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1.  A transparent broadband ultrasonic detector based on an optical micro-ring resonator for photoacoustic microscopy 
Scientific Reports  2014;4:4496.
Photoacoustic microscopy (PAM) does not rely on contrast agent to image the optical absorption contrast in biological tissue. It is uniquely suited for measuring several tissue physiological parameters, such as hemoglobin oxygen saturation, that would otherwise remain challenging. Researchers are designing new clinical diagnostic tools and multimodal microscopic systems around PAM to fully unleash its potential. However, the sizeable and opaque piezoelectric ultrasonic detectors commonly used in PAM impose a serious constraint. Our solution is a coverslip-style optically transparent ultrasound detector based on a polymeric optical micro-ring resonator (MRR) with a total thickness of 250 μm. It enables highly-sensitive ultrasound detection over a wide receiving angle with a bandwidth of 140 MHz, which corresponds to a photoacoustic saturation limit of 287 cm−1, at an estimated noise-equivalent pressure (NEP) of 6.8 Pa. We also established a theoretical framework for designing and optimizing the MRR for PAM.
doi:10.1038/srep04496
PMCID: PMC3968454  PMID: 24675547
2.  REGULATION OF GLUCOSE HOMEOSTASIS THROUGH XBP1-FOXO1 INTERACTION 
Nature medicine  2011;17(3):356-365.
To date, our understanding of the role of X-Box Binding Protein 1 (XBP1) in metabolic processes was limited to its ability to up-regulate ER folding capacity and thereby, to increase insulin sensitivity. Here, we demonstrate that XBP1s interacts with Forkhead box O1 (FoxO1) transcription factor and directs it to proteasome-mediated degradation. Our results provide the first evidence that, in addition to its regulatory effects on the ER system and insulin sensitivity, XBP1s can independently regulate glucose homeostasis through its interaction with FoxO1. Indeed, a DNA binding defective mutant of XBP1s, which does not have the ability to increase ER folding capacity, is still capable of reducing blood glucose levels and increasing glucose tolerance in the severely obese and diabetic ob/ob mice. XBP1-mediated degradation of FoxO1 might lead to development of new therapeutic approaches for treatment of type 2 diabetes.
doi:10.1038/nm.2293
PMCID: PMC3897616  PMID: 21317886
3.  C-Terminal Domain of ICA69 Interacts with PICK1 and Acts on Trafficking of PICK1-PKCα Complex and Cerebellar Plasticity 
PLoS ONE  2013;8(12):e83862.
Background
PICK1 (protein interacting with C-kinase 1) is a PKC (protein kinase C)-binding protein, which is essential for synaptic plasticity. The trafficking of PKCα-PICK1 complex to plasma membrane is critical for the internalization of GluR2 and induction of long-term depression. ICA69 (islet cell autoantigen 69 kDa) is identified as a major binding partner of PICK1. While heteromeric BAR domain complex is suggested to underlie the interaction between PICK1 and ICA69, the role of C-terminal domain of ICA69 (ICAC) in PICK1-ICA69 complex is unknown.
Methodology/Principal Findings
We found that ICAC interacted with PICK1 and regulated the trafficking of PICK1-PKCα complex. ICAC and ΔICAC (containing BAR domain) might function distinctly in the association of ICA69 with PICK1. While ΔICAC domain inclined to form clusters, the distribution of ICAC was diffuse. The trafficking of PICK1 to plasma membrane mediated by activated PKCα was inhibited by ICA69. This action might ascribe to ICAC, because overexpression of ICAC, but not ΔICAC, interrupted PKCα-mediated PICK1 trafficking. Notably, infusion of maltose binding protein (MBP) fusion protein, MBP-ICA69 or MBP-ICAC, in cerebellar Purkinje cells significantly inhibited the induction of long-term depression at parallel fiber- and climbing fiber-Purkinje cell synapses.
Conclusions
Our experiments showed that ICAC is an important domain for the ICA69-PICK1 interaction and plays essential roles in PICK1-mediated neuronal plasticity.
doi:10.1371/journal.pone.0083862
PMCID: PMC3865253  PMID: 24358315
4.  20-Hydroxyeicosatetraenoic Acid Contributes to the Inhibition of K+ Channel Activity and Vasoconstrictor Response to Angiotensin II in Rat Renal Microvessels 
PLoS ONE  2013;8(12):e82482.
The present study examined whether 20-hydroxyeicosatetraenoic acid (HETE) contributes to the vasoconstrictor effect of angiotensin II (ANG II) in renal microvessels by preventing activation of the large conductance Ca2+-activated K+ channel (KCa) in vascular smooth muscle (VSM) cells. ANG II increased the production of 20-HETE in rat renal microvessels. This response was attenuated by the 20-HETE synthesis inhibitors, 17-ODYA and HET0016, a phospholipase A2 inhibitor AACOF3, and the AT1 receptor blocker, Losartan, but not by the AT2 receptor blocker, PD123319. ANG II (10-11 to 10-6 M) dose-dependently decreased the diameter of renal microvessels by 41 ± 5%. This effect was blocked by 17-ODYA. ANG II (10-7 M) did not alter KCa channel activity recorded from cell-attached patches on renal VSM cells under control conditions. However, it did reduce the NPo of the KCa channel by 93.4 ± 3.1% after the channels were activated by increasing intracellular calcium levels with ionomycin. The inhibitory effect of ANG II on KCa channel activity in the presence of ionomycin was attenuated by 17-ODYA, AACOF3, and the phospholipase C (PLC) inhibitor U-73122. ANG II induced a peak followed by a steady-state increase in intracellular calcium concentration in renal VSM cells. 17-ODYA (10-5 M) had no effect on the peak response, but it blocked the steady-state increase. These results indicate that ANG II stimulates the formation of 20-HETE in rat renal microvessels via the AT1 receptor activation and that 20-HETE contributes to the vasoconstrictor response to ANG II by blocking activation of KCa channel and facilitating calcium entry.
doi:10.1371/journal.pone.0082482
PMCID: PMC3853207  PMID: 24324797
5.  Quantitative Imaging of Rapidly Decaying Evanescent Fields Using Plasmonic Near-Field Scanning Optical Microscopy 
Scientific Reports  2013;3:2803.
Non-propagating evanescent fields play an important role in the development of nano-photonic devices. While detecting the evanescent fields in far-field can be accomplished by coupling it to the propagating waves, in practice they are measured in the presence of unwanted propagating background components. It leads to a poor signal-to-noise ratio and thus to errors in quantitative analysis of the local evanescent fields. Here we report on a plasmonic near-field scanning optical microscopy (p-NSOM) technique that incorporates a nanofocusing probe for adiabatic focusing of propagating surface plasmon polaritons at the probe apex, and for enhanced coupling of evanescent waves to the far-field. In addition, a harmonic demodulation technique is employed to suppress the contribution of the background. Our experimental results show strong evidence of background free near-field imaging using the new p-NSOM technique. Furthermore, we present measurements of surface plasmon cavity modes, and quantify their contributing sources using an analytical model.
doi:10.1038/srep02803
PMCID: PMC3786296  PMID: 24076563
6.  Reductive Degradation of Tetrabromobisphenol Using Iron–Silver and Iron–Nickel Bimetallic Nanoparticles with Microwave Energy 
Environmental Engineering Science  2012;29(6):453-460.
Abstract
In this work, a novel combined system by Fe-Ag or Fe-Ni nanoparticles and microwave (MW) radiation were used for the debromination of tetrabromobisphenol A (TBBPA) in aqueous solutions. Core-shell structure bimetallic nanoparticles were prepared by replacement reaction in liquid phase and then characterized by X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy techniques. MW radiation can enhance the degradation of TBBPA by Fe-Ag or Fe-Ni observably. The rate of reduction reactions for bimetallic nanoparticles under MW were first compared with those under conventional heating conditions. Compared with nano-iron, the deposition of Ag or Ni also accelerated the debromination, and Fe-Ag was more reactive than Fe-Ni toward TBBPA reduction. Removal efficiencies increased with increasing Fe-Ag dosage and MW energy level. Major reduction products of TBBPA identified by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) were tri-BBPA, di-BBPA, mono-BBPA, and BPA, which indicated a stepwise debromination process. It provides an effective technology for TBBPA laden wastewater treatment.
doi:10.1089/ees.2010.0376
PMCID: PMC3363012  PMID: 22693414
debromination; TBBPA; bimetallic; nanoparticles; microwave radiation
7.  NMR Studies of Localized Water and Protein Backbone Dynamics in Mechanically Strained Elastin 
The journal of physical chemistry. B  2011;115(47):13935-13942.
We report on measurements of the dynamics of localized waters of hydration and the protein backbone of elastin, a remarkable resilient protein found in vertebrate tissues, as a function of the applied external strain. Using deuterium 2D T1–T2 NMR, we separate four reservoirs in the elastin–water system characterized by water with distinguishable mobilities. The measured correlation times corresponding to random tumbling of water localized to the protein is observed to decrease with increasing strain and is interpreted as an increase in its orientational entropy. The NMR T1 and T1ρ relaxation times of the carbonyl and aliphatic carbons of the protein backbone are measured and indicate a reduction in the correlation time as the elastomer strain is increased. It is argued, and supported by MD simulation of a short model elastin peptide [VPGVG]3, that the observed changes in the backbone dynamics give rise to the development of an entropic elastomeric force that is responsible for elastins’ remarkable elasticity.
doi:10.1021/jp207607r
PMCID: PMC3622950  PMID: 22017547
8.  Complete genome sequencing and analysis of six enterovirus 71 strains with different clinical phenotypes 
Virology Journal  2013;10:115.
Background
Hand, foot and mouth diseases (HFMD) caused by enterovirus 71(EV71) presents a broad spectrum of clinical manifestations ranging from mild febrile disease to fatal neurolocal disease. However, the mechanism of virulence is unknown.
Methods
We isolated 6 strains of EV71 from HFMD patients with or without neurological symptoms, and sequenced the whole genomes of the viruses to reveal the virulence factors of EV71.
Results
Phylogenetic tree based on VP1 region showed that all six strains clustered into C4a of C4 sub-genotype. In the complete polypeptide, 298 positions were found to be variable in all strains, and three of these positions (ValP814/IleP814 in VP1, ValP1148/IleP1148 in 3A and Ala P1728/Cys P1728/Val P1728 in 3C) were conserved among the strains with neurovirulence, but variable in strains without neurovirulence. In the 5′-UTR region, it showed that the first 10 nucleotides were mostly conserved, however from the 11th nucleotide, nucleotide insertions and deletions were quite common. The secondary structure prediction of 5′-UTR sequences showed that two of three strains without neurovirulence (SDLY11 and SDLY48) were almost the same, and all strains with neurovirulence (SDLY96, SDLY107 and SDLY153) were different from each other. SDLY107 (a fatal strain) was found different from other strains on four positions (CP241/TP241, AP571/TP571, CP579/TP579 in 5′-UTR and TP7335/CP7335 in 3′-UTR).
Conclusions
The three positions (ValP814/IleP814 in VP1, ValP1148/IleP1148 in 3A and Ala P1728/Cys P1728/Val P1728 in 3C), were different between two phenotypes. These suggested that the three positions might be potential virulent positions. And the three varied positions were also found to be conserved in strains with neurovirulence, and variable in strains without neurovirulence. These might reveal that the conservation of two of the three positions or the three together were specific for the strains with neurovirulence. Varation of secondary structure of 5′-UTR, might be correlated to the changes of viral virulence. SDLY107 (a fatal strain) was found different from other strains on four positions, these positions might be related with death.
doi:10.1186/1743-422X-10-115
PMCID: PMC3669102  PMID: 23577963
Enterovirus 71; Virulent determinant; Hand, foot and mouth disease
9.  Thermal hysteresis in the backbone and side chain dynamics of the elastin mimetic peptide [VPGVG]3 revealed by 2H NMR 
We report on experimental measurements of the backbone and side chain dynamics of the elastin mimetic peptide [VPGVG]3 by 2H NMR echo spectroscopy and 2D T1-T2 correlation relaxometry. The T1 and T2 relaxation times of the Gly α-deuterons and Val α-, β- and γ- deuterons of a hydrated sample reveal a thermal hysteresis when the temperature is raised from −10°C to 45°C and then subsequently cooled back to −10°C. In addition, near 30°C we observe a reduction in the slope of the T1(T) and T2(T) heating curves, indicating a structural change that appears to be correlated well to the known inverse temperature transition of this peptide. The thermal dependence of the correlation times of the Gly α-deuterons are well fit by an Arrhenius Law, from which we have measured Eact =(20.0 ± 3.1) kJ/mol when the sample is heated, and Eact =(10.9 ± 2.8) kJ/mol when cooled. Molecular dynamics simulations support the notion that the measured activation energy is determined largely by the extent of localized water, which is observed to decrease with increasing temperature from approximately 25°C to 42°C.
doi:10.1021/jp208966k
PMCID: PMC3257400  PMID: 22142235
10.  Highly Efficient Light-Trapping Structure Design Inspired By Natural Evolution 
Scientific Reports  2013;3:1025.
Recent advances in nanophotonic light trapping open up the new gateway to enhance the absorption of solar energy beyond the so called Yablonovitch Limit. It addresses the urgent needs in developing low cost thin-film solar photovoltaic technologies. However, current design strategy mainly relies on the parametric approach that is subject to the predefined topological design concepts based on physical intuition. Incapable of dealing with the topological variation severely constrains the design of optimal light trapping structure. Inspired by natural evolution process, here we report a design framework driven by topology optimization based on genetic algorithms to achieve a highly efficient light trapping structure. It has been demonstrated that the optimal light trapping structures obtained in this study exhibit more than 3-fold increase over the Yablonovitch Limit with the broadband absorption efficiency of 48.1%, beyond the reach of intuitive designs.
doi:10.1038/srep01025
PMCID: PMC3535673  PMID: 23289067
11.  Slow DNA Loss in the Gigantic Genomes of Salamanders 
Genome Biology and Evolution  2012;4(12):1340-1348.
Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ∼1–30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes—the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis, Danio rerio, Gallus gallus, Homo sapiens, and Xenopus tropicalis. Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.
doi:10.1093/gbe/evs103
PMCID: PMC3542557  PMID: 23175715
indel spectrum; insertion; deletion; mutation; genome size; transposable element
12.  Correction: Cytosolic Phospholipase A2 alpha/Arachidonic Acid Signaling Mediates Depolarization-Induced Suppression of Excitation in the Cerebellum 
PLoS ONE  2012;7(11):10.1371/annotation/d08032c8-4a27-4c9c-8ef7-b3ec64351cde.
doi:10.1371/annotation/d08032c8-4a27-4c9c-8ef7-b3ec64351cde
PMCID: PMC3552745
13.  Tissue interaction is required for glenoid fossa development during temporomandibular joint formation 
The mammalian temporomandibular joint (TMJ) develops from two distinct mesenchymal condensations that grow towards each other and ossify through different mechanisms, with the glenoid fossa undergoing intramembranous ossification while the condyle being endochondral in origin. In this study, we used various genetically modified mouse models to investigate tissue interaction between the condyle and glenoid fossa during TMJ formation in mice. We report that either absence or dislocation of the condyle results in an arrested glenoid fossa development. In both cases, glenoid fossa development was initiated, but failed to sustain, and became regressed subsequently. However, condyle development appears to be independent upon the presence of the forming glenoid fossa. In addition, we show that substitution of condyle by Meckel’s cartilage is able to sustain glenoid fossa development. These observations suggest that proper signals from the developing condyle or Meckel’s cartilage are required to sustain the glenoid fossa development.
doi:10.1002/dvdy.22748
PMCID: PMC3197963  PMID: 21953591
TMJ formation; glenoid fossa development; condyle; tissue interaction; Sox9
14.  Cytosolic Phospholipase A2 alpha/Arachidonic Acid Signaling Mediates Depolarization-Induced Suppression of Excitation in the Cerebellum 
PLoS ONE  2012;7(8):e41499.
Background
Depolarization-induced suppression of excitation (DSE) at parallel fiber-Purkinje cell synapse is an endocannabinoid-mediated short-term retrograde plasticity. Intracellular Ca2+ elevation is critical for the endocannabinoid production and DSE. Nevertheless, how elevated Ca2+ leads to DSE is unclear.
Methodology/Principal Findings
We utilized cytosolic phospholipase A2 alpha (cPLA2α) knock-out mice and whole-cell patch clamp in cerebellar slices to observed the action of cPLA2α/arachidonic acid signaling on DSE at parallel fiber-Purkinje cell synapse. Our data showed that DSE was significantly inhibited in cPLA2α knock-out mice, which was rescued by arachidonic acid. The degradation enzyme of 2-arachidonoylglycerol (2-AG), monoacylglycerol lipase (MAGL), blocked DSE, while another catabolism enzyme for N-arachidonoylethanolamine (AEA), fatty acid amide hydrolase (FAAH), did not affect DSE. These results suggested that 2-AG is responsible for DSE in Purkinje cells. Co-application of paxilline reversed the blockade of DSE by internal K+, indicating that large conductance Ca2+-activated potassium channel (BK) is sufficient to inhibit cPLA2α/arachidonic acid-mediated DSE. In addition, we showed that the release of 2-AG was independent of soluble NSF attachment protein receptor (SNARE), protein kinase C and protein kinase A.
Conclusions/Significance
Our data first showed that cPLA2α/arachidonic acid/2-AG signaling pathway mediates DSE at parallel fiber-Purkinje cell synapse.
doi:10.1371/journal.pone.0041499
PMCID: PMC3425552  PMID: 22927908
15.  Ectopic expression of Nkx2.5 suppresses the formation of the sinoatrial node in mice 
Developmental biology  2011;356(2):359-369.
The sinoatrial node (SAN), functionally known as the pacemaker, regulates the cardiac rhythm or heart beat. Several genes are expressed in the developing SAN and form a genetic network regulating the fate of the SAN cells. The short stature homeobox gene Shox2 is an important player in the SAN genetic network by regulating the expression of different cardiac conduction molecular markers including the early cardiac differentiation marker Nkx2.5. Here we report that the expression patterns of Shox2 and Nkx2.5 are mutually exclusive from the earliest stages of the venous pole and the SAN formation. We show that tissue specific ectopic expression of Shox2 in the developing mouse heart downregulates the expression of Nkx2.5 and causes cardiac malformations; however, it is not sufficient to induce a SAN cell fate switch in the working myocardium. On the other hand, tissue specific overexpression of Nkx2.5 in the heart leads to severe hypoplasia of the SAN and the venous valves, dis-regulation of the SAN genetic network, and change of the SAN cell fate into working myocardium, and causes embryonic lethality, recapitulating the phenotypes including bradycardia observed in Shox2−/− mutants. These results indicate that Nkx2.5 activity is detrimental to the normal formation of the SAN. Taken together, our results demonstrate that Shox2 downregulation of Nkx2.5 is essential for the proper development of the SAN and that Shox2 functions to shield the SAN from becoming working myocardium by acting upstream of Nkx2.5.
doi:10.1016/j.ydbio.2011.05.663
PMCID: PMC3143305  PMID: 21640717
Shox2; Nkx2.5; sinoatrial node; pacemaker; heart development
16.  Investigation of the effect of a variety of pulse errors on spin I=1 quadrupolar alignment echo spectroscopy 
We report on an analysis of a well known three-pulse sequence for generating and detecting spin I=1 quadrupolar order when various pulse errors are taken into account. In the situation of a single quadrupolar frequency, such as the case found in a single crystal, we studied the potential leakage of single and/or double quantum coherence when a pulse flip error, finite pulse width effect, RF transient or a resonance offset is present. Our analysis demonstrates that the four-step phase cycling scheme studied is robust in suppressing unwanted double and single quantum coherence as well as Zeeman order that arise from the experimental artifacts, allowing for an unbiased measurement of the quadrupolar alignment relaxation time, T1Q. This work also reports on distortions in quadrupolar alignment echo spectra in the presence of experimental artifacts in the situation of a powdered sample, by simulation. Using our simulation tool, it is demonstrated that the spectral distortions associated with the pulse artifacts may be minimized, to some extent, by optimally choosing the time between the first two pulses. We highlight experimental results acquired on perdeuterated hexamethylbenzene and polyethelene that demonstrate the efficacy of the phase cycling scheme for suppressing unwanted quantum coherence when measuring T1Q. It is suggested that one employ two separate pulse sequences when measuring T1Q to properly analyze the short time behavior of quadrupolar alignment relaxation data.
doi:10.1016/j.jmr.2011.05.003
PMCID: PMC3148855  PMID: 21664160
Quadrupolar Relaxation; Quadrupolar Interaction; Multiple Quantum Filtering; T1Q
17.  The association of leptin and C-reactive protein with the cardiovascular risk factors and metabolic syndrome score in Taiwanese adults 
Background
Serum C-reactive protein (CRP) and leptin levels have been independently associated with the cardiovascular risk factors. The aim of the present study was to determine if their serum levels were associated with cardiovascular risk factors or metabolic syndrome as well as their correlation in the Taiwanese population.
Methods
This retrospective study included 999 subjects (> 18 y), who underwent a physical examination in Chang-Gung Memorial Hospital-Linkou and Chiayi in Taiwan. The associations between CRP and/or leptin levels and cardiovascular risk factors and metabolic syndrome were determined using independent two sample t-tests to detect gender differences and chi-square tests to evaluate differences in frequencies. To compare the means of the variables measured among the four groups (high and low leptin and high and low CRP), analysis of variance (ANOVA) was used.
Results
Both CRP and leptin levels were independently associated with several cardiovascular risk factors, including diabetes, hypercholesterolemia and metabolic syndrome in both men and women (P < 0.05). In addition, a positive correlation between leptin and CRP levels was observed in both genders. Both high-CRP and high-leptin were associated with high blood glucose, waist circumference and serum triglyceride. Whereas increased metabolic syndrome incidence was observed in males with elevated leptin regardless of CRP levels, females with elevated CRP or leptin had increased incidence of metabolic syndrome.
Conclusion
Both leptin and CRP levels were associated with cardiovascular risk factors as well as metabolic syndrome score in both men and women although gender-specific differences were observed. Thus, CRP and leptin may represent useful biomarkers for predicting the onset of cardiovascular disease or metabolic syndrome in Taiwanese adults.
Trial registration
IRB/CGMH 100-3514B
doi:10.1186/1475-2840-11-40
PMCID: PMC3471043  PMID: 22533665
C-reactive protein; Leptin; Cardiovascular disease; Metabolic syndrome; Taiwan
18.  MicroRNA159 Can Act as a Switch or Tuning MicroRNA Independently of Its Abundance in Arabidopsis 
PLoS ONE  2012;7(4):e34751.
The efficacy of gene silencing by plant microRNAs (miRNAs) is generally assumed to be predominantly determined by their abundance. In Arabidopsis the highly abundant miRNA, miR159, acts as a molecular “switch” in vegetative tissues completely silencing the expression of two GAMYB-like genes, MYB33 and MYB65. Here, we show that miR159 has a diminished silencing efficacy in the seed. Using reporter gene constructs, we determined that MIR159 and MYB33 are co-transcribed in the aleurone and embryo of germinating seeds. However in contrast to vegetative tissues, MYB33 is not completely silenced. Instead, miR159 appears to shape the spatio-temporal expression pattern of MYB33 during seed germination. Transcript profiling in a time course during seed germination in wild-type and a mir159 mutant in which miR159 is almost absent, revealed that transcript levels of the GAMYB-like genes were similar between these two genotypes during germination, but much higher in the mir159 mutant once germination had completed. This attenuation in the silencing of the GAMYB-like genes was not explained by a decrease in mature miR159 levels, which remained constant at all time points during seed germination. We propose that miR159 acts as a tuner of GAMYB-like levels in Arabidopsis germinating seeds and that the activity of this miRNA is attenuated in the seed compared to vegetative tissues. This implies that the efficacy of miRNA-mediated silencing is not solely determined by miRNA abundance and target transcript levels, but is being determined through additional mechanisms.
doi:10.1371/journal.pone.0034751
PMCID: PMC3325262  PMID: 22511963
19.  TGF-β1 Down-Regulation of NKG2D/DAP10 and 2B4/SAP Expression on Human NK Cells Contributes to HBV Persistence 
PLoS Pathogens  2012;8(3):e1002594.
The mechanism underlying persistent hepatitis B virus (HBV) infection remains unclear. We investigated the role of innate immune responses to persistent HBV infection in 154 HBV-infected patients and 95 healthy controls. The expression of NKG2D- and 2B4-activating receptors on NK cells was significantly decreased, and moreover, the expression of DAP10 and SAP, the intracellular adaptor proteins of NKG2D and 2B4 (respectively), were lower, which then impaired NK cell-mediated cytotoxic capacity and interferon-γ production. Higher concentrations of transforming growth factor-beta 1 (TGF-β1) were found in sera from persistently infected HBV patients. TGF-β1 down-regulated the expression of NKG2D and 2B4 on NK cells in our in vitro study, leading to an impairment of their effector functions. Anti-TGF-β1 antibodies could restore the expression of NKG2D and 2B4 on NK cells in vitro. Furthermore, TGF-β1 induced cell-cycle arrest in NK cells by up-regulating the expression of p15 and p21 in NK cells from immunotolerant (IT) patients. We conclude that TGF-β1 may reduce the expression of NKG2D/DAP10 and 2B4/SAP, and those IT patients who are deficient in these double-activating signals have impaired NK cell function, which is correlated with persistent HBV infection.
Author Summary
NK cells have been viewed as the most important effectors of the initial antiviral innate immune response. Their activation depends on the integration of signals from “co-activation” receptors, and the cytotoxic effects of NK cells on target cells are tempered by a need for combined signals from multiple activating receptors, such as NKG2D and 2B4. In this study, we showed that NKG2D and 2B4 expression levels were decreased on NK cells from patients in the IT phase of HBV infection. We further demonstrated that lower levels of intracellular adaptor proteins (DAP10 and SAP) were associated with lower surface expression of NKG2D and 2B4. As a result, the synergistically co-activated signalling pathway initiated by NKG2D and 2B4 did not operate properly in IT-phase patients. We demonstrated that high levels of soluble TGF-β1 were associated with the reduction of NKG2D and 2B4 in patients. In addition, we showed that TGF-β1 causes the cell-cycle arrest of NK cells by up-regulating the levels of p15 and p21 in NK cells from IT patients. Collectively, these findings may contribute to our understanding of the immune tolerance mechanism and aid in the development of novel therapeutic methods to clear HBV infection during the initial phase.
doi:10.1371/journal.ppat.1002594
PMCID: PMC3305436  PMID: 22438812
20.  Measurement of the Exchange Rate of Waters of Hydration in Elastin by 2D T2-T2 Correlation Nuclear Magnetic Resonance Spectroscopy 
New journal of physics  2011;13:2-16.
We report on the direct measurement of the exchange rate of waters of hydration in elastin by T2-T2 exchange spectroscopy. The exchange rates in bovine nuchal ligament elastin and aortic elastin at temperatures near, below and at the physiological temperature are reported. Using an Inverse Laplace Transform (ILT) algorithm, we are able to identify four components in the relaxation times. While three of the components are in good agreement with previous measurements that used multi-exponential fitting, the ILT algorithm distinguishes a fourth component having relaxation times close to that of free water and is identified as water between fibers. With the aid of scanning electron microscopy, a model is proposed allowing for the application of a two-site exchange analysis between any two components for the determination of exchange rates between reservoirs. The results of the measurements support a model (described elsewhere [1]) wherein the net entropy of bulk waters of hydration should increase upon increasing temperature in the inverse temperature transition.
doi:10.1088/1367-2630/13/2/025026
PMCID: PMC3144479  PMID: 21804764
21.  Nuclear translocation of AMPK-α1 potentiates striatal neurodegeneration in Huntington’s disease 
The Journal of Cell Biology  2011;194(2):209-227.
Nuclear accumulation of AMPK-α1 induces brain atrophy, neuronal loss, and formation of Htt aggregates in a Huntington’s disease model.
Adenosine monophosphate–activated protein kinase (AMPK) is a major energy sensor that maintains cellular energy homeostasis. Huntington’s disease (HD) is a neurodegenerative disorder caused by the expansion of CAG repeats in the huntingtin (Htt) gene. In this paper, we report that activation of the α1 isoform of AMPK (AMPK-α1) occurred in striatal neurons of humans and mice with HD. Overactivation of AMPK in the striatum caused brain atrophy, facilitated neuronal loss, and increased formation of Htt aggregates in a transgenic mouse model (R6/2) of HD. Such nuclear accumulation of AMPK-α1 was activity dependent. Prevention of nuclear translocation or inactivation of AMPK-α1 ameliorated cell death and down-regulation of Bcl2 caused by mutant Htt (mHtt). Conversely, enhanced expression of Bcl2 protected striatal cells from the toxicity evoked by mHtt and AMPK overactivation. These data demonstrate that aberrant activation of AMPK-α1 in the nuclei of striatal cells represents a new toxic pathway induced by mHtt.
doi:10.1083/jcb.201105010
PMCID: PMC3144412  PMID: 21768291
22.  LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders 
Genome Biology and Evolution  2011;4(2):168-183.
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.
doi:10.1093/gbe/evr139
PMCID: PMC3318908  PMID: 22200636
LTR retrotransposon; transposable element landscape; genomic expansion; TE age distributions; genome size evolution; plethodontid salamanders
23.  Spectral-domain optical coherence tomography in patients with congenital nystagmus 
AIM
To study macular features in patients with congenital nystagmus and to assess the utility of spectral-domain optical coherence tomography (SD-OCT) in nystagmus.
METHODS
The macular areas of 51 outpatients with congenital nystagmus were examined using SD-OCT. Morphological changes in the retinal layers of the macular area were analysed.
RESULTS
Macular images were successfully obtained with SD-OCT from 50 (98%) patients. Patients with ocular albinism mainly have macular hypoplasia, abnormal foveal depression, and increased foveal thickness with persistence of an inner nuclear layer, an inner plexiform layer, a ganglion cell layer and a nerve fiber layer. Macular morphology similar to albinism was observed in three patients with idiopathic macular hypoplasia. The OCT findings of cone dystrophy included unclear, disrupted or invisible photoreceptor outer segment/inner segment in the fovea; fusion, thickening and uneven reflection of the outer segment/inner segment with external limiting membrane. Some patients with congenital idiopathic nystagmus showed normal macular morphology and structure, and others showed indistinct macular external limiting membrane reflection.
CONCLUSION
SD-OCT is an effective and reliable method to detect the macular morphology of congenital nystagmus patients. This technique has diagnostic value in particular for patients with macular hypoplasia and cone cell dystrophy with no distinct abnormality on fundoscopy.
doi:10.3980/j.issn.2222-3959.2011.06.10
PMCID: PMC3340786  PMID: 22553733
optical coherence tomography; congenital nystagmus; macular disease.
24.  Maskless Plasmonic Lithography at 22 nm Resolution 
Scientific Reports  2011;1:175.
Optical imaging and photolithography promise broad applications in nano-electronics, metrologies, and single-molecule biology. Light diffraction however sets a fundamental limit on optical resolution, and it poses a critical challenge to the down-scaling of nano-scale manufacturing. Surface plasmons have been used to circumvent the diffraction limit as they have shorter wavelengths. However, this approach has a trade-off between resolution and energy efficiency that arises from the substantial momentum mismatch. Here we report a novel multi-stage scheme that is capable of efficiently compressing the optical energy at deep sub-wavelength scales through the progressive coupling of propagating surface plasmons (PSPs) and localized surface plasmons (LSPs). Combining this with airbearing surface technology, we demonstrate a plasmonic lithography with 22 nm half-pitch resolution at scanning speeds up to 10 m/s. This low-cost scheme has the potential of higher throughput than current photolithography, and it opens a new approach towards the next generation semiconductor manufacturing.
doi:10.1038/srep00175
PMCID: PMC3240963  PMID: 22355690
25.  ENU-Induced Mutagenesis in Grass Carp (Ctenopharyngodon idellus) by Treating Mature Sperm 
PLoS ONE  2011;6(10):e26475.
N-ethyl-N-nitrosourea (ENU) mutagenesis is a useful approach for genetic improvement of plants, as well as for inducing functional mutants in animal models including mice and zebrafish. In the present study, mature sperm of grass carp (Ctenopharyngodon idellus) were treated with a range of ENU concentrations for 45 min, and then wild-type eggs were fertilized. The results indicated that the proportion of embryos with morphological abnormalities at segmentation stage or dead fry at hatching stage increased with increasing ENU dose up to 10 mM. Choosing a dose that was mutagenic, but provided adequate numbers of viable fry, an F1 population was generated from 1 mM ENU-treated sperm for screening purposes. The ENU-treated F1 population showed large variations in growth during the first year. A few bigger mutants with morphologically normal were generated, as compared to the controls. Analysis of DNA from 15 F1 ENU-treated individuals for mutations in partial coding regions of igf-2a, igf-2b, mstn-1, mstn-2, fst-1and fst-2 loci revealed that most ENU-treated point mutations were GC to AT or AT to GC substitution, which led to nonsense, nonsynonymous and synonymous mutations. The average mutation rate at the examined loci was 0.41%. These results indicate that ENU treatment of mature sperm can efficiently induce point mutations in grass carp, which is a potentially useful approach for genetic improvement of these fish.
doi:10.1371/journal.pone.0026475
PMCID: PMC3195716  PMID: 22022617

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