The evolution of novel fungal genes from non-retroviral RNA viruses

<p>Abstract</p> <p>Background</p> <p>Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles.</p> <p>Results</p> <p>Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated <it>Totivirus</it>-like sequences in three fungi (<it>Candida parapsilosis</it>, <it>Penicillium marneffei </it>and <it>Uromyces appendiculatus</it>). The phylogenetic evidence strongly indicated that the direction of transfer was from <it>Totivirus </it>to fungus. However, there was evidence of transfer of <it>Totivirus</it>-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning.</p> <p>Conclusions</p> <p>Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.</p

Structural rRNA Characters Support Monophyly of Raptorial Limbs and Paraphyly of Limb Specialization in Water Fleas

The evolutionary success of arthropods has been attributed partly to the diversity of their limb morphologies. Large morphological diversity and increased specialization are observed in water flea (Cladocera) limbs, but it is unclear whether the increased limb specialization in different cladoceran orders is the result of shared ancestry or parallel evolution. We inferred a robust among–order cladoceran phylogeny using small–subunit and large–subunit rRNA nuclear gene sequences, signature sequence regions, novel stem–loops and secondary structure morphometrics to assess the phylogenetic distribution of limb specialization. The sequence–based and structural rRNA morphometric phylogenies were congruent and suggested monophyly of orders with raptorial limbs, but paraphyly of orders with reduced numbers of specialized limbs. These results highlight the utility of complex molecular structural characters in resolving ancient rapid radiations

Transglobal comparisons of nuclear and mitochondrial genetic structure in a marine polyploid clam ( Lasaea , Lasaeidae)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75076/1/j.1365-2540.2000.00673.x.pd

Evaluation of Qatari and Canadian Pharmacy Students Learning Together about Cultural Competency using Videoconference Educational Activities

Background: Pharmacists are under pressure to provide patient centered care within increasingly culturally diverse settings. Pharmacy schools play an important role in educating learners regarding culture and its impact on patient care. Objectives: The objectives of this study were to determine if a novel cultural competency learning activity, which involved students from two culturally and ethnically different pharmacy schools learning together using videoconference education activities, improved: (1) student knowledge and confidence pertaining to cultural competency concepts, (2) attitudes and perceptions towards being a culturally competent pharmacist, and (3) academic performance related to cultural competency case studies. Methods: Pharmacy students from Qatar University in Doha, Qatar (n=25) and the University of Saskatchewan in Saskatoon, Canada (n=85) participated in a cultural competency activity comprised of small group work on a patient case study, followed by tutorial discussions. Some Canadian students (n=31/85) worked collaboratively (via video conference) with the students from Qatar. The evaluation used a convergent mixed methods design comprised of: (1) a pre and post session survey measuring student knowledge and confidence; (2) pre and post session student self-reflections; and, (3) student academic performance on care plans and an observed structured clinical exam (OSCE). Results: The survey identified small but statistically significant (p&lt;0.05) improvements in knowledge and confidence with respect to 11 of the 12 questionnaire items in the students from Canada and 2 of the 12 items in the students from Qatar. The self-reflections found that 44.4% (n=36/81) of students who completed the pre and post reflective questions reported a change in knowledge and attitudes regarding cultural competency, but a reason for the change was not evident. Student grades on the cultural competency care plans and the OSCE were not different between the students who worked collaboratively across the two schools compared with those who did not. Conclusion: The cultural competency student activity showed small improvements in pharmacy student knowledge, attitudes and confidence, but did not affect academic performance. Future research in this area could utilize a greater diversity of methodological approaches, including a focus on student self-reflection and qualitative assessment, to better capture student competency. &nbsp; Type:&nbsp;Original Researc

Evolutionary maintenance of filovirus-like genes in bat genomes

<p>Abstract</p> <p>Background</p> <p>Little is known of the biological significance and evolutionary maintenance of integrated non-retroviral RNA virus genes in eukaryotic host genomes. Here, we isolated novel filovirus-like genes from bat genomes and tested for evolutionary maintenance. We also estimated the age of filovirus VP35-like gene integrations and tested the phylogenetic hypotheses that there is a eutherian mammal clade and a marsupial/ebolavirus/Marburgvirus dichotomy for filoviruses.</p> <p>Results</p> <p>We detected homologous copies of VP35-like and NP-like gene integrations in both Old World and New World species of <it>Myotis </it>(bats). We also detected previously unknown VP35-like genes in rodents that are positionally homologous. Comprehensive phylogenetic estimates for filovirus NP-like and VP35-like loci support two main clades with a marsupial and a rodent grouping within the ebolavirus/Lloviu virus/Marburgvirus clade. The concordance of VP35-like, NP-like and mitochondrial gene trees with the expected species tree supports the notion that the copies we examined are orthologs that predate the global spread and radiation of the genus <it>Myotis</it>. Parametric simulations were consistent with selective maintenance for the open reading frame (ORF) of VP35-like genes in <it>Myotis</it>. The ORF of the filovirus-like VP35 gene has been maintained in bat genomes for an estimated 13. 4 MY. ORFs were disrupted for the NP-like genes in <it>Myotis</it>. Likelihood ratio tests revealed that a model that accommodates positive selection is a significantly better fit to the data than a model that does not allow for positive selection for VP35-like sequences. Moreover, site-by-site analysis of selection using two methods indicated at least 25 sites in the VP35-like alignment are under positive selection in <it>Myotis</it>.</p> <p>Conclusions</p> <p>Our results indicate that filovirus-like elements have significance beyond genomic imprints of prior infection. That is, there appears to be, or have been, functionally maintained copies of such genes in mammals. "Living fossils" of filoviruses appear to be selectively maintained in a diverse mammalian genus (<it>Myotis</it>).</p

Virus-host co-evolution under a modified nuclear genetic code

Among eukaryotes with modified nuclear genetic codes, viruses are unknown. However, here we provide evidence of an RNA virus that infects a fungal host (Scheffersomyces segobiensis) with a derived nuclear genetic code where CUG codes for serine. The genomic architecture and phylogeny are consistent with infection by a double-stranded RNA virus of the genus Totivirus. We provide evidence of past or present infection with totiviruses in five species of yeasts with modified genetic codes. All but one of the CUG codons in the viral genome have been eliminated, suggesting that avoidance of the modified codon was important to viral adaptation. Our mass spectroscopy analysis indicates that a congener of the host species has co-opted and expresses a capsid gene from totiviruses as a cellular protein. Viral avoidance of the host’s modified codon and host co-option of a protein from totiviruses suggest that RNA viruses co-evolved with yeasts that underwent a major evolutionary transition from the standard genetic code

Cryptic species within the Chydorus sphaericus species complex (Crustacea: Cladocera) revealed by molecular markers and sexual stage morphology

a b s t r a c t The cosmopolitanism paradigm in the biogeography of freshwater invertebrates is currently being replaced by non-cosmopolitanism or continental endemism. Benthic water fleas (Cladocera) from the family Chydoridae were the first group of freshwater invertebrates for which non-cosmopolitanism and cryptic diversity was substantiated by morphological studies. Yet, little is known about genetic differentiation and evolutionary history of chydorid species complexes. Here we present the first analysis of the genetic versus morphological differentiation in a benthic cladoceran species complex-Chydorus sphaericus s. str. using sequence variation in a nuclear (ribosomal internal transcribed spacer 2, ITS-2) and a mitochondrial (cytochrome c oxidase subunit I, COI) genes in 50 Holarctic localities. We tested for continental endemism and cryptic diversity predicted by previous morphological studies. We found evidence for the presence of at least seven putative regional species in the Holarctic, at least three of them being distributed beyond a single continent. While the molecular and sexual stage characters showed general concordance on species lineages, parthenogenetic female characters lacked resolution or were unassociated with molecular lineages. We conclude that cryptic regional lineages of benthic cladocerans are apparent and that the sexual stages represent the most informative morphological source of species characters for this environmental indicator group

Environmental and genetic factors associated with Solanesol accumulation in potato leaves

Solanesol is a high value 45-carbon, unsaturated, all-trans-nonaprenol isoprenoid. Recently solanesol has received particular attention because of its utility, both in its own right and as a precursor in the production of numerous compounds used in the treatment of disease states. Solanesol is found mainly in solanaceous crops such as potato, tomato, tobacco and pepper where it accumulates in the foliage. There is considerable potential to explore the extraction of solanesol from these sources as a valuable co-product. In this study we have characterised the genetic variation in leaf solanesol content in a biparental, segregating diploid potato population. We demonstrate that potato leaf solanesol content is genetically controlled and identify several quantitative trait loci associated with leaf solanesol content. Transient over-expression of genes from the methylerythritol 4-phosphate (MEP) and mevalonic acid (MVA) pathways, either singly or in combination, resulted in enhanced accumulation of solanesol in leaves of Nicotiana benthamiana, providing insights for genetically engineering the pathway. We also demonstrate that in potato, leaf solanesol content is enhanced by up to six-fold on exposure to moderately elevated temperature and show corresponding changes in expression patterns of MEP and MVA genes. Our combined approaches offer new insights into solanesol accumulation and strategies for developing a bio-refinery approach to potato production

A comparison of sex offenders and other types of offenders referred to intellectual disability forensic services

This study compared 131 sex offenders with ID and 346 other types of offenders with ID using case file records. All the females in the study were non sexual offenders. Significantly more sexual offenders were referred from court and criminal justice services while significantly fewer were referred from secondary healthcare. A higher percentage of sex offenders had some form of legal status at time of referral. Greater proportions of non sexual offenders were referred for aggression, damage to property, substance abuse and fire setting while only the sex offenders had an index sex offence. For previous offending, the non sexual offenders had higher rates of aggression, cruelty and neglect of children, property damage and substance abuse while the sexual offenders had higher rates of previous sexual offending. For psychiatric disturbance and adversity in childhood, only ADHD showed a significant difference between groups with the non sexual offenders recording higher rates