Differential gene expression in Escherichia coli following exposure to nonthermal atmospheric pressure plasma

Aim:  Nonthermal atmospheric-pressure plasmas offer significant advantages as an emerging disinfection approach. However the mechanisms of inactivation, and thus the means of optimizing them, are still poorly understood. The objective of this study, therefore, was to explore differential gene expression on a genome-wide scale in Escherichia coli following exposure to a nonthermal atmospheric-pressure argon plasma plume using high-density oligonucleotide microarrays.
Methods and Results:  Plasma exposure was found to significantly induce the SOS mechanism, consisting of about 20 genes. Other genes involved in regulating response to oxidative stress were also observed to be up-regulated. Conversely, the expression of several genes responsible for housekeeping functions, ion transport, and metabolism was observed to be down-regulated.
Conclusions:  Elevated yet incomplete induction of various DNA damage repair processes, including translesion synthesis, suggests substantial DNA damage in E. coli . Oxidative stress also appeared to play a role. Thus it is proposed that the efficacy of plasma is due to the synergistic impact of UV photons and oxygen radicals on the bacteria.
Significance and Impact of the Study:  This study represents the first investigation of differential gene expression on a genome-wide scale in an organism following plasma exposure. The results of this study will help enable the design of safe and effective plasma decontamination devices.     

Gene expression profiles in the liver and kidney of metallothionein-null mice

It has been reported that the expression of certain genes was altered in rodent cells lacking metallothioneins (MTs). To further explore the effects of MT deficiency, we screened genes differentially expressed in the liver and kidney of MT-null mice by cDNA microarray analysis. In the liver, 29 of 8737 genes analyzed were altered in their expression levels: 19 and 10 genes were up-regulated and down-regulated, respectively. Particularly, 14 of the 29 genes were related to energy metabolism, and some of these suggested that loss of MTs might lead to obesity and irregular ATP synthesis. In the kidney, 41 differentially expressed genes were observed: 27 and 14 genes were up-regulated and down-regulated, respectively. Eleven of the 41 genes were also related to energy metabolism. Microarray results were confirmed by Northern blot analysis for five of the energy metabolism-related genes.     

Gene expression profile in the liver of Rana catesbeiana tadpoles exposed to low temperature in the presence of thyroid hormone

Studies of insulin producing β-cells have reported conflicting responses to NF-κB activation, encompassing both pro- and anti-apoptotic effects, possibly reflecting the use of β-cells from different species. Therefore, the aim of this study was to compare the temporal activation of NF-κB in rat and human insulin producing cells and relate this to the dynamics of cell death, STAT-1 activation and the production of nitric oxide (NO). Rat RIN5AH and human islet cells were exposed to the cytokines IL-1β and IFN-γ and the NOS inhibitor aminoguanidine. Cell death, NO production, IκBα phosphorylation, p65 methylation, STAT-1 phosphorylation and cIAP-2 levels were analyzed at different time-points. Cytokine-induced RIN5AH cell death occurred on day 1, and this was paralleled by NF-κB activation, STAT-1 phosphorylation and production of NO. On the other hand, the human islet cells instead died by an NO-independent mechanism on day 3 and 5. This later occurring cell death was associated with a gradual decrease in IκBα phosphorylation and p65 methylation, and a lowered expression of the NF-κB target genes IκBα and cIAP-2. STAT-1 phosphorylation was persistently high during the entire cytokine exposure period in human islet cells. The results favor a pro-survival role of NF-κB and a pro-apoptotic role of STAT-1 in human islet cells. Thus, rodent insulin producing cells may not be suitable as models for human β-cells in the context of cytokine-induced damage.     

Kin recognition by larval wood frogs (Rana sylvatica): effects of diet and prior exposure to conspecifics

Summary We investigated kin recognition by larval wood frogs (Rana sylvatica) in blind laboratory experiments using spatial affinity as a recognition assay. Tadpoles reared with full-sibs displayed a significant preference for familiar full-sibs over unfamiliar non-kin, but failed to discriminate between unfamiliar full-sibs and unfamiliar paternal half-sibs. Tadpoles reared in social isolation (with or without maternal egg jelly) from the two-celled embryonic stage displayed a significant preference for unfamiliar full-sibs over unfamiliar non-kin. Tadpoles reared on a meat diet with their full-sibs: 1) exhibited a significant preference for unfamiliar full-sibs fed meat over unfamiliar non-kin fed meat, 2) failed to discriminate between unfamiliar full-sibs fed lettuce and unfamiliar non-kin fed meat, 3) exhibited a significant preference for unfamiliar non-kin fed meat over unfamiliar non-lin fed lettuce, 4) failed to discriminate between unfamiliar full-sibs fed meat and unfamiliar full-sibs fed lettuce, and 5) displayed a significant spatial preference for odors associated with meat (a familiar food) over odors associated with lettuce (an unfamiliar food). Our results, together with those of Cornell et al. (1989), indicate that the recognition cue of larval R. sylvatica has both genetic and environmental (dietary) components. Our findings establish that previous exposure to maternal egg jelly, kin, or conspecifics is not necessary for the development of kin recognition ability in larval R. sylvatica. Our results are more consistent with the self-learning of recognition cues (a form of phenotype matching) than with a recognition mechanism that involves a genetically fixed recognition template. Finally, our results indicate that increasing similarity between the recognition template and perceived cue does not necessarily result in increasing spatial affinity for kin.     

Cardiac function-related gene expression profiles in human atrial myocytes

To obtain insights into the molecular pathogenesis of heart failure in humans, we have analyzed the expression profiles of>12,000 genes in a total of 17 human specimens of right atrial myocytes. From this large data set, we here tried to identify gene clusters, expression level of which is correlated precisely with clinical parameter values of cardiac function. We could reveal that cardiac myocytes with normal sinus rhythm were clearly differentiated, in the point of view of gene expression, from those with atrial fibrillation. Further, an expression profile-based prediction of arrhythmia by a newly developed "weighted-distance method" could efficiently diagnose our samples. We could even construct calculation formulae for the values of left ventricular ejection fraction based on the expression level of selected genes. To our best knowledge, this is the first report to indicate that pumping ability of heart can be predicted by any measures of atrium.     

Gene expression profiles of the Southern house mosquito Culex quinquefasciatus during exposure to permethrin

Insecticide resistance is a major obstacle to the management of disease‐vectoring mosquitoes worldwide. The genetic changes and detoxification genes involved in insecticide resistance have been extensively studied in populations of insecticide‐resistant mosquitoes, however few studies have focused on the resistance genes upregulated upon insecticide exposure and the possible regulation pathways involved in insecticide resistance. To characterize the changes in gene expression during insecticide exposure, and to investigate the possible connection of known regulation pathways with insecticide resistance, we conducted RNA‐Seq analysis of a highly permethrin‐resistant strain of Culex quinquefasciatus following permethrin exposure. Gene expression profiles revealed a total of 224 upregulated and 146 downregulated genes when compared to a blank acetone carrier treated control, respectively, suggesting that there were multiple, but specific genes involved in permethrin resistance. Functional enrichment analysis showed that the upregulated genes contained multiple detoxification genes including a glutathione S‐transferase and multiple cytochrome P450 genes, as well as several immune‐related genes, while the downregulated genes consisted primarily of proteases and carbohydrate metabolism and transport. Further analysis showed that permethrin exposure resulted in a decrease in the expression of serum storage proteins and likely represented a delay in the development of the fourth instar possibly due to a decrease in feeding. This effect was more pronounced in an insecticide‐resistant strain than in an insecticide‐susceptible strain and may represent a behavioral mechanism of insecticide resistance in Culex mosquitoes.     

Gene expression profiles during short‐term heat stress in the red sea coral Stylophora pistillata

During the past several decades, corals worldwide have been affected by severe bleaching events leading to wide‐spread coral mortality triggered by global warming. The symbiotic Red Sea coral Stylophora pistillata from the Gulf of Eilat is considered an opportunistic ‘r’ strategist. It can thrive in relatively unstable environments and is considered a stress‐tolerant species. Here, we used a S. pistillata custom microarray to examine gene expression patterns and cellular pathways during short‐term (13‐day) heat stress. The results allowed us to identify a two‐step reaction to heat stress, which intensified significantly as the temperature was raised to a 32 °C threshold, beyond which, coping strategies failed at 34 °C. We identified potential ‘early warning genes’ and ‘severe heat‐related genes’. Our findings suggest that during short‐term heat stress, S. pistillata may divert cellular energy into mechanisms such as the ER‐unfolded protein response (UPR) and ER‐associated degradation (ERAD) at the expense of growth and biomineralization processes in an effort to survive and subsequently recover from the stress. We suggest a mechanistic theory for the heat stress responses that may explain the success of some species which can thrive under a wider range of temperatures relative to others.     

Novel Rana keratin genes and their expression during larval to adult epidermal conversion in bullfrog tadpoles

The conversion of the larval to adult epidermis during metamorphosis of tadpoles of bullfrog, Rana catesbeiana, was investigated utilizing newly cloned Rana keratin cDNAs as probes. Rana larval keratin (RLK) cDNA (rlk) was cloned using highly specific antisera against Xenopus larval keratin (XLK). Tail skin proteins of bullfrog tadpoles were separated by 2-dimensional gel electrophoresis and subjected to Western blot analysis with anti-XLK antisera. The Rana antigen detected by this method was sequenced and identified as a type II keratin. We cloned rlk from tadpole skin by PCR utilizing primers designed from these peptide sequences of RLK. RLK predicted by nucleotide sequences of rlk was a 549 amino acid -long type II keratin. Subtractive cloning between the body and the tail skin of bullfrog tadpole yielded a cDNA (rak) of Rana adult keratin (RAK). RAK was a 433 amino acid-long type I keratin. We also cloned a Rana keratin 8 (RK8) cDNA (rk8) from bullfrog tadpole epidermis. RK8 was 502 amino acid-long and homologous to cytokeratin 8. Northern blot analyses and in situ hybridization experiments showed that rlk was actively expressed through prometamorphosis in larva-specific epidermal cells called skein cells and became completely inactive at the climax stage of metamorphosis and in the adult skin. RAK mRNA was expressed in basal cells of the tadpole epidermis and germinative cells in the adult epidermis. The expression of rlk and rak was down- and up-regulated by thyroid hormone (TH), respectively. In contrast, there was no change in the expression of RK8 during spontaneous and TH-induced metamorphosis. RK8 mRNA was exclusively expressed in apical cells of the larval epidermis. These patterns of keratin gene expression indicated that the expression of keratin genes is differently regulated by TH depending on the type of larval epidermal cells. The present study demonstrated the usefulness of these genes for the study of molecular mechanism of postembryonic epidermal development and differentiation.     

Gene expression profiles of the one-carbon metabolism pathway

One-carbon metabolism plays a critical role in both DNA methylation and DNA synthesis. Accumulating evidence has shown that interruptions of this pathway are associated with many disease outcomes including cardiovascular diseases and cancers. Mechanistic studies have been performed on genetic polymorphisms involved in one-carbon metabolism. However, expression profiles of these inter-related genes are not well-known. In this study, we examined the gene expression profiles of 11 one-carbon metabolizing genes by quantifying the mRNA level of the lymphocyte among 54 healthy individuals and explored the correlations of these genes. We found these genes were expressed in lymphocytes at moderate levels and showed significant inter-person variations, We also applied principle component analysis to explore potential patterns of expression. The components identified by the program agreed with existing knowledge about one-carbon metabolism. This study helps us better understand the biological functions of one-carbon metabolism.     

Context-dependent aggregation in Common Frog Rana temporaria tadpoles: influence of developmental stage, predation risk and social environment

1. This study examines the aggregation behaviour and activity of larvae of the Common Frog Rana temporaria in relation to the early social environment, ontogeny and the presence of chemical cues from a predatory fish to address three main questions: (i) Does previous social interaction influence aggregation behaviour in later developmental stages? (ii) To what extent does aggregation behaviour depend upon the risk level perceived by the individual? (iii) Does aggregation behaviour change through ontogeny?
2. Tadpoles were reared from eggs either in small groups or in complete isolation. In relatively early stages of development, tadpoles showed no preference for the side of the test container containing siblings over the side containing no larvae regardless of the social context experienced (isolation or contact with siblings).
3. The presence of chemical cues from a potential predator did not trigger the aggregation behaviour of tadpoles, but it had a remarkable effect on their activity and spatial distribution. Tadpoles exposed to water preconditioned by a predator spent significantly less time swimming and avoided the central area of the test container more frequently than did controls exposed to unconditioned water.
4. Tadpoles were more active, avoided the central section and associated preferentially with conspecifics (siblings) at later stages of development regardless of the social conditioning they had previously experienced.
5. Individuals reared in groups were twice as active as individuals reared in isolation. This suggests that the early social environment experienced by larvae can influence future behaviour and thereby growth and development rates.
6. The expression of conspecific attraction is probably linked to an ontogenetic shift in larval behaviour. However, reduced activity, rather than aggregation, appears to be the basic antipredator mechanism in larval Common Frog.     

Gene expression profiling identifies a set of transcripts that are up-regulated inhuman testicular seminoma.

Seminoma constitutes one subtype of human testicular germ cell tumors and is uniformly composed of cells that are morphologically similar to the primordial germ cells and/or the cells in the carcinoma in situ. We performed a genome-wide exploration of the genes that are specifically up-regulated in seminoma by oligonucleotide-based microarray analysis. This revealed 106 genes that are significantly and consistently up-regulated in the seminomas compared to the adjacent normal tissues of the testes. The microarray data were validated by semi-quantitative RT-PCR analysis. Of the 106 genes, 42 mapped to a small number of specific chromosomal regions, namely, 1q21, 2p23, 6p21-22, 7p14-15, 12pll, 12p13, 12q13-14 and 22q12-13. This list of up-regulated genes may be useful in identifying the causative oncogene(s) and/or the origin of seminoma. Furthermore, immunohistochemical analysis revealed that the seminoma cells specifically expressed the six gene products that were selected randomly from the list. These proteins include CCND2 and DNMT3A and may be useful as molecular pathological markers of seminoma.     

Mechanism of food detection in the tadpoles of the bronze frog <Emphasis Type="Italic">Rana temporalis</Emphasis>

Mechanism of food detection in Rana temporalis tadpoles was studied using a rectangular choice tank with end compartments (stimulus zones) providing exclusively visual and/or chemical food cues. Boiled spinach served as the food. The test tadpoles were starved for 24 h before use. They were released from the center of the choice tank (n=24) after 5 min of acclimation to test for end bias and food-detecting mechanism. The number of tadpoles in the two stimulus zones was recorded at 5-min intervals from 10 to 30 min. In the end-bias tests (without food cues) tadpole distribution was comparable at all times in the two compartments of the choice tank, exhibiting no end bias. In tests with the visual food cues provided in one of the stimulus zones, the tadpole distribution was also random. On the other hand, in experiments involving chemical cues emanating from food the tadpoles preferentially associated with the food source in significantly greater numbers compared to the zone lacking food or providing only a visual cue. The experiments with individual test tadpoles also revealed that they detect food based on chemical cues and ruled out copycat behavior. These findings on R. temporalis tadpoles reveal that chemical senses predominate over the visual senses in detection of food and foraging.