Heavy and light inertial particle aggregates in homogeneous isotropic turbulence: A study on breakup and stress statistics

The breakup of inertial, solid aggregates in an incompressible, homogeneous and isotropic three-dimensional turbulent flow is studied by means of a direct numerical simulation, and by a Lagrangian tracking of the aggregates at varying Stokes number and fluid-to-particle density ratio. Within the point-particle approximation of the Maxey-Riley-Gatignol equations of motion, we analyse the statistics of the time series of shear and drag stresses, which are here both deemed as responsible for particle breakup. We observe that, regardless of the Stokes number, the shear stresses produced by the turbulent velocity gradients similarly impact the breakup statistics of inertial and neutrally buoyant aggregates, and dictate the breakup rate of loose aggregates. When the density ratio is different from unity, drag stresses become dominant and are seen to be able to cause to breakup of also the most resistant aggregates. The present work paves the way for including the role of inertia in population balance models addressing particle breakup in turbulent flows

Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species

<p>Abstract</p> <p>Background</p> <p>The results of transcriptome microarray analysis are usually presented as a list of differentially expressed genes. As these lists can be long, it is hard to interpret the desired experimental treatment effect on the physiology of analysed tissue, e.g. via selected metabolic or other pathways. For some organisms, gene ontologies and data visualization software have been implemented to overcome this problem, whereas for others, software adaptation is yet to be done.</p> <p>Results</p> <p>We present the classification of tentative potato contigs from the potato gene index (StGI) available from Dana-Farber Cancer Institute (DFCI) into the MapMan ontology to enable the application of the MapMan family of tools to potato microarrays. Special attention has been focused on mapping genes that could not be annotated based on similarity to Arabidopsis genes alone, thus possibly representing genes unique for potato. 97 such genes were classified into functional BINs (i.e. functional classes) after manual annotation. A new pathway, focusing on biotic stress responses, has been added and can be used for all other organisms for which mappings have been done. The BIN representation on the potato 10 k cDNA microarray, in comparison with all putative potato gene sequences, has been tested. The functionality of the prepared potato mapping was validated with experimental data on plant response to viral infection. In total 43,408 unigenes were mapped into 35 corresponding BINs.</p> <p>Conclusion</p> <p>The potato mappings can be used to visualize up-to-date, publicly available, expressed sequence tags (ESTs) and other sequences from GenBank, in combination with metabolic pathways. Further expert work on potato annotations will be needed with the ongoing EST and genome sequencing of potato. The current MapMan application for potato is directly applicable for analysis of data obtained on potato 10 k cDNA microarray by TIGR (The Institute for Genomic Research) but can also be used by researchers working on other potato gene sets. The potato mapping file and the stress mapping diagram are available from the MapMan website <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

Habitat selection and movement by spotted bass and shorthead redhorse downstream of a hydropeaking dam in Missouri

Flow alteration caused by hydropeaking dams may disrupt the natural flow regime and impact physical habitat and biological community, thus threatening the health of freshwater ecosystems. Life history strategies of fish evolved with their environments, including mobility to access habitats for feeding, spawning, refuge, and rearing. However, behavioral responses among species to artificially extreme flow and the influence of spatial and temporal scale, are not clearly understood. We used radio telemetry (from April 2016 to June 2017) to determine the habitat selection and daily and seasonal movement of two native fishes downstream of a hydropeaking dam on the Osage River, Missouri, where river stage may fluctuate up to 5 m daily. We selected two fishes from different habitat and spawning guilds, Spotted Bass (Micropterus punctulatus) and Shorthead Redhorse (Moxostoma macrolepidotum), that are common throughout the Midwestern United States and Canada and represent diverse life history strategies of riverine fishes. We used a Bayesian discrete choice analysis to determine seasonal and flow-related habitat selection and linear regression to evaluate predictors of movement rate of fishes. We determined flow to be "steady" or "fluctuating" based on the range of discharge measured during the 24-hour period prior to a fish location, where the threshold corresponded to minimum or maximum daily discharge being within (steady) or exceeding (fluctuating) 30% of the mean daily flow. Fluctuating flow corresponded to increased movement rate of Spotted Bass and Shorthead Redhorse and selection of slower velocity (1 m/s) during steady flow. Both Spotted Bass and Shorthead Redhorse selected moderate depth (1.5 - 4.0 m) with submerged cover during both steady and fluctuating flow. Spotted Bass movement rate peaked when 3-day average discharge was 500 m3/s, which occurred during consecutive days of hydropeaking or flood management at the dam. This discharge occurred or was exceeded during 25% of the study period, primarily during spring and summer, but did not occur during winter. Smaller adult Spotted Bass had greater movement rates than larger bass, whereas increased movement rate of Shorthead Redhorse was related to increased barometric pressure and Julian day. Both Spotted Bass and Shorthead Redhorse movement rates were greatest during spring (10 - 23[degrees]C) and differed among seasons. The mean longitudinal dispersal by Spotted Bass and Shorthead Redhorse was approximately 20 and 30 rkm, respectively, although 50% and 60% of Spotted Bass and Shorthead Redhorse, respectively, made movements between 5 and 91 rkm from the tagging location. Spotted Bass and Shorthead Redhorse selected similar habitats among steady and fluctuating flow regimes, however, both species responded to flow disturbance by moving more during fluctuating flow than during steady flow, presumably to relocate to suitable habitat. These effects occurred on a short timescale (10 hours to 3 days) and should be could be considered when informing ecologically-sustainable river management in highly flow-altered systems.Includes bibliographical reference

Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation

<p>Abstract</p> <p>Background</p> <p><it>Staphylococcus aureus </it>is a highly adaptable human pathogen and there is a constant search for effective antibiotics. Fosfomycin is a potent irreversible inhibitor of MurA, an enolpyruvyl transferase that uses phosphoenolpyruvate as substrate. The goal of this study was to identify the pathways and processes primarily affected by fosfomycin at the genome-wide transcriptome level to aid development of new drugs.</p> <p>Results</p> <p><it>S. aureus </it>ATCC 29213 cells were treated with sub-MIC concentrations of fosfomycin and harvested at 10, 20 and 40 minutes after treatment. <it>S. aureus </it>GeneChip statistical data analysis was complemented by gene set enrichment analysis. A visualization tool for mapping gene expression data into biological pathways was developed in order to identify the metabolic processes affected by fosfomycin. We have shown that the number of significantly differentially expressed genes in treated cultures increased with time and with increasing fosfomycin concentration. The target pathway - peptidoglycan biosynthesis - was upregulated following fosfomycin treatment. Modulation of transport processes, cofactor biosynthesis, energy metabolism and nucleic acid biosynthesis was also observed.</p> <p>Conclusions</p> <p>Several pathways and genes downregulated by fosfomycin have been identified, in contrast to previously described cell wall active antibiotics, and was explained by starvation response induced by phosphoenolpyruvate accumulation. Transcriptomic profiling, in combination with meta-analysis, has been shown to be a valuable tool in determining bacterial response to a specific antibiotic.</p

Network modeling unravels mechanisms of crosstalk between ethylene and salicylate signaling in potato

To develop novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modeling represents a powerful tool that can unravel properties of complex biological systems. In this study, we aimed to use network modeling to better understand immune signaling in potato (Solanum tuberosum). For this, we first built on a reliable Arabidopsis (Arabidopsis thaliana) immune signaling model, extending it with the information from diverse publicly available resources. Next, we translated the resulting prior knowledge network (20,012 nodes and 70,091 connections) to potato and superimposed it with an ensemble network inferred from time-resolved transcriptomics data for potato. We used different network modeling approaches to generate specific hypotheses of potato immune signaling mechanisms. An interesting finding was the identification of a string of molecular events illuminating the ethylene pathway modulation of the salicylic acid pathway through Nonexpressor of PR Genesi gene expression. Functional validations confirmed this modulation, thus supporting the potential of our integrative network modeling approach for unraveling molecular mechanisms in complex systems. In addition, this approach can ultimately result in improved breeding strategies for potato and other sensitive crops

Screening Study of Potassium Carbonate Solvents for Bio-energy Carbon Capture and Storage (BECCS)

The present work aims at investigating absorption of CO2 into promoted and unpromoted aqueous K2CO3. For this we performed a series of lab experiments in a thermostated batch stirred tank gas-liquid reactor containing the solvent. The absorption of CO2 was monitored by the decrease in the reactor pressure. To compare the different solvent blends, the experimental conditions, i.e., injection pressure, reactor temperature, stirring speed, and solvent volume were kept constant. For the interpretation of the experiments a simple absorption model is formulated based on which an apparent absorption rate is derived. Among the different rate promoters studied, we found that V2O5 results in a substantial increase of the absorption rate, while the use of B(OH)3 in conjunction with V2O5 does not provide any tangible benefits. A semi-qualitative comparison with rate constants reported in the literature suggests that this hindering effect of B(OH)3 is due to the lower pH of the solvent containing B(OH)3. The solvent blends containing amine-promoters MEA and piperazine demonstrated rapid absorption. Comparison with the literature indicates that absorption in the presence of these promoters is mass transfer limited under the experimental conditions

Potentially toxic planktic and benthic Cyanobacteria in Slovenian freshwater bodies: detection by quantitative PCR

Due to increased frequency of cyanobacterial blooms and emerging evidence of cyanotoxicity in biofilm, reliable methods for early cyanotoxin threat detection are of major importance for protection of human, animal and environmental health. To complement the current methods of risk assessment, this study aimed to evaluate selected qPCR assays for detection of potentially toxic cyanobacteria in environmental samples. In the course of one year, 25 plankton and 23 biofilm samples were collected from 15 water bodies in Slovenia. Three different analyses were performed and compared to each other; qPCR targeting mcyE, cyrJ and sxtA genes involved in cyanotoxin production, LC-MS/MS quantifying microcystin, cylindrospermopsin and saxitoxin concentration, and microscopic analyses identifying potentially toxic cyanobacterial taxa. qPCR analyses detected potentially toxic Microcystis in 10 lake plankton samples, and potentially toxic Planktothrix cells in 12 lake plankton and one lake biofilm sample. A positive correlation was observed between numbers of mcyE gene copies and microcystin concentrations. Potential cylindrospermopsin- and saxitoxin-producers were detected in three and seven lake biofilm samples, respectively. The study demonstrated a potential for cyanotoxin production that was left undetected by traditional methods in both plankton and biofilm samples. Thus, the qPCR method could be useful in regular monitoring of water bodies to improve risk assessment and enable timely measures