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Summative assessments are often underused for feedback, despite them being rich with data of students' applied knowledge and clinical and professional skills. To better inform teaching and student support, this study aims to gain insights from summative assessments through profiling students' performance patterns and identify those students missing the basic knowledge and skills in medical specialities essential for their future career. We use Latent Profile Analysis to classify a senior undergraduate year group (n = 295) based on their performance in applied knowledge test (AKT) and OSCE, in which items and stations are pre-classified across five specialities (e.g. Acute and Critical Care, Paediatrics, ). Four distinct groups of students with increasing average performance levels in the AKT, and three such groups in the OSCE are identified. Overall, these two classifications are positively correlated. However, some students do well in one assessment format but not in the other. Importantly, in both the AKT and the OSCE there is a mixed group containing students who have met the required standard to pass, and those who have not. This suggests that a conception of a borderline group at the exam-level can be overly simplistic. There is little literature relating AKT and OSCE performance in this way, and the paper discusses how our analysis gives placement tutors key insights into providing tailored support for distinct student groups needing remediation. It also gives additional information to assessment writers about the performance and difficulty of their assessment items/stations, and to wider faculty about student overall performance and across specialities.
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BACKGROUND: Glutamate-rich WD repeat containing 1 (GRWD1) is over-expressed in a variety of malignant tumors and is considered to be a potential oncogene. However, its mechanism of action in gastric cancer (GC) is still unclear. METHODS: Data analysis, Immunohistochemistry, and Western Blot (WB) were performed to verify the expression of GRWD1 in GC and para-cancerous tissues. The association between GRWD1 expression and tumor size, tissue differentiation, lymph node metastasis, TNM stage, and prognosis was analyzed according to the high and low expression levels of GRWD1. The relationship between GRWD1 and Notch pathway was verified by data analysis and WB. The effects of GRWD1 on the proliferation, migration, and invasion of GC cells were verified by cell proliferation, migration, and invasion assays. We confirmed that the high expression of GRWD1 promoted the proliferation of GC cells in vivo through the tumor formation assay in nude mice. RESULTS: The expression of GRWD1 was higher in GC tissues than in para-cancerous tissues, and its expression was positively correlated with tumor size, lymph node metastasis, and TNM stage, but negatively correlated with differentiation grade and prognosis. GRWD1 over-expression increased ADAM metallopeptidase domain 17 (ADAM17) expression and promoted Notch1 intracellular domain (NICD) release to promote GC cell proliferation, migration, and invasion in vitro. Results from animal studies have shown that high GRWD1 expression could promote GC cell proliferation in vivo by activating the Notch signaling pathway. CONCLUSION: GRWD1 promotes GC progression through ADAM17-dependent Notch signaling, and GRWD1 may be a novel tumor marker and therapeutic target.
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Proteína ADAM17 , Proteínas Portadoras , Neoplasias Gástricas , Animales , Ratones , Línea Celular Tumoral , Movimiento Celular , Proliferación Celular , Regulación Neoplásica de la Expresión Génica , Metástasis Linfática , Ratones Desnudos , Invasividad Neoplásica , Transducción de Señal , Neoplasias Gástricas/patología , Regulación hacia Arriba , Proteínas Portadoras/metabolismo , Proteína ADAM17/metabolismoRESUMEN
In recent years, with the continuous in-depth exploration of the molecular mechanisms of tumorigenesis, numerous potential new targets for cancer treatment have been identified, some of which have been further developed in clinical practice and have produced positive outcomes. Notably, researchers' initial motivation for studying copper metabolism in cancer stems from the fact that copper is a necessary trace element for organisms and is closely connected to body growth and metabolism. Moreover, over the past few decades, considerable progress has been made in understanding the molecular processes and correlations between copper and cancer. Certain achievements have been made in the development and use of relevant clinical medications. The concept of "cuproptosis," a novel concept that differs from previous forms of cell death, was first proposed by a group of scientists last year, offering fresh perspectives on the targeting capabilities of copper in the treatment of cancer. In this review, we introduced the fundamental physiological functions of copper, the key components of copper metabolism, and a summary of the current research contributions on the connection between copper and cancer. In addition, the development of new copper-based nanomaterials and their associated mechanisms of action are discussed. Finally, we described how the susceptibility of cancer cells to this metallic nutrition could be leveraged to further improve the existing cancer treatment paradigm in the new setting.
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Cobre , Neoplasias , Humanos , Cobre/metabolismo , Cobre/uso terapéutico , Neoplasias/tratamiento farmacológico , CarcinogénesisRESUMEN
This study explored the connection between KDM6A expression and patient prognosis and the mechanism of KDM6A's role in developing GC (GC). From the immunohistochemical Analysis of 107 GC patients' tumors, we discovered that patients with reduced KDM6A expression had a shorter survival time. There was a correlation between KDM6A expression and the degree of differentiation of tumor tissue, T stage, N stage, and TNM stage. KDM6A gene expression was positively connected with the expression level of E-cadherin and negatively connected with the expression level of N-cadherin and vimentin in vitro tests. KDM6A gene suppression prevented GC cell proliferation, migration, and invasion, whereas high KDM6A gene expression promoted these processes. Second, low expression of KDM6A down-regulates GSK3ß, p-GSK3ß, up-regulates C-Myc, CyclinD1, and promotes ß-catenin protein expression in the nucleus, while the high expression does the opposite. Then, we used ICG001 to block the Wnt/ß-catenin signal transduction pathway, and the results revealed that ICG001 could reduce the promoting effect of low KDM6A expression on aggressiveness and EMT in GC cells. KDM6A down-regulation stimulates the proliferation of GC cells, while ICG001 reverses this action in vivo tests. Patients whose KDM6A expression was found to be low had a poor prognosis, as this study found. The EMT is inhibited by regulating theWnt/ß-catenin signaling by KDM6A, which reduces GC cell proliferation, migration, and invasion. KDM6A may be a viable target for GC in clinical therapy.
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Neoplasias Gástricas , beta Catenina , Humanos , beta Catenina/metabolismo , Carcinogénesis/genética , Línea Celular Tumoral , Movimiento Celular/genética , Proliferación Celular/genética , Transición Epitelial-Mesenquimal/genética , Regulación Neoplásica de la Expresión Génica , Glucógeno Sintasa Quinasa 3 beta/metabolismo , Neoplasias Gástricas/patología , Vía de Señalización Wnt/genéticaRESUMEN
Data management is a critical challenge required to improve the rigor and reproducibility of large projects. Adhering to Findable, Accessible, Interoperable, and Reusable (FAIR) standards provides a baseline for meeting these requirements. Although many existing repositories handle data in a FAIR-compliant manner, there are limited tools in the public domain to handle the metadata burden required to connect data from multi-omic projects that span multiple institutions and are deposited in diverse repositories. One promising approach is the SEEK platform, which allows for diverse metadata and provides an established repository. SEEK is challenged by the assumption of single deposition events where a sample is immutable once entered in the database. This is structured for published data but presents a limitation for ongoing studies where multiple sequential events may occur in a single sample at different sites. To address this issue, we have created a modified wrapper around the SEEK platform that allows for active data management by establishing more discrete sample types that are mutable to permit the expansion of the types of metadata, allowing researchers to track additional information. The use of discrete nodes also converts assays from nodes to edges, creating a network model of the study and more accurately representing the experimental process. With these changes to SEEK, users are able to collect and organize the information that researchers need to improve reusability and reproducibility as well as make data and metadata available to the scientific community through public repositories.
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Metadatos , Bases de Datos Factuales , Reproducibilidad de los ResultadosRESUMEN
BACKGROUND: The tumor-promoting role of tumor microenvironment (TME) in colorectal cancer has been widely investigated in cancer biology. Cancer-associated fibroblasts (CAFs), as the main stromal component in TME, play an important role in promoting tumor progression and metastasis. Hence, we explored the crosstalk between CAFs and microenvironment in the pathogenesis of colorectal cancer in order to provide basis for precision therapy. METHODS: We integrated spatial transcriptomics (ST) and bulk-RNA sequencing datasets to explore the functions of CAFs in the microenvironment of CRC. In detail, single sample gene set enrichment analysis (ssGSEA), gene set variation analysis (GSVA), pseudotime analysis and cell proportion analysis were utilized to identify the cell types and functions of each cell cluster. Immunofluorescence and immunohistochemistry were applied to confirm the results based on bioinformatics analysis. RESULTS: We profiled the tumor heterogeneity landscape and identified two distinct types of CAFs, which myo-cancer-associated fibroblasts (mCAFs) is associated with myofibroblast-like cells and inflammatory-cancer-associated fibroblasts (iCAFs) is related to immune inflammation. When we carried out functional analysis of two types of CAFs, we uncovered an extensive crosstalk between iCAFs and stromal components in TME to promote tumor progression and metastasis. Noticeable, some anti-tumor immune cells such as NK cells, monocytes were significantly reduced in iCAFs-enriched cluster. Then, ssGSEA analysis results showed that iCAFs were related to EMT, lipid metabolism and bile acid metabolism etc. Besides, when we explored the relationship of chemotherapy and microenvironment, we detected that iCAFs influenced immunosuppressive cells and lipid metabolism reprogramming in patient who underwent chemotherapy. Additionally, we identified the clinical role of iCAFs through a public database and confirmed it were related to poor prognosis. CONCLUSIONS: In summary, we identified two types of CAFs using integrated data and explored their functional significance in TME. This in-depth understanding of CAFs in microenvironment may help us to elucidate its cancer-promoting functions and offer hints for therapeutic studies.
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Fibroblastos Asociados al Cáncer , Neoplasias Colorrectales , Fibroblastos Asociados al Cáncer/metabolismo , Fibroblastos Asociados al Cáncer/patología , Neoplasias Colorrectales/patología , Humanos , Monocitos/metabolismo , Transcriptoma/genética , Microambiente Tumoral/genéticaRESUMEN
Long-term treatment outcomes for patients with high grade ovarian cancers have not changed despite innovations in therapies. There is no recommended assay for predicting patient response to second-line therapy, thus clinicians must make treatment decisions based on each individual patient. Patient-derived xenograft (PDX) tumors have been shown to predict drug sensitivity in ovarian cancer patients, but the time frame for intraperitoneal (IP) tumor generation, expansion, and drug screening is beyond that for tumor recurrence and platinum resistance to occur, thus results do not have clinical utility. We describe a drug sensitivity screening assay using a drug delivery microdevice implanted for 24 h in subcutaneous (SQ) ovarian PDX tumors to predict treatment outcomes in matched IP PDX tumors in a clinically relevant time frame. The SQ tumor response to local microdose drug exposure was found to be predictive of the growth of matched IP tumors after multi-week systemic therapy using significantly fewer animals (10 SQ vs 206 IP). Multiplexed immunofluorescence image analysis of phenotypic tumor response combined with a machine learning classifier could predict IP treatment outcomes against three second-line cytotoxic therapies with an average AUC of 0.91.
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Long intergenic nonprotein-coding RNA 02163 (LINC02163) has been reported to be upregulated and work as an oncogene in gastric cancer. The aims of the present study were to determine the expression profile and clinical value of LINC02163 in breast cancer. Additionally, the detailed functions of LINC02163 in breast cancer were explored, and relevant molecular events were elucidated. In this study, LINC02163 was upregulated in breast cancer, and its expression level was closely associated with tumor size, lymph node metastasis, and TNM stage. Patients with breast cancer presenting high LINC02163 expression exhibited shorter overall survival than those presenting low LINC02163 expression. Knockdown of LINC02163 resulted in a decrease in breast cancer cell proliferation, migration, and invasion and an increase in cell apoptosis in vitro. In addition, silencing of LINC02163 impeded breast cancer tumor growth in vivo. Mechanistic investigation revealed that LINC02163 served as a competing endogenous RNA for microRNA-511-3p (miR-511-3p) and consequently upregulated the expression of the high-mobility group A2 (HMGA2), a downstream target of miR-511-3p. Intriguingly, miR-511-3p inhibition and HMGA2 restoration counteracted the effects of LINC02163 deficiency on the malignant properties of breast cancer cells. LINC02163 exerts cancer-promoting effects during the initiation and progression of breast cancer via regulation of the miR-511-3p/HMGA2 axis. Our findings add to our understanding of the roles of the LINC02163/miR-511-3p/HMGA2 pathway as a regulator of breast cancer pathogenesis and may be useful in the development of lncRNA-directed cancer diagnosis, prognosis, and therapy.
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Neoplasias de la Mama/genética , Proteína HMGA2/genética , MicroARNs/genética , ARN Largo no Codificante/genética , Animales , Apoptosis/genética , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/patología , Línea Celular Tumoral , Movimiento Celular/genética , Proliferación Celular/genética , Progresión de la Enfermedad , Femenino , Regulación Neoplásica de la Expresión Génica , Proteína HMGA2/metabolismo , Humanos , Metástasis Linfática/genética , Ratones , Ratones Endogámicos BALB C , MicroARNs/metabolismo , Pronóstico , ARN Largo no Codificante/metabolismo , Regulación hacia Arriba/genéticaRESUMEN
Bone morphogenetic protein 9 (BMP9) (or GDF2) was originally identified from fetal mouse liver cDNA libraries. Emerging evidence indicates BMP9 exerts diverse and pleiotropic functions during postnatal development and in maintaining tissue homeostasis. However, the expression landscape of BMP9 signaling during development and/or in adult tissues remains to be analyzed. Here, we conducted a comprehensive analysis of the expression landscape of BMP9 and its signaling mediators in postnatal mice. By analyzing mouse ENCODE transcriptome datasets we found Bmp9 was highly expressed in the liver and detectable in embryonic brain, adult lungs and adult placenta. We next conducted a comprehensive qPCR analysis of RNAs isolated from major mouse tissues/organs at various ages. We found that Bmp9 was highly expressed in the liver and lung tissues of young adult mice, but decreased in older mice. Interestingly, Bmp9 was only expressed at low to modest levels in developing bones. BMP9-associated TGFß/BMPR type I receptor Alk1 was highly expressed in the adult lungs. Furthermore, the feedback inhibitor Smads Smad6 and Smad7 were widely expressed in mouse postnatal tissues. However, the BMP signaling antagonist noggin was highly expressed in fat and heart in the older age groups, as well as in kidney, liver and lungs in a biphasic fashion. Thus, our findings indicate that the circulating BMP9 produced in liver and lungs may account for its pleiotropic effects on postnatal tissues/organs although possible roles of BMP9 signaling in liver and lungs remain to be fully understood.
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Kidney stones and ureteral stents can cause ureteral colic and pain. By decreasing contractions in the ureter, clinically prescribed oral vasodilators may improve spontaneous stone passage rates and reduce the pain caused by ureteral stenting. We hypothesized that ureteral relaxation can be improved via the local administration of vasodilators and other smooth muscle relaxants. Here, by examining 18 candidate small molecules in an automated screening assay to determine the extent of ureteral relaxation, we show that the calcium channel blocker nifedipine and the Rho-kinase inhibitor ROCKi significantly relax human ureteral smooth muscle cells. We also show, by using ex vivo porcine ureter segments and sedated pigs that, with respect to the administration of a placebo, the local delivery of a clinically deployable formulation of the two drugs reduced ureteral contraction amplitude and frequency by 90% and 50%, respectively. Finally, we show that standard oral vasodilator therapy reduced contraction amplitude by only 50% and had a minimal effect on contraction frequency. Locally delivered ureteral relaxants therefore may improve ureter-related conditions.
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Contracción Muscular/efectos de los fármacos , Miocitos del Músculo Liso/efectos de los fármacos , Uréter/efectos de los fármacos , Vasodilatadores/administración & dosificación , Animales , Células Cultivadas , Evaluación Preclínica de Medicamentos , Humanos , Nifedipino/administración & dosificación , Inhibidores de Proteínas Quinasas/administración & dosificación , Sus scrofaRESUMEN
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.
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Ácidos Nucleicos Libres de Células/genética , ADN de Neoplasias/genética , Secuenciación del Exoma/métodos , Metástasis de la Neoplasia/genética , Antígenos de Neoplasias/genética , Neoplasias de la Mama/tratamiento farmacológico , Neoplasias de la Mama/genética , Neoplasias de la Mama/secundario , Ácidos Nucleicos Libres de Células/sangre , Análisis Mutacional de ADN , ADN de Neoplasias/sangre , Femenino , Dosificación de Gen , Humanos , Masculino , Metástasis de la Neoplasia/tratamiento farmacológico , Estudios Prospectivos , Neoplasias de la Próstata/tratamiento farmacológico , Neoplasias de la Próstata/genética , Neoplasias de la Próstata/secundario , Programas Informáticos , Secuenciación del Exoma/estadística & datos numéricosRESUMEN
The extracellular matrix (ECM) is a complex meshwork of insoluble fibrillar proteins and signaling factors interacting together to provide architectural and instructional cues to the surrounding cells. Alterations in ECM organization or composition and excessive ECM deposition have been observed in diseases such as fibrosis, cardiovascular diseases, and cancer. We provide here optimized protocols to solubilize ECM proteins from normal or tumor tissues, digest the proteins into peptides, analyze ECM peptides by mass spectrometry, and interpret the mass spectrometric data. In addition, we present here two novel R-script-based web tools allowing rapid annotation and relative quantification of ECM proteins, peptides, and intensity/abundance in mass spectrometric data output files. We illustrate this protocol with ECMs obtained from two pairs of tissues, which differ in ECM content and cellularity: triple-negative breast cancer and adjacent mammary tissue, and omental metastasis from high-grade serous ovarian cancer and normal omentum. The complete proteomics data set generated in this study has been deposited to the public repository ProteomeXchange with the data set identifier: PXD005554.
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Matriz Extracelular/química , Neoplasias Ováricas/química , Proteómica/métodos , Neoplasias de la Mama Triple Negativas/química , Mama/citología , Matriz Extracelular/patología , Proteínas de la Matriz Extracelular/análisis , Femenino , Humanos , Espectrometría de Masas , Anotación de Secuencia Molecular , Epiplón/citología , Neoplasias Ováricas/secundario , Neoplasias Ováricas/ultraestructura , Neoplasias de la Mama Triple Negativas/patología , Neoplasias de la Mama Triple Negativas/ultraestructuraRESUMEN
A continuing rise in acid deposition can cause forest degradation. In China, acid deposition has converted gradually from sulfuric acid deposition (SAD) to nitric acid deposition (NAD). However, the differing responses of photosynthesis and growth to depositions of sulfuric vs. nitric acid have not been well studied. In this study, 1-year-old seedlings of Schima superba, a dominant species in subtropical forests, were treated with two types of acid deposition SO4 (2-)/NO3 (-) ratios (8:1 and 0.7:1) with two applications (foliar spraying and soil drenching) at two pH levels (pH 3.5 and pH 2.5) over a period of 18 months. The results showed that the intensity, acid deposition type, and spraying method had significant effects on the physiological characteristics and growth performance of seedlings. Acid deposition at pH 2.5 via foliar application reduced photosynthesis and growth of S. superba, especially in the first year. Unlike SAD, NAD with high acidity potentially alleviated the negative effects of acidity on physiological properties and growth, probably due to a fertilization effect that improved foliar nitrogen and chlorophyll contents. Our results suggest that trees were damaged mainly by direct acid stress in the short term, whereas in the long term, soil acidification was also likely to be a major risk to forest ecosystems. Our data suggest that the shift in acid deposition type may complicate the ongoing challenge of anthropogenic acid deposition to ecosystem stability.
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Ácido Nítrico/toxicidad , Fotosíntesis/efectos de los fármacos , Plantones/fisiología , Ácidos Sulfúricos/toxicidad , Tracheophyta/fisiología , China , Clorofila/metabolismo , Ecosistema , Bosques , Nitrógeno/análisis , Plantones/metabolismo , Suelo/química , Tracheophyta/efectos de los fármacos , Árboles/metabolismoRESUMEN
The transcriptomic responses of bacteria to environmental stresses have been studied extensively, yet we know little about how the stressed cells respond to bacteriophage infection. Here, we conducted the first whole transcriptome sequencing (RNA-seq) study of stressed bacteria to phage infection by infecting the marine picocyanobacterium Prochlorococcusâ NATL2A with cyanomyovirus P-SSM2 under P limitation, a strong selective force in the oceans. Transcripts of the P-acquisition genes in the uninfected cells were enriched after P limitation, including the high-affinity phosphate-binding protein gene pstS. They were still enriched in the infected cells under P-limited conditions. In contrast, transcripts of adenosine triphosphate (ATP) synthase and ribosomal protein genes were depleted in the uninfected cells after P limitation but were enriched during phage infection of P-starved cells. Cyanophage P-SSM2 contains pstS, and pstS and its adjacent gene g247 of unknown function were the only phage genes that were enriched under P-limited conditions. We further found that the host pstS transcript number per cell decreased after infection, however, it was still much higher in the P-limited infected cells than that in the nutrient-replete cells. Moreover, phage pstS transcript number per cell was â¼ 20 times higher than the host copy, which may help maintain the host phosphate uptake rate during infection.
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Bacteriófagos/genética , Fósforo/deficiencia , Prochlorococcus/genética , Prochlorococcus/virología , Estrés Fisiológico/genética , Transcriptoma , Microbiología del Agua , Secuencia de Bases , ADN Bacteriano/genética , Perfilación de la Expresión Génica , ATPasas de Translocación de Protón Mitocondriales/genética , Datos de Secuencia Molecular , Océanos y Mares , Proteínas de Unión a Fosfato/genética , Fosfatos/deficiencia , Prochlorococcus/metabolismo , Análisis de Secuencia de ADNRESUMEN
The extracellular matrix (ECM) is a fundamental component of multicellular organisms that provides mechanical and chemical cues that orchestrate cellular and tissue organization and functions. Degradation, hyperproduction or alteration of the composition of the ECM cause or accompany numerous pathologies. Thus, a better characterization of ECM composition, metabolism, and biology can lead to the identification of novel prognostic and diagnostic markers and therapeutic opportunities. The development over the last few years of high-throughput ("omics") approaches has considerably accelerated the pace of discovery in life sciences. In this review, we describe new bioinformatic tools and experimental strategies for ECM research, and illustrate how these tools and approaches can be exploited to provide novel insights in our understanding of ECM biology. We also introduce a web platform "the matrisome project" and the database MatrisomeDB that compiles in silico and in vivo data on the matrisome, defined as the ensemble of genes encoding ECM and ECM-associated proteins. Finally, we present a first draft of an ECM atlas built by compiling proteomics data on the ECM composition of 14 different tissues and tumor types.
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Biología Computacional/métodos , Proteínas de la Matriz Extracelular/metabolismo , Matriz Extracelular/metabolismo , Proteómica/métodos , Animales , Bases de Datos de Proteínas , Humanos , Internet , Neoplasias/metabolismo , Especificidad de ÓrganosRESUMEN
New therapeutic strategies are needed to treat infections caused by drug-resistant bacteria, which constitute a major growing threat to human health. Here, we use a high-throughput technology to identify combinatorial genetic perturbations that can enhance the killing of drug-resistant bacteria with antibiotic treatment. This strategy, Combinatorial Genetics En Masse (CombiGEM), enables the rapid generation of high-order barcoded combinations of genetic elements for high-throughput multiplexed characterization based on next-generation sequencing. We created â¼ 34,000 pairwise combinations of Escherichia coli transcription factor (TF) overexpression constructs. Using Illumina sequencing, we identified diverse perturbations in antibiotic-resistance phenotypes against carbapenem-resistant Enterobacteriaceae. Specifically, we found multiple TF combinations that potentiated antibiotic killing by up to 10(6)-fold and delivered these combinations via phagemids to increase the killing of highly drug-resistant E. coli harboring New Delhi metallo-beta-lactamase-1. Moreover, we constructed libraries of three-wise combinations of transcription factors with >4 million unique members and demonstrated that these could be tracked via next-generation sequencing. We envision that CombiGEM could be extended to other model organisms, disease models, and phenotypes, where it could accelerate massively parallel combinatorial genetics studies for a broad range of biomedical and biotechnology applications, including the treatment of antibiotic-resistant infections.
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Farmacorresistencia Bacteriana/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Técnicas Genéticas , Carbapenémicos/farmacología , Código de Barras del ADN Taxonómico , Escherichia coli/enzimología , Proteínas de Escherichia coli/genética , Biblioteca de Genes , Genes Bacterianos , Secuenciación de Nucleótidos de Alto Rendimiento , Ensayos Analíticos de Alto Rendimiento , Humanos , Biología Sintética , Biología de Sistemas , Factores de Transcripción/genética , Resistencia betalactámica/genética , beta-Lactamasas/genéticaRESUMEN
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct "genomic backbones," each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.
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Variación Genética , Genoma Bacteriano , Prochlorococcus/genética , Prochlorococcus/fisiología , Agua de Mar/microbiología , Océano Atlántico , Evolución Biológica , Ecosistema , Genes Bacterianos , Metagenómica , Datos de Secuencia Molecular , Mutación , Filogenia , Polimorfismo de Nucleótido Simple , Prochlorococcus/clasificación , Estaciones del Año , Análisis de Secuencia de ADN , Análisis de la Célula IndividualRESUMEN
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity-both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.
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Genoma Bacteriano , Prochlorococcus/genética , Genómica , Océanos y Mares , Filogenia , Prochlorococcus/aislamiento & purificaciónRESUMEN
Viruses that infect marine cyanobacteria-cyanophages-often carry genes with orthologs in their cyanobacterial hosts, and the frequency of these genes can vary with habitat. To explore habitat-influenced genomic diversity more deeply, we used the genomes of 28 cultured cyanomyoviruses as references to identify phage genes in three ocean habitats. Only about 6-11% of genes were consistently observed in the wild, revealing high gene-content variability in these populations. Numerous shared phage/host genes differed in relative frequency between environments, including genes related to phosphorous acquisition, photorespiration, photosynthesis and the pentose phosphate pathway, possibly reflecting environmental selection for these genes in cyanomyovirus genomes. The strongest emergent signal was related to phosphorous availability; a higher fraction of genomes from relatively low-phosphorus environments-the Sargasso and Mediterranean Sea-contained host-like phosphorus assimilation genes compared with those from the N. Pacific Gyre. These genes are known to be upregulated when the host is phosphorous starved, a response mediated by pho box motifs in phage genomes that bind a host regulatory protein. Eleven cyanomyoviruses have predicted pho boxes upstream of the phosphate-acquisition genes pstS and phoA; eight of these have a conserved cyanophage-specific gene (PhCOG173) between the pho box and pstS. PhCOG173 is also found upstream of other shared phage/host genes, suggesting a unique regulatory role. Pho boxes are found upstream of high light-inducible (hli) genes in cyanomyoviruses, suggesting that this motif may have a broader role than regulating phosphorous-stress responses in infected hosts or that these hlis are involved in the phosphorous-stress response.
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Bacteriófagos/clasificación , Ecosistema , Variación Genética , Fósforo/metabolismo , Prochlorococcus/virología , Agua de Mar/virología , Estrés Fisiológico/genética , Bacteriófagos/genética , Frecuencia de los Genes , Genes Virales/genética , Mar Mediterráneo , Metagenoma , Filogenia , Agua de Mar/microbiologíaRESUMEN
Long noncoding RNAs (lncRNAs) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. Here, we identified Braveheart (Bvht), a heart-associated lncRNA in mouse. Using multiple embryonic stem cell (ESC) differentiation strategies, we show that Bvht is required for progression of nascent mesoderm toward a cardiac fate. We find that Bvht is necessary for activation of a core cardiovascular gene network and functions upstream of mesoderm posterior 1 (MesP1), a master regulator of a common multipotent cardiovascular progenitor. We also show that Bvht interacts with SUZ12, a component of polycomb-repressive complex 2 (PRC2), during cardiomyocyte differentiation, suggesting that Bvht mediates epigenetic regulation of cardiac commitment. Finally, we demonstrate a role for Bvht in maintaining cardiac fate in neonatal cardiomyocytes. Together, our work provides evidence for a long noncoding RNA with critical roles in the establishment of the cardiovascular lineage during mammalian development.