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 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 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 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 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.

scholarly journals Development of 3D Tissue Reconstruction Method from Single-cell RNA-seq Data

2017 ◽  
Vol 3 (1) ◽  
pp. 53 ◽  
Author(s):  
Tomoya Mori ◽  
Junko Yamane ◽  
Kenta Kobayashi ◽  
Nobuko Taniyama ◽  
Takanori Tano ◽  
...  
Keyword(s):  
Single Cell ◽  
In Silico ◽  
Expression Profiles ◽  
Marker Gene ◽  
Three Dimensional ◽  
Principal Component ◽  
Marker Genes ◽  
Reconstruction Method ◽  
Reconstruction Methods ◽  
Tissue Reconstruction

In silico three-dimensional (3D) reconstruction of tissues/organs based on single-cell profiles is required to comprehensively understand how individual cells are organized in actual tissues/organs. Although several tissue reconstruction methods have been developed, they are still insufficient to map cells on the original tissues in terms of both scale and quality. In this study, we aim to develop a novel informatics approach which can reconstruct whole and various tissues/organs in silico. As the first step of this project, we conducted single-cell transcriptome analysis of 38 individual cells obtained from two mouse blastocysts (E3.5d) and tried to reconstruct blastocyst structures in 3D. In reconstruction step, each cell position is estimated by 3D principal component analysis and expression profiles of cell adhesion genes as well as other marker genes. In addition, we also proposed a reconstruction method without using marker gene information. The resulting reconstructed blastocyst structures implied an indirect relationship between the genes of Myh9 and Oct4.

scholarly journals Differentiation of lines of Sychevka cattle using marker genes

2020 ◽  
pp. 87-93
Author(s):  
Dmitry Nikolaevich Koltsov ◽  
Mikhail Eliseevich Gontov ◽  
Valentina Ivanovna Dmitrieva
Keyword(s):  
Genetic Differentiation ◽  
Genetic Markers ◽  
Genetic Similarity ◽  
Marker Gene ◽  
Wide Distribution ◽  
Genetic Differences ◽  
Marker Genes ◽  
Present Stage ◽  
Concentration Degree ◽  
Breed Improvement

The results of genetic differentiation of 10 main genealogical groups of sires of the breed of Sychevka cattle of the Smolensk region, using as genetic markers the genes of the B-locus of erythrocyte antigens of blood groups (n = 2949). At the present stage of breed improvement, 56 marker genes of the EAB locus were found in the studied animals, of which 16 are common to all lines and related groups. The most common are: b, G2Y2E'1Q', I1Y2E'3G'G'', I1Y2I', O1I'Q', O2A'2J'2K'O', Q', Y1A'1. Lines and related groups were differentiated by the level of marker gene concentration, degree of homozygosity, and genetic similarity. The coefficient of genetic similarity (r) between different lines ranged from 0.58 to 0.85. The high similarity between animals of individual lines and the wide distribution of identical inherited material marked with the G2Y2E'1Q' allele indicate that there are no genetic differences between them. The lines that originate from sires of Sychevska and Holstein origin do not have significant genetic differences between them (r = 0.9). It is proposed to direct breeding work using genetic markers to increase the genetic differentiation of existing and breeding new lines.

scholarly journals Regeneration of black ash (Fraxinus nigra Marsh.) in hardwood swamps of the Great Lakes – St. Lawrence Forest Region

2021 ◽  
Vol 97 (3) ◽  
pp. 343-358
Author(s):  
Amanda Springer ◽  
Jeffery P. Dech
Keyword(s):  
Great Lakes ◽  
Abiotic Factors ◽  
Principal Component ◽  
High Standard ◽  
Diameter Distribution ◽  
Topographic Wetness Index ◽  
Randomized Sampling ◽  
High Soil Moisture ◽  
Forest Region ◽  
Black Ash

An inductive, ordination-based approach was used to explore patterns in the microenvironment and natural regeneration of black ash across a range of representative stands in the central Ontario portion of the Great Lakes -St. Lawrence Forest Region (GLSL) near Lake Nipissing, Ontario, Canada. The objective of this study was to describe patterns of regeneration of black ash and determine the associations between multiple indicators of black ash regeneration success and biotic and abiotic factors. Using a randomized sampling design with specific selection criteria, 12 black ash stands were sampled, each with three 400 m2 circular sample plots that contained three 4 m2 sub-plots. A suite of environmental variables such as elevation, topographic wetness index, slope, and soil characteristics (percent moisture, pH, total nitrogen, exchangeable phosphorus, potassium, magnesium) were determined for each stand. Variables capturing regeneration potential, including density, diameter, and height of all germinants, seedlings, saplings and sprouts were also collected. A sample of 15 dominant or co-dominant trees in each stand, as well as numerous black ash seedlings, saplings and sprouts were examined using dendrochronological methods to estimate ages. Principal component analysis ordinations were performed exploring the variation in environment and black ash regeneration variables among the stands. High soil moisture and the presence of canopy gaps, (as indicated by high standard deviation of canopy closure), were key variables associated with greater abundance of regeneration. Black ash was the dominant species in all stands, which were also generally characterized by a common reverse-J diameter distribution. It was observed that black ash in the sapling layer reached substantial ages (up to 60 years), indicating they are capable of withstanding long periods of suppression below the canopy. Collectively, these findings suggest that black ash-dominated stands in the study area are regenerating in multiple cohorts. Based on these patterns, it appears that regeneration in these stands is occurring through gap-phase mechanisms, suggesting single tree selection as the best management option for black ash in the GLSL.

scholarly journals Digital Morphometrics: A Tool for Leaf Morpho- Taxonomical Studies

2021 ◽  
Vol 1 (2) ◽  
pp. 1-7
Author(s):  
Kavi K. Oza ◽  
Rinku J. Desai ◽  
Vinay M. Raole*
Keyword(s):  
Principal Component Analysis ◽  
Abiotic Factors ◽  
Leaf Shape ◽  
Principal Component ◽  
Component Analysis ◽  
Herbarium Specimens ◽  
Fourier Descriptors ◽  
Shape Variation ◽  
Quantitative Analysis Method ◽  
Elliptic Fourier Descriptors

Leaves are most important part of the plant and can be used for the identification of a taxon. An appropriate understanding of leaf development in terms of shape and responsible abiotic factors is necessary for improvement in plant. Leaf shape variation could be evaluated successfully, and the symmetrical and asymmetrical elements of the overall shape variation could be detected. The aim of the present study was to establish a quantitative analysis method of leaf shape by elliptic Fourier descriptors and principal component analysis (EF-PCA). EF-PCA describes an overall shape mathematically by transforming coordinate information concerning its contours into elliptic Fourier descriptors (EFDs) and summarizing the EFDs by principal component analysis. We can be able to extract six variables by using leaf specimen images from field and herbarium specimens. In the present study, total leaf area with respect to notch area is more variable within species. Within a species the major source of the symmetrical elements may be governed by genotypic features and the asymmetrical elements are strongly affected by the environment. We could discuss the value of morphometrics to detect subtle morphological variation which may be undetectable by human eye.

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