scholarly journals Molecular Variation of Satellite DNAβ Molecules Associated with Malvastrum yellow vein virus and Their Role in Pathogenicity

2008 ◽  
Vol 74 (6) ◽  
pp. 1909-1913 ◽  
Author(s):  
Wei Guo ◽  
Tong Jiang ◽  
Xian Zhang ◽  
Guixin Li ◽  
Xueping Zhou
Keyword(s):  
Petunia Hybrida ◽  
Yunnan Province ◽  
Geographical Origin ◽  
Geographical Location ◽  
Yellow Vein ◽  
Molecular Variation ◽  
Infectious Clones ◽  
Malvastrum Coromandelianum ◽  
Geographical Locations ◽  
Limited Sequence

ABSTRACT Previous studies have found that the diversity of begomovirus-associated DNAβ satellites is related to host and geographical origin. In this study, we have cloned and sequenced 20 different isolates of DNAβ molecules associated with Malvastrum yellow vein virus (MYVV) isolated from Malvastrum coromandelianum plants in different geographical locations of Yunnan Province, China. Analyses of their molecular variation indicate that the satellites are clustered together according to their geographical location but that they have only limited sequence diversity. Infectivity tests using infectious clones of MYVV and its associated DNAβ molecule indicate that MYVV DNAβ is indispensable for symptom induction in Nicotiana benthamiana, N. glutinosa, Petunia hybrida, and M. coromandelianum plants. Furthermore, we showed that MYVV interacts functionally with heterologous DNAβ molecules in N. benthamiana plants.

scholarly journals The Evolutionary History of Beet necrotic yellow vein virus Deduced from Genetic Variation, Geographical Origin and Spread, and the Breaking of Host Resistance

2011 ◽  
Vol 24 (2) ◽  
pp. 207-218 ◽  
Author(s):  
Soutaro Chiba ◽  
Hideki Kondo ◽  
Masaki Miyanishi ◽  
Ida Bagus Andika ◽  
Chenggui Han ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Host Resistance ◽  
Evolutionary History ◽  
Sequence Variation ◽  
Geographical Origin ◽  
Geographical Location ◽  
Yellow Vein ◽  
Resistance Breaking ◽  
History Of ◽  
Report Analysis

Beet necrotic yellow vein virus (BNYVV) is an economically important pathogen of sugar beet and has been found worldwide, probably as the result of recent worldwide spread. The BNYVV genome consists of four or five RNA components. Here, we report analysis of sequence variation in the RNA3-p25, RNA4-p31, RNA2-CP, and RNA5-p26 genes of 73 worldwide isolates. The RNA3-p25 gene encodes virulence and avirulence factors. These four sets of gene sequences each fell into two to four groups, of which the three groups of p25 formed eight subgroups with different geographical distributions. Each of these subgroup isolates (strains) could have arisen from four original BNYVV population and their mixed infections. The genetic diversity for BNYVV was relatively small. Selection pressure varied greatly depending on the BNYVV gene and geographical location. Isolates of the Italy strain, in which p25 was subject to the strongest positive selection, were able to overcome the Rz1-host resistance gene to differing degrees, whereas other geographically limited strains could not. Resistance-breaking variants were generated by p25 amino acid changes at positions 67 and 68. Our studies suggest that BNYVV originally evolved in East Asia and has recently become a pathogen of cultivated sugar beet followed by the emergence of new resistance-breaking variants.

scholarly journals Identification of two distinct begomoviruses infecting Malvastrum coromandelianum

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Yaqin Wang ◽  
Xinyue Zhang ◽  
Tao Hu ◽  
Xueping Zhou
Keyword(s):  
Yunnan Province ◽  
Phylogenetic Analyses ◽  
Yellow Vein ◽  
Universal Primers ◽  
Genome Sequences ◽  
Sequence Alignments ◽  
Total Dna ◽  
Malvastrum Coromandelianum ◽  
Complete Viral Genome ◽  
Virus Isolates

AbstractMalvastrum coromandelianum is a common weed plant frequently found around agricultural fields. Three virus isolates (Y249, Y278 and Y281) were obtained from M. coromandelianum with yellow vein symptoms in Honghe and Baoshan, Yunnan Province, China. Specific 500 bp products were amplified from total DNA extracts using universal primers for members of the genus Begomovirus. The complete viral genome sequences of both Y278 and Y281 were determined to be 2743 nucleotides, and that of Y249 was determined to be 2740 nucleotides. Sequence alignments and phylogenetic analyses support the proposal of creating new species in the genus Begomovirus, for which the name malvastrum yellow vein Baoshan virus (MaYVBsV) is proposed for Y278 and Y281, and malvastrum yellow vein Honghe virus (MaYVHhV) is proposed for Y249.

scholarly journals Bayesian Geographical Multi-Dimensional Scaling

2019 ◽  
Vol 1 ◽  
pp. 1-2
Author(s):  
Hayato Nishi ◽  
Yasushi Asami
Keyword(s):  
Three Dimensional ◽  
Geographical Location ◽  
Point Of View ◽  
Statistical Point ◽  
Dimensional Scaling ◽  
Regional Features ◽  
Geographical Distances ◽  
Strong Relation ◽  
Geographical Locations ◽  
Multi Dimensional Scaling

<p><strong>Abstract.</strong> Multi-dimensional scaling (MDS) is a popular method of visualizing the similarity of individuals in a dataset. When dissimilarities between individuals in a dataset are measured, MDS projects these individuals into the (typically two- or three-dimensional) map. In this map, because similar individuals are projected to be close to one another, distances between individuals correspond to their dissimilarities. In other words, MDS makes a similarity map of a dataset.</p><p>Some of the dissimilarities and distances have a strong relation to the geographical location. For example, time distances are similar to geographical distances, and regional features will be similar if the regions are close together. Therefore, it will be useful to compare the MDS projection and geographical locations. However, because MDS projection is not concerned with the rotation, parallel translation, and similarity expansion, it might be difficult to compare the projection to the actual geographical locations. When geographically related similarities are visualized, projected locations should be bound to the geographical locations.</p><p>In this article, we propose Bayesian Geographical Multidimensional Scaling (BGMDS), in which geographical restrictions of projections are given from a statistical point of view. BGMDS gives not only geographically bound projections, but also incorporates the uncertainty of the projections.</p>

scholarly journals Etiology of Ageratum Yellow Vein Diseases in South China

Plant Disease ◽  
2013 ◽  
Vol 97 (11) ◽  
pp. 1497-1503 ◽  
Author(s):  
Xiaoyang Jiao ◽  
Huanran Gong ◽  
Xuejian Liu ◽  
Yan Xie ◽  
Xueping Zhou
Keyword(s):  
Yellow Vein ◽  
Cultivated Plants ◽  
Polymerase Chain Reaction Detection ◽  
Ageratum Conyzoides ◽  
Chain Reaction ◽  
Infectious Clones ◽  
Tobacco Curly Shoot Virus ◽  
Polymerase Chain ◽  
Agricultural Regions ◽  
Dual Infections

Ageratum conyzoides is a common weed in agricultural regions in Asia. A. conyzoides plants exhibiting yellow vein symptoms were collected from Yunnan and Guangxi provinces of China. Polymerase chain reaction detection and sequence analysis showed that samples collected from Yunnan were mainly infected by Tobacco curly shoot virus (TbCSV) associated with Ageratum yellow vein China betasatellite (AYVCNB), while samples from Guangxi were mostly infected by Papaya leaf curl China virus (PaLCuCNV) and AYVCNB, or by Ageratum yellow vein China virus (AYVCNV) and AYVCNB, with a few exhibiting dual infections by PaLCuCNV, AYVCNV, and AYVCNB. Agrobacterium-mediated inoculation of infectious clones showed that both TbCSV and AYVCNB or PaLCuCNV and AYVCNB produced typical yellow vein symptoms in A. conyzoides. Consequently, Ageratum yellow vein diseases in Yunnan and Guangxi provinces were caused by TbCSV/AYVCNB, PaLCuCNV/AYVCNB, or AYVCNV/ AYVCNB. The implications of these results in relation to the prevalence of begomoviruses in cultivated plants are discussed.

Alignment of Chartered SUCs Information Technology Program to the Commission on Higher Education (CHED) Policies and Standards

2015 ◽  
Vol 13 (1) ◽  
Author(s):  
Unife O. Cagas
Keyword(s):  
Higher Education ◽  
Information Technology ◽  
Technology Education ◽  
Statistical Treatment ◽  
Geographical Location ◽  
Survey Questionnaire ◽  
Global Challenge ◽  
Information Technology Education ◽  
Excellence In Education ◽  
Geographical Locations

Considering the global challenge of achieving excellence in education, it is imperative that the Philippine Higher Education Institutions should align to the standards set by the accrediting bodies. The study aimed to determine the alignment of chartered SUCs IT program in the Caraga Region to CHED Policies and Standards. Employing mixed methods, the study considered three types of instruments: survey questionnaire, interview schedule, and observation/ocular visit checklist. The survey questionnaire and observation/ocular visit checklist, which was based on CMO no. 53, series 2006 for Information Technology Education Programs, were used. Data were subjected to statistical treatment as frequency, mean, standard deviation and Analysis of Variance (ANOVA). The results revealed that in terms of alignment percentage by geographical location, generally, the areas – curriculum outline, instructional standards, admission and residence requirements, garnered the highest alignment percentage of 100.00% in four geographical locations. The study, therefore, concludes that one geographical location is not significantly better than the other, or that one is not significantly more aligned than other geographical locations. It is recommended that chartered SUC administrations should continuously upgrade and update the school’s physical facilities and equipment in conformity to the CHED standards and other recognized accrediting agencies that require standardization to support the IT faculty in the delivery of instruction.   Keywords - Technology Education, alignment, chartered SUCs, CHED policies and standards, descriptive design, Philippines

scholarly journals Diversity of Intestinal Microbiota in Coilia ectenes from Lake Taihu, China

2017 ◽  
Vol 12 (1) ◽  
pp. 315-325 ◽  
Author(s):  
Jinrong Duan ◽  
Dongpo Xu ◽  
Kai Liu ◽  
Yanfeng Zhou ◽  
Pao Xu
Keyword(s):  
Chlorophyll A ◽  
Total Nitrogen ◽  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Lake Taihu ◽  
Geographical Location ◽  
Operational Taxonomic Units ◽  
Coilia Ectenes ◽  
Geographical Locations

AbstractTo investigate the community structure and species composition of intestinal microbiota in Coilia ectenes, sixty-seven samples were collected from Lake Taihu in China. The intestinal microbiota of the C. ectenes were identified by the V4 of the 16S ribosomal RNA gene using high-throughput sequencing. Furthermore, the water quality of different sampling sites was also evaluated. A total of 53 phyla and 730 classified genera were found in all the samples. The eight dominant phyla Planctomycetes, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, Crenarchaeota, Actinobacteria, and Verrucomicrobia were included. The intestinal microbiota compositions of the C. ectenes obtained from the same location presented more similar profiles, and the intestinal microbiota compositions of the C. ectenes from different geographical locations showed considerable differences. The operational taxonomic units (OTUs) abundance of the intestinal microbiota was significantly correlated with both the concentrations of total nitrogen and chlorophyll-a of the aquatic environment (p<0.05). Geographical location was an important determinant for the fish’s intestinal microbiota composition. The intestinal microbiota of C. ectenes would be affected by the concentrations of total nitrogen and chlorophyll-a in the water. These findings achieve a basic understanding of fish’s gut microbiota, and are helpful for the protection of fish resources in Lake Taihu and provided the cornerstone to sustainable utlization of C. ectenes.

scholarly journals A Street-Level IP Geolocation Method Based on Delay-Distance Correlation and Multilayered Common Routers

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Shichang Ding ◽  
Fan Zhao ◽  
Xiangyang Luo
Keyword(s):  
Geographical Location ◽  
Capital City ◽  
Smart Devices ◽  
5G Networks ◽  
Distance Correlation ◽  
Ip Geolocation ◽  
Street Level ◽  
Relative Delay ◽  
Geolocation Accuracy ◽  
Geographical Locations

The geographical locations of smart devices can help in providing authentication information between multimedia content providers and users in 5G networks. The IP geolocation methods can help in estimating the geographical location of these smart devices. The two key assumptions of existing IP geolocation methods are as follows: (1) the smallest relative delay comes from the nearest host; (2) the distance between hosts which share the closest common routers is smaller than others. However, the two assumptions are not always true in weakly connected networks, which may affect accuracy. We propose a novel street-level IP geolocation algorithm (Corr-SLG), which is based on the delay-distance correlation and multilayered common routers. The first key idea of Corr-SLG is to divide landmarks into different groups based on relative-delay-distance correlation. Different from previous methods, Corr-SLG geolocates the host based on the largest relative delay for the strongly negatively correlated groups. The second key idea is to introduce the landmarks which share multilayered common routers into the geolocation process, instead of only relying on the closest common routers. Besides, to increase the number of landmarks, a new street-level landmark collection method called WiFi landmark is also presented in this paper. The experiments in one province capital city of China, Zhengzhou, show that Corr-SLG can improve the geolocation accuracy remarkably in a real-world network.

scholarly journals A Portfolio of Geographically Distinct Laboratory-adapted Plasmodium Falciparum Clones With Consistent Infection Rates in Anopheles Mosquitoes

2021 ◽  
Author(s):  
Marga van de Vegte-Bolmer ◽  
Wouter Graumans ◽  
Rianne Stoter ◽  
Geert-Jan van Gemert ◽  
Robert Sauerwein ◽  
...  
Keyword(s):  
Geographical Origin ◽  
Production Capacity ◽  
Infection Intensity ◽  
Infection Rates ◽  
Malaria Research ◽  
Anopheles Mosquitoes ◽  
Mature Gametocyte ◽  
Malaria Interventions ◽  
Geographical Locations

Abstract BackgroundThe ability to culture P. falciparum continuously in vitro has enabled stable access to asexual and sexual parasites for malaria research. The portfolio of isolates has remained limited and research is still largely based on NF54 and its derived clone 3D7. Since 1978, isolates were collected and cryopreserved at Radboudumc from patients presenting at the hospital. Here, procedures are described for culture adaptation of asexual parasites, cloning and production of sexual stage parasites responsible for transmission (gametocytes) and production of oocysts in Anopheles mosquitoes. This study aimed to identify new culture adapted transmissible P. falciparum isolates, originating from distinct geographical locations.ResultsOut of a collection of 121 P. falciparum isolates stored in liquid nitrogen, 21 from different geographical origin were selected for initial testing. Isolates were evaluated for their ability to be asexually cultured in vitro, their gametocyte production capacity, and consistent generation of oocysts. Out of 21 isolates tested, twelve were excluded from further analysis due to lack of mature gametocyte production (n = 1) or generation of satisfactory numbers of oocysts in mosquitoes (n = 11). Nine isolates fulfilled selection criteria and were cloned by limiting dilution and retested. After cloning, one isolate was excluded for not showing transmission. The remaining eight isolates transmitted to A. stephensi or A. coluzzii mosquitoes and were categorized into two groups with a reproducible mean oocyst infection intensity above (n = 5) or below five (n = 3). ConclusionsThese new P. falciparum culture adapted isolates with reproducible transmission to Anopheles mosquitoes are a valuable addition to the malaria research tool box. They can aid in the development of malaria interventions and will be particularly useful for those studying malaria transmission.

scholarly journals Geography as non-genetic modulation factor of chicken cecal microbiota

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244724
Author(s):  
Natalia Pin Viso ◽  
Enzo Redondo ◽  
Juan María Díaz Carrasco ◽  
Leandro Redondo ◽  
Julia Sabio y. Garcia ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Geographical Origin ◽  
Dominant Role ◽  
Geographical Location ◽  
Threshold Value ◽  
Production Performance ◽  
Rrna Gene ◽  
Cecal Microbiota ◽  
Chicken Gut Microbiota

The gastrointestinal tract of chickens harbors a highly diverse microbiota contributing not only to nutrition, but also to the physiological development of the gastrointestinal tract. Microbiota composition depends on many factors such as the portion of the intestine as well as the diet, age, genotype, or geographical origin of birds. The aim of the present study was to demonstrate the influence of the geographical location over the cecal microbiota from broilers. We used metabarcoding sequencing datasets of the 16S rRNA gene publicly available to compare the composition of the Argentine microbiota against the microbiota of broilers from another seven countries (Germany, Australia, Croatia, Slovenia, United States of America, Hungary, and Malaysia). Geographical location played a dominant role in shaping chicken gut microbiota (Adonis R2 = 0.6325, P = 0.001; Mantel statistic r = 0.1524, P = 4e-04) over any other evaluated factor. The geographical origin particularly affected the relative abundance of the families Bacteroidaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. Because of the evident divergence of microbiota among countries we coined the term “local microbiota” as convergent feature that conflates non-genetic factors, in the perspective of human-environmental geography. Local microbiota should be taken into consideration as a native overall threshold value for further appraisals when testing the production performance and performing correlation analysis of gut microbiota modulation against different kind of diet and/or management approaches. In this regard, we described the Argentine poultry cecal microbiota by means of samples both from experimental trials and commercial farms. Likewise, we were able to identify a core microbiota composed of 65 operational taxonomic units assigned to seven phyla and 38 families, with the four most abundant taxa belonging to Bacteroides genus, Rikenellaceae family, Clostridiales order, and Ruminococcaceae family.

scholarly journals Effect of Geographical Location, Year, and Cultivar on Survival of Malus sp. Dormant Buds Stored in Vapors of Liquid Nitrogen

HortScience ◽  
2011 ◽  
Vol 46 (9) ◽  
pp. 1230-1234 ◽  
Author(s):  
Maria M. Jenderek ◽  
Phil Forsline ◽  
Joseph Postman ◽  
Ed Stover ◽  
David Ellis
Keyword(s):  
Cold Hardiness ◽  
Geographical Location ◽  
Germplasm Collections ◽  
Dormant Bud ◽  
Apple Cultivars ◽  
Woody Crop ◽  
Crop Germplasm ◽  
Winter Buds ◽  
Cryopreservation Method ◽  
Geographical Locations

Clonal woody crop germplasm collections often originate and are grown in distinct geographical locations. Because the degree of cold-hardiness is known to be a factor in the successful use of dormant bud cryopreservation for Malus, it was suggested that material from relatively warmer climates would not respond to cryopreservation as well as material from colder environments. To test this hypothesis, the effect of growing provenance on cryosurvival of dormant buds from three Malus (apple) cultivars grown in three locations (Geneva, NY; Davis, CA; and Corvallis, OR) was tested in 3 consecutive years. Dormant winter buds were harvested at the three locations, cryopreserved, and bud viability was tested by grafting. The collective 3-year mean viability for cryopreserved dormant apple buds for the three locations ranged from 63% to 81% of the buds surviving with the highest survival from the Corvallis site; however, the Geneva twigs were exposed to the lowest preharvest temperature. These results suggest that the temperature at the growing location may not hinder application of the dormant bud cryopreservation method with Malus to the extent previously speculated.

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