Abstract：
:This paper presents a robust two-step segmentation procedure for the study of biofilm structure. Without user intervention, the procedure segments volumetric biofilm images generated by a confocal laser scanning microscopy (CLSM). This automated procedure implements an anisotropic diffusion filter as a preprocessing step and a 3D extension of the Otsu method for thresholding. Applying the anisotropic diffusion filter to even low-contrast CLSM images significantly improves the segmentation obtained with the 3D Otsu method. A comparison of the results for several CLSM data sets demonstrated that the accuracy of this procedure, unlike that of the objective threshold selection algorithm (OTS), is not affected by biofilm coverage levels and thus fills an important gap in developing a robust and objective segmenting procedure. The effectiveness of the present segmentation procedure is shown for CLSM images containing different bacterial strains. The image saturation handling capability of this procedure relaxes the constraints on user-selected gain and intensity settings of a CLSM. Therefore, this two-step procedure provides an automatic and accurate segmentation of biofilms that is independent of biofilm coverage levels and, in turn, lays a solid foundation for achieving objective analysis of biofilm structural parameters.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Yerly J,Hu Y,Jones SM,Martinuzzi RJdoi
10.1016/j.mimet.2007.05.022subject
Has Abstractpub_date
2007-09-01 00:00:00pages
424-33issue
3eissn
0167-7012issn
1872-8359pii
S0167-7012(07)00205-9journal_volume
70pub_type
杂志文章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：:Representational Difference Analysis (RDA) is an established technique used for isolation of specific genetic differences between or within bacterial species. This method was used to investigate the genetic basis of serovar-specificity and the relationship between serovar and virulence in Haemophilus parasuis. An RDA ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2006.09.011
更新日期：2007-02-01 00:00:00
abstract：:The need for improved pathogen separation and concentration methods to reduce time-to-detection for foodborne pathogens is well recognized. Apolipoprotein H (ApoH) is an acute phase human plasma protein that has been previously shown to interact with viruses, lipopolysaccharides (LPS) and bacterial proteins. The purpo...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.07.014
更新日期：2016-09-01 00:00:00
abstract：:We modified Wayne's pyrazinamidase test against Mycobacterium tuberculosis to indirectly measure pyrazinamidase activity via pyrazinoic acid in liquid medium. The modified pyrazinamidase test was easy to perform and its results were in complete agreement with those of the conventional Wayne's method, highlighting its ...
journal_title：Journal of microbiological methods
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doi：10.1016/j.mimet.2018.09.018
更新日期：2018-11-01 00:00:00
abstract：:Culture-independent studies using next generation sequencing have revolutionized microbial ecology, however, oomycete ecology in soils is severely lagging behind. The aim of this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete communities. The ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.01.013
更新日期：2015-03-01 00:00:00
abstract：:Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) was used to study compositional characteristics of Extracellular Polymeric Substances (EPS) and compared these to characteristics of the EPS-matrix of intact diatom biofilms. Three benthic diatoms species were investigated, Cylindrotheca closterium, Navicula mu...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.10.001
更新日期：2006-06-01 00:00:00
abstract：:A rapid immunological method for trapping and selection of functionally regulated prokaryotic promoters is described. The method is based on application of a novel mini-Tn5 derived promoter probe (pUTTKZY-promoterless lacZY as a reporter and kanamycin resistance) to mutagenise a plant growth promoting fluorescent pseu...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(00)00139-1
更新日期：2000-06-01 00:00:00
abstract：:Much of our knowledge concerned with microbial cells is based on population-based analysis of cultures, which give useful insights into average responses but neither on individual cells nor subpopulations. In this work we demonstrate how to access and utilise large amounts of valuable information concerned with cell p...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.01.011
更新日期：2009-04-01 00:00:00
abstract：:The present study describes the development of a simple and efficient screening system that allows identification and quantification of nine bacteriocins produced by Lactococcus lactis. Cell-free L. lactis extracts presented a broad spectrum of antibacterial activity, including Gram-negative bacteria, Gram-positive ba...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.06.003
更新日期：2016-08-01 00:00:00
abstract：:Many methods are developed to assess antimicrobial action of ZnO nanoparticles (NPs). A large number of methods associated with the use of fluorescent probes are developed, including Spectrofluorometry, fluorescence microscopy, and cytometry. In this study, flowcytometry, Spectrofluorometry and fluorescent microscopy ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.105920
更新日期：2020-06-01 00:00:00
abstract：:Bacterial biofilms are populations of bacteria within a self-produced adherent extracellular matrix that are notoriously resistant to treatment. Existing methods for biofilm quantification are often limited in their dynamic range of detection (signal-to-background), throughput, and require modifications to the protoco...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.02.018
更新日期：2019-04-01 00:00:00
abstract：:Serological tests, such as agglutination and indirect hemagglutination assay (IHA), have been used to identify antibodies against Pasteurella multocida in poultry sera, but none are highly sensitive. An enzyme-linked immunosorbent assays (ELISA) has been used with varying degrees of success in attempts to monitor sero...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.08.018
更新日期：2017-11-01 00:00:00
abstract：:We report here the construction of a plasmid vector designed for the efficient electrotransformation of the periodontal pathogen Porphyromonas gingivalis. The novel Escherichia coli-Bacteroides/P. gingivalis shuttle vector, designated pTIO-1, is based on the 11.0-kb E. coli-Bacteroides conjugative shuttle vector, pVAL...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.07.032
更新日期：2014-10-01 00:00:00
abstract：:Transposon Integration mediated Mutagenesis (TIM) is a broadly applicable tool for protein engineering. This method combines random integration of modified bacteriophage Mu transposons with their subsequent defined excision employing type IIS restriction endonuclease AarI. TIM enables deletion or insertion of an arbit...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.06.017
更新日期：2008-10-01 00:00:00
abstract：:We aimed to establish the role of MALDI-TOF MS on species discrimination of phenotypically indistinguishable A. baumannii, A. pittii and A. nosocomialis. Compared to multiplex PCR, the gold standard, MALDI-TOF MS yielded a high sensitivity for A. baumannii (97.9%) and specificity for A. pittii (98.9%) and A. nosocomia...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.06.019
更新日期：2017-09-01 00:00:00
abstract：:Recently, we demonstrated that a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) can be used to determine the molecular weight of polymerase chain reaction (PCR) products of intact 16S rRNA regions and to profile their restriction digests. This is the first time that MALDI-T...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(01)00314-1
更新日期：2002-02-01 00:00:00
abstract：:Streptococcus agalactiae (or group B streptococcus; GBS) is a leading cause of neonatal morbidity and mortality in the developed countries. Several epidemiological typing tools have been developed for GBS to investigate the association between genotype and disease and to assess genetic variations within genogroups. Th...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.02.010
更新日期：2011-05-01 00:00:00
abstract：:Sequences in public databases may contain a number of sequencing errors. A double binomial model describing the distribution of indel-excluded similarity coefficients (S) among repeatedly sequenced 16S rRNA was previously developed and it produced a confidence interval of S useful for testing sequence identity among s...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.11.013
更新日期：2008-02-01 00:00:00
abstract：:We developed an immunocapture-based polymerase chain reaction (PCR) assay for simultaneous detection of Cryptosporidium parvum oocysts and Giardia intestinalis cysts in surface water. Using primer pairs Cry9/Cry15 and LaxA/LaxB for Cryptosporidium and Gdh1/Gdh4 for Giardia, the sensitivity of the entire detection proc...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(02)00047-7
更新日期：2002-08-01 00:00:00
abstract：:Staphylococcus aureus is a Gram-positive coccus and one of the major causes of community-acquired and hospital-acquired infections. We established the convenient and reliable experimental system for analyzing the essentiality and function of genes, the plasmid integration (PI) method. This method is based on plasmid i...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.05.017
更新日期：2012-09-01 00:00:00
abstract：:Industrial biotechnology aims to compete as a stronger alternative ensuring environmental friendly microbial-based production that seeks to curb the predicament of pollution. However, the high cost of bioprocessing is a severe drawback, and therefore, new approaches must be developed to overcome this challenge. Haloph...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/j.mimet.2019.105704
更新日期：2019-11-01 00:00:00
abstract：:The ELISA is recognized as an efficient diagnostic tool for antibody detection, but there is no standard ELISA assay for detection of antibodies against hemorrhagic septicemia (HS) in cattle. The present study reports on an indirect ELISA assay for antibody detection of HS in dairy cows, and evaluates the sensitivity ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.12.005
更新日期：2018-02-01 00:00:00
abstract：:In this study, food-borne yeast isolates (n=96), comprising at least 33 species, were identified using MALDI-TOF MS and conventional methods (API ID 32 C and Phoenix Yeast ID). Discrepancies of both methods were resolved by sequencing the ITS1-5.8S-rRNA-ITS2 region. For ten isolates, mainly classified to Rhodotorula a...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.08.021
更新日期：2014-11-01 00:00:00
abstract：:Molecular methods for bacterial pathogen identification are gaining increased importance in routine clinical diagnostic laboratories. Achieving reliable results using DNA based technologies is strongly dependent on pre-analytical processes including isolation of target cells and their DNA of high quality and purity. I...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.03.003
更新日期：2011-06-01 00:00:00
abstract：:Freeze-thaw DNA extraction methods and PCR primers were compared to optimize detection of Cryptosporidium parvum and Toxoplasma gondii oocysts in different matrices. Increasing FT cycles did not increase parasite DNA detection, and primers targeting the 18S ssrRNA gene yielded the most sensitive detection of C. parvum...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.11.017
更新日期：2019-01-01 00:00:00
abstract：:Traditional culture and biochemical tests (CBT) were compared with PCR for sensitivity and detection of Brachyspira hyodysenteriae and Brachyspira pilosicoli in seeded faeces and clinical samples from diarrhoeic pigs. A duplex PCR system was developed based on primers detecting the tlyA-gene of B. hyodysenteriae and t...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.12.008
更新日期：2006-08-01 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：:Limited biological samples of microbial origin often yield insufficient amounts of genomic DNA, making application of standard techniques of genetic analysis, like amplified fragment length polymorphism (AFLP), virtually impossible. The Phi29 DNA polymerase based whole genome amplification (WGA) method has the potenti...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.03.009
更新日期：2005-11-01 00:00:00
abstract：:Thanks to their photosynthetic and nutritive properties, cyanobacteria of the Arthrospira genus are of interest as food supplements, as efficient oxygen producing life support system organisms for manned space flight, and for the production of biofuels. Despite these potential valuable applications, full genome sequen...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.11.012
更新日期：2010-02-01 00:00:00
abstract：:A 384-well-based antibacterial assay amenable for high-throughput screening and combination testing is described. The assay uses 100-500nL of test compounds and tolerates up to 2.5% dimethyl sulfoxide concentrations. It can be used for screening compound libraries and testing combinatory/synergistic/antagonistic effec...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.09.019
更新日期：2015-11-01 00:00:00
