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2.  The miR-7 Identified from Collagen Biomaterial-Based Three-Dimensional Cultured Cells Regulates Neural Stem Cell Differentiation 
Stem Cells and Development  2013;23(4):393-405.
Increasing evidence suggests that three-dimensional (3D) cultures provide more appropriate microenvironments to control stem cell response compared with traditional two-dimensional (2D) cultures. However, the molecular mechanism involved in 3D cultured stem cells is not well known. Several microRNAs whose target genes involved in the regulation of self-renewal and differentiation of stem cells were found to be downregulated in 3D cultured PA-1 cells. Among them, miR-7 was predicted to target Kruppel-like factor 4 (Klf4), a key gene for self-renewal of neural stem cells (NSCs). We showed that the differentiation of NSCs was inhibited in 3D collagen scaffolds compared with 2D cultured cells. The quantitative real-time PCR (qPCR) analysis indicated that the expression of miR-7 and Klf4 changed significantly in 2D cultures, whereas the expression stability of miR-7 and Klf4 was detected in 3D cultures. Using luciferase assay and western blot, Klf4 was identified as a target of miR-7 indicating that miR-7 plays a critical role in maintaining the self-renewal capacity through a Klf4-dependent mechanism in 3D cultured cells. Thus, the collagen scaffold-based 3D cell cultures may provide a platform to reveal the regulatory mechanism of cell regulators, which are difficult to find in traditional 2D cell cultures.
doi:10.1089/scd.2013.0342
PMCID: PMC3920754  PMID: 24200387
3.  Efficacy and Safety of Transcutaneous Electrical Acupoint Stimulation to Treat Muscle Spasticity following Brain Injury: A Double-Blinded, Multicenter, Randomized Controlled Trial 
PLoS ONE  2015;10(2):e0116976.
Objective
This study was aimed at evaluating the clinical efficacy and safety of transcutaneous electrical acupoint stimulation (TEAS) to treat muscle spasticity after brain injury (Chinese Clinical Trial Registry: ChiCTR-TRC-11001310).
Methods
A total of 60 patients with muscle spasticity after brain injury were randomized to the following 3 groups: 100, 2, and 0 Hz (sham) TEAS. The acupoints Hegu (LI4)—Yuji (LU10) and Zusanli (ST36)—Chengshan (BL57) on the injured side were stimulated at 0, 2, or 100 Hz, 5 times per week for 4 weeks. The patients were followed up for 1 and 2 months after the treatments. The effects of the treatments on muscle spasticity at the wrist, thumb, the other 4 fingers, elbow, shoulder, knee, and ankle were evaluated by the Modified Ashworth Scale, and the effects on disability were assessed by the Disability Assessment Scale. The walking capability was evaluated by the Holden functional ambulation classification score. The overall performance was assessed by the Global Assessment Scale score and the improved Barthel Index. The safety of the treatments administered was also monitored.
Results
The wrist spasticity was significantly reduced from baseline at weeks 2, 3, and 4 of treatment and at the 1- and 2-month follow-up visits in the 100 Hz group (P < 0.01). Compared with 2 Hz or sham TEAS, 100 Hz TEAS decreased wrist spasticity at weeks 2, 3, and 4 of treatment and 1 month after treatment (P < 0.001). The other endpoints were not affected by the treatments. No treatment-emergent adverse events were reported during treatments and follow-up visits.
Conclusions
TEAS appears to be a safe and effective therapy to relieve muscle spasticity after brain injury, although large-scale studies are required to further verify the findings.
Trial Registration
Chinese Clinical Trial Registry ChiCTR-TRC-11001310 http://www.chictr.org
doi:10.1371/journal.pone.0116976
PMCID: PMC4314074  PMID: 25643051
4.  Discovery of New Candidate Genes Related to Brain Development Using Protein Interaction Information 
PLoS ONE  2015;10(1):e0118003.
Human brain development is a dramatic process composed of a series of complex and fine-tuned spatiotemporal gene expressions. A good comprehension of this process can assist us in developing the potential of our brain. However, we have only limited knowledge about the genes and gene functions that are involved in this biological process. Therefore, a substantial demand remains to discover new brain development-related genes and identify their biological functions. In this study, we aimed to discover new brain-development related genes by building a computational method. We referred to a series of computational methods used to discover new disease-related genes and developed a similar method. In this method, the shortest path algorithm was executed on a weighted graph that was constructed using protein-protein interactions. New candidate genes fell on at least one of the shortest paths connecting two known genes that are related to brain development. A randomization test was then adopted to filter positive discoveries. Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development.
doi:10.1371/journal.pone.0118003
PMCID: PMC4311913  PMID: 25635857
5.  T-cell acute lymphoid leukemia resembling Burkitt leukemia cell morphology: A case report 
Oncology Letters  2014;9(3):1236-1238.
Biphenotypic acute leukemia (BAL) is an uncommon type of cancer, which accounts for <5% of all adult ALs. Based upon a previously described scoring system, the European Group for the Immunological Classification of Leukemias (EGIL) proposed a set of diagnostic criteria for BAL. This scoring system is based upon the number and degree of specificity of several markers for myeloid or T/B-lymphoid blasts. The present study describes a case of T-cell acute lymphoblastic leukemia (T-ALL) with Burkitt-like cytology, which according to the French-American-British classification, corresponded to a diagnosis of Burkitt type L3 ALL. Flow cytometry analysis demonstrated that the blasts were positive for T-lymphoid markers, cytoplasmic cluster of differentiation (CD)3, CD7 and CD56, and myeloid markers, CD13, CD33 and CD15. At first, a diagnosis of BAL was suggested by the EGIL score, however, according to the 2008 World Health Organization criteria, a case of T-ALL with aberrant myeloid markers was established. The study also reviewed the literature and discussed the limitations of the EGIL scoring system in clinical decision making, to aid in the selection of an appropriate therapeutic regimen.
doi:10.3892/ol.2014.2825
PMCID: PMC4314994  PMID: 25663889
biphenotypic acute leukemia; acute lymphoblastic leukemia; Burkitt leukemia
6.  Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri 
Scientific Reports  2014;4:7478.
Microbial syntrophic metabolism has been well accepted as the heart of how methanogenic and other anaerobic microbial communities function. In this work, we applied a single-cell RT-qPCR approach to reveal gene-expression heterogeneity in a model syntrophic system of Desulfovibrio vulgaris and Methanosarcina barkeri, as compared with the D. vulgaris monoculture. Using the optimized primers and single-cell analytical protocol, we quantitatively determine gene-expression levels of 6 selected target genes in each of the 120 single cells of D. vulgaris isolated from its monoculture and dual-culture with M. barkeri. The results demonstrated very significant cell-to-cell gene-expression heterogeneity for the selected D. vulgaris genes in both the monoculture and the syntrophic dual-culture. Interestingly, no obvious increase in gene-expression heterogeneity for the selected genes was observed for the syntrophic dual-culture when compared with its monoculture, although the community structure and cell-cell interactions have become more complicated in the syntrophic dual-culture. In addition, the single-cell RT-qPCR analysis also provided further evidence that the gene cluster (DVU0148-DVU0150) may be involved syntrophic metabolism between D. vulgaris and M. barkeri. Finally, the study validated that single-cell RT-qPCR analysis could be a valuable tool in deciphering gene functions and metabolism in mixed-cultured microbial communities.
doi:10.1038/srep07478
PMCID: PMC4265775  PMID: 25504148
7.  Response of endothelial cells to decellularized extracellular matrix deposited by bone marrow mesenchymal stem cells 
Objective: Evaluate the behavior and function of human umbilical vein endothelial cells (HUVECs) on decellularized extracellular matrix (ECM) deposited by bone marrow mesenchymal stem cells (BMSCs). Methods: Prepared through chemical approach, decellularized ECM was characterized by use of immunofluorescence staining. The morphology, attachment, proliferation and migration of HUVECs cultured on six-well tissue culture plastic (TCP) and decellularized ECM were investigated. Results: Decellularized ECM was successfully prepared without three-dimensional architecture disruption. This biological scaffold is similar to nature vascular ECM, preserved various matrix proteins such as type I collagen, type III collagen and fibronection. HUVECs on decellularized ECM showed well attachment and regular arrangement. Decellularized ECM could also significantly enhance the migration and proliferation potential of HUVECs in contrast to TCP. Conclusion: Deposited by BMSCs, ECM can affect the behavior of endothelial cell and could be used as a promising material in tissue engineering.
PMCID: PMC4307445  PMID: 25663998
Decellularized extracellular matrix; tissue engineering; vascularization
8.  Gastrointestinal symptom due to lupus peritonitis: a rare form of onset of SLE 
Serositis is commonly seen in systemic lupus erythematosus (SLE). Approximately 16% of patients with SLE have pleural or pericardial involvement. However, peritoneal involvement is extremely rare, and SLE with ascites as the first manifestation is an even rarer condition. This is the case report of a 19-year old male with discoid lupus who evolved with gastrointestinal symptoms as the first manifestation of the disease, characterized by significant abdominal distension and pain, asthenia, vomiting, and signs of ascites. An abdominal CT scan demonstrated ascites and marked edematous thickening of the bowel wall, which appeared as “target sign”, and “double-track sign”. Laboratory tests showed that his serum complement levels decreased and that he was positive for anti-nRNP/Sm antibodies, anti-Sm antibodies, anti-SS-A antibody, and anti-nuclear antibodies. The patient was treated with prednisone and chloroquine, with substantial improvement of his condition.
PMCID: PMC4307580  PMID: 25664133
Systemic lupus erythematosus; serositis; ascites; lupus peritonitis; CT
9.  Prevalence, histologic and clinical characteristics of heterotopic gastric mucosa in Chinese patients 
World Journal of Gastroenterology : WJG  2014;20(46):17588-17594.
AIM: To determine the prevalence, demographic, clinical and histopathologic features of heterotopic gastric mucosa (HGM) in Chinese patients.
METHODS: Patients referred to three endoscopy units were enrolled in this study. The macroscopic characteristics of HGM were documented. Biopsies were obtained and observed using hematoxylin and eosin staining. Helicobacter pylori colonization was examined by Whartin-Starry staining.
RESULTS: HGM was observed in 420 Chinese patients, yielding a prevalence of 0.4%. The majority of patients had a single patch (300/420; 71.4%), while the remainder had two (84/420; 20%) or multiple patches (36/420; 8.6%). The size of the patches and the distance from the patch to the frontal incisor teeth varied significantly. The large majority of HGM patches were flat (393/420; 93.6%), whereas the remaining patches were slightly elevated. The primary histological characteristic was fundic-type (216/420; 51.4%) within the HGM patch, and antral- (43/420; 10.2%) and transitional-type (65/420; 15.5%) mucosa were also observed. The prevalence of intestinal metaplasia was 3.1% (13/420) and the prevalence of dysplasia was 1.4% (6/420), indicating the necessity for endoscopic follow-up in patients with HGM. Esophageal and extraesophageal complaints were also observed in patients with HGM. Dysphagia and epigastric discomfort (odds ratios: 6.836 and 115.826, respectively; Ps < 0.05) were independent risk factors for HGM.
CONCLUSION: Clinical complaints should be considered to improve the detection rate of HMG. The prevalence of intestinal metaplasia and dysplasia also indicates a need for endoscopic follow-up.
doi:10.3748/wjg.v20.i46.17588
PMCID: PMC4265621  PMID: 25516674
Chinese population; Clinical characteristics; Heterotopic gastric mucosa; Histologic characteristics; Prevalence
10.  Copy number variation analysis based on AluScan sequences 
Background
AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing.
Results
In this study, an AluScanCNV package has been assembled for efficient CNV calling from AluScan sequencing data employing a Geary-Hinkley transformation (GHT) of read-depth ratios between either paired test-control samples, or between test samples and a reference template constructed from reference samples, to call the localized CNVs, followed by use of a GISTIC-like algorithm to identify recurrent CNVs and circular binary segmentation (CBS) to reveal large extended CNVs. To evaluate the utility of CNVs called from AluScan data, the AluScans from 23 non-cancer and 38 cancer genomes were analyzed in this study. The glioma samples analyzed yielded the familiar extended copy-number losses on chromosomes 1p and 9. Also, the recurrent somatic CNVs identified from liver cancer samples were similar to those reported for liver cancer WGS with respect to a striking enrichment of copy-number gains in chromosomes 1q and 8q. When localized or recurrent CNV-features capable of distinguishing between liver and non-liver cancer samples were selected by correlation-based machine learning, a highly accurate separation of the liver and non-liver cancer classes was attained.
Conclusions
The results obtained from non-cancer and cancerous tissues indicated that the AluScanCNV package can be employed to call localized, recurrent and extended CNVs from AluScan sequences. Moreover, both the localized and recurrent CNVs identified by this method could be subjected to machine-learning selection to yield distinguishing CNV-features that were capable of separating between liver cancers and other types of cancers. Since the method is applicable to any human DNA sample with or without the availability of a paired control, it can also be employed to analyze the constitutional CNVs of individuals.
Electronic supplementary material
The online version of this article (doi:10.1186/s13336-014-0015-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s13336-014-0015-z
PMCID: PMC4273479  PMID: 25558350
AluScan sequencing; CNV calling; Cancer classification; Machine learning
11.  Store-operated Ca2+ entry regulates glioma cell migration and invasion via modulation of Pyk2 phosphorylation 
Background
The ubiquitous second messenger Ca2+ has been demonstrated to play an important role in cancer progression. Store-operated Ca2+ entry (SOCE) is the main Ca2+ entry pathway regulating intracellular Ca2+ concentration in a variety of cancer types. The present study aimed to explore the specific mechanisms of SOCE in the processes of glioma migration and invasion.
Methods
The expression of Orai1, a key component of SOCE, was examined in glioma samples and glioma cell lines by immunohistochemistry and western blot analysis. Both pharmacological intervention and RNA interference were employed to investigate the role of SOCE in glioma cell migration and invasion in vitro. The intracellular Ca2+ was certified through Fluo-4/AM based Ca2+ measurement. The effect of SOCE on cell viability, migration, and invasion was explored by methyl thiazolyl tetrazolium (MTT) assay, wound healing assay, transwell invasion assay. Western blot analysis and immunofluorescence assay were used to observe the changes of downstream related protein and cell morpholog.
Results
Orai1 expression was elevated in glioma tissues and several glioma cell lines compared with non-neoplastic brain tissues. Either inhibition of SOCE by a pharmacological inhibitor or Orai1 downregulation suppressed glioma cell migration and invasion. However, re-expression of Orai1 could rescue glioma cell motility. Furthermore, phosphorylation of proline-rich tyrosine kinase 2 (Pyk2) participated in the mechanisms by which SOCE regulated focal adhesion turnover and epithelial-to-mesenchymal (−like) transition in glioma cells, both of which are considered to be critical for tumor progression.
Conclusions
The SOCE-Pyk2 pathway is essential for glioma migration and invasion. The study indicates the potential value of Orai1 as a molecular target for anti-invasion therapy.
Electronic supplementary material
The online version of this article (doi:10.1186/s13046-014-0098-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s13046-014-0098-1
PMCID: PMC4258251  PMID: 25433371
Store-operated Ca2+ entry; Glioma; Focal adhesion turnover; Epithelial-to-mesenchymal (−like) transition; Proline-rich tyrosine kinase 2
12.  Whole Genome Sequence of the Treponema pallidum subsp. endemicum Strain Bosnia A: The Genome Is Related to Yaws Treponemes but Contains Few Loci Similar to Syphilis Treponemes 
Background
T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe.
Methodology/Principal Findings
The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6–2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.
Conclusions/Significance
The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.
Author Summary
Uncultivable treponemes represent bacterial species and subspecies that are obligate pathogens of humans and animals causing diseases with distinct clinical manifestations. Treponema pallidum subsp. pallidum causes sexually transmitted syphilis, a multistage disease characterized in humans by localized, disseminated, and chronic forms of infection, whereas Treponema pallidum subsp. pertenue (agent of yaws) and Treponema pallidum subsp. endemicum (agent of bejel) cause milder, non-venereally transmitted diseases affecting skin, bones and joints. The genetic basis of the pathogenesis and evolution of these microorganisms are still unknown. In this study, a high quality whole genome sequence of the T. pallidum subsp. endemicum Bosnia A strain was obtained using a combination of next-generation sequencing approaches and compared to the genomes of available uncultivable pathogenic treponemes. Relative to all known genomes of Treponema pallidum subspecies, no major genome rearrangements were found in the Bosnia A. The Bosnia A strain clustered with other yaws-causing strains, while syphilis-causing strains clustered separately. In general, the Bosnia A genome showed similar genetic characteristics to yaws treponemes but also contained several sequences thought to be unique to syphilis-causing strains. This finding suggests a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.
doi:10.1371/journal.pntd.0003261
PMCID: PMC4222731  PMID: 25375929
13.  3Cpro of Foot-and-Mouth Disease Virus Antagonizes the Interferon Signaling Pathway by Blocking STAT1/STAT2 Nuclear Translocation 
Journal of Virology  2014;88(9):4908-4920.
ABSTRACT
Foot-and-mouth disease virus (FMDV) causes a highly contagious, debilitating disease in cloven-hoofed animals with devastating economic consequences. To survive in the host, FMDV has evolved to antagonize the host type I interferon (IFN) response. Previous studies have reported that the leader proteinase (Lpro) and 3Cpro of FMDV are involved in the inhibition of type I IFN production. However, whether the proteins of FMDV can inhibit type I IFN signaling is less well understood. In this study, we first found that 3Cpro of FMDV functioned to interfere with the JAK-STAT signaling pathway. Expression of 3Cpro significantly reduced the transcript levels of IFN-stimulated genes (ISGs) and IFN-stimulated response element (ISRE) promoter activity. The protein level, tyrosine phosphorylation of STAT1 and STAT2, and their heterodimerization were not affected. However, the nuclear translocation of STAT1/STAT2 was blocked by the 3Cpro protein. Further mechanistic studies demonstrated that 3Cpro induced proteasome- and caspase-independent protein degradation of karyopherin α1 (KPNA1), the nuclear localization signal receptor for tyrosine-phosphorylated STAT1, but not karyopherin α2, α3, or α4. Finally, we showed that the protease activity of 3Cpro contributed to the degradation of KPNA1 and thus blocked STAT1/STAT2 nuclear translocation. Taken together, results of our experiments describe for the first time a novel mechanism by which FMDV evolves to inhibit IFN signaling and counteract host innate antiviral responses.
IMPORTANCE We show that 3Cpro of FMDV antagonizes the JAK-STAT signaling pathway by blocking STAT1/STAT2 nuclear translocation. Furthermore, 3Cpro induces KPNA1 degradation, which is independent of proteasome and caspase pathways. The protease activity of 3Cpro contributes to the degradation of KPNA1 and governs the ability of 3Cpro to inhibit the JAK-STAT signaling pathway. This study uncovers a novel mechanism evolved by FMDV to antagonize host innate immune responses.
doi:10.1128/JVI.03668-13
PMCID: PMC3993825  PMID: 24554650
14.  Metabolomic basis of laboratory evolution of butanol tolerance in photosynthetic Synechocystis sp. PCC 6803 
Microbial Cell Factories  2014;13(1):151.
Background
Recent efforts demonstrated the potential application of cyanobacteria as a “microbial cell factory” to produce butanol directly from CO2. However, cyanobacteria have very low tolerance to the toxic butanol, which limits the economic viability of this renewable system.
Results
Through a long-term experimental evolution process, we achieved a 150% increase of the butanol tolerance in a model cyanobacterium Synechocystis sp. PCC 6803 after a continuous 94 passages for 395 days in BG11 media amended with gradually increased butanol concentration from 0.2% to 0.5% (v/v). To decipher the molecular mechanism responsible for the tolerance increase, we employed an integrated GC-MS and LC-MS approach to determine metabolomic profiles of the butanol-tolerant Synechocystis strains isolated from several stages of the evolution, and then applied PCA and WGCNA network analyses to identify the key metabolites and metabolic modules related to the increased tolerance. The results showed that unstable metabolites of 3-phosphoglyceric acid (3PG), D-fructose 6-phosphate (F6P), D-glucose 6-phosphate (G6P), NADPH, phosphoenolpyruvic acid (PEP), D-ribose 5-phosphate (R5P), and stable metabolites of glycerol, L-serine and stearic acid were differentially regulated during the evolution process, which could be related to tolerance increase to butanol in Synechocystis.
Conclusions
The study provided the first time-series description of the metabolomic changes related to the gradual increase of butanol tolerance, and revealed a metabolomic basis important for rational tolerance engineering in Synechocystis.
Electronic supplementary material
The online version of this article (doi:10.1186/s12934-014-0151-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12934-014-0151-y
PMCID: PMC4234862  PMID: 25366096
Butanol; Tolerance; Evolution; Metabolomics; Synechocystis
15.  Metastasis to the proximal ureter from prostatic adenocarcinoma: A rare metastatic pattern 
Canadian Urological Association Journal  2014;8(11-12):E859-E861.
Prostate cancer is one of the most common male malignancies, but it rarely metastasizes to the proximal ureter. We report a case of a 76-year-old man who presented with flank pain and lower urinary tract symptoms. Abdominal computed tomography scan revealed multiple filling defects at the middle of the left ureter, enlarged retroperitoneal lymph nodes, and probable psoas invasion. The patient underwent nephroureterectomy with excision of a cuff of bladder, and was found to have an adhesion between the middle part of left ureter and psoas intraoperatively. The pathological examination displayed positive immunohistochemical staining with prostate-specific antigen and prostate acid phostate, supporting the diagnosis of metastatic ureteral tumour from prostate cancer. In this case, periureteral soft tissue and ureteral muscular layer were infiltrated by metastatic tumour, whereas the mucosa was spared. The periureteral lymphatic pathway played an important role in the metastatic procedure of prostate cancer to the proximal ureter.
doi:10.5489/cuaj.2169
PMCID: PMC4250253  PMID: 25485016
16.  Synthesis and Antibacterial Activities of Antibacterial Peptides with a Spiropyran Fluorescence Probe 
Scientific Reports  2014;4:6860.
In this report, antibacterial peptides1-3 were prepared with a spiropyran fluorescence probe. The probe exhibits a change in fluorescence when isomerized from a colorless spiro-form (spiropyran, Sp) to a colored open-form (merocyanine, Mc) under different chemical environments, which can be used to study the mechanism of antimicrobial activity. Peptides 1-3 exhibit a marked decrease in antimicrobial activity with increasing alkyl chain length. This is likely due to the Sp-Mc isomers in different polar environments forming different aggregate sizes in TBS, as demonstrated by time-dependent dynamic light scattering (DLS). Moreover, peptides 1-3 exhibited low cytotoxicity and hemolytic activity. These probe-modified peptides may provide a novel approach to study the effect of structural changes on antibacterial activity, thus facilitating the design of new antimicrobial agents to combat bacterial infection.
doi:10.1038/srep06860
PMCID: PMC4215325  PMID: 25358905
17.  Advances in genome editing technology and its promising application in evolutionary and ecological studies 
GigaScience  2014;3:24.
Genetic modification has long provided an approach for “reverse genetics”, analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace with the soaring progress of the genome sequencing era, as a result of their inefficiency, time-consuming and labor-intensive methods. Recently, invented genome modification technologies, such as ZFN (Zinc Finger Nuclease), TALEN (Transcription Activator-Like Effector Nuclease), and CRISPR/Cas9 nuclease (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 nuclease) can initiate genome editing easily, precisely and with no limitations by organism. These new tools have also offered intriguing possibilities for conducting functional large-scale experiments. In this review, we begin with a brief introduction of ZFN, TALEN, and CRISPR/Cas9 technologies, then generate an extensive prediction of effective TALEN and CRISPR/Cas9 target sites in the genomes of a broad range of taxonomic species. Based on the evidence, we highlight the potential and practicalities of TALEN and CRISPR/Cas9 editing in non-model organisms, and also compare the technologies and test interesting issues such as the functions of candidate domesticated, as well as candidate genes in life-environment interactions. When accompanied with a high-throughput sequencing platform, we forecast their potential revolutionary impacts on evolutionary and ecological research, which may offer an exciting prospect for connecting the gap between DNA sequence and phenotype in the near future.
doi:10.1186/2047-217X-3-24
PMCID: PMC4238018  PMID: 25414792
Genetic modification; Genetic innovations; Domestication; Life-environment interaction
18.  Comparison of Long-Term Survival and Toxicity of Cisplatin Delivered Weekly versus Every Three Weeks Concurrently with Intensity-Modulated Radiotherapy in Nasopharyngeal Carcinoma 
PLoS ONE  2014;9(10):e110765.
Background
We aimed to compare the long-term survival outcomes and acute toxicity of cisplatin administered weekly versus every three weeks concurrently with intensity-modulated radiotherapy (IMRT) in patients with nasopharyngeal carcinoma (NPC).
Methods
This was a retrospective review of 154 patients with histologically proven, non-disseminated NPC who were treated using IMRT between January 2003 and December 2007. Seventy-three patients (47.4%) received 5–7 weeks of 30–40 mg/m2 cisplatin weekly; 81 patients (52.6%) received two or three cycles of 80 mg/m2 cisplatin every three weeks. IMRT was delivered at 68 Gy/30 fractions to the nasopharyngeal gross target volume and 60–66 Gy to the involved neck area.
Results
The clinical characteristics and treatment factors of the two groups were well-balanced. The median follow-up was 74 months (range, 6–123 months), and the 5-year overall survival, disease-free survival, locoregional relapse-free survival, and distant metastasis–free survival rates were 85.2% vs. 78.9% (P = 0.318), 71.6% vs. 71.0% (P = 0.847), 93.5% vs. 92.6% (P = 0.904), and 80.9% vs. 80.1% (P = 0.925) for the group treated every three weeks and weekly, respectively. Subgroup analyses indicated no significant differences in the survival rates of the two groups among patients with early- or advanced-stage disease. The incidence of acute toxicities was similar between groups.
Conclusion
IMRT with concurrent cisplatin administered weekly or every three weeks leads to similar long-term survival outcomes and acute toxicity in NPC regardless of whether patients have early- or advanced-stage disease.
doi:10.1371/journal.pone.0110765
PMCID: PMC4199726  PMID: 25329593
19.  New Types of Wheat Chromosomal Structural Variations in Derivatives of Wheat-Rye Hybrids 
PLoS ONE  2014;9(10):e110282.
Background
Chromosomal rearrangements induced by wheat-rye hybridization is a very well investigated research topic. However, the structural alterations of wheat chromosomes in wheat-rye hybrids are seldom reported.
Methodology/Principal Findings
Octoploid triticale lines were derived from common wheat Triticum. aestivum L. ‘Mianyang11’×rye Secale cereale L. ‘Kustro’. Some progeny were obtained by the controlled backcrossing of triticale with ‘Mianyang11’ and common wheat T. aestivum L. ‘Chuannong27’ followed by self-fertilization. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) using Oligo-pSc119.2-1, Oligo-pTa535-1 and rye genomic DNA as probes were used to analyze the mitotic chromosomes of these progeny. Alterations of wheat chromosomes including 5A, 6A, 1B, 2B, 6B, 7B, 1D, 3D and 7D were observed. 5AL arm carrying intercalary Oligo-pSc119.2-1, Oligo-pTa535-1 or both Oligo-pSc119.2-1 and Oligo-pTa535-1 signals, 6AS, 1BS and 1DL arms containing terminal Oligo-pSc119.2-1 signal, 6BS and 3DS arms without terminal Oligo-pSc119.2-1 signal, 7BS without subtelomeric Oligo-pSc119.2-1 signal and 7DL with intercalary Oligo-pSc119.2-1 signal have been observed. However, these changed wheat chromosomes have not been detected in ‘Mianyang11’ and Chuannong 27. The altered 5A, 6A, 7B and 7D chromosomes in this study have not been reported and represent several new karyotype structures of common wheat chromosomes.
Conclusions/Significance
These rearranged wheat chromosomes in the present study afford some new genetic variations for wheat breeding program and are valuable materials for studying the biological function of tandem repetitive DNA sequences.
doi:10.1371/journal.pone.0110282
PMCID: PMC4193885  PMID: 25302962
20.  The association between the rs6495309 polymorphism in CHRNA3 gene and lung cancer risk in Chinese: a meta-analysis 
Scientific Reports  2014;4:6372.
The association between the rs6495309 polymorphism in CHRNA3 gene and lung cancer risk has been studied in Chinese by several number case-control control studies with small number of cases and controls, and these studies might be underpowered to reveal the true association. Thus we sought to investigate the association with the risk of lung cancer by performing a comprehensive meta-analysis on the polymorphism. Five case-control studies were extracted from 3 articles on the polymorphism involving 4608 lung cancer cases and 4617 controls. The results of meta-analysis showed that significant increased risk were found for the polymorphism with the risk of lung cancer in Chinese: OR = 1.47, 95%CI = 1.33–1.63, P < 0.00001 for CC + TC vs. TT; OR = 1.24, 95%CI = 1.07–1.44, P = 0.005 for CC vs. TT + TC; OR = 1.62, 95%CI = 1.32–2.00, P < 0.00001 for CC vs. TT; OR = 1.42, 95%CI = 1.26–1.61, P < 0.00001 for CT vs. TT; OR = 1.42, 95%CI = 1.26–1.61, P < 0.00001. No significant publication bias was found for the five genetic models. Our findings demonstrated that CHRNA3 gene rs6495309 polymorphism might be a risk factor for the development of lung cancer in Chinese.
doi:10.1038/srep06372
PMCID: PMC4187012  PMID: 25288178
21.  Loop-mediated isothermal amplification assays for screening of bacterial integrons 
Biological Research  2014;47(1):53.
Background
The occurrence and prevalence of integrons in clinical microorganisms and their role played in antimicrobial resistance have been well studied recently. As screening and detection of integrons are concerned, current diagnostic methodologies are restricted by significant drawbacks and novel methods are required for integrons detection.
Results
In this study, three loop-mediated isothermal amplification (LAMP) assays targeting on class 1, 2 and 3 integrons were implemented and evaluated. Optimization of these detection assays were performed, including studing on the reaction temperature, volume, time, sensitivity and specificity (both primers and targets). Application of the established LAMP assays were further verified on a total of 1082 isolates (previously identified to be 397 integron-positive and 685 integron-negative strains). According to the results, the indispensability of each primer had been confirmed and the optimal reaction temperature, volume and time were found to be 65°C, 45 min and 25 μL, respectively. As application was concerned, 361, 28 and 8 isolates carrying intI1, intI2 and intI3 yielded positive amplicons, respectively. Other 685 integron-negative bacteria were negative for the integron-screening LAMP assays, totaling the detection rate and specificity to be 100%.
Conclusions
The intI1-, intI2- and intI3-LAMP assays established in this study were demonstrated to be the valid and rapid detection methodologies for the screening of bacterial integrons.
doi:10.1186/0717-6287-47-53
PMCID: PMC4222780  PMID: 25418445
Loop-mediated isothermal amplification (LAMP); Integron screening; Bacterial integrons; Class 1 integron; Class 2 integron; Class 3 integron
22.  Neonatal Seizures: Soothing a Burning Topic 
Pediatric emergency care  2013;29(10):10.1097/PEC.0b013e3182a62fd6.
Neonatal seizures are a potentially life-threatening pediatric problem with a variety of causes, such as birth trauma, asphyxia, congenital anomalies, metabolic disturbances, infections, and drug withdrawal or intoxication. Thorough and timely evaluations of such patients are necessary to identify and treat the underlying etiology, therefore reducing potential morbidity and mortality. We review neonatal seizures and hypocalcemia, and present the case of a 6 day old male who presented to a tertiary pediatric emergency department with seizure-like episodes. He was found to have markedly low serum calcium, magnesium, and parathyroid hormone concentrations, as well as a significantly elevated serum phosphate concentration. The etiology of these abnormalities was found to be maternal ingestion of extremely high doses of calcium carbonate during the third trimester of her pregnancy, an occurrence that has been reported only once in the literature. Education pertaining to the dangers of excessive calcium carbonate intake during pregnancy may be an important piece of anticipatory guidance for pregnant mothers with symptoms of gastroesophageal reflux, and questioning the mother of a neonate presenting with seizures about such over-the-counter medications may help to elucidate the diagnosis.
doi:10.1097/PEC.0b013e3182a62fd6
PMCID: PMC3822764  PMID: 24084610
neonatal seizure; hypocalcemia; calcium carbonate
23.  Selective ligands of estrogen receptor β discovered using pharmacophore mapping and structure-based virtual screening 
Acta Pharmacologica Sinica  2014;35(10):1333-1341.
Aim:
To discover novel ligands of estrogen receptor (ER) β using pharmacophore mapping and structure-based screening.
Methods:
A computer-aided strategy combining pharmacophore mapping and structure-based screening was used to screen the Maybridge and Enamine databases. Yeast two-hybrid (Y2H) assay was used to detect the activity and selectivity of the chosen compounds. The transcriptional activities of the chosen compounds were demonstrated with luciferase reporter assays. The anti-proliferative effects of ER antagonists against MCF-7 and MDA-MB-231 breast cancer cells were examined using MTT assay, and the mechanisms of action were analyzed with flow cytometry analysis and Western blotting.
Results:
Through in silico screen, 95 compounds were chosen for testing in Y2H assay, which led to 20 potent ligands, including 10 agonists, 8 antagonists and 2 partial agonists with EC50 or IC50 values at μmol/L. Furthermore, 6 agonists exhibited absolute selectivity for ERβ, and 3 agonists showed higher selectivity for ERβ. The agonists 1g and 1h (10, 25, and 50 μmol/L) dose-dependently increased ER transcriptional activities, whereas the antagonists 2a and 2d (10, 25, and 50 μmol/L) caused dose-dependent inhibition on the activities. The antagonists and partial agonists at 100 μmol/L suppressed the proliferation of ERα positive MCF-7 cells and ERβ positive MDA-MB-231 cells, but were more effective against MDA-MB-231 cells. Treatment of MDA-MB-231 cells with antagonists 2a and 2d (25 and 50 μmol/L) dose-dependently increased the population of cells in the S phase. Both 2a and 2d treatment dose-dependently decreased the expression levels of cyclin A and CDK2. Meanwhile, the downregulation of cyclin E was only caused by 2d, while 2a treatment did not cause significant changes in the protein levels of cyclin E.
Conclusion:
The selective ligands discovered in this study are promising drug candidates to be used as molecular probes to explore the differences between ERα and ERβ.
doi:10.1038/aps.2014.69
PMCID: PMC4186986  PMID: 25176400
estrogen receptor; subtype-selective ligand; estradiol; tamoxifen; pharmacophore mapping; structure-based virtual screening; breast cancer; anti-proliferation; cell cycle arrest
24.  Finding Candidate Drugs for Hepatitis C Based on Chemical-Chemical and Chemical-Protein Interactions 
PLoS ONE  2014;9(9):e107767.
Hepatitis C virus (HCV) is an infectious virus that can cause serious illnesses. Only a few drugs have been reported to effectively treat hepatitis C. To have greater diversity in drug choice and better treatment options, it is necessary to develop more drugs to treat the infection. However, it is time-consuming and expensive to discover candidate drugs using experimental methods, and computational methods may complement experimental approaches as a preliminary filtering process. This type of approach was proposed by using known chemical-chemical interactions to extract interactive compounds with three known drug compounds of HCV, and the probabilities of these drug compounds being able to treat hepatitis C were calculated using chemical-protein interactions between the interactive compounds and HCV target genes. Moreover, the randomization test and expectation-maximization (EM) algorithm were both employed to exclude false discoveries. Analysis of the selected compounds, including acyclovir and ganciclovir, indicated that some of these compounds had potential to treat the HCV. Hopefully, this proposed method could provide new insights into the discovery of candidate drugs for the treatment of HCV and other diseases.
doi:10.1371/journal.pone.0107767
PMCID: PMC4166673  PMID: 25225900
25.  Discriminating between Lysine Sumoylation and Lysine Acetylation Using mRMR Feature Selection and Analysis 
PLoS ONE  2014;9(9):e107464.
Post-translational modifications (PTMs) are crucial steps in protein synthesis and are important factors contributing to protein diversity. PTMs play important roles in the regulation of gene expression, protein stability and metabolism. Lysine residues in protein sequences have been found to be targeted for both types of PTMs: sumoylations and acetylations; however, each PTM has a different cellular role. As experimental approaches are often laborious and time consuming, it is challenging to distinguish the two types of PTMs on lysine residues using computational methods. In this study, we developed a method to discriminate between sumoylated lysine residues and acetylated residues. The method incorporated several features: PSSM conservation scores, amino acid factors, secondary structures, solvent accessibilities and disorder scores. By using the mRMR (Maximum Relevance Minimum Redundancy) method and the IFS (Incremental Feature Selection) method, an optimal feature set was selected from all of the incorporated features, with which the classifier achieved 92.14% accuracy with an MCC value of 0.7322. Analysis of the optimal feature set revealed some differences between acetylation and sumoylation. The results from our study also supported the previous finding that there exist different consensus motifs for the two types of PTMs. The results could suggest possible dominant factors governing the acetylation and sumoylation of lysine residues, shedding some light on the modification dynamics and molecular mechanisms of the two types of PTMs, and provide guidelines for experimental validations.
doi:10.1371/journal.pone.0107464
PMCID: PMC4164654  PMID: 25222670

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