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2.  Crystal Structures of EF-G-Ribosome Complexes Trapped in Intermediate States of Translocation 
Science (New York, N.Y.)  2013;340(6140):1236086.
Translocation of mRNA and tRNA through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome·tRNA·mRNA·EF-G complexes trapped with GDPNP or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem-loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S rRNA that intercalate between bases of the mRNA may act as “pawls” of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.
doi:10.1126/science.1236086
PMCID: PMC3979973  PMID: 23812722
3.  Berberine Attenuates Axonal Transport Impairment and Axonopathy Induced by Calyculin A in N2a Cells 
PLoS ONE  2014;9(4):e93974.
Berberine is a primary component of the most functional extracts of Coptidis rhizome used in traditional Chinese medicine for centuries. Recent reports indicate that Berberine has the potential to prevent and treat Alzheimer's disease (AD). The previous studies reported that Calyculin A (CA) impaired the axonal transport in neuroblastoma-2a (N2a) cells. Berberine attenuated tau hyperphosphorylation and cytotoxicity induced by CA. Our study aimed at investigating the effects of Berberine on the axonal transport impairment induced by CA in N2a cells. The results showed that Berberine could protect the cell from CA -induced toxicity in metabolism and viability, as well as hyperphosphorylation of tau and neurofilaments (NFs). Furthermore, Berberine could reverse CA-induced axonal transport impairment significantly. Berberine also partially reversed the phosphorylation of the catalytic subunit of PP-2A at Tyrosine 307, a crucial site negatively regulating the activity of PP-2A, and reduced the levels of malondialdehyde and the activity of superoxide dismutase, markers of oxidative stress, induced by CA. The present work for the first time demonstrates that Berberine may play a role in protecting against CA-induced axonal transport impairment by modulating the activity of PP-2A and oxidative stress. Our findings also suggest that Berberine may be a potential therapeutic drug for AD.
doi:10.1371/journal.pone.0093974
PMCID: PMC3979860  PMID: 24713870
4.  Discovery of a super-strong promoter enables efficient production of heterologous proteins in cyanobacteria 
Scientific Reports  2014;4:4500.
Cyanobacteria are oxygenic photosynthetic prokaryotes that play important roles in the global carbon cycle. Recently, engineered cyanobacteria capable of producing various small molecules from CO2 have been developed. However, cyanobacteria are seldom considered as factories for producing proteins, mainly because of the lack of efficient strong promoters. Here, we report the discovery and verification of a super-strong promoter Pcpc560, which contains two predicted promoters and 14 predicted transcription factor binding sites (TFBSs). Using Pcpc560, functional proteins were produced at a level of up to 15% of total soluble protein in the cyanobacterium Synechocystis sp. 6803, a level comparable to that produced in Escherichia coli. We demonstrated that the presence of multiple TFBSs in Pcpc560 is crucial for its promoter strength. Genetically transformable cyanobacteria neither have endotoxins nor form inclusion bodies; therefore, Pcpc560 opens the possibility to use cyanobacteria as alternative hosts for producing heterogeneous proteins from CO2 and inorganic nutrients.
doi:10.1038/srep04500
PMCID: PMC3968457  PMID: 24675756
5.  Tumor-suppressive effects of CDK8 in endometrial cancer cells 
Cell Cycle  2013;12(6):987-999.
CDK8 is either amplified or mutated in a variety of human cancers, and CDK8 functions as an oncoprotein in melanoma and colorectal cancers. Previously, we reported that loss or reduction of CDK8 results in aberrant fat accumulation in Drosophila and mammals, suggesting that CDK8 plays an important role in inhibiting lipogenesis. Epidemiological studies have identified obesity and overweight as the major risk factors of endometrial cancer, thus we examined whether CDK8 regulates endometrial cancer cell growth by using several endometrial cancer cell lines, including KLE, which express low levels of CDK8, as well as AN3 CA and HEC-1A cells, which have high levels of endogenous CDK8. We observed that ectopic expression of CDK8 in KLE cells inhibited cell proliferation and potently blocked tumor growth in an in vivo mouse model. In addition, gain of CDK8 in KLE cells blocked cell migration and invasion in transwell, wound healing and persistence of migratory directionality assays. Conversely, we observed the opposite effects in all of the aforementioned assays when CDK8 was depleted in AN3 CA cells. Similar to AN3 CA cells, depletion of CDK8 in HEC-1A cells strongly enhanced cell migration in transwell assays, while overexpression of CDK8 in HEC-1A cells blocked cell migration. Furthermore, gene profiling of KLE cells overexpressing CDK8 revealed genes whose protein products are involved in lipid metabolism, cell cycle and cell movement pathways. Finally, depletion of CDK8 increased the expression of lipogenic genes in endometrial cancer cells. Taken together, these results show a reverse correlation between CDK8 levels and several key features of the endometrial cancer cells, including cell proliferation, migration and invasion as well as tumor formation in vivo. Therefore, in contrast to the oncogenic effects of CDK8 in melanoma and colorectal cancers, our results suggest that CDK8 plays a tumor-suppressive role in endometrial cancers.
doi:10.4161/cc.24003
PMCID: PMC3637357  PMID: 23454913
cyclin-dependent kinae 8 (CDK8); endometrial cancer; tumorigenesis; cell growth; cell migration
6.  RAGE gene three polymorphisms with Crohn's disease susceptibility in Chinese Han population 
AIM: To investigate the association of three polymorphisms in the receptor for advanced glycation end product (RAGE) gene with Crohn’s disease (CD) risk in a Chinese population.
METHODS: A hospital-based case-control association study involving 312 CD patients and 479 healthy controls was conducted. Peripheral blood samples were collected from 791 study subjects, and genomic DNA was extracted. Genotyping was performed using polymerase chain reaction-ligase detection reaction method. The association between polymorphic genotype and CD predisposition was determined using odds ratio and 95% confidence interval (CI). Data were analyzed using Haplo.stats program.
RESULTS: Significant differences were observed between patients and controls in allele/genotype distributions of rs1800624 (Pallele=0.012; Pgenotype=0.005) and in allele distributions of rs2070600 (P=0.02). The risk for CD associated with the rs1800624-A mutant allele decreased by 36% (95%CI: 0.47-0.88, P = 0.005) under the additive model and by 35% (95%CI: 0.46-0.91, P=0.013) under the dominant model. Carriers of rs2070600-A mutant allele showed a 37% (95%CI: 1.02-1.83, P=0.036) increased risk of developing CD relative to the GG genotype carriers. In haplotype analysis, haplotype T-A-G (in the order rs1800625, rs1800624, and rs2070600) decreased the odds of CD by 33% (95%CI: 0.49-0.94, P=0.018).
CONCLUSION: CD is an immune-related disease with genetic predisposition. Genetic defects in the RAGE gene are strongly associated with CD in Chinese population.
doi:10.3748/wjg.v20.i9.2397
PMCID: PMC3942844  PMID: 24605038
Receptor for advanced glycation end product; Polymorphism; Crohn’s diseases; Susceptibility; Association study
7.  Gene-Based Sequencing Identifies Lipid-Influencing Variants with Ethnicity-Specific Effects in African Americans 
PLoS Genetics  2014;10(3):e1004190.
Although a considerable proportion of serum lipids loci identified in European ancestry individuals (EA) replicate in African Americans (AA), interethnic differences in the distribution of serum lipids suggest that some genetic determinants differ by ethnicity. We conducted a comprehensive evaluation of five lipid candidate genes to identify variants with ethnicity-specific effects. We sequenced ABCA1, LCAT, LPL, PON1, and SERPINE1 in 48 AA individuals with extreme serum lipid concentrations (high HDLC/low TG or low HDLC/high TG). Identified variants were genotyped in the full population-based sample of AA (n = 1694) and tested for an association with serum lipids. rs328 (LPL) and correlated variants were associated with higher HDLC and lower TG. Interestingly, a stronger effect was observed on a “European” vs. “African” genetic background at this locus. To investigate this effect, we evaluated the region among West Africans (WA). For TG, the effect size among WA was the same in AA with only African local ancestry (2–3% lower TG), while the larger association among AA with local European ancestry matched previous reports in EA (10%). For HDLC, there was no association with rs328 in AA with only African local ancestry or in WA, while the association among AA with European local ancestry was much greater than what has been observed for EA (15 vs. ∼5 mg/dl), suggesting an interaction with an environmental or genetic factor that differs by ethnicity. Beyond this ancestry effect, the importance of African ancestry-focused, sequence-based work was also highlighted by serum lipid associations of variants that were in higher frequency (or present only) among those of African ancestry. By beginning our study with the sequence variation present in AA individuals, investigating local ancestry effects, and seeking replication in WA, we were able to comprehensively evaluate the role of a set of candidate genes in serum lipids in AA.
Author Summary
Most of the work on the genetic epidemiology of serum lipids in African Americans (AA) has focused on replicating findings that were identified in European ancestry individuals. While this can be very informative about the generalizability of lipids loci across populations, African ancestry-specific variation will be missed using this approach. Our aim was to comprehensively evaluate five lipid candidate genes in an AA population, from the identification of variants of interest to population-level analysis of high-density lipoprotein cholesterol (HDLC) and triglycerides (TG). We sequenced five genes in individuals with extreme lipids (n = 48) drawn from a population-based study of AA. The variants identified were genotyped in 1,694 AA and analyzed. Notable among the findings were the observation of ancestry specific effect for several variants in the LPL gene among these admixed individuals, with a greater effect observed among those with European ancestry in this region. These associations were further elucidated by replication in West Africans. By beginning with the sequence variation present among AA, investigating ancestry effects, and seeking replication in West Africans, we were able to comprehensively evaluate these candidate genes with a focus on African ancestry individuals.
doi:10.1371/journal.pgen.1004190
PMCID: PMC3945436  PMID: 24603370
8.  Identification of Serum microRNA Biomarkers for Tuberculosis Using RNA-seq 
PLoS ONE  2014;9(2):e88909.
Tuberculosis (TB) remains a significant human health issue. More effective biomarkers for use in tuberculosis prevention, diagnosis, and treatment, including markers that can discriminate between healthy individuals and those with latent infection, are urgently needed. To identify a set of such markers, we used Solexa sequencing to examine microRNA expression in the serum of patients with active disease, healthy individuals with latent TB, and those with or without prior BCG inoculation. We identified 24 microRNAs that are up-regulated (2.85–1285.93 fold) and 6 microRNAs that are down-regulated (0.003–0.11 fold) (P<0.05) in patients with active TB relative to the three groups of healthy controls. In addition, 75 microRNAs were up-regulated (2.05–2454.58 fold) and 11 were down-regulated (0.001–0.42 fold) (P<0.05) in latent-TB infected individuals relative to BCG- inoculated individuals. Of interest, 134 microRNAs were differentially-expressed in BCG-inoculated relative to un-inoculated individuals (18 up-regulated 2.9–499.29 fold, 116 down-regulated 0.0002–0.5 fold), providing insights into the effects of BCG inoculation at the microRNA level. Target prediction of differentially-expressed microRNAs by microRNA-Gene Network analysis and analysis of pathways affected suggest that regulation of the host immune system by microRNAs is likely to be one of the main factors in the pathogenesis of tuberculosis. qRT-PCR validation indicated that hsa-miR-196b and hsa-miR-376c have potential as markers for active TB disease. The microRNA differential-expression profiles generated in this study provide a good foundation for the development of markers for TB diagnosis, and for investigations on the role of microRNAs in BCG-inoculated and latent-infected individuals.
doi:10.1371/journal.pone.0088909
PMCID: PMC3930592  PMID: 24586438
9.  HLJ1 is a novel biomarker for colorectal carcinoma progression and overall patient survival 
The implication of HLJ1, a member of the heat shock protein-40 chaperone family, in colorectal carcinoma (CRC) remains unclear. The aim of this study was to determine the dynamic changes of HLJ1 in CRC both in vitro and in vivo, and the relationship between its level and the survival rate of CRC patients. Both real-time RT-PCR and Western blot were used to detect the expression of HLJ1 in CRC cells, while the distribution of HLJ1 in CRC and its adjacent normal mucosa tissues from CRC patients was determined with immunohistochemistry. Moreover, MTT and in vitro invasive assays were performed to determine the effect of HLJ1 overexpression on cell proliferation and invasion of CRC cells. The results indicated that in highly metastatic CRC cells, the HLJ1 expression was lower than that in lowly metastatic ones, and that the overexpression of HLJ1 significantly inhibited CRC cell proliferation and invasion in vitro. Interestingly, the HLJ1 expression was significantly down-regulated in CRC or lymphatic metastatic tissues from patient, compared to that in the normal mucosa (P<0.05), and the HLJ1 expression was correlated strongly with lymph metastasis, Dukes’ stage, and remote metastasis (P<0.05). Most surprisingly, patients with a higher HLJ1 level had a better overall survival rate, compared to that in patients with lower HLJ1 level (P<0.05). Based on all these findings, we conclude that HLJ1 is a strong tumor suppressor for CRC, and thus the down-regulation of the HLJ1 expression may be used as a biomarker to predict clinical outcome of patients with CRC.
PMCID: PMC3971299
HLJ1; colorectal carcinoma (CRC); biomarker; metastasis; survival rate
10.  Surveillance of a 2D Plane Area with 3D Deployed Cameras 
Sensors (Basel, Switzerland)  2014;14(2):1988-2011.
As the use of camera networks has expanded, camera placement to satisfy some quality assurance parameters (such as a good coverage ratio, an acceptable resolution constraints, an acceptable cost as low as possible, etc.) has become an important problem. The discrete camera deployment problem is NP-hard and many heuristic methods have been proposed to solve it, most of which make very simple assumptions. In this paper, we propose a probability inspired binary Particle Swarm Optimization (PI-BPSO) algorithm to solve a homogeneous camera network placement problem. We model the problem under some more realistic assumptions: (1) deploy the cameras in the 3D space while the surveillance area is restricted to a 2D ground plane; (2) deploy the minimal number of cameras to get a maximum visual coverage under more constraints, such as field of view (FOV) of the cameras and the minimum resolution constraints. We can simultaneously optimize the number and the configuration of the cameras through the introduction of a regulation item in the cost function. The simulation results showed the effectiveness of the proposed PI-BPSO algorithm.
doi:10.3390/s140201988
PMCID: PMC3958228  PMID: 24469353
camera network placement; coverage; particle swarm optimization (PSO); task constraints; camera constraints; scene constraints
11.  E3 Ubiquitin Ligase CHIP and NBR1-Mediated Selective Autophagy Protect Additively against Proteotoxicity in Plant Stress Responses 
PLoS Genetics  2014;10(1):e1004116.
Plant stress responses require both protective measures that reduce or restore stress-inflicted damage to cellular structures and mechanisms that efficiently remove damaged and toxic macromolecules, such as misfolded and damaged proteins. We have recently reported that NBR1, the first identified plant autophagy adaptor with a ubiquitin-association domain, plays a critical role in plant stress tolerance by targeting stress-induced, ubiquitinated protein aggregates for degradation by autophagy. Here we report a comprehensive genetic analysis of CHIP, a chaperone-associated E3 ubiquitin ligase from Arabidopsis thaliana implicated in mediating degradation of nonnative proteins by 26S proteasomes. We isolated two chip knockout mutants and discovered that they had the same phenotypes as the nbr1 mutants with compromised tolerance to heat, oxidative and salt stresses and increased accumulation of insoluble proteins under heat stress. To determine their functional interactions, we generated chip nbr1 double mutants and found them to be further compromised in stress tolerance and in clearance of stress-induced protein aggregates, indicating additive roles of CHIP and NBR1. Furthermore, stress-induced protein aggregates were still ubiquitinated in the chip mutants. Through proteomic profiling, we systemically identified heat-induced protein aggregates in the chip and nbr1 single and double mutants. These experiments revealed that highly aggregate-prone proteins such as Rubisco activase and catalases preferentially accumulated in the nbr1 mutant while a number of light-harvesting complex proteins accumulated at high levels in the chip mutant after a relatively short period of heat stress. With extended heat stress, aggregates for a large number of intracellular proteins accumulated in both chip and nbr1 mutants and, to a greater extent, in the chip nbr1 double mutant. Based on these results, we propose that CHIP and NBR1 mediate two distinct but complementary anti-proteotoxic pathways and protein's propensity to aggregate under stress conditions is one of the critical factors for pathway selection of protein degradation.
Author Summary
Environmental stresses such as heat cause generation of misfolded and damaged proteins, which are highly toxic and must be efficiently removed. In plants, NBR1, the first isolated autophagy receptor with an ubiquitin-association domain, plays a critical role in plant stress tolerance by targeting ubiquitinated protein aggregates under stress conditions for degradation by autophagy. To study how stress-induced misfolded and damaged proteins are detected and ubiquitinated in plant cells, we analyzed the chaperone-associated E3 ubiquitin ligase CHIP from Arabidopsis thaliana for its role in protection against proteotoxicity in plant stress responses. Disruption of Arabidopsis CHIP caused increased sensitivity to a spectrum of abiotic stresses as found in the Arabidopsis nbr1 mutants. Disruption of both Arabidopsis CHIP and NBR1 further compromised plant stress tolerance, indicating that their roles are additive. Furthermore, in the chip nbr1 double mutant, compromised heat tolerance was associated with increased accumulation of insoluble proteins derived mostly from heat-sensitive but biologically important proteins such as Rubisco activase, catalases and proteins required for protein synthesis and folding. Importantly, stress-induced protein aggregates were still highly ubiquitinated in the chip mutants. These results strongly suggest that CHIP and NBR1 function in two distinct but complementary anti-proteotoxic pathways in plant stress responses.
doi:10.1371/journal.pgen.1004116
PMCID: PMC3907298  PMID: 24497840
12.  Salvage Liver Transplantation for Recurrent Hepatocellular Carcinoma after Liver Resection: Retrospective Study of the Milan and Hangzhou Criteria 
PLoS ONE  2014;9(1):e87222.
Background
Salvage liver transplantation (SLT) has recently been proposed for recurrent hepatocellular carcinoma after liver resection; however, criteria for candidate assessment in SLT have not been thoroughly evaluated.
Methods and Findings
We retrospectively analyzed outcomes and factors affecting survival of 53 recipients who received SLT in the Liver Transplantation Center, The First Affiliated Hospital of Zhejiang University between 2004 and 2012. Thirty recipients fulfilled the Hangzhou criteria, of which 16 also fulfilled the Milan criteria, while the remaining 23 exceeded both criteria. The 1-year, 3-year and 5-year overall survival rates and tumor-free survival rates were both superior in patients fulfilling Milan or Hangzhou criteria compared with those exceeding the criteria. For recipients outside Milan criteria but within Hangzhou criteria, the 1-year, 3-year overall survival rates were 70.1%, 70.1%, similar to recipients within Milan criteria, with the 1-year, 3-year and 5-year overall survival of 93.8%%, 62.1% and 62.1% (P = 0.586). The tumor-free survival rates were also similar between these two subgroups, with 51.9% and 51.9% vs. 85.6%, 85.6% and 64.2% during the same time interval, respectively (P = 0.054). Cox regression analysis identified Hangzhou criteria (within vs. outside, hazard ratio (HR) 0.376) and diameter of the largest tumor (HR 3.523) to be independent predictors for overall survival. The only predictor for tumor-free survival was diameter of the largest tumor (HR 22.289).
Conclusions
Hangzhou criteria safely expanded the candidate pool and are feasible in assessment of candidates for SLT. This is helpful in donor liver allocation in transplant practice.
doi:10.1371/journal.pone.0087222
PMCID: PMC3903638  PMID: 24475255
13.  Specific Expression of DR5 Promoter in Rice Roots Using a tCUP Derived Promoter-Reporter System 
PLoS ONE  2014;9(1):e87008.
Variation of transgene expression caused by either position effect at the insertion site or the promoter/enhancer elements employed for the expression of selectable marker genes has complicated phenotype characterization and caused misinterpretation. We have developed a reporter system in rice to analyze the influence of vector configuration, spacer and selectable marker gene promoter on the expression of the promoterless GUS reporter and DR5 promoter. Our results indicate that a spacer inserted between the reversed 35S promoter and the GUS reporter could reduce leaky expression of the reporter but was unable to block the nonspecific expression of DR5::GUS. Stacking the selectable marker unit in head to tail with the GUS reporter aided the gene specific expression of the GUS reporter under the DR5 promoter even when the 35S promoter is used for expression of the selectable marker. Compared to 35S under this configuration, a quick and distinctive expression of DR5::GUS was observed in the root cap, quiescent center and xylem cells in the root apical meristem by using the tCUP derived promoter (tCUP1) for selection, that is similar to the pattern obtained by a sensitive DR5 variant (DR5rev) in Arabidopsis. These data suggest a conserved property of the tCUP promoter in preventing enhancer-promoter interactions in rice as it does in Arabidopsis, and also demonstrate that an analogous distal auxin maximum exists in roots of rice. Therefore, the tCUP promoter based selection system provides a new strategy for specific expression of transgenes in rice.
doi:10.1371/journal.pone.0087008
PMCID: PMC3899362  PMID: 24466314
14.  Vocal Emotion of Humanoid Robots: A Study from Brain Mechanism 
The Scientific World Journal  2014;2014:216341.
Driven by rapid ongoing advances in humanoid robot, increasing attention has been shifted into the issue of emotion intelligence of AI robots to facilitate the communication between man-machines and human beings, especially for the vocal emotion in interactive system of future humanoid robots. This paper explored the brain mechanism of vocal emotion by studying previous researches and developed an experiment to observe the brain response by fMRI, to analyze vocal emotion of human beings. Findings in this paper provided a new approach to design and evaluate the vocal emotion of humanoid robots based on brain mechanism of human beings.
doi:10.1155/2014/216341
PMCID: PMC3920811  PMID: 24587712
15.  Accuracy of 16/18G core needle biopsy for ultrasound-visible breast lesions 
Background
To assess the accuracy of ultrasound-guided 16G or 18G core needle biopsy (CNB) for ultrasound-visible breast lesions, and to analyze the effects of lesion features.
Methods
Between July 2005 and July 2012, 4,453 ultrasound-detected breast lesions underwent ultrasound-guided CNB and were retrospectively reviewed. Surgical excision was performed for 955 lesions (566 with 16G CNB and 389 with 18G CNB) which constitute the basis of the study. Histological findings were compared between the ultrasound-guided CNB and the surgical excision to determine sensitivity, false-negative rate, agreement rate, and underestimation rate, according to different lesion features.
Results
Final pathological results were malignant in 84.1% (invasive carcinoma, ductal carcinoma in situ, lymphoma, and metastases), high-risk in 8.4% (atypical lesions, papillary lesions, and phyllodes tumors), and benign in 7.5%. False-negative rates were 1.4% for 16G and 18G CNB. Agreement rates between histological findings of CNB and surgery were 92.4% for 16G and 92.8% for 18G CNB. Overall underestimate rates (high-risk CNB becoming malignant on surgery and ductal carcinoma in situ becoming invasive carcinoma) were 47.4% for 16G and 48.9% for 18G CNB. Agreements were better for mass lesions (16G: 92.7%; 18G: 93.7%) than for non-mass lesions (16G, 85.7%; 18G, 78.3%) (P <0.01). For mass lesions with a diameter ≤10 mm, the agreement rates (16G, 83.3%; 18G, 86.7%) were lower (P <0.01).
Conclusions
Ultrasound-guided 16G and 18G CNB are accurate for evaluating ultrasound-visible breast mass lesions with a diameter >10 mm.
doi:10.1186/1477-7819-12-7
PMCID: PMC3895748  PMID: 24400744
Breast; Beast cancer; Core needle biopsy; Surgical excision; Ultrasound
16.  Labour-Efficient In Vitro Lymphocyte Population Tracking and Fate Prediction Using Automation and Manual Review 
PLoS ONE  2014;9(1):e83251.
Interest in cell heterogeneity and differentiation has recently led to increased use of time-lapse microscopy. Previous studies have shown that cell fate may be determined well in advance of the event. We used a mixture of automation and manual review of time-lapse live cell imaging to track the positions, contours, divisions, deaths and lineage of 44 B-lymphocyte founders and their 631 progeny in vitro over a period of 108 hours. Using this data to train a Support Vector Machine classifier, we were retrospectively able to predict the fates of individual lymphocytes with more than 90% accuracy, using only time-lapse imaging captured prior to mitosis or death of 90% of all cells. The motivation for this paper is to explore the impact of labour-efficient assistive software tools that allow larger and more ambitious live-cell time-lapse microscopy studies. After training on this data, we show that machine learning methods can be used for realtime prediction of individual cell fates. These techniques could lead to realtime cell culture segregation for purposes such as phenotype screening. We were able to produce a large volume of data with less effort than previously reported, due to the image processing, computer vision, tracking and human-computer interaction tools used. We describe the workflow of the software-assisted experiments and the graphical interfaces that were needed. To validate our results we used our methods to reproduce a variety of published data about lymphocyte populations and behaviour. We also make all our data publicly available, including a large quantity of lymphocyte spatio-temporal dynamics and related lineage information.
doi:10.1371/journal.pone.0083251
PMCID: PMC3880260  PMID: 24404133
17.  Profiles of Serum Cytokines in Acute Drug-Induced Liver Injury and Their Prognostic Significance 
PLoS ONE  2013;8(12):e81974.
Drug-induced liver injury (DILI) is the most common cause of acute liver failure in the United-States. The aim of the study was to describe serum immune profiles associated with acute DILI, to investigate whether there are profiles associated with clinical features or types of DILI and/or with prognosis, and to assess temporal changes in levels. Twenty-seven immune analytes were measured in the sera of 78 DILI subjects in the Drug-Induced Liver Injury Network (DILIN) and compared with 40 healthy controls. Immune analytes (14 cytokines, 7 chemokines and 6 growth factors) were measured by BioPlex multiplex ELISA at DILI onset and after 6 months. A modeling process utilizing immune principles was used to select a final set of variables among 27 immune analytes and several additional clinical lab values for prediction of early death (within 6 months of DILI onset). Nineteen of the 27 immune analytes were differentially expressed among healthy control, DILI onset and 6-month cohorts. Disparate patterns of immune responses, especially innate and adaptive cellular (mostly TH17) immunity were evident. Low values of four immune analytes (IL-9, IL-17, PDGF-bb and RANTES) and serum albumin are predictive of early death [PPV = 88% (95% CI, 65%-100%), NPV = 97% (95% CI, 93%-100%), accuracy = 96% (95% CI, 92%-100%)].
Conclusions
Acute DILI is associated with robust and varying immune responses. High levels of expression of cytokines associated with innate immunity are associated with a poor prognosis, whereas high levels of expression of adaptive cytokines are associated with good long-term prognosis and eventual recovery. Serum immune analyte profiles at DILI onset appear to be of prognostic, and perhaps, diagnostic significance.
doi:10.1371/journal.pone.0081974
PMCID: PMC3873930  PMID: 24386086
18.  Association of ATP1B1, RGS5 and SELE polymorphisms with hypertension and blood pressure in African–Americans 
Journal of hypertension  2011;29(10):10.1097/HJH.0b013e32834b000d.
Objective
Although an increasing number of hypertension-associated genetic variants is being reported, replication of these findings in independent studies has been challenging. Several genes in a human chromosome 1q linkage region have been reported to be associated with hypertension. We examined polymorphisms in three of these genes (ATP1B1, RGS5 and SELE) in relation to hypertension and blood pressure in a cohort of African–Americans.
Methods
We genotyped 87 single nucleotide polymorphisms (SNPs) from the ATP1B1, RGS5 and SELE genes in a well characterized cohort of 968 African–Americans and performed a case–control study to identify susceptibility alleles for hypertension and blood pressure regulation. Single SNP and haplotype association testing was done under an additive genetic model with adjustment for age, sex, BMI and ancestry-by-genotype (principal components).
Results
A total of 12 SNPs showed nominal association with hypertension and/or blood pressure. The strongest signal for hypertension was for rs2815272 in the RGS5 gene (P = 9.3 × 10–3). For SBP, rs3917420 in the SELE gene (P = 9.0 × 10–4) and rs4657251 in the RGS5 gene (P = 9.7 × 10–3) were the top hits. Effect size for each of these variants was approximately 2–3 mmHg. A five-SNP haplotype in the SELE gene also showed significant association with SBP after correction for multiple testing (P < 0.01).
Conclusion
These findings provide additional support for the genetic role of ATP1B1, RGS5 and SELE in hypertension and blood pressure regulation.
doi:10.1097/HJH.0b013e32834b000d
PMCID: PMC3862027  PMID: 21881522
African–Americans; candidate gene; haplotype; hypertension; single nucleotide polymorphism
19.  RBOH1-dependent H2O2 production and subsequent activation of MPK1/2 play an important role in acclimation-induced cross-tolerance in tomato 
Journal of Experimental Botany  2013;65(2):595-607.
H2O2 and mitogen-activated protein kinase (MAPK) cascades play important functions in plant stress responses, but their roles in acclimation response remain unclear. This study examined the functions of H2O2 and MPK1/2 in acclimation-induced cross-tolerance in tomato plants. Mild cold, paraquat, and drought as acclimation stimuli enhanced tolerance to more severe subsequent chilling, photooxidative, and drought stresses. Acclimation-induced cross-tolerance was associated with increased transcript levels of RBOH1 and stress- and defence-related genes, elevated apoplastic H2O2 accumulation, increased activity of NADPH oxidase and antioxidant enzymes, reduced glutathione redox state, and activation of MPK1/2 in tomato. Virus-induced gene silencing of RBOH1, MPK1, and MPK2 or MPK1/2 all compromised acclimation-induced cross-tolerance and associated stress responses. Taken together, these results strongly suggest that acclimation-induced cross-tolerance is largely attributed to RBOH1-dependent H2O2 production at the apoplast, which may subsequently activate MPK1/2 to induce stress responses.
doi:10.1093/jxb/ert404
PMCID: PMC3904713  PMID: 24323505
Cross-tolerance; hydrogen peroxide; mitogen-activated protein kinase; reactive oxygen species; Respiratory burst oxidase homologue 1; signal transduction; Solanum lycopersicum.
20.  Receptor binding and transmission studies of H5N1 influenza virus in mammals 
The H5N1 influenza A virus that is currently circulating in Asia, Africa and Europe has resulted in persistent outbreaks in poultry with sporadic transmission to humans. Thus far, it is believed that H5N1 does not possess sufficient ability for human-to-human transmission and subsequent pandemic infection. Both receptor binding specificity and virus infectivity are key factors in determining whether influenza A virus becomes pandemic. The use of human viral isolates in various studies has helped to illustrate the changes in receptor binding specificity and virulence as a result of adaptation in humans. In this review, we highlight the important amino acids and domains of viral proteins related to receptor binding specificity that have been reported for humans and avians using mammalian models. Thus, this review will consolidate findings from studies that have shed light on the receptor binding and transmission characteristics of the H5N1 influenza virus, with the goal of improving our ability to predict the transmission efficiency or pandemic potential of new viral strains.
doi:10.1038/emi.2013.89
PMCID: PMC3880874
receptor binding; transmission; H5N1; mammal; influenza A virus
21.  How Affectively-Based and Cognitively-Based Attitudes Drive Intergroup Behaviours: The Moderating Role of Affective-Cognitive Consistency  
PLoS ONE  2013;8(11):e82150.
The moderating role of affective-cognitive consistency in the effects of affectively-based and cognitively-based attitudes on consummatory and instrumental behaviors was explored using two experimental studies in the intergroup context. Study 1 revealed that affectively-based attitudes were better predictors than cognitively-based attitudes regardless of affective-cognitive consistency for consummatory behaviors (e.g., undergraduates’ supportive behaviors toward government officials). Study 2, which investigated task groups’ supportive behaviors toward an immediate supervisory group, found that for these instrumental behaviors cognitively-based attitudes were better predictors than affectively-based attitudes only when affective-cognitive consistency was high. The present research also examined the mechanism by which affective-cognitive consistency moderates the relative roles of affectively-based and cognitively-based attitudes in attitude-behavior consistency. Results indicated that attitude-behavior consistency is eroded primarily because of the weaker relationship of affective or cognitive components to behaviors than to general attitudes. The reciprocal implications of research on attitudes and work on intergroup relations are considered.
doi:10.1371/journal.pone.0082150
PMCID: PMC3828264  PMID: 24244751
22.  Responses of Populus trichocarpa galactinol synthase genes to abiotic stresses 
Journal of Plant Research  2013;127:347-358.
Galactinol synthase (GolS; EC 2.4.1.123) is a member of the glycosyltransferase eight family that catalyzes the first step in the biosynthesis pathway of the raffinose family of oligosaccharides (RFOs). The accumulation of RFOs in response to abiotic stress indicates a role for RFOs in stress adaptation. To obtain information on the roles of RFOs in abiotic stress adaptation in trees, we investigated the expression patterns of nine Populus trichocarpaGolS (PtrGolS) genes with special reference to stress responses. PtrGolS genes were differentially expressed in different organs, and the expressions of PtrGolS4 and PtrGolS6 were relatively high in all tested organs. The expression levels of all PtrGolS genes, except PtrGolS9, changed in response to abiotic stress in gene- and stress-type-specific manners. Moreover, short- and long-term stress treatments revealed that induction of PtrGolS by salt stress is obvious only in the early period of treatment (within 24 h), whereas water-deficit stress treatments continued to upregulate PtrGolS gene expression after two days of treatment, in addition to induction within 24 h of treatment. Consistent with these expression patterns, the galactinol content in leaves increased after four days of drought stress, but not under salt stress. Our findings suggest divergent roles for PtrGolS genes in abiotic stress responses in poplars.
Electronic supplementary material
The online version of this article (doi:10.1007/s10265-013-0597-8) contains supplementary material, which is available to authorized users.
doi:10.1007/s10265-013-0597-8
PMCID: PMC3932401  PMID: 24190064
Galactinol synthase; PtrGolS; Populus; RFO; Abiotic stress
23.  Genome-wide association study identifies novel loci association with fasting insulin and insulin resistance in African Americans 
Human Molecular Genetics  2012;21(20):4530-4536.
Insulin resistance (IR) is a key determinant of type 2 diabetes (T2D) and other metabolic disorders. This genome-wide association study (GWAS) was designed to shed light on the genetic basis of fasting insulin (FI) and IR in 927 non-diabetic African Americans. 5 396 838 single-nucleotide polymorphisms (SNPs) were tested for associations with FI or IR with adjustments for age, sex, body mass index, hypertension status and first two principal components. Genotyped SNPs (n = 12) with P < 5 × 10−6 in African Americans were carried forward for de novo genotyping in 570 non-diabetic West Africans. We replicated SNPs in or near SC4MOL and TCERG1L in West Africans. The meta-analysis of 1497 African Americans and West Africans yielded genome-wide significant associations for SNPs in the SC4MOL gene: rs17046216 (P = 1.7 × 10−8 and 2.9 × 10−8 for FI and IR, respectively); and near the TCERG1L gene with rs7077836 as the top scoring (P = 7.5 × 10−9 and 4.9 × 10−10 for FI and IR, respectively). In silico replication in the MAGIC study (n = 37 037) showed weak but significant association (adjusted P-value of 0.0097) for rs34602777 in the MYO5A gene. In addition, we replicated previous GWAS findings for IR and FI in Europeans for GCKR, and for variants in four T2D loci (FTO, IRS1, KLF14 and PPARG) which exert their action via IR. In summary, variants in/near SC4MOL, and TCERG1L were associated with FI and IR in this cohort of African Americans and were replicated in West Africans. SC4MOL is under-expressed in an animal model of T2D and plays a key role in lipid biosynthesis, with implications for the regulation of energy metabolism, obesity and dyslipidemia. TCERG1L is associated with plasma adiponectin, a key modulator of obesity, inflammation, IR and diabetes.
doi:10.1093/hmg/dds282
PMCID: PMC3459464  PMID: 22791750
24.  BIOCAT: a pattern recognition platform for customizable biological image classification and annotation 
BMC Bioinformatics  2013;14:291.
Background
Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effective and efficient image classification and annotation for the ever-increasing microscopic images, it is desirable to have tools that can combine and compare various algorithms, and build customizable solution for different biological problems. However, current tools often offer a limited solution in generating user-friendly and extensible tools for annotating higher dimensional images that correspond to multiple complicated categories.
Results
We develop the BIOimage Classification and Annotation Tool (BIOCAT). It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and annotation. We also propose a 3D anisotropic wavelet feature extractor for extracting textural features from 3D images with xy-z resolution disparity. The extractor is one of the about 20 built-in algorithms of feature extractors, selectors and classifiers in BIOCAT. The algorithms are modularized so that they can be “chained” in a customizable way to form adaptive solution for various problems, and the plugin-based extensibility gives the tool an open architecture to incorporate future algorithms. We have applied BIOCAT to classification and annotation of images and ROIs of different properties with applications in cell biology and neuroscience.
Conclusions
BIOCAT provides a user-friendly, portable platform for pattern recognition based biological image classification of two- and three- dimensional images and ROIs. We show, via diverse case studies, that different algorithms and their combinations have different suitability for various problems. The customizability of BIOCAT is thus expected to be useful for providing effective and efficient solutions for a variety of biological problems involving image classification and annotation. We also demonstrate the effectiveness of 3D anisotropic wavelet in classifying both 3D image sets and ROIs.
doi:10.1186/1471-2105-14-291
PMCID: PMC3854450  PMID: 24090164
25.  Detection of Urinary Metabolomics before and after Pringle Maneuver-Induced Liver Ischemia and Reperfusion Injury in Rats Using Gas Chromatography-Mass Spectrometry 
Disease markers  2013;35(5):345-351.
Background. Metabolomics studies can quantitatively detect the dynamic metabolic response of living systems. Objective. To detect urinary metabolomics after hepatic ischemia/reperfusion (I/R) injury induced by the Pringle maneuver using gas chromatography-mass spectrometry (GC-MS). Methods. Male Sprague-Dawley rats (N = 80) were randomly divided into 4 groups (n = 20/group): sham operation, day 1, day 3, and day 5. Rats in the day 1, day 3, and day 5 groups underwent the Pringle maneuver. Serum alanine transaminase (ALT) and total bilirubin (TBIL) were measured, and hematoxylin and eosin (HE) staining of the liver tissue was performed. GC-MS was used to detect urinary metabolomics. Results. Compared with the sham group, the serum ALT and TBIL levels at day 1 were significantly elevated (P < 0.01) and then decreased and reached close to normal levels at day 5. GC-MS detected 7 metabolites which had similar changes as those of liver tissue revealed by histological examination. Significant differences in lactic acid, pyruvic acid, alanine, serine, and glycerol-3-phosphate were found among the groups (P < 0.001). Principle component analysis showed that 7 metabolites distinguished the day 1 and day 3 groups from the sham group. Conclusions. Noninvasive urinary metabolomic analysis is a potential means for the early detection and diagnosis of hepatic I/R injury.
doi:10.1155/2013/792391
PMCID: PMC3794546  PMID: 24191128

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