scholarly journals The Process Pathway Model of bacterial growth

2019 ◽  
Author(s):  
Daniel Biro ◽  
Ximo Pechuan ◽  
Maryl Lambros ◽  
Aviv Bergman
Keyword(s):  
Temperature Dependence ◽  
Bacterial Growth ◽  
Large Scale ◽  
Growth Curves ◽  
Population Level ◽  
Growth Data ◽  
Pathway Model ◽  
Growth Profile ◽  
Simplifying Assumptions ◽  
Multiple Species

AbstractThe growth profile of microorganisms in an enclosed environment, such as a bioreactor or flask, is a well studied and characterized system. Despite a long history of examination, there are still many competing mathematical models used to describe an output of the microorganisms, namely the number of bacteria as a function of time. However, these descriptions are either purely phenomenological and give no intuition as to the biological mechanisms underlying the growth curves, or extremely complex and become computationally unfeasible at the population level. In this paper, we develop the Process Pathway Model by modifying a model of sequential processes, which was first used to model robustness in metabolic pathways, and demonstrate that the Process Pathway Model encapsulates many features and temperature dependence of bacterial growth. We verify the predictions of the model against growth data for multiple species of microorganisms, and confirm that the model generates accurate predictions on temperature dependence of bacterial growth. The model has five free parameters, and the simplifying assumptions used to build the model are built upon biologically realistic notions. The Process Pathway Model accurately models a microorganism’s growth profile at an intermediate level of complexity that is computationally feasible. This model can be used as both an conceptual model for thinking about systems of bacterial growth, as well as a computational model that operates at level of complexity that is amenable to large scale simulation. This balance in accuracy and intuitiveness was accomplished by using realistic biological assumptions to simplify the underlying biology, which may point the way forward for future models of this type.

More than simply microbial growth curves

2016 ◽  
Vol 1 (2) ◽  
pp. 63 ◽  
Author(s):  
Ji-Dong Gu
Keyword(s):  
Bacterial Growth ◽  
Microbial Growth ◽  
Growth Curves ◽  
Lag Phase ◽  
Growth Data ◽  
Phase Growth ◽  
Simple Task ◽  
Wide Range ◽  
Comparative Results ◽  
Comparative Information

Bacterial growth is a very important piece of information in a wide range of investigation and, in most of the time the data are simply shown directly without any further processing. In a single factor investigation without comparative information to be extracted, this simple approach can be used together with other data to form a comprehensive set of results. When comparison is involved, such direct showing of bacterial growth curves without processing cannot warrant a meaningful comparison thoroughly and further processing of data is necessary. In addition, there is little, if any, quantitative data for the comparison from the display of growth curves and description of a number of curves is not a simple task, especially in a meaningful way for assimilation of the data to readers. With this in mind, I would like to remind of those who plan to show such data as growth curves for their potential publication to carry this further to generate comparative results for a much meaningful interpretation by modeling and calculation from the raw growth data over time of incubation. By calculating with existing equations, the lag phase, growth rate and the biomass can be derived from a series of growth curves for a more effective and meaningful analysis. This approach is not new, but remembrance of such available tool is more important so that research data are shown professionally and also scientifically for meaning presentation and effective assimilation.

scholarly journals Effect of erythritol and xylitol on Streptococcus pyogenes causing peritonsillar abscesses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Siiri Kõljalg ◽  
Risto Vaikjärv ◽  
Imbi Smidt ◽  
Tiiu Rööp ◽  
Anirikh Chakrabarti ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Bacterial Growth ◽  
Growth Curves ◽  
Culture Collection ◽  
Exponential Phase ◽  
Clinical Isolates ◽  
Growth Inhibitors ◽  
Throat Culture ◽  
Potent Growth

AbstractPolyols are effective against caries-causing streptococci but the effect on oropharynx-derived pyogenic streptococci is not well characterised. We aimed to study the effect of erythritol (ERY) and xylitol (XYL) against Streptococcus pyogenes isolated from peritonsillar abscesses (PTA). We used 31 clinical isolates and 5 throat culture collection strains. Inhibition of bacterial growth by polyols at 2.5%, 5% and 10% concentrations was studied and the results were scored. Amylase levels in PTA pus were compared to polyol effectivity scores (PES). Growth curves of four S. pyogenes isolates were analysed. Our study showed that XYL was more effective than ERY inhibiting 71–97% and 48–84% of isolates, respectively, depending of concentrations. 48% of clinical and all throat strains were inhibited by polyols in all concentrations (PES 3). PES was negative or zero in 26% of the isolates in the presence of ERY and in 19% of XYL. ERY enhanced the growth of S. pyogenes isolated from pus with high amylase levels. Polyols in all concentrations inhibited the growth in exponential phase. In conclusion, ERY and XYL are potent growth inhibitors of S. pyogenes isolated from PTA. Therefore, ERY and XYL may have potential in preventing PTA in the patients with frequent tonsillitis episodes.

scholarly journals 214 Longitudinal Changes in Sleep Duration, Timing, Variability, and Stages during the COVID-19 Pandemic: Large-Scale Fitbit Data

SLEEP ◽  
2021 ◽  
Vol 44 (Supplement_2) ◽  
pp. A86-A86
Author(s):  
Michael Grandner ◽  
Naghmeh Rezaei
Keyword(s):  
New York ◽  
Los Angeles ◽  
San Francisco ◽  
Sleep Duration ◽  
Large Scale ◽  
Age Groups ◽  
Population Level ◽  
Sleep Stages ◽  
Longitudinal Changes ◽  
Timing Variability

Abstract Introduction The COVID-19 pandemic has resulted in societal-level changes to sleep and other behavioral patterns. Objective, longitudinal data would allow for a greater understanding of sleep-related changes at the population level. Methods N= 163,524 deidentified active Fitbit users from 6 major US cities contributed data, representing areas particularly hard-hit by the pandemic (Chicago, Houston, Los Angeles, New York, San Francisco, and Miami). Sleep variables extracted include nightly and weekly mean sleep duration and bedtime, variability (standard deviation) of sleep duration and bedtime, and estimated arousals and sleep stages. Deviation from similar timeframes in 2019 were examined. All analyses were performed in Python. Results These data detail how sleep duration and timing changed longitudinally, stratified by age group and gender, relative to previous years’ data. Overall, 2020 represented a significant departure for all age groups and both men and women (P<0.00001). Mean sleep duration increased in nearly all groups (P<0.00001) by 5-11 minutes, compared to a mean decrease of 5-8 minutes seen over the same period in 2019. Categorically, sleep duration increased for some and decreased for others, but more extended than restricted. Sleep phase shifted later for nearly all groups (p<0.00001). Categorically, bedtime was delayed for some and advanced for others, though more delayed than advanced. Duration and bedtime variability decreased, owing largely to decreased weekday-weekend differences. WASO increased, REM% increased, and Deep% decreased. Additional analyses show stratified, longitudinal changes to sleep duration and timing mean and variability distributions by month, as well as effect sizes and correlations to other outcomes. Conclusion The pandemic was associated with increased sleep duration on average, in contrast to 2019 when sleep decreased. The increase was most profound among younger adults, especially women. The youngest adults also experienced the greatest bedtime delay, in line with extensive school-start-times and chronotype data. When given the opportunity, the difference between weekdays and weekends became smaller, with occupational implications. Sleep staging data showed that slightly extending sleep minimally impacted deep sleep but resulted in a proportional increase in REM. Wakefulness during the night also increased, suggesting increased arousal despite greater sleep duration. Support (if any) This research was supported by Fitbit, Inc.

Superlubricity Relevant in Hard Disk Drive Applications

2016 ◽  
Author(s):  
Shou-Mo Zhang ◽  
Cuong-C. Vu ◽  
Qun-Yang Li ◽  
Norio Tagawa ◽  
Quan-Shui Zheng
Keyword(s):  
Temperature Dependence ◽  
Hard Disk Drive ◽  
Large Scale ◽  
Hard Disk Drives ◽  
Hard Disk ◽  
Disk Drive ◽  
Force Sensor ◽  
Lubricant Layer ◽  
Single Crystalline ◽  
Crystalline Graphite

Reduction of head-media spacing (HMS) keeps crucial during the increase of areal density of hard disk drives (HDD). The design of hard disk drive with a superlubric interface is reported with two schemes for HDI design to realize superlubricity. For the first scheme, the DLC layer is kept on the disk while removing the lubricant layer. The DLC layer on the transducer is replaced by graphene-like layer. The direct contact between head and disk could reduce the HMS to about 2.3 nm. For the second scheme, the DLC layer on disk is further replaced by graphene and the HMS could be reduced to below 1 nm. For the first scheme, the basic proof of concept experiments are conducted using micro-scale graphite island samples. Ultralow COF, with the average of 0.0344 on the interface of single crystalline graphite surface and DLC substrate is demonstrated by AFM. What’s more, the temperature dependence of friction between single crystalline graphite and DLC is measured by micro-force sensor mounted on micro-manipulator. The results show that heating helps to significantly decrease the friction. Desorption of contaminants along the interface is speculated to be the key mechanism for temperature dependence of friction. This work provides the concept of large-scale superlubricity relevant in HDD applications, which could be a promising technology to ultimately reduce HMS for future HDI development.

Decomposition of Growth Curves into Growth Rate and Acceleration: a Novel Procedure to Monitor Bacterial Growth and the Time-Dependent Effect of Antimicrobials

2021 ◽  
Author(s):  
M. Luisa Navarro-Pérez ◽  
M. Coronada Fernández-Calderón ◽  
Virginia Vadillo-Rodríguez
Keyword(s):  
Growth Rate ◽  
Mathematical Models ◽  
Bacterial Growth ◽  
Time Course ◽  
Antimicrobial Agents ◽  
Numerical Procedure ◽  
Growth Curves ◽  
Predictive Microbiology ◽  
Insight Into ◽  
Over Time

In this paper, a simple numerical procedure is presented to monitor the growth of Streptococcus sanguinis over time in the absence and presence of propolis, a natural antimicrobial. In particular, it is shown that the real-time decomposition of growth curves obtained through optical density measurements into growth rate and acceleration can be a powerful tool to precisely assess a large range of key parameters [ i.e. lag time ( t 0 ), starting growth rate ( γ 0 ), initial acceleration of the growth ( a 0 ), maximum growth rate ( γ max ), maximum acceleration ( a max ) and deceleration ( a min ) of the growth and the total number of cells at the beginning of the saturation phase ( N s )] that can be readily used to fully describe growth over time. Consequently, the procedure presented provides precise data of the time course of the different growth phases and features, which is expected to be relevant, for instance, to thoroughly evaluate the effect of new antimicrobial agents. It further provides insight into predictive microbiology, likely having important implications to assumptions adopted in mathematical models to predict the progress of bacterial growth. Importance: The new and simple numerical procedure presented in this paper to analyze bacterial growth will possibly allow identifying true differences in efficacy among antimicrobial drugs for their applications in human health, food security, and environment, among others. It further provides insight into predictive microbiology, likely helping in the development of proper mathematical models to predict the course of bacterial growth under diverse circumstances.

Calculation of NQR v's and T1-1' s being proportional to T4 and T5 , respectively

1990 ◽  
Vol 45 (3-4) ◽  
pp. 536-540
Author(s):  
Mariusz Máckowiak ◽  
Costas Dimitropoulos
Keyword(s):  
Temperature Dependence ◽  
Relaxation Rate ◽  
Spin System ◽  
Low Frequency ◽  
Lattice Relaxation ◽  
Spin Lattice Relaxation ◽  
Lattice Vibrations ◽  
Spin Lattice ◽  
Simplifying Assumptions ◽  
The One

Abstract The second-order Raman phonon process for a multilevel spin system is shown to give a quadru-polar spin-lattice relaxation rate T1-1varying as T5 at very low temperatures. This relaxation rate for quadrupole spins is similar to the one discussed for a paramagnetic spin system having a multilevel ground state. The temperature dependence of T1 is discussed on the basis of some simplifying assumptions about the nature of the lattice vibrations in the Debye approximation. This type of relaxation process has been observed below 20 K in tetramethylammonium hydrogen bis-trichloroacetate for the 35Cl T1-1 . Below 20 K the NQR frequency in the same crystal reveals a T4 temperature dependence due to the induced modulations of the vibrational and librational coordinates by the low-frequency acoustic phonons.

Modelling the dynamics of a minimal protocell container

2005 ◽  
Vol 4 (1) ◽  
pp. 81-91 ◽  
Author(s):  
Martin Nilsson Jacobi ◽  
Steen Rasmussen ◽  
Kolbjørn Tunstrøm
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Lattice Gas ◽  
Three Dimensional ◽  
Initial Distribution ◽  
Energy Potential ◽  
Time Dynamics ◽  
Amphiphilic Molecules ◽  
Head Groups ◽  
Simplifying Assumptions

This paper is a discussion on how reaction kinetics and three-dimensional (3D) lattice simulations can be used to elucidate the dynamical properties of micelles as a possible minimal protocell container. We start with a general discussion on the role of molecular self-assembly in prebiotic and contemporary biological systems. A simple reaction kinetic model of a micellation process of amphiphilic molecules in water is then presented and solved analytically. Amphiphilic molecules are polymers with hydrophobic (water-fearing), e.g. hydrocarbon tail groups, and hydrophilic (water-loving) head groups, e.g. fatty acids. By making a few simplifying assumptions an analytical expression for the size distribution of the resulting micelles can be derived. The main part of the paper presents and discusses a lattice gas technique for a more detailed 3D simulation of molecular self-assembly of amphiphilic polymers in aqueous environments. Water molecules, hydrocarbon tail groups and hydrophilic head groups are explicitly represented on a three-dimensional discrete lattice. Molecules move on the lattice proportional to their continuous momentum. Collision rules preserve momentum and kinetic energy. Potential energy from molecular interactions are also included explicitly. The non-trivial thermodynamics of large-scale and long-time dynamics are studied. In this paper we specifically demonstrate how, from a random initial distribution, micelles are formed and grow until they destabilize and can divide. Eventually a steady state of growing and dividing micelles is formed. Towards the end of the paper we discuss the relevance of the presented results to the design of a minimal artificial protocell.

scholarly journals Nonlinear visuoauditory integration in the mouse superior colliculus

2021 ◽  
Author(s):  
Shinya Ito ◽  
Yufei Si ◽  
Alan M. Litke ◽  
David A. Feldheim
Keyword(s):  
Superior Colliculus ◽  
Sensory Integration ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Critical Role ◽  
Sensory Information ◽  
Population Level ◽  
Object Identification ◽  
Response Properties ◽  
The Individual

AbstractSensory information from different modalities is processed in parallel, and then integrated in associative brain areas to improve object identification and the interpretation of sensory experiences. The Superior Colliculus (SC) is a midbrain structure that plays a critical role in integrating visual, auditory, and somatosensory input to assess saliency and promote action. Although the response properties of the individual SC neurons to visuoauditory stimuli have been characterized, little is known about the spatial and temporal dynamics of the integration at the population level. Here we recorded the response properties of SC neurons to spatially restricted visual and auditory stimuli using large-scale electrophysiology. We then created a general, population-level model that explains the spatial, temporal, and intensity requirements of stimuli needed for sensory integration. We found that the mouse SC contains topographically organized visual and auditory neurons that exhibit nonlinear multisensory integration. We show that nonlinear integration depends on properties of auditory but not visual stimuli. We also find that a heuristically derived nonlinear modulation function reveals conditions required for sensory integration that are consistent with previously proposed models of sensory integration such as spatial matching and the principle of inverse effectiveness.

scholarly journals Orientation and color tuning of the human visual gamma rhythm

2021 ◽  
Author(s):  
Ye Li ◽  
William Bosking ◽  
Michael S Beauchamp ◽  
Sameer A Sheth ◽  
Daniel Yoshor ◽  
...  
Keyword(s):  
Visual Cortex ◽  
Large Scale ◽  
Brain Activity ◽  
Population Level ◽  
Gamma Oscillations ◽  
Cell Orientation ◽  
Population Activity ◽  
Color Tuning ◽  
Human Visual Cortex ◽  
Gamma Rhythm

Narrowband gamma oscillations (NBG: ~20-60Hz) in visual cortex reflect rhythmic fluctuations in population activity generated by underlying circuits tuned for stimulus location, orientation, and color. Consequently, the amplitude and frequency of induced NBG activity is highly sensitive to these stimulus features. For example, in the non-human primate, NBG displays biases in orientation and color tuning at the population level. Such biases may relate to recent reports describing the large-scale organization of single-cell orientation and color tuning in visual cortex, thus providing a potential bridge between measurements made at different scales. Similar biases in NBG population tuning have been predicted to exist in the human visual cortex, but this has yet to be fully examined. Using intracranial recordings from human visual cortex, we investigated the tuning of NBG to orientation and color, both independently and in conjunction. NBG was shown to display a cardinal orientation bias (horizontal) and also an end- and mid-spectral color bias (red/blue and green). When jointly probed, the cardinal bias for orientation was attenuated and an end-spectral preference for red and blue predominated. These data both elaborate on the close, yet complex, link between the population dynamics driving NBG oscillations and known feature selectivity biases in visual cortex, adding to a growing set of stimulus dependencies associated with the genesis of NBG. Together, these two factors may provide a fruitful testing ground for examining multi-scale models of brain activity, and impose new constraints on the functional significance of the visual gamma rhythm.

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