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1.
Int J Biol Macromol ; 180: 484-493, 2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-33689774

RESUMO

Two polysaccharide fractions (GLSB50 and GLSB70) with total sugar content of 82.07 wt% and 53.79 wt%, respectively, were obtained from the water extracts of unbroken Ganoderma lucidum spores by sequential ethanol precipitation treatment. Compared with GLSB70, GLSB50 exhibited better activity on stimulation of humoral immune responses in immunosuppressed mice. A novel ß-D-glucan (GLSB50A-III-1) with weight average molecular weight (Mw) of 1.93 × 105 g/mol was purified from GLSB50 through chromatography separation. The exponent α value of Mark-Houwink-Sakurada equation was calculated to be 0.13, indicating that GLSB50A-III-1 presented globular spheres conformation in aqueous solution. Structural analysis showed that GLSB50A-III-1 mainly consisted of (1 â†’ 3), (1 â†’ 4), (1 â†’ 6)-linked ß-d-glucose residues in the backbone, with two single ß-D-Glcp attached at O-6 of ß-(1 â†’ 3) and ß-(1 â†’ 4)-linked residues separately as side chains. The repeat unit of GLSB50A-III-1 was deduced as follows.


Assuntos
Polissacarídeos/química , Reishi/química , Esporos Fúngicos/química , beta-Glucanas/química , Animais , Sequência de Carboidratos , Cromatografia Gasosa-Espectrometria de Massas , Espectroscopia de Ressonância Magnética , Metilação , Camundongos Endogâmicos ICR , Conformação Molecular , Dados de Sequência Molecular , Estrutura Molecular , Peso Molecular , Espectroscopia de Infravermelho com Transformada de Fourier , Água/química , beta-Glucanas/isolamento & purificação
2.
Int J Biol Macromol ; 180: 753-759, 2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-33727189

RESUMO

Polymeric wood hemicelluloses are depicted to join cellulose, starch and chitosan as key polysaccharides for sustainable materials engineering. However, the approaches to incorporate hemicelluloses in emerging bio-based products are challenged by lack of specific benefit, other than the biomass-origin, although their utilization would contribute to sustainable material use since they currently are a side stream that is not valorized. Here we demonstrate wood-xylans as swelling modifiers for neutral and charged nanocellulose films that have already entered the sustainable packaging applications, however, suffer from humidity sensitivity. The oxidative modification is used to modulate the water-solubility of xylan and hence enable adsorption in an aqueous environment. A high molecular weight grade, hence less water-soluble, adsorbed preferentially on the neutral surface while the adsorbed amount on a negatively charged surface was independent of the molecular weight, and hence, solubility. The adsorption of the oxidized xylans on a neutral cellulose surface resulted in an increase in the amount of water in the film while on the negatively charged cellulose the total amount of water decreased. The finding of synergy of two hygroscopic materials to decrease swelling in hydrophilic bio-polymer films demonstrates the oxidized macromolecule xylan as structurally functional component in emerging cellulose products.


Assuntos
Celulose/química , Nanoestruturas/química , Madeira/química , Xilanos/química , Adsorção , Sequência de Carboidratos , Elasticidade , Interações Hidrofóbicas e Hidrofílicas , Microscopia de Força Atômica , Dados de Sequência Molecular , Oxirredução , Solubilidade , Propriedades de Superfície , Viscosidade , Água/química
3.
Int J Biol Macromol ; 180: 643-653, 2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-33744248

RESUMO

In this study, a novel polysaccharide fraction from Ocimum album seed was extracted and then purified by Cellulose DEAE-52 and Sephadex G-200 anion exchange chromatography. The structural, physicochemical and antioxidant properties of the main polysaccharide fraction (OAP-1A) were evaluated. The purified polysaccharide contained 94.3% carbohydrate, 3.56% moisture and 2.14% ash and result of gel permeation chromatography (GPC) showed average molecular weight of 593 kDa. The results of high-performance liquid chromatography (HPLC) showed that OAP-1A was a neutral hetero-polysaccharide composed of mannose (35.7%), glucose (33.32%), galactose (19.6%) and rhamnose (11.38%). In addition, GC-MS data, nuclear magnetic resonance (NMR) spectrum and Fourier transform infrared (FT-IR) analysis revealed that the backbone of OAP-1A consists of →3)-ß-D-Manp-(1→, →3,4)-ß-D-Manp-(1→, →3,6)-ß-D-Manp-(1→, →3)-α-D-Glcp-(1→, →6)-ß-D-Galp-(1→, →4)-α-L-Rhap-(1→ and α-D-Glcp-(1→. X-ray diffraction (XRD) analysis showed semi-crystalline structure in OAP-1A. Differential scanning colorimeter (DSC) and thermo-gravimetry analysis (TGA) indicated that OAP-1A had relatively high thermal stability. Moreover, OAP-1A showed strong scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals.


Assuntos
Antioxidantes/química , Ocimum/química , Polissacarídeos/química , Sementes/química , Antioxidantes/isolamento & purificação , Antioxidantes/farmacologia , Sequência de Carboidratos , Cromatografia Líquida de Alta Pressão , Cromatografia Gasosa-Espectrometria de Massas , Espectroscopia de Ressonância Magnética , Dados de Sequência Molecular , Peso Molecular , Monossacarídeos/análise , Oxirredução/efeitos dos fármacos , Polissacarídeos/isolamento & purificação , Polissacarídeos/farmacologia , Espectroscopia de Infravermelho com Transformada de Fourier , Difração de Raios X
4.
BMC Microbiol ; 21(1): 58, 2021 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-33618668

RESUMO

BACKGROUND: A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization is widespread on the whole world. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was proved to be the main agent of COVID-19. In the present study, we conducted an in depth analysis of the SARS-COV-2 nucleocapsid to identify potential targets that may allow identification of therapeutic targets. METHODS: The SARS-COV-2 N protein subcellular localization and physicochemical property was analyzed by PSORT II Prediction and ProtParam tool. Then SOPMA tool and swiss-model was applied to analyze the structure of N protein. Next, the biological function was explored by mass spectrometry analysis and flow cytometry. At last, its potential phosphorylation sites were analyzed by NetPhos3.1 Server and PROVEAN PROTEIN. RESULTS: SARS-COV-2 N protein composed of 419 aa, is a 45.6 kDa positively charged unstable hydrophobic protein. It has 91 and 49% similarity to SARS-CoV and MERS-CoV and is predicted to be predominantly a nuclear protein. It mainly contains random coil (55.13%) of which the tertiary structure was further determined with high reliability (95.76%). Cells transfected with SARS-COV-2 N protein usually show a G1/S phase block company with an increased expression of TUBA1C, TUBB6. At last, our analysis of SARS-COV-2 N protein predicted a total number of 12 phosphorylated sites and 9 potential protein kinases which would significantly affect SARS-COV-2 N protein function. CONCLUSION: In this study, we report the physicochemical properties, subcellular localization, and biological function of SARS-COV-2 N protein. The 12 phosphorylated sites and 9 potential protein kinase sites in SARS-COV-2 N protein may serve as promising targets for drug discovery and development for of a recombinant virus vaccine.


Assuntos
COVID-19/virologia , Proteínas do Nucleocapsídeo/metabolismo , SARS-CoV-2/metabolismo , SARS-CoV-2/patogenicidade , Sequência de Aminoácidos , COVID-19/genética , COVID-19/imunologia , Genoma Viral/genética , Células HCT116 , Humanos , Dados de Sequência Molecular , Proteínas do Nucleocapsídeo/química , Proteínas do Nucleocapsídeo/genética , Fosforilação , Reprodutibilidade dos Testes , SARS-CoV-2/genética , Vacinas Virais/uso terapêutico
5.
Nucleic Acids Res ; 49(2): 1046-1064, 2021 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-33410911

RESUMO

Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.


Assuntos
DNA Helicases/metabolismo , DNA de Cadeia Simples/metabolismo , Desoxirribonuclease I/metabolismo , Conformação de Ácido Nucleico , Conformação Proteica , Engenharia de Proteínas/métodos , Endonucleases Específicas para DNA e RNA de Cadeia Simples/metabolismo , Transativadores/metabolismo , Proteínas Virais/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Circoviridae/enzimologia , Sequência Conservada , Cristalografia por Raios X , DNA Helicases/química , DNA de Cadeia Simples/química , Desoxirribonuclease I/química , Biblioteca Gênica , Modelos Moleculares , Simulação de Acoplamento Molecular , Dados de Sequência Molecular , Vírus de Plantas/enzimologia , Ligação Proteica , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/metabolismo , Origem de Replicação , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Endonucleases Específicas para DNA e RNA de Cadeia Simples/química , Especificidade por Substrato , Transativadores/química , Proteínas Virais/química
6.
Methods Mol Biol ; 2231: 241-260, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33289897

RESUMO

We present Seaview version 5, a multiplatform program to perform multiple alignment and phylogenetic tree building from molecular sequence data. Seaview provides network access to sequence databases, alignment with arbitrary algorithm, parsimony, distance and maximum likelihood tree building with PhyML, and display, printing, and copy-to-clipboard or to SVG files of rooted or unrooted, binary or multifurcating phylogenetic trees. While Seaview is primarily a program providing a graphical user interface to guide the user into performing desired analyses, Seaview possesses also a command-line mode adequate for user-provided scripts. Seaview version 5 introduces the ability to reconcile a gene tree with a reference species tree and use this reconciliation to root and rearrange the gene tree. Seaview is freely available at http://doua.prabi.fr/software/seaview .


Assuntos
Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos , Software , Algoritmos , Códon/genética , Evolução Molecular , Código Genético , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , Filogenia
7.
Sci Rep ; 10(1): 21394, 2020 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-33288798

RESUMO

The high degree of conservation of toll-like receptors (TLRs), and yet their subtle variations for better adaptation of species in the host-pathogen arms race make them worthy candidates for understanding evolution. We have attempted to track the trend of TLR evolution in the most diverse vertebrate group-teleosts, where Clarias batrachus was given emphasis, considering its traits for terrestrial adaptation. Eleven C. batrachus TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 22, 25, 26) were identified in this study which clustered in proximity to its Siluriformes relative orthologues in the phylogenetic analysis of 228 TLRs from 25 teleosts. Ten TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 21, 22) with at least 15 member orthologues for each alignment were processed for selection pressure and coevolutionary analysis. TLR1, 7, 8 and 9 were found to be under positive selection in the alignment-wide test. TLR1 also showed maximum episodic diversification in its clades while the teleost group Eupercaria showed the maximum divergence in their TLR repertoire. Episodic diversification was evident in C. batrachus TLR1 and 7 alignments. These results present a strong evidence of a divergent TLR repertoire in teleosts which may be contributing towards species-specific variation in TLR functions.


Assuntos
Peixes-Gato/metabolismo , Receptores Toll-Like/química , Receptores Toll-Like/metabolismo , Sequência de Aminoácidos , Animais , Evolução Molecular , Dados de Sequência Molecular , Filogenia , Homologia de Sequência de Aminoácidos
9.
PLoS One ; 15(11): e0241679, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33253167

RESUMO

Plant defensins possess diverse biological functions that include antifungal and antibacterial activities and α-amylase and trypsin inhibitory properties. Two mutations, G9R and V39R, were confirmed to increase the antifungal activity of Raphanus sativus antifungal protein 2 (RsAFP2). Accelerated Molecular Dynamics (aMD) were carried out to examine the conformational changes present in these RsAFP2 mutants, and its two closest homologs compared to the wild-type protein. Specifically, the root mean square fluctuation values for the eight cysteine amino acids involved in the four disulfide bonds were low in the V39R mutant compared to the wild-type. Additionally, analysis of the free energy change revealed that G9R and V39R mutations exert a neutral and stabilizing effect on RsAFP2 conformation, and this is supported by the observed lower total energy of mutants compared to the wild-type, suggesting that enhanced stability of the mutants. However, MD simulations to a longer time scale would aid in capturing more conformational state of the wild-type and mutants defensin protein. Furthermore, the aMD simulations on fungal mimic membranes with RsAFP2 and its mutants and homologs showed that the mutant proteins caused higher deformation and water diffusion than the native RsAFP2, especially the V39R mutant. The mutant variants seem to interact by specifically targeting the POPC and POPI lipids amongst others. This work highlights the stabilizing effect of mutations at the 9th and 39th positions of RsAFP2 and their increased membrane deformation activity.


Assuntos
Defensinas/química , Defensinas/genética , Simulação de Dinâmica Molecular , Sequência de Aminoácidos , Deutério/química , Dados de Sequência Molecular , Mutação/genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
10.
Zootaxa ; 4811(1): zootaxa.4811.1.1, 2020 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-33055724

RESUMO

The planthopper genus Chionomus Fennah, 1971 (Hemiptera: Fulgoroidea: Delphacidae) currently includes three Neotropical species, removed from the polyphyletic genus Delphacodes Fieber, 1866. Morphological and molecular evidence further redefine Chionomus to include ten additional species (eight species removed from Delphacodes, two described as new, viz. Chionomus dolonus n. sp. and C. herkos n. sp.), with another four species synonymized. Phylogenetic analyses of morphological and molecular sequence data of the mitochondrial gene Cytochrome Oxidase I provide support for the monophyly of Chionomus. We use a mixed model Bayesian optimality criterion to define phylogenetic relationships among Chionomus and support paraphyly of the original definition of Chionomus (with respect to Delphacodes) and monophyly of the revised genus.


Assuntos
Hemípteros , Animais , Teorema de Bayes , Genes Mitocondriais , Dados de Sequência Molecular , Filogenia
11.
PLoS One ; 15(7): e0235669, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32634151

RESUMO

MOTIVATION: Annotation of large amounts of generated sequencing data is a demanding task. Most of the currently available robust annotation tools, like ANNOVAR, are command-line based tools which require a certain degree of programming skills. User-friendly tools for variant annotation of sequencing data with graphical interface are under-represented. RESULTS: We have developed an interactive application, which harnesses the easy usability of R Shiny and combines it with the versatile annotation features of ANNOVAR. This application is easy to use and gives comprehensive annotations for user supplied vcf files using multiples databases. The output table contains the list of variants and their corresponding annotation presented within the graphical interface. In addition, the annotation results are downloadable as text file.


Assuntos
Anotação de Sequência Molecular/métodos , Software , Bases de Dados Genéticas , Conjuntos de Dados como Assunto , Humanos , Dados de Sequência Molecular
12.
J Hematol Oncol ; 13(1): 93, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32665005

RESUMO

Tissue factor (TF) is the primary initiator of the coagulation cascade, though its effects extend well beyond hemostasis. When TF binds to Factor VII, the resulting TF:FVIIa complex can proteolytically cleave transmembrane G protein-coupled protease-activated receptors (PARs). In addition to activating PARs, TF:FVIIa complex can also activate receptor tyrosine kinases (RTKs) and integrins. These signaling pathways are utilized by tumors to increase cell proliferation, angiogenesis, metastasis, and cancer stem-like cell maintenance. Herein, we review in detail the regulation of TF expression, mechanisms of TF signaling, their pathological consequences, and how it is being targeted in experimental cancer therapeutics.


Assuntos
Proteínas de Neoplasias/fisiologia , Neoplasias/sangue , Trombofilia/sangue , Tromboplastina/fisiologia , Sequência de Aminoácidos , Hipóxia Celular , Fator VIIa/fisiologia , Regulação Neoplásica da Expressão Gênica , Humanos , Imunoterapia Adotiva , Integrinas/metabolismo , Dados de Sequência Molecular , Terapia de Alvo Molecular , Invasividade Neoplásica , Metástase Neoplásica , Proteínas de Neoplasias/antagonistas & inibidores , Neoplasias/irrigação sanguínea , Neoplasias/fisiopatologia , Neoplasias/terapia , Células-Tronco Neoplásicas/patologia , Neovascularização Patológica/fisiopatologia , Conformação Proteica , Domínios Proteicos , Isoformas de Proteínas/fisiologia , Receptores Proteína Tirosina Quinases/metabolismo , Receptores Ativados por Proteinase/metabolismo , Transdução de Sinais/fisiologia , Trombofilia/etiologia , Tromboplastina/antagonistas & inibidores
13.
Mem Inst Oswaldo Cruz ; 115: e190401, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32401897

RESUMO

Bacillus Calmette Guerin (BCG) vaccines comprise a family of related strains. Whole genome sequencing has allowed the better characterisation of the differences between many of the BCG vaccines. As sequencing technologies improve, updating of publicly available sequence data becomes common practice. We hereby announce the draft genome of four commonly used BCG vaccines in Brazil, Argentina and Venezuela.


Assuntos
Vacina BCG/genética , Mapeamento Cromossômico , Mycobacterium bovis/genética , Argentina , Sequência de Bases , Brasil , Humanos , Dados de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Venezuela
14.
Mar Drugs ; 18(5)2020 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-32370018

RESUMO

RES-701-3 and RES-701-4 are two class II lasso peptides originally identified in the fermentation broth of Streptomyces sp. RE-896, which have been described as selective endothelin type B receptor antagonists. These two lasso peptides only differ in the identity of the C-terminal residue (tryptophan in RES-701-3, 7-hydroxy-tryptophan in RES-701-4), thus raising an intriguing question about the mechanism behind the modification of the tryptophan residue. In this study, we describe the identification of their biosynthetic gene cluster through the genome mining of the marine actinomycete Streptomyces caniferus CA-271066, its cloning and heterologous expression, and show that the seven open reading frames (ORFs) encoded within the gene cluster are sufficient for the biosynthesis of both lasso peptides. We propose that ResE, a protein lacking known putatively conserved domains, is likely to play a key role in the post-translational modification of the C-terminal tryptophan of RES-701-3 that affords RES-701-4. A BLASTP search with the ResE amino acid sequence shows the presence of homologues of this protein in the genomes of eight other Streptomyces strains, which also harbour the genes encoding the RES-701-3, -4 precursor peptide, split-B proteins and ATP-dependent lactam synthetase required for the biosynthesis of these compounds.


Assuntos
Peptídeos Cíclicos/biossíntese , Streptomyces/metabolismo , Sequência de Aminoácidos , Animais , Clonagem Molecular , Regulação da Expressão Gênica , Dados de Sequência Molecular , Peptídeos Cíclicos/genética
15.
Nat Commun ; 11(1): 1871, 2020 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-32313011

RESUMO

Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.


Assuntos
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Edição de Genes/métodos , Ensaios de Triagem em Larga Escala , Proteoma/genética , Leveduras/genética , Sequência de Bases , Sistemas CRISPR-Cas , Genes Essenciais , Genoma , Genoma Fúngico , Sequenciamento de Nucleotídeos em Larga Escala , Dados de Sequência Molecular , Mutagênese , Mutação , RNA Guia/genética
16.
Int J Biol Sci ; 16(6): 981-993, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32140067

RESUMO

Ly6/uPAR/α-neurotoxin domain (LU-domain) is characterized by the presence of 4-5 disulfide bonds and three flexible loops that extend from a core stacked by several conversed disulfide bonds (thus also named three-fingered protein domain). This highly structurally stable protein domain is typically a protein-binder at extracellular space. Most LU proteins contain only single LU-domain as represented by Ly6 proteins in immunology and α-neurotoxins in snake venom. For Ly6 proteins, many are expressed in specific cell lineages and in differentiation stages, and are used as markers. In this study, we report the crystal structures of the two LU-domains of human C4.4A alone and its complex with a Fab fragment of a monoclonal anti-C4.4A antibody. Interestingly, both structures showed that C4.4A forms a very compact globule with two LU-domain packed face to face. This is in contrast to the flexible nature of most LU-domain-containing proteins in mammals. The Fab combining site of C4.4A involves both LU-domains, and appears to be the binding site for AGR2, a reported ligand of C4.4A. This work reports the first structure that contain two LU-domains and provides insights on how LU-domains fold into a compact protein and interacts with ligands.


Assuntos
Moléculas de Adesão Celular/metabolismo , Neurotoxinas/metabolismo , Receptores de Ativador de Plasminogênio Tipo Uroquinase/metabolismo , Sequência de Aminoácidos , Moléculas de Adesão Celular/química , Proteínas Ligadas por GPI/química , Proteínas Ligadas por GPI/metabolismo , Humanos , Immunoblotting , Dados de Sequência Molecular , Neurotoxinas/química , Estrutura Secundária de Proteína , Receptores de Ativador de Plasminogênio Tipo Uroquinase/química
17.
Sci Rep ; 10(1): 4196, 2020 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-32144374

RESUMO

Tail Tubular Protein A (TTPA) was long thought to be strictly a structural protein of environmental bacteriophages. However, our recent work has suggested that some TTPAs have additional functional features and thus are dual-function proteins. This study introduces a new TTPA family member, TTPAgp11, which belongs to Yersinia phage phiYeO3-12. We cloned the gene, expressed it and then purified the phage protein. The protein, including its hydrolytic activity, was characterized. Our enzymatic activity tests showed that TTPAgp11 displayed hydrolytic activity towards Red-starch, suggesting that this enzyme could be classified as part as the α - 1, 4-glucosidase family. Protein folding and aggregation tests indicated that TTPAgp11 is a single-domain protein whose aggregation can be induced by maltose or N-acetylglucosamine. The spatial structure of TTPAgp11 seemed to resemble that of the first reported dual-function TTPA, TTPAgp31, which was isolated from Klebsiella pneumoniae phage 32.


Assuntos
Proteínas Virais/química , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Bacteriófagos/genética , Genoma Viral/genética , Hidrólise , Dados de Sequência Molecular , Proteínas Virais/genética
18.
Euro Surveill ; 25(7)2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32098644

RESUMO

Interim results from Canada's Sentinel Practitioner Surveillance Network show that during a season characterised by early co-circulation of influenza A and B viruses, the 2019/20 influenza vaccine has provided substantial protection against medically-attended influenza illness. Adjusted VE overall was 58% (95% confidence interval (CI): 47 to 66): 44% (95% CI: 26 to 58) for A(H1N1)pdm09, 62% (95% CI: 37 to 77) for A(H3N2) and 69% (95% CI: 57 to 77) for influenza B viruses, predominantly B/Victoria lineage.


Assuntos
Vírus da Influenza A Subtipo H1N1/isolamento & purificação , Vírus da Influenza A Subtipo H3N2/isolamento & purificação , Vírus da Influenza B/isolamento & purificação , Vacinas contra Influenza/administração & dosagem , Influenza Humana/epidemiologia , Influenza Humana/prevenção & controle , Adolescente , Adulto , Idoso , Antígenos Virais/análise , Canadá/epidemiologia , Criança , Pré-Escolar , Feminino , Genótipo , Testes de Inibição da Hemaglutinação , Humanos , Lactente , Vírus da Influenza A Subtipo H1N1/genética , Vírus da Influenza A Subtipo H1N1/imunologia , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/imunologia , Vírus da Influenza B/genética , Vírus da Influenza B/imunologia , Vacinas contra Influenza/imunologia , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Nasofaringe/virologia , Nariz/virologia , Reação em Cadeia da Polimerase em Tempo Real , Estações do Ano , Vigilância de Evento Sentinela , Análise de Sequência de DNA , Adulto Jovem
19.
Phys Chem Chem Phys ; 22(8): 4343-4367, 2020 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-32067019

RESUMO

Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must include structural representation as an indispensable component. Mathematical representations that simplify the biomolecular structural complexity and reduce ML dimensionality have emerged as a prime winner in D3R Grand Challenges. This review is devoted to the recent advances in developing low-dimensional and scalable mathematical representations of biomolecules in our laboratory. We discuss three classes of mathematical approaches, including algebraic topology, differential geometry, and graph theory. We elucidate how the physical and biological challenges have guided the evolution and development of these mathematical apparatuses for massive and diverse biomolecular data. We focus the performance analysis on protein-ligand binding predictions in this review although these methods have had tremendous success in many other applications, such as protein classification, virtual screening, and the predictions of solubility, solvation free energies, toxicity, partition coefficients, protein folding stability changes upon mutation, etc.


Assuntos
Biologia Computacional , Modelos Biológicos , Algoritmos , Dados de Sequência Molecular
20.
J Agric Food Chem ; 68(8): 2366-2372, 2020 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-32017555

RESUMO

Spermidine possesses multiple healthy functions, and soybeans contain the most abundant spermidine. In this study, spermidine contents of soybeans from different varieties and production regions in China were evaluated, and a spermidine synthase gene (speE) was identified by recombinant expression, transcriptional verification, and sequence analysis. Spermidine contents of soybean samples from 18 varieties ranged 72.38-228.82 mg/kg, and those from 19 production regions ranged 134.64-242.32 mg/kg. The highest-spermidine sample GZ was used to clone four predicted speE genes. Expressing the gene speE5 improved the spermidine titer by 54% in Bacillus amyloliquefaciens, confirming that speE5 was involved in spermidine synthesis. Transcriptional verification was performed through a soybean germination model. Germination for 48 h led to a onefold increase of spermidine in samples SHX and HB, and corresponding speE5 transcriptional levels were improved by 26-fold and 18-fold, respectively, further verifying the function of speE5. Finally, the sequences of the speE5 gene and deduced amino acids were analyzed, and the conserved sites and catalysis mechanisms were presented. This study identified an active spermidine synthase gene from soybean for the first time, which provided an important gene resource for genetic breeding of spermidine-rich soybean or microbial cell factory.


Assuntos
Proteínas de Plantas/genética , Soja/enzimologia , Espermidina Sintase/genética , Sequência de Aminoácidos , Bacillus amyloliquefaciens/genética , Bacillus amyloliquefaciens/metabolismo , Germinação , Dados de Sequência Molecular , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Sementes/enzimologia , Sementes/genética , Sementes/crescimento & desenvolvimento , Sementes/metabolismo , Alinhamento de Sequência , Soja/genética , Soja/crescimento & desenvolvimento , Soja/metabolismo , Espermidina/metabolismo , Espermidina Sintase/química , Espermidina Sintase/metabolismo , Transcrição Genética
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