scholarly journals Dataset of Oyster Virome and the Remarkable Virus Diversity in Filter-Feeding Oysters

2021 ◽  
Author(s):  
Jing-Zhe Jiang ◽  
Yi-Fei Fang ◽  
Hong-Ying Wei ◽  
Ying-Xiang Guo ◽  
Li-Ling Yang ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Operational Taxonomic Unit ◽  
Filter Feeding ◽  
High Quality ◽  
Comprehensive Overview ◽  
Dna Viruses ◽  
Viral Ecology ◽  
Marine Virus ◽  
Viral Genomes ◽  
Virus Diversity

Abstract Background:Viruses are the most abundant biological entities, and they play critical roles in entire ecosystems. Nevertheless, current knowledge about them is no more than 1% of the estimated diversity of the Earth’s virosphere. Oysters are filter-feeding molluscan bivalves and are ideal sentinels for marine virus exploration and viral ecology studies. Results: Here we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit (vOTU) contigs and 3,473 high-quality viral genomes, enabling the first comprehensive overview of viral communities in oysters. As in other marine viromes, families Siphoviridae, Podoviridae, and Myoviridae are dominant in the DOV. However, Circoviridae is the most abundant family among the high-quality genomes, indicating that oysters may be their potential hotspots. Despite performing target amplification for RNA genomes, the diversity of RNA viruses was much lower than the diversity of DNA viruses. Notably, most of the vOTUs in the DOV were previously undescribed viruses and could not be clustered with any sequences in three reference datasets. Three approaches (based on references, vOTUs, and auxiliary metabolic genes) consistently showed that host health status, location, and sampling date had potential impacts on virome structures. Conclusions: This study highlights the practicality of oysters for marine virus exploration and provides a new direction to understand the relationship between marine bivalves and the environment.

scholarly journals Significance of indeterminate pulmonary nodules in resectable pancreatic adenocarcinoma—a review

2021 ◽  
Author(s):  
Li Lian Kuan ◽  
Ashley R. Dennison ◽  
Giuseppe Garcea
Keyword(s):  
Overall Survival ◽  
Pancreatic Adenocarcinoma ◽  
Median Overall Survival ◽  
Current Knowledge ◽  
Pulmonary Nodules ◽  
Preoperative Imaging ◽  
Significant Finding ◽  
Comprehensive Overview ◽  
Significant Difference ◽  
Clinical Dilemma

Abstract Background The clinical significance of indeterminate pulmonary nodules (IPN) in patients with resectable pancreatic adenocarcinoma (PDAC) is unknown. The rate of detection on IPN has risen due to enhanced staging investigations to determine resectability. IPNs detected on preoperative imaging represent a clinical dilemma and complicate decision-making. Currently, there are no recommendations on the management of IPN. This review provides a comprehensive overview of the current knowledge on the natural history of IPN detected among patients with resectable PDAC. Methods A systematic review based on a search in Medline and Embase databases was performed. All clinical studies evaluating the significance of IPN in patients with resectable PDAC were included. PRISMA guidelines were followed. Results Five studies met the inclusion criteria. The total patient population was 761. The prevalence of IPN reported ranged from 18 to 71%. The median follow-up duration was 17 months. The median overall survival was 19 months. Patients with pre-operative IPN which subsequently progressed to clinically recognizable pulmonary metastases, ranged from 1.5 to 16%. Four studies found that there was no significant difference in median overall survival in patients with or without IPNs. Conclusion This is a first review on the significance of IPN in patients with resectable PDAC. The preoperative presence of IPN does not demonstrate an association with overall survival after surgery. The identification of IPN is a significant finding however it should not preclude patients with resectable PDAC from undergoing curative resection.

scholarly journals Latest Advances of Virology Research Using CRISPR/Cas9-Based Gene-Editing Technology and Its Application to Vaccine Development

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 779
Author(s):  
Man Teng ◽  
Yongxiu Yao ◽  
Venugopal Nair ◽  
Jun Luo
Keyword(s):  
Biological Sciences ◽  
Gene Therapy ◽  
Genetic Engineering ◽  
Gene Function ◽  
Viral Genome ◽  
Gene Editing ◽  
Vaccine Development ◽  
Future Prospects ◽  
Dna Viruses ◽  
Viral Genomes

In recent years, the CRISPR/Cas9-based gene-editing techniques have been well developed and applied widely in several aspects of research in the biological sciences, in many species, including humans, animals, plants, and even in viruses. Modification of the viral genome is crucial for revealing gene function, virus pathogenesis, gene therapy, genetic engineering, and vaccine development. Herein, we have provided a brief review of the different technologies for the modification of the viral genomes. Particularly, we have focused on the recently developed CRISPR/Cas9-based gene-editing system, detailing its origin, functional principles, and touching on its latest achievements in virology research and applications in vaccine development, especially in large DNA viruses of humans and animals. Future prospects of CRISPR/Cas9-based gene-editing technology in virology research, including the potential shortcomings, are also discussed.

Obtaining High-Quality Blood Specimens for Downstream Applications: A Review of Current Knowledge and Best Practices

2018 ◽  
Vol 16 (6) ◽  
pp. 411-418 ◽  
Author(s):  
Qiyuan Li ◽  
Xian Wang ◽  
Xue Li ◽  
Xuheng He ◽  
Qian Wan ◽  
...  
Keyword(s):  
Best Practices ◽  
Current Knowledge ◽  
High Quality ◽  
Blood Specimens

scholarly journals A Comprehensive Review on Eryptosis

2016 ◽  
Vol 39 (5) ◽  
pp. 1977-2000 ◽  
Author(s):  
Etheresia Pretorius ◽  
Jeanette N. du Plooy ◽  
Janette Bester
Keyword(s):  
Current Knowledge ◽  
Cell Model ◽  
Health Indicators ◽  
Comprehensive Overview ◽  
Ultrastructural Studies ◽  
Important Health ◽  
Membrane Changes ◽  
Cell Model System ◽  
Cell Changes

Erythrocytes (RBCs) are extremely sensitive cells, and although they do not have nuclei and mitochondria, are important health indicators. This is particularly true because, during inflammation, whether it is systemic or chronic, the haematological system is constantly exposed to circulating inflammatory mediators. RBCs have a highly specialized and organized membrane structure, which interacts and reacts to inflammatory molecule insults, and undergo programmed cell death, similar to apoptosis, known as eryptosis. Over the past years, eryptosis studies have focussed on determining if membrane changes have occurred, particularly whether a phosphatidylserine (PS) flip, Ca2+ leakage into the cell, changes to ceramide and cell shrinkage have occurred. Mostly, flow cytometry is used, but confocal microscopy and ultrastructural studies also confirm eryptosis. Here, we provide a comprehensive overview of eryptosis, where we revisit the biochemical process of the process, review all literature in PUBMED, that is shown under the search word, “eryptosis”, and also discuss current methodologies to determine the presence of eryptosis; included in the discussion of the methodologies, we discuss a pitfalls section for each method. This paper is therefore a comprehensive synopsis of current knowledge of eryptosis and discusses how RBCs may provide an essential in vivo cell model system to study not only inflammation in disease, but also track disease progression and treatment regimes.

scholarly journals Date Components as Promising Plant-Based Materials to Be Incorporated into Baked Goods—A Review

2022 ◽  
Vol 14 (2) ◽  
pp. 605
Author(s):  
Meththa Ranasinghe ◽  
Ioannis Manikas ◽  
Sajid Maqsood ◽  
Constantinos Stathopoulos
Keyword(s):  
Current Knowledge ◽  
Value Added ◽  
Phoenix Dactylifera ◽  
Research Area ◽  
Bakery Products ◽  
Comprehensive Overview ◽  
Food Ingredients ◽  
Baked Goods ◽  
Industry Standards ◽  
By Products

Date (Phoenix dactylifera L. Arecaceae) fruits and their by-products are rich in nutrients. The health benefits of dates and their incorporation into value-added products have been widely studied. The date-processing industry faces a significant sustainability challenge as more than 10% (w/w) of the production is discarded as waste or by-products. Currently, food scientists are focusing on bakery product fortification with functional food ingredients due to the high demand for nutritious food with more convenience. Utilizing date components in value-added bakery products is a trending research area with increasing attention. Studies where the researchers tried to improve the quality of bakery goods by incorporating date components have shown positive results, with several drawbacks that need attention and further research. The objective of this review is to present a comprehensive overview of the utilization of date components in bakery products and to identify gaps in the current knowledge. This review will help focus further research in the area of valorization of date by-products and thereby contribute to the generation of novel functional bakery products that meet consumer expectations and industry standards, thus generating income for the relevant industry and considerable alleviation of the environmental burden this waste and by-products contribute to. Only a few studies have been focused on utilizing date by-products and their extracts for baked goods, while a research area still remaining under-explored is the effect of incorporation of date components on the shelf life of bakery products.

scholarly journals The Flavonoid Biosynthesis Network in Plants

2021 ◽  
Vol 22 (23) ◽  
pp. 12824
Author(s):  
Weixin Liu ◽  
Yi Feng ◽  
Suhang Yu ◽  
Zhengqi Fan ◽  
Xinlei Li ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Current Knowledge ◽  
Anthocyanin Biosynthesis ◽  
Basic Structure ◽  
Ring Structure ◽  
Flavonoid Biosynthesis ◽  
Comprehensive Overview ◽  
Flavonoid Biosynthetic Pathway ◽  
Intermediate Metabolites ◽  
Important Intermediate

Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.

scholarly journals Unique viruses that infect Archaea related to eukaryotes

2021 ◽  
Author(s):  
Ian M Rambo ◽  
Valerie De Anda ◽  
Marguerite V Langwig ◽  
Brett J Baker
Keyword(s):  
Transcriptional Regulation ◽  
Deep Sea ◽  
Structural Proteins ◽  
Genome Replication ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Archaeal Viruses ◽  
Hydrothermal Sediments ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Globally Distributed

Asgard archaea are newly described microbes that are related to eukaryotes. Asgards are diverse and globally distributed, however, their viruses have not been described. Here we characterize seven viral genomes that infected Lokiarchaeota, Helarchaeota, and Thorarchaeota in deep-sea hydrothermal sediments. These viruses code for structural proteins similar to those in Caudovirales, as well as proteins distinct from those described in archaeal viruses. They also have genes common in eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs), and are predicted to be capable of semi-autonomous genome replication, repair, epigenetic modifications, and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. This first glimpse of Asgard viruses reveals they have features of both prokaryotic and eukaryotic viruses, and provides insights into their roles in the ecology and evolution of these globally distributed microbes.

scholarly journals Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

2020 ◽  
Vol 14 (10) ◽  
pp. 2527-2541 ◽  
Author(s):  
Jessica K. Jarett ◽  
Mária Džunková ◽  
Frederik Schulz ◽  
Simon Roux ◽  
David Paez-Espino ◽  
...  
Keyword(s):  
Single Cell ◽  
Hot Spring ◽  
Current Knowledge ◽  
Single Cells ◽  
Metagenomic Data ◽  
Viral Genomes ◽  
Active Viral Replication ◽  
High Layer ◽  
Host Virus Interactions ◽  
Virus Interactions

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

scholarly journals Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1022 ◽  
Author(s):  
Pacifica Sommers ◽  
Rafaela S. Fontenele ◽  
Tayele Kringen ◽  
Simona Kraberger ◽  
Dorota L. Porazinska ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Reading Frames ◽  
Pairwise Identity ◽  
Capsid Protein Gene ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Freshwater Pond ◽  
Dry Valley ◽  
Population Structures

Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.

scholarly journals High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics

Viruses ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 385 ◽  
Author(s):  
Asimina Katsiani ◽  
Varvara Maliogka ◽  
Nikolaos Katis ◽  
Laurence Svanella-Dumas ◽  
Antonio Olmos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sour Cherry ◽  
Prunus Species ◽  
Cherry Tree ◽  
High Genetic Diversity ◽  
Viral Genomes ◽  
Virus Diversity ◽  
First Time

Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.

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