EGGTART: A tool to visualize the dynamics of biophysical transport under the inhomogeneous l-TASEP

The totally asymmetric simple exclusion process (TASEP), which describes the stochastic dynamics of interacting particles on a lattice, has been actively studied over the past several decades and applied to model important biological transport processes. Here, we present a software package, called EGGTART (Extensive GUI gives TASEP-realization in Real Time), which quantifies and visualizes the dynamics associated with a generalized version of the TASEP with an extended particle size and heterogeneous jump rates. This computational tool is based on analytic formulas obtained from deriving and solving the hydrodynamic limit of the process. It allows an immediate quantification of the particle density, flux, and phase diagram, as a function of a few key parameters associated with the system, which would be difficult to achieve via conventional stochastic simulations. Our software should therefore be of interest to biophysicists studying general transport processes and can in particular be used in the context of gene expression to model and quantify mRNA translation of different coding sequences.     

CK2 inhibitor CX4945 induces sequential inactivation of proteins in the signaling pathways related with cell migration and suppresses metastasis of A549 human lung cancer cells

Casein kinase 2 (CK2) is known to be involved in various cellular processes such as cell cycle, apoptosis and proliferation. It has been reported that the inhibition of CK2 induced by recently developed small molecule CX4945 shows anti-cancer effects including anti-proliferation and anti-angiogenesis in several different cancers including prostate cancer. Here we report that migration and invasion of A549 human lung cancer cells are suppressed by the inhibition of CK2 induced by CX4945. We found that CX4945 sequentially attenuates the proteins in PI3K/Akt and MAPK pathways, two signaling pathways related with cell migration. This sequential control of signal pathways inhibits the expression of membrane type 1-matrix metalloproteinase and this leads to the selective attenuation of one of the gelatinases, MMP-2, which can degrade components of extracellular matrix, and metastasis of A549 human lung cancer cell.     

Strategic Pore Architecture for Accommodating Volume Change from High Si Content in Lithium‐Ion Battery Anodes

To be a thinner and more lightweight lithium‐ion battery with high energy density, the next‐generation anode with high gravimetric and volumetric capacity is a prerequisite. In this regard, utilizing high silicon (3579 mAh g^?1) content in the electrode for the anode has been highlighted as a practically relevant approach. However, there still remains a crucial issue related to intrinsic volume expansion (>300%) of silicon upon lithiation, which can directly affect severe electrode swelling as well as accelerate its capacity fading by triggering structural degradation and electrical contact loss between particles. Herein, macropore‐exploited design, which can accommodate the volume change of high silicon content within the extended pore of graphite upon repeated cycling, is introduced. Such unique macropore‐exploited design leads to much less electrode swelling, by preserving its morphological integrity and contact between particles, than that of the comparative group with different sized pore and silicon distribution. As a result, this anode (914 mAh g^?1) demonstrates notable gravimetric (220 Wh kg^?1 at 6000 W kg^?1) and volumetric energy density (623 Wh L^?1 upon full lithiation after 100 cycles), exceeding that of a nano‐silicon blended graphite anode (127 Wh kg^?1 and 229 Wh L^?1) in the full‐cell system.     

Facile and Scalable Preparation of Ruthenium Oxide‐Based Flexible Micro‐Supercapacitors

Tremendous efforts have been invested in the development of the internet of things during the past 10 years. Implantable sensors still need embedded miniaturized energy harvesting devices, since commercialized thin films and microbatteries do not provide sufficient power densities and suffer from limited lifetime. Therefore, micro‐supercapacitors are good candidates to store energy and deliver power pulses while providing non‐constant voltage output with time. However, multistep expensive protocols involving mask aligners and sophisticated cleanrooms are used to prepare these devices. Here, a simple and versatile laser‐writing procedure to integrate flexible micro‐supercapacitors and microbatteries on current‐collector‐free polyimide foils is reported, starting from commercial powders. Ruthenium oxide (RuO₂)‐based micro‐supercapacitors are prepared by laser irradiation of a bilayered tetrachloroauric acid (HAuCl₄ · 3H₂O)–cellulose acetate/RuO₂ film deposited by spin‐coating, which leads to adherent Au/RuO₂ electrodes with a unique pillar morphology. The as‐prepared microdevices deliver 27 mF cm^?2/540 F cm^?3 in 1 m H₂SO₄ and retain 80% of the initial capacitance after 10 000 cycles. This simple process is applied to make carbon‐based micro‐supercapacitors, as well as metal oxide based pseudocapacitors and battery electrodes, thus offering a straightforward solution to prepare low‐cost flexible microdevices at a large scale.     

Salmonella enterica Diversity in Central Californian Coastal Waterways

Salmonella enterica is one of the most important bacterial enteric pathogens worldwide. However, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over 2 years from 12 coastal waterways in central California. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found, including 18 newly described STs. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium, and other frequently detected STs were associated with the serovars Heidelberg and Enteritidis; all of these serovars are important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxon-time relationship but no taxon-area or taxon-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest that the lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.     

Multiple FAS1 domains and the RGD motif of TGFBI act cooperatively to bind αvβ3 integrin,leading to anti-angiogenic and anti-tumor effects

TGFBI, a transforming growth factor β-induced extracellular matrix protein, circulates at a level of ~ 300 ng/ml in humans and modulates several integrin-mediated cellular functions. The protein contains an N-terminal EMI domain, four consecutive FAS1 domains, and the RGD motif. Each FAS1 domain and the RGD motif have been known to interact with avb3 integrin. Here, we found that the binding affinity (K_d) of TGFBI for αvβ3 integrin was approximately 3.8 × 10^? 8 M, a value ~ 2300-fold higher than that of a single FAS1 domain, and demonstrated that this greater affinity was due to the cooperative action of the four FAS1 domains and the RGD motif. Moreover, TGFBI exhibited more potent anti-angiogenic and anti-tumorigenic activities, even at a 100-fold lower molar dose than the reported effective dose of the FAS1 domain. Finally, our data showed that TGFBI specifically targeted the tumor vasculature and accumulated at the tumor site. Collectively, our results support the theory that TGFBI acts as a potent endogenous anti-tumor and anti-angiogenic molecule by targeting αvβ3 integrin, and highlights the importance of physiological circulating TGFBI levels in inhibiting tumor growth.     

A nucleic acid hydrolyzing recombinant antibody confers resistance to curtovirus infection in tobacco

A catalytic single chain variable antibody (scFv), 3D8 scFv, which has DNase activities, was functionally expressed in Nicotiana tabacum. The subcellular localization of the GFP-fused 3D8 indicated that the 3D8 protein was expressed in the cytosol of the N. tabacum protoplasts. Progenies of the transgenic tobacco plants exhibited complete resistance against two single stranded (ss) DNA geminiviruses, including the Beet curly top virus and the Beet severe curly top virus, without viral accumulation or disease symptoms. We presented a novel strategy for targeting the viral DNA itself in a sequence non-specific manner, rather than the viral proteins or RNAs, in order to generate virus-resistant transgenic plants. No noticeable adverse effects on the growth and reproduction of the transgenic plants were observed. Our results demonstrated that targeting viral DNA is an effective strategy for protecting plants from ssDNA viruses.     

Study on intraspecific diversity of Ralstonia solanacearum strains in West Malaysia using whole cell fatty acid analysis

Abstract

Surveys were conducted between the years of 2005 and 2006 at several locations in the northern, central and southern parts of West Malaysia to study the polymorphism of Ralstonia solanacearum strains. These sites included vegetables and farms with known hosts of the pathogen, such as banana, tomato, eggplant, chili and tobacco. Samples were collected from the suspected wilted plants and weeds, including soil and water samples, in selected areas. The bacterium was isolated in all samples using semi-selective tetrazolium chloride medium (TZC). The bacteria strains were detected by using the BIOLOG identification system and were confirmed by nested-PCR. Fatty Acid Methyl Esters (FAME) profiling was performed to determine polymorphism among 58 bacterial isolates. The results showed that the fatty acid composition varied for all R. solanacearum isolates. Grouping of R. solanacearum isolates by fatty acid composition suggested that the existence of distinct groups that were significantly related to host of bacteria but low correlation between fatty acid profiles and biovar or sampling site was detected. A unique FAME profile was found among the strains that have been isolated from banana.