Maternal attachment insecurity, maltreatment history, and depressive symptoms are associated with broad DNA methylation signatures in infants.

The early environment, including maternal characteristics, provides many cues to young organisms that shape their long-term physical and mental health. Identifying the earliest molecular events that precede observable developmental outcomes could help identify children in need of support prior to the onset of physical and mental health difficulties. In this study, we examined whether mothers' attachment insecurity, maltreatment history, and depressive symptoms were associated with alterations in DNA methylation patterns in their infants, and whether these correlates in the infant epigenome were associated with socioemotional and behavioral functioning in toddlerhood. We recruited 156 women oversampled for histories of depression, who completed psychiatric interviews and depression screening during pregnancy, then provided follow-up behavioral data on their children at 18 months. Buccal cell DNA was obtained from 32 of their infants for a large-scale analysis of methylation patterns across 5 × 106 individual CpG dinucleotides, using clustering-based significance criteria to control for multiple comparisons. We found that tens of thousands of individual infant CpGs were alternatively methylated in association with maternal attachment insecurity, maltreatment in childhood, and antenatal and postpartum depressive symptoms, including genes implicated in developmental patterning, cell-cell communication, hormonal regulation, immune function/inflammatory response, and neurotransmission. Density of DNA methylation at selected genes from the result set was also significantly associated with toddler socioemotional and behavioral problems. This is the first report to identify novel regions of the human infant genome at which DNA methylation patterns are associated longitudinally both with maternal characteristics and with offspring socioemotional and behavioral problems in toddlerhood.

Knockdown of HSP110 attenuates hypoxia-induced pulmonary hypertension in mice through suppression of YAP/TAZ-TEAD4 pathway.

BACKGROUND: Pulmonary hypertension (PH) is a progressive and fatal cardiopulmonary disease characterized by pulmonary vascular remodeling and increased pulmonary vascular resistance and artery pressure. Vascular remodeling is associated with the excessive cell proliferation and migration of pulmonary artery smooth muscle cells (PASMCs). In this paper, the effects of heat shock protein-110 (HSP110) on PH were investigated. METHODS: The C57BL/6 mice and human PASMCs (HPASMCs) were respectively exposed to hypoxia to establish and simulate PH model in vivo and cell experiment in vitro. To HSP110 knockdown, the hypoxia mice and HPASMCs were infected with adeno-associated virus or adenovirus carring the shRNAs (short hairpin RNAs) for HSP110 (shHSP110). For HSP110 and yes-associated protein (YAP) overexpression, HPASMCs were infected with adenovirus vector carring the cDNA of HSP110 or YAP. The effects of HSP110 on PH development in mice and cell proliferation, migration and autophagy of PASMCs under hypoxia were assessed. Moreover, the regulatory mechanisms among HSP110, YAP and TEA domain transcription factor 4 (TEAD4) were investigated. RESULTS: We demonstrated that expression of HSP110 was significantly increased in the pulmonary arteries of mice and HPASMCs under hypoxia. Moreover, knockdown of HSP110 alleviated hypoxia-induced right ventricle systolic pressure, vascular wall thickening, right ventricular hypertrophy, autophagy and proliferation of PASMCs in mice. In addition, knockdown of HSP110 inhibited the increases of proliferation, migration and autophagy of HPASMCs that induced by hypoxia in vitro. Mechanistically, HSP110 knockdown inhibited YAP and transcriptional co-activator with PDZ-binding motif (TAZ) activity and TEAD4 nuclear expression under hypoxia. However, overexpression of HSP110 exhibited the opposite results in HPASMCs. Additionally, overexpression of YAP partially restored the effects of shHSP110 on HPASMCs. The interaction of HSP110 and YAP was verified. Moreover, TEAD4 could promote the transcriptional activity of HSP110 by binding to the HSP110 promoter under hypoxia. CONCLUSIONS: Our findings suggest that HSP110 might contribute to the development of PH by regulating the proliferation, migration and autophagy of PASMCs through YAP/TAZ-TEAD4 pathway, which may help to understand deeper the pathogenic mechanism in PH development.

Determination of pyraclostrobin dynamic residual distribution in tilapia tissues by UPLC-MS/MS under acute toxicity conditions.

As a lipophilic fungicide, pyraclostrobin is highly toxic to aquatic organisms, especially to fish. In recent years, research has mainly focused on the pyraclostrobin residue in fish tissues under chronic toxicity, but less is known about its distribution in fish tissues under acute toxicity conditions. In this study, the distribution of pyraclostrobin in fish tissues (blood, liver, muscle and gill) was determined by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The purification effects of different purification materials [1) mixtures of PSA, C18 and MgSO4; 2) QuEChERS-PC; and 3) Oasis HLB SPE] were compared for the detection of pyraclostrobin in fish tissues. Finally, the quick and easy clean-up tool of the Oasis HLB SPE procedure was selected. Under optimum conditions, the linearities had a good relationship (determination coefficient R2 > 0.999). The mean recoveries of the analyte for all tested concentrations ranged from 86.94% to 108.81% with RSDs of 0.7%-4.9%. The pyraclostrobin residue amount was much different in fish tissues. Furthermore, the pyraclostrobin residue in different fish tissues increased initially and then decreased gradually. The concentrations in each tissue were initially ranked before 120 min in the following order: gill > liver > blood > muscle. These phenomena may be attributed to the stress response of fish under acute poisoning. This is the first study to document the distribution of pyraclostrobin in fish tissues under acute toxicity conditions, and it provides reference for the management of agrochemicals in terms of aquatic ecological risks.

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.

BACKGROUND: Decoding the temporal control of gene expression patterns is key to the understanding of the complex mechanisms that govern developmental decisions during heart development. High-throughput methods have been employed to systematically study the dynamic and coordinated nature of cardiac differentiation at the global level with multiple dimensions. Therefore, there is a pressing need to develop a systems approach to integrate these data from individual studies and infer the dynamic regulatory networks in an unbiased fashion. RESULTS: We developed a two-step strategy to integrate data from (1) temporal RNA-seq, (2) temporal histone modification ChIP-seq, (3) transcription factor (TF) ChIP-seq and (4) gene perturbation experiments to reconstruct the dynamic network during heart development. First, we trained a logistic regression model to predict the probability (LR score) of any base being bound by 543 TFs with known positional weight matrices. Second, four dimensions of data were combined using a time-varying dynamic Bayesian network model to infer the dynamic networks at four developmental stages in the mouse [mouse embryonic stem cells (ESCs), mesoderm (MES), cardiac progenitors (CP) and cardiomyocytes (CM)]. Our method not only infers the time-varying networks between different stages of heart development, but it also identifies the TF binding sites associated with promoter or enhancers of downstream genes. The LR scores of experimentally verified ESCs and heart enhancers were significantly higher than random regions (p <10(-100)), suggesting that a high LR score is a reliable indicator for functional TF binding sites. Our network inference model identified a region with an elevated LR score approximately -9400 bp upstream of the transcriptional start site of Nkx2-5, which overlapped with a previously reported enhancer region (-9435 to -8922 bp). TFs such as Tead1, Gata4, Msx2, and Tgif1 were predicted to bind to this region and participate in the regulation of Nkx2-5 gene expression. Our model also predicted the key regulatory networks for the ESC-MES, MES-CP and CP-CM transitions. CONCLUSION: We report a novel method to systematically integrate multi-dimensional -omics data and reconstruct the gene regulatory networks. This method will allow one to rapidly determine the cis-modules that regulate key genes during cardiac differentiation.

ER71 directs mesodermal fate decisions during embryogenesis.

Er71 mutant embryos are nonviable and lack hematopoietic and endothelial lineages. To further define the functional role for ER71 in cell lineage decisions, we generated genetically modified mouse models. We engineered an Er71-EYFP transgenic mouse model by fusing the 3.9 kb Er71 promoter to the EYFP reporter gene. Using FACS and transcriptional profiling, we examined the EYFP(+) population of cells in Er71 mutant and wild-type littermates. In the absence of ER71, we observed an increase in the number of EYFP-expressing cells, increased expression of the cardiac molecular program and decreased expression of the hemato-endothelial program, as compared with wild-type littermate controls. We also generated a novel Er71-Cre transgenic mouse model using the same 3.9 kb Er71 promoter. Genetic fate-mapping studies revealed that the ER71-expressing cells give rise to the hematopoietic and endothelial lineages in the wild-type background. In the absence of ER71, these cell populations contributed to alternative mesodermal lineages, including the cardiac lineage. To extend these analyses, we used an inducible embryonic stem/embryoid body system and observed that ER71 overexpression repressed cardiogenesis. Together, these studies identify ER71 as a critical regulator of mesodermal fate decisions that acts to specify the hematopoietic and endothelial lineages at the expense of cardiac lineages. This enhances our understanding of the mechanisms that govern mesodermal fate decisions early during embryogenesis.

An observational study of symmetrical VSD occluder for transcatheter closure of ruptured sinus of Valsalva aneurysm.

This study evaluated the immediate and 1-year postoperative outcomes of 14 patients with ruptured Valsalva aneurysmal sinus (RSVA) using symmetric ventricular septal defect (VSD) occluder for transcatheter closure (TCC). The sites of rupture were from the non-coronary sinus to the right atrium (RA) in 10 cases (71.4%), the right coronary sinus (RCS) to the RA in 3 cases (21.4%) and the RCS to the right ventricle in 1 case (7.2%). The defects (5-11 mm) were closed with a symmetrical VSD device. During the follow-up (12 months), the enlarged heart of the patients had significantly shrunk and the NYHA improved after closure. In 1 case, a moderate residual shunt was present and the patient suffered from hemolysis at 2 h after the operation, and 1 patient was transferred to surgery for aortic regurgitation 1 year after the initial treatment of RSVA. In conclusion, the TCC of RSVA with the China made symmetrical VSD occluder is safe and effective.

Etv2 is expressed in the yolk sac hematopoietic and endothelial progenitors and regulates Lmo2 gene expression.

During embryogenesis, the endothelial and the hematopoietic lineages first appear during gastrulation in the blood island of the yolk sac. We have previously reported that an Ets variant gene 2 (Etv2/ER71) mutant embryo lacks hematopoietic and endothelial lineages; however, the precise roles of Etv2 in yolk sac development remains unclear. In this study, we define the role of Etv2 in yolk sac blood island development using the Etv2 mutant and a novel Etv2-EYFP reporter transgenic line. Both the hematopoietic and the endothelial lineages are absent in the Etv2 mutant yolk sac. In the Etv2-EYFP transgenic mouse, the EYFP reporter is activated in the nascent mesoderm, expressed in the endothelial and blood progenitors, and in the Tie2(+), c-kit(+), and CD41(+) hematopoietic population. The hematopoietic activity in the E7.75 yolk sac was exclusively localized to the Etv2-EYFP(+) population. In the Etv2 mutant yolk sac, Tie2(+) cells are present but do not express hematopoietic or endothelial markers. In addition, these cells do not form hematopoietic colonies, indicating an essential role of Etv2 in the specification of the hematopoietic lineage. Forced overexpression of Etv2 during embryoid body differentiation induces the hematopoietic and the endothelial lineages, and transcriptional profiling in this context identifies Lmo2 as a downstream target. Using electrophoretic mobility shift assay, chromatin immunoprecipitation, transcriptional assays, and mutagenesis, we demonstrate that Etv2 binds to the Lmo2 enhancer and transactivates its expression. Collectively, our studies demonstrate that Etv2 is expressed during and required for yolk sac hematoendothelial development, and that Lmo2 is one of the downstream targets of Etv2.

dbCRID: a database of chromosomal rearrangements in human diseases.

Chromosomal rearrangement (CR) events result from abnormal breaking and rejoining of the DNA molecules, or from crossing-over between repetitive DNA sequences, and they are involved in many tumor and non-tumor diseases. Investigations of disease-associated CR events can not only lead to important discoveries about DNA breakage and repair mechanisms, but also offer important clues about the pathologic causes and the diagnostic/therapeutic targets of these diseases. We have developed a database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org), a comprehensive database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and--when possible--detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event. With 2643 records of disease-associated CR events curated from 1172 original studies, dbCRID is a comprehensive and dynamic resource useful for studying DNA breakage and repair mechanisms, and for analyzing the genetic basis of human tumor and non-tumor diseases.

Drosha processing controls the specificity and efficiency of global microRNA expression.

microRNAs (miRNAs) are a large family of approximately 22-nucleotide-long RNAs that regulate gene expression. They are first transcribed as long, primary transcripts, which then undergo a series of processing steps to generate the single-stranded, mature miRNAs. Here, we showed that Drosha cleaved hundreds of human primary miRNA transcript substrates with different efficiencies in vitro. The differential Drosha susceptibility of the primary miRNA transcripts significantly correlated with the expression of the corresponding, mature miRNAs in vivo. Conserved miRNAs were more efficiently expressed in vivo, and their primary transcripts were also better Drosha substrates in vitro. Combining secondary structure prediction and statistical analyses, we identified features in human primary miRNA transcripts that predisposed miRNAs to efficient Drosha processing in vitro as well as to better expression in vivo. We propose that the selectivity of Drosha action contributes greatly to the specificity and efficiency of miRNA biogenesis. Moreover, this study serves as an example of substrate specificity of a biochemical reaction regulating gene expression at a global scale in vivo. This article is part of a Special Issue entitled: MicroRNA's in viral gene regulation.

miRecords: an integrated resource for microRNA-target interactions.

MicroRNAs (miRNAs) are an important class of small noncoding RNAs capable of regulating other genes' expression. Much progress has been made in computational target prediction of miRNAs in recent years. More than 10 miRNA target prediction programs have been established, yet, the prediction of animal miRNA targets remains a challenging task. We have developed miRecords, an integrated resource for animal miRNA-target interactions. The Validated Targets component of this resource hosts a large, high-quality manually curated database of experimentally validated miRNA-target interactions with systematic documentation of experimental support for each interaction. The current release of this database includes 1135 records of validated miRNA-target interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets component of miRecords stores predicted miRNA targets produced by 11 established miRNA target prediction programs. miRecords is expected to serve as a useful resource not only for experimental miRNA researchers, but also for informatics scientists developing the next-generation miRNA target prediction programs. The miRecords is available at http://miRecords.umn.edu/miRecords.

siRecords: a database of mammalian RNAi experiments and efficacies.

RNAi-based gene-silencing techniques offer a fast and cost-effective way of knocking down genes' functions in an easily regulated manner. Exciting progress has been made in recent years in the application of these techniques in basic biomedical research and therapeutic development. However, it remains a difficult task to design effective siRNA experiments with high efficacy and specificity. We present siRecords, an extensive database of mammalian RNAi experiments with consistent efficacy ratings. This database serves two purposes. First, it provides a large and diverse dataset of siRNA experiments. This dataset faithfully represents the general, diverse RNAi experimental practice, and allows more reliable siRNA design tools to be developed with the overfitting problem well curbed. Second, the database helps experimental RNAi researchers directly by providing them with the efficacy and other information about the siRNAs experiments designed and conducted previously against the genes of their interest. The current release of siRecords contains the records of 17,192 RNAi experiments targeting 5086 genes.

Ecotoxicological effects of pyraclostrobin on tilapia (Oreochromis niloticus) via various exposure routes.

Pyraclostrobin is a widely used and highly efficient fungicide that also has high toxicity to aquatic organisms, especially fish. Although some research has reported the toxic effects of pyraclostrobin on fish, the main toxic pathways of pyraclostrobin in fish remain unclear. The present study has integrated histopathological, biochemical and hematological techniques to reveal the main toxic pathways and mechanisms of pyraclostrobin under different exposure routes. Our results indicated that pyraclostrobin entered fish mainly through the gills. The highest accumulation of pyraclostrobin was observed in the gills and heart compared with accumulation in other tissues and gill tissue showed the most severe damage. Hypoxia symptoms (water jacking, tummy turning and cartwheel formation) in fish were observed throughout the experiment. Taken together, our results suggested that the gills are important target organs. The high pyraclostrobin toxicity to gills might be associated with oxidative damage to the gills, inducing alterations in ventilation frequency, oxygen-carrying substances in blood and disorders of energy metabolism. Our research facilitates a better understanding of the toxic mechanisms of pyraclostrobin in fish, which can promote the ecotoxicological research of agrochemicals on aquatic organisms.

The γ-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.

Changes in the location of γ-tubulin ensure cell survival and preserve genome integrity. We investigated whether the nuclear accumulation of γ-tubulin facilitates the transport of proliferating cell nuclear antigen (PCNA) between the cytosolic and the nuclear compartment in mammalian cells. We found that the γ-tubulin meshwork assists in the recruitment of PCNA to chromatin. Also, decreased levels of γ-tubulin reduce the nuclear pool of PCNA. In addition, the γ-tubulin C terminus encodes a PCNA-interacting peptide (PIP) motif, and a γ-tubulin-PIP-mutant affects the nuclear accumulation of PCNA. In a cell-free system, PCNA and γ-tubulin formed a complex. In tumors, there is a significant positive correlation between TUBG1 and PCNA expression. Thus, we report a novel mechanism that constitutes the basis for tumor growth by which the γ-tubulin meshwork maintains indefinite proliferation by acting as an opportune scaffold for the transport of PCNA from the cytosol to the chromatin.

Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection.

Meta-predictors make predictions by organizing and processing the predictions produced by several other predictors in a defined problem domain. A proficient meta-predictor not only offers better predicting performance than the individual predictors from which it is constructed, but it also relieves experimentally researchers from making difficult judgments when faced with conflicting results made by multiple prediction programs. As increasing numbers of predicting programs are being developed in a large number of fields of life sciences, there is an urgent need for effective meta-prediction strategies to be investigated. We compiled four unbiased phosphorylation site datasets, each for one of the four major serine/threonine (S/T) protein kinase families-CDK, CK2, PKA and PKC. Using these datasets, we examined several meta-predicting strategies with 15 phosphorylation site predictors from six predicting programs: GPS, KinasePhos, NetPhosK, PPSP, PredPhospho and Scansite. Meta-predictors constructed with a generalized weighted voting meta-predicting strategy with parameters determined by restricted grid search possess the best performance, exceeding that of all individual predictors in predicting phosphorylation sites of all four kinase families. Our results demonstrate a useful decision-making tool for analysing the predictions of the various S/T phosphorylation site predictors. An implementation of these meta-predictors is available on the web at: http://MetaPred.umn.edu/MetaPredPS/.

PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.

Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions. Our motivation is to provide the research community with a rich information source emphasizing the reported, experimentally validated data for specific PPBD-PPEP interactions. This information is not only useful for designing, comparing and validating the relevant experiments, but it also serves as a knowledge-base for computationally constructing systems signaling pathways and networks. PepCyber:P approximately PEP is accessible through the URL, http://www.pepcyber.org/PPEP/. The current release of the database contains 7044 PPBD-mediated interactions involving 337 PPBD-containing proteins and 1123 substrate proteins.

Feedback regulation of NEUROG2 activity by MTGR1 is required for progression of neurogenesis.

The sequential steps of neurogenesis are characterized by highly choreographed changes in transcription factor activity. In contrast to the well-studied mechanisms of transcription factor activation during neurogenesis, much less is understood regarding how such activity is terminated. We previously showed that MTGR1, a member of the MTG family of transcriptional repressors, is strongly induced by a proneural basic helix-loop-helix transcription factor, NEUROG2 in developing nervous system. In this study, we describe a novel feedback regulation of NEUROG2 activity by MTGR1. We show that MTGR1 physically interacts with NEUROG2 and represses transcriptional activity of NEUROG2. MTGR1 also prevents DNA binding of the NEUROG2/E47 complex. In addition, we provide evidence that proper termination of NEUROG2 activity by MTGR1 is necessary for normal progression of neurogenesis in the developing spinal cord. These results highlight the importance of feedback regulation of proneural gene activity in neurodevelopment.

Sirt6-Mediated Endothelial-to-Mesenchymal Transition Contributes Toward Diabetic Cardiomyopathy via the Notch1 Signaling Pathway.

BACKGROUND: Endothelial-to-mesenchymal transition (EndMT) is an important source of myofibroblasts that directly affects cardiac function in diabetic cardiomyopathy (DCM) via an unknown underlying mechanism. Sirt6 is a member of the Sirtuin family of NAD(+)-dependent enzymes that plays an important role in glucose and fatty acid metabolism. In this study, we investigated whether Sirt6 participates in EndMT during the development of T2DM and the possible underlying regulatory mechanisms. METHODS: Endothelium-specific Sirt6 knockout (Sirt6-KOEC) mice (C57BL/6 genetic background) were generated using the classic Cre/loxp gene recombination system. T2DM was induced in eight-week-old male mice by feeding with a high-fat diet for three weeks followed by i.p. injection with 30 mg/kg of streptozotocin. The weight, lipids profiles, insulin, food intake and water intake of experimental animals were measured on a weekly basis. Cardiac microvascular endothelial cells (CMECs) were obtained from adult male mice; the isolated cells were cultured with high glucose (HG; 33 mmol/L) and palmitic acid (PA; 500 µmol/L) in DMEM for 24 h, or with normal glucose (NG; 5 mmol/L) as the control. RESULTS: Sirt6 expression is significantly downregulated in CMECs treated with HG+PA. Additionally, Sirt6-KOEC was found to worsen DCM, as indicated by aggravated perivascular fibrosis, cardiomyocyte hypertrophy, and decreased cardiac function. In vitro, Sirt6 knockdown exacerbated the proliferation, and migration of CMECs exposed to HG+PA. Mechanistically, Sirt6 knockdown significantly enhanced Notch1 activation in CMECs treated with HG+PA, whereas Notch1 adenoviral interference significantly blunted the effects of Sirt6 knockdown on CMECs. CONCLUSION: This study is the first to demonstrate that Sirt6 participates in EndMT via the Notch1 signaling pathway in CMECs stimulated with HG+PA. Therefore, the findings of this study suggest that Sirt6 could provide a potential treatment strategy for DCM.

Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression.

Early life adversity and insecure attachment style are known risk factors for perinatal depression. The biological pathways linking these experiences, however, have not yet been elucidated. We hypothesized that overlap in patterns of DNA methylation in association with each of these phenomena could identify genes and pathways of importance. Specifically, we wished to distinguish between allostatic-load and role-transition hypotheses of perinatal depression. We conducted a large-scale analysis of methylation patterns across 5 × 106 individual CG dinucleotides in 54 women participating in a longitudinal prospective study of perinatal depression, using clustering-based criteria for significance to control for multiple comparisons. We identified 1580 regions in which methylation density was associated with childhood adversity, 3 in which methylation density was associated with insecure attachment style, and 6 in which methylation density was associated with perinatal depression. Shorter telomeres were observed in association with childhood trauma but not with perinatal depression or attachment insecurity. A detailed analysis of methylation density in the oxytocin receptor gene revealed similar patterns of DNA methylation in association with perinatal depression and with insecure attachment style, while childhood trauma was associated with a distinct methylation pattern in this gene. Clinically, attachment style was strongly associated with depression only in pregnancy and the early postpartum, whereas the association of childhood adversity with depression was time-invariant. We concluded that the broad DNA methylation signature and reduced telomere length associated with childhood adversity could indicate increased allostatic load across multiple body systems, whereas perinatal depression and attachment insecurity may be narrower phenotypes with more limited DNA methylation signatures outside the CNS, and no apparent association with telomere length or, by extension, allostatic load. In contrast, the finding of matching DNA methylation patterns within the oxytocin receptor gene for perinatal depression and attachment insecurity is consistent with the theory that the perinatal period is a time of activation of existing attachment schemas for the purpose of structuring the mother-child relationship, and that such activation may occur in part through specific patterns of methylation of the oxytocin receptor gene.

siDRM: an effective and generally applicable online siRNA design tool.

Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a large and diverse dataset compiled from siRecords, and implemented the resulting rule sets in siDRM, a new online siRNA design tool. siDRM also implements a few high-sensitivity rule sets and fast rule sets, links to siRecords, and uses several filters to check unwanted detrimental effects, including innate immune responses, cell toxic effects and off-target activities in selecting siRNAs. A performance comparison using an independent dataset indicated that siDRM outperforms 19 existing siRNA design tools in identifying effective siRNAs.

Meta-prediction of protein subcellular localization with reduced voting.

Meta-prediction seeks to harness the combined strengths of multiple predicting programs with the hope of achieving predicting performance surpassing that of all existing predictors in a defined problem domain. We investigated meta-prediction for the four-compartment eukaryotic subcellular localization problem. We compiled an unbiased subcellular localization dataset of 1693 nuclear, cytoplasmic, mitochondrial and extracellular animal proteins from Swiss-Prot 50.2. Using this dataset, we assessed the predicting performance of 12 predictors from eight independent subcellular localization predicting programs: ELSPred, LOCtree, PLOC, Proteome Analyst, PSORT, PSORT II, SubLoc and WoLF PSORT. Gorodkin correlation coefficient (GCC) was one of the performance measures. Proteome Analyst is the best individual subcellular localization predictor tested in this four-compartment prediction problem, with GCC = 0.811. A reduced voting strategy eliminating six of the 12 predictors yields a meta-predictor (RAW-RAG-6) with GCC = 0.856, substantially better than all tested individual subcellular localization predictors (P = 8.2 x 10(-6), Fisher's Z-transformation test). The improvement in performance persists when the meta-predictor is tested with data not used in its development. This and similar voting strategies, when properly applied, are expected to produce meta-predictors with outstanding performance in other life sciences problem domains.