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En la actualidad, más de la mitad de las pacientes con cáncer de mama receptor hormonal positivo recibe algún esquema de quimioterapia adyuvante. Sin embargo, sólo algunas de ellas obtendrían un beneficio real en términos de sobrevida. Las plataformas genómicas permiten un mejor entendimiento de la heterogeneidad tumoral entre carcinomas con receptores hormonales positivos, Her2 negativos, habiendo sido validadas como herramientas para identificar aquellas. pacientes que obtendrían un beneficio claro con el tratamiento quimioterápico. El objetivo de nuestro estudio es describir el uso de la plataforma genómica Oncotype Dx® y evaluar su impacto sobre la indicación del tratamiento adyuvante, evaluado principalmente a través del cambio de conducta en relación con la indicación final del tratamiento adyuvante. Material y método: Estudio multicéntrico observacional de cohorte llevado a cabo en distintas Unidades de Mastología de la República Argentina que utilizaran el Oncotype Dx* para esclarecer la indicación del tratamiento adyuvante en pacientes luminales Her2neu negativas en estadio inicial. Se registraron las decisiones relacionadas con el tratamiento antes y luego de realizar la prueba genómica. El objetivo secundario consistió en describir los eventos en aquellas pacientes en quiénes se solicitó dicho estudio. Resultados: Entre enero de 2013 y diciembre de 2018, 211 pacientes con carcinomas luminales A o B, Her2neu negativas realizaron el Oncotype Dx* y fueron incluidas en el estudio. Según nuestros registros, 40% de las pacientes experimentó un cambio en la indicación del tratamiento adyuvante luego de realizada la plataforma genómica. De aquellas pacientes que tenían indicación inicial de hormonoterapia según parámetros tradicionales clínico-patológicos, 24% recibió adicionalmente quimioterapia. En relación con las pacientes que tenían indicación inicial de quimio y hormonoterapia, 49% experimentó un cambio en la indicación de su adyuvancia pudiendo realizar únicamente hormonoterapia. En relación a los eventos descriptos en las pacientes participantes del trabajo, se registraron 4 muertes específicas por la enfermedad, una muerte por otra causa, 2 recaídas a distancia y un cáncer de mama contralateral. Conclusiones: En nuestra población de estudio el uso del Score de Recurrencia (RS) resultó clínicamente significativo en relación al cambio de conducta en la toma de decisión para adyuvancia. En consecuencia, para este grupo de investigadores, ha demostrado ser una herramienta de significativa importancia en la decisión del tratamiento adyuvante de pacientes con cáncer de mama temprano, luminal, Her2neu negativo(AU)
Objetive: Currently, over half of all patients diagnosed with hormone-receptor positive early stage breast cancer will receive some type of adjuvant chemotherapy (CHT), but only a few of them will actually benefit in terms of survival. Genomic platforms allow a better understanding of the heterogeneity among the different types of hormone receptor positive, her2 negative breast cancer, and have proven their validity as tools for identifying those patients who will obtain a clear benefit from CHT. The aim of our study was to analyze the use of the genomic platform Oncotype Dx® in our population and describe its impact on the decision of adjuvant treatment assessed through change in treatment decision. Material and method: this was a real world collaborative observational study, which was performed across several Breast Units in Argentina. Patients who underwent Oncotype Dx® testing to determine adjuvant treatment were included. Decisions regarding treatment were settled before and after the oncotype was performed by the tumor boards of each Breast Unit. Results: From January 2013 to December 2018, 211 patients with luminal A or B, her 2 negative breast cancer who underwent Oncotype Dx" testing were included. We found that treatment decisions were modified after Oncotype DX in approximately 40% of patients. In 24% percent of cases, chemotherapy was added to the initial treatment plan although endocrine therapy alone had initially been considered (potential subtreatment); and on the other hand, 49% of all patients were able to receive endocrine therapy only when, due to traditional prognostic factors, they would have received chemotherapy (potential overtreatment). Conclusions: In our population, we found that the use of the Recurrence Score was associated with a significant change in treatment recommendation We therefore consider it to be a very important tool and a decisive factor for the selection of adjuvant treatment in patients with hormone receptor positive, her2neu negative early breast cancer(AU)
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Yersinia bacteriophage is a virus that hosts Yersinia bacteria, which not only affects the survival and evolution of the host bacteria, but also plays an important role in biomass cycling and energy flow. As of November 2022, the National Center for Biotechnology Information (NCBI) in the United States has uploaded the complete genome sequences of 119 Yersinia bacteriophages. The genome size and genetic content of different Yersinia bacteriophages vary, and the similarity between the genomes is relatively low. This article reviews the basic genomic characteristics and gene functions of Yersinia bacteriophages, and studies the differences between the genomes of different species of Yersinia bacteriophages, in order to provide reference for understanding the functional differences and genetic evolution of Yersinia bacteriophage.
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Stroke is an acute cerebrovascular disease, and a group of diseases that cause brain tissue damage due to sudden rupture of brain blood vessels or blockage of blood vessels, mainly including ischemic stroke and hemorrhagic stroke. In recent years, although some progresses have been achieved, there are still few biomarkers that can be used for effective warning and monitoring for people at high risk of stroke. Omics research is an important research strategy for discovering differential genes, molecules, and epigenetic markers in the process of disease occurrence and development. A systematic summary of progress made in recent years, in stroke genomics, transcriptomics, proteomics, and metabolomics in recent years, as well as their potential applications in stroke warning, diagnosis, and monitoring, was systematically discussed in the presence review, in order to provide reference for future research on stroke biomarkers.
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The prevalence rate of nonalcoholic fatty liver disease （NAFLD） reaches up to 30% around the world， and the disease has a serious impact on human health and constitutes a public health burden. Due to difficulties in the diagnosis and monitoring of NAFLD， it is important to identify potential drug targets and biomarkers， and multi-omics techniques hold great promise in the search for early diagnostic markers， therapeutic targets， and outcome and prognostic assessment of NAFLD. This article reviews the research advances in multi-omics techniques in the field of NAFLD in recent years， in order to provide a richer theoretical basis and new strategies for the prevention and treatment of NAFLD.
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ObjectiveTo investigate the mechanism of Baitouweng Tang in inhibiting the growth of esophageal cancer （EC） cells by regulating budding uninhibited by benzimidazoles 1 （BUB1）/signal transducer and activator of transcription 3 （STAT3） signaling pathway. MethodGene chip technology was used to explore the differential gene expression between esophageal cancer tissues and normal tissues and identified differentially expressed genes. The differentially expressed genes were analyzed by bioinformatics methods. EC cells were treated with 25， 50， 100， 200， 400， 800 mg·L-1 Baitouweng Tang. EC cell viability was detected by Thiazolyl Blue （MTT） colorimetry. Cell cycle and apoptosis were measured by flow cytometry. The expression of BUB1 was measured by real time quantitative polymerase chain reaction （Real-time PCR）. The protein levels of BUB1， STAT3， phosphorylated （p）-STAT3， Cyclin B1 （CCNB1）， cyclin-dependent kinase 1 （CDK1）， B-cell lymphoma-2 （Bcl-2）， cysteinyl aspartate-specific proteinase（Caspase）-3， and Caspase-9 were measured by Western blot. The migration and invasion abilities of the cells were measured by wound-healing and Transwell invasion assays. ResultDifferentially expressed genes were primarily involved in biological processes， signaling pathways， and network construction related to cell mitosis， with BUB1 identified as a key core gene. Compared with the control group， Baitouweng Tang inhibited BUB1 expression （P<0.05，P<0.01）. In vitro experiments showed that compared with the control group， Baitouweng Tang could significantly inhibit the growth （P<0.05，P<0.01）， migration and invasion （P<0.05，P<0.01） of EC cells， induce apoptosis （P<0.05，P<0.01）， and cause G2/M phase increase （P<0.01）. After treatment with Baitouweng Tang， compared with the results in the control group， the expression of Caspase-3， and Caspase-9 in EC cells increased significantly （P<0.05，P<0.01）， while the expression of Bcl-2， BUB1， CCNB1， and CDK1 decreased significantly （P<0.05，P<0.01）. Moreover， the STAT3 signaling pathway was also found to play an important role in this process. ConclusionBaitouweng Tang may inhibit the growth of EC cells by downregulating BUB1 and mediating the STAT3 signaling pathway.
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Abstract Familial chylomicronemia syndrome (FCS) is an autosomal recessive disorder, characterized by alterations in the catabolism of chylomicrons and by increased levels of plasma triglycerides. It has been shown that about 60-90% of FCS patients have biallelic mutations in the LPL gene and the remaining patients have mutations in genes encoding proteins closely related to LPL function. The objective of this manuscript is to illustrate the different clinical scenarios of FCS presentation, and to guide practitioners on the usefulness of genetic tests in each of them. To this end, several published papers about recommendations for the diagnosis of FCS are discussed briefly, in addition to the presentation of several hypothetical cases, highlighting different clinical presentations and possible associated genetic findings. These cases illustrate the multiplicity of potential aspects of family history, clinical manifestations, biochemical parameters, and patterns of genetic variants found in genomic analyses of FCS.
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ABSTRACT Molecular medicine opened new horizons in understanding disease mechanisms and discovering target interventions. The wider availability of DNA and RNA sequencing, immunohistochemical analysis, proteomics, and other molecular tests changed how physicians manage diseases. The gastric cancer molecular classification proposed by The Cancer Genome Atlas Program divides gastric adenocarcinomas into four subtypes. However, the available targets and/or immunotherapies approved for clinical use seem to be dissociated from these molecular subtypes. Until a more reliable interpretation of the stupendous amount of data provided by the molecular classifications is presented, the clinical guidelines will rely on available actionable targets and approved therapies to guide clinicians in conducting cancer management in the era of molecular therapies.
RESUMO A medicina molecular abriu novos horizontes na compreensão dos mecanismos das doenças e na descoberta de intervenções alvo. A maior disponibilidade de sequenciação de DNA e RNA, análise imuno-histoquímica, proteômica e outros testes moleculares mudou a forma como os médicos conduzem as doenças. A classificação molecular do câncer gástrico proposta pelo Atlas do Genoma do Câncer divide os adenocarcinomas gástricos em quatro subtipos. No entanto, os alvos disponíveis e/ou imunoterapias aprovadas para uso clínico parecem estar dissociados desses subtipos moleculares. Até que seja apresentada uma interpretação mais confiável da estupenda quantidade de dados fornecidos pelas classificações moleculares, as diretrizes clínicas irão se basear nos alvos acionáveis disponíveis e nas terapias aprovadas para orientar os médicos na condução da gestão do câncer na era das terapias moleculares.
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Desde el advenimiento de la ecografía obstétrica y estudios invasivos además genéticos fetales han ayudado en la detección antenatal de anormalidades congénitas siendo uno de los objetivos básicos de la vigilancia fetal anteparto. La combinación de ambas técnicas ofrece, hoy en día un abordaje completo en términos de diagnóstico prenatal. Se cree que muchos trastornos del desarrollo surgen de factores de riesgos genéticos y ambientales. Uno de estos es la holoprosencefalia, sirve como modelo para comprender diversas formas de etiología multifactorial. El análisis genómico, la epidemiología y estudios mecánicos de modelos animales han revelado que factores de riesgo interactúan para producir resultados de desarrollo adversos. La holoprosencefalia es consecuencia de factores genéticos y/o ambientales que interrumpen la especificación de la línea media del prosencéfalo en formación. Estas alteraciones dan lugar a una amplia gama de consecuencias fenotípicas para el cerebro y la cara del nuevo ser humano en formación. Son comunes en 1 de 250 fetos humanos, pero el 97% no sobrevive al nacimiento. La patogenia molecular precisa de la holoprosencefalia sigue siendo desconocida. Aquí, describimos nuestra comprensión de los principales factores impulsores que conducen a patologías de holoproscencefalia y elaboramos nuestro enfoque de genómica integrada multifactorial. Las tecnologías genómicas proporcionan una visión sin precedentes de la variación asociada a la enfermedad. A continuación, se describe un caso de diagnóstico prenatal de trisomía 13 y holoprosencefalia. En éste, se logró establecer un diagnóstico antenatal anatómico y genético preciso.
Since the advent of obstetric ultrasound and invasive studies, fetal genetics have helped in the antenatal detection of congenital abnormalities, being one of the basic objectives of antepartum fetal surveillance. The combination of both techniques currently offers a complete approach in terms of prenatal diagnosis. Many developmental disorders are thought to arise from genetic and environmental risk factors. One of these is holoprosencephaly, which serves as a model for understanding various forms of multifactorial etiology. Genomic analysis, epidemiology, and mechanistic studies of animal models have revealed that risk factors interact to produce adverse developmental outcomes. Holoprosencephaly results from genetic and/or environmental factors that disrupt the specification of the midline of the forming forebrain. These alterations result in a wide range of phenotypic consequences for the brain and face of the newly developing human being. They are common in 1 in 250 human fetuses, but 97% do not survive birth. The precise molecular pathogenesis of holoprosencephaly remains unknown. Here, we describe our understanding of the main drivers leading to holoproscencephaly pathologies and elaborate on our multifactorial integrated genomics approach. Genomic technologies provide unprecedented insight into disease-associated variation. A case of prenatal diagnosis of trisomy 13 and holoprosencephaly is described below. In this study, it was possible to establish an accurate anatomical and genetic antenatal diagnosis.
摘要
Resumen Las novedades en el campo de los errores innatos del metabolismo (EIM) son espectaculares. Se han descrito nuevos EIM, se conoce mejor sus bases fisiopatológicas y las implicaciones para el organismo. Con la llegada de las nuevas técnicas de metabolómica, lípidomica y genómica se han multiplicado los avances en el diag nóstico y permiten explorar nuevas opciones terapéu ticas. Se ha establecido una nueva clasificación de los EIM en base a los más de 1.450 EIM identificados. Está irrumpiendo una nueva especialidad, que es la medici na metabólica. El cribado neonatal se estáempezando a universalizar y nos permite hoy en día, con tándem masas, el diagnóstico de más de 20 enfermedades me tabólicas del período neonatal que tienen opciones de tratamiento. Se están creando unidades de EIM para adultos para seguir niños con EIM que sobreviven a la enfermedad y con cada vez mejor calidad de vida y se diagnostican EIM que debutan en la adolescencia o laedad adulta. Aparecen las terapias personalizadas y las guías de práctica clínica para muchos EIM. Finalmente están emergiendo cada vez nuevas opciones terapéuticas que permiten una mayor supervivencia y mejor calidad de vida. La terapia génica convencional ya se está aplicando en algunos EIM.Sin embargo, las estrategias de edición de genes con terapias de ARN pueden permitir corregir la mutación genética mini mizando los problemas asociados con la terapia génica de compensación convencional.
Abstract The advances in the field of inborn errors of metabo lism (IEM) are spectacular. New IEM have been described, their pathophysiological bases and implications for the organism are better known. With the advent of new metabolomics, lipidomics and genomics techniques, advances in diagnosis have multiplied and allow new therapeutic options to be explored. A new IEM classi fication has been established based on the more than 1.450 IEM identified. A new specialty is emerging, which is metabolic medicine. Neonatal screening is becom ing universal and allows us today, with tandem mass, to diagnose more than 20 metabolic diseases of the neonatal period, with treatment options. IEM units for adults are being created to follow-up children with IEM who survive the disease and with an increasingly better quality of life, and some IEM that start in adolescence or adulthood are diagnosed. Personalized therapies and clinical practice guidelines appear for any IEM. Finally, new therapeutic options are emerging day to day that allow a longer survival and better quality of life. Con ventional gene therapy is already being applied in some IEM. However, gene editing strategies with RNA thera pies may allow the correction of the genetic mutation, minimizing the problems associated with conventional compensation gene therapy.
摘要
La mayoría de los trastornos psiquiátricos tienen una heredabilidad de moderada a alta, con diferentes arquitecturas genéticas. Aunque la investigación genética en psiquiatría ha tenido un avance progresivo, sus hallazgos, interpretación e impacto en la psiquiatría clínica resultan desconocidos para la mayoría de los profesionales de salud mental. En este artículo se abordan conceptos clave sobre genética para el entendimiento de algunas entidades clínicas, con énfasis en la nomenclatura genética y los tipos de mutaciones. Particularmente, se plantea el rol de la herencia en los inicios de la investigación genética en psiquiatría, los diseños de estudio más utilizados y sus principales objetivos. Por otro lado, se revisan algunas bases de datos genéticas y genómicas que pueden ser de utilidad para la práctica clínica. Entre ellas destacan , ClinVar, Ensembl y . Finalmente, se plantea una viñeta clínica en donde es posible aplicar algunas de las herramientas de la medicina genómica. Debido a que la evidencia en genética psiquiátrica se basa en estudios realizados en poblaciones con origen ancestral europeo o norteamericano, es de suma relevancia desarrollar estudios locales para incrementar el conocimiento y la aplicación de la medicina genómica sobre poblaciones subrepresentadas.
Most psychiatric disorders are moderate to highly heritable, often with different genetic architectures. Although genetic research in psychiatry has progressed, its findings, interpretation, and impact on clinical psychiatry are unknown to most mental healthcare professionals. This article addresses key genetic concepts to understand some clinical entities, emphasizing genetic terminology and types of mutations. Particularly, we describe the role of heritability in the early days of psychiatry genetic research, the most used study designs, and their main objectives. On the other hand, we review some genetic and genomic databases useful for clinical practice. These include Online Mendelian Inheritance in Man, ClinVar, Ensembl, and The Single Nucleotide Polymorphism Database. Finally, a clinical vignette is presented in which we can apply genomic medicine tools. Since the evidence in psychiatric genetics is based on studies carried out in European or North American ancestral populations, we must develop local studies to increase the knowledge and application of genomic medicine on underrepresented populations.
Subject(s)
Humans , Psychiatry , Mental Disorders/genetics , Mental Disorders/therapy , Health Personnel , Genomic Medicine , Mutation摘要
El Hospital Garrahan ha sido pionero en el diagnóstico molecular de patologías pediátricas en Argentina. Los avances tecnológicos de las últimas décadas en el área de la biología molecular, sentaron las bases para la optimización y ampliación del diagnóstico molecular a partir de la secuenciación masiva en paralelo de múltiples genes. El presente trabajo describe el proceso de implementación de los estudios de secuenciación de nueva generación y el desarrollo de la Unidad de Genómica en un hospital público pediátrico de alta complejidad, así como su impacto en las capacidades diagnósticas de enfermedades poco frecuentes de origen genético. La creación del Grupo Interdisciplinario de Estudios Genómicos constituyó la vía institucional para la toma de decisiones que implican la implementación de nuevos estudios genómicos y el establecimiento de prioridades diagnósticas, extendiendo la disponibilidad del diagnóstico molecular a más disciplinas. La Unidad de Genómica trabaja en diseñar las estrategias que permitan la mayor optimización de los recursos con los que cuenta el hospital, teniendo en cuenta el equipamiento disponible, las prioridades establecidas y la frecuencia de las distintas patologías. Se demuestra el salto significativo operado en nuestras capacidades diagnósticas, tanto en la variedad de enfermedades como en el número de genes analizados, habiendo estudiado a la fecha alrededor de 2.000 pacientes, muchos de los cuales ven de este modo finalizada su odisea diagnóstica. Los estudios de NGS se han convertido en una herramienta de la práctica diaria para la atención de un número importante de pacientes de nuestro hospital. Continuaremos trabajando para ampliar su aplicación a la mayor cantidad de patologías, a través de los mecanismos institucionales ya existentes (AU)
The Garrahan Hospital has been a pioneer in the molecular diagnosis of pediatric diseases in Argentina. The technological advances of the last decades in the area of molecular biology have laid the foundations for the optimization and expansion of molecular diagnostics through massive parallel sequencing of multiple genes. This study describes the process of implementation of next-generation sequencing studies and the development of the Genomics Unit in a public pediatric tertiary hospital, and its impact on the capacity to diagnose rare diseases of genetic origin. The creation of the Interdisciplinary Group of Genomic Studies constituted the institutional pathway for decision-making involving the implementation of new genomic studies and the establishment of diagnostic priorities, extending the availability of molecular diagnostics to additional disciplines. The Genomics Unit is working to design strategies that allow for optimization of the resources available to the hospital, taking into account the equipment available, the priorities established, and the frequency of the different diseases. It demonstrates the significant leap in our diagnostic capabilities, both in the variety of diseases and in the number of genes analyzed. To date, around 2,000 patients have been studies, many of whom have thus completed their diagnostic odyssey. NGS studies have become a tool in daily practice for the care of a significant number of patients in our hospital. We will continue working to expand its application to as many diseases as possible, through the existing institutional mechanisms (AU)
Subject(s)
Humans , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Genomics/instrumentation , Molecular Diagnostic Techniques/methods , High-Throughput Nucleotide Sequencing , Genomic Medicine/trends , Genetic Diseases, Inborn/diagnosis , Laboratories, Hospital , Hospitals, Pediatric摘要
A generation of new science has evolved with the development of bioinformatics and computational biology, which have molecular biology as an integrated part. In the past decade, technological advances have promoted a prominent development in expertise and knowledge in the molecular basis of phenotypes. In Bioinformatics, biological data is evaluated by computational science and processed in a more statistical and meaningful way. It includes the collection classification storage and evaluation of biochemical and organic statistics using computers in particular as implemented in molecular genetics and genomics. Computational Biology and Bioinformatics are emerging branches of science and include the use of techniques and concepts from informatics statistics, mathematics, chemistry, biochemistry, physics and linguistics. Therefore, bioinformatics and computational biology have sought to triumph over many challenges of which a few are listed in this overview. This evaluation intends to provide insight into numerous bioinformatics databases and their uses in the analysis of biological records exploring approaches emerging methodologies strategies tools that can provide scientific meaning to the information generated.
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Resumen Introducción: La prueba genómica de recurrencia de 21 genes (PGR21) permite determinar la utilidad de la quimioterapia adyuvante en pacientes con cáncer de mama temprano luminal (CMTL). Se han desarrollado modelos predictivos adicionales, como las ecuaciones de Magee (EM), el modelo Predict (MP) y la puntuación del nomograma de la Universidad de Tennessee (NT). Objetivo: Evaluar la concordancia entre PGR21, EM, MP y NT. Métodos: Se incluyeron pacientes con CMTL unifocal y con resultados de PGR21, EM, MP y NT. Se efectuó subanálisis de mujeres mayores de 50 años. La concordancia se evaluó mediante índice kappa de Cohen (IK). Resultados: Se incluyeron 122 mujeres. La concordancia entre PGR21 y EM (IK = 0.35) y MP (IK = 0.24) fue aceptable (p < 0.001); entre PGR21 y NT fue inferior (IK = 0.16, p = 0.04). Se incluyeron 80 pacientes mayores de 50 años con datos suficientes para calcular los tres modelos. Se encontró concordancia entre la clasificación de bajo riesgo mediante PGR21 y los tres modelos combinados en 36/37 pacientes (valor predictivo negativo de 97.3 %). Conclusión: Se puede omitir la PGR21 en las mujeres mayores de 50 años con CMTL que se clasifica de bajo riesgo en los tres modelos predictivos.
Abstract Introduction: The genomic-based 21-gene recurrence score assay (21-GRSA) allows to determine the usefulness of adjuvant chemotherapy in patients with luminal-type early breast cancer (LTEBC). Additional predictive models have also been developed, such as Magee equations (ME), the Predict model (PM), and the Tennessee nomogram score (TNS). Objective: To evaluate the concordance between 21-GRSA, ME, PM and TNS. Methods: Patients with unifocal LTEBC and 21-GRSA, ME, PM and TNS results were included. A subgroup analysis of women older than 50 years was carried out. Concordance between the models and 21-GRSA was evaluated using Cohen's kappa index (KI). Results: One-hundred and twenty-two women were included. Concordance between 21-GRSA and ME (KI = 0.35) and PM (KI = 0.24) was fair (p < 0.001). Concordance between 21-GRSA and TNS was inferior (KI = 0.16, p = 0.04). Eighty patients older than 50 years with sufficient data to calculate all three predictive models were included. Concordance was found between the low-risk classification on 21-GRSA and all three combined models in 36/37 patients (negative predictive value of 97.3%). Conclusion: 21-GRSA can be omitted in women older than 50 years with LTEBC classified with low risk scores on all three predictive models.
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With the advancements in analytical and molecular techniques, Dried Blood Spots (DBS) are re-emerging as attractive and cost-effective alternatives for global health surveillance. The use of DBS has been well-characterized in the neonatal screening of metabolic diseases, therapeutic screening as well as in epidemiological studies for biomonitoring. Malaria is one such infectious disease where DBS use can expedite molecular surveillance for assessing drug resistance and for refining drug usage policies. In India, malaria cases have reduced significantly over the past decade but to achieve malaria elimination by 2030, country-wide DBS-based screening should be conducted to identify the presence of molecular markers of artemisinin resistance and to study parasite reservoirs in asymptomatic populations. DBS has wide applications in genomics, proteomics, and metabolomic studies concerning both host and pathogen factors. Hence, it is a comprehensive tool for malaria surveillance that can capture both host and parasite information. In this review, we elucidate the current and prospective role of DBS in malaria surveillance and its applications in studies ranging from genetic epidemiology, parasite and vector surveillance, drug development and polymorphisms to ultimately how they can pave the roadmap for countries aiming malaria elimination
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Abstract@#Hypertensive disorders of pregnancy (HDP) are a common severe complication during pregnancy, which is characterized by complex etiology, unclear pathogenesis and lack of effective tools for early diagnosis and prediction. Recently, the development of omics technology provides new insights into the research into HDP. Based on national and international publications from 2011 to 2022, this review summarizes the application of genomics, proteomics, metabolomics, and microbiomics in the pathogenesis and prediction of HDP, so as to provide insights into the prediction, prevention and precise treatment of HDP.
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OBJECTIVE@#Campylobacter jejuni NCTC11168 is commonly used as a standard strain for flagellar biosynthesis research. In this report, two distinguished phenotypic isolates (CJ1Z, flhA mutant strain, lawn; CJ2S, flhA complemented strain, normal colony) appeared during laboratory passages for NCTC11168.@*METHODS@#Phenotypic assessments, including motility plates, transmission electron microscopy, biofilm formation assay, autoagglutination assay, and genome re-sequencing for these two isolates (CJ1Z, flhA mutant strain; CJ2S, flhA complemented strain) were carried out in this study.@*RESULTS@#Transmission electron microscopy revealed that the flagellum was lost in CJ1Z. Phenotypic assessments and genome sequencing of the two isolates were performed in this study. The capacity for biofilm formation, colony auto-agglutination, and isolate motility was reduced in the mutant CJ1Z. Comparative genomic analysis indicated a unique native nucleotide insertion in flhA (nt, 2154) that caused the I719Y and I720Y mutations and early truncation in flhA.@*CONCLUSION@#FlhA has been found to influence the expression of flagella in C. jejuni. To the best of our knowledge, this is the first study to describe the function of the C-terminal of this protein.
Subject(s)
Campylobacter jejuni/genetics , Bacterial Proteins/metabolism , Mutation , Biological Variation, Population摘要
Stenotrophomonas species are non-fermentative Gram-negative bacteria that are widely distributed in environment and are highly resistant to numerous antibiotics. Thus, Stenotrophomonas serves as a reservoir of genes encoding antimicrobial resistance (AMR). The detection rate of Stenotrophomonas is rapidly increasing alongside their strengthening intrinsic ability to tolerate a variety of clinical antibiotics. This review illustrated the current genomics advances of antibiotic resistant Stenotrophomonas, highlighting the importance of precise identification and sequence editing. In addition, AMR diversity and transferability have been assessed by the developed bioinformatics tools. However, the working models of AMR in Stenotrophomonas are cryptic and urgently required to be determined. Comparative genomics is envisioned to facilitate the prevention and control of AMR, as well as to gain insights into bacterial adaptability and drug development.
Subject(s)
Stenotrophomonas/genetics , Drug Resistance, Bacterial/genetics , Anti-Bacterial Agents/pharmacology , Gram-Negative Bacteria , Genomics , Microbial Sensitivity Tests摘要
Dracaena marginata is a widely cultivated horticultural plant in the world, which has high ornamental and medicinal value. In this study, the whole genome of leaves from D. marginata was sequenced by Illumina HiSeq 4000 platform. The chloroplast genome were assembled for functional annotation, sequence characteristics and phylogenetic analysis. The results showed that the chloroplast genome of D. marginata composed of four regions with a size of 154 926 bp, which was the smallest chloroplast genome reported for Dracaena species to date. A total of 132 genes were identified, including 86 coding genes, 38 tRNA genes and 8 rRNA genes. Codon bias analysis found that the codon usage bias was weak and there was a bias for using A/U base endings. 46 simple sequence repeat and 54 repeats loci were detected in the chloroplast genome, with the maximum detection rate in the large single copy region and inverted repeat region, respectively. The inverted repeats boundaries of D. marginata and Dracaena were highly conserved, whereas gene location differences occurred. Phylogenetic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, which was the closest relationship and conformed to the morphological classification characteristics. The analysis of the chloroplast genome of D. marginata provides important data basis for species identification, genetic diversity and chloroplast genome engineering of Dracaena.
Subject(s)
Phylogeny , Dracaena , Genome, Chloroplast/genetics , Base Sequence , Genes, Plant摘要
Pseudoexfoliative glaucoma(PEXG)is an eye disease that seriously endangers vision. It is more invasive than primary open-angle glaucoma(POAG), with more serious damage to the optic nerve, worse prognosis and higher resistance to treatment. Early diagnosis of PEXG can help to treat the disease in time and delay the progress of the disease, so it is important to determine appropriate biomarkers. In recent years, more and more people have begun to study the biomarkers of PEXG, hoping to understand the pathogenesis of the disease, find out the potential early diagnosis and treatment targets of PEXG, and provide some help to the disease through the research of genomics, transcriptomics, proteomics, metabolomics and lipomics markers. This article will review the progress of biomarkers of PEXG in recent years, some biomarkers may provide new ideas for early diagnosis of PEXG in the future.
摘要
Objective:To investigate the feasibility of classifying imaging patterns of dermatomyositis/polymyositis-related interstitial lung disease (DM/PM-ILD) into subtypes based on chest CT radiomics features and a model was constructed by machine learning algorithms.Methods:From November 2011 to November 2020, 107 patients diagnosed with PM/DM-ILD at the First Affiliated Hospital of Xi′an Jiaotong University were retrospectively analyzed. A total of 315 cases with chest CT were collected. Doctors pre-classified image patterns, including 105 cases with non-specific interstitial pneumonia (NSIP), 90 cases with organizing pneumonia (OP), and 66 cases with non-specific interstitial pneumonia combined with organizing pneumonia (NSIP+OP), 35 cases with common interstitial pneumonia (UIP), and 19 cases with diffuse alveolar damage (DAD), ANOVA was used to test the difference of baseline clinical information among the imaging classification groups. All images were divided into the training set and the est set by stratified random sampling at a ratio of 4∶1. In each CT scan, 3D slicer was used to segment each lung lobe, and then reconstructed into 3 mm 3 of voxels, and Pyradiomics library was used to extract the radiomic features of the whole lung and each lobe. The multi-classification goal was achieved by constructing random forest base classifiers for each of the five groups and then voting as the final model. In the process of constructing the base classifier, firstly, the balance between sample groups was achieved by SMOTETomek comprehensive sampling, and the optimal feature set was selected by independent sample t test and L1 regularized least absolute shrinkage and selection operator (LASSO) regression. In this study, the Radiomics model was constructed based on chest CT radiomics features, and the Radiomics + model was constructed by introducing gender and age information. The base classifier and the integration model use the mean accuracy and the area under the receiver operator characteristics analysis curve (AUC) to evaluate the performance, respectively. Results:There was a statistically significant difference ( P<0.05) between the ages of the NSIP, OP, NSIP+OP, UIP, and DAD groups [(57±13),(53±8),(54±10),(44±11), and (46±8)years old, respectively], F=11.82, P<0.001. In the Radiomics model, for each group of NSIP, OP, NSIP+OP, UIP, and DAD, the AUCs of the training set were 0.87, 0.91, 0.91, 0.96, and 0.99, respectively, and the AUC of the test set were 0.81, 0.82, 0.79, 0.93, 0.89. In the final Radiomics + model, for each group of NSIP, OP, NSIP+OP, UIP, and DAD, the AUCs of the training set were 0.89, 0.91, 0.92, 0.97, and 0.99, respectively, and the AUCs of the test set were 0.84, 0.82, 0.78, 0.94, 0.90. Conclusion:Based on chest CT radiomics features and key clinical features (sex, age), the Radiomics + model constructed by machine learning has good classification performance for the imaging patterns of PM/DM-LD.