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1. Effect of Magnetic Field Gradient on Effectiveness of the Magnetic Sifter for Cell Purification

Ooi, Chinchun | Earhart, Christopher M. | Wilson, Robert J. | Wang, Shan X.

IEEE transactions on magnetics 2013;49(1):316-320.

In our experiments with NCI-H1650 lung cancer cell lines labeled with magnetic nanoparticles via the Epithelial Cell Adhesion Molecule (EpCAM) antigen, we demonstrate capture efficiencies above 90% even at sample flow rates of 5 ml/h through our microfabricated magnetic sifter. We also improve the elution efficiencies from between 50% and 60% to close to 90% via optimization of the permanent magnet size and position used to magnetize the sifter. We then explain our observations via the use of finite element software for magnetic field and field gradient distributions, and a particle tracing algorithm, illustrating the impact of magnetic field gradients on the performance of the magnetic sifter. The high capture and elution efficiencies observed here is especially significant for magnetic separation of biologically interesting but rare moieties such as cancer stem cells for downstream analysis.

doi:10.1109/TMAG.2012.2224851

PMCID: PMC3600415

Cell separation; magnetic devices; magnetic forces; magnetic microspheres; magnetic nanoparticles; magnetic separation

2. Creation of Lung-Targeted Dexamethasone Immunoliposome and Its Therapeutic Effect on Bleomycin-Induced Lung Injury in Rats

PLoS ONE 2013;8(3):e58275.

Objective

Acute lung injury (ALI), is a major cause of morbidity and mortality, which is routinely treated with the administration of systemic glucocorticoids. The current study investigated the distribution and therapeutic effect of a dexamethasone(DXM)-loaded immunoliposome (NLP) functionalized with pulmonary surfactant protein A (SP-A) antibody (SPA-DXM-NLP) in an animal model.

Methods

DXM-NLP was prepared using film dispersion combined with extrusion techniques. SP-A antibody was used as the lung targeting agent. Tissue distribution of SPA-DXM-NLP was investigated in liver, spleen, kidney and lung tissue. The efficacy of SPA-DXM-NLP against lung injury was assessed in a rat model of bleomycin-induced acute lung injury.

Results

The SPA-DXM-NLP complex was successfully synthesized and the particles were stable at 4°C. Pulmonary dexamethasone levels were 40 times higher with SPA-DXM-NLP than conventional dexamethasone injection. Administration of SPA-DXM-NLP significantly attenuated lung injury and inflammation, decreased incidence of infection, and increased survival in animal models.

Conclusions

The administration of SPA-DXM-NLP to animal models resulted in increased levels of DXM in the lungs, indicating active targeting. The efficacy against ALI of the immunoliposomes was shown to be superior to conventional dexamethasone administration. These results demonstrate the potential of actively targeted glucocorticoid therapy in the treatment of lung disease in clinical practice.

doi:10.1371/journal.pone.0058275

PMCID: PMC3597622

3. A Magneto-Nanosensor Immunoassay for Sensitive Detection of Aspergillus Fumigatus Allergen Asp f 1

Kim, Dokyoon | Wang, Shan X.

IEEE transactions on magnetics 2012;48(11):3266-3268.

We report a magneto-nanosensor biochip for fungal detection. The chip is made of arrays of giant magnetoresistive (GMR) spin-valve sensors, and is able to detect protein biomarkers at low concentrations in solutions. As a demonstration, a standard curve for fungal pathogen Asp f 1 was obtained by measuring signals from various concentrations of Asp f 1 spiked in PBS solutions, indicating a detection limit of ~100 pg/ml. Five positive and negative Asp f 1 solution samples were discriminated correctly in blind experiments. Our data suggest that the magneto-nanosensor biochips are very promising as sensitive diagnostic devices for fungal pathogens. Given the generality of the detection scheme used in the magneto-nanosensor, we anticipate that the platform will be very useful for the detection of many types of biomarkers.

doi:10.1109/TMAG.2012.2195163

PMCID: PMC3594507 PMID: 23494403

magneto-nanosensor; biochip; immunoassay; magnetic nanoparticles

4. Raman-Active Two-Tiered Ag Nanoparticles with a Concentric Cavity

Small (Weinheim an der Bergstrasse, Germany) 2011;7(23):3276-3280.

doi:10.1002/smll.201101523

PMCID: PMC3595186 PMID: 21990231

5. FCHSD1 and FCHSD2 Are Expressed in Hair Cell Stereocilia and Cuticular Plate and Regulate Actin Polymerization In Vitro

PLoS ONE 2013;8(2):e56516.

Mammalian FCHSD1 and FCHSD2 are homologous proteins containing an amino-terminal F-BAR domain and two SH3 domains near their carboxyl-termini. We report here that FCHSD1 and FCHSD2 are expressed in mouse cochlear sensory hair cells. FCHSD1 mainly localizes to the cuticular plate, whereas FCHSD2 mainly localizes along the stereocilia in a punctuate pattern. Nervous Wreck (Nwk), the Drosophila ortholog of FCHSD1 and FCHSD2, has been shown to bind Wsp and play an important role in F-actin assembly. We show that, like its Drosophila counterpart, FCHSD2 interacts with WASP and N-WASP, the mammalian orthologs of Drosophila Wsp, and stimulates F-actin assembly in vitro. In contrast, FCHSD1 doesn’t bind WASP or N-WASP, and can’t stimulate F-actin assembly when tested in vitro. We found, however, that FCHSD1 binds via its F-BAR domain to the SH3 domain of Sorting Nexin 9 (SNX9), a well characterized BAR protein that has been shown to promote WASP-Arp2/3-dependent F-actin polymerization. FCHSD1 greatly enhances SNX9’s WASP-Arp2/3-dependent F-actin polymerization activity. In hair cells, SNX9 was detected in the cuticular plate, where it colocalizes with FCHSD1. Our results suggest that FCHSD1 and FCHSD2 could modulate F-actin assembly or maintenance in hair cell stereocilia and cuticular plate.

doi:10.1371/journal.pone.0056516

PMCID: PMC3577914 PMID: 23437151

6. Phylogeographic Evidence for a Link of Species Divergence of Ephedra in the Qinghai-Tibetan Plateau and Adjacent Regions to the Miocene Asian Aridification

PLoS ONE 2013;8(2):e56243.

The Qinghai-Tibetan Plateau (QTP) has become one of the hotspots for phylogeographical studies due to its high species diversity. However, most previous studies have focused on the effects of the Quaternary glaciations on phylogeographical structures and the locations of glacial refugia, and little is known about the effects of the aridization of interior Asia on plant population structure and speciation. Here the chloroplast DNA (cpDNA) trnT-trnF and trnS-trnfM sequences were used to investigate the differentiation and phylogeographical history of 14 Ephedra species from the QTP and northern China, based on a sampling of 107 populations. The phylogeographical analysis, together with phylogenetic reconstruction based on combined four cpDNA fragments (rbcL, rpl16, rps4, and trnS-trnfM), supports three main lineages (eastern QTP, southern QTP, and northern China) of these Ephedra species. Divergence of each lineage could be dated to the Middle or Late Miocene, and was very likely linked to the uplift of the QTP and the Asian aridification, given the high drought and/or cold tolerance of Ephedra. Most of the Ephedra species had low intraspecific variation and lacked a strong phylogeographical structure, which could be partially attributed to clonal reproduction and a relatively recent origin. In addition, ten of the detected 25 cpDNA haplotypes are shared among species, suggesting that a wide sampling of species is helpful to investigate the origin of observed haplotypes and make reliable phylogeographical inference. Moreover, the systematic positions of some Ephedra species are discussed.

doi:10.1371/journal.pone.0056243

PMCID: PMC3571962 PMID: 23418542

7. Rapid screening for Chlamydia trachomatis infection by detecting α-mannosidase activity in urogenital tract specimens

BMC Infectious Diseases 2013;13:36.

Background

Chlamydia trachomatis may cause multiple different urogenital tract disorders, but current non-culture assays for rapid screening of C. trachomatis typically use immunochromatography-based methods. We established another new rapid non-culture method for detection of C. trachomatis based on the measurement of α-mannosidase enzymatic activity in urogenital tract specimens.

Method

To evaluate the performance of this method, α-mannosidase activities of C. trachomatis serotype D strain 、 and 29 standard strains related to clinical urogenital pathogens were investigated. Furthermore, 553 urogenital tract specimens were used for clinical assays via cell culture method and ligase chain reaction method (LCR), adopting an expanded gold standard.

Results

Only C. trachomatis was positive for α-mannosidase activity among different types of microbes tested in the research. When prostate fluid specimens, which have some interfering activity, were excluded, the sensitivity and specificity of the enzymatic method were 91.8% (78/85) and 98.3% (409/416), respectively. There were no significant differences (P > 0.05).

Conclusions

These results showed that α-mannosidase activity could be utilised as a screening marker of C. trachomatis infection.

doi:10.1186/1471-2334-13-36

PMCID: PMC3568413 PMID: 23347393

Chlamydia trachomatis; α-mannosidase; Activity; Gold standard; Marker

8. The CREB-miR-9 Negative Feedback Minicircuitry Coordinates the Migration and Proliferation of Glioma Cells

PLoS ONE 2012;7(11):e49570.

Migration-proliferation dichotomy is a common mechanism in gliomagenesis; however, an understanding of the exact molecular mechanism of this “go or grow” phenomenon remains largely incomplete. In the present study, we first found that microRNA-9 (miR-9) is highly expressed in glioma cells. MiR-9 inhibited the proliferation and promoted the migration of glioma cells by directly targeting cyclic AMP response element-binding protein (CREB) and neurofibromin 1 (NF1), respectively. Our data also suggested a migration-inhibitory role for CREB through directly regulating the transcription of NF1. Furthermore, we found that the transcription of miR-9-1 is under CREB's control, forming a negative feedback minicircuitry. Taken together, miR-9 inhibits proliferation but promotes migration, whereas CREB plays a pro-proliferative and anti-migratory role, suggesting that the CREB-miR-9 negative feedback minicircuitry plays a critical role in the determination of “go or grow” in glioma cells.

doi:10.1371/journal.pone.0049570

PMCID: PMC3502497 PMID: 23185366

9. Efficacy study of CyberKnife stereotactic radiosurgery combined with CIK cell immunotherapy for advanced refractory lung cancer

Experimental and Therapeutic Medicine 2012;5(2):453-456.

CyberKnife (CK), hypofractionated stereotactic radiosurgery, is a preferred option for the treatment of advanced refractory lung cancer which is usually inoperable. Cytokine-induced killer (CIK) cell immunotherapy has a marked radiosensitization effect which aids the elimination of residual tumor cells in distant areas. The main purpose of the present study was to evaluate the clinical efficacy of CK alone and combined with CIK cell therapy for advanced refractory lung cancer. In one year, 22 patients with advanced lung cancer underwent CK therapy at a CyberKnife Center. Of these patients, 11 received CIK cell therapy before or after the CK therapy course. The median prescribed dose in the combined CK and CIK group was 35 Gy (mean, 33.8±5.0 Gy) with a median number of fractions of 5. The median dose for patients who underwent CK alone was 35 Gy (mean, 35.2±6.0 Gy). CIK cell therapy was administered according to the condition of each patient, generally 2 continuous therapeutic sessions in 2 months. The median follow-up period was 3 months. The preliminary curative efficiency rate was 81.82% for patients who underwent CK/CIK and 72.73% for those who received CK alone, according to radiographic re-examination (P>0.05). The median improvement in the Karnofsky scores of the CK/CIK group was 20 (18±10.51) compared with 10 (8.6±11.85) for those who underwent CK alone (P<0.05). The median expression of carcinoembryonic antigen (CEA) before and after treatment was 40.81 and 12.21 ng/ml, respectively, for the CK/CIK group compared with 39.04 and 26.36 ng/ml for CK alone. The median percentage of phenotype expression of the CIK cells (CD3+/CD8+ and CD3+/CD56+) in the patients who underwent CK/CIK was recorded as 64.35% (57.08±16.94%) and 15.27% (18.80±7.00%), respectively, prior to transfusion. The preliminary results of the present study suggest that CK combined with CIK cell immunotherapy improved the short-term outcomes of patients for curative efficacy, Karnofsky scores, tumor marker levels and immune status compared with alternative CK treatments, although further studies are required.

doi:10.3892/etm.2012.818

PMCID: PMC3570163 PMID: 23403795

CyberKnife; stereotactic radiosurgery; cytokine-induced killer; immunotherapy; clinical efficacy

10. DNA Repair and Cell Cycle Biomarkers of Radiation Exposure and Inflammation Stress in Human Blood

PLoS ONE 2012;7(11):e48619.

DNA damage and repair are hallmarks of cellular responses to ionizing radiation. We hypothesized that monitoring the expression of DNA repair-associated genes would enhance the detection of individuals exposed to radiation versus other forms of physiological stress. We employed the human blood ex vivo radiation model to investigate the expression responses of DNA repair genes in repeated blood samples from healthy, non-smoking men and women exposed to 2 Gy of X-rays in the context of inflammation stress mimicked by the bacterial endotoxin lipopolysaccharide (LPS). Radiation exposure significantly modulated the transcript expression of 12 genes of 40 tested (2.2E-06

doi:10.1371/journal.pone.0048619

PMCID: PMC3492462 PMID: 23144912

11. Role of Alvimopan (Entereg) in Gastrointestinal Recovery And Hospital Length of Stay After Bowel Resection

Pharmacy and Therapeutics 2012;37(9):518-525.

A retrospective chart review revealed that patients receiving alvimopan after bowel surgery had faster recovery times, better surgical care, and lower costs of care compared with patients who did not receive the drug.

Purpose:

Postoperative ileus (POI) can delay gastrointestinal (GI) recovery after bowel resection. Alvimopan (Entereg), a peripherally acting mu-opioid receptor antagonist, is thought to favorably reduce various outcome measures such as the length of stay (LOS) and time from surgery to hospital discharge following partial-bowel, large-bowel, or small-bowel resection surgery with primary anastomosis. We undertook a study to compare these outcome measures in alvimopan-treated patients undergoing laparoscopic or open-bowel resection against a control group. We also sought to determine whether any other factors—Diagnosis-Related Group (DRG) status, complications, inflammatory bowel disease, type of surgery, age, sex, intestinal cancer, diverticular disease, number of chronic conditions, and operative time—were predictive of a more favorable (shorter) time to GI recovery.

Methods:

Patients’ charts were retrospectively reviewed at a large 591-bed teaching hospital in suburban New York City between June and August 2010. We applied descriptive statistics for five outcome variables to compare alvimopan-treated patients with non-users. The main outcome variable was the time from surgery to hospital discharge. Secondary outcome variables were the time to pass gas, time to a liquid diet, time to a solid diet, and total LOS. We compared the outcome variables for three groups of DRG codes (329, the most complicated cases; 330, intermediate; and 331, least complicated) to determine which variables influenced these outcome measures. Multivariate analysis with stepwise multiple linear regression analysis was performed to determine independent predictors of shorter times of outcome variables.

Results:

Of 80 patients, 43 received alvimopan (53.75%), and 37 (46.25%) did not. The female-to-male ratio was about 50:50 (56.25% vs. 43.75%). The mean age (standard deviation) was 66.0 (14.9) years (range, 30–92 years). In the multivariate analysis (adjusted for demographics, DRG status, type of surgery, complications, comorbidities, and operative time), for all of our outcome variables (except for time to a liquid diet), patients receiving alvimopan had shorter times to GI recovery (about 25% less) than controls did (p < 0.05). DRG status, complications, inflammatory bowel disease, type of surgery, and age were also significantly predictive of one or more outcome variables, whereas sex, intestinal cancer, diverticular disease, the number of chronic conditions, and operative time were not predictive of any outcomes.

Conclusion:

GI recovery times were generally shorter for alvimopan-treated patients than for those who did not receive the study drug (P < 0.05). Alvimopan improved quality of life and reduced the cost of surgical care. This medication was considered to be a good choice for the perioperative management of patients requiring segmental bowel resection with primary anastomosis.

PMCID: PMC3462601 PMID: 23066346

12. Cell survival, DNA damage, and oncogenic transformation after a transient and reversible apoptotic response

Molecular Biology of the Cell 2012;23(12):2240-2252.

Dying primary liver, NIH 3T3, and HeLa cells can reverse the advanced stage of apoptosis and survive even after incurring DNA damage. Some surviving cells harbor genetic alterations that result in phenotypic diversity, including oncogenic transformation.

Apoptosis serves as a protective mechanism by eliminating damaged cells through programmed cell death. After apoptotic cells pass critical checkpoints, including mitochondrial fragmentation, executioner caspase activation, and DNA damage, it is assumed that cell death inevitably follows. However, this assumption has not been tested directly. Here we report an unexpected reversal of late-stage apoptosis in primary liver and heart cells, macrophages, NIH 3T3 fibroblasts, cervical cancer HeLa cells, and brain cells. After exposure to an inducer of apoptosis, cells exhibited multiple morphological and biochemical hallmarks of late-stage apoptosis, including mitochondrial fragmentation, caspase-3 activation, and DNA damage. Surprisingly, the vast majority of dying cells arrested the apoptotic process and recovered when the inducer was washed away. Of importance, some cells acquired permanent genetic changes and underwent oncogenic transformation at a higher frequency than controls. Global gene expression analysis identified a molecular signature of the reversal process. We propose that reversal of apoptosis is an unanticipated mechanism to rescue cells from crisis and propose to name this mechanism “anastasis” (Greek for “rising to life”). Whereas carcinogenesis represents a harmful side effect, potential benefits of anastasis could include preservation of cells that are difficult to replace and stress-induced genetic diversity.

doi:10.1091/mbc.E11-11-0926

PMCID: PMC3374744 PMID: 22535522

13. Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

BMC Plant Biology 2012;12:138.

Background

Identification of the novel genes relevant to plant cell-wall (PCW) synthesis represents a highly important and challenging problem. Although substantial efforts have been invested into studying this problem, the vast majority of the PCW related genes remain unknown.

Results

Here we present a computational study focused on identification of the novel PCW genes in Arabidopsis based on the co-expression analyses of transcriptomic data collected under 351 conditions, using a bi-clustering technique. Our analysis identified 217 highly co-expressed gene clusters (modules) under some experimental conditions, each containing at least one gene annotated as PCW related according to the Purdue Cell Wall Gene Families database. These co-expression modules cover 349 known/annotated PCW genes and 2,438 new candidates. For each candidate gene, we annotated the specific PCW synthesis stages in which it is involved and predicted the detailed function. In addition, for the co-expressed genes in each module, we predicted and analyzed their cis regulatory motifs in the promoters using our motif discovery pipeline, providing strong evidence that the genes in each co-expression module are transcriptionally co-regulated. From the all co-expression modules, we infer that 108 modules are related to four major PCW synthesis components, using three complementary methods.

Conclusions

We believe our approach and data presented here will be useful for further identification and characterization of PCW genes. All the predicted PCW genes, co-expression modules, motifs and their annotations are available at a web-based database: http://csbl.bmb.uga.edu/publications/materials/shanwang/CWRPdb/index.html.

doi:10.1186/1471-2229-12-138

PMCID: PMC3463447 PMID: 22877077

Plant cell wall; Arabidopsis; Co-expression network analysis; Bi-clustering; Cis regulatory motifs

14. Role of Glycine Receptors in Glycine-Induced LTD in Hippocampal CA1 Pyramidal Neurons

Neuropsychopharmacology 2011;36(9):1948-1958.

Glycine in the hippocampus can exert its effect on both synaptic NMDA receptors (NMDARs) and extrasynaptic functional glycine receptors (GlyRs) via distinct binding sites. Previous studies have reported that glycine induces long-term potentiation (LTP) through the activation of synaptic NMDARs. However, little is known about the potential role of the activated GlyRs that are largely located in extrasynaptic regions. We report here that relatively high levels of glycine achieved either by exogenous glycine application or by the elevation of endogenous glycine accumulation with an antagonist of the glycine transporter induced long-term depression (LTD) of excitatory postsynaptic currents (EPSCs) in hippocampal CA1 pyramidal neurons. The co-application of glycine with the selective GlyR antagonist strychnine changed glycine-induced LTD (Gly-LTD) to LTP. Blocking the postsynaptic GlyR-gated net chloride flux by manipulating intracellular chloride concentrations failed to elicit any changes in EPSCs. These results suggest that GlyRs are involved in Gly-LTD. Furthermore, this new form of chemical LTD was accompanied by the internalization of postsynaptic AMPA receptors and required the activation of NMDARs. Therefore, our present findings reveal an important function of GlyR activation and modulation in gating the direction of synaptic plasticity.

doi:10.1038/npp.2011.86

PMCID: PMC3154115 PMID: 21593734

glycine; glycine receptor; NMDA receptor; LTP; LTD; synaptic plasticity; glutamate; neurophysiology; molecular & cellular neurobiology; neuropharmacology; glycine; glycine receptor; NMDA receptor; LTP; LTD

15. Visualizing Implanted Tumors in Mice with Magnetic Resonance Imaging Using Magnetotactic Bacteria

Clinical cancer research : an official journal of the American Association for Cancer Research 2009;15(16):5170-5177.

Purpose

To determine if magnetotactic bacteria can target tumors in mice and provide positive contrast for visualization using magnetic resonance imaging.

Experimental Design

The ability of the magnetotactic bacterium, Magnetospirillum magneticum AMB-1 (referred to from here as AMB-1), to confer positive magnetic resonance imaging contrast was determined in vitro and in vivo. For the latter studies, AMB-1 were injected either i.t. or i.v. Bacterial growth conditions were manipulated to produce small (~25-nm diameter) magnetite particles, which were observed using transmission electron microscopy. Tumor targeting was confirmed using 64Cu-labeled bacteria and positron emission tomography and by determination of viable cell counts recovered from different organs and the tumor.

Results

We show that AMB-1 bacteria with small magnetite particles generate T1-weighted positive contrast, enhancing in vivo visualization by magnetic resonance imaging. Following i.v. injection of 64Cu-labeled AMB-1, positron emission tomography imaging revealed increasing colonization of tumors and decreasing infection of organs after 4 hours. Viable cell counts showed that, by day 6, the bacteria had colonized tumors but were cleared completely from other organs. Magnetic resonance imaging showed a 1.22-fold (P = 0.003) increased positive contrast in tumors on day 2 and a 1.39-fold increase (P = 0.0007) on day 6.

Conclusion

Magnetotactic bacteria can produce positive magnetic resonance imaging contrast and colonize mouse tumor xenografts, providing a potential tool for improved magnetic resonance imaging visualization in preclinical and translational studies to track cancer.

doi:10.1158/1078-0432.CCR-08-3206

PMCID: PMC3409839 PMID: 19671860

16. Silicon Nano-well Arrays for Reliable Pattern Transfer and Locally Confined High Temperature Reactions

Wi, Jung-Sub | Wilson, Robert J. | Lee, Donkoun | White, Robert M. | Wang, Shan X.

Nanotechnology 2011;22(30):305304.

Si nano-well arrays, with precisely controlled undercut Si sidewall profiles and flat bottomed pockets, enable uniform nanoscale pattern transfer from resists to metal deposits without degradation of the initial lithographic resolution, as verified by formation of arrays of Au nano-dots with 10 nm diameter. An additional functionality of the Si nano-wells as local nano-reactors, where the patterned material is enclosed in a Si pocket during high temperature reaction, is demonstrated by thermally inducing a phase transformation of the as-deposited A1 phase of FePt nano-dots to the high coercivity, chemically ordered L10 phase.

doi:10.1088/0957-4484/22/30/305304

PMCID: PMC3167870 PMID: 21709347

17. Isolation and characterization of ZZ1, a novel lytic phage that infects Acinetobacter baumannii clinical isolates

BMC Microbiology 2012;12:156.

Background

Acinetobacter baumannii, a significant nosocomial pathogen, has evolved resistance to almost all conventional antimicrobial drugs. Bacteriophage therapy is a potential alternative treatment for multidrug-resistant bacterial infections. In this study, one lytic bacteriophage, ZZ1, which infects A. baumannii and has a broad host range, was selected for characterization.

Results

Phage ZZ1 and 3 of its natural hosts, A. baumanni clinical isolates AB09V, AB0902, and AB0901, are described in this study. The 3 strains have different sensitivities to ZZ1, but they have the same sensitivity to antibiotics. They are resistant to almost all of the antibiotics tested, except for polymyxin. Several aspects of the life cycle of ZZ1 were investigated using the sensitive strain AB09V under optimal growth conditions. ZZ1 is highly infectious with a short latent period (9 min) and a large burst size (200 PFU/cell). It exhibited the most powerful antibacterial activity at temperatures ranging from 35°C to 39°C. Moreover, when ZZ1 alone was incubated at different pHs and different temperatures, the phage was stable over a wide pH range (4 to 9) and at extreme temperatures (between 50°C and 60°C). ZZ1 possesses a 100-nm icosahedral head containing double-stranded DNA with a total length of 166,682 bp and a 120-nm long contractile tail. Morphologically, it could be classified as a member of the Myoviridae family and the Caudovirales order. Bioinformatic analysis of the phage whole genome sequence further suggested that ZZ1 was more likely to be a new member of the Myoviridae phages. Most of the predicted ORFs of the phage were similar to the predicted ORFs from other Acinetobacter phages.

Conclusion

The phage ZZ1 has a relatively broad lytic spectrum, high pH stability, strong heat resistance, and efficient antibacterial potential at body temperature. These characteristics greatly increase the utility of this phage as an antibacterial agent; thus, it should be further investigated.

doi:10.1186/1471-2180-12-156

PMCID: PMC3438129 PMID: 22838726

Acinetobacter baumannii ; Bacteriophage; Characterization

18. Fabrication of Planar, Layered Nanoparticles Using Tri-layer Resist Templates

Nanotechnology 2011;22(18):185302.

A simple and universal pathway to produce free multilayer synthetic nanoparticles is developed based on lithography, vapor phase deposition and a tri-layer resist lift off and release process. The fabrication method presented in this work is ideal for production of a broad range of nanoparticles, either free in solution or still attached to an intact release layer, with unique magnetic, optical, radioactive, electronic and catalytic properties. Multi-modal capabilities are implicit in the layered architecture. As an example, directly fabricated magnetic nanoparticles are evaluated to illustrate the structural integrity of thin internal multilayers and the nanoparticle stability in aggressive biological environments, which is highly desired for biomedical applications.

doi:10.1088/0957-4484/22/18/185302

PMCID: PMC3143003 PMID: 21415483

19. Portable Biomarker Detection with Magnetic Nanotags

Hall, Drew A. | Wang, Shan X. | Murmann, Boris | Gaster, Richard S.

The ... Midwest Symposium on Circuits and Systems conference proceedings : MWSCAS. Midwest Symposium on Circuits and Systems 2010;1779-1782.

This paper presents a hand-held, portable biosensor platform for quantitative biomarker measurement. By combining magnetic nanoparticle (MNP) tags with giant magnetoresistive (GMR) spin-valve sensors, the hand-held platform achieves highly sensitive (picomolar) and specific biomarker detection in less than 20 minutes. The rapid analysis and potential low cost make this technology ideal for point-of-care (POC) diagnostics. Furthermore, this platform is able to detect multiple biomarkers simultaneously in a single assay, creating a promising diagnostic tool for a vast number of applications.

doi:10.1109/ISCAS.2010.5537639

PMCID: PMC3321410 PMID: 22495252

20. Transcriptome Sequencing and Characterization for the Sea Cucumber Apostichopus japonicus (Selenka, 1867)

PLoS ONE 2012;7(3):e33311.

Background

Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus.

Results

In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome.

Conclusion

Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.

doi:10.1371/journal.pone.0033311

PMCID: PMC3299772 PMID: 22428017

21. Proteomic analysis of primary colon cancer-associated fibroblasts using the SELDI-ProteinChip platform*

Journal of Zhejiang University. Science. B 2012;13(3):159-167.

Objective: Cancer-associated fibroblasts (CAFs) are one of the hallmarks of the cancer microenvironment. Recent evidence has indicated that CAFs are more competent in enhancing cancer cell growth and migration than normal fibroblasts. However, the unique protein expression of CAFs has not been fully elucidated. This study aims to investigate the characterizations of colon CAFs by comparing the differential protein expression between CAFs and normal fibroblasts. Methods: Primary fibroblasts were isolated from surgical specimen of human colon cancer and matched normal colonic tissue. Purity of the cell population was verified through immunostain analysis. Total cell lysates and conditioned media from each group of cells were extracted, and protein expression analysis was conducted using the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) ProteinChip platform. Results: Most primary cells showed typical fibroblast-like features after two weeks. Increased proportion of α-smooth muscle actin-positive myofibroblasts was detected within the CAFs in four of the six pairs of primary cells. Fibroblast activation protein was weakly expressed in most cells without differences. Using SELDI-TOF-MS ProteinChip platform, four protein peaks mass over charge ratio (m/z) 1142, 3011, 4035, and 4945 were detected in the total cell lysates, and two protein peaks m/z 1368 and 1389 were detected in the conditioned media. The potential candidate proteins found in the Swiss-Prot database include morphogenetic neuropeptides, FMRFamide-related peptides, insulin-like growth factor II, thymosin β-4-like protein 3, and tight junction-associated protein 1. Conclusions: Using the SELDI-ProteinChip platform, differential protein expressions were identified in colon CAFs compared with normal colonic stromal fibroblasts. The complex proteomic alternations in colon CAFs may play important roles related to the colon cancer microenvironment.

doi:10.1631/jzus.B1100266

PMCID: PMC3296066 PMID: 22374607

Colon cancer; Cancer microenvironment; Cancer-associated fibroblasts; Proteomics; Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS)

22. Axial pain after posterior cervical spine surgery: a systematic review

Wang, Shan-Jin | Jiang, Sheng-Dan | Jiang, Lei-Sheng | Dai, Li-Yang

European Spine Journal 2010;20(2):185-194.

Posterior operative approach has been the standard treatment for cervical compressive myelopathy, and axial pain after laminoplasty or laminectomy as a postoperative complication is now gradually receiving more and more attention. The objective of this study was to provide a systematic review of the current understanding of axial pain after cervical laminoplasty and laminectomy, and summarize clinical features, influence factors and preventive measures of axial pain after posterior decompressive surgery based on a review of literature published in the English language. Axial pain distributes over nuchal, periscapular and shoulder regions. Posterior surgery is not the major cause of axial pain, but axial pain can be worsened by the procedure. There are many clinical factors that influence postoperative axial pain such as age, preoperative axial pain, different surgical technique and postoperative management, but most of them are still controversial. Several surgical modifications have been innovated to reduce axial pain. Less invasive surgery, reconstruction of the extensor musculature, avoiding detachment of the semispinalis cervicis muscle and early removal of external immobilization have proved to be effective. Axial pain is under the influence of multiple factors, so comprehensive methods are required to reduce and avoid the postoperative axial pain. Because of methodological shortcomings in publications included in this systematic review, different results from different studies may be produced due to differences in study design, evaluation criteria, sample size, and incidence or severity of axial pain. More high-quality studies are necessary for drawing more reliable and convincing conclusions.

doi:10.1007/s00586-010-1600-x

PMCID: PMC3030716 PMID: 20941514

Axial pain; Laminoplasty; Laminectomy; Cervical spine; Systematic review

23. Histone H3 Lysine 4 Hypermethylation Prevents Aberrant Nucleosome Remodeling at the PHO5 Promoter ▿

Wang, Shan-Shan | Zhou, Bo O. | Zhou, Jin-Qiu

Molecular and Cellular Biology 2011;31(15):3171-3181.

Recent studies have highlighted the histone H3K4 methylation (H3K4me)-dependent transcriptional repression in Saccharomyces cerevisiae; however, the underlying mechanism remains inexplicit. Here, we report that H3K4me inhibits the basal PHO5 transcription under high-phosphate conditions by suppressing nucleosome disassembly at the promoter. We found that derepression of the PHO5 promoter by SET1 deletion resulted in a labile chromatin structure, allowing more binding of RNA polymerase II (Pol II) but not the transactivators Pho2 and Pho4. We further showed that Pho23 and Cti6, two plant homeodomain (PHD)-containing proteins, cooperatively anchored the large Rpd3 (Rpd3L) complex to the H3K4-methylated PHO5 promoter. The deacetylation activity of Rpd3 on histone H3 was required for the function of Set1 at the PHO5 promoter. Taken together, our data suggest that Set1-mediated H3K4me suppresses nucleosome remodeling at the PHO5 promoter so as to reduce basal transcription of PHO5 under repressive conditions. We propose that the restriction of aberrant nucleosome remodeling contributes to strict control of gene transcription by the transactivators.

doi:10.1128/MCB.05017-11

PMCID: PMC3147609 PMID: 21646424

24. Requirement of cannabinoid CB1 receptor in cortical pyramidal neurons for appropriate development of corticothalamic and thalamocortical projections

The European journal of neuroscience 2010;null.

A role for endocannabinoid signaling in neuronal morphogenesis as the brain develops has recently been suggested. Here we used the developing somatosensory circuit as a model system to examine the role of endocannabinoid signaling in neural circuit formation. We first show that deficiency of cannabinoid receptor type 1 (CB1R), but not G-protein coupled receptor 55 (GPR55), leads to aberrant fasciculation and pathfinding in both corticothalamic and thalamocortical axons despite normal target recognition. Next, we localize CB1R expression to developing corticothalamic projections, and find little if any expression in thalamocortical axons, using a newly established reporter mouse expressing GFP in thalamocortical projections. A similar thalamocortical projection phenotype is observed following removal of CB1R from cortical principal neurons, clearly demonstrating that CB1R in corticothalamic axons is required to instruct their complimentary connections, thalamocortical axons. When reciprocal thalamic and cortical connections meet, CB1R-containing corticothalamic axons are intimately associated with elongating thalamocortical projections containing DGLβ, a 2-arachidonoyl glycerol (2-AG) synthesizing enzyme. Thus, 2-AG produced in thalamocortical axons and acting at CB1Rs on corticothalamic axons is likely to modulate axonal patterning. The presence of MGL, a 2-AG degrading enzyme, in both thalamocortical and corticothalamic tracts likely serves to restrict 2-AG availability. In summary, our study provides strong evidence that endocannabinoids are a modulator for the proposed handshake interactions between corticothalamic and thalamocortical axons, especially for fasciculation. These findings are important in understanding the long-term consequences of alterations in CB1R activity during development, a potential etiology for the mental health disorders linked to prenatal Cannabis use.

doi:10.1111/j.1460-9568.2010.07337.x

PMCID: PMC2970673 PMID: 21143665

neural circuit; endocannabinoids; ECS; cortex; thalamus

25. The peak bispectral index time cannot predict early phase propofol pharmacodynamics with effect site-controlled infusion algorithm

Indian Journal of Pharmacology 2012;44(1):41-45.

Objectives:

The plasma-effect site equilibration rate constant (ke0) of propofol was determined with peak bispectral index (BIS) time (TPEAK) in our previous study. The present study has been conducted to evaluate the ke0's performance with effect site-controlled infusion algorithm.

Materials and Methods:

Forty unpremedicated patients were randomized to group TE1 (Schnider's pharmacokinetic model with ke0 adapted to TPEAK = 74s) and TE2 (TPEAK = 96s). In stage 1, all patients received propofol with effect-site concentration (Ce) controlled infusion. Once the pump had injected the mass of propofol necessary to achieve pre-set Ce and while the infusion was stopped, target was reset at 0 μg/ml. When BIS returned to 80 or above, then, in stage 2, the patients received plasma concentration controlled infusion for 10 min. The time of loss of responsiveness (LOR) and BIS were recorded. The differences of Ce at the time of LOR, lowest BIS between stages 1 and 2, hysteresis loop were used to evaluate the performance of ke0.

Results:

In both groups, the calculated propofol Ce at the time of LOR in stages 1 and 2 differed significantly (P<0.01); the mean lowest BIS in stage 1 were significantly higher than those in stage 2 (P < 0.05).The relations of propofol Ce versus BIS revealed the apparent hysteresis loop.

Conclusions:

The study cannot clinically validate the accuracy of application of ke0 derived from the TPEAK = 74 s of BIS with Schnider propofol pharmacokinetic model.

doi:10.4103/0253-7613.91865

PMCID: PMC3271538 PMID: 22345868

Bispectral index; propofol; the plasma effect site equilibration rate constant

Results 1-25 (81)

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