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In nature, plants continuously face the attack from insect herbivores. To defend themselves, plants have evolved a plethora of direct and indirect defence mechanisms that are present either constitutively or induced upon insect herbivory. In response to insect herbivory, plants activate phytohormonal signal-transduction pathways, transcriptional responses and biological processes. These changes in transcriptional and biological processes level influence the plant’s phenotype and consequently plant ecology during the current season or over seasons. To gain more insight into the dynamics of plant phenotype, elucidating transcriptomic responses to insect herbivory is critical. Various studies have investigated whole-genome transcriptional responses of plants against different insect herbivores, but only few have reported on responses to cell-content feeding thrips. Thrips (Thysanoptera) are minute cell-content feeding insects and are serious pests on many commercial and ornamental plants. Thrips species such as western flower thrips (WFT) and onion thrips are among the most devastating pests on e.g. sweet pepper and white cabbage plants, respectively. Therefore, using a high-density time-series approach, the focus of this thesis was to investigate whole-genome transcriptional responses of sweet pepper and white cabbage plants upon WFT and onion thrips feeding, respectively, and the underlying genetic mechanisms. In addition, I focussed on one particular gene family, the lipoxygenases and a gene in this family that is involved in thrips-induced crop resistance. Chapter 2 was focused on the identification of the lipoxygenase gene family in pepper (Capsicum annuum). Lipoxygenases (LOXs) are non-heme, iron-containing dioxygenases involved in several developmental and defence-related plant processes, such as seed germination, fruit ripening, tuber development and JA-regulated plant defences. Through multiple in-silico analysis, a total of eight LOX genes were identified in pepper classifying four LOXs (CaLOX1, CaLOX3, CaLOX4 and CaLOX5) as 9-LOXs and four (CaLOX2, CaLOX6, CaLOX7 and CaLOX8) as 13-LOXs. Chapter 3 further narrowed down the LOX gene-family to one lipoxygenase (CaLOX2) gene through in-silico analysis and functionally characterized its involvement in jasmonate-dependent induced defence against WFT. Overall, this chapter shows involvement of CaLOX2 in JA-mediated plant resistance to thrips feeding. Chapter 4 elucidates the dynamics of transcriptional reprogramming of sweet pepper in response to WFT feeding. Approximately 8.6% (2060 up and 1002 downregulated) of the pepper genes were differentially expressed that categorized into 23 clusters (16 upregulated and 7 downregulated), each possessing a unique temporal expression pattern. Upregulated gene clusters were overrepresented with defence-related biological processes, whereas downregulated gene clusters were overrepresented with developmental processes. The transcription factor families ERF, MYB, NAC, bHLH and WRKY emerged as pivotal regulators in response to WFT feeding. The data show a chronological order in the activation of hormonal (JA, ET) and secondary metabolite (phenylpropanoids, flavonoids and terpenoids) pathways. Eventually, the comparative analysis of the WFT-induced transcriptional responses of Arabidopsis and sweet pepper plants to WFT feeding shows a conservation in the induction of the JA-pathway in both plants, whereas the majority of transcriptional responses are plant-specific. Chapter 5 focused on 1) elucidating whole-genome transcriptional reprogramming of white cabbage plants in response to onion thrips feeding and 2) comparative transcriptomics to disentangle similarities and differences in transcriptional responses between WFT-induced Arabidopsis and sweet pepper as well as onion-thrips-induced white cabbage. Approximately 9.7 % of the white cabbage genes showed differential expression with 48 (32 upregulated and 16 downregulated) gene clusters with upregulated clusters associated with defence and downregulated clusters with development-related biological processes. Phytohormone-related processes (JA, ET and SA) and secondary metabolite (phenylpropanoids, flavonoids, green-leaf volatiles and indolic glucosinolates) biosynthesis genes were induced, whereas aliphatic glucosinolate biosynthetic genes were suppressed. Comparative analysis of the transcriptional responses of Arabidopsis and sweet pepper to WFT and of white cabbage to onion thrips showed 1) conservation of the JA biosynthesis and signalling pathways, 2) conservation of involvement of TF families, such as MYB, bHLH and WRKY in regulating responses, 3) that the majority of the transcriptional responses to thrips are system-specific, 4) that genes involved in indole glucosinolate biosynthesis are upregulated, whereas genes involved in aliphatic glucosinolate biosynthesis are downregulated in both brassicaceous plants Arabidopsis and white cabbage and 5) that the white-cabbage transcriptomic response to onion thrips is relatively rapid and complex compared to the WFT-induced Arabidopsis and sweet pepper transcriptomic responses. The data presented in this thesis contributes to understand the intensity and complexity of dynamic plant transcriptional responses to thrips feeding, and this is discussed in Chapter 6.

Insect herbivory can seriously hinder plant performance and reduce crop yield. Thrips are minute cell‐content‐feeding insects that are important vectors of viral plant pathogens, and are serious crop pests. We investigated the role of a sweet pepper (Capsicum annuum) lipoxygenase gene, CaLOX2, in the defense of pepper plants against Western flower thrips (Frankliniella occidentalis). This was done through a combination of in‐silico, transcriptional, behavioral and chemical analyses. Our data show that CaLOX2 is involved in jasmonic acid (JA) biosynthesis and mediates plant resistance. Expression of the JA‐related marker genes, CaLOX2 and CaPIN II, was induced by thrips feeding. Silencing of CaLOX2 in pepper plants through virus‐induced gene silencing (VIGS) resulted in low levels of CaLOX2 transcripts, as well as significant reduction in the accumulation of JA, and its derivatives, upon thrips feeding compared to control plants. CaLOX2‐silenced pepper plants exhibited enhanced susceptibility to thrips. This indicates that CaLOX2 mediates JA‐dependent signaling, resulting in defense against thrips. Furthermore, exogenous application of JA to pepper plants increased plant resistance to thrips, constrained thrips population development and made plants less attractive to thrips. Thus, a multidisciplinary approach shows that an intact lipoxygenase pathway mediates various components of sweet pepper defense against F. occidentalis., Through a combination of in‐silico, transcriptional, behavioural and chemical analyses, here we demonstrate that the lipoxygenase gene, CaLOX2, mediates jasmonate‐dependent induced defence of sweet pepper plants against Western flower thrips.

RAG1 protein is one of the key component of RAG complex regulating the V(D)J recombination. There are only few studies for RAG1 concerning evolutionary history, detailed sequence and mutational hotspots. Herein, we present out datasets used for the recent comprehensive study of RAG1 based on sequence, phylogenetic and genetic variant analyses (Kumar et al., 2015) [1]. Protein sequence alignment helped in characterizing the conserved domains and regions of RAG1. It also aided in unraveling ancestral RAG1 in the sea urchin. Human genetic variant analyses revealed 751 mutational hotspots, located both in the coding and the non-coding regions. For further analysis and discussion, see (Kumar et al., 2015) [1].

Electromagnetising of water and using it in various field is not a new concept. It has been done in agriculture, dairy, health care industries etc. But in the past few years owing to unpredictable rainfall there is a serious shortage of water. Also about 75% of the water available is hard water. Because of unavailability of water for construction practices, there is a serious need to use alternative water resources. This paper investigates whether different sources of water other than potable water can be used for construction works. Concrete mix for bore well water as well as electromagnetised bore well water were prepared and an another set of concrete mix of same proportion were prepared of the water flowing out of the STP and the electromagnetic water flowing out of the STP. Compressive strength tests conducted on the electromagnetic samples were very encouraging and can be used for replacing potable water.

The growing uses of functional polymers in different domains and the well-established remanence of synthetic polymers underline the necessity to study their microbial biodegradation. A phylloplane bacterial collection was screened for its potential to overcome documented factors limiting polymer biodegradation, i.e. low cleavable long chain linear polymers and low bioavailable hydrophobic compounds. Acrylate-based polymers, namely poly(2-hydroxyethyl methacrylate) (pHEMA), poly(N-isopropylacrylamide) (pNIPAM), poly(acrylamide) (pAM) and poly(acrylic acid sodium salt) (pAS), and a hydrophobic crosslinker Epoxidized Soybean Oil Acrylate (ESOA) were used as selective substrates. OD monitoring of growth with these molecules as sole carbon sources were correlated with substrates alterations determined by 1H NMR, GPC and FTIR. Selected strains belong to Bacillales Family XII. Incertae Sedis, Bacillaceae, Nocardiaceae, Micrococcaceae, Enterobacteriaceae and Pseudomonadaceae. Bacillus species mainly developed with ESOA. Exiguobacterium sibiricum strains could grow with pHEMA and pNIPAM leading to polymer molecular weight decreases. Arthrobacter koreensis showed the highest alteration capacities of pHEMA with molecular weight decreases from 22,000 to 3,148 g/mol and the production of presumed aromatics and carbon chains.

Tumor hypoxia is a negative prognostic factor that is implicated in oncogenic signal activation, immune escape, and resistance to treatment. Identifying the mechanistic role of hypoxia in immune escape and resistance to immune-checkpoint inhibitors may aid the identification of therapeutic targets. We and others have shown that V-domain Ig suppressor of T-cell activation (VISTA), a negative checkpoint regulator in the B7 family, is highly expressed in the tumor microenvironment in tumor models and primary human cancers. In this study, we show that VISTA and HIF1α activity are correlated in a cohort of colorectal cancer patients. High VISTA expression was associated with worse overall survival. We used the CT26 colon cancer model to investigate the regulation of VISTA by hypoxia. Compared with less hypoxic tumor regions or draining lymph nodes, regions of profound hypoxia in the tumor microenvironment were associated with increased VISTA expression on tumor-infiltrating myeloid-derived suppressor cells (MDSC). Using chromatin immunoprecipitation and genetic silencing, we show that hypoxia-inducible factor (HIF)-1α binding to a conserved hypoxia response element in the VISTA promoter upregulated VISTA on myeloid cells. Further, antibody targeting or genetic ablation of VISTA under hypoxia relieved MDSC-mediated T-cell suppression, revealing VISTA as a mediator of MDSC function. Collectively, these data suggest that targeting VISTA may mitigate the deleterious effects of hypoxia on antitumor immunity.

O Enxame de Dique de Florianópolis (EDF) é parte do sistema de alimentação das lavas da Província Magmática Paraná-Etendeka (PEMP), de idade eocretácea, que constitui a segunda maior província de basaltos continentais do mundo em área preservada. Nas exposições do extremo norte da Ilha de Santa Catarina, predominam largamente diques básicos (microgabros) de direção NNE, quimicamente equivalentes aos basaltos do tipo Urubici, do qual devem constituir o sistema de alimentação, como indicado por evidências estruturais, geoquímicas e geocronológicas. Esses diques são cortados por diques mais jovens e menos espessos (em parte de direção NNW), mas também existem diques NNW que não mostram relações de corte. Foram considerados parte de um mesmo sistema conjugado de fraturas, o que está em conformidade com a interpretação de reativação de estruturas prévias do embasamento. A componente principal de maior compressão, ?1, tem direção NE-SW. Cálculos da dilatação crustal realizados neste trabalho indicam valores mínimos em torno de 5,4% quando da colocação dos diques (~ 134 Ma). Outros tipos de diques básicos menos expressivos podem ser distinguidos especialmente pelos conteúdos de P2O5(%) e Sr (ppm), e são semelhantes ao magma-tipo Pitanga, do qual no entanto se diferenciam por razões de elementos traço, como (Tb/Yb)N levemente mais alto, em relação ao magma-tipo em sua área de ocorrência. Diques ácidos de composição dacítica são subordinados, e ocorrem no centro de diques compostos, cujas bordas podem ser de microgabros tipo Pitanga ou, em um caso, andesito. Os dacitos mostram semelhanças com rochas vulcânicas Chapecó, que se diferenciam por razões de elementos traço e isotópicas, por exemplo, maiores razões (La/Yb)N e maiores 87Sr/86Sr(i). Modelagem geoquímica de elementos traços mostram que os dacitos podem ser geneticamente associados aos microgabros por processos de fracionamento de ca. 65-70% de um cumulato com ~45% de plagioclásio, ~40% de clinopiroxênio e ~15% de magnetita acompanhados de assimilação (massa de assimilado/cristalizado= 0,1) de granitos neoproterozoicos encaixantes. Os melhores resultados são obtidos para os microgabros que formam borda dos diques compostos, caracterizados por teores intermediários de Sr e altos de P2O5, mas os testes com outras composições de microgabros, incluindo o tipo de alto Sr-P2O5 (Urubici), também proporcionaram resultados satisfatórios. The Florianópolis Dike Swarm (FDS) is part of the lava feeding system of the Paraná-Etendeka Magmatic Province (PEMP), of eocretaceous age, which is the second largest province of continental basalts in the world in preserved área. The northern part of the Santa Catarina Island show basic dikes (microgabbros) of NNE-trends, chemically equivalent to basalts of Urubici type, which should constitute the feeding system, as indicated by structural, geochemical and geochronological evidences. These dikes are cut by lower occurence younger dikes (in part of NNW direction), but there are also NNW dikes that do not show crosscut relations. They were considered part of the same conjugate system of fractures, which is in accordance with the interpretation of reactivation of previous structures of the basement. The main component of higher compression, ?1, has NE-SW direction. Calculations of the crustal dilation, performed in this study, indicate minimum values of around 5.4% (~ 134 Ma). Other types of less expressive basic dikes can be distinguished specially by the contents of P2O5 (%) and Sr (ppm). They are similar to the Pitanga magma-type, but differ on ratios of trace elements such as (Tb/Yb)N slightly higher, relative to the magma-type in its area of occurrence. Acidic dykes of dacitic composition are subordinate and occur in the center of composite dikes, whose borders may be of Pitanga type of microgabbro or, in one case, andesite. Dacites show similarities with Chapecó volcanic rocks, but they differ for ratios of trace and isotopic elements, for example, higher ratios (La / Yb)N and higher 87Sr / 86Sr(i). Geochemical modeling of trace elements shows that dacites can be genetically associated to microgabbros by fractionation processes of 65-70% of a cumulus with ~ 45% of plagioclase, ~ 40% of clinopyroxene and ~ 15% of magnetite accompanied by assimilation (assimilated / crystallized mass = 0.1) of host neoproterozoic granites. The best results are obtained from microgabbros that form the edge of the composite dikes, characterized by intermediate levels of Sr and high P2O5. However, the tests with other compositions of microgabbros, including the type of high Sr-P2O5 (Urubici), also yielded satifactory results.

Made available in DSpace on 2018-11-26T16:04:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01. Added 1 bitstream(s) on 2021-07-15T15:20:22Z : No. of bitstreams: 1 S2317-48892018000200177.pdf: 10956683 bytes, checksum: 288814a4f6468b50e5c268cb527734e2 (MD5) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The Parana Continental Flood Basalt (PCFB) province is one of the largest igneous provinces on Earth, but little is known about the architecture and geochemical characteristics of the lava flows. In this context, a set of borehole samples arranged in an NEE-SWW profile - more than 600 km long - located in the northern PCFB was used to define its chemostratigraphy. In this region, the outcrops are rare, and the volcanic piles are covered by hundreds of meters of sedimentary rocks from the Bauru Sub-Basin. This study aimed to explore the chemostratigraphic column from northern PCFB to improve the understanding of its internal architecture and to characterize the flood basalt sequences by using the petrography and elemental geochemistry of surface and borehole samples. The results showed the presence of the main four magma types, which were essentially distinguished by their P2O5, TiO2 and Sr concentrations, as well as Zr/Y ratios, with excellent chemostratigraphy relations. Univ Fed Sao Paulo, Inst Ciencias Ambientais, Dept Ciencias Ambientais, Sao Paulo, SP, Brazil Univ Fed Bahia, Dept Fis Terra & Meio Ambiente, Inst Fis, Salvador, BA, Brazil Univ Sao Paulo, Inst Astron Geofis & Ciencias Atmosfer, Sao Paulo, SP, Brazil Univ Estadual Paulista Julia Mesquita Filho, Inst Geociencias & Ciencias Exatas, Rio Claro, SP, Brazil Univ Sao Paulo, Inst Geociencias, Sao Paulo, SP, Brazil Univ Estadual Paulista Julia Mesquita Filho, Inst Geociencias & Ciencias Exatas, Rio Claro, SP, Brazil CNPq: 482911/2011-5 FAPESP: 2012/06082-6

Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology. This work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080).

Orientador: Prof. Dr. Sylvio Fausto Gil Filho Tese (doutorado) - Universidade Federal do Paraná, Setor de Ciências da Terra, Programa de Pós-Graduação em Geografia. Defesa : Curitiba, 29/06/2018 Inclui referências: p.189-197 Resumo: O povo Karipuna constitui-se num dos mais significativos para a história de Rondônia, em vários momentos foram afetados pelas frentes pioneiras de conquista e exploração. A ocupação da Amazônia foi fortemente marcada no período compreendido entre as décadas de 1960 e 1980, em razão da estratégia nas Políticas de Integração Nacional e pela migração de colonizadores que acarretou duro golpe nas integridades dos indígenas. No momento atual os projetos de grande porte previstos no Programa de Aceleração do Crescimento (PAC), entre outros grandes empreendimentos, causam novos impactos socioculturais e intensificam as pressões já existentes, refletindo nas suas relações com a sociedade envolvente. Este estudo acompanha a trajetória dos contatos dos Karipuna, avaliando o dilema da depopulação e seus processos de territorialização através dos seus etnotextos, é o resultado da junção de dados coletados em diferentes momentos a partir do ano de 2001, com expedições a campo, pesquisa participante e análise dos etnotextos - provenientes das memórias coletivas. Coletaram-se informações relevantes à cerca da situação real dos Karipuna, sendo possível constatar que a etnia compreende que o papel do Estado está em assegurar seus direitos, entretanto, estas mesmas instituições mostram-se incapazes de fazer verdadeira oposição ao assédio da sociedade envolvente sobre seu território, modificaram suas representações, produziram transversalidades culturais e novas territorialidades. Palavras-chave: Karipuna. Rondônia. Territorialidade. Hibridação. Etnotexto. Abstract: The Karipuna people constitute one of the most significant for the history of Rondônia, in several moments they were affected for the pioneering fronts of conquest and exploration. The occupation of the Amazonian was marked strongly in the period understood among the decades of 1960 and 1980, in reason of the Politics of National Integration and the migration of colonizers that caused a severe blow to the integrity of the indigenous. At present, the large projects foreseen in the Growth Acceleration Program (PAC), and other large enterprises, bring new sociocultural impacts and intensify existing pressures, reflecting on its relations with the surrounding society. This study follows the trajectory of the Karipuna contacts, evaluating the depopulation dilemma and its territorialization processes through their ethnotexts, is the result of the gathering of data collected at different times from the year 2001, with expeditions to the field, participant research and analysis of ethnotexts - from the collective memories. Relevant information was gathered about the actual situation of the Karipuna, being possible to verify that the ethnicity understands that the role of the State is in securing its rights, however, these same institutions show themselves unable to make real opposition to the harassment of the surrounding society on their territory, modified their representations, produced cultural transversality and new territorialities. Keywords: Karipuna. Rondônia. Territoriality. Hybridization. Ethnotext.

Designated verifier signature schemes allow a signer to convince only the designated verifier that a signed message is authentic. A designated verifier signature scheme is a special type of digital signature scheme which provides message authentication without non-repudiation. In such a scheme, signer designated the verifier and designated verifier can verify the validity of signer's signature. In this paper, we propose strong designated verier signature(SDVS) scheme scheme based on discrete logarithm problem and compare to Saeednia et al.'s [10] strong designated verifier signature scheme and further discuss its security requirement.

In a proxy signature scheme, a user delegates his/her signing capability to another user in such a way that the latter can sign messages on behalf of the former. Proxy signature helps the proxy signer to sign messages on behalf of the original signer. It is very useful when the original signer is not available to sign a specific document. In this paper, we propose a secure an identity based proxy signature scheme from bilinear pairings. The proposed scheme satisfy all the security property of proxy signature scheme.

The recombination-activating genes (RAGs) encode for V(D)J recombinases responsible for rearrangements of antigen-receptor genes during T and B cell development, and RAG expression is known to correlate strictly with the process of rearrangement. There have been several studies of RAG1 illustrating biochemical, physiological and immunological properties. Hitherto, there are limited studies on RAG1 focusing molecular phylogenetic analyses, evolutionary traits, and genetic variants in human populations. Hence, there is a need of a comprehensive study on this topic. In the current report, we have shed light into insights of evolutionary traits and genetic variants of human RAG1 gene using 1092 genomes from human populations. Syntenic analyses revealed that two RAG genes are physically linked and conserved on the same locus in head-to-head orientation from sea urchin to human for about 550 MY. Spliceosomal introns have been in invaded in fishes and sea urchin, whereas gene structures of RAG1 gene from tetrapods remained single exon architecture. We compiled 751 genetic variants in human RAG1 gene using 1092 human genomes; where major stockholders of variant classes are 79% single nucleotide polymorphisms (SNPs), 12.2% somatic single nucleotide variants (somatic SNVs) and 6.8% deletion. Out of 267 missense variants, 140 are deleterious mutations. We identified 284 non-coding variants with 94% regulatory in nature.

Our article describes findings from a project exploring sexual agency and desire among young women, focusing on the negotiation of sexuality within relationship contexts. Adopting a social constructionist framework, we used discourse analysis to examine semi-structured, audio-taped interviews with 39 Canadian young women (aged 18–26). Three related interpretive repertoires were identified, namely, (a) Sex as Relationship Hygiene (i.e., beneficial to the health of one’s relationship), (b) Sex as Exercise-esque (i.e., part of a wellness regime), and (c) Sex as Economy Exchange (i.e., a commodifiable practice within the heterosexual marketplace). Desire was not absent from participants’ accounts, however, it was channeled into specific forms of sexual expression and mediated by multiple and competing cultural imperatives. The interpretive repertoires provided spaces for agentic sex within which subjective sexual desire was not the primary motive but rather was subordinate to a rhetoric of self- and relationship improvement as a key register of sexuality. We discuss these findings in the context of postfeminist directives about sexual desirability and proficiency that young women must traverse as they develop ideas about successful female sexuality within heterosexual relationships.

A diverging diamond interchange is a freeway and arterial interchange design that uses crossovers at the ramp intersections to eliminate conflicts between arterial through traffic and the left turning traffic, from both the arterial and the ramps. The traffic switches which side of the roadway it is travelling, from right to left, at the crossovers. This allows unopposed left turns from the arterial to the ramps. This project will conduct an analysis on a high traffic growth interchange in Alabama by examining the location and adjusting the traffic volumes through a simulation.

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Nous avons realise une etude qualitative qui avait pour objectif d'apprehender les representations que les patients associent a l'experience de leur maladie et a l'education therapeutique (ETP) en les mettant en lien avec leurs caracteristiques socioeconomiques (niveau d'etude, activite professionnelle, revenu) et leur participation a un programme d'ETP. Vingt-trois entretiens semi-directifs ont ete realises aupres de patients atteints de diabete de type 2 issus de divers milieux socioeconomiques. La moitie des patients a participe a un programme d'ETP. Les entretiens ont ete traites a l'aide du logiciel d'analyse textuelle Alceste© . Les resultats montrent que les caracteristiques socioeconomiques sont associees de maniere significative aux discours portes sur la maladie et l'ETP. En revanche, la variable « participation a un programme » n'est associee a aucune des classes. La maniere dont les patients pensent la maladie et l'ETP est etroitement liee au contexte social dans lequel ils sont inscrits. La participation a l'ETP se doit d'etre frequente et inscrite dans la duree pour attenuer les effets de l'inscription sociale des patients.

Molecular networks governing responses to targeted therapies in cancer cells are complex dynamic systems that demonstrate nonintuitive behaviors. We applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell-cycle arrest caused by inhibition of MEK1/2. Through simulation of a reverse-engineered Bayesian network model, we generated predictions of G1–S transition. The model identified known components of the cell-cycle machinery, such as CCND1, CCNE2, and CDC25A, as well as revealed novel regulators of G1–S transition, IER2, TRIB1, TRIM27. Experimental validation of model predictions confirmed 10 of 12 predicted genes to have a role in G1–S progression. Further analysis showed that TRIB1 regulated the cyclin D1 promoter via NFκB and AP-1 sites and sensitized cells to TRAIL-induced apoptosis. In clinical specimens of breast cancer, TRIB1 levels correlated with expression of NFκB and its target genes (IL8, CSF2), and TRIB1 copy number and expression were predictive of clinical outcome. Together, our results establish a critical role of TRIB1 in cell cycle and survival that is mediated via the modulation of NFκB signaling. Cancer Res; 77(7); 1575–85. ©2017 AACR.

Utilization of negative checkpoint regulators (NCRs) for cancer immunotherapy has garnered significant interest with the completion of clinical trials demonstrating efficacy. While the results of monotherapy treatments are compelling, there is increasing emphasis on combination treatments in an effort to increase response rates to treatment. One of the most recently discovered NCRs is VISTA (V-domain Ig-containing Suppressor of T cell Activation). In this review, we describe the functions of this molecule in the context of cancer immunotherapy as a target for the management of inflammatory diseases. We also discuss factors that may influence the use of anti-VISTA antibody in combination therapy and how genomic analysis may assist in providing indications for treatment.

Conjugated linoleic acids (CLAs) have been found to have beneficial effects on human health when used as dietary supplements. However, their availability is limited because pure, chemistry-based production is expensive, and biology-based fermentation methods can only create small quantities. In an effort to enhance microbial production of CLAs, four genetically modified strains of the oleaginous yeast Yarrowia lipolytica were generated. These mutants presented various genetic modifications, including the elimination of beta-oxidation (pox1-6a dagger), the inability to store lipids as triglycerides (dga1a dagger dga2a dagger are1a dagger lro1a dagger), and the overexpression of the Y. lipolytica a dagger 12-desaturase gene (YlFAD2) under the control of the constitutive pTEF promoter. All strains received two copies of the pTEF-oPAI or pPOX-oPAI expression cassettes; PAI encodes linoleic acid isomerase in Propionibacterium acnes. The strains were cultured in neosynthesis or bioconversion medium in flasks or a bioreactor. The strain combining the three modifications mentioned above showed the best results: when it was grown in neosynthesis medium in a flask, CLAs represented 6.5% of total fatty acids and in bioconversion medium in a bioreactor, and CLA content reached 302 mg/L. In a previous study, a CLA degradation rate of 117 mg/L/h was observed in bioconversion medium. Here, by eliminating beta-oxidation, we achieved a much lower rate of 1.8 mg/L/h.

HSP47/SERPINH1 is key-regulator for collagen biosynthesis and its structural assembly. To date, there is no comprehensive study on the phylogenetic history of HSP47. Herein we illustrate the evolutionary history of HSP47/SERPINH1 along with sequence, structural and syntenic traits for HSP47/SERPINH1. We have identified ancestral HSP47/SERPINH1 locus in Japanese lamprey (Lethenteron japonicum). This gene remains on the same or similar locus for ~500 million years (MY), but chromosomal duplication was observed in ray-finned fishes, leading into three sets of three sets (I-III) of HSP47/SERPINH1. Two novel introns were inserted at the positions 36b and 102b in the first exon of only HSP47_1 gene from the selected ray-finned fishes. On the evolutionary time scale, the events of HSP47 duplications took placed between 416–360 MY ago (MYA) while intron insertion dates back to 231–190 MYA after early divergence of ray-finned fishes.

O artigo propõe discutir os tipos de mudança da percepção que o povo indígena Paiter Suruí obteve a partir do processo de desenvolvimento econômico nos estados de Rondônia e Mato Grosso (ambos na Amazônia Legal brasileira) a partir de sua experiência vivida e do estabelecimento de relações com o mundo não indígena no uso do valor econômico de seu território, isto é, utilizando-se de técnicas de diálogos entre dois conhecimentos, o próprio e o científico. O desenvolvimento da Amazônia contribuiu de forma significativa para a mudança na estabilidade econômica da etnia, seja com a influência sobre a comercialização da madeira, do extrativismo mineral e vegetal, do agronegócio e da introdução de novos valores culturais, sociais e políticos. Parte-se daqui que é quase impossível o retorno de certas práticas verificadas nos modos de vida indígenas antes do contato, no entanto, é necessário dialogar com esse encontro. Desse modo, pretende-se debater os desdobramentos que as atividades socioeconômicas trouxeram para esses povos, bem como de iniciativas e perspectivas relacionadas a projetos que se relacionam ao exercício das práticas e do etnoconhecimento como ferramentas indispensáveis ao processo de permanência cultural e de sobrevivência física e territorial – a educação para os Paiter Suruí é um dos pilares estratégicos que possibilitará a aquisição de novos conhecimentos, a ampliação de seus direitos e a conquista plena da cidadania. The article proposes to discuss the changes of perception that the indigenous people Paiter Suruí obtained from the process of economic development in the States of Rondônia and Mato Grosso (both in the Brazilian Legal Amazon) from their experience and the establishment of relations with the non-indigenous world in the use of the economic value of their territory; that is, using dialogue techniques between two knowledges: the scientific one and their own. The development of the Amazon has contributed significantly to the change in economic stability of ethnicity, with influence over the marketing of wood, vegetables, and mineral extraction of agribusiness and the introduction of new cultural, social and political values. Given this, the return of certain practices observed in the indigenous ways of life before the contact is almost impossible; however, due to this encounter, it is necessary to create a dialogue. In thus, we intend to discuss the unfolding that socio-economic activities have brought to these peoples, as well as initiatives and perspectives related to projects that refer to the exercise of practices and of ethnics knowledge, as essential tools for the process of cultural permanence and physical and territorial survival– education for the Paiter Suruí is one of the strategic pillars that will allow the acquisition of new knowledge, the expansion of their rights and the achievement of full citizenship. El artículo se propone discutir los tipos de cambio de la percepción que el pueblo indígena Paiter Suruí obtuvo a partir del proceso de desarrollo económico en los Estados de Rondonia y Mato Grosso (ambos en la Amazonia Legal brasileña) desde su experiencia y el establecimiento de relaciones con el mundo no-indígena en el uso del valor económico de su territorio, esto es, utilizando técnicas de diálogos entre dos tipos de conocimientos, el científico y el propio. El desarrollo de la Amazonia ha contribuido significativamente al cambio en la estabilidad económica de la etnicidad, con influencia sobre la comercialización de la madera, del extractivismo mineral y vegetal, de la agroindustria y de la introducción de nuevos valores culturales, sociales y políticos. De aquí se desprende que es casi imposible el retorno de ciertas prácticas observadas en las formas indígenas de vida antes del contacto, sin embargo, es necesario construir un diálogo en este proceso de encuentro. De esta manera, tenemos la intención de discutir los despliegues que las actividades socio-económicas han significado para estos pueblos, así como iniciativas y perspectivas relacionadas con proyectos que se vinculan con el ejercicio de las prácticas y del etno-conocimiento como herramientas fundamentales para el proceso de permanencia cultural y de supervivencia física y territorial – educación para los Paiter Suruí es uno de los pilares estratégicos que permitirán la adquisición de nuevos conocimientos, la ampliación de sus derechos y el logro de la plena ciudadanía.

C1 inhibitor (C1IN) is a multi-facet serine protease inhibitor in the plasma cascades, inhibiting several proteases, notably, regulates both complement and contact system activation. Despite huge advancements in the understanding of C1IN based on biochemical properties and its roles in the plasma cascades, the phylogenetic history of C1IN remains uncharacterized. To date, there is no comprehensive study illustrating the phylogenetic history of C1IN. Herein, we explored phylogenetic history of C1IN gene in vertebrates. Fishes have C1IN with two immunoglobulin like domains attached in the N-terminal region. The RCL regions of CIIN from fishes and tetrapod genomes have variations at the positions P2 and P1′. Gene structures of C1IN gene from selected ray-finned fishes varied in the Ig domain region with creation of novel intron splitting exon Im2 into Im2a and Im2b. This intron is limited to ray-finned fishes with genome size reduced below 1 Gb. Hence, we suggest that genome compaction and associated double-strand break repairs are behind this intron gain. This study reveals the evolutionary history of C1IN and confirmed that this gene remains the same locus for ∼450 MY in 52 vertebrates analysed, but it is not found in frogs and lampreys.

Angiotensinogen (AGT) belongs to the serpin superfamily. It acts as the unique substrate of all angiotensin peptides, which generates a spectrum of angiotensin peptides in the renin-angiotensin system and regulates hypertension. This serpin belongs to the multiple member group V2 of the intron encoded vertebrate serpin classification. Despite huge advancements in the understanding of angiotensinogen based on biochemical properties and its roles in the RAS, phylogenetic history of AGT remains forgotten. To date, there is no comprehensive study illustrating the phylogenetic history of AGT. Herein, we investigated phylogenetic traits of AGT gene across vertebrates. Gene structures of AGT gene from selected ray-finned fishes varied in exon I and II with insertions of two novel introns in the core domain for ray-finned fishes at the position 77c and 233c. We that found AGT loci is conserved from lampreys to human and estimated to be older than 500 MY. By comparing AGT protein in 57 vertebrate genomes, we illustrated that the reactive center loop (RCL) of AGT protein became from inhibitory (in lampreys, GTEAKAETVVGIMPI†SMPPT) to non-inhibitory (in human, EREPTESTQQLNKPE†VLEVT) during period of 500 MY. We identified 690 AGT variants by analysis of 1092 human genomes with top three variation classes belongs to SNPs (89.7%), somatic SNVs (5.2%) and deletion (2.9%). There are 32 key residues out of 121 missense variants, which are deleterious for AGT protein, computed by combination of SIFT and PolyPhen V2 methods. These results may have clinical implications for understanding hypertension.

Background:V-domain Ig suppressor of T cell activation (VISTA) is an immune checkpoint receptor with an established role as an inhibitory receptor on T cells. However, its role in myeloid cell biology remains unclear. Owing to the much higher expression of VISTA on monocytes and macrophages, we investigated its role in regulating myeloid biology. Methods: Mouse bone marrow-derived macrophages (BMDMs) were differentiated and treated with agonistic anti-VISTA mAb under steady-state and conditions of M1 inflammatory polarization (LPS + IFN-𝛾). Human CD14+ monocytes were isolated from peripheral blood and treated with anti-VISTA in vitro. Phosphoarrays were used to assess signaling downstream of VISTA engagement and Luminex analysis was used to evaluate cytokine production. Time-course total RNA-seq was performed on BMDMs (at 1, 2, 4, 8 and 16 hours of anti-VISTA treatment). To evaluate the effect of anti-VISTA in vivo, single-cell RNA-seq (scRNA-seq) was performed on FACS sorted CD11b+ myeloid populations 12 hours after mice were treated with intravenous anti-VISTA. Results: Anti-VISTA treatment of BMDMs and human monocytes in vitro induced rapid phosphorylation events including robust phosphorylation of Raf-1 kinase at the suppressive serine residue 43.Next, we generated a comprehensive timestamp of VISTA activation in BMDMs in vitro by time-course deep RNA-seq analysis of agonistic anti-VISTA treated cells under rigorous M1 inflammatory polarization. This revealed a unique activation state marked by the upregulation of inhibitory cytokines IL-10 and IL1RA as well as ablation of IL-12 family cytokines, suggestive of an M2-like signature. The presence of an M2-like immunoregulatory signature defined by upregulation of the IL-10 was also seen in macrophages identified post clustering of in vivo scRNA-seq data on myeloid cells. Conclusion: Using novel agonistic anti-VISTA antibodies, we reveal that VISTA triggering on myeloid cells can induce an alternative anti-inflammatory cell-state, even under conditions of strong inflammatory polarization. This introduces VISTA as an intrinsic checkpoint of macrophage tolerance. Disclosures Noelle: Immunext: Employment, Equity Ownership, Patents & Royalties, Research Funding.

Antithrombin III (ATIII) performs a critical anticoagulant function by precluding the activation of blood clotting proteinases, aided by its two cofactors, heparin and heparan sulfate. Though several studies have been carried out on physiological, biochemical and structural perspectives on ATIII, so far there are lim- ited studies on the molecular evolution of ATIII. Herein, we carried out molecular phylogenetic analyses of ATIII genes, combining gene structures, synteny and sequence-structural features for ATIII spanning 50 vertebrate genomes. ATIII is maintained over 450 MY on same genomic loci in vertebrates with few changes in ray-finned fishes and lost one intron 262c in tetrapods and coelacanth. In ray-finned fishes, ATIII gene has additional intron at the position 262c, which shared by group V1 members, corroborating that it is lost in other vertebrates and also in lobed-finned fish coelacanth (Latimeria chalumnae). We found that heparin binding basic residues, hD helix, three pairs of Cys-Cys salt bridges, N-glycosylation sites, serpin motifs and inhibitory reactive center loop (RCL) of ATIII protein are highly conserved. Using 1092 human genomes available from 1000G project, we also compiled 1997 ATIII variants, which reveals 76.2% single nucleotide polymorphisms (SNPs), 11.8% deletions and 8.1% insertions as three major classes of gene variations. These understandings may have medical importance as well.

Background: Cardiac transplantation is an excellent treatment for end-stage heart disease. However, rejection of the donor graft, in particular, by chronic rejection leading to cardiac allograft vasculopathy, remains a major cause of graft loss. The lymphatic system plays a crucial role in the alloimmune response, facilitating trafficking of antigen-presenting cells to draining lymph nodes. The encounter of antigen-presenting cells with T lymphocytes in secondary lymphoid organs is essential for the initiation of alloimmunity. Donor lymphatic vessels are not anastomosed to that of the recipient during transplantation. The pathophysiology of lymphatic disruption is unknown, and whether this disruption enhances or hinders the alloimmune responses is unclear. Although histological analysis of lymphatic vessels in donor grafts can yield information on the structure of the lymphatics, the function following cardiac transplantation is poorly understood. Methods: Using single-photon emission computed tomography/computed tomography lymphoscintigraphy, we quantified the lymphatic flow index following heterotrophic cardiac transplantation in a murine model of chronic rejection. Results: Ten weeks following transplantation of a minor antigen (HY) sex-mismatched heart graft, the lymphatic flow index was significantly increased in comparison with sex-matched controls. Furthermore, the enhanced lymphatic flow index correlated with an increase in donor cells in the mediastinal draining lymph nodes; increased lymphatic vessel area; and graft infiltration of CD4 + , CD8 + T cells, and CD68 + macrophages. Conclusions: Chronic rejection results in increased lymphatic flow from the donor graft to draining lymph nodes, which may be a factor in promoting cellular trafficking, alloimmunity, and cardiac allograft vasculopathy.

Plants-microorganisms interactions play a fundamental role in terrestrial ecosystems and various methods have been reported for plant-associated bacteria extraction. However, these methods exhibit notable variations and lack of some procedural details that may impact the interpretations of results. We propose here a standardized and detailed protocol for the independent extraction of bulk, rhizosphere and rhizoplan soil fractions. This protocol was applied to the sampling of different polluted soil fractions collected in the vicinity of Arabidopsis halleri dense root system. It allowed us to determine the cultivable bacterial densities in each fraction and to confirm the existence of a bacterial gradient linked to roots distance, with a higher amount of bacteria in the rhizospheric area. We suggest to use this unified procedure as a common basis for soil sampling and bacterial communities analysis from other roots systems.

A large number of spliceosomal proteins are required for proper RNA splicing. While spliceosomal proteins from several model organisms have been analysed, only limited studies are available for fungal species. Hence, we have performed a comparative genomic analysis using eight fungal species belonging to three taxa (Ascomycetes, Basidiomycetes and Glomeromycota). We identified variable number of spliceosomal proteins in fungal species. From the small nuclear ribonucleoproteins (snRNPs), all the snRNPs were identified. In non-snRNPs, only some sub-groups were found extensively conserved in all fungal species, including PRP19 complex proteins, catalytic step II and late-acting proteins. In heterogeneous nuclear ribonucleoproteins (hnRNPs), variable number of proteins was identified. The number of spliceosomal proteins identified in filamentous fungi was higher than that in yeast. The collection of these spliceosomal proteins provides further insight into pre-mRNA splicing in fungi.

The development of optimal in situ bioremediation strategies requires a better knowledge of their impact on the soil microbial communities. We have evaluated the impact of hexadecane contamination and different nutrient amendments on soil microbial density and activity. Microbial density was measured via total DNA quantification, and microbial activity via respiration and RNA variation. The RNA/DNA ratio was also determined, as it is a potential indicator of microbial activity. PCR-amplified 16S rRNA genes were cloned and sequenced to analyze the diversity of bacterial communities. Nutrient addition significantly increased respiration and DNA and RNA concentrations in contaminated soil, indicating a limitation of degradation and growth by the availability of nitrogen and phosphorus in unamended microcosms. Hexadecane treatment slightly affected the diversity of the bacterial community, while it was dramatically reduced by nutrient treatments, particularly the addition of nitrogen and phosphorus. Microbial community composition was also altered with the enrichment of populations related to Nocardia in bioremediated soils, while uncultured Proteobacteria were mostly detected in uncontaminated soil.