Transported probability density function (TPDF) methods are well suited to modelling turbulent, reacting, variable density flows. One of the main challenges to the successful deployment of TPDF ...methods is accurately modelling the unclosed molecular mixing term. This study examines three of the most widely used mixing models: the Interaction by Exchange with the Mean (IEM), Modified Curl (MC) and Euclidean Minimum Spanning Tree (EMST) models. Direct numerical simulation (DNS) data-sets were used to provide both initial conditions and inputs needed over the course of the runs, including the mean flow velocities, mixing frequency, and the turbulent diffusion coefficient. The same chemical mechanism and thermodynamic properties were used, allowing the study to focus on the mixing model. The simulation scenario was a one-dimensional, nonpremixed, turbulent jet flame burning either a syngas or ethylene fuel stream that featured extinction and reignition. This test scenario was selected because extinction and reignition phenomena are sensitive to the mixing model. Three DNS cases were considered for both the syngas and ethylene cases with a parametric variation of Reynolds and Damköhler numbers, respectively. Extinction events became more prevalent with increasing Reynolds number in the syngas cases and with decreasing Damköhler number in the ethylene cases. The model was first tested with the mixing frequency defined from the dissipation rate and variance of mixture fraction. With this definition, for the syngas cases this study finds that the TPDF method is successful at predicting flame extinction and reignition using all three mixing models for the relatively lower and intermediate Reynolds number cases, but that all models under-predict reignition in the relatively higher Reynolds number case. In the ethylene fuelled cases, only the EMST mixing model correctly predicts the reignition event for the two higher Damköhler number cases, however, in the lowest Damköhler number case the EMST model over-predicts reignition and the IEM and MC models under-predict it. Mixing frequency was then modelled based on the turbulence frequency and a model constant Cϕ, the ratio of scalar to mechanical mixing rates. The DNS cases were reexamined with this definition and the results suggested that the optimal value for Cϕ is mixing model and case dependent. In particular, it was found in the ethylene case considered that reignition could be achieved with the IEM and MC models by adjusting the value of Cϕ.
In the present work, nonpremixed temporally evolving planar spray jet flames are simulated using both direct numerical simulation (DNS) and the composition transported probability density function ...(TPDF) method. The objective is to assess the performance of various mixing and evaporation source term distribution models which are required to close the PDF transport equation in spray flames. Quantities which would normally be provided to the TPDF solver by spray models and turbulence models are provided from the DNS: the mean flow velocity, turbulent diffusivity, mixing frequency, and cell-mean evaporation source term. Two cases with different Damköhler numbers (Da) are considered. The low Da case (Da-) features extinction followed by reignition while extinction in the high Da case (Da+) is insignificant. The TPDF modelling considers two mixing models: interaction by exchange with the mean (IEM) and Euclidean minimum spanning trees (EMST). Three models for distribution of the evaporation source terms are considered: EQUAL which distributes them in proportion to notional particles’ mass weight, NEW which creates new particles of pure fuel, and SAT which distributes the sources preferentially to notional particles close to saturation. It is found that the IEM model overpredicts the extinction when used with any evaporation model for both Da- and Da+ cases. The EMST model captures well the trend for extinction and reignition for the Da- case when it is coupled with the EQUAL evaporation model, but it overpredicts the extinction when coupled with the NEW or SAT evaporation model. For the Da+ case, all evaporation models reasonably capture the flame dynamics when coupled with EMST. The flame temperature in the mixture fraction space was examined to further assess the model performance. In general the EMST model results in narrow PDFs with little conditional fluctuation, while the IEM model produces bimodal PDFs with burning and partial extinction branches.
Modeling of premixed turbulent flames is challenging due to the effects of strong turbulence-chemistry interaction. In the transported probability density function (TPDF) methods, chemical reactions ...are treated exactly, while molecular mixing needs to be modeled. In the present study, the performance of three widely used mixing models, namely the Interaction by Exchange with the Mean (IEM), Modified Curl (MC), and Euclidean Minimum Spanning Tree (EMST) models, are assessed using direct numerical simulation (DNS) data of a lean premixed hydrogen–air slot jet flame simulated at Sandia. The DNS provides initial conditions and time varying input quantities, including the mean velocity, turbulent diffusion coefficient, and scalar mixing rate for the TPDF simulations. A number of progress variable definitions are explored, as well as the commonly used constant mechanical-to-scalar mixing timescale model. It is found that the EMST model provides the best prediction of the flame structure and flame propagation speed out of the models tested. The IEM model implies a qualitatively incorrect conditional mean and RMS diffusion rate, while the MC model can qualitatively capture the conditional mean diffusion rate. Only the EMST model can accurately predict the conditional mean diffusion rate for this flame, which can be attributed to its enforcement of mixing that is local in composition space. Finally, a parametric study on the mechanical-to-scalar timescale ratio is performed. It is found that the optimal choice for the timescale ratio varies by a factor of 2 for the two DNS cases study, despite the cases having the same configuration. Therefore, this commonly used approach does not appear to be viable for turbulent premixed flames and further attention to mixing timescale models for reactive scalars is merited.
With the pressure to reduce antibiotics use in poultry production, cost-effective alternative products need to be developed to enhance the bird's immunity. The present study evaluated the efficacy of ...cranberry fruit by-products to modulate immunity in broiler chickens. Broiler Cobb 500 chicks were fed a control basal diet, basal diet supplemented with bacitracin (BACI, 55 ppm), cranberry pomace at 1% and 2% (CP2), or cranberry pomace ethanolic extract at 150 and 300 ppm (COH300) for 30 d. Blood sera were analyzed at days 21 and 28 of age for Ig levels by ELISA. The innate and adaptive immune-related gene expression levels in the liver and bursa of Fabricius were investigated at 21 d of age by quantitative polymerase chain reaction arrays. At day 21, the highest IgY level was found in the blood serum of the CP2-fed birds. In the liver, 13 of the 22 differentially expressed genes were downregulated across all treatments compared with the control. Expression of genes belonging to innate immunity such as caspase 1 apoptosis–related cysteine peptidase, chemokine receptor 5, interferon gamma, myeloid differentiation primary response gene 88, and Toll-like receptor 3 were significantly downregulated mainly in BACI- and COH300-fed birds. In the bursa, 5 of 9 genes associated with the innate immunity were differentially expressed. The expression of anti-inflammatory IL-10 gene was upregulated in all treatment groups in bursa compared with the control. The expression of transferrin gene was significantly upregulated in livers of birds fed COH300 and in bursa of birds fed BACI, indicating feeding practices and organ-dependant modulation of this gene in broiler. Overall results of this study showed that cranberry product feed supplementation modulated the innate immune and suppressed proinflammatory cytokines in broilers, providing a platform for future investigations to develop berry products in poultry feeding.
There exists over 2.5 million publicly available gene expression samples across 101,000 data series in NCBI's Gene Expression Omnibus (GEO) database. Due to the lack of the use of standardised ...ontology terms in GEO's free text metadata to annotate the experimental type and sample type, this database remains difficult to harness computationally without significant manual intervention.
In this work, we present an interactive R/Shiny tool called GEOracle that utilises text mining and machine learning techniques to automatically identify perturbation experiments, group treatment and control samples and perform differential expression. We present applications of GEOracle to discover conserved signalling pathway target genes and identify an organ specific gene regulatory network.
GEOracle is effective in discovering perturbation gene targets in GEO by harnessing its free text metadata. Its effectiveness and applicability has been demonstrated by cross validation and two real-life case studies. It opens up new avenues to unlock the gene regulatory information embedded inside large biological databases such as GEO. GEOracle is available at https://github.com/VCCRI/GEOracle.
Understanding the survival mechanisms used by Shiga toxin-producing Escherichia coli (STEC), including O157:H7 and non-O157 serotypes, is important for minimizing contamination of fresh produce and ...occurrence of foodborne outbreaks. Recent outbreaks linked to leafy green vegetables and sprouted seeds have prompted researchers to focus on investigating decontamination strategies. Several studies showed that hydrogen peroxide (H2O2) treatment has been effective in reducing pathogens on fresh produce. As such, the effect of hydrogen peroxide on stress-associated and virulence gene expression in six STEC isolates was investigated in this study. Logarithmic phase cells of E. coli O157:H7 (EDL933) and non-O157 serotypes, including E. coli O26:H11 (EC20070549), O103:H2 (EC19970811), O104:H4 (NML#11-3088), O111:NM (EC20070546) and O145:NM (EC19970355) were exposed to 2.5mM H2O2 for 40min and gene expression was evaluated using quantitative real-time PCR. Different patterns of gene expression were observed in E. coli O157:H7 and non-O157 serotypes. Particularly, Shiga toxin gene stx2 was upregulated in O157:H7, but not in O104:H4. Moreover, stx1 was significantly upregulated in STEC O157:H7, but only slightly upregulated Stx1-positive non-O157 serotypes. However genes related to motility (fliC) and intimin gene (eae) were downregulated in most strains. Stress-associated sodA gene encoding manganese superoxide dismutase was significantly upregulated in all serotypes. The dps gene coding for non-specific DNA binding protein was upregulated in O145:NM, O111:NM, O103:H2 and O26:H11. However genes related to cold shock (cspC) and acid resistance (gadW) were significantly downregulated in all strains tested. The results of this study provide a basic understanding of the oxidative stress impact on survival and virulence of non-O157 serotype STEC strains.
•Oxidative stress response in Shiga toxin-producing E. coli O157:H7 and five non-O157 serotypes was investigated.•Different patterns of expression of stress-associated and virulence genes were observed under oxidative stress.•Oxidative damage related sodA gene encoding manganese superoxide dismutase was significantly upregulated in all serotypes.•Hydrogen peroxide treatment induced expression of Shiga toxin 2 gene (stx2A) in serotype O157:H7, but not in O104:H4.
Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have ...variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads. We showed that Scavenger could recover unaligned reads in a range of simulated and real RNA-seq datasets, including single-cell RNA-seq data. We found that recovered reads tend to contain more genetic variants with respect to the reference genome compared to previously aligned reads, indicating that divergence between personal and reference genomes plays a role in the false-negative non-alignment problem. Even when the number of recovered reads is relatively small compared to the total number of reads, the addition of these recovered reads can impact downstream analyses, especially in terms of estimating the expression and differential expression of lowly expressed genes, such as pseudogenes.
This study evaluated the performance, gut microbiota, and blood metabolites in broiler chickens fed cranberry and blueberry products for 30 days. A total of 2,800 male day-old broiler Cobb-500 chicks ...were randomly distributed between 10 diets: control basal diet; basal diet with bacitracin (BACI); four basal diets with 1 and 2% of cranberry (CP1, CP2) and blueberry (BP1, BP2) pomaces; and four basal diets supplemented with ethanolic extracts of cranberry (COH150, COH300) or blueberry (BOH150, BOH300) pomaces. All groups were composed of seven replicates (40 birds per replicate). Cecal and cloacal samples were collected for bacterial counts and 16S rRNA gene sequencing. Blood samples and spleens were analyzed for blood metabolites and gene expressions, respectively. The supplementation of COH300 and BOH300 significantly increased the body weight (BW) during the starting and growing phases, respectively, while COH150 improved (
P
< 0.05) the overall cumulated feed efficiency (FE) compared to control. The lowest prevalence (
P
= 0.01) of necrotic enteritis was observed with CP1 and BP1 compared to BACI and control. Cranberry pomace significantly increased the quinic acid level in blood plasma compared to other treatments. At days 21 and 28 of age, the lowest (
P
< 0.05) levels of triglyceride and alanine aminotransferase were observed in cranberry pomace and blueberry product–fed birds, respectively suggesting that berry feeding influenced the lipid metabolism and serum enzyme levels. The highest relative abundance of
Lactobacillaceae
was found in ceca of birds fed CP2 (
P
< 0.05). In the cloaca, BOH300 significantly (
P
< 0.005) increased the abundances of
Acidobacteria
and
Lactobacillaceae
.
Actinobacteria
showed a significant (
P
< 0.05) negative correlation with feed intake (FI) and FE in COH300-treated birds, whereas
Proteobacteria
positively correlated with the BW but negatively correlated with FI and FE, during the growing phase. In the spleen, cranberry products did not induce the release of any pro-inflammatory cytokines but upregulated the expression of several genes (IL4, IL5, CSF2, and HMBS) involved in adaptive immune responses in broilers. This study demonstrated that feed supplementation with berry products could promote the intestinal health by modulating the dynamics of the gut microbiota while influencing the metabolism in broilers.
Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have ...variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads. We showed that Scavenger could recover unaligned reads in a range of simulated and real RNA-seq datasets, including single-cell RNA-seq data. We found that recovered reads tend to contain more genetic variants with respect to the reference genome compared to previously aligned reads, indicating that divergence between personal and reference genomes plays a role in the false-negative non-alignment problem. Even when the number of recovered reads is relatively small compared to the total number of reads, the addition of these recovered reads can impact downstream analyses, especially in terms of estimating the expression and differential expression of lowly expressed genes, such as pseudogenes.
Extraintestinal pathogenic
Escherichia coli
(ExPEC) includes several serotypes that have been associated with colibacillosis in poultry, as well as urinary tract infections and newborn meningitis in ...humans. This study investigated the antimicrobial activities of ceftriaxone (AXO) and cranberry pomace extracts (CRAN) alone or in combination (CC) against multidrug-resistant (MDR) ExPEC from broiler. The growth-inhibitory activity of CRAN and synergy tests by a checkerboard method were determined in cation-adjusted Mueller–Hinton broth (CAMHB). The transcriptomic profile of the MDR
E. coli
O7:H18 (ST38) grown in CAMHB supplemented with sub-inhibitory concertation of CRAN and AXO alone or in combination was obtained by RNA-seq. The MIC of CRAN for all isolates was 16 mg/mL. An additive activity was observed between 4 mg/mL of CRAN and 4 μg/mL of AXO. Compared to the control, the transcriptomic analysis revealed that 4 mg/ml of (1/4MIC) CRAN and its combination with 4 μg/mL of (1/8MIC) AXO (CC) exposures resulted in 727 and 712 differentially expressed genes, respectively (false discovery rate < 0.001 and log
2
-fold change > 2), in the studied
E. coli
. Major virulence genes including adhesins (
fim, flg, csg
, and
yad
), protectins (
omp, tra, waa
, and
hly
), secretion systems (
hof, pho
, and
vir
), and quorum sensing (
lsr
), which are energetically expensive for bacteria, were downregulated. Most importantly, 1/4MIC of CRAN or CC downregulated the β-lactamase
bla
CMY-2
and efflux pump including
tolC, mdtEIJ, gadEW
, and their regulator gene
evgS
, while upregulating the cysteine biosynthesis and oxidative stress-related regulatory genes including
cys, dmlA, sbp, nrdGHI, soxSR
, and
rpoH
. Downregulation of multiple enzymes involved in TCA cycles and upregulation of Fe–S cluster coordinated by Cys and Isc proteins reflect the regulation of energy metabolism of the studied
E. coli
upon CRAN or CC exposure. The downregulation of outer membrane protein genes that control permeability barriers, along with different antimicrobial resistance genes, demonstrates that CRAN may have the unique potential to enhance the antimicrobial activities of third-generation cephalosporins such as AXO against MDR
E. coli
.
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