Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 93
Filtrar
1.
Sci Transl Med ; 16(747): eadj7685, 2024 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-38748774

RESUMEN

Intrahepatic cholangiocarcinoma (ICC) is an aggressive bile duct malignancy that frequently exhibits isocitrate dehydrogenase (IDH1/IDH2) mutations. Mutant IDH (IDHm) ICC is dependent on SRC kinase for growth and survival and is hypersensitive to inhibition by dasatinib, but the molecular mechanism underlying this sensitivity is unclear. We found that dasatinib reduced p70 S6 kinase (S6K) and ribosomal protein S6 (S6), leading to substantial reductions in cell size and de novo protein synthesis. Using an unbiased phosphoproteomic screen, we identified membrane-associated guanylate kinase, WW, and PDZ domain containing 1 (MAGI1) as an SRC substrate in IDHm ICC. Biochemical and functional assays further showed that SRC inhibits a latent tumor-suppressing function of the MAGI1-protein phosphatase 2A (PP2A) complex to activate S6K/S6 signaling in IDHm ICC. Inhibiting SRC led to activation and increased access of PP2A to dephosphorylate S6K, resulting in cell death. Evidence from patient tissue and cell line models revealed that both intrinsic and extrinsic resistance to dasatinib is due to increased phospho-S6 (pS6). To block pS6, we paired dasatinib with the S6K/AKT inhibitor M2698, which led to a marked reduction in pS6 in IDHm ICC cell lines and patient-derived organoids in vitro and substantial growth inhibition in ICC patient-derived xenografts in vivo. Together, these results elucidated the mechanism of action of dasatinib in IDHm ICC, revealed a signaling complex regulating S6K phosphorylation independent of mTOR, suggested markers for dasatinib sensitivity, and described a combination therapy for IDHm ICC that may be actionable in the clinic.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales , Colangiocarcinoma , Dasatinib , Isocitrato Deshidrogenasa , Mutación , Familia-src Quinasas , Colangiocarcinoma/tratamiento farmacológico , Colangiocarcinoma/patología , Colangiocarcinoma/metabolismo , Colangiocarcinoma/genética , Humanos , Dasatinib/farmacología , Mutación/genética , Familia-src Quinasas/metabolismo , Familia-src Quinasas/antagonistas & inhibidores , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Línea Celular Tumoral , Isocitrato Deshidrogenasa/metabolismo , Isocitrato Deshidrogenasa/genética , Animales , Moléculas de Adhesión Celular/metabolismo , Proliferación Celular/efectos de los fármacos , Fosforilación/efectos de los fármacos , Transducción de Señal/efectos de los fármacos , Ratones , Neoplasias de los Conductos Biliares/patología , Neoplasias de los Conductos Biliares/metabolismo , Neoplasias de los Conductos Biliares/genética , Neoplasias de los Conductos Biliares/tratamiento farmacológico , Proteínas Quinasas S6 Ribosómicas 70-kDa/metabolismo
2.
Nucleic Acids Res ; 52(8): 4466-4482, 2024 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-38567721

RESUMEN

A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of Escherichia coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37°C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65°C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.


Asunto(s)
Emparejamiento Base , Escherichia coli , Fluoruros , Conformación de Ácido Nucleico , Riboswitch , Transcripción Genética , Riboswitch/genética , Fluoruros/química , Escherichia coli/genética , Simulación de Dinámica Molecular , ARN Polimerasas Dirigidas por ADN/metabolismo , ARN Polimerasas Dirigidas por ADN/química , ARN Polimerasas Dirigidas por ADN/genética , Pliegue del ARN , Magnesio/química , Secuencia de Bases , ARN Bacteriano/química , ARN Bacteriano/genética , ARN Bacteriano/metabolismo , Thermus/genética , Thermus/enzimología
3.
bioRxiv ; 2024 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-38585958

RESUMEN

Decision-making in noisy, changing, and partially observable environments entails a basic tradeoff between immediate reward and longer-term information gain, known as the exploration-exploitation dilemma. Computationally, an effective way to balance this tradeoff is by leveraging uncertainty to guide exploration. Yet, in humans, empirical findings are mixed, from suggesting uncertainty-seeking to indifference and avoidance. In a novel bandit task that better captures uncertainty-driven behavior, we find multiple roles for uncertainty in human choices. First, stable and psychologically meaningful individual differences in uncertainty preferences actually range from seeking to avoidance, which can manifest as null group-level effects. Second, uncertainty modulates the use of basic decision heuristics that imperfectly exploit immediate rewards: a repetition bias and win-stay-lose-shift heuristic. These heuristics interact with uncertainty, favoring heuristic choices under higher uncertainty. These results, highlighting the rich and varied structure of reward-based choice, are a step to understanding its functional basis and dysfunction in psychopathology.

4.
Med Sci Educ ; 34(2): 429-437, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38686160

RESUMEN

Industry funds nearly two-thirds of US healthcare research, and industry-sponsorship may produce more favorable research results and conclusions. Medical students report feeling inadequately prepared to avoid negative industry influence. Research of educational interventions that educate students on the potential effects of industry influence is lacking, and no interventions have demonstrated long-term benefit. Surveying and assessing student opinions of the relationship between industry and research may help improve future educational interventions. We surveyed preclinical and clinical students at seven US medical schools regarding their attitudes towards industry conflicts of interest (COIs) in medical research. A total of 466 medical students including 232 preclinical and 234 clinical students completed the survey. Of those who had research experience, clinical students were more likely than preclinical students to look for COIs (62.0% v 45.9%, p = .014) and to consider whether author COIs are pertinent to the article (68.1% v 54.1%, p = .023). Many disagreed that they felt adequately educated on the issue of COIs (42.7%), but most agreed that medical school should take a role in guiding student interactions with industry (65.0%). Students responded that all listed financial relationships between industry and investigator, except for providing food and/or beverage, would likely bias the investigator's research. Many students feel inadequately educated on industry issues in biomedical research, and most believe medical schools should help guide interactions with industry. Our findings support further development of educational interventions that prepare students to navigate the relationship between industry and medical research during and after medical school.

5.
Nat Struct Mol Biol ; 30(12): 1947-1957, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38087090

RESUMEN

JTE-607 is an anticancer and anti-inflammatory compound and its active form, compound 2, directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-messenger RNA (pre-mRNA) 3' processing. Surprisingly, compound 2-mediated inhibition of pre-mRNA cleavage is sequence specific and the drug sensitivity is predominantly determined by sequences flanking the cleavage site (CS). Using massively parallel in vitro assays, we identified key sequence features that determine drug sensitivity. We trained a machine learning model that can predict poly(A) site (PAS) relative sensitivity to compound 2 and provide the molecular basis for understanding the impact of JTE-607 on PAS selection and transcription termination genome wide. We propose that CPSF73 and associated factors bind to the CS region in a sequence-dependent manner and the interaction affinity determines compound 2 sensitivity. These results have not only elucidated the mechanism of action of JTE-607, but also unveiled an evolutionarily conserved sequence specificity of the mRNA 3' processing machinery.


Asunto(s)
Precursores del ARN , Procesamiento Postranscripcional del ARN , Línea Celular , Precursores del ARN/genética , Precursores del ARN/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo
6.
bioRxiv ; 2023 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-38106011

RESUMEN

A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of E. coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37 °C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65 °C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.

7.
PLoS One ; 18(9): e0290633, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37713433

RESUMEN

BACKGROUND: Severe childhood infection has a dose-dependent association with adult cardiovascular events and with adverse cardiometabolic phenotypes. The relationship between cardiovascular outcomes and less severe childhood infections is unclear. AIM: To investigate the relationship between common, non-hospitalised infections, antibiotic exposure, and preclinical vascular phenotypes in young children. DESIGN: A Dutch prospective population-derived birth cohort study. METHODS: Participants were from the Wheezing-Illnesses-Study-Leidsche-Rijn (WHISTLER) birth cohort. We collected data from birth to 5 years on antibiotic prescriptions, general practitioner (GP)-diagnosed infections, and monthly parent-reported febrile illnesses (0-1 years). At 5 years, carotid intima-media thickness (CIMT), carotid artery distensibility, and blood pressure (BP) were measured. General linear regression models were adjusted for age, sex, smoke exposure, birth weight z-score, body mass index, and socioeconomic status. RESULTS: Recent antibiotic exposure was associated with adverse cardiovascular phenotypes; each antibiotic prescription in the 3 and 6 months prior to vascular assessment was associated with an 18.1 µm (95% confidence interval, 4.5-31.6, p = 0.01) and 10.7 µm (0.8-20.5, p = 0.03) increase in CIMT, respectively. Each additional antibiotic prescription in the preceding 6 months was associated with an 8.3 mPa-1 decrease in carotid distensibility (-15.6- -1.1, p = 0.02). Any parent-reported febrile episode (compared to none) showed weak evidence of association with diastolic BP (1.6 mmHg increase, 0.04-3.1, p = 0.04). GP-diagnosed infections were not associated with vascular phenotypes. CONCLUSIONS: Recent antibiotics are associated with adverse vascular phenotypes in early childhood. Mechanistic studies may differentiate antibiotic-related from infection-related effects and inform preventative strategies.


Asunto(s)
Antibacterianos , Grosor Intima-Media Carotídeo , Adulto , Humanos , Preescolar , Estudios de Cohortes , Estudios Prospectivos , Antibacterianos/efectos adversos , Cohorte de Nacimiento
8.
Sci Transl Med ; 15(694): eabn9674, 2023 05 03.
Artículo en Inglés | MEDLINE | ID: mdl-37134154

RESUMEN

Pancreatic ductal adenocarcinoma (PDAC) is classified into two key subtypes, classical and basal, with basal PDAC predicting worse survival. Using in vitro drug assays, genetic manipulation experiments, and in vivo drug studies in human patient-derived xenografts (PDXs) of PDAC, we found that basal PDACs were uniquely sensitive to transcriptional inhibition by targeting cyclin-dependent kinase 7 (CDK7) and CDK9, and this sensitivity was recapitulated in the basal subtype of breast cancer. We showed in cell lines, PDXs, and publicly available patient datasets that basal PDAC was characterized by inactivation of the integrated stress response (ISR), which leads to a higher rate of global mRNA translation. Moreover, we identified the histone deacetylase sirtuin 6 (SIRT6) as a critical regulator of a constitutively active ISR. Using expression analysis, polysome sequencing, immunofluorescence, and cycloheximide chase experiments, we found that SIRT6 regulated protein stability by binding activating transcription factor 4 (ATF4) in nuclear speckles and protecting it from proteasomal degradation. In human PDAC cell lines and organoids as well as in murine PDAC genetically engineered mouse models where SIRT6 was deleted or down-regulated, we demonstrated that SIRT6 loss both defined the basal PDAC subtype and led to reduced ATF4 protein stability and a nonfunctional ISR, causing a marked vulnerability to CDK7 and CDK9 inhibitors. Thus, we have uncovered an important mechanism regulating a stress-induced transcriptional program that may be exploited with targeted therapies in particularly aggressive PDAC.


Asunto(s)
Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Sirtuinas , Humanos , Ratones , Animales , Quinasas Ciclina-Dependientes , Línea Celular Tumoral , Neoplasias Pancreáticas/patología , Carcinoma Ductal Pancreático/patología , Sirtuinas/genética , Sirtuinas/uso terapéutico , Neoplasias Pancreáticas
9.
Transl Psychiatry ; 13(1): 179, 2023 05 26.
Artículo en Inglés | MEDLINE | ID: mdl-37236924

RESUMEN

Cognitive control deficits are a hallmark of attention deficit hyperactivity disorder (ADHD) in children. Theoretical models posit that cognitive control involves reactive and proactive control processes but their distinct roles and inter-relations in ADHD are not known, and the contributions of proactive control remain vastly understudied. Here, we investigate the dynamic dual cognitive control mechanisms associated with both proactive and reactive control in 50 children with ADHD (16F/34M) and 30 typically developing (TD) children (14F/16M) aged 9-12 years across two different cognitive controls tasks using a within-subject design. We found that while TD children were capable of proactively adapting their response strategies, children with ADHD demonstrated significant deficits in implementing proactive control strategies associated with error monitoring and trial history. Children with ADHD also showed weaker reactive control than TD children, and this finding was replicated across tasks. Furthermore, while proactive and reactive control functions were correlated in TD children, such coordination between the cognitive control mechanisms was not present in children with ADHD. Finally, both reactive and proactive control functions were associated with behavioral problems in ADHD, and multi-dimensional features derived from the dynamic dual cognitive control framework predicted inattention and hyperactivity/impulsivity clinical symptoms. Our findings demonstrate that ADHD in children is characterized by deficits in both proactive and reactive control, and suggest that multi-componential cognitive control measures can serve as robust predictors of clinical symptoms.


Asunto(s)
Trastorno por Déficit de Atención con Hiperactividad , Trastornos del Conocimiento , Humanos , Niño , Trastorno por Déficit de Atención con Hiperactividad/diagnóstico , Cognición
10.
bioRxiv ; 2023 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-37090613

RESUMEN

JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3' processing. Although CPSF73 is universally required for mRNA 3' end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3' processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3' processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3' processing machinery.

11.
Mol Psychiatry ; 28(7): 3055-3062, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37106117

RESUMEN

The neurocomputational processes underlying bulimia nervosa and its primary symptoms, out-of-control overeating and purging, are poorly understood. Research suggests that the brains of healthy individuals form a dynamic internal model to predict whether control is needed in each moment. This study tested the hypothesis that this computational process of inhibitory control is abnormally affected by metabolic state (being fasted or fed) in bulimia nervosa. A Bayesian ideal observer model was fit to behavioral data acquired from 22 women remitted from bulimia nervosa and 20 group-matched controls who completed a stop-signal task during two counterbalanced functional MRI sessions, one after a 16 h fast and one after a meal. This model estimates participants' trial-by-trial updating of the probability of a stop signal based on their experienced trial history. Neural analyses focused on control-related Bayesian prediction errors, which quantify the direction and degree of "surprise" an individual experiences on any given trial. Regardless of group, metabolic state did not affect behavioral performance on the task. However, metabolic state modulated group differences in neural activation. In the fed state, women remitted from bulimia nervosa had attenuated prediction-error-dependent activation in the left dorsal caudate. This fed-state activation was lower among women with more frequent past binge eating and self-induced vomiting. When they are in a fed state, individuals with bulimia nervosa may not effectively process unexpected information needed to engage inhibitory control. This may explain the difficulties these individuals have stopping eating after it begins.


Asunto(s)
Bulimia Nerviosa , Bulimia , Trastornos de Alimentación y de la Ingestión de Alimentos , Humanos , Femenino , Teorema de Bayes , Encéfalo
12.
J Immunol ; 210(6): 764-773, 2023 03 15.
Artículo en Inglés | MEDLINE | ID: mdl-36723033

RESUMEN

Implementation of conjugate vaccine technology revolutionized the ability to effectively elicit long-lasting immune responses to bacterial capsular polysaccharides. Although expansion of conjugate vaccine serotype coverage is designed to target residual disease burden to pneumococcal serotypes not contained in earlier vaccine versions, details of polysaccharide Ag structure, heterogeneity, and epitope structure components contributing to vaccine-mediated immunity are not always clear. Analysis of Streptococcus pneumoniae serotype 12F polysaccharide by two-dimensional nuclear magnetic resonance spectroscopy and mass spectrometry revealed a partial substitution of N-acetyl-galactosamine by the keto sugar 2-acetamido-2,6-dideoxy-xylo-hexos-4-ulose (Sug) in up to 25% of the repeat units. This substitution was not described in previous published structures for 12F. Screening a series of contemporary 12F strains isolated from humans (n = 17) identified Sug incorporation at varying levels in all strains examined. Thus, partial Sug substitution in S. pneumoniae serotype 12F may have always been present but is now detectable by state-of-the-art analytical techniques. During the steps of conjugation, the serotype 12F Sug epitope is modified by reduction, and both polysaccharide PPSV23 and conjugate PCV20 vaccines contain 12F Ags with little to no Sug epitope. Both PCV20 and PPSV23 vaccines were evaluated for protection against circulating 12F strains with varying amounts of Sug in their repeat unit based on an opsonophagocytic killing assay involving HL-60 cells and rabbit complement. Both vaccines elicited human-derived neutralizing Abs against serotype 12F, independent of Sug level between ∼2 and 25 mol%. These findings suggest that the newly identified serotype 12F Sug epitope is likely not an essential epitope for vaccine-elicited protection.


Asunto(s)
Inmunogenicidad Vacunal , Streptococcus pneumoniae , Humanos , Serogrupo , Vacunas Conjugadas , Espectroscopía de Resonancia Magnética
13.
Hu Li Za Zhi ; 69(4): 88-98, 2022 Aug.
Artículo en Chino | MEDLINE | ID: mdl-35893340

RESUMEN

BACKGROUND: The scholarly evidence on the timing and practice of interventional care administered to preterm infants in high-humidity environments is unclear. This makes evaluating the prognosis of preterm infants with comorbidities difficult and means that clinical medical staff lack clear guidelines for care. PURPOSE: This systematic review was designed to explore the prognostic effects of interventions for comorbidities performed on very low birthweight preterm infants in high humidity environments to provide an empirical basis for developing related clinical-care guidelines. METHODS: An electronic database was searched for all relevant documents published between 1930 and September 2021. The keywords used were "premature infants" OR "very low weight premature infants" OR "very low weight premature infants" AND "humidity", and the target groups were premature infants weighing ≤ 1,500 grams or delivered at ≤ 34 weeks of gestation. The timing and practice of interventions in high humidity environments and the occurrence and prognosis of related comorbidities were explored. The main findings cover the issues of body weight, total water intake, electrolytes, urine output, insensitivity water loss, infection, common complications, and mortality in preterm infants. After reviewing the methods, quality, and efficacy of the research in the identified studies, 9 articles were selected for integrated synthesis. RESULTS: Recommendations for the use of high humidity with infants delivered at ≤ 30 weeks of gestation or at birth weights ≤ 1,000 grams were integrated. An environment with a relative humidity of 70%-80% should be used during the first postpartum week and 50%-60% during the second postpartum week. The recommended total duration of use of a high-humidity environment is two weeks to avoid delaying the development of the stratum corneum. Physiological indicators shown to exhibit significant improvement under this regimen include reduced total water intake, increased urine output, and a lower incidence of hypernatremia. CONCLUSIONS / IMPLICATIONS FOR PRACTICE: The appropriate timing and practice of high humidity intervention were integrated in this study. It is hoped that this review provides an evidence-based clinical practice guideline for preterm infant care.


Asunto(s)
Enfermedades del Prematuro , Recien Nacido Prematuro , Peso al Nacer , Femenino , Humanos , Recién Nacido , Recién Nacido de muy Bajo Peso
14.
Nutrients ; 14(3)2022 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-35276880

RESUMEN

Dietary intake is an important predictor of health and disease outcomes. This cross-sectional study evaluated the relative validity and reproducibility of a semi-quantitative food frequency questionnaire (FFQ) for assessing energy and nutrient intake in older adults. Dietary data were collected 2018-2019 in Auckland, New Zealand from a convenience sample of community-dwelling adults (65-74 years, n = 294, 37% male) using a 109-item self-administered FFQ at baseline (FFQ1) and four weeks later to assess reproducibility. FFQ1 was compared to a four-day food record to determine relative validity. Agreement between dietary assessment tools was assessed for both raw and energy-adjusted nutrient intakes using paired t-tests, correlation coefficients, weighted kappa statistic, Bland-Altman plots, and linear regression analysis. Energy adjustments moderately improved the relative validity and reproducibility for most nutrients. For energy and energy-adjusted nutrient intakes, the mean correlation coefficients were 0.38 (validity) and 0.65 (reproducibility); the mean weighted kappa statistics were 0.27 (validity) and 0.51 (reproducibility). A significant slope of bias was present in 54% (validity) and 25% (reproducibility) of Bland-Altman plots. The Researching Eating, Activity, and Cognitive Health (REACH) FFQ has acceptable relative validity and good reproducibility for ranking nutrient intakes in older New Zealand adults, but is less suitable for assessing absolute nutrient intakes.


Asunto(s)
Ingestión de Alimentos , Anciano , Estudios Transversales , Femenino , Humanos , Masculino , Nueva Zelanda , Reproducibilidad de los Resultados , Encuestas y Cuestionarios
15.
Nucleic Acids Res ; 50(21): 12001-12018, 2022 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-35348734

RESUMEN

RNA folds cotranscriptionally to traverse out-of-equilibrium intermediate structures that are important for RNA function in the context of gene regulation. To investigate this process, here we study the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional riboswitch that downregulates a nucleoside transporter in response to binding guanine. Although the aptamer and expression platform domain sequences of the yxjA riboswitch do not completely overlap, we hypothesized that a strand exchange process triggers its structural switching in response to ligand binding. In vivo fluorescence assays, structural chemical probing data and experimentally informed secondary structure modeling suggest the presence of a nascent intermediate central helix. The formation of this central helix in the absence of ligand appears to compete with both the aptamer's P1 helix and the expression platform's transcriptional terminator. All-atom molecular dynamics simulations support the hypothesis that ligand binding stabilizes the aptamer P1 helix against central helix strand invasion, thus allowing the terminator to form. These results present a potential model mechanism to explain how ligand binding can induce downstream conformational changes by influencing local strand displacement processes of intermediate folds that could be at play in multiple riboswitch classes.


Riboswitches have challenged our understanding of biological regulation for almost two decades. The ability of small molecules to bind to RNA and control gene expression offers another layer of regulation and the potential for direct action by compounds in the environment. While some riboswitches have been well studied, we lack a general understanding of how changes in RNA structure switch genetic expression from "On" to "Off". In this study, the authors propose an elegant "strand displacement" model to explain how the RNA structure shifts between "On" and "Off" states as the concentration of small molecule ligand changes. These observations help us to understand how riboswitches enable genetic decision-making. The data provide a possible general mechanism for understanding how the competition between different strand displacement outcomes can influence RNA folding. Understanding RNA folding pathways could advance the successful design of drugs that target RNA.


Asunto(s)
Bacillus subtilis , Regulación de la Expresión Génica , Riboswitch , Aptámeros de Nucleótidos/química , Ligandos , Conformación de Ácido Nucleico , Purinas , Pliegue del ARN , Transcripción Genética , Bacillus subtilis/genética
17.
Cogsci ; 43: 2045-2051, 2021 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-34368809

RESUMEN

Humans are often faced with an exploration-versus-exploitation trade-off. A commonly used paradigm, multi-armed bandit, has shown humans to exhibit an "uncertainty bonus", which combines with estimated reward to drive exploration. However, previous studies often modeled belief updating using either a Bayesian model that assumed the reward contingency to remain stationary, or a reinforcement learning model. Separately, we previously showed that human learning in the bandit task is best captured by a dynamic-belief Bayesian model. We hypothesize that the estimated uncertainty bonus may depend on which learning model is employed. Here, we re-analyze a bandit dataset using all three learning models. We find that the dynamic-belief model captures human choice behavior best, while also uncovering a much larger uncertainty bonus than the other models. More broadly, our results also emphasize the importance of an appropriate learning model, as it is crucial for correctly characterizing the processes underlying human decision making.

18.
Cancer Res ; 81(20): 5176-5189, 2021 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-34433584

RESUMEN

Epithelial ovarian carcinomas are particularly deadly due to intratumoral heterogeneity, resistance to standard-of-care therapies, and poor response to alternative treatments such as immunotherapy. Targeting the ovarian carcinoma epigenome with DNA methyltransferase inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi) increases immune signaling and recruits CD8+ T cells and natural killer cells to fight ovarian carcinoma in murine models. This increased immune activity is caused by increased transcription of repetitive elements (RE) that form double-stranded RNA (dsRNA) and trigger an IFN response. To understand which REs are affected by epigenetic therapies in ovarian carcinoma, we assessed the effect of DNMTi and HDACi on ovarian carcinoma cell lines and patient samples. Subfamily-level (TEtranscripts) and individual locus-level (Telescope) analysis of REs showed that DNMTi treatment upregulated more REs than HDACi treatment. Upregulated REs were predominantly LTR and SINE subfamilies, and SINEs exhibited the greatest loss of DNA methylation upon DNMTi treatment. Cell lines with TP53 mutations exhibited significantly fewer upregulated REs with epigenetic therapy than wild-type TP53 cell lines. This observation was validated using isogenic cell lines; the TP53-mutant cell line had significantly higher baseline expression of REs but upregulated fewer upon epigenetic treatment. In addition, p53 activation increased expression of REs in wild-type but not mutant cell lines. These data give a comprehensive, genome-wide picture of RE chromatin and transcription-related changes in ovarian carcinoma after epigenetic treatment and implicate p53 in RE transcriptional regulation. SIGNIFICANCE: This study identifies the repetitive element targets of epigenetic therapies in ovarian carcinoma and indicates a role for p53 in this process.


Asunto(s)
Azacitidina/farmacología , Epigénesis Genética , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Inhibidores de Histona Desacetilasas/farmacología , Neoplasias Ováricas/genética , Secuencias Repetitivas de Ácidos Nucleicos , Proteína p53 Supresora de Tumor/metabolismo , Antimetabolitos Antineoplásicos/farmacología , Apoptosis , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Proliferación Celular , Femenino , Humanos , Neoplasias Ováricas/tratamiento farmacológico , Neoplasias Ováricas/patología , Células Tumorales Cultivadas , Proteína p53 Supresora de Tumor/genética
19.
Transl Psychiatry ; 11(1): 408, 2021 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-34312367

RESUMEN

As massive amounts of information are becoming available to people, understanding the mechanisms underlying information-seeking is more pertinent today than ever. In this study, we investigate the underlying motivations to seek out information in healthy and addicted individuals. We developed a novel decision-making task and a novel computational model which allows dissociating the relative contribution of two motivating factors to seek out information: a desire for novelty and a general desire for knowledge. To investigate whether/how the motivations to seek out information vary between healthy and addicted individuals, in addition to healthy controls we included a sample of individuals with gambling disorder-a form of addiction without the confound of substance consumption and characterized by compulsive gambling. Our results indicate that healthy subjects and problem gamblers adopt distinct information-seeking "modes". Healthy information-seeking behavior was mostly motivated by a desire for novelty. Problem gamblers, on the contrary, displayed reduced novelty-seeking and an increased desire for accumulating knowledge compared to healthy controls. Our findings not only shed new light on the motivations driving healthy and addicted individuals to seek out information, but they also have important implications for the treatment and diagnosis of behavioral addiction.


Asunto(s)
Conducta Adictiva , Juego de Azar , Estado de Salud , Humanos , Motivación
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA