Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyses of All Possible Point Mutations within a Protein Reveals Relationships between Function and Experimental Fitness: A Dissertation

The primary amino acid sequence of a protein governs its specific cellular functions. Since the cracking of the genetic code in the late 1950’s, it has been possible to predict the amino acid sequence of a given protein from the DNA sequence of a gene. Nevertheless, the ability to predict a protein’s function from its primary sequence remains a great challenge in biology. In order to address this problem, we combined recent advances in next generation sequencing technologies with systematic mutagenesis strategies to assess the function of thousands of protein variants in a single experiment. Using this strategy, my dissertation describes the effects of most possible single point mutants in the multifunctional Ubiquitin protein in yeast. The effects of these mutants on the essential activation of ubiquitin by the ubiquitin activating protein (E1, Uba1p) as well as their effects on overall yeast growth were measured. Ubiquitin mutants defective for E1 activation were found to correlate with growth defects, although in a non-linear fashion. Further examination of select point mutants indicated that E1 activation deficiencies predict downstream defects in Ubiquitin function, resulting in the observed growth phenotypes. These results indicate that there may be selective pressure for the activity of the E1enzyme to selectively activate ubiquitin protein variants that do not result in functional downstream defects. Additionally, I will describe the use of similar techniques to discover drug resistant mutants of the oncogenic protein BRAFV600E in human melanoma cell lines as an example of the widespread applicability of our strategy for addressing the relationship between protein function and biological fitness.
The effect of woodland proximity and wetland characteristics on larval anuran assemblages in an agricultural landscapeThis is contribution No. 82 of the MacArthur Agro-Ecology Research Center.

Changes to landscapes for agricultural activities often result in reduction and fragmentation of forested habitat. Land conversion for cattle ranching in south-central Florida has resulted in increases in pasture land interspersed with remnant patches of hardwood hammock. To examine the importance of these hammocks to anurans, we sampled 78 seasonally inundated wetlands to examine the relative importance of proximity of hardwood hammock patches (>20 ha) and wetland characteristics and used generalized linear models to determine which factors had a significant effect on larval anuran species richness or abundance. Species richness was significantly influenced by pH, conductivity, and water depth. Proximity to hammock did not influence species richness; however, assemblage composition differed between wetlands near hammocks and wetlands surrounded by pasture. Barking treefrogs (Hyla gratiosa LeConte, 1856), pine woods treefrogs (Hyla femoralis Bosc in Daudin, 1800), and oak toads (Bufo quercicus Holbrook, 1.
Molecular Characterization of Mitofilin, a Novel, Mitochondrial, Coiled Coil Protein, and the Relationship Between Organism Complexity and Coiled Coil Protein-Mediated Structure: A Dissertation

In the course of experiments designed to identifY and characterize structural proteins of the nuclear matrix, one antibody was generated which recognized an extraction-resistant cyoplasmic protein, This antibody was used as the starting point in the cloning and molecular characterization of a novel protein of the inter-membrane space of the mitochondrion which has been named mitofiin. Mitofiin is expressed in all human cell tys, and murine homologues also exist. Mitofiin associates only with mitochondria and not with other membrane-bounded organelles such as Golgi or endoplasmic reticulum. This observation has been confrmed both by biochemical fractionation and multi-label fluorescence microscopy. Recombinant mitofilin, purified to homogeneity by afnity chromatography and preparative electrophoresis, was used to raise second-generation antibodies. Results of Western blot and immunofluorescence microscopy experiments, identical to those obtained using the original monoclonal antiboy, verify the cloning and biochemical characterization. The mitofiin polypptide contains several regions which are predicted to interact by forming coiled coils; a mitochondrial targeting signal; and a hydrophobic, mcmbrane-spanning domain. During thc course of this work, a sequence match was found with a cDNA rcported by Icho. et al (1994) for a mRNA preferentially exprcsscd in heart muscle, which they have called HM. Evidence is presented which contradicts those authors ' contention that HM is kinesin-like motor protein. In the course of these investigations, methods were developed to detect and quantitate the expression of solubilization-resistant proteins of the nuclcar matrix and the nuclear matrix-intermediate filament scafTold. This was accomplished by combining SDS-PAGE. high sensitivity chemiluminescent Western blots. and scanning densitometl)' . Sensitivity in the picogram range was obtained , and reproducibility was assessed. For semi-quantitative measurements of protein expression in tissue samples, cell number was normalized by measurement of lamin B , the major protein of the nuclear envelope, Results of screening several cell and tissuc types for the expression of mitofiin and for the nuclear matrix proteins NuMA , the nucleoporin tpr, and lamin B are presented. These preliminary data suggest a
Effects of Anthropogenic Noise on Songbird Social Networks

Anthropogenic noise, which is increasing globally, affects birds from gene expression up through alteration of community composition. As urbanization pushes further into undisturbed habitat, noise often disperses birds away from the point source. The impacts of this dispersal on surrounding quieter areas is not well understood. Therefore, in the first chapter, we sought to understand how noiserelated dispersal affected the sociality of groups of songbirds as they moved away from the source of noise. As the displaced birds would likely be forced to occupy a smaller area that may already have resident individuals, we predicted that displaced birds would show a tighter clustered social network that may include new individuals, and that individuals within the flock would have more social connections overall. In the second chapter, we were interested in chronic, inescapable noise, the kind that birds living in urbanized areas might experience, and how that affects sociality. We predicted that birds would distribute themselves along a noise gradient and prefer the quieter areas and that the resulting density of birds would increase both flock clustering and individual sociality. We tested these ideas in two songbird systems, free-living red-backed fairy wrens (Malurus melanocephalus) to study dispersal and captive domesticated zebra finches (Taeniopygia guttata) to study chronic noise exposure. Contrary to our prediction, the free-living red-backed fairywrens became less social when dispersing from noise, as measured by node strength, during experimental noise treatments. Additionally, these birds tended to shift their space use away from the sound source. In our captive system, our hypothesis was supported that both flock cluster and individual sociality increased with noise treatments. However, the birds did not alter their distribution in accordance to the noise gradient, thus we propose support for the Increased Threat Hypothesis and suggest that increased vigilance was responsible for flock clustering and sociality. If social networks are altered consistently, there may be implications for future breeding success, detection of communication signals, and even for pathways of disease transmission among individuals.
Bovine infertility: a field oriented categorisation based on investigation among crossbred cattle in a district of Kerala

Animals (500) were examined for gynaecological reasons and the infertility conditions were suitably categorised for easier description. Out of these animals, 374 (75%) were diagnosed to be infertile cases, which included 148 cows and 226 heifers. Infertility cases mainly were of 2 types based on manifestation such as anoestrum (65%) and repeat breeding (35%). Out of the 242 anoestrum cases, 178 (74%) were true' anoestrum and rest (26%) were cases of false anoestrum. Among 132 repeat breeding animals 26 (20%) had ovulatory disturbances, 70 (53%) had reproductive tract infections (RTI) and in 33 (25%) both ovulatory disturbances and RTI together were seen. Major reasons for the conditions were nutritional deficiencies, reproductive tract infections and functional disturbances suspected out of elimination of males. It is concluded that most infertility conditions among crossbred cattle are arising out of management defects either of the farmers or technician, which in turn form indirect Consequences of intensive crossbreeding and widespread AI programme.
INVESTIGATION OF IN VITRO ANTHELMINTIC ACTIVITY OF FICUS ELASTICA LEAVES

The World Health Organization estimates that a staggering two billion people harbor parasitic worm infections.The increasing of anthelmintic drug resistance and the high cost of anthelmintic drugs led to the development of herbalmedicine as an alternative source of anthelmintic. In the current study, in-vitro experiments were conducted todetermine the possible anthelmintic effects of Ficus elastic (FE) Linn which are traditionally used for treatment of variousdiseases. The main aim of this study is to investigate the anthelmintic activity of Ficus elastica using earth-worms(Pheritima posthuma). Intestinal worms affect a host of individuals resulting in malnutrition, intellectual retardation,stunted growth and cognitive deficits. The leaves of the plant were taken for anthelmentic activity against Indianearthworm Pheritima posthuma. The Methanol and Ethanol extract of the Ficus elactica were evaluated for theiranthelmintic activity against metronidazole (10mg/ml) as a reference and distilled water as a control group and theresults were expressed in terms of time for paralysis and time for death of worms.KEY WORDS: - Ficus elastica Linn. anthelmintic activity, metronidazole, Pheritima posthuma, Death time, Paralysis time.
Potency Assay for AAV Vector Encoding Retinal Pigment Epithelial 65 Protein

• A validated potency assay for release of a medicinal product is required by the FDA prior to commercialization. SPK-RPE65 is a gene transfer vector being developed for the treatment of inherited retinal degeneration due to mutations in the retinal pigment epithelial 65 (RPE65) gene. In a Phase 3 trial, it demonstrated restoration of functional vision in subjects progressing toward blindness. We developed a non-radioactive in vitro assay to measure the activity of SPK-RPE65, in anticipation of potential commercialization of this product.
Controlling the delivery of glucose in foods

Abstract: Glucose is the principal biological fuel for the body, and it has been classified into rapidly available glucose (RAG) and slowly available glucose (SAG) based on glycemic carbohydrate digestion rate that is related to human health. This chapter first reviews the concept of glycemic index (GI), and the digestion and nutritional classification of glycemic carbohydrates. The structural properties, slow digestion mechanism, and the biological functions of slowly digestible carbohydrates (SDC), mainly slowly digestible starch (SDS), are then discussed. Finally, potential formulation and testing of low-GI foods, using SDCs to control the glucose delivery, are described for the purpose of improving human health.
Study of the pathosystem: Begomovirus Bemisia tabaci I tomato on the South West islands of the Indian Ocean

Tomato yellow leaf curl virus (TYLCV) belongs to the genus Begomovirus within the Geminiviridae family, and is exclusively transmitted by the whitefly species Bemisia tabaci (Hemiptera: Aleyrodidae) (Gennadius). It is an emerging virus which since the 1980's has globally spread over many tropical, subtropical, and Mediterranean countries. By now it has even reached such isolated places as La Reunion, an island situated in the south-western part of the Indian Ocean. Since its first introduction in 1997, the virus has spread quickly throughout this island, becoming a great constraint for tomato cultivation. At the same time an upsurge of white flies was reported on vegetable crops
The Dynamics of Chronically Bioaccumulated Cd in Rainbow Trout ( Oncorhynchus mykiss ) During Both Moderately Hard and Soft Waterborne Exposures

Aquatic organisms respond to metal exposures by modulating uptake, elimination and detoxification capacity and, therefore, it is difficult to link accumulation within fish to adverse chronic effects. When fish are exposed to sublethal concentrations of metal, physiological responses follow a damage-repair scenario with rapid uptake into the gills followed by transfer via the circulatory system and accumulation into key organs such as the liver and kidney. Anthropogenic sources of cadmium (Cd) arise mainly from mining, smelting, and refining sulphide ores of Zn, Pb and Cu (Norton et al., 1990). The free divalent ion (Cd) is the toxic form of Cd in water. Cd competes with calcium ions (Ca) for binding sites and transport channels across the basolateral membrane of the gill. Ambient Ca is the primary cation responsible for reduced Cd toxicity to species of trout, during both acute and chronic waterborne exposures. The objective of this research was to examine the dynamics of chronically accumulated Cd within tissues of rainbow trout (Oncorhynchus mykiss) during chronic (one month) sublethal waterborne exposures to Cd (0.75 and 2.0 ng/L) in both moderately hard (140 mg/L as CaC03) and moderately soft (50 mg/L as CaC03) water. Accumulation was assessed on a tissue (gills, liver and kidney) and subcellular levels. Tissues accumulated Cd in a timeand dosedependent manner. Results indicate that fish exposed to sublethal Cd concentrations in moderately soft water attained higher amounts of Cd in gills, and more Cd bound to metal-sensitive fractions (mitochondria and proteins) in all tissues in comparison to fish exposed to Cd in moderately hard water. Early mortality and ion-loss may link to accumulation in metal-sensitive fractions (particularly within the gills). However, Cd concentrations in metal-sensitive fractions continued to rise throughout both sublethal exposures suggesting damage-repair mechanisms other than metallothionein are induced, or threshold Cd concentrations in tissues and metalsensitive fractions associated with adverse effects have not been exceeded. The kidney appeared to be most capable organ to offer protection from Cd accumulation in metal-sensitive fractions, as Cd dissipated from metal-sensitive fractions with time and dose. Also kidneys displayed the highest capacity to induce detoxification of Cd by metallothionein.
Composition and distribution of the Orthoptera assemblage (Insecta) in an arid basin in North-Central Chile.

La cuenca del valle del rio Elqui (Region de Coquimbo, Chile) es un importante foco de actividad agrofruticola y turistica dentro de la zona norte-centro de Chile cuyas condiciones climaticas se caracterizan por el aumento de la temperatura y la disminucion de la precipitacion. En el contexto del calentamiento global es esperable que la hoya hidrografica del rio Elqui experimente una tendencia ascendente en la aridez, alteraciones en la fenologia de plantas y artropodos y cambios en la riqueza y biodiversidad local de los ecosistemas. En este sentido, en el presente trabajo, mediante colectas manuales en sectores de secano y cultivo de las localidades de Marquesa, Diaguitas y Pisco Elqui en el valle de Elqui, se documento la composicion taxonomica y abundancia del ensamble de Orthoptera (Insecta) en la cuenca del valle del Elqui, se analizo la distribucion espacial de las especies constituyentes del ensamble mediante SIG y se documento la importancia de Orthoptera como potenciales plagas dentro de esta cuenca arida del norte-centro de Chile. Se capturo Rev. FCA UNCUYO. ISSN 0370-4661. Tomo 43. N° 1. Ano 2011. 97-110.
Comparative analysis of the sperm ultrastructure of three species of Phyllomedusa (Anura, Hylidae)

Costa, G.C. , Garda, A.A, Teixeira, R.D. , Colli, G.R. and Bao, S.N. 2004. Comparative analysis of the sperm ultrastructure of three species of Phyllomedusa (Anura, Hylidae). — Acta Zoologica (Stockholm) 85 : 257-262 We describe the sperm ultrastructure of three species of frogs in the genus Phyllomedusa . According to micrographs, total size of the spermatozoon of Phyllomedusa hypochondrialis is significantly smaller than those of Phyllomedusa bicolor and Phyllomedusa tarsius . The acrosome complex consists of two conical structures covering the nucleus, the acrosome vesicle and the subacrosomal cone. The subacrosomal cone of P. bicolor and P. tarsius is less electron-dense and appears more granular in transverse section than in P. h ypochondrialis . In P. bicolor and P. tarsius , the nuclear space is reduced and the subacrosomal cone fills most of the space between the acrosome vesicle and nucleus. The anterior region of the nucleus in the spermatozoa of P. bicolor and P. tarsius ends abruptly, while in P. hypochondrialis it is sharp-ended. In P. bicolor and P. tarsius , the axial fibre is much larger than in P. hypochondrialis . The sperm ultrastructure of Phyllomedusa appears conservative at the intrageneric level. Future studies on the sperm ultrastructure of hylids can provide new insights on the systematics of the group and a larger database for a cladistic analysis.
INIBIDORES DA BOMBA DE PRÓTONS: REVISÃO E ANÁLISE FARMACOECONÔMICA

Os inibidores da bomba de protons (IBPs), sao medicamentos que inibem a enzima H + , K + -ATPase (ou bomba de protons) realizando a supressao acida gastrica. Atualmente, sao comercializados seis representantes desta classe: omeprazol, lansoprazol, pantoprazol, rabeprazol, esomeprazol e dexlansoprazol. Um novo IBP, tenatoprazol, esta ainda em fase de desenvolvimento. O presente estudo propoe-se a revisar os estudos disponiveis a fim de expor informacoes sobre os IBPs e realizar um estudo farmacoeconomico entre doses-padrao desses medicamentos para o tratamento da ulcera peptica gastroduodenal. Evidencias atuais sugerem que os IBPs possuem eficacia semelhante no tratamento de varias desordens gastricas e no protocolo de erradicacao do Helicobacter pylori . A partir da analise farmacoeconomica ora realizada, constatou-se que o lansoprazol apresenta perfil mais favoravel.
The Coelomycetes. Fungi imperfecti with pycnidia, acervuli and stromata.

Cytokines are regulatory proteins that act as intercellular communication signals in a variety of processes, including embryonic development, haematopoiesis, stress, inflammation, immunity and tissue repair. Studies since the early 1980s have established the vital role of cytokines in humans and rodent models for the immune, endocrine and neuronal systems. More recently, attention has turned to the cytokines of animals of veterinary importance. This book addresses basic research on cytokines and its clinical potential for veterinary medicine. Cytokines in cattle, sheep, pigs, horses, cats, dogs and birds are considered. It is shown how recent knowledge has exploded, particularly through the use of recombinant DNA and PCR technologies. The role of cytokines in the pathogenesis, diagnosis and therapy of animal diseases is reviewed, as is the utility of animal models to investigate diseases analogous to those in humans. It is shown how measurements of cytokines might be used as immunological monitors of disease progression and prognosis, how their administration to production animals might improve health status and how they might be used as vaccine adjuvants or as adjuncts to chemotherapy. Written by leading authorities from Europe, North America, Africa and Australia, the book is essential for research workers in veterinary microbiology and immunology, as well as medical scientists interested in applying this work to human health.
Enhancing the Foundation of Official Economic Statistics with Big Data

espanolLas estadisticas economicas oficiales elaboradas por la United States Census Bureau han servido durante mucho tiempo como punto de referencia de alta calidad para los usuarios de los datos. Para mantener esta calidad y mejorar los fundamentos de sus programas economicos, la Census Bureau ha comenzado a explorar el potencial de las fuentes de Big Data, tales como datos de transacciones de tarjetas de credito, datos de puntos de venta y datos de permisos de construccion disponibles al publico. Si bien este tipo de datos puede permitir a la Census Bureau mejorar la puntualidad, el detalle geografico y la cobertura de la linea de produccion de sus productos de datos economicos, existen preocupaciones tales como la transparencia metodologica y la coherencia de los datos. Este documento cubre los hallazgos relacionados con Big Data que la Direccion Economica de la Oficina del Censo ha descubierto hasta el momento, asi como la vision respecto a Big Data de la Direccion para el futuro. EnglishOfficial economic statistics produced by the United States Census Bureau have long served as a high-quality benchmark for data users. To maintain this quality and enhance the foundation of its economic programs, the Census Bureau has begun exploring the potential of Big Data sources such as credit card transaction data, point-of-sale data, and publicly available building permit data. While this type of data may allow the Census Bureau to improve the timeliness, geographic detail, and product-line coverage of its economic data products, there are concerns such as methodological transparency and consistency of the data. This paper covers the Big Data findings that the Economic Directorate of the Census Bureau has discovered so far as well as the Directorate’s Big Data vision for the future.
Combined Vehicle Type and Fuel Type Choices of Private Households: An Empirical Analysis for Germany

This paper examines joint consumer purchasing decisions of vehicle type and fuel type based on a dataset from a Germany-wide survey among 1500 potential car buyers. The goal is to study the buyer segments that are considering to purchase the different types of vehicles and to identify the main determinants influencing the joint choice decision: socio-demographic and household characteristics, attitudes and preferences, as well as vehicle-related attributes. Based on a nested logit model, our results suggest that although German car buyers’ are very heterogeneous regarding their preferences, several similarities are found between buyers of specific vehicle types (10 vehicle classes) and specific fuel types (gasoline, diesel, alternative fuel), e.g. smaller cars and alternative fuel vehicles (AFVs) have commonalities regarding individual’s environmental awareness/behavior and fuel consumption/costs. Policy-makers, when tailoring their policies, can benefit from making use of the specific insights gained from this particularly comprehensive study, and the comparisons made with the German and international scientific literature on the topic. For instance, the similarities between buyers preferring specific fuel types and specific vehicle types can be used for tailorized measures to incentivize individuals’ vehicle type shifting (e.g from larger to smaller vehicles), fuel type switching (e.g. from fossil-fuelled vehicles to AFVs), or both.