Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo, in vitro and in silico

In vivo and in vitro are commonly used in biology and refer to experiments done in living organisms and outside of living organisms, respectively. On the other hand , in silico is an expression used to mean "performed on computer or via computer simulation . " In silico was coined in 1989 as an analogy to the Latin phrases in vivo and in vitro that had been in vogue in the biological sciences for some time In silico research in medicine has the potential to speed the rate of discovery while reducing the need for expensive laboratory work and clinical trials; this includes producing and screening drug candidates more effectively. Using the molecular modeling technique called Protein-ligand docking, the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme can be predicted. Pharmaceutical research employs such docking techniques for a variety of purposes, most notably in the rapid in silico assessment of large libraries of chemical structures in order to identify those structures that are most likely to bind to a drug target, typically a protein receptor or enzyme ; this helps to select likely drug candidates. Several protein-ligand docking software applications are available, such as Autodock or EADock . There is a web service, Molecular Docking Server that calculates the site, geometry and energy of small molecules interacting with proteins. Indeed, the protein docking algorithm EADock has been used to find potential inhibitors to an enzyme associated with cancer activity in silico . Fifty percent of the molecules identified were later shown to be active inhibitors of the enzymes in vitro . This result is far better than that of expensive high-throughput screening (HTS) which uses robotics, data processing and control software, liquid handling devices, and sensitive detectors, to quickly conduct millions of biochemical, genetic or pharmacological tests to identify active compounds, antibodies or genes for modulating particular biomolecular pathways. HTS involves testing thousands of diverse compounds a day often with an expected hit rate on the order of 1% or less with still fewer expected to be real leads following further testing. In silico models of tuberculosis have been developed in order to aid in identifying anti-tuberculosis drug candidates within minutes rather than months. Many cellular processes are being modeled on the computer, although no exact, fully predictive, computer model of a cell's entire behavior is yet available. These limitations are a result of the limitation of knowledge not only in molecular dynamics and cell biology, but also in computer processing power. In vitro and in vivo experiments have largely contributed to the much knowledge we have in the biological sciences today. The stage is set for in silico experimentation to throw more light on cellular processes, and contribute to the improvement of human welfare.
Original Contribution Biomarkers of oxidative stress study III. Effects of the nonsteroidal anti-inflammatory agents indomethacin and meclofenamic acid on measurements of oxidative products of lipids in CCl 4 poisoning

Plasma and urinary levels of malondialdehyde-like products (MDA) and isoprostanes were identified as markers of in vivo lipid peroxidation in an animal model of CCl4 poisoning. We sought to determine the extent to which the formation of these oxidation products is influenced by inhibition of the cyclooxygenase enzymes which catalytically generate proinflammatory lipid peroxidation products known as prostaglandins and thromboxane. In the present studies, after induction of oxidant stress in rats with CCl4, lipid peroxidation products measured in plasma and urine demonstrate that isoprostanes and MDA can be partially inhibited by cyclooxygenase inhibitors, albeit to different extents. The lowering of isoprostane and MDA formation, however, may not to due primarily to the diminution of catalytic generation of isoprostanes or MDA by the cyclooxygenases but, rather, may be the result of the suppression of nonenzymatic lipid
The complete mitochondrial genome of the cave shrimp Typhlatya miravetensis (Decapoda, Atyidae) and its systematic position

Abstract The complete mitochondrial genome of Typhlatya miravetensis from one of its only three known localities (Ullal de la Rabla de Miravet, Castellón, Spain) is presented here. The mitogenome is 15,865 bp in length and includes the standard set of two rRNAs, two non-coding regions plus 13 protein-coding genes. The later have been used to perform a phylogenetic analysis together with other Caridea representatives with mitogenome data in GenBank, inferring a close relationship with the Hawaiian volcano shirmp (Halocaridina rubra) within the family Atyidae.
The prevalence of Infectious Bronchitis (IB) in some chicken farms in Egypt: I. Spotlight on the status of IB outbreaks in some chicken flocks

Twenty five isolates of IBV were isolated from 36 broiler and layer chicken farms collected from 13 governorates during 2 years started from January 2003. Sixteen farms were vaccinated against IB, and 9 farms were not vaccinated. The cardinal signs of the disease in layers were drop in egg production, with watery albumen, inferior (pale and misshape shell) eggs, un-noticed respiratory distress and pectoral myopathy, and those in broilers were respiratory distress, renal urate deposition and death beyond 4 weeks of age (late mortality). The viruses were isolated and identified by chicken embryo, and CEK cell culture inoculation.
Exploitation of micro refuges and epibiosis: survival strategies of a calcareous sponge

Sponges interact in various ways with a wide variety of organisms in benthic communities and ecological interactions may influence the distribution, abundance and diversity of these organisms in different sites. Although several studies have already been developed for Demospongiae, knowledge of ecological interactions in the class Calcarea is lacking. Some calcareous sponges are considered weak competitors for space and to have developed strategies to survive in highly dynamic environments, such as exploitation of micro refuges and epibiosis. We aimed to investigate the influence of intra- and interspecific interactions in the abundance, growth and lifespan of the calcareous sponge Clathrina aurea in south-eastern Brazil. Two peaks of abundance and area coverage were observed during the studied year, probably associated with reproductive effort. We found no evidence of intra- or interspecific competition between the sponge and the benthic community. Clathrina aurea was found using parts of other organisms as substrate (epibiosis), such as algae, demosponges and corals. It was seen that the interaction of the sponge with coral polyps positively affects the lifespan of sponge individuals and the interstices of corals probably promote a micro refuge for C. aurea against competitors for space and predators.
Amplification of virD1 and opine synthase genes from tumorigenic rose and aster strains of Agrobacterium in Taiwan by polymerase chain reaction

We tried to amplify the vir D1 gene and opine synthase genes from tumorigenic strains of Agrobacterium in Taiwan by polymerase chain reaction (PCR). The vir D1 gene was amplified from tumorigenic strains of Agrobacterium isolated from rose gall tissues; but could not be amplified from tumorigenic strains of Agrobacterium isolated from aster gall tissues. In the PCR analysis of three opine synthase genes, the segment of agrocinopine synthase gene was amplified from the tumorigenic rose strains whereas the octopine synthase gene was amplified from tumorigenic aster strains. None of these tumorigenic strains could generate PCR product with oligonucleotide primers for nopaline synthase gene. These results implicate that the sequence of vir D1 virulence gene may be distinct among different groups of phytopathogenic Agrobacterium. In addition, the type of tumor-inducing plasmid may be quickly determined by PCR amplification of opine synthase gene(s) from the agrobacterial cell.
Production and Purification of Alkaline Protease from Bacillus sp. MPTK 712 Isolated from Dairy Sludge

3 Abstract: Proteolytic bacteria were isolated from dairy sludge with the help of Skim milk agar plates. The isolate showing maximum activity was selected (MPTK 712) and characterized based on Bergey's manual. Upon 16S rDNA analysis, it displayed maximum similarity with Bacillus spp. and the sequence has been deposited in Genbank. For the production of alkaline protease, the strain MPTK 712 was grown on modified production medium containing dairy sludge as substrate. Different cultural parameters were optimized for maximal enzyme production. Peak proteolytic activity was observed at pH-9.0 and temperature at 55°C with 2% inoculums. Cetrimide exhibited the highest inhibitory activity followed by Tween-80, SDS and Tween-20. Alkaline protease was purified to homogeneity by Q-Sepharose revealing a molecular weight of 24 kDa. The enzyme was active and more stable at pH-9 and 55°C.
Gut Microbiota-Metabolome Changes in Children With Diarrhea by Diarrheagenic E. coli

Background: Diarrheagenic Escherichia coli (DEC) strains are a main cause of diarrhea worldwide in children under 5 years old. DEC virulence is strongly regulated by environmental conditions and metabolites produced by the gut microbiota in the intestinal tract. In this study, we evaluated changes in gut microbiota-metabolome in children with or without diarrhea produced by DEC pathotypes. Goal: To determine gut microbiota composition and metabolome in stool samples obtained from healthy children and children with diarrhea positive for DEC pathotypes. Methods: We analyzed a total of 16 age-paired stool samples: 8 diarrheal samples positive for one DEC pathotype and 8 stool samples from healthy children. To identify the microbiota composition, we sequenced the V3-V4 region of the 16S rRNA and determined operational phylogenetic units (OPU). OPU were then used to predict metabolic pathways using the PICRUSt2 software. The presence of metabolites in stool samples was determined by LC-MS. A correlation analysis was performed with the main genera from each group and main metabolites. Bacteria associated with variance of main metabolites were identified using the MIMOSA2 software. Results: DEC and healthy groups showed a statistically different microbiota composition. A decrease in Firmicutes together with an increase in Bacteroidetes and Proteobacteria was found in the DEC group compared to the healthy group. Metabolic pathway predictions based on microbiota diversity showed that pathways involved in histidine and L-ornithine metabolism were significantly different between groups. A total of 88 metabolites detected by LC-MS were included in the metabolome analysis. We found higher levels of histamine and lower levels of ornithine in DEC samples than in the healthy group. Histamine and L-ornithine were associated with a specific microbiota species and the corresponding metabolic pathways. Conclusion: Stool samples from healthy children and children positive for DEC displayed a differential metabolome and microbiota composition. A strong correlation between a gut microbiota species and certain metabolites, such as histamine and L-ornithine, was found in the DEC group. This information might be useful to identify mechanisms and signaling molecules involved in the crosstalk between microbiota and DEC pathotypes.
Plankton food-webs: to what extent can they be simplified?

Plankton is a hugely diverse community including both unicellular and multicellular organisms, whose individual dimensions span over seven orders of magnitude. Plankton is a fundamental part of biogeochemical cycles and food-webs in aquatic systems. While knowledge has progressively accumulated at the level of single species and single trophic processes, the overwhelming biological diversity of plankton interactions is insufficiently known and a coherent and unifying trophic framework is virtually lacking. We performed an extensive review of the plankton literature to provide a compilation of data suitable for implementing food-web models including plankton trophic processes at high taxonomic resolution. We identified the components of the plankton community at the Long Term Ecological Research Station MareChiara in the Gulf of Naples. These components represented the sixty-three nodes of a plankton food-web. To each node we attributed biomass and vital rates, i.e. production, consumption, assimilation rates and ratio between autotrophy and heterotrophy in mixotrophic protists. Biomasses and rates values were defined for two opposite system’s conditions; relatively eutrophic and oligotrophic states. We finally identified 817 possible trophic links within the web and provided each of them with a relative weight, in order to define a diet-matrix, valid for both trophic states, which included all consumers, fromn anoflagellates to carnivorous plankton. Vital rates for plankton resulted, as expected, very wide; this strongly contrasts with the narrow ranges considered in plankton system models implemented so far. Moreover, the amount and variety of trophic links highlighted by our review is largely excluded by state-of-the-art biogeochemical and food-web models for aquatic systems. Plankton models could potentially benefit from the integration of the trophic diversity outlined in this paper: first, by using more realistic rates; second, by better defining trophic roles of consumers in the planktonic web. We suggest that most trophic habits present in planktonic organisms must be contemplated in new generation plankton models.
Potential of Ginger (Zingiber officinale) Rhizome and Watermelon (Citrullus lanatus) Seeds in Mitigating Aspartame-Induced Oxidative Stress in Rat Model

Aspartame (ASP) consumption has been reported to implicate oxidative stress and antioxidant supplements from plant origin are one of the safest ways of averting their effect in the body. The current study was aimed at ascertaining the ability of aspartame (ASP) to induce oxidative stress in rats as well as assessing the potential of ginger (Zingiber officinale) rhizome and watermelon (Citrullus lanatus) seeds extracts in averting the aspartame induced oxidative stress. This was done using sperm parameters and biochemical assays such as superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase, melonaldehyde (MDA), aspartate aminotransferase (AST), alanine aminotransferase and alkaline phosphate (ALP). Forty eight sexually matured male albino rats were divided into six groups (A-F) with eight rats in each group. Group A served as the positive control and received physiological saline. Group B served as the negative control and were administered with 1000 mg kgG b.wt. , of aspartame (ASP). Rats in group C were administered with 1000 mg kgG b.wt. , ASP+500 mg kgG b.wt. , of ginger extracts while rats in group D were administered with 1000 ASP+1000 mg kgG b.wt. , of ginger extracts. On the other hand, rats in group E received 1000 mg kgG b.wt. , ASP+500 mg kgG b.wt. , of watermelon seed extracts while rats in group F received 1000 mg kgG b.wt. , ASP+1000 mg kgG b.wt. , of watermelon seed extracts. The result revealed that administration of ASP reduced sperm viability, sperm count and increased sperm head abnormalities significantly (p<0.05) while sperm motility was not affected by ASP administration in the rats. Superoxide dismutase and GPx levels were increased significantly by ginger and watermelon seeds extracts. Although ginger extract reduced more of lipid peroxidation (MDA), watermelon seeds extract increased the activities of SOD, GPx and reduced AST, ALT and ALP in the liver of rats at 1000 mg kgG b.wt. , than the extract of ginger. Thus, the extracts of these two medicinal plants are possible antioxidant reservoir and may provide reliable solution in averting oxidative stress pathologies.
Direct determination of arsenic species in arsenic hyperaccumulator Pteris vittata by EXAFS

Synchrotron radiation extended X-ray absorption fine structure (SR EXAFS) was used to study the transformation of coordination and redox state of arsenic (As) in a newly discovered As hyperaccumulator, Pteris vittata L. , which is considered to have great potential for phytoremediating the As contaminated soil. It is shown that the As in this plant was mainly coordinated with oxygen in the reduced state, As (III), and the reduction of As (V) occurred in the root after it was taken up. No oxidation of As (III) was found during the translocation of As, from root to shoot. Only a small amount of As was coordinated with sulfur in root and petiole, but not distinct in pinna.
Polyphagy in an uncertain environment: Helicoverpa punctigera in inland Australia

We investigated potential primary hosts for Helicoverpa punctigera, a polyphagous lepidopteran pest which affects many crops, but also has many native hosts in non-cropping regions of inland Australia. The most common hosts are Asteraceae and Fabaceae, but there is little information on the relative importance of different species in these families for the population dynamics of H. punctigera in the inland. We tested three common hosts, one legume (Cullen cinereum) and two daisies, Rhodanthe floribunda and Polycalymma stuartii, for their suitability for survival and growth of early instar larvae. Survival was high on the flowers of all three species, and on the leaves of C. cinereum and R. floribunda, but low on leaves of P. stuartii. There were significant differences in growth rates, measured by head widths, in the order of C. cinereum > R. floribunda > P. stuartii, and flowers > leaves. They were strongly correlated with nitrogen content, measured by fresh weight. Field surveys of larval populations in western Queensland indicated that two legume species, C. cinereum and Cullen pallidum, were widely utilized and supported many larvae. Daisies were generally less widely used and/or had lower numbers of larvae. When C. cinereum or C. pallidum was found near daisies, the legume had more larvae if both the daisy and the legume were flowering, but this was reversed if only the daisy was flowering. The seasonality and habitats of the daisies and legumes are different. C. cinereum and C. pallidum (a new host record for H. punctigera) may be primary hosts of H. punctigera in inland Australia and key hosts for maintaining populations in flood plains. However the areas occupied by daisies can be more extensive depending on rainfall, and some species may be critical in generating outbreaks that affect cropping areas in southeast Australia.
Theoretical modeling of Replication Association Protein of Indian Cassava Mosaic Virus and its docking with N-Acetyl D-Glucosamine

The Bean golden mosaic virus (BGMV), also known as the Begomovirus, belongs to the family Geminiviridae and is transmitted through the whitefly. One of the forms of it is Indian cassava mosaic virus (ICMV) which adversely affects the yields of tomatoes, guavas, green chillies, potatoes, etc. ICMV has been modelled theoretically in the present work with the help of tools of homology modelling. The latter is concerned with insilico approaches to build, predict and analyse the 3-D structure of proteins (for which the crystal structure is unavailable). The closest homologue of Association Protein of Tomato was 1L2M_A, with the highest sequence identity. Both consensus and chimera models were made and studied. The best one was then used for the docking studies. Thereafter, the putative binding sites to be attacked by various inhibitors were located and then docked with N-Acetyl-D-glucosamine (NAG). NAG was optimized using B3LYP/6-31G(d,p) methods and its properties are studies. The docking scores of NAG on the active sites of Replication Association Protein of Indian Cassava Mosaic Virus were checked and it was found that NAG proves to be an effective inhibitor for ICMV. This study will now be tried in the wet lab to check the efficiency of our theoretical findings.
Biochemical study of root extract of Withania somnifera (L.) plant through HPLC analysis

Secondary metabolite contents of W. somnifera varied remarkably between seasons and genotypes under ex vitro condition. In vitro studies provide an optimum culture condition for steady and quality production of bioactive chemicals throughout the year without involvement of environmental stresses. Mass production of micro-shoots and plantlets by exploring the organogenic totipotency of shoot tip explants (ex vitro and in vitro grown) considering two elite genotypes (Poshita and Jawahar 22) of W. somnifera, and assessment of their capability in production and accumulation of bioactive metabolites (total alkaloid and withanolides amount were quantified; withanolide A and withaferin A contents were estimated by High Performance Liquid Chromatography-HPLC).
Functional Characterization of Novel PFN1 Mutations Causative for Familial Amyotrophic Lateral Sclerosis: A Dissertation

The signatures of the Dissertation Defense Committee signify completion and approval as to style and content of the Dissertation iii ACKNOWLEDGEMENTS There are many people whom I would like to thank for their support throughout the course of my graduate study. First and foremost, I would like to thank my thesis advisor, John Landers, for taking me as your first student and providing a dynamic and interactive research environment. I am also grateful that you always encourage me as a scientist, and are open-minded and supportive for my projects throughout the years. I have also learned greatly from our discussions, brainstorming, and your feedback for my proposals. Thank you very much for everything! I have also enjoyed working with all the members of Landers lab. In particular, I would like to thank Claudia Fallini. You never hesitate to provide me with your help and critical comments. You also teach me to keep positive despite the downtime in research, which I really appreciate. Apart from the scientific stuffs, from you I have also learned what authentic pizza should be like. And many thanks to all post-docs in the lab, Anthony Giampretruzzi, for your help, encouragement and good laughs, especially when I was applying for post-doc positions. Also, I would like to thank all the current and former members of Bosco lab, especially Sivakumar Boopathy, Catherine Ward, Melissa Rotunno, and Maeve Tischbein. You guys have encouraged me tremendously and are always generous enough to share with me your reagents and equipment. iv I would also like to thank Helene Tran-Ladam from Gao lab. You have been there for me since the day one I started the fly project. You not only support me, encourage me how to move forward as a researcher, help me with all kinds of experiments but also give me the most critical feedback on my proposals, experiment designs and research rationales. Likewise, I would like to thank Tsai-Yi Lu from Freeman lab. You have always made my life a lot easier but sharing your experience and humor. And many thanks to all the fly people in Gao lab for your support: I really appreciate that you guys are always willing to help me and answer my all kinds of questions about flies. For their advice and guidance throughout the years I would also like to thank the members of my thesis advisory committee: also like to thank Dr. …