Chongjun Xu - Academia.edu (original) (raw)

Papers by Chongjun Xu

Reusable and sensitive exonuclease III activity detection on DNB nanoarrays based on cPAS sequencing technology

Enzyme and microbial technology, Oct 1, 2021

In this article we describe a sensitive exonuclease III detection method using a DNB nanoarray fr... more In this article we describe a sensitive exonuclease III detection method using a DNB nanoarray from a BGISEQ-500 sequencing kit and demonstrate a detection limit as low as 0.001 U/mL. The flow cell of the sequencing kit was loaded with billions of DNA nanoballs (DNBs) to form the DNB nanoarray and initially used for massively parallel sequencing. The 3'-end recessed dsDNA structure formed by sequencing was shown to be a perfect substrate for exonuclease III, but not for other nucleases such as exonuclease I, RecJf and nuclease P1. We developed an exonuclease III assay using the DNB nanoarray, together with other reagents within the BGISEQ-500 sequencing kit, which only required one additional cycle of sequencing. The DNB nanoarray can be reused for the exonuclease III assay at least five times. This method demonstrated superior sensitivity, selectivity, and reusability compared with other assay methods and is accompanied by low cost and simple setup.

DNA Sequencing by Hybridization with Arrays of Samples or Probes

DNA Arrays

SBH with Arrays of Samples or Probes ... DNA Sequencing by Hybridization with Arrays of Samples o... more SBH with Arrays of Samples or Probes ... DNA Sequencing by Hybridization with Arrays of Samples or Probes ... Radoje Drmanac, Snezana Drmanac, Joerg Baier, Gloria Chui, Dan Coleman, Robert Diaz, Darryl Gietzen, Aaron Hou, Hui Jin, Tatjana Ukrainczyk, and Chongjun Xu

Machine learning modelling assisting function-oriented enzyme engineering is normally built on pr... more Machine learning modelling assisting function-oriented enzyme engineering is normally built on predefined protein sequence space. However, efficient defining the determinant amino acid positions upon which the combinatorial mutation library is constructed is still a challenge in protein science. Herein, we present a comprehensive investigation of modifying a recombinant DNA polymerase for efficient incorporating one unnatural nucleotide, including the identification of key sites/regions, machine learning-assisted mutants screening, and the underlying mechanism of kinetics boosting. By using hundreds of training points and only dozens of testing samples, we found that one highly engineered enzyme’s catalytic efficiency can be further improved by one order of magnitude by specific mutation on two sites, 485I and 451L. Compared to the position 485 which is known to dominate local conformation of B-family DNA polymerases, 451 is a split-new active site discovered by our approach. A nove...

Additional file 6: Figure S3. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Full interaction network. Predicted miRNAs are represented in large nodes, colored by type (red: ... more Full interaction network. Predicted miRNAs are represented in large nodes, colored by type (red: blood specific, blue: tissue specific, green: all others) and genes are represented by smaller gray nodes. (PNG 1033Â kb)

Additional file 1: Table S3. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

miRNA read count of the BGISEQ-500. (XLSX 250Â kb)

Additional file 4: Table S2. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

List of novel miRNA candidates. (XLSX 6531Â kb)

Additional file 5: Figure S2. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Histogram of the decade logarithm of the context++ scores (multiplied by â 1) of predicted target... more Histogram of the decade logarithm of the context++ scores (multiplied by â 1) of predicted targets for the candidate miRNAs. Since negative context++ scores are favorable, the miRNA targets on the right of the diagram are more likely true interactions. (PNG 78Â kb)

Energies, 2022

Nonionic–anionic surfactants are expected to be applied in chemical flooding due to their importa... more Nonionic–anionic surfactants are expected to be applied in chemical flooding due to their important properties such as ultralow IFT values, good salt tolerance, and no chromatographic separation in porous media. In this study, a new type of nonionic–anionic–hydrophobic group structure surfactant N,N-dihydroxyethylalkylamide carboxylate (EAMC) was synthesized. The synergistic effects between petroleum sulfonate (KPS) and EAMC in reducing interfacial tension (IFT) and emulsification properties were studied. The influences of salt, alkali and Ca2+ on the IFTs of surfactant solutions were also investigated. One-dimensional core flooding experiments were used to characterize the enhanced oil recovery capability of the KPS and EAMC mixed system. The experimental results show that both EAMC and KPS have high interfacial activity and can reduce IFTs to about 0.01 mN/m order of magnitude against decane at optimized concentrations. The area occupied by the hydrophilic group of EAMC on the int...

Additional file 7: Figure S4. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Core network characteristics as node degree distribution (top) and shortest path length (bottom).... more Core network characteristics as node degree distribution (top) and shortest path length (bottom). (PNG 129Â kb)

Additional file 3: Table S1. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Comparison of BGISEQ-500 to Agilent. (XLSX 135Â kb)

Additional file 8: Figure S5. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Venn diagram showing the distribution of predicted target genes for tissue-specific miRNA candida... more Venn diagram showing the distribution of predicted target genes for tissue-specific miRNA candidates, blood-specific miRNA candidates, and all other miRNA candidates. (PNG 156Â kb)

Additional file 9: Figure S6. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Comparison of the pathway enrichment analysis for the GeneTrail2 analysis with respect to the thr... more Comparison of the pathway enrichment analysis for the GeneTrail2 analysis with respect to the three target sets. Red arrows represent significant enrichments. (PNG 289Â kb)

Acides nucleiques et polypeptides

L'invention concerne des acides nucleiques, des sequences polypeptidiques codees par ces acid... more L'invention concerne des acides nucleiques, des sequences polypeptidiques codees par ces acides nucleiques et leurs utilisations correspondantes.

Neuartige nukleinsäure und polypeptide

AIP Advances, 2020

Almost fully dense pure alumina could be prepared by fast firing (FF) at a high temperature (grea... more Almost fully dense pure alumina could be prepared by fast firing (FF) at a high temperature (greater than 1689 ○ C) and a high heating rate (∼350 ○ C/s) with a whole sintering cycle in approximately 2 min without pressure. Dynamics of the ultrafast densification was explored by comparing the densifying characters of FF sintering and conventional sintering. Results show that overlapping of surface/grain boundary diffusion and lattice diffusion caused by the high heating rate, as well as rapid migration of nanoscale particles caused by the high heating rate and the sufficiently high sintering temperature, leads to the ultrafast densification, which differs from conventional time-cost material diffusion. The ultrafast densification dynamics is expected to be helpful for understanding or developing new fast sintering methods for ceramics.

ABSTRACTHere we report a highly sensitive DNB-based on-chip Motif Finding (DocMF) system that uti... more ABSTRACTHere we report a highly sensitive DNB-based on-chip Motif Finding (DocMF) system that utilizes high throughput next-generation-sequencing (NGS) chips to profile protein binding or cleaving activity. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer-adjacent-motif (PAM) sequences of different CRISPR systems. Our DocMF platform can simultaneously screen both 5’ and 3’ PAM regions with high coverage using the same NGS library/chip. For the well-studied SpCas9, our DocMF platform identified a small proportion of noncanonical 5’-NAG-3’ (∼5%) and 5’-NGA-3’ (∼1.6%), in addition to its common PAMs, 5’-NGG-3’ (∼89.9%). We also used the DocMF to assay two uncharacterized Cas endonucleases, VeCas9 and BvCpf1. VeCas9 PAMs were not detected by the conventional PAM depletion method. However, DocMF discovered that both VeCas9 and BvCpf1 required broader and more complicated PAM sequences for target recognition. VeCas9 preferred the R-ri...

Genome Research, 2019

Here, we describe single-tube long fragment read (stLFR), a technology that enables sequencing of... more Here, we describe single-tube long fragment read (stLFR), a technology that enables sequencing of data from long DNA molecules using economical second-generation sequencing technology. It is based on adding the same barcode sequence to subfragments of the original long DNA molecule (DNA cobarcoding). To achieve this efficiently, stLFR uses the surface of microbeads to create millions of miniaturized barcoding reactions in a single tube. Using a combinatorial process, up to 3.6 billion unique barcode sequences were generated on beads, enabling practically nonredundant cobarcoding with 50 million barcodes per sample. Using stLFR, we demonstrate efficient unique cobarcoding of more than 8 million 20- to 300-kb genomic DNA fragments. Analysis of the human genome NA12878 with stLFR demonstrated high-quality variant calling and phase block lengths up to N50 34 Mb. We also demonstrate detection of complex structural variants and complete diploid de novo assembly of NA12878. These analyses ...

Background:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-5... more Background:Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well studied. In this study, we evaluated the performance of BGISEQ-500 on WES by side-to-side comparison with Hiseq4000, on wellcharacterized human sample NA12878.Results:BGISEQ demonstrated similarly high reproducibility as Hiseq for variation detection. Also, the SNPs from BGISEQ data is highly consistent with Hiseq results (concordance 96.5%∼97%). Variation detection accuracy was subsequently evaluated with data from the genome in a bottle project as the benchmark. Both platforms showed similar sensitivity and precision in SNP detection. While in indel detection, BGISEQ showed slightly higher sensitivity and lower precision. The impact of sequence depth and read length on variation detection accuracy was further analyzed, and showed that variation detection sensitivi...

Methods and materials relating to novel polypeptides and polynucleotides

Journal of Biological Chemistry, 1998