Effect of nucleic acid stain Syto9 on nascent biofilm architecture of Acinetobacter sp. BD413

2005 ◽  
Vol 52 (7) ◽  
pp. 195-202 ◽  
Author(s):  
R. GrayMerod ◽  
L. Hendrickx ◽  
L.N. Mueller ◽  
J.B. Xavier ◽  
S. Wuertz
Keyword(s):  
Nucleic Acid ◽  
Microbial Population ◽  
Separate Flow ◽  
Flow Cell ◽  
Cellular Level ◽  
Flow Cells ◽  
Biofilm Architecture ◽  
Acinetobacter Sp ◽  
Nucleic Acid Stain ◽  
Architecture Development

Flow cells were utilized to determine the effects of repetitive Syto9 staining on developing Acinetobacter sp. BD413 biofilm and to identify features describing reproducible biofilm architecture at 63× magnification. Syto9 is a general nucleic acid stain employed to visualize the entire microbial population of the biofilm and a component in the LIVE/DEAD® BacLight™ Bacterial Viability kits. CLSM images were quantified with the biofilm analysis software PHLIP to calculate six commonly used biofilm architecture characteristics. The characteristics biovolume and mean thickness were most reproducible when biofilms were grown in separate flow cells under controlled conditions, while roughness, porosity, total spreading and surface area to biovolume ratio exhibited inherent variability. Biovolume was more variable in separate flow cells than in channels of the same flow cell. However, even biofilms grown in channels of the same flow cell did not generate reproducible architectures based on the six characteristics. Results suggest difficulties in differentiating the effect of changes due to treatment from the natural variability of architecture development at the cellular level. Despite this high variability, biofilms only stained once developed into thicker structures containing more biomass than biofilms stained multiple times, suggesting that repeated staining with Syto9 affects architecture development. The application of Syto9 to monitor developing biofilms is not recommended.

Underestimation of bacterial numbers in starvation-survival mode using the nucleic acid stain DAPI

2003 ◽  
Vol 157 (3) ◽  
pp. 309-319 ◽  
Author(s):  
Christopher J. McNamara ◽  
Michael J. Lemke ◽  
Laura G. Leff
Keyword(s):  
Nucleic Acid ◽  
Starvation Survival ◽  
Nucleic Acid Stain ◽  
Survival Mode

Flow Cytometry to EvaluateAnaplasma marginaleParasitemia Using a Fluorescent Nucleic Acid Stain

2008 ◽  
Vol 1149 (1) ◽  
pp. 111-113 ◽  
Author(s):  
Rosalía Moretta ◽  
Paula Ruybal ◽  
María Mesplet ◽  
Romina Petrigh ◽  
Pablo Nuñez ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Nucleic Acid ◽  
Nucleic Acid Stain

Packaging of Beef Loin Steaks in 75% O2 Plus 25% CO2. II. Microbiological Properties

1981 ◽  
Vol 44 (12) ◽  
pp. 928-933 ◽  
Author(s):  
M. O. HANNA ◽  
C. VANDERZANT ◽  
G. C. SMITH ◽  
J. W. SAVELL
Keyword(s):  
Microbial Population ◽  
Microbial Flora ◽  
Refrigerated Storage ◽  
Ph Values ◽  
Acinetobacter Sp ◽  
Retail Conditions ◽  
Microbiological Properties

Numbers and types of bacteria were determined on steaks after refrigerated storage (1 ± 1 C) in 75% O2 plus 25% CO2 for 9 days in the dark plus display at 2 ± 2 C for 4 days under simulated retail conditions. Steaks were prepared from strip loins (IMPS #180) as received from the supplier (trial 1) and also from the same or similar loins that were vacuum-packaged at day 0 (trial 1) and then stored under refrigeration for 14 (trial 2) or 28 days (trial 3). Initially (day 0, trial 1), the microflora of steaks consisted primarily of Micrococcus and Moraxella-Acinetobacter sp. Following refrigerated storage in vacuum packages for either 14 or 28 days, Lactobacillus and Leuconostoc sp. became dominant. Refrigerated storage and display of steaks in 75%O2 plus 25% CO2 shifted the microbial population in favor of Leuconostoc sp. Initial log counts of steaks (day 0, trial 1) ranged from 0.88 to 2.02. Counts of steaks stored for 9 or 13 days in 75% O2 plus 25% CO2 nearly always exceeded 106 per cm2 when steaks were prepared from loins which had been stored in vacuum packages for either 14 or 28 days. The pH values of steaks prepared from loins which had been stored under refrigeration for 14 days were lower (0.27–0.56) than those of steaks prepared from comparable loins as they were received from the supplier (day 0, trial 1). Refrigerated storage of vacuum-packaged loins for an additional 14 days did not cause marked changes in pH of the steaks. No consistent differences in microbial flora were detected between green- and normal-pigmented areas of steaks prepared from vacuum-packaged loins which had been stored refrigerated for 14–28 days.

scholarly journals Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 381 ◽  
Author(s):  
Olivier Tytgat ◽  
Yannick Gansemans ◽  
Jana Weymaere ◽  
Kaat Rubben ◽  
Dieter Deforce ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Massively Parallel Sequencing ◽  
Flow Cell ◽  
Nanopore Sequencing ◽  
Flow Cells ◽  
Pattern Complexity ◽  
Str Loci ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies ◽  
Short Tandem

Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the occurrence of homopolymers in STR loci. The goal of this study was to apply the latest progress in nanopore sequencing by Oxford Nanopore Technologies in the field of STR genotyping. The experiments were performed using the state of the art R9.4 flow cell and the most recent R10 flow cell, which was specifically designed to improve consensus accuracy of homopolymers. Two single-contributor samples and one mixture sample were genotyped using Illumina sequencing, Nanopore R9.4 sequencing, and Nanopore R10 sequencing. The accuracy of genotyping was comparable for both types of flow cells, although the R10 flow cell provided improved data quality for loci characterized by the presence of homopolymers. We identify locus-dependent characteristics hindering accurate STR genotyping, providing insights for the design of a panel of STR loci suited for nanopore sequencing. Repeat number, the number of different reference alleles for the locus, repeat pattern complexity, flanking region complexity, and the presence of homopolymers are identified as unfavorable locus characteristics. For single-contributor samples and for a limited set of the commonly used STR loci, nanopore sequencing could be applied. However, the technology is not mature enough yet for implementation in routine forensic workflows.

scholarly journals Development of a Novel Biofilm Continuous Culture Method for Simultaneous Assessment of Architecture and Gaseous Metabolite Production

2008 ◽  
Vol 74 (17) ◽  
pp. 5429-5435 ◽  
Author(s):  
Yutaka Yawata ◽  
Nobuhiko Nomura ◽  
Hiroo Uchiyama
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Flow Reactor ◽  
Culture Method ◽  
Model System ◽  
Metabolite Production ◽  
Biofilm Architecture ◽  
Novel Method ◽  
Architecture Development ◽  
Simultaneous Assessment ◽  
Gaseous Metabolites

ABSTRACT The way that gaseous metabolite production changes along with biofilm architecture development is poorly understood. To address this question, we developed a novel flow reactor biofilm culture method that allows for simultaneous assessment of gaseous metabolite production and architecture visualization. In this report, we establish the utility of this method using denitrification by Pseudomonas aeruginosa biofilms as a model system. Using this method, we were able to collect and analyze gaseous metabolites produced by denitrification and also visualize biofilm architecture in a nondestructive manner. Thus, we propose that this novel method is a powerful tool to investigate potential relationships between biofilm architecture and the gas-producing metabolic activity of biofilms, providing new insights into biofilm ecology.

ACRIDINE ORANGE FLUOROCHROMING AND ULTRAVIOLET ABSORPTION OF STAPHYLOCOCCUS AUREUS CELLS MODIFIED BY UNBALANCED NUCLEIC ACID AND CELL WALL SYNTHESIS

1966 ◽  
Vol 12 (4) ◽  
pp. 677-682
Author(s):  
Jacques de Repentigny ◽  
Sorin Sonea ◽  
Armand Frappier
Keyword(s):  
Staphylococcus Aureus ◽  
Nucleic Acid ◽  
Fluorescence Microscopy ◽  
Nucleic Acids ◽  
Acridine Orange ◽  
Dry Weight ◽  
Cellular Level ◽  
Cellular Heterogeneity ◽  
Nucleic Acid Content ◽  
Bacterial Populations

Cultures of Staphylococcus aureus were grown in the presence of five different antimetabolites (5-fluorodeoxyuridine, aminopterin, 8-azaguanine, mitomycm-C, 5-fluorouracil) active against ceil walls and (or) nucleic acids. Fluorescence microscopy of smears stained with acridine orange revealed reddish and green cells in both treated and untreated cultures. There were less than 20% of reddish cells in untreated cultures and more than 40% in treated cultures. Treated cultures contained fewer viable organisms. All antimetabolites except mitomycin-C produced a diminution in the nucleic acids, chemically determined as percentage of dry weight of bacteria. Only 5-fluorouracil increased the RNA/DNA ratio. However, with ultraviolet microscopy at 260 mμ wavelength the absorption of reddish cells is much higher than that of the green cells, which, at the cellular level, seemed to indicate a greater nucleic acid content. With ultraviolet or with fluorescence microscopy we have obtained similar evidence of the cellular heterogeneity produced by antimetabolites in bacterial populations.

Influence of Ambient Airflow on Free Surface Deformation and Flow Pattern Inside Liquid Bridge With Large Prandtl Number Fluid (Pr > 100) Under Gravity

2017 ◽  
Vol 139 (12) ◽  
Author(s):  
Shuo Yang ◽  
Ruquan Liang ◽  
Song Xiao ◽  
Jicheng He ◽  
Shuo Zhang
Keyword(s):  
Free Surface ◽  
Prandtl Number ◽  
Liquid Bridge ◽  
Thermocapillary Convection ◽  
Surface Deformation ◽  
Flow Cell ◽  
Thermocapillary Force ◽  
Flow Cells ◽  
Lower Disk ◽  
Free Surface Deformation

The influence of airflow shear on the free surface deformation and the flow structure for large Prandtl number fluid (Pr = 111.67) has been analyzed numerically as the parallel airflow shear is induced into the surrounding of liquid bridge from the lower disk or the upper disk. Contrasted with former studies, an improved level set method is adopted to track any tiny deformation of free surface, where the area compensation is carried out to compensate the nonconservation of mass. Present results indicate that the airflow shear can excite flow cells in the isothermal liquid bridge. The airflow shear induced from the upper disk impulses the convex region of free interface as the airflow shear intensity is increased, which may exceed the breaking limit of liquid bridge. The free surface is transformed from the “S”-shape into the “M”-shape as the airflow shear is induced from the lower disk. For the nonisothermal liquid bridge, the flow cell is dominated by the thermocapillary convection at the hot corner if the airflow shear comes from the hot disk, and another reversed flow cell near the cold disk appears. While the shape of free surface depends on the competition between the thermocapillary force and the shear force when the airflow is induced from the cold disk.

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