Plant D-2-hydroxyglutarate dehydrogenase participates in the catabolism of lysine especially during senescence

D-2-Hydroxyglutarate dehydrogenase (D-2HGDH) catalyzes the specific and efficient oxidation of D-2-hydroxyglutarate (D-2HG) to 2-oxoglutarate using FAD as a cofactor. In this work, we demonstrate that D-2HGDH localizes to plant mitochondria and that its expression increases gradually during developmental and dark-induced senescence in Arabidopsis thaliana, indicating an enhanced demand of respiration of alternative substrates through this enzymatic system under these conditions. Using loss-of-function mutants in D-2HGDH (d2hgdh1) and stable isotope dilution LC-MS/MS, we found that the D-isomer of 2HG accumulated in leaves of d2hgdh1 during both forms of carbon starvation. In addition to this, d2hgdh1 presented enhanced levels of most TCA cycle intermediates and free amino acids. In contrast to the deleterious effects caused by a deficiency in D-2HGDH in humans, d2hgdh1 and overexpressing lines of D-2HGDH showed normal developmental and senescence phenotypes, indicating a mild role of D-2HGDH in the tested conditions. Moreover, metabolic fingerprinting of leaves of plants grown in media supplemented with putative precursors indicated that D-2HG most probably originates during the catabolism of lysine. Finally, the L-isomer of 2HG was also detected in leaf extracts, indicating that both chiral forms of 2HG participate in plant metabolism.     

The natural frequency of the foot-surface cushion during the stance phase of running

Researchers have reported on the stiffness of running in holistic terms, i.e. for the structures that are undergoing deformation as a whole rather than in terms of specific locations. This study aimed to estimate both the natural frequency and the viscous damping coefficient of the human foot-surface cushion, during the period between the heel strike and the mid-stance phase of running, using a purposely developed one degree-of-freedom inverted pendulum state space model of the leg. The model, which was validated via a comparison of measured and estimated ground reaction forces, incorporated a novel use of linearized and extended Kalman filter estimators. Investigation of the effect of variation of the natural frequency and/or the damping of the cushioning mechanism during running, using the said model, revealed the natural frequency of running on said foot-surface cushion, during the stance phase, to lie between 5 and 11 Hz. The "extended Kalman filter (EKF)" approach, that was used here for the first time to directly apply measured ground forces, may be widely applicable to the identification process of combined estimation of both unknown physiological state and mechanical characteristics of the environment in an inverse dynamic model.     

Taxonomic versus allometric constraints on non‐linear interaction strengths

Recently, the importance of body mass and allometric scaling for the structure and dynamics of ecological networks has been highlighted in several ground‐breaking studies. However, advances in the understanding of generalities across ecosystem types are impeded to a considerable extent by a methodological dichotomy contrasting a considerable portion of marine ecology on the one hand opposite to traditional community ecology on the other hand. Many marine ecologists are bound to the taxonomy‐neglecting size spectrum approach when describing and analysing community patterns. In contrast, the mindset of the other school is focused on taxonomies according to the Linnean system at the cost of obscuring information due to applying species or population averages of body masses and other traits. Following other pioneering studies, we addressed this lingering gap, and studied non‐linear interaction strengths (i.e. functional responses) between two taxonomically‐distinct terrestrial arthropod predators (centipedes and spiders) of varying individual body masses and their prey. We fitted three non‐linear functional response models to the data: (1) a taxonomic model not accounting for variance in body masses amongst predator individuals, (2) an allometric model ignoring taxonomic differences between predator individuals, and (3) a combined model including body mass and taxonomic effects. Ranked according to their AICs, the combined model performs better than the allometric model, which provides a superior fit to the data than the taxonomic model. These results strongly indicate that the body masses of predator and prey individuals were responsible for most of the variation in non‐linear interaction strengths. Taxonomy explained some specific patterns in allometric exponents between groups and revealed mechanistic insights in predation efficiencies. Reconciling quantitative allometric models as employed by the marine size‐spectrum approach with taxonomic information may thus yield quantitative results that are generalized across ecosystem types and taxonomic groups. Using these quantitative models as novel null models should also strengthen subsequent taxonomic analyses.     

The Bantu expansion revisited: a new analysis of Y chromosome variation in Central Western Africa

The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3-5kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of interpopulation genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.     

Cutting edge: transgenic expression of human MUC1 in IL-10-/- mice accelerates inflammatory bowel disease and progression to colon cancer

Epithelial cell MUC1 is aberrantly expressed on human epithelial adenocarcinomas where it functions as a regulator of immune responses and an oncogene. Normally expressed at low levels in healthy colonic epithelium, MUC1 was reported to be overexpressed in human inflammatory bowel disease (IBD) and thus may be expected to play an important role in regulating chronic inflammation and its progression to colitis-associated colon cancer. Studies in the immunobiology and pathology of IBD and colitis-associated colon cancer have been done in various mouse models but none could properly address the role of MUC1 due to low homology between the mouse and the human molecule. We report that IL-10(-/-) mice, a widely accepted mouse model of IBD, crossed to human MUC1-transgenic mice, develop MUC1(+) IBD characterized by an earlier age of onset, higher inflammation scores, and a much higher incidence and number of colon cancers compared with IL-10(-/-) mice.     

Physiologically regulated transgenic ABCA1 does not reduce amyloid burden or amyloid-beta peptide levels in vivo

ABCA1-deficient mice have low levels of poorly lipidated apolipoprotein E (apoE) and exhibit increased amyloid load. To test whether excess ABCA1 protects from amyloid deposition, we crossed APP/PS1 mice to ABCA1 bacterial artificial chromosome (BAC) transgenic mice. Compared with wild-type animals, the ABCA1 BAC led to a 50% increase in cortical ABCA1 protein and a 15% increase in apoE abundance, demonstrating that this BAC supports modest ABCA1 overexpression in brain. However, this was observed only in animals that do not deposit amyloid. Comparison of ABCA1/APP/PS1 mice with APP/PS1 controls revealed no differences in levels of brain ABCA1 protein, amyloid, Abeta, or apoE, despite clear retention of ABCA1 overexpression in the livers of these animals. To further investigate ABCA1 expression in the amyloid-containing brain, we then compared ABCA1 mRNA and protein levels in young and aged cortex and cerebellum of APP/PS1 and ABCA1/APP/PS1 animals. Compared with APP/PS1 controls, aged ABCA1/APP/PS1 mice exhibited increased ABCA1 mRNA, but not protein, selectively in cortex. Additionally, ABCA1 mRNA levels were not increased before amyloid deposition but were induced only in the presence of extensive Abeta and amyloid levels. These data suggest that an induction of ABCA1 expression may be associated with late-stage Alzheimer's neuropathology.     

Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO

Plasmodium falciparum is the causative agent of the most severe type of malaria, a life-threatening disease affecting the lives of over three billion people. Factors like widespread resistance against available drugs and absence of an effective vaccine are seriously compounding control of the malaria parasite. Thus, there is an urgent need for the identification and validation of new drug targets. The enzymes of the polyamine biosynthesis pathway have been suggested as possible targets for the treatment of malaria. One of these enzymes is spermidine synthase (SPDS, putrescine aminopropyltransferase), which catalyzes the transfer of an aminopropyl moiety from decarboxylated S-adenosylmethionine (dcAdoMet) to putrescine, leading to the formation of spermidine and 5'-methylthioadenosine. Here we present the three-dimensional structure of P. falciparum spermidine synthase (pfSPDS) in apo form, in complex with dcAdoMet and two inhibitors, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and trans-4-methylcyclohexylamine (4MCHA). The results show that binding of dcAdoMet to pfSPDS stabilizes the conformation of the flexible gatekeeper loop of the enzyme and affects the conformation of the active-site amino acid residues, preparing the protein for binding of the second substrate. The complexes of AdoDATO and 4MCHA with pfSPDS reveal the mode of interactions of these compounds with the enzyme. While AdoDATO essentially fills the entire active-site pocket, 4MCHA only occupies part of it, which suggests that simple modifications of this compound may yield more potent inhibitors of pfSPDS.     

Heparanase enhances syndecan-1 shedding: a novel mechanism for stimulation of tumor growth and metastasis

When shed from the cell surface, the heparan sulfate proteoglycan syndecan-1 can facilitate the growth, angiogenesis, and metastasis of tumors. Here we report that tumor cell expression of heparanase, an enzyme known to be a potent promoter of tumor progression and metastasis, regulates both the level and location of syndecan-1 within the tumor microenvironment by enhancing its synthesis and subsequent shedding from the tumor cell surface. Heparanase regulation of syndecan-1 is detected in both human myeloma and breast cancer cell lines. This regulation requires the presence of active enzyme, because mutated forms of heparanase lacking heparan sulfate-degrading activity failed to influence syndecan-1 expression or shedding. Removal of heparan sulfate from the cell surface using bacterial heparitinase dramatically accelerated syndecan-1 shedding, suggesting that the effects of heparanase on syndecan-1 expression by tumor cells may be due, at least in part, to enzymatic removal or reduction in the size of heparan sulfate chains. Animals bearing tumors formed from cells expressing high levels of heparanase or animals transgenic for heparanase expression exhibited elevated levels of serum syndecan-1 as compared with controls, indicating that heparanase regulation of syndecan-1 expression and shedding can occur in vivo and impact cancer progression and perhaps other pathological states. These results reveal a new mechanism by which heparanase promotes an aggressive tumor phenotype and suggests that heparanase and syndecan-1 act synergistically to fine tune the tumor microenvironment and ensure robust tumor growth.     

Novel conantokins from Conus parius venom are specific antagonists of N-methyl-D-aspartate receptors

We report the discovery and characterization of three conantokin peptides from the venom of Conus parius. Each peptide (conantokin-Pr1, -Pr2, and -Pr3) contains 19 amino acids with three gamma-carboxyglutamate (Gla) residues, a post-translationally modified amino acid characteristic of conantokins. The new peptides contain several amino acid residues that differ from previous conantokin consensus sequences. Notably, the new conantokins lack Gla at the 3rd position from the N terminus, where the Gla residue is replaced by either aspartate or by another post-translationally modified residue, 4-trans-hydroxyproline. Conantokin-Pr3 is the first conantokin peptide to have three different post-translational modifications. Conantokins-Pr1 and -Pr2 adopt alpha-helical conformations in the presence of divalent cations (Mg2+ and Ca2+) but are generally unstructured in the absence of divalent cations. Conantokin-Pr3 adopts an alpha-helical conformation even in the absence of divalent cations. Like other conantokins, the new peptides induced sleep in young mice and hyperactivity in older mice upon intracranial injection. Electrophysiological assays confirmed that conantokins-Pr1, -Pr2, and -Pr3 are N-methyl-d-aspartate (NMDA) receptor antagonists, with highest potency for NR2B-containing NMDA receptors. Conantokin-Pr3 demonstrated approximately 10-fold selectivity for NR2B-containing NMDA receptors. However, conantokin-Pr2 showed minimal differences in potency between NR2B and NR2D. Conantokins-Pr1, -Pr2, and -Pr3 all demonstrated high specificity of block for NMDA receptors, when tested against various ligand-gated ion channels. Conus parius conantokins allow for a better definition of structural and functional features of conantokins as ligands targeting NMDA receptors.