U3 snoRNA genes are multi-copy and frequently linked to U5 snRNA genes in Euglena gracilis§

<p>Abstract</p> <p>Background</p> <p>U3 snoRNA is a box C/D small nucleolar RNA (snoRNA) involved in the processing events that liberate 18S rRNA from the ribosomal RNA precursor (pre-rRNA). Although U3 snoRNA is present in all eukaryotic organisms, most investigations of it have focused on fungi (particularly yeasts), animals and plants. Relatively little is known about U3 snoRNA and its gene(s) in the phylogenetically broad assemblage of protists (mostly unicellular eukaryotes). In the euglenozoon <it>Euglena gracilis</it>, a distant relative of the kinetoplastid protozoa, Southern analysis had previously revealed at least 13 bands hybridizing with U3 snoRNA, suggesting the existence of multiple copies of U3 snoRNA genes.</p> <p>Results</p> <p>Through screening of a λ genomic library and PCR amplification, we recovered 14 U3 snoRNA gene variants, defined by sequence heterogeneities that are mostly located in the U3 3'-stem-loop domain. We identified three different genomic arrangements of <it>Euglena </it>U3 snoRNA genes: <it>i</it>) stand-alone, <it>ii</it>) linked to tRNA^Arggenes, and <it>iii</it>) linked to a U5 snRNA gene. In arrangement <it>ii</it>), the U3 snoRNA gene is positioned upstream of two identical tRNA^Arggenes that are convergently transcribed relative to the U3 gene. This scenario is reminiscent of a U3 snoRNA-tRNA gene linkage previously described in trypanosomatids. We document here twelve different U3 snoRNA-U5 snRNA gene arrangements in <it>Euglena</it>; in each case, the U3 gene is linked to a downstream and convergently oriented U5 gene, with the intergenic region differing in length and sequence among the variants.</p> <p>Conclusion</p> <p>The multiple U3 snoRNA-U5 snRNA gene linkages, which cluster into distinct families based on sequence similarities within the intergenic spacer, presumably arose by genome, chromosome, and/or locus duplications. We discuss possible reasons for the existence of the unusually large number of U3 snoRNA genes in the <it>Euglena </it>genome. Variability in the signal intensities of the multiple Southern hybridization bands raises the possibility that <it>Euglena </it>contains a naturally aneuploid chromosome complement.</p

The Formal Dynamism of Categories: Stops vs. Fricatives, Primitivity vs. Simplicity

Minimalist Phonology (MP; Pöchtrager 2006) constructs its theory based on the phonological epistemological principle (Kaye 2001) and exposes the arbitrary nature of standard Government Phonology (sGP) and strict-CV (sCV), particularly with reference to their confusion of melody and structure. For Pöchtrager, these are crucially different, concluding that place of articulation is melodic (expressed with elements), while manner of articulation is structural. In this model, the heads (xN and xO) can license and incorporate the length of the other into their own interpretation, that is xN influences xO projections as well as its own and vice versa. This dynamism is an aspect of the whole framework and this paper in particular will show that stops and fricatives evidence a plasticity of category and that, although fricatives are simpler in structure, stops are the more primitive of the two. This will be achieved phonologically through simply unifying the environment of application of the licensing forces within Pöchtrager's otherwise sound onset structure. In doing so, we automatically make several predictions about language acquisition and typology and show how lenition in Qiang (Sino-Tibetan) can be more elegantly explained

Whole genome sequencing of a Canadian Bovine gammaherpesvirus 4 strain and possible link between the viral infection and respiratory and reproductive clinical manifestations in dairy cattle

Bovine gammaherpesvirus 4 (BoHV-4) is a herpesvirus widespread in cattle populations, and with no clear disease association. Its genome contains a long unique coding region (LUR) flanked by polyrepetitive DNA and 79 open reading frames (ORFs), with unique 17 ORFs, named Bo1 to Bo17. In 2009, a BoHV-4 strain was isolated (FMV09-1180503: BoHV-4-FMV) from cattle with respiratory disease from Quebec, Canada, and its LUR was sequenced. Despite the overall high similarity, BoHV-4-FMV had the most divergent LUR sequence compared to the two known BoHV-4 reference strain genomes; most of the divergences were in the Bo genes and in the repeat regions. Our phylogenetic analysis based on DNA polymerase and thymidine kinase genes revealed that virus isolate was BoHV-4 gammaherpesvirus and clustered it together with European BoHV-4 strains. Because BoHV-4-FMV was isolated from animals presenting respiratory signs, we have updated the BoHV-4 Canadian cattle seroprevalence data and tried to find out whether there is a link between clinical manifestation and BoHV-4 seropositivity. An indirect immunofluorescence assay (IFA) was performed with nearly 200 randomized sera of dairy cattle from two Canadian provinces, Quebec (n = 100) and Ontario (n = 91). An additional set of sera obtained from Quebec, from the healthy (n = 48) cows or from the animals experiencing respiratory or reproductive problems (n = 75), was also analyzed by IFA. BoHV-4 seroprevalence in Canadian dairy cattle was 7.9% (Quebec: 6% and Ontario: 9.9%). Among animals from the Quebec-based farms, diseased animals showed higher BoHV-4 seropositivity than healthy animals (P < 0.05), with a significant 2.494 odds ratio of being seropositive in sick compared to healthy animals. Although there is no established direct link between BoHV-4 and specific diseases, these seroprevalence data suggest the possible involvement of BoHV-4 in dairy cattle diseases

Recent Advances of the Halogen–Zinc Exchange Reaction

For the preparation of zinc organometallics bearing highly sensitive functional groups such as ketones, aldehydes or nitro groups, especially mild halogen–zinc exchange reagents have proven to be of great potential. In this Minireview, the latest research in the area of the halogen–zinc exchange reaction is reported, with a special focus lying on novel dialkylzinc reagents complexed with lithium alkoxides. Additionally, the preparation and application of organofluorine zinc reagents and transition‐metal‐catalyzed halogen–zinc exchange reactions are reviewed

Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya

Box C/D ribonucleoprotein (RNP) particles mediate O(2′)-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts, containing four core protein components (Snu13p, Nop56p, Nop58p and fibrillarin) compared with three in Archaea. This increase in complexity raises questions about the evolutionary emergence of the eukaryote-specific proteins and structural conservation in these RNPs throughout the eukaryotic domain. In protists, the primarily unicellular organisms comprising the bulk of eukaryotic diversity, the protein composition of box C/D RNPs has not yet been extensively explored. This study describes the complete gene, cDNA and protein sequences of the fibrillarin homolog from the protozoon Euglena gracilis, the first such information to be obtained for a nucleolus-localized protein in this organism. The E.gracilis fibrillarin gene contains a mixture of intron types exhibiting markedly different sizes. In contrast to most other E.gracilis mRNAs characterized to date, the fibrillarin mRNA lacks a spliced leader (SL) sequence. The predicted fibrillarin protein sequence itself is unusual in that it contains a glycine-lysine (GK)-rich domain at its N-terminus rather than the glycine-arginine-rich (GAR) domain found in most other eukaryotic fibrillarins. In an evolutionarily diverse collection of protists that includes E.gracilis, we have also identified putative homologs of the other core protein components of box C/D RNPs, thereby providing evidence that the protein composition seen in the higher eukaryotic complexes was established very early in eukaryotic cell evolution

Kinetics of thorium and particle cycling along the U.S. GEOTRACES North Atlantic Transect

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 125 (2017): 106-128, doi:10.1016/j.dsr.2017.05.003.The high particle reactivity of thorium has resulted in its widespread use in tracing processes impacting marine particles and their chemical constituents. The use of thorium isotopes as tracers of particle dynamics, however, largely relies on our understanding of how the element scavenges onto particles. Here, we estimate apparent rate constants of Th adsorption (k1), Th desorption (k−1), bulk particle degradation (β-1), and bulk particle sinking speed (w) along the water column at 11 open-ocean stations occupied during the GEOTRACES North Atlantic Section (GA03). First, we provide evidence that the budgets of Th isotopes and particles at these stations appear to be generally dominated by radioactive production and decay sorption reactions, particle degradation, and particle sinking. Rate parameters are then estimated by fitting a Th and particle cycling model to data of dissolved and particulate 228,230,234Th, 228Ra, particle concentrations, and 234,238U estimates based on salinity, using a nonlinear programming technique. We find that the adsorption rate constant (k1) generally decreases with depth across the section: broadly, the time scale 1/k1 averages 1.0 yr in the upper 1000 m and (1.4–1.5) yr below. A positive relationship between k1 and particle concentration (P) is found, i.e., , k1 ∝ Pb where b ≥ 1, consistent with the notion that k1 increases with the number of surface sites available for adsorption. The rate constant ratio, K = k1/(k-1 + β-1), which measures the collective influence of rate parameters on Th scavenging, averages 0.2 for most stations and most depths. We clarify the conditions under which K/P is equivalent to the distribution coefficient, KD, test that the conditions are met at the stations, and find that decreases with P, in line with a particle concentration effect (dKD/dP < 0). In contrast to the influence of colloids as envisioned by the Brownian pumping hypothesis, we provide evidence that the particle concentration effect arises from the joint effect of P on the rate constants for thorium attachment to, and detachment from, particles.We acknowledge the U.S. National Science Foundation for providing funding for this study (grant OCE-1232578) and for U.S. GEOTRACES North Atlantic section ship time, sampling, and data analysis. The U.S. NSF also supported the generation of 230Th data (OCE-0927064 to LDEO, OCE-O092860 to WHOI, and OCE-0927754 to UMN) and 228,234Th data (OCE-0925158 to WHOI)

Revisiting \u3csup\u3e228\u3c/sup\u3eTh as a Tool for Determining Sedimentation and Mass Accumulation Rates

The use of 228Th has seen limited application for determining sedimentation and mass accumulation rates in coastal and marine environments. Recent analytical advances have enabled rapid, precise measurements of particle-bound 228Th using a radium delayed coincidence counting system (RaDeCC). Herein we review the 228Th cycle in the marine environment and revisit the historical use of 228Th as a tracer for determining sediment vertical accretion and mass accumulation rates in light of new measurement techniques. Case studies comparing accumulation rates from 228Th and 210Pb are presented for a micro-tidal salt marsh and a marginal sea environment. 228Th and 210Pb have been previously measured in mangrove, deltaic, continental shelf and ocean basin environments, and a literature synthesis reveals that 228Th (measured via alpha or gamma spectrometry) derived accumulation rates are generally equal to or greater than estimates derived from 210Pb, reflecting different integration periods. Use of 228Th is well-suited for shallow (\u3c15 cm) cores over decadal timescales. Application is limited to relatively homogenous sediment profiles with minor variations in grain size and minimal bioturbation. When appropriate conditions are met, complimentary use of 228Th and 210Pb can demonstrate that the upper layers of a core are undisturbed and can improve spatial coverage in mapping accumulation rates due to the higher sample throughput for sediment 228Th

Intégration et inclusion : interconnexions et oppositions dans deux domaines éducatifs au Québec

Plusieurs systèmes éducatifs dans le monde, comme c’est le cas au Québec, tendent vers l’adoption de politiques d’éducation inclusive qui visent à répondre de façon équitable aux besoins de tous les élèves. Alors que le paradigme d’éducation inclusive concernait initialement les élèves qui présentaient des handicaps ou considérés comme ayant des besoins particuliers, il englobe maintenant d’autres sous-groupes d’élèves, dont les élèves minorisés sur les plans de la diversité ethnoculturelle, religieuse et linguistique. Cet article propose une lecture critique de l’évolution du paradigme de l’éducation inclusive et du concept d’intégration dans deux domaines éducatifs au Québec : celui de l’adaptation scolaire et celui qui concerne la diversité ethnoculturelle, religieuse et linguistique (ERL). L’exploration du chemin parcouru dans les deux domaines éducatifs illustre l’ancrage de l’évolution des concepts dans les débats sociaux, qui eux-mêmes s’articulent selon des courants politiques, des sensibilités particulières de la société, et qui se reflètent dans les pratiques des milieux scolaires. La conclusion invite le milieu de la recherche et les autorités éducatives à contribuer à la clarification des concepts et des paradigmes, en leur rappelant que ces derniers peuvent enfermer les individus et les groupes dans des rapports sociaux parfois teintés de dynamique de domination