scholarly journals Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 959
Author(s):  
Katrine Wacenius Skov Alanin ◽  
Laura Milena Forero Junco ◽  
Jacob Bruun Jørgensen ◽  
Tue Kjærgaard Nielsen ◽  
Morten Arendt Rasmussen ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
High Throughput Sequencing ◽  
Plaque Assay ◽  
Significant Shift ◽  
Host Matrix ◽  
Related Phage ◽  
Waste Sample ◽  
Solid Media ◽  
Long Reads

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community’s shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome–host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.

scholarly journals Metaviromes reveal the dynamics of Pseudomonas host-specific phages cultured and uncultured by plaque assay

2021 ◽  
Author(s):  
Katrine Wacenius Skov Alanin ◽  
Laura Milena Forero Junco ◽  
Jacob Bruun Jørgensen ◽  
Tue Kjærgaard Nielsen ◽  
Morten Arendt Rasmussen ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
High Throughput Sequencing ◽  
Plaque Assay ◽  
Significant Shift ◽  
Host Matrix ◽  
Related Phage ◽  
Waste Sample ◽  
Solid Media ◽  
Long Reads

AbstractIsolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or the ones with highest ability to plaque on solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in envi-ronmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community’s shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media corresponds to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum 2-fold change above 0 in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, was highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlights how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.

scholarly journals Pengaruh Penambahan Campuran Kapur Tohor dan Kapur Barus (C10H16O) Terhadap Kepadatan Lalat Pada Sampah Organik

2019 ◽  
Vol 16 (1) ◽  
pp. 747
Author(s):  
Fadya Artha Aristanova ◽  
Gunung Setiadi ◽  
Isnawati Isnawati
Keyword(s):  
Organic Waste ◽  
T Test ◽  
Effective Dosage ◽  
P Value ◽  
Test Results ◽  
Waste Sample ◽  
Significant Difference ◽  
Before And After ◽  
Quasi Experimental ◽  
Test Result

Abstract: The Effect Of Lime (C10H16O) And Camphor (C10H16O) Against The Density Of Flies On Organic Waste. Fly is a disease-carrying vector so it is important to measure the density for control purposes. One of the controls that is done is on organic waste which is a breading source place of flies. Control is done by affixing the mixture of lime and camphor. This research aimed to determine the effect of mixture of lime and camphor against the density of flies in organic waste that is carried out in the garbage construction site while Southern Loktabat. This type of research is quasi-experimental that experimenting the provision of nine variations of dosage mixture of lime and camphor against the density of flies in organic waste with the organic waste sample was about 0,16m3. This research design used Pretest-posttest design. The analysis using statistical paired sample t-test, Kruskal Wallis test, and Least Significant Differences Test. The measurements showed a decrease in the density of the flies after administration of the lime and camphor mixture. Paired T-test results showed that in each treatment the p-value (2-tailed) <α (0.05) means that there is significant difference of flies density before and after treatment. Kruskal Wallis test result showed the p value (0,000) <α (0.05) which means there are significant differences between dosages. LSD test result showed that the most effective dosage is sixth dosage (35gr camphor+ 55gr lime/0,16m3 waste).

scholarly journals SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification

2017 ◽  
Author(s):  
Manuel Tardaguila ◽  
Lorena de la Fuente ◽  
Cristina Marti ◽  
Cécile Pereira ◽  
Francisco Jose Pardo-Palacios ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Full Length ◽  
The Novel ◽  
Extensive Evaluation ◽  
Long Reads ◽  
Long Read ◽  
Novel Transcripts ◽  
Mouse Transcriptome

ABSTRACTHigh-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the classification of long-read transcripts that computes 47 descriptors that can be used to assess the quality of the data and of the preprocessing pipelines. We applied SQANTI to a neuronal mouse transcriptome using PacBio long reads and illustrate how the tool is effective in readily describing the composition of and characterizing the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach, and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, result more frequently in novel ORFs than novel UTRs and are enriched in both general metabolic and neural specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases we find that alternative isoforms are elusive to proteogenomics detection and are variable in protein changes with respect to the principal isoform of their genes. SQANTI allows the user to maximize the analytical outcome of long read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes. SQANTI is available at https://bitbucket.org/ConesaLab/sqanti.

Biopolymers modulate microbial communities in municipal organic waste digestion

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Francesca Bandini ◽  
Chiara Misci ◽  
Eren Taskin ◽  
Pier Sandro Cocconcelli ◽  
Edoardo Puglisi
Keyword(s):  
Organic Matter ◽  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Organic Waste ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Organic Fraction ◽  
Thermophilic Anaerobic Digestion ◽  
A Minor ◽  
Real Plant

ABSTRACT The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.

scholarly journals Probably Correct: Rescuing Repeats with Short and Long Reads

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 48
Author(s):  
Monika Cechova
Keyword(s):  
Human Genome ◽  
High Throughput Sequencing ◽  
Genome Project ◽  
Read Length ◽  
Single Individual ◽  
Sequencing Errors ◽  
Long Reads ◽  
Repeat Masking ◽  
The Human Genome Project ◽  
Methylation Patterns

Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome—estimated 50–69%—is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chromosomes from “telomere to telomere”. Moreover, identical reads or repeat arrays can be differentiated based on their epigenetic marks, such as methylation patterns, aiding in the assembly process. This is despite the fact that long reads still contain a modest percentage of sequencing errors, disorienting the aligners and assemblers both in accuracy and speed. Here, I review the proposed and implemented solutions to the repeat resolution and the multi-mapping read problem, as well as the downstream consequences of reference choice, repeat masking, and proper representation of sex chromosomes. I also consider the forthcoming challenges and solutions with regards to long reads, where we expect the shift from the problem of repeat localization within a single individual to the problem of repeat positioning within pangenomes.

scholarly journals Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads

2019 ◽  
Author(s):  
Maria Artesi ◽  
Vincent Hahaut ◽  
Fereshteh Ashrafi ◽  
Ambroise Marçais ◽  
Olivier Hermine ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Recurrent Selection ◽  
High Efficiency ◽  
Large Population ◽  
Insertion Site ◽  
Endogenous Retroviruses ◽  
Inverse Pcr ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Insertion Sites

AbstractRetroviral infections create a large population of cells, each defined by a unique proviral insertion site. Methods based on short-read high throughput sequencing can identify thousands of insertion sites, but the proviruses within remain unobserved. We have developed Pooled CRISPR Inverse PCR sequencing (PCIP-seq), a method that leverages long reads on the Oxford Nanopore MinION platform to sequence the insertion site and its associated provirus. We have applied the technique to three exogenous retroviruses, HTLV-1, HIV-1 and BLV, as well as endogenous retroviruses in both cattle and sheep. The long reads of PCIP-seq improved the accuracy of insertion site identification in repetitive regions of the genome. The high efficiency of the method facilitated the identification of tens of thousands of insertion sites in a single sample. We observed thousands of SNPs and dozens of structural variants within proviruses and uncovered evidence of viral hypermutation, recombination and recurrent selection.

scholarly journals Estimating backyard waste burning emission: A case study of Tembalang Campus, Diponegoro University

2021 ◽  
Vol 894 (1) ◽  
pp. 012038
Author(s):  
E Sutrisno ◽  
B S Ramadan ◽  
H S Huboyo ◽  
N Ikhlas ◽  
A Karmilia
Keyword(s):  
Organic Waste ◽  
Nox Emissions ◽  
Test Results ◽  
Gas Analyzer ◽  
Waste Sample ◽  
Surrounding Environment ◽  
Random Samples ◽  
Enormous Amount ◽  
Waste Burning

Abstract This study analyzes the distribution and amount of CO, CO2, HC, and NOx gas emissions resulting from the open burning of backyard waste in Diponegoro University. The burned waste sample is taken from surrounding environment of Diponegoro University (Tembalang Campus) by taking 4 random samples (3 kg each). Emissions from CO, CO2, HC, and NOx gases were obtained from the 24 minutes combustion test. Furthermore, the gaseous pollutant emitted is measured using a gas analyzer. The burned waste comprised 73.77% of organic waste, 17.45% of plastic; 4.33% of paper; and 4.45% of other waste. The emission test results show that the highest CO, CO2, HC, and NOx emissions have occurred at 14, 20, 18, and 18 minutes, respectively. The combustion test reveals that an enormous amount of CO, CO2, HC, and NOx gas is emitted during uncontrolled waste burning. Because backyard wastes burning produce significant gaseous pollutants, several efforts are needed to reduce this practice.

scholarly journals Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

scholarly journals The Impact of Exogenous Aerobic Bacteria on Sustainable Methane Production Associated with Municipal Solid Waste Biodegradation: Revealed by High-Throughput Sequencing

2020 ◽  
Vol 12 (5) ◽  
pp. 1815 ◽  
Author(s):  
Sai Ge ◽  
Jun Ma ◽  
Lei Liu ◽  
Zhiming Yuan
Keyword(s):  
Municipal Solid Waste ◽  
Microbial Communities ◽  
Solid Waste ◽  
Methane Production ◽  
Organic Waste ◽  
High Throughput Sequencing ◽  
Methane Yield ◽  
Aerobic Bacteria ◽  
Waste Degradation ◽  
The Impact

In this work, the impact of exogenous aerobic bacteria mixture (EABM) on municipal solid waste (MSW) is well evaluated in the following aspects: biogas production, leachate analysis, organic waste degradation, EABM population, and the composition of microbial communities. The study was designed and performed as follows: the control bioreactor (R1) was filled up with MSW and the culture medium of EABM and the experimental bioreactor (R2) was filled up with MSW and EABM. The data suggests that the composition of microbial communities (bacterial and methanogenic) in R1 and R2 were similar at day 0, while the addition of EABM in R2 led to a differential abundance of Bacillus cereus, Bacillus subtilis, Staphylococcus saprophyticus, Staphlyoccus xylosus, and Pantoea agglomerans in two bioreactors. The population of exogenous aerobic bacteria in R2 greatly increased during hydrolysis and acidogenesis stages, and subsequently increased the degradation of volatile solid (VS), protein, lipid, and lignin by 59.25%, 25.68%, 60.47%, and 197.62%, respectively, compared to R1. The duration of hydrolysis and acidogenesis in R2 was 33.33% shorter than that in R1. At the end of the study, the accumulative methane yield in R2 (494.4 L) was almost three times more than that in R1 (187.4 L). In addition, the abundance of acetoclasic methanogens increased at acetogenesis and methanogenesis stages in both bioreactors, which indicates that acetoclasic methanogens (especially Methanoseata) could contribute to methane production. This study demonstrates that EABM can accelerate organic waste degradation to promote MSW biodegradation and methane production. Moreover, the operational parameters helped EABM to generate 20.85% more in accumulative methane yield. With a better understanding of how EABM affects MSW and the composition of bacterial community, this study offers a potential practical approach to MSW disposal and cleaner energy generation worldwide.

scholarly journals Experimental Infection and Genetic Characterization of Two Different Capripox Virus Isolates in Small Ruminants

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1098 ◽  
Author(s):  
Janika Wolff ◽  
Jacqueline King ◽  
Tom Moritz ◽  
Anne Pohlmann ◽  
Donata Hoffmann ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Clinical Signs ◽  
Small Ruminants ◽  
Long Reads ◽  
Animal Trial ◽  
Severity Of The Disease ◽  
Production Animals ◽  
Inoculation Route ◽  
High Quality Genome

Capripox viruses, with their members “lumpy skin disease virus (LSDV)”, “goatpox virus (GTPV)” and “sheeppox virus (SPPV)”, are described as the most serious pox diseases of production animals. A GTPV isolate and a SPPV isolate were sequenced in a combined approach using nanopore MinION sequencing to obtain long reads and Illumina high throughput sequencing for short precise reads to gain full-length high-quality genome sequences. Concomitantly, sheep and goats were inoculated with SPPV and GTPV strains, respectively. During the animal trial, varying infection routes were compared: a combined intravenous and subcutaneous infection, an only intranasal infection, and the contact infection between naïve and inoculated animals. Sheep inoculated with SPPV showed no clinical signs, only a very small number of genome-positive samples and a low-level antibody reaction. In contrast, all GTPV inoculated or in-contact goats developed severe clinical signs with high viral genome loads observed in all tested matrices. Furthermore, seroconversion was detected in nearly all goats and no differences concerning the severity of the disease depending on the inoculation route were observed. Conclusively, the employed SPPV strain has the properties of an attenuated vaccine strain, consistent with the genetic data, whereas the GTPV strain represents a highly virulent field strain.

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