PubMed Health⌕ Search

Biomedical subjects

Xuemei Han

Publications and source records attributed to Xuemei Han.

10 recordsLinked to original sources
PubMed2026

Screening for dual sgRNAs with comparable indel efficiencies enhances CRISPR-mediated large-fragment deletion.

CRISPR-mediated large-fragment deletion provides a powerful approach for gene clusters, noncoding regions and structural variants, but its broader application is limited by low and variable deletion efficiency. Here, we systematically designed and evaluated 78 sgRNAs targeting nine representative gene clusters (ttn.1-ttn.2 cluster, 7 hox clusters and nppb-nppa cluster), containing 31 large fragments (5 kb-340 kb) to investigate the determinants of deletion efficiency. We found two key rules for achieving high deletion efficiency: (i) using dual sgRNAs with similar indel efficiencies, and (ii) applying a single sgRNA pair rather than multiple sgRNAs. Based on those rules, a 340 kb deletion is detected in the progenies of 95% of founders. Whereas the deletion size showed no significant linear correlation with deletion efficiency within the tested range. Implementing these rules resulted in an average of 70% of founders transmitting deletions across all tested sgRNA pairs. Therefore, screening sgRNAs can effectively enhance CRISPR utility in deletions, thereby facilitating the application of genomic manipulation in vertebrates and other species.

CRISPR↗
PubMed2006

Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons.

For characterization of sequence and posttranslational modifications, molecular and fragment ion mass data from ionizing and dissociating a protein in the mass spectrometer are far more specific than are masses of peptides from the protein's digestion. We extend the approximately 500-residue, approximately 50-kilodalton (kD) dissociation limitation of this top-down methodology by using electrospray additives, heated vaporization, and separate noncovalent and covalent bond dissociation. This process can cleave 287 interresidue bonds in the termini of a 1314-residue (144-kD) protein, specify previously unidentified disulfide bonds between 8 of 27 cysteines in a 1714-residue (200-kD) protein, and correct sequence predictions in two proteins, one with 2153 residues (229 kD).

Acyltransferases↗
PubMed2006

High frame rate ultrasonic imaging system based on the angular spectrum principle.

A kind of high frame rate (HFR) 2D and 3D imaging method was developed by Jianyu Lu in 1997. Because only one transmission is required to construct a frame of image, this method can reach an ultra high frame rate (about 3750 volumes or frames per second for biological soft tissues at a depth of 200 mm). In this paper, a new HFR method is presented in the view of angular spectrum. Compared with conventional dynamic focusing method which uses delay-and-sum processing, and Lu's HFR method which uses a kind of special weighting on the received signal, the new method only uses the Fourier transform algorithm to construct image. So the system implementation of the method could be greatly simplified. During constructing image, several array beams with different parameter are used as transmitted signal, and the spectrum of a frame of image is obtained by synthesizing the image spectrums related to different transmit event. The simulation result shows that the solution not only suppresses the sidelobe of system greatly and obtains the high quality image, but also still keeps high frame rate to some extent.

Algorithms↗
PubMed2006

Study on application of complementary Golay code into high frame rate ultrasonic imaging system.

The high frame rate (HFR) ultrasonic imaging system, which is developed with limited diffraction beams, constructs images at a high frame rate. However the rectangular imaging area, to some extent, restricts the far field imaging information. At the same time, by virtue of one transmission event for constructing image, the system suffers from low SNR. In this paper we present a computationally efficient method to construct sector mode image and to increase the SNR in HFR system. The method uses orthogonal complementary Golay coded excitation to realize two transmit and receive events. Each emission simultaneously transmits two plane waves with different transmission angle. Then according to Golay code orthogonality, the received echo signals related to different angles are isolated and used to construct two images of different imaging area by HFR method. Finally the two images are synthesized to one frame of sector mode image.

Algorithms↗
PubMed2006

Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry.

Although deamidation at asparagine and glutamine has been found in numerous studies of a variety of proteins, in almost all cases the analytical methodology that was used could detect only a single site of deamidation. For the extensively studied case of reduced bovine ribonuclease A (13,689 Da), only Asn67 deamidation has been demonstrated previously, although one study found three monodeamidated fractions. Here top down tandem mass spectrometry shows that Asn67 deamidation is extensive before Asn71 and Asn94 react; these are more than half deamidated before Asn34 reacts, and its deamidation is extensive before that at Gln74 is initiated. Except for the initial Asn67 site, these large reactivity differences correlate poorly with neighboring amino acid identities and instead indicate residual conformational effects despite the strongly denaturing media that were used; deamidation at Asn67 could enhance that at Asn71, and these enhance that at Gln74. This success in the site-specific quantitation of deamidation in a 14 kDa protein mixture, despite the minimal 1 Da (-NH2 --> -OH) change in the molecular mass, is further evidence of the broad applicability of the top down MS/MS methodology for characterization of protein posttranslational modifications.

Amides↗
PubMed2006

[Implementation of sector imaging mode with high signal-to-noise ratio in the high frame rate ultrasonic imaging system].

The high frame rate (HFR) ultrasonic imaging system, which is developed with limited diffraction beams, constructs images at a high frame rate. However the rectangular imaging area, to some extent, restricts the far field imaging information. At the same time, because of one transmission for constructing image, the system suffers from low SNR. In this paper we present a computationally efficient method to construct sector mode image and to increase the SNR in HFR system. The method uses Golay complementary sequence as excitation to realize two transmission events. Each event simultaneously transmits two plane waves with different transmission angle. Then the received echo signals related to different angle are separated according to orthogonality of Golay complementary sequence and used to construct two images of different area by HFR method. Finally the two images are synthesized to one frame of sector mode image.

Image Enhancement↗
PubMed2005

Consecutive ion activation for top down mass spectrometry: improved protein sequencing by nozzle-skimmer dissociation.

Mass spectra produced by nozzle-skimmer dissociation (NSD) have been little used in the past for structural characterization. NSD cannot be used on mass-separated ions (MS/MS), and for electrosprayed protein ions, previous NSD spectra showed backbone cleavages similar to those from energetic methods such as collisionally activated dissociation (CAD) or infrared multiphoton dissociation (IRMPD). However, our experimental configuration with Fourier transform (FT) MS makes possible three consecutive steps of NSD ion activation: thermal in the entrance capillary and collisional in both the nozzle-skimmer (N-S) region and the region after the skimmer before the quadrupole entrance lens (S-Q). In the high-pressure N-S region of adjustable path length, ions undergo high-frequency, low-energy collisions to rupture weak noncovalent or covalent bonds, with these "denatured" products then subjected to high-energy collisions in the low-pressure S-Q region to cleave strong backbone bonds. These NSD spectra, plus those from variable capillary thermal activation, of 8+ to 11+ ubiquitin ions electrosprayed from denatured solution show backbone cleavages between 74 of 75 amino acid pairs, vs 66 for CAD and 50 for IRMPD in the FTMS cell. Thermal activation by the inlet capillary of the newly desolvated 6+, 7+ ubiquitin ions from electrospraying the native conformer increases the NSD yield from 8% at 56 degrees C to 96% at 76 degrees C, but with little change in product branching ratios; this capillary heating has no effect on CAD or IRMPD of these ions collected in the FTMS cell. Ion desolvation with its concomitant H-bond strengthening appears to produce a transiently stable conformer whose formation can be prevented by capillary heating. The far more complex and stable noncovalent tertiary structures of large protein ions in the gas phase have made MS/MS difficult; initial inhibition of tertiary structure formation with immediate NSD ("prefolding dissociation") appears promising for the top down characterization of a 200-kDa protein.

Amino Acid Sequence↗
PubMed2005

Lipid segregation and IgE receptor signaling: a decade of progress.

Recent work to characterize the roles of lipid segregation in IgE receptor signaling has revealed a mechanism by which segregation of liquid ordered regions from disordered regions of the plasma membrane results in protection of the Src family kinase Lyn from inactivating dephosphorylation by a transmembrane tyrosine phosphatase. Antigen-mediated crosslinking of IgE receptors drives their association with the liquid ordered regions, commonly called lipid rafts, and this facilitates receptor phosphorylation by active Lyn in the raft environment. Previous work showed that the membrane skeleton coupled to F-actin regulates stimulated receptor phosphorylation and downstream signaling processes, and more recent work implicates cytoskeletal interactions with ordered lipid rafts in this regulation. These and other results provide an emerging view of the complex role of membrane structure in orchestrating signal transduction mediated by immune and other cell surface receptors.

Animals↗
PubMed2005

Phosphoinositide3-kinase regulates actin polymerization during delayed phagocytosis of Helicobacter pylori.

We have shown previously that ulcerogenic (type I) strains of Helicobacter pylori (Hp) retard their entry into macrophages. However, the signaling pathways that regulate Hp phagocytosis are largely undefined. We show here that Hp strongly activated class IA phosphoinositide3-kinases (PI3Ks) in macrophages, coincident with phagocytosis, and endogenous p85 and active protein kinase Balpha accumulated on forming phagosomes. PI3K inhibitors, wortmannin and LY294002, inhibited phagocytosis of Hp in a dose-dependent manner, and blockade of engulfment correlated directly with loss of 3'-phosphoinositides in the membrane subjacent to attached bacteria. During uptake of large immunoglobulin G (IgG)-coated particles, PI3Ks regulate pseudopod extension and phagosome closure. In marked contrast, we show here that 3'-phosphoinositides regulated actin polymerization at sites of Hp uptake. Moreover, Hp and IgG beads activated distinct PI3K isoforms. Phagosomes containing IgG-coated particles accumulated 3'-phosphatase and tensin homologue deleted on chromosome 10 and Src homology 2 domain-containing inositol 5'-phosphatase, yet Hp phagosomes did not. Finally, rapid uptake of IgG-opsonized Hp or a less-virulent type II Hp was PI3K-independent. We conclude that Hp and IgG beads are ingested by distinct mechanisms and that PI3Ks regulate the actin cytoskeleton during slow phagocytosis of ulcerogenic Hp.

Actins↗