scholarly journals Post-synthesis DNA modifications using a trans-cyclooctene click handle

2015 ◽  
Vol 13 (3) ◽  
pp. 909-915 ◽  
Author(s):  
Ke Wang ◽  
Danzhu Wang ◽  
Kaili Ji ◽  
Weixuan Chen ◽  
Yueqin Zheng ◽  
...  
Keyword(s):  
Dna Labeling ◽  
Dna Modifications ◽  
Thymidine Triphosphate ◽  
Post Synthesis ◽  
Dna Incorporation

Efficient enzymatic DNA incorporation of trans-cyclooctene thymidine triphosphate (TCO-TTP) is reported. The general handle of trans-cyclooctene can undergo a rapid bioorthogonal cycloaddition with tetrazine, which is suitable for further DNA labeling work.

scholarly journals Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Leena Malayil ◽  
Suhana Chattopadhyay ◽  
Emmanuel F. Mongodin ◽  
Amy R. Sapkota
Keyword(s):  
16S Rrna ◽  
Irrigation Water ◽  
Brackish Water ◽  
Water Sources ◽  
16S Rrna Sequencing ◽  
Vbnc State ◽  
Recycled Water ◽  
Dna Labeling ◽  
Rrna Sequencing ◽  
Brdu Labeling

AbstractNontraditional irrigation water sources (e.g., recycled water, brackish water) may harbor human pathogens, including Vibrio spp., that could be present in a viable-but-nonculturable (VBNC) state, stymieing current culture-based detection methods. To overcome this challenge, we coupled 5-bromo-2′-deoxyuridine (BrdU) labeling, enrichment techniques, and 16S rRNA sequencing to identify metabolically-active Vibrio spp. in nontraditional irrigation water (recycled water, pond water, non-tidal freshwater, and tidal brackish water). Our coupled BrdU-labeling and sequencing approach revealed the presence of metabolically-active Vibrio spp. at all sampling sites. Whereas, the culture-based method only detected vibrios at three of the four sites. We observed the presence of V. cholerae, V. vulnificus, and V. parahaemolyticus using both methods, while V. aesturianus and V. shilonii were detected only through our labeling/sequencing approach. Multiple other pathogens of concern to human health were also identified through our labeling/sequencing approach including P. shigelloides, B. cereus and E. cloacae. Most importantly, 16S rRNA sequencing of BrdU-labeled samples resulted in Vibrio spp. detection even when our culture-based methods resulted in negative detection. This suggests that our novel approach can effectively detect metabolically-active Vibrio spp. that may have been present in a VBNC state, refining our understanding of the prevalence of vibrios in nontraditional irrigation waters.

Post-synthesis of biomimetic chitosan with honeycomb-like structure for sensitive recognition of phosphorylated peptides

2021 ◽  
Vol 1643 ◽  
pp. 462072
Author(s):  
Canhong Zhu ◽  
Jiani Wu ◽  
Xueting Jin ◽  
Yinghua Yan ◽  
Chuan-Fan Ding ◽  
...  
Keyword(s):  
Phosphorylated Peptides ◽  
Post Synthesis

scholarly journals Post-Synthesis Modification of Photoluminescent and Electrochemiluminescent Au Nanoclusters with Dopamine

Nanomaterials ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 46
Author(s):  
Jae Hyun Kim ◽  
Joohoon Kim
Keyword(s):  
Near Infrared ◽  
Au Nanoclusters ◽  
Metallic Core ◽  
Thiolate Ligand ◽  
Pl Intensity ◽  
Post Synthesis

Here, we report a post-synthesis functionalization of the shell of Au nanoclusters (NCs) synthesized using glutathione as a thiolate ligand. The as-synthesized Au NCs are subjected to the post-synthesis functionalization via amidic coupling of dopamine on the cluster shell to tailor photoluminescence (PL) and electrochemiluminescence (ECL) features of the Au NCs. Because the NCs’ PL at ca. 610 nm is primarily ascribed to the Au(I)-thiolate (SG) motifs on the cluster shell of the NCs, the post-synthesis functionalization of the cluster shell enhanced the PL intensity of the Au NCs via rigidification of the cluster shell. In contrast to the PL enhancement, the post-synthesis modification of the cluster shell does not enhance the near-infrared (NIR) ECL of the NCs because the NIR ECL at ca. 800 nm is ascribed to the Au(0)-SG motifs in the metallic core of the NCs.

scholarly journals 4mCPred-CNN—Prediction of DNA N4-Methylcytosine in the Mouse Genome Using a Convolutional Neural Network

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 296
Author(s):  
Zeeshan Abbas ◽  
Hilal Tayara ◽  
Kil To Chong
Keyword(s):  
Mouse Genome ◽  
Matthews Correlation Coefficient ◽  
Biological Functions ◽  
Independent Dataset ◽  
Validation Test ◽  
Single Feature ◽  
Proposed Model ◽  
Dna Modifications ◽  
Feature Encoding ◽  
Feature Encoding Scheme

Among DNA modifications, N4-methylcytosine (4mC) is one of the most significant ones, and it is linked to the development of cell proliferation and gene expression. To know different its biological functions, the accurate detection of 4mC sites is required. Although we have several techniques for the prediction of 4mC sites in different genomes based on both machine learning (ML) and convolutional neural networks (CNNs), there is no CNN-based tool for the identification of 4mC sites in the mouse genome. In this article, a CNN-based model named 4mCPred-CNN was developed to classify 4mC locations in the mouse genome. Until now, we had only two ML-based models for this purpose; they utilized several feature encoding schemes, and thus still had a lot of space available to improve the prediction accuracy. Utilizing only a single feature encoding scheme—one-hot encoding—we outperformed both of the previous ML-based techniques. In a ten-fold validation test, the proposed model, 4mCPred-CNN, achieved an accuracy of 85.71% and Matthews correlation coefficient (MCC) of 0.717. On an independent dataset, the achieved accuracy was 87.50% with an MCC value of 0.750. The attained results exhibit that the proposed model can be of great use for researchers in the fields of biology and bioinformatics.

scholarly journals Application of microwave radiation in the grafting of acidic sites on SBA-15 type material

2021 ◽  
Author(s):  
Maciej Trejda ◽  
Magdalena Drobnik ◽  
Ardian Nurwita
Keyword(s):  
Microwave Radiation ◽  
Thermal Analyses ◽  
Conventional Heating ◽  
Material Surface ◽  
Test Reaction ◽  
Study Materials ◽  
Mesoporous Support ◽  
Acidic Sites ◽  
Post Synthesis ◽  
Adsorption Desorption

AbstractMesoporous silica of SBA-15 type was modified for the first time with 3-(trihydroxysiyl)-1-propanesulfonic acid (TPS) by post-synthesis modification involving microwave or conventional heating in order to generate the Brønsted acidic centers on the material surface. The samples structure and composition were examined by low temperature N2 adsorption/desorption, XRD, HRTEM, elemental and thermal analyses. The surface properties were evaluated by esterification of acetic acid with n-hexanol used as the test reaction. A much higher efficiency of TPS species incorporation was reached with the application of microwave radiation for 1 h than conventional modification for 24 h. It was found that the structure of mesoporous support was preserved after modification using both methods applied in this study. Materials obtained with the use of microwave radiation showed a superior catalytic activity and high stability.

scholarly journals Cytosolic Ribosomal Mutations That Abolish Accumulation of Circular Intron in the Mitochondria Without Preventing Senescence of Podospora anserina

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 697-705 ◽  
Author(s):  
Philippe Silar ◽  
France Koll ◽  
Michèle Rossignol
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Proteins ◽  
Podospora Anserina ◽  
Cox1 Gene ◽  
Accuracy Control ◽  
Additional Function ◽  
Mutant Proteins ◽  
Double Stranded Dna ◽  
Dna Modifications

The filamentous fungus Podospora anserina presents a degeneration syndrome called Senescence associated with mitochondrial DNA modifications. We show that mutations affecting the two different and interacting cytosolic ribosomal proteins (S7 and S19) systematically and specifically prevent the accumulation of senDNAα (a circular double-stranded DNA plasmid derived from the first intron of the mitochondrial cox1 gene or intron α) without abolishing Senescence nor affecting the accumulation of other usually observed mitochondrial DNA rearrangements. One of the mutant proteins is homologous to the Escherichia coli S4 and Saccharomyces cerevisiae S13 ribosomal proteins, known to be involved in accuracy control of cytosolic translation. The lack of accumulation of senDNAα seems to result from a nontrivial ribosomal alteration unrelated to accuracy control, indicating that S7 and S19 proteins have an additional function. The results strongly suggest that modified expression of nucleus-encoded proteins contributes to Senescence in P. anserina. These data do not fit well with some current models, which propose that intron α plays the role of the cytoplasmic and infectious Determinant of Senescence that was defined in early studies.

scholarly journals Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Chen ◽  
Min Bai ◽  
Xiaowen Cao ◽  
Jing Xue ◽  
Yue Zhao ◽  
...  
Keyword(s):  
Fluorescence Imaging ◽  
Spatial Organization ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Chromatin Modifications ◽  
Dynamic Changes ◽  
Recognition Mechanism ◽  
Cell Cycles ◽  
Dna Modifications ◽  
Relationship Of

AbstractExploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3’-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.

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