"Guilt by association" is the exception rather than the rule in gene networks

Gene networks are commonly interpreted as encoding functional information in their connections. An extensively validated principle called guilt by association states that genes which are associated or interacting are more likely to share function. Guilt by association provides the central top-down principle for analyzing gene networks in functional terms or assessing their quality in encoding functional information. In this work, we show that functional information within gene networks is typically concentrated in only a very few interactions whose properties cannot be reliably related to the rest of the network. In effect, the apparent encoding of function within networks has been largely driven by outliers whose behaviour cannot even be generalized to individual genes, let alone to the network at large. While experimentalist-driven analysis of interactions may use prior expert knowledge to focus on the small fraction of critically important data, large-scale computational analyses have typically assumed that high-performance cross-validation in a network is due to a generalizable encoding of function. Because we find that gene function is not systemically encoded in networks, but dependent on specific and critical interactions, we conclude it is necessary to focus on the details of how networks encode function and what information computational analyses use to extract functional meaning. We explore a number of consequences of this and find that network structure itself provides clues as to which connections are critical and that systemic properties, such as scale-free-like behaviour, do not map onto the functional connectivity within networks.     

Elevated CO2 stimulates grassland soil respiration by increasing carbon inputs rather than by enhancing soil moisture

It is not clear whether the consistent positive effect of elevated CO₂ on soil respiration (soil carbon flux, SCF) results from increased plant and microbial activity due to (i) greater C availability through CO₂‐induced increases in C inputs or (ii) enhanced soil moisture via CO₂‐induced declines in stomatal conductance and plant water use. Global changes such as biodiversity loss or nitrogen (N) deposition may also affect these drivers, interacting with CO₂ to affect SCF. To determine the effects of these factors on SCF and elucidate the mechanism(s) behind the effect of elevated CO₂ on SCF, we measured SCF and soil moisture throughout a growing season in the Biodiversity, CO₂, and N (BioCON) experiment. Increasing diversity and N caused small declines in soil moisture. Diversity had inconsistent small effects on SCF through its effects on abiotic conditions, while N had a small positive effect that was unrelated to soil moisture. Elevated CO₂ had large consistent effects, increasing soil moisture by 26% and SCF by 45%. However, CO₂‐induced changes in soil moisture were weak drivers of SCF: CO₂ effects on SCF and soil moisture were uncorrelated, CO₂ effect size did not change with soil moisture, within‐day CO₂ effects via soil moisture were neutral or weakly negative, and the estimated effect of increased C availability was 14 times larger than that of increased soil moisture. Combined with previous BioCON results indicating elevated CO₂ increases C availability to plants and microbes, our results suggest that increased SCF is driven by CO₂‐induced increases in substrate availability. Our results provide further support for increased rates of belowground C cycling at elevated CO₂ and evidence that, unlike the response of productivity to elevated CO₂ in BioCON, the response of SCF is not strongly N limited. Thus, N limited grasslands are unlikely to act as a N sink under elevated CO₂.     

Desensitization of pigment granule aggregation in Xenopus leavis melanophores: melatonin degradation rather than receptor down-regulation is responsible

Xenopus laevis melanophores express a high density (B(max) 1224 fmol/mg protein) of high-affinity (K(d) 37 pm) cell membrane melatonin receptors. Treatment of melanophores with melatonin resulted in a loss of membrane melatonin receptors reaching a maximum (approximately 60%) by 6 h. In addition to receptor loss, a decline in the potency of melatonin to produce pigment aggregation was observed on prolonged treatment. However, the loss of potency (3.8-fold in 24 h and 162-fold in 96 h) was much slower than loss of receptors, and was completely prevented by inclusion of eserine (100 microm), an inhibitor of melatonin deacetylation in the culture medium. Incubation of melanophores with [(3)H]-melatonin showed that eserine prevented metabolism of melatonin to 5-methoxytryptamine. These results indicate that although receptor density does decline on prolonged treatment, this is not responsible for the diminishing melatonin potency, which is entirely due to degradation of melatonin by deacetylation and subsequent deamination in melanophores.     

Measurement of leaf and canopy photosynthetic CO2 exchange in the field

The principles and limitations of leaf gas exchange measurementsin portable gas exchange systems are described. Attention isgiven to the design and developments in infrared gas analysersused in portable systems, and the basic structure of singleand dual beam instruments is presented. The significance offlow measurement in these systems and the principles of thermalmass flow measurement are illustrated. Considerations of leafarea measurement, chamber design and choice of materials areoutlined. Two specific developments in field gas exchange systemsare described and their significance in field measurements isillustrated with examples. (1) An integrating sphere leaf chamberfor the determination of the quantum yield of photosynthesis,on the basis of absorbed light, is explained and equations forits use are developed. The significance of this approach isillustrated by a comparison of data for contrasting leaves plottedon an absorbed and incident light basis. This measurement oflight-limited photosynthesis is also critical in understandingthe contribution of shaded leaves to canopy photosynthesis.(2) A system for the measurement of canopy photosynthesis fromarable crops and low stature natural vegetation is described.Results from a season-long study of wheat CO₂ exchange are shownto illustrate its application. Key words: Leaf gas exchange, photosynthetic quantum efficiency, infrared gas analysis, canopy photosynthesis, integrating sphere     

Regulation of gene expression by photosynthetic signals triggered through modified CO2 availability

Background  

To coordinate metabolite fluxes and energy availability, plants adjust metabolism and gene expression to environmental changes through employment of interacting signalling pathways.     

Water deficit tolerance in sugarcane is dependent on the accumulation of sugar in the leaf

Sugarcane productivity is severely affected by the occurrence of water deficit in the field, causing inhibition of growth and sugar production. Evaluating physiological responses of sugarcane under water deficit conditions is essential to understand physiological variables responsible for reaching homeostasis. Therefore, we analysed physiological traits of two sugarcane genotypes, RB835486 (Tolerant) and RB855453 (Susceptible), under water deficit conditions: well-watered (WW-Control), water deficit (WD) and rewatered (RW). The physiological response was evaluated using linear regression and multivariate analysis. Some characteristics such as water potential in leaves, photosynthesis, chlorophyll fluorescence, chlorophyll index, sucrose and starch contents did not show differences between the genotypes under water deficit conditions. However, the tolerant genotype showed increased reducing sugars content in the leaves, whereas the susceptible genotype had increased non-photochemical quenching (qN). After rewatering, the susceptible sugarcane genotype showed higher electron transport rate (ETR) and efficiency of PSII (Y). Multivariate analysis revealed that non-photochemical quenching and reducing sugars in the leaves were physiological variables responsible for reaching homestasis under water deficit conditions. Therefore, the reducing sugars concentration should be considered a physiological variable responsible for the adjustment made by the tolerant sugarcane genotype when submitted to water deficit.     

PARK2-mediated mitophagy is involved in regulation of HBEC senescence in COPD pathogenesis

Cigarette smoke (CS)-induced mitochondrial damage with increased reactive oxygen species (ROS) production has been implicated in COPD pathogenesis by accelerating senescence. Mitophagy may play a pivotal role for removal of CS-induced damaged mitochondria, and the PINK1 (PTEN-induced putative kinase 1)-PARK2 pathway has been proposed as a crucial mechanism for mitophagic degradation. Therefore, we sought to investigate to determine if PINK1-PARK2-mediated mitophagy is involved in the regulation of CS extract (CSE)-induced cell senescence and in COPD pathogenesis. Mitochondrial damage, ROS production, and cell senescence were evaluated in primary human bronchial epithelial cells (HBEC). Mitophagy was assessed in BEAS-2B cells stably expressing EGFP-LC3B, using confocal microscopy to measure colocalization between TOMM20-stained mitochondria and EGFP-LC3B dots as a representation of autophagosome formation. To elucidate the involvement of PINK1 and PARK2 in mitophagy, knockdown and overexpression experiments were performed. PINK1 and PARK2 protein levels in lungs from patients were evaluated by means of lung homogenate and immunohistochemistry. We demonstrated that CSE-induced mitochondrial damage was accompanied by increased ROS production and HBEC senescence. CSE-induced mitophagy was inhibited by PINK1 and PARK2 knockdown, resulting in enhanced mitochondrial ROS production and cellular senescence in HBEC. Evaluation of protein levels demonstrated decreased PARK2 in COPD lungs compared with non-COPD lungs. These results suggest that PINK1-PARK2 pathway-mediated mitophagy plays a key regulatory role in CSE-induced mitochondrial ROS production and cellular senescence in HBEC. Reduced PARK2 expression levels in COPD lung suggest that insufficient mitophagy is a part of the pathogenic sequence of COPD.     

Cellular acidosis in rodents exposed to cadmium is caused by adaptation of the tissue rather than an early effect of toxicity

Proton (¹H) Nuclear Magnetic Resonance (NMR) spectroscopy was used to investigate the biochemical response of bank voles and wood mice (two wild rodent species frequently found on metal-contaminated sites) to chronic cadmium (Cd) insult. Similar effects, in terms of both metabolic changes (consistent with cellular acidosis) and induced metallothionin (MT) production were observed in all animals. These changes appeared to be an adaptation of the liver to toxic insult rather than onset of a toxic effect, and, in common with previous studies, were more marked in bank voles than wood mice. This may have reflected the greater Cd intake and assimilation of the former but was not explained by differences in concentrations of free (non MT-bound) Cd; concentrations of which were negligible in both voles and mice. Responses to Cd insult were detected in both species even though their bodies contained cadmium concentrations well below the World Health Organisation critical renal concentration of 200 μg/g dry mass.     

Relationship between ammonium accumulation and senescence of detached rice leaves caused by excess copper

The possibility that ammonium (NH ₄ ⁺ ) accumulation is linked to the senescence of detached rice (Oryza sativa) leaves induced by copper (Cu) was investigated. CuSO₄ was effective in promoting senescence of detached rice leaves. Both CuSO₄ and CuCl₂ induced NH ₄ ⁺ accumulation in detached rice leaves, indicating that NH ₄ ⁺ accumulation is induced by copper. Sulfate salts of Mg, Mn, Zn, and Fe were ineffective in inducing NH ₄ ⁺ accumulation in detached rice leaves. The senescence of detached rice leaves induced by Cu was found to be prior to NH ₄ ⁺ accumulation. Free radical scavengers, such as glutathione and thiourea, inhibited senescence caused by Cu and at the same time inhibited Cu-induced NH ₄ ⁺ accumulation. The current results suggest that NH ₄ ⁺ accumulation is not associated with senescence induced by Cu, but is part of the overall expression of oxidative damage caused by an excess of Cu. Evidence was presented to show that copper-induced ammonium accumulation in detached rice leaves is attributed to a decrease in glutamine synthetase activity and an increase in reduction of nitrate.     

FGF-2 suppresses cellular senescence of human mesenchymal stem cells by down-regulation of TGF-beta2

Human mesenchymal stem cells (hMSCs) are able to both self-replicate and differentiate into a variety of cell types. Fibroblast growth factor-2 (FGF-2) stimulates the growth of hMSCs in vitro, but its mechanisms have not been clarified yet. In this study, we investigated whether cellular senescence was involved in the stimulation of hMSCs growth by FGF-2 and the expression levels of transforming growth factor-beta1 and -beta2 (TGF-betas). Because hMSCs were induced cellular senescence due to long-term culture, FGF-2 decreased the percentage of senescent cells and suppressed G1 cell growth arrest through the suppression of p21(Cip1), p53, and p16(INK4a) mRNA expression levels. Furthermore, the levels of TGF-betas mRNA expression in hMSCs were increased by long-term culture, but FGF-2 suppressed the increase of TGF-beta2 mRNA expression due to long-term culture. These results suggest that FGF-2 suppresses the hMSCs cellular senescence dependent on the length of culture through down-regulation of TGF-beta2 expression.     

Effects of temperature and CO2 concentration on photosynthetic CO2 fixation by Chlorella

The rates of photosynthetic ¹⁴CO₂ fixation by Chlorella vulgarisllh, grown under high CO₂, were determined between 4 to 37°Cwith air containing from 300 to 13,000 ppm ¹⁴CO₂. When the CO₂level was increased, both the rate of photosynthesis and theoptimum temperature for maximum photosynthesis increased. Themaximum photosynthetic rate was reached at 12°C with 300ppm ^l4CO₂. Among the photosynthetic products fromed at 300 ppm ¹⁴CO₂, glycolatedecreased greatly when the temperature was raised from 20 to30°C. At 3,000 ppm ¹⁴CO₂ an insignificant amount of glycolatewas formed at all temperatures, whereas ¹⁴C-incorporation intothe insoluble fraction, sucrose, and the lipid fraction wassignificantly higher than at 300 ppm ¹⁴CO₂. The ¹⁴C in sucrosewas greatly increased and the radioactivity in the insolublefraction decreased when the temperature was raised from 28 to36°C. (Received April 8, 1980; )     

Gibberellin-induced delay of leaf senescence of Alstroemeria cut flowering stems is not caused by an increase in the endogenous cytokinin content

The effects of various chemically pure gibberellins and cytokinins on leaf yellowing of Alstroemeria were described. The loss of chlorophyll was measured both in leaves of cut flowering stems and in a model system consisting of detached leaf tips. It was demonstrated that plant growth substances affected chlorophyll loss in both systems to the same extent. Leaf senescence was delayed by various gibberellins and cytokinins. The results demonstrated that some of the gibberellins (GA₄ and GA₇) are far more effective in delaying chlorophyll loss than GA₃, which is commonly used as a postharvest treatment for Alstroemeria cut flowering stems. Immunoassays were used to demonstrate that the effect of gibberellins on leaf yellowing does not involve an increase in the endogenous cytokinin concentrations in the leaves as an intermediate step.Abbreviations GA gibberellin A - HPLC high performance liquid chromatography - GA_3Mc GA₃-methyl ester - ZR zeatin riboside - IPAR isopentenyl adenine riboside.     

The photosynthetic limitation posed by internal conductance to CO2 movement is increased by nutrient supply

The internal conductance to CO(2) supply from substomatal cavities to sites of carboxylation may pose a large limitation to photosynthesis, but little is known of how it is affected by nutrient supply. Knowing how internal conductance responds to nutrient supply is critical for interpreting the biochemical responses from A-C(i) curves. The aim of this paper was to examine the response of g(i) and photosynthetic parameters to nutrient supply in glasshouse-grown seedlings of the evergreen perennial Eucalyptus globulus Labill. Seedlings were grown with five different nutrient treatments and g(i) was estimated from concurrent measurements of gas exchange and fluorescence. Internal conductance varied between 0.12 and 0.19 mol m(-2) s(-1) and the relative limitation of photosynthesis due to internal conductance was greater than the stomatal limitation. In most species these two limitations are rather similar, but in E. globulus stomatal limitations were abnormally low due to high stomatal conductance (0.31 to 0.39 mol m(-2) s(-1)). The large positive response of photosynthesis to nutrient supply was not matched by changes in internal conductance, and thus the relative limitation of photosynthesis due to internal conductance increased with increasing nutrient supply. Failure to account for finite internal conductance led to estimates of V(cmax) that were 60% of the true value, which, in turn, led to an underestimation of in vivo Rubisco specific activity (as V(cmax)/Rubisco content). The specific activity of Rubisco in E. globulus (21 mol mol(-1) s(-1)) was close to the maximum published estimates, and thus, despite these leaves containing a large fraction of N as Rubisco (38-44%) there was no evidence that Rubisco activity was down-regulated or that the enzyme was in excess.     

Mechanisms of biocontrol by Pantoea dispersa of sugar cane leaf scald disease caused by Xanthomonas albilineans

Albicidins, a family of phytotoxins and antibiotics produced by Xanthomonas albilineans , are important in sugar cane leaf scald disease development. The albicidin detoxifying bacterium Pantoea dispersa (syn. Erwinia herbicola ) SB1403 provides very effective biocontrol against leaf scald disease in highly susceptible sugar cane cultivars. The P. dispersa gene ( albD ) for enzymatic detoxification of albicidin has recently been cloned and sequenced. To test the role of albicidin detoxification in biocontrol of leaf scald disease, albD was inactivated in P. dispersa by site-directed mutagenesis. The mutants, which were unable to detoxify albicidin, were less resistant to the toxin and less effective in biocontrol of leaf scald disease than their parent strain. This indicates that albicidin detoxification contributes to the biocontrol capacity of P. dispersa against X. albilineans . Rapid growth and ability to acidify media are other characteristics likely to contribute to the competitiveness of P. dispersa against X. albilineans at wound sites used to invade sugar cane.     

A loss of insulin-like growth factor-2 imprinting is modulated by CCCTC-binding factor down-regulation at senescence in human epithelial cells

The imprinted insulin-like growth factor-2 (IGF2) gene is an auto/paracrine growth factor expressed only from the paternal allele in adult tissues. In tissues susceptible to aging-related cancers, including the prostate, a relaxation of IGF2 imprinting is found, suggesting a permissive role for epigenetic alterations in cancer development. To determine whether IGF2 imprinting is altered in cellular aging and senescence, human prostate epithelial and urothelial cells were passaged serially in culture to senescence. Allelic analyses using an IGF2 polymorphism demonstrated a complete conversion of the IGF2 imprint status from monoallelic to biallelic, in which the development of senescence was associated with a 10-fold increase in IGF2 expression. As a mechanism, a 2-fold decrease in the binding of the enhancer-blocking element CCCTC-binding factor (CTCF) within the intergenic IGF2-H19 region was found to underlie this switch to biallelic IGF2 expression in senescent cells. This decrease in CTCF binding was associated with reduced CTCF expression in senescent cells. No de novo increases in methylation at the IGF2 CTCF binding site were seen. The forced down-regulation of CTCF expression using small interfering RNA in imprinted prostate cell lines resulted in an increase in IGF2 expression and a relaxation of imprinting. Our data suggest a novel mechanism for IGF2 imprinting regulation, that is, the reduction of CTCF expression in the control of IGF2 imprinting. We also demonstrate that altered imprinting patterns contribute to changes in gene expression in aging cells.     

NK cell activity during human cytomegalovirus infection is dominated by US2-11-mediated HLA class I down-regulation

A highly attractive approach to investigate the influence and hierarchical organization of viral proteins on cellular immune responses is to employ mutant viruses carrying deletions of various virus-encoded, immune-modulating genes. Here, we introduce a novel set of deletion mutants of the human CMV (HCMV) lacking the UL40 region either alone or on the background of a deletion mutant devoid of the entire US2-11 region. Deletion of UL40 had no significant effect on lysis of infected cells by NK cells, indicating that the expected enhancement of HLA-E expression by specific peptides derived from HCMV-encoded gpUL40 leader sequences was insufficient to confer target cell protection. Moreover, the kinetics of MHC class I down-regulation by US2-11 genes observed at early and late phases postinfection with wild-type virus correlated with increased susceptibility to NK lysis. Thus, the influence of HCMV genes on NK reactivity follows a hierarchy dominated by the US2-11 region, which encodes all viral genes capable of down-modulating expression of classical and non-classical MHC class I molecules. The insights gained from studies of such virus mutants may impact on future therapeutic strategies and vaccine development and incorporate NK cells in the line of defense mechanisms against HCMV infection.     

Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene

Autophagy is an intracellular process for vacuolar bulk degradation of cytoplasmic components. The molecular machinery responsible for yeast and mammalian autophagy has recently begun to be elucidated at the cellular level, but the role that autophagy plays at the organismal level has yet to be determined. In this study, a genome-wide search revealed significant conservation between yeast and plant autophagy genes. Twenty-five plant genes that are homologous to 12 yeast genes essential for autophagy were discovered. We identified an Arabidopsis mutant carrying a T-DNA insertion within AtAPG9, which is the only ortholog of yeast Apg9 in Arabidopsis (atapg9-1). AtAPG9 is transcribed in every wild-type organ tested but not in the atapg9-1 mutant. Under nitrogen or carbon-starvation conditions, chlorosis was observed earlier in atapg9-1 cotyledons and rosette leaves compared with wild-type plants. Furthermore, atapg9-1 exhibited a reduction in seed set when nitrogen starved. Even under nutrient growth conditions, bolting and natural leaf senescence were accelerated in atapg9-1 plants. Senescence-associated genes SEN1 and YSL4 were up-regulated in atapg9-1 before induction of senescence, unlike in wild type. All of these phenotypes were complemented by the expression of wild-type AtAPG9 in atapg9-1 plants. These results imply that autophagy is required for maintenance of the cellular viability under nutrient-limited conditions and for efficient nutrient use as a whole plant.