Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S. cerevisiae, D. melanogaster, C. elegans, M. musculus, T. rubripes and H. sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P. falciparum sheds light on possible strategies in host-pathogen interactions.

Structural, magnetic and electrochemical investigation of novel binary Na2-x(Fe1-yMny)P2O7 (0 <= y <= 1) pyrophosphate compounds for rechargeable sodium-ion batteries

Pyrophosphate cathodes have been recently reported as a competent family of insertion compounds for sodium-ion batteries. In the current study, we have investigated the binary Na2 - x(Fe1 - yMny)P2O7 (0 <= y <= 1) pyrophosphate family, synthesized by the classical solid-state method. They form a continuous solid solution maintaining triclinic P-1 (#2) symmetry. The local structural coordination differs mainly by different degrees of Na site occupancy and preferential occupation of the Fe2 site by Mn. The structural and magnetic properties of these mixed-metal pyrophosphate phases have been studied. In each case, complete Fe3+/Fe2+ redox activity has been obtained centered at 3 V vs. Na. The Fe3+/Fe2+ redox process involves multiple steps between 2.5 and 3 V owing to Na-cation ordering during electrochemical cycling, which merge to form a broad single Fe3+/Fe2+ redox peak upon progressive Mn-doping. (C) 2014 Elsevier B.V. All rights reserved.

Oxygen-participated electrochemistry of new lithium-rich layered oxides Li3MRuO5 M = Mn, Fe)

We describe the synthesis, crystal structure and lithium deinsertion-insertion electrochemistry of two new lithium-rich layered oxides, Li3MRuO5 (M = Mn, Fe), related to rock salt based Li2MnO3 and LiCoO2. The Li3MnRuO5 oxide adopts a structure related to Li2MnO3 (C2/m) where Li and (Li0.2Mn0.4Ru0.4) layers alternate along the c-axis, while the Li3FeRuO5 oxide adopts a near-perfect LiCoO2 (R (3) over barm) structure where Li and (Li0.2Fe0.4Ru0.4) layers are stacked alternately. Magnetic measurements indicate for Li3MnRuO5 the presence of Mn3+ and low spin configuration for Ru4+ where the itinerant electrons occupy a pi*-band. The onset of a net maximum in the chi vs. T plot at 9.5 K and the negative value of the Weiss constant (theta) of -31.4 K indicate the presence of antiferromagnetic superexchange interactions according to different pathways. Lithium electrochemistry shows a similar behaviour for both oxides and related to the typical behaviour of Li-rich layered oxides where participation of oxide ions in the electrochemical processes is usually found. A long first charge process with capacities of 240 mA h g(-1) (2.3 Li per f.u.) and 144 mA h g(-1) (1.38 Li per f.u.) is observed for Li3MnRuO5 and Li3FeRuO5, respectively. An initial sloping region (OCV to ca. 4.1 V) is followed by a long plateau (ca. 4.3 V). Further discharge-charge cycling points to partial reversibility (ca. 160 mA h g(-1) and 45 mA h g(-1) for Mn and Fe, respectively). Nevertheless, just after a few cycles, cell failure is observed. X-ray photoelectron spectroscopy (XPS) characterisation of both pristine and electrochemically oxidized Li3MRuO5 reveals that in the Li3MnRuO5 oxide, Mn3+ and Ru4+ are partially oxidized to Mn4+ and Ru5+ in the sloping region at low voltage, while in the long plateau, O2- is also oxidized. Oxygen release likely occurs which may be the cause for failure of cells upon cycling. Interestingly, some other Li-rich layered oxides have been reported to cycle acceptably even with the participation of the O2- ligand in the reversible redox processes. In the Li3FeRuO5 oxide, the oxidation process appears to affect only Ru (4+ to 5+ in the sloping region) and O2- (plateau) while Fe seems to retain its 3+ state.

Evolution of Aromatic beta-Glucoside Utilization by Successive Mutational Steps in Escherichia coli

The bglA gene of Escherichia coli encodes phospho-beta-glucosidase A capable of hydrolyzing the plant-derived aromatic beta-glucoside arbutin. We report that the sequential accumulation of mutations in bglA can confer the ability to hydrolyze the related aromatic beta-glucosides esculin and salicin in two steps. In the first step, esculin hydrolysis is achieved through the acquisition of a four-nucleotide insertion within the promoter of the bglA gene, resulting in enhanced steady-state levels of the bglA transcript. In the second step, hydrolysis of salicin is achieved through the acquisition of a point mutation within the bglA structural gene close to the active site without the loss of the original catabolic activity against arbutin. These studies underscore the ability of microorganisms to evolve additional metabolic capabilities by mutational modification of preexisting genetic systems under selection pressure, thereby expanding their repertoire of utilizable substrates.

HCN channels enhance spike phase coherence and regulate the phase of spikes and LFPs in the theta-frequency range

What are the implications for the existence of subthreshold ion channels, their localization profiles, and plasticity on local field potentials (LFPs)? Here, we assessed the role of hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels in altering hippocampal theta-frequency LFPs and the associated spike phase. We presented spatiotemporally randomized, balanced theta-modulated excitatory and inhibitory inputs to somatically aligned, morphologically realistic pyramidal neuron models spread across a cylindrical neuropil. We computed LFPs from seven electrode sites and found that the insertion of an experimentally constrained HCN-conductance gradient into these neurons introduced a location- dependent lead in the LFP phase without significantly altering its amplitude. Further, neurons fired action potentials at a specific theta phase of the LFP, and the insertion of HCN channels introduced large lags in this spike phase and a striking enhancement in neuronal spike-phase coherence. Importantly, graded changes in either HCN conductance or its half-maximal activation voltage resulted in graded changes in LFP and spike phases. Our conclusions on the impact of HCN channels on LFPs and spike phase were invariant to changes in neuropil size, to morphological heterogeneity, to excitatory or inhibitory synaptic scaling, and to shifts in the onset phase of inhibitory inputs. Finally, we selectively abolished the inductive lead in the impedance phase introduced by HCN channels without altering neuronal excitability and found that this inductive phase lead contributed significantly to changes in LFP and spike phase. Our results uncover specific roles for HCN channels and their plasticity in phase-coding schemas and in the formation and dynamic reconfiguration of neuronal cell assemblies.

A novel Monoclonal Antibody against Notch1 Targets Leukemia-associated Mutant Notch1 and Depletes Therapy Resistant Cancer Stem Cells in Solid Tumors

Higher Notch signaling is known to be associated with hematological and solid cancers. We developed a potential immunotherapeutic monoclonal antibody (MAb) specific for the Negative Regulatory Region of Notch1 (NRR). The MAb604.107 exhibited higher affinity for the ``Gain-offunction'' mutants of Notch1 NRR associated with T Acute lymphoblastic Leukemia (T-ALL). Modeling of the mutant NRR with 12 amino-acid insertion demonstrated ``opening'' resulting in exposure of the S2-cleavage site leading to activated Notch1 signaling. The MAb, at low concentrations (1-2 mu g/ml), inhibited elevated ligand-independent Notch1 signaling of NRR mutants, augmented effect of Thapsigargin, an inhibitor of mutant Notch1, but had no effect on the wild-type Notch1. The antibody decreased proliferation of the primary T-ALL cells and depleted leukemia initiating CD34/CD44 high population. At relatively high concentrations, (10-20 mu g/ml), the MAb affected Notch1 signaling in the breast and colon cancer cell lines. The Notch-high cells sorted from solid-tumor cell lines exhibited characteristics of cancer stem cells, which were inhibited by the MAb. The antibody also increased the sensitivity to Doxorubucinirubicin. Further, the MAb impeded the growth of xenografts from breast and colon cancer cells potentiated regression of the tumors along with Doxorubucin. Thus, this antibody is potential immunotherapeutic tool for different cancers.

Energy-savvy solid-state and sonochemical synthesis of lithium sodium titanate as an anode active material for Li-ion batteries

Lithium sodium titanate insertion-type anode has been synthesized by classical solid-state (dry) and an alternate solution-assisted (wet) sonochemical synthesis routes. Successful synthesis of the target compound has been realized using simple Na- and Li-hydroxide salts along with titania. In contrast to the previous reports, these energy-savvy synthesis routes can yield the final product by calcination at 650 -750 degrees C for limited duration of 1-10 h. Owing to the restricted calcination duration (dry route for 1-2 h and wet route for 1-5 h), they yield homogeneous nanoscale lithium sodium titanate particles. Sono-chemical synthesis reduces the lithium sodium titanate particle size down to 80-100 nm vis-a-vis solid-state method delivering larger (200-500 nm) particles. Independent of the synthetic methods, the end products deliver reversible electrochemical performance with reversible capacity exceeding 80 mAh.g(-1) acting as a 1.3 V anode for Li-ion batteries. (C) 2015 Elsevier B.V. All rights reserved.

Review: Overcoming the paradox of strength and ductility in ultrafine-grained materials at low temperatures

Ultrafine-grained (UFG) materials with grain sizes in the submicrometer or nanometer range may be prepared through the application of severe plastic deformation (SPD) to bulk coarse-grained solids. These materials generally exhibit high strength but only very limited ductility in low-temperature testing, thereby giving rise to the so-called paradox of strength and ductility. This paradox is examined and a new quantitative diagram is presented which permits the easy insertion of experimental data. It is shown that relatively simple procedures are available for achieving both high strength and high ductility in UFG materials including processing the material to a very high strain and/or applying a very short-term anneal immediately after the SPD processing. Significant evidence is now available demonstrating the occurrence of grain boundary sliding in these materials at low temperatures, where this is attributed to the presence of non-equilibrium grain boundaries and the occurrence of enhanced diffusion along these boundaries.

Experimental characterisation and performance evaluation of a coaxial current transformer for measurement of insulated gate bipolar transistor switching current

Measurement of device current during switching characterisation of an insulated gate bipolar transistor (IGBT) requires a current sensor with low insertion impedance and high bandwidth. This study presents an experimental procedure for evaluating the performance of a coaxial current transformer (CCT), designed for the above purpose. A prototype CCT, which can be mounted directly on a power terminal of a 1200 V/50 A half-bridge IGBT module, is characterised experimentally. The measured characteristics include insertion impedance, gain and phase of the CCT at different frequencies. The bounds of linearity within which the CCT can operate without saturation are determined theoretically, and are also verified experimentally. The experimental study on linearity of the CCT requires a high-amplitude current source. A proportional-resonant (PR) controller-based current-controlled half-bridge inverter is developed for this purpose. A systematic procedure for selection of PR controller parameters is also reported in this study. This set-up is helpful to determine the limit of linearity and also to measure the frequency response of the CCT at realistic amplitudes of current in the low-frequency range.

A Facile Synthesis of 1,5-Disubstituted Tetrazole Peptidomimetics by Desulfurization/Electrocyclization of Thiopeptides

The cis-amide bond isostere, 1,5-disubstituted tetrazole,has been introduced in the peptide backbone by a simple route starting from the thiopeptide. The desired 1,5-disubstituted tetrazole peptidomimetics were synthesized by the desulfurization of thiopeptides by using HgCl2 in the presence of NaN3/TEA in DMF in good yields. Various other thiophilic reagents including hypervalent iodine reagents failed to deliver the tetrazole product with the exception of CBr4/PPh3, which resulted in moderate yields. The advantage of the present protocol over previous methods has been demonstrated by the selective insertion of tetrazole into peptide-thiopeptide hybrids. Also, the protocol is compatible with commonly employed urethane protecting groups (Fmoc, Boc, and Cbz) in peptide chemistry. Thiopeptide Boc-Pro-CSNH]-Val-OMe (2i) and two tetrazole peptidomimetics Cbz-Ala-CN4]-Phe-OMe (3d) and Boc-Pro-CN4]-Val-OMe (3i) were obtained as single crystals and their molecular structures have been confirmed by X-ray crystallography.

Two-Phase Metallic Thermal Interface Materials Processed Through Liquid Phase Sintering Followed by Accumulative Roll Bonding

Thermal interface materials (TIMs) form a mechanical and thermal link between a heat source and a heat sink. Thus, they should have high thermal conductivity and high compliance to efficiently transfer heat and accommodate any differential strain between the heat source and the sink, respectively. This paper reports on the processing and the characterization of potential metallic TIM composite solders comprising of Cu, a high conductivity phase, uniformly embedded in In matrix, a highly compliant phase. We propose the fabrication of such a material by a two-step fabrication technique comprising of liquid phase sintering (LPS) followed by accumulative roll bonding (ARB). To demonstrate the efficacy of the employed two-step processing technique, an In-40 vol. % Cu composite solder was produced first using LPS with short sintering periods (30 or 60 s at 160 degrees C) followed by ARB up to five passes, each pass imposing a strain of 50%. Mechanical response and electrical and thermal conductivities of the fabricated samples were evaluated. It was observed that processing through ARB homogenizes the distribution of Cu in an In matrix, disintegrates the agglomerates of Cu powders, and also significantly increases thermal and electrical conductivities, almost attaining theoretically predicted values, without significantly increasing the flow stress. Furthermore, the processing technique also allows the insertion of desired foreign species, such as reduced graphene oxide, in In-Cu for further enhancing a target property, such as electrical conductivity.

Pursuit of Sustainable Iron-Based Sodium Battery Cathodes: Two Case Studies

Rechargeable batteries have been the torchbearer electrochemical energy storage devices empowering small-scale electronic gadgets to large-scale grid storage. Complementing the lithium-ion technology, sodium-ion batteries have emerged as viable economic alternatives in applications unrestricted by volume/weight. What is the best performance limit for new-age Na-ion batteries? This mission has unravelled suites of oxides and polyanionic positive insertion (cathode) compounds in the quest to realize high energy density. Economically and ecologically, iron-based cathodes are ideal for mass-scale dissemination of sodium batteries. This Perspective captures the progress of Fe-containing earth-abundant sodium battery cathodes with two best examples: (i) an oxide system delivering the highest capacity (similar to 200 mA h/g) and (ii) a polyanionic system showing the highest redox potential (3.8 V). Both develop very high energy density with commercial promise for large-scale applications. Here, the structural and electrochemical properties of these two cathodes are compared and contrasted to describe two alternate strategies to achieve the same goal, i.e., improved energy density in Fe-based sodium battery cathodes.

Na2M2(SO4)(3) (M = Fe, Mn, Co and Ni): towards high-voltage sodium battery applications

Sodium-ion-based batteries have evolved as excellent alternatives to their lithium-ion-based counterparts due to the abundance, uniform geographical distribution and low price of Na resources. In the pursuit of sodium chemistry, recently the alluaudite framework Na2M2(SO4)(3) has been unveiled as a high-voltage sodium insertion system. In this context, the framework of density functional theory has been applied to systematically investigate the crystal structure evolution, density of states and charge transfer with sodium ions insertion, and the corresponding average redox potential, for Na2M2(SO4)(3) (M = Fe, Mn, Co and Ni). It is shown that full removal of sodium atoms from the Fe-based device is not a favorable process due to the 8% volume shrinkage. The imaginary frequencies obtained in the phonon dispersion also reflect this instability and the possible phase transition. This high volume change has not been observed in the cases of the Co- and Ni-based compounds. This is because the redox reaction assumes a different mechanism for each of the compounds investigated. For the polyanion with Fe, the removal of sodium ions induces a charge reorganization at the Fe centers. For the Mn case, the redox process induces a charge reorganization of the Mn centers with a small participation of the oxygen atoms. The Co and Ni compounds present a distinct trend with the redox reaction occurring with a strong participation of the oxygen sublattice, resulting in a very small volume change upon desodiation. Moreover, the average deintercalation potential for each of the compounds has been computed. The implications of our findings have been discussed both from the scientific perspective and in terms of technological aspects.

Signature-tagged transposon mutagenesis studies demonstrate the dynamic nature of cecal colonization of 2-week-old chickens by Campylobacter jejuni.

We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of Campylobacter jejuni and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the C. jejuni NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.

Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth reveals a stationary-phase physiological switch.

Campylobacter jejuni is a prevalent cause of food-borne diarrhoeal illness in humans. Understanding of the physiological and metabolic capabilities of the organism is limited. We report a detailed analysis of the C. jejuni growth cycle in batch culture. Combined transcriptomic, phenotypic and metabolic analysis demonstrates a highly dynamic 'stationary phase', characterized by a peak in motility, numerous gene expression changes and substrate switching, despite transcript changes that indicate a metabolic downshift upon the onset of stationary phase. Video tracking of bacterial motility identifies peak activity during stationary phase. Amino acid analysis of culture supernatants shows a preferential order of amino acid utilization. Proton NMR (1H-NMR) highlights an acetate switch mechanism whereby bacteria change from acetate excretion to acetate uptake, most probably in response to depletion of other substrates. Acetate production requires pta (Cj0688) and ackA (Cj0689), although the acs homologue (Cj1537c) is not required. Insertion mutants in Cj0688 and Cj0689 maintain viability less well during the stationary and decline phases of the growth cycle than wild-type C. jejuni, suggesting that these genes, and the acetate pathway, are important for survival.