In vivo bicarbonate requirement for water oxidation by Photosystem II in the hypercarbonate-requiring cyanobacterium Arthrospira maxima

While the presence of inorganic carbon in the form of (bi)carbonate has been known to be important for activity of Photosystem II (PSII), the vast majority of studies on this "bicarbonate effect" have been limited to in vitro studies of isolated thylakoid membranes and PSII complexes. Here we report an in vivo requirement for bicarbonate that is both reversible and selective for this anion for efficient water oxidation activity in the hypercarbonate-requiring cyanobacterium Arthrospira (Spirulina) maxima, originally isolated from highly alkaline soda lakes. Using a non-invasive internal probe of PSII charge separation (variable fluorescence), primary electron acceptor (Q(A)(-)/Q(A)) reoxidation rate, and flash-induced oxygen yield, we report the largest reversible bicarbonate effect on PSII activity ever observed, which is due to the requirement for bicarbonate at the water-oxidizing complex. Temporal separation of this donor side bicarbonate requirement from a smaller effect of bicarbonate on the Q(A)(-) reoxidation rate was observed. We expect the atypical way in which Arthrospira manages intracellular pH, sodium, and inorganic carbon concentrations relative to other cyanobacteria is responsible for this strong in vivo bicarbonate requirement.     

Use of a cyanine dye as a probe for albumin and collagen in the extracellular matrix

The aim of this work was to develop a quick method for analysis of macromolecules of the extracellular matrix. Of great interest are soluble components of the extracellular matrix, in particular, carrier proteins, whose variation dynamics can characterize the studied tissue in its development, adult stage, and aging. We suggest the method of analysis of the extracellular matrix to reveal the presence of albumin and collagen by using an anionic cyanine dye as a spectral and fluorescence probe. The method was applied for the analysis of the human vitreous body in the course of its development. Albumin was detected by the appearance of the trans monomer absorption and fluorescence bands in the dye spectra, and collagen was detected by the absorption and fluorescence bands of J aggregates. Hyaluronic acid present in the vitreous body does not interfere with the results of the analysis. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis confirmed the presence of albumin in the vitreous body. We suppose that albumin as a protein carrying biologically active macromolecules plays an important role in the processes of differentiation and functional establishment of ocular tissues in the course of their prenatal development.     

In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures

The molecular basis of the tyrosine kinases binding specificity and drug resistance against cancer drugs Imatinib and Dasatinib is elucidated using Monte Carlo simulations of the inhibitor-receptor binding with the ensembles of protein kinase crystal structures. In silico proteomics analysis unravels mechanisms by which structural plasticity of the tyrosine kinases is linked with the conformational preferences of Imatinib and Dasatinib in achieving effective drug binding with a distinct spectrum of the tyrosine kinome. The differences in the inhibitor sensitivities to the ABL kinase mutants are rationalized based on variations in the binding free energy profiles with the conformational states of the ABL kinase. While Imatinib binding is highly sensitive to the activation state of the enzyme, the computed binding profile of Dasatinib is remarkably tolerant to the conformational state of ABL. A comparative analysis of the inhibitor binding profiles with the clinically important ABL kinase mutants has revealed an excellent agreement with the biochemical and proteomics data. We have found that conformational adaptability of the kinase inhibitors to structurally different conformational states of the tyrosine kinases may have pharmacological relevance in acquiring a specific array of potent activities and regulating a scope of the inhibitor resistance mutations. This study outlines a useful approach for understanding and predicting the molecular basis of the inhibitor sensitivity against potential kinase targets and drug resistance.     

Genes of the extinct Caucasian bison still roam the Białowieża Forest and are the source of genetic discrepances between Polish and Belarusian populations of the European bison,Bison bonasus

European bison (Bison bonasus) populations from both the Polish (PL) and the Belarusian (BY) sides of the Bia?owie?a Forest represent the Lowland genetic line (LB line) – progeny of the Lowland bison (Bison bonasus bonasus) that inhabited western, central, and south‐eastern Europe in historical times. During the species recovery, one of the founders was a descendant of the extinct Caucasian bison (Bison bonasus caucasicus) and its descendants formed the other genetic line – Lowland–Caucasian (LC). There have been justified suspicions that LB European bison in the former Soviet Union had undergone cross‐mating with the LC line. We performed a comparative genetic analyses on European bison from the BY and PL parts of the Bia?owie?a Forest, the LC line and extinct Caucasian bison, based on a set of 19 microsatellite markers and 1512 bovine single nucleotide polymorphism (SNP) markers, polymorphic in at least one of the studied populations. Although genetic variability (mean allele number and expected heterozygosity) for both populations were similar, the F_ST jack‐knifing and principal component analyses PCA revealed highly significant differences between PL and BY bison from the Bia?owie?a Forest. Examining DNA of the extinct Caucasian bison revealed that at least part of the genetic variants found in the BY, but not the PL, population were of Caucasian origin. The results indicate that the contemporary population of European bison from the BY part of the Bia?owie?a Forest should not be regarded as a LB line. The results also suggest that the actual global population size of the LB line European bison is only a half of its official status. Consideration of the presented results are crucial in determining management actions and policy decisions in order to conserve LB line bison within the Bia?owie?a Forest – its natural refuge. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 752–763.     

A new trap-jaw ant species of the genus <Emphasis Type="Italic">Odontomachus</Emphasis> (Hymenoptera: Formicidae: Ponerinae) from the Early Miocene (Burdigalian) of the Czech Republic

Odontomachus paleomyagra sp. nov. is described from the Early Miocene of the Most Basin (Czech Republic) on the basis of a single-winged female, representing one of the rare reports of fossil Odontomachini. The new species is separated easily from other trap-jaw ant species groups by differences in mandibular morphology (without denticles on the inner side) and distributional occurrence. The evolutionary and biogeographic history of the Odontomachini is briefly discussed.     

The animat: new frontiers in whole brain modeling

The researchers at Boston University (BU)'s Neuromorphics Laboratory, part of the National Science Foundation (NSF)-sponsored Center of Excellence for Learning in Education, Science, and Technology (CELEST), are working in collaboration with the engineers and scientists at Hewlett-Packard (HP) to implement neural models of intelligent processes for the next generation of dense, low-power, computer hardware that will use memristive technology to bring data closer to the processor where computation occurs. The HP and BU teams are jointly designing an optimal infrastructure, simulation, and software platform to build an artificial brain. The resulting Cog Ex Machina (Cog) software platform has been successfully used to implement a large-scale, multicomponent brain system that is able to simulate some key rat behavioral results in a virtual environment and has been applied to control robotic platforms as they learn to interact with their environment.     

Simulating molecular mechanisms of the MDM2-mediated regulatory interactions: a conformational selection model of the MDM2 lid dynamics

Diversity and complexity of MDM2 mechanisms govern its principal function as the cellular antagonist of the p53 tumor suppressor. Structural and biophysical studies have demonstrated that MDM2 binding could be regulated by the dynamics of a pseudo-substrate lid motif. However, these experiments and subsequent computational studies have produced conflicting mechanistic models of MDM2 function and dynamics. We propose a unifying conformational selection model that can reconcile experimental findings and reveal a fundamental role of the lid as a dynamic regulator of MDM2-mediated binding. In this work, structure, dynamics and energetics of apo-MDM2 are studied as a function of posttranslational modifications and length of the lid. We found that the dynamic equilibrium between "closed" and "semi-closed" lid forms may be a fundamental characteristic of MDM2 regulatory interactions, which can be modulated by phosphorylation, phosphomimetic mutation as well as by the lid size. Our results revealed that these factors may regulate p53-MDM2 binding by fine-tuning the thermodynamic equilibrium between preexisting conformational states of apo-MDM2. In agreement with NMR studies, the effect of phosphorylation on MDM2 interactions was more pronounced with the truncated lid variant that favored the thermodynamically dominant closed form. The phosphomimetic mutation S17D may alter the lid dynamics by shifting the thermodynamic equilibrium towards the ensemble of "semi-closed" conformations. The dominant "semi-closed" lid form and weakened dependence on the phosphorylation seen in simulations with the complete lid can provide a rationale for binding of small p53-based mimetics and inhibitors without a direct competition with the lid dynamics. The results suggested that a conformational selection model of preexisting MDM2 states may provide a robust theoretical framework for understanding MDM2 dynamics. Probing biological functions and mechanisms of MDM2 regulation would require further integration of computational and experimental studies and may help to guide drug design of novel anti-cancer therapeutics.     

An efficient method for transient gene expression in monocots applied to modify the Brachypodium distachyon cell wall

Background

Agrobacterium-mediated transformation is widely used to produce insertions into plant genomes. There are a number of well-developed Agrobacterium-mediated transformation methods for dicotyledonous plants, but there are few for monocotyledonous plants.

Methods

Three hydrolase genes were transiently expressed in Brachypodium distachyon plants using specially designed vectors that express the gene product of interest and target it to the plant cell wall. Expression of functional hydrolases in genotyped plants was confirmed using western blotting, activity assays, cell wall compositional analysis and digestibility tests.

Key Results

An efficient, new, Agrobacterium-mediated approach was developed for transient gene expression in the grass B. distachyon, using co-cultivation of mature seeds with bacterial cells. This method allows transformed tissues to be obtained rapidly, within 3–4 weeks after co-cultivation. Also, the plants carried transgenic tissue and maintained transgenic protein expression throughout plant maturation. The efficiency of transformation was estimated at around 5 % of initially co-cultivated seeds. Application of this approach to express three Aspergillus nidulans hydrolases in the Brachypodium cell wall successfully confirmed its utility and resulted in the expected expression of active microbial proteins and alterations of cell wall composition. Cell wall modifications caused by expression of A. nidulans α-arabinofuranosidase and α-galactosidase increased the biodegradability of plant biomass.

Conclusions

This newly developed approach is a quick and efficient technique for expressing genes of interest in Brachypodium plants, which express the gene product throughout development. In the future, this could be used for broad functional genomics studies of monocots and for biotechnological applications, such as plant biomass modification for biofuel production.     

Nucleotide- and nucleoside-converting ectoenzymes: Important modulators of purinergic signalling cascade

The involvement of extracellular nucleotides and adenosine in an array of cell-specific responses has long been known and appreciated, but the integrative view of purinergic signalling as a multistep coordinated cascade has emerged recently. Current models of nucleotide turnover include: (i) transient release of nanomolar concentrations of ATP and ADP; (ii) triggering of signalling events via a series of ligand-gated (P2X) and metabotropic (P2Y) receptors; (iii) nucleotide breakdown by membrane-bound and soluble nucleotidases, including the enzymes of ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase) family, ecto-nucleotide pyrophosphatase/phosphodiesterase (E-NPP) family, ecto-5'-nucleotidase/CD73, and alkaline phosphatases; (iv) interaction of the resulting adenosine with own nucleoside-selective receptors; and finally, (v) extracellular adenosine inactivation via adenosine deaminase and purine nucleoside phosphorylase reactions and/or nucleoside uptake by the cells. In contrast to traditional paradigms that focus on purine-inactivating mechanisms, it has now become clear that "classical" intracellular ATP-regenerating enzymes, adenylate kinase, nucleoside diphosphate (NDP) kinase and ATP synthase can also be co-expressed on the cell surface. Furthermore, data on the ability of various cells to retain micromolar ATP levels in their pericellular space, as well as to release other related compounds (adenosine, UTP, dinucleotide polyphosphates and nucleotide sugars) gain another important insight into our understanding of mechanisms regulating a signalling cascade. This review summarizes recent advances in this rapidly evolving field, with particular emphasis on the nucleotide-releasing and purine-converting pathways in the vasculature.     

Conformational changes in the selectivity filter of the open-state KcsA channel: an energy minimization study

Potassium channels switch between closed and open conformations and selectively conduct K⁺ ions. There are at least two gates. The TM2 bundle at the intracellular site is the primary gate of KcsA, and rearrangements at the selectivity filter (SF) act as the second gate. The SF blocks ion flow via an inactivation process similar to C-type inactivation of voltage-gated K⁺ channels. We recently generated the open-state conformation of the KcsA channel. We found no major, possibly inactivating, structural changes in the SF associated with this massive inner-pore rearrangement, which suggests that the gates might act independently. Here we energy-minimize the open state of wild-type and mutant KcsA, validating in silico structures of energy-minimized SFs by comparison with crystallographic structures, and use these data to gain insight into how mutation, ion depletion, and K⁺ to Na⁺ substitution influence SF conformation. Both E71 or D80 protonations/mutations and the presence/absence of protein-buried water molecule(s) modify the H-bonding network stabilizing the P-loops, spawning numerous SF conformations. We find that the inactivated state corresponds to conformations with a partially unoccupied or an entirely empty SF. These structures, involving modifications in all four P-loops, are stabilized by H-bonds between amide H and carbonyl O atoms from adjacent P-loops, which block ion passage. The inner portions of the P-loops are more rigid than the outer parts. Changes are localized to the outer binding sites, with innermost site S4 persisting in the inactivated state. Strong binding by Na⁺ locally contracts the SF around Na⁺, releasing ligands that do not participate in Na⁺ coordination, and occluding the permeation pathway. K⁺ selectivity primarily appears to arise from the inability of the SF to completely dehydrate Na⁺ ions due to basic structural differences between liquid water and the “quasi-liquid” SF matrix.