Non-coding RNA and pseudogenes in neurodegenerative diseases: “The (un)Usual Suspects”

Neurodegenerative disorders and cancer are severe diseases threatening human health. The glaring differences between neurons and cancer cells mask the processes involved in their pathogenesis. Defects in cell cycle, DNA repair, and cell differentiation can determine unlimited proliferation in cancer, or conversely, compromise neuronal plasticity, leading to cell death and neurodegeneration. Alteration in regulatory networks affecting gene expression contribute to human diseases onset, including neurodegenerative disorders, and deregulation of non-coding RNAs – particularly microRNAs (miRNAs) – is supposed to have a significant impact. Recently, competitive endogenous RNAs (ceRNAs) – acting as sponges – have been identified in cancer, indicating a new and intricate regulatory network. Given that neurodegenerative disorders and cancer share altered genes and pathways, and considering the emerging role of miRNAs in neurogenesis, we hypothesize ceRNAs may be implicated in neurodegenerative diseases. Here we propose, and computationally predict, such regulatory mechanism may be shared between the diseases. It is predictable that similar regulation occurs in other complex diseases, and further investigation is needed

Pharmacogenomics of Drug Response in Type 2 Diabetes: Toward the Definition of Tailored Therapies?

Type 2 diabetes is one of the major causes of mortality with rapidly increasing prevalence. Pharmacological treatment is the first recommended approach after failure in lifestyle changes. However, a significant number of patients shows—or develops along time and disease progression—drug resistance. In addition, not all type 2 diabetic patients have the same responsiveness to drug treatment. Despite the presence of nongenetic factors (hepatic, renal, and intestinal), most of such variability is due to genetic causes. Pharmacogenomics studies have described association between single nucleotide variations and drug resistance, even though there are still conflicting results. To date, the most reliable approach to investigate allelic variants is Next-Generation Sequencing that allows the simultaneous analysis, on a genome-wide scale, of nucleotide variants and gene expression. Here, we review the relationship between drug responsiveness and polymorphisms in genes involved in drug metabolism (CYP2C9) and insulin signaling (ABCC8, KCNJ11, and PPARG). We also highlight the advancements in sequencing technologies that to date enable researchers to perform comprehensive pharmacogenomics studies. The identification of allelic variants associated with drug resistance will constitute a solid basis to establish tailored therapeutic approaches in the treatment of type 2 diabetes

Reconhecimento automático de parâmetros de sinais num contexto linguístico utilizando redes neurais

Há uma grande quantidade de surdos em todo o mundo. Os surdos, em sua grande maioria, não têm proficiência numa língua oral, enquanto que é comum grande parte dos ouvintes não ter conhecimento de línguas de sinais. Isto gera uma barreira comunicativa entre os dois grupos gerando, como consequência, problemas sociais como a falta inclusão. Um meio de se reconhecer os sinais realizados pelos surdos automaticamente pode ser uma maneira de amenizar esta dificuldade de comunicação. Realizamos uma sequência de processamento de imagem e a implementação de um pequeno protótipo capaz de identificar os principais atributos linguísticos dos sinais e fornecer tais atributos em forma de características, permitindo assim o desenvolvimento de diversas aplicações voltadas para o reconhecimento de sinais não necessariamente num contexto linguístico. Consideramos classificar dois parâmetros das línguas de sinais, a configuração manual e o ponto de articulação, de um video capturado por uma câmera RGB simples, visando o fácil acesso para o usuário final, dado como entrada do sistema. Criamos uma pequena base de dados para cada parâmetro considerado e uma outra de sinais em LIBRAS para validação dos objetivos do sistema. Para obtenção das características classificamos cada parâmetro linguístico individualmente, por meio de detectores localizamos a face e as mãos que são dois dos três canais de composição dos sinais. Realizamos a extração das características de cada um dos parâmetros linguísticos utilizando o processamento do resultado das detecções com auxilio de redes neurais e calculo de distâncias entre os canais de composição. A classificação da configuração manual foi realizada com a construção de uma pequena rede neural convolucional de uma dimensão e obtivemos como resultado uma taxa de precisão de aproximadamente 87.1% de uma mão detectada pelo sistemas enquanto que para a o ponto de articulação realizamos uma comparação entre três classificadores são eles: KNN, Random Forest e rede neural convolucional. Obtivemos como resultado uma taxa de precisão semelhante entre os três classificadores variando de 95.2% à 96.3%. O método utilizado possuí limitações e falhas que devem ser sanadas para viabilizar futuramente o uso do sistema num cenário real. Tais limitações incluem não haver contato entre as mãos, tendo em vista que nosso detector de mão utilizado não era capaz de funcionar corretamente nesta situação. Identificar a mão entre direita e esquerda também é um problema não solucionado totalmente em nosso sistema, sendo esta uma tarefa crucial para a obtenção correta das características manuais por meio do método utilizado para extração de tais características. Podemos concluir que, apesar dos erros, com os resultados obtidos pudemos detectar atributos da imagem para predizer dois parâmetros da língua de sinais em relação ao tempo, que servem como características para múltiplas utilidades não necessariamente linguísticas. O protótipo não é adequado para o uso em cenários reais e não considera todos os parâmetros linguísticos existentes nas línguas de sinais. Porém os métodos podem ser substituídos ou melhorados afim de tornar o protótipo mais próximo de ser utilizado em ambientes reais em que há o uso da língua de sinais.There are many deaf people around the world. The deaf, for the most part, are not proficient in an oral language, while it is common for hearing people to have no knowledge of sign languages. This creates a communicative barrier between the two groups resulting in social problems such as lack of inclusion. One way of recognizing the signals made by deaf people automatically can be one way of easing this communication difficulty. In this work, we performed an image processing sequence and an implementation of a small prototype capable of identifying the main linguistic attributes of the signals and providing such attributes in the form of features. It allows the development of several applications aimed at the recognition of signals not necessarily in a linguistic context. We consider classifying two parameters of signal languages, handshape and the location, of a video captured by a simple RGB camera, aiming at the easy access for the end user, given as input of the system. We created a small database for each parameter considered and another one of signs in LIBRAS for validation of objectives of the system. To obtain the characteristics we classify each language parameter individually, through detectors we locate the face and hands that are two of the three channels of signal composition. We performed the extraction of characteristics for each linguistic parameters using the processing of detections results with the aid of neural networks and calculating distances between the composition channels. The classification of handshape was performed with the construction of a small one dimension convolutional neural network and we obtained as result a precision rate of approximately 87.1 % of a hand detected by the hand detector while for the location we made a comparison between three classifiers are: KNN, Random Forest and convolutional neural network. We obtained as result a similar precision rate among the three classifiers ranging from 95.2% to 96.3%. The method used has limitations and shortcomings that must be solved in order to make future use of the system in a real scenario. Such limitations include no contact between the hands, since the hand detector used was not able to function properly in this situation. Identifying the hand between right and left is also an unresolved problem in our system, being this a crucial task for the correct obtaining of the manual features through the method used for extraction of such features. We can conclude, despite the errors, with the results obtained we were able to detect image attributes to predict two parameters of sign language in relation to time, which serve as features for multiple uses not necessarily linguistic. The prototype is not suitable for use in real scenarios and does not consider all the linguistic parameters of sign languages. However, the methods can be replaced or improved in order to make the prototype closer to being used in real environments where sign language is used

O piano expandido no seculo XX nas obras para piano preparado de John Cage

Orientador: Denise Hortensia Lopes GarciaDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ArtesResumo: Na presente pesquisa foi estudada a obra para piano preparado do compositor norte-americano John Cage (1912-1992), composta durante a década de 40 até 1952, com o intuito de desvendar as implicações sonoras da fixação de objetos entre as cordas do piano no processo de transformação dos sons do instrumento. Para tal foi realizado estudo biográfico do compositor referente ao período de composição das obras estudadas, preparação dessas obras em pianos diversos, realização de comentários sobre resultados sonoros das preparações caso a caso, desenvolvimento de método de preparação de pianos não danoso ao instrumento, além da composição de duas peças para piano preparado ilustrativas dos processos estudadosMestradoMusicaMestre em Músic

Reduced fire blight susceptibility in apple cultivars using a high-efficiency CRISPR/Cas9-FLP/FRT-based gene editing system

The bacterium Erwinia amylovora, the causal agent of fire blight disease in apple, triggers its infection through the DspA/E effector which interacts with the apple susceptibility protein MdDIPM4. In this work, an MdDIPM4 knock-out has been produced in two Malus x domestica susceptible cultivars using the CRISPR/Cas9 system delivered via Agrobacterium tumefaciens. Fifty-seven transgenic lines were screened to identify CRISPR/Cas9-induced mutations. An editing efficiency of 75% was obtained. Seven edited lines with a loss-of-function mutation were inoculated with the pathogen. Highly significant reduction of susceptibility was observed compared to control plants. Sequencing of 5 potential off-target sites revealed no mutation event. Moreover, our construct contained a heat shock-inducible FLP/FRT recombination system designed specifically to remove the T-DNA harbouring expression cassettes for CRISPR/Cas9, marker gene and FLP itself. Six plant lines with reduced susceptibility to the pathogen were heat-treated and screened by real-time PCR to quantify the exogenous DNA elimination. The T-DNA removal was further validated by sequencing in one plant line. To our knowledge, this work demonstrates for the first time the development and application of a CRISPR/Cas9-FLP/FRT gene editing system for the production of edited apple plants carrying a minimal trace of exogenous DN

Limitação probatória da técnica de infiltração policial à luz da lei de organizações criminosas

A presente monografia aborda o tema da limitação probatória de agentes infiltrados à luz da Lei de Organizações Criminosas. Será feita uma análise conceitual, doutrinária e legal acerca do fenômeno da organização criminosa e sua crescente complexidade e sofisticação. Tal evolução da criminalidade organizada exige que o Estado adote novas medidas de combate ao crime, como o meio extraordinário de obtenção de prova ilustrado pelo instituto da infiltração policial. Adiante, será estudado o conceito de agente infiltrado, com seus respectivos requisitos para implementação, espécies e direitos do agente. A seguir, serão feitas considerações acerca do instituto da prova no processo penal brasileiro, suas espécies, fontes, assim como suas eventuais ilicitudes. Por fim, serão analisados os limites que as provas obtidas pela infiltração policial possuem ao longo do procedimento, a partir de análises doutrinárias, jurisprudenciais e legais, a fim de servir de instrumento para uma eventual condenação criminal

PPARG: Gene Expression Regulation and Next-Generation Sequencing for Unsolved Issues

Peroxisome proliferator-activated receptor gamma (PPARγ) is one of the most extensively studied ligand-inducible transcription factors (TFs), able to modulate its transcriptional activity through conformational changes. It is of particular interest because of its pleiotropic functions: it plays a crucial role in the expression of key genes involved in adipogenesis, lipid and glucid metabolism, atherosclerosis, inflammation, and cancer. Its protein isoforms, the wide number of PPARγ target genes, ligands, and coregulators contribute to determine the complexity of its function. In addition, the presence of genetic variants is likely to affect expression levels of target genes although the impact of PPARG gene variations on the expression of target genes is not fully understood. The introduction of massively parallel sequencing platforms—in the Next Generation Sequencing (NGS) era—has revolutionized the way of investigating the genetic causes of inherited diseases. In this context, DNA-Seq for identifying—within both coding and regulatory regions of PPARG gene—novel nucleotide variations and haplotypes associated to human diseases, ChIP-Seq for defining a PPARγ binding map, and RNA-Seq for unraveling the wide and intricate gene pathways regulated by PPARG, represent incredible steps toward the understanding of PPARγ in health and disease

The role of a new class of long noncoding RNAs transcribed from ultraconserved regions in cancer

Ultraconserved regions (UCRs) represent a relatively new class of non-coding genomic sequences highly conserved between human, rat and mouse genomes. These regions can reside within exons of protein-coding genes, despite the vast majority of them localizes within introns or intergenic regions. Several studies have undoubtedly demonstrated that most of these regions are actively transcribed in normal cells/tissues, where they contribute to regulate many cellular processes. Interestingly, these non-coding RNAs exhibit aberrant expression levels in human cancer cells and their expression profiles have been used as prognostic factors in human malignancies, as well as to unambiguously distinguish among distinct cancer types. In this review, we first describe their identification, then we provide some updated information about their genomic localization and classification. More importantly, we discuss about the available literature describing an overview of the mechanisms through which some transcribed UCRs (T-UCR) contribute to cancer progression or to the metastatic spread. To date, the interplay between T-UCRs and microRNAs is the most convincing evidence linking T-UCRs and tumorigenesis. The limitations of these studies and the future challenges to be addressed in order to understand the biological role of T-UCRs are also discussed herein. We envision that future efforts are needed to convincingly include this class of ncRNAs in the growing area of cancer therapeutics

Hepatic Insulin Resistance in Hyperthyroid Rat Liver: Vitamin E Supplementation Highlights a Possible Role of ROS

Thyroid hormones are normally involved in glycaemic control, but their excess can lead to altered glucose metabolism and insulin resistance (IR). Since hyperthyroidism-linked increase in ROS results in tissue oxidative stress that is considered a hallmark of conditions leading to IR, it is conceivable a role of ROS in the onset of IR in hyperthyroidism. To verify this hypothesis, we evaluated the effects of vitamin E on thyroid hormone-induced oxidative damage, insulin resistance, and on gene expression of key molecules involved in IR in the rat liver. The factors involved in oxidative damage, namely the total content of ROS, the mitochondrial production of ROS, the activity of antioxidant enzymes, the in vitro susceptibility to oxidative stress, have been correlated to insulin resistance indices, such as insulin activation of hepatic Akt and plasma level of glucose, insulin and HOMA index. Our results indicate that increased levels of oxidative damage ROS content and production and susceptibility to oxidative damage, parallel increased fasting plasma level of glucose and insulin, reduced activation of Akt and increased activation of JNK. This last result suggests a role for JNK in the insulin resistance induced by hyperthyroidism. Furthermore, the variation of the genes Pparg, Ppara, Cd36 and Slc2a2 could explain, at least in part, the observed metabolic phenotypes. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

Clinical-pathological features and treatment of acute appendicitis in the very elderly: an interim analysis of the FRAILESEL Italian multicentre prospective study

Emergency abdominal surgery in the elderly represents a global issue. Diagnosis of AA in old patients is often more difficult. Appendectomy remains the gold standard of treatment and, even though it is performed almost exclusively with a minimally invasive technique, it can still represent a great risk for the elderly patient, especially above 80 years of age. A careful selection of elderly patients to be directed to surgery is, therefore, fundamental. The primary aim was to critically appraise and compare the clinical-pathological characteristics and the outcomes between oldest old (≥ 80 years) and elderly (65-79 years) patients with Acute Appendicitis (AA)