Project description:Bacterial biofilm infections associated with wounded skin are prevalent, recalcitrant and in urgent need of treatments. Additionally, host responses in the skin to biofilm infections are not well understood. Here we employed a human organoid skin model to explore the transcriptomic changes of thermally-injured epidermis to Methicillin-resistant Staphylococcus aureus (MRSA) biofilm colonization. MRSA biofilm impaired skin barrier function, enhanced extracellular matrix remodelling, elicited inflammatory responses including IL-17, IL-12 family and IL-6 family interleukin signalling and modulated skin metabolism. Synthetic antibiofilm peptide DJK-5 effectively diminished MRSA biofilm associated with wounded human ex vivo skin. In the epidermis, DJK-5 shifted the overall skin transcriptome towards homeostasis including modulating the biofilm induced inflammatory response, promoting the skin DNA repair function, and downregulating MRSA invasion of thermally damaged skin. These data revealed the intrinsic promise of synthetic peptides in treating inflammation and biofilm infections.
Project description:In a thermal proteome profiling experiment we have identified 300 unique proteins that become thermally stabilized or destabilized downstream of signal activation of the melanocortin 3 receptor (MC3R) when expressed in HEK293 cells. Upon stimulation with either one of the endogenous MC3R-agonists ACTH, alpha-, or gamma-MSH, derived from the pro-opiomelanocortin (POMC) prohormone, we found that the majority of these thermally affected proteins is related to immunoregulatory processes including signaling cascades up- and downstream of the key transcription factors IRF, STAT and NFkappaB. Here, we have developed a computational pipeline that allows assessment of thermal melting curves from data obtained with label-free quantitation from ion-mobility enhanced LC-MS data. It enables differential expression analysis within the data obtained from a thermal proteome profiling experiment, since all relative abundance information is retained. We found with principal component analysis that the three POMC-peptides act in very distinguished ways on the expression pattern in the MC3R-expressing HEK293 cells. This is consistent with our findings from thermal proteome profiling analysis where we identified 142, 107 and 95 proteins to be thermally affected by ACTH, alpha- and gamma-MSH, respectively, with only 4 proteins identified across all three agonists, and an additional 36 proteins shared pairwise between the agonists. Interestingly, we found proteins involved in immune responses to be enriched according to gene set enrichment analysis with Reactome pathways. As a result of these findings, we inferred transcription factor activities of the involved thermally affected transcription factors using Bayesian analysis based on differential expression data. Our findings on transcription factor activity were validated with patterns of peptide phosphorylation abundance analysis. These combined efforts revealed that all three agonists act via the cAMP-PKA-CREB pathway but that there are differences in the further downstream affected pathways and the identities of the thermally affected pathways proteins in particular kinases.
Project description:This SuperSeries is composed of the following subset Series: GSE17517: Microarray analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation GSE17532: RT-PCR analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation Refer to individual Series
Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in hypothalamus tissues of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.
Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in muscle tissues (Pectoralis major) of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation.