Imperfect Matches Research Articles

Flexiplex: a versatile demultiplexer and search tool for omics data.

The process of analyzing high throughput sequencing data often requires the identification and extraction of specific target sequences. This could include tasks, such as identifying cellular barcodes and UMIs in single-cell data, and specific genetic variants for genotyping. However, existing tools, which perform these functions are often task-specific, such as only demultiplexing barcodes for a dedicated type of experiment, or are not tolerant to noise in the sequencing data. To overcome these limitations, we developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell-line-specific sequences in Illumina short-read single-cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single-cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools. Flexiplex is available at https://davidsongroup.github.io/flexiplex/.

Telescope Matching for Reducing Model Dependence in the Estimation of the Effects of Time-Varying Treatments: An Application to Negative Advertising

Abstract Time-varying treatments are prevalent in the social sciences. For example, a political campaign might decide to air attack ads against an opponent, but this decision to go negative will impact polling and, thus, future campaign strategy. If an analyst naively applies methods for point exposures to estimate the effect of earlier treatments, this would lead to post-treatment bias. Several existing methods can adjust for this type of time-varying confounding, but they typically rely on strong modelling assumptions. In this paper, we propose a novel two-step matching procedure for estimating the effect of two-period treatments. This method, telescope matching, reduces model dependence without inducing post-treatment bias by using matching with replacement to impute missing counterfactual outcomes. It then employs flexible regression models to correct for bias induced by imperfect matches. We derive the asymptotic properties of the telescope matching estimator and provide a consistent estimator for its variance. We illustrate telescope matching by investigating the effect of negative campaigning in US Senate and gubernatorial elections. Using the method, we uncover a positive effect on turnout of negative ads early in a campaign and a negative effect of early negativity on vote shares.

γCas stars: Normal Be stars with discs impacted by the wind of a helium-star companion?

γCas stars are a ∼1% minority among classical Be stars with hard (≥5−10 keV), but only moderately strong continuous thermal X-ray flux, and mostly very early-B spectral type. The X-ray flux has been suggested to originate from matter accelerated via magnetic disc-star interaction, by a rapidly rotating neutron star (NS) companion via the propeller effect, or by accretion onto a white dwarf (WD) companion. In view of the growing number of identifiedγCas stars and the only imperfect matches between these suggestions and the observations, alternative models should be pursued. Two of the three best-observedγCas stars,γCasitself andπAqr, have a low-mass companion with low optical flux, whereas interferometry ofBZ Cruis inconclusive. Binary-evolution models are examined for their ability to produce such systems. The OB+He-star stage of post-mass transfer binaries, which is otherwise observationally unaccounted, can potentially reproduce many observed properties ofγCas stars. The interaction of the fast wind of helium stars with the circumstellar disc and/or with the wind of Be stars may give rise to the production of hard X-rays. While not modelling this process, it is shown that the energy budget is favourable, and that the wind velocities may lead to hard X-rays, as observed inγCas stars. Furthermore, the observed number of these objects appears to be consistent with the evolutionary models. Within the Be+He-star binary model, the Be stars inγ-Cas stars are conventional classical Be stars. They are encompassed by O-star+Wolf-Rayet systems towards higher mass, where no stable Be decretion discs exist, and by Be+sdO systems at lower mass, where the sdO winds may be too weak to cause theγCas phenomenon. In decreasing order of the helium-star mass, the descendants could be Be+black-hole, Be+NS, or Be+WD binaries. The interaction between the helium-star wind and the disc may provide new diagnostics of the outer disc.

Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants

BackgroundWe investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated.MethodsGenomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis.ResultsHigh-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches).ConclusionsThese data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.

Learned feature variance is encoded in the target template and drives visual search

ABSTRACTReal-world visual search targets are frequently imperfect perceptual matches to our internal templates. For example, a friend on different occasions will have different clothes, hairstyles, and accessories, but some of these may vary more than others. The ability to deal with template-to-target variability is important to visual search in natural environments, but we know relatively little about how this is handled by the attentional system. Here, we test the hypothesis that top-down attentional biases are sensitive to the variance of target features and prioritize less-variable dimensions. Subjects were shown target cues composed of coloured dots moving in a specific direction followed by a working memory probe (30%) or visual search display (70%). Critically, the target features in the visual search display differed from the cue, with one feature drawn from a narrow distribution (low-variance dimension), and the other sampled from a broader distribution (high-variance dimension). The results demonstrate that subjects used knowledge of the likely cue-to-target variance to set template precision and bias attentional selection. Our results suggest that observers are sensitive to the variance of feature dimensions within a target and use this information to weight mechanisms of attentional selection.

Controlling the FDR in Imperfect Matches to an Incomplete Database

ABSTRACTWe consider the problem of controlling the false discovery rate (FDR) among discoveries from searching an incomplete database. This problem differs from the classical multiple testing setting because there are two different types of false discoveries: those arising from objects that have no match in the database and those that are incorrectly matched. We show that commonly used FDR controlling procedures are inadequate for this setup, a special case of which is tandem mass spectrum identification. We then derive a novel FDR controlling approach which extensive simulations suggest is unbiased. We also compare its performance with problem-specific as well as general FDR controlling procedures using both simulated and real mass spectrometry data.

Identification of treatment effects under imperfect matching with an application to Chinese elite schools

This paper extends the treatment effect framework for causal inference to contexts in which the instrument appears in a data set that can only be linked imperfectly to the treatment and outcome variables contained in another data set. To overcome this problem, I form all pairwise links between information on the instrument and information on the treatment and outcome matched by the commonly recorded personal characteristics in both data sets. I show how these imperfect conditional matches can be used to identify both the average and distributional treatment effects for compliers of the common units of the two data sets. This multiple data source approach is then applied to analyze the effect of attending an elite middle school in a Chinese city where schools' admissions lottery records can only be linked imperfectly to the administrative student records.

Suboptimization of developmental enhancers.

Transcriptional enhancers direct precise on-off patterns of gene expression during development. To explore the basis for this precision, we conducted a high-throughput analysis of the Otx-a enhancer, which mediates expression in the neural plate of Ciona embryos in response to fibroblast growth factor (FGF) signaling and a localized GATA determinant. We provide evidence that enhancer specificity depends on submaximal recognition motifs having reduced binding affinities ("suboptimization"). Native GATA and ETS (FGF) binding sites contain imperfect matches to consensus motifs. Perfect matches mediate robust but ectopic patterns of gene expression. The native sites are not arranged at optimal intervals, and subtle changes in their spacing alter enhancer activity. Multiple tiers of enhancer suboptimization produce specific, but weak, patterns of expression, and we suggest that clusters of weak enhancers, including certain "superenhancers," circumvent this trade-off in specificity and activity.

Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis.

BackgroundTargeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive.ResultsHere we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified.ConclusionsUsing this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1263-4) contains supplementary material, which is available to authorized users.

MIMO: an efficient tool for molecular interaction maps overlap.

BackgroundMolecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps.ResultsOur approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database.ConclusionsMIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways.

Biological and Therapeutic Applications of Small RNAs

In the past decade, small RNAs including small interfering RNA (siRNA) and microRNA (miRNA) have attracted intense interest due to their unique roles in fundamental biological processes by regulating the stabilities and functions of mRNAs. As illustrated in Fig. 1, the numbers of publications related to siRNA and miRNA have increased dramatically in recent years. Although miRNA was discovered earlier than siRNA, its importance was not fully realized as siRNA from 2000 to 2005. However, while the siRNA publications reached a plateau after 2007, the number of publications on miRNA has increased exponentially since 2005. siRNAs are artificial double-stranded RNAs of 21–23 nt in length, while miRNAs are endogenous singlestranded RNAs of 21–25 nt. Both siRNA and miRNA are non-coding RNAs that post-transcriptionally suppress gene expressions by binding to their complementary mRNAs. The major difference between siRNA and miRNA is that each siRNA only specifically targets a single mRNA and induces its degradation, while a single miRNA targets hundreds of mRNAs either by blocking protein translation or destabilizing the mRNA molecules. This difference comes from the fact that siRNA always forms a perfect match to its complementary mRNA, while miRNA only forms imperfect matches to its multiple mRNA targets (1–3). This theme issue focuses on recent advances in the biological and therapeutic applications of siRNA and miRNA. There are six articles in this issue highlighting research from studying gene functions to delivery to therapeutic application of siRNA. Since its discovery, siRNA has been widely applied as a powerful tool to study genetic functions of a specific gene. To further expand the applications of siRNA in gene function studies, Friedman et al. describe a novel light-activated RNA interference (RNAi) strategy by incorporating photolabile groups (di-methoxy nitro phenyl ethyl or DMNPE) to multiple double-stranded precursors of siRNA (dsRNA). Phosphorothioate linkages are also incorporated to increase the serum stability of the dsRNA. This strategy allows the control of the spacing, timing, and amount of gene expressions by adjusting light exposure. A successful light-controllable RNAi is particularly useful for the study of developmental biology or targeted delivery to specific sites in the body. Another promising application of siRNA is the treatment of various diseases by silencing their key modulators. Currently, there are 13 ongoing clinical trials using siRNA for numerous diseases. A review by Schaffer et al. discusses basic action mechanisms and therapeutic applications of RNAi in antiviral therapy. Design considerations, delivery strategies, computational insight, and areas for future improvement are described. Another article by Nemunaitis and colleagues summarizes the potentials, challenges, and current status of small RNA-based cancer therapies. As an example of developing siRNA therapy, Cheng’s group explore the potential therapeutic application of PCBP2 siRNA in treating alcoholic liver fibrosis which is characK. Cheng (*) Division of Pharmaceutical Sciences, School of Pharmacy University of Missouri—Kansas City 2464 Charlotte Street, HSB 5250 Kansas City, Missouri 64108-2718, USA e-mail: chengkun@umkc.edu

Letters in time and retinotopic space.

Various phenomena in tachistoscopic word identification and priming (WRODS and LTRS are confused with and prime WORDS and LETTERS) suggest that position-specific channels are not used in the processing of letters in words. Previous approaches to this issue have sought alternative matching rules because they have assumed that these phenomena reveal which stimuli are good but imperfect matches to a particular word-such imperfect matches being taken by the word recognition system as partial evidence for that word. The new Letters in Time and Retinotopic Space model (LTRS) makes the alternative assumption that these phenomena reveal the rates at which different features of the stimulus are extracted, because the stimulus is ambiguous when some features are missing from the percept. LTRS is successfully applied to tachistoscopic identification and form priming data with manipulations of duration and target-foil and prime-target relationships.

Building and Searching Tandem Mass Spectral Libraries for Peptide Identification

Spectral library searching is an emerging approach in peptide identifications from tandem mass spectra, a critical step in proteomic data analysis. Conceptually, the premise of this approach is that the tandem MS fragmentation pattern of a peptide under some fixed conditions is a reproducible fingerprint of that peptide, such that unknown spectra acquired under the same conditions can be identified by spectral matching. In actual practice, a spectral library is first meticulously compiled from a large collection of previously observed and identified tandem MS spectra, usually obtained from shotgun proteomics experiments of complex mixtures. Then, a query spectrum is then identified by spectral matching using recently developed spectral search engines. This review discusses the basic principles of the two pillars of this approach: spectral library construction, and spectral library searching. An overview of the software tools available for these two tasks, as well as a high-level description of the underlying algorithms, will be given. Finally, several new methods that utilize spectral libraries for peptide identification in ways other than straightforward spectral matching will also be described.

Seawater nutrient and carbonate ion concentrations recorded as P/Ca, Ba/Ca, and U/Ca in the deep-sea coral Desmophyllum dianthus

As paleoceanographic archives, deep sea coral skeletons offer the potential for high temporal resolution and precise absolute dating, but have not been fully investigated for geochemical reconstructions of past ocean conditions. Here we assess the utility of skeletal P/Ca, Ba/Ca and U/Ca in the deep sea coral D. dianthus as proxies of dissolved phosphate (remineralized at shallow depths), dissolved barium (trace element with silicate-type distribution) and carbonate ion concentrations, respectively. Measurements of these proxies in globally distributed D. dianthus specimens show clear dependence on corresponding seawater properties. Linear regression fits of mean coral Element/Ca ratios against seawater properties yield the equations: P/Ca coral (μmol/mol) = (0.6 ± 0.1) P/Ca sw(μmol/mol) – (23 ± 18), R 2 = 0.6, n = 16 and Ba/Ca coral(μmol/mol) = (1.4 ± 0.3) Ba/Ca sw(μmol/mol) + (0 ± 2), R 2 = 0.6, n = 17; no significant relationship is observed between the residuals of each regression and seawater temperature, salinity, pressure, pH or carbonate ion concentrations, suggesting that these variables were not significant secondary dependencies of these proxies. Four D. dianthus specimens growing at locations with Ω arag ⩽ 0.6 displayed markedly depleted P/Ca compared to the regression based on the remaining samples, a behavior attributed to an undersaturation effect. These corals were excluded from the calibration. Coral U/Ca correlates with seawater carbonate ion: U/Ca coral(μmol/mol) = (−0.016 ± 0.003) [ CO 3 2 - ] (μmol/kg) + (3.2 ± 0.3), R 2 = 0.6, n = 17. The residuals of the U/Ca calibration are not significantly related to temperature, salinity, or pressure. Scatter about the linear calibration lines is attributed to imperfect spatial-temporal matches between the selected globally distributed specimens and available water column chemical data, and potentially to unresolved additional effects. The uncertainties of these initial proxy calibration regressions predict that dissolved phosphate could be reconstructed to ±0.4 μmol/kg (for 1.3–1.9 μmol/kg phosphate), and dissolved Ba to ±19 nmol/kg (for 41–82 nmol/kg Ba sw). Carbonate ion concentration derived from U/Ca has an uncertainty of ±31μmol/kg (for 60 – 120 μ mol / kg CO 3 2 - ). The effect of microskeletal variability on P/Ca, Ba/Ca, and U/Ca was also assessed, with emphasis on centers of calcification, Fe–Mn phases, and external contaminants. Overall, the results show strong potential for reconstructing aspects of water mass mixing and biogeochemical processes in intermediate and deep waters using fossil deep-sea corals.

Transcriptional regulation of neuropeptide and peptide hormone expression by theDrosophila dimmedandcryptocephalgenes

The regulation of neuropeptide and peptide hormone gene expression is essential for the development and function of neuroendocrine cells in integrated physiological networks. In insects, a decline in circulating ecdysteroids triggers the activation of a neuroendocrine system to stimulate ecdysis, the behaviors used to shed the old cuticle at the culmination of each molt. Here we show that two evolutionarily conserved transcription factor genes, the basic helix-loop-helix (bHLH) gene dimmed (dimm) and the basic-leucine zipper (bZIP) gene cryptocephal (crc), control expression of diverse neuropeptides and peptide hormones in Drosophila. Central nervous system expression of three neuropeptide genes, Dromyosuppressin, FMRFamide-related and Leucokinin, is activated by dimm. Expression of Ecdysis triggering hormone (ETH) in the endocrine Inka cells requires crc; homozygous crc mutant larvae display markedly reduced ETH levels and corresponding defects in ecdysis. crc activates ETH expression though a 382 bp enhancer, which completely recapitulates the ETH expression pattern. The enhancer contains two evolutionarily conserved regions, and both are imperfect matches to recognition elements for activating transcription factor-4 (ATF-4), the vertebrate ortholog of the CRC protein and an important intermediate in cellular responses to endoplasmic reticulum stress. These regions also contain a putative ecdysteroid response element and a predicted binding site for the products of the E74 ecdysone response gene. These results suggest that convergence between ATF-related signaling and an important intracellular steroid response pathway may contribute to the neuroendocrine regulation of insect molting.

Mycobacterial linear plasmids have an invertron-like structure related to other linear replicons in actinomycetes.

The authors previously identified large plasmids in Mycobacterium xenopi, M. branderi and M. celatum which appeared to have a linear topology. This study has confirmed the presence of such linear plasmids in mycobacteria, including M. avium, and demonstrated that the ends of these replicons are covalently bound with protein(s), suggesting an invertron-like structure. The termini of one 25 kb plasmid, designated pCLP, from M. celatum were cloned and the first 500 bp of each terminus were sequenced. The termini of this plasmid show the characteristic features of invertrons with terminal inverted repeats of 45 bp (with imperfect matches) and several palindromic sequences. Moreover, similarity existed in the structure and terminal nucleotide sequence of pCLP and the termini of linear replicons of Streptomyces and Rhodococcus species, indicating a conservation of these linear extrachromosomal elements within the Actinomycetales.

Labor-Market Imperfections and the Agglomeration of Firms: Evidence from the Emergent Period of the US Semiconductor Industry

The regional literature suggests that local labor markets offer significant operating advantages to firms in knowledge-intensive industries and thus influence the development of contemporary industrial location patterns. Utilizing two data sets containing information on the employment changes of US semiconductor engineers during the critical formative period (1950–75), the author tests the pooling and anchoring hypotheses of urban economic theory while extending the theory to incorporate the effects of labor and firm specialization. Findings include: (1) moderate evidence of locality-centered labor pooling in this occupation during this early time period; (2) no evidence of anchoring by nonmarket actors, such as universities and government laboratories or by early labor markets; and (3) evidence that agglomerations of firms develop as a result of imperfect skill-opportunity matches. The results discount frequently offered explanations for the emergence of industrial agglomerations and suggest that agglomerations are not the outcome of firms' searches for operating efficiencies but may be a product of entrepreneurship induced by particular ‘permanently failing’ firms.

Heat shock-induced interactions of heat shock transcription factor and the human hsp70 promoter examined by in vivo footprinting.

Genomic footprinting of the human hsp70 promoter reveals that heat shock induces a rapid binding of a factor, presumably heat shock transcription factor, to a region encompassing five contiguous NGAAN sequences, three perfect and two imperfect matches to the consensus sequence. Arrays of inverted NGAAN sequences have been defined as the heat shock element. No protein is bound to the heat shock element prior to or after recovery from heat shock. Heat shock does not perturb the binding of factors to other regulatory elements in the promoter which contribute to basal expression of the hsp70 gene.

Heat Shock-Induced Interactions of Heat Shock Transcription Factor and the Human hsp70 Promoter Examined by In Vivo Footprinting

Genomic footprinting of the human hsp70 promoter reveals that heat shock induces a rapid binding of a factor, presumably heat shock transcription factor, to a region encompassing five contiguous NGAAN sequences, three perfect and two imperfect matches to the consensus sequence. Arrays of inverted NGAAN sequences have been defined as the heat shock element. No protein is bound to the heat shock element prior to or after recovery from heat shock. Heat shock does not perturb the binding of factors to other regulatory elements in the promoter which contribute to basal expression of the hsp70 gene.

Improved Identification of Clastic Depositional Environments by Process and Facies Models in Expert System: ABSTRACT

A previously described expert system for identification of clastic depositional environments (XEOD) has been substantially redesigned and improved as XEOD-II. Whereas the original design utilized simple checklist relationships between environments and features (sedimentary structures, lithology, etc), the new version is more meaningful in that it uses features to characterize facies as intermediate steps to an environmental interpretation. Some facies correspond directly to particular environments (e.g., tractive unidirectional currents). Facies classification is hierarchical, and identification proceeds to the most specific level allowable by the input data. More contexturally accurate interpretations for coastal and fluvial systems are possible using a series of data sets representing facies in a vertical sequence. Tentative facies identifications are verified by imperfect matching against a set of idealized vertical-sequence models. Incomplete and imperfect matches are diagnosed using alternative interpretations which combine two or more models. In spite of considerable difficulty in accepting both specific and varietal terms, improvements in the user interface have resulted in a relatively forgiving program. XEOD-II thus represents a second-generation system utilizing both factual knowledge and logical reasoning in sedimentological facies analysis.