Miracle-dz/UniFAR-FTUs huggingface dataset:
Purification and Fluorometric Analysis of Leucine-Responsive Regulatory Protein from Escherichia coli

We describe the construction of derivatives of wild type and mutant lrp genes that encode 6XHis-tag Lrps. These derivatives of wild type and mutant Lrp could be useful for in vitro studies including Lrp conformational changes. We show that 6XHis-tag Lrp wild type and 6XHis-tag Lrp R145W bind with similar patterns in vitro to 21 bp duplex DNA containing the consensus sequences of Lrp sites of upstream of the ilvIH operon. In addition, we report here the 6XHis-tag Lrp R145W is useful to investigate the conformational changes of Lrp in solution by using its own intrinsic fluorescence characteristics.
Pollen morphology of selected Central European species from subgenera Vignea and Carex (Carex, Cyperaceae) and its relation to taxonomy

This study analysed the taxonomic utility of selected features of pollen grains of 45 Central European species of subgenera Vignea and Carex of the genus Carex. Seven quantitative features were analysed: [length of polar axis (P), length of equatorial axis (E), exine thickness on the pole (Exp), exine thickness on the equator plane (Exe), P/E ratio and the relative thickness of exine (Exp/P and Exe/E ratio)] and outline, shape and exine sculpture. Among the biometrical features, the most important for Carex taxonomy (particularly at the level of subgenus) is the thickness of exine (Exp). Marked differences in the morphological structure of inflorescences at the subgenus level are reflected in the differences of pollen features. Results of our studies clearly show an explicit (and not previously described in the palynological literature) taxonomic division of the genus Carex on the basis of pollen biometrical features into two units corresponding exactly to the subgenera (Vignea and Carex). However, the features of pollen grains analysed did not contribute any essential taxonomic criteria at levels lower than subgenus (e.g. sections). An exception was for C. disticha, where it was observed that the poroid areas occurred in pairs, a new feature for sedges. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164, 422–439.
IDENTIFICATION OF LOCI CONTRIBUTING TO THE SMITH-MAGENIS SYNDROME-LIKE PHENOTYPE AND MOLECULAR EVALUATION OF THE RETINOIC ACID INDUCED 1 GENE

IDENTIFICATION OF LOCI CONTRIBUTING TO THE SMITH-MAGENIS SYNDROMELIKE PHENOTYPE AND MOLECULAR EVALUATION OF THE RETINOIC ACID INDUCED 1 GENE A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University By STEPHEN RICHARDSON WILLIAMS Bachelor of Science (B.S.) James Madison University, Harrisonburg, Virginia, 2001 Smith-Magenis syndrome (SMS) is a multiple congenital abnormalities intellectual disability syndrome that results from a deletion of chromosome 17p11.2 or mutation of the retinoic acid inducted one gene (RAI1). SMS is characterized by a multitude of phenotypic features including craniofacial defects, short stature, obesity, intellectual disability, self-abusive behavior, sleep disturbance and behavioral abnormalities. Interestingly, although SMS is a clearly defined syndrome with a known molecular change at its foundation, ~40% of all candidate cases sent to the Elsea lab for evaluation do not have a mutation or deletion of RAI1. We hypothesize that at least one other locus must be responsible for this Smith-Magenis-like (SMS-like) phenotype. To address this hypothesis, we first compiled a cohort of 52 subjects who had been referred to the Elsea lab for a clinical diagnosis of SMS. Once these individuals were confirmed to not have an RAI1 mutation or deletion, their phenotypes were compiled and statically analyzed to distinguish whether SMS and SMS-like cohorts are different in the prevalence of the core phenotypes of SMS such as, but not limited to, sleep disturbance, self-abusive behavior and
Manifestation of heterosis in chilli

Three lines of chilli (Capsicum annuum) were crossed with fourteen pollen parents in a line x tester fashion. Seventeen parents along with forty-two hybrids were grown in randomized block design in three replications. The extent of heterosis over better parent was 55% for fruit length, 24.48% for fruit width, 111.27% for fruit weight, 66.55% for fruit number, 316.26% for early yield and 108.17% for total yield. The cross Punjab Guchhedar x RHCH up and Lt-2 x Lorai manifested maximum heterosis for fruit number and total yield, respectively.
Analysis of variability in segregating generation of soybean (Glycine max (L.) Merrill)

An investigation was carried out at Main Agricultural Research Station, University of Agricultural Sciences, Dharwad during kharif 2006 to analyze the extent of variability in F3 segregating generation of cross JS-93-05 x JS-335 of soybean. All the segregants were classified based on leaflet shapes viz., oval, ovate, lanceolate and linear leaflets. It was observed that considerable range of variation exhibited by all the leaflet types. The characters viz., plant height, days to flowering, days to maturity, specific leaf weight, number of pods per plant, harvest index and 100-seed weight showed very narrow differences between phenotypic and genotypic coefficient of variation in all the four leaflet types. High heritability coupled with high genetic advance as per cent of mean was observed for traits viz., number of pods per plant, specific leaf weight in oval, ovate and lanceolate leaflet types.
Determinación de la fijación biológica de N2 usando la técnica de abundancia natural del N15 en tres ecotipos de cacahuate forrajero

Se midio la proporcion de nitrogeno atmosferico (N2) biologicamente fijado, utilizando el metodo de abundancia natural de N, en tres ecotipos de la leguminosa forrajera Arachis pintoi (Ap): CIAT 17434, 18744 y 18748, empleando el inoculante mejorado Bradyrhizobium CIAT 3101 (BS), y una mezcla de cepas nativas (NS) de un suelo de Veracruz, Mexico. Como plantas de referencia, se usaron la leguminosa no-nodulante Arachis hypogaea, y las gramineas forrajeras Brachiaria arrecta, Brachiaria brizantha y Cynodon nlemfuensis.
Foraging pattern of birds during the breeding season in thorn forest of Mudumalai Wildlife Sanctuary, Tamil Nadu, Southern India.

Foraging pattern of birds in thorn forest was studied in Mudumalai Wildlife Sanctuary in 1995 and 1996 during January to April (dry spell) as most of the birds start breeding during this period, demands for energy are greatest and birds spend most of their time in foraging. This study examines the foraging pattern of birds in a 10 ha plot laid in the thorn forest. Information on foraging height, substrate, and method was collected. In total, 1386 observations were made on the above said three dimension for 33 species of birds. Cluster analysis of these three dimension shows that the most important factor dividing the bird community into foraging guilds related to the physical structure of the habitat followed by the foraging substrates and methods. In total, nine foraging heights, six foraging substrates, and nine foraging methods were identified for the bird species present in the study plot. All the birds overlapped considerably with other species at least in any one of the three dimensions. Niche overlap was observed high in the usage of height followed by foraging substrate and method. As the birds are evolved with special morphological adaptations to use particular foraging method and exploit particular substrate, overlap was less and specialization was more among birds in these two dimensions.
Ground Beetles as Indicators of Land Type Diversity in the Green Mountains of Vermont

Ground beetles (Coleoptera: Carabidae) captured in pitfall traps were compared within and among three Ecological Land Types in the Green Mountain National Forest, Vermont, to determine if beetle distributions can be linked to an ecological classification system designed to reflect biological diversity. Beetles were sampled in a nested‐scale design comprising three ecological land types, three polygons representing each ecological land type, five sites within each polygon, and six individual traps at each site. A nested analysis of variance showed only 2 of 35 species to vary significantly in relative abundance across ecological land types; most of the significant effects were at the site scale. To determine whether sites might sort into groups based on their beetle assemblages, sites were ordinated by detrended correspondence analysis and classified by two‐way indicator species analysis. Ordinations suggested that the distribution of ground beetles was somewhat influenced by site moisture; classification separated groups of hygrophilous species and wet sites from other ecologically uninterpretable species assemblages and site‐groups. Several of the site‐groups contained sites affiliated primarily with one ecological land type. However, a nested analysis of variance using the relative abundance of each of the species assemblages again showed most significant effects to be at the site scale. Results indicated that ground beetle distributions were not significantly linked with ecological land types and that the ground beetle fauna of the mid‐elevation forests of the western Green Mountains is comprised mainly of forest generalists, with some specialist species responding to a moisture gradient at the site scale. Because the ecological land type units did not explain distributions of carabids, these organisms should next be related to higher and lower scales within the classification system. Distributions of other invertebrate and vertebrate species should also be studied to test the utility of this ecological classification system for monitoring forest biodiversity.
Effect of testing and removal of feeder calves persistently infected with bovine viral diarrhea virus at the time of feedlot arrival and outcome on health, performance, and carcass characteristics

Twelve lots of auction-derived steers totaling 1,577 head with an unknown health history (initial body weight 660 lb [300 kg]) were used to investigate testing and removal of feeder calves persistently infected with bovine viral diarrhea virus (PI-BVDV) upon arrival at a single feedlot in central Kansas. Pens with a PI-BVDV calf present at arrival were considered exposed and were compared to pens of steers that arrived without a PI-BVDV calf in the group. Both exposed and non-exposed pens of steers were followed from arrival through harvest to investigate the impact of exposure on health, performance, and carcass characteristics of feedlot cattle. A significant difference in the morbidity between exposed (2.3%) and non-exposed (7.2%) cattle was found (P<0.01). No differences in retreatment or mortality rates were found between groups. Exposure to a PI-BVDV animal for less than 48 hours after arrival did not have an effect on performance parameters. There was an increased percentage of USD A yield grade 4 and 5 (P=0.01) carcasses in the exposed cattle, but no other differences in carcass characteristics were found between groups.
Dynamics of soybean leaf hydraulic conductance and diurnal soybean transcriptome analysis

Leaf hydraulic properties are strongly linked with transpiration and photosynthesis in many species. However, it is not known if gas exchange and hydraulics will have coordinated responses to climate change. Our objective was to investigate the responses of leaf hydraulic conductance (Kleaf) in Glycine max (soybean) to growth at elevated [CO2] and increased temperature compared with the responses of leaf gas exchange and leaf water status. Two controlled environment growth chamber experiments were conducted with soybean to measure Kleaf, stomatal conductance (gs), and photosynthesis (A) during growth at elevated [CO2] and temperature relative to ambient levels. These results were validated with field experiments on soybean grown under free-air elevated [CO2] (FACE) and canopy warming. In chamber studies, Kleaf did not acclimate to growth at elevated [CO2], even though stomatal conductance decreased and photosynthesis increased. Growth at elevated temperature also did not affect Kleaf, although gs and A showed significant but inconsistent decreases. The lack of response of Kleaf to growth at increased [CO2] and temperature in chamber-grown plants was confirmed with field-grown soybean at a FACE facility. Leaf hydraulic and leaf gas exchange responses to these two climate change factors were not strongly linked in soybean, although stomatal conductance responded to [CO2] and increased temperature as previously reported. This differential behavior could lead to an imbalance between hydraulic supply and transpiration demand under extreme environmental conditions likely to become more common as global climate continues to change. 1 Reprinted with permission from Locke AM, Sack L, Bernacchi CJ, and Ort DR (2013) Soybean leaf hydraulic conductance does not acclimate to growth at elevated [CO2] or temperature in growth chambers or in the field. Annals of Botany doi: 10.1093/aob/mct143.
Music of life : biology beyond the genome

1. The CD of Life: the genome 2. The organ of 30,000 pipes 3. The Score: is it written down? 4. The Conductor: downward causation 5. The Rhythm Section: the heartbeat and other rhythms 6. The Orchestra: the organs and systems of the body 7. Modes and Keys: cellular harmony 8. The Composer: evolution 9. The Opera Theatre: the brain 10. Curtain Call: The artist disappears
Regulation of gastrulation movements by planar cell polarity genes in zebrafish.

During vertebrate gastrulation, mesodermal and ectodermal cells undergo convergent extension (CE), a process characterised by cellular rearrangements in which polarised cells intercalate along the medio-lateral axis leading to elongation of the antero-posterior axis. This thesis aims to prove that genes which have been implicated in the establishment of planar cell polarity (PCP) in Drosophila are conserved in the non-canonical Wnt pathway that regulates CE in zebrafish during gastrulation. Firstly, I analyzed functions of Wnt5 and Wnt 11 ligands and of Fz2 and Fz7 receptors in regulating CE movements. Here, I will show that pipetail (ppt/wnt5) mutant is required for regulating CE movements in posterior mesendoderm and ectoderm while its function in the anterior mesendoderm is redundant to siberblick (slb/wntl 1). Based on gene expression analyses, loss of function and gain of function analyzes, the interaction between these Wnt ligands and Fz receptors is dependent on time, concentration and position of expression during gastrulation. Secondly, I will describe the isolation and functional characterisation of the zebrafish homologue of Drosophila prickle (pkl) during gastrulation. Zebrafish pkl functions together with Sib/Wnt 11 and Ppt/Wnt5 to regulate CE movements due to abrogation of Pkl function by morpholino that leads to defective CE movements, enhances the slb/wntl 1 and ppt/wnt5 phenotypes and suppresses the ability of wnt 11 to rescue the sib phenotype. Gain-of- function of Pkl also inhibits CE movements. Additionally, I found that Pkl could destabilise Dsh and thereby block the ability of Fz to target Dsh to the cell membrane by down-regulating levels of Dsh protein. These results suggest that Pkl acts in the non- canonical Wnt pathway to regulate CE, but it is unlikely to be a simply linear component of this pathway. I will describe the isolation of zebrafish flamingo (fmi) genes and characterise the expression pattern during gastrulation. I also describe functional characterisation of those genes during gastrulation. Initially, abrogation of Fmi function by morpholino leads to weakly defective CE movements enhances the slb/wntl 1 phenotype and defective epiboly phenotypes of the offroad (ord)/fmil mutants. In contrast, a dominant negative approach with a mutant form of Fmi, led me to conclude that Fmi is involved in the regulation of CE movements. Together with analyses of Fmi protein, I will discuss how Fmi regulates different gastrulation movements, such as convergent extension and epiboly.
Molecular Mechanisms of Antibiotic Resistance in Helicobacter pylori

textabstractAn estimated 4 to 5 million individuals in the Netherlands are actively infected with Helicobacter pylori. Eradication of this bacterium becomes more difficult as the prevalence of antibiotic resistance is increasing worldwide. Most H. pylori infections are now diagnosed by non-invasive testing (i.e. urea breath test, serology, stool test), and thus data on antibiotic susceptibility are lacking. Furthermore, once the antibiotic susceptibility is assessed using conventional culture-based methods by means of an E-test, agar dilution or disc-diffusion, then data are difficult to compare between different centers due to lack of standardization. Molecular-based methods are reproducible and easily standardized, and thus they can offer an attractive alternative. To develop molecular-based methods knowledge of molecular mechanisms underlying antibiotic resistance is mandatory. The research presented in this thesis aims to obtain information on molecular mechanisms of antibiotic resistance in H. pylori.
Comparative analysis of structural and functional hair coat characteristics, including heat loss regulation, in the Lutrinae (Carnivora: Mustelidae)

In this thesis, different characteristics of the hair coat of the Lutrinae were investigated: - variability of the primary hair structure in the Eurasian otter (Lutra lutra) - hair structure of the 13 otter species - hair density of the Eurasian otter (Lutra lutra) and the Sea otter (Enhydra lutris) Also, the regulation of heat loss through the surface of the body was studied using an infrared thermographic camera.
Immunology and Evolution of Infectious Disease

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Effect on Grain Yield in Pigeonpea Genotypes with Different Levels of Resistance to the Pod Borer, Helicoverpa armigera

Twelve pigeon pea genotypes with different levels of resistance to Helicoverpa armigera were evaluated for their ability to withstand pod borer damage or recover from damage based on loss in grain yield under field conditions (Andhra Pradesh, India). Under unprotected conditions, ICPL 332, ICPL 84060, and ICPL 98001 suffered low pod damage compared to the susceptible control, ICPL 87, and there were >40 pods per plant in ICP 7203-1, ICPL 98001, ICPL 98008, ICPL 84060, and ICPL 332 compared to <25 pods in case of ICPL 87. The loss in grain yield was <29% in ICPL 332, ICPL 84060, and ICPL 187-1 compared to 87.2% in ICPL 87. Genotypes such as ICPL 332, ICPL 187-1, and ICPL 84060, which suffered low pod damage and/or low reduction in grain yield can be used for the management of H. armigera, or as sources of resistance in the pigeon pea improvement programme.
Antibacterial Activities of different Solvent Extracts of Carica Papaya Fruit Parts on some Gram Positive and Gram Negative Organisms

Aside its nutritional values, there are speculations that Carica papaya , also known as paw paw, has antibacterial potentials. This study evaluates the antibacterial potentials of different extracts of C.papaya parts, in comparison with standard drugs (perflacine and cefuroxine). Dried and grinded papaya leaves (5g), fruit peels (5g); and seeds (5g), respectively mixed with 95ml of extraction solvent (water, ethanol, 1% HCl, acetone and petroleum ether) for 24 hours, were used for this study. The constituent compounds were filtered aseptically and inoculated unto MacConkey and Nutrient agars to verify the sterility of the solutions for utilization. Results showed high antimicrobial activity for the extracts of C.papaya in petroleum ether with a Minimun Inhibitory Concentration (MIC) of 2mg/ml as against 4mg/ml and 6mg/ml for perflacine and cefuroxine respectively. Extracts in 1% HCl and ethanol however, showed antimicrobial activity against the gram positive and negative organisms investigated, while extracts in water was only active against Escherichia coli and S. aureus . No statistical difference (P<0.05) was observed in the antimicrobial activities between the extracts of petroleum ether and the standard antimicrobial drugs. These suggest that C. papaya may be used as an antibiotic, and extracts in petroleum ether seems more potent. Key words : Carica papaya, Antimicrobial, Extraction solvents, Plant parts.
Fatty Acid Metabolism Mediated by 12/15-Lipoxygenase is a Novel Regulator of Hematopoietic Stem Cell Function and Myelopoiesis

Fatty acid metabolism governs critical cellular processes in multiple cell types. The goal of my dissertation was to investigate the intersection between fatty acid metabolism and hematopoiesis. Although fatty acid metabolism has been extensively studied in mature hematopoietic subsets during inflammation, in developing hematopoietic cells the role of fatty acid metabolism, in particular by 12/15-Lipoxygenase (12/15-LOX), was unknown. The observation that 12/15-LOX-deficient (Alox15) mice developed a myeloid leukemia instigated my studies since leukemias are often a consequence of dysregulated hematopoiesis. This observation lead to the central hypothesis of this dissertation which is that polyunsaturated fatty acid metabolism mediated by 12/15-LOX participates in hematopoietic development. Using genetic mouse models and in vitro and in vivo cell development assays, I found that 12/15-LOX indeed regulates multiple stages of hematopoiesis including the function of hematopoietic stem cells (HSC) and the differentiation of B cells, T cells, basophils, granulocytes and monocytes. Within hematopoietic development, I concentrated on the mechanisms that underlie the defects in HSC function and monocyte development since these defects likely contribute to the myeloid leukemogenesis in Alox15 mice. Interestingly, I determined that 12/15-LOX promotes HSC selfrenewal and quiescence, which is associated with the activation of canonical Wnt signaling. Moreover, my studies demonstrate that 12/15-LOX-mediated redox signaling of SHP-2 and the transcription factor ICSBP/ IRF-8 promotes monocyte development while inhibiting granulocyte development. This pathway is also conserved in IL-12p40 expression in macrophages. Therefore, I establish 12/15LOX as a critical regulator of hematopoiesis and provide insight into novel mechanisms whereby HSC function and monocyte cell fate decisions are regulated. These findings have implications for leukemogenesis and immunity. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Immunology First Advisor Ellen Pure