An adaptive threshold determination method of feature screening for genomic selection

Background

Although the dimension of the entire genome can be extremely large, only a parsimonious set of influential SNPs are correlated with a particular complex trait and are important to the prediction of the trait. Efficiently and accurately selecting these influential SNPs from millions of candidates is in high demand, but poses challenges. We propose a backward elimination iterative distance correlation (BE-IDC) procedure to select the smallest subset of SNPs that guarantees sufficient prediction accuracy, while also solving the unclear threshold issue for traditional feature screening approaches.

Results

Verified through six simulations, the adaptive threshold estimated by the BE-IDC performed uniformly better than fixed threshold methods that have been used in the current literature. We also applied BE-IDC to an Arabidopsis thaliana genome-wide data. Out of 216,130 SNPs, BE-IDC selected four influential SNPs, and confirmed the same FRIGIDA gene that was reported by two other traditional methods.

Conclusions

BE-IDC accommodates both the prediction accuracy and the computational speed that are highly demanded in the genomic selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1617-9) contains supplementary material, which is available to authorized users.

Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models

Leaf shape traits have long been a focus of many disciplines, but the complex genetic and environmental interactive mechanisms regulating leaf shape variation have not yet been investigated in detail. The question of the respective roles of genes and environment and how they interact to modulate leaf shape is a thorny evolutionary problem, and sophisticated methodology is needed to address it. In this study, we investigated a framework-level approach that inputs shape image photographs and genetic and environmental data, and then outputs the relative importance ranks of all variables after integrating shape feature extraction, dimension reduction, and tree-based statistical models. The power of the proposed framework was confirmed by simulation and a Populus szechuanica var. tibetica data set. This new methodology resulted in the detection of novel shape characteristics, and also confirmed some previous findings. The quantitative modeling of a combination of polygenetic, plastic, epistatic, and gene-environment interactive effects, as investigated in this study, will improve the discernment of quantitative leaf shape characteristics, and the methods are ready to be applied to other leaf morphology data sets. Unlike the majority of approaches in the quantitative leaf shape literature, this framework-level approach is data-driven, without assuming any pre-known shape attributes, landmarks, or model structures.

A Proof of Concept Study of Function-Based Statistical Analysis of fNIRS Data: Syntax Comprehension in Children with Specific Language Impairment Compared to Typically-Developing Controls

Functional near infrared spectroscopy (fNIRS) is a neuroimaging technology that enables investigators to indirectly monitor brain activity in vivo through relative changes in the concentration of oxygenated and deoxygenated hemoglobin. One of the key features of fNIRS is its superior temporal resolution, with dense measurements over very short periods of time (100 ms increments). Unfortunately, most statistical analysis approaches in the existing literature have not fully utilized the high temporal resolution of fNIRS. For example, many analysis procedures are based on linearity assumptions that only extract partial information, thereby neglecting the overall dynamic trends in fNIRS trajectories. The main goal of this article is to assess the ability of a functional data analysis (FDA) approach for detecting significant differences in hemodynamic responses recorded by fNIRS. Children with and without SLI wore two, 3 × 5 fNIRS caps situated over the bilateral parasylvian areas as they completed a language comprehension task. FDA was used to decompose the high dimensional hemodynamic curves into the mean function and a few eigenfunctions to represent the overall trend and variation structures over time. Compared to the most popular GLM, we did not assume any parametric structure and let the data speak for itself. This analysis identified significant differences between the case and control groups in the oxygenated hemodynamic mean trends in the bilateral inferior frontal and left inferior posterior parietal brain regions. We also detected significant group differences in the deoxygenated hemodynamic mean trends in the right inferior posterior parietal cortex and left temporal parietal junction. These findings, using dramatically different approaches, experimental designs, data sets, and foci, were consistent with several other reports, confirming group differences in the importance of these two areas for syntax comprehension. The proposed FDA was consistent with the temporal characteristics of fNIRS, thus providing an alternative methodology for fNIRS analyses.

Production and genetic analysis of resynthesized Brassica napus from a B. rapa landrace from the Qinghai-Tibet Plateau and B. alboglabra

This study aimed to reveal the genetic and epigenetic variations involved in a resynthesized Brassica napus (AACC) generated from a hybridization between a B. rapa (AA) landrace and B. alboglabra (CC). Amplified fragment length polymorphism (AFLP), methylation-sensitive amplified polymorphism, and the cDNA-AFLP technique were performed to detect changes between different generations at the genome, methylation, and transcription levels. We obtained 30 lines of resynthesized B. napus with a mean 1000-seed weight of over 7.50 g. All of the lines were self-compatible, probably because both parents were self-compatible. At the genome level, the S0 generation had the lowest frequency of variations (0.18%) and the S3 generation had the highest (6.07%). The main variation pattern was the elimination of amplified restriction fragments on the CC genome from the S0 to the S4 generations. At the methylation level, we found three loci that exhibited altered methylation patterns on the parental A genome; the variance rate was 1.35%. At the transcription level, we detected 43.77% reverse mutations and 37.56% deletion mutations that mainly occurred on the A and C genomes, respectively, in the S3 generation. Our results highlight the genetic variations that occur during the diploidization of resynthesized B. napus.

Identification of candidate causal genes and their associated pathogenic mechanisms underlying teratozoospermia based on the spermatozoa transcript profiles

Teratozoospermia with unclear pathomechanism is one of the common causes for failed fertilisation. This study aimed to further explore the pathological mechanism for teratozoospermia. Spermatozoal transcript profiles generated from 13 normal fertile men and eight infertile males with a consistent severe heterogeneous teratozoospermia were used. These data were pre-processed, and differentially expressed genes were screened. Besides, gene ontology and pathway enrichment analysis were performed, and then, protein-protein interaction (PPI) network was constructed, and spermatogenesis-related genes in the PPI network were extracted. As a result, 366 up-regulated and 2158 down-regulated genes were identified. Multiple gene ontology terms and pathways including cell-cell signalling and reproduction enriched by differentially expressed genes were obtained. Moreover, four clusters including cluster 1 associated with RNA catabolic process were identified from the PPI network. In addition, genes including cyclin B1, proteasome (prosome, macropain) activator subunit 4, Rac GTPase-activating protein 1 and pituitary tumour-transforming 1 were received. In conclusion, abnormal expression of cyclin B1 and Rac GTPase-activating protein 1, still proteasome (prosome, macropain) activator subunit 4 and pituitary tumour-transforming 1 would impede cell cycle progression during sperm development and maturation, which may contribute to the occurrence and development of teratozoospermia.

Tigecycline exerts an antitumoral effect in oral squamous cell carcinoma

OBJECTIVE

To explore whether antibacterial drug tigecycline could exert an antitumoral effect in oral squamous cell carcinoma (OSCC).

MATERIALS AND METHODS

Two OSCC cell lines Tca8113 and KB were used in this study. To investigate the cytostatic effects of tigecycline in OSCC, cell growth was tested by trypan blue staining, MTT assay, and Brdu immunofluorescence staining. Then, the apoptosis proportion was measured by FITC Annexin-V and PI labeling, and cell cycle was determined by PI staining. The expression of caspase 3 (CASP3) and cell cycle regulatory protein was detected by Western blot assay. Finally, the clonogenesis and tumorigenesis capacity were analyzed by soft agar growth and xenograft model.

RESULTS

Here, we showed that tigecycline significantly inhibited cell growth and proliferation in OSCC cell lines Tca8113 and KB. It did not induce cell apoptosis but led to an increase of cells in G0/G1 phase with down-regulation of cyclin E2 (CCNE2) and cyclin-dependent kinase4 (CDK4) protein expression. We also showed that tigecycline inhibited colony formation in soft agar and reduced tumor growth in a xenograft model.

CONCLUSION

Our results suggested that tigecycline might be used as a novel candidate agent for the treatment of OSCC.

First Report of Neofusicoccum parvum Causing Panicle Blight and Leaf Spot on Vitis heyneana in China

The climbing vine, Vitis heyneana Roem. & Schult, is a member of the grape family endemic to Asia. Its fruits are used in wine production, and its roots, stems, and leaves can be used in medicinal materials. This plant is grown in Southwest China, as well as in India, Bhutan, and Nepal. Mulao Autonomous County in Guangxi Province is the only artificial cultivation area in China. During the summer of 2013, a panicle blight and leaf spot were detected on V. heyneana on four farms in Mulao Autonomous County. The symptoms were observed from the onset of florescence through fruit harvest. Brown lesions initially appeared at the base of a panicle and then extended to the whole panicle, finally causing the panicle to die and fruit to drop. When the disease developed on leaves, the symptom initially appeared as small dark brown circular spots, later enlarging into irregular spots (average diameter 6 mm) with a light brown center and dark brown rim. With severe disease, some individual leaves were affected by numerous spots, leading to premature senescence. Small sections of diseased tissue excised from 10 panicle and 10 leaf samples were plated on potato dextrose agar (PDA) and incubated at 28°C. Fungal colonies developed, initially with abundant white aerial mycelium, which turned olivaceous gray after 5 days and formed black pycnidia after 25 days. The conidia were hyaline, ellipsoidal to fusiform, externally smooth, thin-walled, and nonseptate. Thirty conidia were measured; the dimensions were 12.0 to 17.5 × 4.0 to 6.0 μm. Morphological characteristics of the isolates were similar to the descriptions of Neofusicoccum parvum (3). The isolate MPT-1 was selected as a representative for molecular identification. Genomic DNA was extracted and used for PCR to amplify the internal transcribed spacer (ITS) region and partial translation elongation factor 1-alpha (EF1-α) gene, using primers ITS1/ITS4 and EF1-728F/EF1-986R, respectively. The obtained ITS sequence (GenBank Accession No. KJ599627) and EF1-α sequence (KM921768) showed >99% homology with several GenBank sequences of N. parvum. Morphological and molecular results confirmed the isolate as N. parvum. For pathogenicity tests, detached, young healthy panicles and leaves of V. heyneana were surface-sterilized, wounded by sterile needle, and inoculated with mycelial plugs (3 mm in diameter) of four N. parvum isolates. Ten panicles and 10 leaves were used for every isolate. Control panicles and leaves were treated with sterile PDA plugs. All the samples were placed in a humid chamber (RH 90%, 28°C, 12 h of light) for 3 days. Symptoms similar to those observed in the field developed on all panicles and leaves inoculated with N. parvum isolates. N. parvum was reisolated from all inoculated, symptomatic tissues. The controls remained symptomless. N. parvum has been reported to cause trunk canker on V. vinifera (2), dieback on Cupressus funebris (3), and a leaf spot on Myristica fragrans (1). To our knowledge, this is the first report of N. parvum causing panicle blight and leaf spot on V. heyneana in China. Panicle blight caused a large number of fruits to drop and reduced the yield seriously. Some effective measures should be taken to control this disease. References: (1) V. Jayakumar et al. New Dis. Rep. 23:19, 2011. (2) J. Kaliternam et al. Plant Dis. 97:1656, 2013. (3) S. B. Li et al. Plant Dis. 94:641, 2010.

A graphical weighted power improving multiplicity correction approach for SNP selections

Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a commonly used approach due to its simplicity, but is conservative and has low power for large-scale tests. The permutation test, which is a powerful and popular tool, is computationally expensive and may mislead in the presence of family structure. We propose a computationally efficient and powerful multiple testing correction approach for Linkage Disequilibrium (LD) based Quantitative Trait Loci (QTL) mapping on the basis of graphical weighted-Bonferroni methods. The proposed multiplicity adjustment method synthesizes weighted Bonferroni-based closed testing procedures into a powerful and versatile graphical approach. By tailoring different priorities for the two hypothesis tests involved in LD based QTL mapping, we are able to increase power and maintain computational efficiency and conceptual simplicity. The proposed approach enables strong control of the familywise error rate (FWER). The performance of the proposed approach as compared to the standard Bonferroni correction is illustrated by simulation and real data. We observe a consistent and moderate increase in power under all simulated circumstances, among different sample sizes, heritabilities, and number of SNPs. We also applied the proposed method to a real outbred mouse HDL cholesterol QTL mapping project where we detected the significant QTLs that were highlighted in the literature, while still ensuring strong control of the FWER.

Holm multiple correction for large-scale gene-shape association mapping

Background

Linkage Disequilibrium (LD) is a powerful approach for the identification and characterization of morphological shape, which usually involves multiple genetic markers. However, multiple testing corrections substantially reduce the power of the associated tests. In addition, the principle component analysis (PCA), used to quantify the shape variations into several principal phenotypes, further increases the number of tests. As a result, a powerful multiple testing correction for simultaneous large-scale gene-shape association tests is an essential part of determining statistical significance. Bonferroni adjustments and permutation tests are the most popular approaches to correcting for multiple tests within LD based Quantitative Trait Loci (QTL) models. However, permutations are extremely computationally expensive and may mislead in the presence of family structure. The Bonferroni correction, though simple and fast, is conservative and has low power for large-scale testing.

Results

We propose a new multiple testing approach, constructed by combining an Intersection Union Test (IUT) with the Holm correction, which strongly controls the family-wise error rate (FWER) without any additional assumptions on the joint distribution of the test statistics or dependence structure of the markers. The power improvement for the Holm correction, as compared to the standard Bonferroni correction, is examined through a simulation study. A consistent and moderate increase in power is found under the majority of simulated circumstances, including various sample sizes, Heritabilities, and numbers of markers. The power gains are further demonstrated on real leaf shape data from a natural population of poplar, Populus szechuanica var tietica, where more significant QTL associated with morphological shape are detected than under the previously applied Bonferroni adjustment.

Conclusion

The Holm correction is a valid and powerful method for assessing gene-shape association involving multiple markers, which not only controls the FWER in the strong sense but also improves statistical power.

Inhibition of farnesyl pyrophosphate synthase prevents angiotensin II-induced cardiac fibrosis in vitro

Farnesyl pyrophosphate synthase (FPPS)-catalysed isoprenoid intermediates are important for the activation of Ras homologue gene family, member A (RhoA) in angiotensin (Ang) II-induced cardiac fibrosis. This study was designed to investigate the specific role of FPPS in the development of cardiac fibrosis. We demonstrated that FPPS expression was elevated in both in-vivo and in-vitro models of Ang II-mediated cardiac fibrosis. FPPS inhibition by zolendronate and FPPS knock-down by a silencing lentivirus decreased the expression of cardiac fibrosis marker genes, including collagen I, collagen III and transforming growth factor (TGF)-β1. FPPS inhibition was reversed by geranylgeraniol (GGOH) and mimicked by RhoA knock-down with siRhoA. The antagonistic effect of GGOH on the zolendronate-mediated modulation of RhoA activation in Ang II-stimulated cardiac fibroblasts was demonstrated by a pull-down assay. Furthermore, FPPS knock-down also prevented RhoA activation by Ang II in vitro. In conclusion, FPPS and RhoA may be part of a signalling pathway that plays an important role in Ang II-induced cardiac fibrosis in vitro.

Clustering analysis of water distribution systems: identifying critical components and community impacts

Large water distribution systems (WDSs) are networks with both topological and behavioural complexity. Thereby, it is usually difficult to identify the key features of the properties of the system, and subsequently all the critical components within the system for a given purpose of design or control. One way is, however, to more explicitly visualize the network structure and interactions between components by dividing a WDS into a number of clusters (subsystems). Accordingly, this paper introduces a clustering strategy that decomposes WDSs into clusters with stronger internal connections than external connections. The detected cluster layout is very similar to the community structure of the served urban area. As WDSs may expand along with urban development in a community-by-community manner, the correspondingly formed distribution clusters may reveal some crucial configurations of WDSs. For verification, the method is applied to identify all the critical links during firefighting for the vulnerability analysis of a real-world WDS. Moreover, both the most critical pipes and clusters are addressed, given the consequences of pipe failure. Compared with the enumeration method, the method used in this study identifies the same group of the most critical components, and provides similar criticality prioritizations of them in a more computationally efficient time.

First Report of Corynespora cassiicola Causing Leaf Spot on Akebia trifoliate

Akebia species have been used for centuries in medicinal practices in a few Asian countries such as China and Japan. The dried stems of Akebia trifoliata are known as mutong in the Chinese pharmacopoeia (4) and mokutsu in Kampo, the traditional Chinese medicine developed in Japan (2). In China, the plant is grown in the provinces of Shandong, Hebei, Shanxi, Henan, Gansu, and some provinces in the south of the Yangtze River basin. During the summer of 2012, a leaf spot disease was detected on A. trifoliata grown in Nanning, Guangxi, China. The disease occurred and spread rapidly in July under conditions of high temperature and high humidity. The symptoms appeared on three sites that we inspected; disease incidences were higher than 80%. Initial symptoms consisted of small (less than 5 mm in diameter), circular, purple-brown leaf spots. Spots later enlarged and became elliptical, circular, or irregular with gray-white centers and dark brown rims. The centers were slightly concave. The spots could coalesce with each other, resulting in leaf desiccation and wilting. A fungal isolate was obtained from symptomatic leaf tissue that taken from a field (22°50'N, 108°22'E) in Nanning, Guangxi, China. Single-spore culture of the isolate was incubated on potato dextrose agar (PDA) for 7 days in the dark at 28°C. Conidiophores were straight to slightly curved, unbranched, and pale brown. Conidia (19.0 to 140.5 μm long and 7.0 to 11.0 μm wide) were formed singly or in chains, obclavate to cylindrical, straight or curved, pale brown, with a rounded apex and truncate base, and 1 to 13 pseudosepta. Morphological characteristics of the isolate were similar to the descriptions of Corynespora cassiicola (Berk. & M.A. Curtis) C.T. Wei (1). Genomic DNA of the isolate was extracted and used for PCR amplification of rDNA-ITS (internal transcribed spacer) sequence with primers ITS1 and ITS4. The PCR products were purified and sequenced. The sequence (GenBank Accession No. KC977496) was used in BLAST searches to interrogate GenBank for sequence similarity. High sequence similarity of 100% was obtained with several C. cassiicola strains. Pathogenicity of the isolate was investigated to demonstrate Koch's postulate. Young, healthy, fully expanded green leaves of A. trifoliata were surface sterilized. Fifteen leaves were inoculated with 10-μl drops of conidia suspension (10⁵ conidia per ml) and 10 leaves were inoculated with the same volume of sterile water to serve as controls. All the leaves were placed in a humid chamber for 5 days. Spots with similar symptoms to those observed in the field developed on all inoculated leaves. The pathogen was reisolated and identified as C. cassiicola. The controls remained symptomless. According to previous reports, A. trifoliata was infected by Alternaria tenuissima in China and by Colletotrichum acutatum in Japan (3). To our knowledge, this is the first report of C. cassiicola found on Akebia species worldwide. Furthermore, this new disease primarily affects plantations and reduces the quality and yield of the medicine. Some effective measures should be taken to control this disease. References: (1) M. B. Ellis and P. Holliday. CMI Description of Pathogenic Fungi and Bacteria, 303, 1971. (2) F. Kitaoka et al. J. Nat. Med. 63:374, 2009. (3) Y. Kobayshi et al. J. Gen. Plant Pathol. 70:295, 2004. (4) L. Li et al. HortScience 45:4, 2010.

Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s^-1·MBq^-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging ^99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using ^99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

Stochastic modeling of systems mapping in pharmacogenomics

As a basis of personalized medicine, pharmacogenetics and pharmacogenomics that aim to study the genetic architecture of drug response critically rely on dynamic modeling of how a drug is absorbed and transported to target tissues where the drug interacts with body molecules to produce drug effects. Systems mapping provides a general framework for integrating systems pharmacology and pharmacogenomics through robust ordinary differential equations. In this chapter, we extend systems mapping to more complex and more heterogeneous structure of drug response by implementing stochastic differential equations (SDE). We argue that SDE-implemented systems mapping provides a computational tool for pharmacogenetic or pharmacogenomic research towards personalized medicine.