Analysis of Single Bacterium Dynamics in a Stochastic Model of Toxin-Producing Bacteria

AbstractWe stochastically model two bacterial populations which can produce toxins. We propose to analyse this biological system by following the dynamics of a single bacterium during its lifetime, as well as its progeny. We study the lifespan of a single bacterium, the number of divisions that this bacterium undergoes, and the number of toxin molecules that it produces during its lifetime. We also compute the mean number of bacteria in the genealogy of the original bacterium and the number of toxin molecules produced by its genealogy. We illustrate the applicability of our methods by considering the bacteria Bacillus anthracis and antibiotic treatment, making use of in vitro experimental data. We quantify, for the first time, bacterial toxin production by exploiting an in vitro assay for the A16R strain, and make use of the resulting parameterised model to illustrate our techniques.

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Statistics of nascent and mature RNA fluctuations in a stochastic model of transcriptional initiation, elongation, pausing, and termination

10.1101/2020.05.13.092650 ◽

2020 ◽

Author(s):

Tatiana Filatova ◽

Nikola Popovic ◽

Ramon Grima

Keyword(s):

Experimental Data ◽

Fluorescence Microscopy ◽

Stochastic Model ◽

Explicit Dependence ◽

Transcriptional Initiation ◽

Estimate Parameter ◽

Mean And Variance ◽

The Mean ◽

Nascent Rna ◽

Parameter Values

AbstractRecent advances in fluorescence microscopy have made it possible to measure the fluctuations of nascent (actively transcribed) RNA. These closely reflect transcription kinetics, as opposed to conventional measurements of mature (cellular) RNA, whose kinetics is affected by additional processes downstream of transcription. Here, we formulate a stochastic model which describes promoter switching, initiation, elongation, premature detachment, pausing, and termination while being analytically tractable. By computational binning of the gene into smaller segments, we derive exact closed-form expressions for the mean and variance of nascent RNA fluctuations in each of these segments, as well as for the total nascent RNA on a gene. We also derive exact expressions for the first two moments of mature RNA fluctuations, and approximate distributions for total numbers of nascent and mature RNA. Our results, which are verified by stochastic simulation, uncover the explicit dependence of the statistics of both types of RNA on transcriptional parameters and potentially provide a means to estimate parameter values from experimental data.

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Fertilization of bovine oocytes grown in vitro

Reproduction Fertility and Development ◽

10.1071/r97044 ◽

1997 ◽

Vol 9 (8) ◽

pp. 781 ◽

Cited By ~ 12

Author(s):

Shigeru Osaki ◽

Kenji Matsumura ◽

Ken Yamamoto ◽

Takashi Miyano ◽

Masashi Miyake ◽

...

Keyword(s):

Granulosa Cell ◽

Calf Serum ◽

Collagen Gels ◽

Normal Morphology ◽

Bovine Spermatozoa ◽

The Mean ◽

First Time ◽

Bovine Oocytes ◽

Meiotic Competence

Early antral follicles 0·5–0·7 mm in diameter were dissected from bovine ovaries, and oocyte–cumulus complexes with pieces of parietal granulosa (OCCGs) were then collected from the follicles. The OCCGs containing oocytes of 90–99 m diameter (94·7 ± 2·8 µm, n = 196) were selected and embedded in collagen gels and cultured for 14 days in TCM199 containing 10% fetal calf serum and 4 mM hypoxanthine. From cultured OCCGs, 144 surviving oocytes were recovered, of which 53 were granulosa cell-enclosed oocytes and 91 were denuded oocytes. The mean diameter of the surviving oocytes was 114·2 ± 8·4 µm, significantly larger than that measured before culture (P < 0·05). The granulosa cell-enclosed oocytes and denuded oocytes were further cultured for maturation for 24 h. After culture, 72% (38/53) of the granulosa cell-enclosed oocytes and 59% (54/91) of the denuded oocytes showed normal morphology. These oocytes were then inseminated with bovine spermatozoa. After 29 h of insemination, all of the denuded oocytes had degenerated, while 32% (12/38) of the granulosa cell-enclosed oocytes showed normal morphology. Of the 12 oocytes, 5 were penetrated by spermatozoa, and 2 formed both male and female pronuclei. These results demonstrate for the first time that bovine oocytes grown in vitro acquire meiotic competence and can be penetrated by spermatozoa.

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Investigating the Effect of Mono- and Dimeric 360A G-Quadruplex Ligands on Telomere Stability by Single Telomere Length Analysis (STELA)

Molecules ◽

10.3390/molecules24030577 ◽

2019 ◽

Vol 24 (3) ◽

pp. 577 ◽

Cited By ~ 3

Author(s):

In Hwang ◽

Patrick Mailliet ◽

Virginie Hossard ◽

Jean-Francois Riou ◽

Anthony Bugaut ◽

...

Keyword(s):

Telomere Length ◽

Dna Binding Protein ◽

Replication Machinery ◽

Telomeric Dna ◽

Full Spectrum ◽

G Quadruplex ◽

The Mean ◽

Length Analysis ◽

First Time

Telomeres are nucleoprotein structures that cap and protect the natural ends of chromosomes. Telomeric DNA G-rich strands can form G-quadruplex (or G4) structures. Ligands that bind to and stabilize G4 structures can lead to telomere dysfunctions by displacing shelterin proteins and/or by interfering with the replication of telomeres. We previously reported that two pyridine dicarboxamide G4 ligands, 360A and its dimeric analogue (360A)2A, were able to displace in vitro hRPA (a single-stranded DNA-binding protein of the replication machinery) from telomeric DNA by stabilizing the G4 structures. In this paper, we perform for the first time single telomere length analysis (STELA) to investigate the effect of G4 ligands on telomere length and stability. We used the unique ability of STELA to reveal the full spectrum of telomere lengths at a chromosome terminus in cancer cells treated with 360A and (360A)2A. Upon treatment with these ligands, we readily detected an increase of ultrashort telomeres, whose lengths are significantly shorter than the mean telomere length, and that could not have been detected by other methods.

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Estimation, morphometry and ultrastructure of ovarian preantral follicle population in agouti (Dasyprocta leporina)

Pesquisa Veterinária Brasileira ◽

10.1590/1678-5150-pvb-4946 ◽

2018 ◽

Vol 38 (1) ◽

pp. 175-182 ◽

Cited By ~ 1

Author(s):

Erica A.A. Santos ◽

Gabriela L. Lima ◽

Erica C.G. Praxedes ◽

Andréia M. Silva ◽

Keilla M. Maia ◽

...

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Ultrastructural Analysis ◽

Preantral Follicle ◽

Transmission Electron ◽

The Mean ◽

First Time ◽

Further Development

ABSTRACT: The aim of this study was to characterize the preantral ovarian follicular population in agoutis (D. leporina) by estimating the number of follicles at each developmental category, and also describe the morphometry and the specific features of the follicle and the oocyte by using light and transmission electron microscopy. The length of each ovary was measured using a caliper rule, longitudinally sectioned into two halves and both were immediately fixed to perform the estimation of follicular population and ultrastructural analysis. The mean (±S.E.M.) population of follicular per pair of ovary was estimated at 4419.8±532.26 and 5397.52±574.91 for right and left ovaries, respectively, but no differences were observed between them. The diameters for follicles, oocyte and nuclei were: 18.62±3.40μm, 12.28±2.37μm and 6.10±0.93μm for primordial, 23.75±5.70μm, 14.22±3.00μm and 6.70±1.24μm for primary and 88.55±17.61μm, 52.85±17.56μm and 22.33±17.61μm for secondary follicles, respectively. The most of the follicles found belonged to the primordial category (86.63%), followed by primary (13.01%) and secondary (0.35%) one. Additionally, polyovular follicles were observed in all the animals and they represented 7.51% of the total follicles counted. The ultrastructural analysis showed that the oocyte presented a central and regular nuclei, displaying a homogenous mass. Among the organelles, the mitochondria were the most abundant and the oocyte Golgi apparatus was rarely observed. In conclusion, this work shows for the first time the characterization of the population of preantral follicles in the ovary of Dasyprocta leporina. Those information will be useful for further development and adaptation of biotechniques such as germplasm cryopreservation and in vitro gametes manipulation.

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Lattice Dynamics of Molybdenum and Chromium

Zeitschrift für Naturforschung A ◽

10.1515/zna-1980-0210 ◽

1980 ◽

Vol 35 (2) ◽

pp. 230-235

Author(s):

B. P. Singh ◽

L. P. Pathak ◽

M. P. Hemkar

Keyword(s):

Experimental Data ◽

Temperature Dependence ◽

Lattice Dynamics ◽

Waller Factor ◽

Mean Square ◽

Frequency Wave ◽

Debye Waller Factor ◽

Nearest Neighbours ◽

The Mean ◽

First Time

Abstract The frequency-wave vector dispersion relations, the frequency spectrum, the Debye temperature, the temperature dependence of the Debye-Waller factor and the mean square displacements of the atoms molybdenum and chromium, the metals for which long range forces are also important, have been computed on the basis of the extended improved Fielek model for BCC transition metals. The model considers, for the first time the d shell-d shell central interactions upto next-nearest-neighbours. The calculated results show a satisfactory agreement with the available experimental data.

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Statistics of Nascent and Mature RNA Fluctuations in a Stochastic Model of Transcriptional Initiation, Elongation, Pausing, and Termination

Bulletin of Mathematical Biology ◽

10.1007/s11538-020-00827-7 ◽

2020 ◽

Vol 83 (1) ◽

Author(s):

Tatiana Filatova ◽

Nikola Popovic ◽

Ramon Grima

Keyword(s):

Experimental Data ◽

Fluorescence Microscopy ◽

Stochastic Model ◽

Explicit Dependence ◽

Transcriptional Initiation ◽

Estimate Parameter ◽

Mean And Variance ◽

The Mean ◽

Nascent Rna ◽

Parameter Values

AbstractRecent advances in fluorescence microscopy have made it possible to measure the fluctuations of nascent (actively transcribed) RNA. These closely reflect transcription kinetics, as opposed to conventional measurements of mature (cellular) RNA, whose kinetics is affected by additional processes downstream of transcription. Here, we formulate a stochastic model which describes promoter switching, initiation, elongation, premature detachment, pausing, and termination while being analytically tractable. We derive exact closed-form expressions for the mean and variance of nascent RNA fluctuations on gene segments, as well as of total nascent RNA on a gene. We also obtain exact expressions for the first two moments of mature RNA fluctuations and approximate distributions for total numbers of nascent and mature RNA. Our results, which are verified by stochastic simulation, uncover the explicit dependence of the statistics of both types of RNA on transcriptional parameters and potentially provide a means to estimate parameter values from experimental data.

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Assessing Mixture Effects of Cereulide and Deoxynivalenol on Intestinal Barrier Integrity and Uptake in Differentiated Human Caco-2 Cells

Toxins ◽

10.3390/toxins13030189 ◽

2021 ◽

Vol 13 (3) ◽

pp. 189 ◽

Cited By ~ 1

Author(s):

Julia Beisl ◽

Elisabeth Varga ◽

Dominik Braun ◽

Benedikt Warth ◽

Monika Ehling-Schulz ◽

...

Keyword(s):

Barrier Function ◽

Intestinal Barrier ◽

Bacterial Toxin ◽

Intestinal Barrier Function ◽

Intestinal Cells ◽

Food Contaminants ◽

Intestinal Integrity ◽

Junction Protein ◽

First Time

The human intestine is regularly exposed to ingested food contaminants, such as fungal and bacterial toxins, which have been described to co-occur in a mixed diet. Thus, it is of utmost importance to understand possible interactions between contaminants of different origin. Hence, we investigated the single and combined effects of one of the most abundant mycotoxins, deoxynivalenol (DON; 0.1 to 10 µg/mL), and the bacterial toxin cereulide (CER; 1 to 100 ng/mL) on differentiated human Caco-2 (C2BBe1) cells cultured in a transwell system. We tested the capacity of the two toxins to alter the intestinal integrity and further investigated the uptake of both compounds and the formation of selected DON metabolites. CER alone (10 and 100 ng/mL) and in combination with DON (10 ng/mL CER with 1 µg/mL DON) was found to alter the barrier function by increasing the transepithelial electrical resistance and the expression of the tight junction protein claudin-4. For the first time, DON-3-sulfate was identified as a metabolite of human intestinal cells in vitro. Moreover, co-incubation of CER and DON led to an altered ratio between DON and DON-3-sulfate. Hence, we conclude that co-exposure to CER and DON may alter the intestinal barrier function and biotransformation of intestinal cells.

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Influence of Platelet Membrane Sialic Acid and Platelet-Associated IgG on Ageing and Sequestration of Blood Platelets in Baboons

Thrombosis and Haemostasis ◽

10.1055/s-0038-1649648 ◽

1993 ◽

Vol 70 (04) ◽

pp. 676-680 ◽

Cited By ~ 24

Author(s):

H F Kotzé ◽

V van Wyk ◽

P N Badenhorst ◽

A du P Heyns ◽

J P Roodt ◽

...

Keyword(s):

Sialic Acid ◽

Life Span ◽

Blood Platelets ◽

Senescent Cell ◽

Platelet Membrane ◽

Antigen Complex ◽

The Mean ◽

Aggregation Of Platelets

SummaryPlatelets were isolated from blood of baboons and treated with neuraminidase to remove platelet membrane sialic acid, a process which artificially ages the platelets. The platelets were then labelled with 111In and their mean life span, in vivo distribution and sites of Sequestration were measured. The effect of removal of sialic acid on the attachment of immunoglobulin to platelets were investigated and related to the Sequestration of the platelets by the spleen, liver, and bone marrow. Removal of sialic acid by neuraminidase did not affect the aggregation of platelets by agonists in vitro, nor their sites of Sequestration. The removal of 0.51 (median, range 0.01 to 2.10) nmol sialic acid/108 platelets shortened their life span by 75 h (median, range 0 to 132) h (n = 19, p <0.001), and there was an exponential correlation between the shortening of the mean platelet life span and the amount of sialic acid removed. The increase in platelet-associated IgG was 0.112 (median, range 0.007 to 0.309) fg/platelet (n = 25, p <0.001) after 0.79 (median, range 0.00 to 6.70) nmol sialic acid/108 platelets was removed (p <0.001). There was an exponential correlation between the shortening of mean platelet life span after the removal of sialic acid and the increase in platelet-associated IgG. The results suggest that platelet membrane sialic acid influences ageing of circulating platelets, and that the loss of sialic acid may have exposed a senescent cell antigen that binds IgG on the platelet membrane. The antibody-antigen complex may then provide a signal to the macrophages that the platelet is old, and can be phagocytosed and destroyed.

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COUNTING TOTAL BACTERIA IN LAND ORGANIC WASTE HOUSEHOLD AND LAND INORGANIC WITH TOTAL PLATE COUNT METHOD (TPC)

Jurnal Penelitian Agrisamudra ◽

10.33059/jpas.v4i2.288 ◽

2017 ◽

Vol 4 (2) ◽

pp. 87-91

Author(s):

Ekamaida Ekamaida

Keyword(s):

Soil Fertility ◽

Bacterial Population ◽

Organic Soil ◽

Biological Properties ◽

Plate Count ◽

Bacterial Populations ◽

Fertility Data ◽

Plate Count Method ◽

The Mean ◽

Total Bacteria

The soil fertility aspect is characterized by the good biological properties of the soil. One important element of the soil biological properties is the bacterial population present in it. This research was conducted in the laboratory of Microbiology University of Malikussaleh in the May until June 2016. This study aims to determine the number of bacterial populations in soil organic and inorganic so that can be used as an indicator to know the level of soil fertility. Data analysis was done by T-Test that is by comparing the mean of observation parameter to each soil sample. The sampling method used is a composite method, which combines 9 of soil samples taken from 9 sample points on the same plot diagonally both on organic soil and inorganic soil. The results showed the highest bacterial population was found in total organic soil cfu 180500000 and total inorganic soil cfu 62.500.000

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Somatic Embryogenesis and In vitro Plant Regeneration in Vigna trilobata (L.) Verd. - A Potential Pasture Legume

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v19i1.4990 ◽

1970 ◽

Vol 19 (1) ◽

pp. 89-99

Author(s):

K. Choudhary ◽

M. Singh ◽

M. S. Rathore ◽

N. S. Shekhawat

Keyword(s):

Somatic Embryogenesis ◽

Growth Regulators ◽

Somatic Embryos ◽

Basal Medium ◽

Long Term Study ◽

Continuous Application ◽

First Time ◽

Pasture Legume

This long term study demonstrates for the first time that it is possible to propagate embryogenic Vigna trilobata and to subsequently initiate the differentiation of embryos into complete plantlets. Initiation of callus was possible on 2,4-D. Somatic embryos differentiated on modified MS basal nutrient medium with 1.0 mg/l of 2,4-D and 0.5 mg/l of Kn. Sustained cell division resulted in globular and heart shape stages of somatic embryos. Transfer of embryos on to a fresh modified MS basal medium with 0.5 mg/l of Kn and 0.5 mg/l of GA3 helped them to attain maturation and germination. However, the propagation of cells, as well as the differentiation of embryos, were inhibited by a continuous application of these growth regulators. For this reason, a long period on medium lacking these growth regulators was necessary before the differentiation of embryos occurred again. The consequences for improving the propagation of embryogenic cultures in Vigna species are discussed. Key words: Pasture legume, Vigna trilobata, Globular, Heart shape, somatic embryogenesis D.O.I. 10.3329/ptcb.v19i1.4990 Plant Tissue Cult. & Biotech. 19(1): 89-99, 2009 (June)

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