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Assessing the genetic diversity of captive populations of endangered species is key to the successful management of conservation-breeding programs. In this study, we sequenced a 393-bp fragment of the mitochondrial DNA (mtDNA) control region of 23 captive individuals of the Endangered François’ langur (Trachypithecus francoisi) to assess the mtDNA diversity of the European captive population and to identify the possible geographical origins of the population founders. Combined with 42 sequences previously published from 29 wild François’ langurs, we identified a total of 40 haplotypes in T. francoisi, including 12 haplotypes in the 23 samples from the European captive population. Only one of the haplotypes from captive animals has previously been reported from wild populations; the remaining 11 haplotypes are newly reported here. Our results suggest that the captive T. francoisi population currently holds a relatively good genetic diversity compared with many other captive populations, that this diversity originates from a fairly broad range across the species’ distribution in the wild, and that the captive population could play a significant role in increasing genetic diversity of isolated wild populations. However, the European captive population is currently quite small, and genetic diversity could be lost rapidly, which has been demonstrated in other captive populations. We recommend further investigation of the genetic diversity of captive and wild T. francoisi populations, as well as the effective conservation of this diversity.

Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the principles of 3D genome folding in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (1) identified different patterns of chromosome folding in across vertebrate species (centromere clustering versus chromosomal territories); (2) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of species representative of the major therian phylogroups; (3) detected lineage-specific chromosome rearrangements; and (4) identified the dynamics of the structural properties of genome reshuffling through therian evolution. We present evidence of chromatin configurational changes that result from ancestral inversions and fusions/fissions. We catalog the close interplay between chromatin higher-order organization and therian genome evolution and introduce an interpretative hypothesis that explains how chromatin folding influences evolutionary patterns of genome reshuffling. This work was supported by the Ministry of Economy, Industry and Competitiveness (CGL2017-83802-P to A.R.-H.) and the Spanish Ministry of Science and Innovation (PID2020-112557GB-I00 to A.R.-H. and PID2020-115696RB-I00 to M.A.M.-R.). Research funding to P.D.W. (Australian Research Council grants DP180100931, DP210103512, and DP220101429) and T.J.R. (South African National Research Foundation) are gratefully acknowledged. C.V. and L.A.-G. were supported by FPI predoctoral fellowships from the Ministry of Economy and Competitiveness (BES-2015-072924 and PRE-2018-083257). L.M.-G. was supported by an FPU predoctoral fellowship from the Spanish Ministry of Science, Innovation and University (FPU18/03867). C.A.-S. was supported by a GTA fellowship from the University of Kent.

The role of genome folding in the heritability and evolvability of structural variations is not well understood. Here the authors investigate the impact of the three-dimensional genome topology of germ cells in the formation and transmission of gross structural genomic changes detected from comparing whole-genome sequences of 14 rodent species. Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. Using a comprehensive integrative computational analysis, we (i) reconstruct seven ancestral rodent genomes analysing whole-genome sequences of 14 species representatives of the major phylogroups, (ii) detect lineage-specific chromosome rearrangements and (iii) identify the dynamics of the structural and epigenetic properties of evolutionary breakpoint regions (EBRs) throughout mouse spermatogenesis. Our results show that EBRs are devoid of programmed meiotic DNA double-strand breaks (DSBs) and meiotic cohesins in primary spermatocytes, but are associated in post-meiotic cells with sites of DNA damage and functional long-range interaction regions that recapitulate ancestral chromosomal configurations. Overall, we propose a model that integrates evolutionary genome reshuffling with DNA damage response mechanisms and the dynamic spatial genome organisation of germ cells.

Approximately one million in vitro produced (IVP) cattle embryos are transferred worldwide each year as a way to improve the rates of genetic gain. The most advanced programmes also apply genomic selection at the embryonic stage by SNP genotyping and the calculation of genomic estimated breeding values (GEBVs). However, a high proportion of cattle embryos fail to establish a pregnancy. Here, we demonstrate that further interrogation of the SNP data collected for GEBVs can effectively remove aneuploid embryos from the pool, improving live births per embryo transfer (ET). Using three preimplantation genetic testing for aneuploidy (PGT-A) approaches, we assessed 1713 cattle blastocysts in a blind, retrospective analysis. Our findings indicate aneuploid embryos have a 5.8% chance of establishing a pregnancy and a 5.0% chance of given rise to a live birth. This compares to 59.6% and 46.7% for euploid embryos (p &lt, 0.0001). PGT-A improved overall pregnancy and live birth rates by 7.5% and 5.8%, respectively (p &lt, 0.0001). More detailed analyses revealed donor, chromosome, stage, grade, and sex-specific rates of error. Notably, we discovered a significantly higher incidence of aneuploidy in XY embryos and, as in humans, detected a preponderance of maternal meiosis I errors. Our data strongly support the use of PGT-A in cattle IVP programmes.

Significance Morphologically and functionally distinct X and Y chromosomes have repeatedly evolved across the tree of life. However, the extent of differentiation between the sex chromosomes varies substantially across species. As sex chromosomes diverge, the Y chromosome gene activity decays, leaving genes on the sex chromosomes reduced to a single functional copy in males. Mechanisms have evolved to compensate for this reduction in gene dosage. Here, we perform a comparative analysis of sex chromosome systems across poeciliid species and uncover extreme variation in the degree of sex chromosome differentiation and Y chromosome degeneration. Additionally, we find evidence for a case of chromosome-wide dosage compensation in fish. Our findings have important implications for sex chromosome evolution and regulation., Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

The speed of muscle contraction is related to body size; muscles in larger species contract at slower rates. Since contraction speed is a property of the myosin isoform expressed in a muscle, we investigated how sequence changes in a range of muscle myosin II isoforms enable this slower rate of muscle contraction. We considered 798 sequences from 13 mammalian myosin II isoforms to identify any adaptation to increasing body mass. We identified a correlation between body mass and sequence divergence for the motor domain of the 4 major adult myosin II isoforms (β/Type I, IIa, IIb, and IIx), suggesting that these isoforms have adapted to increasing body mass. In contrast, the non-muscle and developmental isoforms show no correlation of sequence divergence with body mass. Analysis of the motor domain sequence of β-myosin (predominant myosin in Type I/slow and cardiac muscle) from 67 mammals from 2 distinct clades identifies 16 sites, out of 800, associated with body mass (padj < 0.05) but not with the clade (padj > 0.05). Both clades change the same small set of amino acids, in the same order from small to large mammals, suggesting a limited number of ways in which contraction velocity can be successfully manipulated. To test this relationship, the 9 sites that differ between human and rat were mutated in the human β-myosin to match the rat sequence. Biochemical analysis revealed that the rat–human β-myosin chimera functioned like the native rat myosin with a 2-fold increase in both motility and in the rate of ADP release from the actin–myosin crossbridge (the step that limits contraction velocity). Thus, these sequence changes indicate adaptation of β-myosin as species mass increased to enable a reduced contraction velocity and heart rate., Heart and skeletal muscles of larger mammals contract more slowly than smaller ones. This study identifies amino acid changes in myosin isoforms that correlate with species size; mutating the residues in human β-myosin to match the rat sequence at these positions increased its in vitro velocity to that of the rat protein.

The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species.

The Helmholtz conditions are necessary and sufficient conditions for a system of second-order differential equations to be variational, that is, equivalent to a system of Euler–Lagrange equations for a regular Lagrangian. On the other hand, matching conditions are sufficient conditions for a class of controlled systems to be variational for a Lagrangian function of a prescribed type, known as the controlled Lagrangian. Using the Helmholtz conditions, we are able to recover the matching conditions from Bloch et al. (IEEE Trans Autom Control 45(12):2253–2270, 2000). Furthermore, we can derive new matching conditions for a particular class of mechanical systems. It turns out that for this class of systems we obtain feedback controls that only depend on the configuration variables. We test this new strategy for the inverted pendulum on a cart and for the inverted pendulum on an incline.

In memory of Ingemar Gustavsson 23rd International Colloquium on Animal Cytogenetics and Genomics (23 ICACG) took place in June 9–12, 2018 in Saint-Petersburg, Russia. Organized biennially, the Colloquium runs from 1970. From its very start this meeting is associated with the name of Ingemar Gustavsson to whom we dedicated the Colloquium 2018. The long and productive career of Ingemar Gustavsson had focused on chromosomes and their fundamental role in animal physiology, fertility, health and production in the context of agriculture and veterinary medicine. His meticulous analysis of breeding data performed back in 1964–69 resulted in the unequivocal identification of an association between heterozygosity for the 1/29 translocation in Swedish cattle and reduction in the fertility of the breed. Eventually, the argument in favor of selective elimination of bulls carrying the translocation from the breeding programs prevailed and the field of modern veterinary cytogenetics was established. Participants from fourteen different countries attended the 23 ICACG in Russia, the country having long lasting traditions in cytogenetics and the Scientific schools of N.K. Koltzov, S.S. Chetverikov and A.S. Serebrovsky, geneticists who made important conceptual contributions to studies of chromosomes and genes, population genetics and evolutionary theory as early as in the beginning of the XX-th century. All the abstracts received were subdivided between plenary and seven scientific sessions covering the issues in evolutionary and comparative cytogenetics, cytogenetics and genomes of domestic animals, meiosis studies, particular chromosome analyses, clinical cytogenetics, karyotypes and genomes of vertebrate and invertebrate animals, chromatin studies. In the abstract text below each presentation is marked with a capital letter: „L” stands for lectures, „O” for oral presentations and „P” for poster presentations. We gratefully acknowledge the support from the Saint-Petersburg Association of Scientists and Scholars (SPbSU), Veterinary Genetics Center ZOOGEN, Russian Foundation for Basic Research (RFBR), VEUK, Helicon, Axioma BIO, BioVitrum, Sartorius, DIA-M companies. The current collected abstracts comprise written contributions of the presentations during the 23 ICACG and were edited by Svetlana Galkina and Maria Vishnevskaya. The next Colloquium – 24 ICACG – will be held at the University of Kent in Canterbury (UK) in 2020. Please, cite abstracts as follows: Gall JG (2018) Giant chromosomes and deep sequences: what the amphibian egg tells us about transcription. In: Galkina SA, Vishnevskaya MS, Mikhailova EI (Eds) 23rd Inernational Colloquium on Animal Cytogenetics and Genomics (23rdICACG), June 9–12, 2018, St Petersburg, Russia. Comparative Cytogenetics 12(3): p–p. https://doi.org/10.3897/CompCytogen.v12i3.27748

Rapid advances in biology demand new tools for more active research dissemination and engaged teaching. This paper presents Synteny Explorer, an interactive visualization application designed to let college students explore genome evolution of mam- malian species. The tool visualizes synteny blocks: segments of homologous DNA shared between various extant species that can be traced back or reconstructed in extinct, ancestral species. We take a karyogram-based approach to create an interactive synteny visualization, leading to a more appealing and engaging design for undergraduate-level genome evolution education. For validation, we conduct three user studies: two focused studies on color and animation design choices and a larger study that performs overall system usability testing while comparing our karyogram-based designs with two more common genome mapping representations in an educational context. While existing views communicate the same information, study participants found the interactive, karyogram- based views much easier and likable to use. We additionally discuss feedback from biology and genomics faculty, who judge Synteny Explorer’s fitness for use in classrooms.

Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, and three inversions. We discuss changes in pecoran ancestral karyotype in the light of new painting data. Variations in the X chromosome structure of four bovid species nilgai bull (Boselaphus tragocamelus), saola (Pseudoryx nghetinhensis), gaur (Bos gaurus), and Kirk&rsquo, s Dikdik (Madoqua kirkii) were further analyzed using 26 cattle BAC-clones. We found the duplication on the X in saola. We show main rearrangements leading to the formation of four types of bovid X: Bovinae type with derived cattle subtype formed by centromere reposition and Antilopinae type with Caprini subtype formed by inversion in XSB3.

AIM Of the few instruments available to measure the important, positive aspects of caring, the Caregiver Reaction Assessment is regarded as the most suitable, but there is no validated Spanish version. The aim of this study was to translate the Caregiver Reaction Assessment into Spanish and assess its psychometric properties. METHODS The Caregiver Reaction Assessment was translated into Spanish and then back translated. Validation included construct validity, criterion validity and reliability: 287 interviews were conducted with informal caregivers of patients with dementia between November 2010 and April 2012. RESULTS Principal component analysis confirmed the original instrument's five subscales. Criterion validity showed a moderate negative correlation between the impact on health and the EQ-5D (r = -.43), that is, a greater impact on health correlated with lower health-related quality of life. The Caregiver Reaction Assessment showed good internal consistency, with a Cronbach alpha of .804, and good temporal stability for the distinct subscales, with intraclass correlation coefficients varying from .683 to .729 (p < .001). CONCLUSION The Caregiver Reaction Assessment is a reliable, valid instrument for the measurement of the reactions of informal caregivers of patients with dementia, with good psychometric properties.

BackgroundThe Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.FindingsUsing SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions.ConclusionsWe have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years.

The sustainability of a large proportion of Spanish olive oil-producing territories depends to a great extent on their capacity to fit into a specific model of food quality. The strategies used in the di erent territories di er with respect to their adherence to the objectifiable conception of quality, based on scientific-technical knowledge, or subjectivating conception of quality, based on tacit and practical knowledge. In this paper, we analyse the route taken by two territories with olive oil protected designation of origin (PDO) status in Spain to construct their quality model, the type of knowledge that has been applied and how knowledge processes a ect the construction of sustainable quality models. This study applies a qualitative methodology based on participative observation and semi-structured interviews with key actors of the territories. The results indicate that processes of production, reproduction and dissemination of knowledge are basic pillars for the construction of sustainable quality projects. The degree of understanding of the objectifiable and subjectivating conception of quality in olive-producing territories and the interaction between them depend on the specific characteristics of the territory, the objectives set in connection to the olive oil quality method, the importance given to the di erent types of knowledge, and its standing on the issue of territorial sustainability

While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Felis catus), dog (Canis lupus familiaris), and grey wolf (Canis lupus lupus), providing the opportunity to examine the red fox (Vulpes vulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.

The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.

Background\ud The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts.\ud \ud Findings\ud Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions.\ud \ud Conclusions\ud Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.

Risk factors associated with admission of people with dementia to long-term care institutions need to be identified to support health-care professionals in dementia care at home. An explorative study, combining quantitative and qualitative data collection methods, was performed in people with dementia in Spain. The sample, consisting of people with dementia receiving formal care from health-care professionals but at risk of institutionalisation, and their informal care-givers; and people with dementia recently admitted to a long-term care institution, and their informal care-givers, was interviewed between November 2010 and April 2012. Perceived reasons for admission were determined through an open-ended question put to both groups. Presumed risk factors were collected with validated questionnaires and analysed using bivariate analysis. A total of 287 people with dementia and informal care-givers were studied. Reasons given by the institutionalised group were mostly related to the level of dependency of the person with dementia. People recently admitted to a long-term care institution had more cognitive impairment, a greater degree of dependency and poorer quality of life than those still living at home. Home-care services in Spain need to develop or improve interventions based on the risk factors identified in this study: informal care-giver profile, high cognitive impairment, high level of dependency and the poor quality of life of the person with dementia.

Background Prevalence of dementia in developed countries is high. Optimising the quality of life (QoL) of both patient and caregiver is the most important treatment goal. The main objective is to measure the QoL of people with dementia living at home or in long-term care institutions (LTCI) and identify related factors. Methods Cross-sectional study. Data of people with dementia who lived at home or who had been recently admitted to an LTCI in Spain was included. QoL was assessed by people with dementia themselves and their proxies using the ‘Quality of Life-Alzheimer's Disease scale' (QoL-AD). Clinical, cognitive and neuropsychiatric data were collected. Results In total, 287 PwD were included; 113 from LTCIs (39.4%) and 174 from home care (HC) (60.6%). Mean age was 83.2 (7.1) years; 201 (70%) patients were women and mean of the MMSE score was 15.1 (5.6). A total of 160 (55.7%) PwD had completed data for both QoL self-reported and proxy-reported (35.4% from LTCI and 69% from HC; P b : –0.534, P =0.001) and neuropsychiatric symptoms ( b : –0.223, P =0.004) were independently associated with self-reported QoL. The Charlson index ( b : –0.637, P =0.032), Katz ( b : 0.481, P =0.019) and Cornell index score ( b : –0.367, P =0.001) were independently associated with proxy-reported QoL. Conclusions Low depressive and neuropsychiatric symptoms were independently associated with better self-reported QoL. On the other hand, low comorbidity, better functional status and low depressive symptoms were independently associated with QoL reported by the informer caregivers.

The language of Lagrangian submanifolds is used to extend a geometric characterization of the inverse problem of the calculus of variations on tangent bundles to regular Lie algebroids. Since not all closed sections are locally exact on Lie algebroids, the Helmholtz conditions on Lie algebroids are necessary but not sufficient, so they give a weaker definition of the inverse problem. As an application the Helmholtz conditions on Atiyah algebroids are obtained so that the relationship between the inverse problem and the reduced inverse problem by symmetries can be described. Some examples and comparison with previous approaches in the literature are provided.

Background Due to the high prevalence of dementia, health care needs are increasing beyond existing formal resources. In Spain, it is the family that takes care of this disease. Aims To analyze the direct (health and non-health) and indirect economic costs related to care of people with dementia living with their informal caregiver in the home care/community environment, from the perspective of illness severity, associated comorbidity and social impact. Design Multicentric, descriptive study. Setting Three primary care public health centers associated with Hospital Clinic, Barcelona (Spain). Participants Patients over 65 years old with a diagnosis of dementia, and included in a home care program. Inclusion criteria People with a diagnosis of dementia made by a specialist neurologist; aged 65 years or older; a score ≤24 on the Mini-Mental State Examination, and identification of an informal caregiver. Exclusion criteria Patients unable to identify an informal caregiver, and those with primary psychiatric pathology or Korsakoff's syndrome. Measurements Use of Resources in Dementia to assess costs; Mini-Mental State Examination to evaluate cognitive capacity; Katz-Index to measure functional capacity; Neuropsychiatric Index for neuropsychiatric symptoms, and the Charlson-Index for comorbidity. Data collection took place between November, 2010 and April, 2012. Results The average estimated monthly care costs for people with dementia in the home setting are 1956.2€ (SD 1463.9). Informal care was the major contributor to this with a mean estimated cost of 1214.86 (SD 902.68)€/month. Greater illness severity, dependency in activities of daily living, comorbidity and behavioral disturbance are associated with higher costs. Behavioral disturbance appeared as the only factor independently associated with cost in dementia care. The group of people with dementia with severe behavioral disturbance requires the most care resources with an average cost of 2545.2 (SD 1753.2)€/month. Conclusions There is a direct association between dementia severity and increased costs. In addition, informal caregivers looking after people with dementia in Spain represent an important social cost. The independent factor associated with an increase in the total costs of patient care was neuropsychiatric symptoms.

Background Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Results Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Conclusions Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically. Electronic supplementary material The online version of this article (10.1186/s13059-018-1544-8) contains supplementary material, which is available to authorized users.

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Background: The aim of this study is to identify the barriers and facilitators in dementia care with respect to information provision, communication, and collaboration from the perspectives of the person with dementia, family caregivers, and health care professionals over the course of the illness. Methods: A qualitative study using Focus-Group methodology was carried out in people with dementia, family caregivers, and health care providers. Results: The categories that emerged from the analysis were insufficient information provided, specific dementia care needs, and acceptance of long-term care institutionalization from the people with dementia and caregivers’ groups and insufficient communication between health care providers, differential information according to disease stage, and home care coordination from the health care providers’ groups. Conclusion: The family is a key element in successful care coordination during dementia care provision. New effective strategies including self-management and emergent roles, such as case managers, could bring great benefits to people with dementia, caregivers, and health care providers.

Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders.

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; Volker 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 organization that show regulatory interactions within and between chromosomes. Finally, reconstruction of evolutionary events allows us to study genome organization and function not only in extant but, by extrapolation, in extinct species also. Reconstruction of avian-reptilian ancestral karyotypes will allow us to define chromosomal rearrangements in long-dead species that have captured the public imagination. Here be dragons!