Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Background: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. Results: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). Conclusions: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level

The effect of urbanization and exposure to multiple environmental factors on life-history traits and breeding success of Barn Swallows (Hirundo rustica) across China

In addition to landscape changes, urbanization also brings about changes in environmental factors that can affect wildlife. Despite the common referral in the published literature to multiple environmental factors such as light and noise pollution, there is a gap in knowledge about their combined impact. We developed a multidimensional environmental framework to assess the effect of urbanization and multiple environmental factors (light, noise, and temperature) on life-history traits and breeding success of Barn Swallows (Hirundo rustica) across rural to urban gradients in four locations spanning over 2500 ​km from North to South China. Over a single breeding season, we measured these environmental factors nearby nests and quantified landscape urbanization over a 1 ​km2 radius. We then analysed the relationships between these multiple environmental factors through a principal component analysis and conducted spatially explicit linear-mixed effects models to assess their effect on life-history traits and breeding success. We were particularly interested in understanding whether and how Barn Swallows were able to adapt to such environmental conditions associated with urbanization. The results show that there is significant variation in the exposure to environmental conditions experienced by Barn Swallows breeding across urbanization gradients in China. These changes and their effects are complex due to the behavioural responses ameliorating potential negative effects by selecting nesting sites that minimize exposure to environmental factors. However, significant relationships between landscape urbanization, exposure to environmental factors, and life-history traits such as laying date and clutch size were pervasive. Still, the impact on breeding success was, at least in our sample, negligible, suggesting that Barn Swallows are extremely adaptable to a wide range of environmental features

A DDoS Attack Detection Method Based on SVM in Software Defined Network

The detection of DDoS attacks is an important topic in the field of network security. The occurrence of software defined network (SDN) (Zhang et al., 2018) brings up some novel methods to this topic in which some deep learning algorithm is adopted to model the attack behavior based on collecting from the SDN controller. However, the existing methods such as neural network algorithm are not practical enough to be applied. In this paper, the SDN environment by mininet and floodlight (Ning et al., 2014) simulation platform is constructed, 6-tuple characteristic values of the switch flow table is extracted, and then DDoS attack model is built by combining the SVM classification algorithms. The experiments show that average accuracy rate of our method is 95.24% with a small amount of flow collecting. Our work is of good value for the detection of DDoS attack in SDN

A comparative analysis for the volatile compounds of various Chinese dark teas using combinatory metabolomics and fungal solid-state fermentation

A total of 98 compounds including 20 aldehydes, eight arenes, six acids, 17 alcohols, 13 ketones, nine esters, nine methoxyphenolics, three alkenes, seven alkanes, and six other components were tentatively identified in six Chinese dark teas (CDTs) using gas chromatography–mass spectrometry. Multivariate statistical analysis revealed that dark teas from Yunnan and Guangxi provinces could be classified into one group, and other CDTs belonged to the other cluster. The diagnostic volatile compounds being responsible for CDTs' discrimination were observed as (E,E)-2,4-decadienal, methoxyphenolics, geraniol, α-terpineol, 2,4-heptadienal, cis-jasmone, linalool oxides, and 2-nonenal. Furthermore, mature tea leaves were separately fermented using Eurotium cristatum and Aspergillus niger. The results showed that E. cristatum increased the contents of cis-jasmone, α-terpineol, ß-ionone, nonanal, and 2-pentylfuran, whereas A. niger advanced the levels of geraniol, linalool oxides, 9,12-octadecadienoic acid, and ß-ionone after short-term fermentation. Fungus species may contribute to forming the flavor of Chinese dark teas by affecting the volatile compounds during postfermentation

RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples.

Clinical tumor tissues that are preserved as formalin-fixed paraffin-embedded (FFPE) samples result in extensive cross-linking, fragmentation, and chemical modification of RNA, posing significant challenges for RNA-seq-based gene expression profiling. This study sought to define an optimal RNA-seq protocol for FFPE samples. We employed a common RNA extraction method and then compared RNA-seq library preparation protocols including RNAaccess, RiboZero and PolyA in terms of sequencing quality and concordance of gene expression using FFPE and case-matched fresh-frozen (FF) triple-negative breast cancer (TNBC) tissues. We found that RNAaccess, a method based on exome capture, produced the most concordant results. Applying RNAaccess to FFPE gastric cancer tissues, we established a minimum RNA DV200 requirement of 10% and a RNA input amount of 10ng that generated highly reproducible gene expression data. Lastly, we demonstrated that RNAaccess and NanoString platforms produced highly concordant expression profiles from FFPE samples for shared genes; however, RNA-seq may be preferred for clinical biomarker discovery work because of the broader coverage of the transcriptome. Taken together, these results support the selection of RNA-seq RNAaccess method for gene expression profiling of FFPE samples. The minimum requirements for RNA quality and input established here may allow for inclusion of clinical FFPE samples of sub-optimal quality in gene expression analyses and ultimately increasing the statistical power of such analyses

Latrophilin participates in insecticide susceptibility through positively regulating CSP10 and partially compensated by OBPC01 in Tribolium castaneum

WOS:000482696800015Latrophilin (LPH) is an adhesion G protein-coupled receptor (aGPCR) that participates in multiple essential physiological processes. Our previous studies have shown that lph is not only indispensable for the development and reproduction of red flour beetles (Tribolium castaneum), but also for their resistance against dichlorvos or carbofuran insecticides. However, the regulatory mechanism of lph-mediated insecticide susceptibility remains unclear. Here, we revealed that knockdown of lph in beetles resulted in opposing changes in two chemoreception genes, chemosensory protein 10 (CSP10) and odorant-binding protein C01 (OBPC01), in which the expression of TcCSP10 was downregulated, whereas the expression of TcOBPC01 was upregulated. TcCSP10 and TcOBPC01 were expressed at the highest levels in early pupal and late larval stages, respectively. High levels of expression of both these genes were observed in the heads (without antennae) of adults. TcCSP10 and TcOBPC01 were significantly induced by dichlorvos or carbofuran between 12 and 72 h (hrs) after exposure, suggesting that they are likely associated with increasing the binding affinity of insecticides, leading to a decrease in sensitivity to the insecticides. Moreover, once these two genes were knocked down, the susceptibility of the beetles to dichlorvos or carbofuran was enhanced. Additionally, RNA interference (RNAi) targeting of lph followed by exposure to dichlorvos or carbofuran also caused the opposing expression levels of TcCSP10 and TcOBPC01 compared to the expression levels of wild-type larvae treated with insecticides alone. All these results indicate that lph is involved in insecticide susceptibility through positively regulating TcCSP10; and the susceptibility could also further partially compensated for through the negative regulation of TcOBPC01 when lph was knockdown in the red flour beetle. Our studies shed new light on the molecular regulatory mechanisms of lph related to insecticide susceptibility

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

Background: Cancers arise through an evolutionary process in which cell populations are subjected to selection; however, to date, the process of bladder cancer, which is one of the most common cancers in the world, remains unknown at a single-cell level. Results: We carried out single-cell exome sequencing of 66 individual tumor cells from a muscle-invasive bladder transitional cell carcinoma (TCC). Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading to two distinct tumor cell subpopulations. By analyzing recurrently mutant genes in an additional cohort of 99 TCC tumors, we identified genes that might play roles in the maintenance of the ancestral clone and in the muscle-invasive capability of subclones of this bladder cancer, respectively. Conclusions: This work provides a new approach of investigating the genetic details of bladder tumoral changes at the single-cell level and a new method for assessing bladder cancer evolution at a cell-population level. © 2012 Li et al.; licensee BioMed Central Ltd