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1.  Mechanisms of antibiotic resistance 
doi:10.3389/fmicb.2015.00034
PMCID: PMC4318422
antibiotics; resistance; mechanisms; resistance reservoirs; metagenomics; combination therapy
2.  Heparanase mediates a novel mechanism in lapatinib-resistant brain metastatic breast cancer12 
Neoplasia (New York, N.Y.)  2015;17(1):101-113.
Heparanase (HPSE) is the dominant mammalian endoglycosidase and important tumorigenic, angiogenic, and pro-metastatic molecule. Highest levels of HPSE activity have been consistently detected in cells possessing highest propensities to colonize the brain, emphasizing the therapeutic potential for targeting HPSE in brain metastatic breast cancer (BMBC). Lapatinib (Tykerb) is a small-molecule and dual inhibitor of human epidermal growth factor receptor1 and 2 (EGFR and HER2, respectively) which are both high-risk predictors of BMBC. It was approved by the US Food and Drug Administration for treatment of patients with advanced or metastatic breast cancer. However, its role is limited in BMBC whose response rates to lapatinib are significantly lower than those for extracranial metastasis. Because HPSE can affect EGFR phosphorylation, we examined Roneparstat, a non-anticoagulant heparin with potent anti-HPSE activity, to inhibit EGFR signaling pathways and BMBC onset using lapatinib-resistant clones generated from HER2-transfected, EGFR-expressing MDA-MB-231BR cells. Cell growth, EGFR pathways, and HPSE targets were assessed among selected clones in the absence or presence of Roneparstat and/or lapatinib. Roneparstat overcame lapatinib resistance by inhibiting pathways associated with EGFR tyrosine residues that are not targeted by lapatinib. Roneparstat inhibited the growth and BMBC abilities of lapatinib-resistant clones. A molecular mechanism was identified by which HPSE mediates an alternative survival pathway in lapatinib-resistant clones and is modulated by Roneparstat. These results demonstrate that the inhibition of HPSE-mediated signaling plays important roles in lapatinib resistance, and provide mechanistic insights to validate the use of Roneparstat for novel BMBC therapeutic strategies.
doi:10.1016/j.neo.2014.11.007
PMCID: PMC4309682  PMID: 25622903
ANOVA, analysis of variance; BR, HER2-transfected MDA-MB-231BR; BMBC, brain metastatic breast cancer; COX-2, cyclooxygenase-2; DME/F-12, Dulbecco’s modified Eagle’s/F-12 medium; ERK, extracellular signal-regulated kinase; EGFR, human epidermal growth factor receptor1; FACS, fluorescence activated cell sorting; FAK, focal adhesion kinase; FBS, fetal bovine serum; HER2, human epidermal growth factor receptor2; HPSE, heparanase; HS, heparan sulfate; Ls/Lr BR clones, lapatinib-sensitive/lapatinib-resistant BR clones; MAPK, mitogen-activated protein kinase; MMP-9, matrix metalloprotease-9; PBS, phosphate-buffered saline; PI3K, phosphoinositide 3-kinase; STR, short tandem repeat.
3.  Predicted Configurations of Oligosaccharide Extensions in the Lipooligosaccharide of Nontypeable Haemophilus influenzae Isolates 
Journal of Clinical Microbiology  2014;52(7):2659-2661.
Lipooligosaccharide configurations were predicted in nontypeable Haemophilus influenzae isolates based on the presence of seven oligosaccharide extension-initiating genes (or alleles). Predicted configurations with 2 to 3 oligosaccharide extensions were more prevalent among middle ear than throat strains. In addition, strains with these configurations averaged higher levels of serum resistance than strains with other configurations.
doi:10.1128/JCM.01113-14
PMCID: PMC4097733  PMID: 24789190
4.  Evaluation of EEG Oscillatory Patterns and Cognitive Process during Simple and Compound Limb Motor Imagery 
PLoS ONE  2014;9(12):e114853.
Motor imagery (MI), sharing similar neural representations to motor execution, is regarded as a window to investigate the cognitive motor processes. However, in comparison to simple limb motor imagery, significantly less work has been reported on brain oscillatory patterns induced by compound limb motor imagery which involves several parts of limbs. This study aims to investigate differences of the electroencephalogram (EEG) patterns as well as cognitive process between simple limb motor imagery and compound limb motor imagery. Ten subjects participated in the experiment involving three tasks of simple limb motor imagery (left hand, right hand, feet) and three tasks of compound limb motor imagery (both hands, left hand combined with right foot, right hand combined with left foot). Simultaneous imagination of different limbs contributes to the activation of larger cortical areas as well as two estimated sources located at corresponding motor areas within beta rhythm. Compared with simple limb motor imagery, compound limb motor imagery presents a network with more effective interactions overlying larger brain regions, additionally shows significantly larger causal flow over sensorimotor areas and larger causal density over both sensorimotor areas and neighboring regions. On the other hand, compound limb motor imagery also shows significantly larger 10–11 Hz alpha desynchronization at occipital areas and central theta synchronization. Furthermore, the phase-locking value (PLV) between central and occipital areas of left/right hand combined with contralateral foot imagery is significantly larger than that of simple limb motor imagery. All these findings imply that there exist apparent intrinsic distinctions of neural mechanism between simple and compound limb motor imagery, which presents a more complex effective connectivity network and may involve a more complex cognitive process during information processing.
doi:10.1371/journal.pone.0114853
PMCID: PMC4260914  PMID: 25489941
5.  Dissecting and engineering of the TetR family regulator SACE_7301 for enhanced erythromycin production in Saccharopolyspora erythraea 
Microbial Cell Factories  2014;13(1):158.
Background
Saccharopolyspora erythraea was extensively utilized for the industrial-scale production of erythromycin A (Er-A), a macrolide antibiotic commonly used in human medicine. Yet, S. erythraea lacks regulatory genes in the erythromycin biosynthetic gene (ery) cluster, hampering efforts to enhance Er-A production via the engineering of regulatory genes.
Results
By the chromosome gene inactivation technique based on homologous recombination with linearized DNA fragments, we have inactivated a number of candidate TetR family transcriptional regulators (TFRs) and identified one TFR (SACE_7301) positively controlling erythromycin biosynthesis in S. erythraea A226. qRT-PCR and EMSA analyses demonstrated that SACE_7301 activated the transcription of erythromycin biosynthetic gene eryAI and the resistance gene ermE by interacting with their promoter regions with low affinities, similar to BldD (SACE_2077) previously identified to regulate erythromycin biosynthesis and morphological differentiation. Therefore, we designed a strategy for overexpressing SACE_7301 with 1 to 3 extra copies under the control of PermE* in A226. Following up-regulated transcriptional expression of SACE_7301, eryAI and ermE, the SACE_7301-overexpressed strains all increased Er-A production over A226 proportional to the number of copies. Likewise, when SACE_7301 was overexpressed in an industrial S. erythraea WB strain, Er-A yields of the mutants WB/7301, WB/2×7301 and WB/3×7301 were respectively increased by 17%, 29% and 42% relative to that of WB. In a 5 L fermentor, Er-A accumulation increased to 4,230 mg/L with the highest-yield strain WB/3×7301, an approximately 27% production improvement over WB (3,322 mg/L).
Conclusions
We have identified and characterized a TFR, SACE_7301, in S. erythraea that positively regulated erythromycin biosynthesis, and overexpression of SACE_7301 in wild-type and industrial S. erythraea strains enhanced Er-A yields. This study markedly improves our understanding of the unusual regulatory mechanism of erythromycin biosynthesis, and provides a novel strategy towards Er-A overproduction by engineering transcriptional regulators of S. erythraea.
Electronic supplementary material
The online version of this article (doi:10.1186/s12934-014-0158-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12934-014-0158-4
PMCID: PMC4258057  PMID: 25391994
Saccharopolyspora erythraea; Erythromycin; SACE_7301; TetR family regulator; Gene overexpression; Metabolic engineering
6.  Practical Implementation, Characterization and Applications of a Multi-Colour Time-Gated Luminescence Microscope 
Scientific Reports  2014;4:6597.
Time-gated luminescence microscopy using long-lifetime molecular probes can effectively eliminate autofluorescence to enable high contrast imaging. Here we investigate a new strategy of time-gated imaging for simultaneous visualisation of multiple species of microorganisms stained with long-lived complexes under low-background conditions. This is realized by imaging two pathogenic organisms (Giardia lamblia stained with a red europium probe and Cryptosporidium parvum with a green terbium probe) at UV wavelengths (320–400 nm) through synchronization of a flash lamp with high repetition rate (1 kHz) to a robust time-gating detection unit. This approach provides four times enhancement in signal-to-background ratio over non-time-gated imaging, while the average signal intensity also increases six-fold compared with that under UV LED excitation. The high sensitivity is further confirmed by imaging the single europium-doped Y2O2S nanocrystals (150 nm). We report technical details regarding the time-gating detection unit and demonstrate its compatibility with commercial epi-fluorescence microscopes, providing a valuable and convenient addition to standard laboratory equipment.
doi:10.1038/srep06597
PMCID: PMC4194433  PMID: 25307702
7.  Efflux-mediated resistance identified among norfloxacin resistant clinical strains of group B Streptococcus from South Korea 
Epidemiology and Health  2014;36:e2014022.
OBJECTIVES:
Group B Streptococcus (GBS), a common bowel commensal, is a major cause of neonatal sepsis and an emerging cause of infection in immune-compromised adult populations. Fluoroquinolones are used to treat GBS infections in those allergic to beta-lactams, but GBS are increasingly resistant to fluoroquinolones. Fluoroquinolone resistance has been previously attributed to quinolone resistance determining regions (QRDRs) mutations. We demonstrate that some of fluoroquinolone resistance is due to efflux-mediated resistance.
METHODS:
We tested 20 GBS strains resistant only to norfloxacin with no mutations in the QRDRs, for the efflux phenotype using norfloxacin and ethidium bromide as substrates in the presence of the efflux inhibitor reserpine. Also tested were 68 GBS strains resistant only to norfloxacin not screened for QRDRs, and 58 GBS strains resistant to ciprofloxacin, levofloxacin or moxifloxacin. Isolates were randomly selected from 221 pregnant women (35-37 weeks of gestation) asymptomatically carrying GBS, and 838 patients with GBS infection identified in South Korea between 2006 and 2008. The VITEK II automatic system (Biomerieux, Durham, NC, USA) was used to determine fluoroquinolone resistance.
RESULTS:
The reserpine associated efflux phenotype was found in more than half of GBS strains resistant only to norfloxacin with no QRDR mutations, and half where QRDR mutations were unknown. No evidence of the efflux phenotype was detected in GBS strains that were resistant to moxifloxacin or levofloxacin or both. The reserpine sensitive efflux phenotype resulted in moderate increases in norfloxacin minimum inhibitory concentration (average=3.6 fold, range=>1-16 fold).
CONCLUSIONS:
A substantial portion of GBS strains resistant to norfloxacin have an efflux phenotype.
doi:10.4178/epih/e2014022
PMCID: PMC4258715  PMID: 25322878
Fluoroquinolones; Norfloxacin; Ciprofloxacin; Levofloxacin; Moxifloxacin; Mutations; Efflux; Minimum inhibitory concentration
8.  Seroprevalence of Merkel Cell Polyomavirus in the General Rural Population of Anyang, China 
PLoS ONE  2014;9(9):e106430.
Background
Despite the probably causal link between Merkel cell polyomavirus (MCPyV) infection and Merkel cell carcinoma (MCC), a rare but aggressive skin malignancy, little is known about the seroepidemiology of MCPyV among healthy adults in China.
Methods
Serum antibodies against MCPyV were evaluated by multiplex serology in a population-based study of 5548 adults (including 1587 heterosexual couples) aged 25–65 years who were enrolled from rural Anyang, China in 2007–2009. Univariate and multivariate logistic regression analyses were performed to assess the risk factors for the seropositivity of MCPyV.
Results
The seroprevalence for MCPyV was 61.0%. MCPyV seropositivity was significantly higher in males than in females (64.5% vs. 57.7%, P<0.001), and for both genders, showed a trend of increase with age (Male: Ptrend<0.001; Female: Ptrend<0.001). Furthermore, among antibody positives, antibody levels of MCPyV increased with advancing age (Ptrend = 0.017). MCPyV seropositivity of one spouse was significantly associated with that of the other partner (Adjusted OR = 1.32, 95% CI: 1.07–1.62). However, there was no association between sexual behaviors and the seropositivity of MCPyV.
Conclusions
High seroprevalence of MCPyV was observed in healthy Chinese individuals. Serological evidence suggests that nonsexual horizontal spread of MCPyV can occur among family members, and further research in this regard is needed.
doi:10.1371/journal.pone.0106430
PMCID: PMC4153645  PMID: 25184447
9.  Real-time Metabolomics on Living Microorganisms Using Ambient Electrospray Ionization Flow-Probe 
Analytical chemistry  2013;85(15):7014-7018.
Microorganisms such as bacteria and fungi produce a variety of specialized metabolites that are invaluable for agriculture, biological research, and drug discovery. However, the screening of microbial metabolic output is usually a time intensive task. Here we utilize a liquid micro-junction surface sampling probe for electrospray ionization mass spectrometry to extract and ionize metabolite mixtures directly from living microbial colonies grown on soft nutrient agar in Petri-dishes without any sample pre-treatment. To demonstrate the method is robust, this technique was applied to observe the metabolic output of more than 30 microorganisms, including yeast, filamentous fungi, pathogens, and marine-derived bacteria, that were collected worldwide. Diverse natural products produced from different microbes, including Streptomyces coelicolor, Bacillus subtilis, and Pseudomonas aeruginosa are further characterized.
doi:10.1021/ac401613x
PMCID: PMC3890442  PMID: 23819546
10.  Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains 
PLoS Biology  2014;12(8):e1001920.
This manuscript calls for an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains.
Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
doi:10.1371/journal.pbio.1001920
PMCID: PMC4122341  PMID: 25093819
11.  MUC1 Positive, Kras and Pten Driven Mouse Gynecologic Tumors Replicate Human Tumors and Vary in Survival and Nuclear Grade Based on Anatomical Location 
PLoS ONE  2014;9(7):e102409.
Activating mutations of Kras oncogene and deletions of Pten tumor suppressor gene play important roles in cancers of the female genital tract. We developed here new preclinical models for gynecologic cancers, using conditional (Cre-loxP) mice with floxed genetic alterations in Kras and Pten. The triple transgenic mice, briefly called MUC1KrasPten, express human MUC1 antigen as self and carry a silent oncogenic KrasG12D and Pten deletion mutation. Injection of Cre-encoding adenovirus (AdCre) in the ovarian bursa, oviduct or uterus activates the floxed mutations and initiates ovarian, oviductal, and endometrial cancer, respectively. Anatomical site-specific Cre-loxP recombination throughout the genital tract of MUC1KrasPten mice leads to MUC1 positive genital tract tumors, and the development of these tumors is influenced by the anatomical environment. Endometrioid histology was consistently displayed in all tumors of the murine genital tract (ovaries, oviducts, and uterus). Tumors showed increased expression of MUC1 glycoprotein and triggered de novo antibodies in tumor bearing hosts, mimicking the immunobiology seen in patients. In contrast to the ovarian and endometrial tumors, oviductal tumors showed higher nuclear grade. Survival for oviduct tumors was significantly lower than for endometrial tumors (p = 0.0015), yet similar to survival for ovarian cancer. Oviducts seem to favor the development of high grade tumors, providing preclinical evidence in support of the postulated role of fallopian tubes as the originating site for high grade human ovarian tumors.
doi:10.1371/journal.pone.0102409
PMCID: PMC4117479  PMID: 25078979
12.  The Distribution and Common Amino Acid Polymorphisms of Human Papillomavirus (HPV)-31 Variants in 2700 Women from Northern China 
PLoS ONE  2014;9(6):e99141.
To investigate the distribution of Human papillomavirus (HPV)-31 A, B and C variants as well as the common amino acid polymorphisms in Chinese women, all 14 HPV-31 positive cervical exfoliated cell specimens identified from a descriptive study including ∼2700 women from Northern China were analyzed. HPV-31 positive specimens were identified by Mass Spectrometry and the fragments of partial Long Control Region, E6 and E7 were amplified and directly sequenced or cloned into vector and then sequenced to confirm the variant information. HPV-31 prevalence in Northern Chinese female population was 0.52%. Six different sequences represented all 14 isolates, and these isolates were subsequently classified into variant lineage A (9), B (0) and C (5) by phylogenetic analysis. Five common amino acid polymorphism sites (2 in E6 and 3 in E7) and a novel non-synonymous mutation were detected in the current study. Our investigation suggested that HPV-31 was much less detected in Chinese women population than that in western countries. A and C variants were commonly detected while B variants were rarely detected in this population.
doi:10.1371/journal.pone.0099141
PMCID: PMC4047102  PMID: 24901850
13.  Multidrug-Resistant Transporter Mdr1p-Mediated Uptake of a Novel Antifungal Compound 
Antimicrobial Agents and Chemotherapy  2013;57(12):5931-5939.
The activity of many anti-infectious drugs has been compromised by the evolution of multidrug-resistant (MDR) pathogens. For life-threatening fungal infections, such as those caused by Candida albicans, overexpression of MDR1, which encodes an MDR efflux pump of the major facilitator superfamily (MFS), often confers resistance to chemically unrelated substances, including the most commonly used azole antifungals. As the development of new and efficacious antifungals has lagged far behind the growing emergence of resistant strains, it is imperative to develop strategies to overcome multidrug resistance. Previous advances have been mainly to deploy combinational therapy to restore azole susceptibility, which, however, requires coordination of two or more compounds. We observed a unique phenotype in which Mdr1p facilitates the uptake of a specific class of compounds. Among them, we describe a novel antifungal small molecule, bis[1,6-a:5′,6′-g]quinolizinium 8-methyl-salt (BQM) (U.S. patent application no. 61/793,090,2013), that has potent and broad antifungal activity. Notably, BQM exploits the MDR phenotype in C. albicans to promote the inhibitory effect. Rather than causing an antagonism of MDR strains, it exhibits a highly potentiated activity against a collection of clinical isolates and lab strains that overexpress MDR1. The activity of BQM against MDR1-overexpressing isolates is due to its facilitated intracellular accumulation. Microarray comparisons showed an extensive upregulation of MDR1 as well as polyamine transporter genes in a fluconazole-resistant strain. We then demonstrated that the polyamine transporters augment the accumulation of BQM. Importantly, BQM had greater activity than fluconazole and itraconazole against various fungal pathogens, including MDR Aspergillus fumigatus. Thus, our findings offer a paradigm shift to overcome MDR and the promise of improving antifungal treatment, especially in MDR pathogens.
doi:10.1128/AAC.01504-13
PMCID: PMC3837910  PMID: 24041896
14.  Genomics-Guided Discovery of Thailanstatins A, B and C as Pre-mRNA Splicing Inhibitors and Antiproliferative Agents from Burkholderia thailandensis MSMB43 
Journal of natural products  2013;76(4):685-693.
Mining the genome sequence of Burkholderia thailandensis MSMB43 revealed a cryptic biosynthetic gene cluster resembling that of FR901464 (4), a prototype spliceosome inhibitor produced by Pseudomonas sp. No. 2663. Transcriptional analysis revealed a cultivation condition in which a regulatory gene of the cryptic gene cluster is adequately expressed. Consequently, three new compounds, named thailanstatins A (1), B (2) and C (3), were isolated from the fermentation broth of B. thailandensis MSMB43. Thailanstatins are proposed to be biosynthesized by a hybrid polyketide synthase-nonribosomal peptide synthetase pathway. They differ from 4 by lacking an unstable hydroxyl group and by having an extra carboxyl moiety; those differences endow thailanstatins with a significantly greater stability than 4 as tested in phosphate buffer at pH 7.4. In vitro assays showed that thailanstatins inhibit pre-mRNA splicing as potently as 4, with half-maximal inhibitory concentrations in the single to sub µM range. Cell culture assays indicated that thailanstatins also possess potent antiproliferative activities in representative human cancer cell lines, with half-maximal growth inhibitory concentrations in the single nM range. This work provides new chemical entities for research and development, and new structure-activity information for chemical optimization of related spliceosome inhibitors.
doi:10.1021/np300913h
PMCID: PMC3696399  PMID: 23517093
Burkholderia thailandensis MSMB43; genomics-guided discovery; natural product; pre-mRNA splicing inhibitor; thailanstatin
15.  Human Mucin MUC1 RNA Undergoes Different Types of Alternative Splicing Resulting in Multiple Isoforms 
MUC1 is a transmembrane mucin with important functions in normal and transformed cells carried out by the extracellular domain or the cytoplasmic tail. A characteristic feature of the MUC1 extracellular domain is the variable number of tandem repeats (VNTR) region. Alternative splicing may regulate MUC1 expression and possibly function. We developed an RT-PCR method for efficient isolation of MUC1 mRNA isoforms that allowed us to evaluate the extent of alternative splicing of MUC1 and elucidate some of the rules that govern this process. We cloned and analyzed 21, 24, and 36 isoforms from human tumor cell lines HeLa, MCF7, and Jurkat respectively, and 16 from normal activated human T cells. Among the 78 MUC1 isoforms we isolated, 76 are new and different cells showed varied MUC1 expression patterns. The VNTR region of exon 2 was recognized as an intron with a fixed 5′ splice site but variable 3′ splice sites. We also report that the 3506 A/G SNP in exon 2 can regulate 3′ splice sites selection in intron 1 and produce different MUC1 short isoform proteins. Furthermore, the SNP A to G mutation was also observed in vivo, during de novo tumor formation in MUC1+/−KrasG12D/+PtenloxP/loxP mice. No specific functions have been associated with previously reported short isoforms. We now report that one new G SNP-associated isoform MUC1/Y-LSP, but not the A SNP-associated isoform MUC1/Y, inhibits tumor growth in immunocompetent but not immunocompromised mice.
doi:10.1007/s00262-012-1325-2
PMCID: PMC3538090  PMID: 22941036
MUC1; alternative splicing; isoforms; tumor
16.  Molecular Networking as a Dereplication Strategy 
Journal of natural products  2013;76(9):1686-1699.
A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogs, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogs.
doi:10.1021/np400413s
PMCID: PMC3936340  PMID: 24025162
17.  An EEG-based mental workload estimator trained on working memory task can work well under simulated multi-attribute task 
Mental workload (MW)-based adaptive system has been found to be an effective approach to enhance the performance of human-machine interaction and to avoid human error caused by overload. However, MW estimated from the spontaneously generated electroencephalogram (EEG) was found to be task-specific. In existing studies, EEG-based MW classifier can work well under the task used to train the classifier (within-task) but crash completely when used to classify MW of a task that is similar to but not included in the training data (cross-task). The possible causes have been considered to be the task-specific EEG patterns, the mismatched workload across tasks and the temporal effects. In this study, cross-task performance-based feature selection (FS) and regression model were tried to cope with these challenges, in order to make EEG-based MW estimator trained on working memory tasks work well under a complex simulated multi-attribute task (MAT). The results show that the performance of regression model trained on working memory task and tested on multi-attribute task with the feature subset picked-out were significantly improved (correlation coefficient (COR): 0.740 ± 0.147 and 0.598 ± 0.161 for FS data and validation data respectively) when compared to the performance in the same condition with all features (chance level). It can be inferred that there do exist some MW-related EEG features can be picked out and there are something in common between MW of a relatively simple task and a complex task. This study provides a promising approach to measure MW across tasks.
doi:10.3389/fnhum.2014.00703
PMCID: PMC4157541  PMID: 25249967
passive brain computer-interface; mental workload; EEG; feature selection; cross-task; working memory task; multi-attribute task
18.  Regulatory factors for the assembly of thylakoid membrane protein complexes 
Major multi-protein photosynthetic complexes, located in thylakoid membranes, are responsible for the capture of light and its conversion into chemical energy in oxygenic photosynthetic organisms. Although the structures and functions of these photosynthetic complexes have been explored, the molecular mechanisms underlying their assembly remain elusive. In this review, we summarize current knowledge of the regulatory components involved in the assembly of thylakoid membrane protein complexes in photosynthetic organisms. Many of the known regulatory factors are conserved between prokaryotes and eukaryotes, whereas others appear to be newly evolved or to have expanded predominantly in eukaryotes. Their specific features and fundamental differences in cyanobacteria, green algae and land plants are discussed.
doi:10.1098/rstb.2012.0065
PMCID: PMC3497070  PMID: 23148269
regulatory factors; biogenesis; assembly; thylakoid membrane protein complex; chloroplast
19.  The identification and characterization of breast cancer CTCs competent for brain metastasis 
Science translational medicine  2013;5(180):10.1126/scitranslmed.3005109.
Brain metastatic breast cancer (BMBC) is uniformly fatal and increasing in frequency. Despite its devastating outcome, mechanisms causing BMBC remain largely unknown. The mechanisms that implicate circulating tumor cells (CTCs) in metastatic disease, notably in BMBC, remain elusive. Here we characterize CTCs isolated from peripheral blood mononuclear cells (PBMCs) of patients with breast cancer, and also develop CTC lines from three of these patients. In epithelial cell adhesion molecule (EpCAM)–negative CTCs, we identified a potential signature of brain metastasis comprising “brain metastasis selected markers (BMSM)” HER2+/EGFR+/HPSE+/Notch1+. These CTCs—which are not captured by the CellSearch platform because of their EpCAM negativity—were analyzed for cell invasiveness and metastatic competency in vivo. CTC lines expressing the BMSM signature were highly invasive and capable of generating brain and lung metastases when xenografted in nude mice. Notably, increased brain metastatic capabilities, frequency, and quantitation were detected in EpCAM− CTCs overexpressing the BMSM signature. The presence of proteins of the BMSM CTC signature was also detected in the metastatic lesions of animals. Collectively, we provide evidence of isolation, characterization, and long-term culture of human breast cancer CTCs, leading to the description of a BMSM protein signature that is suggestive of CTC metastatic competency to the brain.
doi:10.1126/scitranslmed.3005109
PMCID: PMC3863909  PMID: 23576814
20.  3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape 
BMC Bioinformatics  2013;14:322.
Background
The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-dimensional visualization tools.
Results
We developed a 3D Cytoscape Client/Server (3DScapeCS) plugin, which adopted Cytoscape in interpreting different types of data, and UbiGraph for three-dimensional visualization. The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies.
Conclusions
Evaluation on several experimental data using 3DScapeCS and its special features, including multilevel graph layout, time-course data animation, and parallel visualization has proven its usefulness in visualizing complex data and help to make insightful conclusions.
doi:10.1186/1471-2105-14-322
PMCID: PMC3835703  PMID: 24225050
21.  EEG feature comparison and classification of simple and compound limb motor imagery 
Background
Motor imagery can elicit brain oscillations in Rolandic mu rhythm and central beta rhythm, both originating in the sensorimotor cortex. In contrast with simple limb motor imagery, less work was reported about compound limb motor imagery which involves several parts of limbs. The goal of this study was to investigate the differences of the EEG patterns between simple limb motor imagery and compound limb motor imagery, and discuss the separability of multiple types of mental tasks.
Methods
Ten subjects participated in the experiment involving three tasks of simple limb motor imagery (left hand, right hand, feet), three tasks of compound limb motor imagery (both hands, left hand combined with right foot, right hand combined with left foot) and rest state. Event-related spectral perturbation (ERSP), power spectral entropy (PSE) and spatial distribution coefficient were adopted to analyze these seven EEG patterns. Then three algorithms of modified multi-class common spatial patterns (CSP) were used for feature extraction and classification was implemented by support vector machine (SVM).
Results
The induced event-related desynchronization (ERD) affects more components within both alpha and beta bands resulting in more broad ERD bands at electrode positions C3, Cz and C4 during left/right hand combined with contralateral foot imagery, whose PSE values are significant higher than that of simple limb motor imagery. From the topographical distribution, simultaneous imagination of upper limb and contralateral lower limb certainly contributes to the activation of more areas on cerebral cortex. Classification result shows that multi-class stationary Tikhonov regularized CSP (Multi-sTRCSP) outperforms other two multi-class CSP methods, with the highest accuracy of 84% and mean accuracy of 70%.
Conclusions
The work implies that there exist the separable differences between simple limb motor imagery and compound limb motor imagery, which can be utilized to build a multimodal classification paradigm in motor imagery based brain-computer interface (BCI) systems.
doi:10.1186/1743-0003-10-106
PMCID: PMC3853015  PMID: 24119261
Compound limb motor imagery; Event-related desynchronization; Event-related spectral perturbation; Power spectral entropy; Spatial distribution coefficient; Common spatial patterns; Support vector machine
22.  Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening 
ACS chemical biology  2012;7(8):1377-1384.
Despite the urgent need for new antitubercular drugs, few are on the horizon. To combat the problem of emerging drug resistance, structurally unique chemical entities that inhibit new targets will be required. Here we describe our investigations using whole cell screening of a diverse collection of small molecules as a methodology for identifying novel inhibitors that target new pathways for Mycobacterium tuberculosis drug discovery. We find that conducting primary screens using model mycobacterial species may limit the potential for identifying new inhibitors with efficacy against M. tuberculosis. In addition, we confirm the importance of developing in vitro assay conditions that are reflective of in vivo biology for maximizing the proportion of hits from whole cell screening that are likely to have activity in vivo. Finally, we describe the identification and characterization of two novel inhibitors that target steps in M. tuberculosis cell wall biosynthesis. The first is a novel benzimidazole that targets mycobacterial membrane protein large 3 (MmpL3), a proposed transporter for cell wall mycolic acids. The second is a nitro-triazole that inhibits decaprenylphosphoryl-β-d-ribose 2′-epimerase (DprE1), an epimerase required for cell wall biosynthesis. These proteins are both among the small number of new targets that have been identified by forward chemical genetics using resistance generation coupled with genome sequencing. This suggests that methodologies currently employed for screening and target identification may lead to a bias in target discovery, and that alternative methods should be explored.
doi:10.1021/cb300151m
PMCID: PMC3560293  PMID: 22577943
23.  Urease Operon and Urease Activity in Commensal and Disease-Causing Nontypeable Haemophilus influenzae 
Journal of Clinical Microbiology  2013;51(2):653-655.
The ure operon was significantly more prevalent in Haemophilus influenzae isolates causing otitis media and chronic obstructive pulmonary disease (COPD)-associated bronchitis than in those from throats of healthy individuals (97% versus 78.1%, P < 0.001). Strains lacking the ure operon are over 8 times more likely to be from the throat than either otitis media or COPD isolates.
doi:10.1128/JCM.03145-12
PMCID: PMC3553914  PMID: 23224103
24.  Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates 
BMC Genomics  2013;14:484.
Background
Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disease. Clinical isolates of H. influenzae display extensive genomic diversity and plasticity. The development of strategies to successfully prevent, diagnose and treat H. influenzae infections depends on tools to ascertain the gene content of individual isolates.
Results
We describe and validate a Haemophilus influenzae supragenome hybridization (SGH) array that can be used to characterize the full genic complement of any strain within the species, as well as strains from several highly related species. The array contains 31,307 probes that collectively cover essentially all alleles of the 2890 gene clusters identified from the whole genome sequencing of 24 clinical H. influenzae strains. The finite supragenome model predicts that these data include greater than 85% of all non-rare genes (where rare genes are defined as those present in less than 10% of sequenced strains). The veracity of the array was tested by comparing the whole genome sequences of eight strains with their hybridization data obtained using the supragenome array. The array predictions were correct and reproducible for ~ 98% of the gene content of all of the sequenced strains. This technology was then applied to an investigation of the gene content of 193 geographically and clinically diverse H. influenzae clinical strains. These strains came from multiple locations from five different continents and Papua New Guinea and include isolates from: the middle ears of persons with otitis media and otorrhea; lung aspirates and sputum samples from pneumonia and COPD patients, blood specimens from patients with sepsis; cerebrospinal fluid from patients with meningitis, as well as from pharyngeal specimens from healthy persons.
Conclusions
These analyses provided the most comprehensive and detailed genomic/phylogenetic look at this species to date, and identified a subset of highly divergent strains that form a separate lineage within the species. This array provides a cost-effective and high-throughput tool to determine the gene content of any H. influenzae isolate or lineage. Furthermore, the method for probe selection can be applied to any species, given a group of available whole genome sequences.
doi:10.1186/1471-2164-14-484
PMCID: PMC3723446  PMID: 23865594
25.  Azole Susceptibility and Transcriptome Profiling in Candida albicans Mitochondrial Electron Transport Chain Complex I Mutants 
Mitochondrial dysfunction in pathogenic fungi or model yeast causes altered susceptibilities to antifungal drugs. Here we have characterized the role of mitochondrial complex I (CI) of Candida albicans in antifungal susceptibility. Inhibitors of CI to CV, except for CII, increased the susceptibility of both patient and lab isolates, even those with a resistance phenotype. In addition, in a C. albicans library of 12 CI null mutants, 10 displayed hypersusceptibility to fluconazole and were severely growth inhibited on glycerol, implying a role for each gene in cell respiration. We chose two other hypersusceptible null mutants of C. albicans, the goa1Δ and ndh51Δ mutants, for transcriptional profiling by RNA-Seq. Goa1p is required for CI activity, while Ndh51p is a CI subunit. RNA-Seq revealed that both the ndh51Δ mutant and especially the goa1Δ mutant had significant downregulation of transporter genes, including CDR1 and CDR2, which encode efflux proteins. In the goa1Δ mutant, we noted the downregulation of genes required for the biogenesis and replication of peroxisomes, as well as metabolic pathways assigned to peroxisomes such as β-oxidation of fatty acids, glyoxylate bypass, and acetyl coenzyme A (acetyl-CoA) transferases that are known to shuttle acetyl-CoA between peroxisomes and mitochondria. The transcriptome profile of the ndh51Δ mutant did not include downregulation of peroxisome genes but had, instead, extensive downregulation of the ergosterol synthesis gene family. Our data establish that cell energy is required for azole susceptibility and that downregulation of efflux genes may be an outcome of that dysfunction. However, there are mutant-specific changes that may also increase the susceptibility of both of these C. albicans mutants to azoles.
doi:10.1128/AAC.01520-12
PMCID: PMC3535965  PMID: 23147730

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