scholarly journals Role of phylogenetic structure in the dynamics of coastal viral assemblages

2021 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Curtis A. Suttle
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Marker Genes ◽  
Marine Microbes ◽  
Phylogenetic Structure ◽  
Genes Encoding ◽  
One Year ◽  
Rna And Dna

Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the foodweb and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, with some of these changes being repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily-related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses, the major capsid protein (gp23) of T4-like phages and their relatives, and the RNA-dependent RNA polymerase (RdRp) of marnavirus-like RNA viruses, as well as their bacterial and eukaryotic host communities, the genes encoding 16S and 18S ribosomal RNA (rRNA). There were strong lagged correlations between viral diversity and community similarity of putative hosts implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically-related viruses shifted over time and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage the ephemeral and persistent taxa were closely related implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages. Importance Viruses are major agents of microbial mortality in marine systems; yet, little is known about changes in the composition of viral assemblages in relation to that of the microbial communities that they infect. Here, we sampled coastal seawater every two weeks for one year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral genotypes is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes the highly dynamic shuffling of viral genotypes largely occurs within a few subsets of related individuals.

scholarly journals Dynamics in coastal RNA viruses and bacteriophages are driven by shifts in the community phylogenetic structure

2019 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Curtis A. Suttle
Keyword(s):  
High Throughput Sequencing ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Phylogenetic Signal ◽  
Marine Ecosystem ◽  
Marker Genes ◽  
Phylogenetic Groups ◽  
Eukaryotic Phytoplankton ◽  
Viral Marker ◽  
Viral Communities

AbstractMarine microbes including viruses are an essential part of the marine ecosystem that forms the base of the foodweb, and drives biogeochemical cycles. Marine viral communities display repeatable changes in abundance and community composition throughout time; however, whether these changes reflect shifts in dominance within evolutionarily related groups of viruses and their hosts is unexplored. To examine these dynamics, changes in the composition and phylogenetic makeup of two ecologically important groups of viruses, and their potential hosts, were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. Changes in the taxonomic composition within DNA bacteriophages related to T4-like viruses and marnavirus-like RNA viruses infecting eukaryotic phytoplankton, as well as bacteria and eukaryotes, were examined using amplicon sequencing of gene fragments encoding the major capsid protein (gp23), the RNA-dependent RNA polymerase (RdRp) and the 16S and 18S ribosomes, respectively. The results showed that for both viral marker genes, the dominant groups of phylogenetically-related viruses shifted over time and contained many transient taxa and few persistent taxa; yet, different community structures were observed in these different viral communities. Additionally, with strong lagged correlations between viral richness and community similarity of putative hosts, the results imply that viruses influence the composition of the host communities.ImportanceUsing high-throughput sequencing of coastal seawater collected every two weeks for one year, the dynamics of two groups of ecologically important groups of viruses were described in the context of their putative hosts and the environment. There was a large diversity of viruses and putative hosts in this study, and groups of phylogenetically-related viruses showed temporal dynamics in dominance. Examining the richness of viruses by phylogenetic groups showed different dynamics of either boom-bust or continued persistence. At the OTU-level, some members of these related groups persisted throughout time, while others were more ephemeral. These findings were put in context of potential quasispecies behaviour, and the dynamics of putative hosts. These results showed that temporal dynamics of viral communities have a phylogenetic signal which is important for understanding the ecology of these viruses since it elucidated one of the drivers of the community structure.

scholarly journals Biological and environmental drivers of deep-sea benthic ecosystem functioning in Canada’s Laurentian Channel Area of Interest (AOI)

2018 ◽  
Author(s):  
Marta Miatta ◽  
Paul V Snelgrove
Keyword(s):  
Deep Sea ◽  
Ecosystem Functioning ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Environmental Drivers ◽  
Biological Traits ◽  
Area Of Interest ◽  
Prokaryotic Abundance

Ongoing environmental changes and accelerating biodiversity loss raise concern and interest about the role of environmental factors and biodiversity in determining marine ecosystem functioning. This study aims to identify the main drivers of benthic ecosystem functioning in deep-sea sedimentary habitats in the Laurentian Channel Area of Interest (AOI), and in particular the role of sea pens (Pennatulacea) as potential keystone species in the area. Using the ROV ROPOS we collected sediment cores and measured environmental variables from 6 stations inside the AOI (depths 348–445m) in September 2017. Through 48-hours incubations and flux measurements (oxygen, inorganic nutrients), we estimated organic matter remineralization, a key benthic function. Preliminary analyses show no significant variation in fluxes among stations, despite significant differences in environmental variables However, the presence/absence of Pennatulacea inside the cores indicated some capability to enhance remineralization and particularly nitrification. Ongoing analyses will address sediment properties, macrofaunal biodiversity, prokaryotic abundance, and biological traits as drivers of remineralization. Shedding new light on the primary drivers of ecosystem functioning in the area will inform the design or monitoring strategies proposed for this AOI and offer new perspectives and tools for MPA design.

scholarly journals Biological and environmental drivers of deep-sea benthic ecosystem functioning in Canada’s Laurentian Channel Area of Interest (AOI)

2018 ◽  
Author(s):  
Marta Miatta ◽  
Paul V Snelgrove
Keyword(s):  
Deep Sea ◽  
Ecosystem Functioning ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Environmental Drivers ◽  
Biological Traits ◽  
Area Of Interest ◽  
Prokaryotic Abundance

Ongoing environmental changes and accelerating biodiversity loss raise concern and interest about the role of environmental factors and biodiversity in determining marine ecosystem functioning. This study aims to identify the main drivers of benthic ecosystem functioning in deep-sea sedimentary habitats in the Laurentian Channel Area of Interest (AOI), and in particular the role of sea pens (Pennatulacea) as potential keystone species in the area. Using the ROV ROPOS we collected sediment cores and measured environmental variables from 6 stations inside the AOI (depths 348–445m) in September 2017. Through 48-hours incubations and flux measurements (oxygen, inorganic nutrients), we estimated organic matter remineralization, a key benthic function. Preliminary analyses show no significant variation in fluxes among stations, despite significant differences in environmental variables However, the presence/absence of Pennatulacea inside the cores indicated some capability to enhance remineralization and particularly nitrification. Ongoing analyses will address sediment properties, macrofaunal biodiversity, prokaryotic abundance, and biological traits as drivers of remineralization. Shedding new light on the primary drivers of ecosystem functioning in the area will inform the design or monitoring strategies proposed for this AOI and offer new perspectives and tools for MPA design.

scholarly journals Identification and verification of seed development related miRNAs in kernel almond by small RNA sequencing and qPCR

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260492
Author(s):  
Marjan Jafari ◽  
Behrouz Shiran ◽  
Gholamreza Rabiei ◽  
Roudabeh Ravash ◽  
Badraldin Ebrahim Sayed Tabatabaei ◽  
...  
Keyword(s):  
Seed Development ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Developmental Stages ◽  
Small Rna Sequencing ◽  
Kernel Size ◽  
Short Rnas ◽  
Genes Encoding ◽  
Negative Effect

Many studies have investigated the role of miRNAs on the yield of various plants, but so far, no report is available on the identification and role of miRNAs in fruit and seed development of almonds. In this study, preliminary analysis by high-throughput sequencing of short RNAs of kernels from the crosses between almond cultivars ‘Sefid’ × ‘Mamaee’ (with small and large kernels, respectively) and ‘Sefid’ × ‘P. orientalis’ (with small kernels) showed that the expressions of several miRNAs such as Pdu-miR395a-3p, Pdu-miR8123-5p, Pdu-miR482f, Pdu-miR6285, and Pdu-miR396a were significantly different. These miRNAs targeted genes encoding different proteins such as NYFB-3, SPX1, PGSIP3 (GUX2), GH3.9, and BEN1. The result of RT-qPCR revealed that the expression of these genes showed significant differences between the crosses and developmental stages of the seeds, suggesting that these genes might be involved in controlling kernel size because the presence of these miRNAs had a negative effect on their target genes. Pollen source can influence kernel size by affecting hormonal signaling and metabolic pathways through related miRNAs, a phenomenon known as xenia.

scholarly journals Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Mimiviridae, and prokaryotes in a coastal ecosystem

2021 ◽  
Author(s):  
Florian Prodinger ◽  
Hisashi Endo ◽  
Yoshihito Takano ◽  
Yanze Li ◽  
Kento Tominaga ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Interspecific Interactions ◽  
Survival Strategies ◽  
Marker Genes ◽  
Sequence Variant ◽  
Dna Viruses ◽  
Seawater Samples ◽  
One Year

AbstractCoastal seawater is the habitat of different microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. In this work, we investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses infecting eukaryotes (i.e. Mimiviridae), as well as prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and the Mimiviridae polB gene as marker genes in 43 seawater samples collected during 20 months. Communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles for eukaryotes, Mimiviridae, and prokaryotes. However, the community dynamics showed intriguing differences in several aspects such as the recovery rate after a year. We further show that the differences in the community dynamics can be explained by differences in the recurrence/persistence levels of individual ASVs among eukaryotes, Mimiviridae, and prokaryotes. Mimiviridae ASVs were less persistent than eukaryotic ASVs, and prokaryotic ASVs were the most persistent. We argue that the differences in the specificity of interactions (i.e. virus-eukaryote vs prokaryote-eukaryote) as well as the survival strategies are at the origin of the distinct community dynamics among eukaryotes, Mimiviridae, and prokaryotes.One sentence summaryA one year observation of coastal microbial communities revealed similar but different community dynamics for eukaryotes, a group of large viruses, and prokaryotes.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

Experience of negative pressure wound therapy over sternal wound healing: A retrospective review

WCET Journal ◽  
2019 ◽  
Vol 39 (2) ◽  
pp. 9-18
Author(s):  
Wai Sze Ho ◽  
Wai Kuen Lee ◽  
Ka Kay Chan ◽  
Choi Ching Fong
Keyword(s):  
Wound Healing ◽  
Negative Pressure ◽  
Negative Pressure Wound Therapy ◽  
Assessment Tool ◽  
Wound Care ◽  
Wound Therapy ◽  
Treatment Pathways ◽  
Wound Assessment ◽  
One Year

Objectives The aim of this study was to retrospectively review the effectiveness of negative pressure wound therapy (NPWT) in sternal wound healing with the use of the validated Bates-Jensen Wound Assessment Tool (BWAT), and explore the role of NPWT over sternal wounds and future treatment pathways. Methods Data was gathered from patients' medical records and the institution's database clinical management system. Seventeen subjects, who had undergone cardiothoracic surgeries and subsequently consulted the wound care team in one year were reviewed. Fourteen of them were included in the analysis. Healing improvement of each sternal wound under continuous NPWT and continuous conventional dressings was studied. In total, 23 continuous NPWT and 13 conventional dressing episodes were analysed with the BWAT. Results Among conventional dressing episodes, sternal wound improvement was 2.5–3% over 10 days to 3.5 weeks, whereas 4–5% sternal healing was achieved in 5 days to 2 weeks with sternal wire presence. Better healing at 11% in 1 week by conventional dressing was attained after sternal wire removal. In NPWT episodes, 8–29%, 13–24%, and 15–46% of healing was observed in 2 weeks, 3.5 to 5 weeks and 6 to 7 weeks, respectively. Only 39% wound healing was acquired at the 13th week of NPWT in one subject. With sternal wire present, 6%–29% wound healing progress was achieved by NPWT in 1–4 weeks, and 16–23% wound improvement in 2 to 4.5 weeks by NWPT after further surgical debridement. After sternal wire removal, 6–34% sternal wound healing occurred by continuous NPWT for 1–2 weeks, and maximum healing at 46% after 2.5 weeks of NPWT were observed. Conclusions Better wound healing was achieved in the NPWT group in comparison to conventional dressings alone. However, suboptimal sternal wound healing by NPWT alone was observed. Removal of sternal wire may improve the effectiveness of NPWT. Successful tertiary closure after NPWT among subjects supports the important bridging role of NPWT in sternal wound healing. Factors causing stagnant sternal wound healing by NPWT alone are discussed.

ANDROST-5-ENE-3β,17β-DIOL IN OVARY OF POST-MENOPAUSAL HYPEROESTROGENIC WOMEN

1968 ◽  
Vol 58 (3) ◽  
pp. 364-376 ◽  
Author(s):  
S. Pesonen ◽  
M. Ikonen ◽  
B-J. Procopé ◽  
A. Saure
Keyword(s):  
Ovarian Tissue ◽  
Cortical Layer ◽  
Vaginal Smears ◽  
Incubation Experiments ◽  
Cell Groups ◽  
Post Menopause ◽  
Reducing Activity ◽  
Post Menopausal ◽  
One Year

ABSTRACT The ovaries of ten patients, at least one year after the post-menopause, were incubated with two Δ5-C19-steroids and also studied histochemically. All these patients had post-menopausal uterine bleeding and increased oestrogen excretion of the urine. The urinary estimations of gonadotrophins, 17-KS, 17-OHCS and pregnanediol were carried out on all patients. Vaginal smears were read according to Papanicolaou, and the endometrium and ovaries were studied histologically. The incubation experiments indicate the presence of Δ5-3β-hydroxysteroid-dehydrogenase. When androst-5-ene-3β,17β-diol was used as precursor the formation of testosterone occurred without any concomitant production of DHA and/or androstenedione. This seems to indicate the possible role of the Δ5-pathway in the formation of testosterone by post-menopausal ovarian tissue. The histochemical reactions indicated a reducing activity on NADH, lactate and glucose-6-phosphate, in certain corpora albicantia, atretic follicles and in diffuse thecoma regions in the cortical layer of the ovary. Steroid-3β-ol-dehydrogenase and β-hydroxybutyrate-dehydrogenase were found only at the edges of certain corpora albicantia, in some individual stroma cell groups and in some atretic follicles. Our studies, both biochemical and histochemical, suggest that the observed increase in the urinary oestrogens of the patients studied might in part at least, be of ovarian origin. This opinion is also supported by the postoperative oestrogen values.

Role of Fibrinolytic Therapy in Empyema Thoracis – A Hospital Based one year Cross Sectional Study

2012 ◽  
Vol 2 (2) ◽  
pp. 345-350
Author(s):  
Dr. Girish.L Dandagi ◽  
◽  
Venkat kalyana kumar. P ◽  
Dr. Dr.Isaac Mathew ◽  
Dr. Dr.G S Gaude Dr. Dr.G S Gaude
Keyword(s):  
Cross Sectional Study ◽  
Fibrinolytic Therapy ◽  
Empyema Thoracis ◽  
Sectional Study ◽  
Cross Sectional ◽  
One Year

The Role of Chess in the Intellectual Development of Childrens from Primary School

2019 ◽  
pp. 58-62
Author(s):  
Vlad Stegariu ◽  
Simona Andreea Popușoi ◽  
Beatrice Abălașei ◽  
Nicolae Lucian Voinea ◽  
Ioan Stelescu ◽  
...  
Keyword(s):  
Cognitive Development ◽  
Primary School ◽  
Intellectual Development ◽  
Resources Allocation ◽  
Control Group ◽  
Cognitive Resources ◽  
One Year ◽  
Better Than ◽  
Chess Playing

Chess playing has a significant role in participants’ resources allocation, both at a psychological level, but mostly concerning the cognitive resources. The aim of the present study was to examine the effect of chess playing on the intellectual development of primary-class students. 67 children were tested using the Raven Standard Progressive Matrices and were distributed in three different groups according to their experience with chess, namely: the control group (formed by students with no experience with chess playing), the beginners group (students with less than one year in chess playing training) and the advanced group (children with more than two years experience with chess). Results indicated that chess playing had a significant effect on the SPM performance, indicating that those in the advanced group performed significantly better than those in the control or in the beginners group. Conclusions of this study tap into the benefits of playing chess with a focus on the children’s’ cognitive development.

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