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Sertoli cells are somatic cells in testis essential for spermatogenesis, that support the development, maturation, and differentiation of germ cells. Sertoli cells are metabolically highly active and physiologically regulated by external signals, particularly factors in the blood stream. In disease conditions, circulating pathological signals may affect Sertoli cells and consequentially, alter germ cells and fertility. While the effects of stress on reproductive cells have been well studied, how Sertoli cells respond to stress remains poorly characterized. We used a mouse model of early postnatal stress to assess the effects of stress on Sertoli cells. We developed an improved strategy based on intracellular stainings and obtained enriched preparations of Sertoli cells from exposed males. We show that adult Sertoli cells have impaired electron transport chain (ETC) pathways and that several components of ETC complexes particularly complex I, III, and IV are persistently affected. We identify serum as potential mediator of the effects of stress on Sertoli cells by showing that it can recapitulate ETC alterations in primary cells. These results highlight Sertoli cells as cellular targets of stress in early life that can keep a trace of exposure until adulthood., Frontiers in Genetics, 13, ISSN:1664-8021

Recent advances in methods for single-cell analyses and barcoding strategies have led to considerable progress in research. The development of multiplexed assays offers the possibility to conduct parallel analyses of multiple factors and processes for comprehensive characterization of cellular and molecular states in health and disease. These technologies have expanded extremely rapidly in the past years and constantly evolve and provide better specificity, precision and resolution. This review summarizes recent progress in single-cell multiomics approaches, and focuses, in particular, on the most innovative techniques that integrate genome, epigenome and transcriptome profiling. It describes the methodologies, discusses their advantages and limitations, and explains how they have been applied to studies on cell heterogeneity and differentiation, and epigenetic reprogramming., Frontiers in Cell and Developmental Biology, 10, ISSN:2296-634X

Sperm RNA can be modified by environmental factors and has been implicated in communicating signals about changes in a father's environment to the offspring. The small RNA composition of sperm could be changed during its final stage of maturation in the epididymis by extracellular vesicles (EVs) released by epididymal cells. We studied the effect of exposure to stress in early postnatal life on the transcriptome of epididymal EVs using a mouse model of transgenerational transmission. We found that the small RNA signature of epididymal EVs, particularly miRNAs, is altered in adult males exposed to postnatal stress. In some cases, these miRNA changes correlate with differences in the expression of their target genes in sperm and zygotes generated from that sperm. These results suggest that stressful experiences in early life can have persistent biological effects on the male reproductive tract that may in part be responsible for the transmission of the effects of exposure to the offspring.

Ocean warming induced by climate change is the greatest threat to the persistence of coral reefs globally. Given the current rate of ocean warming, there may not be sufficient time for natural acclimation or adaptation by corals. This urgency has led to the exploration of active management techniques aimed at enhancing thermal tolerance in corals. Here, we test the capacity for transgenerational acclimation in the reef-building coral Pocillopora acuta as a means of increasing offspring performance in warmer waters. We exposed coral colonies from a reef influenced by intermittent upwelling and constant warm-water effluent from a nuclear power plant to temperatures that matched (26 °C) or exceeded (29.5 °C) season-specific mean temperatures for three reproductive cycles; offspring were allowed to settle and grow at both temperatures. Heated colonies reproduced significantly earlier in the lunar cycle and produced fewer and smaller planulae. Recruitment was lower at the heated recruitment temperature regardless of parent treatment. Recruit survival did not differ based on parent or recruitment temperature. Recruits from heated parents were smaller and had lower maximum quantum yield (Fv/Fm), a measurement of symbiont photochemical performance. We found no direct evidence that thermal conditioning of adult P. acuta corals improves offspring performance in warmer water; however, chronic exposure of parent colonies to warmer temperatures at the source reef site may have limited transgenerational acclimation capacity. The extent to which coral response to this active management approach might vary across species and sites remains unclear and merits further investigation. Supplementary Information The online version contains supplementary material available at 10.1007/s00338-021-02123-9.

Biotic resistance is the ability of an ecological community to prevent or limit the establishment or success of non-indigenous species. Native species can confer resistance by outcompeting or directly consuming non-native invaders. The fear of being eaten could also limit invader success, but non-consumptive effects of native predators have rarely been documented as a source of biotic resistance. Here, we test whether native groupers on Caribbean coral reefs can promote biotic resistance to invasive Indo-Pacific lionfish through competition, consumption, and/or through non-consumptive effects. Stomach content analysis of more than 200 groupers, comprising five species, revealed no instances of predation on lionfish. To test for competitive and non-consumptive effects of groupers, we released tagged juvenile lionfish onto reef patches that varied in grouper densities and monitored lionfish behaviours over five weeks. At dawn, during peak grouper and lionfish hunting times, juvenile lionfish hid more on reefs with more grouper predators. Juvenile lionfish were also less active during the day on reefs with high grouper densities. Hiding and inactivity are incompatible with foraging and thus should result in lionfish eating fewer prey and having reduced somatic growth rates. Although there was no substantial effect of interspecific competition on lionfish behaviours, we found that lionfish swam greater distances with increasing densities of intraspecific competitors at dawn. We did not detect a cascading effect of grouper predators on smaller fishes, perhaps because the seasonal peak in prey fish recruitment masked the effects of lower lionfish predation. Fear of native predators by lionfish has the potential to reduce invader foraging success, although it might not fully mitigate the negative effects on native prey communities. Efforts to rebuild grouper populations throughout the Caribbean may still aid in controlling the lionfish invasion despite weak evidence of interspecific competition and lack of direct predation on lionfish, but further research is needed. At broader scales, our findings highlight that the global depletion of large predators can have implications beyond demographic effects on prey.

Dihaploid production from elite tetraploid cultivars is key to both traditional and novel breeding approaches that seek to simplify potato genetics. For this purpose, efficient and widely compatible haploid inducers (HIs) are needed. We compared PL-4, a new HI developed at the International Potato Center, to known HIs IvP101 and IvP35. By pollination of elite tetraploid breeding lines, we showed that PL-4 performed significantly better and had a homogeneous response regardless of the genetic background of the pistillate parents, on the most important efficiency traits—number of dihaploids per 100 fruits and haploid induction rate. Moreover, PL-4 exhibited a reduced proportion of hybrid seeds, a convenient trait for efficient screening. In this context, we recommend PL-4 as an enhanced HI for the potato breeding community.

Implementing new and effective control strategies to reduce populations of invasive species is needed to offset their negative impacts worldwide. The spread of Indo-Pacific lionfish (Pterois sp.) through much of the western Atlantic has been one of the most publicized marine invasions globally, and is considered a major biodiversity threat whose longer-term impacts are still uncertain. Marine managers have explored several strategies to control lionfish, such as fishing tournaments (derbies) and commercial fisheries. Commercial fisheries for invasive species are controversial because they could create perverse incentives to maintain these populations, and they have never been demonstrated to successfully control target populations. We analyzed the development and impacts of an opportunistic fishing operation aimed at commercializing invasive lionfish in the Mexican Caribbean. We examined official lionfish landings and compared them to catches from lionfish derbies and lionfish densities from locations in the state of Quintana Roo, Mexico. We found that commercial fishers, particularly from one fishing cooperative on Cozumel Island, were effective at catching lionfish, with landings peaking at 20,000 individuals in 2014. This number is comparable to the number of lionfish caught in derbies across the entire Caribbean in the same year. Ecological survey data suggest a ~ 60% reduction in lionfish density on Cozumel reefs over two years (2013–2015), matching the peak landings in the lionfish fishing operation. However, the fishery’s apparent success as a control tool during the time window analyzed seemed to trigger its own demise: a decline in landings was followed by evaporating market interest and loss of economic viability. If fisheries are to be established and used as management strategies to control future invasions, managers must develop strategic collaboration plans with commercial fishing partners.

Life experiences and environmental conditions in childhood can change the physiology and behaviour of exposed individuals and, in some cases, of their offspring. In rodent models, stress/trauma, poor diet, and endocrine disruptors in a parent have been shown to cause phenotypes in the direct progeny, suggesting intergenerational inheritance. A few models also examined transmission to further offspring and suggested transgenerational inheritance, but such multigenerational inheritance is not well characterized. Our previous work on a mouse model of early postnatal stress showed that behaviour and metabolism are altered in the offspring of exposed males up to the 4th generation in the patriline and up to the 2nd generation in the matriline. The present study examined if symptoms can be transmitted beyond the 4th generation in the patriline. Analyses of the 5th and 6th generations of mice revealed that altered risk-taking and glucose regulation caused by postnatal stress are still manifested in the 5th generation but are attenuated in the 6th generation. Some of the symptoms are expressed in both males and females, but some are sex-dependent and sometimes opposite. These results indicate that postnatal trauma can affect behaviour and metabolism over many generations, suggesting epigenetic mechanisms of transmission., Environmental Epigenetics, 8 (1), ISSN:2058-5888

Metamorphosis undeniably shaped the evolutionary success of winged insects. So far, what we know about the hormonal regulation and molecular mechanisms controlling insect metamorphosis lies on the understanding of complete and incomplete metamorphosis. Rarer types of metamorphosis are overlooked, yet they could provide important insights as they represent deviations in life history strategies that are associated with unique ecological traits. The molecular mechanisms of these atypical metamorphoses are still poorly understood. With the rise of next-generation sequencing, and increasing interest in emerging organismal systems, it is now possible to start exploring the molecular mechanisms underlying atypical metamorphoses in insects. By focusing on neometaboly and paedomorphosis, we discuss how exploring their molecular mechanisms can complete our understanding on the evolution of insects and impact applied research areas. Continued decrease in next-generation sequencing costs and progress in genome editing will help decipher the proximate mechanisms of unusual life history strategies in insects.

Seagrass meadows are among the most productive and diverse marine ecosystems, providing essential structure, functions, and services. They are also among the most impacted by human activities and in urgent need of better management and protection. In Canada, eelgrass ( Zostera marina) meadows are found along the Atlantic, Pacific, and Arctic coasts, and thus occur across a wide range of biogeographic conditions. Here, we synthesize knowledge of eelgrass ecosystems across Canada’s coasts, highlighting commonalities and differences in environmental conditions, plant, habitat, and community structure, as well as current trends and human impacts. Across regions, eelgrass life history, phenology, and general species assemblages are similar. However, distinct regional differences occur in environmental conditions, particularly with water temperature and nutrient availability. There is considerable variation in the types and strengths of human activities among regions. The impacts of coastal development are prevalent in all regions, while other impacts are of concern for specific regions, e.g., nutrient loading in the Atlantic and impacts from the logging industry in the Pacific. In addition, climate change represents a growing threat to eelgrass meadows. We review current management and conservation efforts and discuss the implications of observed differences from coast to coast to coast.

Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.

In crude oil contaminant plumes, the dissolved organic carbon (DOC) is mainly hydrocarbon degradation intermediates only partly quantified by the diesel range total petroleum hydrocarbon (TPHd) method. To understand potential biological effects of degradation intermediates, we tested three fractions of DOC: (1) solid-phase extract (HLB); (2) dichloromethane (DCM-total) extract used in TPHd; and (3) DCM extract with hydrocarbons isolated by silica gel cleanup (DCM-SGC). Bioactivity of extracts from five wells spanning a range of DOC was tested using an in vitro multiplex reporter system that evaluates modulation of the activity of 46 transcription factors; extracts were evaluated at concentrations equivalent to the well water samples. The aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR) transcription factors showed the greatest upregulation, with HLB exceeding DCM-total, and no upregulation in the hydrocarbon fraction (DCM-SGC). The HLB extracts were further studied with HepG2 chemically activated luciferase expression (CALUX) in vitro assays at nine concentrations ranging from 40 to 0.01 times the well water concentrations. Responses decreased with distance from the source but were still present at two wells without detectable hydrocarbons. Thus, our in vitro assay results indicate that risks associated with degradation intermediates of hydrocarbons in groundwater will be underestimated when protocols that remove these chemicals are employed.

Exposure to predation should affect prey responses to predators by selecting for threat recognition and/or general risk avoidance. We investigated whether native and non-native predator density on the home reefs of juvenile striped parrotfish, Scarus iseri, which reflects their early exposure to predation risk, influences their behavioural responses and survival when faced with some of these predators under controlled conditions. In aquaria, parrotfish exhibited evasive behaviour, in the form of increased immobility and increased distance from threat, in response to visual and chemical cues from native predatory grouper (Epinephelus striatus) but not from invasive Indo-Pacific lionfish (Pterois sp.), suggesting no evidence of risk perception in relation to the non-native predator. However, parrotfish from high-risk reefs exhibited more evasive behaviours and colour responses (i.e. more mottled coloration) in response to all stimuli than parrotfish from low-risk reefs. Moreover, more parrotfish from high-risk reefs than from low-risk reefs survived in direct encounters with lionfish, and those parrotfish that survived were those that had displayed increased immobility when exposed to lionfish cues. We suggest that predation, especially by non-native lionfish, targeting risk-taking fish could result in greater overall cautiousness in some prey populations. This heightened risk avoidance ultimately aids prey fish to evade non-native lionfish, even in the absence of predator recognition.

Childhood trauma (CT) can have persistent effects on the brain and is one of the major risk factors for neuropsychiatric diseases in adulthood. Recent advances in the field of epigenetics suggest that epigenetic factors such as DNA methylation and histone modifications, as well as regulatory processes involving non-coding RNA are associated with the long-term sequelae of CT. This narrative review summarizes current knowledge on the epigenetic basis of CT and describes studies in animal models and human subjects examining how the epigenome and transcriptome are modified by CT in the brain. It discusses psychological and pharmacological interventions that can counteract epigenetic changes induced by CT and the need to establish longitudinal assessment after CT for developing more effective diagnostics and treatment strategies based on epigenetic targets. ISSN:0149-7634 ISSN:1873-7528

The extraction of high-quality ribonucleic acid (RNA) from tissues and cells is a key step in many biological assays. Guanidinium thiocyanate-phenol-chloroform (AGPC) is a widely used and efficient method to obtain pure RNA from most tissues and cells. However, it is not efficient with some cells like sperm cells because they are resistant to chaotropic lysis solutions containing guanidinium thiocyanate such as Buffer RLT+ and Trizol. Here, we show that disulfide bonds are responsible for the chemical resistance of sperm cells to RNA extraction reagents. We show that while β-mercaptoethanol (βME) can increase sperm lysis in Buffer RLT+, it has no effect in Trizol and leaves sperm cells intact. We measured the reduction of disulfide bonds in 2,2′-dithiodipyridine (DTDP) and observed that βME has a pH-dependent activity in chaotropic solutions, suggesting that pH is a limiting factor. We identified tris(2-carboxyethyl)phosphine (TCEP) as an efficient lysis enhancer of AGPC solutions that can retain reducing activity even at acidic pH. Trizol supplemented with TCEP allows the complete and rapid lysis of sperm cells, increasing RNA yield by 100-fold and resulting in RNA with optimal quality for reverse transcription and polymerase chain reaction. Our findings highlight the importance of efficient cell lysis and extraction of various macromolecules for bulk and single-cell assays, and can be applied to other lysis-resistant cells and vesicles, thereby optimizing the amount of required starting material and animals., Frontiers in Cell and Developmental Biology, 9, ISSN:2296-634X

Epigenetic inheritance has emerged as a new research discipline that aims to study the mechanisms underlying the transmission of acquired traits across generations. Such transmission is well established in plants and invertebrates but remains not well characterized and understood in mammals. Important questions are how life experiences and environmental factors induce phenotypic changes that are passed to the offspring of exposed individuals, sometimes across several successive generations, what is the contribution of germ cells and what are the consequences for health and disease. These questions were recently discussed at the symposium Epigenetic Inheritance: Impact for Biology and Society organized every 2 years in Zürich, Switzerland. This review provides a summary of the research presented during the symposium and discusses current important questions, perspectives and challenges for the feld in the future., Environmental Epigenetics, 8 (1), ISSN:2058-5888

Environmental factors can change phenotypes in exposed individuals and offspring and involve the germline, likely via biological signals in the periphery that communicate with germ cells. Here, using a mouse model of paternal exposure to traumatic stress, we identify circulating factors involving peroxisome proliferator‐activated receptor (PPAR) pathways in the effects of exposure to the germline. We show that exposure alters metabolic functions and pathways, particularly lipid‐derived metabolites, in exposed fathers and their offspring. We collected data in a human cohort exposed to childhood trauma and observed similar metabolic alterations in circulation, suggesting conserved effects. Chronic injection of serum from trauma‐exposed males into controls recapitulates metabolic phenotypes in the offspring. We identify lipid‐activated nuclear receptors PPARs as potential mediators of the effects from father to offspring. Pharmacological PPAR activation in vivo reproduces metabolic dysfunctions in the offspring and grand‐offspring of injected males and affects the sperm transcriptome in fathers and sons. In germ‐like cells in vitro, both serum and PPAR agonist induce PPAR activation. Together, these results highlight the role of circulating factors as potential communication vectors between the periphery and the germline., The EMBO Journal, 39 (23), ISSN:0261-4189, ISSN:1460-2075

The possibility that parental life experiences and environmental exposures influence mental and physical health across generations is an important concept in biology and medicine. Evidence from animal models has established the existence of a non-genetic mode of inheritance. This form of heredity involves transmission of the effects of parental exposure to the offspring through epigenetic changes in the germline. Studying the mechanisms of epigenetic inheritance in humans is challenging because it is difficult to obtain multigeneration cohorts, to collect reproductive cells in exposed parents, and to exclude psychosocial and cultural confounders. Nonetheless, epidemiological studies in humans exposed to famine, stress/trauma, or toxicants have provided evidence that parental exposure can impact the health of descendants, in some cases, across several generations. A few studies have also started to reveal epigenetic changes in the periphery and sperm after certain exposures. This article reviews these studies and evaluates the current evidence for the potential contribution of epigenetic factors to heredity in humans. The challenges and limitations of this fundamental biological process, its implications, and its societal relevance are also discussed.

BACKGROUND The treatment of glioblastoma (GBM) poses many challenges. The use of immune checkpoint inhibition (ICI) has been disappointing as GBM is characterized by a low mutational burden and low infiltration by T cells. The combination of ICI with other treatment modalities may improve efficacy. METHODS Patients with recurrent GBM were treated with 800 mg avelumab, a human IgG1 antibody directed against PD-L1, either alone (in part A) or within a week after MRI-guided laser interstitial thermal therapy (LITT, in part B) and by-weekly thereafter (NCT03341806). To spare steroid use, bevacizumab was allowed to be combined with avelumab. The primary objective was to characterize the tolerability and safety of the regimen. The secondary objectives included overall survival, progression-free survival, and signature of plasma analytes. RESULTS A total of 12 patients (median age 64, range 37 - 73) enrolled from June 2018 to November 2019, 5 in part A and 7 in part B. Three serious adverse events (SAE) occurred in the same patient, not leading to death. There were 94 AEs reported, 5 grade 3, 28 grade 2, and 61 grade 1. The median PFS was 16.7 weeks (range 7.4-56.7) for patients in Part A and 30.9 weeks (range 8.5-77.7) for patients in Part B. The median survival for patients in part A was 11 months and 13.5 months for part B. The risk ratio of death by combining bevacizumab was 0.573 (p=0.258) with significantly decreased levels of peripheral blood plasma inflammatory markers such as EGF, CXCL5, VEGFA, LAP.TGβ1, ANGPT2 in women. CONCLUSIONS Avelumab was generally well-tolerated, and the combination with LITT had a manageable safety profile and increased survival in a subset of patients. The addition of bevacizumab may increase survival by lowering cytokine expression in a gender-dependent manner. These results warrant further investigation in the next phase study.

Significance Seagrasses are important for ecosystem services, including climate regulation and fisheries production. But they are threatened by multiple pressures including poor water quality and coastal development. Seagrass extent is not monitored in many places, so areas at most risk of decline and the management actions needed in these places are largely unknown. We examine associations between change in seagrass meadow area and key pressures globally, helping predict the trajectory of meadows in unmonitored regions. We find rapidly shrinking seagrass meadows in areas where water quality is poor and destructive fishing occurs. Trajectories of change also vary with seagrass life-history strategy. Finally, we identify several unmonitored locations at risk of decline, highlighting where urgent monitoring and management are required., Seagrass meadows are threatened by multiple pressures, jeopardizing the many benefits they provide to humanity and biodiversity, including climate regulation and food provision through fisheries production. Conservation of seagrass requires identification of the main pressures contributing to loss and the regions most at risk of ongoing loss. Here, we model trajectories of seagrass change at the global scale and show they are related to multiple anthropogenic pressures but that trajectories vary widely with seagrass life-history strategies. Rapidly declining trajectories of seagrass meadow extent (>25% loss from 2000 to 2010) were most strongly associated with high pressures from destructive demersal fishing and poor water quality. Conversely, seagrass meadow extent was more likely to be increasing when these two pressures were low. Meadows dominated by seagrasses with persistent life-history strategies tended to have slowly changing or stable trajectories, while those with opportunistic species were more variable, with a higher probability of either rapidly declining or rapidly increasing. Global predictions of regions most at risk for decline show high-risk areas in Europe, North America, Japan, and southeast Asia, including places where comprehensive long-term monitoring data are lacking. Our results highlight where seagrass loss may be occurring unnoticed and where urgent conservation interventions are required to reverse loss and sustain their essential services.

Summary: The hippocampal formation is a brain structure essential for higher-order cognitive functions. It has a complex anatomical organization and cellular composition, and hippocampal subregions have different properties and functional roles. In this study, we used SWATH-MS to determine whether the proteomes of hippocampus areas CA1 and CA3 can explain the commonalities or specificities of these subregions in basal conditions and after recognition memory. We show that the proteomes of areas CA1 and CA3 are largely different in basal conditions and that differential changes and dynamics in protein expression are induced in these areas after recognition of an object or object location. While changes are consistent across both recognition paradigms in area CA1, they are not in area CA3, suggesting distinct proteomic responses in areas CA1 and CA3 for memory formation. : How does the proteome differ in hippocampus areas CA1 and CA3? von Ziegler et al. identify the proteomes of areas CA1 and CA3 and characterize their dynamics during different recognition processes in adult mice. Keywords: hippocampus, areas CA1 and CA3, proteome, dynamics, object memory, object location memory, mass spectrometry, SWATH-MS, mice, bioinformatic tools

Climate change-induced increases in seawater temperature continue to impact coral reef ecosystems globally. There is a consequent need to characterize the responses of corals to thermal stress to understand the molecular processes underpinning these responses and identify hallmarks of resilience. Here we used an iTRAQ approach to compare the proteomes of adult corals (Pocillopora acuta) that had been thermally conditioned at a control (26°C) or elevated temperature (29.5°C) for three reproductive cycles, as well as the larvae released by these corals. We found that larvae responded more to high-temperature exposure at the protein level than their parents and that different proteins were affected between life stages; a single protein was up-regulated at high temperatures in both adults and their offspring, and its identity is currently unknown. Similarly, different cellular pathways were affected by high-temperature exposure between the coral hosts and their dinoflagellate endosymbionts; proteins involved in translation and protein trafficking were most likely to be affected by high-temperature exposure in the former, with photosynthesis being the most thermo-sensitive process in the latter. Collectively, these findings highlight the importance of considering both life stage and the composition of the coral holobiont when using molecular-scale data to model cellular processes associated with responses to future ocean warming.

Cholesterol synthesis is a tightly regulated process, both transcriptionally and post-translationally. Transcriptional control of cholesterol synthesis is relatively well-understood. However, of the ∼20 enzymes in cholesterol biosynthesis, post-translational regulation has only been examined for a small number. Three of the four sterol reductases in cholesterol production, 7-dehydrocholesterol reductase (DHCR7), 14-dehydrocholesterol reductase (DHCR14), and lamin-B receptor (LBR), share evolutionary ties with a high level of sequence homology and predicted structural homology. DHCR14 and LBR uniquely share the same Δ-14 reductase activity in cholesterol biosynthesis, yet little is known about their post-translational regulation. We have previously identified specific modes of post-translational control of DHCR7, but it is unknown whether these regulatory mechanisms are shared by DHCR14 and LBR. Using CHO-7 cells stably expressing epitope-tagged DHCR14 or LBR, we investigated the post-translational regulation of these enzymes. We found that DHCR14 and LBR undergo differential post-translational regulation, with DHCR14 being rapidly turned over, triggered by cholesterol and other sterol intermediates, whereas LBR remained stable. DHCR14 is degraded via the ubiquitin-proteasome system, and we identified several DHCR14 and DHCR7 putative interaction partners, including a number of E3 ligases that modulate DHCR14 levels. Interestingly, we found that gene expression across an array of human tissues showed a negative relationship between the C14-sterol reductases; one enzyme or the other tends to be predominantly expressed in each tissue. Overall, our findings indicate that whereas LBR tends to be the constitutively active C14-sterol reductase, DHCR14 levels are tunable, responding to the local cellular demands for cholesterol.

The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.

Significance This investigation provides a comprehensive evaluation of the geochemical and biological effects of shale gas development on 25 small watersheds over the course of 2 y. Sampling headwater streams seasonally over two consecutive years yielded no statistically significant relationships between the intensity, presence, or absence of shale gas development and any signal in a comprehensive set of chemical constituents (including those recognized as oil and gas geochemical tracers) or any changes in microbial or benthic macroinvertebrate community composition. This work provides a framework for investigations of anthropogenic effects stemming from natural resource development, and highlights the importance of conducting studies which control for regional and temporal variability., The number of horizontally drilled shale oil and gas wells in the United States has increased from nearly 28,000 in 2007 to nearly 127,000 in 2017, and research has suggested the potential for the development of shale resources to affect nearby stream ecosystems. However, the ability to generalize current studies is limited by the small geographic scope as well as limited breadth and integration of measured chemical and biological indicators parameters. This study tested the hypothesis that a quantifiable, significant relationship exists between the density of oil and gas (OG) development, increasing stream water concentrations of known geochemical tracers of OG extraction, and the composition of benthic macroinvertebrate and microbial communities. Twenty-five headwater streams that drain lands across a gradient of shale gas development intensity were sampled. Our strategy included comprehensive measurements across multiple seasons of sampling to account for temporal variability of geochemical parameters, including known shale OG geochemical tracers, and microbial and benthic macroinvertebrate communities. No significant relationships were found between the intensity of OG development, shale OG geochemical tracers, or benthic macroinvertebrate or microbial community composition, whereas significant seasonal differences in stream chemistry were observed. These results highlight the importance of considering spatial and temporal variability in stream chemistry and biota and not only the presence of anthropogenic activities in a watershed. This comprehensive, integrated study of geochemical and biological variability of headwater streams in watersheds undergoing OG development provides a robust framework for examining the effects of energy development at a regional scale.

Cholesterol synthesis is a tightly controlled pathway, with over 20 enzymes involved. Each of these enzymes can be distinctly regulated, helping to fine-tune the production of cholesterol and its functional intermediates. Several enzymes are degraded in response to increased sterol levels, whilst others remain stable. We hypothesised that an enzyme at a key branch point in the pathway, lanosterol 14α-demethylase (LDM) may be post-translationally regulated. Here, we show that the preceding enzyme, lanosterol synthase is stable, whilst LDM is rapidly degraded. Surprisingly, this degradation is not triggered by sterols. However, the E3 ubiquitin ligase membrane-associated ring-CH-type finger 6 (MARCH6), known to control earlier rate-limiting steps in cholesterol synthesis, also control levels of LDM and the terminal cholesterol synthesis enzyme, 24-dehydrocholesterol reductase. Our work highlights MARCH6 as the first example of an E3 ubiquitin ligase that targets multiple steps in a biochemical pathway and indicates new facets in the control of cholesterol synthesis.

Colonic and intestinal epithelial cells (EC) attach to a basement membrane of laminins, fibronectin, and collagen IV. Wounding of the epithelial layer can change the types of extracellular matrix (ECM) proteins to which the EC attach. In this study, we determined the effect of culturing Caco-2 cells on different ECM proteins on the capacity of EC to produce TNF-α- or IL-1-stimulated CXCL8. The effect of the ECM proteins was such that CXCL8 secretion by cells cultured on collagen I > collagen IV > fibronectin or laminin-111. However, suppression of ROCK activity resulted in a similar 75 to 85% suppression of CXCL8 secretion regardless of the ECM protein type. This suggests that EC can produce different levels of CXCL8 depending on the type of ECM proteins they attach to, but all cases result in a similar requirement for ROCK activity for optimal CXCL8 secretion. Furthermore, when confluent cells were compared to subconfluent cells, the level of TNF- or IL-1-stimulated CXCL8 secretion was greatly elevated with the subconfluent cells and inhibiting ROCK had no effect on CXCL8 secretion levels by the confluent cells. These experiments suggest that CXCL8 responses by confluent cells, which would model for intact, unwounded epithelial, do not involve ROCK activation. However, CXCL8 responses by subconfluent cells, which would model for cells attaching to and moving on ECM proteins in wounded epithelia, require ROCK activation for greatly elevated CXCL8 responses. These results provide a model to examine the important conditions which regulate chemokine production by EC in wounded epithelia.

Dominant, habitat-forming plant species, such as seagrasses, are key components of coastal ecosystems worldwide. Multiple stressors, including invasive species that directly alter, remove, or replace the foundation plant species, threaten these ecosystems. On the Atlantic coast of North America, ecosystem engineering by invasive European green crab (Carcinus maenas) has been linked to the loss of some eelgrass (Zostera marina) beds. However, the interaction of the same co-occurring species on the Pacific coast has not been investigated. We conducted an enclosure experiment in Barkley Sound, British Columbia, to determine if the engineering impacts of green crabs on Pacific eelgrass ecosystems mirror those previously identified on the Atlantic coast. Eelgrass shoot density declined rapidly over 4 weeks, with a 73–81% greater loss in enclosures with high crab density compared to the low-density and control treatments. The low ratio of eelgrass blades to rhizomes in the high-density treatment suggests that blade shredding, rather than bioturbation of whole plants, was the main mechanism of eelgrass loss. Eelgrass was detected in green crab stomach contents, consistent with observations from the Atlantic coast. Crab density did not have a detectable effect on the biomass or community composition of benthic fauna associated with eelgrass over the duration of the experiment. The eelgrass loss we observed was consistent with losses observed on the Atlantic coast, which raises management concerns on the Pacific coast, particularly in areas where green crabs co-occur with other coastal stressors and with ecologically and economically important species such as salmon.

The widely divergent species 4xTrifolium ambiguum and 2xT.occidentale are inter-fertile long after speciation (including polyploidisation) has occurred. Tri-species hybrids (T. repens × T. ambiguum × T. occidentale) have the potential to achieve introgression of stress resistant traits from both wild species into white clover. Trifolium ambiguum and T. occidentale are geographically, adaptionally and phenotypically contrasting species in the white clover section (Trifoliastrum) of the genus. T. ambiguum occurs as a high-altitude polyploid series (2x, 4x, 6x) in W Asia and NE Europe. T. occidentale is a diploid coastal species, occurring at sea level in W Europe. This study investigated hybridisation between 4xT. ambiguum and 2xT. occidentale and considered the significance of the hybrids for introgression breeding of white clover. Partially fertile F1 hybrids between 4xT. ambiguum and 2x and 4xT. occidentale were generated by embryo rescue. Hybrid plant morphology and fertility varied widely and hybrids generally expressed traits from both species. Advanced generation (F2–F5) 4x hybrids were highly fertile and constitute a new synthetic allotetraploid species. FISH analyses of 4x hybrids showed multivalent chromosome configurations with homoeologous associations between T. ambiguum and T. occidentale chromosomes. Crosses of the hybrids with T. repens produced fertile tri-species progeny. These very divergent species remain inter-fertile long after speciation (including polyploidisation) has occurred. Tri-species hybrids have the potential to achieve introgression of stress resistance traits from both wild species into white clover.

Many successful invasive species have generalist diets, but the extent to which they can track changing resources has seldom been documented. Stable isotope analysis was used to measure dietary shifts with ontogeny and over time in relation to changes in prey availability for Indo-Pacific lionfish (Pterois sp.). These are invasive predators that are well established throughout the western North Atlantic and Caribbean where they have caused significant decreases in native reef fish populations in some areas. Samples and observations were made off New Providence Island, Bahamas during the summers of 2008 and 2010. Lionfish δ15N and δ13C values increased only weakly with body length, suggesting that processes other than growth also contribute to stable isotope variability. The trophic niche of lionfish changed significantly between years, concomitant with large changes in native fish prey abundance and community structure. The trophic niche of large lionfish expanded, increasing in trophic diversity at the population level and showing lower individual trophic similarity, while that of small lionfish remained similar in size but shifted towards more 15N-enriched and 13C-depleted prey sources. The ability of lionfish to modify their diet over time may have facilitated their expansion and persistence at high densities in some areas despite local prey depletion.

Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.

Th17 cells of the intestine and colon can produce several important cytokines during mucosal inflammation. However, few studies have focused on the role of IL-26 in intestinal inflammations. Colonic epithelial cells express receptors for IL-26, and this cytokine has been shown to induce the HT-29 colonic epithelial cell line to produce the chemokine CXCL8. However, epithelial cells would function in a cytokine network environment during mucosal inflammation and any effect of IL-26 on colonic epithelial cell chemokine responses could be affected by the presence of other potent pro-inflammatory cytokines like TNF-α and IL-1. Therefore, we investigated the effect of IL-26 with TNF-α or IL-1 on colonic epithelial cell line secretion of CXCL8. IL-26 alone had no effect on HT-29 or DLD1 cell line CXCL8 secretion. Yet, IL-26 was found to significantly enhance TNF-α-induced, but not IL-1-induced, CXCL8 secretion, but only at high levels of TNF-α. Similar results were seen with DLD1 cells. IL-26 did not enhance TNF-α-induced CXCL8 mRNA levels and did not affect TNF-α-induced IκBα phosphorylation or degradation. However, signaling through ERK and p38 MAPK were determined to be involved in the enhancing effect of IL-26 on the TNF-α-induced CXCL8 secretion, perhaps through known post-translational effects. These results suggest that the role of IL-26 in intestinal inflammation may be limited to enhancing CXCL8 secretion in the presence high levels of TNF-α, such as may occur in inflammatory bowel disease. Abbreviations: DMEM, Dulbecco's Modified Eagle's Medium; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; IBD, inflammatory bowel disease; IL, interleukin; ITS, insulin, transferrin, selenium; TBS, Tris buffered saline; TNF, tumor necrosis factor.

Produced water (PW) from oil and gas extraction processes has been shown to contain elevated concentrations of major ions. The objective of this study was to determine the potential effects of elevated major ions in PW-contaminated surface water on a fish (fathead minnow, Pimephales promelas) and a unionid mussel (fatmucket, Lampsilis siliquoidea) in short-term (7-day) exposures. The test organisms were exposed in 3 reconstituted waters formulated with 1, 2, and 4 times the major ions measured at a PW-contaminated stream site 1 month after a PW spill from an oil production wastewater pipeline in the Williston Basin, North Dakota. A reconstituted water mimicking the ionic composition of an upstream site from the spill was used as a reference water. Significant reductions in survival and growth of the fish were observed in the 4× treatment compared with the reference. The mussels were more sensitive than the fish, with significant reductions in survival in the 2× and 4× treatments, and significant reductions in length in the 1× and 2× treatments. Overall, these results indicate that elevated concentrations of major ions in PW-contaminated surface waters could adversely affect the fish and mussels tested and potentially other aquatic organisms.

Meiosis, the key process underlying sexual reproduction, is generally a fair process: each chromosome has a 50% chance of being included into each gamete. However in some organisms meiosis has become highly aberrant with some chromosomes having a higher chance of making it into gametes than others. Yet why and how such systems evolve remains unclear. Here we study the unusual reproductive genetics of mealybugs, in which only maternal-origin chromosomes are included into the gametes during male meiosis, while paternally-derived chromosomes degrade. This “whole genome meiotic drive” occurs in all males and is evolutionarily conserved. However one species - the obscure mealybug Pseudococcus viburni - has a segregating B chromosome that increases in frequency by escaping paternal genome elimination. Here we present whole-genome and gene expression data from laboratory lines with and without B chromosomes. These data allow us to identify B-linked sequences including >70 protein-coding genes as well as a B-specific satellite repeat that makes up a significant proportion of the chromosome. We also used these data to investigate the evolutionary origin of the B chromosome. The few paralogs between the B and the core genome are distributed throughout the genome, showing that it is unlikely that the B originated through a simple duplication of one of the autosomes. We also find that while many of the B-linked genes do not have paralogs within the P.viburni genome, but they do show orthology with genes in other hemipteran insects suggesting that the B might have originated from fission of one of the autosomes, possibly followed by further translocations of individual genes. Finally in order to understand the mechanisms by which the B is able to escape elimination when paternally-derived we generated gene expression data for males and females with and without B chromosomes. We find that at the developmental stage when meiosis is taking place only a small number of B-linked genes show significant expression. Only one gene was significantly over-expressed during male meiosis, which is when the drive occurs: a acetyltransferase involved in H3K56Ac, which has a putative role in meiosis and is therefore a promising candidate for further studies. Together, these results form a promising foundation for studying the mechanisms of meiotic drive in a system that is uniquely suited for this approach.

Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1 Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between chromosomes (chr.) 7 and 8 resulted in a 5–3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma,” the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.

During secondary growth, forest trees can modify the anatomy of the wood produced by the vascular cambium in response to environmental conditions. Notably, the trees of the model angiosperm genus, Populus, reduce the risk of cavitation and hydraulic failure under water stress by producing water-conducting vessel elements with narrow lumens, which are more numerous and more interconnected with each other. Here, we determined the genetic architecture of vessel traits affecting hydraulic physiology and resilience to water stress. Vessel traits were measured for clonally replicated genotypes of a unique Populus deltoides x nigra population carrying genomically defined insertions and deletions that create gene dosage variation. We found significant phenotypic variation for all traits measured (mean vessel diameter, height-corrected mean vessel diameter, vessel frequency, height-corrected vessel frequency, vessel grouping index, and mean vessel circularity), and that all traits were under genetic control and showed moderate heritability values, ranging from 0.32 to 0.53. Whole-genome scans of correlations between gene dosage and phenotypic traits identified quantitative trait loci for tree height, mean vessel diameter, height-corrected mean vessel diameter, height-corrected vessel frequency, and vessel grouping index. Our results demonstrate that vessel traits affecting hydraulic physiology are under genetic control, and both pleiotropic and trait-specific quantitative trait loci are found for these traits.

The sustainability of many crops is hindered by the lack of genomic resources and a poor understanding of natural genetic diversity. Particularly, application of modern breeding requires high-density linkage maps that are integrated into a highly contiguous reference genome. Here, we present a rapid method for deriving haplotypes and developing linkage maps, and its application to Mentha suaveolens, one of the diploid progenitors of cultivated mints. Using sequence-capture via DNA hybridization to target single nucleotide polymorphisms (SNPs), we successfully genotyped ∼5000 SNPs within the genome of >400 individuals derived from a self cross. After stringent quality control, and identification of nonredundant SNPs, 1919 informative SNPs were retained for linkage map construction. The resulting linkage map defined a total genetic space of 942.17 cM divided among 12 linkage groups, ranging from 56.32 to 122.61 cM in length. The linkage map is in good agreement with pseudomolecules from our preliminary genome assembly, proving this resource effective for the correction and validation of the reference genome. We discuss the advantages of this method for the rapid creation of linkage maps.

A prophylactic vaccine that confers durable protection against human immunodeficiency virus (HIV) would provide a valuable tool to prevent new HIV/AIDS cases. As herpesviruses establish lifelong infections that remain largely subclinical, the use of persistent herpesvirus vectors to deliver HIV antigens may facilitate the induction of long-term anti-HIV immunity. We previously developed recombinant (r) forms of the gamma-herpesvirus rhesus monkey rhadinovirus (rRRV) expressing a replication-incompetent, near-full-length simian immunodeficiency virus (SIVnfl) genome. We recently showed that 8/16 rhesus macaques (RMs) vaccinated with a rDNA/rRRV-SIVnfl regimen were significantly protected against intrarectal (i.r.) challenge with SIVmac239. Here we investigated the longevity of this vaccine-mediated protection. Despite receiving no additional booster immunizations, the protected rDNA/rRRV-SIVnfl vaccinees maintained detectable cellular and humoral anti-SIV immune responses for more than 1.5 years after the rRRV boost. To assess if these responses were still protective, the rDNA/rRRV-SIVnfl vaccinees were subjected to a second round of marginal-dose i.r. SIVmac239 challenges, with eight SIV-naive RMs serving as concurrent controls. After three SIV exposures, 8/8 control animals became infected, compared to 3/8 vaccinees. This difference in SIV acquisition was statistically significant (P = 0.0035). The three vaccinated monkeys that became infected exhibited significantly lower viral loads than those in unvaccinated controls. Collectively, these data illustrate the ability of rDNA/rRRV-SIVnfl vaccination to provide long-term immunity against stringent mucosal challenges with SIVmac239. Future work is needed to identify the critical components of this vaccine-mediated protection and the extent to which it can tolerate sequence mismatches in the challenge virus. IMPORTANCE We report on the long-term follow-up of a group of rhesus macaques (RMs) that received an AIDS vaccine regimen and were subsequently protected against rectal acquisition of simian immunodeficiency virus (SIV) infection. The vaccination regimen employed included a live recombinant herpesvirus vector that establishes persistent infection in RMs. Consistent with the recurrent SIV antigen expression afforded by this herpesvirus vector, vaccinees maintained detectable SIV-specific immune responses for more than 1.5 years after the last vaccination. Importantly, these vaccinated RMs were significantly protected against a second round of rectal SIV exposures performed 1 year after the first SIV challenge phase. These results are relevant for HIV vaccine development because they show the potential of herpesvirus-based vectors to maintain functional antiretroviral immunity without the need for repeated boosting.

The difference in body size between females and males, or sexual size dimorphism (SSD), is almost ubiquitous, and yet we have a remarkably poor understanding of the developmental-genetic mechanisms that generate it. Such an understanding is important if we are to distinguish between the many theoretical models of SSD evolution. One such model is the condition dependence hypothesis, which proposes that the body size of the larger sex is also more environmentally sensitive, a phenomenon called sex-specific plasticity (SSP). Because SSP generates differences in female and male body size, selection on plasticity may underlie the evolution of sexual size dimorphism. To test this hypothesis, however, we need to know the genetic architecture of both SSD and SSP, which is challenging because both are characteristics of populations not individuals. Here, we overcome this challenge by using isogenic lineages of Drosophila to measure both SSD and SSP for a genotype. We demonstrate extensive genetic variation for SSD among genotypes that is tightly correlated with variation in SSP, indicating that the same developmental-genetic mechanisms regulate both phenomena. These data support the condition dependence hypothesis and suggest that the observed SSD is a consequence of selection on the developmental-genetic mechanisms that regulate SSP.

Success and impact metrics in science are based on a system that perpetuates sexist and racist “rewards” by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals’ meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change., This Essay argues that success and impact metrics in science are based on a system that perpetuates sexist and racist ‘rewards’ by prioritizing citations and impact factors; the authors advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion.

Skeletal muscle is a dynamic tissue the size of which can be remodeled through the concerted actions of various cues. Here, we investigated the skeletal muscle transcriptional program and identified key tissue-specific regulatory genetic elements. Our results show that Myod1 is bound to numerous skeletal muscle enhancers in collaboration with the glucocorticoid receptor (GR) to control gene expression. Remarkably, transcriptional activation controlled by these factors occurs through direct contacts with the promoter region of target genes, via the CpG-bound transcription factor Nrf1, and the formation of Ctcf-anchored chromatin loops, in a myofiber-specific manner. Moreover, we demonstrate that GR negatively controls muscle mass and strength in mice by down-regulating anabolic pathways. Taken together, our data establish Myod1, GR and Nrf1 as key players of muscle-specific enhancer-promoter communication that orchestrate myofiber size regulation.

Background Psoriasis is an inflammatory, IL-17–driven skin disease in which autoantigen-induced CD8+ T cells have been identified as pathogenic drivers. Objective Our study focused on comprehensively characterizing the phenotypic variation of CD8+ T cells in psoriatic lesions. Methods We used single-cell RNA sequencing to compare CD8+ T-cell transcriptomic heterogeneity between psoriatic and healthy skin. Results We identified 11 transcriptionally diverse CD8+ T-cell subsets in psoriatic and healthy skin. Among several inflammatory subsets enriched in psoriatic skin, we observed 2 Tc17 cell subsets that were metabolically divergent, were developmentally related, and expressed CXCL13, which we found to be a biomarker of psoriasis severity and which achieved comparable or greater accuracy than IL17A in a support vector machine classifier of psoriasis and healthy transcriptomes. Despite high coinhibitory receptor expression in the Tc17 cell clusters, a comparison of these cells with melanoma-infiltrating CD8+ T cells revealed upregulated cytokine, cytolytic, and metabolic transcriptional activity in the psoriatic cells that differed from an exhaustion program. Conclusion Using high-resolution single-cell profiling in tissue, we have uncovered the diverse landscape of CD8+ T cells in psoriatic and healthy skin, including 2 nonexhausted Tc17 cell subsets associated with disease severity.

Chromoanagenesis is a genomic catastrophe that results in chromosomal shattering and reassembly. These extreme single chromosome events were first identified in cancer, and have since been observed in other systems, but have so far only been formally documented in plants in the context of haploid induction crosses. The frequency, origins, consequences, and evolutionary impact of such major chromosomal remodeling in other situations remain obscure. Here, we demonstrate the occurrence of chromoanagenesis in poplar (Populus sp.) trees produced from gamma-irradiated pollen. Specifically, in this population of siblings carrying indel mutations, two individuals exhibited highly frequent copy number variation (CNV) clustered on a single chromosome, one of the hallmarks of chromoanagenesis. Using short-read sequencing, we confirmed the presence of clustered segmental rearrangement. Independently, we identified and validated novel DNA junctions and confirmed that they were clustered and corresponded to these rearrangements. Our reconstruction of the novel sequences suggests that the chromosomal segments have reorganized randomly to produce a novel rearranged chromosome but that two different mechanisms might be at play. Our results indicate that gamma irradiation can trigger chromoanagenesis, suggesting that this may also occur when natural or induced mutagens cause DNA breaks. We further demonstrate that such events can be tolerated in poplar, and even replicated clonally, providing an attractive system for more in-depth investigations of their consequences., Author summary Plant breeders often use radiation treatment to produce variation, with the goal of identifying new varieties with superior traits. We studied a population of poplar trees produced by gamma irradiation of pollen, and asked what kind of DNA changes were associated with this variation. We found many changes, most often in the form of added (insertions) or removed (deletions) pieces of DNA. We also found two lines with much more drastic changes. In those lines, we observed massive reorganization. We characterized these two lines in detail and found that catastrophic pulverization and random reassembly only occurred on a single chromosome. Looking closely at how the pieces were put back together suggest that the rearrangements in these two lines may have resulted from two slightly different mechanisms. This type of rearrangement is commonly observed in human cancer cells, but has rarely been observed in plants. We demonstrated here that they can be induced by gamma irradiation, indicating this type of event might be more widespread than we expected. Characterizing such genome restructuring instances helps to understand how genome instability can remodel chromosomes and affect genome function.

Sperm RNA can be modified by environmental factors and has been implicated in communicating signals about changes in a father’s environment to the offspring. The RNA composition of sperm is influenced during its final stage of maturation in the epididymis by extracellular vesicles released by epididymal cells. We studied the effect of exposure to stress in postnatal life on the transcriptome of epididymal extracellular vesicles using a mouse model of transgenerational transmission. We found that the small RNA signature of epididymal extracellular vesicles, particularly miRNAs, is altered in adult males exposed to postnatal stress. miRNAs changes correlate with differences in the expression of their target genes in sperm and zygotes generated from that sperm. These results suggest that stressful experiences in early life can have persistent biological effects on the male reproductive tract that may in part be responsible for the transmission of the effects of exposure to the offspring.Summary SentencemiRNA cargo of extracellular vesicles in cauda epididymis is changed by paternal exposure to early life stress, which correlates with differences in the expression of their target genes in sperm and zygotes generated from that sperm

As human impacts increase in coastal regions, there is concern that critical habitats that provide the foundation of entire ecosystems are in decline. Seagrass meadows face growing threats such as poor water quality and coastal development. To determine the status of seagrass meadows over time, we reconstructed time series of meadow area from 175 studies that surveyed 547 sites around the world. We found an overall trajectory of decline in all seven bioregions with a global net loss of 5602 km2 (19.1% of surveyed meadow area) occurring since 1880. Declines have typically been non-linear, with rapid and historical losses observed in several bioregions. The greatest net losses of area occurred in four bioregions (Tropical Atlantic, Temperate North Atlantic East, Temperate Southern Oceans and Tropical Indo-Pacific), with declining trends being the slowest and most consistent in the latter two bioregions. In some bioregions, trends have recently stabilised or reversed. Losses, however, still outweigh gains. Despite consistent global declines, meadows show high variability in trajectories, within and across bioregions, highlighting the importance of local context. Studies identified 12 different drivers of meadow area change, with coastal development and water quality as the most commonly cited. Overall, however, attributions were primarily descriptive and only 10% of studies used inferential attributions. Although ours is the most comprehensive dataset to date, it still represents only one-tenth of known global seagrass extent, with conspicuous historical and geographic biases in sampling. It therefore remains unclear whether the bioregional patterns of change documented here reflect changes in the world's unmonitored seagrass meadows. The variability in seagrass meadow trajectories, and the attribution of change to numerous drivers, suggest we urgently need to improve understanding of the causes of seagrass meadow loss if we are to improve local-scale management.