Broad spectrum microarray for fingerprint-based bacterial species identification.

Abstract:

BACKGROUND:Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. RESULTS:A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. CONCLUSIONS:These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

journal_name

BMC Biotechnol

journal_title

BMC biotechnology

authors

Pasquer F,Pelludat C,Duffy B,Frey JE

doi

10.1186/1472-6750-10-13

subject

Has Abstract

pub_date

2010-02-17 00:00:00

pages

13

issn

1472-6750

pii

1472-6750-10-13

journal_volume

10

pub_type

杂志文章
  • Production of recombinant VP1-derived virus-like particles from novel human polyomaviruses in yeast.

    abstract:BACKGROUND:Eleven new human polyomaviruses (HPyVs) have been identified in the last decade. Serological studies show that these novel HPyVs sub-clinically infect humans at an early age. The routes of infection, entry pathways, and cell tropism of new HPyVs remain unknown. VP1 proteins of polyomaviruses can assembly int...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-015-0187-z

    authors: Norkiene M,Stonyte J,Ziogiene D,Mazeike E,Sasnauskas K,Gedvilaite A

    更新日期:2015-08-04 00:00:00

  • Keratinocyte cytoskeletal roles in cell sheet engineering.

    abstract:BACKGROUND:There is an increasing need to understand cell-cell interactions for cell and tissue engineering purposes, such as optimizing cell sheet constructs, as well as for examining adhesion defect diseases. For cell-sheet engineering, one major obstacle to sheet function is that cell sheets in suspension are fragil...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-13-17

    authors: Wei Q,Reidler D,Shen MY,Huang H

    更新日期:2013-02-26 00:00:00

  • Biosynthesis of methylated resveratrol analogs through the construction of an artificial biosynthetic pathway in E. coli.

    abstract:BACKGROUND:Methylated resveratrol analogs show similar biological activities that are comparable with those of the resveratrol. However, the methylated resveratrol analogs exhibit better bioavailability as they are more easily transported into the cell and more resistant to degradation. Although these compounds are wid...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-14-67

    authors: Kang SY,Lee JK,Choi O,Kim CY,Jang JH,Hwang BY,Hong YS

    更新日期:2014-07-17 00:00:00

  • Identification of the gene for β-fructofuranosidase from Ceratocystis moniliformis CMW 10134 and characterization of the enzyme expressed in Saccharomyces cerevisiae.

    abstract:BACKGROUND:β-Fructofuranosidases (or invertases) catalyse the commercially-important biotransformation of sucrose into short-chain fructooligosaccharides with wide-scale application as a prebiotic in the functional foods and pharmaceutical industries. RESULTS:We identified a β-fructofuranosidase gene (CmINV) from a Ce...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-13-100

    authors: van Wyk N,Trollope KM,Steenkamp ET,Wingfield BD,Volschenk H

    更新日期:2013-11-14 00:00:00

  • Generation and characterization of a human single-chain fragment variable (scFv) antibody against cytosine deaminase from yeast.

    abstract:BACKGROUND:The ability of cytosine deaminase (CD) to convert the antifungal agent 5-fluorocytosine (5-FC) into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU) raised considerable interest in this enzyme to model gene or antibody - directed enzyme-prodrug therapy (GDEPT/ADEPT) a...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-8-68

    authors: Mallano A,Zamboni S,Carpinelli G,Santoro F,Flego M,Ascione A,Gellini M,Tombesi M,Podo F,Cianfriglia M

    更新日期:2008-09-10 00:00:00

  • Stable high-level expression of factor VIII in Chinese hamster ovary cells in improved elongation factor-1 alpha-based system.

    abstract:BACKGROUND:Recombinant factor VIII (FVIII), used for haemophilia A therapy, is one of the most challenging among the therapeutic proteins produced in heterologous expression systems. Deletion variant of FVIII, in which the entire domain B is replaced by a short linker peptide, was approved for medical use. Efficacy and...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-017-0353-6

    authors: Orlova NA,Kovnir SV,Gabibov AG,Vorobiev II

    更新日期:2017-03-24 00:00:00

  • Antibody degradation in tobacco plants: a predominantly apoplastic process.

    abstract:BACKGROUND:Interest in using plants for production of recombinant proteins such as monoclonal antibodies is growing, but proteolytic degradation, leading to a loss of functionality and complications in downstream purification, is still a serious problem. RESULTS:In this study, we investigated the dynamics of the assem...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-11-128

    authors: Hehle VK,Paul MJ,Drake PM,Ma JK,van Dolleweerd CJ

    更新日期:2011-12-30 00:00:00

  • Characterization of mutations and loss of heterozygosity of p53 and K-ras2 in pancreatic cancer cell lines by immobilized polymerase chain reaction.

    abstract:BACKGROUND:The identification of known mutations in a cell population is important for clinical applications and basic cancer research. In this work an immobilized form of the polymerase chain reaction, referred to as polony technology, was used to detect mutations as well as gene deletions, resulting in loss of hetero...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-3-11

    authors: Butz J,Wickstrom E,Edwards J

    更新日期:2003-07-23 00:00:00

  • Synergistic interaction of hTGF-β3 with hBMP-6 promotes articular cartilage formation in chitosan scaffolds with hADSCs: implications for regenerative medicine.

    abstract:BACKGROUND:Human TGF-β3 has been used in many studies to induce genes coding for typical cartilage matrix components and accelerate chondrogenic differentiation, making it the standard constituent in most cultivation media used for the assessment of chondrogenesis associated with various stem cell types on carrier matr...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-020-00641-y

    authors: Huang Y,Seitz D,Chevalier Y,Müller PE,Jansson V,Klar RM

    更新日期:2020-08-27 00:00:00

  • Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10.

    abstract:BACKGROUND:Nitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explo...

    journal_title:BMC biotechnology

    pub_type: 杂志文章,收录出版

    doi:10.1186/1472-6750-11-2

    authors: Kaplan O,Bezouška K,Plíhal O,Ettrich R,Kulik N,Vaněk O,Kavan D,Benada O,Malandra A,Sveda O,Veselá AB,Rinágelová A,Slámová K,Cantarella M,Felsberg J,Dušková J,Dohnálek J,Kotik M,Křen V,Martínková L

    更新日期:2011-01-06 00:00:00

  • Pharmacological characteristics and efficacy of a novel anti-angiogenic antibody FD006 in corneal neovascularization.

    abstract:BACKGROUND:Vascular endothelial growth factor (VEGF) is a key angiogenic factors. It plays an important role in both physiologic and pathologic angiogenesis and increases permeability across the vessels. Using antibody phage display technology, we obtained a novel anti-VEGFA IgG, named as FD006. In this study, the phar...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-14-17

    authors: Wang Q,Yang J,Tang K,Luo L,Wang L,Tian L,Jiang Y,Feng J,Li Y,Shen B,Lv M,Huang Y

    更新日期:2014-02-27 00:00:00

  • In vitro cell cultures obtained from different explants of Corylus avellana produce Taxol and taxanes.

    abstract:BACKGROUND:Taxol is an effective antineoplastic agent, originally extracted from the bark of Taxus brevifolia with a low yield. Many attempts have been made to produce Taxol by chemical synthesis, semi-synthesis and plant tissue cultures. However, to date, the availability of this compound is not sufficient to satisfy ...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-6-45

    authors: Bestoso F,Ottaggio L,Armirotti A,Balbi A,Damonte G,Degan P,Mazzei M,Cavalli F,Ledda B,Miele M

    更新日期:2006-12-06 00:00:00

  • Intrabodies against the Polysialyltransferases ST8SiaII and ST8SiaIV inhibit Polysialylation of NCAM in rhabdomyosarcoma tumor cells.

    abstract:BACKGROUND:Polysialic acid (polySia) is a carbohydrate modification of the neural cell adhesion molecule (NCAM), which is implicated in neural differentiation and plays an important role in tumor development and metastasis. Polysialylation of NCAM is mediated by two Golgi-resident polysialyltransferases (polyST) ST8Sia...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-017-0360-7

    authors: Somplatzki S,Mühlenhoff M,Kröger A,Gerardy-Schahn R,Böldicke T

    更新日期:2017-05-12 00:00:00

  • Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA.

    abstract:BACKGROUND:Construction of high quality cDNA libraries from the usually low amounts of eukaryotic mRNA extracted from environmental samples is essential in functional metatranscriptomics for the selection of functional, full-length genes encoding proteins of interest. Many of the inserts in libraries constructed by sta...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-14-80

    authors: Yadav RK,Barbi F,Ziller A,Luis P,Marmeisse R,Reddy MS,Fraissinet-Tachet L

    更新日期:2014-09-03 00:00:00

  • Effect of supercritical carbon dioxide on the enzymatic production of biodiesel from waste animal fat using immobilized Candida antarctica lipase B variant.

    abstract:BACKGROUND:Waste animal fat is a promising feedstock to replace vegetable oil that widely used in commercial biodiesel process, however the high content of free fatty acid in waste fat makes it unfeasible to be processed with commercial base-catalytic process. Enzymatic process is preferable to convert waste fat into b...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-017-0390-1

    authors: Pollardo AA,Lee HS,Lee D,Kim S,Kim J

    更新日期:2017-09-09 00:00:00

  • Dynamic in vivo imaging and cell tracking using a histone fluorescent protein fusion in mice.

    abstract:BACKGROUND:Advances in optical imaging modalities and the continued evolution of genetically-encoded fluorescent proteins are coming together to facilitate the study of cell behavior at high resolution in living organisms. As a result, imaging using autofluorescent protein reporters is gaining popularity in mouse trans...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-4-33

    authors: Hadjantonakis AK,Papaioannou VE

    更新日期:2004-12-24 00:00:00

  • Enhancing the thermostability of α-L-rhamnosidase from Aspergillus terreus and the enzymatic conversion of rutin to isoquercitrin by adding sorbitol.

    abstract:BACKGROUND:Thermally stable α-L-rhamnosidase with cleaving terminal α-L-rhamnose activity has great potential in industrial application. Therefore, it is necessary to find a proper method to improve the thermal stability of α-L-rhamnosidase. RESULTS:In this study, addition of sorbitol has been found to increase the th...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-017-0342-9

    authors: Ge L,Chen A,Pei J,Zhao L,Fang X,Ding G,Wang Z,Xiao W,Tang F

    更新日期:2017-02-27 00:00:00

  • Nicotiana benthamiana is a suitable transient system for high-level expression of an active inhibitor of cotton boll weevil α-amylase.

    abstract:BACKGROUND:Insect resistance in crops represents a main challenge for agriculture. Transgenic approaches based on proteins displaying insect resistance properties are widely used as efficient breeding strategies. To extend the spectrum of targeted pathogens and overtake the development of resistance, molecular evolutio...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-019-0507-9

    authors: Prado GS,Bamogo PKA,de Abreu JAC,Gillet FX,Dos Santos VO,Silva MCM,Brizard JP,Bemquerer MP,Bangratz M,Brugidou C,Sérémé D,Grossi-de-Sa MF,Lacombe S

    更新日期:2019-03-08 00:00:00

  • Metabolic evolution of Corynebacterium glutamicum for increased production of L-ornithine.

    abstract:BACKGROUND:L-ornithine is effective in the treatment of liver diseases and helps strengthen the heart. The commercial applications mean that efficient biotechnological production of L-ornithine has become increasingly necessary. Adaptive evolution strategies have been proven a feasible and efficient technique to achiev...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-13-47

    authors: Jiang LY,Chen SG,Zhang YY,Liu JZ

    更新日期:2013-06-01 00:00:00

  • Purification of functional baculovirus particles from silkworm larval hemolymph and their use as nanoparticles for the detection of human prorenin receptor (PRR) binding.

    abstract:BACKGROUND:Baculovirus, which has a width of 40 nm and a length of 250-300 nm, can display functional peptides, receptors and antigens on its surface by their fusion with a baculovirus envelop protein, GP64. In addition, some transmembrane proteins can be displayed without GP64 fusion, using the native transmembrane do...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-11-60

    authors: Kato T,Suzuki F,Park EY

    更新日期:2011-06-02 00:00:00

  • Ultrasound and microbubble induced release from intracellular compartments.

    abstract:BACKGROUND:Ultrasound and microbubbles (USMB) have been shown to enhance the intracellular uptake of molecules, generally thought to occur as a result of sonoporation. The underlying mechanism associated with USMB-enhanced intracellular uptake such as membrane disruption and endocytosis may also be associated with USMB...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-017-0364-3

    authors: Hussein F,Antonescu C,Karshafian R

    更新日期:2017-05-18 00:00:00

  • Manipulation of gene expression by an ecdysone-inducible gene switch in tumor xenografts.

    abstract:BACKGROUND:Rapid, robust and reversible induction of transgene expression would significantly facilitate cancer gene therapy as well as allow the in vivo functional study of newly discovered genes in tumor formation and progression. The popularity of the ecdysone inducible gene switch system has led us to investigate w...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-1-11

    authors: Karns LR,Kisielewski A,Gulding KM,Seraj JM,Theodorescu D

    更新日期:2001-01-01 00:00:00

  • Design and characterization of genetically engineered zebrafish aquaporin-3 mutants highly permeable to the cryoprotectant ethylene glycol.

    abstract:BACKGROUND:Increasing cell membrane permeability to water and cryoprotectants is critical for the successful cryopreservation of cells with large volumes. Artificial expression of water-selective aquaporins or aquaglyceroporins (GLPs), such as mammalian aquaporin-3 (AQP3), enhances cell permeability to water and cryopr...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-11-34

    authors: Chauvigné F,Lubzens E,Cerdà J

    更新日期:2011-04-08 00:00:00

  • gRNA validation for wheat genome editing with the CRISPR-Cas9 system.

    abstract:BACKGROUND:The CRISPR-Cas9 system is a powerful and versatile tool for crop genome editing. However, achieving highly efficient and specific editing in polyploid species can be a challenge. The efficiency and specificity of the CRISPR-Cas9 system depends critically on the gRNA used. Here, we assessed the activities and...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-019-0565-z

    authors: Arndell T,Sharma N,Langridge P,Baumann U,Watson-Haigh NS,Whitford R

    更新日期:2019-10-30 00:00:00

  • Ex vivo evolution of human antibodies by CRISPR-X: from a naive B cell repertoire to affinity matured antibodies.

    abstract:: ...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-019-0504-z

    authors: Devilder MC,Moyon M,Gautreau-Rolland L,Navet B,Perroteau J,Delbos F,Gesnel MC,Breathnach R,Saulquin X

    更新日期:2019-02-18 00:00:00

  • Dye decolorization and detoxification potential of Ca-alginate beads immobilized manganese peroxidase.

    abstract:BACKGROUND:In view of compliance with increasingly stringent environmental legislation, an eco-friendly treatment technology of industrial dyes and effluents is a major environmental challenge in the color industry. In present study, a promising and eco-friendly entrapment approach was adopted to immobilize purified ma...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/s12896-015-0227-8

    authors: Bilal M,Asgher M

    更新日期:2015-12-10 00:00:00

  • CdSe/ZnS quantum dots trigger DNA repair and antioxidant enzyme systems in Medicago sativa cells in suspension culture.

    abstract:BACKGROUND:Nanoparticles appear to be promising devices for application in the agriculture and food industries, but information regarding the response of plants to contact with nano-devices is scarce. Toxic effects may be imposed depending on the type and concentration of nanoparticle as well as time of exposure. A num...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-13-111

    authors: Santos AR,Miguel AS,Macovei A,Maycock C,Balestrazzi A,Oliva A,Fevereiro P

    更新日期:2013-12-20 00:00:00

  • A novel carboxyl-terminal protease derived from Paenibacillus lautus CHN26 exhibiting high activities at multiple sites of substrates.

    abstract:BACKGROUND:Carboxyl-terminal protease (CtpA) plays essential functions in posttranslational protein processing in prokaryotic and eukaryotic cells. To date, only a few bacterial ctpA genes have been characterized. Here we cloned and characterized a novel CtpA. The encoding gene, ctpAp (ctpA of Paenibacillus lautus), wa...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-13-89

    authors: Li Y,Pan Y,She Q,Chen L

    更新日期:2013-10-25 00:00:00

  • Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers.

    abstract:BACKGROUND:MicroRNAs are important regulators of gene expression at the post-transcriptional level and play an important role in many biological processes. Due to the important biological role it is of great interest to quantitatively determine their expression level in different biological settings. RESULTS:We descri...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-11-70

    authors: Balcells I,Cirera S,Busk PK

    更新日期:2011-06-25 00:00:00

  • Controlling pH in shake flasks using polymer-based controlled-release discs with pre-determined release kinetics.

    abstract:BACKGROUND:There are significant differences in the culture conditions between small-scale screenings and large-scale fermentation processes. Production processes are usually conducted in fed-batch cultivation mode with active pH-monitoring and control. In contrast, screening experiments in shake flasks are usually con...

    journal_title:BMC biotechnology

    pub_type: 杂志文章

    doi:10.1186/1472-6750-11-25

    authors: Scheidle M,Dittrich B,Klinger J,Ikeda H,Klee D,Büchs J

    更新日期:2011-03-23 00:00:00