Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Direct repeats in the flavivirus 3' untranslated region; a strategy for survival in the environment?

Previously, direct repeats (DRs) of 20-70 nucleotides were identified in the 3' untranslated regions (3'UTR) of flavivirus sequences. To address their functional significance, we have manually generated a pan-flavivirus 3'UTR alignment and correlated it with the corresponding predicted RNA secondary structures. This approach revealed that intra-group-conserved DRs evolved from six long repeated sequences (LRSs) which, as approximately 200-nucleotide domains were preserved only in the genomes of the slowly evolving tick-borne flaviviruses. We propose that short DRs represent the evolutionary remnants of LRSs rather than distinct molecular duplications. The relevance of DRs to virus replication enhancer function, and thus survival, is discussed.

Origin and evolution of flavivirus 5'UTRs and panhandles: trans-terminal duplications?

Flavivirus replication is mediated by interactions between complementary ssRNA sequences of the 5'- and 3'-termini that form dsRNA cyclisation stems or panhandles, varying in length, sequence and specific location in the mosquito-borne, tick-borne, non-vectored and non-classified flaviviruses. In this manuscript we manually aligned the flavivirus 5'UTRs and adjacent capsid genes and revealed significantly more homology than has hitherto been identified. Analysis of the alignments revealed that the panhandles represent evolutionary remnants of a long cyclisation domain that probably emerged through duplication of one of the UTR termini.

A model for self-directed problem-based learning for renal therapeutics

Objective To introduce a new approach to problem-based learning (PBL) for self-directed learning in renal therapeutics. Design This 5-week course, designed for large student cohorts using minimal teaching resources, was based on a series of case studies and subsequent pharmaceutical care plans, followed by intensive and regular feedback from the instructor. Assessment Assessment of achievement of the learning outcomes was based on weekly-graded care plans and peer review assessment, allowing each student to judge the contributions of each group member and their own, along with a written case-study based examination. The pharmaceutical care plan template, designed using a “tick-box” system, significantly reduced staff time for feedback and scoring. Conclusion The proposed instructional model achieved the desired learning outcomes with appropriate student feedback, while promoting skills that are essential for the students' future careers as health care professionals.

Lyme borreliosis in the UK: ecology and risks to domestic animals and man

The different associations of Borrelia burgdorferi sensu lato spirochaetes with their natural reservoir hosts and tick vectors are slowly being unravelled. This review discusses the interactions of different genospecies of Lyme borreliosis spirochaetes and their differing tick vectors, vertebrate reservoirs and 'accidental hosts'. Particular reference is made to spirochaete-host interactions and occurrence of pathological consequences. Attention is focused on the unique prevalence of enzoonotic cycles in operation within the UK. Risk factors for acquiring Lyme borreliosis in man are discussed. (C) 2001 Lippincott Williams & Wilkins.

Evolutionary and revolutionary effects of transcomputation

Mathematics in Defence 2011 Abstract. We review transreal arithmetic and present transcomplex arithmetic. These arithmetics have no exceptions. This leads to incremental improvements in computer hardware and software. For example, the range of real numbers, encoded by floating-point bits, is doubled when all of the Not-a-Number(NaN) states, in IEEE 754 arithmetic, are replaced with real numbers. The task of programming such systems is simplified and made safer by discarding the unordered relational operator,leaving only the operators less-than, equal-to, and greater than. The advantages of using a transarithmetic in a computation, or transcomputation as we prefer to call it, may be had by making small changes to compilers and processor designs. However, radical change is possible by exploiting the reliability of transcomputations to make pipelined dataflow machines with a large number of cores. Our initial designs are for a machine with order one million cores. Such a machine can complete the execution of multiple in-line programs each clock tick

Molecular archaeology of Flaviviridae untranslated regions: duplicated RNA structures in the replication enhancer of flaviviruses and pestiviruses emerged via convergent evolution.

RNA secondary structures in the 3'untranslated regions (3'UTR) of the viruses of the family Flaviviridae, previously identified as essential (promoters) or beneficial (enhancers) for replication, have been analysed. Duplicated enhancer elements are revealed as a global feature in the evolution of the 3'UTR of distantly related viruses within the genera Flavivirus and Pestivirus. For the flaviviruses, duplicated structures occur in the 3'UTR of all four distantly related ecological virus subgroups (tick-borne, mosquito-borne, no known vector and insect-specific flaviviruses (ISFV). RNA structural differences distinguish tick-borne flaviviruses with discrete pathogenetic characteristics. For Aedes- and Culex-associated ISFV, secondary RNA structures with different conformations display numerous short ssRNA direct repeats, exposed as loops and bulges. Long quadruplicate regions comprise almost the entire 3'UTR of Culex-associated ISFV. Extended duplicated sequence and associated RNA structures were also discovered in the 3'UTR of pestiviruses. In both the Flavivirus and Pestivirus genera, duplicated RNA structures were localized to the enhancer regions of the 3'UTR suggesting an adaptive role predominantly in wild-type viruses. We propose sequence reiteration might act as a scaffold for dimerization of proteins involved in assembly of viral replicase complexes. Numerous nucleotide repeats exposed as loops/bulges might also interfere with host immune responses acting as a molecular sponge to sequester key host proteins or microRNAs.

Transmathematical basis of infinitely scalable pipeline machines

We describe infinitely scalable pipeline machines with perfect parallelism, in the sense that every instruction of an inline program is executed, on successive data, on every clock tick. Programs with shared data effectively execute in less than a clock tick. We show that pipeline machines are faster than single or multi-core, von Neumann machines for sufficiently many program runs of a sufficiently time consuming program. Our pipeline machines exploit the totality of transreal arithmetic and the known waiting time of statically compiled programs to deliver the interesting property that they need no hardware or software exception handling.