title: Development of a pest threshold decision support system for minimising damage to winter wheat from wheat bulb fly, Delia coarctata

abstract:
Graphical AbstractIn this article we describe two predictive models that can be used for the integrated management of wheat bulb fly. Our first model is a pest level prediction model and our second model predicts the number of shoots a winter wheat crop will achieve by the terminal spikelet developmental stage. We revise and update current wheat bulb fly damage thresholds and combine this with our two models to devise a tolerance-based decision support system that can be used to minimise the risk of crop damage by wheat bulb fly.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/435242v1_ufig1.gif" ALT="Figure 1">
View larger version (37K):
org.highwire.dtl.DTLVardef@ee5b9aorg.highwire.dtl.DTLVardef@c0197corg.highwire.dtl.DTLVardef@1c9519eorg.highwire.dtl.DTLVardef@d6a52_HPS_FORMAT_FIGEXP  M_FIG C_FIG SummaryWheat bulb fly, Delia coarctata, is an important pest of winter wheat in the UK, causing significant damage of up to 4 t ha-1. Accepted population thresholds for D. coarctata are 250 eggs m-2 for crops sown up to the end of October and 100 eggs m-2 for crops sown from November. Fields with populations of D. coarctata that exceed the thresholds are at higher risk of experiencing economically damaging pest infestations. In the UK, recent withdrawal of insecticides means that only a seed treatment is available for chemical control of D. coarctata, however this is only effective for late-sown crops (November onwards) and accurate estimations of annual population levels are required to ensure a seed treatment is applied if needed. As a result of the lack of post-drilling control strategies, the management of D. coarctata is becoming increasingly reliant on non-chemical methods of control. Control strategies that are effective in managing similar stem-boring pests of wheat include sowing earlier and using higher seed rates to produce crops with more shoots and greater tolerance to shoot damage.

In this study we develop two predictive models that can be used for integrated D. coarctata management. The first is an updated pest level prediction model that predicts D. coarctata populations from meteorological parameters with a predictive accuracy of 70%, which represents a significant improvement on the previous D. coarctata population prediction model. Our second model predicts the maximum number of shoots for a winter wheat crop that would be expected at the terminal spikelet development stage. This shoot number model uses information about the thermal time from plant emergence to terminal spikelet, leaf phyllochron length, plant population, and sowing date to predict the degree of tolerance a crop will have against D. coarctata. The shoot number model was calibrated against data collected from five field experiments and tested against data from four experiments. Model testing demonstrated that the shoot number model has a predictive accuracy of 70%. A decision support system using these two models for the sustainable management of D. coarcata risk is described.

category: plant biology


title: Symmetry processing in the macaque visual cortex

abstract:
Symmetry is a highly salient feature of the natural world that is perceived by many species of the animal kingdom and that impacts a large array of behaviours such as partner selection or food choice. In humans, the cerebral areas processing symmetry are now well identified from neuroimaging measurements. However, we currently lack an animal model to explore the underlying neural mechanisms. Macaque is a potentially good candidate, but a previous comparative study (1) found that functional magnetic resonance imaging (fMRI) responses to mirror symmetry in this species were substantially weaker than those observed in humans under similar experimental conditions. Here, we re-examined symmetry processing in macaques from a broader perspective, using both rotation (experiment 1) and reflection (experiment 2) symmetry. Our experimental design was directly derived from that of a previous human fMRI study (2), in order to facilitate the comparison between the two primate species. Highly consistent responses to symmetry were found in a large network of areas (notably V3, V3A, V4, V4A and PITd), in line with what has been observed in humans. Within this network, response properties in areas V3 and V4 (notably their dependency on the rotation symmetry order) were strikingly similar to those observed in their human counterparts. Our results suggest that the cortical networks that process symmetry in humans and macaques are much more similar than previously reported and point toward macaque as a relevant model for understanding symmetry processing.

Significance statementSymmetry processing is an important aspect of human visual perception. We currently lack an animal model for characterizing the neural mechanisms that underlie it at the microscopic scale. Here, we use fMRI measurements in macaques to demonstrate that the cortical responses to symmetry in this species are comparable to those observed in humans under similar experimental conditions to a much higher extent than previously documented. Our results call for a re-examination of the relevance of the macaque model for symmetry processing in humans and open the door to an exploration of the underlying neural mechanisms at the single-cell level, notably in V3, an area often neglected in most current models of visual processing.

category: neuroscience


title: Integrative Analysis of Sorghum Bicolor Green Prop Roots Under Elevated CO2 and Water Deficit Conditions

abstract: Elevated CO2 (E[CO2]) improves the biomass and yield when combined with water-stress in C4 plants. Although several studies described the molecular response of the C4 plant Sorghum bicolor during drought exposure, none reported its combinatorial effect with E[CO2] in the roots. We decided to perform a molecular analysis using green prop roots, the portion of the radicular system photosynthetically active and more sensible to drought. Whole-transcriptome analysis identified 394 up- and 1,471 down-regulated genes. Among the E[CO2] induced pathways, photosynthesis stood out. Carbon fixation, phenylpropanoid, phenolic compounds, and fatty acid biosynthesis-related pathways were repressed. Protein family analysis showed induction of chlorophyll a-b binding protein family, and repression of glutathione-related enzymes. Protein-protein interaction networks exhibited well-defined clusters, including genes related to cell organization and biogenesis, oxi-reduction process, and photosynthesis being induced. The findings suggest that the E[CO2] mitigates the water deficit by antioxidant and osmoregulation activity, as well as by accumulation of sugar-alcohols in the green prop roots, which may be responsible by the increase in biomass together with the cell proliferation. The higher carbon uptake explains the increase in photosynthetic and primary metabolism activities. Our data revealed that green prop roots present an intriguing metabolism under water deficit and E[CO2], showing its crucial role in the drought tolerance acquisition in a predicted future global atmosphere.

category: molecular biology


title: Idefix: identifying accidental sample mix-ups in biobanks using polygenic scores

abstract:
Structured abstractIdentifying sample mix-ups in biobanks is essential to allow the repurposing of genetic data for clinical pharmacogenetics. Pharmacogenetic advice based on the genetic information of another individual is potentially harmful. Existing methods for identifying mix-ups are limited to datasets in which additional omics data (e.g. gene expression) is available. Cohorts lacking such data can only use sex, which can reveal only half of the mix-ups. Here, we describe Idefix, a method for the identification of accidental sample mix-ups in biobanks using polygenic scores. In the Lifelines population-based biobank we calculated polygenic scores (PGSs) for 25 traits for 32,786 participants. Idefix then compares the actual phenotypes to PGSs and uses the relative discordance that is expected for mix-ups, compared to correct samples.

In a simulation, using induced mix-ups, Idefix reaches an AUC of 0.90 using 25 polygenic scores and sex. This is a substantial improvement over using only sex, which has an AUC of 0.75. Idefix therefore is not yet able to identify every sample mix-up. However, this will likely improve soon, with highly powered GWAS summary statistics that will likely become available for more commonly measured traits.

Nevertheless, Idefix can already be used to identify a high-quality set of participants for whom it is very unlikely that they reflect sample mix-ups, and therefore could be offered a pharmacogenetic passport. For instance, when selecting the 10% of participants for whom predicted phenotypes adhere best to the actually measured phenotypes, we estimate that the proportion of sample mix-ups is reduced 250-fold.

Availability and implementationIdefix is freely available at https://github.com/molgenis/systemsgenetics/wiki/Idefix

Contactl.h.franke@umcg.nl

category: bioinformatics


title: Engaging the complexity of diet and healthy aging in humans

abstract:
Little is known about how normal variation in dietary patterns in humans affects the aging process, largely because both nutrition and the physiology of aging are highly complex and multidimensional. Here, we apply the nutritional geometry framework to data from 1560 older adults followed over four years to assess how nutrient intake patterns affect the aging process. Aging was quantified via blood biomarkers integrated to measure loss of homeostasis. Additionally, we extend nutritional geometry to 19 micronutrients. Salient results include benefits of intermediate protein and vitamin E intake. Broadly, we show that there are few simple answers of "good" or "bad" nutrients - optimal levels are generally intermediate, but dependent on other nutrients. Simpler linear/univariate analytical approaches are insufficient to capture such associations. We present an interactive tool to explore the results, and our approach presents a roadmap for future studies to explore the full complexity of the nutrition-aging landscape.

Impact StatementMultidimensional nutritional analyses reveal how the association between diet and healthy aging is hard to untangle, as most nutrients have non-linear and interactive effects in humans.


title: Non-linearity matters: a deep learning solution to the generalization of hidden brain patterns across population cohorts

abstract: The increasing number of neuroimaging scans in recent years has facilitated the use of complex nonlinear approaches to analyzing such data. More specifically, deep learning, which has been previously hindered by the curse of dimensionality is now feasible. However, it remains challenging to use these techniques develop reliable biomarkers and find an optimal representation of data that explains the biological underpinnings of the mental disorders Here, we employed a 3-dimensional autoencoder with an architecture designed from the ground up for task-fMRI data. Our study presented a coherent strategy for optimizing model parameters and architecture and a method for visualizing, exploring and interpreting the latent space representation. We trained our model with multi-task fMRI data derived from the Human Connectome Project (HCP) that provides whole-brain coverage across a range of cognitive tasks. Next, in a transfer learning setting, we tested the generalization of our latent space on UK Biobank data as an independent dataset. We showed that the model did not only learn salient features such as age but also high-level behavioral characteristics and that this representation was highly generic and generalizable to an independent dataset. Furthermore, we demonstrated that the projection of latent space back into the original space is meaningful and interpretable. Finally, our results show that with careful implementation, nonlinear features can provide complementary information that accessible to purely linear methods. Our results provide an important step toward learning interpretable and generalizable latent representations that link cognition with underlying brain systems.


title: Human AdV-20-42-42, a promising novel adenoviral vector for gene therapy and vaccine product development

abstract:
Pre-existing immune responses towards adenoviral vector limit the use of a vector based on particular serotypes and its clinical applicability for gene therapy and/or vaccination. Therefore, there is a significant interest to vectorize novel adenoviral types that have low seroprevalence in the human population. Here, we describe the discovery and vectorization of a chimeric human adenovirus, which we call HAdV-20-42-42. Full genome sequencing revealed that this virus is closely related to human serotype 42, except for the penton-base which is derived from serotype 20. The HAdV-20-42-42 vector could be propagated stably to high titers on existing E1-complementing packaging cell lines. Receptor binding studies revealed that the vector utilized both CAR and CD46 as receptors for cell entry. Furthermore, the HAdV-20-42-42 vector was potent in transducing human and murine cardiovascular cells and tissues, irrespective of the presence of blood coagulation factor X. In addition, the vector did not sequester in the liver upon intravenous administration in rodents. Finally, we demonstrate that potent T-cell responses against vector-delivered antigens could be induced upon vaccination. In summary, from the data obtained we conclude that HAdV-20-42-42 provides a valuable addition to the portfolio of adenoviral vectors available to develop safe and efficacious products in the fields of gene therapy and vaccination.

IMPORTANCEAdenoviral vectors are currently under investigation for a broad range of therapeutic indications in diverse fields, such as oncology and gene therapy, as well as for vaccination both for human and veterinary use. A wealth of data shows that pre-existing immune responses may limit the use of a vector. Particularly in the current climate of global pandemic, there is a need to expand the toolbox with novel adenoviral vectors for vaccine development. Our data demonstrates that we have successfully vectorized a novel adenovirus serotype with low seroprevalence. The cell transduction data and antigen-specific immune responses induced in vivo demonstrate that this vector is highly promising for the development of gene therapy and vaccine products.

category: immunology


title: Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex

abstract:
Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA-protein crosslinking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3-segment of the product-RNA generated by backtracking extrudes through the RdRp NTP-entry tunnel, that a mismatched nucleotide at the product-RNA 3-end frays and enters the NTP-entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.

Significance StatementThe COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome is replicated and transcribed by its RNA-dependent RNA polymerase (RdRp), which is the target for antivirals such as remdesivir. We use a combination of approaches to show that backtracking (backwards motion of the RdRp on the template RNA) is a feature of SARS-CoV-2 replication/transcription. Backtracking may play a critical role in proofreading, a crucial process for SARS-CoV-2 resistance against many antivirals.

category: biochemistry


title: Clomipramine suppresses ACE2-mediated SARS-CoV-2 entry

abstract: Myocardial damage caused by the newly emerged coronavirus (SARS-CoV-2) infection is one of key determinants of COVID-19 severity and mortality. SARS-CoV-2 entry to host cells are initiated by binding with its receptor, angiotensin converting enzyme (ACE) 2, and the ACE2 abundance is thought to reflect the susceptibility to infection. Here, we found that clomipramine, a tricyclic antidepressant, potently inhibits SARS-CoV-2 infection and metabolic disorder in human iPS-derived cardiomyocytes. Among 13 approved drugs that we have previously identified as potential inhibitor of doxorubicin-induced cardiotoxicity, clomipramine showed the best potency to inhibit SARS-CoV-2 spike glycoprotein pseudovirus-stimulated ACE2 internalization. Indeed, SARS-CoV-2 infection to human iPS-derived cardiomyocytes (iPS-CMs) and TMPRSS2-expressing VeroE6 cells were dramatically suppressed even after treatment with clomipramine. Furthermore, the combined use of clomipramine and remdesivir was revealed to synergistically suppress SARS-CoV-2 infection. Our results will provide the potentiality of clomipramine for the breakthrough treatment of severe COVID-19.

category: pharmacology and toxicology


title: Increased Risk for Cerebral Small Vessel Disease is Associated with Quantitative Susceptibility Mapping in HIV Infected and Uninfected Individuals

abstract: The aim of this study was to assess in the context of cerebral small vessel disease (CSVD), cardiovascular risk factors and white matter hyperintensities (WMHs) were associated with brain tissue susceptibility as measured by quantitative susceptibility mapping (QSM). Given that CSVD is diagnosed by the presence of lacunar strokes, periventricular and deep WMHs, increased perivascular spaces, and microbleeds, we expected that QSM could capture changes in brain tissue due to underlying CSVD pathology. We compared a cohort of 101 HIV-infected individuals (mean age (SD) = 53.2 (10.9) years) with mild to moderate cardiovascular risk scores, as measured by the Reynolds risk score, to 102 age-matched controls (mean age (SD) = 50.3 (15.7) years) with similar Reynold scores. We performed brain MRI to assess CSVD burden by acquiring 3D T1-MPRAGE, 3D FLAIR, 2D T2-TSE, and mGRE for QSM. We found that signs of CSVD are significantly higher in individuals with HIV-infection compared to controls and that WMH volumes are significantly correlated with age and cardiovascular risk scores. Regional QSM was associated with cardiovascular risk factors, age, sex, and WMH volumes but not HIV status. These results suggest that QSM may be an early imaging marker reflective of alterations in brain microcirculation.

category: pathology


title: Independent mechanisms underlie the protective effect of dietary polyunsaturated fatty acid supplementation and G&alphaz deficiency on the early type 1 diabetes phenotype of Non-obese diabetic (NOD) mice

abstract: Non-obese diabetic (NOD) mice deficient in Gz alpha subunit (Gz) are protected from developing hyperglycemia, even with early islet insulitis similar to wild-type mice. Similarly, wild-type (WT) NOD mice are protected from glucose intolerance when fed a diet enriched in eicosapentaneoic acid (EPA). In the beta-cell, Prostaglandin EP3 receptor (EP3), whose primary endogenous ligand is the arachidonic acid (AA) metabolite, prostaglandin E2, is specifically coupled to Gz. In this work, we tested whether dietary EPA supplementation, thereby reducing systemic PGE2 levels, would complement Gz loss in the NOD mouse model. WT and Gz-null NOD mice were fed an AA-enriched diet, EPA-enriched diet, or control diet upon weaning. After 12 weeks of diet feeding, glucose tolerance tests were performed and pancreatic islets and whole pancreas collected for ex vivo analyses, with the longer-term effect of an EPA-enriched diet on splenic T-cell populations quantified via flow cytometry. Our results reveal a polyunsaturated fatty acid-enriched diet, whether AA or EPA, improves wild-type NOD glucose tolerance by the same magnitude as Gz loss, but through almost completely different physiological and cellular mechanisms. Our results shed critical light on future research into novel pharmacological and dietary adjuvant therapies for T1D.

category: physiology


title: Increasing stimulus similarity drives nonmonotonic representational change in hippocampus

abstract: Studies of hippocampal learning have obtained seemingly contradictory results, with manipulations that increase coactivation of memories sometimes leading to differentiation of these memories, but sometimes not. These results could potentially be reconciled using the nonmonotonic plasticity hypothesis, which posits that representational change (memories moving apart or together) is a U-shaped function of the coactivation of these memories during learning. Testing this hypothesis requires manipulating coactivation over a wide enough range to reveal the full U-shape. To accomplish this, we used a novel neural network image synthesis procedure to create pairs of stimuli that varied parametrically in their similarity in high-level visual regions that provide input to the hippocampus. Sequences of these pairs were shown to human participants during high-resolution fMRI. As predicted, learning changed the representations of paired images in the dentate gyrus as a U-shaped function of image similarity, with neural differentiation occurring only for moderately similar images.


title: PD-1 dependent expansion of Amphregulin+FOXP3+ cells is associated with oral immune dysfunction in HIV patients on therapy

abstract:
Residual systemic inflammation and mucosal immune dysfunction persist in people living with HIV (PLWH) despite treatment with combined anti-retroviral therapy (cART), but the underlying immune mechanisms are poorly understood. Here we report an altered immune landscape involving upregulation of TLR- and inflammasome signaling, localized CD4+ T cell hyperactivation, and counterintuitively, an enrichment of CD4+CD25+FOXP3+ regulatory T cells (Tregs) in the oral mucosa of HIV+ patients on therapy. Using human oral tonsil cultures, we found that HIV infection causes an increase in a unique population of FOXP3+ cells expressing PD-1, IFN-{gamma}, Amphiregulin (AREG), and IL-10. These cells persisted even in the presence of the anti-retroviral drug and underwent further expansion driven by TLR-2 ligands and IL-1{beta}. IL-1{beta} also promoted PD-1 upregulation in AKT1 dependent manner. PD-1 stabilized FOXP3 and AREG expression in these cells through a mechanism requiring the activation of Asparaginyl Endopeptidase (AEP). Importantly, these FOXP3+ cells were incapable of suppressing CD4+ T cells in vitro. Concurrently, HIV+ patients harbored higher levels of PD-1, IFN-{gamma}, Amphiregulin (AREG), and IL-10 expressing FOXP3+ cells, which strongly correlated with CD4+ T cell hyperactivation, suggesting an absence of CD4+ T cell regulation in the oral mucosa. Taken together, this study provides insights into a novel mechanism of FOXP3+ cell dysregulation and reveals a critical link in the positive feedback loop of oral mucosal immune activation events in HIV+ patients on therapy.

One Sentence SummaryHIV-induced immune dysfunction in lymphoid and mucosal tissues


title: Embryo Lethality Assay for Evaluating Virulence of Isolates from Bacterial Chondronecrosis with Osteomyelitis in Broilers

abstract:
We used an embryo lethality assay (ELA) to assess virulence for different isolates from cases of bacterial chondronecrosis with osteomyelitis (BCO) in broilers. ELA has been used to measure virulence and lethal dosage of Enterococcus faecalis and Enterococcus cecorum. We hypothesized that ELA could substitute for more laborious and costly assessments of BCO isolate pathogenicity using live birds. We evaluated two different levels of bacteria injected into eggs from layer and commercial broiler embryos. Significant findings include a) Escherichia coli from neighboring farms operated by the same integrator had very different embryo lethality, b) isolate Staphylococcus agnetis 908 had low virulence in ELA, even though this isolate can induce more than 50% BCO lameness, c) Enterococcus cecorum 1415 also had low pathogenicity; even though it was recovered from severe bilateral tibial dyschondroplasia, d) human and chicken isolates of S. aureus had significant pathogenicity, e) virulence for some isolates was highly variable possibly corresponding with quality of the embryos/fertile eggs used, and f) ELA pathogenicity was much lower for our BCO isolates than previous reports which may reflect maternal environment. Overall, ELA virulence and BCO virulence are not always concordant indicating that that ELA may not be an effective measure for assessing virulence with respect to BCO.

ImportanceLameness is among the most significant animal welfare issues in the poultry industry. Bacterial infections are a major cause of lameness and different bacterial species have been obtained from lame broilers. Reliable lab-based assays are required to assess relative virulence of bacteria obtained from lame broilers. Embryo Lethality Assays have been used to compare virulence. Our results suggest that this assay may not be an effective measure of virulence related to lameness.

category: microbiology


title: Efficacy of Anti-Staphylococcal Lysin, LSVT-1701, in Combination with Daptomycin in Experimental Left-Sided Infective Endocarditis Due to Methicillin-Resistant Staphylococcus aureus (MRSA)

abstract: MRSA endovascular infections are frequently recalcitrant to treatment with standard-of-care antibiotics. Anti-staphylococcal phage lysins represent important candidate adjunctive agents against invasive MRSA infections because of both their microbicidal and anti-biofilm properties. We utilized the rabbit model of aortic valve infective endocarditis (using the prototype MRSA strain, MW2) to examine the combined efficacy of the lysin, LSVT-1701, plus daptomycin. LSVT-1701 was given at two dose-regimens (32.5 mg/kg and 50 mg/kg) with different dose-durations (single dose vs daily dose for 2 d vs daily dose for 4 d); daptomycin was given at a sub-lethal daily dose of 4 mg/kg for 4 d to maximize potential synergistic interaction outcomes. The combination of LSVT-1701 plus daptomycin was highly effective at reducing target tissue MRSA counts (cardiac vegetations, kidneys, and spleen), especially when the lysin was given for multiple days and/or at higher daily doses. Of importance, when given for four daily doses, both lysin dose-regimens in combination with daptomycin sterilized all target tissues. These findings suggest that LSVT-1701 warrants further clinical evaluation as adjunctive therapy for the treatment of invasive MRSA infections.


title: Changes and composition of microbial community during aerobic composting of household food waste

abstract:
In order to explore the effect of added bacteria on microbial community and determine the dominant bacteria in the aerobic composting process of household food waste (HFW), two groups of HFW composting experiments were conducted for 30 days. The final degradation rates of the two groups were 69.95% (group A, natural composting) and 73.52% (Group C, composting with added bacteria), respectively. 16S rRNA high-throughput sequencing was used to analyze the changes of microbial community in the composting process. As the result displays, at the classification of phylum level, the relatively abundant bacteria of two groups were Firmicutes, Proteobacteria and Cyanobacteria. At the classification of genus level, Pediococcus is the dominant bacteria of group A, which performed better in maintaining the microbial community stable in the later stage of composting, while Weissella accounted for a relatively large proportion of group C and behaved well in promoting the final degradation rate of composting. The proportion of Ochrobactrum in the early stage of group C is considerable and it is closely related to the removal of odour during composting. The relative abundance of added bacteria was always in a rather low level, suggested that the way they affect the composting process is to change the proportion of dominant bacteria in different stage of composting. This experiment provides an important reference for improving the microbial degradation efficiency of HFW.

IMPORTANCEIn recent years, food waste has gradually become a global problem, the annual waste of food is as high as 1.3 billion tons. FW, especially HFW, as a high content of organic matter waste, has a pretty good recycling value. So how to deal with and recycle it efficiently, quickly and conveniently becomes more and more important. Among many treatment and recovery methods, microbial treatment (including anaerobic digestion and aerobic composting) has gradually become a research hotspot due to its advantages of low pollution and low energy consumption, and microorganisms play a crucial role in these process.

In this study we use 16S rRNA high-throughput sequencing method to explore aerobic composting of HFW. The purpose of this study is to find out the dominant bacteria which can improve the degradation efficiency, remove the odor and prolong the treatment cycle, and then provide further theoretical reference for future HFW related research.


title: Age-related increase in matrix stiffness downregulates α-Klotho in chondrocytes and induces cartilage degeneration

abstract: Enhanced mechanistic insight into age-related knee osteoarthritis (KOA) is an essential step to promote successful translation of animal research to bedside interventions. To this end, the goal of these studies was to interrogate molecular mechanisms driving age-related KOA in a mouse model and correspond findings to human knee cartilage. Unbiased mass spectrometry proteomics of cartilage tissue revealed PI3K/Akt signaling was the predominant pathway disrupted over time in male, but not female, mice. This finding was consistent with a significantly accelerated KOA progression in males when compared to female counterparts. In probing for upstream regulators of these age-dependent alterations, we found that -Klotho, a suppressor of PI3K/Akt signaling and potent longevity protein, significantly decreased with aging in both mouse and human knee cartilage. Upstream of these alterations, we found that age-related increases in matrix stiffness initiated a cascade of altered nuclear morphology and downregulated -Klotho expression, ultimately impairing chondrocyte health. Conversely, reducing matrix stiffness increased -Klotho expression in chondrocytes, thus enhancing their chondrogencity and cartilage integrity. Collectively, our findings establish a novel mechanistic link between age-related alterations in ECM biophysical properties and regulation of cartilage health by -Klotho.


title: A Creb3-Like Transcription Factor Coordinates ER Function uponFood Intake to Regulate Lipid Metabolism

abstract: Ingestion of nutrients elicits essential physiological responses, including absorption, digestion, cessation of feeding and nutrient storage. The endoplasmic reticulum (ER) is central to this nutritional homeostasis, since it regulates intracellular organelle function, drives intercellular communication and promotes metabolite distribution. We identified the Drosophila Creb3L-family transcription factor, CrebA, as the key metabolic regulator of ER function, thereby affecting lipid metabolism and feeding behavior. In response to feeding, CrebA activity is rapidly and transiently activated. CrebA directly drives the expression of the ER protein sorting machinery. We demonstrate that CrebA levels regulate lipid metabolism through lipoprotein secretion into the hemolymph and suppress feeding behavior. Further, CrebA mouse homologs are also upregulated in the liver following feeding and drive the transcriptional activation of ER protein sorting machinery genes in mammals. Our results reveal an evolutionarily conserved transcription switch which is turned on in response to food ingestion and orchestrates a negative feedback loop that promotes satiety by regulating ER function and protein secretion.

category: cell biology


title: Svep1 stabilizes developmental vascular anastomosis in reduced flow conditions.

abstract: We report the discovery that flow and Svep1 are modulator of vessel anastomosis during developmental angiogenesis in zebrafish embryos. We show that loss of Svep1 and blood flow reduction both contribute to defective anastomosis of intersegmental vessels. We show that this defect in primary angiogenic sprouts is associated with an expansion of Apelin-positive tip cells and with reduced formation and lumenisation of the dorsal longitudinal anastomotic vessel. Mechanistically, our results suggest that flow and Svep1 act synergistically to modulate vascular network formation in the zebrafish trunk.

category: developmental biology


title: Intergenerational niche differentiation in filmy ferns (Hymenophyllaceae)

abstract: Desiccation tolerance was a key trait that allowed plants to colonize land. However, little is known about the transition from desiccation tolerant non-vascular plants to desiccation sensitive vascular ones. Filmy ferns (Hymenophyllaceae) represent a useful system to investigate how water-stress strategies differ between non-vascular and vascular stages within a single organism because they have vascularized sporophytes and nonvascular gametophytes that are each capable of varying degrees of desiccation tolerance. To explore this, we surveyed sporophytes and gametophytes of 19 species (22 taxa including varieties) of filmy ferns on Moorea (French Polynesia) and used chlorophyll fluorescence to measure desiccation tolerance and light responses. We conducted phylogenetically informed analyses to identify differences in physiology between life stages and growth habits. Gametophytes had similar or less desiccation tolerance (ability to recover from 2 d desiccation at -86 MPa) and lower photosynthetic optima (maximum electron transport rate of photosystem II and light level at 95% of that rate) than sporophytes. Epiphytes were more tolerant of desiccation than terrestrial species in both life stages. Despite their lack of greater physiological tolerances, gametophytes of several species occurred over a wider elevational range than conspecific sporophytes. Our results demonstrate that filmy fern gametophytes and sporophytes differ in their physiology and niche requirements, and point to the importance of microhabitat in shaping the evolution of water-use strategies in vascular plants.

category: ecology


title: Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae)


title: Accurate analysis of short read sequencing in complex genomes: A case study using QTL-seq to target blanchability in peanut (Arachis hypogaea)

abstract: Next Generation sequencing was a step change for molecular genetics and genomics. Illumina sequencing in particular still provides substantial value to animal and plant genomics. A simple yet powerful technique, referred to as QTL sequencing (QTL-seq) is susceptible to high levels of noise due to ambiguity of alignment of short reads in complex regions of the genome. This noise is particularly high when working with polyploid and/or outcrossing crop species, which impairs the efficacy of QTL-seq in identifying functional variation. By filtering loci based on the optimal alignment of short reads, we have developed a pipeline, named Khufu, that substantially improves the accuracy of QTL-seq analysis in complex genomes, allowing de novo variant discovery directly from bulk sequence. We first demonstrate the pipeline by identifying and validating loci contributing to blanching percentage in peanut using lines from multiple related populations. Using other published datasets in peanut, Brassica rapa, Hordeum volgare, Lactua satvia, and Felis catus, we demonstrate that Khufu produces more accurate results straight from bulk sequence. Khufu works across species, genome ploidy level, and data types. In cases where identified QTL were fine mapped, the fine mapped region corresponds to the top of the peak identified by Khufu. The accuracy of Khufu allows the analysis of population sequencing at very low coverage (<3x), greatly decreasing the amount of sequence needed to genotype even the most complex genomes.

category: genomics


title: Hydroxyl-radical scavenging activity of hydrogen does not significantly contribute to its biological function

abstract: Since Ohsawa et al. reported a biological antioxidant function of hydrogen in 2007, researchers have now shown it to exert protective effects in a wide range of human and animal disease models. Clinical observations and scientific arguments suggest that a selective scavenging property of H2 cannot adequately explain the beneficial effects of hydrogen. However, there is no experiment challenging the original published data, which suggested that molecular hydrogen dissolved in solution reacts with hydroxyl radicals in cell-free systems. Here we report that a hydrogen-saturated solution (0.6 mM) did not significantly reduce hydroxyl radicals in the Fenton system using 1 mM H2O2. We replicated the same condition as Ohsawas study (i.e. 5 {micro}M H2O2), and observed a decrease in *OH radicals in both the H2-rich and N2-rich solutions, which may be caused by a decreased dissolved oxygen concentration. Finally, we determined the effect of hydrogen on a high-valence iron enzyme, horseradish peroxidase (HRP), and found that hydrogen could directly increase HRP activity in a dose-dependent manner. Overall, these results indicate that although H2 and *OH can react, the reaction rate is too low to have physiological function. The target of hydrogen is more complex, and its interaction with enzymes or other macro-molecules deserve more attention and in-depth study.


title: MCKAT, a multi-dimensional copy numbervariant kernel association test

abstract:
BackgroundCopy number variants (CNVs) are the gain or loss of DNA segments in the genome. Studies have shown that CNVs are linked to various disorders, including autism, intellectual disability, and schizophrenia.

Consequently, the interest in studying a possible association of CNVs to specific disease traits is growing. However, due to the specific multi-dimensional characteristics of the CNVs, methods for testing the association between CNVs and the disease-related traits are still underdeveloped. We propose a novel multi-dimensional CNV kernel association test (MCKAT) in this paper. We aim to find significant associations between CNVs and disease-related traits using kernel-based methods.

ResultsWe address the multi-dimensionality in CNV characteristics. We first design a single pair CNV kernel, which contains three sub-kernels to summarize the similarity between two CNVs considering all CNV characteristics. Then, aggregate single pair CNV kernel to the whole chromosome CNV kernel, which summarizes the similarity between CNVs in two or more chromosomes. Finally, the association between the CNVs and disease-related traits is evaluated by comparing the similarity in the trait with kernel-based similarity using a score test in a random effect model. We apply MCKAT on genome-wide CNV datasets to examine the association between CNVs and disease-related traits, which demonstrates the potential usefulness the proposed method has for the CNV association tests. We compare the performance of MCKAT with CKAT, a uni-dimensional kernel method. Based on the results, MCKAT indicates stronger evidence, smaller p-value, in detecting significant associations between CNVs and disease-related traits in both rare and common CNV datasets.

ConclusionA multi-dimensional copy number variant kernel association test can detect significantly associated CNVs with any disease-related trait. MCKAT can help biologists detect significantly associated CNVs with any disease-related trait across a patient group instead of examining the CNVs case by case in each subject.


title: Folds induced by multiple parallel or antiparallel double-helices: (pseudo)knotting of single-stranded RNA.

abstract: We develop tools to explore and catalogue the topologies of knotted or pseudoknotted circular folds due to secondary and tertiary interactions within a closed loop of RNA which generate multiple double-helices due (for example) to strand complementarity. The fold topology is captured by a  contracted fold which merges helices separated by bulges and removes hairpin loops. Contracted folds are either trivial or pseudoknotted. Strand folding is characterised by a rigid-vertex  polarised strand graph, whose vertices correspond to double-helices and edges correspond to strands joining those helices. Each vertex has a plumbline whose polarisation direction defines the helical axis. That polarised graph has a corresponding circular ribbon diagram and canonical alphanumeric fold label. Key features of the  fully-flagged fold are the arrangement of complementary domains along the strand, described by a numerical bare fold label, and a pair of binary  flags: a parity flag that specifies the twist in each helix (even or odd half-twists), and an orientation flag that characterises each double-helix as parallel or antiparallel. A simple algorithm is presented to translate an arbitrary fold label into a polarised strand graph. Any embedding of the graph in 3-space is an admissible fold geometry; the simplest embeddings minimise the number of edge-crossings in a planar graph drawing. If that number is zero, the fold lies in one of two classes: (a)-type  relaxed folds, which contain conventional junctions and (b)-type folds whose junctions are described as meso-junctions in H. Wang and N.C. Seeman, Biochem, vol. 34, pp920-929. (c)-type folds induce polarised strand graphs with edge-crossings, regardless of the planar graph drawing. Canonical fold labelling allows us to sort and enumerate all  semi-flagged folds with up to six contracted double-helices as windings around the edges of a graph-like fold skeleton, whose cyclomatic number - the  fold genus - ranges from 0 - 3, resulting in a pair of duplexed strands along each skeletal edge. Those semi-flagged folds admit both even and odd double-helical twists. Appending specific parity flags to those semi-flagged folds gives fully-flagged (a)-type folds, which are also enumerated up to genus-3 cases. We focus on all-antiparallel folds, characteristic of conventional ssRNA and enumerate all distinct (a), (b) and (c)-type folds with up to five double-helices. Those circular folds lead to pseudoknotted folds for linear ssRNA strands. We describe all linear folds derived from (a) or (b)-type circular folds with up to four contracted double-helices, whose simplest cases correspond to so-called H, K and L pseudoknotted folds, detected in ssRNA. Fold knotting is explored in detail, via constructions of so-called antifolds and isomorphic folds. We also tabulate fold knottings for (a) and (b)-type folds whose embeddings minimise the number of edge-crossings and outline the procedure for (c)-type folds. The inverse construction - from a specific knot to a suitable nucleotide sequence - results in a hierarchy of knots. A number of specific alternating knots with up to 10 crossings emerge as favoured fold designs for ssRNA, since they are readily constructed as (a)-type all-antiparallel folds.

category: biophysics


title: Primordial capsid and spooled ssDNA genome structures penetrate ancestral events of eukaryotic viruses

abstract: Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the ssDNA viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus, Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.3 [A] resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold, but has additional unique features; a third {beta}-sheet and a long C-terminal tail. Further, low-resolution reconstructions of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organisation.


title: A Serpin27A-dependent Toll Signaling Underlies Host Genetics of Cancer Resistance in Drosophila

abstract: Cancer resistance varies amongst individuals, although its host genetic underpinnings remain largely elusive. Remissions of sarcomas were first reported following repeated injections of patients with mixtures of killed bacteria--Coleys toxins--a phenomenon, which was subsequently causally traced to induction of innate immunity. Here we reveal remission of Drosophila epithelial neoplasms by genetically triggered host innate immunity via Toll signaling. These neoplasms display capacities to receive and, in rare instances, induce Toll signaling. A tumor-induced and progressive Toll signaling, however, did not culminate in tumor suppression. By contrast, Drosophila hosts heterozygous for spn27A1 mutation, which constitutively produce activated Toll ligand, SpzAct, displayed comprehensive tumor remission via Toll-induced, NF-{kappa}B-mediated, tumor cell death. Our results reveal a novel node of host genetic cancer resistance via serpin-dependent Toll signaling.

category: cancer biology


title: In Vitro Assessment of Efficacy and Cytotoxicity of Prunus africana Extracts on Prostate Cancer C4-2 Cells

abstract: Phenolic compounds are products of secondary plant metabolism known for their biological activity including their antimicrobial, antioxidant, analgesic, stimulant, anti- carcinogenic, and aphrodisiac properties. The main objective of this study was to assess the potency/cytotoxic effects of Prunus africana extracts on prostate cancer cells in vitro. Using different concentrations of P. africana extracts, prostate cancer C4-2 cells, a hormonally insensitive subline of LNCaP cells, were treated in a proliferation assay. A concentration dependent inhibition of cell growth in cells treated with P. africana bark and root extracts was present from days 1 through 3 of incubation, with the methanol extract of the bark showing the strongest effect. Compared to other plant parts, leaf extracts were significantly less cytotoxic at the same concentrations. As C4-2 cells are hormonally insensitive and designed to mimic advanced prostate cancer, crude extracts of P. africana are a possible treatment option, not only for hormone sensitive prostate cancer, but also advanced, hormonally insensitive prostate cancer.


title: Updating the steady state model of C4 photosynthesis

abstract:
C4 plants play a key role in world agriculture. For example, C4 crops such as maize and sorghum are major contributors to both first and third world food production and the C4 grasses sugarcane; miscanthus and switchgrass are major plant sources of bioenergy. In the challenge to manipulate and enhance C4 photosynthesis, steady state models of leaf photosynthesis provide and important tool for gas exchange analysis and thought experiments that can explore photosynthetic pathway changes. Here the C4 photosynthetic model by von Caemmerer and Furbank (1999) has been updated with new kinetic parameterisation and temperature dependencies added. The parameterisation was derived from experiments on the C4 monocot, Setaria viridis, which for the first time provides a cohesive parametrisation. Mesophyll conductance and its temperature dependence have also been included, as this is an important step in the quantitative correlation between the initial slope of the CO2 response curve of CO2 assimilation and in vitro PEP carboxylase activity. Furthermore, the equations for chloroplast electron transport have been updated to include cyclic electron transport flow and equations have been added to calculate electron transport rate from measured CO2 assimilation rates.

HighlightThe C4 photosynthesis model by von Caemmerer and Furbank (1999) has been updated. It now includes temperature dependencies and equations to calculate electron transport rate from measured CO2 assimilation rates.


title: A completely resolved phylogenetic tree of British spiders

abstract: The recent accumulation of increasingly densely sampled phylogenetic analyses of spiders has greatly advanced our understanding of evolutionary relationships within this group. Here, this diverse literature is reviewed and combined with earlier morphological analyses in an attempt to reconstruct the first fully resolved phylogeny for the spider fauna of the British Isles. The resulting tree highlights parts of the group where data are still too limited for a confident assessment of relationships, proposes a number of deviations from previously suggested phylogenetic hypotheses, and can serve as a framework for evolutionary and ecological interpretations of the biology of British spiders, as well as a starting point for future studies on a larger geographical scale.

category: zoology


title: Selective Corticofugal Modulation on Sound Processing in Auditory Thalamus of Awake Marmosets

abstract: Cortical feedback has long been considered crucial for modulation of sensory processing. In the mammalian auditory system, studies have suggested that corticofugal feedback can have excitatory, inhibitory, or both effects on the response of subcortical neurons, leading to controversies regarding the role of corticothalamic influence. This has been further complicated by studies conducted under different brain states. In the current study, we used cryo-inactivation in the primary auditory cortex (A1) to examine the role of corticothalamic feedback on medial geniculate body (MGB) neurons in awake marmosets. The primary effects of A1 inactivation were a frequency-specific decrease in the auditory response of MGB neurons coupled with an increased spontaneous firing rate, which together resulted in a decrease in the signal-to-noise ratio. In addition, we report for the first-time that A1 robustly modulated the long-lasting sustained response of MGB neurons which changed the frequency tuning after A1 inactivation, e.g., neurons with sharp tuning increased tuning bandwidth whereas those with broad tuning decreased tuning bandwidth. Taken together, our results demonstrate that corticothalamic modulation in awake marmosets serves to enhance sensory processing in a way similar to center-surround models proposed in visual and somatosensory systems, a finding which supports common principles of corticothalamic processing across sensory systems.


title: Crosstalk between enterocytes and innate lymphoid cells drives early IFN-g-mediated control of Cryptosporidium

abstract: The intestinal parasite, Cryptosporidium, is a major contributor to global child mortality and causes opportunistic infection in immune deficient individuals. Innate resistance to Cryptosporidium, which specifically invades enterocytes, is dependent on the production of IFN-{gamma}, yet whether enterocytes contribute to parasite control is poorly understood. In this study, utilizing the natural mouse pathogen, Cryptosporidium tyzzeri, we show that epithelial-derived IL-18 synergized with IL-12 to stimulate innate lymphoid cell (ILC) production of IFN-{gamma}. This innate IFN-{gamma} was required for early parasite control. Loss of STAT1 in enterocytes, but not dendritic cells or macrophages, antagonized early parasite control. Transcriptional profiling of enterocytes from infected mice identified an IFN-{gamma} signature and enrichment of anti-microbial effectors like IDO, GBP and IRG. Deletion experiments identified a role for Irgm1/m3 in parasite control. Thus, enterocytes promote ILC production of IFN-{gamma} that acts on enterocytes to restrict the growth of C. tyzzeri.


title: Discovery of viral myosin genes with complex evolutionary history within plankton

abstract: Nucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Interestingly, these genes were often accompanied by kinesin genes in the environmental genomes, suggesting a role of these viral proteins in the intracellular viral particle transport. Phylogenetic analyses indicate that most viral myosins (named "virmyosins") belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host.


title: RNA-BINDING PROTEINS DIRECT MYOGENIC CELL FATE DECISIONS

abstract: RNA-binding proteins (RBPs) are essential for skeletal muscle regeneration and RBP dysfunction causes muscle degeneration and neuromuscular disease. How ubiquitously expressed RBPs orchestrate complex tissue regeneration and direct cell fate decisions in skeletal muscle remains poorly understood. Single cell RNA-sequencing of regenerating skeletal muscle reveals that RBP expression, including numerous neuromuscular disease-associated RBPs, is temporally regulated in skeletal muscle stem cells and correlates to stages of myogenic differentiation. By combining machine learning with RBP engagement scoring, we discover that the neuromuscular disease associated RBP Hnrnpa2b1 is a differentiation-specifying regulator of myogenesis controlling myogenic cell fate transitions during terminal differentiation. The timing of RBP expression specifies cell fate transitions by providing a layer of post-transcriptional regulation needed to coordinate stem cell fate decisions during complex tissue regeneration.


title: Heat wave event facilitates defensive responses in invasive C3 plant Ambrosia artemisiifolia L. under elevated CO2 concentration to the detriment of insect herbivores

abstract: To predict and mitigate the effects of climate change on communities and ecosystems, the joint effects of extreme climatic events on species interactions need to be understood. Using the common ragweed (Ambrosia artemisiifolia L.)--leaf beetle (Ophraella communa) system, we investigated the effects of heat wave and elevated CO2 on common ragweed growth, secondary metabolism, and the consequent impacts on the beetle. The results showed that elevated CO2 and heat wave facilitated A. Artemisiifolia growth; further, A. artemisiifolia accumulated large amounts of defensive secondary metabolites. Being fed on A. artemisiifolia grown under elevated CO2 and heat wave conditions resulted in the poor performance of O. communa (high mortality, long development period, and low reproduction). Overall, under elevated CO2, heat wave improved the defensive ability of A. artemisiifolia against herbivores. This implies that heat wave event will relieve harm of A. artemisiifolia to human under elevated CO2. On the other hand, super adaptability to climatic changes may aggravate invasive plant distribution, posing a challenge to the control of invasive plants in the future.


title: Massively parallel characterization of CYP2C9 variant enzyme activity and abundance

abstract: CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect patient response leading to an increased risk of hemorrhage. We developed Click-seq, a pooled yeast-based activity assay to test thousands of variants. Using Click-seq, we measured the activity of 6,142 missense variants expressed in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants expressed in a human cell line using Variant Abundance by Massively Parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity, and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.


title: Fracture Mechanics of Human Blood Clots: Measurements of Toughness and Critical Length scales

abstract: Blood coagulates to plug vascular damage and stop bleeding, and thus the function of blood clots in hemostasis depends on their resistance against rupture (toughness). Despite the significance, fracture mechanics of blood clots remains largely unexplored, particularly the measurements of toughness and critical length scales governing clot fracture. Here, we study the fracture behavior of human whole blood clots and platelet-poor plasma clots. The fracture energy of whole blood clots and platelet-poor plasma clots determined using modified lap-shear method is 5.90{+/-}1.18 J/m2 and 0.96{+/-}0.90 J/m2, respectively. We find that the measured toughness is independent of the specimen geometry and loading conditions. These results reveal a significant contribution of blood cells to the clot fracture, as well as the dissipative length scale and nonlinear elastic length scale governing clot fracture.

category: bioengineering


title: Paired feed-forward excitation with delayed inhibition allows high frequency computations across brain regions

abstract: The transmission of high-frequency temporal information across brain regions is critical to perception, but the mechanisms underlying such transmission remain unclear. Long-range projection patterns across brain areas are often comprised of paired feedforward excitation followed closely by delayed inhibition, including the thalamic triad synapse, thalamic projections to cortex, and projections within hippocampus. Previous studies have shown that these joint projections produce a shortened period of depolarization, sharpening the timing window over which the postsynaptic neuron can fire. Here we show that these projections can facilitate the transmission of high-frequency computations even at frequencies that are highly filtered by neuronal membranes. This temporal facilitation occurred over a range of synaptic parameter values, including variations in synaptic strength, synaptic time constants, short-term synaptic depression, and the delay between excitation and inhibition. Further, these projections can coordinate computations across multiple network levels, even amid ongoing local activity. We suggest that paired feedforward excitation and inhibition provides a hybrid signal - carrying both a value and a clock-like trigger - to allow circuits to be responsive to input whenever it arrives.

category: neuroscience


title: A potential clue for the application of prime editing in tomato, a dicot plant

abstract: Precision genome editing is highly desired for crop improvement. The recently emerged CRISPR/Cas technology offers great potential applications in precision plant genome engineering. A prime editing (PE) approach combining a reverse transcriptase (RT) with a Cas9 nickase and a "priming" extended guide RNA has shown a high frequency for precise genome modification in mammalian cells and several plant species. Nevertheless, the applications of the PE approach in dicot plants are still limited and inefficient. We designed and tested prime editors for precision editing of a synthetic sequence in a transient assay and for desirable alleles of 10 loci in tomato by stable transformation. Our data obtained by targeted deep sequencing also revealed only low PE efficiencies in both the tobacco and tomato systems. Further assessment of the activities of the PE components uncovered potential reasons for the inefficiency of the PE complexes. Modifying the pegRNA sequences by shortening or introducing mismatches to the primer binding sequences (PBS) in order to reduce their melting temperatures (Tm) did not enhance the PE efficiency at the SlBMP21, SlALC and SlALS1 loci. Our data show challenges of PE approach in tomato, indicating a further improvement of the PE system for the successful applications such as use of improved expression systems. Our work provides an important clue for the successful application of the PE approach in crop improvement.

category: molecular biology


title: The obstacles and potential clues of prime editing applications in tomato, a dicot plant

category: synthetic biology


title: Gene body methylation mediates epigenetic inheritance of plant traits

abstract: Genetic variation is regarded as a prerequisite for evolution. Theoretical models suggest epigenetic information inherited independently of DNA sequence can also enable evolution. However, whether epigenetic inheritance mediates phenotypic evolution in natural populations is unknown. Here we show that natural epigenetic DNA methylation variation in gene bodies regulates genes expression, and thereby influences the natural variation of complex traits in Arabidopsis thaliana. Notably, the effects of methylation variation on phenotypic diversity and gene expression variance are comparable with those of DNA sequence polymorphism. We also identify methylation epialleles in numerous genes associated with environmental conditions in native habitats, suggesting that intragenic methylation facilitates adaptation to fluctuating environments. Our results demonstrate that methylation variation fundamentally shapes phenotypic diversity in natural populations and provides an epigenetic basis for adaptive Darwinian evolution independent of genetic polymorphism.

category: evolutionary biology


title: Epigenetic inheritance mediates phenotypic diversity in natural populations


title: Rootstocks influence the response of ripening grape berries to leafroll associated viruses

abstract: Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms with varying severity. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study identified several molecular levers that participate in responses to GLRaVs, including those that are condition-dependent. This included describing common responses to GLRaVs that were reproduced in two consecutive years, in plants grafted to different rootstocks, and in more than one infection condition. Though different infections were inconsistently distinguishable from one another overall, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of pathogen detecting genes, increases in abscisic acid signaling and cytoskeleton remodeling gene expression. The abundance of abscisic acid (ABA), related metabolites, ABA and hormone signaling-related gene expression, and the expression of several transcription factor families differentiated rootstocks overall. These data show that rootstock influences the effect of GLRaVs in ripening berries.

category: plant biology


title: A population of neurons that produce hugin and express the diuretic hormone 44 receptor gene projects to the corpora allata in Drosophila melanogaster

abstract: The corpora allata (CA) are essential endocrine organs that biosynthesize and secrete the sesquiterpenoid hormone, namely juvenile hormone (JH), to regulate a wide variety of developmental and physiological events in insects. Previous studies had demonstrated that the CA are directly innervated with neurons in many insect species, implying the innervations to be important for regulating JH biosynthesis in response to internal physiology and external environments. While this is also true for the model organism, Drosophila melanogaster, which neurotransmitters are produced in the CA-projecting neurons are yet to be clarified. In this study on D. melanogaster, we aimed to demonstrate that a subset of neurons producing the neuropeptide hugin, the invertebrate counterpart of the vertebrate neuromedin U, directly projects to the adult CA. A synaptic vesicle marker in the hugin neurons was observed at their axon termini located on the CA, which were immunolabeled with a newly-generated antibody to the JH biosynthesis enzyme JH acid O-methyltransferase (JHAMT). We also found the CA-projecting hugin neurons to likely express a gene encoding the specific receptor for diuretic hormone 44 (Dh44). Moreover, our data suggested that the CA-projecting hugin neurons have synaptic connections with the upstream neurons producing Dh44. To the best of our knowledge, this is the first study to identify a specific neurotransmitter of the CA-projecting neurons in D. melanogaster, and to anatomically characterize a neuronal pathway of the CA-projecting neurons and their upstream neurons.


title: Evaluation of UV-A LED technology on the reduction of spiked aflatoxin B1 and aflatoxin M1 in whole milk: toxicity analysis using liver hepatocellular cells

abstract: The effectiveness of a UV-A light emitting diode system (LED) to reduce the concentrations of aflatoxin B1, aflatoxin M1 (AFB1, AFM1) in whole milk (WM) was investigated. Irradiation experiments were conducted using an LED system operating at 365 nm. Known concentrations of aflatoxins were spiked in WM and irradiated at quantified UV doses which was calculated based on the average volumetric intensity. LC-MS/MS product ion scans were used to identify and semi-quantify photodegraded products of AFB1 and AFM1. It was observed that UV irradiation significantly reduced aflatoxins in WM, p<0.05. In comparison to control, the maximum UV-A exposure reduced AFB1 and AFM1 concentrations to 78.2 {+/-} 2.36 % (at 836 mJ/cm2) and 65.7 {+/-} 1.65% (at 857 mJ/cm2), respectively. In cell culture studies, our results demonstrated that the increase of UV-A dosage decreased the aflatoxins-induced cytotoxicity in HepG2 cells, and no significant aflatoxin-induced cytotoxicity was observed at highest given UV-A irradiation of 777 (AFB1), 838 (AFM1), and 746 (total AFs) mJ/cm2. Sensory quality of product, cytotoxicity, and mutagenicity of UV exposed aflatoxins in WM using animal models is warranted in the future.


title: Cell cycle-independent integration of stress signals promotes Non-G1/G0 cellular quiescence

abstract: Cellular quiescence is a non-proliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial upregulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside of G1/G0.


title: Cell cycle-independent integration of stress signals promotes Non-G1/G0 quiescence entry


title: Evaluation of the OsTIR1 and AtAFB2 AID systems for chromatin protein degradation in mammalian cells

abstract: Auxin-inducible degron (AID) system is a promising tool for dynamic protein degradation. In mammalian cells, this approach has become indispensable to study fundamental molecular functions, such as replication, chromatin dynamics or transcription, that are otherwise difficult to dissect. We present evaluation of the two prominent AID systems based on OsTIR1 and AtAFB2 auxin receptor F-box proteins (AFBs). We analyzed degradation dynamics of cohesin/condensin complexes subunits in mouse embryonic stem cells (mRad21, mSMC2, mCapH, mCapH2) and human haploid HAP1 line (hRad21, hSMC2). Double antibiotic selection helped to achieve high homozygous AID targeting efficiency for all genes, ranging from 11 to 77%. We found that the main challenge for successful protein degradation is obtaining cell clones with high and stable AFB expression levels due to mosaic expression of AFBs, which also tends to decline with passages in the absence of constant puromycin selection, even at the AAVS1 safe-harbor locus. Comparing two AFBs, we found that OsTIR1 system showed weak dynamics of protein degradation. At the same time, AtAFB2 approach was very efficient even in random integration. Other factors such as degradation dynamics and low basal depletion were also in favor of AtAFB2 system. Our main conclusion is that repeated addition of puromycin to culture medium prevents AtAFB2 silencing and restores auxin sensitivity, facilitating robust protein degradation. We hope that our report will be useful for researchers that plan to establish AID method in their lab.


title: Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae

abstract: Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the "greenhouse-like" colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.


title: Hülle-cell-mediated protection of fungal reproductive and overwintering structures against fungivorous animals

abstract: Fungal Hulle cells with nuclear storage and developmental backup functions are reminiscent of multipotent stem cells. In the soil, Hulle cells nurse the overwintering fruiting bodies of Aspergillus nidulans. The genome of A. nidulans harbors genes for the biosynthesis of xanthones. We show that enzymes and metabolites of this biosynthetic pathway accumulate in Hulle cells under the control of the regulatory velvet complex, which coordinates development and secondary metabolism. Deletion strains blocked in the conversion of anthraquinones to xanthones are delayed in maturation and growth of fruiting bodies. Xanthones are not required for sexual development but exert antifeedant effects on fungivorous animals such as springtails and woodlice. These findings reveal a novel role of Hulle cells in establishing secure niches for A. nidulans by accumulating metabolites with antifeedant activity that protect reproductive structures from animal predators.

category: biochemistry


title: PlotMI: visualization of pairwise interactions and positional preferences learned by a deep learning model from sequence data

abstract: Deep learning models have recently gained success in various tasks related to understanding information coded in biological sequences. Although offering state-of-the art predictive performance, the predictions made by deep learning models can be difficult to understand. In virtually all biological research, the understanding of how a predictive model works is as, or even more important as the raw predictive performance. Thus interpretation of deep learning models is an emerging hot topic especially in context of biological research. Here we describe PlotMI, a mutual information based model interpretation tool that can intuitively visualize positional preferences and pairwise dependencies learned by any machine learning model trained on sequence data such as DNA, RNA or amino acid sequence. PlotMI can also be used to compare dependencies present in training data to the dependencies learned by the model and to compare dependencies learned by different types of models that are trained to perform the same task. PlotMI is freely available at https://github.com/hartonen/plotMI.

category: bioinformatics


title: PlotMI: interpretation of pairwise dependencies and positional preferences learned by deep learning models from sequence data


title: Spontaneous dimensional reduction and novel ground state degeneracy in a simple chain model

abstract: Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple analytic arguments complemented by extensive computer simulations. We find several striking results: there is a first order transition from a high temperature random coil phase to a highly unusual low temperature phase; the modular ground states exhibit significant degeneracy; the ground state structures exhibit spontaneous dimensional reduction and have a two-layer structure; and the ground states are assembled from secondary motifs of helices and strands connected by tight loops. We discuss the similarities and notable differences between the ground state structures (we call these PoSSuM - Planar Structures with Secondary Motifs) in the novel phase and protein native state structures.


title: SARS-CoV-2 Nsp8 N-terminal domain dimerizes and harbors autonomously folded elements

abstract: The SARS-CoV-2 Nsp8 protein is a critical component of the RNA replicase, as its N-terminal domain (NTD) anchors Nsp12, the RNA, and Nsp13. Whereas its C-terminal domain (CTD) structure is well resolved, there is an open debate regarding the conformation adopted by the NTD as it is predicted as disordered but found in a variety of complex-dependent conformations or missing from many other structures. Using NMR spectroscopy, we show that the SARS CoV-2 Nsp8 NTD features both well folded secondary structure and disordered segments. Our results suggest that while part of this domain corresponding to two long -helices forms autonomously, the folding of other segments would require interaction with other replicase components. When isolated, the -helix population progressively declines towards the C-termini, and dynamics measurements indicate that the Nsp8 NTD behaves as a dimer under our conditions.


title: Redox Nanomedicine Cures Chronic Kidney Disease (CKD) by Mitochondrial Reconditioning

abstract: Targeting reactive oxygen species (ROS) while maintaining cellular redox signaling is crucial in the development of redox medicine for the therapeutic benefit as the origin of several prevailing diseases including chronic kidney disease (CKD) is linked to ROS imbalance and associated mitochondrial dysfunction. Here, we have shown that an indigenously developed nanomedicine comprising of Mn3O4 nanoparticles duly functionalized by biocompatible ligand citrate (C-Mn3O4 NPs) can maintain cellular redox balance in an animal model. We developed a cisplatin-induced CKD model in C57BL/6j mice where severe mitochondrial dysfunction resulting in oxidative distress lead to the pathogenesis. Four weeks of treatment with C-Mn3O4 NPs restored renal function, preserved normal kidney architecture, ameliorated overexpression of pro-inflammatory cytokines, and arrested glomerulosclerosis and interstitial fibrosis in CKD mice. A detailed study involving human embryonic kidney (HEK 293) cells and isolated mitochondria from experimental animals revealed that the molecular mechanism behind the pharmacological action of the nanomedicine involves protection of structural and functional integrity of mitochondria from oxidative damage, the subsequent reduction in intracellular ROS, and maintenance of cellular redox homeostasis. To the best of our knowledge, such studies that efficiently treated a multifaceted disease like CKD using a biocompatible redox nanomedicine are sparse in the literature. Successful clinical translation of this nanomedicine may open a new avenue in redox-mediated therapeutics of several other diseases (e.g., diabetic nephropathy, neurodegeneration, and cardiovascular disease) where oxidative distress plays a central role in pathogenesis.

category: pharmacology and toxicology


title: Redox Buffering Capacity of Nanomaterials as an Index of ROS-based Therapeutics and Toxicity: A Preclinical Animal Study

abstract: Precise control of intracellular redox status, i.e., maintenance of physiological level of reactive oxygen species (ROS) for mediating normal cellular functions (oxidative eustress) while evading the excess ROS stress (distress) is central to the concept of redox medicine. In this regard, engineered nanoparticles with unique ROS generation, transition, or depletion functions have the potential to be the choice of redox therapeutics. However, it is always challenging to estimate whether ROS-induced intracellular events are beneficial or deleterious to the cell. Here, we propose the concept of redox buffering capacity as a therapeutic index of engineered nanomaterials. As a steady redox state is maintained for normal functioning cells, we hypothesize that the ability of a nanomaterial to preserve this homeostatic condition will dictate its therapeutic efficacy. Additionally, the redox buffering capacity is expected to provide information about the nanoparticle toxicity. Here, using citrate functionalized trimanganese tetroxide nanoparticles (C-Mn3O4 NPs) as a model nanosystem we explored its redox buffering capacity in erythrocytes. Furthermore, we went on to study the chronic toxic effect (if any) of this nanomaterial in animal model in order to co-relate with the experimentally estimated redox buffering capacity. This study could function as a framework for assessing the capability of a nanomaterial as redox medicine (whether maintains eustress or damages by creating distress), thus orienting its application and safety for clinical use.


title: Individualized precision targeting of dorsal attention and default mode networks with rTMS in traumatic brain injury-associated depression

abstract:
BackgroundAt the group level, antidepressant efficacy of rTMS targets is inversely related to their normative connectivity with subgenual anterior cingulate cortex (sgACC). Individualized connectivity may yield better targets, particularly in patients with neuropsychiatric disorders who may have aberrant connectivity. However, sgACC connectivity shows poor test-retest reliability at the individual level. Individualized resting-state network mapping (RSNM) can reliably map inter-individual variability in brain network organization.

ObjectiveTo identify individualized RSNM-based rTMS targets that reliably target the sgACC connectivity profile.

MethodsWe used RSNM to identify network-based rTMS targets in 10 healthy controls and 13 individuals with traumatic brain injury-associated depression (TBI-D). These "RSNM targets" were compared with consensus structural targets and targets based on individualized anti-correlation with a group-mean-derived sgACC region ("anti-group-mean sgACC targets"). The TBI-D cohort was randomized to receive active (n=9) or sham (n=4) rTMS to RSNM targets.

ResultsThe group-mean sgACC connectivity profile was reliably estimated by individualized correlation with default mode network (DMN) and anti-correlation with dorsal attention network (DAN). Individualized RSNM targets were then identified based on DAN anti-correlation and DMN correlation. Counterintuitively, anti-correlation with the group-mean sgACC connectivity profile was stronger and more reliable for RSNM-derived targets than for "anti-group-mean sgACC targets". Improvement in depression after RSNM-targeted rTMS was predicted by target anti-correlation with the portions of sgACC. Active treatment led to increased connectivity within and between several relevant regions.

ConclusionsRSNM may enable reliable individualized rTMS targeting, although further research is needed to determine whether this personalized approach can improve clinical outcomes.


title: The Neurodata Without Borders ecosystem for neurophysiological data science

abstract: The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWBs impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.


title: Discrete ripples reflect a spectrum of synchronous spiking activity in human association cortex

abstract: Direct brain recordings have provided important insights into how persistent oscillatory activity support human memory retrieval, but the extent to which transient fluctuations in intracranial EEG (iEEG) captures the dynamic coordination of underlying neurons involved in memory processing remains unclear. Here, we simultaneously record iEEG, local field potential (LFP), and single unit activity in the human temporal cortex. We demonstrate that cortical ripples contribute to broadband high frequency activity and exhibit a spectrum of amplitudes and durations related to the amount of underlying neuronal spiking. Ripples in the macro-scale iEEG are related to the number and synchrony of ripples in the micro-scale LFP, which in turn are related to the synchrony of neuronal spiking. Our data suggest that neural activity in the human cortex is organized into dynamic, discrete packets of information.


title: Contrast adaptation improves spatial integration

abstract: The effects of contrast adaptation and contrast area summation were investigated using a contrast discrimination task. The task consisted of a target of variable size, and a pedestal with a fixed base contrast. Discrimination performance was examined for a condition in which the pedestal size was fixed, equal to the largest target size, and for a condition in which the pedestal size matched the target size and thus varied with it. Repeated performance of the task produced rapid within-session improvements for both conditions. For stimuli with a matching size of target and pedestal, the performance improved only for the larger targets, indicating the development of area summation, which was initially absent for these stimuli. However, the improvements were mostly temporary, and were not fully retained between subsequent sessions. The temporary nature of the sensitivity gains implies that they resulted, at least in part, from rapid adaptation to the stimulus contrast. We suggest that adaptation decorrelates and thus reduces the spatial noise generated by a high-contrast pedestal, leading to improved area summation and better contrast sensitivity. A decorrelation model successfully predicted our experimental results.


title: Using synthetic MR images for field map-less distortion correction

abstract: Functional MRI (fMRI) data acquired using echo-planar imaging (EPI) is highly distorted by magnetic field inhomogeneity. Distortion combined with underlying differences in image contrast between EPI and T1-weighted and T2-weighted (T1w/T2w) structural images makes the alignment of functional and anatomical images a challenge. Typically, separately acquired field map data are used to correct fMRI distortions and a flexible cost function insensitive to cross-modal differences in image contrast and intensity is used for aligning fMRI and anatomical images. The quality of alignment achieved with this approach can vary greatly and depends on the availability and quality of field map data. To address this issue, we developed Synth, a software package for distortion correction and cross-modal image registration that does not require separately acquired field map data. Synth combines information from T1w/T2w anatomical images to construct an idealized undistorted synthetic image that has similar contrast and intensity properties to fMRI data. The undistorted synthetic image then serves as an effective reference for individual-specific nonlinear unwarping to correct fMRI distortions. We demonstrate that Synth reliably outperforms other standard registration and distortion correction approaches that utilize field maps in both pediatric (ABCD: Adolescent Brain Cognitive Development) and adult (MSC: Midnight Scan Club) data. Field map-less distortion correction with Synth allows accurate and precise registration of fMRI data with missing or corrupted field map information.


title: GPR15 in colon cancer development and anti-tumor immune responses.

abstract: G protein-coupled receptor 15 (GPR15) is a chemoattractant receptor which in response to its ligand, C10orf99/GPR15L, promotes colon homing of T cells in health and colitis. The functional role of GPR15 in colon cancer is largely unexplored, motivating our current studies using murine colon cancer models and human colorectal cancer (CRC) tissues. Our initial analysis of human CRC specimen revealed significant reduction in GPR15 expression and frequency of GPR15+ immune cells in tumors compared to  tumor-free surgical margins. In the AOM/DSS murine model of colitis associated colon cancer (CAC), we observed increased colonic polyps/tumor burden and lower survival rate in Gpr15-deficient (KO) compared to Gpr15-sufficient (Het) mice. Analysis of immune cell infiltrates in the colonic polyps showed significantly decreased CD8+ T cells and increased IL-17+ CD4+ and IL-17+ CD8+ T cells in Gpr15-KO than in Het mice. GPR15 deficiency thus alters the immune environment in colonic polyps to mitigate T cell-mediated anti-tumor responses resulting in severe disease. Consistent with a protective role of GPR15, administration of GPR15L to established tumors in the MC38 CRC mouse model increased CD45+ cell infiltration, enhanced TNF expression on CD4+ and CD8+ T cells at the tumor site and dramatically reduced tumor burden. Our findings highlight an important, unidentified role of the GPR15-GPR15L axis in promoting a tumor-suppressive immune microenvironment and unveils a novel, colon-specific therapeutic target for CRC.

category: immunology


title: A meta-analysis of single visit pollination effectiveness

abstract:
Many animals provide essential ecosystem services in the form of plant pollination. A rich literature documents considerable variation in the single visit pollination effectiveness of different plant visitors, but this literature has yet to be comprehensively synthesized. We conducted a hierarchical meta-analysis of 193 studies and extracted 1716 single visit effectiveness (SVE) comparisons for 252 plant species. We paired SVE data with visitation frequency data for 75 of these studies. Given the global dominance of honeybees in pollinator communities, we used these data to ask: 1) Do honeybees (Apis mellifera) and other floral visitors vary in their SVE?; 2) To what extent do plant and pollinator attributes predict the difference in SVE between honeybees and other visitors?; and 3) Is there a correlation between floral visitation frequency and SVE? We found that honeybees were significantly less effective than the most effective non-honeybee pollinator. Although not significantly different, honeybees also tended to be less effective than the mean community effectiveness. Honeybees were less effective as pollinators of crop plants and when compared to birds and other bees. Visitation frequency and pollination effectiveness were positively correlated, but this trend was largely driven by data from communities where honeybees were absent, suggesting that honeybees generally combine high visitation frequency and lower SVE. Our study demonstrates that non-honeybee floral visitors are highly effective pollinators of many crop and non-crop plants. While the high visitation frequency typically displayed by honeybees undoubtably makes them important pollinators, we show that honeybees are slightly less effective than the average pollinator and rarely the most effective pollinator of the plants they visit. As such, honeybees may be imperfect substitutes for the loss of wild pollinators and safeguarding global crop production will benefit from conservation of non-honeybee taxa.

Open Research StatementAlthough we are fully committed to data transparency, we are also aware of different research teams working on related meta-analyses. As such, we prefer to wait until our paper is accepted to make data publicly available but are happy to share data upon request. Data will be permanently archived on Figshare following acceptance.


title: Co-variation between glucocorticoids, behaviour and immunity supports the pace-of-life syndrome hypothesis: an experimental approach

abstract: The biomedical literature has consistently highlighted that long-term elevation of glucocorticoids might impair immune functions. In wild animals, patterns are less clear. Here, we re-explored the stress-immunity relationship considering the potential effects of behavioural profiles. Thirteen captive roe deer (Capreolus capreolus) were monitored over an eight-week period encompassing two capture events. We assessed how changes in baseline faecal cortisol metabolite (FCM) concentrations following a standardised capture protocol and vaccination affected changes in thirteen immune parameters of the innate and adaptive immunity, and whether behavioural profiles were linked to changes in baseline FCM levels and immune parameters. We found that individuals showing an increase in baseline FCM levels also exhibited an increase in immunity and were characterised by more reactive behavioural profiles (low activity levels, docility to manipulation and neophilia). Our results suggest that immunity of large mammals may be influenced by glucocorticoids, but also behavioural profiles, as it is predicted by the pace-of-life syndrome hypothesis. Our results highlight the need to consider co-variations between behaviour, immunity and glucocorticoids in order to improve our understanding of the among-individual variability in the stress-immunity relationships observed in wildlife, as they may be underpinned by different life-history strategies.


title: Gene duplications and genomic conflict underlie major pulses of phenotypic evolution in gymnosperms

abstract: Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the Tree of Life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation1, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here we examine the relationship of various facets of genomic evolution--including gene and genome duplication, genome size, and chromosome number--with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.


title: Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms


title: Profiling epigenetic age in single cells

abstract: DNA methylation of a defined set of CpG dinucleotides emerged as a critical and precise biomarker of the aging process. Multi-variate machine learning models, known as epigenetic clocks, can exploit quantitative changes in the methylome to predict the age of bulk tissue with remarkable accuracy. However, intrinsic sparsity and digitized methylation in individual cells have so far precluded the assessment of aging in single cell data. Here, we present scAge, a probabilistic approach to determine the epigenetic age of single cells, and validate our results in mice. scAge tissue-specific and multi-cell type single cell clocks correctly recapitulate chronological age of the original tissue, while uncovering the inherent heterogeneity that exists at the single-cell level. The data suggest that while tissues age in a coordinated fashion, some cells age more or less rapidly than others. We show that individual embryonic stem cells exhibit an age close to zero, that certain stem cells in a tissue show a reduced age compared to their chronological age, and that early embryogenesis is associated with the reduction of epigenetic age of individual cells, the latter supporting a natural rejuvenation event during gastrulation. scAge is both robust against the low coverage that is characteristic of single cell sequencing techniques and is flexible for studying any cell type and vertebrate organism of interest. This study demonstrates for the first time the potential for accurate epigenetic age profiling at single-cell resolution.


title: AKAP79 enables calcineurin to directly suppress protein kinase A activity

abstract: Interplay between the second messengers cAMP and Ca2+ is a hallmark of dynamic cellular processes. A common motif is the opposition of the Ca2+-sensitive phosphatase calcineurin and the major cAMP receptor, protein kinase A (PKA). Calcineurin dephosphorylates sites primed by PKA to bring about changes including synaptic long-term depression (LTD). AKAP79 supports signaling of this type by anchoring PKA and calcineurin in tandem. In this study, we discovered that AKAP79 increases the rate of calcineurin dephosphorylation of type II PKA regulatory subunits by an order of magnitude. Fluorescent PKA activity reporter assays, supported by kinetic modeling, show how AKAP79-enhanced calcineurin activity enables suppression of PKA without altering cAMP levels by increasing PKA catalytic subunit capture rate. Experiments with hippocampal neurons indicate that this mechanism contributes towards LTD. This non- canonical mode of PKA regulation may underlie many other cellular processes.