Biomedical subjects

Xiaojun Zhao

Publications and source records attributed to Xiaojun Zhao.

At least 19 recordsLinked to original sources

PubMed2026

Highly Conserved Allelic Substitutions S202F, L244P, and H248P/R/Y in FsSdhB and A83 V in FsSdhC1 Trigger Gradual Resistance to Pydiflumetofen in Fusarium solani.

Pydiflumetofen (Pyd), one of the new-generation SDHIs, has been applied to control various diseases in economic crops. Fusarium solani, a soil-borne pathogen with a broad host range, is the agent of quinoa basal-stem rot (QBSR). In this study, three PydLR (4.64 < RF < 9.31), six PydMR (51.24 < RF < 86.91), and seven PydHR mutants (RF > 6000) were generated by Pyd-taming. Most F. solani PydR mutants showed no fitness penalties. The sequence alignment of FsSdh genes revealed that substitutions S202F, L244P, and H248P/R/Y in FsSdhB, or A83 V in FsSdhC1, caused Pyd resistance. Notably, the mutation S202F causing HR was first reported. Molecular docking demonstrated that these aforementioned mutations significantly reduced affinity between Pyd and the Qp-binding pocket. These results provide pivotal data for the resistance management strategies of F. solani and advance our understanding of the resistance mechanisms of SDHIs.

Fusarium↗

PubMed2007

Designer self-assembling peptide materials.

Understanding of macromolecular materials at the molecular level is becoming increasingly important for a new generation of nanomaterials for nanobiotechnology and other disciplines, namely, the design, synthesis, and fabrication of nanodevices at the molecular scale from bottom up. Basic engineering principles for microfabrication can be learned through fully grasping the molecular self-assembly and programmed assembly phenomena. Self- and programmed-assembly phenomena are ubiquitous in nature. Two key elements in molecular macrobiological material productions are chemical complementarity and structural compatibility, both of which require weak and non-covalent interactions that bring building blocks together during self-assembly. Significant advances have been made during the 1990s at the interface of materials chemistry and biology. They include the design of helical ribbons, peptide nanofiber scaffolds for three-dimensional cell cultures and tissue engineering, peptide surfactants for solubilizing and stabilizing diverse types of membrane proteins and their complexes, and molecular ink peptides for arbitrary printing and coating surfaces as well as coiled-coil helical peptides for multi-length scale fractal structures. These designer self-assembling peptides have far reaching implications in a broad spectrum of applications in biology, medicine, nanobiotechnology, and nanobiomedical technology, some of which are beyond our current imaginations. [image: see text]

Lipids↗

PubMed2006

Designer short peptide surfactants stabilize G protein-coupled receptor bovine rhodopsin.

Membrane proteins play vital roles in every aspect of cellular activities. To study diverse membrane proteins, it is crucial to select the right surfactants to stabilize them for analysis. Despite much effort, little progress has been made in elucidating their structure and function, largely because of a lack of suitable surfactants. Here we report the stabilization of a G protein-coupled receptor bovine rhodopsin in solution, using a new class of designer short and simple peptide surfactants. These surfactants consist of seven amino acids with a hydrophilic head, aspartic acid or lysine, and a hydrophobic tail with six consecutive alanines. These peptide surfactants not only enhance the stability of bovine rhodopsin in the presence of lipids and the common surfactants n-dodecyl-beta-D-maltoside and octyl-D-glucoside, but they also significantly stabilize rhodopsin under thermal denaturation conditions, even after lipids are removed. These peptide surfactants are simple, versatile, effective, and affordable. They represent a designer molecular nanomaterial for use in studies of diverse elusive membrane proteins.

Amino Acid Sequence↗

PubMed2006

Molecular designer self-assembling peptides.

Chemistry has generally been associated with inorganic and organic syntheses, metal-organic composites, coordinate metal chemistry, catalyses, block copolymer, coating, thin film, industrial surfactants and small-molecule drug development. That is about to change. Chemistry will also expand to the discovery and fabrication of biological and molecular materials with diverse structures, functionalities and utilities. The advent of biotechnology, nanotechnology and nanobiotechnology has accelerated this trend. Nature has selected and evolved numerous molecular architectural motifs at nanometer scale over billions of years for particular functions. These molecular nanomotifs can now be designed for new materials and nanodevices from the bottom up. Chemistry will again harness Nature's enormous power to benefit other disciplines and society. This tutorial review focuses on two self-assembling peptide systems.

Biotechnology↗

PubMed2006

Allelic dilution obscures detection of a biologically significant resistance mutation in EGFR-amplified lung cancer.

EGFR is frequently mutated and amplified in lung adenocarcinomas sensitive to EGFR inhibitors gefitinib and erlotinib. A secondary mutation, T790M, has been associated with acquired resistance but has not been shown to be sufficient to render EGFR mutant/amplified lung cancers resistant to EGFR inhibitors. We created a model for studying acquired resistance to gefitinib by prolonged exposure of a gefitinib-sensitive lung carcinoma cell line (H3255; EGFR mutated and amplified) to gefitinib in vitro. The resulting resistant cell line acquired a T790M mutation in a small fraction of the amplified alleles that was undetected by direct sequencing and identified only by a highly sensitive HPLC-based technique. In gefitinib-sensitive lung cancer cells with EGFR mutations and amplifications, exogenous introduction of EGFR T790M effectively conferred resistance to gefitinib and continued ErbB-3/PI3K/Akt signaling when in cis to an activating mutation. Moreover, continued activation of PI3K signaling by the PIK3CA oncogenic mutant, p110alpha E545K, was sufficient to abrogate gefitinib-induced apoptosis. These findings suggest that allelic dilution of biologically significant resistance mutations may go undetected by direct sequencing in cancers with amplified oncogenes and that restoration of PI3K activation via either a T790M mutation or other mechanisms can provide resistance to gefitinib.

Alleles↗

PubMed2006

Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays.

Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and counterpart normal DNA and noting regions where heterozygous alleles in the normal DNA become homozygous in the tumor. However, paired normal samples for tumors and cell lines are often not available. With the advent of oligonucleotide arrays that simultaneously assay thousands of single-nucleotide polymorphism (SNP) markers, genotyping can now be done at high enough resolution to allow identification of LOH events by the absence of heterozygous loci, without comparison to normal controls. Here we describe a hidden Markov model-based method to identify LOH from unpaired tumor samples, taking into account SNP intermarker distances, SNP-specific heterozygosity rates, and the haplotype structure of the human genome. When we applied the method to data genotyped on 100 K arrays, we correctly identified 99% of SNP markers as either retention or loss. We also correctly identified 81% of the regions of LOH, including 98% of regions greater than 3 megabases. By integrating copy number analysis into the method, we were able to distinguish LOH from allelic imbalance. Application of this method to data from a set of prostate samples without paired normals identified known regions of prevalent LOH. We have developed a method for analyzing high-density oligonucleotide SNP array data to accurately identify of regions of LOH and retention in tumors without the need for paired normal samples.

Alleles↗

PubMed2006

Epidermal growth factor receptor variant III mutations in lung tumorigenesis and sensitivity to tyrosine kinase inhibitors.

The tyrosine kinase inhibitors gefitinib (Iressa) and erlotinib (Tarceva) have shown anti-tumor activity in the treatment of non-small cell lung cancer (NSCLC). Dramatic and durable responses have occurred in NSCLC tumors with mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR). In contrast, these inhibitors have shown limited efficacy in glioblastoma, where a distinct EGFR mutation, the variant III (vIII) in-frame deletion of exons 2-7, is commonly found. In this study, we determined that EGFRvIII mutation was present in 5% (3/56) of analyzed human lung squamous cell carcinoma (SCC) but was not present in human lung adenocarcinoma (0/123). We analyzed the role of the EGFRvIII mutation in lung tumorigenesis and its response to tyrosine kinase inhibition. Tissue-specific expression of EGFRvIII in the murine lung led to the development of NSCLC. Most importantly, these lung tumors depend on EGFRvIII expression for maintenance. Treatment with an irreversible EGFR inhibitor, HKI-272, dramatically reduced the size of these EGFRvIII-driven murine tumors in 1 week. Similarly, Ba/F3 cells transformed with the EGFRvIII mutant were relatively resistant to gefitinib and erlotinib in vitro but proved sensitive to HKI-272. These findings suggest a therapeutic strategy for cancers harboring the EGFRvIII mutation.

Animals↗

PubMed2006

Synthesis, structure, and luminescent properties of microporous lanthanide metal-organic frameworks with inorganic rod-shaped building units.

A series of microporous lanthanide metal-organic frameworks, Tb3(BDC)(4.5)(DMF)2(H2O)3.(DMF)(H2O) (1) and Ln3(BDC)(4.5)(DMF)2(H2O)3.(DMF)(C2H5OH)(0.5)(H2O)(0.5) [Ln = Dy (2), Ho (3), Er (4)], have been synthesized by the reaction of the lanthanide metal ion (Ln3+) with 1,4-benzenedicarboxylic acid and triethylenetetramine in a mixed solution of N,N'-dimethylformamide (DMF), water, and C(2)H(5)OH. X-ray diffraction analyses reveal that they are extremely similar in structure and crystallized in triclinic space group P. An edge-sharing metallic dimer and 4 metallic monomers assemble with 18 carboxylate groups to form discrete inorganic rod-shaped building units [Ln6(CO2)18], which link to each other through phenyl groups to lead to three-dimensional open frameworks with approximately 4 x 6 A rhombic channels along the [0,-1,1] direction. A water sorption isotherm proves that guest molecules in the framework of complex 1 can be removed to create permanent microporosity and about four water molecules per formula unit can be adsorbed into the micropores. These complexes exhibit blue fluorescence, and complex 1 shows a Tb3+ characteristic emission in the range of 450-650 nm.

Journal Article↗

PubMed2006

A sensitive sandwich DNA array using fluorescent nanoparticle probes.

An ultrasensitive sandwich DNA array using highly fluorescent and photostable dyedoped silica nanoparticles is described. Compared to traditional sandwich arrays in which fluorophores have been used to signal target DNA molecules, the developed nanoparticle probes provide a much stronger fluorescent emission. Signal amplification of the dyedoped silica nanoparticles originates from the large number of dye molecules doped inside each individual nanoparticle. In addition, the silica matrix of the nanoparticles protects dye molecules from photobleaching. Thus, the dye-doped nanoparticles provide a constant fluorescent signal that is sufficient for detection of trace amounts of target DNA. By immobilizing a complementary DNA sequence to the target onto the nanoparticle surface, a fluorescent nanoparticle-DNA probe is formed. These nanoparticle probes are then used as superemitting reagents to perform a typical sandwich assay. By using a high-resolution fluorescent microscope, individual nanoparticle-DNA probes that have been hybridized to capture target strands can be observed clearly at low target DNA concentrations. More important, the number of the nanoparticle-DNA probes hybridized to the target DNA is proportional to the target DNA concentration in solution. By counting the number of localized fluorescent "spots" on the array, the target DNA concentration can be determined. In this chapter, detailed methods used to synthesize nanoparticle-DNA probes, fabricate the sandwich array, prepare the substrate, and quantitatively determine DNA concentration are described.

Fluorescent Dyes↗

PubMed2005

Allele-specific amplification in cancer revealed by SNP array analysis.

Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, loss-of-heterozygosity events have been finely mapped using high-throughput genotyping technologies. We have developed a probe-level allele-specific quantitation procedure that extracts both copy number and allelotype information from single nucleotide polymorphism (SNP) array data to arrive at allele-specific copy number across the genome. Our approach applies an expectation-maximization algorithm to a model derived from a novel classification of SNP array probes. This method is the first to our knowledge that is able to (a) determine the generalized genotype of aberrant samples at each SNP site (e.g., CCCCT at an amplified site), and (b) infer the copy number of each parental chromosome across the genome. With this method, we are able to determine not just where amplifications and deletions occur, but also the haplotype of the region being amplified or deleted. The merit of our model and general approach is demonstrated by very precise genotyping of normal samples, and our allele-specific copy number inferences are validated using PCR experiments. Applying our method to a collection of lung cancer samples, we are able to conclude that amplification is essentially monoallelic, as would be expected under the mechanisms currently believed responsible for gene amplification. This suggests that a specific parental chromosome may be targeted for amplification, whether because of germ line or somatic variation. An R software package containing the methods described in this paper is freely available at http://genome.dfci.harvard.edu/~tlaframb/PLASQ.

Alleles↗

PubMed2005

A transforming MET mutation discovered in non-small cell lung cancer using microarray-based resequencing.

We have designed resequencing microarrays to test the performance of this platform when interrogating a large number of exons (164 total) from genes associated with cancer. To evaluate false positive and negative rates, dideoxy sequencing was done for 335,420 bases interrogated by the arrays. From the array data, calls could be made for approximately 97.5% of the bases, and false positive rates were very low with only a single mutation reported from the array dataset for which the corresponding dideoxy trace had a clean wildtype sequence. For the nucleotide positions where array calls were made, false negative rates were 1.41% for heterozygous mutations. All the homozygous mutations were detected, but 8.11% were erroneously reported as heterozygous changes from the reference sequence by the array analysis software. In addition, 20 non-small cell lung cancer (NSCLC) samples were analyzed using the arrays, and both somatic and germline mutations were found. The most interesting findings were two MET mutations that have recently been implemented in NSCLC. Large scale MALDI-TOF genotyping indicated that one of these mutations (T1010I) might represent a true cancer-causing genotype, whereas the other (N375S) appears to be a common germline polymorphism.

Carcinoma, Non-Small-Cell Lung↗

PubMed2005

Phase I study of gefitinib plus celecoxib in recurrent or metastatic squamous cell carcinoma of the head and neck.

PURPOSE: Effective and tolerable palliative treatments are needed for patients with incurable squamous cell carcinoma of the head and neck (SCCHN). Single-agent targeted therapies have limited activity in this setting. The feasibility of adding celecoxib to gefitinib for the treatment of incurable SCCHN is unknown. PATIENTS AND METHODS: Nineteen patients with unresectable recurrent locoregional and/or distant metastatic SCCHN with progressive disease after at least one prior chemotherapy or chemoradiotherapy regimen were enrolled onto this single-institution phase I study. Three dose levels were explored: (1) celecoxib 200 mg twice daily plus gefitinib 250 mg daily; (2) celecoxib 400 mg twice daily plus gefitinib 250 mg daily; and (3) celecoxib 400 mg twice daily plus gefitinib 500 mg daily. RESULTS: No dose-limiting toxicities were encountered at any dose level. The most common toxicities were acneiform rash, diarrhea, hand reaction, dyspepsia, and anemia. Four of 18 patients assessable for response (22%; 95% CI, 2% to 42%) achieved a confirmed partial response. CONCLUSION: The combination of gefitinib 500 mg daily plus celecoxib 400 mg twice daily is well-tolerated. The encouraging responses seen in this early study suggest further evaluation of epidermal growth factor receptor and cyclooxygenase-2 inhibitors in SCCHN is warranted.

Administration, Oral↗

PubMed2005

Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis.

Genome-wide copy number changes were analyzed in 70 primary human lung carcinoma specimens and 31 cell lines derived from human lung carcinomas, with high-density arrays representing approximately 115,000 single nucleotide polymorphism loci. In addition to previously characterized loci, two regions of homozygous deletion were found, one near the PTPRD locus on chromosome segment 9p23 in four samples representing both small cell lung carcinoma (SCLC) and non-small cell lung carcinoma (NSCLC) and the second on chromosome segment 3q25 in one sample each of NSCLC and SCLC. High-level amplifications were identified within chromosome segment 8q12-13 in two SCLC specimens, 12p11 in two NSCLC specimens and 22q11 in four NSCLC specimens. Systematic copy number analysis of tyrosine kinase genes identified high-level amplification of EGFR in three NSCLC specimens, FGFR1 in two specimens and ERBB2 and MET in one specimen each. EGFR amplification was shown to be independent of kinase domain mutational status.

Carcinoma, Non-Small-Cell Lung↗

PubMed2005

Self-assembling peptide detergents stabilize isolated photosystem I on a dry surface for an extended time.

We used a class of designed peptide detergents to stabilize photosystem I (PS-I) upon extended drying under N2 on a gold-coated-Ni-NTA glass surface. PS-I is a chlorophyll-containing membrane protein complex that is the primary reducer of ferredoxin and the electron acceptor of plastocyanin. We isolated the complex from the thylakoids of spinach chloroplasts using a chemical detergent. The chlorophyll molecules associated with the PS-I complex provide an intrinsic steady-state emission spectrum between 650 and 800 nm at -196.15 degrees C that reflects the organization of the pigment-protein interactions. In the absence of detergents, a large blue shift of the fluorescence maxima from approximately 735 nm to approximately 685 nm indicates a disruption in light-harvesting subunit organization, thus revealing chlorophyll-protein interactions. The commonly used membrane protein-stabilizing detergents, N-dodecyl-beta-D-maltoside and N-octyl-beta-D-glucoside, only partially stabilized the approximately 735-nm complex with approximately 685-nm spectroscopic shift. However, prior to drying, addition of the peptide detergent acetyl-AAAAAAK at increasing concentration significantly stabilized the PS-I complex. Moreover, in the presence of acetyl-AAAAAAK, the PS-I complex is stable in a dried form at room temperature for at least 3 wk. Another peptide detergent, acetyl-VVVVVVD, also stabilized the complex but to a lesser extent. These observations suggest that the peptide detergents may effectively stabilize membrane proteins in the solid-state. These designed peptide detergents may facilitate the study of diverse types of membrane proteins.

Detergents↗

PubMed2005

Directed cell migration via chemoattractants released from degradable microspheres.

Chemotaxis, cell migration directed by spatial concentration gradients of chemoattractant molecules, is critical for proper function of the immune system. Materials capable of generating defined chemoattractant gradients via controlled release may be useful for the design of improved vaccines and immunotherapies that draw specific cells to an immunization site. To this end, we encapsulated formyl-Nle-Leu-Phe-Nle-Tyr-Lys (fN'LFN'YK) peptides or macrophage inflammatory protein-3alpha (MIP-3alpha or CCL20) in degradable poly(lactide-co-glycolide) microspheres that provided sustained release for more than 2 weeks in vitro. fN'LFN'YK and MIP-3alpha chemoattract dendritic cells (DCs), the key antigen-presenting cells involved in generation of primary immune responses, and their precursors, monocytes. Using an in vitro videomicroscopy migration assay, we detected strong chemotaxis of human monocytes and monocyte-derived DCs through 3D collagen gels toward microspheres releasing fN'LFN'YK. Similarly, microparticles releasing MIP-3alpha were able to attract mouse bone marrow-derived dendritic cells. Strikingly, prolonged attraction of DCs from distances up to 500 microm from the source to the point of contact with individual microspheres was observed. Such microspheres could be of general interest for the design of vaccines that promote adaptive immunity and as a platform for studying the biology of chemotaxis in vitro and in vivo.

Absorbable Implants↗

PubMed2005

Designer self-assembling peptide nanofiber scaffolds for 3D tissue cell cultures.

Biomedical researchers have become increasingly aware of the limitations of time-honored conventional 2D tissue cell cultures where most tissue cell studies have been carried out. They are now searching for 3D cell culture systems, something between a petri dish and a mouse. It has become apparent that 3D cell culture offers a more realistic micro- and local-environment where the functional properties of cells can be observed and manipulated that is not possible in animals. A newly designer self-assembling peptide scaffolds may provide an ideally alternative system. The important implications of 3D tissue cell cultures for basic cell biology, tumor biology, high-content drug screening, and regenerative medicine and beyond could be profound.

Animals↗

PubMed2004

A rapid bioassay for single bacterial cell quantitation using bioconjugated nanoparticles.

The rapid and sensitive determination of pathogenic bacteria is extremely important in biotechnology, medical diagnosis, and the current fight against bioterrorism. Current methods either lack ultrasensitivity or take a long time for analysis. Here, we report a bioconjugated nanoparticle-based bioassay for in situ pathogen quantification down to single bacterium within 20 min. The bioconjugated nanoparticle provides an extremely high fluorescent signal for bioanalysis and can be easily incorporated with biorecognition molecules, such as antibody. The antibody-conjugated nanoparticles can readily and specifically identify a variety of bacterium, such as Escherichia coli O157:H7, through antibody-antigen interaction and recognition. The single-bacterium-detection capability within 20 min has been confirmed by the plate-counting method and realized by using two independent optical techniques. The two detection methods correlated extremely well. Furthermore, we were able to detect multiple bacterial samples with high throughput by using a 384-well microplate format. To show the usefulness of this assay, we have accurately detected 1-400 E. coli O157 bacterial cells in spiked ground beef samples. Our results demonstrate the potential for a broad application of bioconjugated nanoparticles in practical biotechnological and medical applications in various biodetection systems. The ultimate power of integrating bionanotechnology into complex biological systems will emerge as a revolutionary tool for ultrasensitive detection of disease markers and infectious agents.

Animals↗

PubMed2004

Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification.

Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome-wide genetic analysis of actual clinical samples is, however, limited by the paucity of genomic DNA available. Here we have tested the fidelity and genome representation of phi29 polymerase-based genome amplification (phi29MDA) using direct sequencing and high density oligonucleotide arrays probing >10,000 SNP alleles. Genome representation was comprehensive and estimated to be 99.82% complete, although six regions encompassing a maximum of 5.62 Mb failed to amplify. There was no degradation in the accuracy of SNP genotyping and, in direct sequencing experiments sampling 500,000 bp, the estimated error rate (9.5 x 10(-6)) was the same as in paired unamplified samples. The detection of cancer-associated loss of heterozygosity and copy number changes, including homozygous deletion and gene amplification, were similarly robust. These results suggest that phi29MDA yields high fidelity, near-complete genome representation suitable for high resolution genetic analysis.

Alleles↗