Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Ascorbic Acid on mRNA Expression of HSP70 Gene in WLH Egg Type Growers During Heat Stress

Meteorological factors such as high ambient temperature and high relative humidity exert adverse effects on poultry production. Heat stress results in poor growth performance, feed efficiency, egg production and higher mortality. The aim of the experiment was to explore and quantify the relative mRNA expression of HSP70 gene in relation to ascorbic acid supplementation in White Leghorn (WLH) egg type growers exposed to heat stress. A total of 96 WLH egg type growers of 10 weeks age, were randomly divided and maintained in controlled comfort (26±1.0°C) condition and heat stressed (40±5.0°C) conditions. Each group was divided into four subgroups with twelve birds each in two replicates for homogeneity of experimental design. G1 was designated to control group whereas, G2, G3 and G4 group was supplemented with 100, 200 and 300 mg ascorbic acid (AA) respectively. Relative expression analysis of HSP70 in liver tissue was done on day 42nd of the experiment using RT-PCR technique. The mRNA expression in egg type grower birds was significantly (p<0.01) down-regulated in all the treatment groups as compared to control group in both comfort and heat stressed condition. In comfort condition, maximum down-regulation (0.32 fold) was found in G3 group followed by G4 group (0.43 fold) as compared to control group. Similarly, in heat stressed condition, maximum down-regulation (0.31 fold) was found in G3 group, followed by G4 group (0.56 fold) in comparison to control group. The present investigation reveals that supplementation of ascorbic acid on the expression patterns of HSP70 gene provide an indication that AA may be useful in combating rigors of heat stress in chickens.
Characterization of a Zygomycete Fungus, Mortierella minutissima from Freshwater of Yeongsan River in Korea

During a survey of fungal diversity of the order Mortierellales, a zygomycete strain, EML-YS717-1, was isolated from a freshwater sample collected from the Yeongsan River in Gwangju, Korea. Based on its morphological characteristics and a phylogenetic analysis of the internal transcribed spacer (ITS1 and ITS2) and 5.8S rDNA sequences, the strain was identified as Mortierella minutissima. To the best of our knowledge, M. minutissima, has not previously been authentically reported in Korea.
Using weighted of ROC in analytical network process for decision making

The use of Analytic Network Process (ANP) with complex model sometimes makes it difficult to fill the numeral by using the pairwise comparison. Therefore, one alternative that can apply is ROC or Rank Order Centroid. ROC implemented in SMARTER and MAGIQ, thus for this study was done using ROC on ANP system. The results obtained in this study is that there is a difference in ranking on ANP by using pairwise Comparison in the previous research while comparing with ROC. The reason is many numbers that lead to the same ranking value in a cluster. Therefore, it can complicate the determination of the best alternative. However, ROC can help in quick counting and support validate the pairwise comparison weights on ANP.
SeqsLab: an integrated platform for cohort-based annotation and interpretation of genetic variants on Spark

Summary SeqsLab is a platform that helps researchers to easily annotate and interpret genetic variants derived from a large quantity of personal genomes. It provides an integrated interface to annotate the variants based on curated databases as well as in silico estimation on the effects of the variants. SeqsLab adopts the scalable cluster computing framework, Spark, and incorporates several customized algorithms to speed up the process of variant annotation and interpretation. The key features of SeqsLab include efficient annotation on large structural variations, diverse combinations of variant filters, easy incorporation with a vast amount of public databases, and scalable architecture of analyzing hundreds of human whole genomes simultaneously. Availability and Implementation SeqsLab is implemented with JAVA. The generated annotation will then be stored in Elasticsearch for real-time query and exploratory analysis. SeqsLab can be accessed by web browsers and is freely available at http://portal.seqslab. net/. Contact chungtsai_su@atgenomix.com Supplementary information Supplementary data are available at Bioinformatics online.
Modelling schizophrenia endophenotypes by overexpression of Neuregulin-1 isoforms in transgenic mice

Neuregulin 1 (NRG1) is the best characterized member of a family of epidermal growth factor (EGF)-like domain containing proteins that serve as ligands for tyrosine kinase receptors of the ErbB family. NRG1 and its main receptor in the brain, ErbB4, have been involved in neural development, neurotransmission and synaptic plasticity. Additionally, NRG1 isoform-specific expression patterns in the brain have been described, but isoform-specific functions remain unclear. Nrg1 is a robustly associated schizophrenia susceptibility gene in many populations. Examination of blood cells and post mortem brain tissue revealed that increased Nrg1 expression occurs in schizophrenia patients, including a notable increase in Ig-Nrg1 mRNA. Together with ErbB4 hyperphosphorylation observed in post mortem brains of schizophrenia patients, this suggests that NRG1/ErbB4 hyperstimulation could represent a component of schizophrenia etiology. However, the underlying pathomechanisms are unknown. In the present study, we investigated brain endophenotypes associated with cortical-restricted Ig-NRG1/ErbB4 hyperstimulation. For this purpose, a conditional transgenic mouse line was produced that permits stage- and cell type-specific overexpression of the Ig-NRG1 isoform under control of the β-actin promoter after Cre-mediated removal of a “floxed” STOP-cassette. A comprehensive analysis of this mouse model revealed that physiologically relevant Ig-NRG1 overexpression in glutamatergic projection neurons resulted in chronic ErbB4 hyperphosphorylation in the neocortex and hippocampus. ErbB4 hyperstimulation was associated with impaired hippocampal -oscillation and altered social behavior. Biochemical analyses revealed a preferential activation of the AKT pathway upon Ig-NRG1 overexpression. Furthermore, moderate projection neuron-specific overexpression of Ig-NRG1 allowed us to investigate the subcellular localization of the protein, which appeared to be associated with the potassium channel Kv2.1 in the somatodendritic compartment. These results provide a first insight into possible molecular pathomechanisms and schizophrenia-relevant endophenotypes induced by Ig-NRG1-mediated ErbB4 hyperstimulation in cortical networks. In a second project, NRG1 signaling functions in ErbB4-expressing GABAergic interneurons have been investigated in conditional NRG1 mutants. Cre-mediated elimination of NRG1 from parvalbumin-positive (Parv+) interneurons resulted in body weight reduction, a shivering phenotype, increased motor activity, and a reduced number of interneurons in cortical layers II-III. Thus, in contrast to projection neuron-specific loss- or (moderate) overexpression of NRG1, these findings suggest that NRG1-mediated autocrine signaling in Parv+ interneurons serves an essential role in the regulation of inhibitory circuit functions. Finally, in a pilot project a new mouse line for the conditional overexpression of NRG2, a closely related ErbB4 ligand in the brain, has been generated by homologous recombination into the Rosa26 locus of embryonic stem cells.
A Rapid Assessment of Vascular Plants in Mt. Kiamo, Mindanao, Philippines

A rapid assessment was conducted to determine the richness of vascular plants in Mt. Kiamo, Mindanao, Philippines. Repeated transect walks revealed 3 vegetation types, viz., Mossy-pygmy forest, Montane forest and Agro-ecosystem. A total of 251 species belonging to 82 families and 168 genera were documented. Of these, 95 species are ferns, 6 species are lycophytes, 6 gymnosperms and 144 angiosperms. Eight species are broadly distributed Philippine endemics and four are found only on Mindanao. New species and new records of plants were also documented in the area. Of the 17 threatened species recorded, 3 are critically endangered, 8 are endangered and 6 are vulnerable. Keywords : survey, threatened, endemic plants, Mindanao, Philippines
Características climáticas da Bacia Hidrográfica do Rio Cachoeira, Joinville (SC)

A Bacia Hidrografica do Rio Cachoeira esta localizada na cidade de Joinville, nordeste de Santa Catarina. O territorio dessa bacia possui importância fundamental no desenvolvimento do municipio, pois nela residem aproximadamente 50% da populacao, e esta localizado na area central, com ampla dinâmica politica, social e economica. O clima de uma regiao se reflete no cotidiano, na cultura, na economia, entre outras influencias, ou seja, e uma caracteristica fisica notoria. Entender a dinâmica climatica dessa bacia e de fundamental importância para o desenvolvimento sustentavel do municipio ante as mudancas climaticas. Portanto, o presente estudo teve o objetivo de realizar uma analise das caracteristicas climaticas. Para tanto, foram utilizados dados de temperatura do ar, ventos (direcao e velocidade), umidade relativa do ar e precipitacao pluviometrica, de diferentes estacoes meteorologicas, buscando assim uma representatividade da bacia. Dentre os principais resultados estao que a precipitacao media anual na bacia e de 1.957,3 mm, o mes mais chuvoso e janeiro, os meses mais secos sao junho e julho. A temperatura media anual e de 22,4°C, sendo fevereiro o mes mais quente, e julho o mes mais frio. A umidade relativa do ar media atinge 80,76%. A direcao predominante dos ventos e de leste.
The impact of advances in molecular virology on the clinical epidemiology and management of central nervous system viral infections in infants

Molecular virological techniques have rapidly replaced cell culture as the diagnostic tool of choice across NHS laboratories. This thesis studies two of the commonest causes of CNS viral infections in infants less than 90 days of age to determine whether the introduction of Polymerase Chain Reaction (PCR) based techniques have impacted significantly on their management and epidemiology. Congenital CMV (cCMV) is the commonest congenital infection in the UK and a leading cause of sensorineural hearing loss (SNHL). In the absence of a screening programme the great majority are detected in early childhood outside the time when antiviral therapy has been shown to be effective. This thesis describes a series of coordinated pilot studies that suggest that it is potentially feasible to integrate testing for cCMV using salivary PCR into the Newborn Hearing Screening Programme (NHSP) and start appropriate antiviral management within the first month of life. A programme of work that needs to be conducted before potential national implementation is also outlined. Conventional molecular techniques were used to characterise the variation of five genetic loci of CMV in congenitally infected infants to better understand the current and future medical interventions available. Enterovirus (EV) infections most commonly infect young infants. PCR has been shown to detect viruses with greater accuracy than cell culture. National data over a 10 year surveillance period were analysed to demonstrate a seven fold increase in viral meningo-encephalitis diagnosis rates associated with increased use of PCR. Enteroviruses accounted for 92% of all cases of viral meningo-encephalitis in those aged less than 90 days. The year on year increase in EV infections coincided with increasing PCR-based laboratory diagnosis, which accounted for 36% of reported cases in 2000 and 92% in 2011. These data provided the rationale for the design and implementation of a British Paediatric Surveillance Unit (BPSU) study characterising the burden of EV and human parechovirus meningitis in children aged less than 90 days. This thesis supports the notion that advances in molecular virology can significantly inform the investigation and management of CNS viral infections (as exemplified by cCMV) and alter the apparent epidemiology (as exemplified by EV infections in infants less than 90 days old).
Functional Characterization of Candidate Tyrosine Phosphoproteins during in Vitro Capacitation of Fresh and Cryopreserved Buffalo Spermatoza.

Before fertilization, mammalian spermatozoa accomplish the capacitation, a wellcontrolled process crucial to fertilize mature oocyte. The protein tyrosine phosphorylation is a meaningful indicator of capacitation. The proteins such as Serine/Threonine protein phosphatase 1γ (PP1γ), lactate dehydrogenase C (LDHC) and actin are likely to play an important role in motility, capacitation and acrosome reaction (AR) of mammalian spermatozoa. These proteins were identified and characterized in terms of their isozymic forms, tyrosine phosphorylation status and immunolocalization patterns in in vitro capacitated and cryopreserved spermatozoa in comparison to freshly ejaculated Buffalo spermatozoa. Western blot, two-dimensional gel electrophoresis, immunoblotting, indirect Immunocytochemistry, double staining and spectrophotometry techniques were used in the studies. Expression levels of these three proteins were significantly (P<0.05) decreased in cryopreserved spermatozoa in comparison to fresh spermatozoa. Differential expression of isoforms, tyrosine phosphorylation status and immunolocalization signals of these proteins were observed in in vitro capacitated and cryopreserved spermatozoa in comparison to freshly ejaculated Buffalo spermatozoa. The tyrosine phosphorylation of these proteins involved cAMP/PKA and Erk dependent and independent pathways during in vitro capacitation of the spermatozoa. Tyrosine phosphorylation of these proteins may play a major role in the regulation of capacitation. Increased actin polymerization was observed during capacitation, whereas, Inhibition of actin polymerization blocked the buffalo sperm capacitation. Tyrosine phosphorylation may regulate the actin polymerization during capacitation. Increased actin polymerization and tyrosine phosphorylation (capacitation like changes) were also observed in cryopreserved spermatozoa. LDHC enzyme activity was significantly (P<0.05) increased during capacitation and significantly (P<0.05) decreased in cryopreserved spermatozoa. Inhibiting the LDHC with sodium oxamate (10mM) significantly (P<0.05) reduced the protein tyrosine phosphorylation. The information generated clearly differentiates the differences between the in vitro sperm capacitation and the capacitation like changes (cryo-capacitation) during cryopreservation. It can be used strategically for the improvement of fertility of cryopreserved spermatozoa.
Protein modelling of triterpene synthase genes from mangrove plants using Phyre2 and Swiss-model

Molecular cloning of five oxidosqualene cyclases (OSC) genes from Bruguiera gymnorrhiza, Kandelia candel, and Rhizophora stylosa had previously been cloned, characterized, and encoded mono and -multi triterpene synthases. The present study analyzed protein modelling of triterpene synthase genes from mangrove using Phyre2 and Swiss-model. The diversity was noted within protein modelling of triterpene synthases using Phyre2 from sequence identity (38-43%) and residue (696-703). RsM2 was distinguishable from others for template structure; it used lanosterol synthase as a template (PDB ID: w6j.1.A). By contrast, other genes used human lanosterol synthase (1w6k.1.A). The predicted bind sites were correlated with the product of triterpene synthase, the product of BgbAS was β-amyrin, while RsM1 contained a significant amount of β-amyrin. Similarly BgLUS and KcMS, both main products was lupeol, on the other hand, RsM2 with the outcome of taraxerol. Homology modelling revealed that 696 residues of BgbAS, BgLUS, RsM1, and RsM2 (91-92% of the amino acid sequence) had been modelled with 100% confidence by the single highest scoring template using Phyre2. This coverage was higher than Swiss-model (85-90%). The present study suggested that molecular cloning of triterpene genes provides useful tools for studying the protein modelling related regulation of isoprenoids biosynthesis in mangrove forests.
Histopathological findings in Dalmatian pelicans (Pelecanus crispus) naturally infected with avian influenza subtype A H5N1 in Bulgaria

The aim of this study is to estimate the histopathological changes in visceral organs of naturally infected with the avian influenza virus (AIV) subtype A H5N1 dalmatian pelicans in Bulgaria. The identified gross lesions are: haemorrhagic small intestine, sparse content in gizzard and proventriculus, well defined hyperemia of the tracheal mucosa associated with petechiae, as well as meningeal and brain congestion. The infected birds exhibited the following histopathological changes: edema of the tracheal mucosa with loss of mucosal glands, mild to moderate congestion with focal necrosis and multifocal non suppurative encephalitis and gliosis, mononuclear infiltration in the cecum, and diffuse mononuclear infiltration in the submucosa of the small intestine. The virus was detected by virus isolation (VI) and RT-PCR from tissue samples (lung, trachea, small intestine, brain, proventriculus, cloaca) from the
Antimicrobial activity of whey protein based edible film incorporated with organic acids

The effect of incorporating organic acids in whey protein based edible film, and its antimicrobial activity has been studied. Four organic acids namely acetic, lactic, propionic and benzoic acids (5% v/v each) were incorporated in whey protein based edible film, and their antimicrobial activity was tested using Lactobacillusbulgaricus, Streptococcus thermophilus, Eschericia coli and Salmonella sp. There was a highly significant effect (P<0.01) of the organic acid on the inhibition zone of microorganisms, due to water vapor permeability (WVP) and protein solubility. A significant effect (P<0.05) was shown by different organic acids incorporated on the antimicrobial activity of the films. The highest inhibition zone was found at theE. coli tested sample (11.6 mm), whilst the lowest one was found at theSalmonella sp tested sample (9.77 mm). The highest inhibition zone was also found in the films that contained benzoic acid (11.76 mm), and the lowest was found in the film that contained lactic acid (10.44 mm). While the highest WVP value (0.0238 g.mm/m2.kPa) was shown by the film that contained propionic acid, the lowest one was shown in the film that contained acetic acid (0.0116 g.mm/m2.kPa). With regards to protein solubility, it was found that the film containing propionic acid had the highest value (44.4444%), while that with acetic acid showed the lowest protein solubility (35.5516%). Key words: Organic acids, whey protein edible film, antimicrobial activity, WVP, protein solubility.
The Specification of Hemogenic Endothelium During Embryogenesis and Beyond

The primary goal of regenerative medicine is the in vitro derivation of cells that are functional and safe for transplantation into patients. Although progress has been made towards this goal there are no clinical applications that utilize cells derived in vitro from pluripotent stem cells or reprogrammed primary cells. The foremost reason for this is an incomplete understanding of the development processes that regulate cell identity. In order to gain a better understanding of the specification of hematopoietic stem cells (HSC), I studied their de novo generation during embryogenesis. Using confocal microscopy, I mapped out hematopoiesis during midgestation and discovered that it is less spatially restricted than previously thought. I identified two new sites of blood formation, the dorsal longitudinal anastomotic vessels and the intersomitic vessels. I also identified three waves of hematopoiesis in the heart. During the final wave of cardiac hematopoiesis, spherical protrusions of endocardium encapsulating hematopoietic cells called cardiac blood islands (CBIs) form on the ventricles. CBIs pinch off from the ventricle and contribute to the coronary vasculature in a novel mechanism of vasculogenesis. Interestingly, loss of the RAS GTPase activating protein Nf1 significantly increases the total number of CBIs. Furthermore, I found that the mechanism of vasculogenesis employed by the heart also occurs from the umbilical and vitelline arteries. During midgestation clusters of hematopoietic cells detach from the artery forming extravascular islands. The extravascular islands than sprout and contribute to nearby vessels. My studies revealed new sites of hematopoiesis and shed light on a novel mechanism of vasculogenesis that is coupled with embryonic hematopoiesis. In the final section of this dissertation, I discuss the precursors of HSCs called hemogenic endothelium (HE). HE undergoes an endothelial to hematopoietic transition (EHT), which is dependent on the transcription factor, Runx1. Runx1 activates hematopoietic genes and inhibits endothelial genes resulting in the endothelial to hematopoietic transition. By ectopically expressing Runx1 in endothelium, I found that embryonic and fetal populations are competent to respecification into multilineage hematopoietic cells but adult endothelium is not. Understanding the specification of HE will be imperative for the successful derivation of HSCs in vitro. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Nancy A. Speck This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2659
Isolation of 11 new polymorphic microsatellites from CA enriched turkey genomic libraries.

Abstract. Microsatellite loci from the ancient Hungarian variety of the Broad Breasted Bronze Turkey (Meleagris gallopavo) were isolated. CA-repeat enriched libraries were constructed from DNA of randomly collected samples. Libraries were screened for repeat-containing clones by PIMA (PCR Isolation of Microsatellite Arrays) and the DNA-sequence of 167 positive clones was determined. A total of 136 microsatellite repeat-containing sequences were found, 59 sequences were unique. Comparing these with the genomic databases, we found 7 previously annotated microsatellite sequences. The newly isolated 52 microsatellites were tested on the mapping population of the University of Minnesota, and the map position of 11 microsatellites was determined.
The complete mitochondrial genome of the axillary seabream, Pagellus acarne (Perciformes: Sparidae)

Abstract The axillary seabream (Pagellus acarne, Risso 1827) belongs to the Sparidae family, order Perciformes. This high-valued commercial fish species is distributed along the northern and eastern Atlantic coasts from Norway to Senegal, and throughout the Mediterranean Sea. Its complete mitochondrial genome is 16,486 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (D-loop, 808 bp and L-origin, 29 bp). Its overall base composition is A: 26,8%, C: 29,0%, G: 17.6%, and T: 26.6%.
Light-sensitive Albino Tea Plants and Their Characterization

Albino tea plants are mutants that grow albino young leaves owing to lack of chlorophylls under certain environmental conditions. There are two types of albino tea plants grown in production, i.e., light- and temperature-sensitive albino tea cultivars. The former grows albino leaves in yellow color under intensive sunlight conditions and the later grows albino leaves with white mesophyll and greenish vein as the environmental temperature is below 20 8 C. Both albino teas attract great attention because of their high levels of amino acids and the ‘‘ umami’’ taste. There have been many studies focusing on the temperature-sensitive albino tea plants, whereas little attention has been given to the light-sensitive albino tea cultivars. The characteristics of the albino tea cultivars and the mechanism underlying them were reviewed in the present article based on the published literatures, including chemical compositions, morphological characteristics, and molecular genetic mechanism.