A Versatile Method for Functionalizing Surfaces with Bioactive Glycans

Microarrays and biosensors owe their functionality to our ability to display surface-bound biomolecules with retained biological function. Versatile, stable, and facile methods for the immobilization of bioactive compounds on surfaces have expanded the application of high-throughput “omics”-scale screening of molecular interactions by nonexpert laboratories. Herein, we demonstrate the potential of simplified chemistries to fabricate a glycan microarray, utilizing divinyl sulfone (DVS)-modified surfaces for the covalent immobilization of natural and chemically derived carbohydrates, as well as glycoproteins. The bioactivity of the captured glycans was quantitatively examined by surface plasmon resonance imaging (SPRi). Composition and spectroscopic evidence of carbohydrate species on the DVS-modified surface were obtained by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), respectively. The site-selective immobilization of glycans based on relative nucleophilicity (reducing sugar vs amine- and sulfhydryl-derived saccharides) and anomeric configuration was also examined. Our results demonstrate straightforward and reproducible conjugation of a variety of functional biomolecules onto a vinyl sulfone-modified biosensor surface. The simplicity of this method will have a significant impact on glycomics research, as it expands the ability of nonsynthetic laboratories to rapidly construct functional glycan microarrays and quantitative biosensors

sj-pdf-1-imr-10.1177_03000605211047074 - Supplemental material for Relationship between non-alcoholic fatty liver disease and cardiac arrhythmia: a systematic review and meta-analysis

Supplemental material, sj-pdf-1-imr-10.1177_03000605211047074 for Relationship between non-alcoholic fatty liver disease and cardiac arrhythmia: a systematic review and meta-analysis by Hang Gong, Xianli Liu and Fang Cheng in Journal of International Medical Research</p

Transcription profile of ChpPV RNA.

<p>(<b>A</b>) <b>Northern blotting analysis</b>. Total RNA was isolated from COS-7 cells transfected with pC1ChpPV, and was used for Northern blotting analysis. The blots were hybridized to three ChpPV DNA probes (<i>NSCap</i>, <i>NS1</i> and <i>Cap</i>) that spanned various regions of the ChpPV genome, as diagramed at the bottom of panel B. Sizes of the RNA bands detected by each probe are indicated in kb to the right side of each lane. The RNA marker ladder is shown in lane 1. (<b>B</b>) <b>Transcription map of ChpPV</b>. The ChpPV genome is shown to scale, with transcription landmarks indicated. All of the RNA species detected in our assays are diagrammed to display their identities and respective sizes in the absence of the polyA tail. The putative ORFs that each can encode are also diagramed, and the predicted sizes (kDa) of translated proteins are indicated to the right.</p

Regioselective Reductive Openings of Acetals; Mechanistic Details and Synthesis of Fluorescently Labeled Compounds

Regioselective reductive openings of mixed phenolic-benzylic acetals, using BH3·NMe3−AlCl3, was investigated, and a mechanism where the outcome is directed by the electrostatic potential of the two oxygen atoms is presented. The regioselective acetal opening was used in the synthesis of a fluorescently labeled analogue to antiproliferative xylosides. The fluorescently labeled xyloside was tested for uptake, antiproliferative activity, and glycosaminoglycan priming in different cell lines. The xyloside was taken up by all cell lines but did not initiate glycosaminoglycan biosynthesis

Transfection of ChpPV NS1 induces apoptosis in B19V-permissive cells.

<p>UT7/Epo-S1 cells were transfected with pGFPHA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015113#pone.0015113-Qiu4" target="_blank">[35]</a> (as negative control), pGFP-B19VNS1HA (positive control), and pGFP-ChpPVNS1HA. (<b>A</b>) Cells were harvested at 24 hrs posttransfection and subjected to Western blotting analysis using an anti-HA monoclonal antibody (Sigma, Clone HA-7). Untransfected cells were used as control (lane 1). A molecular marker is shown to the right with sizes in kDa. (<b>B</b>) Cells were stained with AnnexinV and propidium iodide (PI) at 24, 48 and 72 hrs posttransfection, respectively, and were then subjected to flow cytometry analysis. GFP-positive populations were gated for plotting by PI <i>vs.</i> AnnexinV staining. Numbers represent average percentage with standard deviation from three independent experiments. A representative experiment is shown. The number shown in the upper right quadrant and the number shown in the lower right quadrant in each plot are percentages of AnnexinV+/PI+ population and AnnexinV+/PI- population, respectively.</p

Phylogenetic analysis of ChpPV with the other 17 representative parvoviruses in each genus of <i>Parvovirinae</i>.

<p>Genome sequences (<b>A</b>), NS1 (<b>B</b>) and VP1 (<b>C</b>) amino acid sequences of representative members in each genus of the subfamily <i>Parvovirinae</i> were used to determine the neighbor-joining phylogenetic tree using BioEdit Version 7. Genbank accession numbers of the sequences used follow the name of the virus.</p

Averaging Strategy for Interpretable Machine Learning on Small Datasets to Understand Element Uptake after Seed Nanotreatment

Understanding plant uptake and translocation of nanomaterials is crucial for ensuring the successful and sustainable applications of seed nanotreatment. Here, we collect a dataset with 280 instances from experiments for predicting the relative metal/metalloid concentration (RMC) in maize seedlings after seed priming by various metal and metalloid oxide nanoparticles. To obtain unbiased predictions and explanations on small datasets, we present an averaging strategy and add a dimension for interpretable machine learning. The findings in post-hoc interpretations of sophisticated LightGBM models demonstrate that solubility is highly correlated with model performance. Surface area, concentration, zeta potential, and hydrodynamic diameter of nanoparticles and seedling part and relative weight of plants are dominant factors affecting RMC, and their effects and interactions are explained. Furthermore, self-interpretable models using the RuleFit algorithm are established to successfully predict RMC only based on six important features identified by post-hoc explanations. We then develop a visualization tool called RuleGrid to depict feature effects and interactions in numerous generated rules. Consistent parameter-RMC relationships are obtained by different methods. This study offers a promising interpretable data-driven approach to expand the knowledge of nanoparticle fate in plants and may profoundly contribute to the safety-by-design of nanomaterials in agricultural and environmental applications

RPA70-AB domain directly interacts with HBoV1.

(A) A diagram of RPA70 domains. The RPA70 N-terminal domain (RPA70-N-ter), AB domain (RPA70-AB), subdomains A and B within AB domain, C-terminal domain (RPA70-C-ter), and Linkers are diagrammed and shown in different colors. AB domin and C-terminus have both protein and ssDNA binding capability, while the C-terminus mediates heterodimerization with RPA32. (B&D) Protein purification. All purified truncated domains of RPA70, RPA70-N-ter, RPA70-AB, RPA70-C-ter, RPA70-A, and RPA70-B domains, indicated by arrowheads, were analyzed on SDS-(4–20%)PAGE gel. (C, E&F) In vitro pull-down assays. 4 μg of purified GST-NP1 or GST were used to pull down 4 μg of purified domains, as indicated, using Glutathione agarose. Pulldown proteins were analyzed by Western blotting with an anti-His antibody (C&E) or with anti-GST as a control (F). Arrowheads denote the interacting domains.</p

Mass spectrometry identification of each protein band (Bands 1–4) and section (Sections 1–2) excised from the gel shown in Fig 1B.

Numbers of the Unique/Total peptides of each identified protein are shown with the identification number and name (Reference), gene, and molecular weight (MW). (XLS)</p

NP1 binding of Ku70 does not affect the stability of Ku70.

(A) Protein controls. 4 μg of purified Ku70His and GST-NP1 proteins were analyzed on SDS-(4–20%)PAGE gel stained with Coomassie brilliant blue. (B) In vitro pulldown assay of GST-NP1 and Ku70. 4 μg of purified Ku70His and GST-NP1 proteins were added into 300 μl binding buffer with addition of 30 μl pre-washed glutathione agarose. After incubation at 4°C for 4 h or overnight, the glutathione agarose were washed three times with wash buffer and pelleted by centrifugation at 3, 000 g for 1 min before addition of 1 × Laemmli sample buffer. The samples were boiled at 95°C for 5 min and separated on SDS-(4–20%)PAGE gel, followed by Coomassie brilliant blue staining. M, protein size ladder marker. O/N, overnight. (TIF)</p