Displaying publications 1 - 20 of 598 in total

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  1. Chang CC, Li C, Webb GI, Tey B, Song J, Ramanan RN
    Sci Rep, 2016;6:21844.
    PMID: 26931649 DOI: 10.1038/srep21844
    Periplasmic expression of soluble proteins in Escherichia coli not only offers a much-simplified downstream purification process, but also enhances the probability of obtaining correctly folded and biologically active proteins. Different combinations of signal peptides and target proteins lead to different soluble protein expression levels, ranging from negligible to several grams per litre. Accurate algorithms for rational selection of promising candidates can serve as a powerful tool to complement with current trial-and-error approaches. Accordingly, proteomics studies can be conducted with greater efficiency and cost-effectiveness. Here, we developed a predictor with a two-stage architecture, to predict the real-valued expression level of target protein in the periplasm. The output of the first-stage support vector machine (SVM) classifier determines which second-stage support vector regression (SVR) classifier to be used. When tested on an independent test dataset, the predictor achieved an overall prediction accuracy of 78% and a Pearson's correlation coefficient (PCC) of 0.77. We further illustrate the relative importance of various features with respect to different models. The results indicate that the occurrence of dipeptide glutamine and aspartic acid is the most important feature for the classification model. Finally, we provide access to the implemented predictor through the Periscope webserver, freely accessible at http://lightning.med.monash.edu/periscope/.
  2. Shu MH, MatRahim N, NorAmdan N, Pang SP, Hashim SH, Phoon WH, et al.
    Sci Rep, 2016;6:22332.
    PMID: 26923424 DOI: 10.1038/srep22332
    Vaccination may be an alternative treatment for infection with multidrug-resistance (MDR) Acinetobacter baumannii. The study reported here evaluated the bactericidal antibody responses following immunization of mice using an inactivated whole-cell vaccine derived from antibiotic-exposed MDR A. baumannii (I-M28-47-114). Mice inoculated with I-M28-47 (non-antibiotic-exposed control) and I-M28-47-114 showed a high IgG antibody response by day 5 post-inoculation. Sera from mice inoculated with I-M28-47-114 collected on day 30 resulted in 80.7 ± 12.0% complement-mediated bacteriolysis in vitro of the test MDR A. baumannii treated with imipenem, which was a higher level of bacteriolysis over sera from mice inoculated with I-M28-47. Macrophage-like U937 cells eliminated 49.3 ± 11.6% of the test MDR A. baumannii treated with imipenem when opsonized with sera from mice inoculated with I-M28-47-114, which was a higher level of elimination than observed for test MDR A. baumannii opsonized with sera from mice inoculated with I-M28-47. These results suggest that vaccination with I-M28-47-114 stimulated antibody responses capable of mounting high bactericidal killing of MDR A. baumannii. Therefore, the inactivated antibiotic-exposed whole-cell vaccine (I-M28-47-114) has potential for development as a candidate vaccine for broad clearance and protection against MDR A. baumannii infections.
  3. Pandy V, Khan Y
    Sci Rep, 2016;6:21944.
    PMID: 26902717 DOI: 10.1038/srep21944
    The present study established a novel mouse model of a runway drug self-administration in our laboratory. The operant runway apparatus consisted of three long runways arranged in a zig-zag manner. The methodology consisted of six distinct phases: habituation, preconditioning, conditioning, post-conditioning, extinction and reinstatement. The effects of saline were compared with escalating doses of either ethanol (0.5-4.0 g/kg, i.p), heroin (5-40 mg/kg, i.p), or nicotine (0.1-0.5mg/kg, i.p) administered in the goal box during the conditioning phase (day 1 to day 5). A significant decrease in the time of trained (conditioned) mice to reach the goal box confirmed the subjects' motivation to seek those drugs on day 6 (expression). The mice were then subjected to non-rewarded extinction trials for 5 days over which run times were significantly increased. After 5 days of abstinence, a priming dose of ethanol or heroin (1/5th of maximum dose used in conditioning) significantly reinstated the drug-seeking behavior. These results suggest that the modified runway model can serve as a powerful behavioral tool for the study of the behavioral and neurobiological bases of drug self-administration and, as such, is appropriate simple but powerful tool for investigating the drug-seeking behavior of laboratory mice.
  4. Tan AW, Liau LL, Chua KH, Ahmad R, Akbar SA, Pingguan-Murphy B
    Sci Rep, 2016;6:21828.
    PMID: 26883761 DOI: 10.1038/srep21828
    One of the major challenges in bone grafting is the lack of sufficient bone vascularization. A rapid and stable bone vascularization at an early stage of implantation is essential for optimal functioning of the bone graft. To address this, the ability of in situ TiO2 nanofibrous surfaces fabricated via thermal oxidation method to enhance the angiogenic potential of human umbilical vein endothelial cells (HUVECs) was investigated. The cellular responses of HUVECs on TiO2 nanofibrous surfaces were studied through cell adhesion, cell proliferation, capillary-like tube formation, growth factors secretion (VEGF and BFGF), and angiogenic-endogenic-associated gene (VEGF, VEGFR2, BFGF, PGF, HGF, Ang-1, VWF, PECAM-1 and ENOS) expression analysis after 2 weeks of cell seeding. Our results show that TiO2 nanofibrous surfaces significantly enhanced adhesion, proliferation, formation of capillary-like tube networks and growth factors secretion of HUVECs, as well as leading to higher expression level of all angiogenic-endogenic-associated genes, in comparison to unmodified control surfaces. These beneficial effects suggest the potential use of such surface nanostructures to be utilized as an advantageous interface for bone grafts as they can promote angiogenesis, which improves bone vascularization.
  5. Goh SY, Khan SA, Tee KK, Abu Kasim NH, Yin WF, Chan KG
    Sci Rep, 2016;6:20702.
    PMID: 26860259 DOI: 10.1038/srep20702
    Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.
  6. Alavi SE, Soltanian MR, Amiri IS, Khalily M, Supa'at AS, Ahmad H
    Sci Rep, 2016;6:19891.
    PMID: 26814621 DOI: 10.1038/srep19891
    5G communications require a multi Gb/s data transmission in its small cells. For this purpose millimeter wave (mm-wave) RF signals are the best solutions to be utilized for high speed data transmission. Generation of these high frequency RF signals is challenging in electrical domain therefore photonic generation of these signals is more studied. In this work, a photonic based simple and robust method for generating millimeter waves applicable in 5G access fronthaul is presented. Besides generating of the mm-wave signal in the 60 GHz frequency band the radio over fiber (RoF) system for transmission of orthogonal frequency division multiplexing (OFDM) with 5 GHz bandwidth is presented. For the purpose of wireless transmission for 5G application the required antenna is designed and developed. The total system performance in one small cell was studied and the error vector magnitude (EVM) of the system was evaluated.
  7. Tan PC, Mackeen A, Khong SY, Omar SZ, Noor Azmi MA
    Sci Rep, 2016 Mar 18;6:23223.
    PMID: 26987593 DOI: 10.1038/srep23223
    A peripheral intravenous catheter is often inserted as part of care during labour. The catheter is inserted into the back of the hand or lower forearm vein in usual practice. There is no trial data to guide the care provider on which is the better insertion site in any clinical setting. 307 women admitted to the labour ward who required insertion of intravenous catheter were randomised to back of hand or lower forearm vein catheter insertion. Catheter insertion is by junior to mid-grade providers. We evaluated insertion success at the first attempt, pain during insertion and catheter replacement due to malfunction as main outcomes. After catheter removal, we recorded patient satisfaction with site, future site preference and insertion site swelling, bruising, tenderness, vein thrombosis and pain. Insertion of a catheter into back of hand vein is more likely to be successful at the first attempt. Insertion pain score, catheter replacement rate, patient satisfaction, patient fidelity to site in a future insertion and insertion site complications rate are not different between trial arms. In conclusion, both insertion sites are suitable; the back of the hand vein maybe easier to cannulate and seems to be preferred by our frontline providers.
  8. Ahmad P, Khandaker MU, Amin YM, Muhammad N
    Sci Rep, 2016;6:21403.
    PMID: 26892366 DOI: 10.1038/srep21403
    Boron niride microflakes of 2-5 μm in diameter and greater than 40 μm in length with multilayer structure and highly crystalline nature are synthesized in two states of catalysts and dual role of nitrogen at 1100 °C. Most of the microflakes are flat, smooth and vertically aligned with a wall-like view from the top. Transmission electron microscopy shows overlapped layers of microflakes with an interlayer spacing of 0.34 nm. The h-BN components of the synthesized microflakes are verified from B 1s and N1 s peaks at 190. 7 and 397.9 eV. Raman shift at 1370 (cm(-1)) and sharp peaks in the XRD pattern further confirm the h-BN phase and crystalline nature of the synthesized microflakes. Microflakes of h-BN with the above characteristics are highly desirable for the development of a solid state neutron detector with higher detection efficiency.
  9. Guest JR, Low J, Tun K, Wilson B, Ng C, Raingeard D, et al.
    Sci Rep, 2016;6:20717.
    PMID: 26876092 DOI: 10.1038/srep20717
    While many studies of coral bleaching report on broad, regional scale responses, fewer examine variation in susceptibility among coral taxa and changes in community structure, before, during and after bleaching on individual reefs. Here we report in detail on the response to bleaching by a coral community on a highly disturbed reef site south of mainland Singapore before, during and after a major thermal anomaly in 2010. To estimate the capacity for resistance to thermal stress, we report on: a) overall bleaching severity during and after the event, b) differences in bleaching susceptibility among taxa during the event, and c) changes in coral community structure one year before and after bleaching. Approximately two thirds of colonies bleached, however, post-bleaching recovery was quite rapid and, importantly, coral taxa that are usually highly susceptible were relatively unaffected. Although total coral cover declined, there was no significant change in coral taxonomic community structure before and after bleaching. Several factors may have contributed to the overall high resistance of corals at this site including Symbiodinium affiliation, turbidity and heterotrophy. Our results suggest that, despite experiencing chronic anthropogenic disturbances, turbid shallow reef communities may be remarkably resilient to acute thermal stress.
  10. Batra J, Tripathi S, Kumar A, Katz JM, Cox NJ, Lal RB, et al.
    Sci Rep, 2016;6:19063.
    PMID: 26750153 DOI: 10.1038/srep19063
    A unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins.
  11. Chindera K, Mahato M, Kumar Sharma A, Horsley H, Kloc-Muniak K, Kamaruzzaman NF, et al.
    Sci Rep, 2016;6:23121.
    PMID: 26996206 DOI: 10.1038/srep23121
    To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance.
  12. Zahari A, Ablat A, Omer N, Nafiah MA, Sivasothy Y, Mohamad J, et al.
    Sci Rep, 2016;6:21517.
    PMID: 26898753 DOI: 10.1038/srep21517
    The UV-vis spectra of isocorydine 1, norisocorydine 2 and boldine 3 were studied in 2% v/v acetonitrile, at constant ionic strength (0.1 M NaCl, 35 degree Celsius). The pK(a) values of isocorydine 1 and norisocorydine 2 were 11.75 and 12.07, respectively. Boldine 3 gave a pK(a) value of 9.16 and 10.44. All of the alkaloids 1-3 were stable at physiological pH; thereby all of them will not ionize, thus permitting the basic nitrogen to be protonated and accumulated within the acidic food vacuole of Plasmodium via pH trapping. Subsequently, acidic food vacuoles that have been neutralized by alkaloids would result in enhancement of the antiplasmodial activity. The alkaloids showed antiplasmodial activity against Plasmodium falciparum and antioxidant activities; DPPH radical scavenging, metal chelating and ferric reducing power. The antioxidant properties of the alkaloids under investigation revealed that in addition to the antiplasmodial activity, the alkaloids can also prevent oxidative damage. It can be prevented by binding free heme and neutralizing the electrons produced during the Plasmodium falciparum mediated haemoglobin destruction in the host. Slightly basic properties of the aforementioned alkaloids, along with their antioxidant activities, are advantageous in improving the suppression of malaria infection that cause less damage to the host.
  13. Nguyen DM, Soci C, Ooi CH
    Sci Rep, 2016;6:21083.
    PMID: 26879520 DOI: 10.1038/srep21083
    Phaseonium is a three-level Λ quantum system, in which a coherent microwave and an optical control (pump) beams can be used to actively modulate the dielectric response. Here we propose a new metamaterial structure comprising of a periodic array of triangular phaseonium metamolecules arranged as a trefoil. We present a computational study of the spatial distribution of magnetic and electric fields of the probe light and the corresponding transmission and reflection, for various parameters of the optical and microwave beams. For specific values of the probing frequencies and control fields, the phaseonium can display either metallic or dielectric optical response. We find that, in the metallic regime, the phaseonium metamaterial structure supports extremely large transmission, with optical amplification at large enough intensity of the microwave thanks to strong surface plasmon coupling; while, in the dielectric regime without microwave excitation, the transmission bandwidth can be tuned by varying the control beam intensity. Implementation of such phaseonium metamaterial structure in solid-state systems, such as patterned crystals doped with rare-earth elements or dielectric matrices embedded with quantum dots, could enable a new class of actively tunable quantum metamaterials.
  14. Low VL, Takaoka H, Pramual P, Adler PH, Ya'cob Z, Huang YT, et al.
    Sci Rep, 2016 Feb 03;6:20346.
    PMID: 26839292 DOI: 10.1038/srep20346
    Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform 'b' as valid species; indicated that S. xuandei, cytoform L, and morphoform 'a' contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G.
  15. Gholamrezaei S, Salavati-Niasari M, Ghanbari D, Bagheri S
    Sci Rep, 2016;6:20060.
    PMID: 26805744 DOI: 10.1038/srep20060
    Different morphologies of Ag2Te nanostructures were synthesized using TeCl4 as a new precursor and hydrazine hydrate as reducing agent by a hydrothermal method. Various parameters that affect on morphology and purity of nanostructures were optimized. According to our experiments the best time and temperature for preparation of this nanostructure are 12 h and 120 °C. The photo-catalytic behaviour of nanostructures in presence of UV-visible light for degradation of methyl orange was investigated. Results show that the presence of UV light is necessary for an efficient degradation of dye in aqueous solution. On the other hand, as observations propose the Ag2Te reveal a strong photoluminescence peak at room temperature that could be attributed to high level transition in the semiconductor. Nanostructures were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) techniques and UV-visible scanning spectrometer (UV-Vis).
  16. Ikeda T, Ong EB, Watanabe N, Sakaguchi N, Maeda K, Koito A
    Sci Rep, 2016;6:19035.
    PMID: 26738439 DOI: 10.1038/srep19035
    APOBEC1 (A1) proteins from lagomorphs and rodents have deaminase-dependent restriction activity against HIV-1, whereas human A1 exerts a negligible effect. To investigate these differences in the restriction of HIV-1 by A1 proteins, a series of chimeric proteins combining rabbit and human A1s was constructed. Homology models of the A1s indicated that their activities derive from functional domains that likely act in tandem through a dimeric interface. The C-terminal region containing the leucine-rich motif and the dimerization domains of rabbit A1 is important for its anti-HIV-1 activity. The A1 chimeras with strong anti-HIV-1 activity were incorporated into virions more efficiently than those without anti-HIV-1 activity, and exhibited potent DNA-mutator activity. Therefore, the C-terminal region of rabbit A1 is involved in both its packaging into the HIV-1 virion and its deamination activity against both viral cDNA and genomic RNA. This study identifies the novel molecular mechanism underlying the target specificity of A1.
  17. Subramaniam M, In LL, Kumar A, Ahmed N, Nagoor NH
    Sci Rep, 2016;6:19833.
    PMID: 26817684 DOI: 10.1038/srep19833
    Mycobacterium indicus pranii (MIP) is a non-pathogenic mycobacterium, which has been tested on several cancer types like lung and bladder where tumour regression and complete recovery was observed. In discovering the potential cytotoxic elements, a preliminary test was carried out using four different fractions consisting of live bacteria, culture supernatant, heat killed bacteria and heat killed culture supernatant of MIP against two human cancer cells A549 and CaSki by 3-(4,5-dimethyl thiazol)-2,5-diphenyl tetrazolium bromide (MTT) assay. Apoptosis was investigated in MCF-7 and ORL-115 cancer cells by poly-(ADP-ribose) polymerase (PARP) and DNA fragmentation assays. Among four MIP fractions, only heat killed MIP fraction (HKB) showed significant cytotoxicity in various cancer cells with inhibitory concentration, IC50 in the range 5.6-35.0 μl/(1.0 × 10(6) MIP cells/ml), while cytotoxicity effects were not observed in the remaining fractions. HKB did not show cytotoxic effects on non-cancerous cells contrary to cancerous cells, suggesting its safe usage and ability to differentially recognize between these cells. Evaluation on PARP assay further suggested that cytotoxicity in cancer cells were potentially induced via caspase-mediated apoptosis. The cytotoxic and apoptotic effects of MIP HKB have indicated that this fraction can be a good candidate to further identify effective anti-cancer agents.
  18. Chan XY, Hong KW, Yin WF, Chan KG
    Sci Rep, 2016 Jan 28;6:20016.
    PMID: 26817720 DOI: 10.1038/srep20016
    Tropical carnivorous plant, Nepenthes, locally known as "monkey cup", utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid.
  19. Teh CK, Ong AL, Kwong QB, Apparow S, Chew FT, Mayes S, et al.
    Sci Rep, 2016;6:19075.
    PMID: 26743827 DOI: 10.1038/srep19075
    GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10(-4)) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential.
  20. Chai KP, Othman NF, Teh AH, Ho KL, Chan KG, Shamsir MS, et al.
    Sci Rep, 2016 Mar 15;6:23126.
    PMID: 26975884 DOI: 10.1038/srep23126
    A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca(2+) ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca(2+) ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.
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