scholarly journals A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris)

2020 ◽  
Vol 165 (12) ◽  
pp. 2999-3002
Author(s):  
Jean-Sébastien Reynard ◽  
Justine Brodard ◽  
Eric Remoliff ◽  
Marie Lefebvre ◽  
Olivier Schumpp ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
International Committee ◽  
Species Demarcation Criterion ◽  
Replicase Gene ◽  
Sequencing Analysis ◽  
Species Demarcation ◽  
Demarcation Criterion ◽  
Wild Grapevine

Abstract We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named “grapevine foveavirus A” (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.

scholarly journals Patterns of Yeast Diversity Distribution and its Drivers in Rhizosphere Soil of Hami Melon Orchards in Different Regions of Xinjiang

2021 ◽  
Author(s):  
ShanShan Zhu ◽  
YongHui Lei ◽  
Chong Wang ◽  
YuMei Wei ◽  
ChunCheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Yeast Species ◽  
Sequence Similarity ◽  
Climatic Conditions ◽  
Community Diversity ◽  
Sequencing Analysis ◽  
Microscopic Fungus ◽  
Yeast Diversity ◽  
Northern Xinjiang

Abstract Background: Yeast is an essential type of microscopic fungus found in the soil. It is vital to develop the resources of yeast to gain a better understanding of its role and potential in maintaining soil ecological balance and providing microbial resources. A special ecological environment is required for the evolution of yeast species. Xinjiang in China has unique climatic conditions with abundant melon and fruit resources. Here, we aimed to evaluate the diversity, community structure, and relationship between yeast species and environmental factors in Hami melon orchards in different regions of Xinjiang, China.Results: We used Illumina MiSeq high-throughput sequencing analysis to cluster 29,090 yeast sequences into 87 operational taxonomic units (OTUs) with 97% sequence similarity and 47 genera and 73 species. Most sequences (93.16%) belonged to the Basidiomycota; only a few (6.84%) belonged to Ascomycota. We detected 10 dominant genera and 11 dominant species with relative abundances > 1% in all sample sequences. We found that the yeast communities were significantly more diverse in the eastern Xinjiang region than in the southern and northern Xinjiang regions. The most dominant genera in the southern, eastern, and northern Xinjiang regions were Pseudozyma (54.77%), Solicoccozyma (28.6%), and Filobasidium (88.08%), respectively. Redundancy analysis (RDA) results indicated that the main factors influencing the structure of yeast in the study sites were CO, total phosphorus (TP), and total potassium (TK) of the soil.Conclusion: Our results suggest the presence of diversity and structural differences in yeast species among the southern, eastern, and northern Xinjiang regions. Eastern Xinjiang had the highest community diversity with a more even distribution of species. Differences in the geographical environment and the physicochemical properties of soils were probably the key factors driving yeast diversity and community structure.

A New Approach for Predicting the Value of Gene Expression: Two-way Collaborative Filtering

2019 ◽  
Vol 14 (6) ◽  
pp. 480-490 ◽  
Author(s):  
Tuncay Bayrak ◽  
Hasan Oğul
Keyword(s):  
Gene Expression ◽  
Regression Model ◽  
Collaborative Filtering ◽  
High Throughput Sequencing ◽  
Mean Squared Error ◽  
Experimental Studies ◽  
Kernel Functions ◽  
Feature Representation ◽  
Sequencing Analysis ◽  
Computational Systems Biology

Background: Predicting the value of gene expression in a given condition is a challenging topic in computational systems biology. Only a limited number of studies in this area have provided solutions to predict the expression in a particular pattern, whether or not it can be done effectively. However, the value of expression for the measurement is usually needed for further meta-data analysis. Methods: Because the problem is considered as a regression task where a feature representation of the gene under consideration is fed into a trained model to predict a continuous variable that refers to its exact expression level, we introduced a novel feature representation scheme to support work on such a task based on two-way collaborative filtering. At this point, our main argument is that the expressions of other genes in the current condition are as important as the expression of the current gene in other conditions. For regression analysis, linear regression and a recently popularized method, called Relevance Vector Machine (RVM), are used. Pearson and Spearman correlation coefficients and Root Mean Squared Error are used for evaluation. The effects of regression model type, RVM kernel functions, and parameters have been analysed in our study in a gene expression profiling data comprising a set of prostate cancer samples. Results: According to the findings of this study, in addition to promising results from the experimental studies, integrating data from another disease type, such as colon cancer in our case, can significantly improve the prediction performance of the regression model. Conclusion: The results also showed that the performed new feature representation approach and RVM regression model are promising for many machine learning problems in microarray and high throughput sequencing analysis.

scholarly journals Evaluation of breeding potential of wild grape originating from Armenia

2019 ◽  
Vol 15 ◽  
pp. 01006
Author(s):  
K. Margaryan ◽  
E. Maul ◽  
Z. Muradyan ◽  
A. Hovhannisyan ◽  
G. Melyan ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Allelic Variation ◽  
Resistance Breeding ◽  
Crop Wild Relatives ◽  
Breeding Programs ◽  
Genetic Traits ◽  
Breeding Potential ◽  
Wild Grape ◽  
Wild Grapevine ◽  
The Future

Crop wild relatives provide a useful source of genetic variation and represent a large pool of genetic diversity for new allelic variation required in breeding programs. Armenia is an important center of origin both for cultivated Vitis vinifera ssp. sativa and wild Vitis vinifera ssp. sylvestris. Owing to recent prospection in Armenian woods and river floodplains many forms of wild grapevine were discovered and inventoried, which is an important prerequisite to unlock their breeding potential in the future. The fact that some genotypes of V. sylvestris can withstand the diseases is likely to be due to a more efficient basal immunity. The overall goal of the proposed research was to characterize the diversity of V. sylvestris from Armenia with respect to its capacity for stilbene biosynthesis, which might be exploited as genetic resource for resistance breeding. The realized research stimulates the recovery, characterization and preservation of wild grape germplasm, presently at risk of extinction. The recovery and characterization of wild genotypes will be the base of selection of genetic traits important in breeding programs for the generation of biotic and changing climate tolerant grapevine varieties and rootstocks, both necessary for the future of viticulture in Armenia and in Europe.

The species evenness of “prey” bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Hang Qian ◽  
Chunli Hou ◽  
Hao Liao ◽  
Li Wang ◽  
Shun Han ◽  
...  
Keyword(s):  
Soil Properties ◽  
Paddy Soil ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Negative Relationship ◽  
Sequencing Analysis ◽  
Nitrogen Use ◽  
Microbial Network ◽  
Α Diversity ◽  
Positive Effect

ABSTRACT To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.

scholarly journals High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Antibiotics ◽  
2018 ◽  
Vol 7 (2) ◽  
pp. 27 ◽  
Author(s):  
Marta Maciejewska ◽  
Magdalena Całusińska ◽  
Luc Cornet ◽  
Delphine Adam ◽  
Igor Pessi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Spatial Diversity ◽  
Sequencing Analysis

Macrophage-derived CXCL9 and CXCL11, T-cell skin homing and disease control in mogamulizumab-treated CTCL patients

Blood ◽  
2021 ◽  
Author(s):  
Adèle de Masson ◽  
Delphine Darbord ◽  
Gabor Dobos ◽  
Marie Boisson ◽  
Marie Roelens ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Disease Control ◽  
High Throughput Sequencing ◽  
Sequencing Analysis ◽  
Cell Clones ◽  
Skin Homing ◽  
T Cell Homing ◽  
T Cell Immune Responses

Cutaneous T-cell lymphoma (CTCL) is a malignancy of skin-homing T-cells. Long-term remissions are rare in CTCL, and the pathophysiology of long-lasting disease control is unknown. Mogamulizumab is a defucosylated anti-human CCR4 antibody that depletes CCR4-expressing CTCL tumor cells and peripheral blood memory regulatory T cells. Prolonged remissions and immune side effects have been observed in mogamulizumab-treated CTCL patients. We report that mogamulizumab induced skin rashes in 32% of 44 CTCL patients. These rashes were associated with long-term CTCL remission, even in the absence of specific CTCL treatment. CTCL patients with mogamulizumab-induced rash had significantly higher overall survival (hazard ratio, 0.16 (0.04-0.73, p=0.01)). Histopathology and immunohistochemistry of the rashes revealed granulomatous and lichenoid patterns with CD163 macrophagic and CD8 T-cell infiltrates. Depletion of skin CTCL cells was confirmed by high-throughput sequencing analysis of TCRβ genes and in blood by flow cytometry. New reactive T-cell clones were recruited in skin. Gene expression analysis showed overexpression of CXCL9 and CXCL11, two chemokines involved in CXCR3-expressing T-cell homing to skin. Single-cell RNA sequencing analysis in skin of CTCL patients confirmed that CXCL9 and CXCL11 were primarily macrophage-derived and that skin T-cells expressed CXCR3. Finally, patients with rashes had a significantly higher proportion of exhausted reactive blood T-cells expressing TIGIT and PD1 at baseline compared to patients without rash, which decreased under mogamulizumab treatment, consistent with an activation of the antitumor immunity. Together, these data suggest that mogamulizumab may induce long-term immune control in CTCL patients by activation of the macrophagic and T-cell immune responses.

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