scholarly journals Genome analysis of the fatal tapeworm Sparganum proliferum unravels the cryptic lifecycle and mechanisms underlying the aberrant larval proliferation

2020 ◽  
Author(s):  
Taisei Kikuchi ◽  
Mehmet Dayi ◽  
Vicky L. Hunt ◽  
Atsushi Toyoda ◽  
Yasunobu Maeda ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Asexual Reproduction ◽  
Sexual Maturity ◽  
Reference Genome ◽  
Cestode Species ◽  
Genome Sequences ◽  
High Quality ◽  
Genetic Sequence ◽  
Future Studies ◽  
Underlying Mechanisms

AbstractBackgroundThe cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, the S. proliferum phylogeny and lifecycle are still an enigma.ResultsTo investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the underlying mechanisms of pathogenicity, we sequenced the entire S. proliferum genome. Additionally, S. proliferum plerocercoid larvae transcriptome analyses were performed to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum genetic sequence is distinct from that of the closely related Spirometra erinaceieuropaei. Moreover, nonordinal extracellular matrix coordination allows for asexual reproduction in the host and loss of sexual maturity in S. proliferum is related to its fatal pathogenicity in humans.ConclusionsThe high-quality reference genome sequences generated should prove valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

scholarly journals Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Taisei Kikuchi ◽  
Mehmet Dayi ◽  
Vicky L. Hunt ◽  
Kenji Ishiwata ◽  
Atsushi Toyoda ◽  
...  
Keyword(s):  
Life Cycle ◽  
Asexual Reproduction ◽  
Sexual Maturity ◽  
Evolutionary History ◽  
Reference Genome ◽  
Cestode Species ◽  
Genome Sequences ◽  
High Quality ◽  
Future Studies ◽  
Life Threatening

AbstractThe cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, S. proliferum’s phylogeny and life cycle remain enigmatic. To investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the mechanisms underlying pathogenicity, we sequenced the entire genomes of S. proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei. Additionally, we performed larvae transcriptome analyses of S. proliferum plerocercoid to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum has experienced a clearly distinct evolutionary history from S. erinaceieuropaei. Moreover, we found that nonordinal extracellular matrix coordination allows asexual reproduction in the host, and loss of sexual maturity in S. proliferum are responsible for its fatal pathogenicity to humans. Our high-quality reference genome sequences should be valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

scholarly journals Genome Analysis of the Fatal Tapeworm Sparganum Proliferum Uncovers the Cryptic Life Cycle and Mechanisms Underlying Aberrant Larval Proliferation

2020 ◽  
Author(s):  
Taisei Kikuchi ◽  
Mehmet Dayi ◽  
Vicky Hunt ◽  
Atsushi Toyoda ◽  
Yasunobu Maeda ◽  
...  
Keyword(s):  
Life Cycle ◽  
Asexual Reproduction ◽  
Sexual Maturity ◽  
Evolutionary History ◽  
Reference Genome ◽  
Cestode Species ◽  
Genome Sequences ◽  
High Quality ◽  
Future Studies ◽  
Life Threatening

Abstract The cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, S. proliferum’s phylogeny and life cycle remain enigmatic. To investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the mechanisms underlying pathogenicity, we sequenced the entire genomes of S. proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei. Additionally, we performed larvae transcriptome analyses of S. proliferum plerocercoid to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum has experienced a clearly distinct evolutionary history from S. erinaceieuropaei. Moreover, we found that nonordinal extracellular matrix coordination allows asexual reproduction in the host, and loss of sexual maturity in S. proliferum are responsible for its fatal pathogenicity to humans. Our high-quality reference genome sequences should be valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

scholarly journals Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 50
Author(s):  
Axel Barlow ◽  
Stefanie Hartmann ◽  
Javier Gonzalez ◽  
Michael Hofreiter ◽  
Johanna L. A. Paijmans
Keyword(s):  
Clustering Analysis ◽  
Error Rates ◽  
Sequencing Error ◽  
Genome Sequences ◽  
High Quality ◽  
Short Read ◽  
Future Studies ◽  
Sequencing Coverage ◽  
Simplifying Assumptions ◽  
Population Clustering

A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.

scholarly journals High-quality assembly of sweet basil genome

2018 ◽  
Author(s):  
Nativ Dudai ◽  
Marie-Jeanne Carp ◽  
Renana Milavski ◽  
David Chaimovitsh ◽  
Alona Shachter ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
High Quality ◽  
Sweet Basil ◽  
Independent Analysis ◽  
Aroma Production ◽  
Culinary Uses ◽  
Underlying Mechanisms ◽  
Sequencing Platforms

AbstractSweet basil, sometimes called the King of Herbs, is well known for its culinary uses, especially in the Italian sauce ‘Pesto’. It is also used in traditional medicine, as a source for essential oils and as an ornamental plant. So far, basil was bred by classical and traditional methods due to lack of a reference genome that will allow optimized application of the most up-to-date sequencing techniques. Here, we report on the first completion of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil, using several next generation sequencing platforms followed by genome assembly with NRGENE’s DeNovoMAGIC assembly tool. We determined that the genome size of sweet basil is 2.13 Gbp and assembled it into 12,212 scaffolds. The high-quality of the assembly is reflected in that more than 90% of the assembly size is composed of only 107 scaffolds. An independent analysis of single copy orthologues genes showed a 93% completeness which reveal also that 74% of them were duplicated, indicating that the sweet basil is a tetraploid organism. A reference genome of sweet basil will enable to develop precise molecular markers for various agricultural important traits such as disease resistance and tolerance to various environmental conditions. We will gain a better understanding of the underlying mechanisms of various metabolic processes such as aroma production and pigment accumulation. Finally, it will save time and money for basil breeders and scientists and ensure higher throughput and robustness in future studies.

scholarly journals Genome sequence data of Leptosphaerulina arachidicola, a causal agent of peanut scorch spot in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Yu-Ting Sheng Sheng ◽  
Xiao-Li Yu ◽  
Ting-Ting Mao ◽  
Juan Zhang ◽  
Xiao-Tong Guo ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Yield Loss ◽  
Reference Genome ◽  
Sequence Data ◽  
High Quality ◽  
Future Studies ◽  
Significant Yield ◽  
High Quality Genome ◽  
Severe Leaf

Peanut scorch spot caused by Leptosphaerulina arachidicola is one of the most severe leaf diseases of peanut that causes significant yield loss. Here, we report the first high quality genome sequence of L. arachidicola JB313 isolated from an infected peanut leaf in China. The genome size is 47.66 Mb, consisting of 65 scaffolds (N50 length = 1.58 Mb) with a G+C content of 49.05%. The information in this report will provide a reference genome for future studies on peanut scorch spot pathogen in peanut.

scholarly journals Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada

2019 ◽  
Vol 8 (41) ◽  
Author(s):  
Shari Tyson ◽  
Christy-Lynn Peterson ◽  
Adam Olson ◽  
Shaun Tyler ◽  
Natalie Knox ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Reference Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Food Animal ◽  
Bovine Strain ◽  
Human Infections ◽  
Reference Genomes

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.

scholarly journals Homogenous overexpression of the extracellular matrix protein Netrin-1 in a hollow fiber bioreactor

2021 ◽  
Author(s):  
Aniel Moya-Torres ◽  
Monika Gupta ◽  
Fabian Heide ◽  
Natalie Krahn ◽  
Scott Legare ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Hollow Fiber ◽  
Mammalian Cells ◽  
Matrix Protein ◽  
Continuous Production ◽  
Extracellular Matrix Protein ◽  
Close Monitoring ◽  
High Quality ◽  
Biolayer Interferometry ◽  
Hollow Fiber Bioreactor

Abstract The production of recombinant proteins for functional and biophysical studies, especially in the field of structural determination, still represents a challenge as high quality and quantities are needed to adequately perform experiments. This is in part solved by optimizing protein constructs and expression conditions to maximize the yields in regular flask expression systems. Still, work flow and effort can be substantial with no guarantee to obtain improvements. This study presents a combination of workflows that can be used to dramatically increase protein production and improve processing results, specifically for the extracellular matrix protein Netrin-1. This proteoglycan is an axon guidance cue which interacts with various receptors to initiate downstream signaling cascades affecting cell differentiation, proliferation, metabolism, and survival. We were able to produce large glycoprotein quantities in mammalian cells, which were engineered for protein overexpression and secretion into the media using the controlled environment provided by a hollow fiber bioreactor. Close monitoring of the internal bioreactor conditions allowed for stable production over an extended period of time. In addition to this, Netrin-1 concentrations were monitored in expression media through biolayer interferometry which allowed us to increase Netrin-1 media concentrations tenfold over our current flask systems while preserving excellent protein quality and in solution behavior. Our particular combination of genetic engineering, cell culture system, protein purification, and biophysical characterization permitted us to establish an efficient and continuous production of high-quality protein suitable for structural biology studies that can be translated to various biological systems. Key points • Hollow fiber bioreactor produces substantial yields of homogenous Netrin-1 • Biolayer interferometry allows target protein quantitation in expression media • High production yields in the bioreactor do not impair Netrin-1 proteoglycan quality Graphical abstract

Female Voice Agents in Fully Autonomous Vehicles Are Not Only More Likeable and Comfortable, But Also More Competent

2020 ◽  
Vol 64 (1) ◽  
pp. 1033-1037
Author(s):  
Jiayuan Dong ◽  
Emily Lawson ◽  
Jack Olsen ◽  
Myounghoon Jeon
Keyword(s):  
Autonomous Vehicles ◽  
Autonomous Driving ◽  
Preference Ranking ◽  
Uncanny Valley ◽  
Tracking Data ◽  
Effective Solution ◽  
User Perception ◽  
Future Studies ◽  
Underlying Mechanisms ◽  
The Voice

Driving agents can provide an effective solution to improve drivers’ trust in and to manage interactions with autonomous vehicles. Research has focused on voice-agents, while few have explored robot-agents or the comparison between the two. The present study tested two variables - voice gender and agent embodiment, using conversational scripts. Twenty participants experienced autonomous driving using the simulator for four agent conditions and filled out subjective questionnaires for their perception of each agent. Results showed that the participants perceived the voice only female agent as more likeable, more comfortable, and more competent than other conditions. Their final preference ranking also favored this agent over the others. Interestingly, eye-tracking data showed that embodied agents did not add more visual distractions than the voice only agents. The results are discussed with the traditional gender stereotype, uncanny valley, and participants’ gender. This study can contribute to the design of in-vehicle agents in the autonomous vehicles and future studies are planned to further identify the underlying mechanisms of user perception on different agents.

scholarly journals Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sten Ilmjärv ◽  
Fabien Abdul ◽  
Silvia Acosta-Gutiérrez ◽  
Carolina Estarellas ◽  
Ioannis Galdadas ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Modelling ◽  
Spike Protein ◽  
Genome Sequences ◽  
Viral Polymerase ◽  
Rna Dependent Rna Polymerase ◽  
High Quality

AbstractThe D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.

scholarly journals Identification of key genes in calcific aortic valve disease via weighted gene co-expression network analysis

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jin-Yu Sun ◽  
Yang Hua ◽  
Hui Shen ◽  
Qiang Qu ◽  
Jun-Yan Kan ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Network Analysis ◽  
Aortic Valve ◽  
Aortic Valve Disease ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Valve Disease ◽  
Hub Genes ◽  
Calcific Aortic Valve Disease ◽  
Underlying Mechanisms

Abstract Background Calcific aortic valve disease (CAVD) is the most common subclass of valve heart disease in the elderly population and a primary cause of aortic valve stenosis. However, the underlying mechanisms remain unclear. Methods The gene expression profiles of GSE83453, GSE51472, and GSE12644 were analyzed by ‘limma’ and ‘weighted gene co-expression network analysis (WGCNA)’ package in R to identify differentially expressed genes (DEGs) and key modules associated with CAVD, respectively. Then, enrichment analysis was performed based on Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, DisGeNET, and TRRUST database. Protein–protein interaction network was constructed using the overlapped genes of DEGs and key modules, and we identified the top 5 hub genes by mixed character calculation. Results We identified the blue and yellow modules as the key modules. Enrichment analysis showed that leukocyte migration, extracellular matrix, and extracellular matrix structural constituent were significantly enriched. SPP1, TNC, SCG2, FAM20A, and CD52 were identified as hub genes, and their expression levels in calcified or normal aortic valve samples were illustrated, respectively. Conclusions This study suggested that SPP1, TNC, SCG2, FAM20A, and CD52 might be hub genes associated with CAVD. Further studies are required to elucidate the underlying mechanisms and provide potential therapeutic targets.

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