scholarly journals Sequence Analysis of Plum pox virus Strain C Isolates from Russia Revealed Prevalence of the D96E Mutation in the Universal Epitope and Interstrain Recombination Events

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 450 ◽  
Author(s):  
Anna Sheveleva ◽  
Peter Ivanov ◽  
Tatiana Gasanova ◽  
Gennady Osipov ◽  
Sergei Chirkov
Keyword(s):  
Sour Cherry ◽  
Viral Disease ◽  
Plum Pox Virus ◽  
Recombination Detection Program ◽  
Detection Program ◽  
Antigenic Properties ◽  
Universal Epitope ◽  
Almost All ◽  
First Time ◽  
Generation Sequencing

The understanding of genetic diversity, geographic distribution, and antigenic properties of Plum pox virus (PPV) is a prerequisite to improve control of sharka, the most detrimental viral disease of stone fruit crops worldwide. Forty new PPV strain C isolates were detected in sour cherry (Prunus cerasus) from three geographically distant (700–1100 km) regions of European Russia. Analysis of their 3’-terminal genomic sequences showed that nineteen isolates (47.5%) bear the D96E mutation in the universal epitope of the coat protein. Almost all of them cannot be detected by the monoclonal antibody 5B in triple antibody sandwich enzyme-linked immunosorbent assayand Western blot analysis that may potentially compromise serological PPV detection in cherries. Full-length genomes of seven PPV-C isolates were determined employing next-generation sequencing. Using the Recombination Detection Program (RDP4), the recombination event covering the region from (Cter)P1 to the middle of the HcPro gene was predicted in all the available PPV-C complete genomes. The isolates Tat-4, belonging to the strain CV, and RU-17sc (PPV-CR) were inferred as major and minor parents, respectively, suggesting possible pathways of evolution of the cherry-adapted strains. Downy cherry (P. tomentosa) was identified as the natural PPV-C host for the first time.

scholarly journals Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China

2020 ◽  
Vol 11 ◽  
Author(s):  
Shaohua Wen ◽  
Guoping Wang ◽  
Zuokun Yang ◽  
Yanxiang Wang ◽  
Min Rao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Molecular Diversity ◽  
Genome Structure ◽  
Viral Disease ◽  
Open Reading Frames ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing

Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.

scholarly journals Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

2021 ◽  
Vol 11 (2) ◽  
pp. 620
Author(s):  
Magdalena Dyda ◽  
Agnieszka Laudy ◽  
Przemyslaw Decewicz ◽  
Krzysztof Romaniuk ◽  
Martyna Ciezkowska ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Microbial Community Composition ◽  
Fungal Communities ◽  
Bacterial Strains ◽  
Microbial Biodiversity ◽  
Acidophilic Bacteria ◽  
Almost All ◽  
Generation Sequencing ◽  
King John

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

scholarly journals Deciphering the effects of kosmotrope and chaotrope salts during aqueous two phase extraction (ATPE) of polyphenolic compounds and glycoalkaloids from the leaves of a nutraceutical plant, Solanum retroflexum, with the aid of UPLC-QTOF-MS

2021 ◽  
Vol 64 (1) ◽  
Author(s):  
Tebogo Mokgehle ◽  
Ntakadzeni Madala ◽  
Wilson Gitari ◽  
Nikita Tavengwa
Keyword(s):  
Polar Compounds ◽  
Ultra Performance Liquid Chromatography ◽  
Polyphenolic Compounds ◽  
Phase Extraction ◽  
Two Phase ◽  
Solanum Retroflexum ◽  
Chaotropic Salts ◽  
Almost All ◽  
First Time ◽  
Aqueous Two Phase Extraction

AbstractSolanum plants (Solanaceae) are renowned source of nutraceuticals and have widely been explored for their phytochemical constituents. This work investigated the effects of kosmotropic and chaotropic salts on the number of phytochemicals extracted from the leaves of a nutraceutical plant, Solanum retroflexum, and analyzed on the ultra-performance liquid chromatography hyphenated to a quadrupole time of flight mass spectrometer (UPLC-QTOF-MS) detector. Here, a total of 20 different compounds were putatively characterized. The majority of the identified compounds were polyphenols and glycoalkaloids. Another compound, caffeoyl malate was identified for the first time in this plant. Glycoalkaloids such as solanelagnin, solamargine, solasonine, β-solanine (I) and β-solanine (II) were found to be extracted by almost all the salts used herein. Kosmotrope salts, overall, were more efficient in extracting polar compounds with 4 more polyphenolic compounds extracted compared to the chaotropes. Chaotropes were generally more selective for the extraction of less polar compounds (glycoalkaloids) with 3 more extracted than the kosmotropes. The chaotrope and the kosmotrope that extracted the most metabolites were NaCl and Na2SO4, respectively, with 12 metabolites extracted for each salt. This work demonstrated that a comprehensive metabolome of S. retroflexum, more than what was previously reported on the same plant, can be achieved by application of kosmotropes and chaotropes as extractants with the aid of the Aqueous Two Phase Extraction approach. The best-performing salts, Na2SO4 or NaCl, could potentially be applied on a commercial scale, to meet the ever-growing demand of the studied metabolites. The Aqueous Two Phase Extraction technique was found to be efficient in simultaneous extraction of multiple metabolites which can be applied in metabolomics.

scholarly journals Comparison on the Nutrient Plunder Capacity of Orychophragmus violaceus and Brassica napus L. Based on Electrophysiological Information

Horticulturae ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 206
Author(s):  
Cheng Zhang ◽  
Yue Su ◽  
Yanyou Wu ◽  
Haitao Li ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Orychophragmus Violaceus ◽  
Nutrient Metabolism ◽  
Brassica Napus L ◽  
Adaptive Mechanisms ◽  
Capacitive Reactance ◽  
Time Determination ◽  
Almost All ◽  
First Time

The nutrient metabolism, growth and development of plants are strongly affected by its nutrient plunder, and plants have different adaptive mechanisms to low-nutrient environments. The electrophysiological activities involve almost all life processes of plants. In this study, the active transport flow of nutrient (NAF) and nutrient plunder capacity (NPC) of plants were defined based on leaf intrinsic impedance (IZ), capacitive reactance (IXc), inductive reactance (IXL) and capacitance (IC) to evaluate the nutrient plunder capacity of plants for the first time. The results indicate that Orychophragmus violaceus had higher (p < 0.01) NPC and IC and lower (p < 0.01) IR, IXc, IXL and IZ as compared to Brassica napus L., which supports a superior ion affinity and that it could be better adapted to low-nutrient environments. UAF and NPC of plants exhibited good correlations with crude protein, crude ash and water content, and precisely revealed the plunder capacity and adaptive strategies of plants to nutrients. The present work highlights that O. violaceus had superior NPC and ion affinity compared with B. napus, and provided a novel, rapid, reliable method based on the plant’s electrophysiological information for real-time determination of the nutrient plunder capacity of plants.

A New Sahidic Fragment of the Gospel of Luke from the Michigan Collection

2014 ◽  
Vol 56 (2) ◽  
pp. 198-204
Author(s):  
Brice C. Jones
Keyword(s):  
Gospel Of Luke ◽  
Almost All ◽  
First Time

AbstractThis article publishes for the first time the extant remains of a Sahidic Coptic manuscript containing portions of Luke 17-19. Almost all of the special Lukan pericope concerning Jesus and Zacchaeus is preserved (19:1-10), as well as most of the parable of the Dishonest Judge (18:1-8). The edition includes a transcription, translation, palaeographical analysis, critical apparatus, as well as images of the fragment.

Descriptive and illustrated diagnosis of Ophiuroidea fauna (Echinodermata) in the shallow waters of North-eastern Brazil

2015 ◽  
Vol 8 ◽  
Author(s):  
Fabilene Gomes Paim ◽  
Maria Cecília Guerrazzi ◽  
Michela Borges
Keyword(s):  
Brittle Star ◽  
Shallow Waters ◽  
Bottom Substrate ◽  
Eastern Brazil ◽  
North Eastern ◽  
Amphipholis Squamata ◽  
Biological Substrates ◽  
Almost All ◽  
First Time ◽  
Ophiocoma Echinata

In this study, we present descriptions, illustrations, comments, and bathymetric and geographic distributions of the brittle star species related to the estuary region of Camamu Bay, located in the State of Bahia, Brazil. The brittle star fauna lives on biological substrates, sand bottoms, mud and rubble in the Camamu Bay and comprises 12 species divided into five families. Almost all of them are common in the tropical and subtropical fauna of the regions of shallow water.Ophiophragmus filograneusis reported for the first time in Bahia, and nine other species are recorded for the first time in Camamu Bay:Amphipholis januarii, Amphipholis squamata, Ophiophragmus filograneus, Ophiostigma isocanthum,Ophioderma cinerea, Ophioderma januarii, Ophiactis lymani, Ophiactis savignyi andOphiocoma echinata.The results suggest that the ophiuroid assemblages are strongly affected by marine currents as well as by different kinds of bottom substrate.

scholarly journals Human papillomavirus genotyping as a tool for cervical cancer prevention: from commercially available human papillomavirus DNA test to next-generation sequencing

2020 ◽  
Vol 6 (9) ◽  
pp. FSO603
Author(s):  
Tauana Christina Dias ◽  
Adhemar Longatto-Filho ◽  
Nathalia C Campanella
Keyword(s):  
Cervical Cancer ◽  
Human Papillomavirus ◽  
Cervical Cancer Prevention ◽  
Cancer Development ◽  
Cervical Carcinogenesis ◽  
Dna Test ◽  
First Time ◽  
Papillomavirus Dna ◽  
Principal Elements ◽  
Generation Sequencing

The biological importance of human papillomavirus (HPV) in the field of medicine – related to cervical carcinogenesis – has been extensively reported in the last decades. For the first time, a direct correlation between cause and effect to explain a cancer development was completely achieved in medical research. Consequently, the Nobel Prize was awarded to HZ Hausen in 2008 for his efforts to understand the effects of persistent infection of oncogenic types of HPV and malignancy transformation. The aim of the present review was to summarize the principal elements of HPV characteristics and their importance in oncology.

scholarly journals Exactly separable version of the Bohr Hamiltonian with the Davidson potential

2020 ◽  
Vol 16 ◽  
pp. 121
Author(s):  
D. Bonatsos ◽  
E. A. McCutchan ◽  
N. Minkov ◽  
R. F. Casten ◽  
P. Yotov ◽  
...  
Keyword(s):  
Dynamical Symmetry ◽  
Transition Rates ◽  
Stiffness Parameter ◽  
Oscillator Potential ◽  
Harmonic Oscillator Potential ◽  
Boson Model ◽  
Two Parameters ◽  
Almost All ◽  
First Time ◽  
Davidson Potential

An exactly separable version of the Bohr Hamiltonian, is obtained by using a potential of the form V (β, γ) = u(β) + u(γ)/β2, with a Davidson potential for u(β) and a stiff harmonic oscillator potential centered around γ = 0o, for u(γ).Using two parameters (β0 and the γ-stiffness parameter) the band features and B(E2) transition rates of almost all well-deformed rare-earth and actinide nuclei are reproduced, while the spectrum of the SU(3) dynamical symmetry of the Interacting Boson Model can be obtained, for the first time using the Bohr Hamiltonian.

Meloidae of Namibia (Coleoptera): taxonomy and faunistics with biogeographic and ecological notes

Zootaxa ◽  
2018 ◽  
Vol 4373 (1) ◽  
pp. 1 ◽  
Author(s):  
MARCO A. BOLOGNA ◽  
VALENTINA AMORE ◽  
MONICA PITZALIS
Keyword(s):  
New Species ◽  
African Country ◽  
General Distribution ◽  
Namib Desert ◽  
Succulent Karoo ◽  
Southern African Country ◽  
Almost All ◽  
Xeric Ecosystems ◽  
First Time ◽  
Blister Beetle

The blister beetle (Coleoptera: Meloidae) fauna of Namibia is studied. The species are arranged within a catalogue containing information on their general distribution, including a list of localities and brief taxonomic remarks. Zoogeographic and ecological analyses were carried out and a photographic appendix, with images and maps of almost all Namibian species, is included. According to a chorological analysis, the Namibian blister beetle fauna appears to be zoogeographically distinct because of the dominance of western southern African elements. The faunistic levels of similarity among distinct areas in Namibia are also analysed. Several of the endemic species are related to the xeric ecosystems referable to the Namib Desert, Succulent Karoo and Nama Karoo biomes, but the highest diversity is related to the ecosystems referable to the Savannah biome. A total of 148 species belonging to 28 genera, eight tribes and three subfamilies (Eleticinae,  Meloinae, Nemognathinae) are recorded from this southern African country. Five new genera (Namibeletica gen. nov., Eleticinae Eleticini; Dilatilydus gen. nov. and Desertilydus gen. nov., Meloinae Lyttini; Paramimesthes gen. nov. and Namylabris gen. nov, Meloinae Mylabrini) and a total of 13 new species are described: 11 new species from Namibia (Psalydolytta gessi sp.nov., Paramimesthes namibicus sp.nov., Namylabris adamantifera sp.nov., Hycleus arlecchinus sp.nov., H. planitiei sp.nov., H. dvoraki sp.nov., H. aridus sp.nov., H. san sp.nov., Nemognatha fluviatilis sp.nov., “Zonitoschema” deserticola sp.nov., Zonitoschema dunalis sp.nov.); a new Namibeletica from the Angolan Namib (N. angolana) and a new Afrolytta Kaszab, 1959 from the S African Namaqualand (A. namaqua), both close to Namibian borders. Fourty-eight species and the genus Apalus Fabricius, 1775 are recorded for the first time from Namibia, and a few other species from South Africa (1), Zambia (1), Botswana (1) and Congo (1). The following new synonymies are proposed: Lytta pleuralis var. inpleuralis Pic, 1911 = Lydomorphus (Lydomorphus) thoracicus (Erichson, 1843), syn. nov.; Lytta benguellana Pic, 1911 = Prionotolytta melanura (Erichson, 1843), syn. nov.; Actenodia amoena ssp.anthicoides Kaszab, 1955b = Hycleus amoenus (Marseul, 1872), syn. nov.; Decapotoma csikii Kaszab, 1953 = Hycleus benguellanus (Marseul, 1879), syn. nov.; Nemognatha capensis Péringuey, 1909 = Nemognatha peringueyi Fairmaire, 1883, syn. nov. Several new combinations in the genus Hycleus Latreille, 1817 are also established. 

scholarly journals Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuqiao Mao ◽  
Xia Li ◽  
Haibo Lou ◽  
Xiaoyu Shang ◽  
Yanjun Mai ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Los Angeles ◽  
Systemic Infection ◽  
High Sensitivity ◽  
Pathological Examination ◽  
Next Generation ◽  
Coccidioides Posadasii ◽  
Dimorphic Fungi ◽  
Almost All ◽  
Generation Sequencing

Abstract Background Coccidioidomycosis is a systemic infection caused by dimorphic fungi Coccidioides spp. endemic to Southwestern United States and Central and South America. A history of residence and travel in these areas is essential for the diagnostic of coccidioidomycosis, which has highly variable symptoms ranging from asymptomatic to severe, disseminated infection, and even death. Immunocompromised patients of coccidioidomycosis experience a high risk of dissemination, chronic infection, and mortality. Meningitis is one of the most deleterious coccidioidomycosis and can cause various life-threatening complications. Case presentation Here we report a case of Coccidioides posadasii meningitis in a 49-year-old female who returned to China after one and a half years residence in Los Angeles, USA. The repeated routine cultures using CSF for bacteria or fungi were all negative. To hunt for an infectious etiology, the state-of-the-art technology metagenomic next-generation sequencing (mNGS) was then utilized, suggesting Coccidioides posadasii. Organizational pathological examination and polymerase-chain-reaction (PCR) results subsequently confirmed the mNGS detection. Conclusion To our knowledge, cases for coccidioidal meningitis have been rarely reported in China. While global travelling may spread this disease across continents and make the diagnosis more difficult. mNGS can detect almost all known pathogens with high sensitivity and specificity, especially for uncommon pathogen, such as Coccidioides posadasii in China.

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