Pattern and pace of morphological change due to variable human impact: the case of Japanese macaques

Primates - Human impact influences morphological variation in animals, as documented in many captive and domestic animal populations. However, there are different levels of human impact, and their...     

Enzymes involved in phthalate degradation in sulphate-reducing bacteria

The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o-phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here, we demonstrate a previously overseen growth of the δ-proteobacterium Desulfosarcina cetonica with phthalate/sulphate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short-lived phthaloyl-CoA by an ATP-dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl-CoA by an UbiD-like phthaloyl-CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulphate-reducing Desulfobacula toluolica, strain NaphS2, and other δ-proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl-CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl-CoA, the possibly most unstable CoA ester in biology.     

Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers

Computation of LOD scores is a valuable tool for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However, computation of exact multipoint likelihoods of large inbred pedigrees with extensive missing data is often beyond the capabilities of a single computer. We present a distributed system called "SUPERLINK-ONLINE," for the computation of multipoint LOD scores of large inbred pedigrees. It achieves high performance via the efficient parallelization of the algorithms in SUPERLINK, a state-of-the-art serial program for these tasks, and through the use of the idle cycles of thousands of personal computers. The main algorithmic challenge has been to efficiently split a large task for distributed execution in a highly dynamic, nondedicated running environment. Notably, the system is available online, which allows computationally intensive analyses to be performed with no need for either the installation of software or the maintenance of a complicated distributed environment. As the system was being developed, it was extensively tested by collaborating medical centers worldwide on a variety of real data sets, some of which are presented in this article.     

The T cell response to IL-10 alters cellular dynamics and paradoxically promotes central nervous system autoimmunity

IL-10 is a critical anti-inflammatory cytokine, the deficiency of which leads to spontaneous autoimmunity. However, therapeutically administered or ectopically expressed IL-10 can either suppress or promote disease. Distinct lineage-specific activities may explain the contradictory effects of IL-10. To dissect the T cell-specific response to IL-10 during organ-specific autoimmunity, we generated mice with a selective deletion of IL-10Rα in T cells and analyzed its effects in an autoimmune model, experimental allergic encephalomyelitis (EAE). Surprisingly, the T cell response to IL-10 increased EAE severity. This did not result from altered T cell functional potential; T cell cytokine profile was preserved. IL-10 also diminished the proliferation of T cells in situ within the target organ, an effect that would be expected to restrain disease. However, IL-10 acted cell autonomously to sustain the autoreactive T cells essential for immunopathogenesis, promoting their accumulation and distorting the regulatory and effector T cell balance. Indeed, in chimeric mice and after adoptive transfer, wild type T cells showed a competitive advantage over cells deficient in IL-10Rα. Therefore, T cell specific actions of IL-10 can support autoimmune inflammation, and this appears to result from an overall increase in the long term fitness of pathologic T cells. Lineage-restricted, disease-promoting activities of IL-10 should be considered in the therapeutic manipulation of the IL-10 pathway.     

Formamidopyrimidine DNA glycosylase in the yeast Saccharomyces cerevisiae.

A DNA glycosylase that excises, 2,6-diamino-4-hydroxy-5N-methylformamidopyrimidine (Fapy) from double stranded DNA has been purified 28,570-fold from the yeast Saccharomyces cerevisiae. Gel filtration chromatography shows that yeast Fapy DNA glycosylase has a molecular weight of about 40 kDa. The Fapy DNA glycosylase is active in the presence of EDTA, but is completely inhibited by 0.2 M KCl. Yeast Fapy DNA glycosylase does not excise N7-methylguanine, N3-methyladenine or uracil. A repair enzyme for 7,8-dihydro-8-oxoguanine (8-OxoG) co-purifies with the Fapy DNA glycosylase. This repair activity causes strand cleavage at the site of 8-OxoG in DNA duplexes. The highest rate of incision of the 8-OxoG-containing strand was observed for duplexes where 8-OxoG was opposite guanine. The mode of incision at 8-OxoG was not established yet. The results however suggest that the Fapy- and 8-OxoG-repair activities are associated with a single protein.     

T cell receptor gene segment utilization by HLA-DR1-alloreactive T cell clones.

Transplantation of histoincompatible tissues leads to allograft rejection, which involves recognition of allogeneic MHC molecules by Ag-specific receptors expressed on T cells. The interaction of these molecules is highly specific yet poorly understood. We have investigated the relationship between TCR gene utilization and allo-MHC restriction patterns by using a one-way polymerase chain reaction to amplify the alpha- and beta-chain mRNA from a panel of 10 HLA-DR1-alloreactive T lymphocyte clones. Two previously unreported V alpha and five J alpha gene sequences were obtained. Although a few V alpha, V beta, and J alpha genes were utilized more than once, no correlation between TCR gene usage and DR1 alloreactivity was identified. At the sequence level, the presumed TCR alpha- and beta-chain CDR1 and CDR2 regions displayed limited diversity, whereas the CDR3 or junctional sequences were highly variable. Although most TCR probably interact with subtly different surface features of the DR1 alloantigen, we predict that TCR with similar CDR1 and CDR2 sequences would contact essentially identical regions of the DR1 molecule. The lack of sequence conservation in the junctional regions suggests that different endogenous peptides also may be recognized. Thus, alloreactive T cells may recognize not only allogeneic MHC molecules but perhaps also bound endogenous peptides.     

Vascular tissue engineering: the next generation

It is the ultimate goal of tissue engineering: an autologous tissue engineered vascular graft (TEVG) that is immunologically compatible, nonthrombogenic, and can grow and remodel. Currently, native vessels are the preferred vascular conduit for procedures such as coronary artery bypass (CABG) or peripheral bypass surgery. However, in many cases these are damaged, have already been harvested, or are simply unusable. The use of synthetic conduits is severely limited in smaller diameter vessels due to increased incidence of thrombosis, infection, and graft failure. Current research has therefore energetically pursued the development of a TEVG that can incorporate into a patient's circulatory system, mimic the vasoreactivity and biomechanics of the native vasculature, and maintain long-term patency.     

Heteromeric AtKC1��AKT1 Channels in Arabidopsis Roots Facilitate Growth under K+-limiting Conditions

Plant growth and development is driven by osmotic processes. Potassium represents the major osmotically active cation in plants cells. The uptake of this inorganic osmolyte from the soil in Arabidopsis involves a root K⁺ uptake module consisting of the two K⁺ channel α-subunits, AKT1 and AtKC1. AKT1-mediated potassium absorption from K⁺-depleted soil was shown to depend on the calcium-sensing proteins CBL1/9 and their interacting kinase CIPK23. Here we show that upon activation by the CBL·CIPK complex in low external potassium homomeric AKT1 channels open at voltages positive of E_K, a condition resulting in cellular K⁺ leakage. Although at submillimolar external potassium an intrinsic K⁺ sensor reduces AKT1 channel cord conductance, loss of cytosolic potassium is not completely abolished under these conditions. Depending on channel activity and the actual potassium gradients, this channel-mediated K⁺ loss results in impaired plant growth in the atkc1 mutant. Incorporation of the AtKC1 subunit into the channel complex, however, modulates the properties of the K⁺ uptake module to prevent K⁺ loss. Upon assembly of AKT1 and AtKC1, the activation threshold of the root inward rectifier voltage gate is shifted negative by approximately −70 mV. Additionally, the channel conductance gains a hypersensitive K⁺ dependence. Together, these two processes appear to represent a safety strategy preventing K⁺ loss through the uptake channels under physiological conditions. Similar growth retardation phenotypes of akt1 and atkc1 loss-of-function mutants in response to limiting K⁺ supply further support such functional interdependence of AKT1 and AtKC1. Taken together, these findings suggest an essential role of AtKC1-like subunits for root K⁺ uptake and K⁺ homeostasis when plants experience conditions of K⁺ limitation.Fundamental plant functions such as control of the membrane potential, osmo-regulation, and turgor-driven growth and movements are based on the availability to gain high cellular potassium concentrations (1). The absorption of this inorganic osmolyte from the soil by the root therefore represents a pivotal process for plant life. Classical experiments by Epstein et al. in 1963 (2) described K⁺ root uptake as a biphasic process mediated by two uptake mechanisms: high affinity potassium transport with apparent affinities of ∼20 μm and a low affinity transport system with K_m values in the millimolar range. During the last decades several molecular components of potassium transport systems have been identified and functionally characterized in plants (3, 4). Mutant analyses, heterologous expression, as well as radiotracer uptake experiments characterized the K⁺ channels AKT1·AtKC1 and members of the HAK·KT·KUP family as major components of the Arabidopsis thaliana root-localized potassium transport system (5–9). In this study we focused on AKT1 and AtKC1, members of the Arabidopsis Shaker-like K⁺ channel family. AKT1 is a voltage-dependent inward-rectifying K⁺ channel mediating potassium uptake over a wide range of external potassium concentrations (10–15). Root cells of the akt1-1 loss-of-function mutant completely lack inward rectifying K⁺ currents (12). As a consequence the growth of akt1-1 seedlings is strongly impaired on low potassium medium (100 μm and less) (11, 12, 15). Rescue of yeast growth on 20 μm K⁺ and patch clamp experiments (16, 17) directly demonstrated that plant inward rectifying K⁺ channels are capable of serving as high affinity potassium uptake transporters. AtKC1 shares its expression pattern with AKT1 (18–20). AtKC1 α-subunits, however, neither form functional channels in akt1-1 knock-out plants nor in heterologous expression systems. In contrast to root cells of akt1-1 loss of function mutants, root protoplasts of AtKC1 null mutants (atkc1-f) still exhibit inward rectifying potassium currents most likely derived from homomeric AKT1 tetramers (20). Inward K⁺ currents in this atkc1-f mutant were characterized by a more positive activation voltage. These data suggested that the AtKC1 α-subunits do not form K⁺ channels per se but modulate the properties of the AKT1·AtKC1 heterocomplex (20–22). Previously, two groups in their ground-breaking studies demonstrated that AKT1 is activated by the CBL²-interacting, serine/threonine kinase, CIPK23, particularly under low K⁺ conditions (23, 24). CIPK23 itself was shown to be activated by the two calcineurin B-like proteins, CBL1 and 9, acting in a Ca²⁺-dependent manner upstream of CIPK23 (25, 26). Genetic disruption of these elements resulted in transgenic plants exhibiting a phenotype comparable with that of the AKT1 loss of function mutant. This regulatory system, based on a calcium sensor, a protein kinase, and a K⁺ channel, was functionally reconstituted in Xenopus oocytes (23, 24, 27), suggesting that these elements are essential and sufficient to operate as a low K⁺-sensitive potassium uptake system. Here we report on the physiological properties of the heteromeric K⁺ uptake module formed by the predominant root potassium uptake channel subunits, AKT1 and AtKC1 and its regulating kinase complex, CBL1 and CIPK23. Our studies show that the physical interaction of the CBL1·CIPK23 complex is specific for AKT1 channels and does not involve the AtKC1 subunit. AKT1 possesses a K⁺ (absence) sensor affecting channel activity at submillimolar K⁺ concentrations by strongly reducing its maximal cord conductance. Despite this K⁺ sensor, upon activation, AKT1 homomeric channels were shown to represent a potassium leak at low external potassium concentrations. Integration of AtKC1 into the K⁺ uptake module, however, prevented potassium loss by modulating both the voltage sensor and conductance in the channel complex. Moreover, activation of the AKT1-like maize channel ZMK1 by CBL1·CIPK23 suggests a conserved interaction and regulation across monocot and dicotyledonous plant species. Our biophysical studies as well as growth assays with plant mutant lines lacking the respective channels underline that acquisition of potassium under limiting K⁺ conditions is mediated via the root AKT1·AtKC1 K⁺ uptake channel complex.