Le principali anomalie evidenziate nelle nocciole avariate riguardano la presenza di macchie necrotiche, imbrunimenti interni rilevati inseguito al taglio dei frutti e la presenza di marciumi parziali o totali su di essi con conseguente riduzione del prodotto disponibile sul mercato e ingenti perdite economiche. Sulla base di quanto premesso, lo scopo principale di questa tesi è stato quello di identificare e caratterizzare l'agente causale/i dei difetti del nocciolo e di definire un protocollo di gestione del problema, secondo i principi IPM. È stata quantificata l'incidenza dei generi fungini isolati da nocciole provenienti da diverse aree geografiche (Caucaso e Turchia), raccolte in diversi anni e in diverse fasi di crescita della coltura. Diaporthe è stato identificato come il principale genere fungino associato ai difetti della nocciola, e la caratterizzazione molecolare ha confermato il ruolo predominante della specie D. eres. Sono state studiate le caratteristiche ecologiche di questo fungo e l'efficacia in vitro di fungicidi chimici e biologici per controllarne la crescita miceliale, lo sviluppo di picnidi e la formazione di cirri. I risultati ottenuti costituiscono una base per definire linee guida per la corretta gestione della coltura al fine di prevenire la comparsa del patogeno identificato e delle difettosità nelle nocciole / Defects on hazelnuts are responsible for a significant reduction in the availability of high-quality hazelnuts with profound economic impacts. A reduction in the occurrence of defects, based on the identification of causal agents and on their control, is critical to improve the quality of raw nut products and reduce yield losses. Based on this background, the main aim of this thesis was to identify and characterize the causal agent/s of kernel defects in hazelnuts and to define a management protocol, according to IPM principles. Defects affecting hazelnuts are cause of brown spots on the kernel surface and darkening/browning inside the kernel, visible after nuts are half-cut. The incidence of fungal genera in hazelnuts coming from different geographical areas (Caucasus and Turkey), collected in different years at different crop growth stages, was quantified. Diaporthe was identified as the main genus involved in hazelnut defects, and the molecular characterization confirmed the predominant role of D. eres. Its ecological needs were investigated, and the in vitro efficacy of chemical and biological fungicide were screened to control D. eres growth, pycnidial conidiomata development and cirrhi occurrence. This would be an essential tool for a sustainable crop protection approach in this economically important crop

Over the last decade, development and application of a set of molecular genomic approaches based on the chromosome conformation capture method (3C), combined with increasingly powerful imaging approaches have enabled high resolution and genome-wide analysis of the spatial organization of chromosomes. The aim of this thesis is two-fold; 1), to provide guidelines for analyzing and interpreting data obtained from genome-wide 3C methods such as Hi-C and 3C-seq and 2), to leverage the 3C technology to solve genome function, structure, assembly, development and dosage problems across a broad range of organisms and disease models. First, through the introduction of cWorld, a toolkit for manipulating genome structure data, I accelerate the pace at which *C experiments can be performed, analyzed and biological insights inferred. Next I discuss a set of practical guidelines one should consider while planning an experiment to study the structure of the genome, a simple workflow for data processing unique to *C data and a set of considerations one should be aware of while attempting to gain insights from the data. Next, I apply these guidelines and leverage the cWorld toolkit in the context of two dosage compensation systems. The first is a worm condensin mutant which shows a reduction in dosage compensation in the hermaphrodite X chromosomes. The second is an allele-specific study consisting of genome wide Hi-C, RNA-Seq and ATAC-Seq which can measure the state of the active (Xa) and inactive (Xi) X chromosome. Finally I turn to studying specific gene – enhancer looping interactions across a panel of ENCODE cell-lines. These studies, when taken together, further our understanding of how genome structure relates to genome function.

Die Bildung von Amyloidablagerungen ist ein Kennzeichen der Alzheimerschen Erkrankung. Hauptbestandteil dieser senilen Plaques sind sogenannte A beta Peptide, die durch proteolytische Prozessierung aus einem Vorläufermolekül (APP) gebildet werden. Die vorliegende Arbeit beschreibt die Klonierung des Meerschweinchen - APP. Diese cDNA-Sequenz zeigt auf DNA-Ebene eine Homologie zum Human-APP von ca. 90%, auf Proteinebene beträgt die Identität ca. 97 %. Damit wird ein weiterer experimenteller Beweis für die evolutionäre Konservierung des Amyloidvorläuferproteins in Säugetieren erbracht. APP mRNA wird in Meerschweinchen-Geweben ubiquitär exprimiert. Durch alternatives Spleißen wird ein zum Human-APP im wesentlichen ähnliches Isoformenmuster gebildet: Isoformen, welche eine Proteaseinhibitordomäne enthalten, werden dominierend in peripheren Organen exprimiert, dagegen ist im Zentralnervensystem das APP 695 mit über 60 % der Gesamttranskripte die bevorzugt exprimierte Isoform. Die klonierte cDNA des Meerschweinchen-APP wurde in prokaryontischen wie auch eukaryontischen Zellsystemen exprimiert. Dabei wurde die Eignung einer Anzahl von gegen Human-APP gewonnenen Antikörpern zur Detektion des Meerschweinchen-APP und seiner Prozessierungsprodukte gezeigt. Die Expression der neuronal dominierend exprimierten Isoform APP 695 des Meerschweinchen-APP in humanen Neuroblastom-Zellen zeigte keine Unterschiede hinsichtlich der APP-Prozessierung und A beta-Bildung im direkten Vergleich zu Human-APP 695. Die proteolytische Prozessierung des Proteins wurde durch Detektion der typischen Spaltprodukte in vivo (im Liquor) als auch in einem neu etablierten in vitro-Modell primär kultivierter neuronaler Zellen untersucht. Diese Zellkulturen wurden zunächst immunhistochemisch und biochemisch charakterisiert und als "mixed brain"-Typ mit einem hohen neuronalen Anteil beschrieben. Die Prozessierung des endogenen Meerschweinchen-APP in kultivierten Zellen führt dabei zur Bildung und Akkumulation aggregationsfähiger A beta - Peptide. Zur Detektion dieser Peptide wurde ein sensitiver Nachweis durch Western-Blot etabliert. Es wird damit ein Modellsystem für in vitro-Untersuchungen vorgeschlagen, welches ein Studium der Expression und Prozessierung des Amyloidvorläuferproteins unter angenähert physiologischen Bedingungen ermöglicht. / A beta peptides, the major component of neuritic plaques found in the brains of patients with Alzheimer’s disease, are derived by proteolytic processing from a larger precursor molecule (amyloid precursor protein - APP). A combination of PCR methods was used to clone and sequence APP cDNA from guinea pig (Cavia porcellus). Guinea pig APP exhibits extensive similarities to human APP in terms of primary structure, mRNA expression of differentially spliced isoforms as shown by Northern blot and RT-PCR analysis as well as proteolytic processing to amyloidogenic A beta peptides. In contrast to rat and mouse APP, guinea pig APP - recombinantly expressed in human neuroblastoma-cells - was processed indistinguishable from human APP thus excluding intrinsic sequence-specific factors influencing processing. Further studies were performed using newly established primary cell cultures of guinea pig neurons. Refined methods have been used to detect and characterize major proteolytic processing products of APP in vitro and in vivo. In conclusion, guinea pigs provide a model to study expression and processing of APP that closely resembles the physiological situation in humans and should, therefore, be important in elucidating potential strategies to prevent amyloid formation in Alzheimers Disease.

<p>  Fetal Alcohol Syndrome (FAS) is the most serious form of Fetal Alcohol Spectrum Disorders (FASD) and the most prevalent neurodevelopmental disorder in North America. Patients with FAS may exhibit cognitive problems with working memory, manipulating information, and reduced executive functioning. Additionally, previous studies exhibited that stress responses are affected by prenatal alcohol consumption Gut microbiota compositions can also influence stress responses and memory, as several studies have shown strong relationships between the enteric gut system and the brain. However, few studies have examined how prenatal alcohol exposure’s effects on the gut microbiome and neuroinflammatory responses. For this study, pregnant HsdBlu:LE Long Evans rats were treated with either a dry diet, liquid diet, or liquid diet with alcohol. On day 28 and 42 after birth, three male and three female adolescent pups from each treatment group had their gut microbiome (fecal samples) analyzed through 16S rRNA amplicon sequencing. Brain histology staining of the cortex and hippocampus regions was also done to evaluate changes in the CNS through microglial counts and morphology analysis. There were no significant differences in alpha diversity of the fecal microbiome between groups of pups based on prenatal alcohol exposure (PAE), sex, age, the interaction of PAE and sex, or in the morphology of cortex microglia. However, analysis of beta diversity using Bray-Curtis dissimilarity and weighted UniFrac suggested distinct microbial communities between the treatment groups based on PAE and the interaction of PAE, sex, and the interaction between PAE and sex. Microglial count comparisons by PAE or sex were only statistically different in the cortex (p ≤ 0.005). The significance of this study suggests that there are some associations between the gut microbiome and CNS inflammation in rats with PAE. Based on these findings, 11 future studies may implement therapeutics such as antibiotics or probiotics to mitigate cognitive or neural symptoms of FASD affected individuals. </p>

<p dir="ltr">Open-access bioinformatics data enables accessible public health research for a variety of stakeholders, including teachers and low-resourced researchers. This project outlines two case studies utilizing open-access bioinformatics data sets and analysis software as proofs of concept for the types of research projects that can be adapted for workforce development purposes. The first case study is a spatial temporal analysis of Lyme disease rates in the United States from 2008 to 2020 using freely available data from the United States Department of Agriculture and Centers for Disease Control and Prevention to determine how urbanization and other changes in land use have impacted Lyme disease rates over time. The second case study conducts a pangenome analysis using bacteriophage data from the Actinobacteriophage Database to determine conserved gene regions related to host specificity.</p>

No / BMP signaling has a crucial role in skin development and homeostasis, whereas molecular mechanisms underlying its involvement in regulating gene expression programs in keratinocytes and fibroblasts remain largely unknown. We show here that several BMP ligands, all BMP receptors, and BMP-associated Smad1/5/8 are expressed in human primary epidermal keratinocytes and dermal fibroblasts. Treatment of both cell types by BMP-4 resulted in the activation of the BMP-Smad, but not BMP-MAPK pathways. Global microarray analysis revealed that BMP-4 treatment induces distinct and cell type-specific changes in gene expression programs in keratinocytes and fibroblasts, which are far more complex than the effects of BMPs on cell proliferation/differentiation described earlier. Furthermore, our data suggest that the potential modulation of cell adhesion, extracellular matrix remodeling, motility, metabolism, signaling, and transcription by BMP-4 in keratinocytes and fibroblasts is likely to be achieved by the distinct and cell-type-specific sets of molecules. Thus, these data provide an important basis for delineating mechanisms that underlie the distinct effects of the BMP pathway on different cell populations in the skin, and will be helpful in further establishing molecular signaling networks regulating skin homeostasis in health and disease.

Yes / Heterozygous germline mutations of BMPR2 contribute to familial clustering of pulmonary arterial hypertension (PAH). To further explore the genetic basis of PAH in isolated cases, we undertook a candidate gene analysis to identify potentially deleterious variation. Members of the bone morphogenetic protein (BMP) pathway, namely SMAD1, SMAD4, SMAD5, and SMAD9, were screened by direct sequencing for gene defects. Four variants were identified in SMADs 1, 4, and 9 among a cohort of 324 PAH cases, each not detected in a substantial control population. Of three amino acid substitutions identified, two demonstrated reduced signaling activity in vitro. A putative splice site mutation in SMAD4 resulted in moderate transcript loss due to compromised splicing efficiency. These results demonstrate the role of BMPR2 mutation in the pathogenesis of PAH and indicate that variation within the SMAD family represents an infrequent cause of the disease.

No / We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Introdução: A cardiomiopatia hipertrófica (CH) é uma doença genética cardíaca primária, caracterizada por hipertrofia do ventrículo esquerdo, sem dilatação, geralmente assimétrica e predominantemente septal, com prevalência estimada em 1:500. Atualmente já foram descobertos 20 genes associados à doença, mas os genes mais frequentemente relacionados são o da Cadeia Pesada da ?-miosina (MYH7), Proteína C de Ligação da Miosina (MYBPC3) e Troponina T (TNNT2). O diagnóstico molecular dos pacientes é importante e custo-efetivo do ponto de vista de saúde pública, além de recomendado pela Sociedade Europeia de Cardiologia. Entretanto, o custo inicial do exame é muito alto, de forma que estudos tentam reduzir esse custo. Uma das propostas descritas utilizou o RNA extraído de leucócitos para sequenciamento com sucesso para o gene MYBPC3. Este trabalho tem como objetivo testar a metodologia de sequenciamento de RNA em larga escala e testar a aplicabilidade da mesma para os genes MYH7 e TNNT2, estimar as principais mutações envolvidas nos pacientes do estudo e estabelecer correlações entre os diferentes genótipos avaliados e os fenótipos dos grupos familiares portadores da doença. Métodos: Os sujeitos incluídos no estudo são portadores de cardiomiopatia hipertrófica nos quais foi feita uma coleta de sangue para extração de DNA e RNA. Foi utilizada nested PCR para amplificação do cDNA e PCR convencional para amplificação de DNA e posterior sequenciamento em sequenciador automático. As análises estatísticas dos dados clínicos foram realizadas utilizando-se ANOVA para comparação de médias e teste exato de Fisher para comparação de frequências. Resultados: O sequenciamento de RNA se mostrou problemático, com baixa taxa de amplificação, falsos positivos e possíveis falsos negativos, de forma que optou-se por utilizar o sequenciamento de DNA para identificação das alterações. Dos 268 pacientes estudados foi identificada uma mutação em 131 deles (48,8%). Das mutações encontradas, 78 (59,5%) estavam no gene MYH7, 50 (38,2%) no gene MYBPC3 e 3 (2,3%) no gene TNNT2. Foram identificadas 69 mutações diferentes, 24 delas ainda não descritas. Pacientes com mutação identificada possuíam em média idade de diagnóstico e idade atual menores, maior frequência cardíaca média e maior frequência de pacientes com taquicardia ventricular não sustentada quando comparados ao grupo sem mutação identificada. Pacientes com mutação no gene MYH7 possuíam maior tamanho de átrio esquerdo, maior frequência de fibrilação atrial e maior frequência de histórico familiar da doença do que pacientes com mutação em MYBPC3. Conclusões: A técnica sequenciamento de RNA extraído de leucócitos não é adequada para uma rotina de rastreamento em larga escala para CH devido à alta frequência de falsos positivos, possibilidade de falsos negativos e baixa taxa de amplificação, mas o sequenciamento de DNA, embora trabalhoso, se mostrou muito sensível para a análise. A identificação de uma mutação específica ainda não pode ser usada para prognóstico de gravidade da CH, mas as comparações de genótipo e fenótipo mostraram algumas relações interessantes que devem ser melhor avaliadas nos pacientes. Este é o primeiro trabalho a caracterizar a epidemiologia molecular da CH em pacientes brasileiros para os genes MYH7, MYBPC3 e TNNT2 / Introduction: Hypertrophic cardiomyopathy (HC) is a primary genetic cardiac disease characterized by left ventricular hypertrophy without dilation, usually asymmetric and predominantly septal, with an estimated prevalence of 1:500. There are 20 genes associated to the HC, but the ones more often related to the disease are ?-myosin heavy chain (MYH7), myosin binding protein C (MYBPC3) and troponin T (TNNT2). The molecular diagnosis of patients is important and cost-effective from the standpoint of public health, and recommended by the European Society of Cardiology. However, the initial cost of the exam is very high, so several studies are attempting to reduce it. One of the proposals described used the RNA extracted from leukocytes for sequencing successfully to the MYBPC3 gene. The present study aims to test the methodology for large-scale sequencing and test it\'s applicability to the MYH7 and TNNT2 genes, to estimate the main mutations involved in the studied patients and establish correlations between their genotypes and phenotypes. Methods: The subjects included in the study were patients previously diagnosed with hypertrophic cardiomyopathy in whom a blood sample was collected to DNA and RNA extraction. It was used nested PCR for cDNA amplification and conventional PCR for DNA amplification for posterior sequencing on an automatic sequencer. Statistical analyzes of clinical data were performed using ANOVA to compare means and Fisher\'s exact test for frequencies comparison. Results: The RNA sequencing was problematic with low rate of amplification, false positives and possible false negatives, so was used DNA sequencing to identify the mutations. Of the 268 patients studied a mutation was identified in 131 of them (48.8%). Among the mutations found, 78 (59.5%) were in the MYH7 gene, 50 (38.2%) in the MYBPC3 gene and three (2.3%) in the TNNT2 gene. We have identified 69 different mutations, 24 of them not yet described. Patients with an identified mutation had an average smaller age of diagnosis and current age, higher average cardiac frequency and higher frequency of patients with nonsustained ventricular tachycardia compared to those without an identified mutation. Patients with mutations in the MYH7 gene had larger left atrium size, higher frequency of atrial fibrillation and higher frequency of family history of the disease than patients with a mutation in the MYBPC3 gene. Conclusions: The technique of sequencing RNA extracted from leucocytes is not suitable for large scale routine screening for CH due to the high frequency of false positives, possibility of false negatives and low rate of amplification, but the DNA sequencing, though laborious, was very sensitive to the analysis. Identification of a specific mutation cannot yet be used for prognosis of the disease\'s severity, but comparisons of genotype and phenotype have shown some interesting relationships that should be further evaluated. The presente study is the first one to characterize the molecular epidemiology of hypertrophic cardiomyopathy in Brazilian patients for those three more important genes mentioned above

Introdução: A cardiomiopatia hipertrófica (CH) é uma doença genética cardíaca primária, caracterizada por hipertrofia do ventrículo esquerdo, sem dilatação, geralmente assimétrica e predominantemente septal, com prevalência estimada em 1:500. Atualmente já foram descobertos 20 genes associados à doença, mas os genes mais frequentemente relacionados são o da Cadeia Pesada da ?-miosina (MYH7), Proteína C de Ligação da Miosina (MYBPC3) e Troponina T (TNNT2). O diagnóstico molecular dos pacientes é importante e custo-efetivo do ponto de vista de saúde pública, além de recomendado pela Sociedade Europeia de Cardiologia. Entretanto, o custo inicial do exame é muito alto, de forma que estudos tentam reduzir esse custo. Uma das propostas descritas utilizou o RNA extraído de leucócitos para sequenciamento com sucesso para o gene MYBPC3. Este trabalho tem como objetivo testar a metodologia de sequenciamento de RNA em larga escala e testar a aplicabilidade da mesma para os genes MYH7 e TNNT2, estimar as principais mutações envolvidas nos pacientes do estudo e estabelecer correlações entre os diferentes genótipos avaliados e os fenótipos dos grupos familiares portadores da doença. Métodos: Os sujeitos incluídos no estudo são portadores de cardiomiopatia hipertrófica nos quais foi feita uma coleta de sangue para extração de DNA e RNA. Foi utilizada nested PCR para amplificação do cDNA e PCR convencional para amplificação de DNA e posterior sequenciamento em sequenciador automático. As análises estatísticas dos dados clínicos foram realizadas utilizando-se ANOVA para comparação de médias e teste exato de Fisher para comparação de frequências. Resultados: O sequenciamento de RNA se mostrou problemático, com baixa taxa de amplificação, falsos positivos e possíveis falsos negativos, de forma que optou-se por utilizar o sequenciamento de DNA para identificação das alterações. Dos 268 pacientes estudados foi identificada uma mutação em 131 deles (48,8%). Das mutações encontradas, 78 (59,5%) estavam no gene MYH7, 50 (38,2%) no gene MYBPC3 e 3 (2,3%) no gene TNNT2. Foram identificadas 69 mutações diferentes, 24 delas ainda não descritas. Pacientes com mutação identificada possuíam em média idade de diagnóstico e idade atual menores, maior frequência cardíaca média e maior frequência de pacientes com taquicardia ventricular não sustentada quando comparados ao grupo sem mutação identificada. Pacientes com mutação no gene MYH7 possuíam maior tamanho de átrio esquerdo, maior frequência de fibrilação atrial e maior frequência de histórico familiar da doença do que pacientes com mutação em MYBPC3. Conclusões: A técnica sequenciamento de RNA extraído de leucócitos não é adequada para uma rotina de rastreamento em larga escala para CH devido à alta frequência de falsos positivos, possibilidade de falsos negativos e baixa taxa de amplificação, mas o sequenciamento de DNA, embora trabalhoso, se mostrou muito sensível para a análise. A identificação de uma mutação específica ainda não pode ser usada para prognóstico de gravidade da CH, mas as comparações de genótipo e fenótipo mostraram algumas relações interessantes que devem ser melhor avaliadas nos pacientes. Este é o primeiro trabalho a caracterizar a epidemiologia molecular da CH em pacientes brasileiros para os genes MYH7, MYBPC3 e TNNT2 / Introduction: Hypertrophic cardiomyopathy (HC) is a primary genetic cardiac disease characterized by left ventricular hypertrophy without dilation, usually asymmetric and predominantly septal, with an estimated prevalence of 1:500. There are 20 genes associated to the HC, but the ones more often related to the disease are ?-myosin heavy chain (MYH7), myosin binding protein C (MYBPC3) and troponin T (TNNT2). The molecular diagnosis of patients is important and cost-effective from the standpoint of public health, and recommended by the European Society of Cardiology. However, the initial cost of the exam is very high, so several studies are attempting to reduce it. One of the proposals described used the RNA extracted from leukocytes for sequencing successfully to the MYBPC3 gene. The present study aims to test the methodology for large-scale sequencing and test it\'s applicability to the MYH7 and TNNT2 genes, to estimate the main mutations involved in the studied patients and establish correlations between their genotypes and phenotypes. Methods: The subjects included in the study were patients previously diagnosed with hypertrophic cardiomyopathy in whom a blood sample was collected to DNA and RNA extraction. It was used nested PCR for cDNA amplification and conventional PCR for DNA amplification for posterior sequencing on an automatic sequencer. Statistical analyzes of clinical data were performed using ANOVA to compare means and Fisher\'s exact test for frequencies comparison. Results: The RNA sequencing was problematic with low rate of amplification, false positives and possible false negatives, so was used DNA sequencing to identify the mutations. Of the 268 patients studied a mutation was identified in 131 of them (48.8%). Among the mutations found, 78 (59.5%) were in the MYH7 gene, 50 (38.2%) in the MYBPC3 gene and three (2.3%) in the TNNT2 gene. We have identified 69 different mutations, 24 of them not yet described. Patients with an identified mutation had an average smaller age of diagnosis and current age, higher average cardiac frequency and higher frequency of patients with nonsustained ventricular tachycardia compared to those without an identified mutation. Patients with mutations in the MYH7 gene had larger left atrium size, higher frequency of atrial fibrillation and higher frequency of family history of the disease than patients with a mutation in the MYBPC3 gene. Conclusions: The technique of sequencing RNA extracted from leucocytes is not suitable for large scale routine screening for CH due to the high frequency of false positives, possibility of false negatives and low rate of amplification, but the DNA sequencing, though laborious, was very sensitive to the analysis. Identification of a specific mutation cannot yet be used for prognosis of the disease\'s severity, but comparisons of genotype and phenotype have shown some interesting relationships that should be further evaluated. The presente study is the first one to characterize the molecular epidemiology of hypertrophic cardiomyopathy in Brazilian patients for those three more important genes mentioned above