Miracle-dz/UniFAR-FTUs huggingface dataset:
Dengue Virus Infection of Human Microvascular Endothelial Cells

ii STATEMENT OF ORIGINALITY . v ACKNOWLEDGMENTS . vi TABLE OF CONTENTS . viii LIST OF FIGURES . xiii LIST OF TABLES . xvii ABBREVATIONS . xviii Chapter I . 1 Literature review . 1 1.1 Family Flaviviridae . 2 1.1.1 History. 2 1.1.2 Classification of Flaviviridae . 2 1.2 Dengue virus . 4 1.2.
Effect of Edible Coatings and Storage Temperatures on Maintenance of Aril Quality and Microbial Population of Pomegranate cv. Bhagwa Packed in Clamshells

Pomegranate (Punica granatum L.) which is regarded as the „elixir of life‟ is a rich source of minerals, vitamins and nutrients. It belongs to the family Punicaceae and originated from Iran. Pomegranate fruits are large round berries called as balusta and aril is the edible material. It has seen a remarkable increase in the commercial farming, due to its potential health benefits such as, its high anti-oxidant, anti-mutagenic, anti-hypertension activities and the ability to reduce liver injury (Violeta Lopez-Rubira, 2005). Pomegranate fruits are consumed fresh or processed as juice, jellies and syrup for industrial production. In recent years, minimally processed ready-to-eat pomegranate arils have become popular due to their convenience and high value. Minimal processing which involves light processing such as peeling is of great importance for adding convenience to the consumers. The processing of externally damaged pomegranates could be an excellent way to obtain a commercial profit from discarded pomegranates that are unacceptable for fresh marketing and consumption. A commercialization of minimally processed and International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 01 (2018) Journal homepage: http://www.ijcmas. com
Screening Antibacterial Agent from Crude Extract of Marine-Derived Fungi Associated with Soft Corals against MDR-Staphylococcus haemolyticus

Multidrug resistant Staphylococcus haemolyticus is a Gram-positive bacteria and member of coagulase negative staphylococci (CoNS) which has the highest level of antimicrobial resistance. This nosocomial pathogen due to skin or soft tissue infections, bacteremia, septicemia, peritonitis, otitis media, meningitis and urinary tract infections. The ability to produce enterotoxins, hemolysins, biofilm, and cytotoxins could be an important characteristic for the successful of infection. Marine-derived fungi have potency as a continuous supply of bioactive compound. The aim of this research was screening antibacterial agent from crude extracts of marine-derived fungi associated with soft corals against MDR-S. haemolyticus. Among 23 isolates of marine-derived fungi isolated from 7 soft corals, there were 4 isolates active against MDR-S. haemolyticus. The screening was conducted by using agar plug diffusion method. Isolate PPSC-27-A4 had the highest antibacterial activity with diameter 23±9,6 mm. The crude extract from this isolate had been confirmed to antibacterial susceptibility test and it had the highest antibacterial activity in 12.2 mm with concentration of 300μg/ml from mycelia extract. PPSC-27-A4 had been characterized in molecular, based on the sequence analysis of 18S rRNA, PPSC-27-A4 isolate was identified as Trichoderma longibrachiatum.
Uterine Contractile Activity of Extract of Icacina trichantha on Albino Non-Pregnant Rat Uterus

The use of medicinal plants to facilitate birth or protect the young foetus is a common practice in Edo and Delta states of Nigeria. Icacina trichantha has been reported to have anti-inflammatory, antioxidants and antimicrobial activities while saponins, chalcones, anthocyanidins have been reported as phytoconstituents. The ‘Ibo’ tribe of Eastern Nigeria considers the plant to be an aphrodisiac, and they use it on soft tumors. In most rural communities in Southern Nigeria, the tuber is used extensively by herbalists and traditional doctors in the treatment of constipation, poisoning, to induce emesis, and to treat malaria. In the work of Otun, isolated oil of Icacina tichanta has been reported to constitute stearolic acid, a monounsaturated fatty acid which is an acetylenic analogue of oleic acid that has been implicated for the hypotensive effect of olive oils. Ethanol extract of I, ttichanta had been reported to significantly protect the liver and the kidneys of carbon tetrachloride-poisoned rats. In another study, I. trichantha extract was observed to exhibit significant analgesic effect and Ferreira corroborated the analgesic activity by implying that the effect is an anti-inflammatory, analgesic, like aspirin or indomethacin, which block the cyclooxygenase pathway of arachidonic acid metabolism. The research of Umoh has shown that I.trichanta, a root/tuber crop contains antinutritional factors like hydrogen cyanide, soluble and total oxalate, tannin, phytate and alkaloids. While the root of I. trichanta is edible, with a strong presence
Oviposition preference and development of rice weevil, Sitophilus oryzae (Lin.) (Coleoptera: Curculionidae) in different stored grains

Oviposition preference and development of rice weevil, Sitophilus oryzae (Coleoptera: Curculionidae) were observed in three varieties of stored grains i.e. parboiled rice ( Oryza sativa ), wheat ( Triticum aestivum ) and pulse ( Cicer arietinum ). In no choice tests, the mean number of eggs laid were 360.3 ±2.60 in rice, 382 ±2.49 in wheat and 394± 2.06 in pulse. In case of choice tests, the mean number of eggs laid were 13.6±0.4 in rice, 14.2 ±0.37 in wheat and 15.6 ±0.4 in pulse. The differences between the number of eggs laid in rice, wheat and pulse varied significantly in both no-choice and choice tests. The respective incubation period, larval and pupal period of the weevil reared on rice, wheat and pulse were 5.7 ±0.27, 5 ±0.47 and 5.4 ±0.27 days, respectively, 21 ±0.47, 20.3 ± 0.27, 19 ±0.47 days, respectively and 10.3 ±0.27, 10.7 ±0.27, 11.3 ±0.27 days, respectively. The total development time from egg to adult recorded in rice, wheat and pulse was 37 ±0.47, 36 ±0.47 and 35.6 ±0.72 days, respectively. The difference between the larval periods was significant (p < 0.05) when they reared in wheat and pulse. The larval and pupal period varied significantly (p < 0.05) between the individuals reared in rice and pulse. The developmental period was shorter in pulse than in rice and wheat. Bangladesh J. Zool. 45 (2): 131-138, 2017
Biological activity of selected plant ethanolic extracts against phytopathogenic fungi, Fusarium oxysporum f.sp. cicer

In this present study six different plants used in traditional Sudanese medicine; Allium sativum L . (Liliaceae), Azadirachta indica (Meliaceae), Capsicum frutescence L. (Solanaceae) , Momordica balsamina (Cucurbitaceae), Petroselinum crispum (Apiaceae) and Pulicaria undulata L. (Asteraceae), were examined against Fusarium oxysporum f.sp . cicer . , the causal agent of vascular wilt in chickpea. We used disc agar method to determine the in vitro antifungal activity of these plants. The ethanolic extracts of studied plants exhibited varying degrees of inhibition activity against the tested fungi. Among the 6 plants studied only two plants ( A. sativum, P. crispum ) showed high activity, other plants ( M. Balsamina, A. indica, C. frutescence, P. undulata ) showed moderate activity. These results suggest that the plants may have individual components that can be useful for managing Fusarium oxysporum f.sp . cicer.
Genetic recombination of poliovirus facilitates subversion of host barriers to infection

The contribution of RNA recombination to viral fitness and pathogenesis is poorly defined. Here, we isolate a recombination-deficient, poliovirus variant and find that, while recombination is detrimental to virus replication in tissue culture, recombination is important for pathogenesis in infected animals. Notably, recombination-defective virus exhibits severe attenuation following intravenous inoculation that is associated with a significant reduction in population size during intra-host spread. Because the impact of high mutational loads manifests most strongly at small population sizes, our data suggest that the repair of mutagenized genomes is an essential function of recombination and that this function may drive the long-term maintenance of recombination in viral species despite its associated fitness costs. Significance Statement RNA recombination is a widespread but poorly understood feature of RNA virus replication. For poliovirus, recombination is involved in the emergence of neurovirulent circulating vaccine-derived poliovirus, which has hampered global poliovirus eradication efforts. This emergence illustrates the power of recombination to drive major adaptive change; however, it remains unclear if these adaptive events represent the primary role of recombination in virus survival. Here, we identify a viral mutant with a reduced rate of recombination and find that recombination also plays a central role in the spread of virus within animal hosts. These results highlight a novel approach for improving the safety of live attenuated vaccines and further our understanding of the role of recombination in virus pathogenesis and evolution.
Veterinary and public health aspects in tilapia (Oreochromis niloticus niloticus) aquaculture in Kenya, Uganda and Ethiopia.

1 Dept. Veterinary Public Health and Animal Pathology, Bologna University, Italy; 2 Dept. Public Health, Comparative Pathology & Veterinary Hygiene, University of Padua, Italy; 3 Environment Agency, Vienna, Austria; 4 Dept. Freshwater Ecology, University of Vienna, Austria ; 5 Egerton University, Kenya; 6 Moi University, Kenya; 7 Sagana Fish Culture Farm, Kenyan Ministry of Fisheries Development, Kenya; 8 Kenya Marine & Fisheries Research Institute, Kenya ; Dept. Zoology, Makerere University, Kampala, Uganda; 10 Dept. of Aquaculture, Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda; 11 Ethiopian Institute of Aquaculture Research, Addis Ababa, Ethiopia. _______________________________
Nutrient composition of full fat and defatted rice bran

The present investigation was conducted to evaluate the nutrient composition of full fat/defatted rice bran. The content of crude protein, crude fiber, ash, total carbohydrates and total dietary fiber of full fat and defatted rice bran were 11, 13.80; 10.90, 13.10; 9.20, 11.60; 49.92, 61.46; 21.63, 24.50 per cent, respectively. The amount of total Ca, P, Mg, Fe and K of full fat and defatted rice bran were 69.23, 69.80; 1331, 1345; 798, 826; 32.80, 33.31 and 1435, 1456 mg per 100g, respectively. The protein digestibility of full fat rice bran (65.86%) was less as compared to that of defatted rice bran (66.56%). Defatted rice bran had 6.21 mg available iron and 17.57 mg available calcium per 100g which were significantly (P<0.05) higher than those of full fat rice bran. Because of removal of fat, the relative amounts of other nutrients changed proportionately in defatted rice bran.
Isolation and cross-amplification of fifteen microsatellites for oil-rewarding Calceolaria species (Calceolariaceae)

Calceolaria is a diversified American genus whose species are mainly visited by oil-collecting bees, representing a highly specialized plant-pollinator system. However, although this is a unique plant system, different aspects of its ecology and evolution remain unexplored. In this study we characterized fifteen polymorphic microsatellites for four Andean Calceolaria species using next-generation sequencing. The number of alleles per locus (Na) for the study species ranged from 2 to 11, and the observed (Ho) and expected (He) heterozygosity ranged from 0 to 0.85 and 0.3 to 0.87, respectively, while FIS ranged from 0.03 to 1.0. Among the four species, C. cana showed the greatest genetic diversity, followed by C. filicaulis. C. arachnoidea and C. lanigera showed similar, lower genetic diversity. These makers are a useful tool to conduct futures studies on population structure and gene flow. Specifically, this set of markers will be helpful to estimate selfing rates as a first approximation to the understanding of the role of specialization in plant mating system evolution
Isolation of Genomic Deoxyxylulose Phosphate Reductoisomerase (DXR) Mutations Conferring Resistance to Fosmidomycin

Sequence to activity mapping technologies are rapidly developing, enabling the isolation of mutations that confer novel phenotypes. Here we used the CRISPR EnAbled Trackable genome Engineering (CREATE) technology to investigate the inhibition of the essential IspC gene in Escherichia coli. IspC gene product, Deoxyxylulose Phosphate Reductoisomerase (DXR), converts 1-deoxy-D-xylulose 5-phosphate to 2-C-methyl-D-erythritol 4-phosphate in the DXP pathway. Since this pathway is shared with many pathogenic bacteria and protozoa and is missing in humans, it is an appealing target for inhibition. We created a full saturation library of 33 sites proximal to ligand binding and other sites and challenged it with the DXR-specific inhibitor, fosmidomycin. We identified several mutations that confer fosmidomycin resistance. All sites are highly conserved and also exist in pathogens including the malaria-inducing Plasmodium falciparum. These findings may have general implications on the isolation of resistance-conferring mutations and specifically, may affect the design of future generations of fosmidomycin-based drugs. Significance The emergence of acquired drug resistance is a natural process that is likely to occur under most circumstances. Recently-developed technologies allow to map relative fitness contribution of multiple mutations in parallel. Such approaches may be used to predict which mutations are most likely to confer resistance, instead of waiting for them to evolve spontaneously. In this study, a rationally-designed IspC mutant library was generated genomically in E. coli. Mutants resistant to fosmidomycin, an antimalarial drug were identified, and most were in the highly conserved proline at position 274. These results may have implications on next-generation fosmidomycin drug design, and more broadly, this approach may be used for predicting mutational acquired resistance.
A possible link between specific transfer RNA methylation and tumorigenic phenotype of breast cancer

The human RNA methyltransferase BCDIN3D is overexpressed in breast cancer cells and involved in cellular invasion and poor prognosis of breast cancer. Several years ago, BCDIN3D was reported to dimethylate the 5'-monophosphate of specific precursor miRNAs (pre-miRNAs), such as the tumor suppressor miR145. Dimethylation of the 5'-monophosphate of the pre-miRNA negatively regulates the subsequent processing by Dicer in vitro , and results in the downregulated expression of the mature form of the miRNA. The depletion of BCDIN3D also reportedly results in the suppression of the tumorigenic phenotype of breast cancer cells. Thus, these findings suggested that BCDIN3D promotes the cellular invasion of breast cancer cells, by downregulating the expression of tumor suppressor miRNAs via the dimethylation of the 5'-monophosphate of the corresponding pre-miRNAs . Recently, we found that cytoplasmic tRNA His is actually the primary target of human BCDIN3D, rather than pre-miR145. BCDIN3D monomethylates the 5'-phosphate of cytoplasmic tRNA His much more efficiently than that of pre-miRNA in vitro , and is responsible for the monomethylation of the 5'-phosphate of cytoplasmic tRNA His in vivo . BCDIN3D recognizes the eight-nucleotide long extended acceptor helix with the G -1 -A 73 mis-pair at the top of the acceptor stem of tRNA His , which are exceptional features among cytoplasmic tRNA species. These results not only reveal the primary target of BCDIN3D, which is overexpressed in breast cancer cells, but also highlight the possible involvement of the 5'-phosphomethylation of tRNA and/or tRNA in the tumorigenesis of breast cancer cells, beyond its established function in protein synthesis.
Preparation of Chitosan/Rosemary Extract Nanoparticles and their Application for Inhibiting Lipid Oxidation in Grass Carp (Ctenopharyngodon idellus) during Cold Storage

ABSTRACT This study investigated a preparation of chitosan/rosemary extract nanoparticles (CS/RE-NPs) based on the principle of ionic gelation and their application for inhibiting grass carp lipid oxidation. CS/RE-NPs were found to have a rosemary extract (RE) encapsulation efficacy of 40.33%, average particle size of 199.90 nm, and zeta-potential of 35.60 mV. Structural analysis using UV–vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and transmission electron microscopy (TEM) indicated that the RE s were well incorporated into the CS-NPs. Treatment of the CS/RE-NPs inhibited lipid oxidation of the grass carp during cold storage, and the peroxide value (PV), thiobarbituric acid-reactive substance (TBARS) value, and lipoxygenase (LOX) activity of the CS/RE-NP-treated samples were lower than those of RE and CS-NP-treated samples, respectively. CS/RE-NP-treated samples also slowed the growth of bacteria, enhanced the organoleptic quality, and prolonged the shelf life of grass carp. This study suggested that CS/RE-NPs can be used as an antioxidant delivery system to inhibit lipid oxidation and improve food quality.
KOMBINASI ENZIM POLIGALAKTURONASE DAN ENZIM PEKTINESTERASE PADA KLARIFIKASI SARI BUAH NAGA SUPER MERAH (Hylocereus Costaricensis) DALAM PEMBUATAN SIRUP

Tujuan dari penelitian ini adalah untuk mengetahui pengaruh penggunaan enzim poligalakturonase (PG) bakteri Bacillus licheniformis strain GD2a AR2 pada konsentrasi 0,09%, 0,1%, dan 0,11 % dengn enzim pektinesterase (PE) Bacillus licheniformis strain GD2a KK2 pada konsentrasi 0,5%, 1%, dan 1,5% pada klarifikasi sari buah naga super merah dalam pembuatan sirup terhadap parameter pH, total padatan terlarut, transmitansi, dan viskositas. Enzim poligalakturonase menghidrolisis ikatan α-1,4- D-glikosidik membentuk asam galakturonat. Enzim pektinesterase bekerja pada ikatan ester senyawa pektin sehingga dihasilkan asam pektat. Enzim poligalakturonase dan enzim pektinesterase bekerja secara sinergis. Enzim pektinesterase mengkatalis pektin menjadi asam pektat yang merupakan substrat untuk enzim poligalakturonase. Pada pH yang rendah, penggunaan enzim poligalakturonase dan enzim pektinesterase dapat menurunkan viskositas dan nilai total padatan terlarut sirup buah naga super merah. Degradasi pektin meningkatkan transimtansi sirup buah naga super merah. Hasil penelitian ini diperoleh enzim poligalakturonase murni parsial dengan aktivitas enzim 0,31 U/ml dan enzim pektinesterase murni parsial dengan aktivitas enzim 1,167 U/ml. Sampel dengan penambahan enzim poligalakturonase 0,11% dan enzim pektinesterase 0,5% dengan nilai pH 4,303, nilai total padatan terlarut 38,133oBrix, nilai transmitansi 74,5%T, nilai viskositas 0,128cP merupakan sampel terpilih. Kata kunci: Buah naga super merah, enzim, klarifikasi, pektin, pektinesterase, poligalakturonase, sirup buah
From genes to function in autoimmunity - a salty story

Autoimmunity is a condition in which the ability to tolerate self breaks down, resulting in immune responses against the body’s own healthy cells and tissues. Autoimmune diseases are complex and multifactorial, and both genetic and environmental factors are known to play a crucial role. Using animal models, it is possible to study different aspects of arthritis disease development in an environmentally and genetically controlled setting. In this thesis, I have investigated the effect of genetic risk loci and the single environmental factor sodium chloride (NaCl) on immune cell function and the development of autoimmune diseases using mouse models. In Paper I, using four congenic sub-loci within the arthritis susceptible Cia9 locus on chromosome 1, we found that the NOD.Q polymorphic Fc gamma receptor gene (FcγR) cluster located within sub-loci Cia9i and Cia9k, regulated arthritis. Polymorphic FcγR2b and FcγR4 were contained in both Cia9i and Cia9k, whereas Cia9i mice also carried polymorphic FcγR3. FcγR2b gene and protein expression were downregulated in Cia9i and Cia9k mice, whereas FcγR3 was upregulated in Cia9i mice and found downregulated in Cia9k mice compared to littermate control mice. This difference in FcγR3 expression affected killing by NK cells and phagocytosis by macrophages in vitro and PC61 antibody induced regulatory T cell depletion in vivo. Interestingly, arthritis development was regulated by interaction between FcγR2b and FcγR3 without affecting anti-collagen type II antibody secretion. These results show that polymorphisms in both FcγR2b and FcγR3 regulate the severity of inflammatory responses. In paper II, we investigated the importance of the system A family of amino acid transporters (SNAT), based on an identified congenic locus, as mediators of immune cell function and arthritis development. We demonstrated that SNAT proteins affect the initial stages of lymphocyte activation by regulating glutamine uptake in the presence of Na, and that the effector phase of arthritis could be suppressed by blocking SNAT proteins. Paper III describes the effect of salt (e.g. NaCl) on the development of autoimmunity. Here we show that a moderate salt intake affects both T cell and macrophage phenotypes in vitro and ex vivo. However, these moderate levels of salt intake did not alter the development of T cell-dependent autoimmunity, whereas the dextran sulphate sodium (DSS)-induced colitis was exacerbated in mice pre-exposed to salt. Taken together, I have shown that the interplay between two genes enhances arthritis disease development, whereas a single environmental factor has no impact on arthritis despite triggering the immune system. These results contribute to the understanding of the mechanism behind complex multifactorial diseases as a small building block towards therapeutic intervention. SUMMARY FOR MY FAMILY
Feedback Regulation between Initiation and Maturation Networks Orchestrates the Chromatin Dynamics of Epidermal Lineage Commitment

Tissue development results from lineage-specific transcription factors (TF) programming a dynamic chromatin landscape through progressive cell fate transitions. Here, we interrogate the epigenomic landscape during epidermal differentiation and create an inference network that ranks the coordinate effects of TF-accessible regulatory element-target gene expression triplets on lineage commitment. We discover two critical transition periods: surface ectoderm initiation and keratinocyte maturation, and identify TFAP2C and p63 as lineage initiation and maturation factors, respectively. Surprisingly, we find that TFAP2C, and not p63, is sufficient to initiate surface ectoderm differentiation, with TFAP2C-initiated progenitor cells capable of maturing into functional keratinocytes. Mechanistically, TFAP2C primes the surface ectoderm chromatin landscape and induces p63 expression and binding sites, thus allowing maturation factor p63 to positively auto-regulate its expression and close a subset of the TFAP2C-initiated early program. Our work provides a general framework to infer TF networks controlling chromatin transitions that will facilitate future regenerative medicine advances.