A systematic analysis of the role of GGDEF-EAL domain proteins in virulence and motility in Xanthomonas oryzae pv. oryzicola

The second messenger c-di-GMP is implicated in regulation of various aspects of the lifestyles and virulence of Gram-negative bacteria. Cyclic di-GMP is formed by diguanylate cyclases with a GGDEF domain and degraded by phosphodiesterases with either an EAL or HD-GYP domain. Proteins with tandem GGDEF-EAL domains occur in many bacteria, where they may be involved in c-di-GMP turnover or act as enzymatically-inactive c-di-GMP effectors. Here, we report a systematic study of the regulatory action of the eleven GGDEF-EAL proteins in Xanthomonas oryzae pv. oryzicola, an important rice pathogen causing bacterial leaf streak. Mutational analysis revealed that XOC_2335 and XOC_2393 positively regulate bacterial swimming motility, while XOC_2102, XOC_2393 and XOC_4190 negatively control sliding motility. The ΔXOC_2335/XOC_2393 mutant that had a higher intracellular c-di-GMP level than the wild type and the ΔXOC_4190 mutant exhibited reduced virulence to rice after pressure inoculation. In vitro purified XOC_4190 and XOC_2102 have little or no diguanylate cyclase or phosphodiesterase activity, which is consistent with unaltered c-di-GMP concentration in ΔXOC_4190. Nevertheless, both proteins can bind to c-di-GMP with high affinity, indicating a potential role as c-di-GMP effectors. Overall our findings advance understanding of c-di-GMP signaling and its links to virulence in an important rice pathogen.

Molecular Characterization of Three Novel Phospholipase A2 Proteins from the Venom of Atheris chlorechis, Atheris nitschei and Atheris squamigera

Secretory phospholipase A2 (sPLA2) is known as a major component of snake venoms and displays higher-order catalytic hydrolysis functions as well as a wide range of pathological effects. Atheris is not a notoriously dangerous genus of snakes although there are some reports of fatal cases after envenomation due to the effects of coagulation disturbances and hemorrhaging. Molecular characterization of Atheris venom enzymes is incomplete and there are only a few reports in the literature. Here, we report, for the first time, the cloning and characterization of three novel cDNAs encoding phospholipase A2 precursors (one each) from the venoms of the Western bush viper (Atheris chlorechis), the Great Lakes bush viper (Atheris nitschei) and the Variable bush viper (Atheris squamigera), using a “shotgun cloning” strategy. Open-reading frames of respective cloned cDNAs contained putative 16 residue signal peptides and mature proteins composed of 121 to 123 amino acid residues. Alignment of mature protein sequences revealed high degrees of structural conservation and identity with Group II venom PLA2 proteins from other taxa within the Viperidae. Reverse-phase High Performance Liquid Chromatography (HPLC) profiles of these three snake venoms were obtained separately and chromatographic fractions were assessed for phospholipase activity using an egg yolk suspension assay. The molecular masses of mature proteins were all identified as approximately 14 kDa. Mass spectrometric analyses of the fractionated oligopeptides arising from tryptic digestion of intact venom proteins, was performed for further structural characterization.

Material characterization and process development for indium-arsenide / indium-gallium-antimonide channel, high electron mobility transistors for low power, high speed applications

Efforts to push the performance of transistors for millimeter-wave and microwave applications have borne fruit through device size scaling and the use of novel material systems. III-V semiconductors and their alloys hold a distinct advantage over silicon because they have much higher electron mobility which is a prerequisite for high frequency operation. InGaAs/InP pseudomorphic heterojunction bipolar transistors (HBTs) have demonstrated fT of 765 GHz at room temperature and InP based high electron mobility transistors (HEMTs) have demonstrated fMax of 1.2 THz. The 6.1 A lattice family of InAs, GaSb, AlSb covers a wide variety of band gaps and is an attractive future material system for high speed device development. Extremely high electron mobilities ~ 30,000 cm^2 V^-1s^-1 have been achieved in modulation doped InAs-AlSb structures. The work described in this thesis involves material characterization and process development for HEMT fabrication on this material system.

Beyond hope: Rhetorics of mobility, possibility, and literacy

When writing teachers enter the classroom, they often bring with them a deep faith in the power of literacy to rectify social inequalities and improve their students’ social and economic standing. It is this faith—this hope for change—that draws some writing teachers to locations of social and economic hardship. I am interested in how teachers and theorists construct their own narratives of social mobility, possibility, and literacy. My dissertation analyzes the production and expression of beliefs about literacy in the narratives of a diverse group of writing teachers and theorists, from those beginning their careers to those who are published and widely read. The central questions guiding this study are: How do teachers’ and theorists’ narratives of becoming literate intersect with literacy theories? and How do such literacy narratives intersect with beliefs in the power of literacy to improve individuals’ lives socially, economically, and personally? I contend that the professional literature needs to address more fully how teachers’ and theorists’ personal histories with literacy shape what they see as possible (and desirable) for students, especially those from marginalized communities. A central focus of the dissertation is on how teachers and theorists attempt to resolve a paradox they are likely to encounter in narratives about literacy. On one hand, they are immersed in a popular culture that cherishes narrative links between literacy and economic advancement (and, further, between such advancement and a “good life”). On the other hand, in professional discourse and in teacher preparation courses, they are likely to encounter narratives that complicate an assumed causal relationship between literacy and economic progress. Understanding, through literacy narratives, how teachers and theorists chart a practical path through or around this paradox can be beneficial to literacy education in three ways. First, it can offer direction in professional development and teacher education, addressing how teachers negotiate the boundaries between personal experience, theory, and pedagogy. Second, it can help teachers create spaces wherein students can explore the impact of paradoxical views about the role of literacy on their own lives. Finally, it can offer direction in public policy discourse, extending awareness of what we want—and need—from English language arts education in the twenty-first century. To explore these issues, I draw on case studies and ethnographic observation as well as narrative inquiry into teachers’ and theorists’ published literacy narratives. I situate my findings within three interrelated frames: 1) the narratives of new teachers, 2) the published works of literacy educators and theorists, and 3) my own literacy narrative. My first chapter, “Beyond Hope,” explores the tenuous connections between hope and critique in literacy studies and provides a methodological overview of the study. I argue that scholarship must move beyond a singular focus on either hope or critique in order to identify the transformative potential of literacy in particular circumstances. Analyzing literacy narratives provides a way of locating a critically informed sense of possibility. My second chapter, “Making Teachers, Making Literacy,” explores the intersection between teachers’ lives and the theories they study, based on qualitative analysis of a preservice course for secondary education English teachers. I examine how these preservice English teachers understood literacy, how their narratives of becoming literate and teaching English connected—and did not connect—with theoretical and pedagogical positions, and how these stories might inform their future work as practitioners. Centering primarily on preservice teachers who resisted Nancie Atwell’s pedagogy of possibility because they found it too good to be true, this research concentrates on moments of disjuncture, as expressed in class discussion and in one-on-one interviews, when literacy theories failed to align with aspiring teachers’ understandings of their own experiences and also with what they imagined as possible in disadvantaged educational settings. In my third and fourth chapters, I analyze the narratives of celebrated teachers and theorists who put forth an agenda that emphasizes possibilities through literacy, examining how they negotiate the relationship between their own literacy stories and literacy theories. Specifically, I investigate the narratives of three proponents of critical literacy: Mike Rose, Paulo Freire, and Myles Horton, all highly respected literacy teachers whose working-class backgrounds influenced their commitment to teaching in disenfranchised communities. In chapter 3, “Reading Lives on the Boundary,” I demonstrate how Mike Rose’s 1989 autobiographical text, Lives on the Boundary, juxtaposes rhetorics of mobility with critiques of such possibility. Through an analysis of work published in professional journals, I offer a reception history of Rose’s narrative, focusing specifically on how teachers have negotiated the tension between hope and critique. I follow this analysis with three case studies, drawn from a larger sampling, that inquire into the personal connections that writing teachers make with Lives on the Boundary. The teachers in this study, who provided written responses and participated in audio-recorded follow-up interviews, were asked to compare Rose’s story to their own stories, considering how their personal literacy histories influenced their teaching. My findings illustrate how a group of teachers and theorists have projected their own assessments of what literacy and higher education can and cannot accomplish onto this influential text. In my fourth chapter, “Horton and Freire’s Road as Literacy Narrative,” I concentrate on Myles Horton and Paulo Freire’s 1990 collaborative spoken book, We Make the Road by Walking. Central to my analysis are the educators’ stories about their formative years, including their own primary and secondary education experiences. I argue that We Make the Road by Walking demonstrates how theories of literacy cannot be divorced from personal histories. I begin by examining the spoken book as a literacy narrative that fuses personal and theoretical knowledge, focusing specifically on its authors’ ideas on theory. Drawing on Bakhtin’s notion of the chronotope—the intersection of time and space within narrative—I then explore the literacy narratives emerging from the production process of the book, in a video production about Horton and Freire’s meeting, and ultimately in the two men’s reflections on their childhood years (Dialogic). Interspersed with these accounts is archival material on the book’s editorial production that illustrates the value of increased dialogue between personal history and theories of literacy. My fifth chapter is both a reflective analysis and a qualitative study of my work at a men’s medium-high security prison in Illinois, where I conducted research and served as the instructor of an upper-level writing course, “Writing for a Change,” in the spring of 2009. Entitled “Doing Time with Literacy Narratives,” this chapter explores the complex ways in which literacy and incarceration are configured in students’ narratives as well as my own. With and against students’ stories, I juxtapose my own experiences with literacy, particularly in relation to being the son of an imprisoned father. In exploring the intersections between such stories, I demonstrate how literacy narratives can function as a heuristic for exploring beliefs about literacy between teachers and students both inside and outside of the prison-industrial complex. My conclusion pulls together the various themes that emerged in the three frames, from the making of new teachers to the published literacy narratives of teachers and theorists to my own literacy narrative. Writing teachers encounter considerable pressure to align their curricula with one or another theory of literacy, which has the effect of negating the authority of knowledge about literacy gleaned from experience as readers and writers. My dissertation contends that there is much to be gained by finding ways of articulating theories of literacy that encompass teachers’ knowledge of reading and writing as expressed in personal narratives of literacy. While powerful cultural rhetorics of upward social mobility often neutralize the critical potential of teachers’ own narratives of literacy—potential that has been documented by scholars in writing studies and allied disciplines—this is not always the case. The chapters in this dissertation offer evidence that hopeful and critical positions on the transformational possibilities of literacy are not mutually exclusive.

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and Clustered Regularly Interspaced Short Palindromic Repeats sequences associated with Cellular apoptosis susceptibility proteins.

Electroreflectance characterization of AlInGaN/GaN high-electron mobility heterostructures

Room temperature electroreflectance (ER) spectroscopy has been used to study the fundamental properties of AlxInyGa${}_{1-x-y}$N/AlN/GaN heterostructures under different applied bias. The (0001)-oriented heterostructures were grown by metal-organic vapor phase epitaxy on sapphire. The band gap energy of the AlxInyGa${}_{1-x-y}{\rm{N}}$ layers has been determined from analysis of the ER spectra using Aspnes' model. The obtained values are in good agreement with a nonlinear band gap interpolation equation proposed earlier. Bias-dependent ER allows one to determine the sheet carrier density of the two-dimensional electron gas and the barrier field strength.

Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group

Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovis isolates that are representative of the most frequent spoligotype in the Iberian Peninsula, SB0121. VNTR typing targeted nine loci: ETR-A (alias VNTR2165), ETR-B (VNTR2461), ETR-D (MIRU4, VNTR580), ETR-E (MIRU31, VNTR3192), MIRU26 (VNTR2996), QUB11a (VNTR2163a), QUB11b (VNTR2163b), QUB26 (VNTR4052), and QUB3232 (VNTR3232). We found a high degree of diversity among the studied isolates (discriminatory index [D] = 0.9856), which were split into 65 different MIRU-VNTR types. An alternative short-format MIRU-VNTR typing targeting only the four loci with the highest variability values was found to offer an equivalent discriminatory index. Minimum spanning trees using the MIRU-VNTR data showed the hypothetical evolution of an apparent clonal group. MIRU-VNTR analysis was also applied to the isolates of 176 animals from 15 farms infected by M. bovis SB0121; in 10 farms, the analysis revealed the coexistence of two to five different MIRU types differing in one to six loci, which highlights the frequency of undetected heterogeneity.

Phosphate Regulated Proteins Of Xanthomonas Citri Subsp. Citri: A Proteomic Approach.

Xanthomonas citri subsp. citri (X. citri) is the causative agent of the citrus canker, a disease that affects several citrus plants in Brazil and across the world. Although many studies have demonstrated the importance of genes for infection and pathogenesis in this bacterium, there are no data related to phosphate uptake and assimilation pathways. To identify the proteins that are involved in the phosphate response, we performed a proteomic analysis of X. citri extracts after growth in three culture media with different phosphate concentrations. Using mass spectrometry and bioinformatics analysis, we showed that X. citri conserved orthologous genes from Pho regulon in Escherichia coli, including the two-component system PhoR/PhoB, ATP binding cassette (ABC transporter) Pst for phosphate uptake, and the alkaline phosphatase PhoA. Analysis performed under phosphate starvation provided evidence of the relevance of the Pst system for phosphate uptake, as well as both periplasmic binding proteins, PhoX and PstS, which were formed in high abundance. The results from this study are the first evidence of the Pho regulon activation in X. citri and bring new insights for studies related to the bacterial metabolism and physiology. Biological significance Using proteomics and bioinformatics analysis we showed for the first time that the phytopathogenic bacterium X. citri conserves a set of proteins that belong to the Pho regulon, which are induced during phosphate starvation. The most relevant in terms of conservation and up-regulation were the periplasmic-binding proteins PstS and PhoX from the ABC transporter PstSBAC for phosphate, the two-component system composed by PhoR/PhoB and the alkaline phosphatase PhoA.

Exposure To Bisphenol-a During Pregnancy Partially Mimics The Effects Of A High-fat Diet Altering Glucose Homeostasis And Gene Expression In Adult Male Mice.

Bisphenol-A (BPA) is one of the most widespread EDCs used as a base compound in the manufacture of polycarbonate plastics. The aim of our research has been to study how the exposure to BPA during pregnancy affects weight, glucose homeostasis, pancreatic β-cell function and gene expression in the major peripheral organs that control energy flux: white adipose tissue (WAT), the liver and skeletal muscle, in male offspring 17 and 28 weeks old. Pregnant mice were treated with a subcutaneous injection of 10 µg/kg/day of BPA or a vehicle from day 9 to 16 of pregnancy. One month old offspring were divided into four different groups: vehicle treated mice that ate a normal chow diet (Control group); BPA treated mice that also ate a normal chow diet (BPA); vehicle treated animals that had a high fat diet (HFD) and BPA treated animals that were fed HFD (HFD-BPA). The BPA group started to gain weight at 18 weeks old and caught up to the HFD group before week 28. The BPA group as well as the HFD and HFD-BPA ones presented fasting hyperglycemia, glucose intolerance and high levels of non-esterified fatty acids (NEFA) in plasma compared with the Control one. Glucose stimulated insulin release was disrupted, particularly in the HFD-BPA group. In WAT, the mRNA expression of the genes involved in fatty acid metabolism, Srebpc1, Pparα and Cpt1β was decreased by BPA to the same extent as with the HFD treatment. BPA treatment upregulated Pparγ and Prkaa1 genes in the liver; yet it diminished the expression of Cd36. Hepatic triglyceride levels were increased in all groups compared to control. In conclusion, male offspring from BPA-treated mothers presented symptoms of diabesity. This term refers to a form of diabetes which typically develops in later life and is associated with obesity.

Otorhinolaryngological Findings In A Group Of Patients With Rheumatic Diseases.

Otorhinolaryngological manifestations of rheumatologic diseases represent a great challenge not only to the generalistphysician but also to the ENT doctor andrheumatologist. They often represent early manifestations of an autoimmune disorder which requires prompt and aggressive immunosuppressive treatment. Auditory, nasal, laryngeal and eye symptoms can be the first manifestation of rheumatic diseases and their proper assessment helps the doctor to identify signs of disease activity. The objective of this study is to identify the ENT manifestations in patients with rheumatic diseases in a high complexity hospital, regarding facilitating an early diagnosis and treatment. We performed clinical and complete otorhinolaryngological evaluations in patients selected from the outpatient rheumatology in a standardized manner by the use of a standardized form filling during the secondhalf of 2010. In the study group, systemic lupus erythematosus (SLE) patients had predominantly laryngeal manifestations, while patients with Sjögren's syndrome showed a higher prevalence of otologic manifestations. Changes in audiometric tests were found in 53% of Wegener's granulomatosis (WG) patients, 80% of relapsing polychondritis (RP), 33% of systemic lupus erythematosus (SLE) and 50% of Churg-Strauss syndrome (SCS). Regarding nasal alterations, these were found so prevalent in all conditions, especially Churg-Strauss syndrome. This study demonstrated that most patients treated in our hospital has the ENT signs and symptoms commonly associated in previous studies on rheumatic diseases, but further studies with a larger number of patients must be made to establish such relations.

Effect Of Aloe Vera Application On The Content And Molecular Arrangement Of Glycosaminoglycans During Calcaneal Tendon Healing.

Although several treatments for tendon lesions have been proposed, successful tendon repair remains a great challenge for orthopedics, especially considering the high incidence of re-rupture of injured tendons. Our aim was to evaluate the pharmacological potential of Aloe vera on the content and arrangement of glycosaminoglycans (GAGs) during tendon healing, which was based on the effectiveness of A. vera on collagen organization previously observed by our group. In rats, a partial calcaneal tendon transection was performed with subsequent topical A. vera application at the injury site. The tendons were treated with A. vera ointment for 7 days and excised on the 7(th) , 14(th) , or 21(st) day post-surgery. Control rats received ointment without A. vera. A higher content of GAGs and a lower amount of dermatan sulfate were detected in the A. vera-treated group on the 14(th) day compared with the control. Also at 14 days post-surgery, a lower dichroic ratio in toluidine blue stained sections was observed in A. vera-treated tendons compared with the control. No differences were observed in the chondroitin-6-sulfate and TGF-β1 levels between the groups, and higher amount of non-collagenous proteins was detected in the A. vera-treated group on the 21(st) day, compared with the control group. No differences were observed in the number of fibroblasts, inflammatory cells and blood vessels between the groups. The application of A. vera during tendon healing modified the arrangement of GAGs and increased the content of GAGs and non-collagenous proteins.

Saturated Fatty Acids Modulate Autophagy's Proteins In The Hypothalamus.

Autophagy is an important process that regulates cellular homeostasis by degrading dysfunctional proteins, organelles and lipids. In this study, the hypothesis that obesity could lead to impairment in hypothalamic autophagy in mice was evaluated by examining the hypothalamic distribution and content of autophagic proteins in animal with obesity induced by 8 or 16 weeks high fat diet to induce obesity and in response to intracerebroventricular injections of palmitic acid. The results showed that chronic exposure to a high fat diet leads to an increased expression of inflammatory markers and downregulation of autophagic proteins. In obese mice, autophagic induction leads to the downregulation of proteins, such as JNK and Bax, which are involved in the stress pathways. In neuron cell- line, palmitate has a direct effect on autophagy even without inflammatory activity. Understanding the cellular and molecular bases of overnutrition is essential for identifying new diagnostic and therapeutic targets for obesity.

Whey And Soy Protein Supplements Changes Body Composition In Patients With Crohn's Disease Undergoing Azathioprine And Anti-tnf-alpha Therapy.

Crohn´s disease (CD) is a chronic transmural inflammation of the gastrointestinal tract of unknown cause. Malnutrition associated with active CD has been reduced although obesity has increased. Dietary strategies such as those with high-protein have been proposed to reduce body fat. This study compares the effects of two supplements on the nutritional status of CD patients. 68 CD patients were randomized in two groups: whey protein group (WP) and soy protein group (SP). Using bioimpedance analysis, anthropometry and albumin and pre-albumin dosages the nutritional status was measured before starting the intervention and after 8 and 16 weeks. The disease activity was determined by Crohn's Disease Activity Index and serum C-reactive protein dosage and dietary intake by 24h dietary recalls. Forty-one patients concluded the study and both supplements changed body composition similarly. Triceps skin fold thickness (p< 0.001) and body fat percentage (p=0.001) decreased, whereas mid-arm muscle circumference (p=0.004), corrected arm muscle area (p=0.005) and body lean percentage (p=0.001) increased. For Crohn's disease patients undergoing anti TNF-alpha and azatioprine therapies, supplementation with whey and soy proteins changes body composition through reduction of body fat and thus contributes to control inflammation.

New Fefe-hydrogenase Genes Identified In A Metagenomic Fosmid Library From A Municipal Wastewater Treatment Plant As Revealed By High-throughput Sequencing.

A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes.