Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 2.401
Filtrar
1.
Artigo em Inglês | MEDLINE | ID: mdl-33017936

RESUMO

Nanopore-based approaches for the sequencing of DNA and RNA molecules are promising technologies with potential applications in clinical genomics. These approaches have generated large numbers of time series objects over the years, however, it remains a challenge to accurately decipher the underlying nucleotide sequence corresponding to a given signal. By using a combination of consensus signal averaging and stream monitoring of variable-length motifs, we outline an online pattern matching framework that can efficiently locate consensus sequences in real world Nanopore datasets. We demonstrate the applicability of our proposed framework across two use-cases: demultiplexing of DNA barcodes and multiple motif site identification in RNA transcripts.


Assuntos
Nanoporos , Sequência de Bases , Consenso , DNA , Nucleotídeos
2.
Commun Biol ; 3(1): 538, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: covidwho-807978

RESUMO

The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo, a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per sample on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome sample, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.


Assuntos
Betacoronavirus/genética , Biologia Computacional/métodos , Genoma Humano , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento Completo do Genoma/métodos , Betacoronavirus/patogenicidade , Telefone Celular/instrumentação , Biologia Computacional/instrumentação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Metilação de DNA , Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Humanos , Nanoporos , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Sequenciamento Completo do Genoma/instrumentação
3.
Commun Biol ; 3(1): 538, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-32994472

RESUMO

The advent of portable nanopore sequencing devices has enabled DNA and RNA sequencing to be performed in the field or the clinic. However, advances in in situ genomics require parallel development of portable, offline solutions for the computational analysis of sequencing data. Here we introduce Genopo, a mobile toolkit for nanopore sequencing analysis. Genopo compacts popular bioinformatics tools to an Android application, enabling fully portable computation. To demonstrate its utility for in situ genome analysis, we use Genopo to determine the complete genome sequence of the human coronavirus SARS-CoV-2 in nine patient isolates sequenced on a nanopore device, with Genopo executing this workflow in less than 30 min per sample on a range of popular smartphones. We further show how Genopo can be used to profile DNA methylation in a human genome sample, illustrating a flexible, efficient architecture that is suitable to run many popular bioinformatics tools and accommodate small or large genomes. As the first ever smartphone application for nanopore sequencing analysis, Genopo enables the genomics community to harness this cheap, ubiquitous computational resource.


Assuntos
Betacoronavirus/genética , Biologia Computacional/métodos , Genoma Humano , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento Completo do Genoma/métodos , Betacoronavirus/patogenicidade , Telefone Celular/instrumentação , Biologia Computacional/instrumentação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Metilação de DNA , Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Humanos , Nanoporos , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Sequenciamento Completo do Genoma/instrumentação
4.
Waste Manag ; 116: 166-178, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32799098

RESUMO

Platinum group metals have gained significant interest due to their unique characteristics, which make them the main constituents in advanced applications. In this work, we introduce new pH-dependent optical mesocaptors for the colorimetric monitoring and separation of Au(III) from E-waste leach liquors without a preconcentration process. The mesoporous silica nanospheres are fabricated via simple, reproducible, and low-cost procedures. The optical mesocaptor is designed via indirect immobilization of thiazole yellow G (TYG) and amacid yellow M (AYM) chromogenic probes onto mesoporous nanostructured scaffolds. The silanol groups in the mesopores of silica surface robustly anchored dilauryl dimethyl ammonium bromide (DDAB) linker to induce the interactions with the TYG and AYM chelates, thereby leading to the fashioning of a stable optical mesocaptors without releasing of the chelates throughout adsorption and sensing assays. The finding provides evidence of the capability of the synthesized decorated new nanostructured sensor shows excellent sensitivity toward Au(III) with a limit of detection (LOD) as low as 1.16 µg L-1. Furthermore, the new sensors were able to selectively detect Au(III) in solution with multi ions components.


Assuntos
Resíduo Eletrônico , Nanoporos , Adsorção , Ouro/análise , Dióxido de Silício
5.
BMC Bioinformatics ; 21(1): 343, 2020 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-32758139

RESUMO

BACKGROUND: Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioinformatic algorithms for the analysis of raw nanopore signal data. However, comparing raw nanopore signals to a biological reference sequence is a computationally complex task. The dynamic programming algorithm called Adaptive Banded Event Alignment (ABEA) is a crucial step in polishing sequencing data and identifying non-standard nucleotides, such as measuring DNA methylation. Here, we parallelise and optimise an implementation of the ABEA algorithm (termed f5c) to efficiently run on heterogeneous CPU-GPU architectures. RESULTS: By optimising memory, computations and load balancing between CPU and GPU, we demonstrate how f5c can perform ∼3-5 × faster than an optimised version of the original CPU-only implementation of ABEA in the Nanopolish software package. We also show that f5c enables DNA methylation detection on-the-fly using an embedded System on Chip (SoC) equipped with GPUs. CONCLUSIONS: Our work not only demonstrates that complex genomics analyses can be performed on lightweight computing systems, but also benefits High-Performance Computing (HPC). The associated source code for f5c along with GPU optimised ABEA is available at https://github.com/hasindu2008/f5c .


Assuntos
Gráficos por Computador , Nanoporos , Processamento de Sinais Assistido por Computador , Algoritmos , Biologia Computacional , Bases de Dados como Assunto , Genoma Humano , Humanos , Análise de Sequência
6.
Ecotoxicol Environ Saf ; 204: 111066, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32781344

RESUMO

In this study, an iron-doped metal-organic framework (MOF) Fe/ZIF-8 was synthesized from ZIF-8 at room temperature. Direct carbonization of Fe/ZIF-8 under a nitrogen atmosphere produced nanoporous nitrogen doped carbon nanoparticles decorated with Fe component (Fe/NC). The Fe/NC exhibited a large surface area (1221.185 m2 g-1) and narrow pore-size distribution (3-5 nm). The nanoporous Fe/NC components along with Nafion were used to modify a glassy carbon electrode for the electrochemical determination of chloramphenicol and metronidazole via linear sweep voltammetry. Under optimal conditions, the reduction peak currents (observed at -0.237 V and -0.071 V vs. Ag/AgCl) of these analytes increased linearly with increasing chloramphenicol and metronidazole concentrations in the range of 0.1-100 µM and 0.5-30 µM, with the detection limits estimated to be 31 nM and 165 nM, respectively. This result was attributed to the large surface area, porous structure, high nitrogen content, and as well as the electrocatalytic effect of Fe atoms embeded in the carbon support. The proposed sensor was used for chloramphenicol and metronidazole analysis in samples, providing satisfactory results.


Assuntos
Carbono/química , Cloranfenicol/análise , Técnicas Eletroquímicas/métodos , Ferro/química , Estruturas Metalorgânicas/química , Metronidazol/análise , Nitrogênio/química , Animais , Cloranfenicol/urina , Eletrodos , Humanos , Limite de Detecção , Metronidazol/urina , Leite/química , Nanoporos , Soluções Oftálmicas/química , Porosidade , Comprimidos/química
7.
Nat Commun ; 11(1): 4025, 2020 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-32788667

RESUMO

Droplet-based high throughput single cell sequencing techniques tremendously advanced our insight into cell-to-cell heterogeneity. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. In consequence, information on splicing and sequence heterogeneity is lost. To overcome this limitation, several approaches that use long-read sequencing were introduced recently. Yet, those techniques are limited by low sequencing depth and/or lacking or inaccurate assignment of unique molecular identifiers (UMIs), which are critical for elimination of PCR bias and artifacts. We introduce ScNaUmi-seq, an approach that combines the high throughput of Oxford Nanopore sequencing with an accurate cell barcode and UMI assignment strategy. UMI guided error correction allows to generate high accuracy full length sequence information with the 10x Genomics single cell isolation system at high sequencing depths. We analyzed transcript isoform diversity in embryonic mouse brain and show that ScNaUmi-seq allows defining splicing and SNVs (RNA editing) at a single cell level.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento por Nanoporos , Nanoporos , Transcriptoma , Animais , Encéfalo , Expressão Gênica , Perfilação da Expressão Gênica , Genômica , Camundongos , Camundongos Endogâmicos C57BL , Isoformas de Proteínas , Receptores de AMPA/genética , Análise de Sequência de DNA/métodos , Análise de Sequência de RNA/métodos
8.
BMC Bioinformatics ; 21(Suppl 12): 302, 2020 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-32703149

RESUMO

BACKGROUND: De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. RESULTS: In this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. CONCLUSION: To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.


Assuntos
Algoritmos , Transcriptoma/genética , Bases de Dados Genéticas , Humanos , Células MCF-7 , Nanoporos , RNA-Seq , Reprodutibilidade dos Testes
9.
Nucleic Acids Res ; 48(15): e88, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32710620

RESUMO

DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no single method can identify the location, direction and speed of replication forks with high resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthesis, which allows for labeling of replicating or repaired DNA. Here, we demonstrate the use of the Oxford Nanopore Technologies MinION to detect 11 different thymidine analogs including CldU, BrdU, IdU as well as EdU alone or coupled to Biotin and other bulky adducts in synthetic DNA templates. We also show that the large adduct Biotin can be distinguished from the smaller analog IdU, which opens the possibility of using analog combinations to identify the location and direction of DNA synthesis. Furthermore, we detect IdU label on single DNA molecules in the genome of mouse pluripotent stem cells and using CRISPR/Cas9-mediated enrichment, determine replication rates using newly synthesized DNA strands in human mitochondrial DNA. We conclude that this novel method, termed Replipore sequencing, has the potential for on target examination of DNA replication in a wide range of biological contexts.


Assuntos
Bromodesoxiuridina/química , Sequenciamento por Nanoporos , Timidina/genética , Animais , Biotina/química , Biotina/genética , Proliferação de Células/efeitos dos fármacos , Proliferação de Células/genética , Reparo do DNA/efeitos dos fármacos , Reparo do DNA/genética , Replicação do DNA/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Camundongos , Nanoporos , Timidina/química
10.
Sheng Wu Gong Cheng Xue Bao ; 36(5): 811-819, 2020 May 25.
Artigo em Chinês | MEDLINE | ID: mdl-32567264

RESUMO

Sequencing technology has been greatly improved in terms of throughput and cost. The single-molecule nanopore DNA sequencing, one of the major branches of the third-generation sequencing technology, has made great contributions in the fields of medicine and life sciences due to its advantages of ultra-long reading length, real-time detection and direct detection of base methylation modification, etc. This article briefly describes the principle of nanopore sequencing technology, and discusses its application in clinical, animal, plant, bacterial and virus fields and its future development direction.


Assuntos
DNA , Sequenciamento por Nanoporos , Nanoporos , Animais , Sequência de Bases , DNA/química , DNA/genética , Humanos , Sequenciamento por Nanoporos/tendências , Pesquisa/tendências , Análise de Sequência de DNA/tendências
11.
Small ; 16(32): e2002169, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32578378

RESUMO

The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates and are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis and impeding epidemic containment. Combining the advantages of targeted amplification and long-read, real-time nanopore sequencing, herein, nanopore targeted sequencing (NTS) is developed to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h, with a limit of detection of ten standard plasmid copies per reaction. Compared with its specificity for five common respiratory viruses, the specificity of NTS for SARS-CoV-2 reaches 100%. Parallel testing with approved real-time reverse transcription-polymerase chain reaction kits for SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases show that NTS identifies more infected patients (22/61) as positive, while also effectively monitoring for mutated nucleic acid sequences, categorizing types of SARS-CoV-2, and detecting other respiratory viruses in the test sample. NTS is thus suitable for COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses and pathogens.


Assuntos
Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Nanoporos , Técnicas de Amplificação de Ácido Nucleico/métodos , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Betacoronavirus/classificação , Infecções por Coronavirus/epidemiologia , DNA Viral/genética , DNA Viral/isolamento & purificação , Genes Virais , Humanos , Limite de Detecção , Mutação , Nanotecnologia , Técnicas de Amplificação de Ácido Nucleico/estatística & dados numéricos , Pandemias , Pneumonia Viral/epidemiologia , RNA Viral/genética , RNA Viral/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Sensibilidade e Especificidade
12.
Small ; 16(32): e2002169, 2020 08.
Artigo em Inglês | MEDLINE | ID: covidwho-612774

RESUMO

The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates and are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis and impeding epidemic containment. Combining the advantages of targeted amplification and long-read, real-time nanopore sequencing, herein, nanopore targeted sequencing (NTS) is developed to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h, with a limit of detection of ten standard plasmid copies per reaction. Compared with its specificity for five common respiratory viruses, the specificity of NTS for SARS-CoV-2 reaches 100%. Parallel testing with approved real-time reverse transcription-polymerase chain reaction kits for SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases show that NTS identifies more infected patients (22/61) as positive, while also effectively monitoring for mutated nucleic acid sequences, categorizing types of SARS-CoV-2, and detecting other respiratory viruses in the test sample. NTS is thus suitable for COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses and pathogens.


Assuntos
Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Nanoporos , Técnicas de Amplificação de Ácido Nucleico/métodos , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Betacoronavirus/classificação , Infecções por Coronavirus/epidemiologia , DNA Viral/genética , DNA Viral/isolamento & purificação , Genes Virais , Humanos , Limite de Detecção , Mutação , Nanotecnologia , Técnicas de Amplificação de Ácido Nucleico/estatística & dados numéricos , Pandemias , Pneumonia Viral/epidemiologia , RNA Viral/genética , RNA Viral/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real , Infecções Respiratórias/diagnóstico , Infecções Respiratórias/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Sensibilidade e Especificidade
13.
Environ Sci Pollut Res Int ; 27(22): 28132-28145, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32410193

RESUMO

To evaluate the adsorption mechanism and performance of phosphate onto the composite of low-cost biochar and iron oxide, four biochar-iron oxides, namely biochar-magnetite (BC-M), biochar-ferrihydrite (BC-F), biochar-goethite (BC-G), and biochar-hematite (BC-H), were prepared by fabricating iron oxide to porous biochar. The biochar-iron oxides had huge surface areas of 691-864 m2/g and average pore diameters of 3.4-4.0 nm. Based on the characterization analysis of FTIR, XRD, XPS, and zeta potential, the interactions of electrostatic attraction, ligand exchange, and deposition dominated the phosphate adsorption onto biochar-iron oxides. The maximum adsorption capacity of phosphate followed the order of BC-G > BC-F > BC-H > BC-M. The isotherm data of BC-M and BC-H were well fitted by the Langmuir and Freundlich models, while those of BC-G and BC-F followed the Langmuir model. In addition, BC-M, BC-F, BC-G, and BC-H owned excellent regeneration ability and adsorption performance in practical (simulated) wastewater environment. Then the biochar-iron oxides exerted extensive and satisfactory prospect in wastewater remediation and recycling application in soil.


Assuntos
Nanoporos , Poluentes Químicos da Água , Adsorção , Carvão Vegetal , Compostos Férricos , Ferro , Cinética , Óxidos , Fosfatos
14.
ACS Nano ; 14(6): 7659-7665, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32432461

RESUMO

Since the outbreak of the severe respiratory disease caused by the novel coronavirus (COVID-19), the use of face masks has become ubiquitous worldwide to control the rapid spread of this pandemic. As a result, the world is currently facing a face mask shortage, and some countries have placed limits on the number of masks that can be bought by each person. Although the surgical grade N95 mask provides the highest level of protection currently available, its filtration efficiency for sub-300 nm particles is around 85% due to its wider pore size (∼300 nm). Because the COVID-19 virus shows a diameter of around 65-125 nm, there is a need for developing more efficient masks. To overcome these issues, we demonstrate the development of a flexible, nanoporous membrane to achieve a reusable N95 mask with a replaceable membrane and enhanced filtration efficiency. We first developed a flexible nanoporous Si-based template on a silicon-on-insulator wafer using KOH etching and then used the template as a hard mask during a reactive ion etching process to transfer the patterns onto a flexible and lightweight (<0.12 g) polymeric membrane. Pores with sizes down to 5 nm were achieved with a narrow distribution. Theoretical calculations show that airflow rates above 85 L/min are possible through the mask, which confirms its breathability over a wide range of pore sizes, densities, membrane thicknesses, and pressure drops. Finally, the membrane is intrinsically hydrophobic, which contributes to antifouling and self-cleaning as a result of droplets rolling and sliding on the inclined mask area.


Assuntos
Betacoronavirus , Infecções por Coronavirus/prevenção & controle , Máscaras , Nanoporos , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Microbiologia do Ar , Betacoronavirus/ultraestrutura , Infecções por Coronavirus/transmissão , Desenho de Equipamento , Humanos , Interações Hidrofóbicas e Hidrofílicas , Membranas Artificiais , Microscopia Eletrônica de Varredura , Nanoporos/ultraestrutura , Pneumonia Viral/transmissão , Polímeros , Porosidade , Silício
15.
ACS Nano ; 14(6): 7659-7665, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: covidwho-324479

RESUMO

Since the outbreak of the severe respiratory disease caused by the novel coronavirus (COVID-19), the use of face masks has become ubiquitous worldwide to control the rapid spread of this pandemic. As a result, the world is currently facing a face mask shortage, and some countries have placed limits on the number of masks that can be bought by each person. Although the surgical grade N95 mask provides the highest level of protection currently available, its filtration efficiency for sub-300 nm particles is around 85% due to its wider pore size (∼300 nm). Because the COVID-19 virus shows a diameter of around 65-125 nm, there is a need for developing more efficient masks. To overcome these issues, we demonstrate the development of a flexible, nanoporous membrane to achieve a reusable N95 mask with a replaceable membrane and enhanced filtration efficiency. We first developed a flexible nanoporous Si-based template on a silicon-on-insulator wafer using KOH etching and then used the template as a hard mask during a reactive ion etching process to transfer the patterns onto a flexible and lightweight (<0.12 g) polymeric membrane. Pores with sizes down to 5 nm were achieved with a narrow distribution. Theoretical calculations show that airflow rates above 85 L/min are possible through the mask, which confirms its breathability over a wide range of pore sizes, densities, membrane thicknesses, and pressure drops. Finally, the membrane is intrinsically hydrophobic, which contributes to antifouling and self-cleaning as a result of droplets rolling and sliding on the inclined mask area.


Assuntos
Betacoronavirus , Infecções por Coronavirus/prevenção & controle , Máscaras , Nanoporos , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Microbiologia do Ar , Betacoronavirus/ultraestrutura , Infecções por Coronavirus/transmissão , Desenho de Equipamento , Humanos , Interações Hidrofóbicas e Hidrofílicas , Membranas Artificiais , Microscopia Eletrônica de Varredura , Nanoporos/ultraestrutura , Pneumonia Viral/transmissão , Polímeros , Porosidade , Silício
16.
Curr Opin Biotechnol ; 63: 200-209, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32387643

RESUMO

Functional nanopores play an essential role in many biotechnological applications such as sensing, or drug delivery. Prominent examples are polymer functionalized ceramic or solid state nanopores. Intensive research efforts led to a discovery of a plethora of polymer functionalized nanopores demonstrating gated molecular transport upon basically all common stimuli. Nevertheless, nature's biological pore transport precision is unreached. This can be, among others, ascribed to limits in design precision especially with respect to functionalization. Recent trends in polymer functionalized nanopores address the role of confinement and polymerization control, strategies toward more sustainable reaction conditions, such as visible light initiation and strategies toward nanoscale local placement of polymer functionalization. The resulting multi-stimuli responsive nanopore performance enables concerted release or transport, side selective separation and selective detection.


Assuntos
Nanoporos , Biotecnologia , Polímeros
17.
PLoS One ; 15(4): e0231423, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32302323

RESUMO

Recent advances in canine intestinal organoids have expanded the option for building a better in vitro model to investigate translational science of intestinal physiology and pathology between humans and animals. However, the three-dimensional geometry and the enclosed lumen of canine intestinal organoids considerably hinder the access to the apical side of epithelium for investigating the nutrient and drug absorption, host-microbiome crosstalk, and pharmaceutical toxicity testing. Thus, the creation of a polarized epithelial interface accessible from apical or basolateral side is critical. Here, we demonstrated the generation of an intestinal epithelial monolayer using canine biopsy-derived colonic organoids (colonoids). We optimized the culture condition to form an intact monolayer of the canine colonic epithelium on a nanoporous membrane insert using the canine colonoids over 14 days. Transmission and scanning electron microscopy revealed a physiological brush border interface covered by the microvilli with glycocalyx, as well as the presence of mucin granules, tight junctions, and desmosomes. The population of stem cells as well as differentiated lineage-dependent epithelial cells were verified by immunofluorescence staining and RNA in situ hybridization. The polarized expression of P-glycoprotein efflux pump was confirmed at the apical membrane. Also, the epithelial monolayer formed tight- and adherence-junctional barrier within 4 days, where the transepithelial electrical resistance and apparent permeability were inversely correlated. Hence, we verified the stable creation, maintenance, differentiation, and physiological function of a canine intestinal epithelial barrier, which can be useful for pharmaceutical and biomedical researches.


Assuntos
Colo/citologia , Células Epiteliais/metabolismo , Subfamília B de Transportador de Cassetes de Ligação de ATP/metabolismo , Animais , Diferenciação Celular , Linhagem da Célula , Células Cultivadas , Desmossomos/metabolismo , Cães , Células Epiteliais/citologia , Células Epiteliais/ultraestrutura , Membranas Artificiais , Microvilosidades/fisiologia , Mucinas/metabolismo , Nanoporos , Células-Tronco/citologia , Células-Tronco/metabolismo , Junções Íntimas/metabolismo
18.
PLoS One ; 15(3): e0226234, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32208422

RESUMO

The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for PacBio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has rarely been quantified. Furthermore, no study has employed reference-based assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven chloroplast genome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines. In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing. The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the errors detected were indels (81.5%), and a large majority of them is part of homopolymer regions. The quality of reference-based assembly is heavily dependent upon the choice of a close-enough reference. When using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a reference-based assembly with Illumina data. For optimal de novo assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential. Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes.


Assuntos
Mapeamento Cromossômico , Genoma de Cloroplastos , Sequenciamento de Nucleotídeos em Larga Escala , Leucanthemum/genética , Nanoporos , Filogenia
19.
Zhonghua Kou Qiang Yi Xue Za Zhi ; 55(2): 104-110, 2020 Feb 09.
Artigo em Chinês | MEDLINE | ID: mdl-32074671

RESUMO

Objective: To investigate the antibacterial properties and the osteoblast-compatibility of chlorhexidine (CHX)-modified porous titanium. Methods: Smooth pure titanium specimen with diameter of 10.0 mm and thickness of 1.5 mm treated with alkali heat method were set as control group. Those with covalent conjugation of aminosilane were set as silane group, and those with CHX grafted by glutaraldehyde were set as CHX group. Scanning electron microscope (SEM) was used to observe the surface morphology and element compositions were detected by X-ray photoelectron spectroscopy. Hydrophilicity was analyzed by surface water contact angle test (n=6), while surface amino/imine groups quantification were performed through acid orangeⅡ(n=5) and the CHX was quantified by optical densitometric method (n=5). Live/dead bacterial staining, the morphology of adherent bacteria by SEM, plate counting method and inhibition zone method were executed to evaluate the antibacterial property of the samples. Osteoblast compatibility was evaluated by methyl thiazolyl tetrazolium. Cell-bacterial co-culture was conducted to evaluated the cell viability on the samples under the circumstance with bacteria. Results: After CHX grafting, pores on the titanium surface were decreased, while the atom ratio of C, N, Cl increased and the water contact angle decreased to 37.5°±4.0°. The density of CHX on the surface was (5.07±0.39) µg/cm(2). The results of live/dead bacterial staining and the morphology of adherent bacteria showed that only little dead bacterial (bacterial wall rupture) adherent on the surface of CHX group, which proved that the modified surface could inhibit bacteria adhesion and even destroyed bacteria; the plate counting displayed sporadic colonies and a transparent inhibition zone could be observed, which demonstrated that CHX group could suppress bacteria multiplication from surrounding environment. When incubating for 1 and 3 days, the cell viability of CHX group showed no significant difference from that of control group (P>0.05) ; when incubating for 5 days, the value of cell viability of CHX group was 0.547±0.087, and this was significantly lower than that of the control group (0.751±0.056) (P<0.05), demonstrating a slight inhibition of cell proliferation by CHX. The results of bacteria-cell co-culture for 3 days showed that a mass of bacteria adhered on the surface of the control group while considerable cells adhered on the surface of CHX group and exhibited a good shape. Conclusions: Porous titanium surface grafted by CHX showed an excellent antibacterial properties and allowed cell adhesion in bacterial circumstance, providing immediate implantation options for patients with bad oral health.


Assuntos
Antibacterianos/farmacologia , Clorexidina/farmacologia , Nanoporos , Osteoblastos/efeitos dos fármacos , Titânio/farmacologia , Bactérias/efeitos dos fármacos , Aderência Bacteriana/efeitos dos fármacos , Células Cultivadas , Humanos , Propriedades de Superfície
20.
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA