Abstract:
:A common method for visualizing bacterial biofilms is through confocal laser scanning microscopy images. Current software packages separate connected-biofilm bacteria from unconnected bacteria, such as planktonic or dispersed bacteria, but do not save both image sequences, making interpretation of the two bacterial populations difficult. Thus we report the development of an algorithm to save separate image sequences and enable qualitative and quantitative evaluation of each bacterial population. To improve bacterial viability assessment using a membrane integrity dye, a colocalization algorithm was also developed. This assigns colocalized pixels to the dead bacteria population, rather than to both the live and dead bacteria groups. Visually, this makes it clearer to distinguish a green live bacteria pixel from a yellow colocalized dead bacteria pixel. This algorithm also aids in the quantification of viability for connected-biofilm bacteria and unconnected bacteria to investigate susceptibility of each population to antimicrobials. The utility of these algorithms was demonstrated with Pseudomonas aeruginosa biofilms treated with ciprofloxacin hydrochloride. Results from this study indicate that quantification with colocalization adjustment can prevent underestimation of dead bacteria. These improvements in image processing will enable researchers to visually differentiate connected-biofilm and unconnected bacteria in a single image and to quantify these populations independently for viability without double counting the colocalized image pixels.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Sommerfeld Ross S,Reinhardt JM,Fiegel Jdoi
10.1016/j.mimet.2012.04.008subject
Has Abstractpub_date
2012-07-01 00:00:00pages
9-14issue
1eissn
0167-7012issn
1872-8359pii
S0167-7012(12)00142-Xjournal_volume
90pub_type
杂志文章abstract::Recently we showed the applicability and sensitivity of the RNA-based sandwich hybridisation assay (SHA) for detection of gram-negative cells in environmental samples [Leskelä, T., Tilsala-Timisjärvi, A., Kusnetsov, J., Neubauer, P., Breitenstein, A., 2005. Sensitive genus-specific detection of Legionella by a 16S rRN...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2006.10.009
更新日期:2007-03-01 00:00:00
abstract::The U.S. Environmental Protection Agency's (EPA) Water Laboratory Alliance (WLA) currently uses ultrafiltration (UF) for concentration of biosafety level 3 (BSL-3) agents from large volumes (up to 100-L) of drinking water prior to analysis. Most UF procedures require comprehensive training and practice to achieve and ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.08.013
更新日期:2015-11-01 00:00:00
abstract::In Europe, alternative methods for the detection of food-borne pathogens can be used instead of the standard ISO/CEN reference protocol, if validated according to the protocol outlined in ISO 16140, 2003. In this study, the performance of two novel methods for the detection of Salmonella sp. using real-time PCR techno...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.10.004
更新日期:2011-01-01 00:00:00
abstract::A real-time quantitative polymerase chain reaction (Q-PCR) assay was developed for detecting and quantifying Escherichia coli in water samples from agricultural watersheds. The assay included optimization of DNA extraction and purification from water samples, and Q-PCR amplification conditions using newly designed spe...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.02.016
更新日期:2007-06-01 00:00:00
abstract::We evaluated the performance of two MALDI-TOF MS systems for the identification of clinically important Gram-positive cocci. Vitek MS and Microflex LT correctly identified 97.2% and 94.7%, respectively. Both systems offer reliable and rapid identification of clinically important Gram-positive cocci isolated in clinica...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.03.020
更新日期:2015-06-01 00:00:00
abstract::Cryptosporidium parvum is an enteric coccidian parasite that is recognised as a frequent cause of water-borne disease in humans. We report for the first time on use of the in vitro HCT-8 cell culture-quantitative PCR (qPCR) assay and the in vivo SCID-mouse bioassay for evaluating critical factors that reduce or elimin...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.01.017
更新日期:2010-03-01 00:00:00
abstract::Fluorescence in situ hybridization has been used for the identification and analysis of populations of the dinoflagellate Symbiodinium that lives symbiotically in marine invertebrates. Conditions for in situ hybridization of Symbiodinium were optimized and used to identify the clade to which the isolate belongs using ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(02)00250-6
更新日期:2003-06-01 00:00:00
abstract::The food industry requires easy, accurate, and cost-effective techniques for microbial identification to ensure safe products and identify microbial contaminations. In this work, FTIR spectroscopy and MALDI-TOF mass spectrometry were assessed for their suitability and applicability for routine microbial diagnostics of...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.05.011
更新日期:2014-08-01 00:00:00
abstract::Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bac...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/0167-7012(85)90023-5
更新日期:1985-01-01 00:00:00
abstract::To facilitate routine laboratories in the effective diagnosis of brucellosis, we report a robust and rapid multiplex PCR assay, which allows for the differentiation of all nine currently recognised Brucella species. This includes the recently described species B. microti, B. inopinata, B. ceti and B. pinnipedialis. ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2009.10.015
更新日期:2010-01-01 00:00:00
abstract::MALDI-ToF MS can be used to identify microorganisms directly from blood cultures. This study compared two methods of sample preparation. Similar levels of genus- (91% vs 90%) and species-level identifications (79% vs 74%) were obtained with differential centrifugation and SDS methods. The SDS method is faster and requ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2016.05.026
更新日期:2016-08-01 00:00:00
abstract::Modified linker-PCR primers were developed to enable complete sequencing of a DGGE band in one reaction. Commonly used bacterial and archaeal 16S rRNA gene PCR-DGGE primers were modified to contain linkers and sequencing primers. This protocol does not involve additional stages, and improves retrieval of sequence from...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2008.08.006
更新日期:2008-12-01 00:00:00
abstract::The immunoglobulin degrading enzyme of Streptococcus pyogenes, IdeS, is an unusual cysteine protease produced by group A streptococci for which the only known substrate is immunoglobulin G (IgG). To date, IdeS has not been found to cleave any of the known synthetic substrates that other cysteine proteases hydrolyse, t...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.04.017
更新日期:2007-08-01 00:00:00
abstract::The antimicrobial activity of lime oil was significantly enhanced against Staphylococcus epidermidis in a pulsed electromagnetic field. These findings support other workers who found that electromagnetic fields augment antimicrobial activity. ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.09.015
更新日期:2010-11-01 00:00:00
abstract::An acute hepatopancreatic necrosis disease (AHPND) causes serious losses to the global shrimp industry. The etiologic agent of AHPND is Vibrio spp. carrying a large plasmid which encodes a binary toxin, PirAB. Currently, AHPND is diagnosed by PCR based methods that detect the presences of both pirA and pirB genes. How...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2020.106002
更新日期:2020-09-01 00:00:00
abstract::Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidi...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.07.020
更新日期:2015-10-01 00:00:00
abstract::MTS or {3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl}-2H-tetrazolium, inner salt) is converted into soluble formazan by mitochondrial dehydrogenase of viable cells, thus serving as an indicator of cell viability. Accordingly, a MTS-based assay was developed to evaluate anti-leishmanial acti...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.10.011
更新日期:2006-07-01 00:00:00
abstract::A direct most-probable-number polymerase chain reaction method (MPN-PCR) was used to monitor populations of Thiobacillus thioparus in compost biofilters used to treat air contaminated with dymethyl disulphide and ammonia. The PCR method quantified this bacterium at numbers ranging from log 2 to log 8 cells per gram of...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.08.001
更新日期:2006-05-01 00:00:00
abstract::Novel noninvasive techniques for the removal of biological contaminants to generate clean or sterile materials are in demand by the medical, pharmaceutical and food industries. The sterilization method described here uses supercritical fluid carbon dioxide (SF-CO(2)) containing 3.3% water and 0.1% hydrogen peroxide (v...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2011.07.008
更新日期:2011-10-01 00:00:00
abstract::In this study an on-line electrochemical method was developed to examine the one-step growth cycle (OSGC) of the bacteriophage Bam35. The on-line conditions for monitoring the OSGC and the effect of aeration on the duration of the OSGC were defined. The data indicate that binding of phenyldicarbaundecaborane anions to...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2006.12.023
更新日期:2007-04-01 00:00:00
abstract::Microarrays have allowed gene expression profiling to progress from the gene level to the genome level, and oligonucleotide microarrays have become the platform of choice for large-scale, targeted gene expression studies. cDNA arrays and spotted oligonucleotide arrays have gradually given way to in situ synthesized ol...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.12.009
更新日期:2014-02-01 00:00:00
abstract::The purpose of this study was to explore the potential of using cationic polyethylenimine (PEI) to deliver green fluorescent protein (GFP) to protozoan parasite Toxoplasma gondii. PEI/DNA polyplexes were formed using branched PEI and pEGFP-N1 plasmid with various N/P ratios that ranged from 5 to 50. With the increment...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2012.08.001
更新日期:2012-10-01 00:00:00
abstract::The description of microbial diversity by molecular culture-independent techniques most often involves the amplification of the 16S rRNA by PCR gene and either analysis of the diversity of amplified molecules (community fingerprinting) that allows the simultaneous study of many samples or the cloning and sequencing of...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(99)00011-1
更新日期:1999-05-01 00:00:00
abstract::In wastewater, biological phosphate removal can fail because of the presence of glycogen accumulating organism (GAO), therefore measuring glycogen stored in microbial cultures provides information on the bacterial population type. Once glycogen is hydrolysed to glucose it was accurately measured using a human glucose ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.03.002
更新日期:2014-05-01 00:00:00
abstract::Recent developments in host-microbe research give rise to a growing demand for rapid and accurate methods to quantify bacterial adhesion to epithelial cells. Here, we describe a new flow cytometric method to determine the amount and viability of gut bacteria, adhered to a monolayer of differentiated cells. The latter ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2011.03.011
更新日期:2011-07-01 00:00:00
abstract::The direct counts of bacteria inhabiting coral mucus were performed by flow cytometry testing four fluorescent dyes (SYBR®Green I, HCS, TOPRO®3, SYTO®62) with three different scleractinian species. Results obtained with SYTO62 were the most reliable based on the comparison with standardized epifluorescence counts and ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2016.05.032
更新日期:2016-09-01 00:00:00
abstract::The S. PneumoStrip test is a recently developed reverse hybridization strip-based commercial assay that allows for the identification of 76 pneumococcal serotypes, 42 individually and 34 in pairs, according to their specific gene sequences. The test was validated with reference strains of 92 different pneumococcal ser...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.08.010
更新日期:2017-12-01 00:00:00
abstract::Host DNA may adversely affect metagenomic studies focusing on the prokaryotic microbiota. This study compared the levels of host DNA in subgingival plaque collected by paper points and curette, using quantitative PCR. Lower proportions of host DNA and higher proportions of bacterial DNA were recovered from samples col...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.01.023
更新日期:2015-04-01 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::We describe a method based on fluorescence in situ hybridisation (FISH) that allows the identification of individual cells by electron microscopy. We hybridised universal and specific fluorescein-labelled oligonucleotide probes to the ribosomal RNA of prokaryotic microorganisms in heterogeneous cell mixtures. We then ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.02.018
更新日期:2005-10-01 00:00:00