The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes

Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair

Temporomandibular joint pathosis related to sex, age, and dentition in autopsy material

The purpose of this autopsy study was to test the hypotheses that temporomandibular joint (TMJ) arthrosis is more common in women than in men, increases with age, and is more common in edentulous persons than in those with natural teeth. Two hundred forty-eight TMJs removed at autopsy from 224 fresh cadavers were investigated macroscopically with dissection or cryosectioning. Age was found to be a significant factor in prediction of TMJ arthrosis (p p p p < 0.001) between arthrosis, disk displacement, disk deformation, and disk perforation. There were no statistically significant differences in the prevalence of morphologic changes in the joints from persons with 10 or more natural teeth in each jaw compared with those from persons without natural teeth. The results of this study showed that TMJ arthrosis is more frequent in older than in younger persons. TMJ disk displacement generally appears necessary for the development of perforations. The findings of this study indicate that sex and dentition are not major factors for the development of TMJ pathosis in elderly individuals.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31264/1/0000170.pd

Amplitude and frequency spectrum of temporomandibular joint sounds from subjects with and without other signs/symptoms of temporomandibular disorders

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72202/1/j.1365-2842.1999.00348.x.pd

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

A Unifying Model of Genome Evolution Under Parsimony

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.Comment: 52 pages, 24 figure

The role of the specialist nurse in comprehensive care for bleeding disorders in Europe: An integrative review

Introduction: Managing bleeding disorders (BDs) is complex, requiring a comprehensive approach coordinated by a multidisciplinary team (MDT). Haemophilia nurses (HNs) play a central role in the MDT, frequently coordinating care. As novel treatments bring change to the treatment landscape, ongoing education and development is key. However, understanding of the roles and tasks of HNs is lacking. Aim: The EAHAD Nurses Committee sought to identify and describe the roles and tasks of the European HN. Methods: A five-step integrative review was undertaken, including problem identification, literature search, data evaluation, data synthesis and presentation. Relevant literature published from 2000 to 2022 was identified through database, hand and ancestry searching. Data were captured using extraction forms and thematically analysed. Results: Seven hundred and seventy-seven articles were identified; 43 were included. Five main roles were identified, with varied and overlapping associated tasks: Educator, Coordinator, Supporter, Treater and Researcher. Tasks related to education, coordination and support were most frequently described. Patient education was often ‘nurse-led’, though education and coordination roles concerned both patients and health care practitioners (HCPs), within and beyond the MDT. The HN coordinates care and facilitates communication. Long-term patient care relationships place HNs in a unique position to provide support. Guidelines for HN core competencies have been developed in some countries, but autonomy and practice vary. Conclusion: As the treatment landscape changes, all five main HN roles will be impacted. Despite national variations, this review provides a baseline to anticipate educational needs to enable HNs to continue to fulfil their role