Dynamic and Functional Characteristics of Predominant Species in Industrial Paocai as Revealed by Combined DGGE and Metagenomic Sequencing

The microbial community during the fermentation of industrial paocai, a lactic acid fermented vegetable food, was investigated via combined denaturing gradient gel electrophoresis (DGGE) and metagenomic sequencing. Firmicutes and Proteobacteria were identified as the dominant phyla during the fermentation. DGGE results of the bacterial community analysis showed that many genera were observed during the fermentation of industrial paocai, but the same predominant genus and species were observed: Lactobacillus and Lactobacillus (L.) alimentarius/L. paralimentarius. The abundance of L. alimentarius/L. paralimentarius increased fast during the initial stage of fermentation and approximately remained constant during the later stage. Metagenomic sequencing was used to finally identify the predominant species and their genetic functions. Metabolism was the primary functions of the microbial community in industrial paocai fermentation, including carbohydrate metabolism (CM), overview (OV), amino acid metabolism (AAM), nucleotide metabolism (NM), energy metabolism (EM), etc. The predominant species L. alimentarius and L. paralimentarius were involved in plenty of pathways in metabolism and played different roles in the metabolism of carbohydrate, amino acid, lipid to form flavor compounds during industrial paocai fermentation. This study provided valuable information about the predominant species in industrial paocai and its functional properties, which could enable us to advance our understanding of the fermentation mechanism during fermentation of industrial paocai. Our results will advance the understanding of the microbial roles in the industrial paocai fermentation and provide a theoretical basis for improving the quality of industrial paocai products

Design of Wide-Spectrum Inhibitors Targeting Coronavirus Main Proteases

The genus Coronavirus contains about 25 species of coronaviruses (CoVs), which are important pathogens causing highly prevalent diseases and often severe or fatal in humans and animals. No licensed specific drugs are available to prevent their infection. Different host receptors for cellular entry, poorly conserved structural proteins (antigens), and the high mutation and recombination rates of CoVs pose a significant problem in the development of wide-spectrum anti-CoV drugs and vaccines. CoV main proteases (M(pro)s), which are key enzymes in viral gene expression and replication, were revealed to share a highly conservative substrate-recognition pocket by comparison of four crystal structures and a homology model representing all three genetic clusters of the genus Coronavirus. This conclusion was further supported by enzyme activity assays. Mechanism-based irreversible inhibitors were designed, based on this conserved structural region, and a uniform inhibition mechanism was elucidated from the structures of M(pro)-inhibitor complexes from severe acute respiratory syndrome-CoV and porcine transmissible gastroenteritis virus. A structure-assisted optimization program has yielded compounds with fast in vitro inactivation of multiple CoV M(pro)s, potent antiviral activity, and extremely low cellular toxicity in cell-based assays. Further modification could rapidly lead to the discovery of a single agent with clinical potential against existing and possible future emerging CoV-related diseases

Enhanced presentation of MHC class Ia, Ib and class II-restricted peptides encapsulated in biodegradable nanoparticles: a promising strategy for tumor immunotherapy

<p>Abstract</p> <p>Background</p> <p>Many peptide-based cancer vaccines have been tested in clinical trials with a limited success, mostly due to difficulties associated with peptide stability and delivery, resulting in inefficient antigen presentation. Therefore, the development of suitable and efficient vaccine carrier systems remains a major challenge.</p> <p>Methods</p> <p>To address this issue, we have engineered polylactic-co-glycolic acid (PLGA) nanoparticles incorporating: (i) two MHC class I-restricted clinically-relevant peptides, (ii) a MHC class II-binding peptide, and (iii) a non-classical MHC class I-binding peptide. We formulated the nanoparticles utilizing a double emulsion-solvent evaporation technique and characterized their surface morphology, size, zeta potential and peptide content. We also loaded human and murine dendritic cells (DC) with the peptide-containing nanoparticles and determined their ability to present the encapsulated peptide antigens and to induce tumor-specific cytotoxic T lymphocytes (CTL) <it>in vitro</it>.</p> <p>Results</p> <p>We confirmed that the nanoparticles are not toxic to either mouse or human dendritic cells, and do not have any effect on the DC maturation. We also demonstrated a significantly enhanced presentation of the encapsulated peptides upon internalization of the nanoparticles by DC, and confirmed that the improved peptide presentation is actually associated with more efficient generation of peptide-specific CTL and T helper cell responses.</p> <p>Conclusion</p> <p>Encapsulating antigens in PLGA nanoparticles offers unique advantages such as higher efficiency of antigen loading, prolonged presentation of the antigens, prevention of peptide degradation, specific targeting of antigens to antigen presenting cells, improved shelf life of the antigens, and easy scale up for pharmaceutical production. Therefore, these findings are highly significant to the development of synthetic vaccines, and the induction of CTL for adoptive immunotherapy.</p

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Relationship between the Vibration Acceleration and Stability of a Continuous Girder Bridge during Horizontal Rotation

To ensure the safety of bridges during horizontal rotation, we propose a method through which it is possible to evaluate the stability of structures in real time by measuring the vibration acceleration of the rotating structure. First, the vibration characteristics collected during the horizontal rotation of a typical high-speed railway bridge were compared with the results of a finite element analysis. Second, the analytic formula to calculate the ratio of vibration acceleration and the pier-bottom-section bending moment for the rotating structure was deduced by considering the beam and pier as an infinite-degree-of-freedom rod. Then, the results of the analytical formula were compared with those of the finite element calculation. Overall, the results showed that the bending moment of the pier bottom (which was related to the stability of the rotating bridge) was affected only by the two asymmetrical vibration modes. The analytic formula built by considering the beam and pier as an infinite degree-of-freedom rod with equal cross-section effectively described the relationship between the vibration acceleration and pier-bottom-bending moment. Finally, the vibration of the rotating bridge was simplified to the superposition of the first two asymmetric vibration modes in the facade. Based on our findings, we were able to provide a formula and some check tables to calculate the permissible value of vibration acceleration for typical high-speed railway bridges

Delineation of Radar Glacier Zones in the Antarctic Peninsula Using Polarimetric SAR

Climate change is a cause of the expansion of snowmelt phenomena in the Antarctic, and shifts in position of wet and dry snow lines have been considered as good indicators of climate changes. The impacts of climate change are observable by the delineation of significant position change of glacier zones. The principal limitation of current glacier zone classification methods by synthetic aperture radar (SAR) image is that it is difficult to discriminate dry-snow and wet-snow zones using only single-polarimetric radar backscattering intensity. This study tried to solve the problem using polarimetric SAR (PolSAR). Analysis indicates that polarimetric decomposition elements could be efficient characteristics to delineate radar glacier zones by recognition of principal backscatter patterns. Further, two radar glacier zone classification processes for polarimetric SAR are proposed: a supervised support vector machine (SVM) classification process and a simple decision-tree classification method. These methods enable reliable delineation of radar glacier zones in the Antarctic Peninsula. Polarimetric SAR, which provides more information about the scattering processes and target structure, proves to be an efficient tool for delineating radar glacier zones and snowmelt detection

Additional file 3 of Targeting Bruton’s tyrosine kinase in vitreoretinal lymphoma: an open-label, prospective, single-center, phase 2 study

Additional file 3. Additional methods

Additional file 1 of Targeting Bruton’s tyrosine kinase in vitreoretinal lymphoma: an open-label, prospective, single-center, phase 2 study

Additional file 1: Table S1. Characteristics of patients with PVRL and PCNSL with vitreoretinal involvement

Development of Monoclonal Hybridoma Cell Lines and Extracting Antibody Against Fummonisin B1

Objective:To acquire monoclonal hybridoma cell lines against fummonisin B1(FB1) and extract monoclonal antibody against FB1.Methods: Coupling antigens of FB1-KLH and FB1-BSA with chemical methods and immune 6-8 weeks old femaleBALB/c mice with FB1-KLH. Integrating spleen cells with sp2/0 myeloma cells to acquire hybridoma cell lines secreting McAb against FB1. The method of multiple subclones was used to select cell lines stably secreting McAb. McAbs was got from ascites and purified. The subclass of antibody was measured and the molecular weight was identified. The specificity and sensitivity of McAb were identified with indirect competitive inhibition ELISA.Results:The results of serum from immuned mice showed that after five times of immunization the titer stables at 1×10-6, and the McAb belongs to IgG1 subclass, the light chain was ?, the molecular weight of heavy and light chain were 55kDa and 32kDa, respectively. ELISA results showed that McAb could react with FB1. The linear range indirect competitive inhibition ELISA is 10-500ng/ml.Conclusion:The monoclonal hybridoma cell lines and the high specificity,high sensitivity of FB1-McAb was got