Miracle-dz/UniFAR-FTUs huggingface dataset:
Bovine Mastitis Resistance: Novel Quantitative Trait Loci and the Role of Bovine Mammary Epithelial Cells

35 Background . 36 Methods . 38 Results . 42 Discussion . 44 Conclusions . 48 ix III. BOVINE MAMMARY EPITHELIAL CELLS FROM MASTITISRESISTANT AND MASTITIS-SUSCEPTIBLE LACTATING HOLSTEIN COWS DISPLAY DIFFERENTIAL EXPRESSION OF INFLAMMATORY GENES IN RESPONSE TO LIPOPOLYSACCHARIDE . 61 Abstract . 61 Background . 62 Methods . 65 Results . 69 Discussion . 71 Conclusions . 75 IV. PRIMARY BOVINE DERMAL FIBROBLASTS DISPLAY SIMILAR INTERLEUKIN 1Β EXPRESSION CHANGES TO PRIMARY BOVINE MAMMARY EPITHELIAL CELLS IN RESPONSE TO LIPOPOLYSACCHARIDE . 80 Abstract . 80 Background . 81 Methods . 84 Results . 89 Discussion . 92 Conclusions . 99 V. EXOGENOUS PHOSPHOLIPASE A2 AFFECTS EXPRESSION OF INTERLEUKIN-8 AND CHEMOKINE (C-X-C MOTIF) LIGAND 1 BY PRIMARY BOVINE MAMMARY EPITHELIAL CELLS IN RESPONSE TO LIPOPOLYSACCHARIDE . 102 Abstract . 102 Background . 103 Methods . 106 Results . 110 Discussion . 111 Conclusions . 113 VI. ESTABLISHMENT OF A MILK-DERIVED BOVINE MAMMARY EPITHELIAL CELL LINE WITH EXTENDED GROWTH CAPABILITIES BY TRANSFECTION WITH A SIMIAN VIRUS 40 LARGE T ANTIGEN-CONTAINING PLASMID CONSTRUCT . 116 Abstract . 116 Background . 117 x Methods and Results . 120 Conclusions . 124 VII. CONCLUSIONS . 127 REFERENCES . 131 APPENDICES . 180 CURRICULUM VITAE . 198
Fatty Acid Profile of Freshwater Crab (Paratelphusha lamellifrons) from Padma River of Rajshahi City, Bangladesh

Freshwater crab Paratelphusha lamellifrons from Padma River were investigated for proximate and fatty acid composition. Proximate analyses of the claw and body meat of crab revealed the presence of moisture, crude protein, crude lipid and ash and their amount ranges between 71.72%-81.30%, 35.01%-49.06%, 13.24%-17.64% and 19.62%-22.12% respectively, on a dry weight basis. Except lipid (17.64%), claw meat content higher amount of moisture (81.30%), protein (49.06%) and ash (22.12%) compared to body meat. The fatty acid composition was analyzed by GC-FID and total 12 types of fatty acid were recorded in the fat isolated from crab. Among the recorded fatty acids MUFA were observed as the highest (42.85%), SFA were the second (25.96%) whereas, polyunsaturated (PUFA) were the lowest (15.02%). The fatty acid compositions showed that the SFA, MUFA and PUFA were dominated by palmitic acid (20.49%), oleic acid (23.99%) and linoleic acid (9.81%) respectively. The proximate and fatty acid composition of the present study demonstrated that these species (P. lamellifrons) are a promising source of essential fatty acids ω-3 and ω-6 namely, DHA and EPA.
Coconut Milk, Soy Milk, and Fish Flour as Bacillus sphaericus’s Alternative Media Material Used in the Control of Anopheles sp.

Some materials can be used to suppress mosquito larvae. One is entopathogenic microbial-based biopesticides, such as Bacillus thuringiensis for the control of Aedes aegypti larvae and Bacillus sphaericus to suppress Culex and Anopheles larvae. B.sphaericus does not require carbohydrates in its growth, because it lacks the enzymes necessary to enter carbohydrates and convert them into energy sources. However, various materials rich in protein and fat are reported to support their growth, even from simple sources. Coconut milk without water, fish flour and soy milk are common food ingredients consumed by the people of Indonesia. The purpose of this research is to know the ability of simple media with 30% v / v coconut milk formula, 30% v / v soy milk, 30% w / v fish flour as a simple medium for B. sphaericus growth. The results showed that a simple medium with a formula of 30% coconut milk showed the most fertile B. sphaericus growth of 296 x 108 cells / ml, fish flour 30% w / v 291 x 108 cells / ml and soy milk 30% v / v 89 x 108 Cell / ml. The results of Bioassay B. sphaericus test on coconut milk media, Anopheles sp larvae that died from 24 hours 15 larvae, at 42 hours and 72 hours killed 20 larvae.
The mRNA sequence polymorphisms of flowering key genesin bolting sensitive or tolerant sugar beet genotypes

One of the most important characteristics of sugar beet planting in temperate climates is the tolerance against early bolting. Understanding the genetic control of sugar beet flowering can help to develop the bolting-tolerant cultivars. In this study, the transcript sequences of 2 VIN3 copies, frigida, VRN1, EMF2, BvFT1, and BTC1 genes in 4 bolting tolerant and sensitive sugar beet genotypes were evaluated. Leaf samples were taken from plants in 2 growing stages, before and during cold exposure. The amplified fragments of both tolerant and sensitive genotypes were similar in length and the comparison of their transcript sequence showed polymorphism. In overall, 18 mutations comprising 1 mutation in frigida sequence, 14 single nucleotide polymorphisms (SNPs) in 2 copies of BvVIN3 sequence, 2 SNPs in BvFT1 sequence, and 1 insertion/deletion mutation for BTC1 were characterized. The last one caused a frameshift in the encoded protein. Despite the key role of the above mentioned genes, results showed that SNPs identified in this study were not associated with bolting tolerance or sensitivity. There may be differences in the expression levels of these proteins, which necessitates further exploration.
MANEJO DE LA NUTRICIÓN DEL CULTIVO DE CACAO EN LA REGIÓN DE SANTO DOMINGO

A long term experiment was initiated to evaluate the effect of the nutritional management over the morphoproductive behavior of two cocoa (Theobroma cacao) cultivars from planting to production stabilization. The study started on March 2009, and this article reports the results obtained during the two years period of the experimental orchard establishment. The site is located at the Experimental Farm of the Universidad Tecnologica Equinoccial, Campus Santo Domingo, Ecuador. A total of 1 130 seedlings were planted 3.5 by 3.5 m apart. Two cocoa genetic materials (National and CCN51) with 7 fertilization treatments (control, N, NP, NPK, NPKSMg + Micros, Chicken manure y NPKSMg + Micros + Chicken manure) were valuated. For the statistical analysis a completely randomized block design with a factorial arrangement (2 x 7) was utilized. The morphometric variables evaluated during the establishment period were stem diameter, and plant height and the productive variables were vigor index, incidence of witch’s broom disease (Moniliophtora perniciosa) and yield. Differences among cocoa cultivars were observed (P 0.05) for witch´s broom. CCN51 cocoa yield was greater than National EET95 (P<0.05) on spite of the lower vegetative growth, suggesting that the nutrient and other metabolic compounds sink in the plant truck consolidates early in the CCN51 genetic material, condition which would promote greater yield during the adult life of the orchard. Evaluation of treatments in the experiment will continue for several years.
Effects of probiotic Lactobacillus pentosus S-PT84 and prebiotic isomaltodexrin on microbiota population in low-grade chronic inflammation in C57BL/6 mouse model

Effects of probiotic Lactobacillus pentosus S-PT84 and prebiotic isomaltodexrin on microbiota population in low-grade chronic inflammation in C57BL/6 mouse model Lingzi Zong Advisor: University of Guelph, 2017 Professor Y. Mine This project aimed to demonstrate the effect of probiotic Lactobacillus pentosus S-PT84 and prebiotic isomaltodexrin (IMD) on disordered gut microflora in lipopolysaccharide (LPS)induced low-grade chronic inflammatory mouse model. LPS administration to mice leads to increased intestinal permeability and elevated LPS, which ultimately causes metabolic endotoxemia and low-grade inflammation. Real-time quantitative polymerase chain reaction (qRT-PCR) was used to determine quantitative changes of Bifidobacteria bifidum, Lactobacillus casei, Escherichia coli, Clostridium difficile, and Bacteroides fragilis. Pre-treatment with L. pentosus S-PT84 or IMD increased the relative population expression of B. bifidum, L. casei, and B. fragilis, and decreased the relative population expression of E. coli and C. difficile. Moreover, probiotic L. pentosus S-PT84 and prebiotic IMD alleviated the disturbance of gut microflora in LPS-treated mice as the number of B. bifidum, L. casei, and B. fragilis increased, and E. coli and C. difficile decreased when compared to LPS-treated mice. The analysis of short chain fatty acids (SCFAs) further supported that the concentrations of acetic and butyric acids were positively correlated with probiotic L. pentosus S-PT84 and prebiotic IMD, as well as the number of beneficial bacteria. This study elucidates that probiotic L. pentosus S-PT84 and prebiotic IMD are potent nutraceuticals, beneficial for gut microbiota improvement.
In search of relevant predictors for marine species distribution modelling using the MarineSPEED benchmark dataset

Ideally, datasets for species distribution modelling (SDM) contain evenly sampled records covering the entire distribution of the species, confirmed absences and auxiliary ecophysiological data allowing informed decisions on relevant predictors. Unfortunately, these criteria are rarely met for marine organisms for which distributions are too often only scantly characterized and absences generally not recorded. Here, we investigate predictor relevance as a function of modelling algorithms and settings for a global dataset of marine species.
Effect of the application of biochar and Acacia mangium litter on maize in Alley cropping in Bateke plateau / DRC

The management of sandy soil in Bateke plateau to feed Kinshasa population in continued growth, is one of the problems that arises in this urban peripheral agriculture. Agroforestry in time, alternating trees and crops on the same land was used as technical means to increase fertility and production. However, agricultural practice in the long term at Bateke plateau showed that agroforestry was not able alone to ensure continuity of production on the same land. In this study, we tested the effect of biochar associated with litter from an agroforestry system could have on improving maize production in Bateke plateau. We observed that forty one and five months respectively after application of biochar and litter maize production was influenced favorably. Among all combinations of biochar doses (0, 2, 4 and 8 kg / m2) and Acacia mangium litter doses (0, 5, 10 and 20 t / ha), the combination of 4 Kg / m2 of biochar with 20 t / ha of litter was the best with 2019 kg / ha of maize cobs with spathe. Moreover, the presence of the clipped hedge has had an effect on the stems and maize cobs differently on plants in his neighborhood and those in the middle of the experimental plot.
Mechanism of Mismatch Repair Induced Mutagenesis in Somatic Hypermutation

B cells produce a diverse array of antibody specificities that are of low affinity during the initial phase of a humoral immune response. However, somatic hypermutation of the rearranged V region in the immunoglobulin locus generates new antibody affinities, accompanied by the selection of B cells that produce superior antibody affinities. Somatic hypermutation is initiated by the conversion of G:C base pairs to G:U lesions by the enzyme activation induced cytosine deaminase. Left unrepaired, G:U lesions will give rise to transition mutations at G:C base pairs, but are converted to transition and transversion mutations at G:C and A:T base pairs by the paradoxical participation of the base excision repair and mismatch repair pathways. The mismatch repair pathway, which evolved to correct errors produced during DNA replication, is co‐opted by hypermutating B cells to produce A:T mutations via the processing of G:U lesions. This process requires the mismatch repair components Msh2, Msh6, and Exo1, but is additionally dependent upon the translesional DNA polymerase η, a known A:T mutator, and on ubiquitinated PCNA, an initiator of translesion synthesis. The presence of certain types of lesions in the template strand during DNA replication leads to the activation of translesion synthesis. I propose
What are the most influencing factors in reconstructing a reliable transcriptome assembly?

Reconstructing the genome and transcriptome for a new or extant species are essential steps in expanding our understanding of the organism’s active RNA landscape and gene regulatory dynamics, as well as for developing therapeutic targets to fight disease. The advancement of sequencing technologies has paved the way to generate high-quality draft transcriptomes. With many possible approaches available to accomplish this task, there is a need for a closer investigation of the factors that influence the quality of the results. We carried out an extensive survey of variety of elements that are important in transcriptome assembly. We utilized the human RNA-Seq data from the Sequencing Quality Control Consortium (SEQC) as a well-characterized and comprehensive resource with an available, well-studied human reference genome. Our results indicate that the quality of the library construction significantly impacts the quality of the assembly. Higher coverage of the genome is not as important as the quality of the input RNA-Seq data. Thus, once a certain coverage is attained, the quality of the assembly is mainly dependent on the base-calling accuracy of the input sequencing reads; and it is important to avoid saturating the assembler with extra coverage.
Technical Advance Detection of 1p and 19q Loss in Oligodendroglioma by Quantitative Microsatellite Analysis, a Real-Time Quantitative Polymerase Chain Reaction Assay

The combined loss of chromosomes 1p and 19q has recently emerged as a genetic predictor of chemosensitivity in anaplastic oligodendrogliomas. Here, we describe a strategy that uses a novel method of realtime quantitative polymerase chain reaction, quantitative microsatellite analysis (QuMA), for the molecular analysis of 1p and 19q loss in oligodendrogliomas and oligoastrocytomas in archival routinely processed paraffin material. QuMA is performed on the ABI 7700 and based on amplifications of microsatellite loci that contain (CA)n repeats where the repeat itself is the target for hybridization by the fluorescently labeled probe. This single probe can therefore be used to determine copy number of microsatellite loci spread throughout the human genome. In genomic DNA prepared from paraffin-embedded brain tumor specimens, QuMA detected combined loss of 1p and 19q in 64% (21 of 32) of oligodendrogliomas and 67% (6 of 9) of oligoastrocytomas. We validate the use of QuMA as a reliable method to detect copy number by showing concordance between QuMA and fluorescence in situ hybridization at 37 of 45 chromosomal arms tested. These results indicate that QuMA is an accurate, highthroughput assay for the detection of copy number at multiple loci; as many as 31 loci of an individual tumor can be analyzed on a 96-well plate in a single 2-hour run. In addition, it has advantages over standard allelic imbalance/loss of heterozygosity assays in that all loci are potentially informative, paired normal tissue is not required, and gain can be distinguished from loss. QuMA may therefore be a powerful molecular tool to expedite the genotypic analysis of human gliomas in a clinical setting for diagnostic/prognostic purposes. (Am J Pathol 2001, 158:1253–1262)
Ichthyo-faunal diversity of Morang district, Nepal

The present paper attempts to report a total of 118 fish species spread over 11 orders, 26 families and 64 genera inhabited indifferent water bodies viz, rivers, reservoirs, streams, ponds, lakes, canals, ditches, paddy fields of Morang district, collected during a one-year survey. The order Cypriniformes is the richest one among 11 orders that comprises 59 species followed by Siluriformes having 31 and Perciformes with 19 representatives, respectively. Orders Anguilliformes, Osteoglossiformes, Beloniformes, Cyprinodontiformes, Synbranchiformes and Tetraodontiformes have only one representative. Olyra longicaudata is the new report from Morang district and the second report from Nepal. Besides this, other hill-stream fishes viz . , Pseudecheneis sulcatus, Schizothorax plagiostomus, Schistura savona and Neolissochilus hexagonolepis recorded during the survey, also have not been previously reported from this district.
Astrocyte networks and intercellular calcium propagation

Astrocytes organize in complex networks through connections by gap junction channels that are regulated by extra‐ and intracellular signals. Calcium signals generated in individual cells, can propagate across these networks in the form of intercellular calcium waves, mediated by diffusion of second messengers molecules such as inositol 1,4,5-trisphosphate. The mechanisms underpinning the large variety of spatiotemporal patterns of propagation of astrocytic calcium waves however remain a matter of investigation. In the last decade, awareness has grown on the morphological diversity of astrocytes as well as their connections in networks, which seem dependent on the brain area, developmental stage, and the ultrastructure of the associated neuropile. It is speculated that this diversity underpins an equal functional variety but the current experimental techniques are limited in supporting this hypothesis because they do not allow to resolve the exact connectivity of astrocyte networks in the brain. With this aim we present a general framework to model intercellular calcium wave propagation in astrocyte networks and use it to specifically investigate how different network topologies could influence shape, frequency and propagation of these waves.
Phytochemical Analysis and Antioxidant Activity Essential Oil of Anaphalis Contorta from Uttrakhand Himalayas

Anaphalis contorta Hook is an erect herb. The stem is branched from the base, branches are often decumbent. The leaves are linear, crowded, shortly lobed at the base, margins recurved sometimes. The heads are in dense terminal corymbs and in involucral bracts are broad, obtuse, erect in flower, spreading in fruit; outer ones often pale purple. A. contorta is widely distributed in temperate region from Kashmir to Sikkim and Afghanistan to South West China at a height of 1500-4500m [1-3].
The stress peptide PACAP-38 protects neurons against ketamine-induced apoptosis in developing rat retina

Early exposure to general anesthetics can cause widespread neuronal apoptosis and long-term neurocognitive deficits. However, the combined effects of general anesthetics and various noxious stimulations on animal neuronal survival are controversial. This study aimed to assess the effects and mechanisms of pituitary adenylate cyclase-activating peptide-38 (PACAP-38, a master stress peptide produced by noxious stimulation) on ketamineinduced neuronal apoptosis. Whole-mount retinas isolated from postnatal day 7 Sprague Dawley rats were cultured and incubated with 150 μM ketamine for 5 hours in the presence or absence of PACAP-38. Then, immunohistochemistry detecting active caspase-3 and TUNEL assay were used to evaluate neuronal apoptosis in the retinal ganglion cell layer. Interestingly, 10-8 M PACAP-38 significantly reduced ketamine-induced neuronal apoptosis in the retinal ganglion cell layer with mean ratios of caspase-3 positive cells decreasing from 6.5±0.7% to 3.2±0.2% (P<0.001) and TUNEL-positive cells from 31.3±4.4% to 16.9±3.0% (P=0.004), respectively. PACAP6-38, a PACAP-38 antagonist, abolished the anti-apoptotic effect of PACAP-38 at 10-7 M. Further assessments showed that PACAP’s anti-apoptotic effects could be partly antagonized by adenylate cyclase (AC) and protein kinase A (PKA) inhibitors, respectively, and mostly counteracted by extracellular signal-regulated kinase (ERK1/2) inhibitor. In summary, our study demonstrated PACAP-38 could protect neurons from ketamine-induced apoptosis in early developmental rat retina. This anti-apoptotic effect PACAP-38 is partly dependent on the cAMP/PKA signaling pathway, and mainly ascribed to ERK1/2.
Shedding light on an East-Mediterranean mesophotic sponge ground community and the regional sponge fauna

Sponges are a diverse and abundant phylum, globally inhabiting many hard-bottom habitats. However, data on the East-Mediterranean sponge communities are scarce, outdated, and limited to the shallow waters. This study sought to expand the knowledge of the poriferan fauna along the Mediterranean shore of Israel. A newly-discovered mesophotic sponge ground at ~100 m depth was studied using a remotely-operated vehicle (ROV), in addition to shallow-water surveys conducted by scuba diving. In the mesophotic ecosystem, sponges, serving as environmental engineers, create complex 3D structures that attract invertebrates and fish. The results of the quantitative survey of this mesophotic sponge ground reveal that it maintains a rich and diverse community with an estimated 63 species, and a high sponge percent coverage (~35%). Several of the mesophotic species are documented for the first time from the Levant basin, while others might be novel species. Here we identified over 100 sponge species along the Mediterranean coast of Israel, 33 of which were sampled from the mesophotic sponge ground. The updated sponge list supports the hypothesis that the Levantine sponge diversity is not as species-poor, compared to other parts of the Mediterranean Sea, as has previously been considered. In addition, shallow and mesophotic sponge community compositions were found to only partially overlap. Moreover, the latter harbors some species that have disappeared from the shallow habitats, and only a few species thrive along the entire depth range. We suggest that mesophotic sponge grounds may serve as refugia for species stressed by the rising temperatures in shallow waters and should be protected from anthropogenic influences such as oil and gas drilling.
Immunity and Sub-Acute Ruminal Acidosis

Sub-acute ruminal acidosis (SARA) can occur as a consequence of feeding high energy rations to dairy cattle. During SARA, the rate of rumen short-chain fatty acid (SCFA) production exceeds SCFA absorption and results in an unhealthy depression of rumen pH. The severity of SARA is quantified based on the duration and magnitude of depression of rumen pH below a threshold (typically 5.6 or 5.8), and has been most well characterized in ruminally cannulated cows.
Evaluation of Grain Yield, Quality and Nutrients Content in Four Rice (Oryza sativa L.) Genotypes

Aims: The main objective of the study is to combining the higher yield and micronutrient content along with good grain cooking quality in polished rice. Study Place and Duration of Study: The experiment was conducted in the farm of Indian Institute of Rice Research, Hyderabad, India. The duration of the study was two successive wet seasons 2013 and 2014. Methodology: The experiment was conducted in a randomized complete block design (RCBD). Four rice accessions consist of two parent lines (Samba Mahsuri and Chittimutyalu) and two derivatives (BPCM1 and BPCM2) were grown under normal agronomical conditions, evaluated for their yield, grain quality and nutritional properties. The four genotypes were profiled with RM markers. Results: Both the derivative lines BPCM1 and BPCM2 have shown higher yield advantage (4.5% and 8.8%) than the parent Samba Mahsuri along with quality parameters like amylose content Original Article (23.3%, 25%) and gel consistency (21.5, 23.7) as well as high zinc content (20.6 ppm, 24 ppm) moderate iron content (3.6 ppm, 4.3 ppm) in polished rice. High heritability (0.91%) was found for the all traits studied. The association of grain yield is significant with harvest index, test weight and straw yield. Grain zinc content was significantly and positively associated with iron content and negatively associated with total protein. The experiment result indicates that, the micronutrient enhancement could be possible along with grain yield and cooking quality.