Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals

Background: Although the mammalian X and Y chromosomes evolved from a single pair of autosomes, they are highly differentiated: the Y chromosome is dramatically smaller than the X and has lost most of its genes. The surviving genes are a specialized set with extraordinary evolutionary longevity. Most mammalian lineages have experienced delayed, or relatively recent, loss of at least one conserved Y-linked gene. An extreme example of this phenomenon is in the Japanese spiny rat, where the Y chromosome has disappeared altogether. In this species, many Y-linked genes were rescued by transposition to new genomic locations, but until our work presented here, this has been considered an isolated case. Results: We describe eight cases of genes that have relocated to autosomes in mammalian lineages where the corresponding Y-linked gene has been lost. These gene transpositions originated from either the X or Y chromosomes, and are observed in diverse mammalian lineages: occurring at least once in marsupials, apes, and cattle, and at least twice in rodents and marmoset. For two genes - EIF1AX/Y and RPS4X/Y - transposition to autosomes occurred independently in three distinct lineages. Conclusions: Rescue of Y-linked gene loss through transposition to autosomes has previously been reported for a single isolated rodent species. However, our findings indicate that this compensatory mechanism is widespread among mammalian species. Thus, Y-linked gene loss emerges as an additional driver of gene transposition from the sex chromosomes, a phenomenon thought to be driven primarily by meiotic sex chromosome inactivation.National Institutes of Health (U.S.) (Grant HG000257

Environmental Drivers of Holocene Forest Development in the Middle Atlas, Morocco

In semi-arid regions subject to rising temperatures and drought, palaeoecological insights into past vegetation dynamics under a range of boundary conditions are needed to develop our understanding of environmental responses to climatic changes. Here, we present a new high-resolution record of vegetation history and fire activity spanning the last 12,000 years from Lake Sidi Ali in the southern Middle Atlas Mountains, Morocco. The record is underpinned by a robust AMS radiocarbon and 210Pb/137Cs chronology and multi-proxy approach allowing direct comparison of vegetation, hydroclimate, and catchment tracers. The record reveals the persistence of steppic landscapes until 10,340 cal yr BP, prevailing sclerophyll woodland with evergreen Quercus until 6,300 cal yr BP, predominance of montane conifers (Cedrus and Cupressaceae) until 1,300 cal yr BP with matorralization and increased fire activity from 4,320 cal yr BP, and major reduction of forest cover after 1,300 cal yr BP. Detailed comparisons between the pollen record of Lake Sidi Ali (2,080m a.s.l.) and previously published data from nearby Tigalmamine (1,626m a.s.l.) highlight common patterns of vegetation change in response to Holocene climatic and anthropogenic drivers, as well as local differences relating to elevation and bioclimate contrasts between the sites. Variability in evergreen Quercus and Cedrus at both sites supports a Holocene summer temperature maximum between 9,000 and 7,000 cal yr BP in contrast with previous large-scale pollen-based climate reconstructions, and furthermore indicates pervasive millennial temperature variability. Millennial-scale cooling episodes are inferred from Cedrus expansion around 10,200, 8,200, 6,100, 4,500, 3,000, and 1,700 cal yr BP, and during the Little Ice Age (400 cal yr BP). A two-part trajectory of Late Holocene forest decline is evident, with gradual decline from 4,320 cal yr BP linked to synergism between pastoralism, increased fire and low winter rainfall, and a marked reduction from 1,300 cal yr BP, attributed to intensification of human activity around the Early Muslim conquest of Morocco. This trajectory, however, does not mask vegetation responses to millennial climate variability. The findings reveal the sensitive response ofMiddle Atlas forests to rapid climate changes and underscore the exposure of the montane forest ecosystems to future warming

Exploring the experiences of having Guillain‐Barré Syndrome: A qualitative interview study

Background: Guillain-Barré syndrome (GBS) is a rare inflammatory disorder affecting the peripheral nerves. Although typically there is full neurological recovery, some people continue to experience residual physical, psychological or social problems longer term. Evidence describing the experiences of people with GBS is limited. Objective: We aimed to explore the experiences of people with GBS in the UK. Design: We used qualitative (face-to-face and telephone) interviews to explore experiences of people with GBS. Audio-recorded data were transcribed verbatim and analysed using the Framework Method supported by NVivo 11. Setting and Participants: We purposively recruited a sample of 16 volunteers with a prior diagnosis of GBS of varying age, sex, ethnicity, location, marital status, time since diagnosis and length of hospital stay to maximize differences in experience. Interviewees were required to have been discharged from hospital, able to give informed consent, able to speak and understand English and currently resident in the United Kingdom. Results: The key themes arising from the analysis were as follows: the importance of early diagnosis; the experiences of inpatient care; the importance of active support for recovery; the need for communication throughout the course of the illness; the need for greater awareness, knowledge and provision of information by health-care staff; and path to achieving function. Conclusion: This is the first qualitative study exploring experiences of people with GBS in the UK through their whole illness journey from onset to recovery. The findings contribute to our understanding of the experiences and support needs of people recovering from GBS

Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome o

The history of the Y chromosome in man

Studies of the Y chromosome over the past few decades have opened a window into the history of our species, through the reconstruction and exploitation of a patrilineal (Y-genealogical) tree based on several hundred single-nucleotide variants (SNVs). A new study validates, refines and extends this tree by incorporating >65,000 Y-linked variants identified in 1,244 men representing worldwide diversity

Hypolocomotion, asymmetrically directed behaviors (licking, lifting, flinching, and shaking) and dynamic weight bearing (gait) changes are not measures of neuropathic pain in mice

<p>Abstract</p> <p>Background</p> <p>Spontaneous (non-evoked) pain is a major clinical symptom of neuropathic syndromes, one that is understudied in basic pain research for practical reasons and because of a lack of consensus over precisely which behaviors reflect spontaneous pain in laboratory animals. It is commonly asserted that rodents experiencing pain in a hind limb exhibit hypolocomotion and decreased rearing, engage in both reflexive and organized limb directed behaviors, and avoid supporting their body weight on the affected side. Furthermore, it is assumed that the extent of these positive or negative behaviors can be used as a dependent measure of spontaneous chronic pain severity in such animals. In the present study, we tested these assumptions via blinded, systematic observation of digital video of mice with nerve injuries (chronic constriction or spared nerve injury), and automated assessment of locomotor behavior using photocell detection and dynamic weight bearing (i.e., gait) using the CatWalk^®system.</p> <p>Results</p> <p>We found no deficits in locomotor activity or rearing associated with neuropathic injury. The frequency of asymmetric (ipsilaterally directed) behaviors were too rare to be seriously considered as representing spontaneous pain, and in any case did not statistically exceed what was blindly observed on the contralateral hind paw and in control (sham operated and unoperated) mice. Changes in dynamic weight bearing, on the other hand, were robust and ipsilateral after spared nerve injury (but not chronic constriction injury). However, we observed timing, pharmacological, and genetic dissociation of mechanical allodynia and gait alterations.</p> <p>Conclusions</p> <p>We conclude that spontaneous neuropathic pain in mice cannot be assessed using any of these measures, and thus caution is warranted in making such assertions.</p

Remission and recovery in the Treatment for Adolescents with Depression Study (TADS): acute and long-term outcomes.

OBJECTIVE: We examine remission rate probabilities, recovery rates, and residual symptoms across 36 weeks in the Treatment for Adolescents with Depression Study (TADS). METHOD: The TADS, a multisite clinical trial, randomized 439 adolescents with major depressive disorder to 12 weeks of treatment with fluoxetine, cognitive-behavioral therapy, their combination, or pill placebo. The pill placebo group, treated openly after week 12, was not included in the subsequent analyses. Treatment differences in remission rates and probabilities of remission over time are compared. Recovery rates in remitters at weeks 12 (acute phase remitters) and 18 (continuation phase remitters) are summarized. We also examined whether residual symptoms at the end of 12 weeks of acute treatment predicted later remission. RESULTS: At week 36, the estimated remission rates for intention-to-treat cases were as follows: combination, 60%; fluoxetine, 55%; cognitive-behavioral therapy, 64%; and overall, 60%. Paired comparisons reveal that, at week 24, all active treatments converge on remission outcomes. The recovery rate at week 36 was 65% for acute phase remitters and 71% for continuation phase remitters, with no significant between-treatment differences in recovery rates. Residual symptoms at the end of acute treatment predicted failure to achieve remission at weeks 18 and 36. CONCLUSIONS: Most depressed adolescents in all three treatment modalities achieved remission at the end of 9 months of treatment

A quantitative assessment of the consistency of projections from five mathematical models of the HIV epidemic in South Africa: a model comparison study

Background: Mathematical models are increasingly used to inform HIV policy and planning. Comparing estimates obtained using different mathematical models can test the robustness of estimates and highlight research gaps. As part of a larger project aiming to determine the optimal allocation of funding for HIV services, in this study we compare projections from five mathematical models of the HIV epidemic in South Africa: EMOD-HIV, Goals, HIV-Synthesis, Optima, and Thembisa. // Methods: The five modelling groups produced estimates of the total population, HIV incidence, HIV prevalence, proportion of people living with HIV who are diagnosed, ART coverage, proportion of those on ART who are virally suppressed, AIDS-related deaths, total deaths, and the proportion of adult males who are circumcised. Estimates were made under a “status quo” scenario for the period 1990 to 2040. For each output variable we assessed the consistency of model estimates by calculating the coefficient of variation and examining the trend over time. // Results: For most outputs there was significant inter-model variability between 1990 and 2005, when limited data was available for calibration, good consistency from 2005 to 2025, and increasing variability towards the end of the projection period. Estimates of HIV incidence, deaths in people living with HIV, and total deaths displayed the largest long-term variability, with standard deviations between 35 and 65% of the cross-model means. Despite this variability, all models predicted a gradual decline in HIV incidence in the long-term. Projections related to the UNAIDS 95–95-95 targets were more consistent, with the coefficients of variation below 0.1 for all groups except children. // Conclusions: While models produced consistent estimates for several outputs, there are areas of variability that should be investigated. This is important if projections are to be used in subsequent cost-effectiveness studies

Motivations for innovation in the built environment: new directions for research

Innovation in the built environment involves multiple actors with diverse motivations. Policy-makers find it difficult to promote changes that require cooperation from these numerous and dispersed actors and to align their sometimes divergent interests. Established research traditions on the economics and management of innovation pay only limited attention to stakeholder choices, engagement and motivation. This paper reviews the insights that emerge as research in these traditions comes into contact with work on innovation from sociological and political perspectives. It contributes by highlighting growing areas of research on user involvement in complex innovation, collective action, distributed innovation and transition management. To differing extents, these provide approaches to incorporate the motivations of different actors into theoretical understanding. These indicate new directions for research that promise to enrich understanding of innovation

Enhancer Sequence Variants and Transcription-Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B-Cell Lymphoma

SummaryMost B-cell lymphomas arise in the germinal center (GC), where humoral immune responses evolve from potentially oncogenic cycles of mutation, proliferation, and clonal selection. Although lymphoma gene expression diverges significantly from GC B cells, underlying mechanisms that alter the activities of corresponding regulatory elements (REs) remain elusive. Here we define the complete pathogenic circuitry of human follicular lymphoma (FL), which activates or decommissions REs from normal GC B cells and commandeers enhancers from other lineages. Moreover, independent sets of transcription factors, whose expression was deregulated in FL, targeted commandeered versus decommissioned REs. Our approach revealed two distinct subtypes of low-grade FL, whose pathogenic circuitries resembled GC B or activated B cells. FL-altered enhancers also were enriched for sequence variants, including somatic mutations, which disrupt transcription-factor binding and expression of circuit-linked genes. Thus, the pathogenic regulatory circuitry of FL reveals distinct genetic and epigenetic etiologies for GC B-cell transformation