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1.
World J Microbiol Biotechnol ; 36(1): 14, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31897771

RESUMO

Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.


Assuntos
Bactérias/crescimento & desenvolvimento , Glucose/metabolismo , Glicogênio/química , Trifosfato de Adenosina/metabolismo , Bactérias/química , Bactérias/metabolismo , Sequência de Carboidratos , Metabolismo Energético , Viabilidade Microbiana , Modelos Teóricos
2.
Chem Asian J ; 15(3): 327-337, 2020 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-31957936

RESUMO

Microbial secondary metabolites (SMs) have long been viewed as a significant source of novel pharmaceutical and agrochemical molecules. With the increasing availability of genomic data, numerous biosynthetic gene clusters (BGCs) have been discovered. Despite the presence of tens of thousands of BGCs that can theoretically produce extremely diverse SMs, many gene clusters remain in a silent state under axenic culture conditions. Co-culture is a promising research approach as it stimulates the expression of cryptic BGCs to produce novel metabolites and also mimics natural interspecies interactions in a laboratory environment. In recent years, the roles of SMs in microbial communication have caught the attention of researchers and our understanding of microbes and their production of remarkable SMs has improved. SMs may be extensively involved in a variety of communication events among microorganisms. We herein summarize certain representative findings in the field of chemical communication involving SMs in co-culture systems.


Assuntos
Bactérias/química , Metabolismo Secundário , Aspergillus fumigatus/química , Aspergillus fumigatus/metabolismo , Aspergillus fumigatus/virologia , Bactérias/metabolismo , Bactérias/virologia , Montagem e Desmontagem da Cromatina , Óxido Nítrico/química , Óxido Nítrico/metabolismo , Streptomyces/química , Streptomyces/metabolismo , Streptomyces/virologia , Vírus/patogenicidade
3.
J Agric Food Chem ; 68(4): 1091-1100, 2020 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-31896257

RESUMO

The physical structure of type 1 resistant starch (RS 1) could influence the metabolite production and stimulate the growth of specific bacteria in the human colon. In the present study, we isolated intact cotyledon cells from pinto bean seeds as whole pulse food and RS 1 model and obtained a series of cell wall integrities through controlled enzymolysis. In vitro human fecal fermentation performance and microbiota responses were tested, and we reported that the cell wall integrity controls the in vitro fecal fermentation rate of heat-treated pinto bean cells. The concentration of butyrate produced by pinto bean cell fermentation enhanced with weakened cell wall integrity, and certain beneficial bacterial groups such as Blautia and Roseburia genera were remarkably promoted by pinto bean cells with damaged cell wall integrity. However, the intact cell sample had a shape more similar to microbiota composition with the purified cell wall polysaccharides, rather than the damaged cells.


Assuntos
Bactérias/metabolismo , Parede Celular/metabolismo , Fezes/microbiologia , Microbioma Gastrointestinal , Phaseolus/metabolismo , Bactérias/química , Bactérias/classificação , Bactérias/isolamento & purificação , Parede Celular/química , Fermentação , Humanos , Phaseolus/química , Polissacarídeos/metabolismo , Sementes/química , Sementes/metabolismo
4.
BMC Bioinformatics ; 21(1): 15, 2020 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-31931703

RESUMO

BACKGROUND: Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints and default parameter sets. Thus, it is hard to impossible for users to estimate the influence of individual restrictions on the prediction results. RESULTS: Here, we present a systematic assessment of the impact of established and new constraints on sRNA target prediction both on a qualitative as well as computational level. This is done exemplarily based on the performance of IntaRNA, one of the most exact sRNA target prediction tools. IntaRNA provides various ways to constrain considered seed interactions, e.g. based on seed length, its accessibility, minimal unpaired probabilities, or energy thresholds, beside analogous constraints for the overall interaction. Thus, our results reveal the impact of individual constraints and their combinations. CONCLUSIONS: This provides both a guide for users what is important and recommendations for existing and upcoming sRNA target prediction approaches.We show on a large sRNA target screen benchmark data set that only by altering the parameter set, IntaRNA recovers 30% more verified interactions while becoming 5-times faster. This exemplifies the potential of seed, accessibility and interaction constraints for sRNA target prediction.


Assuntos
Bactérias/genética , Biologia Computacional/métodos , RNA Bacteriano/genética , Pequeno RNA não Traduzido/genética , Bactérias/química , Bactérias/metabolismo , RNA Bacteriano/química , RNA Bacteriano/metabolismo , Pequeno RNA não Traduzido/química , Pequeno RNA não Traduzido/metabolismo
5.
Food Microbiol ; 86: 103339, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31703886

RESUMO

The study of microbial communities associated with spontaneous fermentation of agave juice for tequila production is required to develop starter cultures that improve both yield and quality of the final product. Quantification by HPLC of primary metabolites produced during the fermentations was determined. A polyphasic approach using plate count, isolation and identification of microorganisms, denaturing gradient gel electrophoresis and next generation sequencing was carried out to describe the diversity and dynamics of yeasts and bacteria during small-scale spontaneous fermentations of agave juice from two-year samplings. High heterogeneity in microbial populations and fermentation parameters were observed, with bacteria showing higher diversity than yeast. The core microorganisms identified were Saccharomyces cerevisiae and Lactobacillus fermentum. Practices in tequila production changed during the two-year period, which affected microbial community structure and the time to end fermentation. Bacterial growth and concomitant lactic acid production were associated with low ethanol production, thus bacteria could be defined as contaminants in tequila fermentation and efforts to control them should be implemented.


Assuntos
Bebidas Alcoólicas/microbiologia , Bactérias/metabolismo , Leveduras/isolamento & purificação , Agave/química , Agave/microbiologia , Bebidas Alcoólicas/análise , Bactérias/química , Bactérias/genética , Bactérias/isolamento & purificação , Biodiversidade , Etanol/metabolismo , Fermentação , Cinética , Lactobacillus fermentum/química , Lactobacillus fermentum/metabolismo , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/metabolismo , Leveduras/química , Leveduras/genética , Leveduras/metabolismo
6.
Chemosphere ; 239: 124787, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31526987

RESUMO

Herein, the mutual effect between azo dye and the performance of electrochemically active bacteria (EAB) is investigated in detail, which is crucial to understand and control the bio-electrochemical systems (BESs) operation for azo dye containing wastewater treatment. EAB is enriched at controlled potential of -0.2 V vs Ag/AgCl in single-chamber BESs. Over 95% azo dye (alizarin yellow R (AYR)) was decolorized regardless of the initial AYR concentration ranging from 30 to 120 mg/L within 24 h. The fastest decolorization rate was obtained at AYR initial concentration of 70 mg/L, which was 4.25 times greater in the closed circuit BESs than that in the open circuit one. 16S rRNA gene based microbial community analysis showed that Geobacter was dominant in EAB with relative abundance increased from 77.98% (0 mg/L AYR) to 92.22% (70 mg/L AYR), indicating that azo dye selectively boosts the growth of exoelectrogens in electrode biofilm communities. Under electricity stimulation, extracellular process can be mutually conducted by azo dye compounds, which is favorable for accelerating reaction rate and avoiding of significant toxic effect on EAB.


Assuntos
Compostos Azo/química , Bactérias/química , Corantes/química , Eliminação de Resíduos Líquidos/métodos , Compostos Azo/metabolismo , Bactérias/genética , Bactérias/metabolismo , Biofilmes , Cor , Corantes/metabolismo , Técnicas Eletroquímicas/instrumentação , Técnicas Eletroquímicas/métodos , Eletrodos/microbiologia , Geobacter/genética , Geobacter/metabolismo , Microbiota/genética , RNA Ribossômico 16S , Águas Residuárias/química
7.
Comput Biol Chem ; 83: 107147, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31698160

RESUMO

Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent of cost-effective and advanced sequencing techniques. To manage the pace of annotation with that of data generation, there is a shift to computational approaches which are based on homology, sequence and structure-based features, protein-protein interaction networks, phylogenetic profiles, and physicochemical properties, etc. A combination of these features has proven to be promising for protein function prediction in terms of improving prediction accuracy. In the present work, we have employed a combination of features based on sequence, physicochemical property, subsequence and annotation features with a total of 9890 features extracted and/or calculated for 171,212 reviewed prokaryotic proteins of 9 bacterial phyla from UniProtKB, to train a supervised deep learning ensemble model with the aim to categorize a bacterial hypothetical/unreviewed protein's function into 1739 GO terms as functional classes. The proposed system being fully dedicated to bacterial organisms is a novel attempt amongst various existing machine learning based protein function prediction systems based on mixed organisms. Experimental results demonstrate the success of the proposed deep learning ensemble model based on deep neural network method with F1 measure of 0.7912 on the prepared Test dataset 1 of reviewed proteins.


Assuntos
Bactérias/química , Proteínas de Bactérias/metabolismo , Aprendizado Profundo , Bactérias/metabolismo , Proteínas de Bactérias/química
8.
BMC Bioinformatics ; 20(1): 541, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31675979

RESUMO

BACKGROUND: An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Inferring potential related microbes for diseases can not only promote disease prevention, diagnosis and treatment, but also provide valuable information for drug development. Considering that experimental methods are expensive and time-consuming, developing computational methods is an alternative choice. However, most of existing methods are biased towards well-characterized diseases and microbes. Furthermore, existing computational methods are limited in predicting potential microbes for new diseases. RESULTS: Here, we developed a novel computational model to predict potential human microbe-disease associations (MDAs) based on Weighted Meta-Graph (WMGHMDA). We first constructed a heterogeneous information network (HIN) by combining the integrated microbe similarity network, the integrated disease similarity network and the known microbe-disease bipartite network. And then, we implemented iteratively pre-designed Weighted Meta-Graph search algorithm on the HIN to uncover possible microbe-disease pairs by cumulating the contribution values of weighted meta-graphs to the pairs as their probability scores. Depending on contribution potential, we described the contribution degree of different types of meta-graphs to a microbe-disease pair with bias rating. Meta-graph with higher bias rating will be assigned greater weight value when calculating probability scores. CONCLUSIONS: The experimental results showed that WMGHMDA outperformed some state-of-the-art methods with average AUCs of 0.9288, 0.9068 ±0.0031 in global leave-one-out cross validation (LOOCV) and 5-fold cross validation (5-fold CV), respectively. In the case studies, 9, 19, 37 and 10, 20, 45 out of top-10, 20, 50 candidate microbes were manually verified by previous reports for asthma and inflammatory bowel disease (IBD), respectively. Furthermore, three common human diseases (Crohn's disease, Liver cirrhosis, Type 1 diabetes) were adopted to demonstrate that WMGHMDA could be efficiently applied to make predictions for new diseases. In summary, WMGHMDA has a high potential in predicting microbe-disease associations.


Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/microbiologia , Biologia Computacional/métodos , Algoritmos , Bactérias/química , Fenômenos Fisiológicos Bacterianos , Simulação por Computador , Humanos , Serviços de Informação
9.
Mikrochim Acta ; 186(12): 820, 2019 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-31748898

RESUMO

This review (with 118 refs.) discusses the progress made in electroanalytical methods based on the use of organic and inorganic nanomaterials for the determination of bacteria, specifically of E. coli, Salmonella, Staphylococcus, Mycobacterium, Listeria and Klebsiella species. We also discuss advantages and limitations of electrochemical methods. Strategies based on the use of aptamers, DNA and antibodies are covered. Following an introduction into electrochemical biosensing, a first large section covers methods for pathogen detection using metal nanoparticles, with subsections on silver nanoparticles, gold nanoparticles, magnetic nanoparticles and carbon-based nanomaterials. A second large section covers methods based on the use of organic nanocomposites, graphene and its derivatives. Other nanoparticles are treated in a final section. Several tables are presented that give an overview on the wealth of methods and materials. A concluding section summarizes the current status, addresses challenges, and gives an outlook on potential future trends. Graphical abstract This review demonstrates the progress made in electroanalytical methods based on the use of organic and inorganic nanomaterials for the detection and determination of pathogenic bacteria. We also discuss advantages and limitations of electrochemical methods. Strategies based on the use of aptamers, DNA and antibodies are covered.


Assuntos
Bactérias/química , Nanoestruturas/química , Técnicas Biossensoriais/métodos , Carbono/química , Técnicas Eletroquímicas/métodos , Eletrodos , Ouro/química , Nanopartículas Metálicas/química , Oxirredução , Prata/química , Propriedades de Superfície
10.
Emerg Microbes Infect ; 8(1): 1688-1700, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31749408

RESUMO

Resistance to ß-lactams is one of the most serious problems associated with Gram-negative infections. ß-Lactamases are able to hydrolyze ß-lactams such as cephalosporins and/or carbapenems. Evolutionary origin of metallo-ß-lactamases (MBLs), conferring critical antibiotic resistance threats, remains unknown. We discovered PNGM-1, the novel subclass B3 MBL, in deep-sea sediments that predate the antibiotic era. Here, our phylogenetic analysis suggests that PNGM-1 yields insights into the evolutionary origin of subclass B3 MBLs. We reveal the structural similarities between tRNase Zs and PNGM-1, and demonstrate that PNGM-1 has both MBL and tRNase Z activities, suggesting that PNGM-1 is thought to have evolved from a tRNase Z. We also show kinetic and structural comparisons between PNGM-1 and other proteins including subclass B3 MBLs and tRNase Zs. These comparisons revealed that the B3 MBL activity of PNGM-1 is a promiscuous activity and subclass B3 MBLs are thought to have evolved through PNGM-1 activity.


Assuntos
Bactérias/enzimologia , Proteínas de Bactérias/genética , Evolução Molecular , Sedimentos Geológicos/microbiologia , beta-Lactamases/genética , Sequência de Aminoácidos , Bactérias/química , Bactérias/classificação , Bactérias/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Domínio Catalítico , Filogenia , beta-Lactamases/química , beta-Lactamases/metabolismo
11.
J Agric Food Chem ; 67(46): 12675-12684, 2019 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-31661963

RESUMO

Metabolic syndrome (MSyn) constitutes a litany of pathophysiological conditions, such as central adiposity, hypertension, dyslipidemia, and hyperglycemia. As a result of the epidemic levels of MSyn, several efforts have been made to identify the etiologies of the condition and develop methods by which to reduce its prevalence. The attenuation of the gut microflora ratio of Firmicutes/Bacteroidetes through bioactive compounds found in the Mediterranean diet, dietary polysaccharides, and pre- and probiotics can be used as functional foods to improve derangements in cardiometabolic markers correlated with the development of MSyn. Although more studies are needed to understand the role of manipulating the gut microbiota in health and disease in human models, this review based on current data from epidemiologic studies and clinical trials will serve as a review to elucidate the role nutrition plays in attenuating the gut microbiota in preventing and managing MSyn.


Assuntos
Bactérias/isolamento & purificação , Microbioma Gastrointestinal , Síndrome Metabólica/dietoterapia , Síndrome Metabólica/microbiologia , Animais , Bactérias/química , Bactérias/classificação , Dieta , Humanos , Prebióticos/análise
12.
Molecules ; 24(20)2019 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-31614904

RESUMO

S1 domain, a structural variant of one of the "oldest" OB-folds (oligonucleotide/oligosaccharide-binding fold), is widespread in various proteins in three domains of life: Bacteria, Eukaryotes, and Archaea. In this study, it was shown that S1 domains of bacterial, eukaryotic, and archaeal proteins have a low percentage of identity, which indicates the uniqueness of the scaffold and is associated with protein functions. Assessment of the predisposition of tertiary flexibility of S1 domains using computational and statistical tools showed similar structural features and revealed functional flexible regions that are potentially involved in the interaction of natural binding partners. In addition, we analyzed the relative number and distribution of S1 domains in all domains of life and established specific features based on sequences and structures associated with molecular functions. The results correlate with the presence of repeats of the S1 domain in proteins containing the S1 domain in the range from one (bacterial and archaeal) to 15 (eukaryotic) and, apparently, are associated with the need for individual proteins to increase the affinity and specificity of protein binding to ligands.


Assuntos
Proteínas de Bactérias/química , Oligonucleotídeos/química , Oligossacarídeos/química , Dobramento de Proteína , Sequência de Aminoácidos/genética , Proteínas Arqueais/química , Bactérias/química , Eucariotos/química , Ligação Proteica/genética , Domínios Proteicos
13.
BMC Genomics ; 20(1): 738, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615397

RESUMO

BACKGROUND: More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need. RESULTS: We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs. CONCLUSIONS: EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.


Assuntos
Bactérias/genética , Cromossomos Bacterianos/química , Algoritmos , Bactérias/química , Biologia Computacional , Modelos Moleculares , Conformação Molecular , Software
14.
Respir Res ; 20(1): 210, 2019 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-31519188

RESUMO

BACKGROUND: Acute exacerbations of chronic obstructive pulmonary disease (AECOPD) and asthma are associated with a variety of precipitating factors including infection. This study assessed the infective viral etiologies by real-time multiplex polymerase chain reaction of patients hospitalized with AECOPD and asthma exacerbations. In addition, infective etiologies were assessed for association with the clinical outcome of the patients. METHODS: Adults admitted with AECOPD and asthma exacerbations between August 2016 and July 2017 were recruited. Nasopharyngeal aspirate (NPA) samples were obtained from the patients within 1-2 days of admission and subjected to pathogen detection and human rhinovirus (HRV) typing. RESULTS: Altogether 402 patients with AECOPD, 80 stable COPD, 100 asthma exacerbation and 21 stable asthma subjects were recruited. Among those admitted for AECOPD and asthma exacerbations, 141(35.1%) and 45(45.0%) respectively had pathogens identified in the NPA specimens. The commonest virus identified was influenza A followed by HRV. HRV typing identified HRV-A and HRV-C as the more common HRV with a wide variety of genotypes. Identification of pathogens in NPA or HRV typing otherwise did not affect clinical outcomes including the hospital length of stay, readmission rates and mortality except that identification of pathogens in asthma exacerbation was associated with a lower rate of readmissions at 30 and 60 days. CONCLUSIONS: Many respiratory viruses were associated with AECOPD and asthma exacerbation. HRV-A and HRV-C were the more common HRV associated with exacerbations. Identification of pathogens in NPA was associated with less readmissions for asthma patients at 30 and 60 days. TRIAL REGISTRATION: ClinicalTrials.gov NCT02866357 .


Assuntos
Asma/microbiologia , Asma/virologia , Bactérias/química , Doença Pulmonar Obstrutiva Crônica/microbiologia , Doença Pulmonar Obstrutiva Crônica/virologia , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Rhinovirus/química , Idoso , Idoso de 80 Anos ou mais , Feminino , Hospitalização , Humanos , Vírus da Influenza A , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular , Readmissão do Paciente/estatística & dados numéricos , Testes de Função Respiratória , Resultado do Tratamento
15.
Nanoscale ; 11(38): 17725-17735, 2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31549120

RESUMO

The intrinsic properties of paper, such as its light weight, flexibility, foldability, portability and degradability, have led to increasing interest in fabricating flexible energy storage devices and power supply devices on paper-based substrates. Hereby, a robust honeycomb-like thermoelectric generator (TEG) inspired by the origami and kirigami techniques was established in the present study. A thermoelectric ink with the properties of high electrical conductivity and low thermal conductivity was formulated by Bi2Te3 and bacterial cellulose (BC). The formulated ink was printed on a paper surface using a facile processing method. The manufactured paper was further folded and bonded to fabricate a honeycomb-like TEG. This honeycomb-like paper-based TEG exhibited 96 p-n junctions, achieving a maximum voltage and output power of ∼70.5 mV and ∼596 nW, respectively, at a 55 K temperature difference. Moreover, the honeycomb structure was able to withstand a large number of bending and stretching cycles while maintaining its pristine structure. This unique honeycomb structure thus provides a new strategy for future development of paper-based TEGs.


Assuntos
Bactérias/química , Celulose/química , Condutividade Elétrica , Fontes de Energia Elétrica , Nanofibras/química
16.
Inorg Chem ; 58(19): 12843-12853, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31502453

RESUMO

A series of five compounds TpMesMFla (TpMes = hydrotris(3-mesityl)pyrazolylborate; M = Mn, Fe, Co, Ni, Zn; Fla = 3-hydroxyflavonolate) has been synthesized as models for the 2,4-quercetin dioxygenase, QueD. The structures have been determined and the complexes proved to be isomorphous. Considering the structures more closely revealed that they differ in the degree of delocalization in the chelate ring formed through the binding of the two O donors of the flavonolate to the metal center, which is also supported by the results of UV-vis and IR spectroscopic investigations. The resulting trend (Zn/Fe > Co > Mn > Ni) is, however, not in line with the one that was found investigating the redox properties of the complexes by cyclic voltammetry (Zn > Fe > Ni > Co > Mn). Notably, from CV clear-cut information could be derived, as the complexes exhibited exceptionally well-behaved quasi-reversible redox transitions, indicating that the Tp ligand stabilizes the flavonolate radical formed in the oxidation process rather well. The fact that the rates, with which the complexes react with O2 in DMF solution, correlate with the position of the flavonolate redox couples, suggest that these reactions proceed via the initial electron transfer from the flavonolate to O2. After the O2 reaction, salicylic acid was identified as one of the products, the formation of which can be explained by the hydrolysis of the depside that should form upon a dioxygenation similar to the QueD enzyme-catalyzed reaction. 18O labeling experiments confirmed the presence of O2 derived O atoms. Mechanistic inferences based on the above results are discussed.


Assuntos
Bactérias/enzimologia , Complexos de Coordenação/química , Dioxigenases/química , Flavonóis/química , Pirazóis/química , Bactérias/química , Materiais Biomiméticos/química , Boratos/química , Catálise , Cristalografia por Raios X , Ligantes , Modelos Moleculares
17.
Phys Chem Chem Phys ; 21(37): 20750-20756, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31513191

RESUMO

"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.


Assuntos
Nanotubos de Peptídeos/química , Peptídeos Cíclicos/química , Anti-Infecciosos/química , Bactérias/química , Concentração de Íons de Hidrogênio , Bicamadas Lipídicas/química , Simulação de Dinâmica Molecular
18.
Biomed Res Int ; 2019: 7851251, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31559313

RESUMO

Over 1,000 compounds, including ecteinascidin-743 and didemnin B, have been isolated from ascidians, with most having bioactive properties such as antimicrobial, antitumor, and enzyme-inhibiting activities. In recent years, direct and indirect evidence has shown that some bioactive compounds isolated from ascidians are not produced by ascidians themselves but by their symbiotic microorganisms. Isolated culturable bacteria associated with ascidians and investigating their potential bioactivity are an important approach for discovering novel compounds. In this study, a total of 269 bacteria were isolated from the ascidian Styela clava collected from the coast of Weihai in the north of the Yellow Sea, China. Phylogenetic relationships among 183 isolates were determined using their 16S rRNA gene sequences. Isolates were tested for antimicrobial activity against seven indicator strains, and an antiproliferative activity assay was performed to test for inhibition of human hepatocellular carcinoma Bel 7402 and human cervical carcinoma HeLa cell proliferation. Our results showed that the isolates belonged to 26 genera from 18 families in four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes). Bacillus and Streptomyces were the most dominant genera; 146 strains had potent antimicrobial activities and inhibited at least one of the indicator strains. Crude extracts from 29 strains showed antiproliferative activity against Bel 7402 cells with IC50 values below 500 µg·mL-1, and 53 strains showed antiproliferative activity against HeLa cells, with IC50 values less than 500 µg·mL-1. Our results suggest that culturable bacteria associated with the ascidian Styela clava may be a promising source of novel bioactive compounds.


Assuntos
Anti-Infecciosos/isolamento & purificação , Bactérias/genética , Filogenia , Urocordados/microbiologia , Animais , Anti-Infecciosos/química , Anti-Infecciosos/farmacologia , Antineoplásicos/química , Antineoplásicos/isolamento & purificação , Antineoplásicos/farmacologia , Bactérias/química , Bactérias/isolamento & purificação , Bactérias/patogenicidade , Biodiversidade , Proliferação de Células/efeitos dos fármacos , China , Inibidores Enzimáticos/química , Inibidores Enzimáticos/isolamento & purificação , Inibidores Enzimáticos/farmacologia , Firmicutes/química , Firmicutes/genética , Firmicutes/isolamento & purificação , Células HeLa , Humanos , Proteobactérias/química , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Urocordados/química , Urocordados/genética
19.
Mater Sci Eng C Mater Biol Appl ; 104: 109963, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31499992

RESUMO

Bacterial nanocellulose (BNC) has emerged as a natural biopolymer of significant importance in diverse technological areas due to its incredible physicochemical and biological characteristics. However, the high capital investments, production cost and lack of well-organized scale-up processes resulting in low BNC production are the major impediments need to be resolved. This review enfolds the three different and important portions of BNC. Firstly, advancement in production technologies of BNC like cell-free extract technology, static intermittent fed batch technology and novel cost-effective substrates that might surmount the barriers associated with BNC production at industrial level. Secondly, as BNC and its composites (with other polymers/nanoparticles) represents the utmost material of preference in current regenerative and diagnostic medicine, therefore recently reported biomedical applications of BNC and functionalized BNC in drug delivery, tissue engineering, antimicrobial wound healing and biosensing are widely been focused here. The third and the most important aspect of this review is an in-depth discussion of various pitfalls associated with BNC production. Recent trends in BNC research to overcome the existing snags that might pave a way for industrial scale production of BNC thereby facilitating its feasible application in various fields are highlighted.


Assuntos
Bactérias/química , Celulose/química , Nanopartículas/química , Animais , Biopolímeros/química , Sistemas de Liberação de Medicamentos/métodos , Humanos
20.
Anal Bioanal Chem ; 411(26): 7027-7038, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31486868

RESUMO

Biotyping using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) mass spectroscopy (MS) has revolutionized microbiology by allowing clinicians and scientists to rapidly identify microbes at genus and species levels. The present study extensively assesses the suitability and reliability of MALDI-ToF biotyping of 14 different aerobic and anaerobic bacterial species as pure and mixed cultures. Reliable identification at species level was possible from biomaterial of older colonies and even frozen biomaterial, although this was species dependent. Using standard instrument settings and direct application of biomaterial onto the MALDI-ToF target plates, it was determined that the cell densities necessary for completely reliable identification of pure cultures varied between 2.40 × 108 and 1.10 × 1010 viable cell counts (VCCs) per mL, depending on the species. Evaluation of the mixed culture algorithm of the Bruker Biotyper® software showed that the performance of the algorithm depends greatly on the targeted species, on their phylogenetic distance, and on their ratio of VCC per mL in the mixed culture. Hence, the use of MALDI-ToF-MS with incorporation of the mixed culture algorithm of the software is a useful pre-screening tool for early identification of contaminants, but due to the great variability in performance between different species and the usually unknown percentage of the possible contaminant in the mixture, it is advisable to combine this method with other microbiology methods.


Assuntos
Bactérias/classificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Bactérias/química , Bactérias/citologia , Infecções Bacterianas/microbiologia , Carga Bacteriana/métodos , Técnicas Bacteriológicas/métodos , Humanos , Viabilidade Microbiana
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