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1.
Nucleic Acids Res ; 49(6): e36, 2021 04 06.
Artículo en Inglés | MEDLINE | ID: mdl-33619540

RESUMEN

Several existing technologies enable short genomic alterations including generating indels and short nucleotide variants, however, engineering more significant genomic changes is more challenging due to reduced efficiency and precision. Here, we developed RecT Editor via Designer-Cas9-Initiated Targeting (REDIT), which leverages phage single-stranded DNA-annealing proteins (SSAP) RecT for mammalian genome engineering. Relative to Cas9-mediated homology-directed repair (HDR), REDIT yielded up to a 5-fold increase of efficiency to insert kilobase-scale exogenous sequences at defined genomic regions. We validated our REDIT approach using different formats and lengths of knock-in templates. We further demonstrated that REDIT tools using Cas9 nickase have efficient gene-editing activities and reduced off-target errors, measured using a combination of targeted sequencing, genome-wide indel, and insertion mapping assays. Our experiments inhibiting repair enzyme activities suggested that REDIT has the potential to overcome limitations of endogenous DNA repair steps. Finally, our REDIT method is applicable across cell types including human stem cells, and is generalizable to different Cas9 enzymes.


Asunto(s)
Proteína 9 Asociada a CRISPR , Proteínas de Unión al ADN , Proteínas de Escherichia coli , Edición Génica/métodos , Línea Celular , Genoma , Humanos , Reparación del ADN por Recombinación , Células Madre/metabolismo
2.
Phys Chem Chem Phys ; 24(40): 24917-24923, 2022 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-36200432

RESUMEN

Based on first-principles calculations in combination with the Boltzmann transport theory, we investigate the effects of onsite Coulomb interaction and strain on the lattice thermal conductivity of the KAgSe monolayer, a recently discovered 2D thermoelectric system with a low lattice thermal conductivity when the onsite Coulomb interaction was not considered (X. Zhang, C. Liu, Y. Tao, Y. Li, Y. Guo, Y. Chen, X. C. Zeng and J. Wang, Adv. Funct. Mater., 2020, 30, 2001200). Our calculations reveal that the onsite Coulomb interaction leads to an increase in the lattice thermal conductivity from 1.22 to 1.82 W m-1 K-1 at room temperature due to the increased phonon group velocity and relaxation time. However, with onsite Coulomb interaction, small 3% biaxial tensile strain can give rise to a 75% considerable decrease in the lattice thermal conductivity at room temperature, from 1.82 to 0.45 W m-1 K-1, which is also much lower than the lattice thermal conductivity of 1.22 W m-1 K-1 without onsite Coulomb interaction and strain. The strain induced decrease of phonon group velocity and enhancement of lattice anharmonicity (large Grüneisen parameter and phase space volume) are responsible for the reduced lattice thermal conductivity. The present work highlights that the onsite Coulomb interaction is indispensable when determining the lattice thermal conductivity of 2D KAgSe, and small tensile strain can greatly decrease the lattice thermal conductivity.

3.
Virus Genes ; 56(6): 724-733, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33033882

RESUMEN

MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression by complementary binding to target mRNAs. Virus-encoded miRNAs play important roles in virus life cycle and virus-host interactions. Viruses from the Megalocytivirus genus, family Iridoviridae, infect a wide range of fishes, bringing great challenges to aquaculture. Infectious spleen and kidney necrosis virus (ISKNV) is the type species of the Megalocytivirus genus. In this study, using Illumina sequencing coupled with miRNA precursor prediction and stem-loop real-time PCR, 14 putative ISKNV-encoded miRNAs were preliminarily identified from ISKNV-infected mandarin fish MFF-1 cells. To initially study their functions, inhibitors of the 14 viral miRNAs were synthesized and transfected into MFF-1 cells, which were further infected with ISKNV. The results showed that these viral miRNAs could affect the virus titers in the supernatant of ISKNV-infected cells and the expression of major capsid protein (MCP). Moreover, we observed that inhibition of several ISKNV miRNAs had different effects on MCP expression and on titer of released virus, suggesting complex roles of viral miRNAs in ISKNV infection. The current study may provide a fundamental information for further identification and functional studies on miRNAs encoded by Megalocytivirus.


Asunto(s)
Infecciones por Virus ADN/virología , Enfermedades de los Peces/virología , Peces/virología , Iridoviridae/genética , MicroARNs , Animales , Línea Celular , Células Epiteliales/virología , Interacciones Huésped-Patógeno
4.
Int J Mol Sci ; 19(8)2018 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-30127315

RESUMEN

Dormancy is an adaptive trait that blocks seed germination until the environmental conditions become favorable for subsequent vegetative plant growth. Seed dormancy is defined as the inability to germinate in favorable conditions. Dormancy is alleviated during after-ripening, a dry storage period, during which dormant (D) seeds unable to germinate become non-dormant (ND), able to germinate in a wide range of environmental conditions. The treatment of dormant seeds with ethylene (D/ET) promotes seed germination, and abscisic acid (ABA) treatment reduces non-dormant (ND/ABA) seed germination in sunflowers (Helianthus annuus). Metabolomic and transcriptomic studies have been performed during imbibition to compare germinating seeds (ND and D/ET) and low-germinating seeds (D and ND/ABA). A PCA analysis of the metabolites content showed that imbibition did not trigger a significant change during the first hours (3 and 15 h). The metabolic changes associated with germination capacity occurred at 24 h and were related to hexoses, as their content was higher in ND and D/ET and was reduced by ABA treatment. At the transcriptional level, a large number of genes were altered oppositely in germinating, compared to the low-germinating seeds. The metabolomic and transcriptomic results were integrated in the interpretation of the processes involved in germination. Our results show that ethylene treatment triggers molecular changes comparable to that of after-ripening treatment, concerning sugar metabolism and ABA signaling inhibition.


Asunto(s)
Etilenos/metabolismo , Germinación , Helianthus/crecimiento & desarrollo , Reguladores del Crecimiento de las Plantas/metabolismo , Semillas/crecimiento & desarrollo , Regulación de la Expresión Génica de las Plantas , Helianthus/genética , Helianthus/metabolismo , Metaboloma , Latencia en las Plantas , Semillas/genética , Semillas/metabolismo , Transcriptoma
5.
Pediatr Surg Int ; 33(7): 793-797, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28584905

RESUMEN

OBJECTIVE: Intussusception secondary to pathologic lead points (PLPs) is a challenging condition for pediatric surgeons, and few studies have been published on this subject. The aim of this study was to review and analyze clinical data on the diagnosis and management of intussusception secondary to PLPs in children. METHODS: Between 2002 and 2016, a total of 65 pediatric patients with a diagnosis of intussusception secondary to PLPs were retrospectively reviewed. RESULTS: The series comprised 47 males and 18 females. The average age of the patients was 4.9 years old. All patients had typical clinical manifestations, and intussusception was proven by ultrasound. Fifty-one patients had recurrent intussusception, of whom 21 had one, 14 had two, 10 had three, and 6 had more than three. There were 20 episodes of recurrence within 24 h (39.2%), 15 episodes were found between 24 and 72 h (29.4%), and the remaining 31.4% (16/51) of recurrences occurred after 72 h. All patients received surgical intussusception reduction. Meanwhile, enterectomy was the procedure of choice in 55 patients, polypectomy in 5 patients, and cystectomy in 3 patients. The types of intussusception secondary to PLPs included small intestinal (n = 25), ileocolic (n = 19), ileocecal (n = 11), ileo-ileocolic (n = 9) and cecalcolic (n = 1). The types of PLPs included Meckel diverticulum (n = 32), intestinal duplication (n = 14), benign polyps (n = 5), malignant lymphoma (n = 4), Peutz-Jeghers syndrome (n = 3), mesenteric cyst (n = 3), intestinal wall hematoma of hemophilia (n = 2), allergic purpura (n = 1), and hamartoma (n = 1). All patients recovered well with no relapse during follow-up, except for one patient who had an intestinal obstruction from adhesions that occurred approximately 3 months after discharge and who was curable after conservative treatment. CONCLUSIONS: Intussusception secondary to PLPs tends to exhibit recurrence. There are various types of intussusception secondary to PLPs. It is necessary to improve auxiliary examinations to identify the etiology and avoid intraoperative omission. Surgical reduction of intussusception secondary to PLPs is the preferred clinical management.


Asunto(s)
Intususcepción/etiología , Intususcepción/cirugía , Niño , Preescolar , Enfermedades del Sistema Digestivo/complicaciones , Femenino , Humanos , Vasculitis por IgA/complicaciones , Lactante , Pólipos Intestinales/complicaciones , Intususcepción/diagnóstico , Masculino , Recurrencia , Estudios Retrospectivos , Ultrasonografía
6.
BMC Cancer ; 16: 238, 2016 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-26993269

RESUMEN

BACKGROUND: In previous investigation, we reported that stably knocking down cyclin-dependent kinase 4(CDK4) induced expression of let-7c, which further suppressed cell cycle transition and cell growth by modulating cell cycle signaling in nasopharyngeal carcinoma (NPC). In this study, we further explored the molecular function and mechanism of CDK4 modulating miRNAs to stimulate cell cycle transition, cell growth, and Cisplatin (DDP) -resistance on in NPC. METHODS: We identified changes in miRNAs by miRNA array and real-time PCR and the effect on DDP after knocking down CDK4 in NPC cells. Further, we investigated the molecular mechanisms by which CDK4 modulated miR-15a in NPC. Moreover, we also explored the role of miR-15a and the effect on DDP in NPC. Finally, we analyzed the correlation of miR-15a and CDK4 expression in NPC tissues. RESULTS: In addition to let-7 family members, we observed that upregulated expression of miR-15a was significantly induced in CDK4-suppressed NPC cells. Further, we found that knocking down CDK4 suppressed c-Myc expression, and the latter directly suppressed the expression of miR-15a in NPC. Furthermore, miR-15a as a tumor suppressor antagonized CDK4 repressing cell cycle progression and cell growth in vitro and in vivo and induced the sensitivity of cells to DDP by regulating the c-Myc/CCND1/CDK4/E2F1 pathway in NPC. Finally, miR-15a was negatively weak correlated with the expression of CDK4 in NPC. CONCLUSIONS: Our studies demonstrate that CDK4 and miR-15a comprise an abnormal automodulatory feedback loop stimulating the pathogenesis and inducing chemotherapy resistance in NPC.


Asunto(s)
Quinasa 4 Dependiente de la Ciclina/genética , MicroARNs/metabolismo , Neoplasias Nasofaríngeas/tratamiento farmacológico , Neoplasias Nasofaríngeas/genética , Carcinoma , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Cisplatino/administración & dosificación , Quinasa 4 Dependiente de la Ciclina/metabolismo , Resistencia a Antineoplásicos/genética , Retroalimentación Fisiológica , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Técnicas de Silenciamiento del Gen , Humanos , MicroARNs/genética , Carcinoma Nasofaríngeo , Neoplasias Nasofaríngeas/patología , Transducción de Señal/efectos de los fármacos
8.
Nanoscale ; 16(5): 2513-2521, 2024 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-38205870

RESUMEN

In recent years, van der Waals heterostructures (vdWHs) with controllable and peculiar properties have attracted extensive attention in the fields of electronics, optoelectronics, spintronics and electrochemistry. However, vdWHs with good thermoelectric performance are few due to the complex coupling of thermoelectric coefficients. Here, we employ density functional theory and Boltzmann's transport equation to explore the thermoelectric properties of the p-n vdWH of GaSe/SnS2, which has been experimentally observed to exhibit high performance as an optoelectronic device. We reveal that GaSe/SnS2 possesses strong anisotropy in terms of electronic transport resulting from the anisotropic carrier relaxation time. The longer carrier relaxation time in the y-direction for n-type induces a high power factor of 0.084 W m-1 K-2 at 300 K, while it is only 0.0087 W m-1 K-2) in the x-direction. The strong coupling of low-mid frequency phonon branches and the relatively weak Sn-S bond-induced anharmonicity hinder the phonon transport, which results in the lattice thermal conductivity of GaSe/SnS2 (14.61 and 15.43 W m-1 K-1 along the x- and y-directions at 300 K) being much smaller than the average value of GaSe and SnS2 (43.44 W m-1 K-1 at 300 K). The optimal thermoelectric figure of merit at 700 K for GaSe/SnS2 reaches 2.99, which is significantly higher than those of the constituents of GaSe (0.58) and SnS2 (1.04). The present work highlights the potential thermoelectric applications and the understanding of the thermoelectric transport mechanism for the recently synthesized p-n vdWH of GaSe/SnS2 with a high thermoelectric figure of merit and strong anisotropy.

9.
Chem Commun (Camb) ; 60(32): 4342-4345, 2024 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-38545842

RESUMEN

Activity-based ubiquitin probes (Ub-ABPs) have recently been developed as effective tools for studying the capabilities of E1-E2-E3 enzymes, but most of them can only be used in cell lysates. Here, we report the first cell-penetrating Ub-Dha probes based on thiazolidine-protected cysteines, which enable successful delivery into cells confirmed by a fluorophore at the N-terminus of Ub and live-cell fluorescence microscopy. A total of 18 E1-E2-E3 enzymes in live cells were labelled and enriched in combination with label-free quantification (LFQ) mass spectrometry. This work provided a new cell-penetrating Ub tool for studying the activity and function of Ub-related enzymes.


Asunto(s)
Ubiquitina-Proteína Ligasas , Ubiquitina , Ubiquitina/química , Ubiquitina-Proteína Ligasas/metabolismo , Colorantes Fluorescentes , Ubiquitinación
10.
BMC Complement Med Ther ; 24(1): 246, 2024 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-38915038

RESUMEN

INTRODUCTION: The clinical symptoms of Lumbar Disc Herniation (LDH) can be effectively ameliorated through Lever Positioning Manipulation (LPM), which is closely linked to the brain's pain-regulating mechanisms. Magnetic Resonance Imaging (MRI) offers an objective and visual means to study how the brain orchestrates the characteristics of analgesic effects. From the perspective of multimodal MRI, we applied functional MRI (fMRI) and Magnetic Resonance Spectrum (MRS) techniques to comprehensively evaluate the characteristics of the effects of LPM on the brain region of LDH from the aspects of brain structure, brain function and brain metabolism. This multimodal MRI technique provides a biological basis for the clinical application of LPM in LDH. METHODS AND ANALYSIS: A total of 60 LDH patients and 30 healthy controls, matched by gender, age, and years of education, will be enrolled in this study. The LDH patients will be divided into two groups (Group 1, n = 30; Group 2, n = 30) using a random number table method. Group 1 will receive LPM treatment once every two days, for a total of 12 times over 4 weeks. Group 2 will receive sham LPM treatment during the same period as Group 1. All 30 healthy controls will be divided into Group 3. Multimodal MRI will be performed on Group 1 and Group 2 at three time points (TPs): before LPM (TP1), after one LPM session (TP2), and after a full course of LPM treatment. The healthy controls (Group 3) will not undergo LPM and will be subject to only a single multimodal MRI scan. Participants in both Group 1 and Group 2 will be required to complete clinical questionnaires. These assessments will focus on pain intensity and functional disorders, using the Visual Analog Scale (VAS) and the Japanese Orthopaedic Association (JOA) scoring systems, respectively. DISCUSSION: The purpose of this study is to investigate the multimodal brain response characteristics of LDH patients after treatment with LPM, with the goal of providing a biological basis for clinical applications. TRIAL REGISTRATION NUMBER: https://clinicaltrials.gov/ct2/show/NCT05613179 , identifier: NCT05613179.


Asunto(s)
Encéfalo , Desplazamiento del Disco Intervertebral , Imagen por Resonancia Magnética , Humanos , Imagen por Resonancia Magnética/métodos , Desplazamiento del Disco Intervertebral/terapia , Desplazamiento del Disco Intervertebral/diagnóstico por imagen , Adulto , Masculino , Femenino , Encéfalo/diagnóstico por imagen , Persona de Mediana Edad , Imagen Multimodal/métodos , Adulto Joven , Degeneración del Disco Intervertebral
11.
Pediatr Rheumatol Online J ; 22(1): 35, 2024 Mar 08.
Artículo en Inglés | MEDLINE | ID: mdl-38459548

RESUMEN

BACKGROUND: Juvenile idiopathic arthritis (JIA) is a type of chronic childhood arthritis with complex pathogenesis. Immunological studies have shown that JIA is an acquired self-inflammatory disease, involving a variety of immune cells, and it is also affected by genetic and environmental susceptibility. However, the precise causative relationship between the phenotype of immune cells and JIA remains unclear to date. The objective of our study is to approach this inquiry from a genetic perspective, employing a method of genetic association analysis to ascertain the causal relationship between immune phenotypes and the onset of JIA. METHODS: In this study, a two-sample Mendelian randomization (MR) analysis was used to select single nucleotide polymorphisms (SNPs) significantly associated with immune cells as instrumental variables to analyze the bidirectional causal relationship between 731 immune cells and JIA. There were four types of immune features (median fluorescence intensity (MFI), relative cellular (RC), absolute cellular (AC), and morphological parameters (MP)). Finally, the heterogeneity and horizontal reproducibility of the results were verified by sensitivity analysis, which ensured more robust results. RESULTS: We found that CD3 on CM CD8br was causally associated with JIA at the level of 0.05 significant difference (95% CI = 0.630 ~ 0.847, P = 3.33 × 10-5, PFDR = 0.024). At the significance level of 0.20, two immunophenotypes were causally associated with JIA, namely: HLA DR on CD14+ CD16- monocyte (95% CI = 0.633 ~ 0.884, P = 6.83 × 10-4, PFDR = 0.16) and HLA DR on CD14+ monocyte (95% CI = 0.627 ~ 0.882, P = 6.9 × 10-4, PFDR = 0.16). CONCLUSION: Our study assessed the causal effect of immune cells on JIA from a genetic perspective. These findings emphasize the complex and important role of immune cells in the pathogenesis of JIA and lay a foundation for further study of the pathogenesis of JIA.


Asunto(s)
Artritis Juvenil , Humanos , Niño , Artritis Juvenil/genética , Genotipo , Predisposición Genética a la Enfermedad , Reproducibilidad de los Resultados , Antígenos HLA-DR/genética , Polimorfismo de Nucleótido Simple , Estudio de Asociación del Genoma Completo
12.
Cancer Cell Int ; 13(1): 47, 2013 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-23688022

RESUMEN

BACKGROUND: Cranial radiation therapy has been used for the treatment of primary and metastatic brain tumors. A prominent feature of brain injury induced by the radiation therapy is hippocampal dysfunction, characterized by a decline in memory. Cdk5 plays an important role in memory formation. Abnormal Cdk5 activity is associated with neuronal apoptosis induced by neurotoxic stimuli. However, the roles of Cdk5 in hippocampal apoptosis in response to X-ray irradiation have not been explored. METHODS: The expression of Cdk5 activators, p35 and p25, in hippocampal neurons was tested in both in vivo animal and in vitro couture after X-ray irradiation. RESULTS: After X-ray irradiation at 20 Gy and 30 Gy in rats, the number of hippocampal neuronal pyknosis was increased, but the number of hippocampal neuron was decreased, in the hippocampal CA1 region of rats. In these animals undergone with X-ray irradiation, the expression of p35 was significantly down-regulated, but it was up-regulated in p25. These opposite expressions were also shown in the primary cultured hippocampal neurons with 30 Gy irradiation. The apoptosis induced by X-ray irradiation were significantly prevented by the pretreatment of Cdk5 inhibitor, roscovitine, in both in vivo and in vitro settings. CONCLUSIONS: X-ray irradiation resulted in a hippocampal neuronal apoptosis through up-regulation of p25, the Cdk5 activator. Hyperactivity of Cdk5 was involved in the pathogenesis of X-ray irradiation-induced hippocampal neuronal apoptosis. Blockade of Cdk5 signal pathway effectively protected neurons from the irradiation-induced brain injury.

13.
Virol J ; 10: 77, 2013 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-23497248

RESUMEN

BACKGROUND: Infectious spleen and kidney necrosis virus (ISKNV) belongs to the genus Megalocytivirus from the family Iridoviridae. Megalocytivirus causes severe economic losses to tropical freshwater and marine culture industry in Asian countries and is devastating to the mandarin fish farm industry in China particularly. METHODS: We investigated the involvement of microfilaments in the early and late stages of ISKNV infection in MFF-1 cells by selectively perturbing their architecture using well-characterized inhibitors of actin dynamics. The effect of disruption of actin cytoskeleton on ISKNV infection was evaluated by indirect immunofluorescence analysis or real-time quantitative PCR. RESULTS: The depolymerization of the actin filaments with cytochalasin D, cytochalasin B, or latrunculin A reduced ISKNV infection. Furthermore, depolymerization of filamentous actin by inhibitors did not inhibit binding of the virus but affected virus internalization in the early stages of infection. In addition, the depolymerization of actin filaments reduced total ISKNV production in the late stages of ISKNV. CONCLUSIONS: This study demonstrated that ISKNV required an intact actin network during infection. The findings will help us to better understand how iridoviruses exploit the cytoskeleton to facilitate their infection and subsequent disease.


Asunto(s)
Citoesqueleto de Actina/metabolismo , Iridoviridae/fisiología , Citoesqueleto de Actina/genética , Animales , Línea Celular , Peces , Técnica del Anticuerpo Fluorescente Indirecta , Reacción en Cadena en Tiempo Real de la Polimerasa
14.
NPJ Digit Med ; 6(1): 160, 2023 Aug 25.
Artículo en Inglés | MEDLINE | ID: mdl-37626155

RESUMEN

While the literature on putting a "human in the loop" in artificial intelligence (AI) and machine learning (ML) has grown significantly, limited attention has been paid to how human expertise ought to be combined with AI/ML judgments. This design question arises because of the ubiquity and quantity of algorithmic decisions being made today in the face of widespread public reluctance to forgo human expert judgment. To resolve this conflict, we propose that human expert judges be included via appeals processes for review of algorithmic decisions. Thus, the human intervenes only in a limited number of cases and only after an initial AI/ML judgment has been made. Based on an analogy with appellate processes in judiciary decision-making, we argue that this is, in many respects, a more efficient way to divide the labor between a human and a machine. Human reviewers can add more nuanced clinical, moral, or legal reasoning, and they can consider case-specific information that is not easily quantified and, as such, not available to the AI/ML at an initial stage. In doing so, the human can serve as a crucial error correction check on the AI/ML, while retaining much of the efficiency of AI/ML's use in the decision-making process. In this paper, we develop these widely applicable arguments while focusing primarily on examples from the use of AI/ML in medicine, including organ allocation, fertility care, and hospital readmission.

15.
Nat Aging ; 3(5): 600-616, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-37118554

RESUMEN

Chronic systemic inflammation is one of the hallmarks of the aging immune system. Here we show that activated T cells from older adults contribute to inflammaging by releasing mitochondrial DNA (mtDNA) into their environment due to an increased expression of the cytokine-inducible SH2-containing protein (CISH). CISH targets ATP6V1A, an essential component of the proton pump V-ATPase, for proteasomal degradation, thereby impairing lysosomal function. Impaired lysosomal activity caused intracellular accumulation of multivesicular bodies and amphisomes and the export of their cargos, including mtDNA. CISH silencing in T cells from older adults restored lysosomal activity and prevented amphisomal release. In antigen-specific responses in vivo, CISH-deficient CD4+ T cells released less mtDNA and induced fewer inflammatory cytokines. Attenuating CISH expression may present a promising strategy to reduce inflammation in an immune response of older individuals.


Asunto(s)
Citocinas , ADN Mitocondrial , Anciano , Humanos , Citocinas/metabolismo , ADN Mitocondrial/genética , Inflamación/genética , Lisosomas/metabolismo
16.
JACS Au ; 3(10): 2873-2882, 2023 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-37885572

RESUMEN

Dynamic monitoring of intracellular ubiquitin (Ub) conjugates is instrumental to understanding the Ub regulatory machinery. Although many biochemical approaches have been developed to characterize protein ubiquitination, chemical tools capable of temporal resolution probing of ubiquitination events remain to be developed. Here, we report the development of the first cell-permeable and stimuli-responsive Ub probe and its application for the temporal resolution profiling of ubiquitinated substrates in live cells. The probe carrying the photolabile group N-(2-nitrobenzyl)-Gly (Nbg) on the amide bond between Ub Gly75 and Gly76 is readily prepared through chemical synthesis and can be delivered to live cells by conjugation via a disulfide bond with the cyclic cell-penetrating peptide cR10D (i.e., 4-((4-(dimethylamino)phenyl)-azo)-benzoic acid-modified cyclic deca-arginine). Both in vitro and in vivo experiments showed that Ub-modifying enzymes (E1, E2s, and E3s) could not install the Ub probe onto substrate proteins prior to removal of the nitrobenzyl group, which was easily accomplished via photoirradiation. The utility and practicality of this probe were exemplified by the time-resolved biochemical and proteomic investigation of ubiquitination events in live cells during a H2O2-mediated oxidative stress response. This work shows a conceptually new family of chemical Ub tools for the time-resolved studies on dynamic protein ubiquitination in different biological processes and highlights the utility of modern chemical protein synthesis in obtaining custom-designed tools for biological studies.

17.
Nat Med ; 29(1): 258-269, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36604540

RESUMEN

Antigen-specific, MHC-restricted αß T cells are necessary for protective immunity against Mycobacterium tuberculosis, but the ability to broadly study these responses has been limited. In the present study, we used single-cell and bulk T cell receptor (TCR) sequencing and the GLIPH2 algorithm to analyze M. tuberculosis-specific sequences in two longitudinal cohorts, comprising 166 individuals with M. tuberculosis infection who progressed to either tuberculosis (n = 48) or controlled infection (n = 118). We found 24 T cell groups with similar TCR-ß sequences, predicted by GLIPH2 to have common TCR specificities, which were associated with control of infection (n = 17), and others that were associated with progression to disease (n = 7). Using a genome-wide M. tuberculosis antigen screen, we identified peptides targeted by T cell similarity groups enriched either in controllers or in progressors. We propose that antigens recognized by T cell similarity groups associated with control of infection can be considered as high-priority targets for future vaccine development.


Asunto(s)
Mycobacterium tuberculosis , Tuberculosis , Humanos , Tuberculosis/genética , Linfocitos T , Receptores de Antígenos de Linfocitos T/genética , Antígenos , Progresión de la Enfermedad
18.
Methods Mol Biol ; 2574: 251-264, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36087206

RESUMEN

Expression of T-cell receptor (TCR) genes is a critical step for TCR characterization and epitope identification. The recent interest in using specific TCRs for cancer immunotherapy has further increased the demand for practical and robust methods to rapidly clone and express TCRs. We show that a recombination-based cloning protocol facilitates simple and rapid transfer of the TCR transgene into different expression systems. In this protocol, we first constructed all the human TRAV and TRBV genes into individual plasmid. To clone any TCR, we only need to ligate a short CDR3 fragment to its corresponding V gene plasmid using Golden Gate cloning. This strategy significantly improves the efficiency of individual TCR cloning and mutagenesis, providing a flexible high-throughput method for TCR analysis and TCR-mediated therapeutics.


Asunto(s)
Genes Codificadores de los Receptores de Linfocitos T , Receptores de Antígenos de Linfocitos T , Clonación Molecular , Humanos , Receptores de Antígenos de Linfocitos T/genética , Receptores de Antígenos de Linfocitos T/metabolismo
19.
J Colloid Interface Sci ; 627: 180-193, 2022 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-35842968

RESUMEN

In this contribution, carbon quantum dots (CQDs) modified 3D-flower like BiOX (X = Cl, Br, I) photocatalyst were successfully prepared via a facile mechanical compounding method. The crystal structure, surface composition, morphologies, optical properties and photocatalytic activities were investigated in detail. The photocatalytic activity of the as-obtained photocatalyst were evaluated by degradation of rhodamine B (RhB) and Levofloxacin (LEV) under near IR-UV-vis light irradiation, the CQDs/BiOX composite displayed enhanced photocatalytic activity as compared with individual BiOX materials. The CQDs/BiOX composite had the outstanding light harvesting and electron transfer ability because of the ordered ultrathin nanosheet structure of the BiOX, the formation of metal Bi under photoinduction, and the synergistic effects between CQDs and pure BiOX. Antibacterial activity and effects on Rye seeds growth of the LEV degradation intermediate were also researched. Reactive-species-trapping experiments exhibited that h+ and O2- were the active reactive species during photodegradation process. This work provided an effective and simple strategy for designing QDs modified Bi-rich oxyhalides in organic pollutant containing wastewater treatment.


Asunto(s)
Contaminantes Ambientales , Puntos Cuánticos , Antibacterianos/química , Antibacterianos/farmacología , Bismuto , Carbono , Catálisis , Levofloxacino , Fotólisis , Puntos Cuánticos/química , Puntos Cuánticos/toxicidad , Rodaminas
20.
Free Radic Biol Med ; 193(Pt 1): 95-107, 2022 11 20.
Artículo en Inglés | MEDLINE | ID: mdl-36243211

RESUMEN

Circulating tumor cells (CTCs) acquire enhanced anti-anoikis abilities after experiencing flow shear stress in the circulatory system. Our previous study demonstrated that low shear stress (LSS) promotes anoikis resistance of human breast carcinoma cells via caveolin-1 (Cav-1)-dependent extrinsic and intrinsic apoptotic pathways. However, the underlying mechanism how LSS enhanced Cav-1 expression in suspended cancer cells remains unclear. Herein, we found that LSS induced redox signaling was involved in the regulation of Cav-1 level and anoikis resistance in suspension cultured cancer cells. Exposure of human breast carcinoma MDA-MB-231 cells to LSS (2 dyn/cm2) markedly induced ROS and •NO generation, which promoted the cell viability and reduced the cancer cell apoptosis. Furthermore, ROS and •NO scavenging inhibited the upregulation of Cav-1 by interfering ubiquitination, and suppressed the anoikis resistance of suspended tumor cells. These findings provide new insight into the mechanism by which LSS-stimulated ROS and •NO generation increases Cav-1 stabilization in suspended cancer cells through inhibition of ubiquitination and proteasomal degradation, which could be a potential target for therapy of metastatic tumors.


Asunto(s)
Neoplasias de la Mama , Caveolina 1 , Femenino , Humanos , Anoicis/fisiología , Neoplasias de la Mama/genética , Caveolina 1/genética , Caveolina 1/metabolismo , Células MDA-MB-231 , Óxido Nítrico/metabolismo , Especies Reactivas de Oxígeno/metabolismo
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