Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 125
Filtrar
Mais filtros

Base de dados
País/Região como assunto
Tipo de documento
Intervalo de ano de publicação
1.
J Proteome Res ; 23(8): 3716-3725, 2024 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-39008777

RESUMO

Proteins undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S-acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 µg of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment. We show that the method is compatible with protein-level detection of S-acylated proteins (e.g., H-Ras) as well as S-acyl site identification and quantification using "on trap" isobaric labeling and LC-MS/MS from as little as 20 µg of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S-acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamline the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.


Assuntos
Cisteína , Espectrometria de Massas em Tandem , Acilação , Animais , Cisteína/química , Cisteína/metabolismo , Camundongos , Espectrometria de Massas em Tandem/métodos , Hidroxilamina/química , Cromatografia Líquida/métodos , Lipoilação , Processamento de Proteína Pós-Traducional , Compostos de Sulfidrila/química , Proteínas/química , Proteínas/metabolismo , Encéfalo/metabolismo
2.
Mol Cancer ; 23(1): 35, 2024 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-38365721

RESUMO

BACKGROUND: circular RNAs (circRNAs) have been reported to exert important effects in the progression of numerous cancers. However, the functions of circRNAs in intrahepatic cholangiocarcinoma (ICC) are still unclear. METHODS: circPCNXL2 (has_circ_0016956) were identified in paired ICC by circRNA microarray. Then, we assessed the biological functions of circPCNXL2 by CCK8, EdU, clone formation, transwell, wound healing assays, and xenograft models. RNA pull-down, mass spectrometry, and RNA immunoprecipitation (RIP) were applied to explore the interaction between cirrcPCNXL2 and serine-threonine kinase receptor-associated protein (STRAP). RNA pull-down, RIP and luciferase reporter assays were used to investigate the sponge functions of circPCNXL2. In the end, we explore the effects of circPCNXL2 and trametinib (a MEK1/2 inhibitor) in vivo. RESULTS: circPCNXL2 was upregulated in ICC tissues and cell lines, which promoted the proliferation and metastasis of ICC in vitro and in vivo. In terms of the mechanisms, circPCNXL2 could directly bind to STRAP and induce the interaction between STRAP and MEK1/2, resulting in the tumor promotion in ICC by activation of ERK/MAPK pathways. Besides, circPCNXL2 could regulate the expression of SRSF1 by sponging miR-766-3p and subsequently facilitated the growth of ICC. Finally, circPCNXL2 could partially inhibit the anti-tumor activity of trametinib in vivo. CONCLUSION: circPCNXL2 played a crucial role in the progression of ICC by interacting with STRAP to activate the ERK signaling pathway, as well as by modulating the miR-766-3p/SRSF1 axis. These findings suggest that circPCNXL2 may be a promising biomarker and therapeutic target for ICC.


Assuntos
Neoplasias dos Ductos Biliares , Colangiocarcinoma , MicroRNAs , Humanos , RNA Circular/genética , Proliferação de Células/genética , Colangiocarcinoma/metabolismo , Transdução de Sinais , Ductos Biliares Intra-Hepáticos/metabolismo , Ductos Biliares Intra-Hepáticos/patologia , Neoplasias dos Ductos Biliares/metabolismo , MicroRNAs/metabolismo , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica , Fatores de Processamento de Serina-Arginina/metabolismo
3.
Virol J ; 21(1): 197, 2024 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-39182136

RESUMO

Serine/threonine kinase receptor-associated protein (STRAP) serves as a scaffold protein and is engaged in a variety of cellular activities, although its importance in antiviral innate immunity is unknown. We discovered that STRAP works as an interferon (IFN)-inducible positive regulator, facilitating type I IFN signaling during pseudorabies virus infection. Mechanistically, STRAP interacts with TBK1 to activate type I IFN signaling. Both the CT and WD40 7 - 6 domains contribute to the function of STRAP. Furthermore, TBK1 competes with PRV-UL50 for binding to STRAP, and STRAP impedes the degradation of TBK1 mediated by PRV-UL50, thereby increasing the interaction between STRAP and TBK1. Overall, these findings reveal a previously unrecognized role for STRAP in innate antiviral immune responses during PRV infection. STRAP could be a potential therapeutic target for viral infectious diseases.


Assuntos
Herpesvirus Suídeo 1 , Imunidade Inata , Interferon Tipo I , Proteínas Serina-Treonina Quinases , Animais , Linhagem Celular , Herpesvirus Suídeo 1/imunologia , Interferon Tipo I/imunologia , Interferon Tipo I/metabolismo , Ligação Proteica , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/imunologia , Proteínas Serina-Treonina Quinases/metabolismo , Pseudorraiva/imunologia , Pseudorraiva/virologia , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/imunologia , Proteínas de Ligação a RNA/metabolismo , Transdução de Sinais , Regulação para Cima
4.
Postgrad Med J ; 100(1185): 496-503, 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38366645

RESUMO

BACKGROUND: Multiple displaced rib fractures often result in a poor prognosis. Open reduction and internal fixation has been shown to provide benefits for patients with displaced rib fractures and flail chest. Nevertheless, for patients who are unwilling or unsuitable for surgery, the therapeutic options are limited. We developed a novel plastic vacuum device for rib fractures external stabilization. This study aims to compare the therapeutic efficacy of this device against a traditional chest strap in polytrauma patients with multiple rib fractures. METHODS: A retrospective investigation was conducted on polytrauma patients with multiple rib fractures admitted to our trauma center between March 2020 and March 2023. Patients were categorized into two groups: vacuum external fixation and chest strap. Comparative analysis was conducted on baseline parameters, injury characteristics, and clinical outcomes between the two groups. RESULTS: In this study, 54 patients were included, with 28 receiving chest strap and 26 undergoing vacuum external fixation. Results showed that, at 3 days and 7 days postintervention, the vacuum external fixation group had significantly lower visual analog scale scores during deep breathing and coughing (P < .05). Vacuum external fixation also reduced pleural drainage duration and volume, as well as lowered the risk of pneumonia and other complications (P < .05). Furthermore, the vacuum external fixation group demonstrated notable improvements in vital capacity, tidal volume, blood-gas test results, and a shorter hospital length of stay. CONCLUSIONS: According to the study findings, vacuum external fixation appears to offer benefits to patients with multiple rib fractures, potentially reducing the risk of complications and improving overall clinical outcomes.


Assuntos
Fixação de Fratura , Traumatismo Múltiplo , Fraturas das Costelas , Humanos , Fraturas das Costelas/cirurgia , Fraturas das Costelas/terapia , Masculino , Feminino , Estudos Retrospectivos , Pessoa de Meia-Idade , Traumatismo Múltiplo/cirurgia , Traumatismo Múltiplo/terapia , Fixação de Fratura/métodos , Fixação de Fratura/instrumentação , Vácuo , Adulto , Fixadores Externos , Idoso , Resultado do Tratamento , Tempo de Internação , Fraturas Múltiplas/cirurgia
5.
J Shoulder Elbow Surg ; 33(1): 172-180, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37543280

RESUMO

BACKGROUND: The supraspinatus (SS) is formed by a larger anterior bipennate muscle with a cord-like tendon and a posterior unipennate muscle with a strap-like tendon. There is a tendinous connection between the 2 SS subunits. Yet, the relative mechanical contribution of the SS cord and SS strap musculotendinous units to load transmission and subsequent shoulder abduction force is unknown. We hypothesized that a simulated SS cord vs. an SS strap tear would generate less shoulder abduction force and, further, an intact SS cord would offset the expected abduction loss from an SS strap tear, but the inverse would not be true. MATERIALS AND METHODS: Twenty fresh-frozen cadaveric specimens were tested in a shoulder simulator with physiological load vectors applied to the upper and lower subscapularis, SS cord, SS strap, infraspinatus, and teres minor. The roles of the SS cord and SS strap muscles were delineated by varying their loads, while keeping constant loads on other muscles. The randomized testing trials included a native condition and 4 test cases that simulated tears by dropping the load and force transfer via the SS cord-to-SS strap connection by adding the load. Testing was completed at both 0° and 30° of abduction. During each test, shoulder abduction force, rotator cuff strains, and humeral translation were measured. RESULTS: Simulated isolated SS cord and SS strap tears led to a significantly lower shoulder abduction force (P < .001). A simulated cord tear at 0° and 30° reduced the abduction force by 53% and 38%, respectively. A simulated strap tear at 0° and 30° dropped the abduction force by 27% and 23%, respectively. The decline in the abduction force was larger for the SS cord tear vs. SS strap tear (P ≤ .001). An SS cord tear with full-load transfer to the strap was able to recover to native values at both 0° and 30° (P ≥ .288). Likewise, an SS strap tear with full-load transfer to the SS cord showed a similar recovery to native values at both 0° and 30° (P ≥ .155). During full-load transfer, the tendon strain followed the loading pattern. An SS cord tear or SS strap tear did not cause a change in humeral translation (P ≥ .303). DISCUSSION: The mechanical findings support the efficacy of nonoperative treatment of small (<10 mm) SS tears,11 because an intact SS strap tendon can effectively offset the abduction loss of a torn SS cord tear and vice versa.


Assuntos
Lacerações , Lesões do Manguito Rotador , Articulação do Ombro , Humanos , Manguito Rotador/cirurgia , Ombro/cirurgia , Articulação do Ombro/cirurgia , Fenômenos Biomecânicos , Tendões , Ruptura , Amplitude de Movimento Articular/fisiologia , Cadáver
6.
Sensors (Basel) ; 24(9)2024 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-38733051

RESUMO

This paper proposes an improved initial alignment method for a strap-down inertial navigation system/global navigation satellite system (SINS/GNSS) integrated navigation system with large misalignment angles. Its methodology is based on the three-dimensional special Euclidean group and extended Kalman filter (SE2(3)/EKF) and aims to overcome the challenges of achieving fast alignment under large misalignment angles using traditional methods. To accurately characterize the state errors of attitude, velocity, and position, these elements are constructed as elements of a Lie group. The nonlinear error on the Lie group can then be well quantified. Additionally, a group vector mixed error model is developed, taking into account the zero bias errors of gyroscopes and accelerometers. Using this new error definition, a GNSS-assisted SINS dynamic initial alignment algorithm is derived, which is based on the invariance of velocity and position measurements. Simulation experiments demonstrate that the alignment method based on SE2(3)/EKF can achieve a higher accuracy in various scenarios with large misalignment angles, while the attitude error can be rapidly reduced to a lower level.

7.
Int J Mol Sci ; 24(6)2023 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-36982423

RESUMO

Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC-MS/MS analysis, and data analysis. LC-MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Cromatografia Líquida/métodos , Espectrometria de Massas em Tandem/métodos , Proteômica/métodos , Reprodutibilidade dos Testes , Peptídeos/análise , Proteoma/análise
8.
J Mol Cell Cardiol ; 162: 20-31, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34437879

RESUMO

The heart is composed of multiple cell types, each with a specific function. Cell-type-specific approaches are necessary for defining the intricate molecular mechanisms underlying cardiac development, homeostasis, and pathology. While single-cell RNA-seq studies are beginning to define the chamber-specific cellular composition of the heart, our views of the proteome are more limited because most proteomics studies have utilized homogenized human cardiac tissue. To promote future cell-type specific analyses of the human heart, we describe the first method for cardiomyocyte isolation from cryopreserved human cardiac tissue followed by flow cytometry for purity assessment. We also describe a facile method for preparing isolated cardiomyocytes and whole cardiac tissue homogenate for bottom-up proteomic analyses. Prior experience in dissociating cardiac tissue or proteomics is not required to execute these methods. We compare different sample preparation workflows and analysis methods to demonstrate how these can impact the depth of proteome coverage achieved. We expect this how-to guide will serve as a starting point for investigators interested in general and cell-type-specific views of the cardiac proteome.


Assuntos
Miócitos Cardíacos , Proteômica , Humanos , Miócitos Cardíacos/metabolismo , Proteoma/metabolismo , Proteômica/métodos , Manejo de Espécimes
9.
J Proteome Res ; 21(10): 2397-2411, 2022 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-36006919

RESUMO

Robust, efficient, and reproducible protein extraction and sample processing is a key step for bottom-up proteomics analyses. While many sample preparation protocols for mass spectrometry have been described, selecting an appropriate method remains challenging since some protein classes may require specialized solubilization, precipitation, and digestion procedures. Here, we present a comprehensive comparison of the 16 most widely used sample preparation methods, covering in-solution digests, device-based methods, and commercially available kits. We find a remarkably good performance of the majority of the protocols with high reproducibility, little method dependency, and low levels of artifact formation. However, we revealed method-dependent differences in the recovery of specific protein features, which we summarized in a descriptive guide matrix. Our work thereby provides a solid basis for the selection of MS sample preparation strategies for a given proteomics project.


Assuntos
Proteínas , Proteômica , Espectrometria de Massas/métodos , Proteínas/análise , Proteoma/análise , Proteômica/métodos , Reprodutibilidade dos Testes , Manejo de Espécimes/métodos
10.
Biochem Biophys Res Commun ; 589: 197-203, 2022 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-34922203

RESUMO

Protein extraction and digestion are important analytical steps in the study of proteomics. The use of sodium dodecyl sulfate (SDS) buffer makes it possible to effectively analyze various proteins. Its use was evaluated using the S-Trap digestion method and compared to the traditional In solution digestion method. Differences in protein composition were examined for each protein preparation method. S-Trap digestion followed by SDS buffer extraction clearly increased the number of identified proteins, including more mitochondrial and membrane-related proteins. The S-Trap digestion method with 5% SDS buffer was applied to the pellet remaining from the removal of RIPA buffer-soluble proteins, which identified more extracellular space proteins than the conventional S-Trap digestion method. S-Trap digestion of the pellet was particularly advantageous for identifying proteins located inside multilayer membranes.


Assuntos
Proteínas/metabolismo , Proteômica/métodos , Animais , Linhagem Celular Tumoral , Espectrometria de Massas , Camundongos , Peptídeos/metabolismo , Soluções
11.
Anal Bioanal Chem ; 414(8): 2585-2595, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35181835

RESUMO

It has been a challenge to analyze minute amounts of proteomic samples in a facile and robust manner. Herein, we developed a quantitative proteomics workflow by integrating suspension trapping (S-Trap)-based sample preparation and label-free data-independent acquisition (DIA) mass spectrometry and then applied it for the analysis of microgram and even nanogram amounts of exosome samples. S-Trap-based sample preparation outperformed the traditional in-solution digestion-based approach and the commonly used filter-aided sample preparation (FASP)-based approach with regard to the number of proteins and peptides identified. Moreover, S-Trap-based sample preparation coupled with DIA mass spectrometry also showed the highest reproducibility for protein quantification. In addition, this approach allowed for identification and quantification of exosome proteins with low starting amounts (down to 50 ~ 200 ng). Finally, the proposed method was successfully applied to label-free quantification of exosomal proteins extracted from MDA-MB-231 breast cancer cells and MCF-10A non-tumorigenic epithelial breast cells. Prospectively, we envision the integrated S-Trap sample preparation coupled with DIA quantification strategy as a promising alternative for highly efficient and sensitive analysis of trace amounts of proteomic samples (e.g., exosomal samples).


Assuntos
Proteômica , Manejo de Espécimes , Espectrometria de Massas , Proteínas/análise , Proteoma/análise , Proteômica/métodos , Reprodutibilidade dos Testes , Manejo de Espécimes/métodos
12.
Sensors (Basel) ; 22(4)2022 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-35214515

RESUMO

The study aimed to investigate the magnitude and shape of the forces applied on the foot rest, foot strap, and paddle. Thirteen elite male kayakers participated in this study and performed a 2-min test simulating 500 m race pace in a kayak ergometer. Forces applied by the kayakers on the paddle, foot rest, and foot strap were measured with load cells and recorded by an electronic measuring system. The magnitude of the peak forces applied on the foot rest (left: 543.27 ± 85.93; right: 524.39 ± 88.36) approximately doubled the ones applied on the paddle (left: 236.37 ± 19.32; right: 243.92 ± 28.89). The forces on the foot strap were similar in magnitude to the paddle forces (left: 240.09 ± 74.92; right: 231.05 ± 52.01). A positive correlation was found between the peak forces applied on the foot rest and paddle on the same side (p < 0.001). When comparing the best and worst kayakers' performance, the best showed greater forces magnitudes and synchronization of the peak forces. Analyses of the force-time curves, including not only the forces applied by the kayaker on the paddle but also the ones applied on the foot rest and strap, should be considered relevant in terms of technique analyses.


Assuntos
Esportes Aquáticos , Animais , Fenômenos Biomecânicos , Ergometria , Masculino , Navios
13.
Sensors (Basel) ; 22(17)2022 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-36081005

RESUMO

Heart rate variability (HRV) is frequently applied in sport-specific settings. The rising use of freely accessible applications for its recording requires validation processes to ensure accurate data. It is the aim of this study to compare the HRV data obtained by the Polar H10 sensor chest strap device and an electrocardiogram (ECG) with the focus on RR intervals and short-term scaling exponent alpha 1 of Detrended Fluctuation Analysis (DFA a1) as non-linear metric of HRV analysis. A group of 25 participants performed an exhaustive cycling ramp with measurements of HRV with both recording systems. Average time between heartbeats (RR), heart rate (HR) and DFA a1 were recorded before (PRE), during, and after (POST) the exercise test. High correlations were found for the resting conditions (PRE: r = 0.95, rc = 0.95, ICC3,1 = 0.95, POST: r = 0.86, rc = 0.84, ICC3,1 = 0.85) and for the incremental exercise (r > 0.93, rc > 0.93, ICC3,1 > 0.93). While PRE and POST comparisons revealed no differences, significant bias could be found during the exercise test for all variables (p < 0.001). For RR and HR, bias and limits of agreement (LoA) in the Bland−Altman analysis were minimal (RR: bias of 0.7 to 0.4 ms with LoA of 4.3 to −2.8 ms during low intensity and 1.3 to −0.5 ms during high intensity, HR: bias of −0.1 to −0.2 ms with LoA of 0.3 to −0.5 ms during low intensity and 0.4 to −0.7 ms during high intensity). DFA a1 showed wider bias and LoAs (bias of 0.9 to 8.6% with LoA of 11.6 to −9.9% during low intensity and 58.1 to −40.9% during high intensity). Linear HRV measurements derived from the Polar H10 chest strap device show strong agreement and small bias compared with ECG recordings and can be recommended for practitioners. However, with respect to DFA a1, values in the uncorrelated range and during higher exercise intensities tend to elicit higher bias and wider LoA.


Assuntos
Eletrocardiografia , Teste de Esforço , Ciclismo/fisiologia , Eletrocardiografia/métodos , Exercício Físico/fisiologia , Feminino , Frequência Cardíaca/fisiologia , Humanos , Masculino
14.
Sensors (Basel) ; 22(23)2022 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-36502180

RESUMO

Navigation and positioning of autonomous underwater vehicles (AUVs) in the complex and changeable marine environment are crucial and challenging. For the positioning of AUVs, the integrated navigation of the strap-down inertial navigation system (SINS), Doppler velocity log (DVL), and pressure sensor (PS) has a common application. Nevertheless, in the complex underwater environment, the DVL performance is affected by the current and complex terrain environments. The outliers in sensor observations also have a substantial adverse effect on the AUV positioning accuracy. To address these issues, in this paper, a novel tightly integrated navigation model of the SINS, DVL, and PS is established. In contrast to the traditional SINS, DVL, and PS tightly integrated navigation methods, the proposed method in this paper is based on the velocity variation of the DVL beam by applying the DVL bottom-track and water-track models. Furthermore, a new robust interacting multiple models (RIMM) information fusion algorithm is proposed. In this algorithm, DVL beam anomaly is detected, and the Markov transfer probability matrix is accordingly updated to enable quick model matching. By simulating the motion of the AUV in a complex underwater environment, we also compare the performance of the traditional loosely integrated navigation (TLIN) model, the tightly integrated navigation (TTIN) model, and the IMM algorithm. The simulation results show that because of the PS, the velocity and height in the up-change amplitude of the four algorithms are small. Compared with the TLIN algorithm in terms of maximum deviation of latitude and longitude, the RIMM algorithm also improves the accuracy by 39.1243 m and 26.4364 m, respectively. Furthermore, compared with the TTIN algorithm, the RIMM algorithm improves latitude and longitude accuracy by 1.8913 m and 11.8274 m, respectively. A comparison with IMM also shows that RIMM improves the accuracy of latitude and longitude by 1.1506 m and 7.2301 m, respectively. The results confirm that the proposed algorithm suppresses the observed noise and outliers of DVL and further achieves quick conversion between different DVL models while making full use of the effective information of the DVL beams. The proposed method also improves the navigation accuracy of AUVs in complex underwater environments.


Assuntos
Algoritmos , Ultrassonografia Doppler , Movimento (Física) , Simulação por Computador , Probabilidade
15.
Int J Mol Sci ; 23(24)2022 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-36555135

RESUMO

The phenomenon of internal initiation of translation was discovered in 1988 on poliovirus mRNA. The prototypic cis-acting element in the 5' untranslated region (5'UTR) of poliovirus mRNA, which is able to direct initiation at an internal start codon without the involvement of a cap structure, has been called an IRES (Internal Ribosome Entry Site or Segment). Despite its early discovery, poliovirus and other related IRES elements of type I are poorly characterized, and it is not yet clear which host proteins (a.k.a. IRES trans-acting factors, ITAFs) are required for their full activity in vivo. Here we discuss recent and old results devoted to type I IRESes and provide evidence that Poly(rC) binding protein 2 (PCBP2), Glycyl-tRNA synthetase (GARS), and Cold Shock Domain Containing E1 (CSDE1, also known as UNR) are major regulators of type I IRES activity.


Assuntos
Poliovirus , Poliovirus/genética , Poliovirus/metabolismo , Sítios Internos de Entrada Ribossomal/genética , Transativadores/metabolismo , Sequências Reguladoras de Ácido Nucleico , Códon de Iniciação/metabolismo , RNA Mensageiro/metabolismo , Biossíntese de Proteínas , Regiões 5' não Traduzidas , RNA Viral/metabolismo
16.
J Proteome Res ; 20(3): 1783-1791, 2021 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-33630606

RESUMO

Stony corals form the foundation of coral reefs, which are of prominent ecological and economic significance. A robust workflow for investigating the coral proteome is essential in understanding coral biology. Here we investigated different preparative workflows and characterized the proteome of Platygyra carnosa, a common stony coral of the South China Sea. We found that a combination of bead homogenization with suspension trapping (S-Trap) preparation could yield more than 2700 proteins from coral samples. Annotation using a P. carnosa transcriptome database revealed that the majority of proteins were from the coral host cells (2140, 212, and 427 proteins from host coral, dinoflagellate, and other compartments, respectively). Label-free quantification and functional annotations indicated that a high proportion were involved in protein and redox homeostasis. Furthermore, the S-Trap method achieved good reproducibility in quantitative analysis. Although yielding a low symbiont:host ratio, the method is efficient in characterizing the coral host proteomic landscape, which provides a foundation to explore the molecular basis of the responses of coral host tissues to environmental stressors.


Assuntos
Antozoários , Animais , Antozoários/genética , China , Proteoma/genética , Proteômica , Reprodutibilidade dos Testes , Simbiose
17.
J Proteome Res ; 20(1): 1027-1039, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-33301673

RESUMO

Well-characterized archival formalin-fixed paraffin-embedded (FFPE) tissues are of much value for prospective biomarker discovery studies, and protocols that offer high throughput and good reproducibility are essential in proteomics. Therefore, we implemented efficient paraffin removal and protein extraction from FFPE tissues followed by an optimized two-enzyme digestion using suspension trapping (S-Trap). The protocol was then combined with TMTpro 16plex labeling and applied to lung adenocarcinoma patient samples. In total, 9585 proteins were identified, and proteins related to the clinical outcome were detected. Because acetylation is known to play a major role in cancer development, a fast on-trap acetylation protocol was developed for studying endogenous lysine acetylation, which allows identification and localization of the lysine acetylation together with quantitative comparison between samples. We demonstrated that FFPE tissues are equivalent to frozen tissues to study the degree of acetylation between patients. In summary, we present a reproducible sample preparation workflow optimized for FFPE tissues that resolves known proteomic-related challenges. We demonstrate compatibility of the S-Trap with isobaric labeling and for the first time, we prove that it is feasible to study endogenous lysine acetylation stoichiometry in FFPE tissues, contributing to better utility of the existing global tissue archives. The MS proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifiers PXD020157, PXD021986, and PXD021964.


Assuntos
Proteoma , Proteômica , Formaldeído , Humanos , Inclusão em Parafina , Estudos Prospectivos , Processamento de Proteína Pós-Traducional , Proteoma/metabolismo , Reprodutibilidade dos Testes , Fixação de Tecidos , Fluxo de Trabalho
18.
EMBO J ; 36(23): 3483-3500, 2017 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-29046333

RESUMO

The tumor suppressor p53 is activated in response to cellular stress to prevent malignant transformation. However, several recent studies have shown that p53 can play protective roles in tumor cell survival under adversity. Whether p53-regulated long noncoding RNAs are involved in this process remains to be fully understood. Here, we show that under glucose starvation condition, p53 directly upregulates a novel lncRNA named TRINGS (Tp53-regulated inhibitor of necrosis under glucose starvation) in human tumor cells. TRINGS binds to STRAP and inhibits STRAP-GSK3ß-NF-κB necrotic signaling to protect tumor cells from cell death. Interestingly, TRINGS appears to respond to glucose starvation specifically, as it is not activated by serum, serine, or glutamine deprivation. Collectively, our findings reveal that p53-induced lncRNA TRINGS controls the necrotic pathway and contributes to the survival of cancer cells harboring wild-type p53 under glucose stress.


Assuntos
Genes p53 , Neoplasias/genética , Neoplasias/metabolismo , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , RNA Neoplásico/genética , RNA Neoplásico/metabolismo , Apoptose , Linhagem Celular Tumoral , Sobrevivência Celular , Técnicas de Silenciamento de Genes , Glucose/metabolismo , Glicogênio Sintase Quinase 3 beta/metabolismo , Humanos , NF-kappa B/metabolismo , Necrose , Proteínas de Neoplasias/metabolismo , Neoplasias/patologia , Ligação Proteica , RNA Longo não Codificante/antagonistas & inibidores , RNA Neoplásico/antagonistas & inibidores , Proteínas de Ligação a RNA , Regulação para Cima
19.
Clin Endocrinol (Oxf) ; 94(3): 449-459, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-32745252

RESUMO

OBJECTIVE: As per the eighth edition of the American Joint Committee on Cancer (AJCC) staging system for differentiated thyroid carcinoma (DTC), minimal extrathyroidal extension (mETE) has been removed. Instead, gross ETE (gETE) invading only strap muscles has been designated as a new T3b category. Our objective was to investigate the impact of the T3b category on survival in order to establish its prognostic value in DTC. DESIGN: In this retrospective study, we included patients who had undergone thyroidectomy between 2004 and 2012. Data from the Surveillance, Epidemiology and End Results (SEER) database were examined. METHODS: We used the Kaplan-Meier method and log-rank test to analyse overall survival (OS) and cancer-specific survival (CSS). The effect of potential predictors associated with survival were estimated using the Cox regression model. To minimize selection bias, propensity-score matching (PSM) was performed. RESULTS: A total of 63 315 patients were included in our study. During the average follow-up duration of nearly 78 months, significant differences were observed in cancer-specific survival among patients with no ETE, mETE, gETE invading only strap muscles (T3b) and gETE invading perithyroidal structures other than strap muscles (T4) (P < .05). In univariable and multivariate analysis, both mETE and T3b exhibited significant poorer CSS compared with no ETE. After adjusting for patient features with PSM, it was confirmed that T3b was associated with worse CSS compared with no ETE and mETE. CONCLUSIONS: Both mETE and gETE are independent factors for DTC, implying that the new T3b category is worthy of reference for medical workers. Furthermore, mETE was significantly associated with poorer outcome. Our conclusion may provide support for the modification of the TNM staging system in the future.


Assuntos
Neoplasias da Glândula Tireoide , Humanos , Estadiamento de Neoplasias , Prognóstico , Estudos Retrospectivos , Programa de SEER , Neoplasias da Glândula Tireoide/patologia , Neoplasias da Glândula Tireoide/cirurgia , Tireoidectomia
20.
Sensors (Basel) ; 21(2)2021 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-33477362

RESUMO

In this paper, a low-cost small-sized strap-down inertial navigation system (SINS)-Gyrolab GL-VG 109-is studied. When the system is installed on an unmanned vehicle and works in autonomous mode, it is difficult to determine the navigation parameters of the unmanned vehicle. Correcting the SINS information from the Global Navigation Satellite System (GNSS) can significantly increase the determination accuracy of the navigation parameters. However, this is only available when the GNSS signals are stable. A new adaptive estimation algorithm that can automatically detect, evaluate, and process the abnormal measurements is proposed in the present work. The determination of the navigation parameters can reach the third accuracy class using the proposed method. The effectiveness of the algorithm is verified by the mathematical simulation and the experimental tests (with a real SINS GL-VG 109), which are conducted in urban environments with a GNSS signal containing 15% and 40% abnormal measurements. The results show that the proposed method can significantly reduce the impact of abnormal measurements and improve the estimation accuracy.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA