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1.
Cell ; 168(6): 1053-1064.e15, 2017 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-28283061

RESUMO

Cytokines are classically thought to stimulate downstream signaling pathways through monotonic activation of receptors. We describe a severe anemia resulting from a homozygous mutation (R150Q) in the cytokine erythropoietin (EPO). Surprisingly, the EPO R150Q mutant shows only a mild reduction in affinity for its receptor but has altered binding kinetics. The EPO mutant is less effective at stimulating erythroid cell proliferation and differentiation, even at maximally potent concentrations. While the EPO mutant can stimulate effectors such as STAT5 to a similar extent as the wild-type ligand, there is reduced JAK2-mediated phosphorylation of select downstream targets. This impairment in downstream signaling mechanistically arises from altered receptor dimerization dynamics due to extracellular binding changes. These results demonstrate how variation in a single cytokine can lead to biased downstream signaling and can thereby cause human disease. Moreover, we have defined a distinct treatable form of anemia through mutation identification and functional studies.


Assuntos
Anemia de Diamond-Blackfan/genética , Anemia de Diamond-Blackfan/patologia , Eritropoetina/genética , Mutação de Sentido Incorreto , Transdução de Sinais , Anemia de Diamond-Blackfan/terapia , Criança , Consanguinidade , Ativação Enzimática , Eritropoese , Eritropoetina/química , Feminino , Humanos , Janus Quinase 2/metabolismo , Cinética , Masculino , Receptores da Eritropoetina/química , Receptores da Eritropoetina/genética , Receptores da Eritropoetina/metabolismo
2.
Nucleic Acids Res ; 2024 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-39435987

RESUMO

The design, analysis and mining of large-scale 'omics studies with the goal of advancing biological and biomedical understanding require use of a range of bioinformatics tools, including approaches tailored to needs specific to a given species and/or technology. The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) Functional Genomics Resources (https://fgr.hms.harvard.edu/tools) supports an increasingly broad group of technologies and species. Recently, for example, we expanded the database to include additional new data-centric resources that facilitate mining and analysis of single-cell transcriptomics. In addition, we have applied our approaches to CRISPR reagent and gene-centric bioinformatics approaches in Drosophila to arthropod vectors of infectious diseases. Building on our previous comprehensive reports on the FlyRNAi database, here we focus on new and updated resources with a primary focus on data-centric tools. Altogether, our suite of online resources supports various stages of functional genomics studies for Drosophila and other arthropods, and facilitate a wide range of reagent design, analysis, data mining and analysis approaches by biologists and biomedical experts studying Drosophila, other common genetic model species, arthropod vectors and/or human biology.

3.
Proc Natl Acad Sci U S A ; 118(10)2021 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-33649236

RESUMO

Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a central regulator of cell growth and metabolism that senses and integrates nutritional and environmental cues with cellular responses. Recent studies have revealed critical roles of mTORC1 in RNA biogenesis and processing. Here, we find that the m6A methyltransferase complex (MTC) is a downstream effector of mTORC1 during autophagy in Drosophila and human cells. Furthermore, we show that the Chaperonin Containing Tailless complex polypeptide 1 (CCT) complex, which facilitates protein folding, acts as a link between mTORC1 and MTC. The mTORC1 activates the chaperonin CCT complex to stabilize MTC, thereby increasing m6A levels on the messenger RNAs encoding autophagy-related genes, leading to their degradation and suppression of autophagy. Altogether, our study reveals an evolutionarily conserved mechanism linking mTORC1 signaling with m6A RNA methylation and demonstrates their roles in suppressing autophagy.


Assuntos
Autofagia , Proteínas de Drosophila/metabolismo , Alvo Mecanístico do Complexo 1 de Rapamicina/metabolismo , Metiltransferases/metabolismo , Receptores Citoplasmáticos e Nucleares/metabolismo , Proteínas Repressoras/metabolismo , Transdução de Sinais , Animais , Linhagem Celular , Proteínas de Drosophila/genética , Drosophila melanogaster , Humanos , Alvo Mecanístico do Complexo 1 de Rapamicina/genética , Metilação , Metiltransferases/genética , Receptores Nucleares Órfãos , Estabilidade de RNA , Receptores Citoplasmáticos e Nucleares/genética , Proteínas Repressoras/genética
4.
Circ J ; 86(4): 687-694, 2022 03 25.
Artigo em Inglês | MEDLINE | ID: mdl-34759121

RESUMO

BACKGROUND: The predictive role of the vasoactive-inotropic score (VIS) for clinical outcomes after venoarterial extracorporeal membrane oxygenation (VA-ECMO) in patients with cardiogenic shock is not well known. This study investigated the predictive value of VIS on in-hospital outcomes and the determination of optimal timing for the initiation of VA-ECMO.Methods and Results:Overall, 160 patients with cardiogenic shock requiring VA-ECMO who were treated between December 2012 and August 2018 were analyzed. The in-hospital outcomes according to VIS were compared. Pre-ECMO VIS had an area under the receiver-operating characteristic curve (AUC) of 0.60 (P=0.03) for the prediction of in-hospital death. When the patients were divided into the high (≥32) and low (<32) VIS groups, the high VIS group had a higher rate of in-hospital death (P=0.002) and a lower rate of ECMO weaning (P=0.004). The difference in in-hospital death according to VIS was significant only in patients with a cardiogenic shock of non-ischemic etiology (P=0.01). Extracorporeal cardiopulmonary resuscitation (hazard ratio [HR], 1.99), age (HR, 1.02), pre-ECMO lactate (HR, 1.06), and VIS ≥32 (HR, 2.46) were independently predictive of in-hospital death. CONCLUSIONS: Among patients with cardiogenic shock requiring VA-ECMO, the initiation of VA-ECMO before reaching high VIS (≥32) showed better in-hospital outcomes, suggesting that VIS may be a potential marker for determining the initiation of hemodynamic support with VA-ECMO.


Assuntos
Oxigenação por Membrana Extracorpórea , Oxigenação por Membrana Extracorpórea/métodos , Mortalidade Hospitalar , Humanos , Curva ROC , Estudos Retrospectivos , Choque Cardiogênico/terapia
5.
BMC Psychiatry ; 22(1): 490, 2022 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-35869454

RESUMO

BACKGROUND: COVID-19 pandemic causes psychological problems such as stress. It is important to accurately identify the level of stress and establish effective intervention. The Impact of Event Scale-6 (IES-6) is widely used for post-traumatic stress disorder (PTSD) screening by measuring the level of subjective stress, but there has been no research on its psychometric properties with individuals who experienced the COVID-19 pandemic. METHODS: A random sample of 600 participants were randomly selected from a COVID-19 survey database (n = 6391). Rasch analysis was conducted to examine item fit, rating scale structure, construct validity, differential item functioning (DIF), and precision of the IES-6. RESULTS: The principal component analysis of Rasch residuals (54.1% of the raw variance explained) and the average of residual correlations (average r = .19) supported the unidimensionality structure in the IES-6. The rating scale was suitable, and the item difficulty hierarchy was logical. The item fit and the DIF contrast were acceptable, except for item 5. The IES-6's person reliability was .76, which was also an acceptable level. CONCLUSIONS: This study showed that the IES-6 has acceptable item-level psychometrics for screening the stress level in adults in the United States for individuals who have experienced the COVID-19 pandemic. The findings suggested that the IES-6 would be useful for the rapid identification of the high-level stressand allow clinicians to quickly provide interventions for people with the COVID-19 related stress and their families.


Assuntos
COVID-19 , Adulto , Humanos , Pandemias , Psicometria , Reprodutibilidade dos Testes , Inquéritos e Questionários , Estados Unidos/epidemiologia
6.
Nature ; 518(7539): 317-30, 2015 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-25693563

RESUMO

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.


Assuntos
Epigênese Genética/genética , Epigenômica , Genoma Humano/genética , Sequência de Bases , Linhagem da Célula/genética , Células Cultivadas , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , Cromossomos Humanos/química , Cromossomos Humanos/genética , Cromossomos Humanos/metabolismo , DNA/química , DNA/genética , DNA/metabolismo , Metilação de DNA , Conjuntos de Dados como Assunto , Elementos Facilitadores Genéticos/genética , Variação Genética/genética , Estudo de Associação Genômica Ampla , Histonas/metabolismo , Humanos , Especificidade de Órgãos/genética , RNA/genética , Valores de Referência
7.
Artif Organs ; 45(4): 390-398, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33001468

RESUMO

We evaluated the benefit of left ventricular (LV) unloading using a percutaneous transseptal left atrial (LA) drain catheter via femoral vein incorporated into the ECMO venous circuit. This single-center retrospective observational study analyzed clinical outcomes of the LA venting group (N = 62) who underwent percutaneous transseptal LA drain placement comparing with the conventionally treated control group (N = 62) with an arterial pulse pressure below 10 mm Hg for at least 24 hours from December 2012 to August 2018. The ECMO weaning rate (61.3% vs. 38.7%, P = .012) and cardiac transplantation rate (29.0% vs. 11.3%, P = .014) were higher in the LA venting group than in the control group. Inhospital mortality was not significantly different (56.5% vs. 69.4%, P = .191). Pulmonary congestion mostly improved after LA decompression (61.3%, P = .003). A serum lactate level at 24 hours after LA venting of more than 2.2 mmol/L was associated with poor outcomes. LA venting via transseptal cannula reduced pulmonary venous congestion and achieved higher rates of successful ECMO weaning and cardiac transplantation. Placement of a transseptal venous drain cannula should be considered in patients with uncontrolled pulmonary edema secondary to severe LV loading undergoing VA-ECMO.


Assuntos
Cateterismo Cardíaco/métodos , Oxigenação por Membrana Extracorpórea , Transplante de Coração , Disfunção Ventricular Esquerda/fisiopatologia , Biomarcadores/sangue , Drenagem/métodos , Feminino , Humanos , Lactatos/sangue , Masculino , Pessoa de Meia-Idade , Veias Pulmonares , República da Coreia , Estudos Retrospectivos , Disfunção Ventricular Esquerda/prevenção & controle
8.
J Clin Immunol ; 40(4): 554-566, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32303876

RESUMO

Studies of genetic blood disorders have advanced our understanding of the intrinsic regulation of hematopoiesis. However, such genetic studies have only yielded limited insights into how interactions between hematopoietic cells and their microenvironment are regulated. Here, we describe two affected siblings with infantile myelofibrosis and myeloproliferation that share a common de novo mutation in the Rho GTPase CDC42 (Chr1:22417990:C>T, p.R186C) due to paternal germline mosaicism. Functional studies using human cells and flies demonstrate that this CDC42 mutant has altered activity and thereby disrupts interactions between hematopoietic progenitors and key tissue microenvironmental factors. These findings suggest that further investigation of this and other related disorders may provide insights into how hematopoietic cell-microenvironment interactions play a role in human health and can be disrupted in disease. In addition, we suggest that deregulation of CDC42 may underlie more common blood disorders, such as primary myelofibrosis.


Assuntos
Mutação/genética , Mielofibrose Primária/diagnóstico , Proteína cdc42 de Ligação ao GTP/genética , Ciclo Celular , Microambiente Celular , Células HEK293 , Hematopoese/genética , Humanos , Lactente , Recém-Nascido , Mielofibrose Primária/genética , Irmãos , Sequenciamento do Exoma
9.
Hepatology ; 66(2): 416-431, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28073164

RESUMO

Free cholesterol (FC) accumulation in the liver is an important pathogenic mechanism of nonalcoholic steatohepatitis (NASH). Plasmalogens, key structural components of the cell membrane, act as endogenous antioxidants and are primarily synthesized in the liver. However, the role of hepatic plasmalogens in metabolic liver disease is unclear. In this study, we found that hepatic levels of docosahexaenoic acid (DHA)-containing plasmalogens, expression of glyceronephosphate O-acyltransferase (Gnpat; the rate-limiting enzyme in plasmalogen biosynthesis), and expression of Pparα were lower in mice with NASH caused by accumulation of FC in the liver. Cyclodextrin-induced depletion of FC transactivated Δ-6 desaturase by increasing sterol regulatory element-binding protein 2 expression in cultured hepatocytes. DHA, the major product of Δ-6 desaturase activation, activated GNPAT, thereby explaining the association between high hepatic FC and decreased Gnpat expression. Gnpat small interfering RNA treatment significantly decreased peroxisome proliferator-activated receptor α (Pparα) expression in cultured hepatocytes. In addition to GNPAT, DHA activated PPARα and increased expression of Pparα and its target genes, suggesting that DHA in the DHA-containing plasmalogens contributed to activation of PPARα. Accordingly, administration of the plasmalogen precursor, alkyl glycerol (AG), prevented hepatic steatosis and NASH through a PPARα-dependent increase in fatty acid oxidation. Gnpat+/- mice were more susceptible to hepatic lipid accumulation and less responsive to the preventive effect of fluvastatin on NASH development, suggesting that endogenous plasmalogens prevent hepatic steatosis and NASH. CONCLUSION: Increased hepatic FC in animals with NASH decreased plasmalogens, thereby sensitizing animals to hepatocyte injury and NASH. Our findings uncover a novel link between hepatic FC and plasmalogen homeostasis through GNPAT regulation. Further study of AG or other agents that increase hepatic plasmalogen levels may identify novel therapeutic strategies against NASH. (Hepatology 2017;66:416-431).


Assuntos
Fígado Gorduroso/metabolismo , Glucosamina 6-Fosfato N-Acetiltransferase/metabolismo , Subunidade 1 do Complexo Mediador/metabolismo , Plasmalogênios/metabolismo , Análise de Variância , Animais , Biomarcadores/metabolismo , Biópsia por Agulha , Modelos Animais de Doenças , Ácidos Graxos Monoinsaturados/farmacologia , Fígado Gorduroso/patologia , Fluvastatina , Glucosamina 6-Fosfato N-Acetiltransferase/efeitos dos fármacos , Imuno-Histoquímica , Indóis/farmacologia , Masculino , Subunidade 1 do Complexo Mediador/efeitos dos fármacos , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Hepatopatia Gordurosa não Alcoólica/metabolismo , Hepatopatia Gordurosa não Alcoólica/patologia , Distribuição Aleatória , Sensibilidade e Especificidade , Transdução de Sinais
10.
Fish Shellfish Immunol ; 55: 434-43, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27320869

RESUMO

The immune tone is defined as an immunological state during which the readiness for immune response is potentiated. The establishment of immune tone in the gut of olive flounder (Paralichthys olivaceus) was investigated by feeding Lactococcus lactis BFE920 (LL) or Lactobacillus plantarum FGL0001 (LP). LL-fed flounder showed significantly increased levels of regulatory genes (FOXP3, IL-10, and TGF-ß1), CD18, and CD83 in the gut. In contrast, LP feeding drastically increased proinflammatory genes (T-bet, IL-1ß, and IFN-γ) and CD18. This indicates that LL and LP establish different types of local immune tones in the gut through differential activation of innate immune cells: LL activates both macrophages and dendritic cells while LP activates macrophages only. Both of the immune tones required at least a total of 6 probiotic feeds during 72 h for a stable establishment. Once established, the type of immune tone remained steady even up to 30 days (a total of 60 feeds) probiotics feeding. The LL-induced regulatory immune tone enhanced the level of occludin, a tight junction molecule, significantly more than that observed with the proinflammatory immune tone established by LP feeding. Consequently, LL-fed fish showed considerably lower gut permeability than that of the LP-fed group. Furthermore, when orally challenged by Edwardsiella tarda, LL-fed flounder survived at a significantly higher rate than LP-fed fish. The data clearly demonstrate that individual probiotics establish distinct types of immune tone in the fish gut, which in turn influences the immunological status as well as the physiology of the gut. Selection of proper probiotics may be essential for optimal effects in aquaculture farming.


Assuntos
Linguados/imunologia , Imunomodulação , Lactobacillus plantarum/química , Lactococcus lactis/química , Probióticos/administração & dosagem , Ração Animal/análise , Animais , Dieta/veterinária , Trato Gastrointestinal/imunologia
11.
PLoS Genet ; 9(2): e1003243, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23468638

RESUMO

Rearrangements of about 2.5 kilobases of regulatory DNA located 5' of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small "spacer" segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2-3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cis-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein-DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory "elements" are not elementary objects.


Assuntos
Proteínas de Drosophila/genética , Drosophila melanogaster , Elementos Facilitadores Genéticos , Rearranjo Gênico/genética , Proteínas de Homeodomínio/genética , Fatores de Transcrição/genética , Animais , Sítios de Ligação , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Evolução Molecular , Regulação da Expressão Gênica no Desenvolvimento , Genoma , RNA não Traduzido/genética , Sítio de Iniciação de Transcrição
12.
Mol Biol Evol ; 31(4): 903-16, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24408913

RESUMO

Upstream regulatory sequences that control gene expression evolve rapidly, yet the expression patterns and functions of most genes are typically conserved. To address this paradox, we have reconstructed computationally and resurrected in vivo the cis-regulatory regions of the ancestral Drosophila eve stripe 2 element and evaluated its evolution using a mathematical model of promoter function. Our feed-forward transcriptional model predicts gene expression patterns directly from enhancer sequence. We used this functional model along with phylogenetics to generate a set of possible ancestral eve stripe 2 sequences for the common ancestors of 1) D. simulans and D. sechellia; 2) D. melanogaster, D. simulans, and D. sechellia; and 3) D. erecta and D. yakuba. These ancestral sequences were synthesized and resurrected in vivo. Using a combination of quantitative and computational analysis, we find clear support for functional compensation between the binding sites for Bicoid, Giant, and Krüppel over the course of 40-60 My of Drosophila evolution. We show that this compensation is driven by a coupling interaction between Bicoid activation and repression at the anterior and posterior border necessary for proper placement of the anterior stripe 2 border. A multiplicity of mechanisms for binding site turnover exemplified by Bicoid, Giant, and Krüppel sites, explains how rapid sequence change may occur while maintaining the function of the cis-regulatory element.


Assuntos
Drosophila melanogaster/genética , Elementos Facilitadores Genéticos , Evolução Molecular , Animais , Teorema de Bayes , Sítios de Ligação , Proteínas de Drosophila/genética , Genes de Insetos , Especiação Genética , Proteínas de Homeodomínio/genética , Modelos Genéticos , Filogenia , Fatores de Transcrição/genética , Transcrição Gênica
13.
Nat Genet ; 38(10): 1159-65, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-16980977

RESUMO

Here we present a quantitative and predictive model of the transcriptional readout of the proximal 1.7 kb of the control region of the Drosophila melanogaster gene even skipped (eve). The model is based on the positions and sequence of individual binding sites on the DNA and quantitative, time-resolved expression data at cellular resolution. These data demonstrated new expression features, first reported here. The model correctly predicts the expression patterns of mutations in trans, as well as point mutations, insertions and deletions in cis. It also shows that the nonclassical expression of stripe 7 driven by this fragment is activated by the protein Caudal (Cad), and repressed by the proteins Tailless (Tll) and Giant (Gt).


Assuntos
Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Elementos Facilitadores Genéticos , Proteínas de Homeodomínio/genética , Modelos Genéticos , Fatores de Transcrição/genética , Transcrição Gênica , Animais , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Proteínas de Drosophila/metabolismo , Regulação da Expressão Gênica , Proteínas de Homeodomínio/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Fatores de Transcrição/metabolismo
14.
Methods ; 62(1): 91-8, 2013 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-23732772

RESUMO

Synthetic biology offers novel opportunities for elucidating transcriptional regulatory mechanisms and enhancer logic. Complex cis-regulatory sequences--like the ones driving expression of the Drosophila even-skipped gene--have proven difficult to design from existing knowledge, presumably due to the large number of protein-protein interactions needed to drive the correct expression patterns of genes in multicellular organisms. This work discusses two novel computational methods for the custom design of enhancers that employ a sophisticated, empirically validated transcriptional model, optimization algorithms, and synthetic biology. These synthetic elements have both utilitarian and academic value, including improving existing regulatory models as well as evolutionary questions. The first method involves the use of simulated annealing to explore the sequence space for synthetic enhancers whose expression output fit a given search criterion. The second method uses a novel optimization algorithm to find functionally accessible pathways between two enhancer sequences. These paths describe a set of mutations wherein the predicted expression pattern does not significantly vary at any point along the path. Both methods rely on a predictive mathematical framework that maps the enhancer sequence space to functional output.


Assuntos
Drosophila melanogaster/genética , Embrião não Mamífero/metabolismo , Elementos Facilitadores Genéticos , Regulação da Expressão Gênica no Desenvolvimento , Modelos Genéticos , Biologia Sintética/métodos , Algoritmos , Animais , Sítios de Ligação , Padronização Corporal/genética , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/embriologia , Drosophila melanogaster/metabolismo , Embrião não Mamífero/citologia , Embrião não Mamífero/ultraestrutura , Perfilação da Expressão Gênica , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Processamento de Imagem Assistida por Computador/estatística & dados numéricos , Hibridização In Situ , Ligação Proteica , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcrição Gênica
15.
iScience ; 27(1): 108747, 2024 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-38222110

RESUMO

Massively parallel reporter assay measures transcriptional activities of various cis-regulatory modules (CRMs) in a single experiment. We developed a thermodynamic computational model framework that calculates quantitative levels of gene expression directly from regulatory DNA sequences. Using the framework, we investigated the molecular mechanisms of cis-regulatory mutations of a synthetic enhancer that cause abnormal gene expression. We found that, in a human cell line, competitive binding between family transcription factors (TFs) with slightly different binding preferences significantly increases the accuracy of recapitulating the transcriptional effects of thousands of single- or multi-mutations. We also discovered that even if various harmful mutations occurred in an activator binding site, CRM could stably maintain or even increase gene expression through a certain form of competitive binding between family TFs. These findings enhance understanding the effect of SNPs and indels on CRMs and would help building robust custom-designed CRMs for biologics production and gene therapy.

16.
Nutrients ; 16(19)2024 Sep 26.
Artigo em Inglês | MEDLINE | ID: mdl-39408221

RESUMO

Muscular strength and endurance are vital for physical fitness. While mistletoe extract has shown efficacy in significantly increasing muscle strength and endurance, its accessibility is limited. This study explores combining mistletoe and apple peel extracts as an effective muscle health supplement. Analyses of histology, RNA, and protein in the combined extract-treated mouse group demonstrated significant enhancements in muscle strength and endurance, evidenced by larger muscle fibers, improved mitochondrial function, and a higher ratio of type I and IIa muscle fibers. Combining half doses of each extract resulted in greater improvements than using each extract separately, indicating a synergistic effect. Pathway analysis suggests that the observed synergy arises from complementary mechanisms, with a mistletoe extract-induced decrease in myostatin (MSTN) and an apple peel extract-induced increase in IGF1, leading to a sharp rise in AKT, S6K, and MuRF1, which promote myogenesis, along with a significant increase in PGC-1α, TFAM, and MEF2C, which are critical for mitochondrial biogenesis. This research provides practical insights into developing cost-effective, natural supplements to enhance muscle performance and endurance, with potential applications in athletic performance, improving muscle growth and endurance in children, and addressing age-related muscle decline.


Assuntos
Malus , Erva-de-Passarinho , Força Muscular , Resistência Física , Extratos Vegetais , Extratos Vegetais/farmacologia , Animais , Força Muscular/efeitos dos fármacos , Camundongos , Resistência Física/efeitos dos fármacos , Malus/química , Erva-de-Passarinho/química , Músculo Esquelético/efeitos dos fármacos , Proteínas Musculares/metabolismo , Miostatina/metabolismo , Masculino , Frutas/química , Sinergismo Farmacológico , Suplementos Nutricionais , Proteínas com Motivo Tripartido/metabolismo , Proteínas com Motivo Tripartido/genética , Ubiquitina-Proteína Ligases/metabolismo , Desenvolvimento Muscular/efeitos dos fármacos , Fator de Crescimento Insulin-Like I/metabolismo , Camundongos Endogâmicos C57BL , República da Coreia
17.
J Eval Clin Pract ; 30(6): 1049-1058, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39031719

RESUMO

INTRODUCTION: Lifestyle, defined as a way of living resulting from an individual's deliberate choices, is a crucial factor in improving and maintaining health. Consequently, the measurement and analysis of lifestyle are of significant importance. This study aims to validate the validity and reliability of the Yonsei Lifestyle Profile-Active, Balance, Connection, Diversity (YLP-ABCD) in measuring health-related lifestyles. METHODS: Data were collected from 300 participants aged 55 and older using the YLP-ABCD. To analyse the validity and reliability of the YLP-ABCD, analysed using frequency, descriptive statistics, confirmatory factor analysis, and Rasch model analysis. RESULTS: The results indicate that the YLP-ABCD, which consists of 35 items, demonstrates unidimensionality and local independence. The Rasch model confirmed the suitability of the 5-point Likert scale for the factors, excluding subfactors Balanced and Unbalanced. The item fit criteria (0.5 < MNSQ < 1.5) were met for all items. The distribution of the respondents' abilities suggests the need for additional items to measure their ability levels. Both the item and respondent separation indices and their reliabilities were satisfactory. CONCLUSION: This study confirmed the utility of the YLP-ABCD as a valuable tool for measuring and understanding the multifaceted diversity of lifestyles. Therefore, by utilising YLP-ABCD to quantitatively measure health lifestyles, we anticipate contributing to improvements in human health and quality of life.


Assuntos
Estilo de Vida , Psicometria , Humanos , Masculino , Feminino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes , Idoso , Inquéritos e Questionários/normas , China , Análise Fatorial , Qualidade de Vida
18.
Front Cardiovasc Med ; 11: 1351431, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38390441

RESUMO

Introduction: There have been few studies on predictors of weaning failure from MV in patients with heart failure (HF). We sought to investigate the predictive value of B-lines measured by lung ultrasound (LUS) on the risk of weaning failure from mechanical ventilation (MV) and in-hospital outcomes. Methods: This was a single-center, prospective observational study that included HF patients who were on invasive MV. LUS was performed immediate before ventilator weaning. A positive LUS exam was defined as the observation of two or more regions that had three or more count of B-lines located bilaterally on the thorax. The primary outcome was early MV weaning failure, defined as re-intubation within 72 h. Results: A total of 146 consecutive patients (mean age 70 years; 65.8% male) were enrolled. The total count of B-lines was a median of 10 and correlated with NT-pro-BNP level (r2 = 0.132, p < 0.001). Early weaning failure was significantly higher in the positive LUS group (9 out of 64, 14.1%) than the negative LUS group (2 out of 82, 2.4%) (p = 0.011). The rate of total re-intubation during the hospital stay (p = 0.004), duration of intensive care unit stay (p = 0.004), and hospital stay (p = 0.010) were greater in the positive LUS group. The negative predictive value (NPV) of positive LUS was 97.6% for the primary outcome. Conclusion: B-lines measured by LUS can predict the risk of weaning failure. Considering the high NPV of positive LUS, it may help guide the decision of weaning in patients on invasive MV due to acute decompensated HF.

19.
bioRxiv ; 2024 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-38712132

RESUMO

Individual tissues perform highly specialized metabolic functions to maintain whole-body homeostasis. Although Drosophila serves as a powerful model for studying human metabolic diseases, a lack of tissue-specific metabolic models makes it challenging to quantitatively assess the metabolic processes of individual tissues and disease models in this organism. To address this issue, we reconstructed 32 tissue-specific genome-scale metabolic models (GEMs) using pseudo-bulk single cell transcriptomics data, revealing distinct metabolic network structures across tissues. Leveraging enzyme kinetics and flux analyses, we predicted tissue-dependent metabolic pathway activities, recapitulating known tissue functions and identifying tissue-specific metabolic signatures, as supported by metabolite profiling. Moreover, to demonstrate the utility of tissue-specific GEMs in a disease context, we examined the effect of a high sugar diet (HSD) on muscle metabolism. Together with 13C-glucose isotopic tracer studies, we identified glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as a rate-limiting enzyme in response to HSD. Mechanistically, the decreased GAPDH activity was linked to elevated NADH/NAD+ ratio, caused by disturbed NAD+ regeneration rates, and oxidation of GAPDH. Furthermore, we introduced a pathway flux index to predict and validate additionally perturbed pathways, including fructose and butanoate metabolism. Altogether, our results represent a significant advance in generating quantitative tissue-specific GEMs and flux analyses in Drosophila, highlighting their use for identifying dysregulated metabolic pathways and their regulation in a human disease model.

20.
Sci Rep ; 14(1): 3018, 2024 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-38321153

RESUMO

Rehabilitation improves symptoms, quality of life, and survival in patients with chronic respiratory or cardiovascular disease. We evaluated smartphone application-based rehabilitation programs for patients with chronic respiratory or cardiovascular diseases. This was a single-center prospective single arm study. Participants underwent smartphone application-based pulmonary or cardiac rehabilitation for 12 weeks. A total of 93 participants were recruited, and 75 visited after rehabilitation. Their median age was 67.0 (interquartile range, 60.0-70.8) years, and 60 (80.0%) were men. For patients with chronic respiratory disease (n = 41), VO2peak (median 13.7 to 15.4 ml/kg/min, P = 0.049), chronic obstructive pulmonary disease assessment test (median 14 to 6, P < 0.001), Euro-QoL 5-Dimension 5-Level (EQ-5D-5L) index (median 0.795 to 0.862, P = 0.001), and Health-related Quality of Life Instrument with 8 Items (HINT-8) index (median 0.784 to 0.855, P < 0.001) were significantly improved. For patients with chronic cardiovascular disease (n = 34), VO2peak (median 21.8 to 23.3, P = 0.007), EQ-5D-5L index (median 0.871 to 1.000, P = 0.037), and HINT-8 index (median 0.890 to 0.903, P < 0.001) were significantly improved. The smartphone application-based rehabilitation program improved exercise capacity and quality of life in patients with chronic respiratory or cardiovascular disease.Trial registration: https://clinicaltrials.gov/ct2/show/NCT05383950 (20/05/2022).


Assuntos
Doenças Cardiovasculares , Doença Pulmonar Obstrutiva Crônica , Masculino , Humanos , Idoso , Feminino , Qualidade de Vida , Smartphone , Estudos Prospectivos , Doença Pulmonar Obstrutiva Crônica/reabilitação
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