Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of axon guidance receptor expression and activity during neuronal morphogenesis

Receptors expressed on the surface of neurons during development direct cell migration, axon guidance, dendrite morphogenesis, and synapse formation by responding to cues in the neuron’s environment. The expression levels and the activity of cell surface receptors must be tightly controlled for a neuron to acquire its unique identity. Transcriptional mechanisms are essential in this process, and many studies have identified requirements for specific transcription factors during the different steps of neural circuit assembly. However, the downstream effectors by which most of these factors control morphology and connectivity remain unknown. In Chapter 1, I highlight recent work that elucidated functional relationships between transcription factors and the cellular effectors through which they regulate neural morphogenesis and synaptogenesis in multiple model systems. In Chapters 2 and 3, I present data demonstrating that the homeodomain transcription factors Hb9 and Islet control motor axon guidance in Drosophila embryos through distinct effectors: Hb9 regulates the (Roundabout) 2 receptor in a subset of motor neurons, while Islet acts in the same cells to regulate the Frazzled/DCC receptor. Genetic rescue experiments indicate that these relationships are functionally important for the guidance of motor axons to their muscle targets. In addition, Islet regulates motor neuron dendrite targeting in the central nervous system (CNS) through Frazzled, demonstrating how an individual transcription factor can control multiple aspects of neuronal connectivity through the same effector. In Chapter 4, I characterize a non-canonical function for the Robo2 receptor during midline crossing, and present data suggesting that this activity requires Robo2 to be expressed in midline cells, providing an example of how mechanisms that regulate guidance receptor gene expression are key to regulating receptor function and nervous system formation. In Chapter 5, I explore the implications of these findings, and propose future directions of research to build upon them. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Greg J. Bashaw
Tadpole and advertisement call of Chiasmocleis albopunctata (Anura, Microhylidae) from Brazil

The advertisement call of Chiasmocleis albopunctata is known from specimens from Bolivia, the tadpole is unknown. Here we present data on tadpole and the advertisement call of a Brazilian population of this species. Tadpoles and calls are from Uberlândia (Minas Gerais, Brazil). Tadpoles are 18.3-21.5 mm TL. Body length about 47% total length; tail triangular, flagellar-tipped. Oral apparatus with two symmetrical semicircular flaps pending over the mouth; flaps border wartyornamented. The tadpoles of C. albopunctata differ in color from that of C. shudikarensis. Different from C. ventrimaculata and C. carvalhoi, tadpoles of C. albopunctata do not possess a pair of parentheses-like mottles between eyes. Calls from the Brazilian population were consistently characterized by nine pulses per notes and two harmonic frequency bands, while calls from Bolivia have 5-8 pulses per note and no harmonics.
Occurrence and diversity of fungal pathogens associated with water hyacinth and their potential as biocontrol agents in the Rift Valley of Ethiopia

ABSTRACT Water hyacinth poses serious socio-economic and environmental problems in Ethiopia. To integrate fungal pathogens into water hyacinth management, a survey was conducted in the Rift Valley of Ethiopia. Based on morphological characterization and DNA sequencing, 25 fungal species were identified that belong to nine genera. Alternaria tenuissima, A. alternata, Aspergillus niger, Phoma sp. , Curvularia trifolii, Mucor fragilis, M. racemosus, A. fumigatus, Fusarium oxysporum, and F. equiseti were the most common fungi detected. However, their occurrence was influenced by water wave action, temperature, season, and altitude. Among the fungal pathogens, A. alternata, A. tenuissima, F. oxysporum, F. equiseti, and Neofisicoccum parvum were highly pathogenic to water hyacinth. Alternaria alternata and A. tenuissima did not cause disease symptoms on ecologically important plant species (e.g. Noug, Tef, and Coffee). Application of the fungal pathogens on water hyacinth plants also showed 11%–67%, 22%–72%, 15%–55%, and 12%–50% reduction in fresh weight, dry weight, plant height, and root length of water hyacinth, respectively. This study suggests that fungal species have the potential to control water hyacinth biologically and provides baseline data for biological control efforts in the future.
Development and characterization of DNA aptamer and microfluidic paper based platform for detection of heart type fatty acid binding protein

i List of Abbreviations and symbols iv List of Figures ix List of Tables xv Introduction 1 Chapter 1 1. Literature Review 7 1.1. Heart type fatty acid binding protein as early marker of acute myocardial infarction 11 1.2. Structure–function relationship of FABP3 15 1.3. Functions of FABP3 18 1.4. Detection techniques 21 1.4. 1. Immunoassays 21 1.4. 2. Immunosensors 25 1.4. 3. Point of care immunotests 32 1.4. 4. Microarray systems 34 1.5. Nucleic acid aptamers as biorecognition elements 38 1.5. 1. General process of SELEX 40 1.5. 2. Aptamer-target interaction studies 41 1.6. Paper based microfluidic device as a sensing platform 44 Chapter 2 2. Cloning, expression and purification of human fatty acid binding proteins 49 2.1. Overview 49
Complete mitochondrial genome of the monogonont rotifer Brachionus rotundiformis (Rotifera, Brachionidae)

Abstract The two complete mitochondrial genomes were sequenced from the monogonont rotifer Brachionus rotundiformis. The genome sequences were 10,268 bp and 11,703 bp in size, and the gene order and contents were identical with those of B. koreanus but were different in tRNA-Cys with B. plicatilis mitochondrial genomes. Of the 12 protein-coding genes (PCGs), five genes (ND1, ATP6, ND5, CO3, ND3) had incomplete stop codons. Furthermore, the start codon of ND4 and CO3 gene was ATA, while the start codon of other PCGs was ATG. The base composition of B. rotundiformis mitogenome shows an anti-G bias (12.05% and 10.24%) on the second and third position of the PCGs, respectively.
Efecto del fuego sobre la germinación de especies de ecosistemas de matorral

En este trabajo se estudio la germinacion de especies de matorral a tres niveles jerarquicos. En el primer nivel considerado, nivel familiar, unicamente las ericaceas resultaron favorecidas por la quema debil. En las cistaceas y ulex, el numero de plantulas aumento con la intensidad de la quema, pero no hubo confirmacion estadistica de los resultados. En sentido inverso, los resultados de las gramineas indicaron una tendencia desfavorable de este grupo con la intensidad. El estudio a nivel especifico del efecto de las altas temperaturas y la concentracion de cenizas en 11 especies detecto que: A) las cenizas deprimen la germinacion, en particular, en las ericaceas y cistaceas. Unicamente A. Marginata resulto ser insensible a este factor. B) las altas temperaturas son favorables en las tres cistaceas (T. guttata, H. alyssoides y C. psilosepalus) y en E. umbellata. Las ericaceas C. vulgaris y D. cantabrica y las gramineas (A. curtisii, A. delicatula y D. cantabrica) son insensibles a este factor. E. ciliaris es la unica especie que resulto ser desfavorecida por la temperatura mas alta (110 grados c, durante 5 min.). En Ulex europaeus se confirmo un efecto claramente favorable de la temperatura sobre las semillas, influyendo ademas el tipo de suelo (quemado o no) en germinacion. Por ultimo, se estudiaron variaciones dentro de la misma especie en tres gramineas, segun la posicion en la inflorescencia, en funcion de la temperatura y las cenizas. La combinacion de los tres factores produce diversificacion en la respuesta, y se relaciono esta con el grado de desarrollo de la semilla.
Ovoteste de Bradybaena similaris (Férussac, 1821) (Mollusca, Xanthonychidae): histologia e produção de gametas

Ovotestis of adult specimens of Bradybaena similaris (Ferussac, 1821) (Mollusca, Xanthonychidae) have been studied, under the microscope. It has been confirmed that the ovotestis of B. similaris lays in the middle of a loose conjunctive tissue, internally the digestive gland, and is constituted of tubular units, surrounded by fusiform cells, which support the germinative lineage in different maturing stages. The oocytes, which are large cells with a finely granular cytoplasm and spherical nuclei with evident nucleoli, are located at the basis of the acinar wall, just beneath the male cells which are always luminal. A halo separates the oocyte from the follicular epithelium, whose visibility is variable. The spermatozoa, attached to the Sertoli cells or free in the tubule lumen, arrange themselves in a parallel way and stand out because of the pronounced basophilia of their heads and their long and eosinophilic tails.
Multi-scale modeling of paracrine PDGF-driven glioma growth and invasion

Multi-scale modeling of paracrine PDGF-driven glioma growth and invasion Susan Christine Massey Chair of the Supervisory Committee: Affiliate Professor Kristin R. Swanson Applied Mathematics The most common primary brain tumor in adults, glioma claims thousands of lives each year. Despite efforts to improve survival rates, the standard of care has remain unchanged for more than a decade. Recent research has started to uncover the role of stromal involvement in the growth of gliomas. Consisting of the supportive cells in the tissue, these stromal cells had long been overlooked in finding strategies for treating cancers. One particular component of this stromal support of gliomas is plateletderived growth factor (PDGF). PDGF is secreted by a number of cells in the brain, and has a number of cellular targets, including oligodendroglial progenitor cells. In animal models, upregulated PDGF signaling leads to the formation of tumors similar to human gliomas through the recruitment of oligodendroglial progenitor cells by PDGF. Central to my work is the mathematical examination of the effects of paracrine PDGF signaling on normal brain tissue and in brain tumor formation using PDE models. Model simulations show that PDGF can drive a number of outcomes in response to brain injury, and that increased PDGF signaling can speed up tumor growth and can alter the steepness of the tumor density gradient extending into adjacent normal brain tissue. Greater understanding of the contributions of PDGF in the development and growth of tumors may lead to much needed new strategies for combating glioma.
Kinetic modeling predicts a role for ribosome collisions at elongation stall sites in bacteria

Ribosomes can stall during translation elongation in bacteria and eukaryotes. To identify mechanisms by which ribosome stalling affects expression of the encoded protein, we develop an inverse approach that combines computational modeling with systematic perturbations of translation initiation rate, the number of stall sites, and the distance between stall sites on a reporter mRNA. By applying this approach to ribosome stalls caused by amino acid starvation in the bacterium Escherichia coli, we find that our measurements are quantitatively inconsistent with two widely used kinetic models for stalled ribosomes: ribosome traffic jams that block initiation, and abortive (premature) termination of stalled ribosomes. To account for this discrepancy, we consider a model in which collision from a trailing ribosome causes abortive termination of the stalled ribosome. This collision-stimulated abortive termination model provides a better fit to measured protein synthesis rates from our reporter library, and is consistent with observed ribosome densities near stall sites. Analysis of this model further predicts that ribosome collisions can selectively stimulate abortive termination of stalled ribosomes without fine-tuning of kinetic rate parameters. Thus ribosome collisions may serve as a robust timer for translational quality control pathways to recognize stalled ribosomes.
Ichthyofauna as an environmental quality indicator of the Bertioga Channel, São Paulo (Brazil)

O objetivo deste estudo foi investigar a estrutura da ictiofauna na regiao da desembocadura norte do Canal de Bertioga (Sao Paulo, Brasil) e os possiveis efeitos da perda da qualidade ambiental. As amostras foram coletadas mensalmente de setembro a dezembro de 2005, em duas estacoes oceanograficas, com rede de arrasto. A estrutura da fauna de peixes foi avaliada por indicadores ecologicos e a qualidade ambiental por curvas ABC e um indice de comunidades de peixes estuarinos (EFCI). Um total de 1553 individuos em 50 especies foi amostrado. Ariidae e Sciaenidae totalizaram 60% e Cathorops spixii representou 36% de todos os especimes coletados. Maior riqueza e diversidade ecologica foram registradas em dezembro, enquanto a maior abundância numerica foi encontrada em outubro. A maioria das especies foi representada por juvenis. As analises de agrupamento e de correspondencia canonica mostraram uma diferenca consistente e clara entre as estacoes de amostragem, e os fatores abioticos analisados (temperatura, profundidade e salinidade) parecem nao ter influencia sobre a estrutura da comunidade. A curva ABC sugeriu um ambiente moderadamente perturbado e o EFCI permitiu classificar a area como "pobre", a partir das 12 metricas analisadas, que consideraram a reducao da diversidade especifica, a composicao e a abundância, bem como a modificacao na funcao de bercario/infantario e a integridade trofica da area. Futuros estudos devem se concentrar em analisar conjuntamente os indicadores quimicos da agua, do sedimento e os indicadores biologicos, para confirmar a condicao da ictiofauna da desembocadura norte do Canal de Bertioga.
Antifungal Activity, Biodegradation and Production Inhibition of Aflatoxins B1 and G1 by a Soil Isolate of Bacillus subtilis against Aspergillus parasiticus NRRL 2999

Aflatoxins, the most potent carcinogenic mycotoxins, are mainly produced by Aspergillus flavus and Aspergillus parasiticus. Different strategies have been used to control aflatoxin-producing fungi in field and storage conditions. In this study, a field isolate of Bacillus subtilis examined for its ability to inhibit the growth, spore germination and aflatoxin production by A. parasiticus NRRL 2999. Aflatoxin degradation and cell wall adsorption were also tested. Aflatoxins B1 and G1, the most potent carcinogens, were measured qualitatively by HPLC. According to the results, B. subtilis culture filtrate suppressed fungal growth and spore germination by 0-100% and 0-38% at different concentrations, respectively. The bacterium inhibited aflatoxins B1 and G1 more than 90% in 750 μl concentration. In addition to the aflatoxin production inhibition, the bacterial cells degraded the aflatoxins B1 and G1 in liquid medium up to 60% but there was no aflatoxin which could be adsorbed by the cell wall of the bacterium. The inhibitory potentials of this isolate could be extended to direct use of this strain in the market or as a biological control agent in the field to prolong the shelf life of commodities.
ANTIFUNGAL ACTIVITY OF EXTRACT OF EUGENIA AROMATICA (L.) BAILL. (MYRTACEAE) AGAINST SOME PLANT PATHOGENIC MOLDS

Extract of Eugenia aromatica (L.) Baill. (Myrtaceae) was tested for antifungal activity. In this study, phytopathogenic molds, Alternaria sp. and Fusarium sp. causing leafspot and wilt disease in Brassica spp. , and Botrytis sp. and Septoria sp. , causing gray mold rot in roses and leafspot in chrysanthemums respectively, were used as test organisms. The extract of Eugenia aromatica, 0.01 1.00% concentration incorporated in PDA, provided inhibitory activity against all tested molds. Botrytis sp. and Fusarium sp. were completely inhibited at a concentration of 0.05%, while Alternaria sp. and Septoria sp. were completely inhibited at concentrations higher than 0.30%. Separation by preparative-TLC and confirmation by TLC-bioassay using Cladosporium cladosporioides as a diagnostic fungus distinguished two active compounds, eugenyl acetate and eugenol. INTRODUCTION Eugenia aromatica (L.) Baill. (Myrtaceae, common name: clove) is a tree reaching a height of 5-10 meters. It is native in Malacca and abundant in Malaysia, Sumatra, Africa, South America, and Thailand. In Thailand, flower buds of this species are used as a spice and traditional medicine, mainly as a carminative, stomachic, antidiarrheal, local anesthetic for toothache, and as a gargle for mouth-wash (Mahidol University, 1996). In spite of this widespread use, information concerning a marked antifungal property of the plant extract has been reported only quite recently (Lima et al., 1993; Tragoolpua, 1996; Wilson et al., 1997; Wonggiratthiti, 2000; Costa et al., 2000). In order to determine the antifungal activity, the dichloromethanic extract of Eugenia aromatica was tested against phytopathogenic molds and the active compounds were evaluated and identified. MATERIALS AND METHODS Plant Material Dried flower buds of Eugenia aromatica were obtained from a grocery in Chiang Mai Province Test Organisms The fungi used for testing antifungal activity of the plant extract were: Alternaria sp. and Fusarium sp. causing leaf spot and wilt disease of cruciferous vegetables, Septoria sp. causing leaf spot of chrysanthemums and Botrytis sp. causing gray mold rot of roses. They were cultured on potato dextrose agar and maintained at 4-8°C. Extraction Procedure Dried flower buds of clove were crushed and extracted with dichloromethane using an ultrasonic bath (40°C) for 1 hour. The solvent was removed under reduced pressure in a rotary evaporator to give a dry crude extract, which was dissolved in a small amount of dichloromethane and mixed with sterile distilled water to obtain a 2% stock
The ability of two fungi to dissolve hardly soluble phosphates in solution

ABSTRACT Low phosphorus availability in soil is one of the major causes that hamper crop yield. The main objectives of this work were to isolate efficient phosphate-solubilising strains from semi-arid soil and to check their efficiency to solubilise different inorganic phosphorus forms (viz., dicalcium phosphate (DCP), tricalcium phosphate and Udaipur rock phosphate) at different temperatures. Initially, 40 strains were isolated from rhizosphere soil of Sesamum indicum grown in semi-arid region of Rajasthan, India, of which 24 isolates showed phosphate-solubilising ability. Further, screening of these isolates for their phosphate solubilisation efficiency in solid media and broth led to the selection of two most competent isolates viz. SI32 and SI39. Both the isolates were effective in solubilising phosphorus at wide range of temperatures with different inorganic insoluble phosphorus sources. Amongst various insoluble phosphate sources tested, DCP was solubilised the most at all the temperatures but the performance was especially good in the range of 25–35°C.
Conflicting Effects of Climate and Vector Behavior on the Spread of a Plant Pathogen

Local climatic conditions are important determinants of disease dynamics through effects on vector population performance or distribution. Yet, climate may also be epidemiologically significant due to effects on host−pathogen infection dynamics. We developed a model to explore interactive effects between climate-mediated acceleration in disease phenology (i.e., faster incubation or symptom onset) and vector preference based on host symptom status. Higher incubation rates favored pathogen outbreaks, but more rapid symptom onset may constrain spread if vectors avoid symptomatic hosts. Next, we tested whether warmer conditions favored greater spread of the plant pathogen, Xylella fastidiosa, by its leafhopper vector, Graphocephala atropunctata. Inoculated and healthy plants were reared in two temperature-controlled greenhouses. At six times postinoculation, a healthy and inoculated plant were exposed to noninfective vectors, after which pathogen spread was evaluated. Incubation rate and symptom onset in infe.
The Economic Value of Biodiversity.

The authors show how cost-benefit techniques can be applied to biodiversity and how they provide a measure of the efficiency of conservation techniques. Only if biodiversity conservation passes a basic economic test such as cost-benefit analysis is it likely to be incorporated into policy. Written with great clarity and accessibility, the book will be invaluable to policy-makers and others grappling with this subject, and is also a very suitable introdution and course-book for students of economics and environmental studies.
Linking plant strategies and plant traits derived by radiative transfer modelling

Question Do spatial gradients of plant strategies correspond to patterns of plant traits obtained from a physically based model and hyperspectral imagery? It has been shown before that reflectance can be used to map plant strategies according to the established CSR scheme. So far, these approaches were based on empirical links and lacked transferability. Therefore, we test if physically-based derivations of plant traits may help in finding gradients in traits that are linked to strategies. Location A raised bog and minerotrophic fen complex, Murnauer Moos, Germany. Methods Spatial distributions of plant traits were modelled by adopting an inversion of the PROSAIL radiative transfer model on airborne hyperspectral imagery. The traits are derived from reflectance without making use of field data but only of known links between reflectance and traits. We tested whether previously found patterns in CSR plant strategies were related to the modelled traits. Results The results confirm close relationships between modelled plant traits and C, S and R strategies that were previously found in the field. The modelled plant traits explained different dimensions of the CSR-space. Leaf Area Index (LAI) and the reciprocal of Specific Leaf Area appeared to be good candidates for reproducing CSR scores as community traits using remote sensing. LAI has not been used in previous studies to allocate plant strategies. Conclusions Combining RTMs and the CSR model is a promising approach for establishing a robust link between airborne or spaceborne imagery and plant functioning. The demonstrated potential to map traits with close relation to CSR gradients using only our understanding of the relation between traits and reflectance is a step forward towards an operational use of the CSR model in remote sensing. This article is protected by copyright. All rights reserved.