Dissertations / Theses on the topic 'Genotype II'

Glycogen storage disease type II (GSDII) is an autosomal recessive lysosomal storage disorder caused by acid alpha-1,4-glucosidase (GAA) deficiency. This study aimed to provide an in-depth description of a late-onset GSDII (LO-GSDII) cohort (n=36) and assess potential genotype-phenotype correlation. We performed a clinical record-based study, some patients (n= 19) were also followed prospectively. Phenotypes were highly variable. We focused our clinical assessment onrespiratory failure, as it is the most frequent cause of death in LO-GSDII. In addition to standard spirometric measures, in a subgroup of patients (n = 10) we utilized a new tool, optoelectronic plethysmography (OEP), to investigate the pathophysiology of respiratory muscle impairment.The GAA gene was sequenced in every patient, and pathogenic mutations were identified inall of them. Almost all (35/36) patients carried the same mutation on one allele, IVS1-32-13T>G, which was in compound heterozygosity with a variety of other GAA mutations. To investigate genotype-phenotype correlation, we divided the patient cohort in two groups, according to the severity of the mutation on the second allele. The respiratory function study focused on diaphragmatic weakness. According to the change in forced vital capacity in supine position (ΔFVC), we defined patients with ΔFVC>25% ashaving diaphragmatic weakness (DW) and those with ΔFVC<25% as without diaphragmatic weakness (noDW). We measured pulmonary function and chest wall volumes using OEP inboth groups. We found a good correlation between the supine abdominal contribution to tidal volume (%VAB) and ΔFVC. Patients showed reduced chest wall and abdominal inspiratory capacity and low abdominal expiratory reserve volume. In terms of genotype-phenotype correlation, we counted more subjects in the group with severe second mutations (n=21) who had severe motor disability and respiratory dysfunction. However, this finding remains preliminary because differences were not significant, likely because of small sample size. Finally, in two smaller substudies, we investigated the occurrence of urinary and fecal incontinence in LO-GSDII, and reported a possibly non-fortuitous association of LO-GSDII and hydromyelia in two individuals. Overall, this work 1) provided new insight into genotype-phenotype correlation in GSDII, suggesting that it is of complex nature; 2) refined the analysis of respiratory muscle impairment and showed the utility of OEP for respiratory assessment in this neuromuscular disorder, and possibly in others as well; 3) indicated some so far little studied phenotypic features of LO-GSD-II that deserve further investigation.
Doctorat en Sciences médicales (Médecine)
info:eu-repo/semantics/nonPublished

Background: Multiple lines of evidence implicate the insulin-like growth factor(IGF) group of proteins in human type 2 diabetes. The actions of IGF-I and IGF-IIare modulated through their interaction with IGF binding proteins. A holisticapproach to study the IGF system is preferable to analyses of individual proteininteractions as the inter-relationships between these proteins are complex. Inparticular, the associations of IGF-II and its associated binding proteins withcardiovascular risk have been inadequately studied. This study aimed to study indetail the genotype and phenotype interactions of the IGF system with longitudinalcardiovascular risk factor trends and phenotypic outcomes in type 2 diabetes.Methods: 1000 subjects of predominantly Caucasian origin from the SalfordDiabetes Cohort were studied. Measurements of IGF proteins (IGF-I, IGF-II,IGFBP-1, IGFBP-2 and IGFBP-3) were performed in 554 of these patients. 991Caucasian subjects were successfully genotyped for 76 single nucleotidepolymorphisms (SNPs) related to ten genes in the IGF system. In this project weanalysed associations of the studied SNPs with the measured IGF proteins as well aslongitudinal risk factor trends. In addition, the baseline concentrations of themeasured proteins were studied for associations with cardiovascular risk factortrends and vascular outcomes.Results: This project demonstrates for the first time that high serum IGF-IIconcentration at baseline predicts longitudinal increases in high-density lipoproteincholesterol. High baseline IGF-II was also observed to predict longitudinal weightloss. High baseline concentration of IGFBP-2 (which has a preferential associationof IGF-II over IGF-I) was associated with a number of favourable longitudinalcardiovascular risk trends like increased HDL cholesterol and decreased diastolicblood pressure. However high IGFBP-2 was also associated with deterioration inrenal function and increased all-cause and cardiovascular mortality. The IGF2 geneand the genes encoding IGFBP-2 and IGFBP-5 (proteins with IGF-II bindingaffinity) were also associated with longitudinal trends in renal function, bloodpressure and cholesterol concentration.Discussion: This study is the most detailed exploration to date of the genotype andphenotype interactions of the IGF system in a Caucasian population with type 2diabetes. Results from this study strongly hint that changes in IGF-II bioavailabilitymay influence inter-individual variations in cardiovascular risk. The precisebiological role of IGF-II merits clarification in future expression studies in renal,adipose and vascular tissues. Replication of significant results in an independentdiabetes cohort and measurement of other IGF binding proteins will be performed inthe next stage of this study.

Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused by the common deletion of 26-28 contiguous genes in the 7q11.23 region, which poses difficulties to the establishment of genotype-phenotype correlations. The use of mouse models would broader the knowledge of the syndrome, the role of deleted genes, affected pathways and possible treatments. In this thesis project, several mouse models, tissues and cells have been used to define the phenotypes at different levels, the deregulated genes and pathways and to discover modifying elements and novel treatments for the cardiovascular phenotype. In addition, a new binding motif has been described for Gtf2i, a deleted gene encoding a transcription factor with a major role in WB, providing new target genes from deregulated pathways. The obtained results reveal the essential role of mouse models for the study of Williams-Beuren syndrome and provide new treatments options and affected pathways and genes which could be future treatment targets.
La síndrome de Williams-Beuren és una malaltia del neurodesenvolupament causada per una deleció comú d’entre 26 i 28 gens contigus a la regió 7q11.23, dificultant l’establiment de relacions genotip-fenotip. L’ús de models de ratolí pot augmentar el coneixement sobre la malaltia, el paper dels gens delecionats, les vies moleculars afectades i els futurs tractaments. En aquesta tesi s’han usat diversos models de ratolí, les seves cèl·lules i teixits per tal de descriure i definir fenotips, gens i vies moleculars desregulades i per descobrir elements modificadors i nous tractaments. Per últim, s’ha definit un nou motiu d’unió per Gtf2i, uns dels gens delecionats que codifica per un factor de transcripció amb un rol central en la síndrome, proporcionats possible nous gens diana de vies moleculars desregulades. Els resultats obtinguts revelen el paper essencial dels models de ratolí per a l’estudi de la síndrome de Williams-Beuren, proporcionen noves opcions terapèutiques i defineixen nous gens i vies moleculars afectades que podrien suposar noves dianes terapèutiques.

Le polymorphisme hla-classe ii, sa definition au niveau genomique et son importance fonctionnelle constituent les objectifs de ce travail. L'etude du polymorphisme de taille des fragments de restriction (rflp) a montre que la technologie rflp permettait de caracteriser la majorite des alleles hla-dr, dq et dp. Une autre methode de biologie moleculaire (pcr-rflp) plus rapide, plus precise et non radioactive est presentee dans ce travail. Elle est basee sur la caracterisation des fragments de restriction apres amplification de l'exon le plus polymorphe des genes. Cette technique a permis une etude de la molecule hla-dp dans la population caucasoide c'est-a-dire frequence des differents alleles, association des genes dpa et dpb. Notre travail a montre que les rflp, bien qu'etant un typage au niveau genomique, permettent de predire dans la majorite (95,23%) des cas les resultats des reactions lymphocytaires mixtes. Elle a egalement montre la capacite de la molecule hla-dp de provoquer une proliferation au cours d'une mlr primaire. Neanmoins, certaines incompatibilites hla-classe ii ne provoquent pas de proliferation en mlr malgre les differences dans leur sequence primaire. Cela suggere que le polymorphisme dans certains cas est non-fonctionnel dans les reactions allogeniques in vitro. L'evaluation de la compatibilite hla-classe ii dans les greffes de moelle entre germains hla-identiques montre que en face de l'identite genetique hla-dr, dq l'incompatibilite hla-dp entre donneur et receveur ne semble pas jouer un role important sur l'evolution de ce type de greffe. Par contre cette molecule semble importante dans les greffes de moelle non-apparentees, bien qu'une correlation significative entre la maladie du greffon contre l'hote et les incompatibilites hla-dp n'ai pas pu etre mise en evidence du fait du nombre trop faible de cas etudies. Quoi qu'il en soit, les techniques developpees dans ce travail ont apporte beaucoup aux greffes de moelle entre sujets non-apparentes en permettant le choix du donneur le plus identique au receveur

Le modèle étudié est l'agent phytopathogène vasculaire Ralstonia solanacearum, en portant une attention particulière aux souches de phylotype II. Cette bactérie d'origine tellurique est très diversifiée, tant au plan génétique que phénotypique. Sa classification en constante évolution témoigne d'une volonté de clarifier cette biodiversité inhabituellement forte, tout en cherchant à reconnaître les écotypes structurant ce complexe d'espèces, i.e., des groupes de souches partageant à la fois des traits génotypiques et biologiques spécifiques. Dans le cadre de ce pathosystème modèle, nous nous sommes attachés dans un premier temps à revisiter de façon précise les pathotypes au sein d'écotypes bien décrits dans la littérature, ou à en faire la description (phylotype III africain). Nous avons observé une forte convergence phénotypique entre les souches de phylotype III des hauts plateaux africains et les souches Brown rot de phylotype IIB-1, capables de flétrir la pomme de terre et d'autres Solanacées à température froide. L'adaptation de souches aussi diverses pour la tolérance au froid nous a conduits à dresser un bilan de la situation R. solanacearum en Europe et in extenso dans le bassin méditerranéen. Cette approche a permis d'apprécier les degrés de divergence significative dans le pouvoir pathogène (virulence et agressivité) sur Solanaceae au sein de souches quasi clonales unifiant l'écotype Brown rot, qui s'établissent aussi sous forme d'infections latentes dans les tissus vasculaires de bananiers (Musacées). Dans le même temps, le phénotype de souches pathogènes du bananier, unifiant l'écotype Moko, a aussi été revisité sur Solanaceae qu'elles parviennent à flétrir, y compris des ressources génétiques résistantes au flétrissement bactérien. L'ensemble de ces données expérimentales a permis de dégager les critères de sélection pour le choix de trois nouvelles souches du complexe d'espèces R. solanacearum, dont nous avons obtenu les séquences génomiques. Notre approche en génomique comparative a permis de décrire le premier pangénome chez cet agent pathogène : l'ensemble les gènes repérés de l'espèce. Ces données ont été exploitées par différentes approches bio-informatiques et permettent de concevoir une refonte pertinente du complexe d'espèces R. solanacearum en trois nouvelles espèces génomiques, regroupant les souches de phylotypes I (Asie) et III (Afrique) d'une part, puis les souches de phylotype II (Amérique), et enfin les souches de phylotype IV (Indonésie) d'autre part. Ce pangénome a ensuite été exploité en concevant et développant une puce à ADN, un outil permettant l'exploration à haut débit d'une grande quantité de souches. La densité des données expérimentales accumulées permet une démarche vers l'écologie moléculaire et de reconstituer certains pans du passé évolutif des souches de phylotype II chez R. solanacearum. Par ailleurs, l'analyse approfondie de ces données de génomique, associant phylogéographie et structuration des populations de l'écotype Brown rot, montre une double situation épidémiologique en Europe, recoupant des influences andines et africaines. De la même façon, l'écotype Moko présente trois structures génétiques distinctes. Ces données ont été analysées de manière à retracer les principaux flux de gènes dans les états ancestraux des phylotypes et de dégager la forte contribution de la partie mobile du génome, des gènes relatifs à l'adaptation environnementale et à la pathogénie, comme moteurs dans l'évolution de cet important organisme phytopathogène.

A doença de Pompe (GSDII), autossômica recessiva, é causada pela deficiência da enzima lisossomal que degrada o glicogênio, -glucosidase ácida (GAA). O quadro clínico varia de acordo com a idade de início da doença, grau de progressão e envolvimento dos tecidos: predominantemente cardíaco e muscular esquelético na forma de início-precoce (FIP) e mais restrito no músculo esquelético na forma de início-tardio (FIT). A sobrevida média na FIP é de 9-12 meses. Com avanço dos métodos histológicos, histoquímicos e imunoistoquímicos intensificou-se a análise estrutural e funcional dos tipos de fibras musculares. O estudo da vascularização também é de importância pelo aporte nutricional e funcional das fibras. O objetivo do presente trabalho é analisar a correlação da distribuição do tipo de fibras com a forma de apresentação clínica da doença de Pompe, seu genótipo correspondente e a quantidade residual da enzima GAA. Analisou-se 10 biópsias musculares de pacientes FIP e 09 de FIT comparados com o grupo controle, pareados por idade e gênero. Os pacientes foram selecionados segundo dados clínicos e laboratoriais, sendo feito o seqüenciamento de toda parte codificante do gene e Western Blotting (WB) com anticorpo monoclonal 15362-157, cedido pela Genzyme (primário 1:200 e secundário 1:10.000). A confirmação do diagnóstico foi feita através da medida da atividade residual de GAA em papel filtro, da presença de miopatia vacuolar com grânulos PAS e fosfatase ácida positivos em biópsia muscular e pela presença de mutação no gene GAA. A reação de imunoistoquímica foi realizada para fibras tipo I (lenta), tipo II (rápida) e densidade capilar (ulex), utilizando anticorpos monoclonais, respectivamente: antimiosina lenta (1:80), anti-miosina rápida (1:40) da Novocastra e ulex da Vector (1:800). A contagem das fibras foi realizada por 2 observadores em todo fragmento do corte transversal da biópsia com auxílio de um programa semi-automatizado. Observou-se predomínio de fibras tipo II em ambos os gêneros na FIP e predomínio de fibras tipo I em mulheres e tipo II em homens, na FIT. Aumento da densidade capilar, em comparação com os controles, foi notada em ambas as formas IP e IT. Verificou-se em média 90% de fibras vacuoladas nos casos FIP com completa distorção da arquitetura, enquanto na FIT, a porcentagem de fibras vacuoladas foi variável (0-88%). Como alguns genes constitutivos influenciam na distribuição das fibras musculares, como o gene ACE, o polimorfismo deste gene foi analisado quanto aos genótipos I/I, D/D e I/D. Observou-se ausência de concordância entre o genótipo do ACE e a distribuição de fibras em 60% dos casos da FIP e FIT, atribuindo-se o resultado da distribuição do tipo de fibras como parte da patologia da doença de Pompe. A gravidade da doença variou inversamente com a quantidade de enzima residual, sendo compatível com o quadro clínico do paciente. A presença de mutação deletéria em ambos os alelos foi observada em 3/10 casos de IP, sendo que todos os 3 casos apresentaram ausência total de enzima no WB. Há maior envolvimento de fibras tipo II em GSDII, sem depleção da microcirculação muscular. Estudos demonstram que a remoção do depósito de glicogênio ocorre diferencialmente nos tipos de fibra, sendo menos eficiente nas fibras tipo II. O achado do presente estudo poderá ter implicações na resposta à recente terapêutica proposta por reposição enzimática.
The glycogen storage disease type II (GSDII), autosomal recessive disorder, is caused by the deficiency of GAA (acid -glucosidase) a lysossomal enzyme that degrades the glycogen. The clinical findings are in accordance to great variability of age onset, degree of disease progression and extent of tissue involvement: predominantly cardiac and skeletal muscle in the infantile form (I) and more restricted to the skeletal muscle in the late-onset form (LO). The average survival time of the infantile form is 9-12 months. With advances of the histological, histochemical and imunohistochemical methods structural and functional analysis of muscle fiber types were intensified. The study of the capillary density is also important for nutritional and functional aspects. The objective of the present work is to analyze the correlations of the fiber type distribution to clinical presentation, genotype and residual GAA enzymatic activity. We analyzed 10 muscle biopsies of infantile and 09 of late-onset patients and compared to age and gender matched controls. The patients were selected according to clinical and laboratorial data, molecular diagnosis by full gene sequencing, and Western Blotting (WB) with monoclonal antibody 15362-157, courtesy Genzyme Science Group (primary 1:200 and secondary 1:10.000). Diagnostic confirmation was made by GAA enzymatic measurement in DBS, presence of vacuolar myopathy in muscle biopsy, and presence of mutation in GAA gene. The imunohistochemical study was carried out by detection of type I (slow), type II (fast) fibers and capillaries, using monoclonal antibodies, respectively: anti-slow myosin (1:80), anti-fast myosin (1:40) (Novocastra) and ulex (1:800) (Vector). Morphometry was performed by 2 observers using a half-automatized program. Type II fiber predominance was observed in both gender in the infantile form, type I fiber predominance in women and type II predominance in men with LO. Increase of the capillary density, in comparison to controls was noticed in both forms. 90% of vacuolated fibers with complete distortion of fiber architecture were demonstrated in I cases, while in LO, the percentage of vacuolated fibers ranged from 0 to 88%. As some constitutive gene, like ACE, influence muscle fiber distribution, its polymorphisms I/I, D/D and I/D gene were analyzed. Absence of agreement was observed between ACE genotype and fiber type distribution in 60% of I and LO cases, which was attributed as consequence of Pompe disease pathology itself. The disease severity varied inversely to the amount of residual GAA enzymatic activity, being compatible with the patient clinical findings. The presence of deleterious mutation in both alleles was observed in 3/10 infantile cases, and all 3 presented total enzyme absence at WB. A greater fiber type II involvement was observed in GSDII, without decrease in muscle capillary density. Recent studies demonstrated that glycogen deposit removal occurs distinctively in different fiber types, being less efficient in type II fibers. The present findings might have implications in the reply to the recent proposed enzyme replacement therapy.

Oral Biology
M.S.
Alpha-actinins are myofibril anchor proteins, which influence contractile properties of skeletal muscle. ACTN2 is expressed in slow type I and fast type II fibers whereas ACTN3 is expressed only in fast fibers. ACTN3 homozygosity for the 577X stop codon (i.e. changing 577RR to 577XX - the R577X polymorphism) results in the absence of alpha-actinin-3 in about 18% of Europeans, diminished fast contractile ability, enhanced endurance performance, and reduced bone mass or bone mineral density. We have examined ACTN3 expression and genetic variation in masseter muscle of orthognathic surgery patients to determine genotype associations with malocclusion. To determine the associations between genotypes and malocclusions, clinical information, masseter muscle biopsies, and saliva samples were obtained from 60 subjects. Genotyping for ACTN3 SNPs, RT-PCR quantitation of muscle gene message, and muscle morphometric fiber type properties were compared to determine statistical differences between genotype and phenotype. We found muscle mRNA expression level was significantly different for ACTN3 SNP genotypes (p<0.01). The frequency of ACTN3 genotypes was significantly different for sagittal and vertical classifications of malocclusion with the clearest association being elevated 577XX genotype in skeletal Class II malocclusion (p = 0.003). This genotype also resulted in significantly smaller diameter of fast type II fibers in masseter muscle (p=0.002). In conclusion, ACTN3 577XX is overrepresented in skeletal Class II malocclusion, suggesting a biologic influence during bone growth. ACTN3 577XX is underrepresented in deep bite malocclusion, suggesting muscle differences contribute to variations in vertical facial dimensions.
Temple University--Theses

Orientadores: Reginaldo Bruno Gonçalves, Cristiane Duque
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
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Resumo: Candida spp. são leveduras comensais que habitam diferentes sítios da cavidade bucal. Em indivíduos saudáveis, sem alterações imunológicas, esses microrganismos não causam doença. Entretanto, diante de condições imunossupressoras, essas leveduras podem se tornar mais virulentas e expressar patogenicidade. Espécies de Candida apresentam diversos fatores de virulência, incluindo mecanismos de adesão e invasão celular associado à produção de enzimas que auxiliam na degradação tecidual e facilitam sua proliferação na mucosa bucal. Estudos têm demonstrado a presença de Candida sp. em sítios periodontais de pacientes com periodontite crônica, principalmente quando estes são imunologicamente comprometidos. Entretanto, ainda é desconhecido o papel desses microrganismos na patogênese da doença periodontal. Os objetivos do presente trabalho foram: 1) identificar a presença de espécies de Candida e periodontopatógenos por PCR em sítios bucais de pacientes diabéticos ou não com periodontite crônica; 2) isolar cepas de Candida albicans desses pacientes e avaliá-las quanto à atividade das enzimas proteinase, fosfolipase e hemolisina e os graus de hidrofobicidade da superfície celular, sob diferentes condições atmosféricas, além de realizar a análise genotípica desses isolados; 3) avaliar a capacidade de adesão e invasão de cepas de Candida albicans com diferentes graus de hidrofobicidade, em fibroblastos gengivais humanos. As reações de PCR mostraram que os diabéticos tiveram maior prevalência de Candida spp. principalmente C. albicans e C. dubliniensis, e menor freqüência de Tannerella forsythia, quando comparado aos pacientes não diabéticos, para bolsa periodontal e furcas. C. glabrata e C. tropicalis não foram encontradas em sítios periodontais de pacientes não diabéticos. Dos pacientes diabéticos, foram isoladas 128 cepas de C. albicans, das quais 51.6% foram determinadas como genótipo B e 48.4% como genótipo A. As condições ambientais consideradas neste estudo, níveis reduzidos de oxigênio ou anaerobiose, não modificaram o tipo de hemólise realizado pelo microrganismo, sendo que a maioria das cepas foi alfa-hemolítica. Nesses ensaios, 100% das cepas em anaerobiose apresentaram as colônias rugosas, enquanto que em ambiente de oxigênio reduzido, houve variação em relação à morfologia e a maioria delas apresentou colônia lisa. Com relação à atividade de proteinase e fosfolipase, cepas de C. albicans não produziram as enzimas na ausência total de oxigênio. Em ambiente com nível reduzido de oxigênio, a maioria das cepas de C. albicans foram fortemente produtoras de proteinase e a maioria das cepas foi positiva para fosfolipase. A hidrofobicidade foi mais alta na condição de anaerobiose. A partir desses resultados, foram selecionadas 16 cepas com alta ou baixa hidrofobicidade e avaliadas quanto à capacidade de adesão e invasão em fibroblastos gengivais humanos. Foi verificado que ambos os processos foram maiores nas cepas com alta hidrofobicidade. A produção de óxido nítrico foi maior para as cepas mais hidrofóbicas. Os resultados demonstraram que as espécies de Candida podem ser encontradas, em grande proporção, em bolsas periodontais e furcas de pacientes portadores de periodontite crônica, principalmente naqueles acometidos por diabetes mellitus. A maioria das cepas de C. albicans apresentou atividade enzimática, que atuaria diretamente na degradação tecidual. Além disso, a hidrofobicidade das cepas de C. albicans mostrou estar relacionada à maior capacidade de adesão e invasão em fibroblastos. Todos esses fatores de virulência aumentam a patogenicidade da Candida, que poderia colaborar na progressão da doença periodontal, principalmente em pacientes imunodeficientes
Abstract: Candida spp. are commensal yeasts that inhabit different sites of the oral cavity. In healthy subjects, without immunological alterations, these microorganisms do not cause disease. However, in immunosuppressive conditions, these yeasts can become more virulent and express pathogenicity. Candida species have different virulence factors, including mechanisms of cell adhesion and invasion associated with the production of enzymes that facilitate tissue degradation and their proliferation in oral mucosa. Studies have shown the presence of Candida spp. in periodontal sites of patients with chronic periodontitis, especially when they are immunologically compromised. However is still unknown their role in the pathogenesis of periodontal disease. The objectives of this study were: 1) to identify the presence of Candida species and putative periodontopathogens by PCR in periodontal sites of diabetic or non-diabetic patients with chronic periodontitis; 2) to isolate strains of Candida albicans in these patients and evaluate the proteinase, phospholipase and haemolysin activities and degrees of cell surface hydrophobicity under different atmospheric conditions, besides to performe the genotypic analysis of these isolates; 3) to evaluate the ability of adhesion and invasion of Candida albicans strains with different degrees of hydrophobicity, in human gingival fibroblasts. The PCR reactions revealed that diabetics had higher prevalence of Candida spp., mainly C. albicans and C. dubliniensis, and lower T. forsythia frequency, when compared to non-diabetic patients, for both periodontal sites. C. glabrata and C. tropicalis were not found in periodontal pockets and furcation sites of non-diabetic patients. From diabetic patients, it was isolated 128 strains of C. albicans and 51.6% were determined as genotype B and 48.4% as genotype A. The atmospheric conditions, reduced oxygen and anaerobiosis, did not change the type of hemolysis, and the most of strains were alpha-hemolytic. From these assays, 100% of the strains under anaerobiosis showed rough colonies, whereas in an environment with reduced oxyen was no change in relation to morphology and most of them had smooth colony. Considering proteinase and phospholipase activities, C. albicans strains did not produce the enzymes in the total absence of oxygen. In reduced oxygen, the majority of C. albicans strains were strong proteinase producers and most strains were positive for phospholipase. Hydrophobicity was higher in anaerobic condition. From these results, 16 hydrophobic or hydrophilic strains were selected and evaluated their ability of adhesion and invasion in human gingival fibroblasts. Both processes were greater in strains with high hydrophobicity. The production of nitric oxide was higher for hydrophobic strains. The results showed that Candida species can be found in large proportion, in periodontal pockets and furcation of patients with chronic periodontitis, especially diabetics. The most of C. albicans strains showed enzymatic activity, which could act directly on tissue degradation. Moreover, the hydrophobicity of C. albicans seems to be related to higher capacity of adhesion and invasion in fibroblasts. All these virulence factors enhance the pathogenicity of Candida that could collaborate for the progression of periodontal disease
Doutorado
Microbiologia e Imunologia
Doutor em Biologia Buco-Dental

Little is known about the crown system and its association with plant growth and development in spring cereals. This study investigated temperature, seeding depth and genotypic effects on crown development of barley; relationships between crown and seminal root systems; and classification and description of crown systems under deep seeding. Two greenhouse experiments were performed using PVC tubes. Low temperature and deep seeding reduced percentage and rate of emergence but increased crown number, crown depth, and crown weight in most genotypes. Crown number, crown depth and crown weight showed increased associations with seminal root, whole root, and shoot weight at low temperature and deep seeding in most genotypes. Deep plantings showed that crown systems of barley can be classified as unicrown, bicrown and multicrown types with some variants. One line produced plants with no subcrown internode under 12.5 cm planting. Our results suggested that the crown is a potential source of crown roots and tillers.

Porphyromonas gingivalis é um dos principais mircrorganismos associados à periodontite. O objetivo do presente estudo foi testar a hipótese de que a colonização por diferentes genótipos fimA de P.gingivalis resultaria em diferenças na resposta ao tratamento periodontal. Foram analisados 20 pacientes com periodontite crônica, fumantes, portadores de P.gingivalis, divididos em 2 grupos: 1 grupo recebeu tratamento periodontal mecânico (RAR) e o outro recebeu, além da RAR, antibioticoterapia (amoxicilina e metronidazol). O efeito do tratamento foi avaliado com relação a parâmetros clínicos, prevalência e níveis subgengivais de P. gingivalis e dos genótipos fimA II e fimA IV em estudo quantitativo por PCR em tempo real, antes e 180 dias após o tratamento. Os dados sugerem que RAR associado a antibiotioticoterapia sistêmica é mais eficiente na redução dos níveis de P.gingivalis do que apenas RAR. Não foram detectadas diferenças na resposta ao tratamento periodontal quanto à presença dos genótipos fimA II ou fimA IV em relação aos demais genótipos de P.gingivalis.
Porphyromonas gingivalis is one of the main mircrorganisms associate to periodontitis. The present study proposed to test the hypothesis that the colonization by different P.gingivalis genotypes fimA would lead to different results on periodontal treatment. Twenty chronic periodontitis patients, smokers, bearers of P. gingivalis was analyzed and divided in 2 groups: one group received mechanic periodontal treatment (SRP) and the other group received, besides SRP, antibiotic therapy (amoxicillin and metronidazole). The effect of treatment was appraised under clinical parameters, prevalence and subgingival levels of P. gingivalis and genotypes fimA II and fimA IV in quantitative study by Real time PCR, before and after 180 days of the treatment. Data suggest that SRP associated with systemic antibiotic administration is more efficient in reducing P. gingivalis levels than SRP only. No difference on periodontal treatment results was detected about the presence of fimA II or fimA IV genotypes related to other P.gingivalis genotypes.

La degradación de las tierras de zonas áridas y semiáridas es un proceso que ocurre mundialmente y que va en aumento. Ha sido atribuido a eventos climáticos como a actividades antrópicas. Ya que la provincia de Mendoza se encuentra en una zona árida, se plantea llevar a cabo actividades de restauración en áreas degradadas. Para ello, es necesario conocer los atributos de las gramíneas nativas ya que son componentes importantes del estrato herbáceo. Leptochloa crinita es un pasto nativo del monte argentino que se comporta como especie pionera en sitios degradados, protege el suelo contra la erosión, posee una buena calidad forrajera, resistencia a la sequía y al pastoreo, lo que le confiere gran potencial para ser utilizada en restauración. En base a esto, la presente tesis tuvo como objetivo determinar y comparar el efecto del estrés hídrico sobre algunos mecanismos fisiológicos de seis genotipos de Leptochloa crinita, con el fin de identificar y seleccionar genotipos tolerantes para restaurar zonas áridas degradadas. Para ello se determinó el efecto del estrés hídrico en la partición de asimilados hacia la parte aérea y subterránea de las plantas de L. crinita. Por otro lado, se evaluó cómo afecta el estrés hídrico el área foliar, la conductancia estomática y el índice de clorofila en los distintos genotipos de L. crinita. Y, por último, se determinó, mediante fluorescencia de la clorofila, como se afecta el aparato fotosintético con el estrés hídrico en los distintos genotipos de L. crinita. El ensayo fue realizado en la parcela de la cátedra de Fisiología Vegetal. Los genotipos seleccionados fueron sembrados y mantenidos en invernáculo hasta que presentaron 5-6 hojas, luego fueron colocados a la intemperie para un periodo de rusticación y por último fueron llevados a campo. Se utilizó un diseño factorial 6 x 2 en parcelas divididas, con dos parcelas principales (testigo y estrés hídrico) y seis subparcelas (genotipos 1, 3, 5, 9, 18, 22) dentro de cada parcela principal. Los tratamientos fueron testigo y estrés hídrico, para evitar el contacto del agua de lluvia el suelo de la parcela experimental fue cubierto con polietileno negro de 200 micrones de espesor. Una vez por semana se determinó para 3 plantas de cada uno de los genotipos: conductancia estomática, índice de clorofila y eficiencia del fotosistema II. Al mismo tiempo, se realizaron cuatro muestreos cada 30 días aproximadamente, en cada muestreo se cosecharon 3 plantas por cada genotipo para ambas parcelas, y a su vez se colectó la parte aérea y subterránea de cada planta. En estos muestreos también se determinó el área foliar y el coeficiente de partición de materia seca. De acuerdo con los resultados obtenidos, es correcto aceptar la hipótesis de trabajo. Por lo tanto, concluimos que la respuesta al estrés hídrico de Leptochloa crinita es genotipo-dependiente. Esta respuesta se manifiesta mediante la expresión diferencial de algunos mecanismos fisiológicos como la partición de fotoasimilados, modificaciones del área foliar y conductancia estomática, como así también de algunos indicadores de daño oxidativo como el índice de clorofila y la eficiencia del fotosistema II. Los genotipos 1, 3 y 9 se desempeñaron mejor ante condiciones de déficit hídrico por lo que podrían ser utilizados para proyectos de restauración de áreas degradadas. Asimismo, el genotipo 9 demostró ser muy productivo aun en condiciones de estrés hídrico por lo que puede ser utilizado en zonas de baja precipitación como forraje para el ganado
Fil: Panasiti Ros, Juana. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias.

Thesis (Ph. D.)--Ohio State University, 2003.
Title from first page of PDF file. Document formatted into pages; contains xviii, 233 p.: ill. Includes abstract and vita. Advisor: Douglas E. Crews, Dept. of Anthropology. Includes bibliographical references (p. 209-233).

Since it was discovered in 1926 in England and Indonesia, Newcastle Disease Virus (NDV), especially from Genotype VII (GVII), has caused death in chickens that have been vaccinated using the NDV vaccine Genotype II (GII), known as a heterologous vaccine. Vaccines from the GVII strain, also known as homologous vaccines, have prevented NDV outbreaks. Determination of the differences between the two vaccines was done using a transcriptomic method to determine the response of chickens at the genetic level; with serology approach and viral loading counting; and differences between the two strains genetically using whole-genome sequences. Thirty, three-week-old specific-pathogen-free (SPF) chickens were divided into three groups. The first group was a negative control, the second group was vaccinated with GIIvacc, and the third group was vaccinated with GVIIvacc. Treatment groups were immunized with vaccines on day 14 and day 28. Sera were obtained from all groups on day 28 for the serology tests. On day 42, the spleen was collected for transcriptomic. Meanwhile, the whole genome sequence samples were obtained from the NDV outbreak in 2015 in Indonesia, Genotype II strain, and challenge strain to determine vaccine effectiveness Spleen transcriptomic showed that GVIIvacc down-regulates the neuroinflammation pathway but increases the communication activity among neurons as part of the synaptogenesis pathway. Thus, it is speculated that suppressing the neuroinflammation pathway is associated with protecting the nervous system in chickens from excess leukocytes and cytokine activity. Meanwhile, GIIvacc only prevents apoptosis by suppressing PERK/ ATF4/CHOP as part of the unfolded protein response (UPR) pathway. Thus, the use of GVIIvacc should be considered in countries where GVII strain causes NDV outbreaks. The transcriptomic result aligned with serological and challenged virus test that homologous vaccine (GVIIvacc) gave better protection by reducing the viral shedding and had higher protective antibodies than a heterologous vaccine (GIIvacc). In particular, the Hemagglutination Inhibition (HI) test showed that antibody titers were higher when tested with homologous antigen. However, the cleavage site of the Fusion (F) protein from GII and GVII were used as alternative antigens in an ELISA, did not perform well to obtain the relevant antibody titer. After being challenged with GVII, viral shedding from vaccinated chickens with GVIIvacc was significantly reduced compared to chickens vaccinated with GIIvacc. Both chicken groups showed no clinical signs. The whole-genome sequence and phylogenetic tree results showed that GVII is still the dominant NDV strain that causes NDV outbreaks in Indonesia. In addition, ITA strains for testing the vaccine's efficacy belong to GVI. Hence, using GVI as a heterologous strain from the field as a challenge strain for effective vaccine testing should be considered in veterinary laboratories, especially in Indonesia. All the results from my research study suggested that to combat NDV, the vaccine, antigen for antibody titer, and antigen as challenge strain for effectivity vaccine need to be homologous or coming from the NDV genotype, which causes an outbreak in the field.
Thesis (Ph.D.) -- University of Adelaide, School of Animal and Veterinary Sciences, 2021

Two species of Cryptosporidium are routinely found in pigs: Cryptosporidium suis and Cryptosporidium pig genotype II. Identification of Cryptosporidium species and genotypes currently relies on molecular methods such as polymerase chain reaction (PCR) followed by restriction fragment lenght polymorphism (RFLP) or gene sequencing. However their applications are limited in identification of mixed infections. To overcome this problem, novel species specific primers were developed in this study. A total of 457 pig fecal samples were collected and examined using microscopy and molecular tools including PCR-RFLP, species or genus specific nested PCR and sequencing. Of these, 12.8 % were microscopicaly positive for oocysts presence and 36.5 % using molecular methods. While PCR-RFLP with genus specific primers revealed 1 case of C. suis and Cryptosporidium pig genotype II mixed infection only, nested PCR with species specific primers identified 41 cases of mixed infections. Our results showed that C. suis is infectious for all age categories of pigs and Cryptosporidium pig genotype II has been found in animals older than 6 weeks of age. Morphometric analysis proved oocyst size difference between both pig specific Cryptosporidium spp. Histological examination revealed that Cryptosporidium pig genotype II infects epithelia of both small and large intestine.

Yes
Background: Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicinresistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance. Methods: We developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data. Results: The MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda. Conclusion: Overall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT.
Erasmus Mundus Joint Doctorate Fellowship grant 2016- 1346.

Yes
Background: Tuberculosis (TB) is the highest-mortality infectious disease in the world and the main cause of death related to antimicrobial resistance, yet its surveillance is still paper-based. Rifampicin-resistant TB (RR-TB) is an urgent public health crisis. The World Health Organization has, since 2010, endorsed a series of rapid diagnostic tests (RDTs) that enable rapid detection of drug-resistant strains and produce large volumes of data. In parallel, most high-burden countries have adopted connectivity solutions that allow linking of diagnostics, real-time capture, and shared repository of these test results. However, these connected diagnostics and readily available test results are not used to their full capacity, as we have yet to capitalize on fully understanding the relationship between test results and specific rpoB mutations to elucidate its potential application to real-time surveillance. Objective: We aimed to validate and analyze RDT data in detail, and propose the potential use of connected diagnostics and associated test results for real-time evaluation of RR-TB transmission. Methods: We selected 107 RR-TB strains harboring 34 unique rpoB mutations, including 30 within the rifampicin resistance–determining region (RRDR), from the Belgian Coordinated Collections of Microorganisms, Antwerp, Belgium. We subjected these strains to Xpert MTB/RIF, GenoType MTBDRplus v2.0, and Genoscholar NTM + MDRTB II, the results of which were validated against the strains’ available rpoB gene sequences. We determined the reproducibility of the results, analyzed and visualized the probe reactions, and proposed these for potential use in evaluating transmission. Results: The RDT probe reactions detected most RRDR mutations tested, although we found a few critical discrepancies between observed results and manufacturers’ claims. Based on published frequencies of probe reactions and RRDR mutations, we found specific probe reactions with high potential use in transmission studies: Xpert MTB/RIF probes A, Bdelayed, C, and Edelayed; Genotype MTBDRplus v2.0 WT2, WT5, and WT6; and Genoscholar NTM + MDRTB II S1 and S3. Inspection of probe reactions of disputed mutations may potentially resolve discordance between genotypic and phenotypic test results. Conclusions: We propose a novel approach for potential real-time detection of RR-TB transmission through fully using digitally linked TB diagnostics and shared repository of test results. To our knowledge, this is the first pragmatic and scalable work in response to the consensus of world-renowned TB experts in 2016 on the potential of diagnostic connectivity to accelerate efforts to eliminate TB. This is evidenced by the ability of our proposed approach to facilitate comparison of probe reactions between different RDTs used in the same setting. Integrating this proposed approach as a plug-in module to a connectivity platform will increase usefulness of connected TB diagnostics for RR-TB outbreak detection through real-time investigation of suspected RR-TB transmission cases based on epidemiologic linking.
KCN was supported by Erasmus Mundus Joint Doctorate Fellowship grant 2016-1346, and BCdJ, LR, and CJM were supported by European Research Council-INTERRUPTB starting grant 311725.

博士
國立陽明大學
微生物暨免疫學研究所
89
Different hepatitis D virus (HDV) genotypes vary in both nucleotide and the encoded hepatitis delta antigen (HDAg) sequences. The significance of these variations is unclear. Previous HDV studies focusing on the most common genotype I have revealed interesting properties of HDAg. The small form HDAg (HDAg-S) activates HDV replication while the large form (HDAg-L) with a C-terminal 19-amino acid extension plays a key role in the assembly of HDV particle by interacting with the helper hepatitis B virus surface antigen (HBsAg). These genotypic differences of HDAg-L scatter along the entire sequences, but two major regions could be identified. One located at the N-terminal residues 3-40 has a 45-50% amino acid difference and overlaps with the coiled-coil domain critical for the HDAg oligomerization. The second located at the C-terminus (residues 196-214) has an amino acid sequence divergence up to 74%. In this study, we have used several different approaches to examine the differences of HDAg between genotypes I and II. (1) Peptides covering the carboxyl-terminal 19 amino acids of HDAg-L were used as immunogens to generate genotype-specific antibodies. These antibodies were proven to be useful in immunohistochemical differentiation of HDV genotypes in liver biopsies. (2) In a cDNA transfection system, two antigens were co-expressed in HuH-7 cells and followed by specific antibody precipitation. HDAgs of different origins were found to interact with each other without genotypic discrimination. (3) The assembling efficiency of virus particle by HDAg-L (in the presence of HBsAg) varied among isolates and genotypes. The genotype II HDAg-L tended to assemble viral particles less efficiently. (4) A comparative analysis of HDV replication between genotypes I and II revealed that the HDV RNA replications of these two genotypes are similar, but vary in HDAg-L production. An RT-PCR based assay demonstrated that genotype I antigenomic HDV RNA was more efficienctly edited than genotype II. In summary, the specific antibodies produced in the first part are valuable in epidemiological, clinical and molecular study of HDV. The functional differences between genotypes I and II HDV may explain, at least in part, why genotype II HDV infection is less frequently associated with poor clinical outcomes.

碩士
國立陽明大學
微生物暨免疫學研究所
87
Hepatitis delta virus (HDV) is a subviral RNA virus that needs the help of hepatitis B virus to supply the surface protein HBsAg for packaging. HDV expresses two forms of a single protein, the small (HDAg-S) and large (HDAg-L) antigens, which are identical except an additional 19 residues present at the C terminus of the large form. While HDAg-S is required for viral replication, HDAg-L suppresses the replication and is critical for viral packaging. The last C-terminal 4 amino acids, CXXX, of the HDAg-L constitute an isoprenylation motif that is necessary for HDV assembly and interaction between HDAg-L and HBsAg. However, variations of HDV are present and the significance is not known. There are two genotypes of HDV reported in Taiwan. Genotype I has been more frequently associated with poor outcomes of the infection than genotype II. Previous studies with HDV replication and package have been limited to genotype I. We investigated whether pathogenic variations could be reflected from the differences of package and isoprenylation between genotypes. By co-transfection of HDAg-expression vector with that expressing HBsAg, empty HDV-like viral particles could be harvested from the tissue culture supernatants. The amounts of these secreted particles were compared among different HDV isolates. The results showed that genotype I HDAg has a greater or equal package capability than HDAg of genotype II. By immunofluorescence staining using anti-farnesyl antibodies, HDAg-L of genotype I was stained far batter than that of genotype II. We further addressed the critical region or residues that may affect these genotype differences. Swapping of the C-terminus 19-residue of the type I to the type II HDAg-L, no effect on packaging was observed. However, when the 19-residue of the type II was placed on the type I HDAg-L, the assembly capacity of this HDAg-L decreased. Therefore, the type II C-terminus seems to have an unfavorable packaging ability that has to be compensated by the N-terminal context of HDAg. We then examined whether this effect is due to the slight difference in the isoprenylation motif. The last five residues of HDAg-L are SCRPQ and ECTPQ for genotypes I and II, respectively. In genotype I, the R to T substitution to create a SCTPQ mutant did not affect the HDAg-L package capability. However, an additional S to E substitution to create ECTPQ at the C-terminus of HDAg-L adversely affected the viral assembly. On the other hand, the C-terminal ECTPQ of the genotype II was changed to ECRPQ and the package of HDAg-L was deminished. When an additional E was substituted with S to create a SCRPQ terminus, the packaging capacity of mutated genotype II HDAg-L was restored. Isoprenylatuin of these mutants were examined by immunofluorescence staining using anti-farnesyl antibody, no significant difference was observed between the mutant and the parental proteins. Therefore, these results consolidate the notion that the isoprenylation alone is not sufficient for viral assembly and reveal that the C-terminal extension of HDAg-L from different genotypes are not completely compatible. Furthermore, we find out the residues upstream and downstream the isoprenylated cysteine are important for HDV packaging. Intergenotypical changes of these residues may not be completely tolerated for different functions of HDAg-L.

Microsporidia are obligate, unicellular intracellular parasites that have a unique way of entering the host cells. Encephalitozoon cuniculi was the first microsporidia found in mammals. This parasite has a broad host spectrum, infects a variety of host?s cells and is found in most tissues of an infected individual. The course of acute and chronic infections caused by various genotypes of Encephalitozoon cuniculi was investigated by using different strains of mice. The aim of this study was to clarify the origin and extent of neglected latent microsporidiosis in immunocompetent hosts. Furthermore, the role of individual lymphocyte subpopulations (CD4+ and CD8+) in protective immunity against microsporidia was examined using CD4 and CD8 knockout mice experiments, and also the efficacy of treatment with albendazole was studied. The obtained data help to elucidate the potential danger of latent microsporidiosis, which may pose a risk to recipients of organs from infected donors in human medicine. A considerable part of this thesis was the study of transplacental transmission of microsporidia from mother to a fetus, which answered the question about the risks associated with prenatal infections of fetuses in chronically infected mothers.

Le pois chiche (Cicer arietinum L.) a l’avantage de pouvoir assimiler l'azote atmosphérique grâce à son association symbiotique avec des bactéries du genre Mesorhizobium. Malgré cet effet bénéfique sur les systèmes culturaux, le pois chiche réduit parfois la productivité du blé qui la suit. Cet effet négatif du pois chiche pourrait provenir d’une réaction allélopathique à ses exsudats racinaires ou résidus, ou de changements inopportuns dans la communauté microbienne du sol induits par la plante. L'amélioration des interactions symbiotiques du pois chiche pourrait améliorer la performance économique et environnementale des systèmes culturaux basés sur le blé. L’objectif à long terme de ce travail est d'améliorer l’influence du pois chiches sur son environnement biologique et sur la productivité du système cultural. À court terme, nous voulons 1) vérifier l'effet des champignons endophytes sur la performance de cultivars de pois chiche de type desi et kabuli, particulièrement en conditions de stress hydrique, ainsi que sur celle d’une culture subséquente de blé dur, 2) identifier des cultivars de pois chiche capables d’améliorer la qualité biologique de sols cultivés, 3) vérifier que des composés biologiquement actifs sont présents dans les racines des différents cultivars de pois chiches et 4) définir la nature de l’activité (stimulation ou inhibition) des ces composés sur les champignons endomycorhiziens à arbuscules (CMA), qui sont des microorganismes bénéfiques du sol reconnus. L’inoculation du pois chiche avec des champignons endophytes indigènes en serre a augmenté la tolérance à la sécheresse du cultivar de type kabuli à feuille simple CDC Xena et amélioré la nutrition azotée et phosphatée d’un cultivar de type desi, cv. CDC Nika, cultivé en conditions de stress hydrique. La germination des graines de blé dur fut meilleure lorsque celles-ci étaient semées dans les débris de pois chiche inoculé de type kabuli. Le sol dans lequel le génotype de pois chiche à feuille simple CDC Xena fut cultivé mais duquel tout le matériel végétal de pois chiche fut retiré a fortement inhibé la germination des semences de blé dur, ce qui suggère un effet des exsudats racinaires sur la communauté microbienne du sol associée à cette variété de pois chiche. En champ, les cultivars de pois chiche ont influencé différemment la composition des communautés de champignons de la rhizosphère. Les espèces de champignons pathogènes étaient infréquentes et les espèces saprotrophiques et de CMA étaient fréquentes dans la zone des racines du cultivar de type desi CDC Anna. L’effet des composés contenus dans les fractions séparées par HPLC et solubles en solution de méthanol à 25% et 50% de l’extrait racinaire de ce cultivar sur la germination de spores de CMA a été testé in vitro. Les deux espèces de CMA utilisées ont répondu différemment à l’exposition aux composés testés, révélant un mécanisme impliqué dans l’association préférentielle entre les plantes hôtes et les CMA qui leurs sont associés. Nous concluons que le génotype de pois chiche influence la composition de la communauté microbienne qui lui est associée et que cette influence est reliée au moins en partie aux molécules bioactives produites par les racines de la plante. D’autre part, la productivité du pois chiche et de la culture subséquente pourrait être favorisée par la manipulation de leurs champignons endophytes par inoculation.
Chickpea (Cicer arietinum L.) has the ability to bring free N into cropping systems, but is only a fair rotation crop, leading to lower yield in following wheat crops, as compared to medic, vetch or lentil. The negative effects of a chickpea plant on the following wheat crops could come from chickpea root exudates, their residues or their influence on the soil microbial community. The identification of chickpea cultivars best able to promote soil biological quality and the growth of a subsequent crop in rotation will help farmers in selecting better crop rotations and, thus, will improve crop management in soil zone growing chickpea. The global objective of this research is to improve the fitness of chickpea crops to their biological environment and to improve the ability of the plant to enhance soil biological quality. The specific objectives were (1) to verify that the productivity of chickpea and subsequent crops could be promoted through the inoculation by some indigenous endophytic fungi particularly under drought stress conditions (2) to verify the existence of variation in the rhizospheric associations of field-grown chickpea, as it is a necessary condition for the selection of genotypes with improved compatibility with beneficial microorganisms. (3) to identify the biologically active compounds present in the root extracts of chickpea cultivars with contrasting phenotypes, and assess their effect on beneficial and pathogenic soil microorganisms. The greenhouse experiments show that inoculation with indigenous endophytes increased drought tolerance of the unifoliate Kabuli chickpea CDC Xena and the N and P nutrition of the drought stressed Desi chickpea CDC Nika. Inoculation of both Kabuli chickpea varieties with indigenous endophytes improved wheat seeds germination in tissues amended soil. Residue-free soil previously growing the unifoliate Kabuli chickpea CDC Xena strongly inhibited durum seed germination suggesting an effect of root exudates on the soil microbial community, with this Kabuli chickpea variety. In a field experiment, the fungal diversity in cultivated Prairie dryland appeared to host a large array of fungal groups known to reduced plant nutrient, water and biotic stresses, and chickpea genotypes influenced differently the composition and biomass of the soil microbial community. The Desi chickpea CDC Anna was associated with high diversity of arbuscular mycorrhizal fungi (AMF) and culturable fungi, favored the proliferation of soil bacteria and fungal genus hosting biocontrol agents, and developed high AM root colonization level, as compared to the three Kabuli genotypes examined. The HPLC fractions of the roots of chickpea cultivar CDC Anna were recovered and the effects of these fractions on AM fungal spore germination were assayed in multi-well plates. Root extract fractions affect in a different ways the percentage of spores’ germination of Glomus etunicatum and Gigaspora Rosea. We concluded that the genotype of chickpea plants influences the composition of the associated microbial community, and this influence may be related to molecular signals produced by the plants. Furthermore, the productivity of chickpea and subsequent crops could be promoted through the inoculation with indigenous endophytic fungi.
réalisé en cotutelle avec la Faculté des Sciences de Tunis, Université Tunis El Manar.