[DNA shuffling of ptr resistance gene leads to improved pristinamycin production in Streptomyces pristinaespiralis]

In order to enhance pristinamycin production, six homologous ptr genes from high pristinamycin-producing strains of Streptomyces pristinaespiralis were selected for DNA shuffling, and the reason for the altered activities of the shuffled ptr gene was speculated by sequence alignment. The highest pristinamycin yield of 0.12 g/L was achieved with a sixfold increase in strain sps16 obtained by DNA shuffling when compared to ancestral strain ATCC 25486. Sequence analysis of theptr gene variant from the sps16 strain indicated that five mutations (H16P, N63D, T75P, Q107R, and P435A) were introduced into the gene, two of them (N63D and T75P) located in the second of the 14 transmembrane segments (TMS). Prediction of the secondary structure of the gene product indicated that mutations at the N-terminus resulted in the shortening of the corresponding α-helix, while the mutation at the C-terminus lengthened the helix. In conclusion, combination of DNA shuffling with genome shuffling is an effective breeding strategy for increasing the antibiotic yield by directed evolution of target genes.

Molecular characterization of enolase gene from Taenia multiceps

Taenia multiceps is a cestode parasite with its larval stage, known as Coenurus cerebralis, mainly encysts in the central nervous system of sheep and other livestocks. Enolase is a key glycolytic enzyme and represents multifunction in most organisms. In the present study, a 1617bp full-length cDNA encoding enolase was cloned from T. multiceps and designated as TmENO. A putative encoded protein of 433 amino acid residues that exhibited high similarity to helminth parasites. The recombinant TmENO protein (rTmENO) showed the catalytic and plasminogen-binding characteristics after the TmENO was subcloned and expressed in the pET30a(+) vector. The TmENO gene was transcribed during the adult and larval stages and was also identified in both cyst fluid and as a component of the adult worms and the metacestode by western blot analysis. Taken together, our results will facilitate further structural characterization for TmENO and new potential control strategies for T. multiceps.

GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature

The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures.

Covalent modification of DNA by α, β-unsaturated aldehydes derived from lipid peroxidation: Recent progress and challenges

Oxidative stress-induced lipid peroxidation (LPO) has been associated with human physiology and pathophysiology. LPO generates an array of oxidation products and among them reactive lipid aldehydes have received intensive research attentions due to their roles in modulating functions of biomolecules through covalent modification. Thus, covalent modification of DNA by these reactive lipid electrophiles has been postulated to be partially responsible for the biological roles of LPO. In this review, we summarized recent progress and challenges in studying the roles of covalent modification of DNA including nuclear and mitochondrial DNA by reactive lipid metabolites from LPO. We focused on the novel mechanistic insights into generation of lipid aldehydes from cellular membranes especially mitochondria through LPO. Recent advances in the technological front using mass spectrometry have also been highlighted in the settings of studying DNA damage caused by LPO and its biological relevance.

Development of Agave as a dedicated biomass source: production of biofuels from whole plants

BACKGROUND

Agave species can grow well in semi-arid marginal agricultural lands around the world. Selected Agave species are used largely for alcoholic beverage production in Mexico. There are expanding research efforts to use the plentiful residues (bagasse) for ethanol production as the beverage manufacturing process only uses the juice from the central core of mature plants. Here, we investigate the potential of over a dozen Agave species, including three from cold semi-arid regions of the United States, to produce biofuels using the whole plant.

RESULTS

Ethanol was readily produced by Saccharomyces cerevisiae from hydrolysate of ten whole Agaves with the use of a proper blend of biomass degrading enzymes including inulinase that overcomes inhibition of most of the species tested. As an example, US grown Agave neomexicana produced 119 ± 11 mg ethanol/g biomass. Unlike yeast fermentations, Clostridium beijerinckii produced n-butanol plus acetone from all species tested. Butyric acid, a precursor of n-butanol, was also present due to incomplete conversion during the screening process. Since Agave contains high levels of free and polyfructose which are readily destroyed by acidic pretreatment, a two-step procedure was developed to depolymerize polyfructose while maintaining its fermentability. The hydrolysate from before and after dilute acid processing was used in C. beijerinckii fermentations with selected Agave species with A. neomexicana producing 144 ± 4 mg fermentation products/g biomass.

CONCLUSIONS

Results showed Agave's potential to be a source of fermentable sugars beyond the existing beverage species to now include many species previously unfermentable by yeast, including cold-tolerant lines. This development should stimulate development of Agave as a dedicated feedstock for biofuels in semi-arid regions throughout the globe.

Changes in expression of an antimicrobial peptide, digestive enzymes, and nutrient transporters in the intestine of E. praecox-infected chickens

Coccidiosis is a major intestinal disease of poultry, caused by several species of the protozoan Eimeria. The objective of this study was to examine changes in expression of digestive enzymes, nutrient transporters, and an antimicrobial peptide following an Eimeria praecox challenge of chickens at days 3 and 6 post-infection. Gene expression was determined by real-time PCR and analyzed by one-way ANOVA. In the duodenum, the primary site of E. praecox infection, a number of genes were downregulated at both d3 and d6 post-infection. These genes included liver expressed antimicrobial peptide 2 (LEAP2), the cationic (CAT1), anionic (EAAT3), and L-type (LAT1) amino acid transporters, the peptide transporter PepT1 and the zinc transporter ZnT1. Other transporters were downregulated either at d3 or d6. At both d3 and d6, there was downregulation of B(o)AT and CAT1 in the jejunum and downregulation of LEAP2 and LAT1 in the ileum. LEAP2, EAAT3, and ZnT1 have been found to be downregulated following challenge with other Eimeria species, suggesting a common cellular response to Eimeria.

Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea

The transition from vegetative to reproductive growth in woody perennials involves pathways controlling flowering timing, bud dormancy and outgrowth in responses to seasonal cues. However little is known about the mechanism governing the adaptation of signaling pathways to environmental conditions in trees. Camellia azalea is a rare species in this genus flowering during summer, which provides a unique resource for floral timing breeding. Here we reported a comprehensive transcriptomics study to capture the global gene profiles during floral bud development in C. azalea. We examined the genome-wide gene expression between three developmental stages including floral bud initiation, floral organ differentiation and bud outgrowth, and identified nine co-expression clusters with distinctive patterns. Further, we identified the differential expressed genes (DEGs) during development and characterized the functional properties of DEGs by Gene Ontology analysis. We showed that transition from floral bud initiation to floral organ differentiation required changes of genes in flowering timing regulation, while transition to floral bud outgrowth was regulated by various pathways such as cold and light signaling, phytohormone pathways and plant metabolisms. Further analyses of dormancy associated MADS-box genes revealed that SVP- and AGL24- like genes displayed distinct expression patterns suggesting divergent roles during floral bud development.

Carrier transport in quantum dot quantum well microstructures of the self-assembled CdTe/CdS/ligand core-shell system

The study on the quantum dot quantum well (QDQW) microstructure modified by choosing different ligands containing a sulfhydryl group is of significance because it enables one to regulate photoexcited free charge carriers' (FCCs') transport behaviours in high-quality CdTe/ligand QDs via a self-assembled way. The photoelectron characteristics of ligand-capped CdTe nanoparticles were probed by a combination of surface photovoltaic (SPV) and photoacoustic technologies, supplemented by a computer simulation method of the CASTEP module. The experiment reveals that the D-value ΔEWi obtained by the associated two parameters of the SPV spectroscopy was closely related to the quantum confinement energy in the self-assembled CdTe/CdS/ligand core-shell system. In the paper the D-value was termed the depth of QWs, which were buried in the space charge regions located in the graded-band-gap and on either side of the shell-CdS. Obvious resonance quantum tunnelling may occur in the energy band structure with deep QWs on using certain ligands, resulting in an extended diffusion length of the FCCs on illumination of the photon energy hν ≥ Eg, core-CdTe, and in a strong SPV response at a specific wavelength region. In addition, the carrier-longitudinal optical phonon interaction is the reciprocal of the carriers' lifetime. The d-frontier orbital in the graded-band-gap plays an important role in both the microstructure and the resonance quantum tunnelling of the QDQW system according to the CASTEP calculations.

Expression and functionality of Toll-like receptor 3 in the megakaryocytic lineage

BACKGROUND

In addition to their key role in hemostasis, platelets and megakaryocytes regulate immune and inflammatory responses, in part through their expression of Toll-like receptors (TLRs). Among the TLRs, TLR3 recognizes dsRNA associated with viral infection. Thrombocytopenia is a frequent complication of viral infection. However, the expression and functionality of TLR3 in megakaryocytes and platelets is not yet well understood.

OBJECTIVE

To study the expression and functionality of TLR3 in the megakaryocytic lineage.

METHODS AND RESULTS

RT-PCR, flow cytometric and immunofluorescence assays showed that TLR3 is expressed in CD34(+) cells, megakaryocytes, and platelets. Immunoblotting assays showed that stimulation of megakaryocytes with two synthetic agonists of TLR3, Poly(I:C) and Poly(A:U), activated the nuclear factor-κB (NF-κB), phosphoinositide 3-kinase (PI3K)/Akt, extracellular signal-related kinase (ERK)1/2 and p38 pathways. TLR3-megakaryocyte activation resulted in reduced platelet production in vitro and interferon-β release through the PI3K-Akt and NF-κB signaling pathways. TLR3 ligands potentiated the aggregation mediated by classic platelet agonists. This effect was also observed for ATP release, but not for P-selectin or CD40L membrane exposure, indicating that TLR3 activation was not involved in α-granule release. In addition, TLR3 agonists induced activation of the NF-κB, PI3K-Akt and ERK1/2 pathways in platelets. Reductions in platelet production and platelet fibrinogen binding mediated by Poly(I:C) or Poly(A:U) were prevented by the presence of an inhibitor of the TLR3-dsRNA complex.

CONCLUSIONS

Our findings indicate that functional TLR3 is expressed in CD34(+) cells, megakaryocytes, and platelets, and suggest a potential role for this receptor in the megakaryopoiesis/thrombopoiesis alterations that occur in viral infections.

Dioxin-enhanced expression of interleukin-1 beta in human epidermal keratinocytes: potential role in the modulation of immune and inflammatory responses

Human keratinocytes are an important source of cytokines that participate in inflammatory and immunological processes of the skin. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) has been shown to enhance the expression of the cytokine, interleukin-1 beta (IL-1 beta), in a human keratinocyte cell line. Here we have expanded this observation to primary cultures of normal human epidermal keratinocytes. Treatment of these cells with TCDD resulted in increased expression of IL-1 beta mRNA. Both the magnitude and relative fold increase of levels of IL-1 beta mRNA were affected by specific culture conditions. In specific analyses of each culture medium supplement, bovine pituitary extract (BPE) was shown to exert the greatest effect on both the constitutive and TCDD-inducible expression of IL-1 beta mRNA, and this effect of BPE was shown to be concentration-dependent. These results indicate that, in vitro, enhanced expression of IL-1 beta is a response of normal human epidermal keratinocytes to TCDD and furthermore, that the intensity of this response may be modulated by additional growth factors, including those present in BPE.

Tevatron constraints on models of the Higgs boson with exotic spin and parity using decays to bottom-antibottom quark pairs

Combined constraints from the CDF and D0 Collaborations on models of the Higgs boson with exotic spin J and parity P are presented and compared with results obtained assuming the standard model value JP=0+. Both collaborations analyzed approximately 10  fb(-) of proton-antiproton collisions with a center-of-mass energy of 1.96 TeV collected at the Fermilab Tevatron. Two models predicting exotic Higgs bosons with JP=0- and JP=2+ are tested. The kinematic properties of exotic Higgs boson production in association with a vector boson differ from those predicted for the standard model Higgs boson. Upper limits at the 95% credibility level on the production rates of the exotic Higgs bosons, expressed as fractions of the standard model Higgs boson production rate, are set at 0.36 for both the JP=0- hypothesis and the JP=2+ hypothesis. If the production rate times the branching ratio to a bottom-antibottom pair is the same as that predicted for the standard model Higgs boson, then the exotic bosons are excluded with significances of 5.0 standard deviations and 4.9 standard deviations for the JP=0- and JP=2+ hypotheses, respectively.

Population genetic structure and historical demography of the ground beetle Chlaenius costiger in the Tsinling-Dabashan Mountains of central China

Population genetic structure and demographic history of the ground beetle Chlaenius costiger (Coleoptera: Carabidae) in the Tsinling-Dabashan Mountains of central China were estimated using mitochondrial DNA sequences (Cox1-tRNALeu-Cox2) of 144 individuals from 16 local populations. The high haplotype diversity was accompanied by low nucleotide diversity. Phylogenetic analysis (Bayesian inference) of the 43 haplotypes revealed no phylogeographic structure. Analysis of molecular variance suggested that most of the variation was attributed to within population variation (79.26%). Mantel test results showed a significant correlation between the genetic distance and geographical distance of the populations with a correlation coefficient equal to 0.216964 (P = 0.0471 < 0.05), indicating the presence of isolation by distance. Spatial AMOVA and PERMUT analyses showed no phylogeographic structure. Gene flow calculated through the number of migrants was high between many pairs of populations. The results of a neutrality test, mismatch distribution analyses, and Bayesian skyline plot analysis together showed a demographic expansion. The estimated expansion time of the whole sampled population was 0.125 million years. The complex topography in the Tsinling-Dabashan Mountains area led to the high level of genetic diversity, and migratory flight resulted in the high level of gene flow, leading to the lack of a phylogeographic structure.

Sudden stoppage of rotor in a thermally driven rotary motor made from double-walled carbon nanotubes

In a thermally driven rotary motor made from double-walled carbon nanotubes, the rotor (inner tube) can be actuated to rotate within the stator (outer tube) when the environmental temperature is high enough. A sudden stoppage of the rotor can occur when the inner tube has been actuated to rotate at a stable high speed. To find the mechanisms of such sudden stoppages, eight motor models with the same rotor but different stators are built and simulated in the canonical NVT ensembles. Numerical results demonstrate that the sudden stoppage of the rotor occurs when the difference between radii is near 0.34 nm at a high environmental temperature. A smaller difference between radii does not imply easier activation of the sudden rotor stoppage. During rotation, the positions and electron density distribution of atoms at the ends of the motor show that a sp(1) bonded atom on the rotor is attracted by the sp(1) atom with the biggest deviation of radial position on the stator, after which they become two sp(2) atoms. The strong bond interaction between the two atoms leads to the loss of rotational speed of the rotor within 1 ps. Hence, the sudden stoppage is attributed to two factors: the deviation of radial position of atoms at the stator's ends and the drastic thermal vibration of atoms on the rotor in rotation. For a stable motor, sudden stoppage could be avoided by reducing deviation of the radial position of atoms at the stator's ends. A nanobrake can be, thus, achieved by adjusting a sp1 atom at the ends of stator to stop the rotation of rotor quickly.

Measurement of the B(s)(0) lifetime in the flavor-specific decay channel B(s)(0)→D(s)(-)μ(+)νX

We present an updated measurement of the B(s)(0) lifetime using the semileptonic decays B(s)(0)→D(s)(-)μ(+)νX, with D(s)(-)→ϕπ(-) and ϕ→K(+)K(-) (and the charge conjugate process). This measurement uses the full Tevatron Run II sample of proton-antiproton collisions at √[s]=1.96  TeV, comprising an integrated luminosity of 10.4  fb(-1). We find a flavor-specific lifetime τ(fs)(B(s)(0))=1.479±0.010(stat)±0.021(syst)  ps. This technique is also used to determine the B(0) lifetime using the analogous B(0)→D(-)μ(+)νX decay with D(-)→ϕπ(-) and ϕ→K(+)K(-), yielding τ(B(0))=1.534±0.019(stat)±0.021(syst)  ps. Both measurements are consistent with the current world averages, and the B(s)(0) lifetime measurement is one of the most precise to date. Taking advantage of the cancellation of systematic uncertainties, we determine the lifetime ratio τ(fs)(B(s)(0))/τ(B(0))=0.964±0.013(stat)±0.007(syst).

Molecular Survey of Anaplasma and Ehrlichia of Red Deer and Sika Deer in Gansu, China in 2013

Anaplasma and Ehrlichia are important emerging tick-borne pathogens in both humans and animals. Here, we conducted a molecular surveillance study in Gansu, China to assess the prevalence of Anaplasma and Ehrlichia spp. in red deer and sika deer based on polymerase chain reaction (PCR) analysis and sequencing of 16S rRNA or msp genes. PCR revealed that the prevalence of Anaplasma ovis, Anaplasma bovis and Anaplasma platys of the Qilian Mountain samples was 32%, 9% and 9%, respectively; the prevalence of Anaplasma ovis, Anaplasma bovis, Anaplasma platys was 20%, 15% and 15% among the Long Mountain samples, respectively. Of the Long Mountain samples, two (5%) of the 40 samples were positive for Ehrlichia canis, but all 44 of the Qilian Mountain samples were negative for E. canis, and no other Anaplasma or Ehrlichia spp. were found in the samples. The phylogenetic tree showed that the newly isolated Anaplasma and Ehrlichia spp. could be classified as belonging to four clades, including an A. bovis cluster, A. ovis cluster, A. platys cluster and E. canis cluster. In addition, Bartonella schoenbuchensis was firstly identified in blood samples from red deer in Gansu, China. Our results provide important data to increase the understanding of the epidemiology of anaplasmosis and ehrlichiosis of red deer and sika deer and will assist with the implementation of measures to control anaplasmosis and ehrlichiosis transmission to red deer, sika deer and other animals in Gansu, China.

Measurement of the forward-backward asymmetry in the production of B(±) mesons in pp̄ collisions at √s=1.96 TeV

We present a measurement of the forward-backward asymmetry in the production of B(±) mesons, A(FB)(B(±)), using B(±)→J/ψK(±) decays in 10.4  fb(-1) of pp̄ collisions at sqrt[s]=1.96  TeV collected by the D0 experiment during Run II of the Tevatron collider. A nonzero asymmetry would indicate a preference for a particular flavor, i.e., b quark or ̄b antiquark, to be produced in the direction of the proton beam. We extract A(FB)(B(±)) from a maximum likelihood fit to the difference between the numbers of forward- and backward-produced B(±) mesons. We measure an asymmetry consistent with zero: A(FB)(B(±))=[-0.24±0.41  (stat)±0.19  (syst)]%.

A possible way that φC31 integrase regulates the recombination direction

φC31 integrase encoded by Streptomyces phage can mediate site-specific recombination between phage and host genomes. The recombination direction is generally considered to be accurately regulated, but the regulatory mechanisms involved are still unclear. Recently, some hyperactive mutants of φC31 integrase that can bypass the regulatory steps have been isolated and extensively studied. A putative coiled-coil region is found to play a critical role in controlling recombination direction. Further analysis led us to the speculation that at least two regions in the N-terminal domain of φC31 integrase are involved in the tetrameric interfaces and that the putative coiled coil interacts with one of the regions to regulate the recombination direction.

In situ Si doping of heteroepitaxially grown c-BN thin films at different temperatures

Phase pure cubic boron nitride (c-BN) films have been epitaxially grown on (001) diamond substrates at 420 °C, 600 °C and 900 °C.

Gradientless temperature-driven rotating motor from a double-walled carbon nanotube

Rotation of the inner tube in a double-walled carbon nanotube (DWCNT) system with a fixed outer tube is investigated and found to be inducible by a relatively high uniform temperature (say, 300 K). We also found the mechanism of a gradientless temperature-driven rotating motor lies in the inner tube losing its geometric symmetry in a high-temperature field. This mechanism can be taken as a guide for designing a motor from such a bi-tube system. Using a computational molecular dynamics (CMD) approach and the adaptive intermolecular reactive empirical bond order (AIREBO) potential, the dynamic behavior of a bi-tube system subjected to uniformly distributed temperature is studied. In particular, the effects of environmental temperature, boundary conditions of the outer tube, and intertube gap on the dynamic behavior of the bi-tube system are investigated. Numerical examples show that a bi-tube system with the inner tube having 0.335 nm of interlayer gap produces the highest rotational speed.