DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1

Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA. The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.status: publishe

Estimation of State Space Models using Particle Filters – applications to Economics and Finance

In recent years, general state space models have been proven to be extremely useful in modelling wide range of economic and financial time series. Subsequently, particle filters, a computational simulation based method along with its related techniques had burst into our spectrum and fill our expectation of estimating general state space models. However, particle methods can be computationally intensive, as well as possibly requiring stringent restrictions on the parameters space to achieve timely convergence. In this thesis, I propose several improvements to particle methods on different aspects. A list of the improvements are: general computational time reduction in particle filters, modified particle smoothing algorithm, more accurate parameter and state variable estimation through the utilizations of Modified Entropy particle filter, and apply novel general state space model estimation method to real economic and financial time series

The complete chloroplast genome of the medicinally important plant <i>Plumbago zeylanica</i> L. (plumbaginaceae) and phylogenetic analysis

Plumbago zeylanica L. 1753 is a medicinally-important herb in family Plumbaginaceae. In this study, we assembled and reported the complete chloroplast genome of P. zeylanica. The plastome of P. zeylanica was 169,178 bp, including a large single-copy region of 92,135 bp, a small single-copy region (SSC) of 13,455 bp and a pair of inverted repeat regions (IRs) of 31,794 bp. It contained 124 genes, including 79 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that P. zeylanica formed a close relationship with P. auriculata in Plumbago. The first complete chloroplast genome report of P. zeylanica providing an opportunity to explore the genetic diversity, and would be also helpful in the species identification and conservation.</p

In-Channel Printing-Device Opening Assay for Micropatterning Multiple Cells and Gene Analysis

Herein we report an easy but versatile method for patterning different cells on a single substrate by using a microfluidic approach that allows not only spatial and temporal control of multiple microenvironments but also retrieval of specific treated cells to profile their expressed genetic information at around 10-cell resolution. By taking advantages of increased surface area of gold nanoparticles on a poly­(dimethylsiloxane) (PDMS) coated substrate, cell adhesive-promotive protein, human fibronectin (hFN) can be significantly accumulated on designed regions where cells can recognize the protein and spread out. Moreover, the whole device can be easily opened by hand without any loss of patterned cells which could be retrieved by mouth-pipet. Consequently, we demonstrate the possibility of analyzing the difference of gene expression patterns between wild type MCF-7 cell and MCF/Adr (drug-resistant cell line) from less than 400 cells in total for a single comprehensive assay, including parallel experiments, controls, and multiple dose treatments. Certain genes, especially the P-glycoprotein coding gene (ABCB1), show high expression level in resistant cells compared with the wild type, suggesting a possible pathway that may contribute to the antidrug mechanism

A Protein-Based Hydrogel for <i>In Vitro</i> Expansion of Mesenchymal Stem Cells

<div><p>Hydrogels are widely used as scaffolds in tissue engineering because they can provide excellent environments for bioactive components including growth factors and cells. We reported in this study on a physical hydrogel formed by a specific protein-peptide interaction, which could be used for the three dimensional (3D) cell culture of murine mesenchymal stem cells (mMSC). The mMSC kept dividing during the 7-day culture period and the metabolic-active cell number at day 7 was 359% more than that at day 1. This kind of physical hydrogel could be converted to a homogeneous solution by firstly adding an equal volume of culture medium and then pipeting for several times. Therefore, mMSC post culture could be easily separated from cell-gel constructs. We believed that the protein-based hydrogel system in this study could be developed into a promising scaffold for <i>in vitro</i> expansion of stem cells and cell therapy. This work would be in the general interests of researchers in the fields of biomaterials and supramolecular chemistry.</p></div

The abundance of carbapenemase and 16S rRNA genes and DNA extraction recoveries for each samples from the WWTP.

<p>The abundance of carbapenemase and 16S rRNA genes and DNA extraction recoveries for each samples from the WWTP.</p

A cartoon representation to illustrate the formation of the hydrogels.

<p>3D networks of the hydrogels are formed by the specific protein-peptide interaction. The blue, green, red and cyan represent ULD tetramer; the yellow represent TIP-1 protein; the grey thick line represent PEG-peptide; the grey balls represent hexapeptide of WRESAI which can bind with TIP-1.</p

Li₅AlO₄‑Assisted Low-Temperature Sintering of Dense Li₇La₃Zr₂O₁₂ Solid Electrolyte with High Critical Current Density

In recent years, solid electrolytes (SEs) have been developed a lot due to the superior safety of solid-state batteries (SSBs) upon liquid electrolyte-based commercial batteries. Among them, garnet-type Li7La3Zr2O12 (LLZO) is one of the few SEs that is stable to lithium anode with high Li+ conductivity and the feasibility of preparation under ambient air, which makes it a promising candidate for fabricating SSBs. However, high sintering temperature (>1200 °C) prevents its large-scale production, further hindering its application. In this work, the Li5AlO4 sintering aid is proposed to decrease the sintering temperature and modify the grain boundaries of LLZO ceramics. Li5AlO4 generates in situ Li2O atmosphere and molten Li–Al–O compounds at relatively low temperatures to facilitate the gas–liquid–solid material transportation among raw LLZO grains, which decreases the densification temperature over 150 °C and strengthens the grain boundaries against lithium dendrites. As an example, Ta-doped LLZO ceramics without excessive Li sintered with 2 wt % Li5AlO4 at 1050 °C delivered high relative density > 94%, an ionic conductivity of 6.7 × 10–4 S cm–1, and an excellent critical current density (CCD) of 1.5 mA cm–2 at room temperature. In comparison, Ta-doped LLZO with 15% excessive Li sintered at 1200 °C delivered low relative density < 89%, a low ionic conductivity of ∼2 × 10–4 S cm–1, and a poor CCD of 0.5 mA cm–2. Li symmetric cells and Li-LFP full cells fabricated with Li5AlO4-assised ceramics were stably cycled at 0.2 mA cm–2 over 2000 h and at 0.8C over 100 cycles, respectively

Resistance profiles of KPC-2 for <i>Klebsiella</i> isolates, <i>E</i>.<i>coli</i> J53 harboring <i>bla</i>_KPC-2 gene, and the <i>E</i>.<i>coli</i> J53 recipient strain.

<p>Resistance profiles of KPC-2 for <i>Klebsiella</i> isolates, <i>E</i>.<i>coli</i> J53 harboring <i>bla</i>_KPC-2 gene, and the <i>E</i>.<i>coli</i> J53 recipient strain.</p

PCR primers used in this study.

<p>PCR primers used in this study.</p