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<p>Articular cartilage is a highly specialized avascular tissue and consists of chondrocytes and two major components, a collagen-rich framework and highly abundant proteoglycans. The chondrocyte morphology and extracellular matrix properties vary with the depth of cartilage. Some past studies have defined the zonal distribution of a broad range of cartilage proteins in different layers. Based on the variations within each layer, the extracellular matrix can be further distinguished to pericellular, territorial and interterritorial regions. However, most of these studies used guanidine-HCl extraction that leaves an unextracted residual with a substantial amount of collagen. The high abundance of anionic polysaccharide molecules from cartilage adversely affects the chromatographic separation. Scatter oriented chondrocytes only account for the small proportion of the whole tissue protein extraction. However, the density of the cell varies with depth of cartilage as well. Moreover, the physiological status may also altered the extracellular matrix properties. Therefore, a comprehensive strategy to solve all these difficulties are necessary to elucidate the molecular structure of cartilage. </p><p>In this study, we used quantitative and qualitative proteomic analysis to investigate various cartilage tissue processing protocols. We established a method for removing chondrocytes from cartilage sections that minimized matrix protein loss. Quantitative and qualitative proteomic analyses were used to evaluate different cartilage extraction methodologies. The addition of surfactant to guanidine-HCl extraction buffer improved protein solubility. Ultrafiltration removed interference from polysaccharides and salts. The different extraction methods yielded different protein profiles. For instance, an overwhelming number of collagen peptides were extracted by the in situ trypsin digestion method. However, as expected, proteoglycans were more abundant within the guanidine-HCl extraction. </p><p>Subsequently we applied these methods to extract cartilage sections from different cartilage layers (superficial, intermediate and deep), joint types (knee and hip), and disease states (healthy and osteoarthritic). We also utilized lase capture microscopy (LCM) to harvest cartilage sample from individual subregions (territorial and interterritorial regions). The results suggested that there is more unique proteins existed in the superficial layer. By removing the chondrocytes, we were able to identify more extracellular matrix proteins. The phenotyping of cartilage subregions provided the chance to precisely localize the protein distribution, such as clusterin protein. We observed that the guanidine-HCl extractability (guanidine-HCl/ guanidine-HCl + in situ digestion extracts) of cartilage proteins. Proteoglycans showed high extractability while collagen and non-collagenous proteins had lower extractability. We also observed that the extractability might differ with depth of cartilage and also disease states might alter the characters as well. </p><p>Laser capture microscopy provides us the access to the cartilage subregions in which only few studies have investigated because of the difficulties to separate them. We established the proteomic analysis compatible-protocol to prepare the cartilage section for LCM application. The results showed that most of the proteoglycans and other proteins were enriched in the interterritorial regions. Type III and VI collagens, and fibrillin-1 were enriched in the territorial regions. We demonstrated that this distribution difference also varied with depth of cartilage. The difference of protein abundance between subregions might be altered because of disease states. </p><p>Last we were looking for the post-transliational modification existed in these subregions of cartilage. Deamidation is one of the modification without the enzyme involved. Previous studies have showed that deamidation may accumulated in the tissue with low turnover rate. Our proteomic analysis results suggests that abundance of deamidated peptides also varied in different layers and subregions of cartilage. </p><p>We have developed the monoclonal antibody based immunoassay to quantify the deamidated cartilage oligomeric matrix protein within cartilage tissue from different joints (hip and knee) and disease states (healthy, para-lesion, and remote lesion). The results suggests that the highest concentration of deamidated COMP was identified in arthritic hip cartilage. </p><p>The results of this study generated several reliable protocols to perform cartilage matrix proteomic analysis and provided data on the cartilage matrix proteome, without confounding by intracellular proteins and an overwhelming abundance of collagens. The discovery results elucidated the molecular architecture of cartilage tissue at different joint sites and disease states. The similarities among these cartilages suggested a constitutive role of some proteins such as collagen, prolargin, biglycan and decorin. Differences in abundance or distribution patterns, for other proteins such as for cartilage oligomaric matrix protein, aggrecan and hyaluronan and proteoglycan link protein, point to intriguing biological difference by joint site and disease state. Decellularization and a combination of extraction methodologies provides a holistic approach in characterizing the cartilage extracellular matrix. Guanidine-HCl extractability is an important marker to characterize the statue of cartilage; however it has not been fully understand. The protein distributions in matrix subregions may also serve as an index to characterize the metabolic status of cartilage in different disease states. A large sample cohort will be necessary to elucidate these characters.</p> / Dissertation

Background. Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth's most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods. We cultured fungi from the interior of surface-sterilized leaves that were living at the time. of sampling (i.e., dophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi,eDn LF), and fallen. leaves (leaf litter.fungi,LLF) from 3-4 species of woody plants in each of five sites in. North America. Our sampling encompassed 18 plant species. representing. two families of Pinophyta.and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial L SU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated'onlyfrom living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi living leays were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed igninolytic or pectinolytic activity in vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes. Discussion. Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiornycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.

Articular cartilage lining joints, such as in the knee, functions to reduce friction and absorb shock. Collagen type II is the largest constituent in the extracellular matrix of articular cartilage and its restoration is of the highest interest to tissue engineers. Cartilage has little ability to naturally regenerate due to the absence of vascularity and the inability of the chondrocytes to proliferate at a high rate. It would be ideal to create a mimicking extracellular matrix/scaffold from type II collagen that could possibly be used to replace damaged articular cartilage that has the same function and morphology. Three different groups of cartilage chips were utilized to extract type II collagen. The yield of the three groups was compared. The extracted type II collagen from the three groups was electrospun at the concentrations of 0.06, 0.08, 0.10 and 0.12 g/mL. Both the pore size and fiber diameter were analyzed. A SDS-Page was performed on the material to assure it was pure type II collagen and that no collagen type I contamination was present.

Chronic respiratory diseases affects many people worldwide with little known about the mechanisms diving the pathology, making it difficult to find a cure. Improving the understanding of smooth muscle and extracellular matrix (ECM) interaction is key to developing a remedy to this leading cause of death. With currently no relevant or controllable in vivo or in vitro model to investigate diseased and normal interactions of small airway components, the development of a physiologically relevant in vitro model with comparable cell attachment, signaling, and organization is necessary to develop new treatments for airway disease. The goal of this study is to create a mechanically, biologically and structurally relevant in vitro model of small airway smooth muscle tissue. Synthetic Poly-L-Lactic Acid (PLLA) and decellularized pig lung ECM (DPLECM) were electrospun to form nanofibrous mats that can closely mimic natural bronchial tissue. The addition of DPLECM significantly changed the PLLA scaffold mechanically, biologically, and physically to bring it closer to the characteristics of the human lung. DPLECM scaffolds exhibited a significant decrease in the elastic modulus compared with PLLA alone. Histological staining and SDS-PAGE showed that after scaffold fabrication, essential proteins or protein fragments in natural ECM are still present after processing. Human bronchial smooth muscle cells (HBSMCs) seeded onto PLECM scaffolds formed multiple layers of cells compared to scaffolds composed solely of PLLA. Phenotype of smooth muscle is better maintained when DPLECM is incorporated into the scaffold shown by enhanced contractile protein expression and increased collagen production for normal smooth muscle remodeling of the scaffold. In summary, this research demonstrates that a PLLA/DPLECM composite electrospun mat is a promising tool to produce an in vitro model with the potential to uncover unknown characteristics of bronchiole smooth muscle behavior in diseased or normal states.

Dans l’environnement marin, les surfaces artificielles sont rapidement colonisées par des bactéries qui s’organisent en communautés appelées biofilms, s’entourant d’une matrice de substances polymériques extracellulaires (EPS). La formation d’un biofilm est une étape critique du processus nommé biofouling, c’est-à-dire l’accumulation de micro- et de macro-organismes sur une surface immergée, pouvant conduire à des conséquences néfastes dans le secteur marin. Dans cette étude, il s’agit d’identifier des souches bactériennes isolées de supports immergés en Mer Méditerranée et de les caractériser phénotypiquement par diverses approches. Leur capacité à former un biofilm in vitro a été évaluée dans différentes conditions avec une attention particulière portée sur leurs capacités à produire une matrice polymérique abondante riche en polysaccharides; l’objectif étant d’isoler des exopolysaccharides originaux à activité antifouling. Treize souches ont ainsi fait l’objet d’analyses phylogénétiques et d’une caractérisation phénotypique. Sept genres et douze espèces différentes ont été identifiés au sein desquelles deux isolats peuvent être affiliés à une nouvelle espèce, nommée Persicivirga mediterranea. Ce genre n’a jamais été décrit en Mer Méditerranée jusqu’à présent. L’extraction des EPS de chaque souche cultivée en biofilm a permis de déterminer leur composition générale en glucides, protéines, acides nucléiques et lipides. Une souche, Pseudoalteromonas ulvae TC14, se distingue par sa capacité à produire des exopolysaccharides en quantité importante. Il s’agit essentiellement de polymères du glucose dont les analyses chromatographiques et spectroscopiques ont révélé la diversité de taille (Mw ~ 1–4000 kDa), de charge (neutre ou anionique) et de fonction associée (lactate ou acétate). Les fractions d’EPS enrichies en polysaccharides inhibent la formation de biofilm par d’autres souches marines. Ces derniers sont également synthétisés par les bactéries en culture planctonique mais en proportions très différentes. / In marine environment, artificial surfaces are promptly colonized by biofilms, which are communities of bacteria surrounded by matrix of extracellular polymeric substances (EPS). Formation of biofilm is a critical step of biofouling development, which corresponds to the accumulation of micro and macro-organisms on immersed surfaces and which can have important negative ramifications in particular in the marine sector. In this study, bacteria isolated from the Mediterranean Sea have been identified and characterized using different phenotypical tools. Their capacity to form a biofilm in vitro has been studied in different conditions, with a particular focus on their ability to produce abundant carbohydrate-rich EPS, the overall objective of the study being the isolation of original antifouling-active exopolysaccharides. Thirteen strains have been phylogenetically and phenotypically characterized. Seven genera and twelve species were identified among which two isolates were affiliated to a new species, named Persicivirga mediterranea. This genus has never been described in the Mediterranean Sea. Extraction of EPS of each strain, grown in biofilm conditions, allowed the determination of their general composition in carbohydrates, proteins, nucleic acids and lipids. One strain, Pseudoalteromonas ulvae TC14, was able to produce large quantities of exopolysaccharides, comprising in majority polymers of glucose whose chromatographic and spectroscopic analyzes revealed a diversity in size (Mw ~ 1-4000 kDa), charge (neutral or anionic) and associated function (acetate or lactate). These polysaccharides inhibited biofilm formed by other marine strains isolated from the Mediterranean Sea. They can also be synthesized by planktonic TC14, but in very different proportions.

Aneurismas e dissecções da aorta ascendente são caracterizados por degradação das fibras elásticas e de colágeno e diminuição de células musculares lisas, predominantemente em áreas mucóides, as quais são relacionadas ao acúmulo de glicosaminoglicanos ou proteoglicanos. Tendo em vistas tais alterações, estudamos a topologia das metaloproteases nestas doenças. Cortes de 5?m de aortas, fixadas em fomol e embebidas em parafina, foram submetidos a reações imuno-histoquímicas para MMP-3 (estromelisina), MMP-7 (matrilisina) e plasminogênio/plasmina na camada média. Em paralelo, cortes de aortas foram submetidos a coloração pela hematoxilina e eosina e azul de Alcian (para material mucóide). Aortas de 8 pacientes com aneurisma de aorta torácica e 10 com dissecções agudas foram analisadas. Adicionalmente, 9 aortas normais foram estudadas como controle. Em todos os casos, MMP-3 e, mais expressivamente, MMP-7 apresentaram marcação dentro dos acúmulos mucóides. Em contrapartida, a marcação para plasmina/plasminogênio situou-se ao redor deles. Fora dessas áreas, a MMP-3 mostrou distribuição intra e extracelular, a MMP-7 apresentou marcação intra e extracelular predominante na segunda metade da túnica média, e plasmina/plasminogênio teve co-localização com células musculares lisas. Considerando que matrilisina e estromelisina atuam sobre os proteoglicanos e sobre outros componentes da matriz extracelular, estas enzimas poderiam estar envolvidas diretamente na gênese dos aneurismas e dissecções da aorta ascendente, com possível modulação por plasminogênio/plasmina / In dissections and non-inflammatory aneurysms of the ascending aorta there is an increase in mucoid (proteoglycan) deposition. We analyzed by immunoperoxidase the distribution of stromelysin (MMP-7), matrilysin (MMP-3) and plasminogen/plasmin, enzymes that act on proteoglycans, in sections of human aortas with these diseases and in controls. In cases with any of these diseases MMP-7 and MMP-3 were accumulated in the areas of mucoid degeneration, and plasmin around them. Such enzymes could thus be involved in these diseases. We also evaluated by morphometry the amount of collagen in the two halves of the aortic media.

A matriz extracelular do endométrio (ECM) é constituída por moléculas secretadas que compõem o microambiente celular e são ativadas ou suprimidas principalmente pelos hormônios esteróides ovarianos, estradiol (E2) e progesterona (P4) durante o ciclo estral. A identificação de genes envolvidos no remodelamento e receptividade pode levar à descoberta de importantes processos biológicos ligados ao sucesso gestacional. Os objetivos foram: 1. identificar a relação de diferentes tamanhos de folículos pré-ovulatórios (FPO) e corpo lúteo (CL) e de seus respectivos hormônios E2 e P4 com a expressão endometrial de genes associados com o remodelamento da ECM durante o período de pré-implantação; e 2. analisar a relação entre a expressão gênica de determinados componentes da ECM avaliada no dia 6 após inseminação artificial (IA) com sucesso gestacional. Para tal, dois experimentos foram realizados. No experimento 1, estudo 1 e estudo 2, 42 e 74 vacas Nelore (Bos indicus) adultas, respectivamente foram sincronizadas obtendo-se ao final dois grupos com distintos tamanhos FPO e CL consequentemente, distintas concentrações de E2 no proestro e P4 no diestro. Os grupos foram: Folículo Grande-CL Grande (FG-CLG; estudo 1, n=20; estudo 2, n=35) e Folículo Pequeno-CL Pequeno (FP-CLP; estudo 1, n=22; estudo 2, n=39). Amostras de tecido endometrial foram coletadas por biópsia no D0 (estro) e pós-mortem no D4 (estudo 1) e D7 (estudo 2). Concentrações de E2 e P4 foram mensuradas por radioimunoensaio (RIA) obtendo- se menores concentrações no grupo FP-CLP. No experimento 2, vacas adultas, Nelore (Bos indicus; n=33) foram sincronizadas utilizando um protocolo a base de prostaglandina F 2&#945; (PGF2&#945;) e observação de estro. As vacas foram inseminadas artificialmente (IA) e seis dias após, uma biópsia endometrial coletada. O diagnóstico de gestação foi realizado após 30 dias por meio de ultrasonografia (US) e então as vacas foram divididas em grupo Prenhe e Não- Prenhe (P e NP) para análise retrospectiva. Abundância de transcritos foi avaliada por sequenciamento (RNAseq) assim como qPCR em amostras de ambos experimentos. Realizaram-se também exames histológicos em amostras do D4 e D7 (estudo 2) para avaliação de colágeno total assim como espessura de fibras colágenas. Resultados determinaram uma maior abundância de transcritos relacionados ao remodelamento de MEC, em destaque TGF&#946;, MMPs, TIMPs e colágenos em vacas pertencentes aos grupos NP e FP-CLP. O mesmo foi observado para abundância de colágeno. No entanto, não observou-se diferença na relação entre fibras grossas e finas entre os tratamentos. Análises de correlação e regressão indicaram que folículos pré-ovulatórios de maior tamanho geram CL maiores e assim maiores concentrações de P4, a qual está negativamente associada à abundância de colágenos. Assim, de acordo com resultados aqui descritos, assume-se que a alteração da homeostase da MEC devido ao incremento na abundância de colágeno pode ser prejudicial à gestação em bovinos. / The endometrial extracellular matrix (ECM) é build up of secretory molecules that make up the cellular microenvironment and suffer activation or suppression mainly by the ovarian steroid hormones, estradiol (E2) and progesterone (P4) during the estrous cycle. The identification of genes involved in endometrial remodeling and receptivity may reveal important biological processes linked to gestational success. The objectives were: 1. identify the relationship among preovulatory follicle (POF) size and corpus luteum (CL) and its respective hormones, E2 and P4 on the endometrial expression of genes related to extracellular matrix remodeling during the pre-implantation period; and 2. analyze the relationship between endometrial ECM gene expression evaluated on day 6 post artificial insemination (AI) with pregnancy outcome. For such, two experiments were carried on. On experiment 1, study 1 and study 2, 42 and 74, respectively, adult Nelore (Bos indicus) cows were synchronized aiming to manipulate the peri-ovulatory endocrine environment, obtaining at the end of the protocol, two groups with distinct pre-ovulatory follicle (POF) and corpus luteum (CL) sizes, leading to groups with distinct E2 and P4 concentrations. The groups were: Large Follicle/CL (LF/CL; study 1, n=20, study 2, n=35) and Small Follicle/Cl (SF/CL; study 1, n=22; study 2, n=39). Endometrial samples were collected by biopsy on D0 (Estrus) and post-mortem on D4 and on study 2 post-mortem on D7. P4 and E2 concentrations were measured by RIA with a significative difference between the groups, being lower hormonal concentrations in the SF- SCL group and higher concentrations in the LF-LCL group . In experiment 2, adult Nelore (Bos indicus) cows (n=33) were synchronized using a prostaglandin 2&#945; (PGF2&#945;) and heat detection based protocol. The cows were AI and six days after an endometrial biopsy was collected. Pregnancy diagnosis was performed on day 30 by ultrasound (US) examination and cows were divided into pregnant and non-pregnant (P vs. NP) groups for a retrospective analysis. Histology was performed on D4 and D7 samples for total collagen abundance as well as fiber thickness. Correlation and regression analysis indicate that larger preovulatory follicles as well as higher P4 concentrations have a negative effect on collagen content. RNA- Seq analysis and confirmation by qPRC was performed on selected samples from experiment 1, study 2 and experiment 2. Comparison of mRNA levels of ECM components samples revealed higher levels of transcripts envolved in ECM remodeling, highlighting TGF&#946; MMPs, TIMPs and collagens in NP cows when compared with P cows as well as in the SF- SCL compared to the LF-LCL group. The same was observed for collagen abundance. However, there was no difference between thin and thick collagen fibers between treatments. Correlation and regression analysis indicate that larger POF lead to larger CL and hence, higher P4 concentrations, which has a negative effects on collagen abundance. Therefore, according to the results presented here, we can imply that an alteration in ECM homeostasis due to increased collagen abundance may be harmful to pregnancy in cows.

The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs). Since unregulated MMP activities are linked to arthritis, cancer, and atherosclerosis, TIMP variants that are selective inhibitors of disease-related MMPs have potential therapeutic value. The structures of TIMP/MMP complexes reveal that most interactions with the MMP involve the N-terminal region of TIMP and the C-D B-strand connector which occupy the primed (right side of the active site) and unprimed (left side) regions of the active site. Substitutions for Thr2 of N-TIMP- 1 strongly influence MMP selectivity. In this study we found that Arg and Gly, which generally reduce MMP affinity, have less effect on binding to MMP-9. When the Arg mutation is added to the NTIMP-1 mutant with AB loop of TIMP-2, it produced a gelatinase-specific inhibitor with Ki values of 2.8 and 0.4 nM for MMP-2 and MMP-9, respectively. The Gly mutant has a Ki of 2.1 nM for MMP-9 and > 40 uM for MMP-2, indicating that engineered TIMPs can discriminate between MMPs in the same subfamily. In collaboration with Dr. Yingnan Zhang at Genentech, we have developed a protocol for the phage display of full-length human TIMP-2 to identify high-affinity selective inhibitors of human MMP-1, a protease that plays a role in cleaving extracellular matrix (ECM) components, connective tissue remodeling during development, angiogenesis, and apoptosis. We have generated a library containing 2x1010 variants of TIMP-2 randomized at residues 2-6 (L1), at residues 34-40 (L2) and 67-70 (L3). / The L1 library yielded a positive signal for MMP-1 binding. Clones from the L1 library, designated TM1, TM8, TM13, and TM14, were isolated after 5 rounds of selection on immobilized MMP-1 and MMP-3 and found to show a greater selectivity for MMP-1 relative to MMP-3. TM8, which has Ser2 to Asp and Ser4 to Ala substitutions, showed the greatest apparent selectivity of 10-fold toward MMP-1 compared to MMP-3. The various mutations identified by phage display were introduced into recombinant Nterminal TIMP-2 and the variants characterized as inhibitors of an array of MMP catalytic domains. The TM8-based mutant showed pronounced selectivity (> 1000-fold for MMP-1 vs. MMP-3) and may be a step towards the generation of MMP-1-specific inhibitors. Molecular modeling was used to rationalize the structural basis of MMP selectivity in the mutants. / by Harinathachari Bahudhanapati. / Thesis (Ph.D.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

The 23 matrix metalloproteinases (MMPs) in humans catalyze the turnover of all protein components of the extracellular matrix (ECM) and have important roles in tissue remodeling, wound healing, embryo implantation, cell migration and shedding of cell surface proteins. Excess MMP activities are associated with many diseases including arthritis, heart disease and cancer. The activities of MMPs are regulated by a family of four protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs), that are endogenous inhibitors of matrix metalloproteinases (MMPs), ADAMs (A Disintegrin And Metalloproteinase) and ADAMTS (disintegrin-metalloproteinase with thrombospmdin motifs) .... The balance between TIMPs and active metzinicins is very important and imbalances are linked to human diseases such as arthritis, cancer, and atherosclerosis. The engineering of TIMPs to produce specific inhibitors of individual MPs could provide new therapeutic principles for disease treatment, but this requires a detailed understanding of the biophysical and structural basis of the interactions of TIMPs and MMPs and ADAMs. / by Wu Ying. / Thesis (Ph.D.)--Florida Atlantic University, 2012. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.