) + soybean meal (SM) + dried skim milk (DSM); B- Pre-cooked corn (PCC) + soybean meal (SM) + dried skim milk (DSM); C- Pre-cooked corn (PCC) + whole soybean dry extrusion (WSDE) + dried skim milk (DSM) and D- Pre-cooked corn (PCC) + whole steam toasted soybean (WSTS)+ dried skim milk (DSM). In the second experiment the treatments were: A1 - Common corn (CC) + soybean meal (SM) + dried skim milk (DSM); B1 - Pre-cooked corn (PCC) + whole steam toasted soybean (WSTS) + dried skim milk (DSM); C1 - Common corn (CC) + whole soybean dry extrusion (WSDE) + dried skim milk (DSM) and D1 - Common corn (CC) + whole steam toasted soybean (WSTS) + dried skim milk (DSM). The experimental period in each experiment was 14 days. The PCC did provide superior results in relation to CC independent of soybean type. Combined with any corn type, the diets with WSDE had poorest (P<0.05) piglets performance. The WSTS combined with CC or PCC may be utilized for weaned piglets of 28 days. The worst economic return was for diets WSDE.
GAD65 antibody prevalence and association with c-peptide, HLA class II alleles in Beninese patients with type 1 diabetes

Background: Antibodies to glutamic acid decarboxylase and particularly their isoforms in 65 kDa are one of markers for the diagnosis of the type 1 diabetes (T1D). The aim of this study is to assess the prevalence of GAD65 antibodies (GAD65Ab) and investigate the association of GAD65Ab with C-peptide values, HLA Class II alleles genotyping. The diagnosis of T1D was set up according to American Diabetes Association criteria. Methods: Radioimmunoassay was used to determine the GAD65Ab and C-peptide values. Class II HLA genotyping was performed in 51 patients with T1D and 51 healthy unrelated as control by using the PCR-SSP method. The sensitivity and specificity of the tests were calculated by standard formula. Results: Result revealed that GAD65Ab were present in 74.5% (38/51) of the patients with T1D. There was no significant difference between the positivity or the negativity of GAD65Ab and gender, onset and duration of diabetes, frequencies of HLA-DR4, HLA-DR3-DR4, HLA-DQB1*0201. However, GAD65Ab values are linked to Cpeptide concentration (χ2 =15.73, P=0.0001), the presence of HLA-DR3 (χ2 =9.75, P= 0.002), HLA-DQA1*0501 (χ2 =4.09, P= 0.043) alleles. The GAD65Ab test sensitivity and specificity were 74.5% and 94.1%, respectively. The Cpeptide test showed a sensitivity around 82.4 % and 86.3 % for the specificity. Conclusions: GAD65Ab showed to be a valuable early predictive marker and is associated with the risk to develop of T1D.
Nutrient Uptake and Dry Matter Production by Intensively Managed Yams Grown In an Ultisol

Intensively managed yams grown in a Ultisol and fertilized with 2,240 kg of 10-5-20-3/ha yielded 51.6 T of marketable tubers/ha, containing 18 T of edible dry matter, over an 8-month crop cycle. Uptake of nutrients by the yams was 190, 25, 215, 90 and 35 kg/ha of N, P, K, Ca, and Mg, respectively.
Genotype-by-milking frequency interaction for milk production traits in New Zealand

ABSTRACT The objective of this study was the estimation of genetic correlation (rg) for milk production traits across milking frequency (MF) in New Zealand dairy cattle milked once-(OAD) or twice-a-day (TAD). Analysis was made of lactation yields of milk, fat and protein, and somatic cell score of Holstein-Friesian (F), Jersey (J) and crossbred F × J breed populations cows herd-tested between 2008 to 2012 while in their first and second lactations. The estimates of rg were, in general, greater than 0.80, providing no evidence of a genotype-by-milking frequency (G × MF) interaction. Genetic correlations tended to be greater in second compared to first lactation cows and greater in J compared to F and F × J breed populations. The results also indicate a scaling effect, due to differences in the genetic variances across breed populations and MF, with the variances being lower in the OAD population. The results demonstrate that there is no need for a separate selection scheme for the OAD milking cow population, as long as there is similarity between breeding objectives and selection indices for both MF systems. The scaling effect indicates that the best animals in TAD system would also perform the best under OAD but genetic progress is expected to be lower in OAD compared to TAD systems because lower genetic variances in breed populations milked OAD.
Properties and Seasonal Variation of Milk Produced by One-humped Camels (Camelus dromedarius) and Two-humped camels (C. bactrianus) in the Republic of Kazakhstan

This study examined the components of the milk of one-humped and two-humped camels kept in same area in Kazakhstan, in May (rainy season) and August (dry season) 2015. Milk was sampled from camels of the same age that grazed on the same pastures. The general component analyses of camel milk involved the nutrition values, protein and fat content. The milk sampled from two-humped camels was found to contain greater densities of these components than milk sampled from one-humped camels. The values of calcium, phosphorus, zinc, aspartic acid, glutamic acid, phenylalanine, and lysine were higher in the two-humped camel milk samples. The densities of general components in the milk from both one-humped and two-humped camels were lower in the August samples than in those from May. Free amino acid densities in all milk samples were, however, higher in August than in May. The observed increase in August was considered to be related to the consumption of dry grasses that require longer rumination time and hence an increased activity of rumen microorganisms, and their nutritional byproducts. It may also be necessary to consider the grass type and nutrition ingested by the camels as well as the season for milking with regard to the quality and composition of milk.
Efficiency of Egyptian Plant Extracts on the Antibiotic Susceptible and Resistant Pathogenic bacterial Isolates

S UCCESSIVE leaf extracts of three Egyptian plant species: Datura stramonium L. , Withania somnifera (L.) Dun. in DC. and Ziziphus spina-christi (L.)Willd were studied for their antimicrobial activity against susceptible and Multi-Drug Resistant (MDR) bacteria isolated from chickens. Four bacterial spp. namely: Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella sp. were isolated from 463 different chicken samples. The sensitivity of these bacterial isolates was tested against 11 types of antibiotics: Ampicillin, Amoxicillin, Cefaclor, Gentamicin, Amikacin, Tobramycin, Ciprofloxacin, Nalidixic acid, Erythromycin, Tetracycline and Vancomycin. The isolates of E. coli, S. aureus, P.aureugenosa and Salmonella sp. showed notable bacterial resistance against the used antibiotics with percentages: (68.18%), (59.09%), (54.54%) and (54.54%); respectively. Chloroform extract of Datura stramonium showed the highest antibacterial activity against all the studied bacterial isolates with MICs values varying from 75.0 to 0.037 mg/ml. In conclusion, the present work indicated the potentiality of Datura stramonium chloroform extract as a promising national source for drug industry to produce antibiotics to be used against pathogenic multidrug resistant bacteria.
Does daily climate variation have an effect on species’ elevational range size?

In their recent paper published in Science (2016, 351, 1437–1439), Chan et al. analysed 137 montane gradients, concluding that they found a novel pattern—a negative relationship between mean elevational range size of species and daily temperature variation, which was claimed as empirical evidence for a novel macrophysiological principle (Gilchrist's hypothesis). This intriguing possibility was their key conceptual contribution. Unfortunately, as we show, the empirical evidence was flawed because of errors in the analyses and substantial sampling bias in the data. First, we re‐ran their analyses using their data, finding that their model should have been rejected. Second, we performed two additional re‐analyses of their data, addressing biases and pseudoreplication in different ways, both times again rejecting the evidence claimed to support Gilchrist's hypothesis. These results overturn the key empirical findings of Chan et al.'s study. Therefore, the “macrophysiological principle” should be regarded as currently remaining unsupported by empirical evidence.
Genetic variation in nutrient uptake and nutrient use efficiency of oil palm

ABSTRACT Observations of the vegetative and reproductive biomass produced annually and the mineral element contents have been conducted on diverse oil palm plant materials tested in a genetic test in Indonesia. The results show that the nutrient uptake (for trunk growth, leaf renewal and bunch export) greatly varies (CV = 10% for N uptake and 17% for K uptake) with the origins of the planting materials considered. For equivalent production, the uptake in nutrients of certain plant material may differ very significantly; for the same level of uptake in nutrients, production can vary significantly. This study supports the hypothesis that the optimal nutrient thresholds are intrinsically linked to the plant material. It assumes that some planting materials have different needs and that a fertilizer regime could be adapted to their specific needs without losses in performance. To confirm these assumptions, the need of implementing specific experimental devices with differentiated fertilization regimes is discussed.
Estimation of Relationship Between In Situ and In Vitro Rumen Protein Degradability of Extruded Full Fat Soybean

The objectives of this study were to estimate the protein degradability of extruded full fat soybean (ESB) by in situ (nylon bag) and in vitro enzymatic method and to develop an equation in order predict in situ degradability from in vitro values. In the study enzymatic technique; hydrolysis after 1 h (INV1) and after 24 h (INV24) by a purified protease extracted from Streptomyces griseus in a borate-phosphate buffer at pH 8 was used as in vitro method. Relationship between in situ effective protein degradability (INSE) and in vitro degradability after 1 and 24 hours incubations (INV1 and INV24) were determined. In situ protein degradability was measured at 0, 2, 4, 8, 16, 24, and 48 and at 72 h incubations in the rumen of 3 Holstein cows. In the study INSE, INV1 and INV24 were determined as 58.05, 20.24 and 41.46% respectively. Despite there were differences between in situ and in vitro protein degradability values, correlation coefficients between in situ and in vitro protein degradability of ESB were high and regression equations for estimation of in situ from in vitro were found significant. As conclusion in vitro enzymatic protein degradability (INV1 and INV24) can be used for estimation of in situ effective protein degradability of extruded full fat soybean.
EGG WEIGHT INFLUENCE ON SOME EGG CHARACTERS AND HATCHLING BODY WEIGHTOF GIMMIZAH CHICKEN STRAIN

The present experiment was carried out for studying the effect of egg size on egg shape index, egg volume, egg surface area, egg weight loss during incubation and their relations with chick body weight at hatch and at pull out. Eight hundred and fifty two hatching eggs obtained from Gimmizah chickens aged 49 weeks were divided into 6 groups based on egg weight with 5 grams differences namely as 1(<44 ), 2 (4448.99), 3 (49 – 53.99), 4 (54 – 58.99), 5 (59 – 63.99) and 6 (≥ 64.00). The obtained results showed that egg weight over 64 grams had the highest significant egg shape index compared to other egg weight groups. Moreover, eggs groups for weights between 59-63.99 and ≥ 64.00had significant increase on both egg volumes and egg surface areas compared to the rest egg groups. Also, negative correlations between egg weight and egg shape index were observed for egg groups < 44, and ≥ 64.00 grams. Moreover, highly significant correlations between egg weight and egg surface area were detected for groups of eggs weighing 44-48.99, 49-53.99, 54-58.99 and 59-63.99 grams. The accumulated egg weight loss% through the setting phase represented significant increase for eggs weighing more than 64 grams compared with those for all the rest egg categories. The increase of egg weight has a significant (p<0.001) influence on chick body weight either at hatch or at pull out as they increased with the increase of egg weight. Moreover, chick body weight loss % inside the hatcher was significantly decreased with the increase of egg weight. The correlations between egg weight and both of chick body weight at hatch are significant (p=0.001) among all experimental groups. The multiple regression equations implied the importance of egg weight and egg weight loss during incubation on chick body weight at hatch and at pull out. Thus, it could be concluded that separating hatching eggs basing on egg weight may be advisable to obtain the best hatchling weight.
Polygenic Adaptation has Impacted Multiple Anthropometric Traits

Our understanding of the genetic basis of human adaptation is biased toward loci of large phenotypic effect. Genome wide association studies (GWAS) now enable the study of genetic adaptation in highly polygenic phenotypes. Here we test for polygenic adaptation among 187 world-wide human populations using polygenic scores constructed from GWAS of 34 complex traits. Comparing these polygenic scores to a null distribution under genetic drift, we identify strong signals of selection for a suite of anthropometric traits including height, infant head circumference (IHC), hip circumference and waist-to-hip ratio (WHR), as well as type 2 diabetes (T2D). In addition to the known north-south gradient of polygenic height scores within Europe, we find that natural selection has contributed to a gradient of decreasing polygenic height scores from West to East across Eurasia. Analyzing a set of ancient DNA samples from across Eurasia, we show that much of this gradient can be explained by selection for increased height in two long diverged hunter-gatherer populations living in western and west-central Eurasia sometime during or shortly after the last glacial maximum. We find that the signal of selection on hip circumference can largely be explained as a correlated response to selection on height. However, our signals in IHC and WHR cannot, suggesting that these patterns are the result of selection along multiple axes of body shape variation. Our observation that IHC and WHR polygenic scores follow a strong latitudinal cline in Western Eurasia support the role of natural selection in establishing Bergmann’s Rule in humans, and are consistent with thermoregulatory adaptation in response to latitudinal temperature variation. One Sentence Summary Natural selection has lead to divergence in multiple quantitative traits in humans across Eurasian populations.