Abstract：
:We have developed and implemented methods of extracting morphological features from images of biofilms in order to quantify the characteristics of the inherent heterogeneity. This is a first step towards quantifying the relationship between biofilm heterogeneity and the underlying processes, such as mass-transport dynamics, substrate concentrations, and species variations. We have examined two categories of features, areal, which quantify the relative magnitude of the heterogeneity and textural, which quantify the microscale structure of the heterogeneous elements. The feature set is not exhaustive and has been restricted to two-dimensional images to this point. Included in this paper are the methods used to extract the structural information and the algorithms used to quantify the data. The features discussed are porosity, fractal dimension, diffusional length, angular second moment, inverse difference moment and textural entropy. We have found that some features are better predictors of biofilm behavior than others and we discuss possible future directions for research in this area.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Yang X,Beyenal H,Harkin G,Lewandowski Zdoi
10.1016/s0167-7012(99)00097-4subject
Has Abstractpub_date
2000-01-01 00:00:00pages
109-19issue
2eissn
0167-7012issn
1872-8359pii
S0167-7012(99)00097-4journal_volume
39pub_type
杂志文章abstract：:A protein database was constructed and validated with identification rate over 90% for the 4 most common Gram-negative bacteria on agar plates. By protein masses comparison, 120 bacteria of the 4 species from blood culture bottles were identified. The concordance was high (Kappa=0.906) between our method and conventio...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.07.021
更新日期：2014-10-01 00:00:00
abstract：:In recent years the global rise in antibiotic resistance and environmental consciousness lead to a renewed fervour to find and develop novel antibiotics, including antifungals. However, the influence of the environment on antifungal activity is often disregarded and many in vitro assays may cause the activity of certa...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.09.025
更新日期：2012-12-01 00:00:00
abstract：:Confocal Raman Microspectroscopy (CRM) can be used as a tool for the in situ evaluation of the chemical composition of living, fully submerged, unstained biofilms. In this study the estimation of the local water content in Pseudomonas aeruginosa PA01 biofilms is given as an example. The ratio of the area of the O-H st...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.05.012
更新日期：2008-09-01 00:00:00
abstract：:Due to technical problems, biofilm biomasses are difficult to be precisely determined. One reliable strategy is based on the colorimetry of formazan compounds derived from tetrazolium salt reduction. XTT presents some desirable properties that make the biofilm measurements easier. However, cells entrapped within the e...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2010.12.018
更新日期：2011-02-01 00:00:00
abstract：:In this study, we aimed to identify the molecular carbapenemase types of the Enterobacteriaceae isolates and to evaluate the performance of manually prepared and commercially available combination disc methods and the modified Hodge test. One hundred and forty carbapenemase producing isolates and 45 isolates as contro...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.03.010
更新日期：2016-06-01 00:00:00
abstract：:Lactic acid bacteria (LAB) play important roles in the food industry, animal husbandry and medicine which are closely related to human life. Modern gene engineering technology is the major means to reveal gene functions, study metabolic pathways and metabolomes of strains and improve the properties of strains. However...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/j.mimet.2020.105944
更新日期：2020-07-01 00:00:00
abstract：:Streptococcus agalactiae, group B streptococci (GBS) is the leading cause of severe bacterial infections in newborns. GBS expression studies allowed the identification and characterization of virulence factors and a better understanding of the host-pathogen-environment interactions. The measurement of transcript level...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.05.011
更新日期：2012-09-01 00:00:00
abstract：:The paper and pulp industry (PPI) produces high quantities of solid and liquid discharge and is regarded as the most polluting industry in the world causing adverse effects to environments and human beings. Hence changes in the way PPI sludge and waste materials are treated is urgently required. Nearly, 10 million ton...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/j.mimet.2019.03.015
更新日期：2019-05-01 00:00:00
abstract：:The U.S. Environmental Protection Agency Alternative Test Procedure protocol outlines a method to produce chlorine-stressed bacteria for water quality testing. Achieving consistent results is challenging due effluent variability. We describe a starting point for generating chlorine-stressed samples from secondary effl...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.105651
更新日期：2019-08-01 00:00:00
abstract：:A quantitative real time reverse transcription polymerase chain reaction (qRT-PCR) assay was utilized to quantify the expression of ElHDO in the fungus Exophiala lecanii-corni during the biodegradation of ethylbenzene and other volatile organic pollutants. The assay was applied to measure the impact of pollutant mixtu...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2006.03.018
更新日期：2006-11-01 00:00:00
abstract：:Exocellulases play a key role in cleaving the accessible ends of cellulose molecules to release soluble glucose and cellobiose. To date, there have been no screens for exocellulase owing to assay protocol limitations, the high cost of substrates, and low activity of exocellulases compared with endocellulases. This stu...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2013.07.010
更新日期：2013-09-01 00:00:00
abstract：:Amplification of high GC content genes by PCR is a major challenge during the creation of recombinant GC-rich DNA constructs. This may be due to the difficulty in DNA denaturation or the possibility of forming secondary structures from DNA templates. Tools have been described to address the technical problems associat...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.106121
更新日期：2020-12-13 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：:One of the known limitations for biosensor assays is the high limit of detection for target cells within complex samples (e.g., Escherichia coli at 10(4) to 10(5) CFU/mL) due to poor capture efficiencies. Currently, researchers can only estimate the cell capture efficiency necessary to produce a positive signal for an...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.11.004
更新日期：2008-01-01 00:00:00
abstract：:Specific fatty acids from phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) recovered from a per 13C-labeled bacteria can be detected in environmental samples and used as measures of bacterial transport in the subsurface. Detection of palmitic acid (16:0) and oleic acid (18:1) at m/z 271 (255+16) and 299 (28...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(00)00245-1
更新日期：2001-04-01 00:00:00
abstract：:AFLP is a selective restriction fragment amplification method generating DNA fingerprints for microbial isolates. We present high-throughput AFLP (htAFLP) to characterize molecular markers associated with bacterial phenotypes. Methicillin-resistant and -susceptible isolates of Staphylococcus aureus have been used for ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.07.013
更新日期：2007-10-01 00:00:00
abstract：:An optimized Citrobacter braakii phytase gene, appA-c, was chemically synthesized by oligonucleotides synthesis and over-lap PCR method. The appA-c gene encoding 423 amino acids was cloned into expression vector pPIC9 and transformed into methylotropic yeast Pichia pastoris. From about 2000 transformants, 400 transfor...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.08.018
更新日期：2009-10-01 00:00:00
abstract：:Recently, a unique method for bacterial transformation using nanofibers to inoculate DNA has been developed by Naoto Yoshida and colleagues. We have verified the principle, transforming Escherichia coli, Yersinia enterocolitica and Acinetobacter baumannii, and have established a user-friendly protocol. A buffered susp...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.12.002
更新日期：2010-02-01 00:00:00
abstract：:Mushrooms are considered as important source of biologically active compounds which include low-molecular-mass protein/peptides (LMMP). In this study, we attempted to profile the LMMP from Lignosus rhinocerus, a wild medicinal mushroom, grown by static cultures (SC) and in stirred tank reactor (STR). Crude water extra...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.07.005
更新日期：2011-10-01 00:00:00
abstract：:Cell wall glycopolymers (CWG) represent an important component of the Gram-positive cell envelope with many biological functions. The mycelial soil bacterium Streptomyces coelicolor A3(2) incorporates two distinct CWGs, polydiglycosylphosphate (PDP) and teichulosonic acid, into the cell wall of its vegetative mycelium...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.07.002
更新日期：2016-09-01 00:00:00
abstract：:The present study for the first time evaluates the serodiagnostic efficacy of two recombinant antigens namely, listeriolysin O (rLLO) and phosphatidyl-inositol phospholipase C (rPI-PLC). Indirect ELISA with the above recombinant antigens was used on samples collected from bovines (n=106), goats (n=138) and pigs (n=92)...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.04.005
更新日期：2017-06-01 00:00:00
abstract：:Development of a high-throughput eukaryotic screening procedure is important to increase success in obtaining improved enzymes through directed enzyme evolution. This procedure was developed for the yeast Yarrowia lipolytica which becomes the second eukaryotic host for this purpose. The extracellular lipase Lip2 was u...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.06.008
更新日期：2007-09-01 00:00:00
abstract：:Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.10.011
更新日期：2015-12-01 00:00:00
abstract：:To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically rele...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.06.008
更新日期：2006-04-01 00:00:00
abstract：:Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within differ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.07.008
更新日期：2012-10-01 00:00:00
abstract：:We have developed an anaerobic biofilm culture system. The system is inexpensive, simple to use and, unlike an anaerobic glovebox, requires no dedicated space. As a test of the system, Porphyromonas gingivalis was cultured under low oxygen (1-2 ppm) and under anaerobic conditions (
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(00)00126-3
更新日期：2000-05-01 00:00:00
abstract：:ERIC (Enterobacterial Repetitive Intergenic Consensus)-PCR was employed to generate stable and reproductive ERIC-PCR fingerprints of Ent. sakazakii ATCC51329. Moreover, this study also cloned and sequenced a major band of Ent. sakazakii (ATCC51329) ERIC-PCR fingerprints. The major band was amplified with primer ERIC2 ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.07.012
更新日期：2008-12-01 00:00:00
abstract：:Permanent staining of faecal smears by Wheatley's trichrome technique has been used by many scientists for the detection of parasites in the past and it was found to be highly sensitive. This study was conducted to evaluate the use of Wintergreen oil in comparison with xylene in Wheatley's trichrome staining technique...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.08.004
更新日期：2012-10-01 00:00:00
abstract：:Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile ele...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2006.03.021
更新日期：2006-11-01 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
