scholarly journals Cyanophage Distribution Across European Lakes of the Temperate-Humid Continental Climate Zone Assessed Using PCR-based Genetic Markers

2021 ◽  
Author(s):  
Aleksandra Jaskulska ◽  
Sigitas Šulčius ◽  
Mikołaj Kokociński ◽  
Judita Koreivienė ◽  
Arnoldo Font Nájera ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Dna Sequences ◽  
Abiotic Factors ◽  
Principal Component ◽  
Marker Genes ◽  
Total Phosphorous ◽  
Physicochemical Factors ◽  
Infected Cells ◽  
Continental Climate ◽  
Cyanobacterial Biomass

Abstract Studies of the diversity and distribution of freshwater cyanophages are generally limited to the small geographical areas, in many cases including only one or few lakes. Data from dozens of various lakes distributed at a larger distance are necessary to understand their spatial distribution and sensitivity to biotic and abiotic factors. Thus, the objective of this study was to analyze the diversity and distribution of cyanophages within the infected cells using marker genes (psbA, nblA, and g91) in 21 Polish and Lithuanian lakes. Physicochemical factors that might be related to them were also analyzed. The results demonstrated that genetic markers representing cyanophages were observed in most lakes studied. The frequently detected gene was psbA with 88% of cyanophage-positive samples, while nblA and g91 were found in approximately 50% of lakes. The DNA sequences analyses for each gene demonstrated low variability between them. Although, the psbA sequences branched within the larger cluster of marine Synechoccocuss counterparts. The principal component analysis allowed to identify significant variation between the lakes that presented high and low cyanobacterial biomass. The lakes with high cyanobacterial biomass were further separated by country and the different diversity of cyanobacteria species, particularly Planktothrix agardhii was dominant in the Polish lakes and Planktolyngbya limnetica in the Lithuanian lakes. The total phosphorous and the presence of cyanophage genes psbA and nblA were the most important factors that allowed differentiation for the Polish lakes, while the pH and the genes g91 and nblA for the Lithuanian lakes.

scholarly journals Cyanophage Distribution Across European Lakes of the Temperate-Humid Continental Climate Zone Assessed Using PCR-Based Genetic Markers

2021 ◽  
Author(s):  
Aleksandra Jaskulska ◽  
Sigitas Šulčius ◽  
Mikołaj Kokociński ◽  
Judita Koreivienė ◽  
Arnoldo Font Nájera ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Abiotic Factors ◽  
Principal Component ◽  
Marker Genes ◽  
Sequence Analyses ◽  
Total Phosphorous ◽  
Physicochemical Factors ◽  
Infected Cells ◽  
Continental Climate ◽  
Cyanobacterial Biomass

AbstractStudies of the diversity and distribution of freshwater cyanophages are generally limited to the small geographical areas, in many cases including only one or few lakes. Data from dozens of various lakes distributed at a larger distance are necessary to understand their spatial distribution and sensitivity to biotic and abiotic factors. Thus, the objective of this study was to analyze the diversity and distribution of cyanophages within the infected cells using marker genes (psbA, nblA, and g91) in 21 Polish and Lithuanian lakes. Physicochemical factors that might be related to them were also analyzed. The results demonstrated that genetic markers representing cyanophages were observed in most lakes studied. The frequently detected gene was psbA with 88% of cyanophage-positive samples, while nblA and g91 were found in approximately 50% of lakes. The DNA sequence analyses for each gene demonstrated low variability between them, although the psbA sequences branched within the larger cluster of marine Synechoccocuss counterparts. The principal component analysis allowed to identify significant variation between the lakes that presented high and low cyanobacterial biomass. The lakes with high cyanobacterial biomass were further separated by country and the different diversity of cyanobacteria species, particularly Planktothrix agardhii, was dominant in the Polish lakes and Planktolyngbya limnetica in the Lithuanian lakes. The total phosphorous and the presence of cyanophage genes psbA and nblA were the most important factors that allowed differentiation for the Polish lakes, while the pH and the genes g91 and nblA for the Lithuanian lakes.

scholarly journals Leaf geometric morphometrics among populations of Dalbergia ecastaphyllum (L.) Taub.

2019 ◽  
Vol 35 (6) ◽  
Author(s):  
Daniel Vieira de Morais ◽  
Lorena Andrade Nunes ◽  
Vandira Pereira da Mata ◽  
Maria Angélica Pereira de Carvalho Costa ◽  
Geni da Silva Sodré ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Geometric Morphometrics ◽  
Cross Validation ◽  
Abiotic Factors ◽  
Principal Component ◽  
Canonical Variate ◽  
Validation Test ◽  
Significant Difference ◽  
Variate Analysis ◽  
Geographical Distances

Leaves are plant structures that express important traits of the environment where they live. Leaf description has allowed identification of plant species as well as investigation of abiotic factors effects on their development, such as gases, light, temperature, and herbivory. This study described populations of Dalbergia ecastaphyllum through leaf geometric morphometrics in Brazil. We evaluated 200 leaves from four populations. The principal component analysis (PCA) showed that the first four principal components were responsible for 97.81% of variation. The non-parametric multivariate analysis of variance (NPMANOVA) indicated significant difference between samples (p = 0.0001). The Mentel test showed no correlation between geographical distances and shape. The canonical variate analysis (CVA) indicated that the first two variables were responsible for 96.77 % of total variation, while the cross-validation test showed an average of 83.33%. D. ecastaphyllum leaves are elliptical and ovate.

scholarly journals Diversity and spatial distribution of black flies (Diptera: Simuliidae) in the Ijuí river drainage basin, Rio Grande do Sul, Brazil

2019 ◽  
Vol 12 (2) ◽  
pp. 47-56
Author(s):  
Tieli Cláudia Menzel ◽  
Sirlei Maria Hentges ◽  
David Augusto Reynalte Tataje ◽  
Milton Norberto Strieder
Keyword(s):  
River Basin ◽  
Indicator Species ◽  
Drainage Basin ◽  
Abiotic Factors ◽  
Principal Component ◽  
Rio Grande ◽  
Anthropogenic Pressure ◽  
Black Flies ◽  
Rio Grande Do Sul ◽  
Significant Difference

Abstract. In southern Brazil there are several problems regarding the hematophageal activity of black flies, and the information on the distribution of species are still insufficient. In this study, our main goals were to recognize Simuliidae species and to analyze abiotic factors regarding the distribution of immature stages (larva and pupa) in streams from the Ijuí River basin, Northwest of Rio Grande do Sul, Brazil. We sampled simulids specimens in 27 study sites, covering three regions (high, intermediate and low altitude). Concomitantly, we recorded abiotic factors in the studied sites, such as: temperature, electrical conductivity, dissolved oxygen, atmospheric pressure, pH, altitude and stream width. For data analysis, we performed Kruskal-Wallis, ANOVA, Principal Component Analysis (PCA), Analysis of Indicator Species and Canonical Correspondence (CCA). A total of 10 species of black Flies was recorded. Simulium pertinax Kollar, Simulium incrustatum Lutz and Simulium orbitale Lutz were the most frequent. There was no significant difference in richness and density of the species between the different regions studied, except for Simulium jujuyense Paterson & Shannon. The sampled environments were segregated according to the location within the basin, and only S. jujuyense was considered an indicator species of the upper region. These results can be explained by the homogeneous conditions of the Ijuí River basin, which have suffered anthropogenic pressure mainly due to agricultural activities, resulting in losses in local aquatic biodiversity. Also, it may indicate that the control must be conducted considering the basin as a whole, and not only as isolated stretches of the streams.Diversidade e distribuição espacial de borrachudos (Diptera: Simuliidae) na bacia hidrográfica do rio Ijuí, Rio Grande do Sul, BrasilResumo. No sul do Brasil existem problemas com atividade hematofágica de borrachudos e as informações referentes à distribuição das espécies ainda são insuficientes. O presente estudo visa reconhecer as espécies de Simuliidae e analisar fatores abióticos quanto a distribuição dos estágios imaturos (larva e pupa) em riachos da Bacia do Rio Ijuí, no Noroeste do Rio Grande do Sul, Brasil. Foram coletados simulídeos em 27 pontos de estudo, cobrindo três regiões da bacia (alta, intermediária e baixa altitude). Concomitantemente, foi feito o registro de fatores abióticos nos trechos estudados, tais como: temperatura, condutividade elétrica, oxigênio dissolvido, pressão atmosférica, pH, altitude e largura do riacho. Foram realizadas análises de Kruskal-Wallis ou ANOVA, Análise de Componentes Principais (PCA), Análise de Espécie Indicadora e de Correspondência Canônica (CCA). Foi registrado um total de 10 espécies de Simuliidae. Simulium pertinax Kollar, Simulium incrustatum Lutz e Simulium orbitale Lutz foram as mais frequentes. Não ocorreu diferença na riqueza e na densidade das espécies entre as diferentes regiões estudadas, exceto para Simulium jujuyense Paterson & Shannon. Os ambientes nos pontos de amostragem foram segregados de acordo com a sua localização na bacia, e apenas S. jujuyense foi considerada uma espécie indicadora da região alta. Tais resultados podem ser explicados pelas condições homogêneas da Bacia do Rio Ijuí, que vêm sofrendo pressão antropogênica principalmente devido às atividades agrícolas, resultando em perdas na biodiversidade aquática local. Também, indicam que o controle deve ser realizado considerando a bacia como um todo e não apenas em trechos isolados dos riachos.

scholarly journals More than efficacy revealed by single-cell analysis of antiviral therapeutics

2019 ◽  
Vol 5 (10) ◽  
pp. eaax4761 ◽  
Author(s):  
Wu Liu ◽  
Mehmet U. Caglar ◽  
Zhangming Mao ◽  
Andrew Woodman ◽  
Jamie J. Arnold ◽  
...  
Keyword(s):  
Viral Infection ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Principal Component ◽  
Cell Analysis ◽  
Infection Cycle ◽  
Reporter Protein ◽  
Fluorescent Reporter ◽  
Infection Dynamics ◽  
Infected Cells

Because many aspects of viral infection dynamics and inhibition are governed by stochastic processes, single-cell analysis should provide more information than approaches using population averaging. We have developed a microfluidic device composed of ~6000 wells, with each well containing a microstructure to capture single, infected cells replicating an enterovirus expressing a fluorescent reporter protein. We have used this system to characterize enterovirus inhibitors with distinct mechanisms of action. Single-cell analysis reveals that each class of inhibitor interferes with the viral infection cycle in a manner that can be distinguished by principal component analysis. Single-cell analysis of antiviral candidates not only reveals efficacy but also facilitates clustering of drugs with the same mechanism of action and provides some indication of the ease with which resistance will develop.

scholarly journals Molecular Diversity of Nematode Parasites in Afrotropical Reed Frogs (Hyperolius spp.)

Diversity ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 265
Author(s):  
Ulrich Sinsch ◽  
J. Maximilian Dehling ◽  
Patrick Scheid ◽  
Carsten Balczun
Keyword(s):  
Dna Sequences ◽  
Nematode Species ◽  
Sub Saharan Africa ◽  
Parasitic Nematodes ◽  
Marker Genes ◽  
Nematode Parasites ◽  
Diversity Assessment ◽  
Wide Range ◽  
Nematode Diversity ◽  
Sub Saharan

The diversity of nematodes infecting amphibians is understudied in tropical Africa and unknown in Rwanda. Diversity assessment is hampered by the fact that species descriptions refer mostly to morphological features that are unlinked to DNA sequences of marker genes available in public databases. In this paper, we explore the abundance and diversity of parasitic nematodes in reed frogs Hyperolius kivuensis (n = 115), H. parallelus (n = 45) and H. viridiflavus (n = 100) collected in Rwanda. Five nematode species were identified morphologically as Orneoascaris chrysanthemoides, O. schoutedeni, Gendria leberrei, Aplectana chamaeleonis and Rhabdias collaris. Corresponding DNA sequences of 18S and COI genes were determined and subsequently deposited in GenBank. Aplectana chamaeleonis showed the highest prevalence (8.7%), but O. chrysanthemoides the highest mean intensity of infection (6.0) and largest number (24) of individuals in H. kivuensis. To the best of our knowledge, all amphibian hosts are new records for these nematode species, which are known to infect a wide range of amphibian and reptile species. Our findings suggest that nematode diversity is probably lower than previously assumed due to low host specificity. As morphological species identification is often challenging, our data facilitate molecular identification of adult and specifically larval nematodes found in amphibians of Sub-Saharan Africa.

Excision of Plastid Marker Genes Using Directly Repeated DNA Sequences

2014 ◽  
pp. 107-123 ◽  
Author(s):  
Elisabeth A. Mudd ◽  
Panagiotis Madesis ◽  
Elena Martin Avila ◽  
Anil Day
Keyword(s):  
Dna Sequences ◽  
Marker Genes ◽  
Repeated Dna ◽  
Repeated Dna Sequences

scholarly journals Seasonal dynamics of cyanobacteria in a eutrophic reservoir (Arcoverde) in a semi-arid region of Brazil

2012 ◽  
Vol 72 (3) ◽  
pp. 533-544 ◽  
Author(s):  
MC. Bittencourt-Oliveira ◽  
SN. Dias ◽  
AN. Moura ◽  
MK. Cordeiro-Araújo ◽  
EW. Dantas
Keyword(s):  
Phytoplankton Community ◽  
Climatic Factors ◽  
Principal Component ◽  
Taxonomic Composition ◽  
Dry Season ◽  
Northeastern Brazil ◽  
Cylindrospermopsis Raciborskii ◽  
Physical And Chemical Variables ◽  
Semi Arid Region ◽  
Cyanobacterial Biomass

Environmental conditions favor the predominance of dense populations of cyanobacteria in reservoirs in northeastern Brazil. The aim of this study was to understand cyanobacterial population dynamics in the rainy and dry seasons at two depths in the Arcoverde reservoir. Microalgae and cyanobacteria samples were collected during 24 hours with intervals of 4 hours (nycthemeral) at sub-surface and 10 m using a van Dorn bottle and a determined biomass. Physical and chemical variables were obtained and the data were analyzed using the principal component analysis (PCA). No nycthemeral variations in the taxonomic composition or distribution of the populations of cyanobacteria were found between the different times of day in either the rainy or dry season. In both seasons, the greatest biomass of the phytoplankton community was made up of cyanobacteria at two depths and all times of the day. Cylindrospermopsis raciborskii (Woloszynska) Seenayya et Subba Raju was dominant at all times of the day on both the surface and at the bottom. In the rainy season, the differences in cyanobacterial biomass between the surface and bottom were less significant than in the dry season. The differences in cyanobacterial biomass between surface and bottom were less pronounced than those found in the dry season. We concluded that a) physical variables better explain the alterations of species in the phytoplankton community in an environment dominated by cyanobacteria throughout the year; b) seasonal climatic factors associated to periods of stratification and de-stratification are important for alterations in the community and variations in biomass and, c) the turbidity caused by rainfall favored the emergence and establishment of other cyanobacteria, especially Planktothrix agardhii (Gomont) Anagnostidis & Komárek.

scholarly journals Investigating the Diversity of Marine Bacteriophage in Contrasting Water Masses Associated with the East Australian Current (EAC) System

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 317 ◽  
Author(s):  
Amaranta Focardi ◽  
Martin Ostrowski ◽  
Kirianne Goossen ◽  
Mark V. Brown ◽  
Ian Paulsen
Keyword(s):  
Microbial Communities ◽  
Dna Sequences ◽  
Abiotic Factors ◽  
Western Boundary Current ◽  
Viral Diversity ◽  
Western Boundary ◽  
East Australian Current ◽  
Boundary Current ◽  
Regional Patterns ◽  
Marine Productivity

Virus- and bacteriophage-induced mortality can have a significant impact on marine productivity and alter the flux of nutrients in marine microbial food-webs. Viral mediated horizontal gene transfer can also influence host fitness and community composition. However, there are very few studies of marine viral diversity in the Southern Hemisphere, which hampers our ability to fully understand the complex interplay of biotic and abiotic factors that shape microbial communities. We carried out the first genetic study of bacteriophage communities within a dynamic western boundary current (WBC) system, the east Australian current (EAC). Virus DNA sequences were extracted from 63 assembled metagenomes and six metaviromes obtained from various depths at 24 different locations. More than 1700 bacteriophage genomic fragments (>9 kbps) were recovered from the assembled sequences. Bacteriophage diversity displayed distinct depth and regional patterns. There were clear differences in the bacteriophage populations associated with the EAC and Tasman Sea euphotic zones, at both the taxonomic and functional level. In contrast, bathypelagic phages were similar across the two oceanic regions. These data provide the first characterisation of viral diversity across a dynamic western boundary current, which is an emerging model for studying the response of microbial communities to climate change.

scholarly journals Structural and mechanistic bases for a potent HIV-1 capsid inhibitor

Science ◽  
2020 ◽  
Vol 370 (6514) ◽  
pp. 360-364 ◽  
Author(s):  
Stephanie M. Bester ◽  
Guochao Wei ◽  
Haiyan Zhao ◽  
Daniel Adu-Ampratwum ◽  
Naseer Iqbal ◽  
...  
Keyword(s):  
Principal Component ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Capsid Shell ◽  
Hydrogen Deuterium ◽  
Infected Cells ◽  
Long Acting ◽  
Structural Insights ◽  
Hiv 1

The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo–electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.

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