scholarly journals SurVirus: a repeat-aware virus integration caller

2021 ◽  
Author(s):  
Ramesh Rajaby ◽  
Yi Zhou ◽  
Yifan Meng ◽  
Xi Zeng ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Human Genome ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Second Generation ◽  
False Positives ◽  
The Other ◽  
False Negatives ◽  
Human Cancers ◽  
Human Genomes ◽  
Virus Integration

Abstract A significant portion of human cancers are due to viruses integrating into human genomes. Therefore, accurately predicting virus integrations can help uncover the mechanisms that lead to many devastating diseases. Virus integrations can be called by analysing second generation high-throughput sequencing datasets. Unfortunately, existing methods fail to report a significant portion of integrations, while predicting a large number of false positives. We observe that the inaccuracy is caused by incorrect alignment of reads in repetitive regions. False alignments create false positives, while missing alignments create false negatives. This paper proposes SurVirus, an improved virus integration caller that corrects the alignment of reads which are crucial for the discovery of integrations. We use publicly available datasets to show that existing methods predict hundreds of thousands of false positives; SurVirus, on the other hand, is significantly more precise while it also detects many novel integrations previously missed by other tools, most of which are in repetitive regions. We validate a subset of these novel integrations, and find that the majority are correct. Using SurVirus, we find that HPV and HBV integrations are enriched in LINE and Satellite regions which had been overlooked, as well as discover recurrent HBV and HPV breakpoints in human genome-virus fusion transcripts.

scholarly journals DNA-Based Herbal Teas’ Authentication: An ITS2 and psbA-trnH Multi-Marker DNA Metabarcoding Approach

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2120
Author(s):  
Jessica Frigerio ◽  
Giulia Agostinetto ◽  
Valerio Mezzasalma ◽  
Fabrizio De De Mattia ◽  
Massimo Labra ◽  
...  
Keyword(s):  
Quality Control ◽  
Quantitative Analysis ◽  
Medicinal Plants ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
The Other ◽  
Plant Component ◽  
Identification Rate ◽  
Dna Metabarcoding ◽  
Therapeutic Properties

Medicinal plants have been widely used in traditional medicine due to their therapeutic properties. Although they are mostly used as herbal infusion and tincture, employment as ingredients of food supplements is increasing. However, fraud and adulteration are widespread issues. In our study, we aimed at evaluating DNA metabarcoding as a tool to identify product composition. In order to accomplish this, we analyzed fifteen commercial products with DNA metabarcoding, using two barcode regions: psbA-trnH and ITS2. Results showed that on average, 70% (44–100) of the declared ingredients have been identified. The ITS2 marker appears to identify more species (n = 60) than psbA-trnH (n = 35), with an ingredients’ identification rate of 52% versus 45%, respectively. Some species are identified only by one marker rather than the other. Additionally, in order to evaluate the quantitative ability of high-throughput sequencing (HTS) to compare the plant component to the corresponding assigned sequences, in the laboratory, we created six mock mixtures of plants starting both from biomass and gDNA. Our analysis also supports the application of DNA metabarcoding for a relative quantitative analysis. These results move towards the application of HTS analysis for studying the composition of herbal teas for medicinal plants’ traceability and quality control.

scholarly journals Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Lasse Vinner ◽  
Tobias Mourier ◽  
Jens Friis-Nielsen ◽  
Robert Gniadecki ◽  
Karen Dybkaer ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Enrichment ◽  
Human Cancers

Diagnostic difficulties of plunging ranula: case series

2012 ◽  
Vol 126 (5) ◽  
pp. 506-510 ◽  
Author(s):  
R Jain ◽  
R P Morton ◽  
Z Ahmad
Keyword(s):  
New Zealand ◽  
Surgical Management ◽  
Case Series ◽  
Cystic Hygroma ◽  
False Positives ◽  
The Other ◽  
Thyroglossal Cyst ◽  
False Negatives ◽  
Diagnostic Difficulties

AbstractObjectives:To evaluate common pitfalls in diagnosing complicated plunging ranula, either due to misidentification of plunging ranula or alternative pathology (i.e. false negatives or false positives, respectively).Methods:A review of cases of plunging ranula seen in Middlemore Hospital, New Zealand, was performed. Diagnostically uncertain cases were identified and reviewed, taking particular note of clinical, radiological and surgical findings.Results:From our database, 12 cases were found to have had a complicated diagnosis of plunging ranula. Ten cases were false negatives: four were treated as abscesses, four as simple cysts, one as a thyroglossal cyst and one as a cystic hygroma. Two cases were false positives: one was found to be a thyroglossal cyst and the other a lipoma.Conclusion:The diagnosis of plunging ranula is usually straightforward, with simple surgical management. Misdiagnosis can lead to recurrence of symptoms and inappropriate management, with the associated risks, complications and frustrations of surgery.

scholarly journals Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

2020 ◽  
Author(s):  
Laura C. Rosenwald ◽  
Michael I. Sitvarin ◽  
Jennifer A. White
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Strain ◽  
High Throughput Sequencing ◽  
Cytoplasmic Incompatibility ◽  
The Other ◽  
Bacterial Endosymbionts ◽  
Different Strains

AbstractMany arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally-inherited symbiont from the genera Wolbachia, Rickettsia, and Rickettsiella. The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella. We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella-infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella, or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally-inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia.

NMR-Based Quality Control Approach for the Identification of False Positives and False Negatives in High Throughput Screening

2006 ◽  
Vol 3 (2) ◽  
pp. 115-124 ◽  
Author(s):  
Claudio Dalvit ◽  
Dannica Caronni ◽  
Nicola Mongelli ◽  
Marina Veronesi ◽  
Anna Vulpetti
Keyword(s):  
Quality Control ◽  
High Throughput ◽  
High Throughput Screening ◽  
False Positives ◽  
False Negatives ◽  
Control Approach

Role of Yeasts in the Cranberry Fruit Rot Disease Complex

Plant Disease ◽  
2020 ◽  
Author(s):  
Zachary David Zalewski ◽  
Rae Page ◽  
Richard Lankau ◽  
Patricia McManus
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
The Other ◽  
Fruit Rot ◽  
Internal Transcribed Spacer Region ◽  
Operational Taxonomic Units ◽  
Inhibition Of Growth ◽  
Hanseniaspora Uvarum ◽  
Rot Disease

Cranberry fruit rot (CFR) is an economically important disease caused by at least 10 species of filamentous fungi. Despite the application of fungicides, incidence of CFR is sometimes high, raising the possibility of a role for microbes other than fungi in the CFR complex. Isolation of microbes from rotten berries on media that favor either bacteria or yeasts resulted in mucoid colonies from fewer than 15% of dry-harvested rotten berries but up to 60% of wet-harvested berries. The mucoid colonies were identified as yeasts, primarily in the family Saccharomycetaceae. Inoculation of sound berries with three yeasts, Hanseniaspora uvarum, Pichia fermentans, and Pichia terricola, resulted in significantly higher incidence and severity of rot symptoms compared to mock-inoculated controls; these yeasts were recovered from inoculated berries, providing evidence of their pathogenicity. The minimum concentrations of azoxystrobin, chlorothalonil, and prothioconazole that resulted in 80% inhibition of growth compared to untreated controls (MIC80) were determined for a subset of yeasts. In general, MIC80s were higher for azoxystrobin and prothioconazole (usually >64 µg/ml) than for chlorothalonil (usually ≤1 µg/ml). To complement culture-dependent studies, DNA was isolated from wet- and dry-harvested rotten berries, and fungi were identified to the level of family by high-throughput sequencing of the fungal internal transcribed spacer region (ITS2). There were no fungal families consistently detected among samples by one method (culturing or high-throughput sequencing) and missed by the other that have not previously been reported in cranberry; however, some fungal families were found to be more abundant by one method versus the other. Harvest method (wet or dry) had a significant effect on the composition of fungal communities of rotten berries (P < 0.001), and operational taxonomic units representing the Saccharomycetaceae were more abundant in wet- than dry-harvested berries. Taken together, the results suggest that some yeasts are pathogenic to cranberry and may be especially relevant in wet-harvested berries.

scholarly journals Effects of keratinocyte-derived and fibroblast-derived exosomes on human epidermal melanocytes

2021 ◽  
Vol 0 ◽  
pp. 1-10
Author(s):  
Hai-Xia Shi ◽  
Ru-Zhi Zhang ◽  
Li Xiao ◽  
Li Wang
Keyword(s):  
Signaling Pathway ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Tyrosinase Activity ◽  
The Other ◽  
Differentially Expressed ◽  
Ras Signaling ◽  
Sequencing Analysis ◽  
Melanin Synthesis

Background: Exosomes have been demonstrated to carry proteins, membrane lipids, mRNAs and microRNAs which can be transferred to surrounding cells and regulate the functions of those recipient cells. Objectives: The objective of the study was to investigate the effects of exosomes released by keratinocytes and fibroblasts on the proliferation, tyrosinase activity and melanogenesis of melanocytes. Methods: Melanocytes, keratinocytes and fibroblasts obtained from human foreskin were cultured and exosomes secreted by keratinocytes and fibroblasts were harvested from the culture supernatants by ultracentrifugation. Each exosome fraction was divided into two parts; one part was subjected to high-throughput sequencing using an Illumina HiSeq sequencer to characterize the microRNA expression profiles, while the other part was labeled with the fluorescent dye PKH67 and was then co-cultivated with epidermal melanocytes. Results: High-throughput sequencing analysis showed 168 differentially expressed microRNA within exosomes derived from keratinocytes and from fibroblasts, 97 of those being up-regulated with the other 71 down-regulated. Gene ontology analysis showed that the target genes responsible for these differentially expressed microRNAs were mainly enriched in the protein-binding region of molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that target genes regulated by differentially expressed microRNA were mainly involved in mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, cAMP signaling pathway and Wnt signaling pathway. Keratinocyte-derived exosomes were taken up by melanocytes co-cultured with them and promoted the proliferation, tyrosinase activity and melanin synthesis of those melanocytes. However, fibroblast-derived exosomes had no similar effects on melanocytes. Conclusion: Keratinocyte-derived exosomes but not fibroblast-derived exosomes were taken up by melanocytes in co-culture and significantly stimulated their proliferation, tyrosinase activity and melanin synthesis. Those different effects may be mainly due to the differential expression of microRNAs in exosomes derived from the different types of cells. Limitations: Electron microscopy of the obtained exosomes and in-depth study of apparently differentially expressed microRNAs were not performed.

scholarly journals Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

2020 ◽  
Vol 287 (1930) ◽  
pp. 20201107 ◽  
Author(s):  
Laura C. Rosenwald ◽  
Michael I. Sitvarin ◽  
Jennifer A. White
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Strain ◽  
High Throughput Sequencing ◽  
Cytoplasmic Incompatibility ◽  
The Other ◽  
Bacterial Endosymbionts ◽  
Different Strains

Many arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here, we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally inherited symbiont from the genera Wolbachia , Rickettsia , and Rickettsiella . The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella . We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella -infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella , or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia .

scholarly journals Evaluating the accuracy of DNA stable isotope probing

2017 ◽  
Author(s):  
Nicholas D. Youngblut ◽  
Daniel H. Buckley
Keyword(s):  
Stable Isotope ◽  
Dna Sequencing ◽  
High Throughput ◽  
False Positives ◽  
Stable Isotope Probing ◽  
Detection Sensitivity ◽  
False Negatives ◽  
Isotope Incorporation ◽  
High Throughput Dna Sequencing

Originality-Significance StatementBy combining DNA Stable Isotope Probing (DNA-SIP) with multiplexed high throughput DNA sequencing (HTS-DNA-SIP), it is now possible to identify patterns of isotope incorporation for thousands of microbial taxa. HTS-DNA-SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. A current limitation is that, due to the expense of these experiments, it has been impossible to evaluate the accuracy of DNA-SIP methods. We have developed a model that simulates DNA-SIP data, and we use the model to systematically evaluate and validate the accuracy of DNA-SIP analyses. This model can determine the analytical accuracy of DNA-SIP experiments in a range of contexts. Furthermore, the ability to predict experimental outcomes, as a function of experimental design and community characteristics, should be of great use in the design and interpretation DNA-SIP experiments.SummaryDNA Stable isotope probing (DNA-SIP) is a powerful method that identifiesin situisotope assimilation by microbial taxa. Combining DNA-SIP with multiplexed high throughput DNA sequencing (HTS-DNA-SIP) creates the potential to mapin situassimilation dynamics for thousands of microbial taxonomic units. However, the accuracy of methods for analyzing DNA-SIP data has never been evaluated. We have developed a toolset (SIPSim) for simulating HTS-DNA-SIP datasets and evaluating the accuracy of methods for analyzing HTS-DNA-SIP data. We evaluated two different approaches to analyzing HTS-DNA-SIP data: “high resolution stable isotope probing” (HR-SIP) and “quantitative stable isotope probing” (q-SIP). HR-SIP was highly specific and moderately sensitive, with very few false positives but potential for false negatives. In contrast, q-SIP had fewer false negatives but many false positives. We also found HR-SIP more robust than q-SIP with respect to experimental variance. Furthermore, we found that the detection sensitivity of HTS-DNA-SIP can be increased without compromising specificity by evaluating evidence of isotope incorporation over multiple windows of buoyant density (MW-HR-SIP). SIPSim provides a platform for determining the accuracy of HTS-DNA-SIP methods across a range of experimental parameters, which will be useful in the design, analysis, and validation of DNA-SIP experiments.

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