Food poisoning is mainly caused by pathogenic microorganisms and is now a severe problem worldwide. Therefore, rapid and sensitive methods are required to detect foodborne pathogens. A locally isolated bacterium, Bacillus licheniformis B38 was selected for this study. The spores of B. licheniformis B38 were induced by Schaeffer’s sporulation medium containing KCl, MgSO4.7H2O, Ca(NO3)4, MnCl2 and FeSO4. Schaeffer-Fulton endospore staining was used to differentiate spores and vegetative cells, where spores were stained green and vegetative cells were stained red. In order to separate the spores from the cells, a two-phase system was used to obtain pure spore suspension for following experiments. Spore coat proteins were extracted by SDS-8 M urea sample buffer and visualized by two different types of coomassie brilliant blue staining solutions. One of the staining solutions was more suitable for gel elution by diffusion. An ~10 kDa spore coat protein was selected for protein purification. Based on the given results, the protein purification by liquid chromatography was less convincing than using gel elution by diffusion technique. The two hypothetical protein sequences, P06552 and P45693, from the ~10 kDa spore coat protein were identified. In the preliminary study of B. licheniformis B38 spores detection by surface plasmon resonance, several binding parameters were studied. Dot blot was done to verify the reaction between the Bacillus spores polyclonal antibody against the B. licheniformis B38 spore coat protein. The most promising result was the binding of 0.1 mg/mL polyclonal antibody (analyte) to the 0.2 mg/mL spore coat protein at pH 2 (ligand) which showed 5.74 RU. The differences between a dot blot and a SPR detection techniques are described.

Sweet potato is one of the 15 most important food crops worldwide. At least 30 different virus species, belonging to different taxonomic groups affect sweet potato. Little is known about the viruses present in sweet potato crops in Central America, which is the primary origin of sweet potato. The objective of this study was to design and implement primers for use in polymerase chain reaction (PCR) and Reverse transcription-PCR (RT-PCR) to identify and survey the diversity of plant viruses infecting sweet potato in Honduras and Guatemala. Primers were designed and used to amplify, clone, and sequence a taxonomically informative fragment of the coat protein (CP) gene for whitefly-transmitted geminiviruses (herein, sweepoviruses) and potyviruses, and of the heat shock protein 70 (HSP70) for the Crinivirus, Sweet potato chlorotic stunt virus (SPCSV). The partial genome sequences were used for identification based on phylogenetic relationships with reference sequences available in the GenBank database. All three of the plant virus groups identified in this study were found to occur either in single or in multiple infections. Results of the sequence analyses indicated that the genomic regions amplified in this study were capable of discriminating among potyvirus species, and strains of SPCSV. With respect to potyvirus, all isolates were identified as Sweet potato feathery mottle virus (SPFMV) species, except for two, which grouped phylogenetically with Sweet potato virus G (SPVG) and Sweet potato virus C (SPVC). All sweepoviruses detected in sweet potato plants belonged to a single phylogenetically, well-supported group that contains all other previously described geminiviruses (sweepoviruses) associated with sweet potato or closely related host species. These results demonstrate that the primers designed for amplification of plant virus species commonly recognized to infect sweet potato, effectively detected the viruses singly and in mixtures from symptomatic plants, and that the resultant fragment, when subjected to cloning and DNA sequenced, was phylogenetically informative at the species and/or strain levels, depending on the virus group.

Object and tasks of work: 1. Analyse and summarize literature about horse coat color and it genetic background. 2. Perform phenotypical analysis of Lithuanian Heavy Darught horse coat color polymorphism. 3. Introduce horse MC1R gene research methodology at K. Janušauskas Laboratory of Animal Genetics, LVA. 4. Investigate MC1R gene polymorphism and distribution of different alleles at Lithuanian heavy draught by PCR-RFLP method. 5. Determine correlation between restriction fragment lenght polymorphism (RFLP) in MC1R gene and horse bay coat color polymorhism. Research methodology: 1. DNA extraction from hair roots. 2. PCR to amplify MC1R gene. 3. RFLP method-MC1R – enzyme Tag I. 3. Electrophoresis in agarose gel. 4. Staining with Etidium bromide. 5. Genotyping. 6. Stasitical analysis of data. Results and conclutions: The following DNA restriction fragments were obtained for the MC1R – Tag I polymorphism: PCR product - 460 bp; genotypes E/E; ea/ea – 460 bp; genotypes e/e – 275 bp; 185 bp; genotypes E/e; e/ea – 460 bp; 275 bp; 185 bp. After phenotypical investigation of coat color from 32 Lithuanian Heavy draught horses following variation have been found: light bay, bay, dark bay, roan and chesnut. Light bay horses with different intensivity of coat color comprised 84,4 %. From total investigated animals 34.4 % had e/e genotype, E/e – 12.5 %, e/ea - 50 % and E/E genotype – 3.1 %. Two different genotypes e/e (40.7 %) and e/ea (59.3) were found among bay color horses... [to full text]

Molecular markers for seed quality traits including erucic acid content genes, seed coat color genes in Brassica napus and seed coat color genes in B. rapa were developed. A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. The single base change was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5´ primer end to increase SNP detection throughput through sample pooling. The two-base deletion in the C genome gene was detected as a sequence characterized amplified region (SCAR) marker in an ABI 3100 Genetic analyzer. To increase the throughput, one genome specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. These multiplexed high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. Trigenic inheritance was observed for seed coat color in B. napus. Three Sequenced Related Amplified Polymorphism (SRAP) markers very closely linked to the three different seed coat color genes were developed. Chromosome-walking technology was used to convert the SRAP marker into a SCAR marker and a SNP marker. Subsequently, the first seed coat color gene (Bn1) marker was converted into a SCAR marker, and the second seed coat color gene (Bn2) marker was converted into a SNP marker. Digenic inheritance was observed for seed coat color genes in B. rapa. A SRAP marker was identified as being tightly linked to the major seed coat color gene (Br1). The SRAP marker was sequenced and extended sequences were obtained using chromosome-walking technology. The flanking sequences of the SRAP marker contained 24 SNPs and a 12-bp deletion position that allowed the marker to be converted into a co-dominant SNP marker and a co-dominant SCAR marker, respectively. The SCAR marker was detected in the ABI 3100 genetic analyzer with four fluorescently labeled M13 primers integrated with different SCAR primers, which permitted pooling of PCR samples for high throughput detection.

Fescue toxicosis can produce negative effects on animal weight gain and physiology. Sixty-four steers were grazed on endophyte-infected (E+) KY-31 tall fescue for 77 days in 2007 and sixty steers grazed for 86 days in 2008 to evaluate interactions with implantation of steroidal implants and concentrate feeding on performance and physiology of yearling steers. Steers were stratified by body weight for assignment to six, 3.0-ha toxic tall fescue pastures. The main plot treatment of with or without pelleted soybean hulls (SBH) were randomly assigned to pastures. Pelleted SBH were group-fed to provide daily consumptions of 2.3 kg/steer/d (as fed). Sub-plot treatments of with or without ear implantation with steroid hormone (200 mg progesterone--20 mg estradiol were assigned to groups of five or six steers within each pasture. Average daily gain in the experiment showed an additive effect of feeding SBH and implanting (P

Molecular markers for seed quality traits including erucic acid content genes, seed coat color genes in Brassica napus and seed coat color genes in B. rapa were developed. A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. The single base change was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5´ primer end to increase SNP detection throughput through sample pooling. The two-base deletion in the C genome gene was detected as a sequence characterized amplified region (SCAR) marker in an ABI 3100 Genetic analyzer. To increase the throughput, one genome specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. These multiplexed high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. Trigenic inheritance was observed for seed coat color in B. napus. Three Sequenced Related Amplified Polymorphism (SRAP) markers very closely linked to the three different seed coat color genes were developed. Chromosome-walking technology was used to convert the SRAP marker into a SCAR marker and a SNP marker. Subsequently, the first seed coat color gene (Bn1) marker was converted into a SCAR marker, and the second seed coat color gene (Bn2) marker was converted into a SNP marker. Digenic inheritance was observed for seed coat color genes in B. rapa. A SRAP marker was identified as being tightly linked to the major seed coat color gene (Br1). The SRAP marker was sequenced and extended sequences were obtained using chromosome-walking technology. The flanking sequences of the SRAP marker contained 24 SNPs and a 12-bp deletion position that allowed the marker to be converted into a co-dominant SNP marker and a co-dominant SCAR marker, respectively. The SCAR marker was detected in the ABI 3100 genetic analyzer with four fluorescently labeled M13 primers integrated with different SCAR primers, which permitted pooling of PCR samples for high throughput detection.

The chicken eggshell possesses physical and chemical barriers to protect the embryo from pathogens. The avian eggshell cuticle is the outmost layer of the eggshell whose protein constituents remain largely unknown. Since eggs with incomplete or absent cuticle are more susceptible to bacterial contamination, we hypothesize that cuticle protein components play an important role in microbial resistance. In our study, at least 47 proteins were identified by LC/MS/MS in the non-calcified cuticle layer. Similar to Kunitz-like protease inhibitor (also annotated as ovocalyxin-25, OCX-25) and ovocalyxin-32 (OCX-32) were two of most abundant proteins of the cuticle proteins. Some proteins that have antimicrobial activity were also detected in the proteomic results, such as lysozyme C, ovotransferrin, ovocalyxin-32, cystatin, ovoinhibitor. This study represents the first comprehensive report of the cuticle proteome. Since the sequence similarity of the kunitz motif in OCX-25 is similar to that of BPTI, it is predicted that it will have the same trypsin inhibitory and antimicrobial activity against Gram-positive and/or Gram-negative bacteria. In order to test the antimicrobial property and trypsin inhibitor activity of OCX-25, cuticle proteins were extracted by 1N HCl. Antimicrobial activity was monitored using the Bioscreen C instrument; and antimicrobial activity was identified primarily against Staphylococcus aureus. Trypsin inhibitor activity was studied by using a specific trypsin assay, and the assay indicated that the cuticle proteins could inhibit the reaction of trypsin and substrate. Therefore, the current research has provided some insight into the antimicrobial and enzymatic aspects of the cuticle proteins, and its function for egg protection. Eggshell membranes are another important component of the chicken eggshell.Due to its insoluble and stable properties, there are still many questions regarding formation and constituents of the eggshell membranes. The purpose of our study was to identify eggshell membrane proteins, particularly these responsible for its structural features, by examining the transcriptome of the white isthmus during its formation. Bioinformatics tools were applied to analyze the differentially expressed genes as well as their encoded proteins. Some interesting proteins were encoded by the over-expressed genes in the white isthmus during the formation of eggshell membranes, such as Collagen X, and similar to spore coat protein SP75. These proteins may have potential applications. Our study provides a detailed description of the chicken white isthmus transcriptome during formation of the eggshell membranes; it could lead to develop the strategies to improve food safety of the table egg.

The pericellular matrix (PCM) is a voluminous polymer network adhered to and surrounding many different types of mammalian cells, and which extends out into the environment outside the cell for distances ranging up to twenty microns. It is comprised of very long flexible polymers (hyaluronan) which are tethered to the cell surface and which have binding sites for large, highly charged bottle brush proteoglycans (aggrecan). The PCM plays an important role in many cell functions such as cell proliferation, cell adhesion, cell migration, and cancer development, however the precise way it influences these processes remains unclear. Three original biophysical tools are developed in this thesis in order to study the PCM: the quantitative particle exclusion assay (qPEA), optical force probe assay (OFPA), and exogenous fluorescent aggrecan mapping assays. These tools are used to measure the polymeric and biophysical properties of the matrix in order to make further advancements in the understanding the PCMs role in adhesion, transport to and from the cell surface, its purported function as a chemical micro-reservoir, as well as basic studies on the kinetics of its formation, turnover and maintenance. The qPEAs measure the penetration and distribution of sub-micron particles after they diffuse into the cell coat, where their distribution maps the interior structure of the PCM. The qPEA assays reveal that the PCM acts a sieve, separating incoming particles by their size, preventing micron sized particles from entering the PCM while allowing sub 100 nm particles to pass to the cell surface. The OFPA uses an optically-trapped bead to study the force response of the matrix as it encounters the probe. The assay not only reveals new details about the PCM such as the fact that it is larger than initially thought, having a two layer structure, but when combined with a polymer physics model which relates the observed equilibrium forces to an existing osmotic pressure gradient within the PCM, the OFPA studies produce the first discovery and measurement of the correlation length distribution in the cell coat. The OFPA and qPEA assays are also performed on cells modified with exogenous aggrecan, resulting in a model for possible proteoglycan mediated cell coat transformations. The fluorescent exogenous aggrecan assays measure the dynamics of the exogenous aggrecan binding to and releasing from the coat, revealing that the PCM can be rapidly modified by a changing environment, and quantitatively measure how the exogenous aggrecan modifies the existing PCM. Together, these assays provide an unprecedented look into the interior structure of the PCM, and the mechanisms responsible both for this structure and its modification.

Caveolae are small plasma membrane invaginations present in many different cell types, which have been linked to diverse cellular functions, including cell signalling, membrane rearrangements and lipid regulation. The caveolae markers, members of the caveolin family of proteins, are essential for caveola formation and function. Recently, however, a protein named PTRF (Polymerase I and Transcript Release Factor) or cavin, originally identified as a nuclear factor that regulates transcription in vitro, was shown to be associated with caveolae in adipocytes. In the first chapter of this thesis, I have used the zebrafish Danio rerio to investigate the relation of PTRF/cavin to caveolae as well as caveola function in vivo. During zebrafish development, PTRF/cavin was highly expressed in the notochord in 18 h, 24 h and 35 h post-fertilization embryos, as detected by in situ hybrydization. Analysis of later development stages showed that PTRF/cavin is also present in the otic vesicle, brachial arches, and periderm. Disruption of PTRF/cavin expression, via morpholino-mediated inhibition, caused severely defective development of the notochord as well as heart edema, in a dose-dependent manner. PTRF/cavin knockdown embryos had curved notochords and were shorter than the controls. Examination of the notochord by electron microscopy showed that the number of caveolae was greatly reduced in PTRF/cavin-morpholino-injected embryos. Similar effects were observed when caveolin-1, the major protein of caveolae in non-muscle cells, was down-regulated. Altogether, these results indicated a role for PTRF/cavin during formation and/or stabilization of caveolae as well as an essential role for caveolae during zebrafish embryo development. Combined with results obtained in mammalian cells, these findings identify PTRF/cavin as the first component of a caveolar coat, required for caveola formation and function (Hill et al., 2008). We subsequently identified a family of PTRF/cavin-related proteins, the cavins, that all associate with caveolae. Using biochemistry, light microscopy, and FRET-based approaches we characterised PTRF/cavin and the new members of this family of proteins SDR/cavin-2, SRBC/cavin-3 and MURC/cavin-4. We have shown that the four members of the cavin family form a multi-protein complex that associates with caveolae. This complex can constitutively assemble in the cytosol and then associate with caveolin at the plasma membrane caveolae; interestingly, caveolin is essential for the plasma membrane translocation of the cavin complex, and in caveolin-1 knockout cells the four cavin proteins are restricted to the cytosol. PTRF/cavin-1, but not other cavins, can induce caveola formation in a heterologous system and is required for the recruitment of the cavin complex to caveolae. The four cavin proteins present distinct patterns of tissue expression, which suggests that caveolae may perform tissue-specific functions regulated by the composition of the cavin complex. MURC/cavin-4 is expressed predominantly in muscle and its distribution is perturbed in human muscle disease associated with caveolin-3 dysfunction, identifying MURC/cavin-4 as a novel muscle disease candidate caveolar protein. To functionally investigate the relation of cavins and caveolae, we explored a caveolar function in mechanosensation. Through the use of hypo-osmotic media, we induced membrane-stretch and showed that the increased membrane tension leads to dissociation of the caveolin-cavin module and caveola disassembly as observed by immunofluorescence and FLIM/FRET techniques. Once released from caveolae, caveolin was seen internalized in late endosomes and lysosomes. Cavin-1, on the other hand, was found to be diffused in the cytosol and from there it was translocated to the nuclear compartment. The nuclear translocation was observed in several different cell types, which suggests a universal role for nuclear cavin-1, and was independent of caveolin expression. Analysis of live cells using real-time FLIM/FRET showed that cells quickly respond to variations in membrane tension by dissociation/re-association of caveolin and cavin-1. Altogether, in the course of this project, I was able to show that cavin-1 is an essential regulator of caveola biogenesis in cultured cells and in vivo. Cavin-1 and the other members of the PTRF/Cavin family form a multiprotein complex that is recruited to caveolae by caveolin and coats plasma membrane caveolae. The association between cavin-1 and caveolin is crucial for caveolae assembly and this interaction has a role in the cellular sensation of plasma membrane tension. Under high membrane tensions, caveolin and cavin-1 dissociate with the consequent flattening of caveolae. Under these circumstances, caveolin is internalized into enlarged endosomes and lysosomes while cavin-1 is translocated to the nucleus, identifying for the first time a caveola- to nucleus signalling pathway. The exact role of nuclear cavin-1 under plasma membrane stretch is now amenable to analysis.

Orientador: Rosangela Zacarias Machado / Banca: Matias Pablo Juan Szabó. / Banca: Mirela Tinucci Costa. / Banca: Odilon Vidotto / Banca: Rodrigo Martins Soares / Resumo: Este estudo foi realizado objetivando-se detectar e identificar a presença de material genômico de agentes pertencentes à Família Anaplasmataceae em 55 cães com inclusões citoplasmáticas encontrados em células leucocitárias granulocíticas, monocíticas e plaquetas, compatíveis com infecção por Ehrlichia canis, E. chaffeensis, E. ewingii, A. phagocytophilum, A. platys ou Neorickettsia risticii. A ocorrência natural de Babesia canis também foi avaliada pois vetor Rhipicephalus sanguineus, é o principal carrapato encontrado em cães no Brasil. Também objetivou-se realizar, através da utilização de técnicas de Seqüenciamento de um fragmento do gene 16S rRNA, a caracterização parcial dos fragmentos das amostras positivas encontradas neste estudo, e comparar as seqüências dos fragmentos obtidos com as seqüências apresentadas previamente no GenBank, iniciando a realização de estudos filogenéticos das seqüências encontradas. Amostras de sangue foram colhidas de 25 e 30 cães atendidos nos Hospitais Veterinários da Universidade Estadual Paulista-Unesp, Câmpus de Jaboticabal-SP e Universidade para o Desenvolvimento do Estado e da região do Pantanal-UNIDERP, Campo Grande- MS, respectivamente. Dentre as inclusões citoplasmáticas encontradas neste estudo foi observado uma grande diversidade na morfologia, tamanho, coloração e localização das inclusões. DNA de agentes Família Anaplasmataceae foram detectados em 45/55 das amostras sangüíneas examinadas (81,8%), sendo destas 32 (58,18%) e 13 (23,63%) positivas para Ehrlichia canis e Anaplasma platys, respectivamente. Dez animais que foram incluídos neste estudo por apresentarem inclusões citoplasmáticas foram negativos quando uma segunda confecção de esfregaço de papa leucocitária corada pelo Giemsa foi realizada, e também... (Resumo completo, clicar aesso eletrônico abaixo) / Abstract: The aim of this study was to evaluate the natural occurrence of Anaplasmataceae agents (Ehrlichia canis, E. chaffeensis, E. ewingii, A. phagocytophilum, A. platys and Neorickettsia risticii) using molecular techniques. For this purpose a group of fifty-five supposedly infected dogs from two different Brazilian states (São Paulo and Mato Grosso do Sul) that showed suggestive Anaplasmataceae agent intracitoplasmic inclusions in white blood cells and platelets were analysed. The natural occurrence of Babesia canis was also evaluated, because its vector is also Brazilian dog tick, Rhipicephalus sanguineus. Sequencing of a partial phragment of 16S rRNA gene from the positive samples were performed to conduct phylogenetic study. The evaluated blood cells of the studied dog population displayed a wide variety in shapes, sizes, stain pattern and localization of the inclusions. Anaplasmataceae DNA were amplified in 45/55 (81.8%) examined blood samples. Thirty-two samples were positive for E. canis (58.18%) and thirteen for Anaplasma platys (23.63%). Ten animals were negative by PCR and an analyses of a second Buffy coat smear. The obtained nucleotide sequences were analysed for similarity of the 16S rRNA gene sequence using Blast with other sequences available in the GenBank database. The sequences obtained from E. canis positive were closely related to E. canis from Spain (Acession number AY 394465) presenting an identity percentage of between 94.82% and 99.67%. Sequences from Anaplasma sp and Anaplasma platys positive samples were closely related to A. platys from Venezuela (Genbank Acession number AF 399917) presenting an identity betwwen 96.52% and 99.69%, and A. platys from Spain (Genbank Acession number AY 530 806\0 presenting... (Complete abstract, click electronic access below) / Doutor