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Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction.

Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction. This review is a comprehensive overview of avian genome (“chromosomic”) organization research based mostly on chromosome painting and BAC-based studies. We discuss traditional and contemporary tools for reliably generating chromosome-level assemblies and analyzing multiple species at a higher resolution and wider phylogenetic distance than previously possible. These results permit more detailed investigations into inter- and intrachromosomal rearrangements, providing unique insights into evolution and speciation mechanisms. The ‘signature’ avian karyotype likely arose ~250 mya and remained largely unchanged in most groups including extinct dinosaurs. Exceptions include Psittaciformes, Falconiformes, Caprimulgiformes, Cuculiformes, Suliformes, occasional Passeriformes, Ciconiiformes, and Pelecaniformes. The reasons for this remarkable conservation may be the greater diploid chromosome number generating variation (the driver of natural selection) through a greater possible combination of gametes and/or an increase in recombination rate. A deeper understanding of avian genomic structure permits the exploration of fundamental biological questions pertaining to the role of evolutionary breakpoint regions and homologous synteny blocks.

The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species ( , and was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from and . Findings suggest that (2 = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for (2 = 88) and demonstrated microchromosomal rearrangements involving plus a single, unique hitherto undescribed rearrangement in . This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.

Subjects: Evolutionary Biology. Contributors: Darren K. Griffin, Denis M. Larkin, Rebecca E. O’Connor, Michael N. Romanov. According to Britannica, dinosaurs are described as “Triceratops, contemporary birds, their most recent common ancestor and all of their descendants.” However, for biologists, it could be simpler to picture dinosaurs as reptiles with hind limbs held erect beneath the trunk, similar to how mammals’ hind limbs are held.

Simple Summary Dinosaurs have been in scientific and popular culture since early fossil discoveries, but increased interest, particularly in their genomes, is expanding. Birds are reptiles, specifically theropod dinosaurs, meaning that if we compare the genomes of related reptile relations, we can get an idea of what the extinct dinosaur genomes looked like. In all animals/plants/fungi, we think of genome organization in terms of chromosomes. Genes sit on chromosomes and each cell of each individual of each species has its own unique organization. Every gene is in exactly the same spot on each chromosome, organized like continents and islands, with the genes as the cities/ towns/villages. All reptiles apart from crocodilians have both big and small chromosomes in their genomes but birds particularly so, like the Philippines or Polynesia. Birds have ~80 chromosomes (far more than most organisms) and this is very consistent in most species. Recent studies suggest that this pattern was probably established ~255 million years ago as it is also mostly present in some turtles. In other words, most dinosaurs probably had chromosomes (genome organization) like chickens or emus. In this paper, we present ideas of how this may have contributed to dinosaurs being so diverse in appearance and function. Abstract Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome‐level genome assemblies cannot be made from long‐extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro‐ and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is

Simple Summary Dinosaurs have been in scientific and popular culture since early fossil discoveries, but increased interest, particularly in their genomes, is expanding. Birds are reptiles, specifically theropod dinosaurs, meaning that if we compare the genomes of related reptile relations, we can get an idea of what the extinct dinosaur genomes looked like. In all animals/plants/fungi, we think of genome organization in terms of chromosomes. Genes sit on chromosomes and each cell of each individual of each species has its own unique organization. Every gene is in exactly the same spot on each chromosome, organized like continents and islands, with the genes as the cities/ towns/villages. All reptiles apart from crocodilians have both big and small chromosomes in their genomes but birds particularly so, like the Philippines or Polynesia. Birds have ~80 chromosomes (far more than most organisms) and this is very consistent in most species. Recent studies suggest that this pattern was probably established ~255 million years ago as it is also mostly present in some turtles. In other words, most dinosaurs probably had chromosomes (genome organization) like chickens or emus. In this paper, we present ideas of how this may have contributed to dinosaurs being so diverse in appearance and function. Abstract Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome‐level genome assemblies cannot be made from long‐extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro‐ and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very scarce in this bird order. Thus, the aim of this study was to provide insight into the Charadriiformes karyotype, with emphasis on microchromosome evolution in three species of shorebirds—Calidris canutus, Jacana jacana, and Vanellus chilensis—combining classical and molecular approaches. Cross-species FISH mapping applied two BAC probes for each microchromosome, GGA10–28 (except GGA16). The experiments revealed different patterns of microchromosome organization in the species investigated. Hence, while in C. canutus, we found two microchromosomes involved in chromosome fusions, they were present as single pairs in V. chilensis. We also described a new chromosome number for C. canutus (2n = 92). Hence, this study contributed to the understanding of genome organization and evolution of three shorebird species.

Fragile X Syndrome is an inherited condition often causing mental retardation in adolescence but difficult to detect in childhood. Early detection allows therapeutic intervention and alerts parents to seek genetic counseling. Symptoms warranting a referral include language delay, autistic behaviors, hand-biting, oversensitivity to touch, large ears, long face, flat feet, a single crease across the hand, and double joints. (ME)

The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.

Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not necessarily present with a recognizable phenotype and may cause significant economic losses for breeders when undetected. Here, we present a reappraisal of the incidence of RTs across several European pig herds, using contemporary methodology, as well as an analysis modelling the economic impact of these abnormalities. Molecular cytogenetic investigation was completed by karyotyping and/or multiprobe FISH (fluorescence in situ hybridisation) between 2016–2021, testing 2673 animals. We identified 19 types of chromosome abnormalities, the prevalence of these errors in the database was 9.1%, and the estimated incidence of de novo errors was 0.90%. Financial modelling across different scenarios revealed the potential economic impact of an undetected RT, ranging from £69,802 for an individual affected terminal boar in a commercial farm selling weaned pigs, to £51,215,378 for a genetics company with an undetected RT in a dam line boar used in a nucleus farm. Moreover, the added benefits of screening by FISH instead of karyotyping were estimated, providing a strong case for proactive screening by this approach.

Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.

Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.

The ultimate aim of a genome assembly is to create a contiguous length of sequence from the p- to q- terminus of each chromosome. Most assemblies are however highly fragmented, limiting their use in studies of gene mapping, phylogenomics and genomic organisation. To overcome these limitations, we developed a novel scaffold-to-chromosome anchoring method combining reference-assisted chromosome assembly (RACA) and fluorescence in situ hybridisation (FISH) to position scaffolds from de novo genomes onto chromosomes. Using RACA, scaffolds were ordered and orientated into ‘predicted chromosome fragments’ (PCFs) against a reference and outgroup genome. PCFs were verified using PCR prior to FISH mapping. A universal set of FISH probes developed through the selection of conserved regions were then used to map PCFs of peregrine falcon (Falco peregrinus Tunstall, 1771), pigeon (Columba livia Gmelin, 1789), ostrich (Struthio camelus Linnaeus, 1758), saker falcon (Falco cherrug Gray, 1834) the budgerigar (Melopsittacus undulatus Shaw, 1805). Using this approach, we were able to improve the N50 of genomes seven-fold. Results revealed that Interchromosomal breakpoint regions are limited to regions with low sequence conservation, shedding light on why most avian species have very stable karyotypes. Our combined FISH and bioinformatics approach represents a step-change in the mapping of genome assemblies, allowing comparative genomic research at a higher resolution than was previously possible. The universal probe set facilitates research into avian karyotype evolution and the role of chromosome rearrangements in adaptation and phenotypic diversity in birds. Indeed, they have been used on over 20 avian species plus non-avian reptiles (including turtles), shedding light into the evolution of dinosaur species. Non-avian dinosaurs remain subjects of intense biological enquiry while pervading popular culture and the creative arts. While organismal studies focus primarily on their morph

Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning.

Background Unlike the chromosome constitution of most snakes (2n=36), the cobra karyotype shows a diploid chromosome number of 38 with a highly heterochromatic W chromosome and a large morphologically different chromosome 2. To investigate the process of sex chromosome differentiation and evolution between cobras, most snakes, and other amniotes, we constructed a chromosome map of the Siamese cobra (Naja kaouthia) with 43 bacterial artificial chromosomes (BACs) derived from the chicken and zebra finch libraries using the fluorescence in situ hybridization (FISH) technique, and compared it with those of the chicken, the zebra finch, and other amniotes. Results We produced a detailed chromosome map of the Siamese cobra genome, focusing on chromosome 2 and sex chromosomes. Synteny of the Siamese cobra chromosome 2 (NKA2) and NKAZ were highly conserved among snakes and other squamate reptiles, except for intrachromosomal rearrangements occurring in NKA2. Interestingly, twelve BACs that had partial homology with sex chromosomes of several amniotes were mapped on the heterochromatic NKAW as hybridization signals such as repeat sequences. Sequence analysis showed that most of these BACs contained high proportions of transposable elements. In addition, hybridization signals of telomeric repeat (TTAGGG)n and six microsatellite repeat motifs ((AAGG)8, (AGAT)8, (AAAC)8, (ACAG)8, (AATC)8, and (AAAAT)6) were observed on NKAW, and most of these were also found on other amniote sex chromosomes. Conclusions The frequent amplification of repeats might involve heterochromatinization and promote sex chromosome differentiation in the Siamese cobra W sex chromosome. Repeat sequences are also shared among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial syntenies. Alternatively, amplification of microsatellite repeat motifs could have occurred independently in each lineage, representing convergent sex chromosomal differe

Background: The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. Results: We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest. Conclusions: The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falc

Background: Granulocyte-colony stimulating factor (G-CSF) mobilises endogenous haematopoietic stem cells and enhances recovery in experimental stroke. Recovery may also be dependent on an enriched environment and physical activity. G-CSF may have the potential to enhance recovery when used in combination with physiotherapy, in patients with disability late after stroke. Methods: A pilot 2 x 2 factorial randomised (1:1) placebo-controlled trial of G-CSF (double-blind), and/or a 6 week course of physiotherapy, in 60 participants with disability (mRS >1), at least 3 months after stroke. Primary outcome was feasibility, acceptability and tolerability. Secondary outcomes included death, dependency, motor function and quality of life measured 90 and 365 days after enrolment. Results: Recruitment to the trial was feasible and acceptable; of 118 screened patients, 92 were eligible and 32 declined to participate. 60 patients were recruited between November 2011 and July 2013. All participants received some allocated treatment. Although 29 out of 30 participants received all 5 G-CSF/placebo injections, only 7 of 30 participants received all 18 therapy sessions. G-CSF was well tolerated but associated with a tendency to more adverse events than placebo (16 vs 10 patients, p=0.12) and serious adverse events (SAE) (9 vs 3, p=0.10). On average, patients received 14 (out of 18 planned) therapy sessions, interquartile range [12, 17]. Only a minority (23%) of participants completed all physiotherapy sessions, a large proportion of sessions (114 of 540, 21%) were cancelled due to patient (94, 17%) and therapist factors (20, 4%). No significant differences in functional outcomes were detected in either the G-CSF or physiotherapy group at day 90 or 365. Conclusions – Delivery of G-CSF is feasible in chronic stroke. However, the study failed to demonstrate feasibility for delivering additional physiotherapy sessions late after stroke. Future work should occur earlier after stroke, along

The Dinosaurs dominated the terrestrial environment for around 170 million years and are probably the most successful land vertebrate group to have existed. They survived several mass extinction events before finally all non-avian species were wiped out 66 million years ago in the Cretaceous-Paleogene extinction event. The neornithes (modern birds) are their living descendants. Despite the huge phenotypic diversity seen in birds, they, and some non-avian reptiles (e.g. some turtle species) display remarkably similar karyotypes with a characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements. This suggests that these were features present early in their evolution. The availability whole genome sequences and the recent sequencing of around 50 avian genomes, 6 of which were assembled at sufficient read depth and coverage to permit visualization at the chromosomal level, has facilitated the reconstruction of the overall genome structure (karyotype) of both Saurian (bird-reptile) and Avian ancestors. Subsequent use of bioinformatic tools permitted the retracing of the gross evolutionary changes that have occurred along the Dinosaur (and various avian) lineages. Gene ontology analysis of homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) of chromosomes has allowed us to search for enrichment for genes involved in chromosome rearrangement (consistent with the formation of the signature fragmented karyotype of birds (and probably dinosaurs)). Preliminary analyses of EBRs suggest that they appear to be enriched for genes involved in body size, consistent with the overall gross reduction in body size as dinosaurs evolved into birds. Our results also suggest a period of inter-and intra-chromosomal rearrangements up until around the divergence of turtles (approximately 210 MYA) with a relatively “fixed” pattern thereafter where intra-chromosomal rearrangement plus a few identifiable fissions predominated. It is

The past 10–15 years have seen a revolution in the field of genomics, first with the human genome project, followed by those of key model and agricultural species (chicken, pig, cattle, sheep) and, most recently, ~ 60 de novo avian genome assemblies. The ultimate aim of a genome assembly is to create a contiguous unbroken length of sequence from p- to q-terminus to facilitate studies of gene mapping, trait linkage, phylogenomics, and gross genomic organization/change. Chromosome rearrangements are biologically relevant both in the context of reduction in reproductive capability of individual animals and in the establishment in reproductive isolation as species evolve and diverge. Moreover, a karyotype effectively represents a low-resolution map of the genome of any species. In investigating all these aspects, FISH remains the tool of choice, and this study describes a step change in its use.

Chromosomal (karyotypic) analysis in animals is performed for three primary reasons: to diagnose genetic disease; to map genes to their place in the genome and to retrace evolutionary events by cross species comparison. Technology for analysis has progressed from chromosome banding (cytogenetics), to fluorescence in-situ hybridisation (FISH - molecular cytogenetics) through to microarrays and ultimately whole genome sequence analysis (cytogenomics or chromonomics). Indeed, the past 10-15 years has seen a revolution in whole genome sequencing, first with the human genome project, followed by those of key model and agricultural species and, more recently, ~60 de novo avian genome assemblies. Whole genome analysis provides detailed insight into the biology of chromosome rearrangements that occur both in individuals (for diagnostic purposes) and at an evolutionary level. It permits the study of gene mapping, trait linkage, phylogenomics, and gross genomic organisation and change. An essential pre-requisite however is an unbroken length of contiguous DNA sequence along the length of each chromosome. Most recent de novo genome assemblies fall short of this level of resolution producing lengths of contiguous sequence that are sub-chromosomal in size (scaffolds). Chromosome rearrangements can affect reproductive capability at an individual level (causing reduced fertility) and at a population level leading to reproductive isolation and subsequent speciation. The purpose of this thesis was to implement a step change in the combination of FISH technology with genome sequence data to provide greater insight into the nature of chromosomal rearrangement at an individual and evolutionary level. It therefore had four specific aims: The first was to isolate sub-telomeric sequences from the pig, cattle and chicken genome assemblies to develop a tool for the rapid screening of chromosome rearrangements. Now routinely used for porcine translocation screening (and in the future bovine

It is now over 10 years since the first avian genome [International Chicken Genome Sequencing Consortium, 2004] and the first complete avian karyotype [Masabanda et al., 2004] were both published; however, until 2014, avian cytogenetics has focused heavily on descriptive studies [e.g. Griffin et al., 2007, 2008; Skinner et al., 2009; Völker et al., 2010] with less attention to its functional relevance. Last year, however, saw 2 landmark efforts in the chromosomal studies of birds: a special issue of Chromosome Research in April and the announcement of recently completed sequences of multiple new avian genomes in Science and the BMC journals (taking the total number sequenced to over 50) in December. Studying the chromosomes of birds is, perhaps for the first time, telling us more about avian biology, function and evolution than it ever has... Conclusions. The most recent advances in avian cytogenetics have culminated in great promise not only for the study of bird karyotypes, but also for providing insight into the mechanisms of chromosome evolution in general. New avenues for investigation include gene regulation; for instance, it will become necessary to map accurately the physical location of polyadenylation and transcription start sites, important reference points that define promoters and post-transcriptional regulation. It will also become possible to sequence full-length transcripts, to allow accurate identification of alternate splicing events and their controlling elements. The ENCODE (Encyclopedia of DNA Elements) project has helped to define functional elements of the human genome, including those aforementioned as well as other chromatin signals, e.g. active chromatin, enhancers, insulators, methylation domains, etc. An effort of agENCODE is underway to include agriculturally important birds such as chicken, turkey, duck, quail, and perhaps ostrich. The study of cytogenetics will be essential here in helping to define higher-order structures in nuclear o

Whole chromosomes (and sub-chromosomal homologous synteny blocks (HSBs)) have great significance in molecular studies of genome evolution. In birds, our ability to define chromosomes and HSBs precisely has however been impeded by a near intractable karyotype and so has focused primarily on comparative molecular cytogenetics (zoo- FISH) of the largest chromosomes (1-10+Z). Availability of multiple avian genome sequence assemblies has however allowed us, for the first time, to identify chromosomal syntenies across species. In recent work we have made use of comparative maps for 20+ avian genome assemblies (plus out-groups) and presented them on “Evolution Highway” an open-access, interactive freely available comparative chromosome browser designed to store and visualise comparative chromosome maps. This browser (http://evolutionhighway.ncsa.uiuc.edu) is used to visualize comparative genome organization and to identify and visualize the different types of evolutionary breakpoint regions (EBRs) in chromosomes, e.g., lineage specific, ordinal, superordinal, and reuse. Comparative analysis of all available genomes is providing insight into the mechanisms of chromosome change through correlation of EBRs with transposable elements and non-allelic homologous recombination. Gene ontology analysis is revealing interesting correlations with avian specific phenotype and function. Focus on six genomes (chicken, turkey, duck, zebra finch, ostrich and budgerigar) with both the largest N50s and supporting molecular cytogenetic information, has allowed us to assemble a putative ancestral avian karyotype and identify the key changes that led to the gross genome organization of representatives in the major avian clades (Palaeognathae, Galliformes, Anseriformes and Neoaves). We describe, for the first time, numerous inter- chromosomal rearrangements in a Paleoganthaeous bird (the ostrich), plus rearrangements in the budgerigar (Psattaciformes) and 15 other species. Intra- chromosomal ev

Dinosaurs hold a unique place both in the history of the earth and the imagination of many. They dominated the terrestrial environment for around 170 million years during which time they diversified into at least 1000 different species. Reptilia, within which they are placed is one of the most remarkable vertebrate groups, consisting of two structurally and physiologically distinct lineages – the birds and the non-avian reptiles, of which there are 10,000 and 7,500 extant species respectively. The dinosaurs are without doubt the most successful group of vertebrate to have existed. They survived several mass extinction events before finally non-avian dinosaurs were defeated 66 million years ago in the Cretaceous-Paleogene extinction event, leaving the neornithes (modern birds) as their living descendants. Aside from the huge phenotypic diversity seen in this group, the birds and non-avian reptiles interestingly display similar karyotypic patterns (with the exception of crocodilians); with the characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements, suggesting that these were features exhibited in their common ancestor. In this study, the availability of multiple reptile genome sequences (including birds) on an interactive browser (Evolution Highway) allowed us to identify multi species homologous synteny blocks (msHSBs) between the putative avian ancestor (derived from six species of extant birds), the Lizard (Anolis carolensis) and the Snake (Boa constrictor). From these msHSBs we were able to produce a series of contiguous ancestral regions (CARs) representing the most likely ancestral karyotype of the Saurian (ancestor of archosaurs and lepidosaurs) that diverged from the mammalian lineage 280 mya. From this we have hypothesised the series of inter and intra-chromosomal rearrangements that have occurred along the dinosaur (archosaur) lineage to the ancestor of modern birds (100 mya) and along the lepidosaur lineage to t

There has been a recent explosion in avian genomics. In December 2014 the Beijing Genomics Institute in collaboration with a number of labs worldwide (including Kent) released 48 new de-novo avian genome sequences in a special edition of Science. This has led to a complete re-evaluation of the phylogenetic tree of birds and presents the opportunity to study avian comparative genomics in far more detail than before. Most of these genome sequences however exist only as “scaffolds” i.e. the depth of sequence and length of read produces contiguous fragments of sub-chromosomal size. This impedes insight into overall genome structure, which is particularly challenging, as one of the most interesting biological features of birds is the peculiarity of their karyotype. This project is an on-going effort to map scaffold assemblies to avian chromosomes using a combination of bioinformatics and Fluorescent in situ Hybridization (FISH). This has traditionally been a very time-consuming and costly procedure, however a combination of bioinformatic approaches coupled with novel hardware innovation has deconstructed the FISH protocol and re-invented it as a high throughput, cheaper procedure. Initial work has helped to reconstruct Pigeon and Peregrine Falcon genomes and will ultimately provide insight into various unanswered questions pertaining to avian gross genome rearrangement. These include why the unique overall genomic structure of birds is so evolutionarily conserved, why intra and inter-chromosomal rearrangements happen (e.g. in response to the development of traits such as vocal learning) and what the karyotypes of extinct species such as dinosaurs may have looked like.

Recent generation of multiple avian genome sequences enables further comparative analysis of their karyotypes, genome structure, and evolutionary changes. Using FISH and bioinformatic tools (e.g., Evolution Highway browser), we explore genome alignment for the sequenced birds, reptiles and mammals to infer ancestral genome organisation based on the information about their homologous synteny blocks and evolutionary breakpoints (EBRs). In EBRs shared between the birds, boa and opossum, we found over 6,000 human-chicken orthologous genes and examined their gene ontology (GO) categories. Four significant gene clusters were identified that embraced GO terms for phosphorylation (important for turning enzymes on and off and other metabolic pathways), and protein transport and maintenance at specific cell location. They were also enriched with genes of key cellular components (e.g. membranes, endoplasmic reticulum, Golgi membrane). Since chromosomal rearrangements occurred in EBRs may lead to new gene variants and, therefore, function changes, we suggest that the observed EBR enrichment could play a crucial part in evolution of metabolic networks and rates in higher vertebrates, including birds, adapted to various environments. We also developed a pipeline for analyzing cross-species FISH data including tools for semi-automated hybridization signal and FLpter identification, and comparative cytogenetic map construction.

In birds, genome is organised into several large chromosomes (macrochromosomes) and many smaller chromosomes (microchromosomes) that usually constitute about 25 and 75 per cent of the karyotype, respectively. Cytogenetic and molecular cytogenetic evidence suggests that avian karyotype is remarkably stable in evolution, with exception of several clades. To date, at least 21 avian genomes have been sequenced and assembled at the chromosome or scaffold level with N50 greater than 2 Mb, thereby allowing cytogenomic studies of chromosome organisation and change. To understand the comparative organisation and evolution of several avian species, we aligned chromosomes and scaffolds using an interactive genome browser (Evolution Highway), identifying homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs). For ancestral karyotype reconstruction, we focused on six species (chicken, turkey, duck, zebra finch, ostrich, and budgerigar; N50 > 10Mb) and reconstructed avian ancestor chromosomes using an outgroup (Anole lizard). In particular, we addressed the following biological questions: (1) whether species-specific EBRs could represent recombination hotspots, and (2) whether entire microchromosomes could be considered as blocks of conserved synteny. Our study did not reveal a significant association between EBRs and recombination. With support from molecular cytogenetic mapping, we did find that microchromosomes are characterised by a high interchromosomal conservation in almost all birds studied, except ostrich and parrots (budgerigar). By analysing HSBs in six birds and using a lizard outgroup,, we reconstructed a tentative avian ancestral genome and chromosomal rearrangements that occurred in the major avian evolutionary lineages. We identified most intrachromosomal changes (mostly inversions) in the zebra finch clade (Passeriformes) since the time when it diverged from the sister group of parrots (Psittaciformes) 54MYA. Our data also suggest the fewest

Background: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Results: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra-and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Conclusions: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lin

BACKGROUND The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g. in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineag

Dinosaurs hold a unique place both in the history of the earth and the imagination of many. They dominated the terrestrial environment for around 170 million years during which time they diversified into at least 1000 different species. Reptilia, within which they are placed is one of the most remarkable vertebrate groups, consisting of two structurally and physiologically distinct lineages – the birds and the non-avian reptiles, of which there are 10,000 and 7,500 extant species respectively. The dinosaurs are without doubt the most successful group of vertebrate to have existed. They survived several mass extinction events before finally non-avian dinosaurs were defeated 66 million years ago in the Cretaceous-Paleogene extinction event, leaving the neornithes (modern birds) as their living descendants. Aside from the huge phenotypic diversity seen in this group, the birds and non-avian reptiles interestingly display similar karyotypic patterns (with the exception of crocodilians); with the characteristic pattern of macro and micro chromosomes, small genome size and few repetitive elements, suggesting that these were features exhibited in their common ancestor. In this study, the availability of multiple reptile genome sequences (including birds) on an interactive browser (Evolution Highway) allowed us to identify multi species homologous synteny blocks (msHSBs) between the putative avian ancestor (derived from six species of extant birds), the Lizard (Anolis carolensis) and the Snake (Boa constrictor). From these msHSBs we were able to produce a series of contiguous ancestral regions (CARs) representing the most likely ancestral karyotype of the Saurian (ancestor of archosaurs and lepidosaurs) that diverged from the mammalian lineage 280 mya. From this we have hypothesised the series of inter and intra-chromosomal rearrangements that have occurred along the dinosaur (archosaur) lineage to the ancestor of modern birds (100 mya) and along the lepidosaur lineage to t

Chromosomes (and sub-chromosomal homologous synteny blocks (HSBs)) have great significance in molecular studies of genome evolution. In birds, our ability to define chromosomes and HSBs precisely has however been impeded by a near intractable karyotype and so has focused primarily on comparative molecular cytogenetics (zoo-FISH) of the largest chromosomes (1-10+Z). Availability of multiple avian genome sequence assemblies has however allowed us, for the first time, to identify chromosomal syntenies across species. In recent work we made use of comparative maps for 20+ avian genome assemblies (plus out-groups) and presented them on “Evolution Highway” an open-access, interactive freely available comparative chromosome browser designed to store and visualize comparative chromosome maps. This browser (http://evolutionhighway.ncsa.uiuc.edu) visualizes comparative genome organization and identifies different types of evolutionary breakpoint regions (EBRs) in chromosomes, e.g., lineage specific, ordinal, superordinal, and reuse. Comparative analysis of all available genomes provides insight into the mechanisms of chromosome change through correlation of EBRs with transposable elements and non-allelic homologous recombination. Gene ontology analysis is revealing interesting correlations with avian specific phenotype and function. Focus on six genomes (chicken, turkey, duck, zebra finch, ostrich, budgerigar) with the large N50s and supporting molecular cytogenetic data, allowed us to assemble a putative ancestral avian karyotype and identify key changes that led to the gross genome organization of representatives in the major avian clades (Palaeognathae, Galliformes, Anseriformes, Neoaves). We describe numerous inter-chromosomal rearrangements in a Paleoganthaeous bird (the ostrich), plus rearrangements in the budgerigar (Psattaciformes) and 15 other species. Intra-chromosomal evolutionary change can be derived, most parsimoniously, by a series of inversions, inter-chromoso

In birds, genome is organised into several large chromosomes (macrochromosomes) and many smaller chromosomes (microchromosomes) that usually constitute about 25 and 75 per cent of the karyotype, respectively. Cytogenetic and molecular cytogenetic evidence suggests that avian karyotype is remarkably stable in evolution, with exception of several clades. To date, at least 21 avian genomes have been sequenced and assembled at the chromosome or scaffold level with N50 greater than 2 Mb, thereby allowing cytogenomic studies of chromosome organisation and change. To understand the comparative organisation and evolution of several avian species, we aligned chromosomes and scaffolds using an interactive genome browser (Evolution Highway), identifying homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs). For ancestral karyotype reconstruction, we focused on six species (chicken, turkey, duck, zebra finch, ostrich, and budgerigar; N50 > 10Mb) and reconstructed avian ancestor chromosomes using an outgroup (Anole lizard). In particular, we addressed the following biological questions: (1) whether species-specific EBRs could represent recombination hotspots, and (2) whether entire microchromosomes could be considered as blocks of conserved synteny. Our study did not reveal a significant association between EBRs and recombination. With support from molecular cytogenetic mapping, we did find that microchromosomes are characterised by a high interchromosomal conservation in almost all birds studied, except ostrich and parrots (budgerigar). By analysing HSBs in six birds and using a lizard outgroup,, we reconstructed a tentative avian ancestral genome and chromosomal rearrangements that occurred in the major avian evolutionary lineages. We identified most intrachromosomal changes (mostly inversions) in the zebra finch clade (Passeriformes) since the time when it diverged from the sister group of parrots (Psittaciformes) 54MYA. Our data also suggest the fewest

Avian genome organization is characterized, in part, by a set of microchromosomes that are unusually small in size and unusually large in number. Although occupying about a quarter of the genome, they contain around half the genes and three quarters of the chromosome count. Nonetheless, they continue to belie analysis by cytogenetic means. Chromosomal rearrangements play a key role in genome evolution, fertility and genetic disease and, thus, tools for the microchromosomes are essential to analyze such phenomena in birds. Here we report the development of chicken microchromosomal paint pools, generation of pairs of specific microchromosome BAC clones in chicken, and tools for in-silico genomic comparison of microchromosomes. We demonstrate the application of these tools cross-species, which can, in principle, be used in combination to generate a clear picture of microchromosomal rearrangements for numerous avian species. With increasing numbers of avian genome sequences being generated, tools such as these will find great utility in assembling genomes de-novo and asking fundamental questions about genome evolution from a chromosome perspective.

The recent availability of whole genome assemblies for multiple bird species has changed the way we can detect and describe patterns of avian genome evolution. Coupled with conventional cytogenetic techniques, in silico comparison and alignment of bird chromosome assemblies offer exciting opportunities for reconstructing chromosomal rearrangement events that occurred in various avian and ancestral lineages. These can later be correlated with the variety of phenotypes observed in birds. We are testing this approach using the chromosome assemblies of zebra finch, turkey, duck, and green anole lizard (as an outgroup genome); analysis of further genomes is in progress. The approach first involves identification of multi-species homologous synteny blocks and reconstruction of a tentative avian ancestral genome from contiguous ancestral regions (CARs) using the multiple genome rearrangement and ancestors tool (MGRA). Secondly, manual comparative analysis of the CARs to reveal the most likely scenarios of inter- and intrachromosomal events in separate avian lineages is performed. Finally, we compare the rearrangement rates in each lineage. We frequently observe that species with the fewest number of chromosomal rearrangements exhibit phenotypes considered being ancestral for birds. In contrast, an increased rate of chromosomal rearrangements often correlates with higher degree of phenotypic variation, diversification, and adaptation.

With Rebecca O'Connor, piano and John Mattern, cello.; Part of the 2004-2005 Faculty Artist Series., Series LIX, Number 24., This archival material has been provided for educational purposes. Ball State University Libraries recognizes that some historic items may include offensive content. Our statement regarding objectionable content is available at: https://dmr.bsu.edu/digital/about

With Rebecca O'Connor, piano and John Mattern, cello.; Part of the 2003-2004 Faculty Artist Series., Series LVIII, Number 16., This archival material has been provided for educational purposes. Ball State University Libraries recognizes that some historic items may include offensive content. Our statement regarding objectionable content is available at: https://dmr.bsu.edu/digital/about

Background Granulocyte-colony stimulating factor (G-CSF) mobilises endogenous haematopoietic stem cells and enhances recovery in experimental stroke. Recovery may also be dependent on an enriched environment and physical activity. G-CSF may have the potential to enhance recovery when used in combination with physiotherapy, in patients with disability late after stroke. Methods A pilot 2 x 2 factorial randomised (1:1) placebo-controlled trial of G-CSF (double-blind), and/ or a 6 week course of physiotherapy, in 60 participants with disability (mRS >1), at least 3 months after stroke. Primary outcome was feasibility, acceptability and tolerability. Secondary outcomes included death, dependency, motor function and quality of life measured 90 and 365 days after enrolment. Results Recruitment to the trial was feasible and acceptable; of 118 screened patients, 92 were eligible and 32 declined to participate. 60 patients were recruited between November 2011 and July 2013. All participants received some allocated treatment. Although 29 out of 30 participants received all 5 G-CSF/placebo injections, only 7 of 30 participants received all 18 therapy sessions. G-CSF was well tolerated but associated with a tendency to more adverse events than placebo (16 vs 10 patients, p = 0.12) and serious adverse events (SAE) (9 vs 3, p = 0.10). On average, patients received 14 (out of 18 planned) therapy sessions, interquartile range [12, 17]. Only a minority (23%) of participants completed all physiotherapy sessions, a large proportion of sessions (114 of 540, 21%) were cancelled due to patient (94, 17%) and therapist factors (20, 4%). No significant differences in functional outcomes were detected in either the G-CSF or physiotherapy group at day 90 or 365. Conclusions Delivery of G-CSF is feasible in chronic stroke. However, the study failed to demonstrate feasibility for delivering additional physiotherapy sessions late after stroke therefore a definitive study using this trial design

Collaborative governance has given rise to decision-making methodologies promoting democracy, inclusivity and transparency. This is exemplified by deliberative priority-setting (DPS) that blends cost-effectiveness analysis with stakeholder deliberation. Little is known however, about the facilitation challenges when ‘technical’ and ‘social’ elements are combined in a methodology. This paper investigates the facilitation challenges of implementing a DPS project within the English National Health Service (NHS). Our study examines the relationship between facilitation and the effectiveness of DPS processes, highlighting the importance of knowledge management as facilitators seek to translate technical information, to enhance the deliberative experience and promote legitimate decisions.

Background Granulocyte-colony stimulating factor (G-CSF) mobilises endogenous haematopoietic stem cells and enhances recovery in experimental stroke. Recovery may also be dependent on an enriched environment and physical activity. G-CSF may have the potential to enhance recovery when used in combination with physiotherapy, in patients with disability late after stroke. Methods A pilot 2 x 2 factorial randomised (1:1) placebo-controlled trial of G-CSF (double-blind), and/ or a 6 week course of physiotherapy, in 60 participants with disability (mRS >1), at least 3 months after stroke. Primary outcome was feasibility, acceptability and tolerability. Secondary outcomes included death, dependency, motor function and quality of life measured 90 and 365 days after enrolment. Results Recruitment to the trial was feasible and acceptable; of 118 screened patients, 92 were eligible and 32 declined to participate. 60 patients were recruited between November 2011 and July 2013. All participants received some allocated treatment. Although 29 out of 30 participants received all 5 G-CSF/placebo injections, only 7 of 30 participants received all 18 therapy sessions. G-CSF was well tolerated but associated with a tendency to more adverse events than placebo (16 vs 10 patients, p = 0.12) and serious adverse events (SAE) (9 vs 3, p = 0.10). On average, patients received 14 (out of 18 planned) therapy sessions, interquartile range [12, 17]. Only a minority (23%) of participants completed all physiotherapy sessions, a large proportion of sessions (114 of 540, 21%) were cancelled due to patient (94, 17%) and therapist factors (20, 4%). No significant differences in functional outcomes were detected in either the G-CSF or physiotherapy group at day 90 or 365. Conclusions Delivery of G-CSF is feasible in chronic stroke. However, the study failed to demonstrate feasibility for delivering additional physiotherapy sessions late after stroke therefore a definitive study using this trial design

Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.

Background The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Results Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Conclusions Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and b

Collaborative governance has given rise to decision-making methodologies promoting democracy, inclusivity and transparency. This is exemplified by deliberative priority-setting (DPS) that blends cost-effectiveness analysis with stakeholder deliberation. Little is known however, about the facilitation challenges when ‘technical’ and ‘social’ elements are combined in a methodology. This paper investigates the facilitation challenges of implementing a DPS project within the English National Health Service (NHS). Our study examines the relationship between facilitation and the effectiveness of DPS processes, highlighting the importance of knowledge management as facilitators seek to translate technical information, to enhance the deliberative experience and promote legitimate decisions.

Background Granulocyte-colony stimulating factor (G-CSF) mobilises endogenous haematopoietic stem cells and enhances recovery in experimental stroke. Recovery may also be dependent on an enriched environment and physical activity. G-CSF may have the potential to enhance recovery when used in combination with physiotherapy, in patients with disability late after stroke. Methods A pilot 2 x 2 factorial randomised (1:1) placebo-controlled trial of G-CSF (double-blind), and/ or a 6 week course of physiotherapy, in 60 participants with disability (mRS >1), at least 3 months after stroke. Primary outcome was feasibility, acceptability and tolerability. Secondary outcomes included death, dependency, motor function and quality of life measured 90 and 365 days after enrolment. Results Recruitment to the trial was feasible and acceptable; of 118 screened patients, 92 were eligible and 32 declined to participate. 60 patients were recruited between November 2011 and July 2013. All participants received some allocated treatment. Although 29 out of 30 participants received all 5 G-CSF/placebo injections, only 7 of 30 participants received all 18 therapy sessions. G-CSF was well tolerated but associated with a tendency to more adverse events than placebo (16 vs 10 patients, p = 0.12) and serious adverse events (SAE) (9 vs 3, p = 0.10). On average, patients received 14 (out of 18 planned) therapy sessions, interquartile range [12, 17]. Only a minority (23%) of participants completed all physiotherapy sessions, a large proportion of sessions (114 of 540, 21%) were cancelled due to patient (94, 17%) and therapist factors (20, 4%). No significant differences in functional outcomes were detected in either the G-CSF or physiotherapy group at day 90 or 365. Conclusions Delivery of G-CSF is feasible in chronic stroke. However, the study failed to demonstrate feasibility for delivering additional physiotherapy sessions late after stroke therefore a definitive study using this trial design

Collaborative governance has given rise to decision-making methodologies promoting democracy, inclusivity and transparency. This is exemplified by deliberative priority-setting (DPS) that blends cost-effectiveness analysis with stakeholder deliberation. Little is known however, about the facilitation challenges when ‘technical’ and ‘social’ elements are combined in a methodology. This paper investigates the facilitation challenges of implementing a DPS project within the English National Health Service (NHS). Our study examines the relationship between facilitation and the effectiveness of DPS processes, highlighting the importance of knowledge management as facilitators seek to translate technical information, to enhance the deliberative experience and promote legitimate decisions.

Background Granulocyte-colony stimulating factor (G-CSF) mobilises endogenous haematopoietic stem cells and enhances recovery in experimental stroke. Recovery may also be dependent on an enriched environment and physical activity. G-CSF may have the potential to enhance recovery when used in combination with physiotherapy, in patients with disability late after stroke. Methods A pilot 2 x 2 factorial randomised (1:1) placebo-controlled trial of G-CSF (double-blind), and/ or a 6 week course of physiotherapy, in 60 participants with disability (mRS >1), at least 3 months after stroke. Primary outcome was feasibility, acceptability and tolerability. Secondary outcomes included death, dependency, motor function and quality of life measured 90 and 365 days after enrolment. Results Recruitment to the trial was feasible and acceptable; of 118 screened patients, 92 were eligible and 32 declined to participate. 60 patients were recruited between November 2011 and July 2013. All participants received some allocated treatment. Although 29 out of 30 participants received all 5 G-CSF/placebo injections, only 7 of 30 participants received all 18 therapy sessions. G-CSF was well tolerated but associated with a tendency to more adverse events than placebo (16 vs 10 patients, p = 0.12) and serious adverse events (SAE) (9 vs 3, p = 0.10). On average, patients received 14 (out of 18 planned) therapy sessions, interquartile range [12, 17]. Only a minority (23%) of participants completed all physiotherapy sessions, a large proportion of sessions (114 of 540, 21%) were cancelled due to patient (94, 17%) and therapist factors (20, 4%). No significant differences in functional outcomes were detected in either the G-CSF or physiotherapy group at day 90 or 365. Conclusions Delivery of G-CSF is feasible in chronic stroke. However, the study failed to demonstrate feasibility for delivering additional physiotherapy sessions late after stroke therefore a definitive study using this trial design

Collaborative governance has given rise to decision-making methodologies promoting democracy, inclusivity and transparency. This is exemplified by deliberative priority-setting (DPS) that blends cost-effectiveness analysis with stakeholder deliberation. Little is known however, about the facilitation challenges when ‘technical’ and ‘social’ elements are combined in a methodology. This paper investigates the facilitation challenges of implementing a DPS project within the English National Health Service (NHS). Our study examines the relationship between facilitation and the effectiveness of DPS processes, highlighting the importance of knowledge management as facilitators seek to translate technical information, to enhance the deliberative experience and promote legitimate decisions.