scholarly journals De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds

2016 ◽  
Author(s):  
Alexander Suh ◽  
Sandra Bachg ◽  
Stephen Donnellan ◽  
Leo Joseph ◽  
Jürgen Brosius ◽  
...  
Keyword(s):  
De Novo ◽  
Bird Species ◽  
Early Evolution ◽  
Template Switching ◽  
Passerine Birds ◽  
Short Interspersed Elements ◽  
Mammalian Genomes ◽  
Rapid Diversification ◽  
The Common ◽  
Avian Genomes

AbstractPasseriformes (“perching birds” or passerines) make up more than half of all extant bird species. Here, we resolve their deep phylogenetic relationships using presence/absence patterns of short interspersed elements (SINEs), a group of retroposons which is abundant in mammalian genomes but considered largely inactive in avian genomes. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous indications derived from sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excl. the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines, following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. We propose that the early evolution of passerines was unusual among birds in that it was accompanied by activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

scholarly journals De-novo emergence of SINE retroposons during the early evolution of passerine birds

Mobile DNA ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Alexander Suh ◽  
Sandra Bachg ◽  
Stephen Donnellan ◽  
Leo Joseph ◽  
Jürgen Brosius ◽  
...  
Keyword(s):  
De Novo ◽  
Early Evolution ◽  
Passerine Birds

scholarly journals SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 777-784
Author(s):  
Jürgen Schmitz ◽  
Martina Ohme ◽  
Hans Zischler
Keyword(s):  
New World ◽  
World Monkey ◽  
Old World ◽  
Alu Elements ◽  
Alu Sequences ◽  
Short Interspersed Elements ◽  
Divergence Point ◽  
Tarsius Bancanus ◽  
Cladistic Analyses ◽  
The Common

Abstract Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

Initial Experience with Percutaneous Angioplasty of the Common Femoral Artery in De Novo Stenotic Lesions

2015 ◽  
Vol 29 (8) ◽  
pp. 1493-1500 ◽  
Author(s):  
Romain de Blic ◽  
Jean-François Deux ◽  
Hicham Kobeiter ◽  
Pascal Desgranges ◽  
Jean-Pierre Becquemin ◽  
...  
Keyword(s):  
Femoral Artery ◽  
De Novo ◽  
Common Femoral Artery ◽  
Initial Experience ◽  
Percutaneous Angioplasty ◽  
The Common ◽  
Stenotic Lesions

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

scholarly journals Blood parasites in passerine birds from the Brazilian Atlantic Forest

2012 ◽  
Vol 21 (1) ◽  
pp. 7-15 ◽  
Author(s):  
Fabiane Sebaio ◽  
Érika Martins Braga ◽  
Felipe Branquinho ◽  
Alan Fecchio ◽  
Miguel Ângelo Marini
Keyword(s):  
Atlantic Forest ◽  
Bird Species ◽  
Parasite Prevalence ◽  
Neotropical Region ◽  
Blood Parasite ◽  
Blood Parasites ◽  
Passerine Birds ◽  
Blood Smears ◽  
Temporal And Spatial ◽  
Low Prevalence

Parasites may lead bird species to extinction, affect host temporal and spatial population dynamics, alter community structure and alter individuals’ social status. We evaluated blood parasite prevalence and intensity according to bird families and species, among 925 birds that were caught in 2000 and 2001, in the Atlantic Forest in the State of Minas Gerais, Brazil. We applied Giemsa staining to thin blood smears, to detect blood parasites. The birds (n = 15.8%) in 11 families, were infected by at least one parasite genus, especially Muscicapidae (28.3%) and Conopophagidae (25%). Among the 146 infected birds, Plasmodium was detected in all bird families and had the highest prevalence (54.8%). Trypanosoma, Haemoproteus and microfilaria had lower prevalence rates (23.3, 23.3 and 2.1%, respectively). Birds caught during the rainy season were more infected than birds caught during the dry season. The overall low prevalence of blood parasites in birds is similar to the patterns found elsewhere in the Neotropical region.

scholarly journals Haemosporidioses in wild Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos): an in situ hybridization study with emphasis on exo-erythrocytic parasite burden

2019 ◽  
Author(s):  
Tanja Himmel ◽  
Josef Harl ◽  
Simone Pfanner ◽  
Nora Nedorost ◽  
Norbert Nowotny ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Bird Species ◽  
Parasite Burden ◽  
Passerine Birds ◽  
Haemosporidian Parasite ◽  
Pathogenic Potential ◽  
Tissue Samples ◽  
Inflammatory Reactions ◽  
Turdus Merula

Abstract Background Passerine birds are frequently infected with diverse haemosporidian parasites. While infections are traditionally considered benign in wild birds, recent studies demonstrated mortalities of passerine species due to exo-erythrocytic development of the parasites, which can damage organs in affected hosts. However, exo-erythrocytic development remains insufficiently investigated for most haemosporidian species and thus little is known about the virulence of tissue stages in wild passerine birds. The aim of the present study was to investigate natural haemosporidian infections in deceased Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos) and to determine parasite burden and associated histological effects.Methods For molecular analysis, blood and tissue samples from 306 thrushes were screened for Plasmodium, Haemoproteus and Leucocytozoon parasites by nested PCR. For the detection of parasite stages in organ samples, tissue sections were subjected to chromogenic in situ hybridization using genus- and species-specific probes targeting the rRNAs of parasites. Exo-erythrocytic parasite load was semi-quantitatively assessed and histological lesions were evaluated in haematoxylin-eosin-stained sections.Results 179 of 277 Eurasian blackbirds and 15 of 29 song thrushes were positive for haemosporidians. Parasites of all three genera were detected, with Plasmodium matutinum LINN1 and P. vaughani SYAT05 showing the highest prevalences. CISH revealed significant differences in exo-erythrocytic parasite burden between lineages in Eurasian blackbirds, with P. matutinum LINN1 frequently causing high parasite loads in various organs that were associated with histological alterations. Song thrushes infected with P. matutinum LINN1 and birds infected with other haemosporidian lineages showed mostly low parasite burdens. Two Eurasian blackbirds infected with Leucocytozoon sp. TUMER01 showed megalomeronts in various organs that were associated with inflammatory reactions and necroses.Conclusion This study suggests that P. matutinum LINN1, a common lineage among native thrushes, regularly causes high exo-erythrocytic parasite burdens in Eurasian blackbirds, which may result in disease and mortalities, indicating its high pathogenic potential. The findings further illustrate that the same parasite lineage may show different levels of virulence in related bird species which should be considered when assessing the pathogenicity of haemosporidian parasite species. Finally, the study provides evidence of virulent Leucocytozoon sp. TUMER01 infections in two Eurasian blackbirds caused by megalomeront formation.

scholarly journals Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Shir Toubiana ◽  
Miriam Gagliardi ◽  
Mariarosaria Papa ◽  
Roberta Manco ◽  
Maty Tzukerman ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Pharmacological Intervention ◽  
Icf Syndrome ◽  
Genome Wide ◽  
Mammalian Genomes ◽  
Induced Pluripotent ◽  
Methylation Patterns

DNA methyltransferase 3B (DNMT3B) is the major DNMT that methylates mammalian genomes during early development. Mutations in human DNMT3B disrupt genome-wide DNA methylation patterns and result in ICF syndrome type 1 (ICF1). To study whether normal DNA methylation patterns may be restored in ICF1 cells, we corrected DNMT3B mutations in induced pluripotent stem cells from ICF1 patients. Focusing on repetitive regions, we show that in contrast to pericentromeric repeats, which reacquire normal methylation, the majority of subtelomeres acquire only partial DNA methylation and, accordingly, the ICF1 telomeric phenotype persists. Subtelomeres resistant to de novo methylation were characterized by abnormally high H3K4 trimethylation (H3K4me3), and short-term reduction of H3K4me3 by pharmacological intervention partially restored subtelomeric DNA methylation. These findings demonstrate that the abnormal epigenetic landscape established in ICF1 cells restricts the recruitment of DNMT3B, and suggest that rescue of epigenetic diseases with genome-wide disruptions will demand further manipulation beyond mutation correction.

Role of three bird species in the life cycle of two Sarcocystis species (Apicomplexa, Sarcocystidae) in the Czech Republic

2021 ◽  
Author(s):  
Ondřej Máca ◽  
David González
Keyword(s):  
Czech Republic ◽  
Intestinal Mucosa ◽  
Bird Species ◽  
Great Cormorant ◽  
Sarcocystis Species ◽  
The Czech Republic ◽  
Leg Muscles ◽  
The Common ◽  
Milvus Milvus

Abstract BackgroundBirds are one of the groups involved in the development of Sarcocystis Lankester, 1882, serving either as intermediate or definitive hosts. The white-tailed sea eagle Haliaeetus albicilla (Linnaeus, 1758), red kite Milvus milvus (Linnaeus, 1758) (both Accipitriformes) and common starlings Sturnus vulgaris Linnaeus, 1758 (Passeriformes) were examined to elucidate their participation in the development of Sarcocystis, as well as to determine the specific identity of the parasites based on morphological and especially molecular analyses.MethodsIn 2020–2021, one white-tailed eagle, one red kite and five common starlings were parasitologically examined for the presence of Sarcocystis using flotation centrifugation coprological method and by wet mounts of intestinal mucosa scrapings and/or muscle samples. Positive samples were processed by light microscopy, histologically and followed molecularly at four genetic markers (18S rRNA, 28S rRNA, ITS1 and cox1).ResultsThe white-tailed eagle harboured oocysts/sporocysts of S. arctica Gjerde et Schulze, 2014 in the intestinal mucosa, while the intestinal mucosa of the red kite and breasts and leg muscles of one common starling were positive to S. halieti Gjerde, Vikøren et Hamnes, 2018. Sequences from eagle shared 99.6 − 100% identity with each other and S. arctica in the red fox (V. vulpes Linnaeus, 1758) from the Czech Republic. Sequences from the common starling and red kite shared 100% identity with each other and with S. halieti in the great cormorant (P. carbo [Linnaeus, 1758]) from Lithuania and H. albicilla from Norway.ConclusionsThe white-tailed sea eagle (H. albicilla) acts as natural definitive host of S. arctica, whereas the common starling (St. vulgaris) and red kite (M. milvus) represent intermediate and definitive hosts, respectively, for S. halieti.

Haemosporidioses in wild Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos): an in situ hybridization study with emphasis on exo-erythrocytic parasite burden

2020 ◽  
Author(s):  
Tanja Himmel ◽  
Josef Harl ◽  
Simone Pfanner ◽  
Nora Nedorost ◽  
Norbert Nowotny ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Bird Species ◽  
Parasite Burden ◽  
Passerine Birds ◽  
Haemosporidian Parasite ◽  
Pathogenic Potential ◽  
Tissue Samples ◽  
Inflammatory Reactions ◽  
Turdus Merula

Abstract Background Passerine birds are frequently infected with diverse haemosporidian parasites. While infections are traditionally considered benign in wild birds, recent studies demonstrated mortalities of passerine species due to exo-erythrocytic development of the parasites, which can damage organs in affected hosts. However, exo-erythrocytic development remains insufficiently investigated for most haemosporidian species and thus little is known about the virulence of tissue stages in wild passerine birds. The aim of the present study was to investigate natural haemosporidian infections in deceased Eurasian blackbirds (Turdus merula) and song thrushes (Turdus philomelos) and to determine parasite burden and associated histological effects. Methods For molecular analysis, blood and tissue samples from 306 thrushes were screened for Plasmodium, Haemoproteus and Leucocytozoon parasites by nested PCR. For the detection of parasite stages in organ samples, tissue sections were subjected to chromogenic in situ hybridization (CISH) using genus- and species-specific probes targeting the rRNAs of parasites. Exo-erythrocytic parasite load was semi-quantitatively assessed and histological lesions were evaluated in haematoxylin-eosin-stained sections. Results By PCR, 179 of 277 Eurasian blackbirds and 15 of 29 song thrushes were positive for haemosporidians. Parasites of all three genera were detected, with Plasmodium matutinum LINN1 and Plasmodium vaughani SYAT05 showing the highest prevalence. CISH revealed significant differences in exo-erythrocytic parasite burden between lineages in Eurasian blackbirds, with P. matutinum LINN1 frequently causing high exo-erythrocytic parasite burdens in various organs that were associated with histological alterations. Song thrushes infected with P. matutinum LINN1 and birds infected with other haemosporidian lineages showed mostly low exo-erythrocytic parasite burdens. Two Eurasian blackbirds infected with Leucocytozoon sp. TUMER01 showed megalomeronts in various organs that were associated with inflammatory reactions and necroses. Conclusion This study suggests that P. matutinum LINN1, a common lineage among native thrushes, regularly causes high exo-erythrocytic parasite burdens in Eurasian blackbirds, which may result in disease and mortalities, indicating its high pathogenic potential. The findings further illustrate that the same parasite lineage may show different levels of virulence in related bird species which should be considered when assessing the pathogenicity of haemosporidian parasite species. Finally, the study provides evidence of virulent Leucocytozoon sp. TUMER01 infections in two Eurasian blackbirds caused by megalomeront formation.

scholarly journals Quantitative analysis of Mycobacterium avium subsp. hominissuis proteome in response to antibiotics and during exposure to different environmental conditions

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Rajoana Rojony ◽  
Matthew Martin ◽  
Anaamika Campeau ◽  
Jacob M. Wozniak ◽  
David J. Gonzalez ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Mycobacterium Avium ◽  
Metabolic Pathways ◽  
De Novo ◽  
Aerobic Condition ◽  
Peptidoglycan Biosynthesis ◽  
Tandem Mass Tag ◽  
Drug Treatments ◽  
The Common

Abstract Mycobacterium avium subsp. hominissuis (MAH) belongs to the clinically important non-tuberculous mycobacterial group that infects immunocompromised patients and individuals with underling lung conditions. The need for prolonged therapy is a major challenge of MAH treatment, influencing the development of persistent and drug-resistant infections. The reason why bactericidal drugs take several months to eliminate MAH is unknown. To investigate MAH proteome remodeling under aerobic, anaerobic and biofilm conditions (as it is encountered in patient lungs) and identify metabolic changes potentially associated with bacterial persistent state, we performed the relative protein quantitative analysis using Tandem Mass Tag Mass Spectrometry sequencing. MAH was exposed to amikacin (4 μg/ml) and clarithromycin (16 μg/ml) under aerobic, anaerobic or biofilm condition for 24 h and the response was compared with bacterial proteomics of the corresponding conditions. Overall, 4000 proteins were identified out of 5313 MAH proteome of across all experimental groups. Numerous sets of de novo synthesized proteins belonging to metabolic pathways not evidenced in aerobic condition were found commonly enriched in both anaerobic and biofilm conditions, including pantothenate and CoA biosynthesis, glycerolipid metabolism, nitrogen metabolism and chloroalkene degradation, known to be associated with bacterial tolerance in M. tuberculosis. The common pathways observed in anaerobic and biofilm conditions following drug treatments were peptidoglycan biosynthesis, glycerophospholipid metabolism and protein export. The LprB lipoprotein, highly synthesized in MAH biofilms during drug treatments and shown to be essential for M. tuberculosis virulence and survival in vivo, was selected and overexpressed in MAH. Results demonstrate that LprB is secreted in MAH biofilms and the overexpression clone is more tolerant to antimicrobials than the wild-type strain. Our study identified promising metabolic pathways that can be targeted to prevent the bacterial tolerance mechanism and, subsequently, reduce the length of MAH therapy.

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