Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Metabolism by Hepatic OXPHOS: A Dissertation

The signature of the Dean of the Graduate School of Biomedical Sciences signifies that the student has met all graduation requirements of the school. Dedication This work is humbly dedicated to my wife Heather, without whose love, support, and friendship these accomplishments would not have been attainable, and to our son Oliver, whose presence has brought us incredible happiness. You are both my inspiration and my joy. iv Acknowledgements I must begin by thanking my thesis mentor, Dr. Marcus Cooper, for inviting me into his laboratory and under his tutelage. Learning from Marcus has been critical in shaping my development as an aspiring investigator. I remain inspired by the enthusiasm, passion, and work ethic which he brings to the laboratory each day, and am thankful to have had the opportunity to learn from him. Marcus' constant encouragement to not only work hard, but think hard, about scientific questions will continue to benefit me throughout my career. Second, I must acknowledge our postdoctoral fellow, Lijun Liu, who initiated the project described herein. Lijun's early experiments were crucial in shaping the direction of this project, and I am indebted to her for her hard work. Moreover, Lijun made significant contributions to my technical and experimental development, and for that I thank her. Additionally, I would like to thank Minwoo Nam, my fellow graduate student and partner in the laboratory. Minwoo's technical assistance, thoughtful conversation, and supportive friendship were immensely helpful during my years in the laboratory. I wish him the best of luck as he completes his thesis work and looks toward his next endeavor. I would also like to recognize my thesis committee, chair Dr. constructive feedback throughout the development of this work. Thank you all for your advice and support, which were integral for my research. v Additionally, I must acknowledge my clinical preceptor, Dr. Howard Sachs. My work with Dr. Sachs has been invaluable on my path to becoming a physician. More, his approach to caring for patients and clinical medicine are inspiring, and my sessions with him will remain a highlight of my clinical education. I am grateful for the members of the Division of Cardiovascular Medicine, who have provided everything from reagents and technical advice to necessary (and at times, not so necessary) distractions during my research. I consider many of you good friends and am grateful to have you as colleagues. Finally, I want to extend …
Island floras as model systems for studies of plant speciation: Prospects and challenges

Oceanic islands have long been called natural laboratories for studying evolution because they are geologically young, isolated, dynamic areas with diverse habitats over small spatial scales. Volcanic substrates of different ages permit the study of different stages of divergence and speciation within plant lineages. In addition to divergence, the dynamic island setting is conducive to hybridization. Discussion will focus on the potential of systematic/ecological studies, in combination with genomic data from high throughput sequencing and an ever‐increasing array of analytical techniques, for studying evolution in island plants. These studies may include: generation of highly resolved phylogenies to clarify the biogeography of speciation and whether divergence has occurred with or without gene flow; identification of the barriers to gene flow (extrinsic vs. intrinsic) of importance during divergence; documentation of historical and current hybridization events within island lineages; and elucidation of the genomic composition and ecology of hybrid populations in order to infer the evolutionary consequences of hybridization, such as the origin of stabilized homoploid hybrid species.
Dessiccation Using Saturated Salt Solutions and Improvement Germination Rate of Walnut (Juglans regia L.) Somatic Embryos

Desiccation of somatic embryos under different air humidities conditioned by saturated salt solutions for different dura-tions; relationships between desiccation and germination or root formation in the dark; and effects of desiccation and gibberellic acid on germinating of 'Su-2' walnut somatic embryonic embryo line were investigated. Survival of embryos was low (about 10%) or zero when loss of fresh weight was about 90% and dry matter was about 70%. The highest germinating percentages (13.3-23.3%) were obtained with about 40.4-77.3% of loss of fresh weight and 9.1-34.6% of dry matter of desiccated embryos in covered plates over saturated MgCl 2 . 6H 2 O for 4 days, Mg(NO 3 ) 2 . 6H 2 O for 5 days or NaCl for 5-6 days, and with uncovered plates over ZnSO 4 . 7H 2 O for 6-7 days or NH 3 SO 4 for 6-8 days. The highest rooting percentage (80.9%) in the dark were obtained with 56.2% of loss of fresh weight and 16.8% of dry matter of desiccated embryos in covered plates over saturated MgCl 2 . 6H 2 O for 4 days. To improve germination, both desiccation and GA 3 treatments were more effective than only desiccation or GA 3 treatments on germination. Germinating was best (46.0%) with desiccation followed by incubation in the dark for 15 days prior to being transferred to a medium containing 9 mg/l GA 3 in the light.
Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of koi carp (Cyprinus carpio, Cyprinidae)

Abstract The complete mitochondrial genome of the koi carp (Cyprinus carpio, Cyprinidae) was sequenced in the present study by using Ion Torrent Personal Genome Machine (PGM) platform for the first time. The mitochondrial genome sequence is 16 581 bp in size and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The gene order and organization were similar to most of the other teleost. The nucleotide compositions of the light strand are 24.82% of A, 31.92% of T, 27.53% of G and 15.73% of C. With the exception of eight tRNA genes and the NADH dehydrogenase subunit 6 (ND6), all other mitochondrial genes are encoded on the heavy strand. The phylogenetic tree constructed using a maximum-likelihood model showed sister relationship of koi carp to other Cyprinidae fishes.
Towards understanding a holobiont : host-microbe interactions in Hydra

Epithelia in all animals, which are exposed to the environment, are colonized by more or less diverse communities of microbes. Since Hydra is an early-branching metazoan and has preserved much of the genetic complexity of the common metazoan ancestor it promises to be highly informative to discover evolutionary conserved mechanisms controlling epithelial host-microbe interactions. To obtain a better understanding of the microbiota associated with phylogenetically ancient epithelia, I identified the epibiotic and endosymbiotic bacteria of two species of the cnidarian Hydra on the basis of rRNA gene comparisons. I discovered that individuals from both species differ greatly in their bacterial microbiota. Hydra oligactis appears to be associated with only a limited number of microbes, while Hydra vulgaris polyps have a more diverse microbiota. Surprisingly, the microbial composition showed similar characteristics comparing polyps from culture maintained in the laboratory for more than 30 years with polyps from the wild. The significant differences in the microbial communities between the two species and the maintenance of specific microbial communities over long periods of time strongly indicate distinct selective pressures imposed on and within the epithelium. To understand the factors involved in the maintenance of the specific association I first analysed how epithelial homeostasis affects the associated microbiota. I could show that eliminating derivates of the interstitial stem cell lineage from the epithelium causes significant changes in hydra´s microbial community. Due to the loss of the interstitial cell lineage, bacteria of the β-Proteobacteria group decreased and bacteria of the Bacteroidetes group increased in relative abundance. These results indicate a previously unrecognized link between cellular tissue composition and microbiota. To elucidate the role of the innate immunity, especially the antimicrobial peptides (AMP), in shaping the commensal microbiota, I made use of transgenic Hydra overexpressing the AMP periculin1a. I could show that overexpression of an endogenous AMP not only reduces the bacterial burden but also leads to drastic changes in the biodiversity of the colonizing microbiota. These findings indicate that AMPs as an evolutionary old ‘invention’ may play a crucial role in shaping the composition of the commensal microbiota. Antimicrobial peptides, until now known as gene–encoded key elements of innate immunity, therefore, appear also to have an essential role in host-microbe co-evolution.
The Prediction of Protein Post-translational Modification Sites

Plenary Sessions 1 The Prediction of Protein Post-translational Modification Sites · · · · · · · · 3 Naiyang Deng, Ling-Yun Wu, Xiaobo Wang Modeling the Roles of miRNA164 in Determining the Age-dependent Cell Death in Plant Leaves · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · 5 Hye Ryun Woo, Seungmin Han, Jin Hee Kim, Il-Hwan Lee, Daehee Hwang, Hong Gil Nam Systems Biology of Cell Signaling · · · · · · · · · · · · · · · · · · · · · · · · 11 Qing Nie Next Generation DNA Sequencing and Bioinformatics: Bottlenecks and Opportunities · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · · 12 Kwok-Wing Stephen Tsui Exploring the Design Principle of Emergent Properties in Biological Systems · 485 Kwang-Hyun Cho
Analysis of parasporin (anti-cancer) proteins of bacillus thuringiensis

Cancer is the leading cause of death in worldwide whose treatments are costly and has different physical and emotional side effects. Parsporal inclusion proteins from B. thuringiensis having specific cytotoxic activity against specific cancer cells can be used for cancer treatment which might have relatively lower side effects and might be cost effective. We have reported in silico analysis that is physico-chemical characteristics, secondary structure, 3-D structure, motifs and phylogenetic relationship among these 19 parasporin proteins to characterize them and predict their cancer cell killing mechanism.
Improving Onion Seed Germination Using Priming Treatments

The effects of osmopriming ‘Wolska’ onion seeds on the percentage of normal and abnormal seedlings as well as the mean germination time (MGT) were studied. The priming was carried out with polyethylene glycol (PEG 6000 and PEG 8000) at ‐1.0 MPa and ‐1.5 MPa solutions. The seeds were treated in a column bioreactor for 6, 24, 48, 72 and 96 hours at 15 and 20oC. Compared to the control (untreated seeds), both PEG 6000 and PEG 8000 osmotics similarly increased the percentage of normal seedlings, reduced the percentage of abnormal seedlings and shortened MGT. Seed priming at ‐1.0 MPa promoted a higher percentage of normal seedlings and shorter MGT than treatment at ‐1.5 MPa, but both osmotic potentials enhanced those germination features relative to the untreated seeds. Compared to the control, both priming temperatures improved the tested germination traits, but treatment at 20oC gave better results than at 15oC. Seeds primed for 48 hours produced the highest percentage of normal seedlings and the lowest number of abnormal seedlings, but treatment for 72 hours reduced MGT the most. The best ratios of normal to abnormal seedlings were obtained after priming at 20oC for 24 hours at ‐1.0 MPa and after treating for 48 hours at ‐1.5 MPa. The seeds primed at 20oC for 72 hours at ‐1.0 MPa germinated two times faster than the control. The study showed that some of the applied priming treatments notably improved the germination characteristics of the tested ‘Wolska’ onion seed lot.
Propanil-Resistant Barnyardgrass (Echinochloa crus-galli) Control in Rice (Oryza sativa)

Six experiments were conducted in three rice fields near Harrisburg, AR in Poinsett County in 1991 and 1992 to confirm barnyardgrass resistance to propanil and to compare herbicide treatments for control of propanil-resistant barnyardgrass. In all experiments, standard treatments of thiobencarb applied delayed PRE or tank mixtures of propanil + thiobencarb applied POST controlled propanil-resistant barnyardgrass. In five of six experiments, propanil failed to control barnyardgrass at 6 to 8 kg ai/ha (three times use rates) and in three experiments it provided inconsistent control at 11 kg/ha. Emulsifiable propanil at 11 kg/ha frequently controlled resistant barnyardgrass better than the dry flowable formulation. Treatments that consistently controlled propanil-resistant barnyardgrass included propanil tank-mixed with pendimethalin or quinclorac applied POST to two-leaf grass; quinclorac applied alone delayed PRE or POST or applied POST tank-mixed with thiobencarb, pendimethalin, or a formulated mixture of molinate and propanil; a formulated mixture of propanil and molinate applied POST in tank mixtures with thiobencarb or pendimethalin; and fenoxaprop or fenoxaprop-P alone applied POST to four-leaf grass prior to flood establishment. Herbicide treatments that failed to control resistant barnyardgrass included POST applications of a formulated mixture of propanil and molinate alone and propanil in tank mixtures with bromoxynil or triclopyr. These studies confirm that barnyardgrass from several farms in Arkansas have resistance to propanil and identified treatments that control propanil-resistant barnyardgrass.
Birds of Madagascar and the Indian Ocean Islands: Seychelles, Comoros, Mauritius, Reunion and Rodrigues

Birds of Madagascar and the Indian Ocean Islands: Seychelles, Comoros, Mauritius, Reunion and Rodrigues by Frank Hawkins, Roger Safford, and Adrian Skerrett; illustrated by John Gale and Brian Small. 2015. Helm Field Guides, Christopher Helm, London, UK. 336 pp., 124 color plates. $45 (paperback). ISBN 9781472924094. Madagascar is famous for its unique, and often bizarre, biological marvels. In fact, along with its island neighbors in the Western Indian Ocean, it possesses the second most distinctive vertebrate fauna of the world’s seven zoogeographic regions, despite being much smaller than the others. Although the bird fauna is not particularly rich, with only 382 regularly occurring species, an extraordinary 41% of them are endemic either to the region or to individual islands within it. Endemism is just as startling at higher taxonomic levels, with no fewer than 6 endemic families (containing 32 extant genera and 45 species) and 18 further endemic genera (containing 43 species). Two of these families, the cuckoo-roller and the mesites, are such ancient and distinctive lineages that they are now recognized as orders of their own, the Leptosomiformes and Mesitornithiformes. For these reasons and more, the region ranks high on most birders’ must-visit lists. And for those birders who do make the journey, there is a clear choice of field guide: this new Helm guide by Hawkins and colleagues. Not that the marketplace is crowded—there is only one other field guide covering the whole region, Ian Sinclair and Olivier Langrand’s (2013) Birds of the Indian Ocean Islands, and the alternatives for Madagascar are now horribly out-of-date. Sinclair and Langrand’s guide is certainly useful and served as my main field resource for most of the decade I lived in Madagascar, but it has the intensely annoying habit of unilaterally elevating certain subspecies to full species—such as the Moheli subspecies of Madagascar Green Pigeon (Treron australis griveaudi) and the Madagascar subspecies of African Black Swift (Apus barbatus balstoni)—despite a lack of supporting research. Not only did this create unnecessary taxonomic confusion, but it also left one questioning the authority of everything else the book said. We can be sure of one thing about the new Helm guide: It is authoritative. For this is not just a field guide but is actually the offshoot of a much grander project, the mammoth 1,024-page bible on the region’s avifauna, Birds of Africa, volume VIII: The Malagasy Region (Safford and Hawkins 2013). An edited
Genotyping in Thousands By Sequencing (GT-seq): A Low Cost, High-Throughput, Targeted SNP Genotyping Method

Abstract GT-seq is a genotyping method which leverages large read numbers from Illumina sequencers to genotype hundreds of single nucleotide polymorphisms within pools of multiplex PCR amplicons generated from thousands of individual samples (Campbell et al. 2015). This method produces genotypes that are 99.9% concordant to those produced using TaqManTM assays at approximately 1/4 the cost. Since its development, GT-seq panels have been created for several species (Chinook salmon, coho salmon, sockeye salmon, rainbow trout, and pacific lamprey) and has become the preferred SNP genotyping method in our laboratory. New genotyping software allows genotypes and summary figures to be produced from a lane of raw sequencing data in under an hour using a desktop linux computer.
ACIDO LINOLEICO CONJUGADO: UN ACIDO GRASO CON ISOMERIA TRANS POTENCIALMENTE BENEFICIOSO. CONJUGATED LINOLEIC ACID: A TRANS ISOMER FATTY ACID POTENTIALLY BENEFICIAL

Conjugated linoleic acid (CLA) is a type of isomeric trans fatty acid that has been demonstrated to have diverse health beneficial effects. The most common naturally existing structural form of CLA is the 9c (cis), 11t (trans) isomeric configuration. CLA, which is commonly found in the tissues and/or secretions (i.e., milk) of ruminants, is formed from the isomerization of linoleic acid by the ruminal bacteria Butyrivibrio fibrisolvens. CLA may also be synthesized, in both ruminants and non ruminants, by desaturation of vaccenic acid (18:1, 11t) at the intestinal tract and/or the at liver of these animals. Daily ingestion of CLA in humans highly variable (0.5g/day-1.5g/day), pending on the individual and the country nutritional habits, and on the amount of meat, milk and milk-derived products consumed. Different biological and nutritional properties have been described for CLA, the most relevant being related to its hipocholesterolemic, antiatherogenic and immuno-stimulant action, the protective action against certain types of cancer, and its antioxidant and body-weight reduction effects ascribed.for the isomeric fatty acid. However, the definitive confirmation of these health beneficial effects needs more experimental and clinical evidences supporting these actions. Meanwhile, diverse products containing CLA are now offered at the retail market with increasing success, especially those preparations claiming body weight reduction properties for the isomeric fatty acid.
New Disease Reports

Figure 2 Capsicum annuum (sweet pepper or bell pepper), known as simla mirch in India is one of the leading vegetables grown in the open as well as under protected cultivation. In the Kashmir valley, India, whitefly infestation and begomovirus-like symptoms viz. malformation, leaf curling, vein clearing and stunting were observed in capsicum plantations (Fig. 1). The incidence under protected cultivation was very high ranging from 10% to 40% whereas under field conditions it was less than 10%. The presence of whiteflies and symptoms called for the investigation of possible begomovirus infection.
Determination of the Geographical Origin of Maltese Honey Using 1H NMR Fingerprinting

The price of honey, as a highly consumed natural product, depends on its botanical source and its production environment, causing honey to be vulnerable to adulteration through mislabeling and inappropriate, fraudulent production. In this study, a fast and simple approach is proposed to tackle this issue through non-target one dimensional zg30 and noesypr1d 1H NMR fingerprint analysis, in combination with multivariate data analysis. Results suggest that composition differences in sugars, amino acids, and carboxylic acid were sufficient to discriminate between the tested honey of Maltese origin and that of non-local origin. Indeed, all chemometric models based on noesypr1d analysis of the whole fraction honey showed better prediction in geographical discrimination. The possibility of discrimination was further investigated through analysis of the honey’s phenolic extract composition. The partial least squares models were deemed unsuccessful to discriminate, however, some of the linear discriminant analysis models achieved a prediction accuracy of 100%. Lastly, the best performing models of both the whole fraction and the phenolic extracts were tested on five samples of unknown geographic for market surveillance, which attained a high agreement within the models. Thus, suggesting the use of non-target 1H NMR coupled with the multivariate-data analysis and machine learning as a potential alternative to the current time-consuming analytical methods.
Bioaminergic Responses in an In Vitro System Studying Human Gut Microbiota–Kiwifruit Interactions

Whole kiwifruit (‘Hayward’ and ‘Zesy002’) were examined for their bioaminergic potential after being subjected to in vitro gastrointestinal digestion and colonic fermentation. Controls included the prebiotic inulin and water, a carbohydrate-free vehicle. The dopamine precursor l-dihydroxyphenylalanine (L-DOPA) and the serotonin precursor 5-hydroxytryptophan were increased in the kiwifruit gastrointestinal digesta (‘Hayward’ > ‘Zesy002’) in comparison to the water digesta. Fermentation of the digesta with human fecal bacteria for 18 h modulated the concentrations of bioamine metabolites. The most notable were the significant increases in L-DOPA (‘Zesy002’ > ‘Hayward’) and γ-aminobutyric acid (GABA) (‘Hayward’ > ‘Zesy002’). Kiwifruit increased Bifidobacterium spp. and Veillonellaceae (correlating with L-DOPA increase), and Lachnospira spp. (correlating with GABA). The digesta and fermenta were incubated with Caco-2 cells for 3 h followed by gene expression analysis. Effects were seen on genes related to serotonin synthesis/re-uptake/conversion to melatonin, gut tight junction, inflammation and circadian rhythm with different digesta and fermenta from the four treatments. These indicate potential effects of the substrates and the microbially generated organic acid and bioamine metabolites on intestinal functions that have physiological relevance. Further studies are required to confirm the potential bioaminergic effects of gut microbiota–kiwifruit interactions.