Recognition of outer membrane proteins using multiple feature fusion

Introduction: Outer membrane proteins are crucial in maintaining the structural stability and permeability of the outer membrane. Outer membrane proteins exhibit several functions such as antigenicity and strong immunogenicity, which have potential applications in clinical diagnosis and disease prevention. However, wet experiments for studying OMPs are time and capital-intensive, thereby necessitating the use of computational methods for their identification.Methods: In this study, we developed a computational model to predict outer membrane proteins. The non-redundant dataset consists of a positive set of 208 outer membrane proteins and a negative set of 876 non-outer membrane proteins. In this study, we employed the pseudo amino acid composition method to extract feature vectors and subsequently utilized the support vector machine for prediction.Results and Discussion: In the Jackknife cross-validation, the overall accuracy and the area under receiver operating characteristic curve were observed to be 93.19% and 0.966, respectively. These results demonstrate that our model can produce accurate predictions, and could serve as a valuable guide for experimental research on outer membrane proteins

Kovács Mihály és a kibernetika oktatás kezdetei a budapesti Piarista gimnáziumban

Genotype-specific transcriptional DEGs results in resistant genotype and susceptible genotype. (XLSX 4357 kb

Passive Filler-Loaded Silicon Oxycarbide Coating on Nickle Alloy with High Thermal Shocking Behavior and Oxidation Resistance

Polymer-derived ceramic (PDC) coatings of considerable thickness can offer promising protection for metallic and superalloy substrates against oxidation and corrosion, yet the preparation remains challenging. Here, a SiOC/Al2O3/YSZ coating was prepared on a nickel alloy with a spraying method using Al2O3 and yttria-stabilized zirconia (YSZ) as passive fillers. The thickness can reach up to 97 μm with the optimal mass fraction and particle sizes of the passive fillers. A small or isolated SiOC phase is formed in the coating, which can effectively alleviate the shrinkage and cracking during the pyrolysis. The SiOC/Al2O3/YSZ coating exhibits low thermal conductivity and high bonding strength with the substrate. Moreover, the coating shows good thermal shock resistance between 800 °C-room temperature cycles and oxidation resistance at 1000 °C for 36 h. This work provides an effective guide for the design of thick PDC coatings to further promote their application in the thermal protective field

The Correlation between Targeted Contrast-Enhanced Ultrasound Imaging and Tumor Neovascularization of Ovarian Cancer Xenografts in Nude Mice

In order to explore the correlation between targeted contrast-enhanced ultrasound imaging and tumor neovascularization of ovarian cancer xenografts in nude mice, a total of 49 nude mice were selected and randomly divided into 1-week group, 2-week group, 3-week group, 4-week group, 5-week group, 6-week group, and 7-week group according to their ovarian cancer xenografts’ growth time, with 7 ovarian cancer xenografts in each group. After preparing antibody-carrying targeted contrast agent, each group of xenografts performed normal and targeted contrast ultrasound examinations to obtain peak intensity, time to peak, and other imaging parameters; then, those ovarian cancer xenografts were sacrificed for pathological analysis: the neovascular density and antibody expression of the cancer xenografts at different stages were observed and counted, and the correlation between targeted contrast-enhanced ultrasound parameters and tumor neovascular densities of the ovarian cancer xenografts was analyzed. The results show that the peak intensities of targeted contrast ultrasound imaging are greater than that of ordinary ultrasound imaging in the 2-, 3-, 4-, and 5-week groups with statistically significant differences (P<0.05); the time to peak of targeted contrast ultrasound imaging is shorter than that of ordinary ultrasound imaging in the 2-, 3-, 4-, and 5-week groups with statistically significant differences (P<0.05); there is a positive correlation between the peak intensities of targeted contrast ultrasound imaging and tumor neovascular densities of the ovarian cancer xenografts in the 2-, 3-, and 4-week group (r2 = 0.645, r3 = 0.668, and r4 = 0.693, P<0.05); there is a negative correlation between the time to peak of targeted contrast ultrasound imaging and tumor neovascular densities of the ovarian cancer xenografts in the 2-, 3-, and 4-week groups (r2 = −0.669, r3 = −0.692, and r4 = −0.704, P<0.05). Therefore, the targeted contrast-enhanced ultrasound imaging parameters have a certain correlation with tumor neovascular density of ovarian cancer xenografts in nude mice and this correlation is more significant in the early stage of ovarian cancer; hence, targeted contrast-enhanced ultrasound imaging may provide a new method, new idea, and new basis for the diagnosis of early ovarian cancer

Large-scale transcriptome comparison of sunflower genes responsive to Verticillium dahliae

Abstract Background Sunflower Verticillium wilt (SVW) is a vascular disease caused by root infection with Verticillium dahliae (V. dahlia) . It is a serious threat to the yield and quality of sunflower. However, chemical and agronomic measures for controlling this disease are not effective. The selection of more resistant genotypes is a desirable strategy to reduce contamination. A deeper knowledge of the molecular mechanisms and genetic basis underlying sunflower Verticillium wilt is necessary to accelerate breeding progress. Results An RNA-Seq approach was used to perform global transcriptome profiling on the roots of resistant (S18) and susceptible (P77) sunflower genotypes infected with V. dahlia . Different pairwise transcriptome comparisons were examined over a time course (6, 12 and 24\ua0h, and 2, 3, 5 and 10 d post inoculation). In RD, SD and D datasets, 1231 genes were associated with SVW resistance in a genotype-common transcriptional pattern. Moreover, 759 and 511 genes were directly related to SVW resistance in the resistant and susceptible genotypes, respectively, in a genotype-specific transcriptional pattern. Most of the genes were demonstrated to participate in plant defense responses; these genes included peroxidase (POD), glutathione peroxidase, aquaporin PIP, chitinase, L-ascorbate oxidase, and LRR receptors. For the up-regulated genotype-specific differentially expressed genes (DEGs) in the resistant genotype, higher average fold-changes were observed in the resistant genotype compared to those in the susceptible genotype. An inverse effect was observed in the down-regulated genotype-specific DEGs in the resistant genotype. KEGG analyses showed that 98, 112 and 52 genes were classified into plant hormone signal transduction, plant-pathogen interaction and flavonoid biosynthesis categories, respectively. Many of these genes, such as CNGC, RBOH, FLS2, JAZ, MYC2 NPR1 and TGA, regulate crucial points in defense-related pathway and may contribute to V. dahliae resistance in sunflower. Conclusions The transcriptome profiling results provided a clearer understanding of the transcripts associated with the crosstalk between sunflower and V. dahliae . The results identified several differentially expressed unigenes involved in the hyper sensitive response (HR) and the salicylic acid (SA)/jasmonic acid (JA)-mediated signal transduction pathway for resistance against V. dahliae . These results are useful for screening resistant sunflower genotypes

The treatment of SARS-CoV2 with antivirals and mitigation of the cytokine storm syndrome: the role of gene expression

In the absence of a vaccine, the treatment of SARS-CoV2 has focused on eliminating the virus with antivirals or mitigating the cytokine storm syndrome (CSS) that leads to the most common cause of death: respiratory failure. Herein we discuss the mechanisms of antiviral treatments for SARS-CoV2 and treatment strategies for the CSS. Antivirals that have shown in vitro activity against SARS-CoV2, or the closely related SARS-CoV1 and MERS-CoV, are compared on the enzymatic level and by potency in cells. For treatment of the CSS, we discuss medications that reduce the effects or expression of cytokines involved in the CSS with an emphasis on those that reduce IL-6 because of its central role in the development of the CSS. We show that some of the medications covered influence the activity or expression of enzymes involved in epigenetic processes and specifically those that add or remove modifications to histones or DNA. Where available, the latest clinical data showing the efficacy of the medications is presented. With respect to their mechanisms, we explain why some medications are successful, why others have failed, and why some untested medications may yet prove useful.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Network-Based Biomarkers for Cold Coagulation Blood Stasis Syndrome and the Therapeutic Effects of Shaofu Zhuyu Decoction in Rats

In this study, the reverse docking methodology was applied to predict the action targets and pathways of Shaofu Zhuyu decoction (SFZYD) bioactive ingredients. Furthermore, Traditional Chinese Medicine (TCM) cold coagulation blood stasis (CCBS) syndrome was induced in female Sprague-Dawley rats with an ice-water bath and epinephrine, and SFZYD was used to treat CCBS syndrome. A metabolomic approach was used to evaluate changes in the metabolic profiles and to analyze the pharmacological mechanism of SFZYD actions. Twenty-three potential protein targets and 15 pathways were discovered, respectively; among these, pathways are associated with inflammation and immunological stress, hormone metabolism, coagulation function, and glycometabolism. There were also changes in the levels of endogenous metabolites of LysoPCs and glucuronides. Twenty endogenous metabolites were identified. Furthermore, the relative quantities of 6 endogenous metabolites in the plasma and 5 in the urine were significantly affected by SFZYD (P<0.05). The pharmacological mechanism of SFZYD was partially associated with glycerophospholipid metabolism and pentose and glucuronate interconversions. In conclusion, our findings demonstrated that TCM CCBS pattern induced by ice water and epinephrine was complex and related to multiple metabolic pathways. SFZYD did regulate the TCM CCBS by multitargets, and biomarkers and SFZYD should be used for the clinical treatment of CCBS syndrome

A multifunctional hierarchical porous SiO2/GO membrane for high efficiency oil/water separation and dye removal

2020 Elsevier Ltd Removing contaminants from wastewater is critical to secure the global water supply. Membrane technologies for water purification are exceptionally attractive due to their high efficiency and low energy consumption. The traditional porous polymer films, however, are easy to be fouled by the organic pollutants, causing pore blockage and deteriorated separation performance. We herein report the rational design of a porous SiO2/GO hybrid membrane by coupling graphene oxide (GO) nanosheets with SiO2 nanoparticles and using ethylenediamine to crosslink them, for efficient oil/water separation and dye removal. The SiO2 nanoparticles provide an excellent hydrophilicity and underwater superoleophobicity interface, resulting in efficient and antifouling oil/water separation with an outstanding rejection rate over 99.4% for different types of oil; and the hierarchical scaffold, formed from the hydrophilic GO nanosheets embedded with SiO2 nanoparticles, greatly facilitates the rapid permeation of water with a high flux rate of up to 2387 L m−2 h−1 for pure water and 470 L m−2 h−1 for oil/water separation. Moreover, the abundant functional groups on the GO surface also render this membrane with a high removal capability for dye blocking, enabling it to remove soluble pollutants in molecular dimensions as well. This design strategy not only provides an outstanding membrane for water purification but also sheds light on the design of multi-purpose functional membranes for a variety of energy and environment-related applications

Observation of a ferromagnetic-to-paramagnetic phase transition in Ce

$\text{Ce}_{1-x}\text{Mg}_{x}\text{Co}_{3}$ are promising candidates for the permanent magnets since they can show ferromagnetism and large anisotropy by substituting Mg for Ce in a paramagnetic $\text{CeCo}_{3}$ compound. In this work, a room-temperature ferromagnetism with a second-order magnetic phase transition is observed in the $\text{Ce}_{0.65}\text{Mg}_{0.35}\text{Co}_{3}$ (CMC) compound prepared by a cold crucible levitation melting method. Based on the DC magnetization data, the critical phenomenon around the phase transition point (${\sim}308\ \text{K}$ ) in CMC is investigated and the critical exponents ${\beta}$ for spontaneous magnetization, ${\gamma}$ for susceptibility and ${\delta}$ for critical isothermal magnetization are determined independently by three different data processing techniques including the modified Arrott plot, Kouvel-Fisher plot, and critical isotherm analysis. It is noteworthy that the magnetizations obey the scaling equation, indicating that the critical parameters including Tc, ${\beta}$ , ${\gamma}$ and ${\delta}$ are reliable and self-consistent. The calculation of spin interaction with the obtained critical exponents further suggests a long-range ferromagnetic coupling with $J(r)\sim r^{-4.622}$ in CMC