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1.  Chinese and Australians showed difference in mental time travel in emotion and content but not specificity 
Mental time travel refers to the ability to recall episodic past and imagine future events. The present study aimed to investigate cultural differences in mental time travel between Chinese and Australian university students. A total of 231 students (108 Chinese and 123 Australians) participated in the study. Their mental time travel abilities were measured by the Sentence Completion for Events from the Past Test (SCEPT) and the Sentence Completion for Events in the Future Test (SCEFT). Results showed that there were no cultural differences in the number of specific events generated for the past or future. Significant differences between the Chinese and Australian participants were found mainly in the emotional valence and content of the events generated. Both Chinese and Australian participants generated more specific positive events compared to negative events when thinking about the future and Chinese participants were more positive about their past than Australian participants when recalling specific events. For content, Chinese participants recalled more events about their interpersonal relationships, while Australian participants imagined more about personal future achievements. These findings shed some lights on cultural differences in episodic past and future thinking.
doi:10.3389/fpsyg.2015.00879
PMCID: PMC4481147  PMID: 26167154
cultural differences; future thinking; mental time travel; autobiographical memory; Chinese; Australian
2.  Genetic Basis of a Cognitive Complexity Metric 
PLoS ONE  2015;10(4):e0123886.
Relational complexity (RC) is a metric reflecting capacity limitation in relational processing. It plays a crucial role in higher cognitive processes and is an endophenotype for several disorders. However, the genetic underpinnings of complex relational processing have not been investigated. Using the classical twin model, we estimated the heritability of RC and genetic overlap with intelligence (IQ), reasoning, and working memory in a twin and sibling sample aged 15-29 years (N = 787). Further, in an exploratory search for genetic loci contributing to RC, we examined associated genetic markers and genes in our Discovery sample and selected loci for replication in four independent samples (ALSPAC, LBC1936, NTR, NCNG), followed by meta-analysis (N>6500) at the single marker level. Twin modelling showed RC is highly heritable (67%), has considerable genetic overlap with IQ (59%), and is a major component of genetic covariation between reasoning and working memory (72%). At the molecular level, we found preliminary support for four single-marker loci (one in the gene DGKB), and at a gene-based level for the NPS gene, having influence on cognition. These results indicate that genetic sources influencing relational processing are a key component of the genetic architecture of broader cognitive abilities. Further, they suggest a genetic cascade, whereby genetic factors influencing capacity limitation in relational processing have a flow-on effect to more complex cognitive traits, including reasoning and working memory, and ultimately, IQ.
doi:10.1371/journal.pone.0123886
PMCID: PMC4393228  PMID: 25860228
3.  Foot Massage and Physiological Stress in People with Dementia: A Randomized Controlled Trial 
Abstract
Background: The anxiety associated with unfamiliar surroundings, the disorientation and mental confusion, and the social isolation that accompanies dementia can often create increased stress for people living in long-term care settings. Such a response is thought to affect the autonomic nervous system and result in emotional and physical symptoms of distress that may be manifested as agitation. There is the potential for such distress to influence the physiological response and in particular Blood Pressure and Heart Rate. A relaxation intervention such as massage may influence the physiological stress response.
Methods: This randomized controlled trial aimed to compare the effect of foot massage (FM) versus a control activity (quiet presence, QP) on physiological stress response (i.e., blood pressure [BP] and heart rate [HR]) in people living with moderate-to-severe dementia in long-term-care settings.
Results: Fifty-three residents were randomized to intervention (10-minute FM) or control group (QP). While the FM group experienced a greater reduction in HR than the control group, these reductions were not significantly different between groups (p=0.83; see Table 1), or across time (p=0.46). Both groups experienced a reduction in systolic BP and diastolic BP, while the mean reduction in systolic BP was greater for those in the FM group.
Conclusions: While the findings do not provide strong support for FM, the finding that both conditions allowed the person with dementia to rest in the presence of another human being is of importance in the care of people with dementia. The close presence of another person may in fact promote relaxation and therefore improve BP and HR measures.
doi:10.1089/acm.2013.0177
PMCID: PMC3994911  PMID: 24047244
4.  Revisiting the therapeutic effect of rTMS on negative symptoms in schizophrenia: A meta-analysis 
Psychiatry research  2013;215(3):505-513.
This study sought to determine the moderators in the treatment effect of repetitive transcranial magnetic stimulation (rTMS) on negative symptoms in schizophrenia. We performed a meta-analysis of prospective studies on the therapeutic application of rTMS in schizophrenia assessing the effects of both low-frequency and high-frequency rTMS on negative symptoms. Results indicate that rTMS is effective in alleviating negative symptoms in schizophrenia. The effect size was moderate (0.63 and 0.53, respectively). The effect size of rTMS on negative symptoms in sham-controlled trials was 0.80 as measured by the SANS and 0.41 as measured by the PANSS. A longer duration of illness was associated with poorer efficacy of rTMS on negative symptoms. A 10 Hz setting, at least 3 consecutive weeks of treatment, treatment site at the left dorsolateral prefrontal cortex (DLPFC) and a 110% motor threshold (MT) were found to be the best rTMS parameters for the treatment of negative symptoms. The results of our meta-analysis suggest that rTMS is an effective treatment option for negative symptoms in schizophrenia. The moderators of rTMS on negative symptoms included duration of illness, stimulus frequency, duration of illness, position and intensity of treatment as well as the type of outcome measures used.
doi:10.1016/j.psychres.2013.12.019
PMCID: PMC4127383  PMID: 24411074
Negative symptoms; Repetitive transcranial magnetic stimulation; Schizophrenia; Intervention; Meta-analysis
5.  Feasibility and Utility of Telephone-Based Psychological Support for People with Brain Tumor: A Single-Case Experimental Study 
Rates of psychological distress are high following diagnosis and treatment of brain tumor. There can be multiple barriers to accessing psychological support, including physical and cognitive impairments and geographical limitations. Tele-based support could provide an effective and more flexible option for delivering psychological interventions. The present study aimed to investigate the feasibility and utility of a telephone-based psychotherapy intervention for people with brain tumor. A single-case multiple-baseline design was employed with a 4–7-week baseline phase, 10-week treatment phase, and 5-week maintenance phase including a booster session. Four participants with a benign or malignant brain tumor (three males and one female; aged 34–49 years), received 10 sessions of tele-based therapy and a booster session at 4 weeks post-treatment. Levels of depression, anxiety, and illness cognitions were monitored on a weekly basis throughout each phase whilst measures of quality of life, stress, and self-concept were administered at the start and end of each phase. Weekly measures were analyzed using a combination of both visual analysis and Tau-U statistics. Of the four participants, two of them demonstrated significant gains in mental health (depression and/or anxiety) and a significant decrease in their levels of helplessness (p < 0.05). The other two participants did not show gains in mental health or change in illness cognitions. All participants reported improvement in quality of life post-treatment. The results of the study provide preliminary support concerning the feasibility and utility of tele-based therapy for some people with brain tumor. Further research examining factors influencing the outcomes of tele-based psychological support is needed.
doi:10.3389/fonc.2015.00071
PMCID: PMC4374457  PMID: 25859430
neuro-oncology; brain tumor; psychological distress; psychotherapy; telephone-based support; counseling
6.  Dimensional schizotypy and social cognition: an fMRI imaging study 
Impairment in empathy has been demonstrated in patients with schizophrenia and individuals with psychosis proneness. In the present study, we examined the neural correlates underlying theory of mind (ToM) and empathy and the relationships between these two social cognitive abilities with schizotypy. Fifty-six first-year college students (31 males, 25 females) between 17 and 21 years of age (M = 19.3, SD = 0.9) from a medical university in China participated. All participants undertook a comic strips functional imaging task that specifically examined both empathy and ToM. In addition, they completed two self-report scales: the Chapman Psychosis Proneness scale and the Interpersonal Responsivity Index (IRI). Results showed that both empathy and ToM conditions of the task were associated with brain activity in the middle temporal gyrus, the temporo-parietal junction (TPJ), the precuneus and the posterior cingulate gyrus. In addition, we found positive correlations between negative schizotypy and brain activity in regions involved in social cognition, namely, the middle temporal gyrus, the TPJ, as well as the medial prefrontal gyrus. These findings highlight that different dimensions of schizotypy may show different associations with brain regions involved in social cognitive abilities. More importantly, the positive correlation between brain activity and anhedonia suggests the presence of compensatory mechanisms in high-risk populations.
doi:10.3389/fnbeh.2015.00133
PMCID: PMC4444828  PMID: 26074796
schizotypy; theory of mind; empathy; fMRI; anhedonia
7.  The development of prospective memory across adolescence: an event-related potential analysis 
Prospective memory (PM) is an important cognitive function vital for day-to-day functioning. Although there has been extensive research into the decline of PM in older adulthood, little is known about its developmental trajectory throughout adolescence, a time of important brain maturation. In the present study, the development of PM was examined in 85 participants across the following groups: 12 to 13-year-olds (n = 19), 14 to 15-year-olds (n = 21), 16 to 17-year-olds (n = 19), and 18 to 19-year-olds (n = 26). A 30-cue (30 min) event-based PM task (with font-color stimuli as PM cues and a lexical-decision task as the ongoing task) was used while recording Event-Related Potentials (ERPs). The well-established neural correlates of PM, the N300 and parietal positivity, were examined across the age groups. In addition, hierarchical multiple regressions were used to examine the unique contribution of executive functioning measures (viz., the Self-Ordered Pointing Task [SOPT], the Stroop task, and Trail Making Test [TMT]) on the ERP components of PM (after controlling for age). First, the established components of ERPs associated with prospective remembering (i.e., N300 and parietal positivity) were detected for each age group. Second, although there were no significant age- group differences on the amplitude of the N300, the amplitude of the parietal positivity was found to be different between the 12 to 13-year-olds and 18 to 19-year-olds (viz., the 12 to 13-year-olds had the highest amplitude). Third, for the contribution of executive functioning measures on the amplitude of the ERP components of PM, the regression on the N300 was not significant, however, the SOPT beta weights were significant predictors of the amplitude of the parietal positivity. This relationship was found to be specific for the central and right electrode region. These findings are discussed within the context of brain development and executive functioning along with particular task demands, which may contribute to age-related PM differences across adolescence. Moreover, the findings suggest that cognitive processes associated with parietal positivity may continue to develop across adolescence.
doi:10.3389/fnhum.2015.00362
PMCID: PMC4475796  PMID: 26157379
prospective memory; adolescence; ERPs; executive functioning; cognitive development
8.  A Meta-Analysis of Cognitive Impairment and Decline Associated with Adjuvant Chemotherapy in Women with Breast Cancer 
A meta-analysis was performed to quantify the magnitude and nature of the association between adjuvant chemotherapy and performance on a range of cognitive domains among breast cancer patients. A total of 27 studies (14 cross-sectional, 8 both cross-sectional and prospective, and 5 prospective) were included in the analyses, involving 1562 breast cancer patients who had undergone adjuvant chemotherapy and 2799 controls that included breast cancer patients who did not receive adjuvant chemotherapy. A total of 737 effect sizes (Cohen’s d) were calculated for cross-sectional and prospective longitudinal studies separately and classified into eight cognitive domains. The mean effect sizes varied across cross-sectional and prospective longitudinal studies (ranging from −1.12 to 0.62 and −0.29 to 1.12, respectively). Each cognitive domain produced small effect sizes for cross-sectional and prospective longitudinal studies (ranging from −0.25 to 0.41). Results from cross-sectional studies indicated a significant association between adjuvant chemotherapy and cognitive impairment that held across studies with varied methodological approaches. For prospective studies, results generally indicated that cognitive functioning improved over time after receiving adjuvant chemotherapy. Greater cognitive impairment was reported in cross-sectional studies comparing chemotherapy groups with healthy control groups. Results suggested that cognitive impairment is present among breast cancer patients irrespective of a history of chemotherapy. Prospective longitudinal research is warranted to examine the degree and persisting nature of cognitive impairment present both before and after chemotherapy, with comparisons made to participants’ cognitive function prior to diagnosis. Accurate understanding of the effects of chemotherapy is essential to enable informed decisions regarding treatment and to improve quality of life among breast cancer patients.
doi:10.3389/fonc.2015.00059
PMCID: PMC4354286  PMID: 25806355
breast cancer; adjuvant chemotherapy; meta-analysis; cognitive functioning; moderators
9.  Neuropsychological Assessment of Individuals with Brain Tumor: Comparison of Approaches Used in the Classification of Impairment 
Approaches to classifying neuropsychological impairment after brain tumor vary according to testing level (individual tests, domains, or global index) and source of reference (i.e., norms, controls, and pre-morbid functioning). This study aimed to compare rates of impairment according to different classification approaches. Participants were 44 individuals (57% female) with a primary brain tumor diagnosis (mean age = 45.6 years) and 44 matched control participants (59% female, mean age = 44.5 years). All participants completed a test battery that assesses pre-morbid IQ (Wechsler adult reading test), attention/processing speed (digit span, trail making test A), memory (Hopkins verbal learning test-revised, Rey–Osterrieth complex figure-recall), and executive function (trail making test B, Rey–Osterrieth complex figure copy, controlled oral word association test). Results indicated that across the different sources of reference, 86–93% of participants were classified as impaired at a test-specific level, 61–73% were classified as impaired at a domain-specific level, and 32–50% were classified as impaired at a global level. Rates of impairment did not significantly differ according to source of reference (p > 0.05); however, at the individual participant level, classification based on estimated pre-morbid IQ was often inconsistent with classification based on the norms or controls. Participants with brain tumor performed significantly poorer than matched controls on tests of neuropsychological functioning, including executive function (p = 0.001) and memory (p < 0.001), but not attention/processing speed (p > 0.05). These results highlight the need to examine individuals’ performance across a multi-faceted neuropsychological test battery to avoid over- or under-estimation of impairment.
doi:10.3389/fonc.2015.00056
PMCID: PMC4356068  PMID: 25815271
cancer; oncology; neoplasm; brain tumor; neuropsychological impairment; assessment
10.  Prospective Memory Performance in Non-Psychotic First-Degree Relatives of Patients with Schizophrenia: A Controlled Study 
PLoS ONE  2014;9(11):e111562.
Objective
We aimed at investigating prospective memory and its socio-demographic and neurocognitive correlates in non-psychotic, first-degree relatives (FDRs) of patients with schizophrenia compared to patients with first episode schizophrenia (FES), and healthy controls (HCs).
Methods
Forty-seven FES patients, 50 non-psychotic FDRs (23 offspring and 27 siblings) of patients with chronic schizophrenia (unrelated to the FES group) and 51 HCs were studied. The Chinese version of the Cambridge Prospective Memory Test (C-CAMPROMPT) was used to measure time-based prospective memory (TBPM) and event-based prospective memory (EBPM) performance. Other cognitive functions (involving respective memory and executive functions) were evaluated with standardized tests.
Results
After controlling for basic demographic characteristics including age, gender and educational level, there was a significant difference between FDRs, FES and HCs with respect to both TBPM (F(2,142) = 10.4, p<0.001) and EBPM (F(2,142) = 10.8, p<0.001). Multiple linear regression analyses revealed that lower scores of the Hopkins Verbal Learning Test-Revised (HVLT-R) and the STROOP Word-Color Test (SWCT) contributed to TBPM impairment, while lower educational level and higher scores of the Color Trails Test-2 (CTT-2) contributed to EBPM deficit in FDRs.
Conclusions
FDRs share similar but attenuated prospective memory impairments with schizophrenia patients, suggesting that prospective memory deficits may represent an endophenotype of schizophrenia.
doi:10.1371/journal.pone.0111562
PMCID: PMC4218767  PMID: 25365028
11.  Inhibition of Dengue Virus Replication by a Class of Small-Molecule Compounds That Antagonize Dopamine Receptor D4 and Downstream Mitogen-Activated Protein Kinase Signaling 
Journal of Virology  2014;88(10):5533-5542.
ABSTRACT
Dengue viruses (DENV) are endemic pathogens of tropical and subtropical regions that cause significant morbidity and mortality worldwide. To date, no vaccines or antiviral therapeutics have been approved for combating DENV-associated disease. In this paper, we describe a class of tricyclic small-molecule compounds—dihydrodibenzothiepines (DHBTs), identified through high-throughput screening—with potent inhibitory activity against DENV serotype 2. SKI-417616, a highly active representative of this class, displayed activity against all four serotypes of DENV, as well as against a related flavivirus, West Nile virus (WNV), and an alphavirus, Sindbis virus (SINV). This compound was characterized to determine its mechanism of antiviral activity. Investigation of the stage of the viral life cycle affected revealed that an early event in the life cycle is inhibited. Due to the structural similarity of the DHBTs to known antagonists of the dopamine and serotonin receptors, we explored the roles of two of these receptors, serotonin receptor 2A (5HTR2A) and the D4 dopamine receptor (DRD4), in DENV infection. Antagonism of DRD4 and subsequent downstream phosphorylation of epidermal growth factor receptor (EGFR)-related kinase (ERK) were found to impact DENV infection negatively, and blockade of signaling through this network was confirmed as the mechanism of anti-DENV activity for this class of compounds.
IMPORTANCE The dengue viruses are mosquito-borne, reemerging human pathogens that are the etiological agents of a spectrum of febrile diseases. Currently, there are no approved therapeutic treatments for dengue-associated disease, nor is there a vaccine. This study identifies a small molecule, SKI-417616, with potent anti-dengue virus activity. Further analysis revealed that SKI-417616 acts through antagonism of the host cell dopamine D4 receptor and subsequent repression of the ERK phosphorylation pathway. These results suggest that SKI-417616, or other compounds targeting the same cellular pathways, may have therapeutic potential for the treatment of dengue virus infections.
doi:10.1128/JVI.00365-14
PMCID: PMC4019099  PMID: 24599995
12.  Plasmid-based shRNA lentiviral particle production for RNAi applications 
Journal of biomolecular screening  2014;19(9):1309-1313.
Lentiviral vectors have become mainstream gene transfer vehicles for their ability to delivery and integrate into host cells. In RNA interference (RNAi) applications, lentiviral constructs constitutively express dsRNA molecules usually as short hairpin RNA (shRNA) enabling long-term gene silencing and when pseudotyped with a broad host glycoprotein envelope; allows a multitude of cell types to be transduced. Their successful use ultimately relies on the production of lentiviral particles in high-titer and uniformity. Typical methods require the transfection of three or more plasmids in which essential viral elements have been encoded separated so as to remain replication deficient. These transfection procedures are of critical importance; however, methods often vary among laboratories making it difficult to assess the overall efficiency of lentiviral particle production. In this report, we focused exclusively on this step and compared the overall impact of the commercial transfection reagent FuGENE 6 to FuGENE HD. We found that FuGENE HD resulted in at least 5-fold improvement in viral particle titer as assessed by the p24 standard ELISA assay. We present the complete optimized workflow and demonstrate this utility in which a single modification of this transfection step improved the lentiviral particle production.
doi:10.1177/1087057114539390
PMCID: PMC4170048  PMID: 24939963
shRNA; FuGENE 6; FuGENE HD; RNAi; lentiviral particles; viral titer; plasmid; DNA
13.  A 1536-well Fluorescence Polarization Assay to Screen for Modulators of the MUSASHI Family of RNA-Binding Proteins 
RNA-binding proteins (RBPs) can act as stem cell modulators and oncogenic drivers, but have been largely ignored by the pharmaceutical industry as potential therapeutic targets for cancer. The MUSASHI (MSI) family has recently been demonstrated to be an attractive clinical target in the most aggressive cancers. Therefore, the discovery and development of small molecule inhibitors could provide a novel therapeutic strategy. In order to find novel compounds with MSI RNA binding inhibitory activity, we have developed a fluorescence polarization (FP) assay and optimized it for high throughput screening (HTS) in a 1536-well microtiter plate format. Using a chemical library of 6,208 compounds, we performed pilot screens, against both MSI1 and MSI2, leading to the identification of 7 molecules for MSI1, 15 for MSI2 and 5 that inhibited both. A secondary FP dose-response screen validated 3 MSI inhibitors with IC50 below 10μM. Out of the 25 compounds retested in the secondary screen only 8 demonstrated optical interference due to high fluorescence. Utilizing a SYBR-based RNA electrophoresis mobility shift assay (EMSA), we further verified MSI inhibition of the top 3 compounds. Surprisingly, even though several aminoglycosides were present in the library, they failed to demonstrate MSI inhibitor activity challenging the concept that these compounds are pan-active against RBPs. In summary, we have developed an in vitro strategy to identify MSI specific inhibitors using an FP HTS platform, which will facilitate novel drug discovery for this class of RBPs.
PMCID: PMC4135234  PMID: 24912481
RNA-binding protein; MUSASHI; HTS; fluorescence polarization; cancer; small-molecule inhibitors
14.  Discovery of a Dicer-Independent, Cell-Type Dependent Alternate Targeting Sequence Generator: Implications in Gene Silencing & Pooled RNAi Screens 
PLoS ONE  2014;9(7):e100676.
There is an acceptance that plasmid-based delivery of interfering RNA always generates the intended targeting sequences in cells, making it as specific as its synthetic counterpart. However, recent studies have reported on cellular inefficiencies of the former, especially in light of emerging gene discordance at inter-screen level and across formats. Focusing primarily on the TRC plasmid-based shRNA hairpins, we reasoned that alleged specificities were perhaps compromised due to altered processing; resulting in a multitude of random interfering sequences. For this purpose, we opted to study the processing of hairpin TRCN#40273 targeting CTTN; which showed activity in a miRNA-21 gain-of-function shRNA screen, but inactive when used as an siRNA duplex. Using a previously described walk-through method, we identified 36 theoretical cleavage variants resulting in 78 potential siRNA duplexes targeting 53 genes. We synthesized and tested all of them. Surprisingly, six duplexes targeting ASH1L, DROSHA, GNG7, PRKCH, THEM4, and WDR92 scored as active. QRT-PCR analysis on hairpin transduced reporter cells confirmed knockdown of all six genes, besides CTTN; revealing a surprising 7 gene-signature perturbation by this one single hairpin. We expanded our qRT-PCR studies to 26 additional cell lines and observed unique knockdown profiles associated with each cell line tested; even for those lacking functional DICER1 gene suggesting no obvious dependence on dicer for shRNA hairpin processing; contrary to published models. Taken together, we report on a novel dicer independent, cell-type dependent mechanism for non-specific RNAi gene silencing we coin Alternate Targeting Sequence Generator (ATSG). In summary, ATSG adds another dimension to the already complex interpretation of RNAi screening data, and provides for the first time strong evidence in support of arrayed screening, and questions the scientific merits of performing pooled RNAi screens, where deconvolution of up to genome-scale pools is indispensable for target identification.
doi:10.1371/journal.pone.0100676
PMCID: PMC4079264  PMID: 24987961
15.  Chemical & RNAi screening at MSKCC: a collaborative platform to discover & repurpose drugs to fight disease 
Memorial Sloan-Kettering Cancer Center (MSKCC) has implemented the creation of a full service state-of-the-art High-throughput Screening Core Facility (HTSCF) equipped with modern robotics and custom-built screening data management resources to rapidly store and query chemical and RNAi screening data outputs. The mission of the facility is to provide oncology clinicians and researchers alike with access to cost-effective HTS solutions for both chemical and RNAi screening, with an ultimate goal of novel target identification and drug discovery. HTSCF was established in 2003 to support the institution’s commitment to growth in molecular pharmacology and in the realm of therapeutic agents to fight chronic diseases such as cancer. This endeavor required broad range of expertise in technology development to establish robust and innovative assays, large collections of diverse chemical and RNAi duplexes to probe specific cellular events, sophisticated compound and data handling capabilities, and a profound knowledge in assay development, hit validation, and characterization. Our goal has been to strive for constant innovation, and we strongly believe in shifting the paradigm from traditional drug discovery towards translational research now, making allowance for unmet clinical needs in patients. Our efforts towards repurposing FDA-approved drugs fructified when digoxin, identified through primary HTS, was administered in the clinic for treatment of stage Vb retinoblastoma. In summary, the overall aim of our facility is to identify novel chemical probes, to study cellular processes relevant to investigator’s research interest in chemical biology and functional genomics, and to be instrumental in accelerating the process of drug discovery in academia.
PMCID: PMC4050342  PMID: 24661215
HTS; HCS; RNAi; siRNA; shRNA; miRNA; automation; robotics; small molecule; chemical; robotics; cell-based assay; target-based assay; screen data analysis; drug discovery
16.  Comparative analysis of RNAi screening technologies at genome-scale reveals an inherent processing inefficiency of the plasmid-based shRNA hairpin 
RNAi screening in combination with the genome-sequencing projects would constitute the Holy Grail of modern genetics; enabling discovery and validation towards a better understanding of fundamental biology leading to novel targets to combat disease. Hit discordance at inter-screen level together with the lack of reproducibility is emerging as the technology's main pitfalls. To examine some of the underlining factors leading to such discrepancies, we reasoned that perhaps there is an inherent difference in knockdown efficiency of the various RNAi technologies. For this purpose, we utilized the two most popular ones, chemically synthesized siRNA duplex and plasmid-based shRNA hairpin, in order to perform a head to head comparison. Using a previously developed gain-of-function assay probing modulators of the miRNA biogenesis pathway, we first executed on a siRNA screen against the Silencer Select V4.0 library (AMB) nominating 1,273, followed by an shRNA screen against the TRC1 library (TRC1) nominating 497 gene candidates. We observed a poor overlap of only 29 hits given that there are 15,068 overlapping genes between the two libraries; with DROSHA as the only common hit out of the seven known core miRNA biogenesis genes. Distinct genes interacting with the same biogenesis regulators were observed in both screens, with a dismal cross-network overlap of only 3 genes (DROSHA, TGFBR1, and DIS3). Taken together, our study demonstrates differential knockdown activities between the two technologies, possibly due to the inefficient intracellular processing and potential cell-type specificity determinants in generating intended targeting sequences for the plasmid-based shRNA hairpins; and suggests this observed inefficiency as potential culprit in addressing the lack of reproducibility.
PMCID: PMC4007059  PMID: 24433414
17.  An Arrayed Genome-Scale Lentiviral-Enabled Short Hairpin RNA Screen Identifies Lethal and Rescuer Gene Candidates 
Abstract
RNA interference technology is becoming an integral tool for target discovery and validation.; With perhaps the exception of only few studies published using arrayed short hairpin RNA (shRNA) libraries, most of the reports have been either against pooled siRNA or shRNA, or arrayed siRNA libraries. For this purpose, we have developed a workflow and performed an arrayed genome-scale shRNA lethality screen against the TRC1 library in HeLa cells. The resulting targets would be a valuable resource of candidates toward a better understanding of cellular homeostasis. Using a high-stringency hit nomination method encompassing criteria of at least three active hairpins per gene and filtered for potential off-target effects (OTEs), referred to as the Bhinder–Djaballah analysis method, we identified 1,252 lethal and 6 rescuer gene candidates, knockdown of which resulted in severe cell death or enhanced growth, respectively. Cross referencing individual hairpins with the TRC1 validated clone database, 239 of the 1,252 candidates were deemed independently validated with at least three validated clones. Through our systematic OTE analysis, we have identified 31 microRNAs (miRNAs) in lethal and 2 in rescuer genes; all having a seed heptamer mimic in the corresponding shRNA hairpins and likely cause of the OTE observed in our screen, perhaps unraveling a previously unknown plausible essentiality of these miRNAs in cellular viability. Taken together, we report on a methodology for performing large-scale arrayed shRNA screens, a comprehensive analysis method to nominate high-confidence hits, and a performance assessment of the TRC1 library highlighting the intracellular inefficiencies of shRNA processing in general.
doi:10.1089/adt.2012.475
PMCID: PMC3619155  PMID: 23198867
18.  An Arrayed RNA Interference Genome-Wide Screen Identifies Candidate Genes Involved in the MicroRNA 21 Biogenesis Pathway 
Abstract
MicroRNAs (miRNAs) are evolutionary conserved noncoding molecules that regulate gene expression. They influence a number of diverse biological functions, such as development and differentiation. However, their dysregulation has been shown to be associated with disease states, such as cancer. Genes and pathways regulating their biogenesis remain unknown and are highly sought after. For this purpose, we have validated a multiplexed high-content assay strategy to screen for such modulators. Here, we describe its implementation that makes use of a cell-based gain-of-function reporter assay monitoring enhanced green fluorescent protein expression under the control of miRNA 21 (miR-21); combined with measures of both cell metabolic activities through the use of Alamar Blue and cell death through imaged Hoechst-stained nuclei. The strategy was validated using a panel of known genes and enabled us to successfully progress to and complete an arrayed genome-wide short interfering RNA (siRNA) screen against the Ambion Silencer Select v4.0 library containing 64,755 siRNA duplexes covering 21,565 genes. We applied a high-stringency hit analysis method, referred to as the Bhinder–Djaballah analysis method, leading to the nomination of 1,273 genes as candidate inhibitors of the miR-21 biogenesis pathway; after several iterations eliminating those genes with only one active duplex and those enriched in seed sequence mediated off-target effects. Biological classifications revealed four major control junctions among them vesicular transport via clathrin-mediated endocytosis. Altogether, our screen has uncovered a number of novel candidate regulators that are potentially good druggable targets allowing for the discovery and development of small molecules for regulating miRNA function.
doi:10.1089/adt.2012.477
PMCID: PMC3619226  PMID: 23153064
19.  Flaviviruses Are Sensitive to Inhibition of Thymidine Synthesis Pathways 
Journal of Virology  2013;87(17):9411-9419.
Dengue virus has emerged as a global health threat to over one-third of humankind. As a positive-strand RNA virus, dengue virus relies on the host cell metabolism for its translation, replication, and egress. Therefore, a better understanding of the host cell metabolic pathways required for dengue virus infection offers the opportunity to develop new approaches for therapeutic intervention. In a recently described screen of known drugs and bioactive molecules, we observed that methotrexate and floxuridine inhibited dengue virus infections at low micromolar concentrations. Here, we demonstrate that all serotypes of dengue virus, as well as West Nile virus, are highly sensitive to both methotrexate and floxuridine, whereas other RNA viruses (Sindbis virus and vesicular stomatitis virus) are not. Interestingly, flavivirus replication was restored by folinic acid, a thymidine precursor, in the presence of methotrexate and by thymidine in the presence of floxuridine, suggesting an unexpected role for thymidine in flavivirus replication. Since thymidine is not incorporated into RNA genomes, it is likely that increased thymidine production is indirectly involved in flavivirus replication. A possible mechanism is suggested by the finding that p53 inhibition restored dengue virus replication in the presence of floxuridine, consistent with thymidine-less stress triggering p53-mediated antiflavivirus effects in infected cells. Our data reveal thymidine synthesis pathways as new and unexpected therapeutic targets for antiflaviviral drug development.
doi:10.1128/JVI.00101-13
PMCID: PMC3754125  PMID: 23824813
20.  Modulators of the microRNA biogenesis pathway via arrayed lentiviral enabled RNAi screening for drug and biomarker discovery 
MicroRNAs (miRNAs) are small endogenous and conserved non-coding RNA molecules that regulate gene expression. Although the first miRNA was discovered well over sixteen years ago, little is known about their biogenesis and it is only recently that we have begun to understand their scope and diversity. For this purpose, we performed an RNAi screen aimed at identifying genes involved in their biogenesis pathway with a potential use as biomarkers. Using a previously developed miRNA 21 (miR-21) EGFP-based biosensor cell based assay monitoring green fluorescence enhancements, we performed an arrayed short hairpin RNA (shRNA) screen against a lentiviral particle ready TRC1 library covering 16,039 genes in 384-well plate format, and interrogating the genome one gene at a time building a panoramic view of endogenous miRNA activity. Using the BDA method for RNAi data analysis, we nominate 497 gene candidates the knockdown of which increased the EGFP fluorescence and yielding an initial hit rate of 3.09%; of which only 22, with reported validated clones, are deemed high-confidence gene candidates. An unexpected and surprising result was that only DROSHA was identified as a hit out of the seven core essential miRNA biogenesis genes; suggesting that perhaps intracellular shRNA processing into the correct duplex may be cell dependent and with differential outcome. Biological classification revealed several major control junctions among them genes involved in transport and vesicular trafficking. In summary, we report on 22 high confidence gene candidate regulators of miRNA biogenesis with potential use in drug and biomarker discovery.
PMCID: PMC3884689  PMID: 23977983
miRNA; biogenesis; shRNA; H score; BDA method; RNAi; HCS; biomarker; HCA; miRNA 21; DROSHA; biomarker; diagnostics
21.  A Novel High-Throughput 1536-well Notch1 γ-Secretase AlphaLISA Assay 
The Notch pathway plays a crucial role in cell fate decisions through controlling various cellular processes. Overactive Notch signal contributes to cancer development from leukemias to solid tumors. γ-Secretase is an intramembrane protease responsible for the final proteolytic step of Notch that releases the membrane-tethered Notch fragment for signaling. Therefore, γ-secretase is an attractive drug target in treating Notch-mediated cancers. However, the absence of high-throughput γ-secretase assay using Notch substrate has limited the identification and development of γ-secretase inhibitors that specifically target the Notch signaling pathway. Here, we report on the development of a 1536-well γ-secretase assay using a biotinylated recombinant Notch1 substrate. We effectively assimilated and miniaturized this newly developed Notch1 substrate with the AlphaLISA detection technology and demonstrated its robustness with a calculated Z’ score of 0.66. We further validated this optimized assay by performing a pilot screening against a chemical library consisting of ~5,600 chemicals and identified known γ-secretase inhibitors e.g. DAPT, and Calpeptin; as well as a novel γ-secretase inhibitor referred to as KD-I-085. This assay is the first reported 1536-well AlphaLISA format and represents a novel high-throughput Notch1-γ-secretase assay, which provides an unprecedented opportunity to discover Notch-selective γ-secretase inhibitors that can be potentially used for the treatment of cancer and other human disorders.
PMCID: PMC3664143  PMID: 23448293
Alzheimer disease; AlphaLISA; cancer; γ-secretase; γ-secretase modulators; Notch signaling
22.  Planning Following Stroke: A Relational Complexity Approach Using the Tower of London 
Planning on the 4-disk version of the Tower of London (TOL4) was examined in stroke patients and unimpaired controls. Overall TOL4 solution scores indicated impaired planning in the frontal stroke but not non-frontal stroke patients. Consistent with the claim that processing the relations between current states, intermediate states, and goal states is a key process in planning, the domain-general relational complexity metric was a good indicator of the experienced difficulty of TOL4 problems. The relational complexity metric shared variance with task-specific metrics of moves to solution and search depth. Frontal stroke patients showed impaired planning compared to controls on problems at all three complexity levels, but at only two of the three levels of moves to solution, search depth and goal ambiguity. Non-frontal stroke patients showed impaired planning only on the most difficult quaternary-relational and high search depth problems. An independent measure of relational processing (viz., Latin square task) predicted TOL4 solution scores after controlling for stroke status and location, and executive processing (Trail Making Test). The findings suggest that planning involves a domain-general capacity for relational processing that depends on the frontal brain regions.
doi:10.3389/fnhum.2014.01032
PMCID: PMC4274981  PMID: 25566042
Tower of London; planning; moves to solution; search depth; goal ambiguity; relational complexity; stroke; frontal lobes
23.  Developmental trajectories of schizotypal personality disorder-like behavioural manifestations: a two-year longitudinal prospective study of college students 
BMC Psychiatry  2013;13:323.
Background
Previous evidence has shown that schizotypal personality disorder (SPD) is part of the schizophrenia spectrum. Few studies have examined latent classes in the developmental trajectories of SPD features over time in individuals with SPD features.
Methods
We adopted a longitudinal prospective study design to follow up a cohort of 660 college students during a two-year period. Participants’ SPD-like symptoms and psychosocial function were measured by a comprehensive set of questionnaires that covered SPD features and cognitive, emotional, and psychosocial functions. Latent class growth analysis was used to examine the trajectory classes.
Results
Three trajectory classes were identified: a low, a medium, and a high SPD features group. Participants in the low group reported few SPD features and their symptoms declined over time. The medium group students had more SPD features than the low group and these symptoms stabilized during the follow up period. Participants in the high group reported the most SPD features and their symptoms increased over time. The three groups differed in paranoid thoughts, psychological distress, neurocognition function, and emotional expression over time. Results of multivariate regression analysis suggested that paranoid thoughts, emotional experience and prospective memory were predictors of social functioning in the high SPD feature group.
Conclusions
Our findings suggest that individuals with SPD features may be delineated into different developmental subgroups and these subgroups differ significantly in psychosocial function. Delusions, emotion, and prospective memory may be important features to consider in early diagnosis and interventions for individuals predisposed to SPD and schizophrenia.
doi:10.1186/1471-244X-13-323
PMCID: PMC3875349  PMID: 24289659
Schizotypal personality disorder; Developmental trajectories; Psychosocial function; Latent class growth analysis
24.  Comparison of error-based and errorless learning for people with severe traumatic brain injury: study protocol for a randomized control trial 
Trials  2013;14:369.
Background
Poor skills generalization poses a major barrier to successful outcomes of rehabilitation after traumatic brain injury (TBI). Error-based learning (EBL) is a relatively new intervention approach that aims to promote skills generalization by teaching people internal self-regulation skills, or how to anticipate, monitor and correct their own errors. This paper describes the protocol of a study that aims to compare the efficacy of EBL and errorless learning (ELL) for improving error self-regulation, behavioral competency, awareness of deficits and long-term outcomes after TBI.
Methods/Design
This randomized, controlled trial (RCT) has two arms (EBL and ELL); each arm entails 8 × 2 h training sessions conducted within the participants’ homes. The first four sessions involve a meal preparation activity, and the final four sessions incorporate a multitasking errand activity. Based on a sample size estimate, 135 participants with severe TBI will be randomized into either the EBL or ELL condition. The primary outcome measure assesses error self-regulation skills on a task related to but distinct from training. Secondary outcomes include measures of self-monitoring and self-regulation, behavioral competency, awareness of deficits, role participation and supportive care needs. Assessments will be conducted at pre-intervention, post-intervention, and at 6-months post-intervention.
Discussion
This study seeks to determine the efficacy and long-term impact of EBL for training internal self-regulation strategies following severe TBI. In doing so, the study will advance theoretical understanding of the role of errors in task learning and skills generalization. EBL has the potential to reduce the length and costs of rehabilitation and lifestyle support because the techniques could enhance generalization success and lifelong application of strategies after TBI.
Trial registration
ACTRN12613000585729.
doi:10.1186/1745-6215-14-369
PMCID: PMC4228339  PMID: 24192067
Brain injury; Metacognition; Self-awareness; Rehabilitation; Functional activities; Randomized controlled trial
25.  A high density assay format for the detection of novel cytotoxicagents in large chemical libraries 
The Alamar Blue (AB) assay, which incorporates a redox indicator that causes a fluorescence signal enhancement in response to metabolic activity, is commonly used to assess the viability of mammalian cells. In response to the need for homogeneous, inexpensive, high throughput assays for anti-cancer drug screening, a 1536-well microtiter plate based assay which utilizes the AB fluorescent dye as a measure of cellular growth was developed and validated in 10 µL assay volume. The performance and robustness of the miniaturized assay was assessed using a human Mantle Cell Lymphoma (MCL) cell line in a pilot screen against a library of 2,000 known bioactive chemicals; with an overall Z’ value of 0.89 for assay robustness, several known cytotoxic agents were identified including and not limited to anthracyclines, cardiac glycosides, gamboges, and quinones. To further test the sensitivity of the assay, IC50 determinations were performed in both 384-well and 1536-well formats and the obtained results show a very good correlation between the two density formats. These findings demonstrate that this newly developed assay is simple to set up, robust, highly sensitive and inexpensive. The non-radiometric strategy employed in this study should also offer the potential for the rapid screening, without a wash or a lysis step, of well established and primary tumor cell lines against large chemical libraries using the 1536-well microtiter plates.
doi:10.1080/14756360701810082
PMCID: PMC3710589  PMID: 18608772
Assay; miniaturization; Alamar Blue; cytotoxicity; anthracyclines; screening; HTS; fluorescence; resazurin; cell viability; NCEB1; cancer

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