Lifting the threshold between life and death: SUMO and HDAC fine-tune HIPK2 to sense redox status

In the current issue of Molecular Cell, de la Vega et al. (2012) propose an intriguing model for HIPK2 posttranslational modifications in response to oxidative stress, explaining how HIPK2 can possess both prosurvival as well as proapoptotic activities.     

Clustering threshold gradient descent regularization: with applications to microarray studies

MOTIVATION: An important goal of microarray studies is to discover genes that are associated with clinical outcomes, such as disease status and patient survival. While a typical experiment surveys gene expressions on a global scale, there may be only a small number of genes that have significant influence on a clinical outcome. Moreover, expression data have cluster structures and the genes within a cluster have correlated expressions and coordinated functions, but the effects of individual genes in the same cluster may be different. Accordingly, we seek to build statistical models with the following properties. First, the model is sparse in the sense that only a subset of the parameter vector is non-zero. Second, the cluster structures of gene expressions are properly accounted for. RESULTS: For gene expression data without pathway information, we divide genes into clusters using commonly used methods, such as K-means or hierarchical approaches. The optimal number of clusters is determined using the Gap statistic. We propose a clustering threshold gradient descent regularization (CTGDR) method, for simultaneous cluster selection and within cluster gene selection. We apply this method to binary classification and censored survival analysis. Compared to the standard TGDR and other regularization methods, the CTGDR takes into account the cluster structure and carries out feature selection at both the cluster level and within-cluster gene level. We demonstrate the CTGDR on two studies of cancer classification and two studies correlating survival of lymphoma patients with microarray expressions. AVAILABILITY: R code is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Effects of species interactions on community organization along a trampling gradient

Abstract. Effects of interspecific interactions on the organization of two trampled communities, Eragrostio ferrugineae - Plantaginetum asiaticae (EP) and Eleusino indicae - Digitarietum violascentis (ED), were examined by 4-yr field experiments. We compared changes in the relative abundance of the main component species of the communities in monoculture and mixed culture along a trampling gradient. At no trampling in mixed culture, Ambrosia artemisiifolia var. elatior and Erigeron annuus (roadside herbs, RH) predominated and excluded the trampled community species. Severe trampling markedly reduced the predominance of these roadside herbs, promoted Eragrostis ferruginea (a perennial grass of EP), but suppressed Eleusine indica (an annual grass of ED). These results suggest that the differentiation of trampled and roadside herb communities under heavy trampling are caused by asymmetric competition between their main species. Several species pairs showed a constant rank order of relative cover at high trampling levels. Pennisetum alopecuroides (a perennial grass of both RH and EP) and Eragrostis coexisted, indicating symmetric competition. Eragrostis and Plantago asiatica (a perennial herb of EP) or Poa annua (a winter-annual grass of both EP and ED) coexisted through separation in phenology. Eragrostis promoted the survival of Plantago by moderating unpredictable drought (commensalistic positive interaction). This suggests that community composition is maintained by several interspecific interactions.     

The threshold responses of phytoplankton community to nutrient gradient in a shallow eutrophic Chinese lake

Excessive nutrient loads resulted in cascading trophic effects and ecosystem responses. Aims of this study were to determine if the thresholds in nutrient gradient related to phytoplankton community composition could be identified in eutrophic lake, and further to analyze the change of phytoplankton assemblage along the nutrient concentration based on Threshold Indicator Taxa ANalysis (TITAN). The results presented the significant community thresholds estimate for negative taxa declining at 1.650 mg/L TN and 131.5 μg/L TP, as well as simultaneously increasing for positive taxa at 1.665 mg/L TN and 151.5 μg/L TP along nutrient enrichment gradient. However, there was unremarkable change point determined for TN:TP ratios in Lake Dianchi. Elevated TN and TP altered the phytoplankton assemblage, even may induce the fade of algal blooms across the threshold in the hypertrophic lake. The findings could provide implications for deeply deciphering abrupt transitions for phytoplankton assemblage and developing nutrient tactics to protect the lake ecosystems.     

Evolution of resource use along a gradient of stress leads to increased facilitation

The stress‐gradient hypothesis (SGH) posits that the relative importance of facilitative interactions versus negative interactions increases as levels of abiotic stress increase. Originally formulated in empirical studies of plant populations, in recent years the SGH has been found to describe how interactions change in response to stress in a wide range of species including algae, mussels and moths. However, there has been little theory attempting to predict patterns from first principles in relation to different types of interactions. Here, we use mathematical models of microbial populations to investigate whether patterns consistent with the SGH arise when species interact through resource use and allelopathy. Evolution alters the degree to which competition for resource use versus facilitation (cross‐feeding) occurs. Our results are consistent with the SGH; species interactions evolve to be more facilitative as average stress intensifies. This occurs because at greater stress the species evolve to become specialists on either of the two resources thereby decreasing overlap in resource use and increasing facilitation through cross‐feeding. In addition, the production of toxic allelopathic compounds decreases as stress intensifies due to density‐dependent effects. Our results suggest that the SGH could arise through fundamental interactions that are common to many organisms and therefore that the SGH could be a more widespread phenomenon than previously recognised.     

The interplay of protein engineering and glycoengineering to fine-tune antibody glycosylation and its impact on effector functions

The N-glycan pattern of an IgG antibody, attached at a conserved site within the fragment crystallizable (Fc) region, is a critical antibody quality attribute whose structural variability can also impact antibody function. For tailoring the Fc glycoprofile, glycoengineering in cell lines as well as Fc amino acid mutations have been applied. Multiple glycoengineered Chinese hamster ovary cell lines were generated, including defucosylated (FUT8KO), α-2,6-sialylated (ST6KI), and defucosylated α-2,6-sialylated (FUT8KOST6KI), expressing either a wild-type anti-CD20 IgG (WT) or phenylalanine to alanine (F241A) mutant. Matrix-assisted laser desorption ionization-time of flight mass spectrometry characterization of antibody N-glycans revealed that the F241A mutation significantly increased galactosylation and sialylation content and glycan branching. Furthermore, overexpression of recombinant human α-2,6-sialyltransferase resulted in a predominance of α-2,6-sialylation rather than α-2,3-sialylation for both WT and heavily sialylated F241A antibody N-glycans. Interestingly, knocking out α-1,6-fucosyltransferase (FUT8KO), which removed core fucose, lowered the content of N-glycans with terminal Gal and increased levels of terminal GlcNAc and Man5 groups on WT antibody. Further complement-dependent cytotoxicity (CDC) analysis revealed that, regardless of the production cells, WT antibody samples have higher cytotoxic CDC activity with more exposed Gal residues compared to their individual F241A mutants. However, the FUT8KO WT antibody, with a large fraction of bi-GlcNAc structures (G0), displayed the lowest CDC activity of all WT antibody samples. Furthermore, for the F241A mutants, a higher CDC activity was observed for α-2,6- compared to α-2,3-sialylation. Antibody-dependent cellular cytotoxicity (ADCC) analysis revealed that the defucosylated WT and F241A mutants showed enhanced in vitro ADCC performance compared to their fucosylated counterparts, with the defucosylated WT antibodies displaying the highest overall ADCC activity, regardless of sialic acid substitution. Moreover, the FcγRIIIA receptor binding by antibodies did not always correspond directly with ADCC result. This study demonstrates that glycoengineering and protein engineering can both promote and inhibit antibody effector functions and represent practical approaches for varying glycan composition and functionalities during antibody development.     

Interferon acts directly on human B lymphocytes to modulate immunoglobulin synthesis

At different times of exposure, interferon (IFN) enhanced and suppressed pokeweed mitogen- (PWM) induced IgG synthesis by human peripheral blood lymphocytes (PBL). Pretreatment of PBL and IFN frequently increased antibody production by more than 100% when compared with that by untreated PBL. Results of experiments in which PBL were separated into T and B subpopulations indicated that IFN preparations acted directly on B cells. Thus, mixtures of IFN-treated B cells and untreated T cells from 5 of 7 persons tested produced 81% to 500% more IgG than untreated, matched control cells. However, IFN-treated monocytes mixed with untreated B and T cells or IFN-treated T cells mixed with untreated B cells failed to enhance IgG production significantly in similar assays. In contrast to the pretreatment protocol, when IFN was present in the incubation mixture throughout the PWM assay, IgG production decreased. Sephadex chromatography of the IFN and tests of the resulting fractions indicated that the IgG production-enhancing activity was located in the fraction carrying the antiviral activity.     

Ghrelin acts on the dorsal vagal complex to stimulate pancreatic protein secretion

Ghrelin receptors are present in the central nervous system. We hypothesized that ghrelin released from the stomach acts as an endocrine substance and stimulates brain stem vagovagal circuitry to evoke pancreatic secretion. In an in vivo anesthetized rat model, an intravenous infusion of ghrelin at doses of 5, 10, and 25 nmol increased pancreatic protein secretion from a basal level of 125 +/- 6 to 186 +/- 8, 295 +/- 12, and 356 +/- 11 mg/h, respectively. Pretreatment with atropine or hexamethonium or an acute vagotomy, but not a perivagal application of capsaicin, completely abolished pancreatic protein secretion responses to ghrelin. In conscious rats, an intravenous infusion of ghrelin at a dose of 10 nmol resulted in a 2.2-fold increase in pancreatic protein secretion over basal volume. Selective ablation of the area postrema abolished pancreatic protein secretion stimulated by intravenous infusion of ghrelin but did not alter the increase in pancreatic protein secretion evoked by diversion of bile-pancreatic juice. Immunohistochemical staining showed a marked increase in the number of c-Fos-expressing neurons in the area postrema, nucleus of the solitary tract, and dorsal motor nucleus of the vagus after an intravenous infusion of ghrelin in sham-lesioned rats; selective ablation of the area postrema eliminated this increase. In conclusion, ghrelin stimulates pancreatic secretion via a vagal cholinergic efferent pathway. Circulating ghrelin gains access to the brain stem vagovagal circuitry via the area postrema, which represents the primary target on which peripheral ghrelin may act as an endocrine substance to stimulate pancreatic secretion.     

Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA

Pseudouridine synthases catalyze the isomerization of uridine to pseudouridine (Psi) in rRNA and tRNA. The pseudouridine synthase RluF from Escherichia coli (E.C. 4.2.1.70) modifies U2604 in 23S rRNA, and belongs to a large family of pseudouridine synthases present in all kingdoms of life. Here we report the domain architecture and crystal structure of the catalytic domain of E.coli RluF at 2.6A resolution. Limited proteolysis, mass spectrometry and N-terminal sequencing indicate that RluF has a distinct domain architecture, with the catalytic domain flanked at the N and C termini by additional domains connected to it by flexible linkers. The structure of the catalytic domain of RluF is similar to those of RsuA and TruB. RluF is a member of the RsuA sequence family of Psi-synthases, along with RluB and RluE. Structural comparison of RluF with its closest structural homologues, RsuA and TruB, suggests possible functional roles for the N-terminal and C-terminal domains of RluF.     

Met acts on Mdm2 via mTOR to signal cell survival during development

Coordination of cell death and survival is crucial during embryogenesis and adulthood, and alteration of this balance can result in degeneration or cancer. Growth factor receptors such as Met can activate phosphatidyl-inositol-3' kinase (PI3K), a major intracellular mediator of growth and survival. PI3K can then antagonize p53-triggered cell death, but the underlying mechanisms are not fully understood. We used genetic and pharmacological approaches to uncover Met-triggered signaling pathways that regulate hepatocyte survival during embryogenesis. Here, we show that PI3K acts via mTOR (Frap1) to regulate p53 activity both in vitro and in vivo. mTOR inhibits p53 by promoting the translation of Mdm2, a negative regulator of p53. We also demonstrate that the PI3K effector Akt is required for Met-triggered Mdm2 upregulation, in addition to being necessary for the nuclear translocation of Mdm2. Inhibition of either mTOR or Mdm2 is sufficient to block cell survival induced by Hgf-Met in vitro. Moreover, in vivo inhibition of mTOR downregulates Mdm2 protein levels and induces p53-dependent apoptosis. Our studies identify a novel mechanism for Met-triggered cell survival during embryogenesis, involving translational regulation of Mdm2 by mTOR. Moreover, they reinforce mTOR as a potential drug target in cancer.