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1.
Mar Drugs ; 22(2)2024 Jan 26.
Artículo en Inglés | MEDLINE | ID: mdl-38393035

RESUMEN

Paralytic shellfish toxins (PSTs) are widely distributed in shellfish along the coast of China, causing a serious threat to consumer health; however, there is still a lack of large-scale systematic investigations and risk assessments. Herein, 641 shellfish samples were collected from March to November 2020, and the PSTs' toxicity was detected via liquid chromatography-tandem mass spectrometry. Furthermore, the contamination status and potential dietary risks of PSTs were discussed. PSTs were detected in 241 shellfish samples with a detection rate of 37.60%. The average PST toxicities in mussels and ark shells were considerably higher than those in other shellfish. The PSTs mainly included N-sulfonylcarbamoyl toxins (class C) and carbamoyl toxins (class GTX), and the highest PST toxicity was 546.09 µg STX eq. kg-1. The PST toxicity in spring was significantly higher than those in summer and autumn (p < 0.05). Hebei Province had the highest average PST toxicity in spring. An acute exposure assessment showed that consumers in Hebei Province had a higher dietary risk, with mussels posing a significantly higher dietary risk to consumers. This research provides reference for the green and sustainable development of the shellfish industry and the establishment of a shellfish toxin prevention and control system.


Asunto(s)
Bivalvos , Intoxicación por Mariscos , Animales , Toxinas Marinas/química , Intoxicación por Mariscos/etiología , Intoxicación por Mariscos/prevención & control , Intoxicación por Mariscos/diagnóstico , Espectrometría de Masas en Tándem/métodos , Mariscos/análisis , Bivalvos/química , Medición de Riesgo , China
2.
Biotechnol Lett ; 45(4): 521-536, 2023 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-36790735

RESUMEN

PURPOSE: Pichia pastoris is well known for its ability to produce short and low-immunogenic humanized glycosyl chains onto recombinant glycoproteins, it was thus speculated to be applicable to synthesize oligosaccharides. In this study, generally recognized as safe (GRAS) microorganism Pichia pastoris GS115 was tested for its potential to be used as a new synthetic chassis to produce the most abundant human milk oligosaccharide 2'-fucosyllactose (2'-FL). METHODS: To enable the de novo synthesis of 2'-FL, lactose transporter lac12, two enzymes of gmd, gmer, and fucosyltransferases futC were integrated into the genome of P. pastoris, under the control of constitutive PGAP promoter. RESULTS: The resulting recombinant yeasts yielded up to 0.276 g/L through culture optimization in a 5 L bioreactor. CONCLUSION: To our knowledge, this is the first report of 2'-FL production in engineered Pichia pastoris. This work is a good starting point to produce 2'-FL using Pichia pastoris as a viable chassis.


Asunto(s)
Saccharomycetales , Trisacáridos , Humanos , Trisacáridos/genética , Oligosacáridos , Pichia/genética
3.
Genomics ; 114(5): 110470, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-36041636

RESUMEN

Germin-like proteins (GLPs) play important roles in plant disease resistance but are rarely reported in cotton. We compared the expression of GLPs in Verticillium dahliae inoculate G. hirsutum (susceptible) and G. barbadense (resistant) and enriched 11 differentially expressed GLPs. 2741 GLP proteins identified from 53 species determined that GLP probably originated from algae and could be classified into 7 clades according to phylogenetic analysis, among which Clade I is likely the most ancient. Cotton GLP (two allopolyploids and two diploids) genes within a shared clade were highly conserved. Intriguingly, clade VII genes were mainly located in gene clusters that derived from the expansion of LTR transposons. Clade VII members expressed mainly in root which is the first battle against Verticillium dahlia and could be induced more intensely in G. barbadense than G. hirsutum. The GLP genes are resistant to Verticillium dahliae, which can be further investigated against Verticillium wilt.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Verticillium , Resistencia a la Enfermedad/genética , Gossypium/genética , Filogenia , Proteínas de Plantas/genética , Verticillium/fisiología
4.
Plant Biotechnol J ; 18(1): 239-253, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31199554

RESUMEN

Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.


Asunto(s)
Fibra de Algodón , Gossypium/genética , Sitios de Carácter Cuantitativo , Mapeo Cromosómico , Marcadores Genéticos , Fenotipo , Fitomejoramiento , RNA-Seq
5.
World J Microbiol Biotechnol ; 35(6): 87, 2019 May 27.
Artículo en Inglés | MEDLINE | ID: mdl-31134386

RESUMEN

Biofilms enable Cronobacter spp. to contaminate food, infect infants and resist different environmental stresses, especially desiccation, which is the main reason why Cronobacter can survive in powdered infant formula (PIF) for a long time. Considering the high lethality of Cronobacter infection in infants, it is important to find efficient and safe inhibitors of Cronobacter biofilms. In this study, we found that chitooligosaccharides (COS) with a molecular weight of 2000 Da efficiently inhibited Cronobacter biofilms, especially in skim milk broth. The minimum biofilm inhibitory concentration (MBIC77) of COS was as low as 20 µg/mL, which is lower than that reported in most previous studies. Besides, the elimination rate of COS for Cronobacter mature biofilms was 50% when the concentration was 10 mg/mL. COS could significantly inhibit soluble polysaccharide secretion and biofilm cell growth, as well as change the cell membrane permeability of Cronobacter. These might be the possible reasons for COS's efficient inhibition of Cronobacter biofilms. However, during the inhibition, five important genes-related to biofilm formation-flhD, flgJ, luxR, ompA, and wcaJ-were all up-regulated after COS treatment, except the gene bcsA. In summary, our findings showed that COS could be used as an efficient and safe inhibitor against Cronobacter biofilms for better control of Cronobacter contamination and infection.


Asunto(s)
Biopelículas/efectos de los fármacos , Quitina/análogos & derivados , Cronobacter/efectos de los fármacos , Animales , Biopelículas/crecimiento & desarrollo , Membrana Celular/efectos de los fármacos , Quitina/química , Quitina/farmacología , Quitosano , Cronobacter/genética , Infecciones por Enterobacteriaceae , Contaminación de Alimentos , Microbiología de Alimentos , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Genes Bacterianos/genética , Pruebas de Sensibilidad Microbiana , Leche , Peso Molecular , Oligosacáridos
7.
Anticancer Drugs ; 29(8): 736-747, 2018 09.
Artículo en Inglés | MEDLINE | ID: mdl-29912010

RESUMEN

Cyclosporin A (CsA) is a calcium antagonist and can enhance the efficacy of some protein drugs, but its mechanism remains unknown. In this study, MAP30, a ribosome-inactivating protein reported to have apoptotic effects on cancer cells, was fused with S3, an epidermal growth factor receptor (EGFR)-targeting peptide. In addition, CsA was used to investigate whether it can further promote the apoptotic effects of S3 fused MAP30 (MAP30-S3). Our result showed that the internalization of FITC-labeled MAP30-S3 was increased significantly by S3 in HeLa cells. Unexpectedly, MAP30-S3 only showed a minor decrease in the viability of EGFR-overexpressing cancer cells, including HeLa, SMMC-7721, and MGC803 (IC50>5 µmol/l). However, 2 µmol/l CsA significantly increased the cytotoxicity of MAP30-S3, especially for HeLa cells (IC50=40.3 nmol/l). In comparison, CsA did not further decrease the cytotoxicity of MAP30-S3 on MRC-5, an EGFR low-expressing cell line from normal lung tissue, indicating that CsA did not affect the cancer-targeting specificity of MAP30-S3. Our results also showed that CsA further increased the apoptotic activity of MAP30-S3 in HeLa cells. CsA could promote the endosomal escape of FITC-MAP30-S3 with a diffused pattern in the cytoplasm. Five endocytic inhibitors were used to investigate the cellular uptake mechanism of MAP30-S3, and the results showed that the endosomal escape-enhancing effect of CsA on MAP30-S3 may be associated with the clathrin-dependent endocytic pathways. Our study suggested that CsA could be a novel endosomal escape enhancer to potentiate the intracellular release of anticancer protein drugs, resulting in their improved therapeutic efficacy.


Asunto(s)
Ciclosporina/farmacología , Endosomas/metabolismo , Neoplasias/tratamiento farmacológico , Neoplasias/metabolismo , Proteínas Recombinantes de Fusión/farmacología , Proteínas Ribosómicas/farmacología , Proteínas Inactivadoras de Ribosomas Tipo 2/farmacología , Antineoplásicos/química , Antineoplásicos/farmacología , Línea Celular Tumoral , Sinergismo Farmacológico , Células HeLa , Humanos , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Ribosómicas/química , Proteínas Ribosómicas/genética , Proteínas Inactivadoras de Ribosomas Tipo 2/química , Proteínas Inactivadoras de Ribosomas Tipo 2/genética
8.
Ann Bot ; 121(4): 665-679, 2018 03 14.
Artículo en Inglés | MEDLINE | ID: mdl-29324975

RESUMEN

Background and Aims: Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Methods: Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species. Key Results: Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG). Conclusions: Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during glacial periods and range expansion during interglacial periods. Our study corroborates the importance of combining multiple lines of evidence when reconstructing Quaternary population evolutionary histories.


Asunto(s)
Populus , China , ADN de Cloroplastos/genética , Demografía , Ecosistema , Variación Genética/genética , Genética de Población , Haplotipos/genética , Repeticiones de Microsatélite/genética , Populus/genética , Refugio de Fauna , Clima Tropical
9.
Appl Microbiol Biotechnol ; 98(1): 207-18, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23615737

RESUMEN

Two native epoxide hydrolases (EHs) were previously discovered from mung bean powder (Vigna radiata), both of which can catalyze the enantioconvergent hydrolysis of p-nitrostyrene oxide (pNSO). In this study, the encoding gene of VrEH1 was successfully cloned from the cDNA of V. radiata by RT-PCR and rapid amplification of cDNA ends (RACE) technologies. High homologies were found to two putative EHs originated from Glycine max (80%) and Medicago truncatula (79%). The vreh1 gene constructed in pET28a(+) vector was then heterologously overexpressed in Escherichia coli BL21(DE3), and the encoded protein was purified to homogeneity by nickel affinity chromatography. It was shown that VrEH1 has an optimum activity at 45 °C and is very thermostable with an inactivation energy of 468 kJ mol(-1). The enzyme has no apparent requirement of metal ions for activity, and its activity was strongly inhibited by 1 mM of Ni(2+), Cu(2+), Fe(2+), or Co(2+). By adding 0.1% Triton X-100, the enzyme activity could be significantly increased up to 340%. VrEH1 shows an unusual ability of enantioconvergent catalysis for the hydrolysis of racemic pNSO, affording (R)-p-nitrophenyl glycol (pNPG). It displays opposite regioselectivity toward (S)-pNSO (83% to Cα) in contrast to (R)-pNSO (87% to Cß). The K M and k cat of VrEH1 were determined to be 1.4 mM and 0.42 s(-1) for (R)-pNSO and 5.5 mM and 6.2 s(-1) for (S)-pNSO. This thermostable recombinant VrEH1 with enantioconvergency is considered to be a promising biocatalyst for the highly productive preparation of enantiopure vicinal diols and also a good model for understanding the mechanism of EH stereoselectivity.


Asunto(s)
Epóxido Hidrolasas/metabolismo , Compuestos Epoxi/metabolismo , Fabaceae/enzimología , Cromatografía de Afinidad , Activadores de Enzimas/metabolismo , Inhibidores Enzimáticos/metabolismo , Estabilidad de Enzimas , Epóxido Hidrolasas/química , Epóxido Hidrolasas/genética , Epóxido Hidrolasas/aislamiento & purificación , Escherichia coli/genética , Fabaceae/genética , Expresión Génica , Glicoles/metabolismo , Hidrólisis , Datos de Secuencia Molecular , Nitrobencenos/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Temperatura
10.
Synth Syst Biotechnol ; 9(4): 713-722, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38868610

RESUMEN

Amino oligosaccharides (AOs) possess various biological activities and are valuable in the pharmaceutical, food industries, and agriculture. However, the industrial manufacturing of AOs has not been realized yet, despite reports on physical, chemical, and biological approaches. In this study, the de novo production of chitin oligosaccharides (CHOS), a type of structurally defined AOs, was achieved in Escherichia coli through combinatorial pathway engineering. The most suitable glycosyltransferase for CHOS production was found to be NodCL from Mesorhizobium Loti. Then, by knocking out the nagB gene to block the flow of N-acetyl-d-glucosamine (NAG) to the glycolytic pathway in E. coli and adjusting the copy number of NodCL-coding gene, the CHOS yield was increased by 6.56 times. Subsequently, by introducing of UDP-N-acetylglucosamine (UDP-GlcNAc) salvage pathway for and optimizing fermentation conditions, the yield of CHOS reached 207.1 and 468.6 mg/L in shake-flask cultivation and a 5-L fed-batch bioreactor, respectively. Meanwhile, the concentration of UDP-GlcNAc was 91.0 mg/L, the highest level reported in E. coli so far. This study demonstrated, for the first time, the production of CHOS with distinct structures in plasmid-free E. coli, laying the groundwork for the biosynthesis of CHOS and providing a starting point for further engineering and commercial production.

11.
J Adv Res ; 58: 13-30, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-37207930

RESUMEN

INTRODUCTION: The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. OBJECTIVES: Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. METHODS: We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. RESULTS: Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6, a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. CONCLUSION: Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.


Asunto(s)
ARN Largo no Codificante , ARN Largo no Codificante/genética , Reproducibilidad de los Resultados , Transcriptoma , Ribosomas/genética , Transcripción Genética , Gossypium/genética
12.
Biotechnol Bioeng ; 110(9): 2395-404, 2013 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-23475631

RESUMEN

Toxic compounds, such as formic acid, furfural, and hydroxymethylfurfural (HMF) generated during pretreatment of corn stover (CS) at high temperature and low pH, inhibit growth of Zymomonas mobilis and lower the conversion efficiency of CS to biofuel and other products. The inhibition of toxic compounds is considered as one of the major technical barriers in the lignocellulose bioconversion. In order to detoxify and/or degrade these toxic compounds by the model ethanologenic strain Z. mobilis itself in situ the fermentation medium, we constructed a recombinant Z. mobilis ZM4 (pHW20a-fdh) strain that is capable of degrading toxic inhibitor, formate. This is accomplished by cloning heterologous formate dehydrogenase gene (fdh) from Saccharomyces cerevisiae and by coupling this reaction of NADH regeneration reaction system with furfural and HMF degradation in the recombinant Z. mobilis strain. The NADH regeneration reaction also improved both the energy efficiency and cell physiological activity of the recombinant organism, which were definitely confirmed by the improved cell growth, ethanol yield, and ethanol productivity during fermentation with CS hydrolysate.


Asunto(s)
Biocombustibles/análisis , Etanol , Zymomonas/genética , Clonación Molecular , Electroforesis en Gel de Poliacrilamida , Etanol/análisis , Etanol/metabolismo , Fermentación , Formiato Deshidrogenasas/genética , Formiatos/análisis , Formiatos/metabolismo , Proteínas Fúngicas/genética , NAD/análisis , NAD/metabolismo , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/genética , Zea mays/metabolismo , Zymomonas/metabolismo , Zymomonas/fisiología
13.
Int J Biol Macromol ; 244: 125241, 2023 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-37301336

RESUMEN

Chitin is the second largest renewable biomass resource in nature, it can be enzymatically degraded into high-value chitin oligosaccharides (CHOSs) by chitinases. In this study, a chitinase (ChiC8-1) was purified and biochemically characterized, its structure was analyzed by molecular modeling. ChiC8-1 had a molecular mass of approximately 96 kDa, exhibited its optimal activity at pH 6.0 and 50 °C. The Km and Vmax values of ChiC8-1 towards colloidal chitin were 10.17 mgmL-1 and 13.32 U/mg, respectively. Notably, ChiC8-1 showed high chitin-binding capacity, which may be related to the two chitin binding domains in the N-terminal. Based on the unique properties of ChiC8-1, a modified affinity chromatography method, which combines protein purification with chitin hydrolysis process, was developed to purify ChiC8-1 while hydrolyzing chitin. In this way, 9.36 ± 0.18 g CHOSs powder was directly obtained by hydrolyzing 10 g colloidal chitin with crude enzyme solution. The CHOSs were composed of 14.77-2.83 % GlcNAc and 85.23-97.17 % (GlcNAc)2 at different enzyme-substrate ratio. This process simplifies the tedious purification and separation steps, and may enable its potential application in the field of green production of chitin oligosaccharides.


Asunto(s)
Quitina , Quitinasas , Quitina/química , Quitinasas/química , Oligosacáridos , Especificidad por Sustrato
14.
Gene ; 885: 147712, 2023 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-37579958

RESUMEN

Chlorophyll biosynthesis and chloroplast development are essential for photosynthesis and plant growth. Gossypium arboreum, a valuable source of genetic variation for cotton improvement, remains poorly studied for the mechanisms regulating chlorophyll biosynthesis and chloroplast development. Here we created a G. arboreum etiolated leaf and stuntedness (els) mutant that displayed a distinct yellow color of leaves, bracts and stems throughout the whole growth, where chlorophyll accumulation in leaves was reduced and chloroplast development was delayed. The GaCHLH gene, which encodes the H subunit of magnesium chelatase (Mg-chelatase), was screened by MutMap and KASP analysis. Compared to GaCHLH, the gene Gachlh of the mutant had a single nucleotide transition (G to A) at 1549 bp, which causes the substitution of a glycine (G) by a serine (S) at the 517th amino acid, resulting in an abnormal secondary structure of the Gachlh protein. GaCHLH-silenced SXY1 and ZM24 plants exhibited a lower GaCHLH expression level, a lower chlorophyll content, and the yellow-leaf phenotype. Gachlh expression affected the expression of key genes in the tetrapyrrole pathway. GaCHLH and Gachlh were located in the chloroplasts and that alteration of the mutation site did not affect the final target position. The BiFC assay result indicated that Gachlh could not bind to GaCHLD properly, which prevented the assembly of Mg-chelatase and thus led to the failure of chlorophyll synthesis. In this study, the Gachlh gene of G. arboreum els was finely localized and identified for the first time, providing new insights into the chlorophyll biosynthesis pathway in cotton.


Asunto(s)
Cloroplastos , Gossypium , Gossypium/metabolismo , Cloroplastos/genética , Cloroplastos/metabolismo , Fotosíntesis/genética , Clorofila/análisis , Hojas de la Planta/metabolismo , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
15.
Front Microbiol ; 14: 1177078, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37362919

RESUMEN

Verticillium dahliae (V. dahliae) is a notorious soil-borne pathogen causing Verticillium wilt in more than 400 dicotyledonous plants, including a wide range of economically important crops, such as cotton, tomato, lettuce, potato, and romaine lettuce, which can result in extensive economic losses. In the last decade, several studies have been conducted on the physiological and molecular mechanisms of plant resistance to V. dahliae. However, the lack of a complete genome sequence with a high-quality assembly and complete genomic annotations for V. dahliae has limited these studies. In this study, we produced a full genomic assembly for V. dahliae VD991 using Nanopore sequencing technology, consisting of 35.77 Mb across eight pseudochromosomes and with a GC content of 53.41%. Analysis of the genome completeness assessment (BUSCO alignment: 98.62%; Illumina reads alignment: 99.17%) indicated that our efforts resulted in a nearly complete and high-quality genomic assembly. We selected 25 species closely related to V. dahliae for evolutionary analysis, confirming the evolutionary relationship between V. dahliae and related species, and the identification of a possible whole genome duplication event in V. dahliae. The interaction between cotton and V. dahliae was investigated by transcriptome sequencing resulting in the identification of many genes and pathways associated with cotton disease resistance and V. dahliae pathogenesis. These results will provide new insights into the pathogenic mechanisms of V. dahliae and contribute to the cultivation of cotton varieties resistant to Verticillium wilt.

16.
Front Plant Sci ; 13: 773107, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35126443

RESUMEN

With the increasing amount of cotton omics data, breeding scientists are confronted with the question of how to use massive cotton data to mine effective breeding information. Here, we construct a Gossypium Resource And Network Database (GRAND), which integrates 18 cotton genome sequences, genome annotations, two cotton genome variations information, and also four transcriptomes for Gossypium species. GRAND allows to explore and mine this data with the help of a toolbox that comprises a flexible search system, BLAST and BLAT suite, orthologous gene ID, networks of co-expressed genes, primer design, Gbrowse and Jbrowse, and drawing instruments. GRAND provides important information regarding Gossypium resources and hopefully can accelerate the progress of cultivating cotton varieties.

17.
Gigascience ; 112022 10 30.
Artículo en Inglés | MEDLINE | ID: mdl-36310248

RESUMEN

BACKGROUND: The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS: We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS: This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.


Asunto(s)
Capparaceae , Capparis , Filogenia , Genómica , Genoma de Planta
18.
J Genet Genomics ; 49(6): 547-558, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-34995812

RESUMEN

Sorbus pohuashanensis (Hance) Hedl. is a potential horticulture and medicinal plant, but its genomic and genetic backgrounds remain unknown. Here, we sequence and assemble the S. pohuashanensis reference genome using PacBio long reads. Based on the new reference genome, we resequence a core collection of 22 Sorbus spp. samples, which are divided into 2 groups (G1 and G2) based on phylogenetic and PCA analyses. These phylogenetic clusters are highly consistent with their classification based on leaf shape. Natural hybridization between the G1 and G2 groups is evidenced by a sample (R21) with a highly heterozygous genotype. Nucleotide diversity (π) analysis shows that G1 has a higher diversity than G2 and that G2 originated from G1. During the evolution process, the gene families involved in photosynthesis pathways expanded and the gene families involved in energy consumption contracted. RNA-seq data suggests that flavonoid biosynthesis and heat-shock protein (HSP)-heat-shock factor (HSF) pathways play important roles in protection against sunburn. This study provides new insights into the evolution of Sorbus spp. genomes. In addition, the genomic resources, and the identified genetic variations, especially those related to stress resistance, will help future efforts to produce and breed Sorbus spp.


Asunto(s)
Sorbus , Quemadura Solar , Filogenia , Fitomejoramiento , Hojas de la Planta/genética , Sorbus/genética , Transcriptoma/genética
19.
Environ Sci Pollut Res Int ; 29(27): 41151-41167, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35088269

RESUMEN

Acrylamide (ACR) is a typical environmental contaminant, presenting potential health hazards that have been attracting increasing attention. Its neurotoxicity is known to cause significant damage to health. However, the mechanisms of ACR-induced neurotoxicity require further clarification. This study uses a mouse model to explore how ACR-induced oxidative stress, neuronal lesions, neurotransmission impairment, and neuroinflammation mutually contribute to neurotoxicity. A distinct increase in the cellular reactive oxygen species (ROS) levels, malondialdehyde (MDA), and 8-hydroxy-2-deoxyguanosine (8-OHdG) content and a significant decrease in the glutathione (GSH) content after ACR exposure were indicative of oxidative stress. Moreover, ACR caused neurological defects associated with gait abnormality and neuronal loss while suppressing the acetylcholine (ACh) and dopamine (DA) levels and increasing the protein expression of α-synuclein (α-syn), further inhibiting cholinergic and dopaminergic neuronal function. Additionally, ACR treatment caused an inflammatory response via nuclear factor-kappa B (NF-κB) activation and increased the protein expression of NOD-like receptor protein-3 (NLRP3), consequently activating the NLRP3 inflammasome constituents, including cysteinyl aspartate specific proteinase 1 (Caspase-1), apoptosis-associated speck-like protein containing CARD (ASC), N domain gasdermin D (N-GSDMD), interleukin-1ß (IL-1ß), and IL-18. The results revealed the underlying molecular mechanism of ACR-induced neurotoxicity via oxidative stress, neurotransmission impairment, and neuroinflammation-related signal cascade. This information will further improve the development of an alternative pathway strategy for investigating the risk posed by ACR. The hypothetical mechanism of ACR-induced neurotoxicity in vivo.


Asunto(s)
Acrilamida , Síndromes de Neurotoxicidad , Acrilamida/toxicidad , Animales , Glutatión/metabolismo , Ratones , FN-kappa B/metabolismo , Proteína con Dominio Pirina 3 de la Familia NLR/metabolismo , Enfermedades Neuroinflamatorias , Síndromes de Neurotoxicidad/metabolismo , Estrés Oxidativo/fisiología , Transmisión Sináptica
20.
Mol Biol Rep ; 38(4): 2649-56, 2011 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-21080077

RESUMEN

Cell-penetrating peptides can carry a variety of biologically active molecules into cells. Here we have identified a novel CPP derived from the C-terminus of human extracellular superoxide dismutase (hC-SOD3) which was shown to be located throughout in the cytoplasm and nucleus by fluorescence microscopy investigation. Furthermore, when apoptin fused to hC-SOD3, it was translocated efficiently into HeLa cells resulting in antitumor activities. This study shows that hC-SOD3 has the potential to penetrate and translocate cargo molecules into cells and has no cytotoxicity at effective concentration.


Asunto(s)
Péptidos de Penetración Celular/genética , Sistemas de Liberación de Medicamentos/métodos , Superóxido Dismutasa/genética , Animales , Western Blotting , Proteínas de la Cápside/metabolismo , Células HeLa , Humanos , Ratones , Ratones Endogámicos C57BL , Microscopía Confocal , Microscopía Fluorescente , Superóxido Dismutasa/metabolismo
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