scholarly journals Eudiplozoon nipponicum (Monogenea, Diplozoidae) and its adaptation to haematophagy as revealed by transcriptome and secretome profiling

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jiří Vorel ◽  
Krystyna Cwiklinski ◽  
Pavel Roudnický ◽  
Jana Ilgová ◽  
Lucie Jedličková ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Proteolytic Enzymes ◽  
Current Knowledge ◽  
Mass Spectrometry Analysis ◽  
Fatty Acid Binding Proteins ◽  
Rna Seq ◽  
Fatty Acid Binding ◽  
Spectrometry Analysis ◽  
Eudiplozoon Nipponicum

Abstract Background Ectoparasites from the family Diplozoidae (Platyhelminthes, Monogenea) belong to obligate haematophagous helminths of cyprinid fish. Current knowledge of these worms is for the most part limited to their morphological, phylogenetic, and population features. Information concerning the biochemical and molecular nature of physiological processes involved in host–parasite interaction, such as evasion of the immune system and its regulation, digestion of macromolecules, suppression of blood coagulation and inflammation, and effect on host tissue and physiology, is lacking. In this study, we report for the first time a comprehensive transcriptomic/secretome description of expressed genes and proteins secreted by the adult stage of Eudiplozoon nipponicum (Goto, 1891) Khotenovsky, 1985, an obligate sanguivorous monogenean which parasitises the gills of the common carp (Cyprinus carpio). Results RNA-seq raw reads (324,941 Roche 454 and 149,697,864 Illumina) were generated, de novo assembled, and filtered into 37,062 protein-coding transcripts. For 19,644 (53.0%) of them, we determined their sequential homologues. In silico functional analysis of E. nipponicum RNA-seq data revealed numerous transcripts, pathways, and GO terms responsible for immunomodulation (inhibitors of proteolytic enzymes, CD59-like proteins, fatty acid binding proteins), feeding (proteolytic enzymes cathepsins B, D, L1, and L3), and development (fructose 1,6-bisphosphatase, ferritin, and annexin). LC-MS/MS spectrometry analysis identified 721 proteins secreted by E. nipponicum with predominantly immunomodulatory and anti-inflammatory functions (peptidyl-prolyl cis-trans isomerase, homolog to SmKK7, tetraspanin) and ability to digest host macromolecules (cathepsins B, D, L1). Conclusions In this study, we integrated two high-throughput sequencing techniques, mass spectrometry analysis, and comprehensive bioinformatics approach in order to arrive at the first comprehensive description of monogenean transcriptome and secretome. Exploration of E. nipponicum transcriptome-related nucleotide sequences and translated and secreted proteins offer a better understanding of molecular biology and biochemistry of these, often neglected, organisms. It enabled us to report the essential physiological pathways and protein molecules involved in their interactions with the fish hosts.

scholarly journals Re-Discovery of Giardiavirus: Genomic and Functional Analysis of Viruses from Giardia duodenalis Isolates

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 654
Author(s):  
Gianluca Marucci ◽  
Ilaria Zullino ◽  
Lucia Bertuccini ◽  
Serena Camerini ◽  
Serena Cecchetti ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Diarrheal Disease ◽  
Current Knowledge ◽  
Biological Significance ◽  
Giardia Duodenalis ◽  
Protozoan Parasite ◽  
Protein Translation ◽  
Mass Spectrometry Analysis ◽  
Animal Origin ◽  
Spectrometry Analysis

Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively studied; moreover, a positive correlation between GLV and parasite virulence is yet to be proved. To understand the biological significance of GLV infection in Giardia, the characterization of several GLV strains from naturally infected G. duodenalis isolates is necessary. Here we report high-throughput sequencing of four GLVs strains, from Giardia isolates of human and animal origin. We also report on a new, unclassified viral sequence (designed GdRV-2), unrelated to Giardiavirus, encoding and expressing for a single large protein with an RdRp domain homologous to Totiviridae and Botybirnaviridae. The result of our sequencing and proteomic analyses challenge the current knowledge on GLV and strongly suggest that viral capsid protein translation unusually starts with a proline and that translation of the RNA-dependent RNA polymerase (RdRp) occurs via a +1/−2 ribosomal frameshift mechanism. Nucleotide polymorphism, confirmed by mass-spectrometry analysis, was also observed among and between GLV strains. Phylogenetic analysis indicated the occurrence of at least two GLV subtypes which display different phenotypes and transmissibility in experimental infections of a GLV naïve Giardia isolate.

scholarly journals Weissellicin 110, a Newly Discovered Bacteriocin from Weissella cibaria 110, Isolated from Plaa-Som, a Fermented Fish Product from Thailand

2007 ◽  
Vol 73 (7) ◽  
pp. 2247-2250 ◽  
Author(s):  
Sirinat Srionnual ◽  
Fujitoshi Yanagida ◽  
Li-Hsiu Lin ◽  
Kuang-Nan Hsiao ◽  
Yi-sheng Chen
Keyword(s):  
Proteolytic Enzymes ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Protein Band ◽  
Proteinase K ◽  
Mass Spectrometry Analysis ◽  
Fermented Fish ◽  
Spectrometry Analysis ◽  
Weissella Cibaria ◽  
Fish Product

ABSTRACT Weissella cibaria 110, isolated from the Thai fermented fish product plaa-som, was found to produce a bacteriocin active against some gram-positive bacteria. Bacteriocin activity was not eliminated by exposure to high temperatures or catalase but was destroyed by exposure to the proteolytic enzymes proteinase K and trypsin. The bacteriocin from W. cibaria 110 was purified, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the purified bacteriocin contained one protein band that was approximately 2.5 kDa in size. Mass spectrometry analysis showed the mass of the peptide to be approximately 3,487.8 Da. N-terminal amino acid sequence analysis was performed, and 27 amino acids were identified. Because it has no similarity to other known bacteriocins, this bacteriocin was defined as a new bacteriocin and termed weissellicin 110.

scholarly journals A preliminary study of Dihydroorotase from Methanococcus jannaschii

2014 ◽  
Vol 70 (a1) ◽  
pp. C481-C481
Author(s):  
Aditya Singh ◽  
Michael Colaneri ◽  
Jacqueline Vitali
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Hydrophobic Interaction Chromatography ◽  
Size Exclusion ◽  
Mass Spectrometry Analysis ◽  
Yale University ◽  
Spectrometry Analysis ◽  
Bacteria And Fungi ◽  
Physics Department ◽  
Research Institute

Dihydroorotase (DHOase) catalyzes the reversible cyclization of N-carbamoyl-L-aspartate to form L-dihydroorotate in the third step of de novo pyrimidine biosynthesis. It is a Zinc metalloenzyme and a member of the aminohydrolase superfamily. There are two classes of the enzyme. Class I, typically ~45 kDa, is found in higher organisms, bacteria and yeast. Class II, typically ~38 kDa, is found in bacteria and fungi. Some organisms have multiple DHOase sequences. The M. jannaschii pyrC gene coding for DHOase was subcloned and expressed in E. coli. Protein purification consisted of ammonium sulfate precipitation, heat treatment at 850C, and phenyl-sepharose hydrophobic interaction chromatography. The protein was confirmed in the SDS gel using Liquid Chromatography-Mass Spectrometry (Proteomics Laboratory, Lerner Research Institute, Cleveland, OH). Size Exclusion Chromatography-Laser Light Scattering (Keck Biotechnology Laboratory, Yale University, New Haven, CT) indicated that the protein is a monomer in solution with a molecular weight of 47 kDa. A model constructed with the I-TASSER server (Zhang, 2008) suggested that the binding site contains only one Zn ion per monomer coordinated by the conserved His56, His58 and Asp302. Asp146 is further away and does not coordinate with the Zn ion. According to the mass spectrometry analysis, the protein does not contain a carboxylated lysine. Our progress on this study will be presented. Acknowledgements: We thank Dr. Belinda Willard (Lerner Research Institute) for the LC-MS and Dr. Ewa Folta-Stogniew (Yale University) for the SEC- LS analysis. The presentation was supported in part by a graduate faculty travel award and by a contribution from the Physics Department at Cleveland State University.

Purification and characterization of enterocin MC13 produced by a potential aquaculture probiontEnterococcus faeciumMC13 isolated from the gut ofMugil cephalus

2011 ◽  
Vol 57 (12) ◽  
pp. 993-1001 ◽  
Author(s):  
R. Satish Kumar ◽  
P. Kanmani ◽  
N. Yuvaraj ◽  
K.A. Paari ◽  
V. Pattukumar ◽  
...  
Keyword(s):  
Molecular Mass ◽  
Enterococcus Faecium ◽  
Vibrio Vulnificus ◽  
Proteolytic Enzymes ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Probiotic Bacterium ◽  
Mass Spectrometry Analysis ◽  
Native Page ◽  
Spectrometry Analysis

A bacteriocin producer strain MC13 was isolated from the gut of Mugil cephalus (grey mullet) and identified as Enterococcus faecium . The bacteriocin of E. faecium MC13 was purified to homogeneity, as confirmed by Tricine sodium dodecyl sulphate – polyacrylamide gel electrophoresis (SDS–PAGE). Reverse-phase high-performance liquid chromatography (HPLC) analysis showed a single active fraction eluted at 26 min, and matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry analysis showed the molecular mass to be 2.148 kDa. The clear zone in native PAGE corresponding to enterocin MC13 band further substantiated its molecular mass. A dialyzed sample (semicrude preparation) of enterocin MC13 was broad spectrum in its action and inhibited important seafood-borne pathogens: Listeria monocytogenes , Vibrio parahaemolyticus , and Vibrio vulnificus . This antibacterial substance was sensitive to proteolytic enzymes: trypsin, protease, and chymotrypsin but insensitive to catalase and lipase, confirming that inhibition was due to the proteinaceous molecule, i.e., bacteriocin, and not due to hydrogen peroxide. Enterocin MC13 tolerated heat treatment (up to 90 °C for 20 min). Enterococcus faecium MC13 was effective in bile salt tolerance, acid tolerance, and adhesion to the HT-29 cell line. These properties reveal the potential of E. faecium MC13 to be a probiotic bacterium. Enterococcus faecium MC13 could be used as potential fish probiotic against pathogens such as V. parahaemolyticus, Vibrio harveyi , and Aeromonas hydrophila in fisheries. Also, this could be a valuable seafood biopreservative against L. monocytogenes.

scholarly journals The Pharmacological or Genetic Blockade of Endogenous De Novo Fatty Acid Synthesis Does Not Increase the Uptake of Exogenous Lipids in Ovarian Cancer Cells

2021 ◽  
Vol 11 ◽  
Author(s):  
Thomas W. Grunt ◽  
Lisa Lemberger ◽  
Ramón Colomer ◽  
María Luz López−Rodríguez ◽  
Renate Wagner
Keyword(s):  
Ovarian Cancer ◽  
Fatty Acid ◽  
De Novo ◽  
Lipid Production ◽  
Growth Arrest ◽  
High Energy ◽  
Cancer Drug ◽  
Fatty Acid Binding Proteins ◽  
Ovarian Cancer Cells ◽  
Fatty Acid Binding

Ovarian cancer(OC) is a serious threat to women worldwide. Peritoneal dissemination, ascites and omental metastasis are typical features for disease progression, which occurs in a micro-environment that is rich in high-energy lipids. OC cells require high amounts of lipids for survival and growth. Not only do they import lipids from the host, they also produce lipids de novo. Inhibitors of fatty acid(FA) synthase(FASN) – the rate-limiting enzyme of endogenous FA synthesis that is overexpressed in OC – induce growth-arrest and apoptosis, rendering them promising candidates for cancer drug development. However, cancer researchers have long hypothesized that the lipid deficiency caused by FASN inhibition can be circumvented by increasing the uptake of exogenous lipids from the host, which would confer resistance to FASN inhibitors. In contrast to a very recent report in colorectal cancer, we demonstrate in OC cells (A2780, OVCAR3, SKOV3) that neither FASN inhibitors (G28UCM, Fasnall) nor FASN-specific siRNAs can stimulate a relief pathway leading to enhanced uptake of extrinsic FAs or low density lipoproteins (LDLs). Instead, we observed that the growth-arrest due to FASN inhibition or FASN knock-down was associated with significant dose- and time-dependent reduction in the uptake of fluorescently labeled FAs and LDLs. Western blotting showed that the expression of the FA receptor CD36, the LDL receptor(LDLR) and the lipid transport proteins fatty acid binding proteins 1–9 (FABP1–9) was not affected by the treatment. Next, we compared experimental blockade of endogenous lipid production with physiologic depletion of exogenous lipids. Lipid-free media, similar to FASN inhibitors, caused growth-arrest. Although lipid-depleted cells have diminished amounts of CD36, LDLR and FABPs, they can still activate a restorative pathway that causes enhanced import of fluorophore-labeled FAs and LDLs. Overall, our data show that OC cells are strictly lipid-depend and exquisitely sensitive to FASN inhibitors, providing a strong rationale for developing anti-FASN strategies for clinical use against OC.

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Julien Richard Albert ◽  
Wan Kin Au Yeung ◽  
Keisuke Toriyama ◽  
Hisato Kobayashi ◽  
Ryutaro Hirasawa ◽  
...  
Keyword(s):  
De Novo ◽  
Cpg Islands ◽  
Blastocyst Stage ◽  
Early Embryo ◽  
Mass Spectrometry Analysis ◽  
Paternal Allele ◽  
Sequencing Data ◽  
Cell Stage ◽  
Paternal Genome ◽  
Spectrometry Analysis

Abstract De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.

scholarly journals Index suffix–prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression

2018 ◽  
Vol 35 (12) ◽  
pp. 2066-2074 ◽  
Author(s):  
Yuansheng Liu ◽  
Zuguo Yu ◽  
Marcel E Dinger ◽  
Jinyan Li
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Reference Sequence ◽  
Supplementary Information ◽  
The Novel ◽  
Rna Seq ◽  
File Size ◽  
Sequencing Technologies ◽  
Efficient Storage ◽  
Merging Process

Abstract Motivation Advanced high-throughput sequencing technologies have produced massive amount of reads data, and algorithms have been specially designed to contract the size of these datasets for efficient storage and transmission. Reordering reads with regard to their positions in de novo assembled contigs or in explicit reference sequences has been proven to be one of the most effective reads compression approach. As there is usually no good prior knowledge about the reference sequence, current focus is on the novel construction of de novo assembled contigs. Results We introduce a new de novo compression algorithm named minicom. This algorithm uses large k-minimizers to index the reads and subgroup those that have the same minimizer. Within each subgroup, a contig is constructed. Then some pairs of the contigs derived from the subgroups are merged into longer contigs according to a (w, k)-minimizer-indexed suffix–prefix overlap similarity between two contigs. This merging process is repeated after the longer contigs are formed until no pair of contigs can be merged. We compare the performance of minicom with two reference-based methods and four de novo methods on 18 datasets (13 RNA-seq datasets and 5 whole genome sequencing datasets). In the compression of single-end reads, minicom obtained the smallest file size for 22 of 34 cases with significant improvement. In the compression of paired-end reads, minicom achieved 20–80% compression gain over the best state-of-the-art algorithm. Our method also achieved a 10% size reduction of compressed files in comparison with the best algorithm under the reads-order preserving mode. These excellent performances are mainly attributed to the exploit of the redundancy of the repetitive substrings in the long contigs. Availability and implementation https://github.com/yuansliu/minicom Supplementary information Supplementary data are available at Bioinformatics online.

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