Global transcriptional response of Caulobacter crescentus to iron availability

Abstract Background In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. Results In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility. Conclusions Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms.

Global transcriptional response of Caulobacter crescentus to iron availability

BACKGROUND: In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. RESULTS: In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility. CONCLUSIONS: Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms

Changes in the intermediate water mass formation rates in the global ocean for the Last Glacial Maximum, mid-Holocene and pre-industrial climates

The paleoclimate version of the National Center for Atmospheric Research Community Climate System Model version 3 (NCAR-CCSM3) is used to analyze changes in the water formation rates in the Atlantic, Pacific, and Indian Oceans for the Last Glacial Maximum (LGM), mid-Holocene (MH) and pre-industrial (PI) control climate. During the MH, CCSM3 exhibits a north-south asymmetric response of intermediate water subduction changes in the Atlantic Ocean, with a reduction of 2 Sv in the North Atlantic and an increase of 2 Sv in the South Atlantic relative to PI. During the LGM, there is increased formation of intermediate water and a more stagnant deep ocean in the North Pacific. The production of North Atlantic Deep Water (NADW) is significantly weakened. The NADW is replaced in large extent by enhanced Antarctic Intermediate Water (AAIW), Glacial North Atlantic Intermediate Water (GNAIW), and also by an intensified of Antarctic Bottom Water (AABW), with the latter being a response to the enhanced salinity and ice formation around Antarctica. Most of the LGM intermediate/mode water is formed at 27.4 < sigma(theta) < 29.0 kg/m(3), while for the MH and PI most of the subduction transport occurs at 26.5 < sigma(theta) < 27.4 kg/m(3). The simulated LGM Southern Hemisphere winds are more intense by 0.2-0.4 dyne/cm(2). Consequently, increased Ekman transport drives the production of intermediate water (low salinity) at a larger rate and at higher densities when compared to the other climatic periods.

Xylella fastidiosa: An in vivo system to study possible survival strategies within citrus xylem vessels based on global gene expression analysis

Xylella fastidiosa inhabits the plant xylem, a nutrient-poor environment, so that mechanisms to sense and respond to adverse environmental conditions are extremely important for bacterial survival in the plant host. Although the complete genome sequences of different Xylella strains have been determined, little is known about stress responses and gene regulation in these organisms. In this work, a DNA microarray was constructed containing 2,600 ORFs identified in the genome sequencing project of Xylella fastidiosa 9a5c strain, and used to check global gene expression differences in the bacteria when it is infecting a symptomatic and a tolerant citrus tree. Different patterns of expression were found in each variety, suggesting that bacteria are responding differentially according to each plant xylem environment. The global gene expression profile was determined and several genes related to bacterial survival in stressed conditions were found to be differentially expressed between varieties, suggesting the involvement of different strategies for adaptation to the environment. The expression pattern of some genes related to the heat shock response, toxin and detoxification processes, adaptation to atypical conditions, repair systems as well as some regulatory genes are discussed in this paper. DNA microarray proved to be a powerful technique for global transcriptome analyses. This is one of the first studies of Xylella fastidiosa gene expression in vivo which helped to increase insight into stress responses and possible bacterial survival mechanisms in the nutrient-poor environment of xylem vessels.

Global pharmacogenomics: Impact of population diversity on the distribution of polymorphisms in the CYP2C cluster among Brazilians

The impact of biogeographical ancestry, self-reported 'race/color' and geographical origin on the frequency distribution of 10 CYP2C functional polymorphisms (CYP2C8*2, *3, *4, CYP2C9*2, *3, *5, *11, CYP2C19*2, *3 and *17) and their haplotypes was assessed in a representative cohort of the Brazilian population (n = 1034). TaqMan assays were used for allele discrimination at each CYP2C locus investigated. Individual proportions of European, African and Amerindian biogeographical ancestry were estimated using a panel of insertion-deletion polymorphisms. Multinomial log-linear models were applied to infer the statistical association between the CYP2C alleles and haplotypes (response variables), and biogeographical ancestry, self-reported Color and geographical origin (explanatory variables). The results showed that CYP2C19*3, CYP2C9*5 and CYP2C9*11 were rare alleles (<1%), the frequency of other variants ranged from 3.4% (CYP2C8*4) to 17.3% (CYP2C19*17). Two distinct haplotype blocks were identified: block 1 consists of three single nucleotide polymorphisms (SNPs) (CYP2C19*17, CYP2C19*2 and CYP2C9*2) and block 2 of six SNPs (CYP2C9*11, CYP2C9*3, CYP2C9*5, CYP2C8*2, CYP2C8*4 and CYP2C8*3). Diplotype analysis generated 41 haplotypes, of which eight had frequencies greater than 1% and together accounted for 96.4% of the overall genetic diversity. The distribution of CYP2C8 and CYP2C9 (but not CYP2C19) alleles, and of CYP2C haplotypes was significantly associated with self-reported Color and with the individual proportions of European and African genetic ancestry, irrespective of Color self-identification. The individual odds of having alleles CYP2C8*2, CYP2C8*3, CYP2C9*2 and CYP2C9*3, and haplotypes including these alleles, varied continuously as the proportion of European ancestry increased. Collectively, these data strongly suggest that the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of pharmacogenomic studies of the CYP2C cluster in order to avoid spurious conclusions based on improper matching of study cohorts. This conclusion extends to other polymorphic pharmacogenes among Brazilians, and most likely to other admixed populations of the Americas. The Pharmacogenomics Journal (2012) 12, 267-276; doi: 10.1038/tpj.2010.89; published online 21 December 2010

Pancreatic islets from dexamethasone-treated rats show alterations in global gene expression and mitochondrial pathways

Chronic administration of glucocorticoids (GC) leads to characteristic features of type 2 diabetes in mammals. The main action of dexamethasone in target cells occurs through modulation of gene expression, although the exact mechanisms are still unknown. We therefore investigated the gene expression profile of pancreatic islets from rats treated with dexamethasone using a cDNA array screening analysis. The expression of selected genes and proteins involved in mitochondria] apoptosis was further analyzed by PCR and immunoblotting. Insulin, triglyceride and free fatty acid plasma levels, as well as glucose-induced insulin secretion, were significantly higher in dexamethasone-treated rats compared with controls. Out of 1176 genes, 60 were up-regulated and 28 were down-regulated by dexamethasone treatment. Some of the modulated genes are involved in apoptosis, stress response, and proliferation pathways. RT-PCR confirmed the cDNA array results for 6 selected genes. Bax alpha protein expression was increased, while Bcl-2 was decreased. In vivo dexamethasone treatment decreased the mitochondrial production of NAD(P)H, and increased ROS production. Concluding, our data indicate that dexamethasone modulates the expression of genes and proteins involved in several pathways of pancreatic-islet cells, and mitochondria dysfunction might be involved in the deleterious effects after long-term GC treatment.

Trends, drivers and impacts of changes in swidden cultivation in tropical forest-agriculture frontiers: A global assessment

This meta-analysis of land-cover transformations of the past 10-15 years in tropical forest-agriculture frontiers world-wide shows that swidden agriculture decreases in landscapes with access to local, national and international markets that encourage cattle production and cash cropping, including biofuels. Conservation policies and practices also accelerate changes in swidden by restricting forest clearing and encouraging commercial agriculture. However, swidden remains important in many frontier areas where farmers have unequal or insecure access to investment and market opportunities, or where multi-functionality of land uses has been preserved as a strategy to adapt to current ecological, economic and political circumstances. In some areas swidden remains important simply because intensification is not a viable choice, for example when population densities and/or food market demands are low. The transformation of swidden landscapes into more intensive land uses has generally increased household incomes, but has also led to negative effects on the social and human capital of local communities to varying degrees. From an environmental perspective, the transition from swidden to other land uses often contributes to permanent deforestation, loss of biodiversity, increased weed pressure, declines in soil fertility, and accelerated soil erosion. Our prognosis is that, despite the global trend towards land use intensification, in many areas swidden will remain part of rural landscapes as the safety component of diversified systems, particularly in response to risks and uncertainties associated with more intensive land use systems. (C) 2011 Elsevier Ltd. All rights reserved.

Global and Regional Ventricular Repolarization Study by Body Surface Potential Mapping in Patients with Left Bundle-Branch Block and Heart Failure Undergoing Cardiac Resynchronization Therapy

Background: The controversial effects promoted by cardiac resynchronization therapy (CRT) on the ventricular repolarization (VR) have motivated VR evaluation by body surface potential mapping (BSPM) in CRT patients. Methods: Fifty-two CRT patients, mean age 58.8 +/- 12.3 years, 31 male, LVEF 27.5 +/- 9.2, NYHA III-IV heart failure with QRS181.5 +/- 14.2 ms, underwent 87-lead BSPM in sinus rhythm (BASELINE) and biventricular pacing (BIV). Measurements of mean and corrected QT intervals and dispersion, mean and corrected T peak end intervals and their dispersion, and JT intervals characterized global and regional (RV, Intermediate, and LV regions) ventricular repolarization response. Results: Global QTm (P < 0.001) and QTcm (P < 0.05) were decreased in BIV; QTm was similar across regions in both modes (P = ns); QTcm values were lower in RV/LV than in Intermediate region in BASELINE and BIV (P < 0.001); only RV/Septum showed a significant difference (P < 0.01) in the BIV mode. QTD values both of BASELINE (P < 0.01) and BIV (P < 0.001) were greater in the Intermediate than in the LV region. CRT effect significantly reduced global/regional QTm and QTcm values. QTD was globally decreased in RV/LV (Intermediate: P = ns). BIV mode significantly reduced global T peak end mean and corrected intervals and their dispersion. JT values were not significant. Conclusions: Ventricular repolarization parameters QTm, QTcm, and QTD global/regional values, as assessed by BSPM, were reduced in patients under CRT with severe HF and LBBB. Greater recovery impairment in the Intermediate region was detected by the smaller variation of its dispersion.

Cellular biomarkers to elucidate global warming effects on Antarctic sea urchin Sterechinus neumayeri

Global warming is a reality and its effects have been widely studied. However, the consequences for marine invertebrates remain poorly understood. Thus, the present study proposed to evaluate the effect of elevated temperature on the innate immune system of Antarctic sea urchin Sterechinus neumayeri. Sea urchins were collected nearby Brazilian Antarctic Station "Comandante Ferraz" and exposed to 0 (control), 2 and 4A degrees C for periods of 48 h, 2, 7 and 14 days. After the experimental periods, coelomic fluid was collected in order to perform the following analyses: coelomocytes differential counting, phagocytic response, adhesion and spreading coelomocytes assay, intranuclear iron crystalloid and ultra structural analysis of coelomocytes. The red sphere cell was considered a biomarker for heat stress, as they increased in acute stress. Besides that, a significant increase in phagocytic indexes was observed at 2A degrees C coinciding with a significant increase of intranuclear iron crystalloid at the same temperature and same time period. Furthermore, significant alterations in cell adhesion and spreading were observed in elevated temperatures. The ultra structural analysis of coelomocytes showed no significant difference across treatments. This was the first time that innate immune response alterations were observed in response to elevated temperature in a Polar echinoid.

Soil-nutrient availability modifies the response of young pioneer and late successional trees to elevated carbon dioxide in a Brazilian tropical environment

The aim of this work was to determine the impact of three levels of [CO2] and two levels of soil-nutrient availability on the growth and physiological responses of two tropical tree species differing in their ecological group: Croton urucurana Baillon, a pioneer (P), and also Cariniana legalis (Martius) Kuntze, a late succession (LS). We aimed to test the hypothesis that P species have stronger response to elevated [CO2] than LS species as a result of differences in photosynthetic capacity and growth kinetics between both functional groups. Seedlings of both species were grown in open-top-chambers under high (HN) or low (LN) soil-nutrient supply and exposed to ambient (380 mu mol mol(-1)) or elevated (570 and 760 mu mol mol(-1)) [CO2]. Measurements of gas exchange, chlorophyll a fluorescence, seedling biomass and allocation were made after 70 days of treatment. Results suggest that elevated [CO2] significantly enhances the photosynthetic rates (A) and biomass production in the seedlings of both species, but that soil-nutrient supply has the potential to modify the response of young tropical trees to elevated [CO2]. In relation to plants grown in ambient [CO2], the P species grown under 760 mu mol mol(-1) [CO2] showed increases of 28% and 91% in A when grown in LN and HN, respectively. In P species grown under 570 mu mol mol(-1) [CO2], A increased by 16% under HN, but there was no effect in LN. In LS species, the enhancement of A by effect of 760 mu mol mol(-1) [CO2] was 30% and 70% in LN and HN, respectively. The exposure to 570 mu mol mol(-1) [CO2] stimulated A by 31% in HN, but was no effect in LN. Reductions in stomatal conductance (g(s)) and transpiration (E), as a result of elevated [CO2] were observed. Increasing the nutrient supply from low to high increased both the maximum rate of carboxylation (V-cmax) and maximum potential rate of electron transport (J(max)). As the level of [CO2] increased, both the V-cmax and the J(max) were found to decrease, whereas the J(max)/V-cmax ratio increased. In the LS species, the maximum efficiency of PSII (F-v/F-m) was higher in the 760 mu mol mol(-1) [CO2] treatment relative to other [CO2] treatments. The results suggest that when grown under HN and the highest [CO2], the performance of the P species C. urucurana, in terms of photosynthesis and biomass enhancement, is better than the LS species C. legalis. However, a larger biomass is allocated to roots when C. legalis seedlings were exposed to elevated [CO2]. This response would be an important strategy for plant survival and productivity of the LS species under drought stresses conditions on tropical environments in a global-change scenario. (C) 2011 Elsevier B.V. All rights reserved.

The Global Paleomonsoon as seen through speleothem records from Asia and the Americas

The regional monsoons of the world have long been viewed as seasonal atmospheric circulation reversal-analogous to a thermally-driven land-sea breeze on a continental scale. This conventional view of monsoons is now being integrated at a global scale and accordingly, a new paradigm has emerged which considers regional monsoons to be manifestations of global-scale seasonal changes in response to overturning of atmospheric circulation in the tropics and subtropics, and henceforth, interactive components of a singular Global Monsoon (GM) system. The paleoclimate community, however, tends to view 'paleomonsoon' (PM), largely in terms of regional circulation phenomena. In the past decade, many high-quality speleothem oxygen isotope (delta O-18) records have been established from the Asian Monsoon and the South American Monsoon regions that primarily reflect changes in the integrated intensities of monsoons on orbital-to-decadal timescales. With the emergence of these high-resolution and absolute-dated records from both sides of the Equator, it is now possible to test a concept of the 'Global-Paleo-Monsoon' (GPM) on a wide-range of timescales. Here we present a comprehensive synthesis of globally-distributed speleothem delta O-18 records and highlight three aspects of the GPM that are comparable to the modern GM: (1) the GPM intensity swings on different timescales; (2) their global extent; and (3) an anti-phased inter-hemispheric relationship between the Asian and South American monsoon systems on a wide range of timescales.

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.