L-lactate metabolism in potato tuber mitochondria

We investigated the metabolism of L-lactate in mitochondria isolated from potato tubers grown and saved after harvest in the absence of any chemical agents. Immunologic analysis by western blot using goat polyclonal anti-lactate dehydrogenase showed the existence of a mitochondrial lactate dehydrogenase, the activity of which could be measured photometrically only in mitochondria solubilized with Triton X-100. The addition of L-lactate to potato tuber mitochondria caused: (a) a minor reduction of intramitochondrial pyridine nucleotides, whose measured rate of change increased in the presence of the inhibitor of the alternative oxidase salicyl hydroxamic acid; (b) oxygen consumption not stimulated by ADP, but inhibited by salicyl hydroxamic acid; and (c) activation of the alternative oxidase as polarographically monitored in a manner prevented by oxamate, an L-lactate dehydrogenase inhibitor. Potato tuber mitochondria were shown to swell in isosmotic solutions of ammonium L-lactate in a stereospecific manner, thus showing that L-lactate enters mitochondria by a proton-compensated process. Externally added L-lactate caused the appearance of pyruvate outside mitochondria, thus contributing to the oxidation of extramitochondrial NADH. The rate of pyruvate efflux showed a sigmoidal dependence on L-lactate concentration and was inhibited by phenylsuccinate. Hence, potato tuber mitochondria possess a non-energy-competent L-lactate/pyruvate shuttle. We maintain, therefore, that mitochondrial metabolism of L-lactate plays a previously unsuspected role in the response of potato to hypoxic stress.     

Establishment and characterization of induced pluripotent stem cells (iPSCs) from central nervous system lupus erythematosus

Involvement of the central nervous system (CNS) is an uncommon feature in systemic lupus erythematosus (SLE), making diagnosis rather difficult and challenging due to the poor specificity of neuropathic symptoms and neurological symptoms. In this work, we used human‐induced pluripotent stem cells (hiPSCs) derived from CNS‐SLE patient, with the aim to dissect the molecular insights underlying the disease by gene expression analysis and modulation of implicated pathways. CNS‐SLE‐derived hiPSCs allowed us to provide evidence of Erk and Akt pathways involvement and to identify a novel cohort of potential biomarkers, namely CHCHD2, IDO1, S100A10, EPHA4 and LEFTY1, never reported so far. We further extended the study analysing a panel of oxidative stress‐related miRNAs and demonstrated, under normal or stress conditions, a strong dysregulation of several miRNAs in CNS‐SLE‐derived compared to control hiPSCs. In conclusion, we provide evidence that iPSCs reprogrammed from CNS‐SLE patient are a powerful useful tool to investigate the molecular mechanisms underlying the disease and to eventually develop innovative therapeutic approaches.     

Plant and animal transglutaminases: do similar functions imply similar structures?

In plants the post-translational modification of proteins by polyamines catalysed by transglutaminases has been studied since 1987; it was identified by the production of glutamyl-polyamine derivatives, biochemical features, recognition by animal antibodies and modification of typical animal substrates. Transglutaminases are widespread in all plant organs and cell compartments studied until now, chloroplast being the most studied. Substrates are: photosynthetic complexes and Rubisco in chloroplasts, cytoskeleton and cell wall proteins. Roles either specific of plants or in common with animals are related to photosynthesis, fertilisation, stresses, senescence and programmed cell death, showing that the catalytic function is conserved across the kingdoms. AtPng1p, the first plant transglutaminase sequenced shows undetectable sequence homology to the animal enzymes, except for the catalytic triad. It is, however, endowed with a calcium-dependent activity that allowed us to build a three-dimensional model adopting as a template the animal tranglutaminase 2.     

Carbon and nitrogen stable isotopic inventory of the most abundant demersal fish captured by benthic gears in southwestern Iceland (North Atlantic)

Stable isotopes (δ¹³C and δ¹⁵N) were used to examine the origin of organic matter for the most representative demersal species of the SW Icelandic fishery, accounting for over 70% of landings of those species in the North Atlantic. Samples were collected during a 2-week period in early September 2004 from landings and directly during fishing cruises. Stable isotopes showed that particulate organic matter and sedimentary organic matter were at the base of the food web and appeared to fill two different compartments: the pelagic and the benthic. The pelagic realm was composed of only capelin and sandeel; krill and redfish occupied an intermediate position between pelagic and benthic realms; while anglerfish, haddock, cod and ling resulted as the true demersal species while tusk, rays and plaice were strongly linked to the benthic habitat.     

Ab initio and homology based prediction of protein domains by recursive neural networks

Background  

Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures.     

Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

Background

Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure.

Results

We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that C _α trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets using a pre-CASP7 PDB, and find that both predictors are state-of-the-art, with the template-based one far outperforming the best CASP7 systems if templates with sequence identity to the query of 10% or better are available. Although this is not the main focus of this paper we also report on reconstructions of C _α traces based on both ab initio and template-based 4-class map predictions, showing that the latter are generally more accurate even when homology is dubious.

Conclusion

Accurate predictions of multi-class maps may provide valuable constraints for improved ab initio and template-based prediction of protein structures, naturally incorporate multiple templates, and yield state-of-the-art binary maps. Predictions of protein structures and 8 Å contact maps based on the multi-class distance map predictors described in this paper are freely available to academic users at the url http://distill.ucd.ie/.     

Process-level controls on CO<Subscript>2</Subscript> fluxes from a seasonally snow-covered subalpine meadow soil,Niwot Ridge,Colorado

Fluxes of CO₂ during the snow-covered season contribute to annual carbon budgets, but our understanding of the mechanisms controlling the seasonal pattern and magnitude of carbon emissions in seasonally snow-covered areas is still developing. In a subalpine meadow on Niwot Ridge, Colorado, soil CO₂ fluxes were quantified with the gradient method through the snowpack in winter 2006 and 2007 and with chamber measurements during summer 2007. The CO₂ fluxes of 0.71 μmol m⁻² s⁻¹ in 2006 and 0.86 μmol m⁻² s⁻¹ in 2007 are among the highest reported for snow-covered ecosystems in the literature. These fluxes resulted in 156 and 189 g C m⁻² emitted over the winter, ~30% of the annual soil CO₂ efflux at this site. In general, the CO₂ flux increased during the winter as soil moisture increased. A conceptual model was developed with distinct snow cover zones to describe this as well as the three other reported temporal patterns in CO₂ flux from seasonally snow-covered soils. As snow depth and duration increase, the factor controlling the CO₂ flux shifts from freeze–thaw cycles (zone I) to soil temperature (zone II) to soil moisture (zone III) to carbon availability (zone IV). The temporal pattern in CO₂ flux in each zone changes from periodic pulses of CO₂ during thaw events (zone I), to CO₂ fluxes reaching a minimum when soil temperatures are lowest in mid-winter (zone II), to CO₂ fluxes increasing gradually as soil moisture increases (zone III), to CO₂ fluxes decreasing as available carbon is consumed. This model predicts that interannual variability in snow cover or directional shifts in climate may result in dramatically different seasonal patterns of CO₂ flux from seasonally snow-covered soils.     

A family of polyamino phenolic macrocyclic ligands. Acid-base and coordination properties towards Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Pb(II) ions

The acid-base and coordination properties towards Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Pb(II) of four polyamino-phenol macrocycles 15-hydroxy-3,6,9-triazabicyclo[9.3.1]pentadeca-11,13,1¹⁵-triene L1, 18-hydroxy-3,6,9,12-tetraazabicyclo[12.3.1]octadeca-14,16,1¹⁸-triene L2, 21-hydroxy-3,6,9,12,15-pentaazabicyclo[15.3.1]enaicosa-17,19,1²¹-triene L3 and 24-hydroxy-3,6,9,12,15,18-hexaazabicyclo[18.3.1]tetraicosa-20,22,1²⁴-triene L4 are reported. The protonation and stability constants were determined by means of potentiometric measurements in 0.15 mol dm⁻³ NMe₄Cl aqueous solution at 298.1 K. L1 forms highly unsaturated Co(II), Cu(II), Zn(II) and Cd(II) mononuclear complexes that are prone to give dimeric dinuclear species with [(MH₋₁L1)₂]²⁺ stoichiometry, in solution. L2 forms stable Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Pb(II) mononuclear complexes that can coordinate external species as OH⁻ anion, giving hydroxylated complexes at alkaline pH. L3 forms stable Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Pb(II) mononuclear complexes and Co(II), Ni(II), Cu(II) and Zn(II) dinuclear [M₂H₋₁L3]³⁺ species. L4 forms stable mono- and dinuclear Co(II), Cu(II), Zn(II) and Cd(II) complexes, but only mononuclear species with Pb(II). The effect of macrocyclic size is considered in the discussion of results.     

Aptian dinosaur footprints from the Apulian platform (Bisceglie,Southern Italy) in the framework of periadriatic ichnosites

New dinosaur tracks have been found near Bisceglie (Bari, Apulia), on loose blocks ascribed to the Corato Member (late Bedoulian to early Gargasian) of the Calcare di Bari Fm. The material consists of isolated footprints as well as of short trackways of quadrupedal and bipedal dinosaurs. The new tracksite has yielded a quite differentiated dinosaur ichnocoenosis, including theropod, sauropod, thyreophoran and ornithopod footprints.The discovery of early Aptian dinosaur footprints in the limestone of the carbonate platform of southern Italy gives new insights on dinosaur distribution, and new palaeontological constraints for the palaeogeographic reconstruction of the Mediterranean Tethys during the Cretaceous. The analysis of this and others ichnosites of the periadriatic carbonate platforms, gives evidence of repeated emersions and of widespread land-vertebrates dwelling. The characteristics of the associations suggest that the trackmakers did not constitute a real coevolved association but the occasional co-occurrence of taxa after migration.The results emphasize the need of both structural and environmental continuity and walking ways between a southern continent and the periadriatic carbonate platforms during the Early Cretaceous.     

In silico pKa Prediction and ADME Profiling

Improving the ADME profile of drug candidates is a critical step in lead optimization, and because pK_a affects most ADME properties such as lipophilicity, solubility, and metabolism, it is extremely advantageous to predict pK_a in order to guide the design of new compounds. However, accurately (<0.5 log units) predicting pK_a by empirical methods can be challenging especially for novel series, because of lack of knowledge on determinants of pK_a (steric effects, ring effects, H‐bonding, etc.), and because of limited experimental data on the effects of specific chemical groups on the ionization of an atom. To address these issues, we recently developed the computational package MoKa, which integrates graphical and command line tools designed for computational and medicinal chemists to predict the pK_a values of organic compounds. Here, we present the major issues considered when we developed MoKa, such as the accurate selection of training data, the fundamentals of the methodology (which has also been extended to predict protein pK_a), the treatment of multiprotic compounds, and the selection of the dominant tautomer for the calculation. Last, we illustrate some specific applications of MoKa to predict solubility, lipophilicity, and metabolism.