Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeographical study of the alpine plant Cassiope lycopodioides (Ericaceae) suggests a range connection between the Japanese archipelago and Beringia during the Pleistocene

Given that East Asia is located south-west of Beringia and was less glaciated during the Pleistocene, species at higher latitudes were able to expand their range in this region during climate cooling. Although southward migration is an inevitable colonization process, the biogeographical history of the disjunct ranges of higher-latitude species in East Asia has been investigated less extensively. Here, we assess whether their disjunct distributions in the Japanese archipelago connected sufficiently with Beringia or persisted in isolation following their establishment. Sequences of nine nuclear loci were determined for Cassiope lycopodioides (Ericaceae) from the Japanese archipelago as well as its surrounding areas, Kamchatka and Alaska. According to the geographical pattern of genetic diversity, the northern populations from Kamchatka to the northern part of the Japanese archipelago were similar genetically and were differentiated from populations in central Japan. Our study suggested that the distribution of C. lycopodioides was connected between the northern part of the Japanese archipelago and south-western Beringia due to Pleistocene climate cooling. Conversely, central Japan harboured a disjunct range after its establishment. These inferences suggest that widespread range expansion in northern East Asia was plausible for species distributed in Beringia. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 497–509.
Determining the suitability of using eye wrinkle patterns for the accurate identification of individual black rhinos

Photograhic identification is used to identify individual black rhinos (Diceros bicornis) with the distinguishing features of sex, the size and shape of the anterior and posterior horns, peculiarities of the ears, the pattern of wrinkle contours on the snout, prominent scars and sores on the body, the state of the tail, body size including the size of a calf in relation to the mother and skin folds. Eye wrinkle patterns have received little attention but were found to be useful when separating a large number of photographs of 19 captive rhinos particularly for distinguishing individual sub-adults where other features such as horn length and shape were very similar. Each rhino was found to have unique eye wrinkle patterns which remained consistent when the eyes were open or closed. By developing and applying a series of tests, judgement errors that occur when reviewing eye wrinkle photographs were determined and are reported. Results show that individual black rhinos can be accurately identified from suitable photographs but, even for the best of the judges, using eye wrinkles alone to identify individual rhinos was not completely reliable.
Governance without Government: Emerging Private Environmental Authority in Taiwan's ICT Industry

In recent years, international nongovernmental organizations have created non-state market-driven (NSMD) governance systems whose purpose is to develop and implement environmentally and socially responsible management practices. These governance systems have relied upon the market's green supply chain to create incentives and force companies to comply. This paper develops an analytical framework designed to understand better the emergence of NSMD governance systems and the conditions under which they may gain authority to create policy. Its empirical focus is on the case of ICT industry in Taiwan. It aims at NGOs-firms interplay through market's green supply chain mechanism in establishing rules, standards and authority that guide the behavior of the participants. This paper argues that this new type of private environmental governance system might challenge existing state-centered authority and public policy-making processes, and reframe power relations within domestic and global environmental governance
Simple, repeatable and low-cost SERS fibre probe for fluorochrome detection

A method for developing the spherical surface-enhanced Raman scattering (SERS) fibre probe is presented cladded with the silver nanoparticles to detect the fluorochrome molecular. By controlling the diameter of the fibre ball, the excellent SERS enhancement effect has been achieved up to about 105 due to the plasmonic silver nanoparticles, the coated parylene-C dielectric layer and the low-energy loss in the spherical resonant cavity. Meanwhile, the repeatability and stability of the fibre probe have been explored by coating the parylene-C with the error of 1%. It has proved an important superiority for potential commercial applications of this technique to detect the bio-molecular with the advantages of high sensitivity, high stability and low cost.
JJRE Outstanding Young Investigator Award in 2005 Prop-1 Activation of Porcine FSHβ Subunit Gene Requires AT-rich Recognition Sites

We have recently cloned the pituitary specific transcription factor Prop-1 as a regulator of the porcine folli- cle-stimulating hormoneβ (pFSHβ) gene (1). This study aimed to establish the characteristics of porcine Prop-1. The deduced amino acid sequence showed considerable diversity in the N-terminal and moderate change in the C-terminal regions among mammalian Prop-1s except for the homeodomain in the middle region. Prop-1 binds to two thirds of the 5' region of Fd2 located between the -852 and -746 base upstream of the pFSHβ gene, which shows a high AT-con- tent (80%). The transfection assay of the pituitary tumor-derived cell line, LβT2, using the chimera genes fused the upstream of the pFSHβ gene as a reporter vector, showed that Prop-1 activates FSHβ promoter but not SV40 promot- er. The gene expression of Prop-1 during porcine pituitary ontogeny was observed from fetal days 40 through 110, and its postnatal expression increased even further. Thus, this study demonstrated that Prop-1 definitely stimulates the porcine FSHβ gene by acting on the AT-rich Fd2 region and plays a role in the fetal and postnatal pituitary.
Tardigrade Phylogenetic Systematics at the Family Level Using Morphological and Molecular Data

iii ACKNOWLEDGEMENTS . iv TABLE OF CONTENTS . v LIST OF FIGURES . vii LIST OF TABLES . ix Chapter 1 : GENERAL INTRODUCTION . 1 1.1 An Overview of Tardigrade Biology . 2 1.2 Morphology and Classification . 3 1.2.1 Cuticle Structure and Body Armour . 3 1.2.2 Cephalic Sensory Appendages . 6 1.2.3 Buccal-Pharyngeal Apparatus . 7 1.2.4 Claw Structure and Morphology . 9 1.2. 5 Sexual Dimorphic Gonopores . 11 1.3 Phylogenetic Systematic Analyses: From Morphology to Molecules . 12 1.3. 1 Morphology-Based Analyses . 12 1.3. 2 Molecular-Based Analyses . 17 1.3. 3 Analyses combining morphology and molecular data . 25 1.4 Research Goals, Hypotheses and Projects . 30 Chapter 2 : MORPHOLOGICAL PHYLOGENETIC SYSTEMATICS OF TARDIGRADES AT THE FAMILY-LEVEL . 32 2.1 Abstract . 33 2.2 Introduction . 33 2.3 Material and Methods . 35 2.3. 1 Glossary of Morphological Characters . 35 2.3. 2 Data Matrix & Phylogenetic Inferences . 48 2.4 Results . 52
Economic Contribution of Bamboo Production and Marketing, in Case of Hula Woreda, Sidama Zone, Southern Ethiopia

Despite becoming one of Ethiopia’s fast growing and most valuable forest, bamboo’s role in livelihoods and rural development is poorly understood. Hence, the general objective was to examine economic contributions of bamboo production and marketing for livelihoods of rural households. To attain this objective, both quantitative and qualitative data from 300 households were collected through structured questionnaires, focus group discussion and key informant interviews using multi-stage sampling technique in 4 Kebeles in Hula Woreda, SNNPR, Ethiopia. Both descriptive statistical tools and binary logit regression model were used to analyze relationship between variables. Binary logit regression model was employed to find out the relationship between dependency level of households on bamboo for their livelihood and some selected socio-economic factors. According to the results, the area of land covered by bamboo has been decreasing from time to time and about 75 percent of respondents said that the area of land covered by bamboo has been decreasing. Bamboo culms and products marketing systems were informal. Bamboo producers simply display their products, mostly on road-sides, and interested buyers buy them. Information helps farmers to get better price to their product, to increase quality and quantity of the bamboo product. And only 7 percent farmers have full access for information on how to supply, where to sell and the level of demand for their bamboo products. This shows there was lack of adequate market information on the marketing of bamboo products they produce in this area. Therefore, the focus on the development of conservation and processing methods and appropriate production system and marketing can enhance the utilization of bamboo resources.
An overview of post-extraction secondary forests in Indonesia

Indonesia has extensive areas of post extraction secondary forests and degraded lands arising from intensive exploitation of forest resources in recent decades. Using the area of forests resulting from selective logging practices as an estimate, in year 2000, post extraction secondary forests covered about 23 million ha, or about 55% of the total concession area. This paper analyses the underlying causes of transformation of primary to secondary forests and degraded lands, including policy and regulations in forestry and forest resources, poor enforcement of regulations, and the lack of recognition of timber exploitation rights for local communities. The government is committed to promoting participation of local communities in managing forests. Recent policy changes for ameliorating some of the degrading factors have resulted in increased pressure on secondary forests due to rampant illegal logging and use claims by local communities and land speculators. While the largest proportion of post extraction secondary forests has been maintained as part of the permanent forest estate, substantial areas have been converted for swidden agriculture, industrial tree and estate crop plantations and transmigration areas. Local community involvement and an understanding of the underlying degradation pressures would be imperative for the effective rehabilitation and sustainable management of post extraction secondary forests.
Action of Rifampicin on the Liver Wort Marchantia Polymorpha

SUMMARY The effect of rifampicin was studied on a multicellular plant in comparison with its effect on unicellular organisms. Marchantia polymorpha L. is sensitive to rifampicin and was chosen as the material. The inhibitory dose on the growth of young gemmae was established. The effect of rifampicin on the ultrastructure of the cells was investigated and it was found to inhibit the formation of plastid ribosomes and dissociate existing ribosomes into their subunits, but probably does not inhibit the synthesis of some plastid proteins, which remain visible as small granules in the stroma. The effect of rifampicin on the chlorophyll content and on the absorption of C02 by intact thalli and isolated chloroplasts has also been studied. Little or no change was observed.
Genetic Dissection of Quantitative Trait Loci for Substances of Abuse

Genetic Dissection of Quantitative Trait Loci for Substances of Abuse By Jo Lynne Harenza, M.S. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2013. Major Director, Michael F. Miles, M.D., Ph.D., Professor, Pharmacology and Toxicology and Neurology It has been reported that an individual’s initial level of response to a drug might be predictive of his or her future risk of becoming dependent, thus basal gene expression profiles underlying those drug responses may be informative for both predicting addiction susceptibility and determining targets for intervention. This dissertation research aims to elucidate genetic risk factors underlying acute alcohol and nicotine dependence phenotypes using mouse genetic models of addiction. Phenotyping, brain region-specific mRNA expression profiling, and genetic mapping of a recombinant inbred panel of over 25 mouse strains were performed in order to identify xxi
A taxonomic revision of the Paramo Tapaculo Scytalopus canus Chapman (Aves: Rhinocryptidae), with description of a new subspecies from Ecuador and Peru

The nominate subspecies of the Paramo Tapaculo (Scytalopus canus Chapman), which is restricted to high elevations of the Western Andes of Colombia, differs substantially in song from S. c. opacus from the Central Andes of Colombia, Ecuador, and northern Peru. In accordance with current taxonomy of the genus, which is primarily based on differences in song, we assign species rank to both taxa. Within opacus, birds from southernmost Ecuador and northernmost Peru sing like northern opacus but call differently. They are indistinguishable morphologically except for a white patch in the wing present in 10 out of 12 of the adult males of the southern population. We describe this population as a new taxon and rank it as a subspecies of S. opacus. Genetically, S. canus, nominate S. opacus, and the new taxon are strongly differentiated (>5% divergence in mtDNA); the first two appear to be sister taxa.
Uso fertilizante de resduo da indstria processadora de goiabas

The guava processing industry waste (GPIW) has been used in some areas, however is not known its effect on soil fertility. A greenhouse experiment was carried out to evaluate the effect of GPIW on soil fertility, using corn as testing plant. The experiment was in randomized blocks design combining five GPIW rates (0; 20; 40; 60 and 80 t ha-1) in the absence and the presence of mineral fertilization. The GPIW increased P and K concentration and behaved as a slow release source of N and P for corn.
An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

Abstract : The amino acid methionine is particularly sensitive to damage by reactive oxygen species. The enzyme methionine sulfoxide reductase A (MsrA) is capable of repairing oxidized methionines [Met-(O)] found in a wide range of damaged substrates, ultimately protecting cells against oxidative damage. How MsrA reverses oxygen modifications to these damaged proteins is well known, but very little is known about how MsrA recognizes the damaged proteins in the first place. Unlike most enzymes which carry out reactions on a single target molecule, MsrA can repair damage to a single methionine, a peptide, or an entire protein. This study focused on understanding how MsrA is able to recognize, then ultimately repair such a range of oxidatively modified substrates. We propose that MsrA functions as a molecular chaperone, recognizing overall characteristics of unfolded proteins due to oxidative damage. Enzyme-ligand interactions were studied between MsrA of E. coli and four target molecules in their normal and oxidized forms: staphylococcal nuclease, staphylococcal nuclease T62P which has an unfolded structure due to a mutation, a 9-amino acid peptide (KKMVENAKK) derived from staphylococcal nuclease, and the non-steroidal anti-inflammatory drug sulindac. Using the hydrophobic marker 8-anilino-1-naphthalene sulfonic acid (ANS), changes in ANS fluorescence were used to identify changes in the exposed hydrophobic surface area of the protein-ligand complex. The investigation reveals an MsrA target molecule recognition mechanism of weak, but specific hydrophobic interactions enhanced by the presence of a sulfoxide. This study represents the first investigation of the interaction of MsrA with physiologically relevant ligands and has laid the foundation for a novel method of investigating the hydrophobic recognition mechanism of MsrA as a chaperone for oxidatively modified target molecules.
Next-Generation Sequencing for Biomedical Applications

Based on the development of current status of Next-Generation Sequencing technologies (NGS), I developed several technologies to improve NGS technologies and exampled to apply the NGS technology to biomedical sciences. In the first chapter, I overviewed most of the NGS technologies, described the characteristics of the technologies, and compared the pits and falls, as well as the applications. Based on the current development status, I developed Dual-Primer emulsion PCR (DPePCR) to simplify the library preparation and elongate the read length, and the details were illustrated in the chapter 2. To minimize the sequencing feature/template and improve sequencing throughput, I developed Rolony sequencing by Synthesis, which was elaborated in chapter 3. To utilize the NGS technologies on biological researches, Haplotype-resolved sequencing was developed to sequence haplotype genome in chapter 4. Haplotype-resolved sequencing technology provided haplotype information, which is very important for fully understanding human genome, completely describing genetic diversities, and identifying the association between genetic variations and diseases. In one word, this dissertation developed several sequencing technologies that improved the next-generation sequencing technologies, and will potentially contribute to biomedical applications.
Conservation genetics and the Australian lungfish Neoceratodus forsteri; a spatio-temporal study of population structure

Neoceratodus forsteri is a phylogenetically distinct ancient lineage with a natural distribution restricted to 3 catchments in the southeast Queensland region. Modifications to the river systems they are restricted to has prompted concern for the persistence of this species in the face of such changes. Accordingly, ecological and molecular surveys have been undertaken to identify the management units in order to design and implement a sound management strategy. Ecological surveys of the Burnett catchment have highlighted that compounding factors of longevity, low reproductive output and loss of suitable spawning sites through seasonal fluctuations as well as habitat degradation have greatly reduced juvenile recruitment rates. Genetic surveys investigating allozyme , mtDNA and microsatellite markers show that despite substantial barriers to gene flow, lungfish populations comprise of one homogenous population. This lack of diversity was attributed to historic and present bottleneck events, as well as to historic fluvial connectivity. To obtain a broader snapshot of the genome, this survey developed and screened RAF and AFLP multi-locus markers, as well as a microsatellite library. Moreover, in a study complementing previous ATPase survey of contemporary populations, sequence data from this region was evaluated from formalin preserved adult specimens (collection dates range between 1912 and 1976). This study has shown that the common ATPase haplotype found in contemporary populations was also present among specimens collected from 1912. Further, the high prevalence of rare alleles recorded from modern Mary populations was also recorded from formalin preserved specimens. AFLP banding profiles were monomorphic; by contrast, variation detected by RAF markers identified significant patterns of substructure between catchments. Significant structure was also recorded between impounded populations and non-impounded populations. Lungfish populations have a relatively narrow range and occur within regulated fluvial systems. Habitat degradation is implicated in reduction of spawning sites. Combined with low juvenile recruitment these effects greatly reduce the effective population size. The phyletic age of this species, in conjunction with low genetic diversity greatly increases its vulnerability to environmental change or novel diseases. In accordance with the World Conservation Union (IUCN), genetic diversity is one of three recognised levels requiring conservation. ; Submitted in fulfillment of the requirements of the degree of Masters of Science, University of the Sunshine Coast, 2003.
Walnut Oil – Unexplored Raw Material for Lipase‐Catalyzed Synthesis of Low‐Calorie Structured Lipids for Clinical Nutrition

Low-calorie structured lipids that contain medium-chain fatty acids in the sn-1 and sn-3 positions of the glycerol backbone, and long-chain fatty acid in the sn-2 (MLM type) were synthesized in one-step acidolysis of walnut oil with caprylic acid. Caprylic acid residues were incorporated selectively into sn-1,3 positions of triacylglycerols using 1,3-specific immobilized lipases from Rhizomucor miehei (Lipozyme) and Rhizopus delemar (PP-RhDL) as catalysts. Under the optimal reaction conditions, we achieved an excellent yield of the desired MLM-type structured lipids (97 mole % with Lipozyme and 96.4 mole % with PP-RhDL). The synthetic activity of PP-RhDL was not influenced by the reaction medium whereas the Lipozyme was more effective in hexane than in solvent-free medium. The same degree of conversion of initial triacylglycerols was observed for the two enzymes in four consecutive reaction cycles. The amount of MLM-type structured lipids, however, decreased with each following cycle at the expense of mono-substituted with caprylic acid triacylglycerols (MLL type). Practical Applications Structured lipids (SLs) that contain medium-chain fatty acids in the sn-1 and sn-3 positions of the glycerol backbone, and long-chain fatty acids in the sn-2 (MLM type) are known to improve liver function, minimize risk of infections, and reduce the number of gastrointestinal complications in patients undergoing major abdominal surgery and are used in clinical nutrition as well as specialized food for athletes because they provide fast energy supply. After an enzymatic modification of walnut oil, high yield of SLs with caprylic acid residue in the sn-1 and sn-3 positions of the glycerol backbone and long-chain fatty acid residue in the sn-2 position of triglycerides was obtained.
Evaluation of Safflower Varieties for Resistance to the Fungal Pathogen, Colletotrichum acutatum

Vichova J., Staňkova B. , Pokorný R. , Vejražka K. (2013): Evaluation of safflower varieties for resistance to the fungal pathogen, Colletotrichum acutatum. Plant Protect. Sci., 49: 132–136. The influence of plant growth stage, inoculum density, and variety on the disease severity and incidence were stud ied. Our results indicated that growth stage of the plant had no influence on infection rate, as the pathogen attacked 100% of tested plants. When applying three different inoculum concentrations to three weeks old safflower plants, no statistical differences were recorded, disease incidence ranged 32.0–47.0%. In this test, the 3 rd and 4 th evaluated leaves (the youngest) were infected more intensively than were the 1 st and 2 nd leaves. Among 11 safflower varieties tested for resistance to this pathogen, cultivar CW 1221 manifested the highest resistance with 8.3% infection, whereas two cultivars, Sabina and AC Sunset, were found to be the most susceptible with 90.0 and 83.3% infection.