No description available.

<p>Human disease and the corresponding immune response occur in three-dimensional space and time. Many diseases are difficult to study, either <em>in vivo</em> or <em>in vitro</em>, due to the complexity of the system. Despite computational models that can address complexity, many do not capture the spatial  aspects  of  disease.  Agent-based  models  are  mechanistic,  spatiotemporal  computational models that can be integrated with other mathematical models to create multiscale models. Here I detail two models to examine spatiotemporal progression and possible treatment strategies for two diseases  with  low  treatment  success: <em>Mycobacterium  avium complex</em>  (MAC)  and  Alzheimer’s Disease.</p> <p>MAC  are  biofilm-forming  environmental  microbes  capable  of  residing  in  human  lung nodules,  causing  MAC  pulmonary  disease  (MAC-PD).  Clinical  drug  susceptibility  tests  and treatment  outcomes  are  poorly  correlated,  and  nodules  are  complex  and  difficult  to  monitor, leading to low MAC cure rates (45-65%)². I have developed an informative model of the initial infection  events  in  MAC-PD. This  model  has  been  used  to  probe  many  different  scenarios  of infection and to predict the effect of potential interventions.</p> <p>Alzheimer’s  Disease  (AD)  is  the  leading  cause  of  dementia,  with  no  disease-altering pharmacological  intervention.  Microglia  are  phagocytotic  neuroimmune  cells,  known  to  form barriers around plaques. There has been increased interest in leveraging microglia to slow the progression of neurodegeneration by manipulating these barriers. I present an agent-based model of microglia barriers at the single plaque level and use knock-out experiments to probe possible targets for immunotherapy and quantify their effects on plaque progression.</p>

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic enteritis in ruminants, and has recently been linked to Crohn's disease in humans. To generate an effective vaccine against MAP, it is necessary to identify MAP antigens that trigger protective immunity. Unfortunately, not much is known about MAP proteins despite decades of research. We have previously shown that a 4.8 kb insert from MAP will produce a 16 kDa recombinant protein when expressed in Escherichia coli and 19 kDa recombinant protein when expressed in M smegmatis ( smeg 19K). The difference of 3 kDa in size of these expressed proteins may be related to posttranslational modificatjons that occur in Mycobacterium species. We hypothesized that smeg19K is a lipoglycoprotein since blast analysis revealed approximately 76 % amino acid identity between the MAP 19 kDa protein and a known lipoglycoprotein, the 19 kDa protein of M tuberculosis. This prediction was confirmed following positive staining of smeg19K with Sudan Black 4B, a postelectrophoresis dye used to stain for lipids. Smeg 19K has also stained positively for glycosylation with the lectin concavalin A, a highly specific stain for mannose residues. As expected, treatment with tunicamycin (an antibiotic known to inhibit N-glycosylation) and treatment with deglycosylation assay (non-specific for mannose ), showed no reduction in size of 19 kDa glycolipoproteins. Since covalent modification of proteins with acyl or glycosyl moieties alter immunogenicity and/or pathogenicity, the study here provides foundation for future experiments regarding the antigenicity of MAP 19 kDa lipoglycoprotein and its role in disease pathogenicity.

No description available.

No description available.

Il presente elaborato intende approfondire le ipotesi avanzate nel mio precedente lavoro di ricerca, Il Codice inedito di falconeria della Biblioteca di Dresda (Mscd.Dresd.Ob.21), stampato e catalogato presso la SLUB, sulla base delle argomentazioni dello studioso croato Grmek riguardo la tradizione letteraria del trattato di Iacobello Vitturi contenuto nel codice Ob.21. L’intento è quello di definire la collocazione spaziale del manoscritto e, al fine di raggiungere tale obbiettivo, la ricerca è stata incentrata sul raffronto linguistico del codice dresdense col manoscritto conservato presso la Biblioteca Universitaria di Bologna, ms. 1349. Le particolarità linguistiche rintracciate nel codice Ob.21 a seguito dell’analisi comparativa mi hanno permesso di chiudere la ricerca nella direzione intrapresa: le forme mantovane del lessico della lingua adoperata in tutto il codice Ob.21, insieme ad altre spie fonetiche e morfologiche, costituiscono un’ulteriore prova a favore della collocazione del manoscritto in area mantovana.

<p>U okviru ove doktorske disertacije ispitane su i<br />poređene različite ekstrakcione tehnike korena<br />gaveza, lista crnog duda i peteljki tre&scaron;nje. Poređene<br />su konvencionalne i savremene ekstrakcione<br />tehnike i izvedena je optimizacija ekstrakcionih<br />postupaka s ciljem dobijanja ekstrakata ispitivanih<br />biljnih vrsta sa najvećom bioaktivno&scaron;ću. Za svaku<br />ekstrakcionu tehniku ispitan je uticaj najznačajnijih<br />parametara: maceracija (rastvarač i vreme<br />ekstrakcije), ubrzana ekstrakcija (temperatura i<br />rastvarač), supekritična ekstrakcija (pritisak i<br />koncentracija ko-rastvarača) i ekstrakcija<br />subkritičnom vodom (temperatura, pritisak, vreme<br />ekstrakcije i brzina me&scaron;anja). Ekstrakcija polifenola<br />korena gaveza, lista crnog duda i peteljki tre&scaron;nje je<br />bila najefikasnija ekstrakcijom subkritičnom<br />vodom. Primenjene su tehnika visokopritisne tečne<br />hromatografije spregnute sa masenom<br />spektrometrijom uz primenu različitih masenih<br />analizatora, masenog analizatora na bazi vremena<br />preleta jona i tandema kvadrupolnog i analizatora<br />na bazi vremena preleta jona. Za karakterizaciju<br />dobijenih ekstrakata instrumentalnom analizom su<br />određene kvalitativne i kvantitativne karakteristike dobijenih ekstrakata korena gaveza, lista crnog duda i peteljki tre&scaron;nje. HPLC-ESI-QTOF-MS/MS analizom ekstrakata identifikovano je vi&scaron;e od 27 novih jedinjenja različitih hemijskih klasa u svakom od ispitivanih biljnih matriksa.</p> / <p>Within the scope of this doctoral dissertation,<br />different extraction techniques of comfrey root,<br />black mulberry leaves and sweet cherry stems were<br />applied and compared. Conventional and novel<br />extraction techniques were optimized and<br />compared in order to obtain plant extracts with the<br />highest content of bioactive compounds. The<br />influence of the most important parameters was<br />investigated for each extraction technique:<br />maceration (solvent and extraction time),<br />accelerated solvent extraction (temperature and<br />solvent), supercritical fluid extraction (co-solvent<br />percentage and pressure) and subcritical water<br />extraction (temperature, pressure, extraction time<br />and agitation rate). Extraction of polyphenolic<br />compounds from comfrey root, black mulberry<br />leaves and sweet cherry stems was the most<br />effective using subcritical water. High-pressure<br />liquid chromatography coupled to mass<br />spectrometry techniques using time-of-flight and<br />quadrupole-time-of-flight mass analyzers have<br />been used to characterize bioactive compounds.<br />Qualitative and quantitative characteristics of the<br />obtained comfrey root, black mulberry leaves and sweet cherry stem extracts were determined. HPLC-ESI-QTOF-MS/MS revealed the presence of more than 27 compounds of different chemical classes that have been identified for the first time in&nbsp; the plant matrix.</p>

Structural investigations on two mycobacterial enzymes were carried out. Tuberculosis still remains a major threat to mankind even though drugs against it have been in use for many decades. The emergence of drug resistant strains of the bacteria calls for the identification of new targets based on which new drugs can be developed to combat the disease. A thorough understanding of the functioning of the target molecules is essential for this approach. We have taken up the structural studies on two such molecules, aspartic proteinases and adenylyl cyclases, of Mycobacterium tuberculosis with a view to obtain insights into their mechanisms of action at the atomic level. The work presented in the thesis includes (i) the identification, cloning, expression, purification and structure determination of a putative aspartic proteinase domain of M. tuberculosis and (ii) the crystal structure of an adenylyl cyclase of M. tuberculosis and its mutant; and also of an adenylyl cyclase from M. avium. Chapter 1 presents an overview of aspartic proteinases and nucleotide cyclases with an emphasis on their structural features. The methods employed during the course of the present work are described in Chapter 2. Work on the putative aspartic proteinase domain identified in M. tuberculosis is presented in Chapter 3. The structure of the aspartic proteinase domain is the first structural report of such domain from any bacteria. A search in the genome of M. tuberculosis showed a weak similarity to the HIV aspartic proteinase sequence. This region corresponds to the C-terminal domain of a PE family protein in M. tuberculosis. The presence of two signature motifs, DTG and DSG, of aspartic proteinases in the full sequence of this domain encouraged us to take up further studies on this domain. Previous reports identifying the protein as a surface antigen and our findings on the occurrence of similar domains in two other PE proteins of M. tuberculosis and also in other pathological strains of Mycobacteria indicated that these domains probably play an important role in infecting the host. The crystal structure of one of the domains showed that it has a pepsin-like fold and the catalytic site architecture of known aspartic proteinases. However, no proteolytic activity was detected. The size of the molecule is intermediate to eukaryotic pepsins and the homodimeric retroviral pepsins. A close examination of the binding site revealed subtle differences when compared to the active enzyme structures. Appropriate mutations of some of the residues in this region to convert it to an active enzyme did not make it active. Once the in vivo function of these putative aspartic proteinase domains is established, their potential to act as drug targets can be probed as the PE proteins are present exclusively in pathogenic Mycobacteria. As part of an ongoing project on adenylyl cyclases of Mycobacteria, we have taken up the structure analysis of the catalytic domains of two adenylyl cyclases; Rv1625c from M. tuberculosis and Ma1120 from M. avium. This work is described in Chapter 4. The wild-type of Rv1625c crystallized as a domain swapped head to head inactive dimer even though it is an active dimer in solution and expected to have a head to tail arrangement as in the previously reported structures of the active forms of the enzyme. Mutation of a phenylalanine residue presumed to occur at the subunit interface of the active dimeric structure of the enzyme to an arginine residue, a conserved residue of guanylyl cyclases, resulted in reduced adenylyl cyclase activity. This mutant crystallized as a monomer though it was expected to be an active dimer. Similarly, Ma1120 also has a monomeric structure in the crystal in spite of showing activity in solution. Though our aim was to capture the active dimers in the crystalline state we did not succeed in this effort in any of the three cases. The catalytic reaction probably takes place very rapidly with the formation of a transient active form of the dimer which cannot be easily crystallized. However, the analysis revealed new structures which are likely to represent the stable states of the enzyme when it is required to stay inactive in certain conditions. We have also established that the N-terminal segments of the enzyme, a loop at the dimeric interface and external factors like pH are involved in determining the oligomeric status of the enzyme thereby regulating its function. Publications 1 Crystal structure of a putative aspartic proteinase domain of the Mycobacterium tuberculosis cell surface antigen PE_PGRS16; Deivanayaga V. Barathy and K. Suguna; FEBS Open Bio (In Press) 2 New structural forms of mycobacterial adenylyl cyclases (in preparation)

Submitted by Cássio da Cruz Nogueira (cassionogueirakk@gmail.com) on 2017-05-05T11:56:57Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_EstudoParatuberculoseBufalos.PDF: 1575243 bytes, checksum: 82baedacd1f3e101d0cc4918e2b8243b (MD5) / Approved for entry into archive by Edisangela Bastos (edisangela@ufpa.br) on 2017-05-10T12:05:55Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_EstudoParatuberculoseBufalos.PDF: 1575243 bytes, checksum: 82baedacd1f3e101d0cc4918e2b8243b (MD5) / Made available in DSpace on 2017-05-10T12:05:55Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_EstudoParatuberculoseBufalos.PDF: 1575243 bytes, checksum: 82baedacd1f3e101d0cc4918e2b8243b (MD5) Previous issue date: 2016-03-11 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / INCT - Instituto Nacional de Ciência e Tecnologia / Este trabalho objetivou estudar a paratuberculose (PTB) em bubalinos no estado do Maranhão (MA). Para isso foram realizadas a utilização da biópsia retal como ferramenta auxiliar na coleta de amostras para o diagnóstico ante mortem da PTB; dosagem de teores de cobre (Cu), zinco (Zn) e ferro (Fe) em animais positivos para PTB, assim como, o relato da detecção de Mycobacterium avium subesp. paratuberculosis (Map) em útero e feto bubalino. No primeiro estudo foram realizadas 140 biopsias retais em bubalinos das raças Murrah, Mediterrâneo e seus mestiços, com idade acima de três anos, no município de São Mateus, MA. Essas biópsias foram processadas por meio das técnicas de Ziehl-Neelsen (ZN) e reação em cadeia da polimerase quantitativa (qPCR). Adicionalmente foi realizada necropsia de 11 búfalos com sinais clínicos sugestivos de PTB, coletadas amostras de íleo e linfonodo mesentério (LM) para a realização de ZN e qPCR. Pela colaboração de ZN das biopsias retais, 4,3% (6/140) apresentaram bacilos álcool-ácidos resistentes (BAAR) e na qPCR, 5% (7/140) tiveram amplificação do material genético. As lesões anatomopatológicas de quatro animais foram compatíveis com lesões sugestivas de PTB, apresentaram BAAR e amplificação de material genético. A concordância entre a biopsia retal e a analise dos tecidos de íleo e LM, segundo o teste Kappa foi alta (k=0,792). No segundo estudo, foram realizadas 13 necropsias em búfalos de raças Murrah, mediterrâneo e seus mestiços, com idade acima de três anos, nos municípios de São Mateus e São Luís, MA. Foram coletadas amostras de íleo e LM para pesquisa de Map e de fígado para dosagem de minerais (Cu, Zn e Fe). Sete búfalos foram positivos PTB e alocados no Grupo 1; e seis búfalos foram negativos e alocados no Grupo 2. Na dosagem dos microminerais, os búfalos do Grupo 1 apresentaram níveis abaixo dos valores de referência para Cu e Zn. observou-se que as medias dos teores de Cu foi 18,0ppm. Os teores de Fe em ambos os grupos foram elevados (>669ppm). O terceiro estudo foi conduzido em uma propriedade em São Luís, MA. Uma búfala prenha, com acentuada debilidade física e com suspeita clinica de PTB foi eutanasiada e necropsiada. Foram coletadas fragmentos de íleo, LM, útero e placenta da fêmea; fragmentos de rim, fígado, vaso umbilical e sistema digestivo (SD) do feto e analisadas através de ZN e qPCR. A fêmea foi positiva em amostras de íleo, LM e útero na qPCR e o feto foi positivo no SD. No íleo, LM e nas fezes foram observados BAAR. Conclui-se que a analise de biopsia retal pode ser empregada para auxiliar no diagnostico ante mortem. A PTB pode induzir quadros de deficiência mineral com consequente piora do quadro clínico da doença. E a presença de Map em búfalos pode ocorrer em vários órgãos, inclusive no sistema reprodutivo e a transmissão intrauterina pode ocorrer nesta espécie. / This study investigated paratuberculosis (PTB) in water buffaloes in the state of Maranhão (MA). For that were performed using the rectal biopsy as an auxiliary tool in the collection of samples for ante mortem diagnosis of PTB; dosages of copper (Cu), zinc (Zn) and iron (Fe) in PTB positive animals was performed, as well as the report of the detection of Mycobacterium avium subsp. paratuberculosis (Map) in the utero and fetus of a buffalo. In the first study were conducted 140 rectal biopsies in buffaloes of Murrah, Mediterranean and their crossbreeds, over the age of three years in São Mateus, MA. These biopsies were processed by Ziehl-Neelsen (ZN) staining and quantitative PCR (qPCR). Postmortem examination of 11 buffaloes with clinical signs suggestive of PTB was performed and samples of ileum and mesenteric lymph nodes (MLN) were collected for performing qPCR and ZN. By ZN staining of rectal biopsies, 4.3% (6/140) acid-fast bacilli and qPCR, 5% (7/140) had amplification of genetic material. The pathological lesions of four animals were consistent with lesions suggestive of PTB showed acid-fast bacilli and amplification of genetic material. The correlation between rectal biopsy and analysis of ileal tissue and LM, according to the Kappa test was high (K=0.792). In the second study, 13 postmortem examination were carried in buffaloes of Murrah, Mediterranean and their crossbreeds, over the age of three years in the cities of São Mateus and São Luís, MA. Ileum and mesenteric lymph nodes samples were collected for Map search and liver to dosage minerals (Cu, Zn and Fe). Seven buffaloes were positive for PTB and allocated in Group 1; six buffaloes were negative and allocated in Group 2. In the dosing of trace minerals in Group 1 showed levels below the reference values for Cu and Zn. It was observed that the average Cu concentration was 18.0ppm and Zn 68.6ppm. In Group 2 the average Cu concentration was 113.7ppm and Zn 110.0ppm. The iron concentrations in both groups were high (>669ppm). The third study was conducted on a property in São Luís, MA. A buffalo cow pregnant with marked physical debility and clinical signs suggestive of PTB was eutanasiada and necropsiada. Fragments ileum, MLN, uterus, and placenta of buffalo cow were collected; fragments of kidney, liver, umbilical vessel and digestive system (DS) of the fetus were collected and were analyzed by Zn and qPCR. The buffalo cow was positive in ileum samples, mesenteric lymph nodes and uterus in qPCR and the fetus was positive in DS. In the ileum, MLN and feces were observed acid-fast bacilli. It is concluded that rectal biopsy analysis can be used to help diagnose ante mortem. The PTB could lead to mineral deficiency and worsen the clinical condition of the buffaloes. The presence of Map in buffalo can occur in various organs, including the reproductive system and intrauterine transmission can occur in this species.

No description available.