Miracle-dz/UniFAR-FTUs huggingface dataset:
Expanding Genetic Code for Protein Lysine and Phenylalanine Modifications

Expanding Genetic Code for Protein Lysine and Phenylalanine Modifications. (August 2012) Yane-Shih Wang, B.S.; M.S., National Cheng-Kung University, Taiwan Chair of Advisory Committee: Dr. Wenshe Liu The naturally occurring pyrrolysine (Pyl) incorporation machinery was discovered in methanogenic archaea and some bacteria. In these organisms, Pyl is cotranslationally inserted into proteins and coded by an in-frame UAG codon. Suppression of this UAG codon is mediated by a suppressor tRNA, , that has a CUA anticodon and is acylated with Pyl by pyrrolysyl-tRNA synthetase (PylRS). The PylRSpair can be directly applied to incorporate Pyl and other lysine derivatives into proteins at amber mutation sites in E. coli and mammalian cells. In the approach of amber codon suppression, evolved PylRSs were selected to synthesize the proteins genetically with lysine and phenylalanine derivatives which contain native or mimic of post-translational modifications (PTMs) or active chemical functional groups for protein labelling and protein folding studies. A photocaged N-methyl-L-lysine has been genetically incorporated into proteins at amber codons in Escherichia coli using an evovled PylRSpair. Its genetic incorporation and following photolysis to recover N-methyl-L-lysine at phsyiological pH provide a convenient method for the biosythesis of proteins with monomethylated lysines.
Determining the Effect of Total Fructose-Containing Sugars and Food Sources of Fructose-Containing Sugars on Glycemic Control

The role of fructose-containing sugars in diabetes remains unclear. We undertook two systematic reviews and meta-analyses (SRMAs) of controlled trials: one to assess the ecological validity of fructose doses used in human interventions and a second to assess the effect of food sources of fructose-containing sugars on glycemic control. The first SRMA identified 80 trials involving 1,432 participants. Average doses of fructose greatly exceeded mean population level intakes. The second SRMA identified 160 trials involving 5139 participants. Fructose-containing sugars from different food sources, especially fruits, did not adversely affect glycemic control and improved HbA1c in isocaloric exchange with other macronutrients. However, supplementing diets with excess energy from fructosecontaining sugars across different food sources, especially sugars-sweetened beverages, impaired fasting glucose and insulin. The available evidence suggest that the fructose doses studied do not represent ‘real world’ exposures and effects of fructose-containing sugars on glycemic control are energy and food source dependent. Abstract word count: 150 /150word count: 150 /150
Assessment of genetic diversity using D2 analysis in warm-season turfgrasses

The present experiment was conducted to estimate the variability and diversity in thirteen warm season turfgrass genotypes. The mean sum of squares due to genotypes showed significant differences for all the characters. High and moderate estimates of heritability (broad sense) were obtained for all growth related traits of turf grasses high genotypic and phenotypic coefficient of variation were recorded for shoot intensity (GCV=111.20, PCV=111.65) followed by leaf width (GCV=82.90, PCV= 83.77) and days to new growth (GCV=71.60, PCV=72.60). The maximum and minimum cluster mean value was observed for fresh weight and vertical leaf growth among all three clusters, respectively. High genetic advance was found for all characters, except monthly colour rating and turf quality. On basis of D2 analysis, the thirteen genotypes were grouped into three clusters. The cluster I was very large and comprised of 9 genotypes and cluster II had 3 genotypes. While, cluster III was comprised only single genotype. The clustering pattern showed that genotypes of different geographical areas were clubbed in one group and also the genotypes of same geographical area were grouped into same cluster as well as in different cluster indicating formal relationship between geographical diversity and genetic diversity.
The Ability of Released, Hatchery Salmonids to Breed and Contribute to the Natural Productivity of Wild Populations

The success and implications of hatchery release programmes are intimately tied to the repro- ductive capabilities of the hatchery fish in the wild. Moreover, reproductive interactions are important in understanding the ecological and genetic threats that hatchery fish may pose to wild populations. Reproductive success is a key to self-sustainability, shaping natural and sexual selection, and influencing the genetic diversity of populations. In this paper, we review the determinants of breeding success in natural populations and the implications of parental traits and decisions for offspring survival and success. We then address how rearing and release programmes affect the reproductive traits and performance of fish. A review of such pro- grammes reveals that in the few cases where adequate assessments have been made released fish frequently fail to attain self-sustainability and/or contribute significantly to populations. Clearly, new approaches based on sound scientific research are needed and these need to be tailored specifically to the management objectives.
Effects of partial replacement of nitrate with different nitrogen forms on the yield, quality and nitrate content of Chinese kale

ABSTRACT In this study, the yields, nutritional qualities and nitrate (NO3) content of Chinese kale were studied with two cultivars, following partial replacement of nitrate (20%) with ammonium (NH4), urea and glycine in hydroponics. The results showed that, compared with the full nitrate treatment, ammonium replacement increased the fresh weight by 18.1% and 8.0% of ‘Zaobao’ and ‘Lvbao’ cultivars respectively, whereas urea and glycine replacements decreased the biomass significantly. Adding different nitrogen (N) forms significantly improved the contents of vitamin C, soluble sugar, free amino acid, protein, soluble phenol and flavonoids in Chinese kale. Adding the three alternative N forms also reduced nitrate content significantly, in which glycine replacement was the lowest. According to the results obtained, different forms of N replacement could be used for different purposes. Glycine replacement could be the best alternative only to improve qualities, while ammonium replacement could be the best alternative to improve both the yield and qualities.
Incidence rate and antibiotic resistance profile of Cronobacter sakazakii isolated
from various food products

Cronobacter sakazakii (C. sakazakii) is a foodborne pathogen which has been linked to various food outbreaks. The current study was aimed to isolate and identify this pathogen from different kind of food products and herbs as well as to reveal its antibacterial resistant profiling. A total of 235 samples were collected, including 130 Powdered Infant Formula (PIF), 55 spices and herbs and 50 samples from Bouillon Flavoured Powder (BFP). These samples were obtained from local markets in Duhok city of Iraq from February to August 2019. The collected items were checked for the presence of C. sakazakii by using conventional biochemical tests and confirmed through molecular techniques. The findings showed that 3.1% of PIF, 24% of BFP and 78.2% of spices and herbs were positive for C. sakazakii. This bacterium expressed a complete susceptibility to each of ampicillin, tetracycline, gentamycin and chloramphenicol and showed high to mild resistance to the rest of the examined antibiotics Microbiological evaluation of imported food is crucial for safeguarding public health. The high contamination rate and high drug-resistant C. sakazakii in the examined food products declared prospective hazards to endangered people.
MutPred2: inferring the molecular and phenotypic impact of amino acid variants

We introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid substitutions, generates molecular mechanisms potentially causative of disease, and returns interpretable pathogenicity score distributions on individual genomes. While its prioritization performance is state-of-the-art, a novel and distinguishing feature of MutPred2 is the probabilistic modeling of variant impact on specific aspects of protein structure and function that can serve to guide experimental studies of phenotype-altering variants. We demonstrate the utility of MutPred2 in the identification of the structural and functional mutational signatures relevant to Mendelian disorders and the prioritization of de novo mutations associated with complex neurodevelopmental disorders. We then experimentally validate the functional impact of several variants identified in patients with such disorders. We argue that mechanism-driven studies of human inherited diseases have the potential to significantly accelerate the discovery of clinically actionable variants. Availability: http://mutpred.mutdb. org/
Water sorption, solubility and monomer elution from three commercial orthodontic adhesives

Objectives: The aims of this study were to study the water sorption, water solubility, and elution of three monomers Bis-GMA, TEGDMA, and BPA of three commercial orthodontic adhesives up to 7 days. Materials and methods: The water sorption, water solubility and monomer elution from three commercial adhesives; one chemically cured; Unite (Unitek Corp., Monrovia, CA, USA), two light-cured; Enlight (Ormco, Glendora, California, USA), and Grengloo (Ormco, Glendora, California, USA) were determined at four interval times of 1,3,5, and 7 days immersion. The adhesive specimen was prepared by polymerization in a cylindrical stainless steel mold with a diameter of 10 mm and 1 mm thickness. The water sorption and solubility protocol were done according to ISO 4049 specification. The concentration of Bis-GMA, TEGDMA, and BPA from the immersion medium was determined using High-performance liquid chromatography (HPLC). One-way ANOVA followed by Dunnett T3 test for water sorption and Tukey’s for elution test were done for multiple comparisons. Results: Water sorption and water solubility were found to increase with storage time. It was found that they had similar water sorption and water solubility at 1 day (p>0.05) but differences were found at other time intervals (p<0.05). All adhesives had significantly differences in water sorption and solubility between 1 day and 7 days (p<0.05). Enlight and Unite had Bis-GMA, TEGDMA, and BPA elution at all time intervals, however in varied amount. Grengloo contains no Bis-GMA in the immersion medium at all time intervals. They were significantly differences among elution of the different adhesives at the same time (p<0.05) and among time intervals of the same adhesive (p<0.05) except Bis-GMA elution of Enlight at 1 day and 7 days (p>0.05) and BPA elution of Unite at 1 day and 7 days (p<0.05) which had similar results. Pearson’s correlation coefficient were found high correlation between water sorption and solubility (R =0.988). Only TEGDMA at 3 and 5 d found correlation with water sorption (R=0.754), and sol (R=0.878) Conclusion: Water sorption and solubility of light-cure and chemically cured adhesives increase with storage time. The amount of monomer leached from the polymerized specimen from all adhesives seems to be varied.
Galloylated Catechins as Potent Inhibitors of Angiotensin Converting Enzyme

In the present study, we investigated the inhibitory effects of four tea catechins, including (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-epicatechin gallate (ECg) and (-)-epigallocatechin gallate (EGCg), on angiotensin converting enzyme (ACE) activity in vitro . Each catechin treatment significantly reduced the ACE activity with the order of potency being EGCg > ECg > EGC = EC. The addition of 1 mM borate significantly recovered the reduced ACE activities by tea catechins, suggesting that hydroxyl groups at the B-ring or at a galloyl moiety play an important role in the ACE-inhibitory mechanism. The covalent modification of ACE by tea catechins was also observed by a redox-cycling staining experiment. A Lineweaver-Burk plot indicated that EGC and ECg were non-competitive inhibitors. The galloylated catechins might more potently inhibit ACE activity in an allosteric manner through the interaction of the galloyl moiety with the non-catalytic site of ACE.
Grazing management of dairy pastures based on tall fescue in southern Australia

Abstract. Tall fescue (Festuca arundinacea (Schreb) Darbysh. ) has the potential to become a useful component of irrigated dairy pastures in northern Victoria owing to its high dry matter (DM) production compared with perennial ryegrass. However, tall fescue is not widely grown because its grazing management is perceived as difficult. In October 2010, a tall fescue–white clover pasture was established and irrigated. In September 2011, six grazing-management treatments were imposed over 3 years, involving grazing: at 1-leaf stage; at 2-leaf stage (1.5-leaf stage during spring); at 3-leaf stage (2.5-leaf stage during spring); at intervals based upon days between grazings ranging from 15 days in October–December to 60 days in winter; at intervals as above except for 21 days in October–December; and at intervals approximating that of a well-managed perennial-ryegrass-based pasture . Measurements included pre- and post-grazing pasture mass, nutritive characteristics, botanical composition and plant frequency. Pasture consumption from the treatment grazed at the 3-leaf stage was >3.5 t DM ha–1 year–1 (30%) greater than from the three most frequently grazed treatments. However, crude protein content was 1–3% DM units lower when grazed at the 3-leaf stage compared with the two most frequently grazed treatments. There was no effect on estimated metabolisable energy or neutral detergent fibre contents of the pasture on offer. Differences in pasture composition between the pastures grazed at the 3-leaf stage and those most frequently grazed emerged over time and were most conspicuous in the third year, with a greater plant frequency (79% v. 66%) and tall fescue content (61% v. 40% DM) and lower weed content (14% v. 28% DM). From the study, a grazing regime for tall fescue based on the 3-leaf stage appears promising because it produced the most DM over the experiment. A disadvantage of this regime was the need for an extra mowing each year. The practicality of this approach to grazing tall fescue needs to be tested at the whole-farm level.
First complete mitochondrial genome of Phoenix dact ylifera var. Khanezi

Abstract In this study, we determined the complete mitochondrial (mt) genome of Phoenix dactylifera var. Khanezi. The results revealed a circular genome of 715,120 bp, having G + C content of 45.1%, containing 40 protein coding genes, 3 rRNA, and 18 rRNA genes. Evolutionary relationship analysis suggested that P. dactylifera var. Khanezi is more closely related to previously reported P. dactylifera var. Khalas.
Parasitism in gills of Centropomus undecimalis (Pisces, Centropomidae) from a protected area in Sao Luis, Maranhao, Brazil

Effects of contaminants in fishes might be manifested in many levels of biological organization, including the cause of lesions in gills. This study aimed to identify damages caused by parasites to Centropomus undecimalis’ gills’ tissue structure (Bloch, 1972) and evaluates the quality of fishes’ community in the Ecological Park of Laguna da Jansen, Sao Luis, Maranhao, Brasil. A number of 33 exemplars of C. undecimalis were used, the first right gill arch was removed from each animal and fixed in 10% formaldehyde, fixed in 10% formalin for 24 hours, afterwards it was decalcified in 10% nitric acid, dehydrated in increasing concentrations of alcohols, diaphanized in in xylene, impregnated and included in paraffin. The 5μm thick cuts were stained with hematoxylin and eosin for histologic description. The parasitological search was performed by light microscopy and the lesions were evaluated through Histological Change Index. From the fishes collected, 48.4% presented parasitic changes associated to structural gills changes, such as epithelial hyperplasia and mucus. It was diagnosed presence of parasites in the gills of the sampled specimens, which belong to three families from the group Monogenea and myxosporean cysts. The Histological Change Index average was 53.3 demonstrating that individuals from species C. undecimalis’s gills collected presented severe tissue modifications. Therefore, the results show that the fishes sampled present a likely imbalanced host-parasite-environment
Hybrid Approach for Software Component Classification using Computational Intelligence

-Software engineering provides solutions of the existing problems coming from different-different areas. Fuzzy C-Means and Subtractive Clustering Algorithm play a vital role in the Software Engineering for Software Components Classification in their respective Clusters. Fuzzy C-Means Clustering Algorithm has a major disadvantage that the number of Clusters formed, intimate before classification of Software Components. How can intimate the number of Software Components beforehand, it depends on the nature of data points used. This is the main cause to produce local optimal solutions instead of optimal solution. Fuzzy Subtractive Clustering Algorithm evaluates the number of required Clusters on the base of nature of Software Components. This paper uses a Hybrid Approach for Software Components Classifications by using Computational intelligence. The problems associated with Fuzzy C-Means can rectify to use to Fuzzy Subtractive Clustering Algorithm, but Computation time required is high that’s why in this paper use rejection ratio, Recall and Precision to classify Software Components. Selecting a Cluster Center is main task in Clustering process because if selection of Cluster center is good then Computation time to classify Software Components in their respective Clusters is small.
Selective effects of floral food sources and honey on life‐history traits of a pest–parasitoid system

Many parasitoids and their herbivorous hosts forage on the same floral resources in agroecosystems. Floral resources that benefit natural enemies without supporting pests can improve the efficacy of biological control agents. Here, we report the results of a study on selective effects of floral and non‐floral food sources on the life‐history traits of the parasitoid Diadegma insulare (Cresson) (Hymenoptera: Ichneumonidae) and its host Plutella xylostella (L.) (Lepidoptera: Plutellidae). Under standard laboratory conditions, insects were exposed to four flowering plant species, 10% honey solution, and water. All food sources increased the longevity of the herbivore and its parasitoid by as much as four‐ to nine‐fold, respectively, compared to the water control diet. Diadegma insulare survived the longest on Thlaspi arvense L. (Brassicaceae) and P. xylostella on Sinapis arvensis L. (Brassicaceae). However, none of the food sources tested was beneficial to the parasitoid alone, though Lobularia maritima L. (Brassicaceae) was found to selectively favor the longevity of D. insulare. Diadegma insulare adults were heavier when fed on S. arvensis, whereas feeding on the honey solution led to higher body weights of P. xylostella. In conclusion, we demonstrated that floral and non‐floral food sources varied in their suitability and acted differently on life‐history traits of a host–parasitoid system. The selective characteristics of nectar‐producing plants and their influence on the herbivore‐natural enemy combination can, therefore, be employed to increase their impact in integrated P. xylostella management.
Augmenting the Detection of Verotoxin-Producing Escherichia coli Through use of Fluorescently-labeled DNA Oligonucleotides

Verotoxin-producing Escherichia coli (VTEC) present a significant risk of foodborne illness and severe patient outcomes. Isolation is laborious and time consuming due to the diversity of strains. Development of a differential agent wouldenhance rate and speed of isolation. Production of verotoxin (VT) is the only phenotypic trait exclusive to VTEC. Aptamers are single-stranded oligonucleotides with high selectivity and affinity for their targets. A VT-targeting aptamer beacon could aid in isolation of VTEC. Proof of concept was demonstrated using an existing aptamer sequence, showing increased fluorescence in the presence of VT1a. Further characterization showed target specificity, but weaker signal contrast in complex media. Comparison of fluorophore-quencher pairs showed Texas Red and Black Hole Quenchers as optimal choices. Finally, a DNA substrate developed to detect VT enzyme activity produced weak fluorescent signalmaking it unlikely to aid in detection.
The impact of news exposure on collective attention in the United States during the 2016 Zika epidemic

In recent years, many studies have drawn attention to the important role of collective awareness and human behaviour during epidemic outbreaks. A number of modelling efforts have investigated the interaction between the disease transmission dynamics and human behaviour change mediated by news coverage and by information spreading in the population. Yet, given the scarcity of data on public awareness during an epidemic, few studies have relied on empirical data. Here, we use fine-grained, geo-referenced data from three online sources – Wikipedia, the GDELT Project and the Internet Archive – to quantify population-scale information seeking about the 2016 Zika virus epidemic in the U.S., explicitly linking such behavioural signal to epidemiological data. Geolocalized Wikipedia pageview data reveal that visiting patterns of Zika-related pages in Wikipedia were highly synchronized across the United States and largely explained by exposure to national television broadcast. Contrary to the assumption of some theoretical models, news volume and Wikipedia visiting patterns were not significantly correlated with the magnitude or the extent of the epidemic. Attention to Zika, in terms of Zika-related Wikipedia pageviews, was high at the beginning of the outbreak, when public health agencies raised an international alert and triggered media coverage, but subsequently exhibited an activity profile that suggests nonlinear dependencies and memory effects in the relation between information seeking, media pressure, and disease dynamics. This calls for a new and more general modelling framework to describe the interaction between media exposure, public awareness and disease dynamics during epidemic outbreaks.