1,720,973 research outputs found
EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing
No full textEdiPy is an online resource appropriately designed to simulate the evolution of plant mitochondrial genes in a biologically realistic fashion. EdiPy takes into account the presence of sites subjected to RNA editing and provides multiple artificial alignments corresponding to both genomic and cDNA sequences. Each artificial data set can successively be submitted to main and widespread evolutionary and phylogenetic software packages such as PAUP, Phyml, PAML and Phylip. ' As an online bioinformatic resource, EdiPy is available at the following web page: http://biologia.unical.it/py_script/index.html. (C) 2005 Elsevier Ltd. All rights reserved
Reproductive healthcare during the Covid-19 outbreak in Italy
No full textThe outbreak of COVID-19 increased gender inequalities worldwide. This paper analyses how adjustments to the pandemic situation introduced in Italy between February and May 2020 affected women and pregnant people’s reproductive healthcare. It illustrates how a national structural approach to maternal and reproductive health was adapted to the Covid-19 epidemic, sometimes delaying essential care and leaving women and pregnant people feeling lonely and uncomfortable. It shows how the measures introduced in antenatal, childbirth and postnatal care, assisted reproduction, and abortion were developed within a clinical and cultural framework, where women’s reproductive health was considered a risky matter and medicalized care the best way to manage it; motherhood was valued as a preferred reproductive trajectory, and a public demographic discourse supporting selective pronatalism entered health settings. At the same time, the pandemic generated unprecedented grassroot demands for more accessible and diverse reproductive car
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from <it>in silico</it> and <it>in vivo</it> data sets
Full text linkAbstract Background In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters. To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations. Results Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (rps3, matR and atp1) no differences in the comparison between inferred genomic and cDNA topologies could be detected. Conclusions Our findings by the here reported in silico and in vivo computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0%) and reduced in length (shorter than 500 bp). In the current lack of direct experimental evidence the results presented here encourage, thus, the use of genomic mitochondrial rather than cDNA sequences for reconstructing phylogenetic events in land plants.</p
Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria
No full textThe ribosomal protein S4 gene (rps4) has been identified as a single copy sequence in the mitochondrial genomes of two distant higher plants, Magnolia and Helianthus. Sequence analysis revealed that the rps4 genes present in the magnolia and sunflower mitochondrial genomes encode S4 polypeptides of 352 and 331 amino acids, respectively, longer than their counterparts in liverwort and bacteria. Expression of the rps4 genes in the investigated higher plant mitochondria was confirmed by Western blot analysis. In Helianthus, one of two short nucleotide insertions at the 3'-end introduces in the coding region a premature termination codon. Northern hybridizations and reverse transcription-polymerase chain reaction analysis demonstrated that the monocistronic RNA transcripts generated from the rps4 locus in Magnolia and Helianthus mitochondria are modified by RNA editing at 28 and 13 positions, respectively. Although evolutionarily conserved, RNA editing requirements of the rps4 appear more extensive in Magnolia than in Helianthus and in the other higher plants so far investigated. Furthermore, our analysis also suggests that selection of editing sites is RNA sequence-specific in a duplicated sequence context. (C) 2002 Elsevier Science B.V. All rights reserved
A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms
No full textComparative analysis of the ribosomal protein S3 gene (rps3) in the mitochondrial genome of Cycas with newly sequenced counterparts from Magnolia and Helianthus and available sequences from higher plants revealed that the positional clustering with the genes for ribosomal protein S19 (rps19) and L16 (rpl16) is preserved in gymnosperms. However, in contrast to the other land plant species, the rps3 gene in Cycas mitochondria is unique in possessing a second intron: rps3i2. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of the transcripts generated from the rps19-rps3-rpl16 cluster in Cycas mitochondria demonstrated that the genes are cotranscribed and extensively modified by RNA editing and that both introns are efficiently spliced. Despite remarkable size heterogeneity, the Cycas rps3i1 can be shown to be homologous to the group IIA introns present within the rps3 gene of algae and land plants, including Magnolia and Helianthus. Conversely, sequences similar to the rps3i2 have not been reported previously. On the basis of conserved primary and secondary structure the second intervening sequence interrupting the Cycas rps3 gene has been classified as a group II intron. The close relationship of the rps3i2 to a group of different plant mitochondrial introns is intriguing and suggestive of a mitochondrial derivation for this novel intervening sequence. Interestingly, the rps3i2 appears to be conserved at the same gene location in other gymnosperms. Furthermore, the pattern of the rps3i2 distribution among algae and land plants provides evidence for the evolutionary acquisition of this novel intron in gymnosperms via intragenomic transposition or retrotransposition
REDIdb: an upgraded bioinformatics resource for organellar RNA editing
No full textRNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/ or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http:// biologia.unical.it/py_script/REDIdb/
Shifting vulnerabilities: gender and reproductive care on the migrant trail to Europe
Full text linkThe reproductive care of pregnant migrants entering the European Union via its Mediterranean borders represents an under-examined topic, despite a growing scholarly emphasis on female migrants and the gendered aspects of migration in the past three decades. This article uses ethnographic data gathered in Greece, Italy, and Spain to examine pregnant migrants’ experiences of crossing, first reception, and reproductive care. We discuss our findings through the conceptual lens of vulnerability, which we understand as a shifting and relational condition attributed to, or dynamically endorsed by, migrant patients within given social contexts and encounters. We focus on two principal aspects of migrant women’s experiences. First, we shed light on their profiles, their journeys to Europe via the three main Mediterranean routes, and the conditions of first reception. Through ethnographic vignettes we examine the diverse ways in which pregnant migrants become vulnerable within these contexts. Second, we turn to the reproductive healthcare they receive in EU borderlands. We explore how declinations of ideas of vulnerability shape the medical encounter between healthcare professionals and migrant women and how vulnerability is dynamically used or contested by migrant patients to engage in meaningful social relations in unpredictable and unstable borderlands
Evolution of the nad3-rps12 gene cluster in angiosperm mitochondria: Comparison of edited and unedited sequences
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