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1.  Up-regulation of long noncoding RNA MALAT1 contributes to proliferation and metastasis in esophageal squamous cell carcinoma 
Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) has been demonstrated to be an important player in various human malignancies; it is thought to promote tumor growth by cell cycle regulating. However, the roles of MALAT1 in esophageal squamous cell carcinoma(ESCC), and the mechanisms involved in cell cycle regulation remain poorly understood. Moreover, the factors contributing to its up-regulation in tumor tissues are still largely unclear.
Expression of MALAT1 was determined from cell lines and clinical samples by qRT-PCR. The effects of MALAT1 knockdown on cell proliferation, cell cycle, apoptosis, migration, and invasion were evaluated by in vitro and in vivo assays. The potential protein expression changes were investigated by Western-blotting. The methylation status of the CpG island in the MALAT1 promoter was explored by bisulfite sequencing, while the copy numbers in tumor tissues and blood samples were detected by a well-established AccuCopyTM method.
MALAT1 was over-expressed in 46.3% of ESCC tissues, mostly in the high-stage tumor samples. Enhanced MALAT1 expression levels were positively correlated with clinical stages, primary tumor size, and lymph node metastasis. Inhibition of MALAT1 suppressed tumor proliferation in vitro and in vivo, as well as the migratory and invasive capacity. MALAT1 depletion also induced G2/M phase arrest and increased the percentage of apoptotic cells. Western-blotting results implicated that the ATM-CHK2 pathway which is associated with G2/M arrest was phosphorylated by MALAT1 knockdown. No effects of CpG island methylation status on MALAT1 expression were found, whereas amplification of MALAT1 was found in 22.2% of tumor tissues, which correlated significantly with its over-expression. However, neither association between tissue copy number amplification and germline copy number variation, nor correlation between germline copy number variation and ESCC risk were identified in the case–control study.
Our data suggest that MALAT1 serves as an oncogene in ESCC, and it regulates ESCC growth by modifying the ATM-CHK2 pathway. Moreover, amplification of MALAT1 in tumor tissues may play an important role for its up-regulation, and it seems that the gene amplification in tumor tissues emerges during ESCC progression, but is not derived from germline origins.
Electronic supplementary material
The online version of this article (doi:10.1186/s13046-015-0123-z) contains supplementary material, which is available to authorized users.
PMCID: PMC4322446  PMID: 25613496
Long noncoding RNA; MALAT1; Esophageal cancer; Copy number; Cell cycle arrest
2.  Identification of a cyclin D1 network in prostate cancer that antagonizes epithelial-mesenchymal restraint 
Cancer research  2013;74(2):508-519.
Improved clinical management of prostate cancer (PCa) has been impeded by an inadequate understanding of molecular genetic elements governing tumor progression. Gene signatures have provided improved prognostic indicators of human PCa. The TGFβ/BMP-SMAD4 signaling pathway, which induces epithelial mesenchymal transition (EMT), is known to constrain prostate cancer progression induced by Pten deletion. Herein, cyclin D1 inactivation reduced cellular proliferation in the murine prostate in vivo and in isogenic oncogene-transformed prostate cancer cell lines. The in vivo cyclin D1-mediated molecular signature predicted poor outcome of recurrence free survival for prostate cancer patients (K-means hazard ratio 3.75, P-value=0.02) and demonstrated that endogenous cyclin D1 restrains TGFβ, Snail, Twist and Goosecoid signaling. Endogenous cyclin D1 enhanced Wnt and ES cell gene expression and expanded a prostate stem cell population. In ChIP-Seq, cyclin D1 occupied genes governing stem cell expansion and induced their transcription. The coordination of EMT restraining and stem cell expanding gene expression by cyclin D1 in the prostate may contribute to its strong prognostic value for poor outcome in biochemical free recurrence in human prostate cancer.
PMCID: PMC3914674  PMID: 24282282
Cyclin D1; gene network; prostate cancer; siRNA; shRNA
3.  Neural representation of orientation relative to gravity in the macaque cerebellum 
Neuron  2013;80(6):10.1016/j.neuron.2013.09.029.
A fundamental challenge for maintaining spatial orientation and interacting with the world is knowledge of our orientation relative to gravity, i.e. tilt. Sensing gravity is complicated because of Einstein’s equivalence principle, where gravitational and translational accelerations are physically indistinguishable. Theory has proposed that this ambiguity is solved by tracking head tilt through multisensory integration. Here we identify a group of Purkinje cells in the caudal cerebellar vermis with responses that reflect an estimate of head tilt. These tilt-selective cells are complementary to translation-selective Purkinje cells, such that their population activities sum to the net gravito-inertial acceleration encoded by the otolith organs, as predicted by theory. These findings reflect the remarkable ability of the cerebellum for neural computation and provide novel quantitative evidence for a neural representation of gravity, whose calculation relies on long-postulated theoretical concepts such as internal models and Bayesian priors.
PMCID: PMC3872004  PMID: 24360549
Vestibular; cerebellum; spatial orientation; internal model; gravity
4.  The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities 
As widely recognized, agarwood formation in Aquilaria trees is induced by external wounding. Because agarwood usually harbors specific microbes, the function of microbes in agarwood formation has been debated for almost a century. In this study, two wounding methods, the burning-chisel-drilling method (BCD) and the whole-tree agarwood-inducing method (Agar-Wit), were used under the non-contamination of environmental microorganisms. After pyrosequencing the small rRNA subunits of the wounds induced by the BCD and Agar-Wit, no substantial variation was observed either in fungal and bacterial enrichment and diversity or in the relative abundances of taxa. By contrast, significant variations in fungal and bacterial communities were detected following the partial tree pruning (PTP)-wounding. The wound-induced sesquiterpene biosynthesis and vessel-occlusion formation, however, were found to be similar in all types of wounded trunks. We thus infer that wounding in the absence of variations in microbial communities may induce agarwood formation. This result does not support the long-standing notion that agarwood formation depends on microbes.
PMCID: PMC4284782  PMID: 25530613
Aquilaria sinensis; wound; microbe; vessel occlusion; sesquiterpene; plant defense response
5.  Challenges and limitations of patient-specific vascular phantom fabrication using 3D Polyjet printing 
Additive manufacturing (3D printing) technology offers a great opportunity towards development of patient-specific vascular anatomic models, for medical device testing and physiological condition evaluation. However, the development process is not yet well established and there are various limitations depending on the printing materials, the technology and the printer resolution. Patient-specific neuro-vascular anatomy was acquired from computed tomography angiography and rotational digital subtraction angiography (DSA). The volumes were imported into a Vitrea 3D workstation (Vital Images Inc.) and the vascular lumen of various vessels and pathologies were segmented using a “marching cubes” algorithm. The results were exported as Stereo Lithographic (STL) files and were further processed by smoothing, trimming, and wall extrusion (to add a custom wall to the model). The models were printed using a Polyjet printer, Eden 260V (Objet-Stratasys). To verify the phantom geometry accuracy, the phantom was reimaged using rotational DSA, and the new data was compared with the initial patient data. The most challenging part of the phantom manufacturing was removal of support material. This aspect could be a serious hurdle in building very tortuous phantoms or small vessels. The accuracy of the printed models was very good: distance analysis showed average differences of 120 μm between the patient and the phantom reconstructed volume dimensions. Most errors were due to residual support material left in the lumen of the phantom. Despite the post-printing challenges experienced during the support cleaning, this technology could be a tremendous benefit to medical research such as in device development and testing.
PMCID: PMC4188370  PMID: 25300886
Vascular phantoms; 3D printing; additive manufacturing; patient specific phantoms; CT; Cone-Beam CT
6.  High Fidelity Virtual Stenting (HiFiVS) for Intracranial Aneurysm Flow Diversion: In Vitro and In Silico 
Annals of biomedical engineering  2013;41(10):2143-2156.
A flow diverter (FD) is a flexible, densely braided stent-mesh device placed endoluminally across an intracranial aneurysm to induce its thrombotic occlusion. FD treatment planning using computational virtual stenting and flow simulation requires accurate representation of the expanded FD geometry. We have recently developed a High Fidelity Virtual Stenting (HiFiVS) technique based on finite element analysis to simulate detailed FD deployment processes in patient-specific aneurysms (Ma et al. J. Biomech. 45: 2256–2263, 2012). This study tests if HiFiVS simulation can recapitulate real-life FD implantation. We deployed two identical FDs (Pipeline Embolization Device) into phantoms of a wide-necked segmental aneurysm using a clinical push-pull technique with different delivery wire advancements. We then simulated these deployment processes using HiFiVS and compared results against experimental recording. Stepwise comparison shows that the simulations precisely reproduced the FD deployment processes recorded in vitro. The local metal coverage rate and pore density quantifications demonstrated that simulations reproduced detailed FD mesh geometry. These results provide validation of the HiFiVS technique, highlighting its unique capability of accurately representing stent intervention in silico.
PMCID: PMC3766425  PMID: 23604850
Flow diverter; Pipeline Embolization Device; Stent deployment; Intracranial aneurysm; Finite element analysis; Braided stent
7.  Tissue Triage and Freezing for Models of Skeletal Muscle Disease 
Skeletal muscle is a unique tissue because of its structure and function, which requires specific protocols for tissue collection to obtain optimal results from functional, cellular, molecular, and pathological evaluations. Due to the subtlety of some pathological abnormalities seen in congenital muscle disorders and the potential for fixation to interfere with the recognition of these features, pathological evaluation of frozen muscle is preferable to fixed muscle when evaluating skeletal muscle for congenital muscle disease. Additionally, the potential to produce severe freezing artifacts in muscle requires specific precautions when freezing skeletal muscle for histological examination that are not commonly used when freezing other tissues. This manuscript describes a protocol for rapid freezing of skeletal muscle using isopentane (2-methylbutane) cooled with liquid nitrogen to preserve optimal skeletal muscle morphology. This procedure is also effective for freezing tissue intended for genetic or protein expression studies. Furthermore, we have integrated our freezing protocol into a broader procedure that also describes preferred methods for the short term triage of tissue for (1) single fiber functional studies and (2) myoblast cell culture, with a focus on the minimum effort necessary to collect tissue and transport it to specialized research or reference labs to complete these studies. Overall, this manuscript provides an outline of how fresh tissue can be effectively distributed for a variety of phenotypic studies and thereby provides standard operating procedures (SOPs) for pathological studies related to congenital muscle disease.
PMCID: PMC4215994  PMID: 25078247
Basic Protocol; Issue 89; Tissue; Freezing; Muscle; Isopentane; Pathology; Functional Testing; Cell Culture
8.  Endothelial Nitric Oxide Synthase and Superoxide Mediate Hemodynamic Initiation of Intracranial Aneurysms 
PLoS ONE  2014;9(7):e101721.
Hemodynamic insults at arterial bifurcations are believed to play a critical role in initiating intracranial aneurysms. Recent studies in a rabbit model indicate that aneurysmal damage initiates under specific wall shear stress conditions when smooth muscle cells (SMCs) become pro-inflammatory and produce matrix metalloproteinases (MMPs). The mechanisms leading to SMC activation and MMP production during hemodynamic aneurysm initiation are unknown. The goal is to determine if nitric oxide and/or superoxide induce SMC changes, MMP production and aneurysmal remodeling following hemodynamic insult.
Bilateral common carotid artery ligation was performed on rabbits (n = 19, plus 5 sham operations) to induce aneurysmal damage at the basilar terminus. Ligated animals were treated with the nitric oxide synthase (NOS) inhibitor LNAME (n = 7) or the superoxide scavenger TEMPOL (n = 5) and compared to untreated animals (n = 7). Aneurysm development was assessed histologically 5 days after ligation. Changes in NOS isoforms, peroxynitrite, reactive oxygen species (ROS), MMP-2, MMP-9, and smooth muscle α-actin were analyzed by immunohistochemistry.
LNAME attenuated ligation-induced IEL loss, media thinning and bulge formation. In untreated animals, immunofluorescence showed increased endothelial NOS (eNOS) after ligation, but no change in inducible or neuronal NOS. Furthermore, during aneurysm initiation ROS increased in the media, but not the intima, and there was no change in peroxynitrite. In LNAME-treated animals, ROS production did not change. Together, this suggests that eNOS is important for aneurysm initiation but not by producing superoxide. TEMPOL treatment reduced aneurysm development, indicating that the increased medial superoxide is also necessary for aneurysm initiation. LNAME and TEMPOL treatment in ligated animals restored α-actin and decreased MMPs, suggesting that eNOS and superoxide both lead to SMC de-differentiation and MMP production.
Aneurysm-inducing hemodynamics lead to increased eNOS and superoxide, which both affect SMC phenotype, increasing MMP production and aneurysmal damage.
PMCID: PMC4081806  PMID: 24992254
9.  High Wall Shear Stress and Spatial Gradients in Vascular Pathology: A Review 
Annals of biomedical engineering  2012;41(7):1411-1427.
Cardiovascular pathologies such as intracranial aneurysms (IAs) and atherosclerosis preferentially localize to bifurcations and curvatures where hemodynamics are complex. While extensive knowledge about low wall shear stress (WSS) has been generated in the past, due to its strong relevance to atherogenesis, high WSS (typically >3 Pa) has emerged as a key regulator of vascular biology and pathology as well, receiving renewed interests. As reviewed here, chronic high WSS not only stimulates adaptive outward remodeling, but also contributes to saccular IA formation (at bifurcation apices or outer curves) and atherosclerotic plaque destabilization (in stenosed vessels). Recent advances in understanding IA pathogenesis have shed new light on the role of high WSS in pathological vascular remodeling. In complex geometries, high WSS can couple with significant spatial WSS gradient (WSSG). A combination of high WSS and positive WSSG has been shown to trigger aneurysm initiation. Since endothelial cells (ECs) are sensors of WSS, we have begun to elucidate EC responses to high WSS alone and in combination with WSSG. Understanding such responses will provide insight into not only aneurysm formation, but also plaque destabilization and other vascular pathologies and potentially lead to improved strategies for disease management and novel targets for pharmacological intervention.
PMCID: PMC3638073  PMID: 23229281
Intracranial aneurysm; Aneurysm initiation; Atherosclerosis; Outward remodeling; Vulnerable plaque; Wall shear stress gradient; Endothelial cell sensing; Hemodynamics
10.  Deleting exon 55 from the nebulin gene induces severe muscle weakness in a mouse model for nemaline myopathy 
Brain  2013;136(6):1718-1731.
Nebulin—a giant sarcomeric protein—plays a pivotal role in skeletal muscle contractility by specifying thin filament length and function. Although mutations in the gene encoding nebulin (NEB) are a frequent cause of nemaline myopathy, the most common non-dystrophic congenital myopathy, the mechanisms by which mutations in NEB cause muscle weakness remain largely unknown. To better understand these mechanisms, we have generated a mouse model in which Neb exon 55 is deleted (NebΔExon55) to replicate a founder mutation seen frequently in patients with nemaline myopathy with Ashkenazi Jewish heritage. NebΔExon55 mice are born close to Mendelian ratios, but show growth retardation after birth. Electron microscopy studies show nemaline bodies—a hallmark feature of nemaline myopathy—in muscle fibres from NebΔExon55 mice. Western blotting studies with nebulin-specific antibodies reveal reduced nebulin levels in muscle from NebΔExon55 mice, and immunofluorescence confocal microscopy studies with tropomodulin antibodies and phalloidin reveal that thin filament length is significantly reduced. In line with reduced thin filament length, the maximal force generating capacity of permeabilized muscle fibres and single myofibrils is reduced in NebΔExon55 mice with a more pronounced reduction at longer sarcomere lengths. Finally, in NebΔExon55 mice the regulation of contraction is impaired, as evidenced by marked changes in crossbridge cycling kinetics and by a reduction of the calcium sensitivity of force generation. A novel drug that facilitates calcium binding to the thin filament significantly augmented the calcium sensitivity of submaximal force to levels that exceed those observed in untreated control muscle. In conclusion, we have characterized the first nebulin-based nemaline myopathy model, which recapitulates important features of the phenotype observed in patients harbouring this particular mutation, and which has severe muscle weakness caused by thin filament dysfunction.
PMCID: PMC3673460  PMID: 23715096
nebulin; nemaline myopathy; muscle fibre weakness; thin filament function
11.  Computation of linear acceleration through an internal model in the macaque cerebellum 
Nature neuroscience  2013;16(11):10.1038/nn.3530.
A combination of theory and behavioral findings has supported a role for internal models in the resolution of sensory ambiguities and sensorimotor processing. Although the cerebellum has been proposed as a candidate for implementation of internal models, concrete evidence from neural responses is lacking. Here we exploit un-natural motion stimuli, which induce incorrect self-motion perception and eye movements, to explore the neural correlates of an internal model proposed to compensate for Einstein’s equivalence principle and generate neural estimates of linear acceleration and gravity. We show that caudal cerebellar vermis Purkinje cells and cerebellar nuclei neurons selective for actual linear acceleration also encode erroneous linear acceleration, as expected from the internal model hypothesis, even when no actual linear acceleration occurs. These findings provide strong evidence that the cerebellum might be involved in the implementation of internal models that mimic physical principles to interpret sensory signals, as previously hypothesized by theorists.
PMCID: PMC3818145  PMID: 24077562
12.  Mutations in the Homeodomain of HOXD13 Cause Syndactyly Type 1-c in Two Chinese Families 
PLoS ONE  2014;9(5):e96192.
Syndactyly type 1 (SD1) is an autosomal dominant limb malformation characterized in its classical form by complete or partial webbing between the third and fourth fingers and/or the second and third toes. Its four subtypes (a, b, c, and d) are defined based on variable phenotypes, but the responsible gene is yet to be identified. SD1-a has been mapped to chromosome 3p21.31 and SD1-b to 2q34–q36. SD1-c and SD1-d are very rare and, to our knowledge, no gene loci have been identified.
Methods and Results
In two Chinese families with SD1-c, linkage and haplotype analyses mapped the disease locus to 2q31-2q32. Copy number variation (CNV) analysis, using array-based comparative genomic hybridization (array CGH), excluded the possibility of microdeletion or microduplication. Sequence analyses of related syndactyly genes in this region identified c.917G>A (p.R306Q) in the homeodomain of HOXD13 in family A. Analysis on family B identified the mutation c.916C>G (p.R306G) and therefore confirmed the genetic homogeneity. Luciferase assays indicated that these two mutations affected the transcriptional activation ability of HOXD13. The spectrum of HOXD13 mutations suggested a close genotype-phenotype correlation between the different types of HOXD13-Syndactyly. Overlaps of the various phenotypes were found both among and within families carrying the HOXD13 mutation.
Mutations (p.R306Q and p.R306G) in the homeodomain of HOXD13 cause SD1-c. There are affinities between SD1-c and synpolydactyly. Different limb malformations due to distinct classes of HOXD13 mutations should be considered as a continuum of phenotypes and further classification of syndactyly should be done based on phenotype and genotype.
PMCID: PMC4006867  PMID: 24789103
13.  Enzyme replacement therapy rescues weakness and improves muscle pathology in mice with X-linked myotubular myopathy 
Human Molecular Genetics  2013;22(8):1525-1538.
No effective treatment exists for patients with X-linked myotubular myopathy (XLMTM), a fatal congenital muscle disease caused by deficiency of the lipid phosphatase, myotubularin. The Mtm1δ4 and Mtm1 p.R69C mice model severely and moderately symptomatic XLMTM, respectively, due to differences in the degree of myotubularin deficiency. Contractile function of intact extensor digitorum longus (EDL) and soleus muscles from Mtm1δ4 mice, which produce no myotubularin, is markedly impaired. Contractile forces generated by chemically skinned single fiber preparations from Mtm1δ4 muscle were largely preserved, indicating that weakness was largely due to impaired excitation contraction coupling. Mtm1 p.R69C mice, which produce small amounts of myotubularin, showed impaired contractile function only in EDL muscles. Short-term replacement of myotubularin with a prototypical targeted protein replacement agent (3E10Fv-MTM1) in Mtm1δ4 mice improved contractile function and muscle pathology. These promising findings suggest that even low levels of myotubularin protein replacement can improve the muscle weakness and reverse the pathology that characterizes XLMTM.
PMCID: PMC3605830  PMID: 23307925
14.  Novel Oncogene Induced Metastatic Prostate Cancer Cell Lines Define Human Prostate Cancer Progression Signatures 
Cancer research  2012;73(2):978-989.
Herein, murine prostate cancer cell lines, generated via selective transduction with a single oncogene (c-Myc, Ha-Ras, and v-Src), demonstrated oncogene-specific prostate cancer molecular signatures that were recapitulated in human prostate cancer, and developed lung metastasis in immune competent mice. Interrogation of two independent retrospective cohorts of patient samples using the oncogene signature demonstrated an ability to distinguish tumor from normal prostate with a predictive value for prostate cancer of 98 – 99%. In a blinded study, the signature algorithm demonstrated independent substratification of reduced recurrence free survival by Kaplan-Meier analysis. The generation of new oncogene-specific prostate cancer cell lines that recapitulate human prostate cancer gene expression, that metastasize in immune-competent mice, are a valuable new resource for testing targeted therapy while the molecular signatures identified herein provides further value over current gene signature markers of prediction and outcome.
PMCID: PMC3561759  PMID: 23204233
15.  Profiling of MicroRNAs under Wound Treatment in Aquilaria sinensis to Identify Possible MicroRNAs Involved in Agarwood Formation 
Agarwood, a kind of highly valued non-timber product across Asia, is formed only when its resource trees -- the endangered genus Aquilaria are wounded or infected by some microbes. To promote the efficiency of agarwood production and protect the wild resource of Aquilaria species, we urgently need to reveal the regulation mechanism of agarwood formation. MicroRNAs (miRNAs) are a group of gene expression regulators with overwhelming effects on a large spectrum of biological processes. However, their roles in agarwood formation remain unknown. This work aimed at identifying possible miRNAs involved in the wound induced agarwood formation. In this study, the high-throughput sequencing was adopted to identify miRNAs and monitor their expression under wound treatment in the stems of A. sinensis. The miR171, miR390, miR394, miR2111, and miR3954 families remained at the reduced level two days after the treatment. 131 homologous miRNAs in the 0.5 h library showed over three-fold variation of read number compared with the control library, of which 12 exhibiting strong expression alterations were further confirmed by real-time quantitative PCR. Target prediction and annotation of the miRNAs demonstrated that the binding, metabolic process, catalytic activity, and cellular process are the most common functions of the predicted targets of these newly identified miRNAs in A.sinensis. The cleaveage sites of three newly predicted targets were verified by 5'RACE.
PMCID: PMC4007363  PMID: 24795531
microRNA; Agarwood; Aquilaria sinensis; wound; small RNA
16.  A Critical Role for Proinflammatory Behavior of Smooth Muscle Cells in Hemodynamic Initiation of Intracranial Aneurysm 
PLoS ONE  2013;8(9):e74357.
Intracranial aneurysm initiation is poorly understood, although hemodynamic insult is believed to play an important role in triggering the pathology. It has recently been found in a rabbit model that while macrophages are absent during hemodynamic aneurysm initiation, matrix metalloproteinases (MMPs) are elevated and co-localize with smooth muscle cells (SMCs). This study investigates whether SMCs play a mechanistic role in aneurysm initiation triggered by hemodynamics.
Aneurysmal damage was induced at the basilar terminus via bilateral common carotid artery ligation in rabbits (n = 45, plus 7 sham controls). 16 ligated rabbits were treated with doxycycline to inhibit MMPs, 7 received clodronate liposomes to deplete circulating monocytes, and the rest received no drug. Effects of the treatments on aneurysm development were assessed histologically 5 days and 6 months after ligation. MMP production and expression of inflammatory markers by SMCs was monitored by immunohistochemistry and in situ hybridization.
Treatment with doxycycline attenuated aneurysmal development examined at 5 days and 6 months, suggesting that MMPs contribute to aneurysm initiation. However, systemic depletion of macrophages did not decrease MMPs or suppress aneurysmal development. Immunofluorescence showed that during aneurysm initiation MMP-2 and MMP-9 were distributed in SMCs, and in situ hybridization indicated that they were transcribed by SMCs. In regions of early aneurysmal lesion, SMCs exhibited decreased expression of smooth muscle actin and increased NF-κB and MCP-1 expressions.
During aneurysm initiation triggered by hemodynamics, SMCs rather than macrophages are responsible for MMP production that is critical for aneurysmal lesion development. These SMCs exhibit proinflammatory behavior.
PMCID: PMC3759467  PMID: 24023941
17.  Reaching the Limit of the Oculomotor Plant: 3D Kinematics after Abducens Nerve Stimulation during the Torsional Vestibulo-Ocular Reflex 
Accumulating evidence shows that the oculomotor plant is capable of implementing aspects of three-dimensional kinematics such as Listing's law and the half-angle rule. But these studies have only examined the eye under static conditions or with movements that normally obey these rules (e.g., saccades and pursuit). Here we test the capability of the oculomotor plant to rearrange itself as necessary for non-half-angle behavior. Three monkeys (Macaca mulatta) fixated five vertically displaced targets along the midsagittal plane while sitting on a motion platform that rotated sinusoidally about the naso-occipital axis. This activated the torsional, rotational vestibuloocular reflex, which exhibits a zero-angle or negative-angle rule (depending on the visual stimulus). On random sinusoidal cycles, we stimulated the abducens nerve and observed the resultant eye movements. If the plant has rearranged itself to implement this non-half-angle behavior, then stimulation should reveal this behavior. On the other hand, if the plant is only capable of half-angle behavior, then stimulation should reveal a half-angle rule. We find the latter to be true and therefore additional neural signals are likely necessary to implement non-half-angle behavior.
PMCID: PMC3676185  PMID: 22993439
18.  Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis 
BMC Genomics  2013;14:227.
Agarwood is an expensive resinous heartwood derived from Aquilaria plants that is widely used in traditional medicines, incense and perfume. Only wounded trees can produce agarwood, and the huge demand for the agarwood products has led all Aquilaria spp. being endangered and listed in the Appendix II of the CITES ( The major components of agarwood are sesquiterpenes and phenylethyl chromones. Owing to a lack of genomic information, the molecular basis of wound-induced sesquiterpenes biosynthesis and agarwood formation remains unknown.
To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65 bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, and a handful of transcription factors and protein kinases were related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being δ-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS.
This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation.
PMCID: PMC3635961  PMID: 23565705
Agarwood; Aquilaria sinensis; GC-MS; Sesquiterpenes; Transcriptome; Wound signal transduction
19.  Reaching the Limit of the Oculomotor Plant: 3D Kinematics after Abducens Nerve Stimulation during the Torsional Vestibulo-Ocular Reflex 
The Journal of Neuroscience  2012;32(38):13237-13243.
Accumulating evidence shows that the oculomotor plant is capable of implementing aspects of three-dimensional kinematics such as Listing's law and the half-angle rule. But these studies have only examined the eye under static conditions or with movements that normally obey these rules (e.g., saccades and pursuit). Here we test the capability of the oculomotor plant to rearrange itself as necessary for non-half-angle behavior. Three monkeys (Macaca mulatta) fixated five vertically displaced targets along the midsagittal plane while sitting on a motion platform that rotated sinusoidally about the naso-occipital axis. This activated the torsional, rotational vestibulo-ocular reflex, which exhibits a zero-angle or negative-angle rule (depending on the visual stimulus). On random sinusoidal cycles, we stimulated the abducens nerve and observed the resultant eye movements. If the plant has rearranged itself to implement this non-half-angle behavior, then stimulation should reveal this behavior. On the other hand, if the plant is only capable of half-angle behavior, then stimulation should reveal a half-angle rule. We find the latter to be true and therefore additional neural signals are likely necessary to implement non-half-angle behavior.
PMCID: PMC3676185  PMID: 22993439
20.  Probabilistic Identification of Cerebellar Cortical Neurones across Species 
PLoS ONE  2013;8(3):e57669.
Despite our fine-grain anatomical knowledge of the cerebellar cortex, electrophysiological studies of circuit information processing over the last fifty years have been hampered by the difficulty of reliably assigning signals to identified cell types. We approached this problem by assessing the spontaneous activity signatures of identified cerebellar cortical neurones. A range of statistics describing firing frequency and irregularity were then used, individually and in combination, to build Gaussian Process Classifiers (GPC) leading to a probabilistic classification of each neurone type and the computation of equi-probable decision boundaries between cell classes. Firing frequency statistics were useful for separating Purkinje cells from granular layer units, whilst firing irregularity measures proved most useful for distinguishing cells within granular layer cell classes. Considered as single statistics, we achieved classification accuracies of 72.5% and 92.7% for granular layer and molecular layer units respectively. Combining statistics to form twin-variate GPC models substantially improved classification accuracies with the combination of mean spike frequency and log-interval entropy offering classification accuracies of 92.7% and 99.2% for our molecular and granular layer models, respectively. A cross-species comparison was performed, using data drawn from anaesthetised mice and decerebrate cats, where our models offered 80% and 100% classification accuracy. We then used our models to assess non-identified data from awake monkeys and rabbits in order to highlight subsets of neurones with the greatest degree of similarity to identified cell classes. In this way, our GPC-based approach for tentatively identifying neurones from their spontaneous activity signatures, in the absence of an established ground-truth, nonetheless affords the experimenter a statistically robust means of grouping cells with properties matching known cell classes. Our approach therefore may have broad application to a variety of future cerebellar cortical investigations, particularly in awake animals where opportunities for definitive cell identification are limited.
PMCID: PMC3587648  PMID: 23469215
21.  MicroRNA and histopathological characterization of pure mucinous breast carcinoma 
Cancer Biology & Medicine  2013;10(1):22-27.
Pure mucinous breast carcinoma (PMBC) is an uncommon histological type of breast cancer characterized by a large amount of mucin production. MicroRNA (miRNA) is a large class of small noncoding RNA of about 22 nt involved in the regulation of various biological processes. This study aims to identify the miRNA expression profile in PMBC.
MiRNA expression profiles in 11 PMBCs were analyzed by miRNA-microarray and real-time polymerase chain reaction (PCR). Thirty-one PMBCs and 27 invasive ductal carcinoma of no special types (IDC-NSTs) were assessed by immunohistochemistry using antibodies against ER, PR-progesterone receptor, HER2, Ki-67, Bcl-2, p53, PCNA, and CK5 and 6.
We analyzed the miRNA expression in 11 PMBCs and corresponding normal tissues using miRNA-microarray and real-time PCR, and found that miR-143 and miR-224-5p were significantly downregulated in mucinous carcinoma tissue. Compared with IDC-NSTs, PMBC showed a significantly higher ER positive rate, lower HER-2 positive rate, and lower cell proliferation rates.
To our knowledge, this is the first study to demonstrate the miRNA expression profile of PMBC, and our findings may lead to further understanding of this type of breast cancer.
PMCID: PMC3643684  PMID: 23691441
Pure mucinous breast carcinoma; microRNA; real-time PCR
22.  Cellular and Molecular Responses of the Basilar Terminus to Hemodynamics during Intracranial Aneurysm Initiation in a Rabbit Model 
Journal of Vascular Research  2011;48(5):429-442.
Hemodynamics constitute a critical factor in the formation of intracranial aneurysms. However, little is known about how intracranial arteries respond to hemodynamic insult and how that response contributes to aneurysm formation. We examined early cellular responses at rabbit basilar termini exposed to hemodynamic insult that initiates aneurysmal remodeling.
Flow in the basilar artery was increased by bilateral carotid artery ligation. After 2 and 5 days, basilar terminus tissue was examined by immunohistochemistry and quantitative PCR.
Within 2 days of flow increase, internal elastic lamina (IEL) was lost in the periapical region of the bifurcation, which experienced high wall shear stress and positive wall shear stress gradient. Overlying endothelium was still largely present in this region. IEL loss was associated with localized apoptosis and elevated expression of matrix metalloproteinases (MMPs) 2 and 9. A small number of inflammatory cells were sporadically scattered in the bifurcation adventitia and were not concentrated in regions of IEL loss and MMP elevation. Elevated MMP expression colocalized with smooth muscle α-actin in the media.
The initial vascular response to aneurysm-initiating hemodynamic insult includes localized matrix degradation and cell apoptosis. Such destructive remodeling arises from intrinsic mural cells, rather than through inflammatory cell infiltration.
PMCID: PMC3121554  PMID: 21625176
Intracranial aneurysm; Hemodynamic forces; Vascular remodeling; Internal elastic lamina; Matrix metalloproteinase; Apoptosis; Inflammatory cells; Wall shear stress
23.  Homonymous Quadrantanopsia as the First Manifestation of Cerebral Metastasis of Invasive Mole: a case report 
Homonymous quadrantanopsia results from retrochiasmal lesions in the visual pathway. Invasive mole is a benign tumor that arises from myometrial invasion of a hydatidiform mole via direct extension through tissue or venous channels. Cerebral metastasis of invasive mole is rare and there has been no report demonstrating homonymous quadrantanopsia as the first manifestation of metastasis in any trophoblastic neoplasms.
Case presentation
We report the case of a 31-year-old Asian woman who presented with right homonymous inferior quadrantanopsia from the mass effect of a solitary cerebral metastasis from an invasive mole. A magnetic resonance image (MRI) of the brain showed a metastatic tumor in the left occipital lobe. The visual field improved slightly after chemotherapy. There was a reduction in the tumor size and the surrounding edema. This is the first case report demonstrating that homonymous quadrantanopsia should be included in the manifestations of the metastasis of an invasive mole.
The presentation of homonymous quadrantanopsia must alert ophthalmologists to conduct a complete medical history and arrange specialist consultation.
PMCID: PMC3353198  PMID: 22531212
Cerebral metastasis; Homonymous Quadrantanopsia; Invasive mole
24.  Transcriptional activation of microRNA-34a by NF-kappa B in human esophageal cancer cells 
miR-34a functions as an important tumor suppressor during the process of carcinogenesis. However, the mechanism of miR-34a dysregulation in human malignancies has not been well elucidated. Our study aimed to further investigate the regulation mechanism of miR-34a.
We found that overexpression of NF-kappa B p65 subunit could increase miR-34a levels in EC109, an esophageal squamous cancer cell line, while ectopic expression of DN IkappaB leaded to a significant reduction of miR-34a expression. Bioinformatics analysis suggested three putative KB sites in promoter region of miR-34a gene. Mutation two of these KB sites impaired p65 induced miR-34a transcriptional activity. Chromatin immunoprecipitation and electrophoretic mobility shift assays both showed that NF-kappaB could specifically bind to the third KB site located in miR-34a promoter. In addition, we found that overexpression of NF-kappaB p65 could not successfully induce miR-34a expression in esophageal cancer cell lines with mutant p53 or decreased p53. Reporter assay further showed that NF-kappaB-induced miR-34a transcriptional activity was reduced by p53 impairment. Nevertheless, CHIP analysis suggested binding of NF-kappaB to miR-34a promoter was not affected in cells with mutant p53.
Our work indicates a novel mechanism of miR-34a regulation that NF-kappaB could elevate miR-34a expression levels through directly binding to its promoter. And wildtype p53 is responsible for NF-kappaB-mediated miR-34a transcriptional activity but not for NF-kappaB binding. These findings might be helpful in understanding miR-34a abnormality in human malignancies and open new perspectives for the roles of miR-34a and NF-kappaB in tumor progression.
PMCID: PMC3311059  PMID: 22292433
miR-34a; NF-kappa B; p53; gene expression regulation
25.  Hemodynamic-Morphologic Discriminants for Intracranial Aneurysm Rupture 
Background and Purpose
To identify significant morphologic and hemodynamic parameters that discriminate intracranial aneurysm (IA) rupture status using 3D angiography and computational fluid dynamics (CFD).
119 IAs (38 ruptured, 81 unruptured) were analyzed from 3D angiographic images and CFD. Six morphologic and seven hemodynamic parameters were evaluated for significance with respect to rupture. Receiver-operating characteristic (ROC) analysis identified area under the curve (AUC) and optimal thresholds separating ruptured from unruptured aneurysms for each parameter. Significant parameters were examined by multivariate logistic regression analysis in 3 predictive models—morphology only, hemodynamics only, and combined—to identify independent discriminants, and the AUC-ROC of the predicted probability of rupture status was compared among these models.
Morphologic parameters (Size Ratio [SR], Undulation Index, Ellipticity Index, and Nonsphericity Index) and hemodynamic parameters (Average Wall Shear Stress [WSS], Maximum intra-aneurysmal WSS, Low WSS Area, Average Oscillatory Shear Index [OSI], Number of Vortices, and Relative Resident Time) achieved statistical significance (p<0.01). Multivariate logistic regression analysis demonstrated SR to be the only independently significant factor in the morphology model (AUC=0.83, 95% confidence interval [CI] 0.75–0.91), whereas WSS and OSI were the only independently significant variables in the hemodynamics model (AUC=0.85, 95% CI 0.78–0.93). The combined model retained all three variables, SR, WSS, and OSI (AUC=0.89, 95% CI 0.82–0.96).
All three models—morphological (based on SR), hemodynamic (based on WSS and OSI), and combined—discriminate IA rupture status with high AUC values. Hemodynamics is as important as morphology in discriminating aneurysm rupture status.
PMCID: PMC3021316  PMID: 21106956
Hemodynamics; Intracranial aneurysm; Morphology; Rupture

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