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1.
Fish Shellfish Immunol ; 149: 109568, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38636741

RESUMO

Pompano fishes have been widely farmed worldwide. As a representative commercial marine species of the Carangidae family, the golden pompano (Trachinotus blochii) has gained significant popularity in China and worldwide. However, because of rapid growth and high-density aquaculture, the golden pompano has become seriously threatened by various diseases. Cell lines are the most cost-effective resource for in vitro studies and are widely used for physiological and pathological research owing to their accessibility and convenience. In this study, we established a novel immortal cell line, GPF (Golden pompano fin cells). GPF has been passaged over 69 generations for 10 months. The morphology, adhesion and extension processes of GPF were evaluated using light and electron microscopy. GPF cells were passaged every 3 days with L-15 containing 20 % fetal bovine serum (FBS) at 1:3. The optimum conditions for GPF growth were 28 °C and a 20 % FBS concentration. DNA sequencing of 18S rRNA and mitochondrial 16S rRNA confirmed that GPF was derived from the golden pompano. Chromosomal analysis revealed that the number pattern of GPF was 48 chromosomes. Transfection experiments demonstrated that GPF could be utilized to express foreign genes. Furthermore, heavy metals (Cd, Cu, and Fe) exhibited dose-dependent cytotoxicity against GPF. After polyinosinic-polycytidylic acid (poly I:C) treatment, transcription of the retinoic acid-inducible gene I-like receptor (RLR) pathway genes, including mda5, mita, tbk1, irf3, and irf7 increased, inducing the expression of interferon (IFN) and anti-viral proteins in GPF cells. In addition, lipopolysaccharide (LPS) stimulation up-regulated the expression of inflammation-related factors, including myd88, irak1, nfκb, il1ß, il6, and cxcl10 expression. To the best of our knowledge, this is the first study on the immune response signaling pathways of the golden pompano using an established fin cell line. In this study, we describe a preliminary investigation of the GPF cell line immune response to poly I:C and LPS, and provide a more rapid and efficient experimental material for research on marine fish immunology.


Assuntos
Doenças dos Peixes , Animais , Linhagem Celular , Doenças dos Peixes/imunologia , Nadadeiras de Animais/imunologia , Poli I-C/farmacologia , Imunidade Inata , Perciformes/imunologia , Perciformes/genética , Peixes/imunologia
2.
Sci Rep ; 14(1): 6707, 2024 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38509164

RESUMO

In order to solve the problems of slow detection speed, large number of parameters and large computational volume of deep learning based gangue target detection method, we propose an improved algorithm for gangue target detection based on Yolov5s. First, the lightweight network EfficientVIT is used as the backbone network to increase the target detection speed. Second, C3_Faster replaces the C3 part in the HEAD module, which reduces the model complexity. once again, the 20 × 20 feature map branch in the Neck region is deleted, which reduces the model complexity; thirdly, the CIOU loss function is replaced by the Mpdiou loss function. The introduction of the SE attention mechanism makes the model pay more attention to critical features to improve detection performance. Experimental results show that the improved model size of the coal gang detection algorithm reduces the compression by 77.8%, the number of parameters by 78.3% the computational cost is reduced by 77.8% and the number of frames is reduced by 30.6%, which can be used as a reference for intelligent coal gangue classification.

3.
J Hazard Mater ; 466: 133636, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38309166

RESUMO

The toxic Cr(VI) from industrial wastewater pose serious threat to the human beings and eco-systems. To reduce the operation processes and enhance the removal efficiency of Cr(VI), targeted design of functionalized material is critical in practical applications. Herein, we developed a one-step strategy for simultaneous Cr(VI) reduction and total Cr capture by a novel phytate modified zero-valent iron (PA-ZVI). The reaction kinetics of Cr(VI) removal by PA-ZVI (0.2225 min-1) was 53 times higher compared to ZVI (0.0042 min-1). The Fe(0) content on the surface of PA-ZVI increased from 2.2% to 15.6% compared to ZVI. Meanwhile, Cr(VI) was liable to adsorb on the surface of PA-ZVI due to its lower adsorption energy compared with the original ZVI (-2.09 eV vs -0.85 eV). The incorporation of the phytate ligand promoted electron transfer from iron core to Cr(VI), leading to the rapid in-situ reduction of Cr(VI) adsorbed on the surface of PA-ZVI to Cr(III). PA-ZVI exhibited a satisfactory performance for Cr(VI) removal at a broad pH range (3-11) and in the presence of coexisting ions and humic acid. Moreover, the reactor with the addition of PA-ZVI achieved more than 90% Cr(VI) removal within 72 h in continuous flow experiments. The feasibility of PA-ZVI for the removal of Cr(VI) is also validated in authentic wastewater. This work provides novel ZVI materials that can effectively address decontamination challenges from Cr(VI) pollution.

4.
Cell Death Discov ; 10(1): 65, 2024 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-38320998

RESUMO

Matrix metalloproteinase-1 (MMP1) has an aberrant expression relevant to various behaviors of cancers. As dominant components of the tumor stroma, fibroblasts constitute an important source of Matrix metalloproteinase (MMPs) including mainly MMP1. The impacts of MMP1 derived from fibroblasts in tumor microenvironment, however, is not well defined. In this study, we demonstrated a part of crosstalk between fibroblasts and cancer cells that enhanced the invasiveness of cancer cells, IL8-induced activation of STAT3 signaling pathway as a key promoter to elevated MMP1 level in fibroblasts that supports the migration and invasion of head and neck squamous cell carcinoma (HNSCC) cells by extracellular matrix degradation. Importantly, once exposed to the inhibitor of STAT3 phosphorylation (TPCA-1), the enhanced induction of HNSCC cells invasion triggered by fibroblasts was significantly impaired.

5.
J Pharm Biomed Anal ; 239: 115901, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38091819

RESUMO

Toad venom is a traditional Chinese medicine (TCM) with various sources and wide-ranging preparations. Previous quality assessment studies primarily concentrated on small molecular compounds like toad dienolactones and indole alkaloids, studies on macromolecular peptides and proteins as quality assessment standards remained at the qualitative stage, lacking the development of practical and convenient quantitative methods. In this study, to explore the peptides from toad venom as a new method for identifying and evaluating its source, a complete scan of the water extract of peptides from toad venom was conducted using HPLC-Quadrupole Time-of-Flight Mass Spectrometer (Q-TOF) 5600, leading to the identification of peptides based on mass spectrometry data. Subsequently, HPLC- Quadrupole-Linear Ion Trap Mass Spectrometer (Q-Trap) 5500 employing Multiple Reaction Monitoring (MRM) mode was utilized to quantitatively analyze peptides in various sources of toad venom, followed by Partial Least Squares Discriminant Analysis (PLS-DA) to further analyze the data and evaluate the effectiveness. This study highlights the importance of exploring macromolecular substance in natural products research and provides a foundation for further studies on toad venom.


Assuntos
Venenos de Anfíbios , Espectrometria de Massa com Cromatografia Líquida , Cromatografia Líquida , Espectrometria de Massas em Tandem/métodos , Venenos de Anfíbios/química , Cromatografia Líquida de Alta Pressão/métodos , Peptídeos
6.
PLoS One ; 18(10): e0292283, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37788250

RESUMO

Innovation has emerged as a crucial factor in the sustenance and growth of enterprises. Nonetheless, small and medium-sized enterprises (SMEs) confront numerous challenges in their pursuit of innovation, owing to constraints in capital, expertise, and knowledge resources. Drawing on the resource-based theory and the input-process-output (IPO) model, this study devises a mechanism model to assess the impact of knowledge heterogeneity and innovation performance on small and medium-sized manufacturing enterprises in Guizhou Province, China. The objective is to offer recommendations for the advancement and innovation of enterprises with relative knowledge resource deficiencies. A total of 324 valid questionnaires were gathered, and the acquired data were analyzed employing SPSS 23.0 and Amos 26.0. The findings reveal that knowledge heterogeneity exerts a significantly positive influence on innovation performance. Task conflict and relationship conflict serve as partial mediators in the effects of knowledge heterogeneity on innovation performance. By capitalizing on the heterogeneity of internal and external knowledge, enterprises can effectively enhance their innovation outcomes. Furthermore, the study demonstrates that knowledge sharing possesses a moderating effect on the impact of knowledge heterogeneity on task conflict, relationship conflict, and innovation performance. In a conducive sharing environment, the ultimate effect of knowledge heterogeneity on innovation is subject to alteration.


Assuntos
Comércio , Conhecimento , China , Organizações
7.
Fish Shellfish Immunol ; 143: 109163, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37838211

RESUMO

The golden pompano (Trachinotus blochii), a pivotal commercial marine species in China, has gained significant popularity worldwide. However, accompanied with rapid growth and high density aquaculture, golden pompano has been seriously threatened by Nervous necrosis virus (NNV), while its molecular biology research regarding the innate immune system remains unexplored, which is crucial for understanding the activation of interferon (IFN) production and antiviral responses. In this study, we aimed to identify the characterization and function of golden pompano TANK-binding kinase 1 (gpTBK1), thereby providing evidence of the conservation of this classical factor in the RLR pathway among marine fish. Initially, we found the expression of gpTBK1 upregulation in diseased golden pompano with NNV infection and we successfully cloned the full-length open reading frame (ORF) of gpTBK1, consisting of 2172 nucleotides encoding 723 amino acids, from the head kidney. Subsequent analysis of the amino acid sequence revealed homology between gpTBK1 and other fish TBK1 proteins, with conserved N-terminal Serine/Threonine protein kinases catalytic domain (S_TKc) and C-terminal coiled coil domain (CCD). Moreover, the expression pattern showed that gpTBK1 exhibited ubiquitous expression across all evaluated tissues. Furthermore, functional identification experiments indicated that gpTBK1 activated interferon promoters' activity in golden pompano and induced the expression of downstream IFN-stimulated genes (ISGs). Notably, gpTBK1 was found to co-localize and interact with gpIRF3 in the cytoplasm. Collectively, these data provide a comprehensive analysis of the characterization and functional role of gpTBK1 in promoting interferon production. This research may facilitate the further study of the innate antiviral response, particularly the anti-NNV mechanisms, in golden pompano.


Assuntos
Peixes , Imunidade Inata , Animais , Imunidade Inata/genética , Proteínas de Peixes/química , Interferons , Antivirais
8.
Microb Genom ; 9(7)2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37402176

RESUMO

Gut microbiomes in infancy have a profound impact on health in adulthood. CRISPRs play an essential role in the interaction between bacteria and phages. However, the dynamics of CRISPRs in gut microbiomes during early life are poorly understood. In this study, using shotgun metagenomic sequencing data from 82 Swedish infants' gut microbiomes, 1882 candidate CRISPRs were identified, and their dynamics were analysed. We found large-scale turnover of CRISPRs and their spacers during the first year of life. As well as changes in relative abundance of the bacteria containing CRISPR, acquisition, loss and mutation of spacers were observed within the same CRISPR array sampled over time. Accordingly, the inferred interaction network of bacteria and phage was distinct at different times. This research underpins CRISPR dynamics and their potential role in the interaction between bacteria and phage in early life.


Assuntos
Bacteriófagos , Humanos , Bacteriófagos/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Bactérias/genética , Metagenoma
9.
Nucleic Acids Res ; 51(W1): W93-W107, 2023 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-37216595

RESUMO

The CRISPR-Cas system is a highly adaptive and RNA-guided immune system found in bacteria and archaea, which has applications as a genome editing tool and is a valuable system for studying the co-evolutionary dynamics of bacteriophage interactions. Here introduces CRISPRimmunity, a new web server designed for Acr prediction, identification of novel class 2 CRISPR-Cas loci, and dissection of key CRISPR-associated molecular events. CRISPRimmunity is built on a suite of CRISPR-oriented databases providing a comprehensive co-evolutionary perspective of the CRISPR-Cas and anti-CRISPR systems. The platform achieved a high prediction accuracy of 0.997 for Acr prediction when tested on a dataset of 99 experimentally validated Acrs and 676 non-Acrs, outperforming other existing prediction tools. Some of the newly identified class 2 CRISPR-Cas loci using CRISPRimmunity have been experimentally validated for cleavage activity in vitro. CRISPRimmunity offers the catalogues of pre-identified CRISPR systems to browse and query, the collected resources or databases to download, a well-designed graphical interface, a detailed tutorial, multi-faceted information, and exportable results in machine-readable formats, making it easy to use and facilitating future experimental design and further data mining. The platform is available at http://www.microbiome-bigdata.com/CRISPRimmunity. Moreover, the source code for batch analysis are published on Github (https://github.com/HIT-ImmunologyLab/CRISPRimmunity).


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Edição de Genes/métodos , Sistemas CRISPR-Cas/genética , Bactérias/genética , Archaea/genética , Computadores
10.
Chemistry ; 29(35): e202300449, 2023 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-37070968

RESUMO

Aromatic ring fusion on BODIPY core can effectively tune its electronic property, and red-shift its absorption and emission wavelength. In this work, we report that a one-pot Pd(II) catalyzed multiple C-H activation to access acenaphtho[b]-fused BODIPYs though the reaction of α,ß-unsubstituted-BODIPYs and 1,8-dibromonaphthalenes. These newly synthesized acenaphtho[b]-fused BODIPYs revealed intensified deep red absorptions (639-669 nm) and emissions (643-683 nm), with high fluorescence quantum yields (0.53-0.84) in dichloromethane. Notably, these acenaphtho[b]-fused BODIPYs exhibited well-defined self-aggregation behavior in water/THF mixture, and for instance, the absorption of 3 a was red-shifted by 53 nm to 693 nm after forming aggregates.


Assuntos
Corantes Fluorescentes , Paládio , Paládio/química , Corantes Fluorescentes/química , Compostos de Boro/química , Catálise
11.
J Clin Immunol ; 43(6): 1193-1207, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-36947335

RESUMO

The dedicator of cytokinesis 2(DOCK2) protein, an atypical guanine nucleotide exchange factor (GEFs), is a member of the DOCKA protein subfamily. DOCK2 protein deficiency is characterized by early-onset lymphopenia, recurrent infections, and lymphocyte dysfunction, which was classified as combined immune deficiency with neutrophil abnormalities as well. The only cure is hematopoietic stem cell transplantation. Here, we report two patients harboring four novel DOCK2 mutations associated with recurrent infections including live attenuated vaccine-related infections. The patient's condition was partially alleviated by symptomatic treatment or intravenous immunoglobulin. We also confirmed defects in thymic T cell output and T cell proliferation, as well as aberrant skewing of T/B cell subset TCR-Vß repertoires. In addition, we noted neutrophil defects, the weakening of actin polymerization, and BCR internalization under TCR/BCR activation. Finally, we found that the DOCK2 protein affected antibody affinity although with normal total serum immunoglobulin. The results reported herein expand the clinical phenotype, the pathogenic DOCK2 mutation database, and the immune characteristics of DOCK2-deficient patients.


Assuntos
Proteínas Ativadoras de GTPase , Síndromes de Imunodeficiência , Humanos , Vacinas Atenuadas , Proteínas Ativadoras de GTPase/genética , Reinfecção , Fatores de Troca do Nucleotídeo Guanina/genética , Síndromes de Imunodeficiência/genética , Síndromes de Imunodeficiência/terapia , Mutação , Receptores de Antígenos de Linfócitos T/genética
12.
Front Genet ; 14: 947466, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36755570

RESUMO

Decades of overconsumption of antimicrobials in the treatment and prevention of bacterial infections have resulted in the increasing emergence of drug-resistant bacteria, which poses a significant challenge to public health, driving the urgent need to find alternatives to conventional antibiotics. Bacteriophages are viruses infecting specific bacterial hosts, often destroying the infected bacterial hosts. Phages attach to and enter their potential hosts using their tail proteins, with the composition of the tail determining the range of potentially infected bacteria. To aid the exploitation of bacteriophages for therapeutic purposes, we developed the PhageTailFinder algorithm to predict tail-related proteins and identify the putative tail module in previously uncharacterized phages. The PhageTailFinder relies on a two-state hidden Markov model (HMM) to predict the probability of a given protein being tail-related. The process takes into account the natural modularity of phage tail-related proteins, rather than simply considering amino acid properties or secondary structures for each protein in isolation. The PhageTailFinder exhibited robust predictive power for phage tail proteins in novel phages due to this sequence-independent operation. The performance of the prediction model was evaluated in 13 extensively studied phages and a sample of 992 complete phages from the NCBI database. The algorithm achieved a high true-positive prediction rate (>80%) in over half (571) of the studied phages, and the ROC value was 0.877 using general models and 0.968 using corresponding morphologic models. It is notable that the median ROC value of 992 complete phages is more than 0.75 even for novel phages, indicating the high accuracy and specificity of the PhageTailFinder. When applied to a dataset containing 189,680 viral genomes derived from 11,810 bulk metagenomic human stool samples, the ROC value was 0.895. In addition, tail protein clusters could be identified for further studies by density-based spatial clustering of applications with the noise algorithm (DBSCAN). The developed PhageTailFinder tool can be accessed either as a web server (http://www.microbiome-bigdata.com/PHISDetector/index/tools/PhageTailFinder) or as a stand-alone program on a standard desktop computer (https://github.com/HIT-ImmunologyLab/PhageTailFinder).

13.
Methods Mol Biol ; 2545: 491-512, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36720830

RESUMO

Research on the evolutionary fate of duplicated genes in recurrent polyploids is scarce due to the difficulties in disentangling the different homeologs and alleles of duplicated genes. This chapter describes the detailed procedures to identify different homeologs and alleles of duplicated genes, to analyze their molecular characteristics, and to reveal their functional divergence by gene editing with CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9). Using the gene editing approach, we efficiently constructed multiple knockout mutant lines with single or simultaneously disrupted different homeologs or alleles in a recurrent polyploid fish, demonstrating its usability for targeting and mutating multiple divergent homeologs and alleles in recurrent duplicated genomes.


Assuntos
Evolução Biológica , Traumatismos Craniocerebrais , Animais , Alelos , Edição de Genes , Poliploidia
14.
Nature ; 612(7940): 519-527, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36477534

RESUMO

In mice and humans, sleep quantity is governed by genetic factors and exhibits age-dependent variation1-3. However, the core molecular pathways and effector mechanisms that regulate sleep duration in mammals remain unclear. Here, we characterize a major signalling pathway for the transcriptional regulation of sleep in mice using adeno-associated virus-mediated somatic genetics analysis4. Chimeric knockout of LKB1 kinase-an activator of AMPK-related protein kinase SIK35-7-in adult mouse brain markedly reduces the amount and delta power-a measure of sleep depth-of non-rapid eye movement sleep (NREMS). Downstream of the LKB1-SIK3 pathway, gain or loss-of-function of the histone deacetylases HDAC4 and HDAC5 in adult brain neurons causes bidirectional changes of NREMS amount and delta power. Moreover, phosphorylation of HDAC4 and HDAC5 is associated with increased sleep need, and HDAC4 specifically regulates NREMS amount in posterior hypothalamus. Genetic and transcriptomic studies reveal that HDAC4 cooperates with CREB in both transcriptional and sleep regulation. These findings introduce the concept of signalling pathways targeting transcription modulators to regulate daily sleep amount and demonstrate the power of somatic genetics in mouse sleep research.


Assuntos
Transdução de Sinais , Duração do Sono , Transcrição Gênica , Animais , Camundongos , Regulação da Expressão Gênica , Fosforilação , Transdução de Sinais/fisiologia , Sono de Ondas Lentas/genética , Perfilação da Expressão Gênica
15.
Gene Expr Patterns ; 46: 119286, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36341978

RESUMO

Foxl2 plays conserved central function in ovarian differentiation and maintenance in several fish species. However, its expression pattern and function in fish embryogenesis are still largely unknown. In this study, we first presented a sequential expression pattern of zebrafish foxl2a and foxl2b during embryo development. They were predominantly expressed in the cranial paraxial mesoderm (CPM) and cranial venous vasculature (CVV) during somitogenesis and subsequently expressed in the pharyngeal arches after 48 h post-fertilization (hpf). Then, we compared the brain structures among zebrafish wildtype (WT) and three homozygous foxl2 mutants (foxl2a-/-, foxl2b-/- and foxl2a-/-;foxl2b-/-) and found the reduction of the fourth ventricle in the three foxl2 mutants, especially in foxl2a-/-;foxl2b-/- mutant. Finally, we detected several key transcription factors involved in the gene regulatory network of midbrain-hindbrain boundary (MHB) patterning, such as wnt1, en1b and pax2a. Their expression levels were obviously downregulated in MHB of foxl2a-/- and foxl2a-/-;foxl2b-/- mutants. Thus, we suggest that Foxl2a and Foxl2b are involved in MHB and the fourth ventricle development in zebrafish. The current study provides insights into the molecular mechanism underlying development of brain ventricular system.


Assuntos
Proteínas de Peixe-Zebra , Peixe-Zebra , Animais , Peixe-Zebra/genética , Peixe-Zebra/metabolismo , Proteínas de Peixe-Zebra/genética , Proteínas de Peixe-Zebra/metabolismo , Rombencéfalo , Mesencéfalo/metabolismo , Desenvolvimento Embrionário , Regulação da Expressão Gênica no Desenvolvimento
16.
Nat Ecol Evol ; 6(9): 1354-1366, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35817827

RESUMO

Triploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexual reproduction has been maintained for over 0.82 million years. Comparative genomics show intensive expansion and alterations of meiotic cell cycle-related genes and an oocyte-specific histone variant. Cytological assays indicate that C. gibelio produces unreduced oocytes by an alternative ameiotic pathway; however, sporadic homologous recombination and a high rate of gene conversion also exist in C. gibelio. These genomic changes might have facilitated purging deleterious mutations and maintaining genome stability in this unisexual amphitriploid fish. Overall, the current results provide novel insights into the evolutionary mechanisms of the reproductive success in unisexual polyploid vertebrates.


Assuntos
Carpas , Poliploidia , Animais , Genoma , Carpa Dourada/genética , Reprodução/genética
17.
Front Genet ; 13: 885048, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35518360

RESUMO

As an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics studies, there is a massive demand for a tool that is capable of fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes. DBSCAN-SWA runs faster than any previous tools. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) for (Multi-) FASTA sequences. Moreover, DBSCAN-SWA outperforms the existing standalone prophage prediction tools for high-throughput sequencing data based on the analysis of 19,989 contigs of 400 bacterial genomes collected from Human Microbiome Project (HMP) project. DBSCAN-SWA also provides user-friendly result visualizations including a circular prophage viewer and interactive DataTables. DBSCAN-SWA is implemented in Python3 and is available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.

18.
ACS Synth Biol ; 11(6): 2108-2120, 2022 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-35549070

RESUMO

Engineering regulatory parts for improved performance in genetic programs has played a pivotal role in the development of the synthetic biology cell programming toolbox. Here, we report the development of a novel high-throughput platform for regulatory part prototyping and analysis that leverages the advantages of engineered DNA libraries, cell-free protein synthesis (CFPS), high-throughput emulsion droplet microfluidics, standard flow sorting adapted to screen droplet reactions, and next-generation sequencing (NGS). With this integrated platform, we screened the activity of millions of genetic parts within hours, followed by NGS retrieval of the improved designs. This in vitro platform is particularly valuable for engineering regulatory parts of nonmodel organisms, where in vivo high-throughput screening methods are not readily available. The platform can be extended to multipart screening of complete genetic programs to optimize yield and stability.


Assuntos
Ensaios de Triagem em Larga Escala , Microfluídica , Biblioteca Gênica , Microfluídica/métodos , Biossíntese de Proteínas , Biologia Sintética
19.
Genomics Proteomics Bioinformatics ; 20(3): 508-523, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35272051

RESUMO

Phage-microbe interactions are appealing systems to study coevolution, and have also been increasingly emphasized due to their roles in human health, disease, and the development of novel therapeutics. Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences, defined as phage-host interaction signals (PHISs), which include clustered regularly interspaced short palindromic repeats (CRISPR) targeting, prophage, and protein-protein interaction signals. In the present study, we developed a novel tool phage-host interaction signal detector (PHISDetector) to predict phage-host interactions by detecting and integrating diverse in silico PHISs, and scoring the probability of phage-host interactions using machine learning models based on PHIS features. We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases. When tested on a dataset of 758 annotated phage-host pairs, PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels, respectively, outperforming other phage-host prediction tools. When applied to on 125,842 metagenomic viral contigs (mVCs) derived from 3042 geographically diverse samples, a detection rate of 54.54% could be achieved. Furthermore, PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant (MDR) bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health (NIH) Human Microbiome Project (HMP). The PHISDetector can be run either as a web server (http://www.microbiome-bigdata.com/PHISDetector/) for general users to study individual inputs or as a stand-alone version (https://github.com/HIT-ImmunologyLab/PHISDetector) to process massive phage contigs from virome studies.


Assuntos
Bacteriófagos , Microbiota , Humanos , Bacteriófagos/genética , Viroma , Prófagos/genética , Bactérias/genética
20.
J Nutr Biochem ; 99: 108843, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34407449

RESUMO

Epigallocatechin-3-gallate (EGCG), the main active ingredient of green tea, exhibits low toxic side effect and versatile bioactivities, and its anti-cancer effect has been extensively studied. Most of the studies used cancer cell lines and xenograft models. However, whether EGCG can prevent tumor onset after cancer-associated mutations occur is still controversial. In the present study, Krt14-cre/ERT-Kras transgenic mice were developed and the expression of K-RasG12D was induced by tamoxifen. Two weeks after induction, the K-Ras mutant mice developed exophytic tumoral lesions on the lips and tongues, with significant activation of Notch signaling pathway. Administration of EGCG effectively delayed the time of appearance, decreased the size and weight of tumoral lesions, relieved heterotypic hyperplasia of tumoral lesions, and prolonged the life of the mice. The Notch signaling pathway was significantly inhibited by EGCG in the tumoral lesions. Furthermore, EGCG significantly induced cell apoptosis and inhibited the proliferation of tongue cancer cells by blocking the activation of Notch signaling pathway. Taken together, these results indicate EGCG as an effective chemotherapeutic agent for tongue cancer by targeting Notch pathway.


Assuntos
Antineoplásicos/administração & dosagem , Catequina/análogos & derivados , Neoplasias Labiais/tratamento farmacológico , Extratos Vegetais/administração & dosagem , Receptores Notch/metabolismo , Neoplasias da Língua/tratamento farmacológico , Animais , Apoptose/efeitos dos fármacos , Camellia sinensis/química , Catequina/administração & dosagem , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Humanos , Neoplasias Labiais/genética , Neoplasias Labiais/metabolismo , Camundongos , Camundongos Transgênicos , Proteínas Proto-Oncogênicas p21(ras)/genética , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Receptores Notch/genética , Transdução de Sinais/efeitos dos fármacos , Neoplasias da Língua/genética , Neoplasias da Língua/metabolismo , Ensaios Antitumorais Modelo de Xenoenxerto
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