Estimating Microbial Population Data from Optical Density

The spectrophotometer has been used for decades to measure the density of bacterial populations using the turbidity expressed as optical density – OD. However, the OD alone is an unreliable metric and is only proportionately accurate to cell titers to about an OD of 0.6. The relationship between OD and cell titer depends on the configuration of the spectrophotometer, the length of the light path through the culture, the size of the bacterial cells, and the cell culture density. We demonstrate the importance of plate reader calibration to identify the exact relationship between OD and cells/ml. We use four bacterial genera and two sizes of micro-titer plates (96-well and 384-well) and show that the cell/ml per unit OD depends heavily on the bacterial cell size and plate size. We applied our calibration curve to real growth curve data and conclude the cells/ml – rather than OD – is a metric that can be used to directly compare results across experiments, labs, instruments, and species.

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HIV and cardiovascular disease in sub-Saharan Africa: Demographic and Health Survey data for 4 countries

BMC Public Health ◽

10.1186/s12889-021-11218-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Leonard E. Egede ◽

Rebekah J. Walker ◽

Patricia Monroe ◽

Joni S. Williams ◽

Jennifer A. Campbell ◽

...

Keyword(s):

South Africa ◽

Cardiovascular Disease ◽

Health Survey ◽

Survey Design ◽

Logistic Models ◽

Population Data ◽

Demographic And Health Survey ◽

Sub Saharan Africa ◽

Sub Saharan ◽

The Relationship

Abstract Background Investigate the relationship between two common cardiovascular diseases and HIV in adults living in sub-Saharan Africa using population data provided through the Demographic and Health Survey. Methods Data for four sub-Saharan countries were used. All adults asked questions regarding diagnosis of HIV, diabetes, and hypertension were included in the sample totaling 5356 in Lesotho, 3294 in Namibia, 9917 in Senegal, and 1051 in South Africa. Logistic models were run for each country separately, with self-reported diabetes as the first outcome and self-reported hypertension as the second outcome and HIV status as the primary independent variable. Models were adjusted for age, gender, rural/urban residence and BMI. Complex survey design allowed weighting to the population. Results Prevalence of self-reported diabetes ranged from 3.8% in Namibia to 0.5% in Senegal. Prevalence of self-reported hypertension ranged from 22.9% in Namibia to 0.6% in Senegal. In unadjusted models, individuals with HIV in Lesotho were 2 times more likely to have self-reported diabetes (OR = 2.01, 95% CI 1.08–3.73), however the relationship lost significance after adjustment. Individuals with HIV were less likely to have self-reported diabetes after adjustment in Namibia (OR = 0.29, 95% CI 0.12–0.72) and less likely to have self-reported hypertension after adjustment in Lesotho (OR = 0.63, 95% CI 0.47–0.83). Relationships were not significant for Senegal or South Africa. Discussion HIV did not serve as a risk factor for self-reported cardiovascular disease in sub-Saharan Africa during the years included in this study. However, given the growing prevalence of diabetes and hypertension in the region, and the high prevalence of undiagnosed cardiovascular disease, it will be important to continue to track and monitor cardiovascular disease at the population level and in individuals with and without HIV. Conclusions The odds of self-reported diabetes in individuals with HIV was high in Lesotho and low in Namibia, while the odds of self-reported hypertension in individuals with HIV was low across all 4 countries included in this study. Programs are needed to target individuals that need to manage multiple diseases at once and should consider increasing access to cardiovascular disease management programs for older adults, individuals with high BMI, women, and those living in urban settings.

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Stochasticity in Colonial Growth Dynamics of Individual Bacterial Cells

Applied and Environmental Microbiology ◽

10.1128/aem.03629-12 ◽

2013 ◽

Vol 79 (7) ◽

pp. 2294-2301 ◽

Cited By ~ 64

Author(s):

Konstantinos P. Koutsoumanis ◽

Alexandra Lianou

Keyword(s):

Kinetic Parameters ◽

Single Cells ◽

Growth Curves ◽

Growth Dynamics ◽

Time Lapse ◽

Initial Population ◽

Bacterial Cells ◽

Stochastic Growth ◽

Bacterial Populations ◽

Content Type

ABSTRACTConventional bacterial growth studies rely on large bacterial populations without considering the individual cells. Individual cells, however, can exhibit marked behavioral heterogeneity. Here, we present experimental observations on the colonial growth of 220 individual cells ofSalmonella entericaserotype Typhimurium using time-lapse microscopy videos. We found a highly heterogeneous behavior. Some cells did not grow, showing filamentation or lysis before division. Cells that were able to grow and form microcolonies showed highly diverse growth dynamics. The quality of the videos allowed for counting the cells over time and estimating the kinetic parameters lag time (λ) and maximum specific growth rate (μmax) for each microcolony originating from a single cell. To interpret the observations, the variability of the kinetic parameters was characterized using appropriate probability distributions and introduced to a stochastic model that allows for taking into account heterogeneity using Monte Carlo simulation. The model provides stochastic growth curves demonstrating that growth of single cells or small microbial populations is a pool of events each one of which has its own probability to occur. Simulations of the model illustrated how the apparent variability in population growth gradually decreases with increasing initial population size (N0). For bacterial populations withN0of >100 cells, the variability is almost eliminated and the system seems to behave deterministically, even though the underlying law is stochastic. We also used the model to demonstrate the effect of the presence and extent of a nongrowing population fraction on the stochastic growth of bacterial populations.

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Study on the Relationship between Spiritual Intelligence and Organizational Commitment for Male Teachers at Elementary Schools in Academic Year of 2013-2014, in Quchan City, Iran

International Journal of Life Sciences ◽

10.3126/ijls.v9i6.12683 ◽

2015 ◽

Vol 9 (6) ◽

pp. 24-32 ◽

Cited By ~ 2

Author(s):

Hamid Saremi ◽

Morteza Rajab Pur Farkhani

Keyword(s):

Elementary Schools ◽

Organizational Commitment ◽

Population Data ◽

Spiritual Intelligence ◽

Male Teachers ◽

Statistical Population ◽

Population Sampling ◽

Central Statistical ◽

Study Population ◽

The Relationship

This study aims at investigating the relationship between spiritual intelligence and organizational commitment in male teachers of elementary schools in Quchan in the 2013-2014 school years. This is an applied research. Since the researcher sought to study the relationship between the two components, this is correlation research. Considering the variables studied, statistical population was all male teachers in grades three and four at elementary school in Quchan in the 2013-2014 school years. Total number of teachers obtained from Quchan Department of Education was 98 and due to the small size of study population, sampling wasn't performed and the sample was considered equal to the population. Data collection tools were Meyer and Allen's organizational commitment questionnaire and Abdullah Zadeh's spiritual intelligence questionnaire. Having completed the questionnaires, the researcher used mean central statistical indicators and standard deviation dispersion measures and variance for data analysis in descriptive statistics level and in inferential statistics level, they used multivariate linear regression statistic method.The results showed that there was not a significant correlation between total spiritual intelligence and total organizational commitment. There was not also a significant correlation between spiritual intelligence and its components with continuance and normative commitments. However, there was a significant correlation between spiritual intelligence and its components with affective commitment.The findings indicated that spiritual intelligence has been effective in maintaining and improving organizational commitment and it should be tried to improve spirituality and spiritual intelligence in employees and teachers.

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Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

10.1101/866244 ◽

2019 ◽

Cited By ~ 3

Author(s):

Sydney B. Blattman ◽

Wenyan Jiang ◽

Panos Oikonomou ◽

Saeed Tavazoie

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Low Cost ◽

Bacterial Cells ◽

Single Experiment ◽

Bacterial Populations ◽

Single Cell Rna Sequencing ◽

Gene Expression Heterogeneity ◽

Mrna Polyadenylation

AbstractDespite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. While single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems, application of scRNA-seq to prokaryotes has been hindered by their extremely low mRNA abundance, lack of mRNA polyadenylation, and thick cell walls. Here, we present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a low-cost, high-throughput, prokaryotic scRNA-seq pipeline that overcomes these technical obstacles. PETRI-seq uses in situ combinatorial indexing to barcode transcripts from tens of thousands of cells in a single experiment. PETRI-seq captures single cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and low bias, with median capture rates >200 mRNAs/cell for exponentially growing E. coli. These characteristics enable robust discrimination of cell-states corresponding to different phases of growth. When applied to wild-type S. aureus, PETRI-seq revealed a rare sub-population of cells undergoing prophage induction. We anticipate broad utility of PETRI-seq in defining single-cell states and their dynamics in complex microbial communities.

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The relationship between the optical density of cataract and its influence on retinal nerve fibre layer thickness measured with spectral domain optical coherence tomography

Acta Ophthalmologica ◽

10.1111/j.1755-3768.2012.02514.x ◽

2012 ◽

Vol 91 (5) ◽

pp. 418-424 ◽

Cited By ~ 23

Author(s):

Pauline H. B. Kok ◽

Thomas J. T. P. van den Berg ◽

Hille W. van Dijk ◽

Marilette Stehouwer ◽

Ivanka J. E. van der Meulen ◽

...

Keyword(s):

Optical Coherence Tomography ◽

Layer Thickness ◽

Nerve Fibre ◽

Optical Density ◽

Retinal Nerve Fibre Layer ◽

Spectral Domain ◽

Optical Coherence ◽

Fibre Layer ◽

Nerve Fibre Layer ◽

The Relationship

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Analysis of relationship between key genes and astaxanthin biosynthesis in Phaffia rhodozyma by transcript level and gene knock-out

10.21203/rs.2.19181/v1 ◽

2019 ◽

Author(s):

Zhipeng Li ◽

Lina Chen ◽

Tianli Li ◽

Xiping Du ◽

Ning He ◽

...

Keyword(s):

Homologous Recombination ◽

Transcript Level ◽

Phaffia Rhodozyma ◽

Knock Out ◽

Astaxanthin Production ◽

Key Genes ◽

Different Strains ◽

The Relationship ◽

Rate Limiting ◽

Exact Relationship

Abstract Background Phaffia rhodozyma is a potential industrial source for production of natural astaxanthin. The synthetic mechanism of astaxanthin in P. rhodozyma is complex and unclear that blocked its development. Results In this study, eight genes related to dicyclic and monocyclic pathway in three different strains of P. rhodozyma were analyzed, and the relationship between the expression and astaxanthin biosynthesis was explored. Among these genes, crtYB (R=0.75, P<0.05) and asy genes (R=0.74, P<0.05) showed the most closely correlation with astaxanthin biosynthesis. In order to further study exact relationship, crtYB and asy genes were knocked out by homologous recombination. After crtYB knock-out, astaxanthin was decreased to be under detected line. It suggested crtYB played a role in dicyclic and monocyclic pathway. Meanwhile, the asy gene was in dicyclic pathway of astaxanthin biosynthesis, and its knock-out would promote the astaxanthin biosynthesis in monocyclic pathway, resulting in a 25.04% increase in astaxanthin production. Conclusion The possible rate-limiting enzymes were asy gene and crtYB illustrated by analysis of regression. Knock-out of asy and crtYB gene was great helpful to understand the synthetic pathway of astaxanthin, and significant to the industrial application of producing astaxanthin.

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Effect of blood platelets on heparin-induced clearing reaction

American Journal of Physiology-Legacy Content ◽

10.1152/ajplegacy.1960.199.5.803 ◽

1960 ◽

Vol 199 (5) ◽

pp. 803-806 ◽

Cited By ~ 15

Author(s):

Charlotte Hollett ◽

P. J. Nestel

Keyword(s):

Optical Density ◽

Blood Platelets ◽

Regression Coefficients ◽

Glycerol Concentration ◽

Optical Clearing ◽

Fasting Plasma ◽

Heparin Plasma ◽

The Relationship

The relationship between the fall in optical density and the rise in glycerol concentration which occur during heparin-induced clearing was studied in platelet-rich and in platelet-poor post-heparin plasmas. This relationship as determined by the significance of the regression coefficients was highly significant with both plasmas. The effect of platelets on clearing was studied in three system containing either fasting plasma or post-heparin plasma or a mixture of both plasmas. In each system platelets inhibited clearing as measured by fall in optical density but did not inhibit lipolysis as measured by production of glycerol. Addition of platelet-poor fasting plasma to platelet-poor post-heparin plasma inhibited lipolysis but did not inhibit clearing. It is concluded that there may be at least two inhibitors against clearing, one associated with platelets and one present in plasma, which inhibit optical clearing and lipolysis, respectively. When fasting plasmas were incubated with substrate endogenous clearing occurred frequently, but sometimes a rise in optical density and a decrease in glycerol concentration were found, suggesting reversal of enzymatic processes.

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Recent improvements of long-path DOAS measurements: impact on accuracy and stability of short-term and automated long-term observations

Atmospheric Measurement Techniques ◽

10.5194/amt-12-4149-2019 ◽

2019 ◽

Vol 12 (8) ◽

pp. 4149-4169 ◽

Cited By ~ 3

Author(s):

Jan-Marcus Nasse ◽

Philipp G. Eger ◽

Denis Pöhler ◽

Stefan Schmitt ◽

Udo Frieß ◽

...

Keyword(s):

Light Source ◽

Optical Density ◽

Measurement Accuracy ◽

Trace Gases ◽

Detection Limits ◽

Trace Gas ◽

Light Sources ◽

Light Path ◽

Mixing Ratios ◽

Spectral Residual

Abstract. Over the last few decades, differential optical absorption spectroscopy (DOAS) has been used as a common technique to simultaneously measure abundances of a variety of atmospheric trace gases. Exploiting the unique differential absorption cross section of trace-gas molecules, mixing ratios can be derived by measuring the optical density along a defined light path and by applying the Beer–Lambert law. Active long-path (LP-DOAS) instruments can detect trace gases along a light path of a few hundred metres up to 20 km, with sensitivities for mixing ratios down to ppbv and pptv levels, depending on the trace-gas species. To achieve high measurement accuracy and low detection limits, it is crucial to reduce instrumental artefacts that lead to systematic structures in the residual spectra of the analysis. Spectral residual structures can be introduced by most components of a LP-DOAS measurement system, namely by the light source, in the transmission of the measurement signal between the system components or at the level of spectrometer and detector. This article focuses on recent improvements by the first application of a new type of light source and consequent changes to the optical setup to improve measurement accuracy. Most state-of-the-art LP-DOAS instruments are based on fibre optics and use xenon arc lamps or light-emitting diodes (LEDs) as light sources. Here we present the application of a laser-driven light source (LDLS), which significantly improves the measurement quality compared to conventional light sources. In addition, the lifetime of LDLS is about an order of magnitude higher than of typical Xe arc lamps. The small and very stable plasma discharge spot of the LDLS allows the application of a modified fibre configuration. This enables a better light coupling with higher light throughput, higher transmission homogeneity, and a better suppression of light from disturbing wavelength regions. Furthermore, the mode-mixing properties of the optical fibre are enhanced by an improved mechanical treatment. The combined effects lead to spectral residual structures in the range of 5-10×10-5 root mean square (rms; in units of optical density). This represents a reduction of detection limits of typical trace-gas species by a factor of 3–4 compared to previous setups. High temporal stability and reduced operational complexity of this new setup allow the operation of low-maintenance, automated LP-DOAS systems, as demonstrated here by more than 2 years of continuous observations in Antarctica.

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Bacteriophages Limit the Existence Conditions for Conjugative Plasmids

mBio ◽

10.1128/mbio.00586-15 ◽

2015 ◽

Vol 6 (3) ◽

Cited By ~ 22

Author(s):

Ellie Harrison ◽

A. Jamie Wood ◽

Calvin Dytham ◽

Jonathan W. Pitchford ◽

Julie Truman ◽

...

Keyword(s):

Mathematical Modeling ◽

Experimental Evolution ◽

Phage Resistance ◽

Bacterial Cells ◽

Resistance Mutations ◽

Weak Selection ◽

Bacterial Populations ◽

Conjugative Plasmids ◽

Existence Conditions ◽

Selection For

ABSTRACTBacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome.IMPORTANCEConjugative plasmids are infectious loops of DNA capable of transmitting DNA between bacterial cells and between species. Because plasmids often carry extra genes that allow bacteria to live in otherwise-inhospitable environments, their dynamics are central to understanding bacterial adaptive evolution. The plasmid-bacterium interaction has typically been studied in isolation, but in natural bacterial communities, bacteriophages, viruses that infect bacteria, are ubiquitous. Using experiments, mathematical models, and computer simulations we show that bacteriophages drive plasmid dynamics through their ecological and evolutionary effects on bacteria and ultimately limit the conditions allowing plasmid existence. These results advance our understanding of bacterial adaptation and show that bacteriophages could be used to select against plasmids carrying undesirable traits, such as antibiotic resistance.

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