Phylogenetic Distribution of Intron Positions in Alpha-Amylase Genes of Bilateria Suggests Numerous Gains and Losses

Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that “resets” of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures

Ultrafast biomolecular dynamics

This thesis describes experimental studies of ultrafast charge transfer processes in molecules which are the building blocks of proteins and DNA; the amino acid phenylalanine and the nucleoside adenosine respectively. This was achieved by using femtosecond (10-15 and attosecond (10-18) laser pulses with a range of wavelengths to create a positive charge in these molecules through ionisation and to probe the subsequent electron motion. This work has been performed using gas phase molecular targets which were liberated from solid samples using a technique known as laser induced acoustic desorption (LlAD). An experimental investigation was performed supported by simulations undertaken using a radiation transport code, HYADES, to optimise and understand this technique. The results presented for the adenosine and the nucleobase adenine suggest that fragmentation of the sugar group following ionisation (which corresponds to strand breakages in DNA) is mostly via relatively slow dissociation processes (nano or microsecond timescales). In vivo such a slow statistical process is likely to be quenched by cooling of the vibrational energy in the molecule by the surrounding environment. This shows that, to a degree, cells can be protected from the direct action of ionising radiation in DNA. In phenylalanine two different ultrafast processes were observed. The first of these was charge transfer to the phenyl group with a time constant of 80 fs, attributed to transfer between electronic states. A second process lasting 30 fs was observed, which is consistent with a number of theoretical predictions of a purely electronic process, termed charge migration. This work provides the first experimental evidence for charge migration in a complex molecule, and is one of the fastest processes ever measured in a biological system. It could ultimately pave the way for control of electron transport in natural or synthetic nanostructures.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Ultrafast charge dynamics in an amino acid induced by attosecond pulses

In the past few years, attosecond techniques have been implemented for the investigation of ultrafast dynamics in molecules. The generation of isolated attosecond pulses characterized by a relatively high photon flux has opened up new possibilities in the study of molecular dynamics. In this paper, we report on experimental and theoretical results of ultrafast charge dynamics in a biochemically relevant molecule, namely, the amino acid phenylalanine. The data represent the first experimental demonstration of the generation and observation of a charge migration process in a complexmolecule, where electron dynamics precede nuclear motion. The application of attosecond technology to the investigation of electron dynamics in biologically relevant molecules represents a multidisciplinary work, which can open new research frontiers: those in which few-femtosecond and even subfemtosecond electron processes determine the fate of biomolecules. It can also open new perspectives for the development of new technologies, for example, in molecular electronics, where electron processes on an ultrafast temporal scale are essential to trigger and control the electron current on the scale of the molecule

Critically Appraised Topics (CATs) in veterinary medicine:Applying evidence in clinical practice

Abstract Critically appraised topics (CATs) are evidence syntheses that provide veterinary professionals with information to rapidly address clinical questions and support the practice of evidence-based veterinary medicine (EBVM). They also have an important role to play in both undergraduate and post-registration education of veterinary professionals, in research and knowledge gap identification, literature scoping, preparing research grants and informing policy. CATs are not without limitations, the primary one relating to the rapid approach used which may lead to selection bias or restrict information identified or retrieved. Furthermore, the narrow focus of CATs may limit applicability of the evidence findings beyond a specific clinical scenario, and infrequently updated CATs may become redundant. Despite these limitations, CATs are fundamental to EBVM in the veterinary profession. Using the example of a dog with osteoarthritis, the five steps involved in creating and applying a CAT to clinical practice are outlined, with an emphasis on clinical relevance and practicalities. Finally, potential future developments for CATs and their role in EBVM, and the education of veterinary professionals are discussed. This review is focused on critically appraised topics (CATs) as a form of evidence synthesis in veterinary medicine. It aims to be a primary guide for veterinarians, from students to clinicians, and for veterinary nurses and technicians (hereafter collectively called veterinary professionals). Additionally, this review provides further information for those with some experience of CATs who would like to better understand the historic context and process, including further detail on more advanced concepts. This more detailed information will appear in pop-out boxes with a double-lined surround to distinguish it from the information core to producing and interpreting CATs, and from the boxes with a single line surround which contain additional resources relevant to the different parts of the review. Keywords: BestBETs; clinical practice; critically appraised topic (CAT); evidence synthesis; evidence-based veterinary medicine; knowledge summary; veterinary medicine

Construction of a Conceptual Framework for Assessment of Health-Related Quality of Life in Dogs With Osteoarthritis

An owner's ability to detect changes in the behavior of a dog afflicted with osteoarthritis (OA) may be a barrier to presentation, clinical diagnosis and initiation of treatment. Management of OA also relies upon an owner's ability to accurately monitor improvement following a trial period of pain relief. The changes in behavior that are associated with the onset and relief of pain from OA can be assessed to determine the dog's health-related quality of life (HRQOL). HRQOL assessments are widely used in human medicine and if developed correctly can be used in the monitoring of disease and in clinical trials. This study followed established guidelines to construct a conceptual framework of indicators of HRQOL in dogs with OA. This generated items that can be used to develop a HRQOL assessment tool specific to dogs with OA. A systematic review was conducted using Web of Science, PubMed and Scopus with search terms related to indicators of HRQOL in dogs with osteoarthritis. Eligibility and quality assessment criteria were applied. Data were extracted from eligible studies using a comprehensive data charting table. Resulting domains and items were assessed at a half-day workshop attended by experts in canine osteoarthritis and quality of life. Domains and their interactions were finalized and a visual representation of the conceptual framework was produced. A total of 1,264 unique articles were generated in the database searches and assessed for inclusion. Of these, 21 progressed to data extraction. After combining synonyms, 47 unique items were categorized across six domains. Review of the six domains by the expert panel resulted in their reduction to four: physical appearance, capability, behavior, and mood. All four categories were deemed to be influenced by pain from osteoarthritis. Capability, mood, and behavior were all hypothesized to impact on each other while physical appearance was impacted by, but did not impact upon, the other domains. The framework has potential application to inform the development of valid and reliable instruments to operationalize measurement of HRQOL in canine OA for use in general veterinary practice to guide OA management decisions and in clinical studies to evaluate treatment outcomes