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1.
Cell ; 174(6): 1492-1506.e22, 2018 09 06.
Artículo en Inglés | MEDLINE | ID: mdl-30173914

RESUMEN

The assembly of phase-separated structures is thought to play an important role in development and disease, but little is known about the regulation and function of phase separation under physiological conditions. We showed that during C. elegans embryogenesis, PGL granules assemble via liquid-liquid phase separation (LLPS), and their size and biophysical properties determine their susceptibility to autophagic degradation. The receptor SEPA-1 promotes LLPS of PGL-1/-3, while the scaffold protein EPG-2 controls the size of PGL-1/-3 compartments and converts them into less dynamic gel-like structures. Under heat-stress conditions, mTORC1-mediated phosphorylation of PGL-1/-3 is elevated and PGL-1/-3 undergo accelerated phase separation, forming PGL granules that are resistant to autophagic degradation. Significantly, accumulation of PGL granules is an adaptive response to maintain embryonic viability during heat stress. We revealed that mTORC1-mediated LLPS of PGL-1/-3 acts as a switch-like stress sensor, coupling phase separation to autophagic degradation and adaptation to stress during development.


Asunto(s)
Autofagia , Proteínas de Caenorhabditis elegans/metabolismo , Diana Mecanicista del Complejo 1 de la Rapamicina/metabolismo , Animales , Arginina/metabolismo , Caenorhabditis elegans/crecimiento & desarrollo , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Embrión no Mamífero/metabolismo , Desarrollo Embrionario , Larva/metabolismo , Diana Mecanicista del Complejo 1 de la Rapamicina/genética , Metilación , Mutagénesis Sitio-Dirigida , Fosforilación , Fosfotransferasas (Aceptor de Grupo Alcohol)/genética , Fosfotransferasas (Aceptor de Grupo Alcohol)/metabolismo , Procesamiento Proteico-Postraduccional , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Transducción de Señal , Temperatura
2.
Cell ; 156(1-2): 359-72, 2014 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-24439388

RESUMEN

Elucidation of complex phenotypes for mechanistic insights presents a significant challenge in systems biology. We report a strategy to automatically infer mechanistic models of cell fate differentiation based on live-imaging data. We use cell lineage tracing and combinations of tissue-specific marker expression to assay progenitor cell fate and detect fate changes upon genetic perturbation. Based on the cellular phenotypes, we further construct a model for how fate differentiation progresses in progenitor cells and predict cell-specific gene modules and cell-to-cell signaling events that regulate the series of fate choices. We validate our approach in C. elegans embryogenesis by perturbing 20 genes in over 300 embryos. The result not only recapitulates current knowledge but also provides insights into gene function and regulated fate choice, including an unexpected self-renewal. Our study provides a powerful approach for automated and quantitative interpretation of complex in vivo information.


Asunto(s)
Caenorhabditis elegans/citología , Linaje de la Célula , Embrión no Mamífero/citología , Células Madre/citología , Animales , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Desarrollo Embrionario , Fenotipo , Transcriptoma
3.
EMBO Rep ; 24(12): e57440, 2023 Dec 06.
Artículo en Inglés | MEDLINE | ID: mdl-37885348

RESUMEN

Embryogenesis is highly dependent on maternally loaded materials, particularly those used for energy production. Different environmental conditions and genetic backgrounds shape embryogenesis. The robustness of embryogenesis in response to extrinsic and intrinsic changes remains incompletely understood. By analyzing the levels of two major nutrients, glycogen and neutral lipids, we discovered stage-dependent usage of these two nutrients along with mitochondrial morphology changes during Caenorhabditis elegans embryogenesis. ATGL, the rate-limiting lipase in cellular lipolysis, is expressed and required in the hypodermis to regulate mitochondrial function and support embryogenesis. The embryonic lethality of atgl-1 mutants can be suppressed by reducing sinh-1/age-1-akt signaling, likely through modulating glucose metabolism to maintain sustainable glucose consumption. The embryonic lethality of atgl-1(xd314) is also affected by parental nutrition. Parental glucose and oleic acid supplements promote glycogen storage in atgl-1(xd314) embryos to compensate for the impaired lipolysis. The rescue by parental vitamin B12 supplement is likely through enhancing mitochondrial function in atgl-1 mutants. These findings reveal that metabolic plasticity contributes to the robustness of C. elegans embryogenesis.


Asunto(s)
Caenorhabditis elegans , Lipólisis , Animales , Caenorhabditis elegans/metabolismo , Lipólisis/genética , Lipasa/genética , Glucosa/metabolismo , Glucógeno/metabolismo
4.
Nat Methods ; 18(8): 893-902, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-34312566

RESUMEN

Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using protein-fusion fluorescent reporters and four-dimensional live imaging, we present a protein expression atlas of transcription factors (TFs) mapped onto developmental cell lineages during Caenorhabditis elegans embryogenesis, at single-cell resolution. This atlas reveals a spatiotemporal combinatorial code of TF expression, and a cascade of lineage-specific, tissue-specific and time-specific TFs that specify developmental states. The atlas uncovers regulators of embryogenesis, including an unexpected role of a skin specifier in neurogenesis and the critical function of an uncharacterized TF in convergent muscle differentiation. At the systems level, the atlas provides an opportunity to model cell state-fate relationships, revealing a lineage-dependent state diversity within functionally related cells and a winding trajectory of developmental state progression. Collectively, this single-cell protein atlas represents a valuable resource for elucidating metazoan embryogenesis at the molecular and systems levels.


Asunto(s)
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/metabolismo , Desarrollo Embrionario , Regulación del Desarrollo de la Expresión Génica , Análisis de la Célula Individual/métodos , Análisis Espacio-Temporal , Factores de Transcripción/metabolismo , Animales , Caenorhabditis elegans/embriología , Diferenciación Celular , Linaje de la Célula
5.
Pacing Clin Electrophysiol ; 47(4): 518-524, 2024 04.
Artículo en Inglés | MEDLINE | ID: mdl-38407374

RESUMEN

BACKGROUND: Left bundle branch block (LBBB) and atrial fibrillation (AF) are commonly coexisting conditions. The impact of LBBB on catheter ablation of AF has not been well determined. This study aims to explore the long-term outcomes of patients with AF and LBBB after catheter ablation. METHODS: Forty-two patients with LBBB of 11,752 patients who underwent catheter ablation of AF from 2011 to 2020 were enrolled as LBBB group. After propensity score matching in a 1:4 ratio, 168 AF patients without LBBB were enrolled as non-LBBB group. Late recurrence and a composite endpoint of stroke, all-cause mortality, and cardiovascular hospitalization were compared between the two groups. RESULTS: Late recurrence rate was significantly higher in the LBBB group than that in the non-LBBB group (54.8% vs. 31.5%, p = .034). Multivariate analysis showed that LBBB was an independent risk factor for late recurrence after catheter ablation of AF (hazard ratio [HR] 2.19, 95% confidence interval [CI] 1.09-4.40, p = .031). LBBB group was also associated with a significantly higher incidence of the composite endpoint (21.4% vs. 6.5%, HR 3.98, 95% CI 1.64-9.64, p = .002). CONCLUSIONS: LBBB was associated with a higher risk for late recurrence and a higher incidence of composite endpoint in the patients underwent catheter ablation.


Asunto(s)
Fibrilación Atrial , Ablación por Catéter , Accidente Cerebrovascular , Humanos , Bloqueo de Rama/etiología , Factores de Riesgo , Accidente Cerebrovascular/etiología , Ablación por Catéter/efectos adversos , Resultado del Tratamiento , Recurrencia
6.
Mol Cell Proteomics ; 21(8): 100261, 2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35738554

RESUMEN

Brain development and function are governed by precisely regulated protein expressions in different regions. To date, multiregional brain proteomes have been systematically analyzed only for adult human and mouse brains. To understand the underpinnings of brain development and function, we generated proteomes from six regions of the postnatal brain at three developmental stages of domestic dogs (Canis familiaris), which are special among animals in terms of their remarkable human-like social cognitive abilities. Quantitative analysis of the spatiotemporal proteomes identified region-enriched synapse types at different developmental stages and differential myelination progression in different brain regions. Through integrative analysis of inter-regional expression patterns of orthologous proteins and genome-wide cis-regulatory element frequencies, we found that proteins related with myelination and hippocampus were highly correlated between dog and human but not between mouse and human, although mouse is phylogenetically closer to human. Moreover, the global expression patterns of neurodegenerative disease and autism spectrum disorder-associated proteins in dog brain more resemble human brain than in mouse brain. The high similarity of myelination and hippocampus-related pathways in dog and human at both proteomic and genetic levels may contribute to their shared social cognitive abilities. The inter-regional expression patterns of disease-associated proteins in the brain of different species provide important information to guide mechanistic and translational study using appropriate animal models.


Asunto(s)
Trastorno del Espectro Autista , Enfermedades Neurodegenerativas , Adulto , Animales , Encéfalo , Perros , Humanos , Ratones , Proteoma , Proteómica
7.
Development ; 146(8)2019 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-30890567

RESUMEN

The sensory nervous system of C. elegans comprises cells with varied molecular and functional characteristics, and is, therefore, a powerful model for understanding mechanisms that generate neuronal diversity. We report here that VAB-3, a C. elegans homolog of the homeodomain-containing protein Pax6, has opposing functions in regulating expression of a specific chemosensory fate. A homeodomain-only short isoform of VAB-3 is expressed in BAG chemosensory neurons, where it promotes gene expression and cell function. In other cells, a long isoform of VAB-3, comprising a Paired homology domain and a homeodomain, represses expression of ETS-5, a transcription factor required for expression of BAG fate. Repression of ets-5 requires the Eyes Absent homolog EYA-1 and the Six-class homeodomain protein CEH-32. We determined sequences that mediate high-affinity binding of ETS-5, VAB-3 and CEH-32. The ets-5 locus is enriched for ETS-5-binding sites but lacks sequences that bind VAB-3 and CEH-32, suggesting that these factors do not directly repress ets-5 expression. We propose that a promoter-selection system together with lineage-specific expression of accessory factors allows VAB-3/Pax6 to either promote or repress expression of specific cell fates in a context-dependent manner. This article has an associated 'The people behind the papers' interview.


Asunto(s)
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/metabolismo , Proteínas de Homeodominio/metabolismo , Factores de Transcripción/metabolismo , Animales , Protocolos de Quimioterapia Combinada Antineoplásica/metabolismo , Bleomicina/metabolismo , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Clorambucilo/metabolismo , Cisplatino/metabolismo , Ciclofosfamida/metabolismo , Dactinomicina/metabolismo , Regulación del Desarrollo de la Expresión Génica/genética , Proteínas de Homeodominio/genética , Péptidos y Proteínas de Señalización Intracelular/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Neuronas/citología , Neuronas/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Regiones Promotoras Genéticas/genética , Proteínas Tirosina Fosfatasas/genética , Proteínas Tirosina Fosfatasas/metabolismo , Proteínas Proto-Oncogénicas c-ets/genética , Proteínas Proto-Oncogénicas c-ets/metabolismo , Factores de Transcripción/genética , Vinblastina/metabolismo
8.
Mol Syst Biol ; 17(4): e10075, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33900055

RESUMEN

Elucidating the chromatin dynamics that orchestrate embryogenesis is a fundamental question in developmental biology. Here, we exploit position effects on expression as an indicator of chromatin activity and infer the chromatin activity landscape in every lineaged cell during Caenorhabditis elegans early embryogenesis. Systems-level analyses reveal that chromatin activity distinguishes cellular states and correlates with fate patterning in the early embryos. As cell lineage unfolds, chromatin activity diversifies in a lineage-dependent manner, with switch-like changes accompanying anterior-posterior fate asymmetry and characteristic landscapes being established in different cell lineages. Upon tissue differentiation, cellular chromatin from distinct lineages converges according to tissue types but retains stable memories of lineage history, contributing to intra-tissue cell heterogeneity. However, the chromatin landscapes of cells organized in a left-right symmetric pattern are predetermined to be analogous in early progenitors so as to pre-set equivalent states. Finally, genome-wide analysis identifies many regions exhibiting concordant chromatin activity changes that mediate the co-regulation of functionally related genes during differentiation. Collectively, our study reveals the developmental and genomic dynamics of chromatin activity at the single-cell level.


Asunto(s)
Caenorhabditis elegans/citología , Caenorhabditis elegans/embriología , Diferenciación Celular , Linaje de la Célula , Cromatina/metabolismo , Embrión no Mamífero/citología , Embrión no Mamífero/metabolismo , Análisis de la Célula Individual , Animales , Tipificación del Cuerpo/genética , Caenorhabditis elegans/genética , Diferenciación Celular/genética , Linaje de la Célula/genética , Desarrollo Embrionario/genética , Regulación del Desarrollo de la Expresión Génica , Genes Reporteros , Genoma , Proteínas Fluorescentes Verdes/metabolismo , Especificidad de Órganos
9.
Cell Mol Biol (Noisy-le-grand) ; 67(6): 55-61, 2022 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-35818214

RESUMEN

A large amount of evidence indicates that the abnormal activation of multiple signal transduction pathways in cells is closely related to the occurrence and development of tumors. TGF-ß and NFAT1 signaling pathways can inhibit cell proliferation and promote apoptosis in the early stage of breast cancer, but with the increase of tumor malignancy, the two appear to promote tumor progression and deterioration. Therefore, the study of the relationship between STIM2 and NFAT1/TGF-ß1 is helpful for the discovery and treatment of breast cancer, which is of great significance for improving the survival rate of breast cancer patients. This article focuses on the effect of STIM2 molecules on breast cancer cell migration through the NFAT1/ TGF-ß1 pathway and discusses the regulatory mechanism of STIM2 affecting breast cancer cell migration. Experimental data shows that the positive rate of breast cancer NFAT1 is 54%, which is significantly lower than that of benign breast Tissue 85%; the positive expression rate of TGF-ß1 in benign breast tissue is 85%, and the positive expression rate in breast cancer tissue is 49%. The results show that STIM2 protein can promote the invasion and metastasis of breast cancer cells through the NFAT1 / TGF-ß1 pathway.


Asunto(s)
Neoplasias de la Mama , Factores de Transcripción NFATC , Molécula de Interacción Estromal 2 , Factor de Crecimiento Transformador beta1 , Neoplasias de la Mama/patología , Línea Celular Tumoral , Movimiento Celular , Proliferación Celular , Femenino , Humanos , Factores de Transcripción NFATC/metabolismo , Invasividad Neoplásica , Metástasis de la Neoplasia , Molécula de Interacción Estromal 2/metabolismo , Factor de Crecimiento Transformador beta1/metabolismo
10.
Cell Mol Biol (Noisy-le-grand) ; 68(2): 132-137, 2022 Feb 28.
Artículo en Inglés | MEDLINE | ID: mdl-35869716

RESUMEN

The analyze the effect of miR-138 on the proliferation and apoptosis of breast cancer cells through the NF-κB/VEGF signaling pathway is the Objective of this experiment. For this aim, the endometrial stem breast cancer cell line MCF-7 was cultured in vitro, and the overexpression mimic miR-138 mimics and the inhibitor anti-miR-138 were transfected into the endometrial stem breast cancer cell line MCF-7, which was set to overexpress miR-138 group and interfere with miR-138, and set up negative control of overexpression and negative control of inhibitor. Observe the cell proliferation and apoptosis ability of each group, and the changes in tumor necrosis factor-α (TNF-α), interleukin 1ß, 6, 18 (IL-1ß, IL-6, IL-18) levels, and compare the Bax of each group, NF-κB, VEGF protein expression level. Results showed that the proliferation ability of the miR-138 overexpression group was significantly lower than that of the miR-138 overexpression control group (P<0.05); the proliferation ability of the miR-138 interference group was significantly higher than that of the miR-138 interference control group (P<0.05). The apoptosis rate, caspase-3 and caspase-9 expression levels of the miR-138 overexpression group were significantly higher than those of the miR-138 overexpression control group (P<0.05);  the apoptosis rate, caspase-3 and caspase-9 expression levels of the miR-138 interference group were significantly lower than those of the miR-138 interference control group (P<0.05). The expression levels of IL-1 ß, IL-6, IL-18 and TNF - α in the miR-138 overexpression group were significantly lower than those in the miR-138 overexpression control group (P < 0.05). The protein expression levels of Bax, NF-κB and VEGF in the miR-138 overexpression group were significantly lower than those in the miR-138 overexpression control group (P < 0.05); the protein expression levels of Bax, NF-κB and VEGF in the miR-138 interference group were significantly higher than those in the miR-138 interference control group (P <0.05). The proliferation ability of the miR-138 overexpression group was significantly lower than that of the miR-138 overexpression control group (P < 0.05); the proliferation ability of the miR-138 + NF-κB overexpression group was significantly higher than that of the miR-138 overexpression group (P<0.05). The apoptosis rate of the miR-138 + NF-κB overexpression group was significantly lower than that of the miR-138 overexpression group (P < 0.05). Then MiR-138 can significantly inhibit the proliferation of breast cancer cells, promote apoptosis, and regulate the expression of inflammatory factors in the cells. It is speculated that the related mechanism may be related to the negative regulation of the NF-κB/VEGF signaling pathway.


Asunto(s)
Neoplasias de la Mama , MicroARNs , Apoptosis , Neoplasias de la Mama/genética , Caspasa 3/metabolismo , Caspasa 9/metabolismo , Proliferación Celular , Femenino , Humanos , Interleucina-18 , Interleucina-6/metabolismo , MicroARNs/genética , MicroARNs/metabolismo , FN-kappa B/metabolismo , Transducción de Señal , Factor de Necrosis Tumoral alfa/metabolismo , Factor A de Crecimiento Endotelial Vascular/genética , Factor A de Crecimiento Endotelial Vascular/metabolismo , Proteína X Asociada a bcl-2/genética , Proteína X Asociada a bcl-2/metabolismo
11.
Catheter Cardiovasc Interv ; 97 Suppl 2: 1080-1088, 2021 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-33780143

RESUMEN

OBJECTIVES: We investigated whether the age shock index (SI) was associated with coronary plaque characteristics in patients with ST-segment elevation myocardial infarction (STEMI) using optical coherence tomography (OCT). BACKGROUND: The age SI is a simple clinical parameter that effectively predicts poor clinical outcomes among patients with STEMI. METHODS: This retrospective study evaluated 408 STEMI patients who underwent 3-vessel OCT during emergency percutaneous coronary interventions at a single center between January 2017 and October 2018. Patients were divided into groups with low or high age SI values (<41 vs. ≥41). Plaque characteristics were compared between the two groups for both culprit lesions (n = 408) and non-culprit lesions (n = 1,077). RESULTS: In culprit lesions, patients with a high age SI (≥41) were more likely to have plaque rupture (61.0% vs. 56.8%, p = .002) and thinner fibrous caps (fibrous cap thickness [FCT]: 40.0 [33.0-53.0] µm vs. 46.0 [36.0-63.8] µm, p = .021). In non-culprit lesions, patients with a high age SI were more likely to have high-risk plaques (29.9% vs. 17.8%, p = .018; simultaneous presence of a minimal lumen area of <3.5 mm2 , maximum lipid arc of >180°, FCT of <75 µm, and macrophage accumulation). Plaque-based analyses revealed that patients with a high age SI had larger lipid cores and lesser FCT. CONCLUSIONS: Patients with STEMI and a high age SI had increased risks of culprit plaque rupture and high-risk non-culprit plaques, and vulnerable plaque features at the culprit and non-culprit lesions. Therefore, a high age SI in patients with STEMI may indicate greater pancoronary vulnerability.


Asunto(s)
Enfermedad de la Arteria Coronaria , Placa Aterosclerótica , Infarto del Miocardio con Elevación del ST , Angiografía Coronaria , Enfermedad de la Arteria Coronaria/diagnóstico por imagen , Vasos Coronarios/diagnóstico por imagen , Humanos , Estudios Retrospectivos , Infarto del Miocardio con Elevación del ST/diagnóstico por imagen , Infarto del Miocardio con Elevación del ST/terapia , Tomografía de Coherencia Óptica , Resultado del Tratamiento
12.
Genome Res ; 27(9): 1525-1535, 2017 09.
Artículo en Inglés | MEDLINE | ID: mdl-28684554

RESUMEN

Translational efficiency is subject to extensive regulation. However, the factors influencing such regulation are poorly understood. In Caenorhabditis elegans, 62% of genes are trans-spliced to a specific spliced leader (SL1), which replaces part of the native 5' untranslated region (5' UTR). Given the pivotal role the 5' UTR plays in the regulation of translational efficiency, we hypothesized that SL1 trans-splicing functions to regulate translational efficiency. With genome-wide analysis on Ribo-seq data, polysome profiling experiments, and CRISPR-Cas9-based genetic manipulation of trans-splicing sites, we found four lines of evidence in support of this hypothesis. First, SL1 trans-spliced genes have higher translational efficiencies than non-trans-spliced genes. Second, SL1 trans-spliced genes have higher translational efficiencies than non-trans-spliced orthologous genes in other nematode species. Third, an SL1 trans-spliced isoform has higher translational efficiency than the non-trans-spliced isoform of the same gene. Fourth, deletion of trans-splicing sites of endogenous genes leads to reduced translational efficiency. Importantly, we demonstrated that SL1 trans-splicing plays a key role in enhancing translational efficiencies of essential genes. We further discovered that SL1 trans-splicing likely enhances translational efficiency by shortening the native 5' UTRs, hence reducing the presence of upstream start codons (uAUG) and weakening mRNA secondary structures. Taken together, our study elucidates the global function of trans-splicing in enhancing translational efficiency in nematodes, paving the way for further understanding the genomic mechanisms of translational regulation.


Asunto(s)
Proteínas del Complejo de Iniciación de Transcripción Pol1/genética , Biosíntesis de Proteínas , ARN Mensajero/genética , Trans-Empalme/genética , Regiones no Traducidas 5'/genética , Animales , Sistemas CRISPR-Cas/genética , Caenorhabditis elegans/genética , Codón Iniciador/genética , Edición Génica , Genoma/genética , Empalme del ARN/genética , ARN Mensajero/biosíntesis
14.
BMC Musculoskelet Disord ; 21(1): 548, 2020 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-32799840

RESUMEN

BACKGROUND: The prognostic value of Neutrophil-to-Lymphocyte Ratio (NLR) for the outcome of acute cervical traumatic spinal cord injury (tSCI) patients has rarely been studied by now throughout the world. METHODS: We performed a single-center retrospective cohort study to evaluate the prognostic value of NLR from peripheral whole blood count in patients with acute cervical tSCI. Patients within 6 h of acute cervical tSCI treated between Dec 2008 and May 2018 in Huashan Hospital of Fudan University were enrolled. Outcomes of patients with tSCI were assessed using American spinal injury association Impairment Scale (AIS). 6-month outcomes were dichotomized into poor outcome group (AIS A to C) and good outcome group (AIS D and E). Uni- and multivariate analyses were performed to assess the independent predictors of 6-month outcome. Two prediction models based on admission characteristics were built to evaluate the prognostic value of NLR. The discriminative ability of predictive models was evaluated using the area under the curve (AUC). RESULTS: A total of 377 patients were identified from our single center in China PR. Multivariate analysis showed that age, AIS grade at admission, NLR (p < 0.001) and coagulopathy (p = 0.003) were independent predictors of the 6-months outcome for acute cervical tSCI patients. The model combing NLR and standard variables (AUC = 0.944; 95% CI, 0.923-0.964) showed a more favorable prognostic value than that without NLR (AUC = 0.841; 95% CI, 0.798-0.885) in terms of 6-month outcome. CONCLUSIONS: NLR is firstly identified as an independent predictor of the 6-month outcome in acute cervical tSCI patients worldwide. The prognostic value of NLR is favorable, and a high NLR is associated with poor outcome in patients with acute cervical tSCI.


Asunto(s)
Médula Cervical , Traumatismos de la Médula Espinal , China , Humanos , Recién Nacido , Linfocitos , Neutrófilos , Estudios Retrospectivos , Traumatismos de la Médula Espinal/diagnóstico
15.
Adv Exp Med Biol ; 1181: 15-58, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31677139

RESUMEN

Species of Ganoderma (Ling-zhi) have been widely researched and cultivated due to their highly prized medicinal value, which is famous as a traditional Chinese medicine. The aims of this chapter are to (1) review the historical taxonomy of the family Ganodermataceae, (2) provide an account of the genera and species of Ganoderma together with the distributions and habitats, (3) evaluate morphological features and phylogenetic methods to define the genera and species and (4) present two commonly used cultivated methods (wood-log cultivation and substitute cultivation) for Ganoderma.


Asunto(s)
Ganoderma , Filogenia , Ganoderma/clasificación , Ganoderma/fisiología , Medicina Tradicional China
16.
Nucleic Acids Res ; 44(D1): D781-5, 2016 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-26503254

RESUMEN

Developmental systems biology is poised to exploit large-scale data from two approaches: genomics and live imaging. The combination of the two offers the opportunity to map gene functions and gene networks in vivo at single-cell resolution using cell tracking and quantification of cellular phenotypes. Here we present Digital Development (http://www.digital-development.org), a database of cell lineage differentiation with curated phenotypes, cell-specific gene functions and a multiscale model. The database stores data from recent systematic studies of cell lineage differentiation in the C. elegans embryo containing ∼ 200 conserved genes, 1400 perturbed cell lineages and 600,000 digitized single cells. Users can conveniently browse, search and download four categories of phenotypic and functional information from an intuitive web interface. This information includes lineage differentiation phenotypes, cell-specific gene functions, differentiation landscapes and fate choices, and a multiscale model of lineage differentiation. Digital Development provides a comprehensive, curated, multidimensional database for developmental biology. The scale, resolution and richness of biological information presented here facilitate exploration of gene-specific and systems-level mechanisms of lineage differentiation in Metazoans.


Asunto(s)
Caenorhabditis elegans/embriología , Diferenciación Celular , Linaje de la Célula , Bases de Datos Factuales , Animales , Caenorhabditis elegans/citología , Caenorhabditis elegans/genética , Diferenciación Celular/genética , Linaje de la Célula/genética , Modelos Biológicos , Fenotipo
17.
Dev Biol ; 398(2): 267-79, 2015 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-25523393

RESUMEN

Regulated choice between cell fate maintenance and differentiation provides decision points in development to progress toward more restricted cell fates or to maintain the current one. Caenorhabditis elegans embryogenesis follows an invariant cell lineage where cell fate is generally more restricted upon each cell division. EMS is a progenitor cell in the four-cell embryo that gives rise to the endomesoderm. We recently found that when ubiquitin-mediated protein degradation is compromised, the anterior daughter of EMS, namely MS, reiterates the EMS fate. This observation demonstrates an essential function of ubiquitin-mediated protein degradation in driving the progression of EMS-to-MS differentiation. Here we report a genome-wide screen of the ubiquitin pathway and extensive lineage analyses. The results suggest a broad role of E3 ligases in driving differentiation progression. First, we identified three substrate-binding proteins for two Cullin-RING ubiquitin ligase (CRL) E3 complexes that promote the progression from the EMS fate to MS, namely LIN-23/ß-TrCP and FBXB-3 for the CRL1/SCF complex and ZYG-11/ZYG-11B for the CRL2 complex. Genetic analyses suggest these E3 ligases function through a multifunctional protein OMA-1 and the endomesoderm lineage specifier SKN-1 to drive differentiation. Second, we found that depletion of components of the CRL1/SCF complex induces fate reiteration in all major founder cell lineages. These data suggest that regulated choice between self-renewal and differentiation is widespread during C. elegans embryogenesis as in organisms with regulative development, and ubiquitin-mediated protein degradation drives the choice towards differentiation. Finally, bioinformatic analysis of time series gene expression data showed that expression of E3 genes is transiently enriched during time windows of developmental stage transitions. Transcription factors show similar enrichment, but not other classes of regulatory genes. Based on these findings we propose that ubiquitin-mediated protein degradation, like many transcription factors, function broadly as regulators driving developmental progression during embryogenesis in C. elegans.


Asunto(s)
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/citología , Caenorhabditis elegans/embriología , Diferenciación Celular , Desarrollo Embrionario , Ubiquitina-Proteína Ligasas/metabolismo , Animales , Caenorhabditis elegans/enzimología , Proteínas de Caenorhabditis elegans/genética , Linaje de la Célula , Embrión no Mamífero/citología , Embrión no Mamífero/metabolismo , Endodermo/embriología , Regulación del Desarrollo de la Expresión Génica , Mesodermo/embriología , Interferencia de ARN , Ubiquitinación , Vía de Señalización Wnt
18.
Development ; 140(15): 3266-74, 2013 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-23861063

RESUMEN

Current imaging technology provides an experimental platform in which complex developmental processes can be observed at cellular resolution over an extended time frame. New computational tools are essential to achieve a systems-level understanding of this high-content information. We have devised a structured approach to systematically analyze complex in vivo phenotypes at cellular resolution, which divides the task into a panel of statistical measurements of each cell in terms of cell differentiation, proliferation and morphogenesis, followed by their spatial and temporal organization in groups and the cohesion within the whole specimen. We demonstrate the approach to C. elegans embryogenesis with in toto imaging and automated cell lineage tracing. We define statistical distributions of the wild-type developmental behaviors at single-cell resolution based on over 50 embryos, cumulating in over 4000 distinct, developmentally based measurements per embryo. These methods enable statistical quantification of abnormalities in mutant or RNAi-treated embryos and a rigorous comparison of embryos by testing each measurement for the probability that it would occur in a wild-type embryo. We demonstrate the power of this structured approach by uncovering quantitative properties including subtle phenotypes in both wild-type and perturbed embryos, transient behaviors that lead to new insights into gene function and a previously undetected source of developmental noise and its subsequent correction.


Asunto(s)
Caenorhabditis elegans/citología , Caenorhabditis elegans/embriología , Animales , Animales Modificados Genéticamente , Caenorhabditis elegans/genética , Puntos de Control del Ciclo Celular , Linaje de la Célula , Movimiento Celular , Regulación del Desarrollo de la Expresión Génica , Genes de Helminto , Mutación , Fenotipo , Interferencia de ARN , Imagen de Lapso de Tiempo
19.
BMC Bioinformatics ; 15: 217, 2014 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-24964866

RESUMEN

BACKGROUND: Advances in fluorescence labeling and imaging have made it possible to acquire in vivo records of complex biological processes. Analysis has lagged behind acquisition in part because of the difficulty and computational expense of accurate cell tracking. In vivo analysis requires, at minimum, tracking hundreds of cells over hundreds of time points in complex three dimensional environments. We address this challenge with a computational framework capable of efficiently and accurately tracing entire cell lineages. RESULTS: The bulk of the tracking problem-tracking cells during interphase-is straightforward and can be executed with simple and fast methods. Difficult cases originate from detection errors and relatively rare large motions. Therefore, our method focuses computational effort on difficult cases identified by local increases in cell number. We force these cases into tentative cell track bifurcations, which define natural semi-local neighborhoods that permit Bayesian judgment about the underlying cell behavior. The bifurcation judgment process not only correctly tracks through cell divisions and large movements, but also offers corrections to detection errors. We demonstrate that this method enables large scale analysis of Caenorhabditis elegans development, an ideal validation platform because of an invariant cell lineage. CONCLUSION: The high accuracy achieved by our method suggests that a bifurcation-based semi-local neighborhood provides sufficient information to recognize dependencies between nearby tracking choices, and to interpret difficult tracking cases without reverting to global optimization. Our method makes large amounts of lineage data accessible and opens the door to new types of statistical analysis of complex in vivo processes.


Asunto(s)
Linaje de la Célula , Probabilidad , Animales , Teorema de Bayes , Caenorhabditis elegans/citología , Caenorhabditis elegans/embriología
20.
Proc Natl Acad Sci U S A ; 108(43): 17708-13, 2011 Oct 25.
Artículo en Inglés | MEDLINE | ID: mdl-22006307

RESUMEN

The Caenorhabditis elegans embryo is a powerful model for studying neural development, but conventional imaging methods are either too slow or phototoxic to take full advantage of this system. To solve these problems, we developed an inverted selective plane illumination microscopy (iSPIM) module for noninvasive high-speed volumetric imaging of living samples. iSPIM is designed as a straightforward add-on to an inverted microscope, permitting conventional mounting of specimens and facilitating SPIM use by development and neurobiology laboratories. iSPIM offers a volumetric imaging rate 30× faster than currently used technologies, such as spinning-disk confocal microscopy, at comparable signal-to-noise ratio. This increased imaging speed allows us to continuously monitor the development of C, elegans embryos, scanning volumes every 2 s for the 14-h period of embryogenesis with no detectable phototoxicity. Collecting ∼25,000 volumes over the entirety of embryogenesis enabled in toto visualization of positions and identities of cell nuclei. By merging two-color iSPIM with automated lineaging techniques we realized two goals: (i) identification of neurons expressing the transcription factor CEH-10/Chx10 and (ii) visualization of their neurodevelopmental dynamics. We found that canal-associated neurons use somal translocation and amoeboid movement as they migrate to their final position in the embryo. We also visualized axon guidance and growth cone dynamics as neurons circumnavigate the nerve ring and reach their targets in the embryo. The high-speed volumetric imaging rate of iSPIM effectively eliminates motion blur from embryo movement inside the egg case, allowing characterization of dynamic neurodevelopmental events that were previously inaccessible.


Asunto(s)
Caenorhabditis elegans/embriología , Linaje de la Célula , Imagenología Tridimensional/métodos , Microscopía/métodos , Sistema Nervioso/citología , Animales , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Homeodominio/metabolismo , Sistema Nervioso/embriología , Factores de Tiempo
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