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1.
Immunity ; 57(6): 1187-1189, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38865963

RESUMO

A major barrier to antitumor immunity in solid tumors is T cell exclusion. In this issue of Immunity, De Sanctis et al.1 elucidate how CLDN18 on pancreatic and lung cancer cells enhances infiltration, immunological synapse formation, and activation of cytotoxic T lymphocytes.


Assuntos
Claudinas , Humanos , Claudinas/metabolismo , Claudinas/imunologia , Claudinas/genética , Neoplasias/imunologia , Animais , Linfócitos T Citotóxicos/imunologia , Neoplasias Pancreáticas/imunologia , Neoplasias Pulmonares/imunologia , Ativação Linfocitária/imunologia , Sinapses Imunológicas/imunologia , Sinapses Imunológicas/metabolismo
2.
Proc Natl Acad Sci U S A ; 120(17): e2218623120, 2023 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-37068248

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads efficiently by spike-mediated, direct cell-to-cell transmission. However, the underlying mechanism is poorly understood. Herein, we demonstrate that the tight junction protein occludin (OCLN) is critical to this process. SARS-CoV-2 infection alters OCLN distribution and expression and causes syncytium formation that leads to viral spread. OCLN knockdown fails to alter SARS-CoV-2 binding but significantly lowers internalization, syncytium formation, and transmission. OCLN overexpression also has no effect on virus binding but enhances virus internalization, cell-to-cell transmission, and replication. OCLN directly interacts with the SARS-CoV-2 spike, and the endosomal entry pathway is involved in OCLN-mediated cell-to-cell fusion rather than in the cell surface entry pathway. All SARS-CoV-2 strains tested (prototypic, alpha, beta, gamma, delta, kappa, and omicron) are dependent on OCLN for cell-to-cell transmission, although the extent of syncytium formation differs between strains. We conclude that SARS-CoV-2 utilizes OCLN as an internalization factor for cell-to-cell transmission.


Assuntos
COVID-19 , Ocludina , Proteínas de Junções Íntimas , Internalização do Vírus , Humanos , Ocludina/genética , Ocludina/metabolismo , SARS-CoV-2/metabolismo , Glicoproteína da Espícula de Coronavírus/genética
3.
PLoS Pathog ; 19(3): e1011201, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36888569

RESUMO

Autophagy plays an important role in the infectious processes of diverse pathogens. For instance, cellular autophagy could be harnessed by viruses to facilitate replication. However, it is still uncertain about the interplay of autophagy and swine acute diarrhea syndrome coronavirus (SADS-CoV) in cells. In this study, we reported that SADS-CoV infection could induce a complete autophagy process both in vitro and in vivo, and an inhibition of autophagy significantly decreased SADS-CoV production, thus suggesting that autophagy facilitated the replication of SADS-CoV. We found that ER stress and its downstream IRE1 pathway were indispensable in the processes of SADS-CoV-induced autophagy. We also demonstrated that IRE1-JNK-Beclin 1 signaling pathway, neither PERK-EIF2S1 nor ATF6 pathways, was essential during SADS-CoV-induced autophagy. Importantly, our work provided the first evidence that expression of SADS-CoV PLP2-TM protein induced autophagy through the IRE1-JNK-Beclin 1 signaling pathway. Furthermore, the interaction of viral PLP2-TMF451-L490 domain and substrate-binding domain of GRP78 was identified to activate the IRE1-JNK-Beclin 1 signaling pathway, and thus resulting in autophagy, and in turn, enhancing SADS-CoV replication. Collectively, these results not only showed that autophagy promoted SADS-CoV replication in cultured cells, but also revealed that the molecular mechanism underlying SADS-CoV-induced autophagy in cells.


Assuntos
Chaperona BiP do Retículo Endoplasmático , Papaína , Papaína/metabolismo , Proteína Beclina-1 , Peptídeo Hidrolases/metabolismo , Autofagia , Transdução de Sinais , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo
4.
Methods ; 223: 65-74, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38280472

RESUMO

MicroRNAs (miRNAs) are vital in regulating gene expression through binding to specific target sites on messenger RNAs (mRNAs), a process closely tied to cancer pathogenesis. Identifying miRNA functional targets is essential but challenging, due to incomplete genome annotation and an emphasis on known miRNA-mRNA interactions, restricting predictions of unknown ones. To address those challenges, we have developed a deep learning model based on miRNA functional target identification, named miTDS, to investigate miRNA-mRNA interactions. miTDS first employs a scoring mechanism to eliminate unstable sequence pairs and then utilizes a dynamic word embedding model based on the transformer architecture, enabling a comprehensive analysis of miRNA-mRNA interaction sites by harnessing the global contextual associations of each nucleotide. On this basis, miTDS fuses extended seed alignment representations learned in the multi-scale attention mechanism module with dynamic semantic representations extracted in the RNA-based dual-path module, which can further elucidate and predict miRNA and mRNA functions and interactions. To validate the effectiveness of miTDS, we conducted a thorough comparison with state-of-the-art miRNA-mRNA functional target prediction methods. The evaluation, performed on a dataset cross-referenced with entries from MirTarbase and Diana-TarBase, revealed that miTDS surpasses current methods in accurately predicting functional targets. In addition, our model exhibited proficiency in identifying A-to-I RNA editing sites, which represents an aberrant interaction that yields valuable insights into the suppression of cancerous processes.


Assuntos
Aprendizado Profundo , MicroRNAs , MicroRNAs/genética , RNA Mensageiro/genética , Nucleotídeos , Edição de RNA
5.
Nat Methods ; 18(1): 51-59, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33288960

RESUMO

Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR-RfxCas13d can effectively discriminate circRNAs from mRNAs by using guide RNAs targeting sequences spanning back-splicing junction (BSJ) sites featured in RNA circles. Using a lentiviral library that targets sequences across BSJ sites of highly expressed human circRNAs, we show that a group of circRNAs are important for cell growth mostly in a cell-type-specific manner and that a common oncogenic circRNA, circFAM120A, promotes cell proliferation by preventing the mRNA for family with sequence similarity 120A (FAM120A) from binding the translation inhibitor IGF2BP2. Further application of RfxCas13d-BSJ-gRNA screening has uncovered circMan1a2, which has regulatory potential in mouse embryo preimplantation development. Together, these results establish CRISPR-RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.


Assuntos
Sistemas CRISPR-Cas , Neoplasias do Colo/patologia , Regulação Neoplásica da Expressão Gênica , RNA Circular/genética , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/metabolismo , Processamento Alternativo , Animais , Apoptose , Proliferação de Células , Neoplasias do Colo/genética , Neoplasias do Colo/metabolismo , Humanos , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , RNA Mensageiro/genética , Proteínas de Ligação a RNA/genética , Células Tumorais Cultivadas , Ensaios Antitumorais Modelo de Xenoenxerto
6.
J Virol ; 97(4): e0012823, 2023 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-36975782

RESUMO

Coronavirus membrane protein is a major component of the viral envelope and plays a central role in the viral life cycle. Studies of the coronavirus membrane protein (M) have mainly focused on its role in viral assembly and budding, but whether M protein is involved in the initial stage of viral replication remains unclear. In this study, eight proteins in transmissible gastroenteritis virus (TGEV)-infected cells coimmunoprecipitated with monoclonal antibodies (MAb) against M protein in PK-15 cells, heat shock cognate protein 70 (HSC70), and clathrin were identified by matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry (MALDI-TOF MS). Further studies demonstrated that HSC70 and TGEV M colocalized on the cell surface in early stages of TGEV infection; specifically, HSC70 bound M protein through its substrate-binding domain (SBD) and preincubation of TGEV with anti-M serum to block the interaction of M and HSC70 reduced the internalization of TGEV, thus demonstrating that the M-HSC70 interaction mediates the internalization of TGEV. Remarkably, the process of internalization was dependent on clathrin-mediated endocytosis (CME) in PK-15 cells. Furthermore, inhibition of the ATPase activity of HSC70 reduced the efficiency of CME. Collectively, our results indicated that HSC70 is a newly identified host factor involved in TGEV infection. Taken together, our findings clearly illustrate a novel role for TGEV M protein in the viral life cycle and present a unique strategy used by HSC70 to promote TGEV infection in which the interaction with M protein directs viral internalization. These studies provide new insights into the life cycle of coronaviruses. IMPORTANCE TGEV is the causative agent of porcine diarrhea, a viral disease that economically affects the pig industry in many countries. However, the molecular mechanisms underlying viral replication remain incompletely understood. Here, we provide evidence of a previously undescribed role of M protein in viral replication during early stages. We also identified HSC70 as a new host factor affecting TGEV infection. We demonstrate that the interaction between M and HSC70 directs TGEV internalization in a manner dependent on CME, thus revealing a novel mechanism for TGEV replication. We believe that this study may change our understanding of the first steps of infection of cells with coronavirus. This study should facilitate the development of anti-TGEV therapeutic agents by targeting the host factors and may provide a new strategy for the control of porcine diarrhea.


Assuntos
Clatrina , Proteínas M de Coronavírus , Endocitose , Proteínas de Choque Térmico HSC70 , Vírus da Gastroenterite Transmissível , Internalização do Vírus , Vírus da Gastroenterite Transmissível/fisiologia , Clatrina/metabolismo , Proteínas M de Coronavírus/metabolismo , Linhagem Celular , Humanos , Animais , Replicação Viral
7.
Opt Express ; 32(2): 2619-2630, 2024 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-38297786

RESUMO

Auto-focusing is an essential task for lens-free holographic microscopy, which has developed many methods for high precision or fast refocusing. In this work, we derive the relationship among intensity derivation, the derivative of spectral distribution, as well as the distribution of the object, and propose a new auto-focusing criterion, the Robert critical function with axial difference (RCAD), to enhance the accuracy of distance estimation for lens-free imaging with the ultra-broadband light source. This method consists of three steps: image acquisition and preprocessing, axial-difference calculation, and distance estimation with sharpness analysis. The simulations and experiments demonstrate that the accuracy of this metric on auto-focusing with the ultra-broadband spectrum can effectively assist in determining the off-focus distance. The experiments are conducted in an ultra-broad-spectrum on-chip system, where the samples including the resolution target and the cross-section of the Tilia stem are employed to maximize the applicability of this method. We believe that the RCAD criterion is expected to be a useful auxiliary tool for lens-free on-chip microscopes with ultra-broadband spectrum illumination.

8.
Nanotechnology ; 35(36)2024 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-38861963

RESUMO

Optimizing the width of depletion region is a key consideration in designing high performance photovoltaic photodetectors, as the electron-hole pairs generated outside the depletion region cannot be effectively separated, leading to a negligible contribution to the overall photocurrent. However, currently reported photovoltaic mid-infrared photodetectors based on two-dimensional heterostructures usually adopt a single pn junction configuration, where the depletion region width is not maximally optimized. Here, we demonstrate the construction of a high performance broadband mid-infrared photodetector based on a MoS2/b-AsP/MoS2npn van der Waals heterostructure. The npn heterojunction can be equivalently represented as two parallel-stacked pn junctions, effectively increasing the thickness of the depletion region. Consequently, the npn device shows a high detectivity of 1.3 × 1010cmHz1/2W-1at the mid-infrared wavelength, which is significantly improved compared with its single pn junction counterpart. Moreover, it exhibits a fast response speed of 12 µs, and a broadband detection capability ranging from visible to mid-infrared wavelengths.

9.
BMC Pediatr ; 24(1): 449, 2024 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-38997661

RESUMO

BACKGROUND: Language delay affects near- and long-term social communication and learning in toddlers, and, an increasing number of experts pay attention to it. The development of prosody discrimination is one of the earliest stages of language development in which key skills for later stages are mastered. Therefore, analyzing the relationship between brain discrimination of speech prosody and language abilities may provide an objective basis for the diagnosis and intervention of language delay. METHODS: In this study, all cases(n = 241) were enrolled from a tertiary women's hospital, from 2021 to 2022. We used functional near-infrared spectroscopy (fNIRS) to assess children's neural prosody discrimination abilities, and a Chinese communicative development inventory (CCDI) were used to evaluate their language abilities. RESULTS: Ninety-eight full-term and 108 preterm toddlers were included in the final analysis in phase I and II studies, respectively. The total CCDI screening abnormality rate was 9.2% for full-term and 34.3% for preterm toddlers. Full-term toddlers showed prosody discrimination ability in all channels except channel 5, while preterm toddlers showed prosody discrimination ability in channel 6 only. Multifactorial logistic regression analyses showed that prosody discrimination of the right angular gyrus (channel 3) had a statistically significant effect on language delay (odd ratio = 0.301, P < 0.05) in full-term toddlers. Random forest (RF) regression model presented that prosody discrimination reflected by channels and brain regions based on fNIRS data was an important parameter for predicting language delay in preterm toddlers, among which the prosody discrimination reflected by the right angular gyrus (channel 4) was the most important parameter. The area under the model Receiver operating characteristic (ROC) curve was 0.687. CONCLUSIONS: Neural prosody discrimination ability is positively associated with language development, assessment of brain prosody discrimination abilities through fNIRS could be used as an objective indicator for early identification of children with language delay in the future clinical application.


Assuntos
Transtornos do Desenvolvimento da Linguagem , Desenvolvimento da Linguagem , Espectroscopia de Luz Próxima ao Infravermelho , Humanos , Feminino , Masculino , Pré-Escolar , Transtornos do Desenvolvimento da Linguagem/diagnóstico , Lactente , Percepção da Fala/fisiologia , Encéfalo/fisiologia , Encéfalo/diagnóstico por imagem
10.
Chin J Cancer Res ; 36(2): 124-137, 2024 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-38751436

RESUMO

Objective: Primary resistance to trastuzumab frequently occurs in human epidermal growth factor receptor 2 (HER2)-positive (+) breast cancer patients and remains a clinical challenge. Pyrotinib is a novel tyrosine kinase inhibitor that has shown efficacy in the treatment of HER2+ breast cancer. However, the efficacy of pyrotinib in HER2+ breast cancer with primary trastuzumab resistance is unknown. Methods: HER2+ breast cancer cells sensitive or primarily resistant to trastuzumab were treated with trastuzumab, pyrotinib, or the combination. Cell proliferation, migration, invasion, and HER2 downstream signal pathways were analyzed. The effects of pyrotinib plus trastuzumab and pertuzumab plus trastuzumab were compared in breast cancer cells in vitro and a xenograft mouse model with primary resistance to trastuzumab. Results: Pyrotinib had a therapeutic effect on trastuzumab-sensitive HER2+ breast cancer cells by inhibiting phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) and rat sarcoma virus (RAS)/rapidly accelerated fibrosarcoma (RAF)/mitogen-activated protein kinase (MAPK)/extracellular-signal regulated kinase (ERK) pathways. In primary trastuzumab-resistant cells, pyrotinib inhibited cell growth, migration, invasion, and HER2 downstream pathways, whereas trastuzumab had no effects. The combination with trastuzumab did not show increased effects compared with pyrotinib alone. Compared with pertuzumab plus trastuzumab, pyrotinib plus trastuzumab was more effective in inhibiting cell proliferation and HER2 downstream pathways in breast cancer cells and tumor growth in a trastuzumab-resistant HER2+ breast cancer xenograft model. Conclusions: Pyrotinib-containing treatments exhibited anti-cancer effects in HER2+ breast cancer cells sensitive and with primary resistance to trastuzumab. Notably, pyrotinib plus trastuzumab was more effective than trastuzumab plus pertuzumab in inhibiting tumor growth and HER2 downstream pathways in HER2+ breast cancer with primary resistance to trastuzumab. These findings support clinical testing of the therapeutic efficacy of dual anti-HER2 treatment combining an intracellular small molecule with an extracellular antibody.

11.
J Am Chem Soc ; 145(42): 23176-23187, 2023 10 25.
Artigo em Inglês | MEDLINE | ID: mdl-37822292

RESUMO

Polymeric nanoparticles (NPs) have been extensively designed for theranostic agent delivery. Previous methods for tracking their biological behavior and assessing theranostic efficacy heavily rely on fluorescence or isotope labeling. However, these labeling techniques may alter the physicochemical properties of the labeled NPs, leading to inaccurate biodistribution information. Therefore, it is highly desirable to develop label-free techniques for accurately assessing the biological fate of polymeric NPs. Here, we create discrete oligourethane amphiphiles (DOAs) with methoxy (OMe), hydroxyl (OH), and maleimide (MI) moieties at the dendritic oligo(ethylene glycol) (dOEG) ends. We obtained four types of digital nanorods (NRs) with distinct surface functional groups through self-assembly of a single DOA (OMe and OH NRs) or coassembly of two DOAs (OMe-MI and OH-MI NRs). These unique NRs can be directly quantified in a label-free manner by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Specifically, OMe-MI NRs exhibited the best blood circulation, and OH-MI showed the highest area under the curve (AUC) value after intravenous injection. Biodistribution studies demonstrated that MI-containing NRs generally had lower accumulation in the liver and spleen compared to that of MI-free NRs, except for the comparison between OMe and OMe-MI NRs in the liver. Proteomics studies unveiled the formation of distinct protein coronas that may greatly affect the biological behavior of NRs. This study not only provides a label-free technique for quantifying the pharmacokinetics and biodistribution of polymeric NRs but also highlights the significant impact of surface functional groups on the biological fate of polymeric NPs.


Assuntos
Nanopartículas , Nanotubos , Distribuição Tecidual , Nanotubos/química , Nanopartículas/química , Espectrometria de Massas
12.
Biochem Biophys Res Commun ; 683: 149110, 2023 11 26.
Artigo em Inglês | MEDLINE | ID: mdl-37866110

RESUMO

Sperm is the key media between the father's aberrant exposure and the offspring's phenotype. Whether paternal hypertension affects offspring through sperm epigenetics remains to be explored. To investigate the underlying mechanisms, we constructed a hypertensive mice model induced by drinking l-NAME and found that spermatocytes and spermatids in the testis were increased significantly after l-NAME treatment. The sequencing of sperm showed that tsRNA profiles changed with 315 tsRNAs (195 up-regulated and 120 down-regulated) altered. Meanwhile, KEGG pathway analysis showed that the target genes of these altered tsRNAs were involved in influencing some important signaling pathways, such as the cAMP signaling path, the mTOR signaling path, the Hippo signaling path, and the Ras signaling path. Bioinformatics of tsRNA-miRNA-mRNA pathway interactions revealed several ceRNA mechanisms, such as tsRNA-00051, the ceRNA of miR-128-1-5p, co-targeting Agap1. This study provides evidence for enriching and further understanding the pathophysiology and paternal epigenetic mechanisms of testicular reproduction, as well as contributing to a rethinking of the transgenerational reprogramming mechanisms of paternal exposure in hypertension.


Assuntos
Sêmen , Espermatozoides , Masculino , Camundongos , Animais , NG-Nitroarginina Metil Éster , Espermatozoides/metabolismo , Espermatogênese/genética , Testículo/metabolismo
13.
Curr Opin Oncol ; 35(2): 132-144, 2023 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-36721897

RESUMO

PURPOSE OF REVIEW: Because the high risk of death and poor prognosis of patients with refractory thyroid cancer (TC), studies related to tyrosine kinase inhibitors (TKIs) in treating different types of refractory TC have gradually attracted attention. Thus, we conducted a meta-analysis of published randomized controlled trials and single-arm trials to evaluate tyrosine kinase inhibitors' efficacy and safety profile treatment in TC patients. RECENT FINDINGS: The studies of 29 in 287 met the criteria, 9 were randomized controlled trials and 20 were single-arm trials, involving 11 TKIs (Apatinib, Anlotinib, Cabozantinib, Imatinib, Lenvatinib, Motesanib, Pazopanib, Sorafenib, Sunitinib, Vandetanib, Vemurafenib). Treatment with TKIs significantly improved progression-free survival [hazard ratio [HR] 0.34 (95% confidence interval [CI]: 0.24, 0.48), P < 0.00001] and overall survival [OS] [HR 0.76, (95% CI: 0.64, 0.91), P = 0.003] in randomized controlled trials, but adverse events (AEs) were higher than those in the control group (P < 0.00001). The result of the objective response rate (ORR) in single-arm trials was statistically significant [odds ratio [OR] 0.49 (95% CI: 0.32, 0.75), P = 0.001]. SUMMARY: TKIs significantly prolonged progression-free survival and OS or improved ORR in patients with different types of TC (P < 0.01). Our recommendation is to select appropriate TKIs to treat different types of TC patients, and to prevent and manage drug-related AEs after using TKIs.


Assuntos
Neoplasias da Glândula Tireoide , Humanos , Neoplasias da Glândula Tireoide/tratamento farmacológico , Sorafenibe , Mesilato de Imatinib , Intervalo Livre de Progressão
14.
Small ; 19(15): e2206404, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36610052

RESUMO

Atomic understanding of a chemical reaction can realize the programmable design and synthesis of desired products with specific compositions and structures. Through directly monitoring the phase transition and tracking the dynamic evolution of atoms in a chemical reaction, in situ transmission electron microscopy (TEM) techniques offer the feasibility of revealing the reaction kinetics at the atomic level. Nevertheless, such investigation is quite challenging, especially for reactions involving multi-phase and complex interfaces, such as the widely adopted carbothermal reduction (CTR) reactions. Herein, in-situ TEM is applied to monitor the CTR of Co3 O4 nanocubes on reduced graphene oxide nanosheets. Together with the first-principle calculation, the migration route of Co atoms during the phase transition of the CTR reaction is revealed. Meanwhile, the interfacial edge-dislocations/stress-gradient is identified as a result of the atomistic diffusion, which in turn can affect the morphology variation of the reactants. Accordingly, controllable synthesis of Co-based nanostructure with a desirable phase and structure has been achieved. This work not only provides atomic kinetic insight into CTR reactions but also offers a novel strategy for the design and synthesis of functional nanostructures for emerging energy technologies.

15.
Small ; 19(52): e2304996, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37635097

RESUMO

Both ternary copolymerization and ternary blending are effective methods to fine-tune polymer structure and manipulate thin-film morphology to improve device performance. In this work, three D-A-A-A (D: donor, A: acceptor) terpolymer donors (FY1, FY2, and FY3) are synthesized by introducing BDD (1,3-bis(2-ethylhexyl)-5,7-di(thiophen-2-yl)benzo[1,2-c:4,5-c']dithiophene-4,8-dione) units into the D-A alternating copolymer PM6 backbone. Owing to the promoted conjugated planarity and excellent absorption of BDD, the obtained terpolymers display an extended absorption range and enhanced π-π stacking orientation, which is a promising third component in ternary device. As a result, the optimal FY1:PM6:BTP-eC9-based ternary device afforded an impressive power conversion efficiency (PCE) as high as 18.52%, owing to the efficient charge transport, negligible energy loss, and suitable domain size. The result provides an efficient method to obtain high-performance polymer solar cells by using analogous polymer donors in ternary device.

16.
Brief Bioinform ; 22(3)2021 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-34020547

RESUMO

Cancer is a highly heterogeneous disease caused by dysregulation in different cell types and tissues. However, different cancers may share common mechanisms. It is critical to identify decisive genes involved in the development and progression of cancer, and joint analysis of multiple cancers may help to discover overlapping mechanisms among different cancers. In this study, we proposed a fusion feature selection framework attributed to ensemble method named Fisher score and Gradient Boosting Decision Tree (FS-GBDT) to select robust and decisive feature genes in high-dimensional gene expression datasets. Joint analysis of 11 human cancers types was conducted to explore the key feature genes subset of cancer. To verify the efficacy of FS-GBDT, we compared it with four other common feature selection algorithms by Support Vector Machine (SVM) classifier. The algorithm achieved highest indicators, outperforms other four methods. In addition, we performed gene ontology analysis and literature validation of the key gene subset, and this subset were classified into several functional modules. Functional modules can be used as markers of disease to replace single gene which is difficult to be found repeatedly in applications of gene chip, and to study the core mechanisms of cancer.


Assuntos
Algoritmos , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , Neoplasias/genética , Máquina de Vetores de Suporte , Análise por Conglomerados , Árvores de Decisões , Perfilação da Expressão Gênica/classificação , Ontologia Genética , Humanos , Neoplasias/patologia , Reprodutibilidade dos Testes
17.
Analyst ; 148(10): 2308-2315, 2023 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-37083189

RESUMO

The simple and efficient detection of nucleic acids is important in the diagnosis of tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis). However, base mismatch will lead to false positive and false negative nucleic acid test, which seriously interferes with the accuracy of the final results. Herein, we demonstrated a CRISPR/Cas-9-mediated fluorescent strategy utilizing fluorescence resonance energy transfer (FRET) for the detection of bacteria. High-variable region of M. tuberculosis 16S rDNA fragment was used as the target, and CRISPR/Cas9 was used as the recognition element. The binding of the P1 probe of upconversion nanoparticles (UCNPs) @SiO2-P1 and the P2 probe of Fe3O4@Au-P2 caused the fluorescence quenching of UCNPs. In the presence of the target, the P2 probe hybridized with the target to form double-stranded DNA (dsDNA), which was recognized and cleaved by CRISPR/Cas9, resulting in the breaking of the P1-P2 duplex linkage. UCNPs moved away from Fe3O4@Au under a magnetic field, and the fluorescence signal was restored; bacteria were detected under the excitation of a 980 nm laser source. Using the CRISPR/Cas-9-mediated system, the sensor could distinguish single-base mismatches in 10 bases from the protospacer adjacent motif (PAM) region. The limit of detection (LOD) was 20 CFU mL-1 and the detection time was 2 h. It developed a new way of accurate nucleic acid detection for disease diagnosis.


Assuntos
Mycobacterium tuberculosis , Tuberculose , Humanos , DNA Ribossômico , Transferência Ressonante de Energia de Fluorescência/métodos , Mycobacterium tuberculosis/genética , Sistemas CRISPR-Cas/genética , Dióxido de Silício , Tuberculose/diagnóstico
18.
Appl Opt ; 62(29): 7678-7688, 2023 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-37855475

RESUMO

Ghost imaging technology has a great application potential in optical security because of its non-local characteristics. In this paper, on the basis of computational ghost imaging, an optical authentication scheme is proposed that utilizes the correspondence imaging technique for the preliminary reconstruction of the object image, and then authenticates the image by a nonlinear correlation algorithm. Different from the previous optical authentication schemes that usually adopted random selection of measurements, this authentication method consciously selects the bucket detector measurement values with large fluctuation and can achieve authentication using ultra-low data volumes less than 1% of the Nyquist limit. In brief, this scheme is easy to implement and has a simpler algorithm and higher stability, which is a tremendous advantage in practical optical authentication systems. The simulation and physical experimental results demonstrate the feasibility of the scheme.

19.
Curr Microbiol ; 80(8): 259, 2023 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-37358649

RESUMO

Trichoderma longibrachiatum SMF2 is an important biocontrol strain isolated by our group that can promote plant growth and induce plant disease resistance. To further study its biocontrol mechanism, the effector proteins secreted by T. longibrachiatum SMF2 were analyzed through bioinformatics and transcriptome sequencing. Overall, 478 secretory proteins produced by T. longibrachiatum were identified, of which 272 were upregulated after treatment with plants. Functional annotation showed that 36 secretory proteins were homologous with different groups of effectors from pathogenic microorganisms. Moreover, the quantitative PCR results of six putative effector proteins were consistent with those of transcriptome sequencing. Taken together, these findings indicate that the secretory proteins secreted by T. longibrachiatum SMF2 may act as effectors to facilitate its own growth and colonization or to induce plant immunity response.


Assuntos
Hypocreales , Trichoderma , Trichoderma/genética , Transcriptoma , Resistência à Doença
20.
BMC Pediatr ; 23(1): 96, 2023 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-36859178

RESUMO

OBJECTIVE: The purpose of this study was to provide evidence for early life care by meta-analyzing the relationship between infection during pregnancy and up to 2 years of age and the risk of subsequent allergic rhinitis (AR). METHODS: Published studies up to April 2022 were systematically searched in PubMed, Embase, Web of Science, Cochrane Library, SinoMed, CNKI, Wanfang Database, and VIP. Literature screening, including quality assessment, was performed, and the effect values (OR, HR, RR) and 95% confidence intervals (95% CI) of infection during pregnancy and up to 2 years of age and allergic rhinitis were extracted from each qualified study. RESULTS: In total, 5 studies with a sample size of 82,256 reported the relationship between infection during pregnancy and offspring AR. Meta-analysis showed that maternal infection during pregnancy was associated with an increased risk of childhood AR in offspring (OR = 1.34, 95% CI: 1.08-1.67). Altogether, 13 studies with a sample size of 78,426 reported evidence of an association between infection within 2 years of age and subsequent AR in children. A pooled meta-analysis of all studies showed that early infection within 2 years of age was closely associated with childhood AR (OR = 1.25, 95% CI: 1.12-1.40), especially upper respiratory tract infection (OR = 1.32, 95% CI: 1.06-1.65) and gastrointestinal infections (OR = 1.37, 95% CI: 1.01-1.86), but ear infection showed similar results in the cohort study (OR = 1.13, 95% CI: 1.04-1.22). CONCLUSION: Current evidence suggests that infection during pregnancy, early upper respiratory infection, gastrointestinal infections and ear infection within 2 years of age would increase the risk of AR in children. Therefore, the prevention of infection during pregnancy and in infancy and young children needs to be emphasized.


Assuntos
Infecções Respiratórias , Rinite Alérgica , Criança , Feminino , Gravidez , Humanos , Pré-Escolar , Estudos de Coortes , Bases de Dados Factuais , Tamanho da Amostra
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