Assembly of 43 human Y chromosomes reveals extensive complexity and variation.

The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.

Imprinted X chromosome inactivation in marsupials: The paternal X arrives at the egg with a silent DNA methylation profile.

X chromosome inactivation (XCI) is an epigenetic process that results in the transcriptional silencing of one X chromosome in the somatic cells of females. This phenomenon is common to both eutherian and marsupial mammals, but there are fundamental differences. In eutherians, the X chosen for silencing is random. DNA methylation on the eutherian inactive X is high at transcription start sites (TSSs) and their flanking regions, resulting in universally high DNA methylation. This contrasts XCI in marsupials where the paternally derived X is always silenced, and in which DNA methylation is low at TSSs and flanking regions. Here, we examined the DNA methylation status of the tammar wallaby X chromosome during spermatogenesis to determine the DNA methylation profile of the paternal X prior to and at fertilization. Whole genome enzymatic methylation sequencing was carried out on enriched flow-sorted populations of premeiotic, meiotic, and postmeiotic cells. We observed that the X displayed a pattern of DNA methylation from spermatogonia to mature sperm that reflected the inactive X in female somatic tissue. Therefore, the paternal X chromosome arrives at the egg with a DNA methylation profile that reflects the transcriptionally silent X in adult female somatic tissue. We present this epigenetic signature as a candidate for the long sought-after imprint for paternal XCI in marsupials.

Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures.

MOTIVATION: Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B DNA play an important role in basic cellular processes and are associated with genomic instability, gene regulation, and oncogenesis. Experimental methods are low-throughput and can detect only a limited set of non-B DNA structures, while computational methods rely on non-B DNA base motifs, which are necessary but not sufficient indicators of non-B structures. Oxford Nanopore sequencing is an efficient and low-cost platform, but it is currently unknown whether nanopore reads can be used for identifying non-B structures. RESULTS: We build the first computational pipeline to predict non-B DNA structures from nanopore sequencing. We formalize non-B detection as a novelty detection problem and develop the GoFAE-DND, an autoencoder that uses goodness-of-fit (GoF) tests as a regularizer. A discriminative loss encourages non-B DNA to be poorly reconstructed and optimizing Gaussian GoF tests allows for the computation of P-values that indicate non-B structures. Based on whole genome nanopore sequencing of NA12878, we show that there exist significant differences between the timing of DNA translocation for non-B DNA bases compared with B-DNA. We demonstrate the efficacy of our approach through comparisons with novelty detection methods using experimental data and data synthesized from a new translocation time simulator. Experimental validations suggest that reliable detection of non-B DNA from nanopore sequencing is achievable. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/bayesomicslab/ONT-nonb-GoFAE-DND.

Translating global evidence into local implementation through technical assistance: a realist evaluation of the Bloomberg philanthropies initiative for global Road safety.

BACKGROUND: Traffic-related crashes are a leading cause of premature death and disability. The safe systems approach is an evidence-informed set of innovations to reduce traffic-related injuries and deaths. First developed in Sweden, global health actors are adapting the model to improve road safety in low- and middle-income countries via technical assistance (TA) programs; however, there is little evidence on road safety TA across contexts. This study investigated how, why, and under what conditions technical assistance influenced evidence-informed road safety in Accra (Ghana), Bogotá (Colombia), and Mumbai (India), using a case study of the Bloomberg Philanthropies Initiative for Global Road Safety (BIGRS). METHODS: We conducted a realist evaluation with a multiple case study design to construct a program theory. Key informant interviews were conducted with 68 government officials, program staff, and other stakeholders. Documents were utilized to trace the evolution of the program. We used a retroductive analysis approach, drawing on the diffusion of innovation theory and guided by the context-mechanism-outcome approach to realist evaluation. RESULTS: TA can improve road safety capabilities and increase the uptake of evidence-informed interventions. Hands-on capacity building tailored to specific implementation needs improved implementers' understanding of new approaches. BIGRS generated novel, city-specific analytics that shifted the focus toward vulnerable road users. BIGRS and city officials launched pilots that brought evidence-informed approaches. This built confidence by demonstrating successful implementation and allowing government officials to gauge public perception. But pilots had to scale within existing city and national contexts. City champions, governance structures, existing political prioritization, and socio-cultural norms influenced scale-up. CONCLUSION: The program theory emphasizes the interaction of trust, credibility, champions and their authority, governance structures, political prioritization, and the implement-ability of international evidence in creating the conditions for road safety change. BIGRS continues to be a vehicle for improving road safety at scale and developing coalitions that assist governments in fulfilling their role as stewards of population well-being. Our findings improve understanding of the complex role of TA in translating evidence-informed interventions to country-level implementation and emphasize the importance of context-sensitive TA to increase impact.

Is economic growth enough to propel rehabilitation expenditures? An empirical analysis of country panel data and policy implications.

PURPOSE: Rehabilitation is a set of services designed to increase functioning and improve wellbeing across the life course. Despite being a core part of Universal Health Coverage, rehabilitation services often receive limited public expenditure, especially in lower income countries. This leads to limited service availability and high out of pocket payments for populations in need of care. The purpose of this research was to assess the association between macroeconomic conditions and rehabilitation expenditures across low-, middle-, and high-income countries and to understand its implications for overall rehabilitation expenditure trajectory across countries. MATERIALS AND METHODS: We utilized a panel data set from the World Health Organization's Global Health Expenditure Database comprising the total rehabilitation expenditure for 88 countries from 2016 to 2018. Basic macroeconomic and population data served as control variables. Multiple regression models were implemented to measure the relationship between macroeconomic conditions and rehabilitation expenditures. We used four different model specifications to check the robustness of our estimates: pooled data models (or naïve model) without control, pooled data models with controls (or expanded naïve model), fixed effect models with all controls, and lag models with all controls. Log-log specifications using fixed effects and lag-dependent variable models were deemed the most appropriate and controlled for time-invariant differences. RESULTS: Our regression models indicate that, with a 1% increase in economic growth, rehabilitation expenditure would be associated with a 0.9% and 1.3% increase in expenditure. Given low baseline levels of existing rehabilitation expenditure, we anticipate that predicted increases in rehabilitation expenditure due to economic growth may be insufficient to meet the growing demand for rehabilitation services. Existing expenditures may also be vulnerable during periods of economic recession. CONCLUSION: This is the first known estimation of the association between rehabilitation expenditure and macroeconomic conditions. Our findings demonstrate that rehabilitation is sensitive to macroeconomic fluctuations and the path dependency of past expenditures. This would suggest the importance of increased financial prioritization of rehabilitation services and improved institutional strengthening to expand access to rehabilitation services for populations.

Health systems challenges, mitigation strategies and adaptations to maintain essential health services during the COVID-19 pandemic: learnings from the six geopolitical regions in Nigeria.

BACKGROUND: The COVID-19 pandemic control strategies disrupted the smooth delivery of essential health services (EHS) globally. Limited evidence exists on the health systems lens approach to analyzing the challenges encountered in maintaining EHS during the COVID-19 pandemic. This study aimed to identify the health system challenges encountered and document the mitigation strategies and adaptations made across geopolitical zones (GPZs) in Nigeria. METHODS: The national qualitative survey of key actors across the six GPZs in Nigeria involved ten states and the Federal Capital Territory (FCT) which were selected based on resilience, COVID-19 burden and security considerations. A pre-tested key informant guide was used to collect data on service utilization, changes in service utilization, reasons for changes in primary health centres' (PHCs) service volumes, challenges experienced by health facilities in maintaining EHS, mitigation strategies implemented and adaptations to service delivery. Emerging sub-themes were categorized under the appropriate pillars of the health system. RESULTS: A total of 22 respondents were interviewed. The challenges experienced in maintaining EHS cut across the pillars of the health systems including: Human resources shortage, shortages in the supply of personal protective equipments, fear of contracting COVID-19 among health workers misconception, ignorance, socio-cultural issues, lockdown/transportation and lack of equipment/waiting area (. The mitigation strategies included improved political will to fund health service projects, leading to improved accessibility, affordability, and supply of consumables. The health workforce was motivated by employing, redeploying, training, and incentivizing. Service delivery was reorganized by rescheduling appointments and prioritizing some EHS such as maternal and childcare. Sustainable systems adaptations included IPC and telehealth infrastructure, training and capacity building, virtual meetings and community groups set up for sensitization and engagement. CONCLUSION: The mitigation strategies and adaptations implemented were important contributors to EHS recovery especially in the high resilience LGAs and have implications for future epidemic preparedness plans.

Prioritizing rehabilitation in low- and middle-income country national health systems: a qualitative thematic synthesis and development of a policy framework.

BACKGROUND: There is a large and growing unmet need for rehabilitation - a diverse category of services that aim to improve functioning across the life course - particularly in low- and middle-income countries. Yet despite urgent calls to increase political commitment, many low- and middle-income country governments have dedicated little attention to expanding rehabilitation services. Existing policy scholarship explains how and why health issues reach the policy agenda and offers applicable evidence to advance access to physical, medical, psychosocial, and other types of rehabilitation services. Drawing from this scholarship and empirical data on rehabilitation, this paper proposes a policy framework to understand national-level prioritization of rehabilitation in low- and middle-income countries. METHODS: We conducted key informant interviews with rehabilitation stakeholders in 47 countries, complemented by a purposeful review of peer-reviewed and gray literature to achieve thematic saturation. We analyzed the data abductively using a thematic synthesis methodology. Rehabilitation-specific findings were triangulated with policy theory and empirical case studies on the prioritization of other health issues to develop the framework. RESULTS: The novel policy framework includes three components which shape the prioritization of rehabilitation on low- and middle-income countries' national government's health agendas. First, rehabilitation lacks a consistent problem definition, undermining the development of consensus-driven solutions which could advance the issue on policy agendas. Second, governance arrangements are fragmented within and across government ministries, between the government and its citizens, and across national and transnational actors engaged in rehabilitation service provision. Third, national legacies - particularly from civil conflict - and weaknesses in the existing health system influences both rehabilitation needs and implementation feasibility. CONCLUSIONS: This framework can support stakeholders in identifying the key components impeding prioritization for rehabilitation across different national contexts. This is a crucial step for ultimately better advancing the issue on national policy agendas and improving equity in access to rehabilitation services.

MyD88 Costimulation in Donor CD8+ T Cells Enhances the Graft-versus-Tumor Effect in Murine Hematopoietic Cell Transplantation.

Donor-derived lymphocytes from allogeneic hematopoietic cell transplantation (allo-HCT) or donor lymphocyte infusion can mediate eradication of host tumor cells in a process labeled the graft-versus-tumor (GVT) effect. Unfortunately, these treatments have produced limited results in various types of leukemia because of an insufficient GVT effect. In this context, molecular engineering of donor lymphocytes to increase the GVT effect may benefit cancer patients. Activating MyD88 signaling in CD8+ T cells via TLR enhances T cell activation and cytotoxicity. However, systemic administration of TLR ligands to stimulate MyD88 could induce hyperinflammation or elicit protumor effects. To circumvent this problem, we devised a synthetic molecule consisting of MyD88 linked to the ectopic domain of CD8a (CD8α:MyD88). We used this construct to test the hypothesis that MyD88 costimulation in donor CD8+ T cells increases tumor control following allo-HCT in mice by increasing T cell activation, function, and direct tumor cytotoxicity. Indeed, an increase in both in vitro and in vivo tumor control was observed with CD8α:MyD88 T cells. This increase in the GVT response was associated with increased T cell expansion, increased functional capacity, and an increase in direct cytotoxic killing of the tumor cells. However, MyD88 costimulation in donor CD8+ T cells was linked to increased yet nonlethal graft-versus-host disease in mice treated with these engineered CD8+ T cells. Given these observations, synthetic CD8α:MyD88 donor T cells may represent a unique and versatile approach to enhance the GVT response that merits further refinement to improve the effectiveness of allo-HCT.

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch).

The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.

Integration measurement and its applications in low- and middle-income country health systems: a scoping review.

BACKGROUND: Despite growing interest in and commitment to integration, or integrated care, the concept is ill-defined and the resulting evidence base fragmented, particularly in low- and middle-income countries (LMICs). Underlying this challenge is a lack of coherent approaches to measure the extent of integration and how this influences desired outcomes. The aim of this scoping review is to identify measurement approaches for integration in LMICs and map them for future use. METHODS: Arksey and O'Malley's framework for scoping reviews was followed. We conducted a systematic search of peer-reviewed literature measuring integration in LMICs across three databases and screened identified papers by predetermined inclusion and exclusion criteria. A modified version of the Rainbow Model for Integrated Care guided charting and analysis of the data. RESULTS: We included 99 studies. Studies were concentrated in the Africa region and most frequently focused on the integration of HIV care with other services. A range of definitions and methods were identified, with no single approach for the measurement of integration dominating the literature. Measurement of clinical integration was the most common, with indicators focused on measuring receipt of two or more services provided at a single point of time. Organizational and professional integration indicators were focused on inter- and intra-organizational communication, collaboration, coordination, and continuity of care, while functional integration measured common information systems or patient records. Gaps were identified in measuring systems and normative integration. Few tools were validated or publicly available for future use. CONCLUSION: We identified a wide range of recent approaches used to measure integration in LMICs. Our findings underscore continued challenges with lack of conceptual cohesion and fragmentation which limits how integration is understood in practice.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.

Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

Introducing the READY Study: DHH Young people's Well-Being and Self-Determination.

READY is a self-report prospective longitudinal study of deaf and hard of hearing (DHH) young people aged 16 to 19 years on entry. Its overarching aim is to explore the risk and protective factors for successful transition to adulthood. This article introduces the cohort of 163 DHH young people, background characteristics and study design. Focusing on self-determination and subjective well-being only, those who completed the assessments in written English (n = 133) score significantly lower than general population comparators. Sociodemographic variables explain very little of the variance in well-being scores; higher levels of self-determination are a predictor of higher levels of well-being, outweighing the influence of any background characteristics. Although women and those who are LGBTQ+ have statistically significantly lower well-being scores, these aspects of their identity are not predictive risk factors. These results add to the case for self-determination interventions to support better well-being amongst DHH young people.

Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition.

Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.

Integrating private health facilities in government-led health systems: a case study of the public-private mix approach in Ethiopia.

BACKGROUND: Private health care facilities working in partnership with the public health sector is one option to create sustainable health systems and ensure health and well-being for all in low-income countries. As the second-most populous country in Africa with a rapidly growing economy, demand for health services in Ethiopia is increasing and one-quarter of its health facilities are privately owned. The Private Health Sector Program (PHSP), funded by the United States Agency for International Development, implemented a series of public-private partnership in health projects from 2004 to 2020 to address several public health priorities, including tuberculosis, malaria, HIV/AIDS, and family planning. We assessed PHSP's performance in leadership and governance, access to medicines, health management information systems, human resources, service provision, and finance. METHODS: The World Health Organization's health systems strengthening framework, which is organized around six health system building blocks, guided the assessment. We conducted 50 key informant interviews and a health facility assessment at 106 private health facilities supported by the PHSP to evaluate its performance. RESULTS: All six building blocks were addressed by the program and key informants shared that several policy and strategic changes were conducive to supporting the functioning of private health facilities. The provision of free medicines from the public pharmaceutical logistics system, relaxation of strict regulatory policies that restricted service provision through the private sector, training of private providers, and public-private mix guidelines developed for tuberculosis, malaria, and reproductive, maternal, newborn, child, and adolescent health helped increase the use of services at health facilities. CONCLUSIONS: Some challenges and threats to sustainability remain, including fragile partnerships between public and private bodies, resource constraints, mistrust between the public and private sectors, limited incentives for the private sector, and oversight of the quality of services. To continue with gains in the policy environment, service accessibility, and other aspects of the health system, the government and international communities must work collaboratively to address public-private partnerships in health areas that can be strengthened. Future efforts should emphasize a mechanism to ensure that the private sector is capable, incentivized, and supervised to deliver continuous, high-quality and equitable services.

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.

The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here, we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400-600 kb) TADs in human and other mammalian species. The colocalization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Last, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.

Seq'ing identity and function in a repeat-derived noncoding RNA world.

Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs that populate cell nuclei and lend insight to the mechanisms by which noncoding RNAs influence chromosome biology and gene expression. This review focuses on some of the recent technological developments that have enabled the isolation of nascent transcripts and chromatin-associated and DNA-interacting RNAs. Coupled with emerging genome assembly and analytical approaches, the field is poised to achieve a comprehensive catalog of nuclear noncoding RNAs, including those derived from repetitive regions within eukaryotic genomes. Herein, particular attention is paid to the challenges and advances in the sequence analyses of repeat and transposable element-derived noncoding RNAs and in ascribing specific function(s) to such RNAs.

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes.

BACKGROUND: One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). The non-Mendelian inheritance and non-pairing abilities of B chromosomes make them an interesting model for genomics studies, thus bringing to bear different questions about their genetic composition, evolutionary survival, maintenance and functional role inside the cell. This study uncovers these phenomena in multiple species that we considered as representative organisms of both vertebrate and invertebrate models for B chromosome analysis. RESULTS: We sequenced the genomes of three animal species including two fishes Astyanax mexicanus and Astyanax correntinus, and a grasshopper Abracris flavolineata, each with and without Bs, and identified their B-localized genes and repeat contents. We detected unique sequences occurring exclusively on Bs and discovered various evolutionary patterns of genomic rearrangements associated to Bs. In situ hybridization and quantitative polymerase chain reactions further validated our genomic approach confirming detection of sequences on Bs. The functional annotation of B sequences showed that the B chromosome comprises regions of gene fragments, novel genes, and intact genes, which encode a diverse set of functions related to important biological processes such as metabolism, morphogenesis, reproduction, transposition, recombination, cell cycle and chromosomes functions which might be important for their evolutionary success. CONCLUSIONS: This study reveals the genomic structure, composition and function of Bs, which provide new insights for theories of B chromosome evolution. The selfish behavior of Bs seems to be favored by gained genes/sequences.

A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive.

A common feature of eukaryotic centromeres is the presence of large tracts of tandemly arranged repeats, known as satellite DNA. However, these centromeric repeats appear to experience rapid evolution under forces such as molecular drive and centromere drive, seemingly without consequence to the integrity of the centromere. Moreover, blocks of heterochromatin within the karyotype, including the centromere, are hotspots for chromosome rearrangements that may drive speciation events by contributing to reproductive isolation. However, the relationship between the evolution of heterochromatic sequences and the karyotypic dynamics of these regions remains largely unknown. Here, we show that a single conserved satellite DNA sequence in the order Rodentia of the genus Peromyscus localizes to recurrent sites of chromosome rearrangements and heterochromatic amplifications. Peromyscine species display several unique features of chromosome evolution compared to other Rodentia, including stable maintenance of a strict chromosome number of 48 among all known species in the absence of any detectable interchromosomal rearrangements. Rather, the diverse karyotypes of Peromyscine species are due to intrachromosomal variation in blocks of repeated DNA content. Despite wide variation in the copy number and location of repeat blocks among different species, we find that a single satellite monomer maintains a conserved sequence and homogenized tandem repeat structure, defying predictions of molecular drive. The conservation of this satellite monomer results in common, abundant, and large blocks of chromatin that are homologous among chromosomes within one species and among diverged species. Thus, such a conserved repeat may have facilitated the retention of polymorphic chromosome variants within individuals and intrachromosomal rearrangements between species-both factors that have previously been hypothesized to contribute towards the extremely wide range of ecological adaptations that this genus exhibits.

Branched Pectic Galactan in Phloem-Sieve-Element Cell Walls: Implications for Cell Mechanics.

A major question in plant biology concerns the specification and functional differentiation of cell types. This is in the context of constraints imposed by networks of cell walls that both adhere cells and contribute to the form and function of developing organs. Here, we report the identification of a glycan epitope that is specific to phloem sieve element cell walls in several systems. A monoclonal antibody, designated LM26, binds to the cell wall of phloem sieve elements in stems of Arabidopsis (Arabidopsis thaliana), Miscanthus x giganteus, and notably sugar beet (Beta vulgaris) roots where phloem identification is an important factor for the study of phloem unloading of Suc. Using microarrays of synthetic oligosaccharides, the LM26 epitope has been identified as a ß-1,6-galactosyl substitution of ß-1,4-galactan requiring more than three backbone residues for optimized recognition. This branched galactan structure has previously been identified in garlic (Allium sativum) bulbs in which the LM26 epitope is widespread throughout most cell walls including those of phloem cells. Garlic bulb cell wall material has been used to confirm the association of the LM26 epitope with cell wall pectic rhamnogalacturonan-I polysaccharides. In the phloem tissues of grass stems, the LM26 epitope has a complementary pattern to that of the LM5 linear ß-1,4-galactan epitope, which is detected only in companion cell walls. Mechanical probing of transverse sections of M x giganteus stems and leaves by atomic force microscopy indicates that phloem sieve element cell walls have a lower indentation modulus (indicative of higher elasticity) than companion cell walls.

Transposable elements: genome innovation, chromosome diversity, and centromere conflict.

Although it was nearly 70 years ago when transposable elements (TEs) were first discovered "jumping" from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive. Finally, we focus on the role of TEs in the establishment, maintenance, and stabilization of critical, yet rapidly evolving, chromosome features: eukaryotic centromeres. Across centromeres, specific types of TEs participate in genomic conflict, a balancing act wherein they are actively inserting into centromeric domains yet are harnessed for the recruitment of centromeric histones and potentially new centromere formation.