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Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.
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Perfilación de la Expresión Génica/métodos , Células Madre Pluripotentes Inducidas/citología , Miocitos Cardíacos/citología , Análisis de la Célula Individual/métodos , Técnicas de Cultivo de Célula , Diferenciación Celular , Línea Celular , Linaje de la Célula , Regulación de la Expresión Génica , Humanos , Células Madre Pluripotentes Inducidas/química , Miocitos Cardíacos/química , RNA-SeqRESUMEN
The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus.
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Elementos Transponibles de ADN , Interacciones Microbiota-Huesped , Neisseria , Animales , Portador Sano/microbiología , Portador Sano/fisiopatología , Elementos Transponibles de ADN/genética , Biblioteca de Genes , Interacciones Microbiota-Huesped/genética , Interacciones Microbiota-Huesped/fisiología , Ratones , Microbiota/genética , Membrana Mucosa/microbiología , Neisseria/genética , Neisseria/patogenicidad , Neisseria gonorrhoeae/genética , Neisseria gonorrhoeae/patogenicidad , Neisseria meningitidis/genética , Neisseria meningitidis/patogenicidad , Simbiosis/genética , Simbiosis/fisiología , Factores de Virulencia/genéticaRESUMEN
Little is known about mismatches between the language of mathematics testing instruments and the rich linguistic repertoires that African American children develop at home and in the community, in part because research paradigms with African American English (AAE) dialect speakers face complex challenges in measurement, historical exclusion, and other social, economic, cultural, and linguistic confounds. The current study aims to provide a proof of concept and novel explanatory item response design that uses error analysis to investigate the relationship between AAE child language and children's mathematics assessment outcomes. Here, we illustrate 2nd and 3rd grade children's qualitative patterns of performance on arithmetic tasks in relation to their AAE dialect use and elaborate a unified framework for examining child and item level linguistic characteristics. Results suggest that children draw upon their emerging (bi)dialectal repertoire with arithmetic problems when selecting appropriate problem-solving strategies on language-formatted problems. The mismatch of assessment language formatting with children's repertoires may disadvantage AAE speakers' strategy selections and result in a language-based performance disadvantage unrelated to mathematical ability. Research designs that look beyond correct/incorrect scoring to examine qualitative patterns of performance in AAE speaking children can provide valuable and oft-overlooked evidence when considering equity in mathematics assessment formats.
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øX174, G4, and α3 represent the three sister genera of a Microviridae subfamily. α3-like genomes are considerably larger than their sister genera genomes, yet they are packaged into capsids of similar internal volumes. They also contain multiple A* genes, which are nested within the larger A gene reading frame. Although unessential under most conditions, A* proteins mediate the fidelity of packaging reactions. Larger genomes and multiple A* genes may indicate that genome packaging is more problematic for α3-like viruses, especially at lower temperatures, where DNA persistence lengths would be longer. Unlike members of the other genera, which reliably form plaques at 20°C, α3-like phages are naturally cold sensitive below 28°C. To determine whether there was a connection between the uniquely α3-like genome characteristics and the cold-sensitive phenotype, the α3 assembly pathway was characterized at low temperature. Although virions were not detected, particles consistent with off-pathway packaging complexes were observed. In a complementary evolutionary approach, α3 was experimentally evolved to grow at progressively lower temperatures. The two major responses to cold adaptation were genome reduction and elevated A* gene expression. IMPORTANCE The production of enzymes, transcription factors, and viral receptors directly influences the niches viruses can inhabit. Some prokaryotic hosts can thrive in widely differing environments; thus, physical parameters, such as temperature, should also be considered. These variables may directly alter host physiology, preventing viral replication. Alternatively, they could negatively inhibit infection processes in a host-independent manner. The members of three sister Microviridae genera (canonical species øX174, G4 and α3) infect the same host, but α3-like viruses are naturally cold sensitive, which could effectively exclude them from low-temperature environments (<28°C). Exclusion appeared to be independent of host cell physiology. Instead, it could be largely attributed to low-temperature packaging defects. The results presented here demonstrate how physical parameters, such as temperature, can directly influence viral diversification and niche determination in a host-independent manner.
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Adaptación Fisiológica , Virus ADN , Genoma Viral , Adaptación Fisiológica/genética , Bacteriófagos/genética , Cápside/metabolismo , Frío , Virus ADN/genética , Ensamble de VirusRESUMEN
Post-translational acetylation is a common protein modification in bacteria. It was recently reported that Neisseria gonorrhoeae acetylates the Type IV pilus retraction motor, PilT. Here, we show recombinant PilT can be acetylated in vitro and acetylation does not affect PilT ultrastructure. To investigate the function of PilT acetylation, we mutated an acetylated lysine, K117, to mimic its acetylated or unacetylated forms. These mutations were not tolerated by wild-type N. gonorrhoeae, but they were tolerated by N. gonorrhoeae carrying an inducible pilE when grown without inducer. We identified additional mutations in pilT and pilU that suppress the lethality of K117 mutations. To investigate the link between PilE and PilT acetylation, we found the lack of PilE decreases PilT acetylation levels and increases the amount of PilT associated with the inner membrane. Finally, we found no difference between wild-type and mutant cells in transformation efficiency, suggesting neither mutation inhibits Type IV pilus retraction. Mutant cells, however, form microcolonies morphologically distinct from wt cells. We conclude that interfering with the acetylation status of PilTK117 greatly reduces N. gonorrhoeae viability, and mutations in pilT, pilU and pilE can overcome this lethality. We discuss the implications of these findings in the context of Type IV pilus retraction regulation.
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Proteínas Fimbrias , Proteínas Motoras Moleculares , Neisseria gonorrhoeae/genética , Neisseria gonorrhoeae/metabolismo , Acetilación , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Fimbrias/genética , Proteínas Fimbrias/metabolismo , Fimbrias Bacterianas/metabolismo , Proteínas Motoras Moleculares/genética , Proteínas Motoras Moleculares/metabolismo , Mutación , Procesamiento Proteico-PostraduccionalRESUMEN
The Strategy Choice Model (SCM) is a highly influential theory of human problem-solving. One strength of this theory is the allowance for both item and person variance to contribute to problem-solving outcomes, but this central tenet of the model has not been empirically tested. Explanatory Item Response Theory (EIRT) provides an ideal approach to testing this core feature of SCM, as it allows for simultaneous estimation of both item and person effects on problem-solving outcomes. We used EIRT to test and confirm this central tenet of the SCM for adolescents' (n = 376) solving of addition problems. The approach also allowed us to identify the strategy choices of adolescents who still struggle with basic arithmetic. The synthesis of SCM theory and EIRT modeling has implications for more fully investigating the sources of individual differences in students' problem solving, and for identifying problem-solving patterns associated with poor academic achievement.
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Commensals are important for the proper functioning of multicellular organisms. How a commensal establishes persistent colonization of its host is little understood. Studies of this aspect of microbe-host interactions are impeded by the absence of an animal model. We have developed a natural small animal model for identifying host and commensal determinants of colonization and of the elusive process of persistence. Our system couples a commensal bacterium of wild mice, Neisseria musculi, with the laboratory mouse. The pairing of a mouse commensal with its natural host circumvents issues of host restriction. Studies are performed in the absence of antibiotics, hormones, invasive procedures, or genetic manipulation of the host. A single dose of N. musculi, administered orally, leads to long-term colonization of the oral cavity and gut. All mice are healthy. Susceptibility to colonization is determined by host genetics and innate immunity. For N. musculi, colonization requires the type IV pilus. Reagents and powerful tools are readily available for manipulating the laboratory mouse, allowing easy dissection of host determinants controlling colonization resistance. N. musculi is genetically related to human-dwelling commensal and pathogenic Neisseria and encodes host interaction factors and vaccine antigens of pathogenic Neisseria Our system provides a natural approach for studying Neisseria-host interactions and is potentially useful for vaccine efficacy studies.
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Infecciones por Bacterias Gramnegativas/inmunología , Infecciones por Bacterias Gramnegativas/transmisión , Interacciones Huésped-Patógeno , Inmunidad Innata , Ratones/microbiología , Neisseria/patogenicidad , Simbiosis , Animales , Modelos Animales de EnfermedadRESUMEN
Burkholderia pseudomallei, the cause of melioidosis, is intrinsically resistant to many antibiotics. Acquired multidrug resistance, including resistance to doxycycline and co-trimoxazole used for melioidosis eradication phase therapy, is mainly attributed to constitutive expression of the BpeEF-OprC efflux pump. Constitutive expression of this pump is caused by mutations affecting two highly similar LysR-type transcriptional regulators (LTTR), BpeT and BpeS, but their interaction with the regulatory region governing BpeEF-OprC expression has not yet been studied. The bpeE-bpeF-oprC genes are distally located in the llpE-bpeE-bpeF-oprC operon. The llpE gene encodes a putative lipase/esterase of unknown function. We show that in a bpeT mutant llpE is constitutively co-transcribed with bpeE-bpeF-oprC. As expected from previous studies with B. cenocepacia, deletion of llpE does not affect antibiotic efflux. Using transcriptional bpeE'-lacZ fusions, we demonstrate that the 188 bp bpeT-llpE intergenic region located between bpeT and the llpE-bpeE-bpeF-oprC operon contains regulatory elements needed for control of bpeT and llpE-bpeE-bpeF-oprC operon expression. By native polyacrylamide gel electrophoresis and electrophoretic mobility shift assays with purified recombinant BpeT and BpeS proteins, we show BpeT and BpeS form oligomers that share a 14 bp binding site overlapping the essential region required for llpE-bpeE-bpeF-oprC expression. The binding site contains the conserved T-N11-A LTTR box motif involved in binding of LysR proteins, which in concert with two other possible LTTR boxes may mediate BpeT and BpeS regulation of BpeEF-OprC expression. These studies form the basis for further investigation of BpeEF-OprC expression and regulation at the molecular level by yet unknown external stimuli.
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Burkholderia pseudomallei/enzimología , Burkholderia pseudomallei/genética , Regulación Bacteriana de la Expresión Génica , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/metabolismo , Antibacterianos/metabolismo , Sitios de Unión , Transporte Biológico Activo , ADN Bacteriano , Farmacorresistencia Bacteriana , Electroforesis en Gel de Poliacrilamida , Ensayo de Cambio de Movilidad Electroforética , Eliminación de Gen , Operón , Unión Proteica , Multimerización de Proteína , Transcripción GenéticaRESUMEN
The genus Burkholderia comprises metabolically diverse and adaptable Gram-negative bacteria, which thrive in often adversarial environments. A few members of the genus are prominent opportunistic pathogens. These include Burkholderia mallei and Burkholderia pseudomallei of the B. pseudomallei complex, which cause glanders and melioidosis, respectively. Burkholderia cenocepacia, Burkholderia multivorans, and Burkholderia vietnamiensis belong to the Burkholderia cepacia complex and affect mostly cystic fibrosis patients. Infections caused by these bacteria are difficult to treat because of significant antibiotic resistance. The first line of defense against antimicrobials in Burkholderia species is the outer membrane penetration barrier. Most Burkholderia contain a modified lipopolysaccharide that causes intrinsic polymyxin resistance. Contributing to reduced drug penetration are restrictive porin proteins. Efflux pumps of the resistance nodulation cell division family are major players in Burkholderia multidrug resistance. Third and fourth generation ß-lactam antibiotics are seminal for treatment of Burkholderia infections, but therapeutic efficacy is compromised by expression of several ß-lactamases and ceftazidime target mutations. Altered DNA gyrase and dihydrofolate reductase targets cause fluoroquinolone and trimethoprim resistance, respectively. Although antibiotic resistance hampers therapy of Burkholderia infections, the characterization of resistance mechanisms lags behind other non-enteric Gram-negative pathogens, especially ESKAPE bacteria such as Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa.
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Antibacterianos/farmacología , Burkholderia mallei/efectos de los fármacos , Burkholderia pseudomallei/efectos de los fármacos , Burkholderia/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Regulación Bacteriana de la Expresión Génica , Genes MDR , Animales , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Burkholderia/genética , Burkholderia/crecimiento & desarrollo , Burkholderia/patogenicidad , Infecciones por Burkholderia/tratamiento farmacológico , Infecciones por Burkholderia/microbiología , Infecciones por Burkholderia/patología , Burkholderia mallei/genética , Burkholderia mallei/crecimiento & desarrollo , Burkholderia mallei/patogenicidad , Burkholderia pseudomallei/genética , Burkholderia pseudomallei/crecimiento & desarrollo , Burkholderia pseudomallei/patogenicidad , Girasa de ADN/genética , Girasa de ADN/metabolismo , Muermo/tratamiento farmacológico , Muermo/microbiología , Muermo/patología , Caballos , Humanos , Melioidosis/tratamiento farmacológico , Melioidosis/microbiología , Melioidosis/patología , Porinas/antagonistas & inhibidores , Porinas/genética , Porinas/metabolismo , Tetrahidrofolato Deshidrogenasa/genética , Tetrahidrofolato Deshidrogenasa/metabolismoRESUMEN
Using multitrait, multimethod data, and confirmatory factor analysis, the current study examined the effects of arithmetic item formatting and the possibility that across formats, abilities other than arithmetic may contribute to children's answers. Measurement hypotheses were guided by several leading theories of arithmetic cognition. With a sample of 1314 3rd grade students (age M=103.24 months, SD=5.41 months), Abstract Code Theory, Encoding Complex Theory, Triple Code Theory, and the Exact versus Approximate Calculations Hypothesis were evaluated, using 11 measures of arithmetic with symbolic problem formats (e.g., Arabic numeral and language-based formats) and various problem demands (e.g., requiring both exact and approximate calculations). In general, results provided support for both Triple Code Theory and Encoding Complex Theory. As predicted by Triple Code Theory, arithmetic outcomes with language formatting, Arabic numeral formatting, and estimation demands (across formats) were related but distinct from one another. As predicted by Encoding Complex Theory, executive attention was a direct predictor of all arithmetic outcomes. Language was no longer a direct predictor of arithmetic outcomes when executive attention was accounted for in the model; however, a strong and enduring relationship between language and executive attention suggested that language may play a facilitative role in reasoning during numeric processing. These findings have important implications for assessing arithmetic in educational settings and suggest that in addition to arithmetic-focused interventions, interventions targeting executive attention, language, and/or the interplay between them (i.e., internal speech during problem-solving) may be a promising avenues of mathematical problem-solving intervention.
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Problem solving encompasses the broad domain of human, goal-directed behaviors. Though we may attempt to measure problem solving using tightly controlled and decontextualized tasks, it is inextricably embedded in both reasoners' experiences and their contexts. Without situating problem solvers, problem contexts, and our own experiential partialities as researchers, we risk intertwining the research of information relevance with our own confirmatory biases about people, environments, and ourselves. We review each of these ecological facets of information relevance in problem solving, and we suggest a framework to guide its measurement. We ground this framework with concrete examples of ecologically valid, culturally relevant measurement of problem solving.
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PURPOSE: Syntax provides critical support for both academic success and linguistic growth, yet it has not been a focus of language research in school-age African American children. This study examines complex syntax performance of African American children in second through fifth grades. METHOD: The current study explores the syntactic performances of African American children (N = 513) in Grades 2-5 on the Test of Language Development-Intermediate who speak African American English. Multilevel modeling was used to evaluate the growth and associated changes between dialect density and syntax. Analyzed data were compared both to the normative sample and within the recruited sample. RESULTS: The results suggest that dialect density exerted its impact early but did not continue to influence syntactic growth over time. Additionally, it was not until dialect density was accounted for in growth models that African American children's syntactic growth resembled normative expectations of a standardized language instrument. CONCLUSION: The current study suggests that failure to consider cultural language differences obscures our understanding of African American students' linguistic competence on standardized language assessments.
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Negro o Afroamericano , Lenguaje Infantil , Lingüística , Humanos , Negro o Afroamericano/psicología , Niño , Femenino , Masculino , Desarrollo del Lenguaje , Pruebas del LenguajeRESUMEN
IMPORTANCE: We describe the importance of Type IV pilus retraction to colonization and persistence by a mouse commensal Neisseria, N. musculi, in its native host. Our findings have implications for the role of Tfp retraction in mediating interactions of human-adapted pathogenic and commensal Neisseria with their human host due to the relatedness of these species.
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Proteínas Fimbrias , Fimbrias Bacterianas , Ratones , Animales , Humanos , Neisseria/genética , Simbiosis , Neisseria gonorrhoeae , Proteínas BacterianasRESUMEN
Identifying the molecular effects of human genetic variation across cellular contexts is crucial for understanding the mechanisms underlying disease-associated loci, yet many cell-types and developmental stages remain underexplored. Here we harnessed the potential of heterogeneous differentiating cultures ( HDCs ), an in vitro system in which pluripotent cells asynchronously differentiate into a broad spectrum of cell-types. We generated HDCs for 53 human donors and collected single-cell RNA-sequencing data from over 900,000 cells. We identified expression quantitative trait loci in 29 cell-types and characterized regulatory dynamics across diverse differentiation trajectories. This revealed novel regulatory variants for genes involved in key developmental and disease-related processes while replicating known effects from primary tissues, and dynamic regulatory effects associated with a range of complex traits.
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BACKGROUND: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS: We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS: Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
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Cuerpos Embrioides , Pan troglodytes , Humanos , Animales , Pan troglodytes/genética , Línea Celular , Perfilación de la Expresión Génica , TranscriptomaRESUMEN
Practically all studies of gene expression in humans to date have been performed in a relatively small number of adult tissues. Gene regulation is highly dynamic and context-dependent. In order to better understand the connection between gene regulation and complex phenotypes, including disease, we need to be able to study gene expression in more cell types, tissues, and states that are relevant to human phenotypes. In particular, we need to characterize gene expression in early development cell types, as mutations that affect developmental processes may be of particular relevance to complex traits. To address this challenge, we propose to use embryoid bodies (EBs), which are organoids that contain a multitude of cell types in dynamic states. EBs provide a system in which one can study dynamic regulatory processes at an unprecedentedly high resolution. To explore the utility of EBs, we systematically explored cellular and gene expression heterogeneity in EBs from multiple individuals. We characterized the various cell types that arise from EBs, the extent to which they recapitulate gene expression in vivo, and the relative contribution of technical and biological factors to variability in gene expression, cell composition, and differentiation efficiency. Our results highlight the utility of EBs as a new model system for mapping dynamic inter-individual regulatory differences in a large variety of cell types.
One major goal of human genetics is to understand how changes in the way genes are regulated affect human traits, including disease susceptibility. To date, most studies of gene regulation have been performed in adult tissues, such as liver or kidney tissue, that were collected at a single time point. Yet, gene regulation is highly dynamic and context-dependent, meaning that it is important to gather data from a greater variety of cell types at different stages of their development. Additionally, observing which genes switch on and off in response to external treatments can shed light on how genetic variation can drive errors in gene regulation and cause diseases. Stem cells can produce more cells like themselves or differentiate acquire the characteristics of many cell types. These cells have been used in the laboratory to research gene regulation. Unfortunately, these studies often fail to capture the complex spatial and temporal dynamics of stem cell differentiation; in particular, these studies are unable to observe gene regulation in the transient cell types that appear early in embryonic development. To overcome these limitations, scientists developed systems such as embryoid bodies: three-dimensional aggregates of stem cells that, when grown under certain conditions, spontaneously develop into a variety of cell types. Rhodes, Barr et al. wanted to assess the utility of embryoid bodies as a model to study how genes are dynamically regulated in different cell types, by different individuals who have distinct genetic makeups. To do this, they grew embryoid bodies made from human stem cells from different individuals to examine which genes switched on and off as the stem cells that formed the embryoid bodies differentiated into different types of cells. The results showed that it was possible to grow embryoid bodies derived from genetically distinct individuals that consistently produce diverse cell types, similar to those found during human fetal development. Rhodes, Barr et al.'s findings suggest that embryoid bodies are a useful model to study gene regulation across individuals with different genetic backgrounds. This could accelerate research into how genetics are associated with disease by capturing gene regulatory dynamics at an unprecedentedly high spatial and temporal resolution. Additionally, embryoid bodies could be used to explore how exposure to different environmental factors during early development affect disease-related outcomes in adulthood in different individuals.
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Diferenciación Celular/genética , Cuerpos Embrioides/citología , Regulación de la Expresión Génica , Línea Celular , Cuerpos Embrioides/metabolismo , Femenino , Genoma Humano , Humanos , Células Madre Pluripotentes Inducidas , Masculino , Análisis de Secuencia de ARNRESUMEN
Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type, and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing and were highly variable across contexts. For thousands of genes, we identified variable allelic expression across contexts and characterized different types of gene-environment interactions, many of which are associated with complex traits. Promoter functional and evolutionary features distinguished genes with elevated allelic imbalance mean and variance. On average, half of the genes with dynamic regulatory interactions were missed by large eQTL mapping studies, indicating the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease.
The activity of the genes in a cell depends on the type of cell they are in, the interactions with other genes, the environment and genetics. Active genes produce a greater number of mRNA molecules, which act as messenger molecules to instruct the cell to produce proteins. The amount of mRNA molecules in cells can be measured to assess the levels of gene activity. Genes produce mRNAs through a process called transcription, and the collection of all the mRNA molecules in a cell is called the transcriptome. Cells obtained from human samples can be grown in the lab under different conditions, and this can be used to transform them into different types of cells. These cells can then be exposed to different treatments such as specific chemicals to understand how the environment affects them. Cells derived from different people may respond differently to the same treatment based on their unique genetics. Exposing different types of cells from many people to different treatments can help explain how genetics, the environment and cell type affect gene activity. Findley et al. grew three different types of cells from six different people in the lab. The cells were exposed to 28 different treatments, which reflect different environmental changes. Studying all these different factors together allowed Findley et al. to understand how genetics, cell type and environment affect the activity of over 53,000 genes. Around half of the effects due to an interaction between genetics and the environment and had not been seen in other larger studies of the transcriptome. Many of these newly observed changes are in genes that have connections to different diseases, including heart disease. The results of Findley et al. provide evidence indicating to which extent lifestyle and the environment can interact with an individual's genetic makeup to impact gene activity and long-term health. The more researchers can understand these factors, the more useful they can be in helping to predict, detect and treat illnesses. The findings also show how genes and the environment interact, which may be relevant to understanding disease development. There is more work to be done to understand a wider range of environmental factors across more cell types. It will also be important to establish how this work on cells grown in the lab translates to human health.
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Regulación de la Expresión Génica/genética , Células Madre Pluripotentes Inducidas/metabolismo , Linfocitos/metabolismo , Miocitos Cardíacos/metabolismo , Empalme Alternativo , Diferenciación Celular/genética , Línea Celular , Femenino , Humanos , Células Madre Pluripotentes Inducidas/citología , Linfocitos/citología , Miocitos Cardíacos/citología , Sitios de Carácter Cuantitativo , Análisis de Secuencia de ARNRESUMEN
Current definitions of asexuality focus on sexual attraction, sexual behavior, and lack of sexual orientation or sexual excitation; however, the extent to which these definitions are accepted by self-identified asexuals is unknown. The goal of Study 1 was to examine relationship characteristics, frequency of sexual behaviors, sexual difficulties and distress, psychopathology, interpersonal functioning, and alexithymia in 187 asexuals recruited from the Asexuality Visibility and Education Network (AVEN). Asexual men (n = 54) and women (n = 133) completed validated questionnaires online. Sexual response was lower than normative data and was not experienced as distressing, and masturbation frequency in males was similar to available data for sexual men. Social withdrawal was the most elevated personality subscale; however, interpersonal functioning was in the normal range. Alexithymia was elevated in 12%. Social desirability was also in the normal range. Study 2 was designed to expand upon these quantitative findings with 15 asexuals from Study 1 through in-depth telephone interviews. The findings suggest that asexuality is best conceptualized as a lack of sexual attraction; however, asexuals varied greatly in their experience of sexual response and behavior. Asexuals partnered with sexuals acknowledged having to "negotiate" sexual activity. There were not higher rates of psychopathology among asexuals; however, a subset might fit the criteria for Schizoid Personality Disorder. There was also strong opposition to viewing asexuality as an extreme case of sexual desire disorder. Finally, asexuals were very motivated to liaise with sex researchers to further the scientific study of asexuality.
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Disfunciones Sexuales Psicológicas/psicología , Adulto , Síntomas Afectivos , Femenino , Humanos , Internet , Relaciones Interpersonales , Entrevistas como Asunto , Masculino , Masturbación/psicología , Modelos Psicológicos , Personalidad , Religión y Sexo , Trastorno de Personalidad Esquizoide/diagnóstico , Factores Sexuales , Conducta Sexual , Disfunciones Sexuales Psicológicas/diagnóstico , Encuestas y Cuestionarios , Terminología como AsuntoRESUMEN
A comprehensive reference map of all cell types in the human body is necessary for improving our understanding of fundamental biological processes and in diagnosing and treating disease. High-throughput single-cell RNA sequencing techniques have emerged as powerful tools to identify and characterize cell types in complex and heterogeneous tissues. However, extracting intact cells from tissues and organs is often technically challenging or impossible, for example in heart or brain tissue. Single-nucleus RNA sequencing provides an alternative way to obtain transcriptome profiles of such tissues. To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes. Clustering of time-series transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics. We then applied DroNc-seq to postmortem heart tissue to test its performance on heterogeneous human tissue samples. Our data confirm that DroNc-seq yields similar results to Drop-seq on matched samples and can be successfully used to generate reference maps for the human cell atlas.
Asunto(s)
Miocitos Cardíacos/metabolismo , RNA-Seq/métodos , Análisis de la Célula Individual/métodos , Secuencia de Bases/genética , Diferenciación Celular/genética , Núcleo Celular/genética , Perfilación de la Expresión Génica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , ARN/genética , Análisis de Secuencia de ARN/métodos , Transcriptoma/genéticaRESUMEN
We have developed a natural mouse model to study persistent colonization by commensal Neisseria. The system couples the ordinary lab mouse with Neisseria musculi (Nmus), a commensal in the oral cavity and gut of the wild mouse, Mus musculus. The pairing of Nmus with its natural reservoir circumvents host restriction barriers that have impeded previous studies of Neisseria in vivo behavior. The model allows, for the first time, for the dissection of host and neisserial determinants of asymptomatic colonization. Inoculation procedures are noninvasive and susceptibility to Nmus colonization varies with host genetic background. In colonized mice, bacterial burdens are detectable up to 1-year post inoculation, making it an ideal model for the study of persistence. As Nmus encodes several Neisseria gonorrhoeae (and Neisseria meningitidis) host interaction factors, the system can be used to query the in vivo functions of these commonly held genes and factors. Nmus also encodes many pathogenic Neisseria vaccine targets including a polysaccharide capsule, making the model potentially useful for vaccine development. The ease of genetic manipulation of Nmus enhances the feasibility of such studies.