Características Fonoaudiológicas de Pacientes Atendidos por um Serviço de Genética Clínica / Speech-language Pathology Characteristics of Patients Assisted by a Clinical Genetics Service / Características de patología del habla y lenguaje de Pacientes Atendidos por un Servicio de Genética Clínica

Introdução: O trabalho conjunto da genética médica e da fonoaudiologia é essencial, contribuindo para o desenvolvimento de procedimentos que auxiliam no tratamento de pacientes com distúrbios da comunicação. Objetivo: Analisar as características fonoaudiológicas de pacientes pediátricos atendidos por um serviço de genética clínica. Método: Estudo transversal observacional, realizado com pacientes atendidos pelo serviço de genética de um hospital em Porto Alegre. Para a coleta de dados, aplicou-se um questionário relacionado as áreas de audição, deglutição, motricidade orofacial, voz e linguagem. Resultados: A amostra foi constituída por 54 participantes com idades entre 8 meses e 17 anos (média de idade 6 anos e 5 meses). 24,07% (n=13) dos pacientes apresentaram diagnóstico de síndrome, e 59,26% (n=32) tinham atraso no desenvolvimento neuropsicomotor. Com relação ao perfil fonoaudiológico, 81,48% (n=44) apresentaram algum hábito oral deletério durante a infância. 16,67% (n=9) percebiam alguma dificuldade para ouvir e 29,62% (n=16) para deglutir. 85,19% (n=46) dos participantes manifestaram a linguagem oral desenvolvida e, destes, 71,74% (n=33) apresentavam trocas na fala. 33,33% (n=18) já estavam em atendimento fonoaudiológico, e outros 24,07% (n=13) estavam na fila de espera para este atendimento. Conclusões: Uma parte significativa dos pacientes apresentou queixas e/ou manifestações nas áreas da comunicação humana, principalmente em relação à linguagem, à fala e aos hábitos orais deletérios. Esses dados destacam a importância do encaminhamento para a equipe de fonoaudiologia. (AU)

Introduction: The collaborative efforts of medical genetics and speech therapy are essential, contributing to the development of procedures that assist in treating patients with communication disorders. Objective: To analyze the speech therapy characteristics of pediatric patients seen by a clinical genetics service. Methods: Observational cross-sectional study conducted with patients seen at the genetics service of a hospital in Porto Alegre. A questionnaire related to hearing, swallowing, orofacial motricity, voice, and language areas was used for data collection. Results: The sample consisted of 54 participants aged between 8 months and 17 years, with an average age of 6 years and 5 months. 24.07% (n=13) of the patients had a diagnosis of syndrome, and 59.26% (n=32) had delayed neuropsychomotor development. Regarding the speech therapy profile, 81.48% (n=44) had some harmful oral habit during childhood. 16.67% (n=9) reported some difficulty in hearing, and 29.62% (n=16) in swallowing. 85.19% (n=46) of the participants showed developed oral language, and of these, 71.74% (n=33) made speech substitutions. 33.33% (n=18) of the patients were already undergoing speech therapy, and another 24.07% (n=13) were on the waiting list for this treatment. Conclusions: A significant portion of the patients presented complaints and/or manifestations in the areas of human communication, especially regarding language, speech, and harmful oral habits. These data highlight the importance of referral to the speech therapy team. (AU)

Introducción: La colaboración entre genética médica y foniatría es esencial para desarrollar procedimientos que ayuden en el tratamiento de pacientes con trastornos de la comunicación. Objetivo:Analizar las características de patología del habla y lenguaje de pacientes pediátricos atendidos por un servicio de genética clínica. Método: Estudio transversal observacional con pacientes atendidos por el servicio de genética de un hospital en Porto Alegre. Se aplicó un cuestionario sobre audición, deglución, motricidad orofacial, voz y lenguaje. Resultados: La muestra consistió en 54 participantes con edades comprendidas entre 8 meses y 17 años (media: 6 años y 5 meses). El 24,07% (n=13) de los pacientes tenían un diagnóstico de síndrome, y el 59,26% (n=32) presentaron retraso en el desarrollo neuropsicomotor. En cuanto al perfil foniatra, el 81,48% (n=44) presentaron algún hábito oral perjudicial durante la infancia. El 16,67% (n=9) reportaron dificultades para oír, y el 29,62% (n=16) para tragar. El 85,19% (n=46) manifestaron lenguaje oral desarrollado y, de ellos, el 71,74% (n=33) realizaban intercambios en el habla. El 33,33% (n=18) de los pacientes ya estaban en tratamiento foniatra y el 24,07% (n=13) estaban en lista de espera para este tratamiento. Conclusiones: Una parte significativa de los pacientes presentó quejas y/o manifestaciones en las áreas de la comunicación humana, especialmente en relación con el lenguaje, el habla y los hábitos orales perjudiciales, enfatizando la importancia de la derivación al equipo de foniatría. (AU)

Survival analysis and associated factors of highgrade glioma patients / Survival analysis and associated factors of highgrade glioma patients

Introduction: High-grade gliomas are the most common primary brain tumors in adults, and they usually have a quick fatal course. Average survival is 18 months, mainly, because of tumor resistance to Stupp protocol. Objective: To determine high-grade glioma patient survival and the effect of persuasion variables on survival. Materials and methods: We conducted a longitudinal descriptive study in which 80 untreated recently diagnosed high-grade glioma patients participated. A survey was conducted regarding their exposure to some risk factors, degree of genetic instability in peripheral blood using micronucleus quantification on binuclear lymphocytes, micronuclei in reticulocytes and sister-chromatid exchanges in lymphocytes. In the statistical analysis, this study constructed life tables, used the Kaplan-Meier, and the log-rank test, and in the multivariate analysis, a Cox proportional hazards model was constructed. Results: Eighty patients' clinical, demographic and lifestyle characteristics were analyzed, as well as their survival rates and the average survival time is 784 days (interquartile range: 928). Factors like age, exposure at work to polycyclic hydrocarbons and the number of sister-chromatid exchanges in lymphocytes in the first sampling was significantly survivalrelated in the multivariate analysis. Conclusion: We determined that only three of the analyzed variables have an important effect on survival time when it comes to high-grade glioma patients.

Introducción. Los gliomas de alto grado son los tumores cerebrales primarios más comunes en adultos y, por lo general, tienen un curso mortal rápido. La supervivencia media es de 18 meses, principalmente, como consecuencia de la resistencia del tumor al protocolo Stupp. Objetivo. Determinar la supervivencia de los pacientes con glioma de alto grado y el efecto de las variables de persuasión en la supervivencia. Materiales y métodos. Se llevó a cabo un estudio descriptivo longitudinal en el que participaron 80 pacientes con diagnóstico reciente de glioma de alto grado no tratados. Se hizo una encuesta sobre su exposición a algunos factores de riesgo, grado de inestabilidad genética en sangre periférica mediante cuantificación de micronúcleos en linfocitos binucleares, micronúcleos en reticulocitos e intercambios de cromátidas hermanas en linfocitos. En el análisis estadístico, se construyeron tablas de vida, se utilizó Kaplan-Meier y la prueba de rangos logarítmicos, y en el análisis multivariado, se construyó un modelo de riesgos proporcionales de Cox. Resultados. Se analizaron las características clínicas, demográficas y de estilo de vida de 80 pacientes, así como sus tasas de supervivencia y el tiempo medio de supervivencia fue de 784 días (rango intercuartílico: 928). Factores como la edad, la exposición laboral a hidrocarburos policíclicos y el número de intercambios de cromátidas hermanas en linfocitos en el primer muestreo se relacionaron significativamente con la supervivencia en el análisis multivariante. Conclusión. Según los resultados, el estudio determinó que solo tres de las variables analizadas tienen un efecto importante en el tiempo de supervivencia cuando se trata de pacientes con glioma de alto grado.

Exploring Atrial Fibrillation: Understanding the Complex Relation Between Lifestyle and Genetic Factors.

Cardiovascular diseases (CVDs) are the leading cause of death worldwide across diverse ethnic groups. Among these, atrial fibrillation (AF) stands as one of the most prevalent types of arrhythmias and the primary cause of stroke. Risk factors associated with AF include alcohol consumption, aging, high blood pressure, hypertension, inflammation, and genetic factors. A family history of CVD could indicate an increased risk. Consequently, genetic, and genomic testing should be performed to identify the molecular etiology of CVDs and assess at-risk patients. It is important to note that CVDs are the results of the complex interplay of genes and environmental factors, including ethnicity. In this case, the proband's clinic story includes a history of smoking abuse for 10 years (10 cigarettes per day), obesity, hypertension, and an associated familial history. These risk factors, along with genetic variants, could trigger the early onset of AF. In recent years, genetic and genomic studies have significantly advanced our understanding of CVD etiology, given that next-generation sequencing (NGS) allows for the identification of genetic variants that could contribute to these pathologies. Furthermore, NGS facilitates early diagnosis, personalized pharmacological approaches, and identification of novel biomarkers. Thus, NGS is a valuable tool in CVD management. However, such studies are limited in Ecuador, a low- and middle-income country. Several challenges contribute to this gap, encompassing economic, infrastructural, and educational obstacles. Notably, the cost of genetic and genomic studies may also pose a barrier, restricting access to a portion of the population. In this case report, we present a 56-year-old Ecuadorian woman, who has been diagnosed with AF; however, after performing NGS no disease-associated variants were found, despite having strong clinical signs and symptoms. In summary, this case report contributes valuable insights into the complex interplay between genetic and lifestyle factors in the development and management of AF. The case report aims to underscore the potential impact of genetic variants on disease risk, even when classified as variants of uncertain significance, and the importance of an integral approach to patient care that includes genetic screening, lifestyle interventions, and tailored pharmacological treatment.

Teaching and training of human resources for genetics and genomics in Brazil.

This manuscript reviewed the state of the art about the teaching and training of human resources for genetics and genomics in Brazil. We presented the national scenario of teaching genetics in medical undergraduate and other health courses. We discussed the training of medical geneticists through medical residency and addressed the training in genetics of physicians from specialties other than genetics. We examined the training of health professionals specializing in genetics through lato sensu and stricto sensu postgraduate programs and presented the proposals for multi-professional residency in genetic counseling and genetics and genomics that are currently the subject of discussion in the country. Finally, we highlighted the importance of training primary health care professionals concerning genetics and genomics for the effective establishment of a line of care for individuals with genetic disorders in the Brazilian Unified Health System. Therefore, we provided a thorough overview of how genetics is (or is not) incorporated into professional training in a comprehensive public healthcare system such as the Brazilian.

The DEFB1 gene rs11362 A/G genetic variant is associated with risk of developing CAD: a case-control study.

BACKGROUND: In the present study, we evaluated whether DEFB1 gene polymorphisms are associated with the presence of coronary artery disease (CAD). METHODS: Two rs11362 A/G, and rs1800972 C/G gene polymorphisms of DEFB1 gene were genotyped by 5'exonuclease TaqMan assays in 219 patients with CAD and 522 control individuals. RESULTS: The distribution of rs1800972 C/G polymorphisms was similar in patients with CAD and healthy controls. Nonetheless, under the co-dominant, dominant, recessive, and additive models, the AA genotype of the rs11362 A/G polymorphism was associated with the risk of developing CAD (OR = 1.89 pCCo-Dom = 0.041, OR = 1.46, pCDom = 0.034, OR = 1.69, pCRes = 0.039, and OR = 1.37, pCAdd = 0.012, respectively). In addition, the linkage disequilibrium showed that the 'AG' haplotype was associated with an increased risk of developing CAD (OR = 1.23, p = 0.042). According, with the Genotype-Tissue Expression (GTEx) consortium data, the rs11362 AA genotype is associated with a low mRNA expression of the ß-defensin-1 in tissues, such as artery aorta, artery coronary, heart left ventricle, and heart atrial appendage (p < 0.001). CONCLUSION: This study demonstrates that rs11362 A/G polymorphism of the DEFB1 gene is involved in the risk of developing CAD, and with a low RNA expression of the ß-defensin-1 in heart tissue.

Targeted Therapy Innovations for Melanoma.

Melanoma, a malignant tumor of melanocytes, poses a significant clinical challenge due to its aggressive nature and high potential for metastasis. The advent of targeted therapy has revolutionized the treatment landscape of melanoma, particularly for tumors harboring specific genetic alterations such as BRAF V600E mutations. Despite the initial success of targeted agents, resistance inevitably arises, underscoring the need for novel therapeutic strategies. This review explores the latest advances in targeted therapy for melanoma, focusing on new molecular targets, combination therapies, and strategies to overcome resistance.

Genetics and sleep bruxism: a systematic review and meta-analysis of studies with twins.

OBJECTIVE: To systematically review the literature regarding the concordance of sleep bruxism (SB) between monozygotic (MZ) and dizygotic (DZ) twins. METHODS: The registration for this systematic review was accomplished in the International Prospective Register of Systematic Reviews (PROSPERO, No. CRD42021251751). As of July 2022, four databases were searched, including PubMed, Scopus, Embase, and Web of Science, as well as the grey literature in Google Scholar and OpenGrey. Observational studies evaluating SB in MZ and DZ twins of any age and sex were included. For the evaluation of the risk of bias, the Joanna Briggs checklist was utilized. The certainty of evidence was assessed via the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. Pooled and subgroup meta-analyses were performed to estimate concordance of SB ​​between twins (p < 0.05). RESULTS: In total, 3,155 records were identified. In the qualitative analysis, eleven studies were included; of these, seven were included in the meta-analysis. The majority of the articles exhibited a low risk of bias (63.6%). Greater SB concordance was observed between MZ twins than between DZ twins in the analysis of general concordance (OR = 1.47; 95% CI = 1.07-2.02) and also positive concordance (OR = 1.53; 95% CI = 1.29-1.81). Within the subgroup analyses, the significance of the findings remained only for the reported/self-reported SB regarding general concordance (OR = 1.44; 95% CI = 1.07-1.95) and positive concordance (OR = 1.55; 95% CI = 1.28-1.88). Low certainty of the evidence was observed for the general concordance analysis, while moderate certainty was observed for the positive concordance. CONCLUSION: There was a higher concordance of SB in MZ twins compared to DZ twins, indicating a possible genetic influence on the condition's occurrence.

Predictive genetic panel for adult asthma using machine learning methods.

Background: Asthma is a chronic inflammatory disease of the airways that is heterogeneous and multifactorial, making its accurate characterization a complex process. Therefore, identifying the genetic variations associated with asthma and discovering the molecular interactions between the omics that confer risk of developing this disease will help us to unravel the biological pathways involved in its pathogenesis. Objective: We sought to develop a predictive genetic panel for asthma using machine learning methods. Methods: We tested 3 variable selection methods: Boruta's algorithm, the top 200 genome-wide association study markers according to their respective P values, and an elastic net regression. Ten different algorithms were chosen for the classification tests. A predictive panel was built on the basis of joint scores between the classification algorithms. Results: Two variable selection methods, Boruta and genome-wide association studies, were statistically similar in terms of the average accuracies generated, whereas elastic net had the worst overall performance. The predictive genetic panel was completed with 155 single-nucleotide variants, with 91.18% accuracy, 92.75% sensitivity, and 89.55% specificity using the support vector machine algorithm. The markers used range from known single-nucleotide variants to those not previously described in the literature. Our study shows potential in creating genetic prediction panels with tailored penalties per marker, aiding in the identification of optimal machine learning methods for intricate results. Conclusions: This method is able to classify asthma and nonasthma effectively, proving its potential utility in clinical prediction and diagnosis.

Genetic knowledge and attitudes towards genetic testing among final-year medical students at a public university in Ecuador.

Background: Genetics plays a crucial role in the field of medicine, offering numerous applications. However, health professionals often have insufficient knowledge in this area. Therefore, it is essential to provide appropriate genetics education during university studies. Aim: This study aimed to assess the knowledge and attitudes towards genetic testing among final-year medical students at a public university in Ecuador. Methods: A cross-sectional study was conducted involving final-year medical students from a public university in Ecuador. The third version of the Genetic Literacy and Attitudes Survey was administered between April and May 2022. The study examined sociodemographic characteristics, genetic knowledge, and attitudes towards genetic testing. Results: The study included 153 medical students, of which 58.2% identified as female. Most participants fell within the age range of 22 to 25 years old (85.0%). Regarding genetic knowledge, three-quarters of the participants (75.2%) demonstrated intermediate proficiency, while only 9.80% possessed a high level of knowledge. Attitudes towards the clinical and therapeutic applications of genetics, scientific advancements, access to conventional medicine, and other related topics were found to be appropriate. Conclusion: The findings suggest that most final-year medical students at a public university in Ecuador have intermediate genetic knowledge and hold appropriate attitudes towards genetic testing. However, higher education institutions should conduct a comprehensive analysis and restructure their curricula to better prepare students for the medical and technological challenges of the 21st century.

Identification and Application of Emerging Biomarkers in Treatment of Non-Small-Cell Lung Cancer: Systematic Review.

Non-small-cell lung cancer (NSCLC) comprises approximately 85% of all lung cancer cases, often diagnosed at advanced stages, which diminishes the effective treatment options and survival rates. This systematic review assesses the utility of emerging biomarkers-circulating tumor DNA (ctDNA), microRNAs (miRNAs), and the blood tumor mutational burden (bTMB)-enhanced by next-generation sequencing (NGS) to improve the diagnostic accuracy, prognostic evaluation, and treatment strategies in NSCLC. Analyzing data from 37 studies involving 10,332 patients from 2020 to 2024, the review highlights how biomarkers like ctDNA and PD-L1 expression critically inform the selection of personalized therapies, particularly beneficial in the advanced stages of NSCLC. These biomarkers are critical for prognostic assessments and in dynamically adapting treatment plans, where high PD-L1 expression and specific genetic mutations (e.g., ALK fusions, EGFR mutations) significantly guide the use of targeted therapies and immunotherapies. The findings recommend integrating these biomarkers into standardized clinical pathways to maximize their potential in enhancing the treatment precision, ultimately fostering significant advancements in oncology and improving patient outcomes and quality of life. This review substantiates the prognostic and predictive value of these biomarkers and emphasizes the need for ongoing innovation in biomarker research.

Coastal dunes as drivers of genetic differentiation in the honeypot ant Myrmecocystus baja (Formicidae: Formicinae).

Coastal dunes are unique habitats, threatened by human activities. In biogeographical terms, coastal dunes are habitat islands, being discrete and distinct patches of similar habitat among themselves, separated from each other by a different type of habitat. Furthermore, coastal dunes harbor endemic species, adapted to living solely in the habitats found on specific dune systems. For example, the honeypot ant Myrmecocystus baja is endemic and restricted to coastal dunes of Mexico's Baja California Pacific coast. This ecological and biogeographical scenario led to the questions whether their geographical isolation is reflected in their genetic diversity and structuring, and how their demographic history is related with the formation of the dune system habitats. To answer these questions, population genetic, isolation-with-migration, and phylogeographical analyses were carried out, based on mitochondrial and five nuclear intronic markers. Minimal gene flow was detected only between two of the dune systems sampled; otherwise, the M. baja populations were found to be isolated and genetically structured, and their divergence generally pre-dated the modern-day dune systems. It is therefore highly likely that these ants were already present in paleodunes and that each of the populations was established from founder populations as the dunes formed. These findings highlight the importance of coastal dunes for species such as the honeypot ant from Baja California, in promoting genetic differentiation.

Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon.

Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = 0.07-0.52 and Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.

Identification of Genomic Predictors of Muscle Fiber Size.

The greater muscle fiber cross-sectional area (CSA) is associated with greater skeletal muscle mass and strength, whereas muscle fiber atrophy is considered a major feature of sarcopenia. Muscle fiber size is a polygenic trait influenced by both environmental and genetic factors. However, the genetic variants underlying inter-individual differences in muscle fiber size remain largely unknown. The aim of our study was to determine whether 1535 genetic variants previously identified in a genome-wide association study of appendicular lean mass are associated with the CSA of fast-twitch muscle fibers (which better predict muscle strength) in the m. vastus lateralis of 148 physically active individuals (19 power-trained and 28 endurance-trained females, age 28.0 ± 1.1; 28 power-trained and 73 endurance-trained males, age 31.1 ± 0.8). Fifty-seven single-nucleotide polymorphisms (SNPs) were identified as having an association with muscle fiber size (p < 0.05). Of these 57 SNPs, 31 variants were also associated with handgrip strength in the UK Biobank cohort (n = 359,729). Furthermore, using East Asian and East European athletic (n = 731) and non-athletic (n = 515) cohorts, we identified 16 SNPs associated with athlete statuses (sprinter, wrestler, strength, and speed-strength athlete) and weightlifting performance. All SNPs had the same direction of association, i.e., the lean mass-increasing allele was positively associated with the CSA of muscle fibers, handgrip strength, weightlifting performance, and power athlete status. In conclusion, we identified 57 genetic variants associated with both appendicular lean mass and fast-twitch muscle fiber size of m. vastus lateralis that may, in part, contribute to a greater predisposition to power sports.

New Perspectives of Deep Brain Stimulation Indications for Parkinson's Disease: A Critical Review.

Deep Brain Stimulation (DBS) is an effective treatment option for patients with dopaminergic complications of Parkinson's disease (PD) and drug-refractory PD tremor. However, DBS and its indications can be challenging, and they are not often debated in the medical community. Through a critical narrative review, the objective of this paper is to improve the comprehension of DBS indications and help to solve the puzzle that this process can be. Proper patient selection is the first step for a good surgical outcome. In this review, then, relevant considerations are discussed, involving PD genes, PD phenotypes, indications of early stages, non-motor symptoms, neuroimaging predictors, comorbidities, and age. Individualized approaches are encouraged, including clinical and radiological factors. Social support during the whole follow-up and expectations alignment are necessary through this process and are also debated.

Genetic Ancestry and Self-Reported "Skin Color/Race" in the Urban Admixed Population of São Paulo City, Brazil.

Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess their relationship with self-reported skin color/race in an admixed population of Sao Paulo city. We analyzed 226,346 single-nucleotide polymorphisms from 841 individuals participating in the population-based ISA-Nutrition study. Our findings confirmed the admixed nature of the population, demonstrating substantial European, significant Sub-Saharan African, and minor Native American ancestries, irrespective of skin color. A correlation was observed between global genetic ancestry and self-reported color-race, which was more evident in the extreme proportions of African and European ancestries. Individuals with higher African ancestry tended to identify as Black, those with higher European ancestry tended to identify as White, and individuals with higher Native American ancestry were more likely to self-identify as Mixed, a group with diverse ancestral compositions. However, at the individual level, this correlation was notably weak, and no deviations were observed for specific regions throughout the individual's genome. Our findings emphasize the significance of accurately defining and thoroughly analyzing race and ancestry, especially within admixed populations.

An overview of key online resources for human genomics: a powerful and open toolbox for in silico research.

Recent advances in high-throughput molecular methods have led to an extraordinary volume of genomics data. Simultaneously, the progress in the computational implementation of novel algorithms has facilitated the creation of hundreds of freely available online tools for their advanced analyses. However, a general overview of the most commonly used tools for the in silico analysis of genomics data is still missing. In the current article, we present an overview of commonly used online resources for genomics research, including over 50 tools. This selection will be helpful for scientists with basic or intermediate skills in the in silico analyses of genomics data, such as researchers and students from wet labs seeking to strengthen their computational competencies. In addition, we discuss current needs and future perspectives within this field.

Genetic cholestasis: classification according to the cellular defect. / Colestasis genéticas: clasificación según el defecto celular.

Advances in molecular biology achieved during the last years have allowed us to know the genes involved in biliary secretion and the mutations capable of generating cholestasis. The mechanisms involved in forming bile and its circulation have been clarified. According to the biology of biliary secretion, we classify the genetic causes of cholestasis as follows: 1) transport abnormalities in canalicular or basolateral membranes, 2) alterations in intracellular vesicle transit, 3) increased paracellular permeability, 4) mutations in nuclear receptors, 5) cholangiopathies, and 6) hepatocellular diseases, due to disturbance of the function of intracellular organelles or errors of metabolism. This physiopathological classification of chronic cholestasis in childhood will facilitate pediatricians' diagnostic guidance and timely specialized referrals, as patients should receive early and appropriate treatment for its complications.

Los avances en biología molecular alcanzados durante los últimos años nos han permitido conocer los genes que intervienen en la secreción biliar y las mutaciones capaces de generar un cuadro de colestasis. Los mecanismos involucrados en la formación de la bilis y su circulación han sido precisados. De acuerdo a la biología de la secreción biliar, clasificamos las causas genéticas de colestasis en 1) anomalías del transporte en las membranas canalicular o basolateral, 2) alteraciones del tránsito de vesículas intracelulares, 3) aumento de la permeabilidad paracelular, 4) mutaciones en los receptores nucleares, 5) colangiopatías, 6) enfermedades hepatocelulares, por perturbación de la función de orgánulos intracelulares o errores del metabolismo. Esta clasificación fisiopatológica de las colestasis crónicas de la infancia facilitará la orientación diagnóstica de los pediatras y la derivación especializada oportuna, ya que los pacientes deben recibir tempranamente un tratamiento adecuado a las complicaciones de la colestasis.

Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data.

BACKGROUND: A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data. RESULTS: The parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima's D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds. CONCLUSIONS: The detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.

Reconstructing the Global Migration History of Phytophthora infestans Toward Colombia.

The evolution of new variants of plant pathogens is one of the biggest challenges to controlling and managing plant diseases. Of the forces driving these evolutionary processes, global migration events are particularly important for widely distributed diseases such as potato late blight, caused by the oomycete Phytophthora infestans. However, little is known about its migration routes outside North America and Europe. This work used genotypic data from population studies to elucidate the migration history originating the Colombian P. infestans population. For this purpose, a dataset of 1,706 P. infestans genotypes was recollected, representing North and South America, Europe, and Asia. Descriptive analysis and historical records from North America and Europe were used to propose three global migration hypotheses, differing on the origin of the disease (Mexico or Peru) and the hypothesis that it returned to South America from Europe. These scenarios were tested using approximate Bayesian computation. According to this analysis, the most probable scenario (posterior probability = 0.631) was the one proposing a Peruvian origin for P. infestans, an initial migration toward Colombia and Mexico, and a later event from Mexico to the United States and then to Europe and Asia, with no return to northern South America. In Colombia, the scenario considering a single migration from Peru and posterior migrations within Colombia was the most probable, with a posterior probability of 0.640. The obtained results support the hypothesis of a Peruvian origin for P. infestans followed by rare colonization events worldwide.

Ecological transcriptomics reveals stress response pathways of a ground-herb species in a waterlogging gradient of Amazonian riparian forests.

Environmental stress is a fundamental facet of life and a significant driver of natural selection in the wild. Gene expression diversity may facilitate adaptation to environmental changes, without necessary genetic change, but its role in adaptive divergence remains largely understudied in Neotropical systems. In Amazonian riparian forests, species distribution is predominantly influenced by species' waterlogging tolerance. The flooding gradient delineates distinct wetland forest types, shaping habitats and species characteristics. Here we investigated the molecular basis of environmental stress response in a tropical ground-herb species (Ischnosiphon puberulus) to environmental variation in Amazonian riparian forests. We compared environmental variables and gene expression profiles from individuals collected in two forest types: Igapó and Terra firme in the Amazonian riparian forests. Predictable seasonal flooding poses a significant challenge in Igapó compared to Terra firme environments, with the former presenting higher water column height and longer flooding duration. Our findings suggest that contrasting environmental conditions related to flooding regimes are important drivers of population genetic differentiation and differential gene expression in I. puberulus. Enriched gene ontology terms highlight associations with environmental stresses, such as defence response, water transport, phosphorylation, root development, response to auxin, salicylic acid and oxidative stress. By uncovering key environmental stress response pathways conserved across populations, I. puberulus offers novel genetic insights into the molecular basis of plant reactions to environmental constraints found in flooded areas of this highly biodiverse neotropical ecosystem.