Lattice Dynamics and Specific Heat of α\alpha - GeTe: a theoretical and experimental study

We extend recent \textit{ab initio} calculations of the electronic band structure and the phonon dispersion relations of rhombohedral GeTe to calculations of the density of phonon states and the temperature dependent specific heat. The results are compared with measurements of the specific heat. It is discovered that the specific heat depends on hole concentration, not only in the very low temperature region (Sommerfeld term) but also at the maximum of $C_p/T^3$ (around 16 K). To explain this phenomenon, we have performed \textit{ab initio} lattice dynamical calculations for GeTe rendered metallic through the presence of a heavy hole concentration ($p$ $\sim$ 2$\times$ 10$^{21}$ cm$^{-3}$). They account for the increase observed in the maximum of $C_p/T^3$.Comment: 8 pages, 7 figures, ref. 19 correcte

OXIDATIVE ENZYMES AND THE INJURY METABOLISM OF DIAPAUSING CECROPIA SILKWORMS *

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75474/1/j.1749-6632.1960.tb27576.x.pd

Enhanced superconducting pairing interaction in indium-doped tin telluride

The ferroelectric degenerate semiconductor Sn$_{1-\delta}$Te exhibits superconductivity with critical temperatures, $T_c$, of up to 0.3 K for hole densities of order 10$^{21}$ cm$^{-3}$. When doped on the tin site with greater than $x_c$ $= 1.7(3)$ indium atoms, however, superconductivity is observed up to 2 K, though the carrier density does not change significantly. We present specific heat data showing that a stronger pairing interaction is present for $x > x_c$ than for $x < x_c$. By examining the effect of In dopant atoms on both $T_c$ and the temperature of the ferroelectric structural phase transition, $T_{SPT}$, we show that phonon modes related to this transition are not responsible for this $T_c$ enhancement, and discuss a plausible candidate based on the unique properties of the indium impurities.Comment: 7 page

Requirements for translation re-initiation in Escherichia coli: roles of initiator tRNA and initiation factors IF2 and IF3

Despite its importance in post-transcriptional regulation of polycistronic operons in Escherichia coli, little is known about the mechanism of translation re-initiation, which occurs when the same ribosome used to translate an upstream open reading frame (ORF) also translates a downstream ORF. To investigate translation re-initiation in Escherichia coli, we constructed a di-cistronic reporter in which a firefly luciferase gene was linked to a chloramphenicol acetyltransferase gene using a segment of the translationally coupled geneV–geneVII intercistronic region from M13 phage. With this reporter and mutant initiator tRNAs, we show that two of the unique properties of E. coli initiator tRNA – formylation of the amino acid attached to the tRNA and binding of the tRNA to the ribosomal P-site – are as important for re-initiation as for de novo initiation. Overexpression of IF2 or increasing the affinity of mutant initiator tRNA for IF2 enhanced re-initiation efficiency, suggesting that IF2 is required for efficient re-initiation. In contrast, overexpression of IF3 led to a marked decrease in re-initiation efficiency, suggesting that a 30S ribosome and not a 70S ribosome is used for translation re-initiation. Strikingly, overexpression of IF3 also blocked E. coli from acting as a host for propagation of M13 phage

Mapping Hidden Potential Identity Elements by Computing the Average Discriminating Power of Individual tRNA Positions

The recently published discrete mathematical method, extended consensus partition (ECP), identifies nucleotide types at each position that are strictly absent from a given sequence set, while occur in other sets. These are defined as discriminating elements (DEs). In this study using the ECP approach, we mapped potential hidden identity elements that discriminate the 20 different tRNA identities. We filtered the tDNA data set for the obligatory presence of well-established tRNA features, and then separately for each identity set, the presence of already experimentally identified strictly present identity elements. The analysis was performed on the three kingdoms of life. We determined the number of DE, e.g. the number of sets discriminated by the given position, for each tRNA position of each tRNA identity set. Then, from the positional DE numbers obtained from the 380 pairwise comparisons of the 20 identity sets, we calculated the average excluding value (AEV) for each tRNA position. The AEV provides a measure on the overall discriminating power of each position. Using a statistical analysis, we show that positional AEVs correlate with the number of already identified identity elements. Positions having high AEV but lacking published identity elements predict hitherto undiscovered tRNA identity elements

The representation of protein complexes in the Protein Ontology (PRO)

BACKGROUND: Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. DESCRIPTION: We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. CONCLUSION: PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species

Detoxifying effect of Nelumbo nucifera and Aegle marmelos on hematological parameters of Common Carp (Cyprinus carpio L.)

The objective of this study was to investigate the efficacy of Nelumbo nucifera and Aegle marmelos on common carp exposed to sub-lethal concentrations of combined heavy metals (5 ppm) under laboratory conditions. The fish were treated with Nelumbo nucifera (500 mg/kg bwt) and Aegle marmelos (500 mg/kgbwt) for 30 days as a dietary supplement. The blood biochemical parameters of the fish were evaluated by analyzing the level of red blood cells (RBC), packed cell volume (PCV), hemoglobin concentration, glucose, cholesterol, iron and copper. The findings of the present investigation showed significant increase in hemoglobin (p<0.001), RBC (p<0.01) and PCV (p<0.01) of herbal drug-treated groups compared with metal-exposed fish. Conversely, glucose and cholesterol level in blood of common carp showed significant reduction compared with heavy-metal-exposed groups. All the values measured in Nelumbo nucifera and Aegle marmelos treated fish were restored comparably to control fish. Our results confirmed that Nelumbo nucifera and Aegle marmelos provide a detoxification mechanism for heavy metals in common carp

Experimental study of negative photoconductivity in n-PbTe(Ga) epitaxial films

We report on low-temperature photoconductivity (PC) in n-PbTe(Ga) epitaxial films prepared by the hot-wall technique on -BaF_2 substrates. Variation of the substrate temperature allowed us to change the resistivity of the films from 10^8 down to 10_{-2} Ohm x cm at 4.2 K. The resistivity reduction is associated with a slight excess of Ga concentration, disturbing the Fermi level pinning within the energy gap of n-PbTe(Ga). PC has been measured under continuous and pulse illumination in the temperature range 4.2-300 K. For films of low resistivity, the photoresponse is composed of negative and positive parts. Recombination processes for both effects are characterized by nonexponential kinetics depending on the illumination pulse duration and intensity. Analysis of the PC transient proves that the negative photoconductivity cannot be explained in terms of nonequilibrium charge carriers spatial separation of due to band modulation. Experimental results are interpreted assuming the mixed valence of Ga in lead telluride and the formation of centers with a negative correlation energy. Specifics of the PC process is determined by the energy levels attributed to donor Ga III, acceptor Ga I, and neutral Ga II states with respect to the crystal surrounding. The energy level corresponding to the metastable state Ga II is supposed to occur above the conduction band bottom, providing fast recombination rates for the negative PC. The superposition of negative and positive PC is considered to be dependent on the ratio of the densities of states corresponding to the donor and acceptor impurity centers.Comment: 7 pages, 4 figure

Synergistic growth inhibition by Iressa and Rapamycin is modulated by VHL mutations in renal cell carcinoma

Epidermal growth factor receptor (EGFR) and tumour growth factor alpha (TGFα) are frequently overexpressed in renal cell carcinoma (RCC) yet responses to single-agent EGFR inhibitors are uncommon. Although von Hippel–Lindau (VHL) mutations are predominant, RCC also develops in individuals with tuberous sclerosis (TSC). Tuberous sclerosis mutations activate mammalian target of rapamycin (mTOR) and biochemically resemble VHL alterations. We found that RCC cell lines expressed EGFR mRNA in the near-absence of other ErbB family members. Combined EGFR and mTOR inhibition synergistically impaired growth in a VHL-dependent manner. Iressa blocked ERK1/2 phosphorylation specifically in wt-VHL cells, whereas rapamycin inhibited phospho-RPS6 and 4E-BP1 irrespective of VHL. In contrast, phospho-AKT was resistant to these agents and MYC translation initiation (polysome binding) was similarly unaffected unless AKT was inhibited. Primary RCCs vs cell lines contained similar amounts of phospho-ERK1/2, much higher levels of ErbB-3, less phospho-AKT, and no evidence of phospho-RPS6, suggesting that mTOR activity was reduced. A subset of tumours and cell lines expressed elevated eIF4E in the absence of upstream activation. Despite similar amounts of EGFR mRNA, cell lines (vs tumours) overexpressed EGFR protein. In the paired cell lines, PRC3 and WT8, EGFR protein was elevated post-transcriptionally in the VHL mutant and EGF-stimulated phosphorylation was prolonged. We propose that combined EGFR and mTOR inhibitors may be useful in the subset of RCCs with wt-VHL. However, apparent differences between primary tumours and cell lines require further investigation

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.ow