Abstract：
:We describe a novel, multiplexed method for focused transcript analysis of tens to hundreds of genes. In this method TRAC (transcript analysis with aid of affinity capture) mRNA targets, a set of amplifiable detection probes of distinct sizes and biotinylated oligo(dT) capture probe are hybridized in solution. The formed sandwich hybrids are collected on magnetic streptavidin-coated microparticles and washed. The hybridized probes are eluted, optionally amplified by a PCR using a universal primer pair and detected with laser-induced fluorescence and capillary electrophoresis. The probes were designed by using a computer program developed for the purpose. The TRAC method was adapted to 96-well format by utilizing an automated magnetic particle processor. Here we demonstrate a simultaneous analysis of 18 Saccharomyces cerevisiae transcripts from two experimental conditions and show a comparison with a qPCR system. The sensitivity of the method is significantly increased by the PCR amplification of the hybridized and eluted probes. Our data demonstrate a bias-free use of at least 16 cycles of PCR amplification to increase probe signal, allowing transcript analysis from 2.5 ng of the total mRNA sample. The method is fast and simple and avoids cDNA conversion. These qualifications make it a potential, new means for routine analysis and a complementing method for microarrays and high density chips.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Kataja K,Satokari RM,Arvas M,Takkinen K,Söderlund Hdoi
10.1016/j.mimet.2006.03.013subject
Has Abstractpub_date
2006-10-01 00:00:00pages
102-13issue
1eissn
0167-7012issn
1872-8359pii
S0167-7012(06)00065-0journal_volume
67pub_type
杂志文章abstract：:The lack of a surrogate-of-immunity assay presents a major barrier to Streptococcus pyogenes research. Modification of the Lancefield assay to include an antibody digestion step reduced inter-donor variation and permitted detection of the anti-streptococcal activity of intravenous immunoglobulin and convalescent serum...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.03.015
更新日期：2016-05-01 00:00:00
abstract：:To target bacterial pathogens that invade and proliferate inside host cells, it is necessary to design intervention strategies directed against bacterial attachment, cellular invasion and intracellular proliferation. We present an automated microscopy-based, fast, high-throughput method for analyzing size and number o...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.05.001
更新日期：2017-08-01 00:00:00
abstract：:Preservation of strains is important to further studies and characterization; we have shown a technique of long-term preservation of Neisseria spp. and Haemophilus spp. by freezing cotton tip swabs impregnated with fastidious organisms at -80 °C without the addition of cryoprotectants. ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.105969
更新日期：2020-08-01 00:00:00
abstract：:Watermelon peel waste (WPW) is a zero value material containing a high amount of nutrients that could be utilized in microbial growth medium production. In the present work, WPW was used to produce universal fungal growth medium with great nutritional profile to use instead of other expensive media particularly the Po...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.105802
更新日期：2020-01-01 00:00:00
abstract：:A simple and sensitive method based on the use of colloidal chitin stained with Remazol Brilliant Blue R (RBB) is proposed to evaluate chitinase activity. If this colloidal-stained substrate is included as a carbon source in a liquid medium, this technique allows the selection or the comparison of chitinolytic microor...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2003.10.011
更新日期：2004-02-01 00:00:00
abstract：:Confocal microscopy-based monitoring of pH in biofilms is gaining increasing interest, as it allows for a quick assessment of horizontal pH gradients without mechanically perturbing the biofilm. Ratiometric monitoring of pH with the fluorescent dye C-SNARF-4 has been used to reliably map extracellular pH in the basal ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.08.007
更新日期：2018-09-01 00:00:00
abstract：:DNA probes specific for rRNA of selected target species were utilised for the detection of beer spoilage bacteria of the genera Pectinatus and Megasphaera using a hybridisation protection assay (HPA). All the probes were modified during synthesis by addition of an amino linker arm at the 5' end or were internally modi...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2013.10.014
更新日期：2014-01-01 00:00:00
abstract：:Host defense responses of animals and plants to pathogenic microbes are mediated in part by the release of antimicrobial substances into tissue fluids. Exploration of the antimicrobial properties of tissue fluids is often limited by their small quantity. We have developed assays of antimicrobial activity that require ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(00)00140-8
更新日期：2000-07-01 00:00:00
abstract：:A novel fluorescent microbead immunoassay (FMIA) using the recombinant polypeptide SpaA415 was developed for detection of anti-Erysipelothrix spp. IgG in pig sera. The diagnostic performance of the FMIA was evaluated on samples from pigs with known and unknown Erysipelothrix spp. exposure and compared to an in-house e...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.07.014
更新日期：2012-10-01 00:00:00
abstract：:Listeria monocytogenes internalin gene inlJ has been described previously for differentiation of virulent from avirulent strains. However, a recent report indicated that there exist some unusual lineage IIIB strains (e.g., serotype 7 strain R2-142) that possess no inlJ gene but have the capacity to cause mouse mortali...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.08.007
更新日期：2007-11-01 00:00:00
abstract：:This paper describes a method that facilitates the extraction of PCR-compatible DNA from different activated sludge samples. The approach involves a novel preprocessing step in DNA extraction, which removes potential PCR inhibitors. The sludge was washed with different ratios of acetone and petroleum ether after pretr...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(02)00185-9
更新日期：2003-03-01 00:00:00
abstract：:Tropheryma whipplei is the causative agent of Whipple's disease (WD), a chronic, life-threatening infection. Laboratory diagnosis is mainly based on PCR and histopathological analysis in duodenal biopsies and other specimens requiring invasive procedures. We have examined the presence of antibodies to recombinant heat...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(01)00336-0
更新日期：2001-12-01 00:00:00
abstract：:This paper describes a simple method for the isolation of salt-tolerant myxobacteria from marine conditions. As the results show in this paper, salt-tolerant myxobacteria are found to be able to grow, but unable to form fruiting bodies at high salt concentrations. The fruiting body structures of the salt-tolerant stra...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(02)00029-5
更新日期：2002-07-01 00:00:00
abstract：:Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefor...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(03)00067-8
更新日期：2003-09-01 00:00:00
abstract：:A novel method for directly increasing the recovery of Escherichia coli O157:H7 and efficiently eliminating PCR inhibitors in oyster tissue without preenrichment was developed with the use of activated carbon coated with bentonite. The recovery of E. coli O157:H7 was significantly affected by the amount of bentonite u...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.10.010
更新日期：2008-01-01 00:00:00
abstract：:Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent y...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.03.016
更新日期：2019-05-01 00:00:00
abstract：:Virulence is the relative capacity of a pathogenic microorganism to cause damage in susceptible host cells such as those found in airway passages and the gut. In this study, the effect of clinical bacterial isolates on the monolayer integrity of cultured human alveolar basal epithelial cells (A549) was evaluated using...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.105833
更新日期：2020-02-01 00:00:00
abstract：:Immunoproteomic technology offers an exceptional tool to fill the blanks that still exist in diagnosis of Toxoplasma gondii infection despite its annotated sequence. The pitfalls of serological assays and current immunoproteomic approaches are accentuated, and new approaches are presented to improve the signal and to ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.09.011
更新日期：2015-12-01 00:00:00
abstract：:Metagenomic sequencing of bacterial samples has become the gold standard for profiling microbial populations, but 16S rRNA profiling remains widely used due to advantages in sample throughput, cost, and sensitivity even though the approach is hampered by primer bias and lack of specificity. We hypothesized that a hybr...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.09.019
更新日期：2018-11-01 00:00:00
abstract：:Silver scurf caused by Helminthosporium solani causes significant economic losses in table stock, seed and processing potatoes. Specific polymerase chain reaction (PCR) primers, Hs1F1/Hs2R1, from H. solani were used for the amplification of a 447-bp product from 20 tissue samples and 54 single spore H. solani isolates...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(00)00240-2
更新日期：2001-02-01 00:00:00
abstract：:Contamination of cereals with Fusarium species is one of the major sources of mycotoxins in food and feed. Quantification of biomass of Fusarium species is essential to understand the interactions of individual species in disease development. In this study quantitative real-time PCR assays based on the elongation fact...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.10.016
更新日期：2009-03-01 00:00:00
abstract：:In this study, a simple and rapid method was developed to transform protein A producing Staphylococcus aureus cells into red color and red fluorescent nanobioparticles, which were homogeneous, dispersive and relatively stable with a uniform size of 800 nm. The method consists of reaction with a monotetrazolium redox d...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.04.018
更新日期：2015-08-01 00:00:00
abstract：:Staphylococcal Cassette Chromosome mec (SCCmec) element plays a key role in development of resistance by carrying different resistance factors. Therefore, routine and rapid diagnostic approach is considered advantageous for the easy detection of SCCmec elements. So, here we have described the use of three sets of mult...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.105733
更新日期：2019-11-01 00:00:00
abstract：:In this study extruded bean was used as a nitrogen source substitute in culture medium formulation. A 3-factor simplex-lattice mixture design was used to establish better growth conditions. Completely substituted medium resulted in 43% of increase in the growth of Saccharomyces cerevisiae. Mixtures containing 1% extru...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2013.01.002
更新日期：2013-03-01 00:00:00
abstract：:There have been many recent reviews published on MALDI-TOF MS (matrix assisted laser desorption/ionization time-of-flight) MS (mass spectrometry) for identification of bacteria particularly with relevance to clinical microbiology. MALDI-TOF MS is now a mature technique for bacterial identification with great promise. ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/j.mimet.2013.01.004
更新日期：2013-03-01 00:00:00
abstract：:Efficient selection of new silage inoculant strains from a collection of over 10,000 isolates of lactic acid bacteria (LAB) requires excellent strain discrimination. Toward that end, we constructed a GelCompar II database of DNA fingerprint patterns of ethidium bromide-stained EcoRI fragments of total LAB DNA separate...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(03)00186-6
更新日期：2003-12-01 00:00:00
abstract：:MALDI-TOF MS identified a 6250-Da protein specific to Sequence Type-1 (ST-1) strains and a 7625-Da protein specific to ST-17 strains when used for identification of Group B streptococci. The strains of these STs are major causes of meningitis and late-onset-disease in neonates. This rapid method of identification coul...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.05.017
更新日期：2011-08-01 00:00:00
abstract：:Bacteriocin activity can be quantified by a simple parallel line model based on an agar diffusion assay. The quotient between the inhibition zone area and the sensitivity of the indicator bacterium can be used to compare different bacteriocins. Deferred calculations of relative potencies are possible, once purified co...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.01.006
更新日期：2005-07-01 00:00:00
abstract：:The aim of the present study was to show the efficiency of multi-factorial experimental design to investigate factors affecting the antimicrobial compound production by Brevibacillus brevis EGS9 isolated from mangrove sediment soil. The isolate utilizing different carbon and nitrogen sources showed different growth ch...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.09.010
更新日期：2017-11-01 00:00:00
abstract：:The development of biofilms in static plates was monitored. Glass coupons were placed on agar covered with filter paper, which was inoculated with suspended bacteria. The viable cell density, biofilms matrix and biomass were quantified. The method is excellent for adhesion and material studies, due to its simplicity a...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.10.008
更新日期：2014-12-01 00:00:00
