Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome.

In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.

A Standard Pipeline for Analyzing the Endometrial Microbiome.

The endometrial microbiome is a rapidly advancing field of research, particularly in obstetrics and gynecology, as it has been found to be linked with obstetric complications and potential impacts on fertility. The diversity of microorganisms presents in the endometrium, along with their metabolites, can influence reproductive outcomes by modulating the local immune environment of the uterus. However, a major challenge in advancing our understanding of the endometrial microbiota lies in the heterogeneity of available studies, which vary in terms of patient selection, control groups, collection methods and analysis methodologies. In this study, we propose a detailed pipeline for endometrial microbiome analysis, based on the most comprehensive prospective of 64 studies that have investigated the endometrial microbiome up to the present. Additionally, our review suggests that a dominance of Lactobacilli in the endometrium may be associated with improved reproductive prognosis, including higher implantation rates and lower miscarriage rates. By establishing a standardized pipeline, we aim to facilitate future research, enabling better comparison and correlation of bacterial communities with the health status of patients, including fertility-related issues.

Viruses as a potential environmental trigger of type 1 diabetes mellitus (Review).

The etiopathogenesis of type 1 diabetes mellitus (T1DM) is a complex multifactorial process that involves an intricate network of genetic, epigenetic, immunological, and environmental factors. Despite the advances in recent years, some aspects of the mechanisms involved in triggering the disease are still unclear. Infections with certain viruses have been suggested as possible environmental triggers for the autoimmune process that leads to selective and progressive destruction of pancreatic ß-cells and insufficiency of insulin production, which is its hallmark. In this review, advances in knowledge and evidence that suggest the participation of certain viruses in the mechanisms of disease initiation and progression are described. It has been accepted that environmental factors, including viruses, can initiate and possibly sustain, accelerate, or slow down the autoimmune process and consequently damage insulin-producing pancreatic ß-cells. Although the role of these agents, especially human enteroviruses, has been exhaustively studied as the most likely triggers of the activation of autoimmunity that destroys pancreatic islets and leads to T1DM, certain doubts remain. Clinical epidemiological and experimental studies in humans and animals provide consistent and increasing evidence that persistent viral infections, especially with human enteroviruses and rotavirus infections, are associated with an increased risk of the disease in individuals genetically predisposed to autoimmunity.

Main topics in assisted reproductive market: A scoping review.

BACKGROUND: Infertility affects around 12% of couples, and this proportion has been gradually increasing. In this context, the global assisted reproductive technologies (ART) market shows significant expansion, hovering around USD 26 billion in 2019 and is expected to reach USD 45 billion by 2025. OBJECTIVES: We realized a scoping review of the ART market from academic publications, market reports, and specialized media news, to identify the main terms and characterize them into the main topics in the area. DESIGN: We apply an LDA topic modeling process to identify the main terms, and clustered them into semantic synonymous topics. We extracted the patterns and information to these topics and purposed a factor/consequence correlation to them. RESULTS: We found 2,232 academic papers and selected 632 to include in the automatic term detection. We also included 34 market reports and seven notices produced by specialized enterprises. Were identified 121 most relevant cited terms covering 7,806 citations. These terms were manually aggregated into 10 topics based on semantic similarity: neutral terms (37.2%), economic aspects (17.6%), in vitro fertilization (IVF) commodities & cross-border reproductive care (CBRC) (10.6%), geographic distribution (9.5%), social aspects (7%), regulation (6%), trends & concerns (3.9%), accessibility (3.4%), internet influence (2.9%), and fertility preservation for non-medical reasons (2%). DISCUSSION: The analysis indicates a market with expressive complexity. Most terms were associated with more than one topic, indicating the synergism of this market's behavior. Only seven terms related to economic aspects, surrogacy and donation represent around 50% of the citations. Except for the topic formed by generic terms, the topic of the economic aspects was the most represented, reflecting macro perspectives such as a-la-carte standard of treatments, many clinics operating on a small/medium scale, and the recent formation of conglomerates. The IVF commodities & CBRC topic brings an overview of gametes pricing and transnational surrogacy, and its regulation. The topic of geographic distribution indicates that that the Asia-Pacific (APAC) market has the most significant growth potential in all fields. Despite the increase in supply and demand for infertility treatments and technological advances in recent decades, the success rate of IVF cycles remains at around 30%. Terms referring to research and development or technical improvement were not identified in a significant way in this review. CONCLUSIONS: The formation of topics by semantic similarity proved to be an initial path for the elaboration of in-depth studies on the dynamics between several factors, for this, we present the panel classifying main terms into factors (demand, pent-up demand, or distributive) or ART market consequences. Through this approach, it was possible to observe that most of the works addresses economic aspects, regulation and geographic aspects and that topics related to research and improvement have not been addressed. In this way, we highlight the need to deepen the analysis of market elements that may be related to increased efficiency of IVF in the technical field.

Biology and Natural History of Type 1 Diabetes Mellitus.

Type 1 diabetes mellitus is a clinical condition characterized by insufficient insulin production due to progressive loss of pancreatic islet ß-cells mediated by an autoimmune response. This deregulation of the immune system is caused by the action of genetic, epigenetic, and environmental factors in varying combinations for each individual. Although the inflammation of the islets with immune cell infiltration, known as insulitis, is an important element in pathogenesis, other factors are necessary for disease initiation. Associations with variants of HLA and other genes related to immune system function, mainly haplotypes HLA-DR3-DQ2 and HLA-DR4-DQ8, are more evident. The influence of polymorphisms and epigenetic modifications, as well as the microbiome, is convincing proof of the existence of a complex interaction between genetic, immune, and environmental factors in the etiology and pathogenesis of this metabolic disorder. Loss of selftolerance to autoimmunity is a critical point in the development of the disease, and regulatory T cells play a key role in this process. Thus, any failure of these cells, either due to an insufficient number or altered expression of cytokines and transcription factors, may be the trigger for the onset of the disease. The protective action of regulatory T cells is controlled by gene expression that is modulated by epigenetic modifications, including the dysregulation of noncoding RNAs. This review takes an updated approach to the natural history of type 1 diabetes, focusing on the factors involved in the etiology and pathogenesis.

Human seminal virome: a panel based on recent literature.

BACKGROUND: The seminal virome and its implications for fertility remain poorly understood. To date, there are no defined panels for the detection of viruses of clinical interest in seminal samples. RESULTS: In this study, we characterized the human seminal virome based on more than 1,000 studies published over the last five years. CONCLUSIONS: The number of studies investigating viruses that occur in human semen has increased, and to date, these studies have been mostly prospective or related to specific clinical findings. Through the joint analysis of all these studies, we have listed the viruses related to the worsening of seminal parameters and propose a new panel with the main viruses already described that possibly affect male fertility and health. This panel can assist in evaluating semen quality and serve as a tool for investigation in cases of infertility.

RéSUMé: CONTEXTE: Le virome séminal et ses implications pour la fertilité restent mal compris. À ce jour, il n'existe pas de panels définis pour la détection des virus d'intérêt clinique dans les échantillons de sperme. RéSULTATS: Dans cette étude, nous avons caractérisé le virome séminal humain sur la base de plus de 1000 études publiées au cours des cinq dernières années. CONCLUSIONS: Le nombre d'études portant sur les virus présents dans le sperme humain a augmenté et, à ce jour, ces études ont principalement été prospectives ou liées à des résultats cliniques spécifiques. Grâce à l'analyse conjointe de toutes ces études, nous avons répertorié les virus liés à l'aggravation des paramètres spermatiques, et nous proposons un nouveau panel avec les principaux virus déjà décrits qui peuvent affecter la fertilité et la santé masculines. Ce panel peut aider à évaluer la qualité du sperme et servir d'outil d'investigation dans les cas d'infertilité.

The role of HPV-induced epigenetic changes in cervical carcinogenesis (Review).

Cervical cancer is associated with infection by certain types of human papillomaviruses (HPVs), and this affects women worldwide. Despite the improvements in prevention and cure of HPV-induced cervical cancer, it remains the second most common type of cancer in women in the least developed regions of the world. Epigenetic modifications are stable long-term changes that occur in the DNA, and are part of a natural evolutionary process of necessary adaptations to the environment. They do not result in changes in the DNA sequence, but do affect gene expression and genomic stability. Epigenetic changes are important in several biological processes. The effects of the environment on gene expression can contribute to the development of numerous diseases. Epigenetic modifications may serve a critical role in cancer cells, by silencing tumor suppressor genes, activating oncogenes, and exacerbating defects in DNA repair mechanisms. Although cervical cancer is directly related to a persistent high-risk HPV infection, several epigenetic changes have been identified in both the viral DNA and the genome of the infected cells: DNA methylation, histone modification and gene silencing by non-coding RNAs, which initiate and sustain epigenetic changes. In the present review, recent advances in the role of epigenetic changes in cervical cancer are summarized.

Single nucleotide polymorphism associated with disease resistance in Penaeus vannamei.

Despite the considerable number of genetic markers published for Penaeus vannamei, the classification of these markers and their standardization in specific databases is still insufficient. As a consequence, access to these markers is difficult, hampering their application in genetic association studies. In this study, all previously described single nucleotide polymorphisms (SNPs) related to resistance for P. vannamei were revised, and 512 SNPs were identified and classified in detail. We observed that most of the SNPs occurred in the proteins including Toll like receptors 1 and 3, hemocyanin large and small subunits, and anti-lipopolysaccharide factors 1 and 2, allowing to propose to use them as targets in association studies involving resistance in P. vannamei. Additionally, the potential effects of the most frequent non-synonymous coding SNPs in the secondary structure of the main target proteins were evaluated using an in silico approach. These data can serve as the starting point for the development of new genetic and computational tools as well as for the design of new association studies that involve resistance in P. vannamei.

A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum.

Nucleic acid detection by electrophoresis is still a quick and accessible technique for many diagnosis methods, primarily at research laboratories or at the point of care units. Standard protocols detect DNA/RNA molecules through specific bound chemical dyes using a UV-transilluminator or UV-photo documentation system. However, the acquisition costs and availability of these devices, mainly the ones with photography and internet connection capabilities, can be prohibitive, especially in developing countries public health units. Also, ultraviolet radiation is a common additional risk factor to professionals that use electrophoresis-based nucleic acid detection. With that in mind, this work describes the development of a low-cost DNA/RNA detection smart system capable of obtaining qualitative and semi-quantitative data from gel analysis. The proposed device explores the visible light absorption range of commonly used DNA/RNA dyes using readily available parts, and simple manufacturing processes, such as light-emitting diodes (LEDs) and 3D impression. By applying IoT techniques, our system covers a wide range of color spectrum in order to detect bands from various commercially used dyes, using Bluetooth communication and a smartphone for hardware control, image capturing, and sharing. The project also enables process scalability and has low manufacturing and maintenance costs. The use of LEDs at the visible spectrum can achieve very reproducible images, providing a high potential for rapid and point-of-care diagnostics as well as applications in several fields such as healthcare, agriculture, and aquaculture.

Biology and pathogenesis of human osteosarcoma.

Osteosarcoma (OS) is a bone tumor of mesenchymal origin, most frequently occurring during the rapid growth phase of long bones, and usually located in the epiphyseal growth plates of the femur or the tibia. Its most common feature is genome disorganization, aneuploidy with chromosomal alterations, deregulation of tumor suppressor genes and of the cell cycle, and an absence of DNA repair. This suggests the involvement of surveillance failures, DNA repair or apoptosis control during osteogenesis, allowing the survival of cells which have undergone alterations during differentiation. Epigenetic events, including DNA methylation, histone modifications, nucleosome remodeling and expression of non-coding RNAs have been identified as possible risk factors for the tumor. It has been reported that p53 target genes or those genes that have their activity modulated by p53, in addition to other tumor suppressor genes, are silenced in OS-derived cell lines by hypermethylation of their promoters. In osteogenesis, osteoblasts are formed from pluripotent mesenchymal cells, with potential for self-renewal, proliferation and differentiation into various cell types. This involves complex signaling pathways and multiple factors. Any disturbance in this process can cause deregulation of the differentiation and proliferation of these cells, leading to the malignant phenotype. Therefore, the origin of OS seems to be multifactorial, involving the deregulation of differentiation of mesenchymal cells and tumor suppressor genes, activation of oncogenes, epigenetic events and the production of cytokines.

Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome.

BACKGROUND: White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. This virus presents a complex genome of ~ 300 kb and viral isolates that present genomes with great identity. Despite this conservation, some variable regions in the WSSV genome occur in coding regions, and these putative proteins may have some relationship with viral adaptation and virulence mechanisms. Until now, the functions of these proteins were little studied. In this work, sequences and putative proteins encoded by WSSV variable regions were characterized in silico. RESULTS: The in silico approach enabled determining the variability of some sequences, as well as the identification of some domains resembling the Formin homology 2, RNA recognition motif, Xeroderma pigmentosum group D repair helicase, Hemagglutinin and Ankyrin motif. The information obtained from the sequences and the analysis of secondary and tertiary structure models allow to infer that some of these proteins possibly have functions related to protein modulation/degradation, intracellular transport, recombination and endosome fusion events. CONCLUSIONS: The bioinformatics approaches were efficient in generating three-dimensional models and to identify domains, thereby enabling to propose possible functions for the putative polypeptides produced by the ORFs wsv129, wsv178, wsv249, wsv463a, wsv477, wsv479, wsv492, and wsv497.

Th17 response in patients with cervical cancer.

Persistent infection by high-risk human papillomavirus (HR-HPV) is the main risk factor for uterine cervical cancer (UCC). However, viral infection alone is not sufficient for the development and progression of premalignant cervical lesions for cancer. In previous years it has been suggested that the adaptive immune response triggered by the differentiation of naïve helper T cells in Th17 cells may serve an important role in disease development. It has been hypothesized that Th17 cells may be involved in the promotion of UCC, as high levels of interleukin 17 (IL17) expression have been detected in the mucosa of the uterine cervix of patients affected by the disease. However, the role of Th17 cells in the tumor development and progression remains unclear. It is believed that the immune response of the Th17 type during persistent infection of the genital tract with HR-HPV triggers chronic inflammation with a long duration with the production of IL17 and other pro-inflammatory cytokines, creating a favorable environment for tumor development. These cytokines are produced by immune system cells in addition to tumor cells and appear to function by modulating the host immune system, resulting in an immunosuppressive response as opposed to inducing an effective protective immune response, thus contributing to the growth and progression of the tumor. In the present review, the latest advances are presented about the function of Th17 cells and the cytokines produced by them in the development and progression of UCC.

Chikungunya fever: a threat to global public health.

Chikungunya fever is an emerging arbovirus infection, representing a serious public health problem. Its etiological agent is the Chikungunya virus (CHIKV). Transmission of this virus is mainly vector by mosquitoes of the genus Aedes, although transmission by blood transfusions and vertical transmission has also been reported. The disease presents high morbidity caused mainly by the arthralgia and arthritis generated. Cardiovascular and neurological manifestations have also been reported. The severity of the infection seems to be directly associated with the action of the virus, but also with the decompensation of preexisting comorbidities. Currently, there are no therapeutic products neither vaccines licensed to the infection CHIKV control, although several vaccine candidates are being evaluated and human polyvalent immunoglobulins anti-CHIKV had been tested. Antibodies can protect against the infection, but in sub-neutralizing concentrations can augment virus infection and exacerbate disease severity. So, the prevention still depends on the use of personal protection measures and vector control, which are only minimally effective.

Macrophage Migration Inhibitory Factor (MIF): Biological Activities and Relation with Cancer.

Macrophage migration inhibitory factor (MIF) emerged in recent years as an important inflammation mediator, playing a prominent role in the pathogenesis of various types of malignant neoplasm. MIF is a glycoprotein that presents a wide spectrum of biological activities and exerts a complex interaction with various cellular signaling pathways, causing imbalance of homeostasis. Experimental and clinical studies show that high levels of MIF are found in almost all types of human cancers and are implicated in seemingly all stages of development of the tumors. The production of MIF is triggered through an autocrine signal emitted by tumor cells, and stimulates the production of cytokines, chemokines, and growth as well as angiogenic factors that lead to growth of the tumor, increasing its aggressiveness and metastatic potential. MIF is produced by virtually all types of human body cells, in response to stress caused by different factors, leading to pathological conditions such as chronic inflammation and immunomodulation with suppression of immune surveillance and of immune response against tumors, angiogenesis, and carcinogenesis. In this review, we present recent advances on the biological activity of MIF, the signaling pathways with which it is involved and their role in tumorigenesis.