Biomedical subjects

Junjie Zhu

Publications and source records attributed to Junjie Zhu.

8 recordsLinked to original sources

PubMed2025

A quick guide to evaluating prime editing efficiency in mammalian cells.

According to the Clinvar database, modeling the diseases associated with pathogenic mutations requires the installation of base substitutions, small insertions or deletions. Prime editor (PE) was recently developed to precisely install any base substitutions and/or small insertions/deletions (indels) in mammalian cells and animals without requiring DSBs or donor DNA templates. PE also offers greater editing and targeting flexibility compared to other precision CRISPR editing methods because the versatile editing information is encoded in the reverse-transcription template of its prime editing guide RNA. However, optimal PE system selection and experimental design can be complex, and there are various factors that can affect PE efficiency. This chapter serves as a rapid entry-level guideline for the application of PE, providing an experimental framework for using PE at a specific genomic locus. RUNX1 was selected as a representative target site to illustrate the detailed methodology for constructing PE plasmids and the process of transfecting these plasmids into 293FT cells. We further examined the efficiency of PE-mediated genome editing in mammalian cells by using next-generation sequencing.

Gene Editing↗

PubMed2006

Morphological control and luminescent properties of YVO4:Eu nanocrystals.

Rodlike, olivelike, pineapplelike, and particlelike nanocrystals of theYVO4:Eu (5 at. % Eu) were synthesized by a hydrothermal reaction with different conditions, respectively. The rodlike nanocrystal has a rectangular cross-section with about 35 x 60 nm2 and a length of about 220 nm. The olivelike nanocrystal has an equatorial diameter of approximately 40 nm and a length of approximately 200 nm. The pineapplelike nanocrystal with an equatorial diameter of approximately 200 nm and a length of approximately 300 nm, is a superstructure consisting of self-organized nanorods with a diameter of approximately 20 nm and a length of approximately 50 nm. The particlelike nanocrystals show globular and polyhedral shape with a diameter of approximately 50 nm. Their UV-vis absorption peaks are at 305, 308, 285, and 280 nm, respectively, and there is such a trend that the absorption peaks shift to higher energy as the size of the particles decreases. Compared with other-shape nanocrystals, the luminescence intensity of the olivelike nanocrystals is obviously enhanced. It suggests that we could obtain the function-improved materials by tailoring the size and shape of theYVO4:Eu nanostructures.

Journal Article↗

PubMed2006

Enrichment of phosphopeptides by Fe3+-immobilized mesoporous nanoparticles of MCM-41 for MALDI and nano-LC-MS/MS analysis.

Fe3+-immobilized mesoporous molecular sieves MCM-41 with particle size of ca. 600 nm and pore size of ca. 3 nm is synthesized and applied to selectively trap and separate phosphopeptides from tryptic digest of proteins. For the capture of phosphopeptides, typically 10 microL of tryptic digest solution was first diluted to 1 mL by solution of ACN/0.1% TFA (50:50, v/v) and incubated with 10 microL of 0.1% acetic acid dispersed Fe3+-immobilized MCM-41 for 1 h under vibration. Fe3+-immobilized MCM-41 with trapped phosphopeptides was separated by centrifugation. The deposition was first washed with a volume of 300 microL of solution containing 100 mM NaCl in ACN/0.1% TFA (50:50, v/v) and followed by a volume of 300 microL of solution of 0.1% acetic acid to remove nonspecifically bound peptides. The nanoparticles with trapped phosphopeptides are mixed with 2,5-dihydroxybenzoic acid (2,5-DHB) and deposited onto the target for analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). It was found that phosphopeptides from tryptic digest of alpha-casein and beta-casein are effectively and specifically trapped on Fe3+-immobilized MCM-41 with few peptides nonspecifically adsorbed. After the extraction by Fe3+-immobilized MCM-41, the suppression to the detection of phosphopeptides caused by abundant nonphosphopeptides from tryptic digest is effectively eliminated, and the detection of phosphopeptides by MALDI is greatly enhanced with the value of signal-to-noise (S/N) increased by more than an order of magnitude. It is demonstrated that the mechanism of the adsorption of phosphopeptides on Fe3+-immobilized MCM-41 is based on the interaction between the Fe3+ and the phosphate group. Finally, Fe3+-immobilized MCM-41 is applied to extract phosphopeptides from tryptic digest of the lysate of mouse liver for phosphoproteome analysis by nano-LC-MS/MS.

Amino Acid Sequence↗

PubMed2005

Molecular cloning and characterization of CD9 cDNA from cartilaginous fish, red stingray, Dasyatis akajei.

CD9 is a glycoprotein of the transmembrane 4 superfamily (TM4SF) and is involved in various cellular processes. In this study, we describe the isolation of the full-length cDNA encoding for CD9 molecule (daCD9) of red stingray, Dasyatis akajei. This 1252 bp cDNA was isolated from leukocyte cDNA library and contains 681 bp open reading frame encoding 226 amino acid residues. Amino acid sequences analysis and structure prediction display approximately 50% identity to higher vertebrates with the presence of conserved structures, including the four transmembrane domains and certain characteristic residues. Southern blot analysis shows that daCD9 exists as a single copy gene. Northern blot analysis reveals that daCD9 is highly expressed in gill and spleen although its expression can be found in other tissues suggesting daCD9 might play an important role in immune defense in this fish.

Amino Acid Sequence↗

PubMed2005

Preparation of single-crystalline NdVO4 nanorods, and their emissions in the ultraviolet and blue under ultraviolet excitation.

This paper describes a facile sacrifical (NH4)0.5V2O5 nanowires approach to single-crystalline NdVO4 nanorods. The nanorods have a rectangular cross section of about 30 x 30 nm2 to 100 x 200 nm2, and length ranging from 400 to 700 nm. Transmission electron microscopy (TEM) and selected area electron diffraction (SAED) show that the nanorods grew respectively along the [312] and [101] direction on the (NH4)0.5V2O5 nanowires. Ultraviolet (362 nm) and blue (467 nm) emissions can be observed under excitation of 310 nm at room temperature, suggesting that the nanorods should be good candidates for fabricating UV and blue nanodevices.

Journal Article↗

PubMed2004

Heterostructured Bi2Se3 nanowires with periodic phase boundaries.

Single and multijunction nanowires with diameters of 10-40 nm were synthesized by an electrically assisted sonochemical method in aqueous solution at room temperature. By properly controlling the reaction conditions and reactants, this method opens a new strategy towards the fabrication of one-dimensional superlattices in nanowires under ambient conditions. Such a chemical approach provides a promising and simple way to synthesize high-performance building blocks for device applications.

Journal Article↗

PubMed2004

Basis for fusion inhibition by peptides: analysis of the heptad repeat regions of the fusion proteins from Nipah and Hendra viruses, newly emergent zoonotic paramyxoviruses.

Nipah virus (NiV) and Hendra virus (HeV) are novel zoonotic members of the Paramyxoviridae family and are the prototypes for a newly designated genus, Genus Henipavirus. Recent studies have shown that paramyxovirus might adopt a similar mechanism of virus fusion-entry. Under this mechanism, the two highly conserved heptad repeat (HR) regions, HR1 and HR2, in the fusion (F) protein, seem to show characteristic structure in the fusion core: the formation of a 6-helix coiled-coil bundle. The three HR1s form the alpha-helix coiled-coil surrounded by three HR2s. In this study, the two HR regions of NiV or HeV were expressed in an Escherichia coli system as a single chain and the results do show that HR1 and HR2 interact with each other in both NiV and HeV and form typical 6-helix coiled-coil bundles. This provides the molecular basis of HR2 inhibition to NiV and HeV fusion as observed in an earlier report.

Amino Acid Sequence↗

PubMed2003

Molecular profile of the unique species of traditional Chinese medicine, Chinese seahorse (Hippocampus kuda Bleeker).

A cDNA library of male Chinese seahorse (Hippocampus kuda Bleeker) was constructed to investigate the molecular profile of seahorse as one of the most famous traditional Chinese medicine materials, and to reveal immunological and physiological mechanisms of seahorse as one of the most primitive vertebrates at molecular level. A total of 3372 expressed sequence tags (ESTs) consisting of 1911 unique genes (345 clusters and 1566 singletons) were examined in the present study. Identification of the genes related to immune system, paternal brooding and physiological regulation provides not only valuable insights into the molecular mechanism of immune system in teleost fish but also plausible explanations for pharmacological activities of Chinese seahorse. Furthermore, the occurrence of high prevalent C-type lectins suggested that a lectin-complement pathway might exert a more dominant function in the innate immune system of teleost than mammal. Carbohydrate recognition domain (CRD) without a collagen-like region in the lectins of seahorse was likely an ancient characteristic of lectins similar to invertebrates.

Amino Acid Sequence↗