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1.  Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates 
Scientific Reports  2014;4:4224.
Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction.
PMCID: PMC3936233  PMID: 24573303
2.  Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX 
Nature structural & molecular biology  2012;19(12):1287-1292.
Mammalian H3.3 is a variant of the canonical histone H3.1 essential for genome reprogramming in the fertilized eggs and maintenance of chromatin structure in neuronal cells. An H3.3-specific histone chaperone, DAXX, directs the deposition of H3.3 onto pericentric and telomeric heterochromatin. H3.3 differs from H3.1 by only five amino acids, yet DAXX can distinguish the two with high precision. By a combination of structural, biochemical and cell-based targeting analyses, here we show that Ala87 and Gly90 are the principal determinants of H3.3 specificity. DAXX uses a shallow hydrophobic pocket to accommodate the small, hydrophobic Ala87 of H3.3, whereas a polar binding environment in DAXX prefers Gly90 in H3.3 over the hydrophobic Met90 in H3.1. An H3.3-H4 heterodimer is bound by the histone-binding domain of DAXX, which makes extensive contacts with both H3.3 and H4.
PMCID: PMC3932182  PMID: 23142979
3.  N-acetyltransferase 2 Polymorphisms and Risk of Esophageal Cancer in a Chinese Population 
PLoS ONE  2014;9(2):e87783.
Esophageal cancer was the fifth most commonly diagnosed cancer and the fourth leading cause of cancer-related death in China in 2009. Genetic factors might play an important role in the carcinogenesis of esophageal squamous cell carcinoma (ESCC). We conducted a hospital-based case-control study to evaluate ten NAT2 tagging single nucleotide polymorphisms (SNPs) on the risk of ESCC. Six hundred and twenty-nine ESCC cases and 686 controls were recruited. Their genotypes were determined using the ligation detection reaction method. In the single locus analyses, there was a borderline statistically significant difference in genotype frequencies of NAT2 rs1565684 T>C SNP between the cases and the controls (p = 0.057). The NAT2 rs1565684 CC genotype was associated with a borderline significantly increased risk for ESCC (CC vs. TT: adjusted OR = 1.77, 95% CI = 0.97–3.21, p = 0.063 and CC vs. TT/TC: adjusted OR = 1.68, 95% CI = 0.93–3.04, p = 0.085). The association was evident among older patients and patients who never drunk. After the Bonferroni correction, in all comparison models, NAT2 rs1565684 T>C SNP was not associated with ESCC risk (p>0.05). For the other nine NAT2 SNPs, after Bonferroni correction, in all comparison models, the nine SNPs were also not associated with ESCC risk (p>0.05). Thus, nine NAT2 tagging SNPs were not associated with risk of ESCC. NAT2 rs1565684 T>C SNP might play a slight role in ESCC etiology. Additional, larger studies and tissue-specific biological characterization are required to confirm the current findings.
PMCID: PMC3929587  PMID: 24586291
4.  Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA41, with Changed Metabolism after Space Flight 
Genome Announcements  2014;2(1):e01124-13.
To explore the effects of space flight on microorganisms, Pseudomonas aeruginosa ATCC 27853 was sent into orbit for 398 h on the spacecraft ShenZhou VIII. Here, we present the draft genome sequence of the P. aeruginosa strain LCT-PA41, determined after space flight.
PMCID: PMC3886951  PMID: 24407638
5.  Single-port video-assisted thoracoscopic surgery for lung cancer 
Journal of Thoracic Disease  2014;6(1):14-21.
In 2004, novel results using pulmonary wedge resection executed through single-port video-assisted thoracoscopic surgery (VATS) was first described. Since that time, single-port VATS has been advocated for the treatment of a spectrum of thoracic diseases, especially lung cancer. Lung cancer remains one of the top three cancer-related deaths in Taiwan, and surgical resection remains the “gold standard” for early-stage lung cancer. Anatomical resections (including pneumonectomy, lobectomy, and segmentectomy) remain the primary types of lung cancer surgery, regardless of whether conventional open thoracotomy, or 4/3/2-ports VATS are used. In the past three years, several pioneers have reported their early experiences with single-port VATS lobectomy, segmentectomy, and pneumonectomy for lung cancer. Our goal was to appraise their findings and review the role of single-port VATS in the treatment of lung cancer. In addition, the current concept of mini-invasive surgery involves not only smaller resections (requiring only a few incisions), but also sub-lobar resection as segmentectomy. Therefore, our review will also address these issues.
PMCID: PMC3895589  PMID: 24455171
Lobectomy; lung cancer; segmentectomy; single-port; video-assisted thoracoscopic surgery (VATS)
6.  The default mode network and social understanding of others: what do brain connectivity studies tell us 
The Default Mode Network (DMN) has been found to be involved in various domains of cognitive and social processing. The present article will review brain connectivity results related to the DMN in the fields of social understanding of others: emotion perception, empathy, theory of mind, and morality. Most of the reviewed studies focused on healthy subjects with no neurological and psychiatric disease, but some studies on patients with autism and psychopathy will also be discussed. Common results show that the medial prefrontal cortex (MPFC) plays a key role in the social understanding of others, and the subregions of the MPFC contribute differently to this function according to their roles in different subsystems of the DMN. At the bottom, the ventral MPFC in the medial temporal lobe (MTL) subsystem and its connections with emotion regions are mainly associated with emotion engagement during social interactions. Above, the anterior MPFC (aMPFC) in the cortical midline structures (CMS) and its connections with posterior and anterior cingulate cortex contribute mostly to making self-other distinctions. At the top, the dorsal MPFC (dMPFC) in the dMPFC subsystem and its connection with the temporo-parietal junction (TPJ) are primarily related to the understanding of other's mental states. As behaviors become more complex, the related regions in frontal cortex are located higher. This reflects the transfer of information processing from automatic to cognitive processes with the increase of the complexity of social interaction. Besides the MPFC and TPJ, the connectivities of posterior cingulate cortex (PCC) also show some changes during tasks from the four social fields. These results indicate that the DMN is indispensable in the social understanding of others.
PMCID: PMC3932552  PMID: 24605094
default mode network; social cognition; brain connectivity; morality; theory of mind; empathy
7.  Bcl-2 expression predicts sensitivity to chemotherapy in breast cancer: a systematic review and meta-analysis 
Numerous studies have yielded inconclusive results regarding the relationship between anti-apoptotic protein Bcl-2 expression and the sensitivity to chemotherapy in the patients with breast cancer. The purpose of the current study was therefore to elaborate their relationship.
Methods, findings
A total of 23 previously published eligible studies involving 2,467 cases were identified and included in this meta-analysis. Negative Bcl-2 expression was associated with good chemotherapy response in breast cancer patients (total objective response [OR]: risk ratio [RR] = 1.16, 95% confidence interval [CI] = 1.02-1.32, p = 0.026; total complete response [CR]: RR = 1.67, 95% CI = 1.24-2.24, p = 0.001; pathological CR: RR = 1.92, 95% CI = 1.38-2.69, p < 0.001). In further stratified analyses, this association remained for sub-groups of response in neoadjuvant chemotherapy setting, especially pathological CR. Besides, negative Bcl-2 expression was significantly associated with good OR and pathological CR in anthracycline-based chemotherapy subgroup. Furthermore, there were significant links between negative Bcl-2 expression and taxane-based chemotherapy with pathological CR, but not OR.
The results of the present meta-analysis suggest that Bcl-2 expression is a predictive factor for chemotherapy sensitivity in breast cancer patients. They could also potentially benefit further clinical treatment for breast cancers.
PMCID: PMC3922829  PMID: 24370277
Bcl-2; Breast cancer; Chemotherapy; Response
8.  Genome-Wide Analyses of Radioresistance-Associated miRNA Expression Profile in Nasopharyngeal Carcinoma Using Next Generation Deep Sequencing 
PLoS ONE  2013;8(12):e84486.
Rapidly growing evidence suggests that microRNAs (miRNAs) are involved in a wide range of cancer malignant behaviours including radioresistance. Therefore, the present study was designed to investigate miRNA expression patterns associated with radioresistance in NPC.
The differential expression profiles of miRNAs and mRNAs associated with NPC radioresistance were constructed. The predicted target mRNAs of miRNAs and their enriched signaling pathways were analyzed via biological informatical algorithms. Finally, partial miRNAs and pathways-correlated target mRNAs were validated in two NPC radioreisitant cell models.
50 known and 9 novel miRNAs with significant difference were identified, and their target mRNAs were narrowed down to 53 nasopharyngeal-/NPC-specific mRNAs. Subsequent KEGG analyses demonstrated that the 53 mRNAs were enriched in 37 signaling pathways. Further qRT-PCR assays confirmed 3 down-regulated miRNAs (miR-324-3p, miR-93-3p and miR-4501), 3 up-regulated miRNAs (miR-371a-5p, miR-34c-5p and miR-1323) and 2 novel miRNAs. Additionally, corresponding alterations of pathways-correlated target mRNAs were observed including 5 up-regulated mRNAs (ICAM1, WNT2B, MYC, HLA-F and TGF-β1) and 3 down-regulated mRNAs (CDH1, PTENP1 and HSP90AA1).
Our study provides an overview of miRNA expression profile and the interactions between miRNA and their target mRNAs, which will deepen our understanding of the important roles of miRNAs in NPC radioresistance.
PMCID: PMC3868612  PMID: 24367666
9.  Effects of sodium polyacrylate on water retention and infiltration capacity of a sandy soil 
SpringerPlus  2013;2(Suppl 1):S11.
Based on the laboratory study, the effects of sodium polyacrylate (SP) was investigated at 5 rates of 0, 0.08, 0.2, 0.5, and 1%, on water retention, saturated hydraulic conductivity(Ks), infiltration characteristic and water distribution profiles of a sandy soil. The results showed that water retention and available water capacity effectively increased with increasing SP rate. The Ks and the rate of wetting front advance and infiltration under certain pond infiltration was significantly reduced by increasing SP rate, which effectively reduced water in a sandy soil leaking to a deeper layer under the plough layer. The effect of SP on water distribution was obviously to the up layer and very little to the following deeper layers. Considering both the effects on water retention and infiltration capacity, it is suggested that SP be used to the sandy soil at concentrations ranging from 0.2 to 0.5%.
PMCID: PMC3973410
sodium polyacrylate; water retention; infiltration; sandy soil; leakage
10.  Control of Angiogenesis by AIBP-mediated Cholesterol Efflux 
Nature  2013;498(7452):118-122.
Cholesterol is a structural component of the cell, indispensable for normal cellular function, but its excess often leads to abnormal proliferation, migration, inflammatory responses and/or cell death. To prevent cholesterol overload, ATP-binding cassette (ABC) transporters mediate cholesterol efflux from the cells to apolipoprotein A-I (ApoA-I) and to the ApoA-I-containing high-density lipoprotein (HDL)1-3. Maintaining efficient cholesterol efflux is essential for normal cellular function4-6. However, the role of cholesterol efflux in angiogenesis and the identity of its local regulators are poorly understood. Here we show that ApoA-I binding protein (AIBP) accelerates cholesterol efflux from endothelial cells (EC) to HDL and thereby regulates angiogenesis. AIBP/HDL-mediated cholesterol depletion reduces lipid rafts, interferes with VEGFR2 dimerization and signaling, and inhibits VEGF-induced angiogenesis in vitro and mouse aortic neovascularization ex vivo. Remarkably, Aibp regulates the membrane lipid order in embryonic zebrafish vasculature and functions as a non-cell autonomous regulator of zebrafish angiogenesis. Aibp knockdown results in dysregulated sprouting/branching angiogenesis, while forced Aibp expression inhibits angiogenesis. Dysregulated angiogenesis is phenocopied in Abca1/Abcg1-deficient embryos, and cholesterol levels are increased in Aibp-deficient and Abca1/Abcg1-deficient embryos. Our findings demonstrate that secreted AIBP positively regulates cholesterol efflux from EC and that effective cholesterol efflux is critical for proper angiogenesis.
PMCID: PMC3760669  PMID: 23719382
11.  Hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A Polymorphisms Are Associated with the Risk of Esophageal Cancer in a Chinese Population 
PLoS ONE  2013;8(11):e80570.
Esophageal cancer is the eighth most common cancer and sixth leading cause of cancer associated death worldwide. Besides environmental risk factors, genetic factors might play an important role in the esophageal cancer carcinogenesis. We conducted a hospital based case–control study to evaluate the genetic susceptibility of functional single nucleotide polymorphisms (SNPs) in the microRNAs on the development of esophageal cancer. A total of 629 esophageal squamous cell carcinoma (ESCC) cases and 686 controls were recruited for this study. The hsa-miR-34b/c rs4938723 T>C, pri-miR-124-1 rs531564 C>G, pre-miR-125a rs12975333 G>T and hsa-miR-423 rs6505162 C>A genotypes were determined using Ligation Detection Reaction (LDR) method. Our results demonstrated that hsa-miR-34b/c rs4938723 CC genotype had a decreased risk of ESCC. The association was evident among patients who never drinking. Hsa-miR-423 rs6505162 C>A might associated with a significantly increased risk of ESCC in patients who smoking. These findings indicated that functional polymorphisms hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A might alter individual susceptibility to ESCC. However, our results were obtained with a limited sample size. Future larger studies with other ethnic populations are required to confirm current findings.
PMCID: PMC3832359  PMID: 24260422
12.  Synthesis, characterization, and evaluation of paclitaxel loaded in six-arm star-shaped poly(lactic-co-glycolic acid) 
Star-shaped polymers provide more terminal groups, and are promising for application in drug-delivery systems.
A new series of six-arm star-shaped poly(lactic-co-glycolic acid) (6-s-PLGA) was synthesized by ring-opening polymerization. The structure and properties of the 6-s-PLGA were characterized by carbon-13 nuclear magnetic resonance spectroscopy, infrared spectroscopy, gel permeation chromatography, and differential scanning calorimetry. Then, paclitaxel-loaded six-arm star-shaped poly(lactic-co-glycolic acid) nanoparticles (6-s-PLGA-PTX-NPs) were prepared under the conditions optimized by the orthogonal testing. High-performance liquid chromatography was used to analyze the nanoparticles’ encapsulation efficiency and drug-loading capacity, dynamic light scattering was used to determine their size and size distribution, and transmission electron microscopy was used to evaluate their morphology. The release performance of the 6-s-PLGA-PTX-NPs in vitro and the cytostatic effect of 6-s-PLGA-PTX-NPs were investigated in comparison with paclitaxel-loaded linear poly(lactic-co-glycolic acid) nanoparticles (L-PLGA-PTX-NPs).
The results of carbon-13 nuclear magnetic resonance spectroscopy and infrared spectroscopy suggest that the polymerization was successfully initiated by inositol and confirm the structure of 6-s-PLGA. The molecular weights of a series of 6-s-PLGAs had a ratio corresponding to the molar ratio of raw materials to initiator. Differential scanning calorimetry revealed that the 6-s-PLGA had a low glass transition temperature of 40°C–50°C. The 6-s-PLGA-PTX-NPs were monodispersed with an average diameter of 240.4±6.9 nm in water, which was further confirmed by transmission electron microscopy. The encapsulation efficiency of the 6-s-PLGA-PTX-NPs was higher than that of the L-PLGA-PTX-NPs. In terms of the in vitro release of nanoparticles, paclitaxel (PTX) was released more slowly and more steadily from 6-s-PLGA than from linear poly(lactic-co-glycolic acid). In the cytostatic study, the 6-s-PLGA-PTX-NPs and L-PLGA-PTX-NPs were found to have a similar antiproliferative effect, which indicates durable efficacy due to the slower release of the PTX when loaded in 6-s-PLGA.
The results suggest that 6-s-PLGA may be promising for application in PTX delivery to enhance sustained antiproliferative therapy.
PMCID: PMC3825676  PMID: 24235829
PTX; polymer; drug delivery; nanoparticles; PLGA; antiproliferative therapy
13.  The Scaling Relationships between Leaf Mass and Leaf Area of Vascular Plant Species Change with Altitude 
PLoS ONE  2013;8(10):e76872.
The scaling relationship between leaf dry mass and leaf surface area has important implications for understanding the ability of plants to harvest sunlight and grow. Whether and how the scaling relationships vary across environmental gradients are poorly understood. We analyzed the scaling relationships between leaf mass and leaf area of 121 vascular plant species along an altitudinal gradient in a subtropical monsoon forest. The slopes increased significantly with altitude, it varied from less than 1 at low altitude to more than 1 at high altitude. This means that plants growing at high altitude allocate proportionately more biomass to support tissues in larger leaves and less in smaller leaves, whereas the reverse is true at low altitude. This pattern can be explained by different leaf strategies in response to environmental pressure and constrains.
PMCID: PMC3795618  PMID: 24146938
14.  Genetic variations of E6 and long control region of human papillomavirus type 16 from patients with cervical lesion in Liaoning, China 
BMC Cancer  2013;13:459.
High-risk human papillomavirus type 16 (HPV16) is a risk factor for cervical cancer. Previous studies suggest that polymorphisms in the E6 gene or the long control region(LCR)of HPV16 may alter the oncogenic potential of the virus. The aims of this study were to investigate the genetic variations of HPV16 E6 gene and LCR in isolates from Chinese population and correlation of the E6 and LCR polymorphisms with disease status of infected patients.
HPV16 positive endocervical specimens were collected from 304 women living in Northeast of China. Sequences of E6 gene and LCR were analyzed by PCR-sequencing.
Two lineages were found in the populations, including EUR lineage and As lineage. Based on the HPV16 prototype, the most frequent variation in the E6 gene was T178A/G (48.7%), followed by mutations of G94A (12.2%) and T350G (9.9%). The rank orders of incidence of E6 variations in amino acid were as follows: D25E (46.3%), L83V (9.9%) and H78Y (4.3%). Nucleotide variations in LCR were found in all the 304 isolates from HPV16 positive cervical samples. The most commonly observed LCR variations were the transition replacement G7193T, 7434CIns, G7521A and 7863ADel (100%). The As lineage was associated with HPV persistent infections and with disease status of ≥CIN2,3. The EUR lineage variants showed a negative trend of association with the severity of ≥CIN2,3. Among 41 variations found in LCR, 25 (61.0%) were located at the binding sites for transcription factors. Occurrence of ≥CIN2,3 was significantly associated with the mutations of R10G/L83V in E6 and the C7294T co-variation in LCR, after adjusting for ages of infected patients.
Associations between As lineage and HPV persistent infections, and with disease status of ≥CIN2,3, and an association between the EUR lineage and negative trend of association with the severity of ≥CIN2,3 were found in this study. An association between a co-variation of R10G/L83V in E6 and C7294T in LCR and an increased risk for developing CIN-2,3 was found in a HPV16 infected population of Chinese women. These findings indicate that HPV16 polymorphism influences development of CIN-2,3.
PMCID: PMC3852402  PMID: 24099556
HPV16; E6; LCR; Cervical lesion
15.  Activation of AMP-activated protein kinase alleviates high glucose-induced dysfunction of brain microvascular endothelial cell tight junction dynamics 
Free radical biology & medicine  2012;53(6):1213-1221.
The blood-brain-barrier, formed by specialized brain endothelial cells that are interconnected by tight junctions, strictly regulates paracellular permeability to maintain an optimal extracellular environment for brain homeostasis. Diabetes is known to compromise the blood-brain-barrier although the underlying mechanism remains unknown.
The aim of this study was to elucidate the molecular mechanisms underlying disruption of the blood-brain-barrier in diabetes and to determine whether activation of AMP-activated protein kinase prevents diabetes-induced blood-brain-barrier dysfunction
Methods and Results
Exposure of human brain microvascular endothelial cells to high glucose (25 mmol/L D-glucose), but not to high osmotic conditions (20 mmol/L L-glucose plus 5 mmol/L D-glucose), for 2 h to 1 week significantly increased the permeability of blood-brain-barrier in parallel with lowered expression levels of zonula occludens-1, occludin, and claudin-5, three proteins that are essential to maintain endothelial cell tight junctions. In addition, high glucose significantly increased generation of superoxide anions. Adenoviral overexpression of superoxide dismutase or catalase significantly attenuated the high glucose-induced reduction of endothelial cell tight junction proteins. Furthermore, administration of apocynin reversed the effects of high glucose on endothelial cell tight junction proteins. Finally, activation of AMP-activated protein kinase with 5-amino-4-imidazole carboxamide riboside (AICAR) or adenoviral overexpression of constitutively active AMP-activated protein kinase mutants (Ad-AMPK-CA) abolished both induction of NAD(P)H oxidase-derived superoxide anions and tight junction protein degradation induced by high glucose.
We conclude that high glucose increases blood-brain-barrier dysfunction in diabetes through induction of superoxide anions and that the activation of AMP-activated protein kinase protects the integrity of the blood-brain-barrier by suppressing the induction of NAD(P)H oxidase-derived superoxide anions.
PMCID: PMC3437014  PMID: 22796592
AMPK; NAD(P)H oxidase; blood brain barrier; tight junctions; diabetes
16.  Impulsive control for synchronizing delayed discrete complex networks with switching topology 
In this paper, global exponential synchronization of a class of discrete delayed complex networks with switching topology has been investigated by using Lyapunov-Ruzimiki method. The impulsive scheme is designed to work at the time instant of switching occurrence. A time-varying delay-dependent criterion for impulsive synchronization is given to ensure the delayed discrete complex networks switching topology tending to a synchronous state. Furthermore, a numerical simulation is given to illustrate the effectiveness of main results
PMCID: PMC3882576  PMID: 24415851
Impulsive synchronization; Complex networks; Switching topology; Lyapunov-Ruzimiki method
17.  Proteomic analysis of extremely severe hand, foot and mouth disease infected by enterovirus 71 
BMC Infectious Diseases  2013;13:383.
To clarify the molecular mechanisms that participate in the severe hand, foot and mouth disease (HFMD) infected by Enterovirus 71 and to detect any related protein biomarkers, we performed proteomic analysis of protein extracts from 5 extremely severe HFMD children and 5 healthy children.
The protein profiles of them were compared using two-dimensional electrophoresis. Differentially expressed proteins were identified using mass spectrometry. Functional classifications of these proteins were based on the PANTHER. The interaction network of the differentially expressed protein was generated with Pathway Studio.
A total of 38 differentially expressed proteins were identified. Functional classifications of these proteins indicated a series of altered cellular processes as a consequence of the severe HFMD. These results provided not only new insights into the pathogenesis of severe HFMD, but also implications of potential therapeutic designs.
Our results suggested the possible pathways that could be the potential targets for novel therapy: viral protection, complement system and peroxide elimination.
PMCID: PMC3765220  PMID: 23961958
Extremely severe HFMD; MALDI-TOF/TOF MS; Proteomic analysis
18.  Molecular Characterization of Larval Peripheral Thermosensory Responses of the Malaria Vector Mosquito Anopheles gambiae 
PLoS ONE  2013;8(8):e72595.
Thermosensation provides vital inputs for the malaria vector mosquito, Anopheles gambiae which utilizes heat-sensitivity within a broad spectrum of behaviors, most notably, the localization of human hosts for blood feeding. In this study, we examine thermosensory behaviors in larval-stage An. gambiae, which as a result of their obligate aquatic habitats and importance for vectorial capacity, represents an opportunistic target for vector control as part of the global campaign to eliminate malaria. As is the case for adults, immature mosquitoes respond differentially to a diverse array of external heat stimuli. In addition, larvae exhibit a striking phenotypic plasticity in thermal-driven behaviors that are established by temperature at which embryonic development occurs. Within this spectrum, RNAi-directed gene-silencing studies provide evidence for the essential role of the Transient Receptor Potential sub-family A1 (TRPA1) channel in mediating larval thermal-induced locomotion and thermal preference within a discrete upper range of ambient temperatures.
PMCID: PMC3737131  PMID: 23940815
19.  Alkaline twin-screw extrusion pretreatment for fermentable sugar production 
The inevitable depletion of fossil fuels has resulted in an increasing worldwide interest in exploring alternative and sustainable energy sources. Lignocellulose, which is the most abundant biomass on earth, is widely regarded as a promising raw material to produce fuel ethanol. Pretreatment is an essential step to disrupt the recalcitrance of lignocellulosic matrix for enzymatic saccharification and bioethanol production. This paper established an ATSE (alkaline twin-screw extrusion pretreatment) process using a specially designed twin-screw extruder in the presence of alkaline solution to improve the enzymatic hydrolysis efficiency of corn stover for the production of fermentable sugars.
The ATSE pretreatment was conducted with a biomass/liquid ratio of 1/2 (w/w) at a temperature of 99°C without heating equipment. The results indicated that ATSE pretreatment is effective in improving the enzymatic digestibility of corn stover. Sodium hydroxide loading is more influential factor affecting both sugar yield and lignin degradation than heat preservation time. After ATSE pretreatment under the proper conditions (NaOH loading of 0.06 g/g biomass during ATSE and 1 hour heat preservation after extrusion), 71% lignin removal was achieved and the conversions of glucan and xylan in the pretreated biomass can reach to 83% and 89% respectively via subsequent enzymatic hydrolysis (cellulase loading of 20 FPU/g-biomass and substrate consistency of 2%). About 78% of the original polysaccharides were converted into fermentable sugars.
With the physicochemical functions in extrusion, the ATSE method can effectively overcome the recalcitrance of lignocellulose for the production of fermentable sugars from corn stover. This process can be considered as a promising pretreatment method due to its relatively low temperature (99°C), high biomass/liquid ratio (1/2) and satisfied total sugar yield (78%), despite further study is needed for process optimization and cost reduction.
PMCID: PMC3718628  PMID: 23834726
Twin-screw extrusion; Pretreatment; Corn stover; Sugar recovery; Enzymatic hydrolysis
20.  Timing and Operating Mode Design for Time-Gated Fluorescence Lifetime Imaging Microscopy 
The Scientific World Journal  2013;2013:801901.
Steady-state fluorence imaging and time-resolved fluorescence imaging are two important areas in fluorescence imaging research. Fluorescence lifetime imaging is an absolute measurement method which is independent of excitation laser intensity, fluorophore concentration, and photobleaching compared to fluorescence intensity imaging techniques. Time-gated fluorescence lifetime imaging microscopy (FLIM) can provide high resolution and high imaging frame during mature FLIM methods. An abstract time-gated FLIM model was given, and important temporal parameters are shown as well. Aiming at different applications of steady and transient fluorescence processes, two different operation modes, timing and lifetime computing algorithm are designed. High resolution and high frame can be achieved by one-excitation one-sampling mode and least square algorithm for steady imaging applications. Correspondingly, one-excitation two-sampling mode and rapid lifetime determination algorithm contribute to transient fluorescence situations.
PMCID: PMC3707217  PMID: 23864834
21.  A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells 
Nature medicine  2011;17(6):738-743.
Cellular immunity has an inherent high level of functional heterogeneity. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. We report a microfluidic platform designed for highly multiplexed (more than ten proteins), reliable, sample-efficient (~1 × 104 cells) and quantitative measurements of secreted proteins from single cells. We validated the platform by assessment of multiple inflammatory cytokines from lipopolysaccharide (LPS)-stimulated human macrophages and comparison to standard immunotechnologies. We applied the platform toward the ex vivo quantification of T cell polyfunctional diversity via the simultaneous measurement of a dozen effector molecules secreted from tumor antigen–specific cytotoxic T lymphocytes (CTLs) that were actively responding to tumor and compared against a cohort of healthy donor controls. We observed profound, yet focused, functional heterogeneity in active tumor antigen–specific CTLs, with the major functional phenotypes quantitatively identified. The platform represents a new and informative tool for immune monitoring and clinical assessment.
PMCID: PMC3681612  PMID: 21602800
22.  Research progress in the radioprotective effect of the canonical Wnt pathway 
Cancer Biology & Medicine  2013;10(2):61-71.
Irradiation from diverse sources is ubiquitous and closely associated with human activities. Radiation therapy (RT), an important component of multiple radiation origins, is a common therapeutic modality for cancer. More importantly, RT provides significant contribution to oncotherapy by killing tumor cells. However, during the course of therapy, irradiation of normal tissues can result in a wide range of side effects, including self-limited acute toxicities, mild chronic symptoms, or severe organ dysfunction. Although numerous promising radioprotective agents have emerged, only a few have successfully entered the market because of various limitations. At present, the widely accepted hypothesis for protection against radiation-caused injury involves the Wnt canonical pathway. Activating the Wnt/β-catenin signaling pathway may protect the salivary gland, oral mucosa, and gastrointestinal epithelium from radiation damage. The underlying mechanisms include inhibiting apoptosis and preserving normal tissue functions. However, aberrant Wnt signaling underlies a wide range of pathologies in humans, and its various components contribute to cancer. Moreover, studies have suggested that Wnt/β-catenin signaling may lead to radioresistance of cancer stem cell. These facts markedly complicate any definition of the exact function of the Wnt pathway.
PMCID: PMC3719192  PMID: 23882420
Signaling transduction; canonical Wnt pathway; β-catenin; radioprotection; radiation
23.  DDX5 Facilitates HIV-1 Replication as a Cellular Co-Factor of Rev 
PLoS ONE  2013;8(5):e65040.
HIV-1 Rev plays an important role in the late phase of HIV-1 replication, which facilitates export of unspliced viral mRNAs from the nucleus to cytoplasm in infected cells. Recent studies have shown that DDX1 and DDX3 are co-factors of Rev for the export of HIV-1 transcripts. In this report, we have demonstrated that DDX5 (p68), which is a multifunctional DEAD-box RNA helicase, functions as a new cellular co-factor of HIV-1 Rev. We found that DDX5 affects Rev function through the Rev-RRE axis and subsequently enhances HIV-1 replication. Confocal microscopy and co-immunoprecipitation analysis indicated that DDX5 binds to Rev and this interaction is largely dependent on RNA. If the DEAD-box motif of DDX5 is mutated, DDX5 loses almost all of its ability to bind to Rev, indicating that the DEAD-box motif of DDX5 is required for the interaction between DDX5 and Rev. Our data indicate that interference of DDX5-Rev interaction could reduce HIV-1 replication and potentially provide a new molecular target for anti-HIV-1 therapeutics.
PMCID: PMC3669200  PMID: 23741449
24.  Arginine68 is an essential residue for the C-terminal cleavage of human Atg8 family proteins 
BMC Cell Biology  2013;14:27.
Autophagy is a conserved cellular process that degrades and recycles cytoplasmic components via a lysosomal pathway. The phosphatidylethanolamine (PE)-conjugation of the Atg8 protein plays an important role in the yeast autophagy process. In humans, six Atg8 homologs, including MAP1LC3A, MAP1LC3B, MAP1LC3C (refer to LC3A, LC3B, and LC3C hereafter), GABARAP, GABARAPL1, and GABARAPL2 have been reported. All of them can be conjugated to PE through a ubiquitin-like conjugation system, and be located to autophagosomes.
In this study, we found 3 new alternative splicing isoforms in LC3B, GABARAP, and GABARAPL1, (designated as LC3B-a, GABARAP-a and GABARAPL1-a, respectively). None of them can go through the PE-conjugation process and be located to autophagosomes. Interestingly, compared with LC3B, LC3B-a has a single amino acid (Arg68) deletion due to the NAGNAG alternative splicing in intron 3. Through structural simulations, we found that the C-terminal tail of LC3B-a is less mobile than that of LC3B, thus affecting its C-terminal cleavage by human ATG4 family proteins. Furthermore, we found that Arg68 is an essential residue facilitating the interaction between human Atg8 family proteins and ATG4B by forming a salt bridge with Asp171 of ATG4B. Depletion of this salt bridge reduces autophagosomes formation and autophagic flux under both normal and nutrition starvation conditions.
These results suggest Arg68 is an essential residue for the C-terminal cleavage of Atg8 family proteins during the autophagy process.
PMCID: PMC3686597  PMID: 23721406
Atg8; MAP1LC3B; Autophagy; Alternative splicing
25.  Serum microRNAs profile from genome-wide serves as a fingerprint for diagnosis of acute myocardial infarction and angina pectoris 
BMC Medical Genomics  2013;6:16.
In order to identify miRNAs expression profiling from genome-wide screen for diagnosis of acute myocardial infarction (AMI) and angina pectoris (AP), we investigated the altered profile of serum microRNAs in AMI and AP patients at a relative early stage.
Serum samples were taken from 117 AMI patients, 182 AP patients and 100 age-and gender-matched controls. An initial screening of miRNAs expression was performed by Solexa sequencing. Differential expression was validated using RT-qPCR in individuals samples, the samples were arranged in a two-phase selection and validation.
The Solexa sequencing results demonstrated marked upregulation of serum miRNAs in AMI patients compared with controls. RT-qPCR analysis identified a profile of six serum miRNAs (miR-1, miR-134, miR-186, miR-208, miR-223 and miR-499) as AMI biomarkers. MiR-208 and miR-499 were elevated higher in AP cases than in AMI cases. The ROC curves indicated a panel of six miRNAs has a great potential to offer sensitive and specific diagnostic tests for AMI. More especially, the panel of six miRNAs presents significantly differences between the AMI and AP cases.
The six-miRNAs signature identified from genome-wide serum miRNA expression profiling may serves as a fingerprint for AMI and AP diagnosis.
PMCID: PMC3655858  PMID: 23641832
Acute myocardial infarction; Angina pectoris; Serum microRNAs

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