Stress Response Categories Research Articles

The Surgical Stress Response and Anesthesia: A Narrative Review.

The human physiological response "to stress" includes all metabolic and hormonal changes produced by a traumatic event at the micro or macro cellular levels. The main goal of the body's first response to trauma is to keep physiological homeostasis. The perioperative non-specific adaptation response can sometimes be detrimental and can produce systemic inflammatory response syndrome (SIRS), characterized by hypermetabolism and hyper catabolism. We performed a narrative review consisting of a description of the surgical stress response's categories of changes (neurohormonal and immunological response) followed by reviewing methods found in published studies to modulate the surgical stress response perioperatively. We described various preoperative measures cited in the literature as lowering the burden of surgical trauma. This article revises the anesthetic drugs and techniques that have an impact on the surgical stress response and proven immune-modulatory effects. We also tried to name present knowledge gaps requiring future research. Our review concludes that proper preoperative measures, adequate general anesthetics, multimodal analgesia, early postoperative mobilization, and early enteral nutrition can decrease the stress response to surgery and ease patient recovery. Anesthetics and analgesics used during the perioperative period may modulate the innate and adaptive immune system and inflammatory system, with a consecutive impact on cancer recurrence and long-term outcomes.

Diurnal transcriptomics analysis reveals the regulatory role of the circadian rhythm in super-hybrid rice LY2186

Heterosis, an important biological phenomenon wherein F1 hybrids exhibit better performance than any of their parents, has been widely applied; however, its underlying mechanism remains largely unknown. Here, we studied and compared the dynamic transcriptional profiles of super-hybrid rice LY2186 and its parents at 17 time points during 2 day/night cycles and identified 1552 rhythmic differentially expressed genes (RDGs). Cluster and functional enrichment analyses revealed that the day- and night-phased RDGs were mainly enriched in the photosynthesis and stress response categories, respectively. Regulatory network analysis indicated that circadian-related RDGs are core components in both the day and night phases and extensively regulate downstream genes involved in photosynthesis, starch synthesis, plant hormone signal transduction, and other pathways. Furthermore, among the 282 RDGs mapped onto the quantitative tract loci of small intervals (≤100 genes), 72.3% were significantly enriched in the yield, vigor, and anatomy categories. These findings provide valuable information for exploring heterosis mechanisms further and guiding breeding practices.

Integrative indices for health assessment in reef corals under thermal stress

• Long-term exposure to heat stress tested in seven reef-building coral species. • Quantification of biomarkers at biochemical and organism levels. • Biomarkers were combined in integrated biomarker response (IBR) indices. • In general, IBR values increased with temperature. • Integrated indices are useful for monitoring heat-induced stress in reef corals. Global warming is one of the major causes of reef coral ecosystems’ degradation. Predictions of further rise in sea surface temperatures call for urgent action. In this study, a holistic method for bio-monitoring heat stress in reef ecosystems was tested and optimized. Long-term induction of antioxidant enzymes and oxidative stress by elevated temperatures (30 °C and 32 °C) was assessed on fragments of reef-building corals and compared to control conditions (26 °C). The quantification of both oxidative stress, through lipid peroxidation (LPO) levels, and antioxidant enzyme activities: superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST) in a long-term experiment (60 days), using seven Indo-Pacific reef-building coral species, provided useful information that was interpreted in combination with the observed partial mortality and growth rate of these organisms. These biomarkers were combined in integrated biomarker response (IBR) indices, either in an antioxidant defense mechanisms and oxidative stress response category (approach A: GST, CAT, LPO, and SOD) or in an integrated stress response category – organism performance (approach B: GST, CAT, LPO, SOD, partial mortality, and growth rate). The results of this study indicate that the IBRs were responsive to temperature treatment and dependent on the coral species. The approach B was the most adequate since it better reflected the stress suffered by the tested species, whereas the set of four biochemical biomarkers (approach A) was not enough to explain the organismal response of most of the tested species to thermal stress conditions.

Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection.

Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.

Genomic and phenotypic assessments of safety and probiotic properties of Streptococcus macedonicus strains of dairy origin.

In this work, we studied the genomes and characterized some probiotic features of four S. macedonicus strains isolated from dairy environments in Italy that already had indicated some technological potential. The genomes of these strains were sequenced and used for genomic in silico studies. All strains were also evaluated for hemolytic activity, susceptibility to most commonly used antibiotics and probiotic potential, such as resistance to simulated gastrointestinal conditions, bile salts hydrolytic activity and adhesion ability to HT-29 human colorectal adenocarcinoma cells. Results revealed that one strain, namely S. macedonicus 211MA, was found to possess probiotic properties, such as resistance to simulated gastrointestinal conditions as well as adherence capability to human epithelial cells. In silico analyses revealed that S. macedonicus 211MA displayed the least number of single copy genes, genomic islands regions and gene content classified as virulence factors when compared to other S. macedonicus and S. gallolyticus strains. Moreover, the maximum gene content associated with bacterial stress response category and the presence of the opuCABCD operon, not detected in the other strains, were correlated with S. macedonicus 211MA capability to resist to low pH and to show higher adhesion to HT-29 human cells. This is the first report on the presence of opuCABCD operon in S. macedonicus and its possible relation with attachment ability and stress response.

Environmental health assessment of warming coastal ecosystems in the tropics – Application of integrative physiological indices

According to climate science, ocean warming is one of the current and future greatest threats to coastal ecosystems. Projection scenarios for the end of this century show that tropical intertidal ecosystems are particularly at risk. In this study we optimized and tested a holistic method for bio-monitoring present and projected thermal pressure in such ecosystems, in order to assess organism vulnerability to ocean warming. Several species representative of different animal groups (fish, crustaceans and gastropods) were collected from the field and subjected to an experimental trial for 28 days, testing two temperatures: control (present seawater summer temperature) and elevated temperature (+3 °C, projected seawater temperature anomaly for 2100). Muscle samples were collected weekly to quantify several biomarkers of: i) macromolecular damage (protein unfolding and denaturation, and lipid peroxidation), ii) reactive oxygen species (ROS) scavengers (antioxidant enzymes), and iii) body condition (energy reserves and body mass). These biomarkers were combined in integrated biomarker response (IBR) indices, either in three separate stress response categories (as previously defined) or in a unique combined analysis of overall physiological performance. Both approaches suggest that temperature affected IBRs, with increasing temperatures significantly impairing the overall health of individuals. Biomarkers of lower levels of biological organization indicated deleterious effects of temperature, whereas biomarkers of higher levels suggested maintenance of performance after chronic exposure. Overall indices combining the estimates of biomarkers across levels of biological organization are essential to predict the vulnerability of species, or populations, to climate warming. Such indices may assist managers and stakeholders in the establishment of monitoring programs and environmental policies toward the conservation of fragile coastal systems.

Identification of Novel Signal Transduction, Immune Function, and Oxidative Stress Genes and Pathways by Topiramate for Treatment of Methamphetamine Dependence Based on Secondary Outcomes.

Topiramate (TPM) is suggested to be a promising medication for treatment of methamphetamine (METH) dependence, but the molecular basis remains to be elucidated. Among 140 METH-dependent participants randomly assigned to receive either TPM (N = 69) or placebo (N = 71) in a previously conducted randomized controlled trial, 50 TPM- and 49 placebo-treated participants had a total 212 RNA samples available at baseline, week 8, and week 12 time points. Following our primary analysis of gene expression data, we reanalyzed the microarray expression data based on a latent class analysis of binary secondary outcomes during weeks 1-12 that provided a classification of 21 responders and 31 non-responders with consistent responses at both time points. Based on secondary outcomes, 1,381, 576, 905, and 711 differentially expressed genes at nominal P values < 0.05 were identified in responders versus non-responders for week 8 TPM, week 8 placebo, week 12 TPM, and week 12 placebo groups, respectively. Among 1,381 genes identified in week 8 TPM responders, 359 genes were identified in both week 8 and week 12 TPM groups, of which 300 genes were exclusively detected in TPM responders. Of them, 32 genes had nominal P values < 5 × 10-3 at either week 8 or week 12 and false discovery rates < 0.15 at both time points with consistent directions of gene expression changes, which include GABARAPL1, GPR155, and IL15RA in GABA receptor signaling that represent direct targets for TPM. Analyses of these 300 genes revealed 7 enriched pathways belonging to neuronal function/synaptic plasticity, signal transduction, inflammation/immune function, and oxidative stress response categories. No pathways were enriched for 72 genes exclusively detected in both week 8 and week 12 placebo groups. This secondary analysis study of gene expression data from a TPM clinical trial not only yielded consistent results with those of primary analysis but also identified additional new genes and pathways on TPM response to METH addiction.

A microRNA-mRNA expression network during oral siphon regeneration in Ciona

Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network-based clustering associated transcripts into 22 non-overlapping groups, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.

Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold.

The genome-wide role of heterotrimeric G-proteins in abiotic stress response in rice has not been examined from a functional genomics perspective, despite the availability of mutants and evidences involving individual genes/processes/stresses. Our rice whole transcriptome microarray analysis (GSE 20925 at NCBI GEO) using the G-alpha subunit (RGA1) null mutant (Daikoku 1 or d1) and its corresponding wild type (Oryza sativa Japonica Nipponbare) identified 2270 unique differentially expressed genes (DEGs). Out of them, we mined for all the potentially abiotic stress-responsive genes using Gene Ontology terms, STIFDB2.0 and Rice DB. The first two approaches produced smaller subsets of the 1886 genes found at Rice DB. The GO approach revealed similar regulation of several families of stress-responsive genes in RGA1 mutant. The Genevestigator analysis of the stress-responsive subset of the RGA1-regulated genes from STIFDB revealed cold and drought-responsive clusters. Meta data analysis at Rice DB revealed large stress-response categories such as cold (878 up/810 down), drought (882 up/837 down), heat (913 up/777 down), and salt stress (889 up/841 down). One thousand four hundred ninety-eight of them are common to all the four abiotic stresses, followed by fewer genes common to smaller groups of stresses. The RGA1-regulated genes that uniquely respond to individual stresses include 111 in heat stress, eight each in cold only and drought only stresses, and two genes in salt stress only. The common DEGs (1498) belong to pathways such as the synthesis of polyamine, glycine-betaine, proline, and trehalose. Some of the common DEGs belong to abiotic stress signaling pathways such as calcium-dependent pathway, ABA independent and dependent pathway, and MAP kinase pathway in the RGA1 mutant. Gene ontology of the common stress responsive DEGs revealed 62 unique molecular functions such as transporters, enzyme regulators, transferases, hydrolases, carbon and protein metabolism, binding to nucleotides, carbohydrates, receptors and lipids, morphogenesis, flower development, and cell homeostasis. We also mined 63 miRNAs that bind to the stress responsive transcripts identified in this study, indicating their post-transcriptional regulation. Overall, these results indicate the potentially extensive role of RGA1 in the regulation of multiple abiotic stresses in rice for further validation.

2D-DIGE-based proteome expression changes in leaves of rice seedlings exposed to low-level gamma radiation at Iitate village, Fukushima

The present study continues our previous research on investigating the biological effects of low-level gamma radiation in rice at the heavily contaminated Iitate village in Fukushima, by extending the experiments to unraveling the leaf proteome. 14-days-old plants of Japonica rice (Oryza sativa L. cv. Nipponbare) were subjected to gamma radiation level of upto 4 µSv/h, for 72 h. Following exposure, leaf samples were taken from the around 190 µSv/3 d exposed seedling and total proteins were extracted. The gamma irradiated leaf and control leaf (harvested at the start of the experiment) protein lysates were used in a 2-D differential gel electrophoresis (2D-DIGE) experiment using CyDye labeling in order to asses which spots were differentially represented, a novelty of the study. 2D-DIGE analysis revealed 91 spots with significantly different expression between samples (60 positive, 31 negative). MALDI-TOF and TOF/TOF mass spectrometry analyses revealed those as comprising of 59 different proteins (50 up-accumulated, 9 down-accumulated). The identified proteins were subdivided into 10 categories, according to their biological function, which indicated that the majority of the differentially expressed proteins consisted of the general (non-energy) metabolism and stress response categories. Proteome-wide data point to some effects of low-level gamma radiation exposure on the metabolism of rice leaves.

Development of a heat-responsive cDNA library from Prosopis cineraria and molecular characterisation of the Pchsp17.9 gene

SummaryHigh temperature adversely affects the growth, yield, and quality of crops. Prosopis cineraria, an indigenous plant in India, is highly tolerant of environmental stresses. In the present study, an expressed sequence tag (EST) library was constructed using pooled RNAs from 1-month-old P. cineraria seedlings subjected to heat stress at 48°C for between 15 min to 48 h. A total of 84 unigenes (20 contigs and 64 singletons) were generated from the cluster assembly of 132 good ESTs. Of these, nine unigenes did not show any homology to sequences in the NCBI database. A BLASTX comparison of the remaining 75 unigenes revealed significant similarities to known genes. The 84 ESTs were classified into 14 functional categories, of which 13.75% were in the stress-response category, including approx. 10% that were for heat-shock proteins. The heat stress-induced ESTs reported here are the first for P. cineraria. A phylogenetic analysis based on the complete coding sequence of the Pchsp17.9 gene showed a close relationship to hsp17.9 of Acacia mangium. Levels of expression of genes related to hsp chaperones were analysed by reverse transcriptionquantitative PCR (RT-qPCR) in 1-month-old heat-stressed seedlings of P. cineraria and were found to be highly upregulated.

Heterologous Microarray Analysis of Transcriptome Alterations inMus spretusMice Living in an Industrial Settlement

This work demonstrates the successful application of a commercial oligonucleotide microarray containing Mus musculus whole-genome probes to assess the biological effects of an industrial settlement on inhabitant Mus spretus mice. The transcriptomes of animals in the industrial settlement contrasted with those of specimens collected from a nearby protected ecosystem. Proteins encoded by the differentially expressed genes were broadly categorized into six main functional classes. Immune-associated genes were mostly induced and related to innate and acquired immunity and inflammation. Genes sorted into the stress-response category were mainly related to oxidative-stress tolerance and biotransformation. Metabolism-associated genes were mostly repressed and related to lipid metabolic pathways; these included genes that encoded 11 of the 20 cholesterol biosynthetic pathway enzymes. Crosstalk between members of different functional categories was also revealed, including the repression of serine-protease genes and the induction of protease-inhibitor genes to control the inflammatory response. Absolute quantification of selected transcripts was performed via RT-PCR to verify the microarray results and assess interindividual variability. Microarray data were further validated by immunoblotting and by cholesterol and protein-thiol oxidation level determinations. Reported data provide a broad impression of the biological consequences of residing in an industrial area.

Early stress responses in Atlantic salmon (Salmo salar) exposed to environmentally relevant concentrations of uranium

Uranium (U) is a naturally occurring heavy metal widely used in many military and civil applications. Uranium contamination and the associated potential adverse effects of U on the aquatic environment have been debated during recent years. In order to understand the effect and mode of action (MoA) of U in vivo, juvenile Atlantic salmon (Salmo salar) were exposed to 0.25mg/L, 0.5mg/L and 1.0mg/L waterborne depleted uranyl acetate, respectively, in a static system for 48h. The U concentrations in the gill and liver were analyzed by inductively coupled plasma mass spectrometry (ICP-MS) and the resulting biological effects were determined by a combination of analysis of gene expression and micronuclei formation. The hepatic transcriptional level of 12 biomarker genes from four stress–response categories, including oxidative stress (γ-glutamyl cysteine synthetase (GCS), glutathione reductase (GR), glutathione peroxidase (GPx)), DNA damage and repair (P53, cyclin-dependent kinase inhibitor 1 (P21), growth arrest and DNA damage-inducible gene gamma (Gadd45G), proliferating cell nuclear antigen (PCNA), Rad51), apoptosis (Bcl2-associated X protein (BAX), Bcl-x, Caspase 6A,) and protein degradation (Ubiquitin) were evaluated by quantitative real-time polymerase chain reaction (q-rtPCR). The results clearly showed accumulation of U in the gill and liver with increasing concentrations of U in the exposure water. The effects of U on differential hepatic gene expression also occurred in a concentration-dependent manner, although deviations from ideal concentration–response relationships were observed at the highest U concentration (1.0mg/L). All the genes tested were found to be up-regulated by U while no significant micronuclei formation was identified. The results suggest that U may cause oxidative stress in fish liver at concentrations greater than 0.25mg/L, giving rise to clear induction of several toxicologically relevant biomarker genes, although no significant adverse effects were observed after the relatively short exposure period.

Diapause specific gene expression in the eggs of multivoltine silkworm Bombyx mori, identified by suppressive subtractive hybridization

Molecular mechanism controlling egg diapause remains obscure in silkworm, Bombyx mori. An attempt is made to decipher various molecular events occurring during embryonic diapause in multivoltine silkworm, B. mori. Using suppressive subtractive hybridization (SSH), 186 cDNA clones isolated from both diapause and nondiapause eggs were sequenced. Of the sequenced clones, 29 matched with silkbase entries and these identified putative genes were classified into six functional groups such as regulatory, food utilization, stress response, metabolic, ribosomal and transposable elements. Among these genes, twelve belonged to regulatory group while, one taste receptor type 2 member 117 gene was related to food utilization. One heat shock cognate 70 kDa protein and 3 of the ubiquitin family were identified under stress response category. Similarly, four genes were identified as metabolic genes, 3 belonging to chitin family and one propanediol utilization protein. Of the seven genes identified in ribosomal groups, most of them were 60s ribosomal protein subunits. However, one negative regulation of transcription gene identified was a transposable element. The qPCR analysis confirmed the expression of 21 of the above genes, wherein, 6 were upregulated during diapause, 12 during non-diapause, while, 3 remained unchanged.

A New Transcriptional Effect Level Index (TELI) for Toxicogenomics-based Toxicity Assessment

This study proposes and demonstrates the potential application of a new Transcriptional Effect Level Index (TELI) to convert the information-rich toxicogenomic data into integrated and quantitative endpoints. A library of transcriptional fusions of green fluorescent protein (GFP) that includes different promoters for 91 stress-related genes in E. coli K12, MG1655 is employed to evaluate the gene expression alteration induced by exposure to four nanomaterials (NMs), nano silver (nAg), nano titanium dioxide anatase (nTiO₂_a), nano titanium dioxide rutile (nTiO₂_r), and fullerene soot. TELI is determined for each toxicogenomic assay, and it incorporates the number and identity of genes that had altered expression, the magnitude of alteration, and the temporal pattern of gene expression change in response to toxicant exposure. TELI values exhibit a characteristic "sigmoid" shaped toxicity dose-response curve, based on which TELI(MAX) (the maximal value of TELI), TELI50 (concentration that yields half of TELI(MAX)), NOTEL(TELI) (TELI-based no observed transcriptional effect level), and Slope(TELI) (the slope of TELI-dose response curve) are obtained. TELI-based endpoints are compared to currently used endpoints such as EC50 and no observed transcriptional effect level (NOTEL). The agreement of NOTEL(TELI) and NOTEL values validates the concept and application of TELI. Multiple endpoints derived from TELI can describe the dose response behavior and characteristics more completely and holistically than single points such as NOTEL alone. TELI values determined for genes in each stress response category (e.g., oxidative stress, DNA repair) indicate mode of action (MOA)-related comparative transcriptional level toxicity among compounds, and it reveals detailed information of toxic response pathways such as different DNA damage and repair mechanisms among the NMs. This study presents a methodology for converting the rich toxicogenomic information into a readily usable and transferable format that can be potentially linked to regulation endpoints and incorporated into a decision-making framework.

Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis

BackgroundPhotorhabdus and Xenorhabdus are Gram-negative, phylogenetically related, enterobacteria, forming mutualism with the entomopathogenic nematodes Heterorhabditis and Steinernema, respectively. The mutualistic bacteria living in the intestines of the nematode infective juveniles are pathogenic to the insect upon release by the nematodes into the insect hemolymph. Such a switch needs activation of genes that promote bacterial virulence. We studied in vivo gene expression in Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the white grub Rhizotrogus majalis using selective capture of transcribed sequences technique.ResultsA total of 40 genes in P. temperata and 39 in X. koppenhoeferi were found to be upregulated in R. majalis hemolymph at 24 h post infection. Genomic presence or upregulation of these genes specific in either one of the bacterium was confirmed by the assay of comparative hybridization, and the changes of randomly selected genes were further validated by quantitative real-time PCR. The identified genes could be broadly divided into seven functional groups including cell surface structure, regulation, virulence and secretion, stress response, intracellular metabolism, nutrient scavenging, and unknown. The two bacteria shared more genes in stress response category than any other functional group. More than 60% of the identified genes were uniquely induced in either bacterium suggesting vastly different molecular mechanisms of pathogenicity to the same insect host. In P. temperata lysR gene encoding transcriptional activator was induced, while genes yijC and rseA encoding transcriptional repressors were induced in X. koppenhoeferi. Lipopolysaccharide synthesis gene lpsE was induced in X. koppenhoeferi but not in P. temperata. Except tcaC and hemolysin related genes, other virulence genes were different between the two bacteria. Genes involved in TCA cycle were induced in P. temperata whereas those involved in glyoxylate pathway were induced in X. koppenhoeferi, suggesting differences in metabolism between the two bacteria in the same insect host. Upregulation of genes encoding different types of nutrient uptake systems further emphasized the differences in nutritional requirements of the two bacteria in the same insect host. Photorhabdus temperata displayed upregulation of genes encoding siderophore-dependent iron uptake system, but X. koppenhoeferi upregulated genes encoding siderophore-independent ion uptake system. Photorhabdus temperata induced genes for amino acid acquisition but X. koppenhoeferi upregulated malF gene, encoding a maltose uptake system. Further analyses identified possible mechanistic associations between the identified gene products in metabolic pathways, providing an interactive model of pathogenesis for each bacterium species.ConclusionThis study identifies set of genes induced in P. temperata and X. koppenhoeferi upon infection of R. majalis, and highlights differences in molecular features used by these two closely related bacteria to promote their pathogenicity in the same insect host.

Stress response proteins’ differential expression in embryogenic and non-embryogenic callus of Vitis vinifera L. cv. Cabernet Sauvignon—A proteomic approach

Co-cultivation of grape embryogenic callus (EC) and somatic embryos with Agrobacterium often leads to necrogenesis, which manifests in tissue browning and subsequent cell death. Interestingly, however, co-cultivation of grape non-embryogenic callus (NEC) does not display any visible symptoms. This paper compares the proteome of EC and NEC of Vitis vinifera L. cv. Cabernet Sauvignon to investigate the underlying mechanism. Analysis of 2-DE gels revealed 1180 spots, with 154 of them detected as differentially responsive proteins in EC versus NEC. Of these, the identity of 108 proteins was determined, with 28 proteins falling in the stress-response category. Those exclusively or predominantly identified in EC were iron-deficiency-responsive protein, acidic ascorbate peroxidase and isoflavone reductase-like protein, and those that were exclusively or predominant in NEC were basic ascorbate peroxidase, catalase, calcineurin B-like protein, 1,3-β-glucanase and cyclin-dependent kinase A1. The abundant protein PR-10 was at a remarkably lower level in EC than in NEC. These results demonstrated that different stress response pathways were activated in EC from those in NEC. A number of additional differentially expressed proteins involved in various functional categories were also identified.

Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions

BackgroundThe Saccharomyces cerevisiae MYO1 gene encodes the myosin II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Myo1p deficiency in yeast (myo1Δ) causes a cell separation defect characterized by the formation of attached cells, yet it also causes abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, increased chitin synthesis, and hypersensitivity to the chitin synthase III inhibitor Nikkomycin Z. To determine how differential expression of genes is related to these diverse cell wall phenotypes, we analyzed the global mRNA expression profile of myo1Δ strains.ResultsGlobal mRNA expression profiles of myo1Δ strains and their corresponding wild type controls were obtained by hybridization to yeast oligonucleotide microarrays. Results for selected genes were confirmed by real time RT-PCR. A total of 547 differentially expressed genes (p ≤ 0.01) were identified with 263 up regulated and 284 down regulated genes in the myo1Δ strains. Gene set enrichment analysis revealed the significant over-representation of genes in the protein biosynthesis and stress response categories. The SLT2/MPK1 gene was up regulated in the microarray, and a myo1Δslt2Δ double mutant was non-viable. Overexpression of ribosomal protein genes RPL30 and RPS31 suppressed the hypersensitivity to Nikkomycin Z and increased the levels of phosphorylated Slt2p in myo1Δ strains. Increased levels of phosphorylated Slt2p were also observed in wild type strains under these conditions.ConclusionFollowing this analysis of global mRNA expression in yeast myo1Δ strains, we conclude that 547 genes were differentially regulated in myo1Δ strains and that the stress response and protein biosynthesis gene categories were coordinately regulated in this mutant. The SLT2/MPK1 gene was confirmed to be essential for myo1Δ strain viability, supporting that the up regulated stress response genes are regulated by the PKC1 cell integrity pathway. Suppression of Nikkomycin Z hypersensitivity together with Slt2p phosphorylation was caused by the overexpression of ribosomal protein genes RPL30 and RPS31. These ribosomal protein mRNAs were down regulated in the myo1Δ arrays, suggesting that down regulation of ribosomal biogenesis may affect cell integrity in myo1Δ strains.

Macroscopic indicators for the retrospective assessment of Norway spruce crown response to stress in the Krkonoše Mountains

The synergistic effect of a number of natural and anthropogenic stress factors is probably responsible for forest decline in Central Europe. The macroscopic indicators of Norway spruce crown status, as well as branch structure transformation, were proposed to reconstruct the retrospective stress response of a tree to stress conditions over a 30-year period. Based on crown defoliation and the proportion of secondary shoots, five categories of tree response to stress factors were introduced: resistant trees (crown defoliation ≤35%, secondary shoots ≤65%); resilient trees (crown defoliation ≤35%, secondary shoots >65%); susceptible moderately transformed trees (crown defoliation >35%, secondary shoots ≤65%); susceptible strongly transformed trees (crown defoliation >35%, 65% 35%, secondary shoots >90%). These stress response categories are discussed assuming a sink/source relationship on carbohydrate allocation. The relationship between stress response categories and current regenerative processes in the crown, assessed by macroscopic markers on bud development and shoot growth, is outlined. The research has been carried out mainly in three permanent research plots of old autochthonous Norway spruce forest stands in the Krkonose Mts. (Czech Republic) under different historical stress loads.

Diaphragm Unloading via Controlled Mechanical Ventilation Alters the Gene Expression Profile

Prolonged controlled mechanical ventilation results in diaphragmatic inactivity and promotes oxidative injury, atrophy, and contractile dysfunction in this important inspiratory muscle. However, the impact of controlled mechanical ventilation on global mRNA alterations in the diaphragm remains unknown. In these experiments, we used an Affymetrix oligonucleotide array to identify the temporal changes in diaphragmatic gene expression during controlled mechanical ventilation in the rat. Adult Sprague-Dawley rats were assigned to either control or mechanical ventilation groups (n = 5/group). Mechanically ventilated animals were anesthetized, tracheostomized, and ventilated with room air for 6 or 18 h. Animals in the control group were acutely anesthetized but not exposed to mechanical ventilation. Compared with control diaphragms, microarray analysis identified 354 differentially expressed, unique gene products after 6 and 18 h of mechanical ventilation. In general, genes in the cell growth/cell maintenance, stress response, and nucleic acid metabolism categories showed predominant upregulation, whereas genes in the structural protein and energy metabolism categories were predominantly downregulated. We conclude that mechanical ventilation results in rapid changes in diaphragmatic gene expression, and subsequently, many of these changes may contribute to atrophy and muscle fiber remodeling associated with unloading this primary inspiratory muscle. Importantly, this study also provides new insights into why the diaphragm, after the onset of contractile inactivity, atrophies more rapidly than locomotor skeletal muscles and also highlights unique differences that exist between these muscles in the mRNA response to inactivity.