title: FGFR3 activating mutations induce luminal-like papillary bladder tumor formation and favor a male gender bias.

abstract:
BackgroundFGFR3 mutations are among the most frequent genetic alterations in bladder cancer and are enriched in the luminal papillary subtype of muscle-invasive tumors (MIBC) and luminal-like classes 1 and 3 of non-MIBC. To study their oncogenic properties in vivo, we developed here a genetically engineered mouse (GEM) model expressing the most frequent FGFR3 mutation, FGFR3-S249C, in urothelial cells.

MethodsBladder tumorigenesis was monitored in FGFR3-S249C mice. FGFR3 expression was assessed by RT-qPCR in the transgenic mice urothelium and in various human epithelia. Transcriptomic data were obtained from mouse bladder tumors and crossspecies comparisons were performed. Sex bias in FGFR3-mutated tumors was evaluated in our GEM model and in the TCGA and UROMOL cohorts of patients including 408 MIBC and 419 NMIBC, respectively. The association of androgen receptor (AR) activity, based on the expression of its target genes, with FGFR3 mutations was examined in these two cohorts. Binding of AR to its response element and AR phosphorylation in FGFR3-dependent cell lines were evaluated.

ResultsFGFR3-S249C expression in the urothelium of mice induced spontaneous low-grade papillary bladder tumors resembling the human counterpart at the histological and transcriptomic levels. Mutant-FGFR3 expression levels impacted tumor formation incidence in mice and mutant-FGFR3-driven human tumors were restricted to epithelia presenting high normal expression levels of FGFR3. The known bladder cancer male gender bias, also found in our model, was even higher in human FGFR3-mutated compared to wild-type tumors and associated with a higher AR regulon activity considering gender adjustment. AR phosphorylation and regulon activity were modulated by FGFR3 in FGFR3-dependent models.

ConclusionsMutant-FGFR3 is an oncogene per se, inducing bladder tumorigenesis. Patients with early stage bladder lesions could thus potentially benefit from FGFR3 targeting. Our results also reinforce the interest in elucidating the role of AR in bladder carcinogenesis, specifically in FGFR3-mutated driven tumors. Finally, our results suggest FGFR3 expression level in epithelium as a determinant for the FGFR3-driven tumors tissue specificity.


title: Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

abstract:
Premise of study"El Chango" is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants.

MethodsWe collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e.,, including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions.

ResultsWe obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most-parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest.

ConclusionsOur findings contribute to the understanding of Cenomanian equatorial regions, and support the hypothesis of a geographically and ecologically structured "rise of angiosperms", with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

category: paleontology


title: A scalable, clinically severe pig model for Duchenne muscular dystrophy

abstract: Large animal models for Duchenne muscular dystrophy (DMD) are crucial for preclinical evaluation of novel diagnostic procedures and treatment strategies. Pigs cloned from male cells lacking DMD exon 52 (DMD{Delta}52) resemble molecular, clinical and pathological hallmarks of DMD, but cannot be propagated by breeding due to death before sexual maturity. Therefore, female DMD+/- carriers were generated. A single founder animal had 11 litters with 29 DMDY/-, 34 DMD+/- as well as 36 male and 29 female wild-type (WT) offspring. Breeding with F1 and F2 DMD+/- carriers resulted in additional 114 DMDY/- piglets. The majority of them survived for 3-4 months, providing large cohorts for experimental studies. Pathological investigations and proteome studies of skeletal muscles and myocardium confirmed the resemblance of human disease mechanisms. Importantly, DMDY/- pigs reveal progressive fibrosis of myocardium and increased expression of connexin-43, associated with significantly reduced left ventricular fractional shortening and ejection fraction already at age 3 months. Furthermore, behavioral tests provided evidence for impaired cognitive ability of DMDY/- pigs. Our breeding cohort of DMD{Delta}52 pigs and standardized tissue repositories from DMDY/- pigs, DMD+/- carriers, and WT littermate controls provide important resources for studying DMD disease mechanisms and for testing novel diagnostic procedures and treatment strategies.

category: pathology


title: A new mathematical model of phyllotaxis to solve the genuine puzzle spiromonostichy

abstract: The view is widely accepted that the inhibitory effect of existing leaf primordia on new primordium formation determines phyllotactic patterning. Previous studies have shown that mathematical models based on such inhibitory effect can generate most of phyllotactic patterns. However, a few types of phyllotaxis still remain unaddressed. A notable example is costoid phyllotaxis showing spiromonostichy, which is characterized by a steep spiral with a small divergence angle and is unique to Costaceae plants. Costoid phyllotaxis has been called a "genuine puzzle" because it seems to disagree with the inhibitory effect-based mechanism. In an attempt to produce a steep spiral pattern, we developed a new mathematical model assuming that each leaf primordium emits not only the inhibitory effect but also some inductive effect. Computer simulations with the new model successfully generated a steep spiral pattern when these two effects met a certain relationship. The obtained steep spiral matched the real costoid phyllotaxis observed with Costus megalobractea. We also found by the mathematical model analysis that the early phyllotactic transition in the seedlings of this plant can be explained by the SAM enlargement.

category: plant biology


title: Wide-Angle, Monocular Head Tracking using Passive Markers

abstract:
Camera images can encode large amounts of visual information of an animal and its environment, enabling high fidelity 3D reconstruction of the animal and its environment using computer vision methods. Most systems, both markerless (e.g. deep learning based) and marker-based, require multiple cameras to track features across multiple points of view to enable such 3D reconstruction. However, such systems can be expensive and are challenging to set up in small animal research apparatuses.

We present an open-source, marker-based system for tracking the head of a rodent for behavioral research that requires only a single camera with a potentially wide field of view. The system features a lightweight visual target and computer vision algorithms that together enable high-accuracy tracking of the six-degree-of-freedom position and orientation of the animals head. The system, which only requires a single camera positioned above the behavioral arena, robustly reconstructs the pose over a wide range of head angles (360{whitebullet} in yaw, and approximately {+/-}120{whitebullet} in roll and pitch).

Experiments with live animals demonstrate that the system can reliably identify rat head position and orientation. Evaluations using a commercial optical tracker device show that the system achieves accuracy that rivals commercial multi-camera systems.

Our solution significantly improves upon existing monocular marker-based tracking methods, both in accuracy and in allowable range of motion.

The proposed system enables the study of complex behaviors by providing robust, fine-scale measurements of rodent head motions in a wide range of orientations.

category: neuroscience


title: A cerebellar-prepontine circuit for tonic immobility triggered by inescapable threat

abstract: Sudden changes in the sensory environment are frequently perceived as threats and may provoke defensive behavioral states. One such state is tonic immobility, a conserved defensive strategy characterized by a powerful suppression of movement and motor reflexes. Tonic immobility has been associated with multiple brainstem regions and cell types, but the underlying circuit is not known. Here, we demonstrate that a strong vibratory stimulus evokes tonic immobility in larval zebrafish defined by suppression of exploratory locomotion and sensorimotor responses. Using a circuit-breaking screen and targeted neuron ablations, we show that cerebellar granule cells and a cluster of glutamatergic ventral prepontine neurons (vPPNs) that express key stress-associated neuropeptides are critical components of the circuit that suppresses movement. The complete sensorimotor circuit transmits information from primary sensory neurons through the cerebellum to vPPNs to regulate reticulospinal premotor neurons. These results show that cerebellar regulation of a neuropeptide-rich prepontine structure governs a conserved and ancestral defensive behavior that is triggered by inescapable threat.


title: Category-specific representational patterns in left inferior frontal and temporal cortex reflect similarities and differences in the sensorimotor and distributional properties of concepts.

abstract: Neuronal populations code similar concepts by similar activity patterns across the human brains networks supporting language comprehension. However, it is unclear to what extent such meaning-to-symbol mapping reflects statistical distributions of symbol meanings in language use, as quantified by word co-occurrence frequencies, or, rather, experiential information thought to be necessary for grounding symbols in sensorimotor knowledge. Here we asked whether integrating distributional semantics with human judgments of grounded sensorimotor semantics better approximates the representational similarity of conceptual categories in the brain, as compared with each of these methods used separately. We examined the similarity structure of activation patterns elicited by action- and object-related concepts using multivariate representational similarity analysis (RSA) of fMRI data. The results suggested that a semantic vector integrating both sensorimotor and distributional information yields best category discrimination on the cognitive-linguistic level, and explains the corresponding activation patterns in left posterior inferior temporal cortex. In turn, semantic vectors based on detailed visual and motor information uncovered category-specific similarity patterns in fusiform and angular gyrus for object-related concepts, and in motor cortex, left inferior frontal cortex (BA 44), and supramarginal gyrus for action-related concepts.


title: Substantia nigra degradation results in widespread changes in medial zona incerta afferent and efferent connectomics

abstract:
Parkinsons disease (PD) is a complex disease affecting many facets of movement, especially gait abnormalities such as shuffling and freezing of gait. The nigrostriatal pathways of the basal ganglia are traditionally targeted by existing therapies; however, other pathways may be more relevant to gait, such as the pedunculopontine nucleus and the zona incerta (ZI). The A13 nucleus may be such a target as it has emerged as an area of interest in dopamine motor function. Yet, this area remains understudied compared to other dopamine nuclei, especially in animal models of PD. In 6-OHDA mice, we found a reduction in locomotion in the open field and gait dysfunction during treadmill tests. Medial ZI dopamine cells, containing the A13 nucleus, were preserved following 6-OHDA, in contrast to a marked reduction in substantia nigra pars compacta (SNc) neurons. There was extensive remodelling of the A13 afferent and efferent connectome following nigrostriatal lesions. Afferent input patterns displayed a marked reduction in cross-correlation across brain regions in 6-OHDA mice, while efferent projections showed an increase. In a human PD patient with advanced gait dysfunction we found that the A13 nucleus was preserved, suggesting that remodelling could also occur in humans. This work points to the A13 region as a potential therapeutic target in PD.

Significance StatementRecently it was found that the medial zona incerta projects to the cuneiform nucleus suggesting a parallel dopaminergic projection onto motor regions. Here we investigated the connectome of the A13 region and examined the afferent and efferent projections in normal mice and mice with a unilateral Parkinsonian mouse model. We found that the connectome was reconfigured following nigrostriatal degeneration. This work provides a comprehensive insight into the plasticity in a dopaminergic-rich area of the zona incerta in PD injury models.


title: Riemannian geometry of functional connectivity matrices for multi-site attention-deficit/hyperactivity disorder data harmonization

abstract: The use of multi-site datasets in neuroimaging provides neuroscientists with more statistical power to perform their analyses. However, it has been shown that imaging-site introduces a variability in the data that cannot be attributed to biological sources. In this work, we show that functional connectivity matrices derived from resting-state multi-site data contain a significant imaging-site bias. To this aim, we exploited the fact that functional connectivity matrices belong to the manifold of symmetric positive-definite matrices, making possible to operate on them with Riemannian geometry. We hereby propose a geometry-aware harmonization approach, Rigid Log-Euclidean Translation, that accounts for this site bias. Moreover, we adapted other Riemannian-geometric methods designed for other domain adaptation tasks, and compared them to our proposal. Based on our results, Rigid Log-Euclidean Translation of multi-site functional connectivity matrices seems to be among the studied methods the most suitable one in a clinical setting. This represents an advance with respect to previous functional connectivity data harmonization approaches, which do not respect the geometric constraints imposed by the underlying structure of the manifold. In particular, when applying our proposed method on data from the ADHD-200 dataset, a multi-site dataset built for the study of attention-deficit/hyperactivity disorder, we obtained results that display a remarkable correlation with established pathophysiological findings and, therefore, represent a substantial improvement when compared to the non-harmonization analysis. Thus, we present evidence supporting that harmonization should be extended to other functional neuroimaging datasets, and provide a simple geometric method to address it.


title: Innate immunity pathways activate cell proliferation after penetrating traumatic brain injury in adult Drosophila

abstract: We are utilizing an adult penetrating traumatic brain injury (PTBI) model in Drosophila to investigate regenerative mechanisms after damage to the central brain. We focused on cell proliferation as an early event in the regenerative process. To identify candidate pathways that may trigger cell proliferation following PTBI, we utilized RNA-Seq. We find that transcript levels for components of both Toll and Immune Deficiency (Imd) innate immunity pathways are rapidly and highly upregulated post-PTBI. We then tested mutants for the NF-{kappa}B transcription factors of the Toll and Imd pathways, Dorsal-related immunity factor (Dif) and Relish (Rel) respectively. We find that loss of either or both Dif and Rel results in loss of cell proliferation after injury. We then tested canonical downstream targets of Drosophila innate immune signaling, the antimicrobial peptides (AMPs), and find that they are not required for cell proliferation following PTBI. This suggests that there are alternative targets of Toll and Imd signaling that trigger cell division after injury. Furthermore, we find that while AMP levels are substantially elevated after PTBI, their levels revert to near baseline within 24 hours. Finally, we identify tissue-specific requirements for Dif and Rel. Taken together, these results indicate that the innate immunity pathways play an integral role in the regenerative response. Innate immunity previously has been implicated as both a potentiator and an inhibitor of regeneration. Our work suggests that modulation of innate immunity may be essential to prevent adverse outcomes. Thus, this work is likely to inform future experiments to dissect regenerative mechanisms in higher organisms.


title: Neural Excursions from Low-Dimensional Manifold Structure Explain Intersubject Variation in Human Motor Learning

abstract: Humans vary greatly in their motor learning abilities, yet little is known about the neural mechanisms that underlie this variability. Recent neuroimaging and electrophysiological studies demonstrate that large-scale neural dynamics inhabit a low-dimensional subspace or manifold, and that learning is constrained by this intrinsic manifold architecture. Here we asked, using functional MRI, whether subject-level differences in neural excursion from manifold structure can explain differences in learning across participants. We had subjects perform a sensorimotor adaptation task in the MRI scanner on two consecutive days, allowing us to assess their learning performance across days, as well as continuously measure brain activity. We find that the overall neural excursion from manifold activity in both cognitive and sensorimotor brain networks is associated with differences in subjects patterns of learning and relearning across days. These findings suggest that off-manifold activity provides an index of the relative engagement of different neural systems during learning, and that intersubject differences in patterns of learning and relearning across days are related to reconfiguration processes in cognitive and sensorimotor networks during learning.


title: The art of snacking: Innovative food extraction in a synanthropic species is associated with food exposure and food categorization

abstract:
Extractive foraging is generally studied from the perspective of behavioral flexibility, cognitive ability, innovation and social learning. Despite its potential to elucidate synanthropic adaptation in species exploiting enclosed anthropogenic food, research on extractive foraging under urban conditions is limited. Since a large extent of anthropogenic food is packaged and contains highly processed food, processes of identification/extraction of food by nonhuman species become intriguing themes of research. We studied how processing status of embedded food determined extraction decisions across groups of a species differing in exposure and familiarity to the food. Further, we tested the generalizability of extraction methods. Experimenting with wild bonnet macaques (Macaca radiata), we found exposure- and form (native/shelled/peeled)-specific familiarity to peanuts, state (raw/boiled/roasted)-specific distinction in depeeling, and exposure- and state-specific differences in methods of depeeling. Group with the highest exposure to peanut differed in its propensity to use sophisticated extraction methods, e.g. depeeling by rubbing between palms (bimanual asymmetric action) and rubbing against horizontal substrata (unimanual action). The innovative methods were also extended to roasted peas and chickpeas by the urban group. Our study establishes a causal relationship between familiarity and processing status of food and shows the generalized extension of extraction methods based on food categorization.

Summary StatementNonhuman species in cities face upheaval challenges of accessing enclosed and highly processed anthropogenic food. We studied the effects of minor processing of enclosed food on its extraction decisions.

category: animal behavior and cognition


title: H3K4me1-marked Enhancer Activation in Resistant Prostate Cancers Implicates SOX4 and MENIN Inhibition as Therapeutic Strategies

abstract: Chromatin elements and regulators play important roles during progression of prostate cancer, however, their involvement in response to therapy is less well understood. Using comprehensive chromatin profiling of patient-derived tumors, we find that enhancer elements marked by H3K4me1 are highly enriched in aggressive therapy-resistant prostate cancers on important resistance-driving genes, such as those involved in FOXA1, NOTCH and TGF-{beta} signaling. Importantly, by targeting H3K4me1-elements through inhibition of the MLL complex, a H3K4 methyltransferase, we reduced the proliferative capacity and H3K4me1-associated loci in enzalutamide-resistant prostate cancer lines. We identify AR, FOXA1, HOXB13 and SOX4 as a subset of core TFs that are critical for establishing transcriptional networks via active enhancer reprogramming during acquisition of resistance to therapy. Knock-down of SOX4 reduced cell proliferation and disrupted the H3K4me1 enhancer landscape, further suggesting a role for this TF in therapy-resistance. Overall, our data implicate H3K4me1-marked enhancers as a key epigenetic feature of therapy-resistance, implicate SOX4 in enhancer reprogramming and suggest use of MLL/MENIN inhibitors as a potential therapeutic strategy in high-grade and locally advanced prostate cancers that do not respond to traditional therapies.

category: cancer biology


title: Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes

abstract:
I.Chewing herbivores activate plant defense responses through a combination of mechanical wounding and elicitation by herbivore associated molecular patterns (HAMPs). HAMPs are wound response amplifiers; however, specific defense outputs may also exist that strictly require HAMP-mediated defense signaling. To investigate HAMP-mediated signaling and defense responses, we characterized cowpea transcriptome changes following elicitation by inceptin, a peptide HAMP common in Lepidoptera larvae oral secretions. Following inceptin treatment, we observed large-scale reprogramming of the transcriptome consistent with 3 different response categories: 1) amplification of mechanical wound responses, 2) temporal extension through accelerated or prolonged responses, and 3) examples of inceptin-specific elicitation and suppression. At both early and late timepoints, namely 1 and 6 hours, large sets of transcripts specifically accumulated following inceptin elicitation but not wounding alone. Further inceptin-regulated transcripts were classified as reversing changes induced by wounding alone. Within key signaling and defense related gene families, inceptin-elicited responses commonly targeted select subsets of wound-induced transcripts. Transcripts displaying the largest inceptin-elicited fold-changes included terpene synthases (TPS) and peroxidases (POX) that correspond with induced volatile production and increased peroxidase activity in cowpea. Characterization of inceptin-elicited cowpea defenses via heterologous expression in Nicotiana benthamiana demonstrated that specific cowpea TPS and POX were able to confer terpene emission and the reduced growth of beet armyworm (Spodoptera exigua) herbivores, respectively. Collectively, our present findings in cowpea support a model where HAMP-elicitation both amplifies concurrent wound responses and specifically contributes to the activation of selective outputs associated with direct and indirect anti-herbivore defenses.

II. Significance StatementPlants recognize herbivore-associated molecular patterns (HAMPs) to induce defenses, but interactions with the more general wound response are not well-understood. We leveraged a known HAMP-receptor interaction to characterize transcriptomic modulation of the wound response by the peptide HAMP, inceptin. Inceptin not only amplifies wound responses, but can specifically induce or suppress transcripts with demonstrated functions in direct and indirect defense against herbivores. The plant immune system thus recognizes HAMPs to fine-tune wound responses against herbivory.


title: A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

abstract:
BackgroundAccurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single molecule long read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation or incomplete cDNA synthesis.

ResultsWe present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 160k transcripts - twice that of the best current Arabidopsis transcriptome and including over 1,500 novel genes. 79% of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We developed novel methods to determine splice junctions and transcription start and end sites accurately. Mis- match profiles around splice junctions provided a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identified high confidence transcription start/end sites and removed fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provided higher resolution of transcript expression profiling and identified cold- and light-induced differential transcription start and polyadenylation site usage.

ConclusionsAtRTD3 is the most comprehensive Arabidopsis transcriptome currently available. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single molecule sequencing analysis from any species.


title: Two Ubiquitin-Activating Systems Occur in Plants with One Playing a Major Role in Plant Immunity

abstract:
Many plants possess two or more ubiquitin-activating enzymes (E1). However, it is unclear whether the E1s of a plant genome play equivalent roles in various pathways. Here we report that tomato and tobacco encode dual ubiquitin-activating systems (DUAS) in which the E1s UBA1 and UBA2 display differential specificities in charging four groups of E2s. The C-terminal ubiquitin-folding domain of the E1s play a major but not sole role in determining the differential specificities of charging the four groups E2s. The dual systems do not play equivalent roles in plant immunity, with silence of UBA2 only compromising host immunity. Among the differentially charged E2s, group IV members UBC32, UBC33 and UBC34 are shown to be essential for ER-associated protein degradation (ERAD) and plant immunity. Like tomato, Arabidopsis UBC32/33/34 E2 triplet are also differentially charged by its E1s and are essential for plant immunity. Loss of function in Arabidopsis UBC32, UBC33 and UBC34 does not affect flg22 and elf18-triggered inhibition of seedling growth but results in alteration of ER stress tolerance, which likely contribute to the diminished plant immunity in the mutants. Our results uncover DUAS in plants and a previously unknown E1-ERAD-associated E2 triplet module in the regulation of host immunity.

One sentence summaryPlant dual ubiquitin E1 systems play distinct roles in plant immunity by differentially charging the ERAD-associated E2s for ER stress tolerance.


title: Dissecting the subtropical adaptation traits and cuticle synthesis pathways via the genome of the subtropical blueberry Vaccinium darrowii

abstract: Vaccinium darrowii is a subtropical wild blueberry species, which was used to breed economically important southern highbush cultivars. The adaptation traits of V. darrowii to subtropical climate would provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochoromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and predicted 41 815 genes using RNAseq evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and V. corymbosum. This conserved genome structure may explain the high fertilization during crossbreeding between V. darrowii and other blueberry cultivars. Gene expansion and tandem duplication analysis indicated possible roles of defense and flowering associated genes in adaptation of V. darrowii to the subtropics. The possible SOC1 genes in V. darrowii were identified with phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA-sequencing, the cuticle biosynthesis pathways of Vaccinium species were delineated here in V. darrowii. This result could serve as a reference for breeding berries with customer-desired colors. The V. darrowii reference genome, together with the unique traits of this species, including diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.


title: Developmental integration cannot explain major features of stomatal anatomical evolution in seed plants

abstract:
O_LIDevelopmental integration can cause traits to covary over macroevolutionary time and in some cases prevent populations from reaching their adaptive optima. Developmental integration between stomatal size and density may contribute to two major features of stomatal anatomical evolution: inverse size-density scaling and bimodal stomatal ratio. If these patterns result from developmental integration, we predicted that in amphistomatous leaves 1) stomatal size and density should covary similarly on both abaxial and adaxial surfaces and 2) stomatal traits (size and density) on each surface should covary isometrically.
C_LIO_LIWe synthesized data on stomatal density and length from amphistomatous leaves of 711 terrestrial seed plant taxa mostly from the literature. We estimated the covariance in divergence between stomatal traits from 327 phylogenetically independent contrasts using a robust Bayesian model.
C_LIO_LIAdaxial stomatal density, but not length, is evolutionarily labile and not strongly integrated with stomatal length or abaxial stomatal density. Hence, developmental integration alone cannot explain inverse size-density scaling nor bimodal stomatal ratio.
C_LIO_LIQuasi-independent evolution of stomatal anatomical traits facilitates largely unfettered access to fitness optima. If stomatal anatomical traits are near their current fitness optimum, this implies that limits on trait (co)variance result from selective rather than developmental constraints. However, we cannot rule out that developmental integration is important in some lineages. Future research should identify the mechanistic basis of (dis)integration in stomatal development.
C_LI


title: How much the response of rice genotypes to water deficit at the reproductive phase is dependent from environmental conditions?

abstract: Rice crop is known as particularly sensitive to water deficit, especially during the reproductive phase when growth of vegetative organs and formation of spikelets are simultaneous. Many works have focused on the response of rice plants to water deficits varying in timing, duration and intensity. Oppositely, the impact of the environmental conditions on the response to a given water deficit remains largely unknown. In order to test it, two experiments under contrasted conditions of temperature, radiation and VPD were conducted on six genotypes in greenhouse in Brazil (S) and in growth chamber in France (GC). The plants were submitted to the same mild water deficit at the reproductive phase, by adjusting FTSW at 0.4. Under irrigation, plant growth rate was reduced and crop duration extended in GC in relation to S: ultimately, this trade-off resulted in similar plant height and biomass in both environments. Under water deficit and in both environments, elongation rate decreased and was associated with an increase in soluble sugars in stem and flag leaf, while starch was reduced in S and negligible in GC because of the low radiation. This common biochemical response displayed a large gradient of values across environments and genotypes, but differentially impacted the branch and spikelet formation on the developing panicle: in carbon limiting conditions (GC), the increase in soluble sugars was associated with the reduction in branch and spikelet number, and conversely in S. At the morphological level, the maintenance of spikelet number on the panicle was correlated with the maintenance of flag leaf width in all genotypes and conditions, that was discussed according to the maintenance of the apical meristem size. Genotypes were discriminated and the study underlined the global tolerance of Cirad 409 and sensitivity of IAC 25.


title: Cluster mean-field theory accurately predicts statistical properties of large-scale DNA methylation patterns

abstract: The accurate establishment and maintenance of DNA methylation patterns is vital for mammalian development and disruption to these processes causes human disease. Our understanding of DNA methylation mechanisms has been facilitated by mathematical modelling, particularly stochastic simulations. Mega-base scale variation in DNA methylation patterns is observed in development, cancer and ageing and the mechanisms generating these patterns are little understood. However, the computational cost of stochastic simulations prevents them from modelling such large genomic regions. Here we test the utility of three different mean-field models to predict large-scale DNA methylation patterns. By comparison to stochastic simulations, we show that a cluster mean-field model accurately predicts the statistical properties of steady-state DNA methylation patterns, including the mean and variance of methylation levels calculated across a system of CpG sites, as well as the covariance and correlation of methylation levels between neighbouring sites. We also demonstrate that a cluster mean-field model can be used within an approximate Bayesian computation framework to accurately infer model parameters from data. As mean-field models can be solved numerically in a few seconds, our work demonstrates their utility for understanding the processes underpinning large-scale DNA methylation patterns.

category: systems biology


title: Kronos scRT: a uniform framework for single-cell replication timing analysis

abstract: Mammalian genomes are replicated in a cell-type specific order and in coordination with transcription and chromatin organization. Although the field of replication is also entering the single-cell era, current studies require cell sorting, individual cell processing and have yielded a limited number (<100) of cells. Here, we have developed Kronos scRT (https://github.com/CL-CHEN-Lab/Kronos_scRT), a software for single-cell Replication Timing (scRT) analysis. Kronos scRT does not require a specific platform nor cell sorting, allowing the investigation of large datasets obtained from asynchronous cells. Analysis of published available data and droplet-based scWGS data generated in the current study, allows exploitation of scRT data from thousands of cells for different mouse and human cell lines. Our results demonstrate that, although most cells replicate within a close timing range for a given genomic region, replication can also occur stochastically throughout S phase. Altogether, Kronos scRT allows investigating the RT program at a single-cell resolution for both homogeneous and heterogeneous cell populations in a fast and comprehensive manner.

category: genomics


title: Bringing TrackMate in the era of machine-learning and deep-learning.

abstract: TrackMate is an automated tracking software used to analyze bioimages and distributed as a Fiji plugin. Here we introduce a new version of TrackMate rewritten to improve performance and usability, and integrating several popular machine and deep learning algorithms to improve versatility. We illustrate how these new components can be used to efficiently track objects from brightfield and fluorescence microscopy images across a wide range of bio-imaging experiments.

category: bioinformatics


title: Bringing TrackMate into the era of machine-learning and deep-learning.


title: A climate-based model for tick life cycle: an infinite system of differential equation approach

abstract:
The distribution of ticks is essentially determined by the presence of climatic conditions and ecological contexts suitable for their survival and development.

We have developed a general tick biology model to study the major trends due to climate change on tick population dynamics under different climate conditions.

We build a model that explicitly takes into account stage into each physiological state through a system of infinite differential equations where tick population density are structured on an infinite discrete set. We suppose that intrastage development process is temperature dependent (Arrhenius temperatures function) and that larvae hatching and adult mortality are temperature and precipitations dependent.

We analysed mathematically the model and have explicit the R0 of the tick population. Therefore, we performed a numerical analysis of the model under three different climate conditions (tropical, Mediterranean and subarctic climates) over the short term using climatic data from 1995 to 2005, as well as long-term simulations from 1902 to 2005.

category: ecology


title: Neural Networks for self-adjusting Mutation Rate Estimation when the Recombination Rate is unknown

abstract:
Estimating the mutation rate, or equivalently effective population size, is a common task in population genetics. If recombination is low or high, the optimal linear estimation methods, namely Fus and Wattersons estimator, are known and well understood. For intermediate recombination rates, the calculation of optimal estimators is more involved. As an alternative to model-based estimation, neural networks and other machine learning tools could help to develop good estimators in these involved scenarios. However, if no benchmark is available it is difficult to assess how well suited these tools are for different applications in population genetics.

Here we investigate feedforward neural networks for the estimation of the mutation rate and compare their performance with the frequently used optimal estimators introduced by Fu and Watterson. We find that neural networks can reproduce the optimal estimators if provided with the appropriate features and training sets. Remarkably, only one hidden layer is necessary to obtain a single estimator that performs almost as well as the optimal estimators for both, low and high recombination rates and provides a superior estimation method for intermediate recombination rates at the same time.

category: evolutionary biology


title: Identification of Arhgef12 and Prkci as Genetic Modifiers of Retinal Dysplasia in the Crb1rd8 Mouse Model

abstract: Mutations in the apicobasal polarity gene CRB1 lead to diverse retinal diseases, such as Leber congenital amaurosis, cone-rod dystrophy, retinitis pigmentosa (with and without Coats-like vasculopathy), foveal retinoschisis, macular dystrophy, and pigmented paravenous chorioretinal atrophy. Limited correlation between disease phenotypes and CRB1 alleles, and evidence that patients sharing the same alleles often present with different disease features, suggest that genetic modifiers contribute to clinical variation. Similarly, the retinal phenotype of mice bearing the Crb1 retinal degeneration 8 (rd8) allele varies with genetic background. Here, we initiated a sensitized chemical mutagenesis screen in B6.Cg-Crb1rd8/Pjn, a strain with a mild clinical presentation, to identify genetic modifiers that cause a more severe disease phenotype. Two models from this screen, Tvrm266 and Tvrm323, exhibited increased retinal dysplasia. Genetic mapping with high-throughput exome and candidate-gene sequencing identified causative mutations in Arhgef12 and Prkci, respectively. Epistasis analysis of both strains indicated that the increased dysplastic phenotype required homozygosity of the Crb1rd8 allele. Retinal dysplastic lesions in Tvrm266 mice were smaller and caused less photoreceptor degeneration than those in Tvrm323 mice, which developed an early, large diffuse lesion phenotype. In both models at one month of age, Muller glia and microglia mislocalization at dysplastic lesions was similar to that in B6.Cg-Crb1rd8/Pjn mice, while photoreceptor cell mislocalization was more extensive. External limiting membrane disruption was comparable in Tvrm266 and B6.Cg- Crb1rd8/Pjn mice but milder in Tvrm323 mice. Immunohistological analysis of mice at postnatal day 0 indicated a normal distribution of mitotic cells in Tvrm266 and Tvrm323 mice, suggesting normal early development. Aberrant electroretinography responses were observed in both models but functional decline was significant only in Tvrm323 mice. These results identify Arhgef12 and Prkci as modifier genes that differentially shape Crb1-associated retinal disease, which may be relevant to understanding clinical variability and underlying disease mechanisms.

category: genetics


title: Alignment of multiple metabolomics LC-MS datasets from disparate diseases to reveal fever-associated metabolites

abstract: Acute febrile illnesses are still a major cause of mortality and morbidity globally, particularly in low to middle income countries. The aim of this study was to determine any possible metabolic commonalities of patients infected with disparate pathogens that cause fever. Three liquid chromatography-mass spectrometry (LC-MS) datasets investigating the metabolic effects of malaria, leishmaniasis and Zika virus infection were used. The retention time (RT) drift between the datasets was determined using landmarks obtained from the standard reference mixtures generally used in the quality control of the LC-MS experiments. We used fitted Gaussian Process models (GPs) to perform a high level correction of the RT drift between the experiments, followed by standard peakset alignment between the samples with corrected RTs of the three LC-MS datasets. Statistical analysis, annotation and pathway analysis of the integrated peaksets were subsequently performed. Metabolic dysregulation patterns common across the datasets were identified, with kynurenine pathway being the most affected pathway between all three fever-associated datasets.


title: High lineage survivorship across the end-Devonian Mass Extinction suggested by a remarkable new Late Devonian actinopterygian

abstract: Actinopterygian (ray-finned) fishes represent the principal vertebrate group in aquatic settings. This dominance is often attributed to their apparent success in the aftermath of the end-Devonian extinction. Increases in taxonomic and morphological diversity in the early Carboniferous, coupled with phylogenetic hypotheses implying the survival of few Devonian lineages, contribute to a model of explosive post-extinction radiation. However, most actinopterygian fossils from within a ca. 20 million year (Myr) window surrounding the end-Devonian extinction remain poorly known, contributing to uncertainty about these patterns. Here we present detailed anatomical data for an exceptionally preserved but diminutive ray-finned fish from within this gap, ~7 Myr prior to the Devonian-Carboniferous boundary. Representing a new genus and species, it bears a series of derived anatomical features otherwise known only from Carboniferous and younger taxa. It nests phylogenetically within a clade of post-Devonian species and, in an expanded phylogenetic analysis incorporating other previously neglected taxa, draws at least ten lineages of Carboniferous actinopterygians into the Late Devonian. This suggests phenotypically cryptic divergence among ray-finned fishes in the latest Devonian, followed by more conspicuous diversification in feeding and locomotor structures in the Carboniferous. Our revised model matches more complicated patterns of divergence, survival, and diversification around the Devonian-Carboniferous boundary in other vertebrate clades such as tetrapods and lungfishes. It also fundamentally recalibrates the onset of diversification early in the history of a group that today contains half of all living vertebrate species.


title: Three-dimensional Super-resolved Imaging of Paraffin-embedded Kidney Samples

abstract: Diseases of the glomeruli, the renal filtration units, are a leading cause of progressive kidney disease. Assessment of the ultrastructure of podocytes at the glomerular filtration barrier is essential for diagnosing diverse disease entities, providing insight into the disease pathogenesis as well as monitoring treatment responses. New technologies, including superresolved nanoscopy and expansion microscopy, as well as new sample preparation techniques, are starting to revolutionize imaging of biopsy specimens. However, our previous approaches for simple and fast three-dimensional imaging of optically cleared samples are to date not compatible with formalin fixed paraffin-embedded (FFPE) tissue, impeding application in clinical routine. Here we provide protocols that circumvent these limitations and allow for three dimensional STED and confocal imaging of FFPE kidney tissue with similar staining and image quality as compared to our previous approaches. This would increase the feasibility to implement these protocols in clinical routines, as FFPE is the gold standard method for storage of patient samples.


title: Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic

abstract: A variational autoencoder (VAE) is a machine learning algorithm, useful for generating a compressed and interpretable latent space. These representations have been generated from various biomedical data types and can be used to produce realistic-looking simulated data. However, standard vanilla VAEs suffer from entangled and uninformative latent spaces, which can be mitigated using other types of VAEs such as {beta}-VAE and MMD-VAE. In this project, we evaluated the ability of VAEs to learn cell morphology characteristics derived from cell images. We trained and evaluated these three VAE variants--Vanilla VAE, {beta}-VAE, and MMD-VAE--on cell morphology readouts and explored the generative capacity of each model to predict compound polypharmacology (the interactions of a drug with more than one target) using an approach called latent space arithmetic (LSA). To test the generalizability of the strategy, we also trained these VAEs using gene expression data of the same compound perturbations and found that gene expression provides complementary information. We found that the {beta}-VAE and MMD-VAE disentangle morphology signals and reveal a more interpretable latent space. We reliably simulated morphology and gene expression readouts from certain compounds thereby predicting cell states perturbed with compounds of known polypharmacology. Inferring cell state for specific drug mechanisms could aid researchers in developing and identifying targeted therapeutics and categorizing off-target effects in the future.

category: pharmacology and toxicology


title: Sigma Oscillations Protect or Reinstate Motor Memory Depending on their Temporal Coordination with Slow Waves

abstract: Targeted memory reactivation (TMR) during post-learning sleep is known to enhance motor memory consolidation but the underlying neurophysiological processes remain unclear. Here, we confirm the beneficial effect of auditory TMR on motor performance. At the neural level, TMR enhanced slow wave (SW) characteristics. Additionally, greater TMR-related phase-amplitude coupling between slow (0.5-2 Hz) and sigma (12-16 Hz) oscillations after the SW peak was related to higher TMR effect on performance. Importantly, sounds that were not associated to learning strengthened SW-sigma coupling at the SW trough and the increase in sigma power nested in the trough of the potential evoked by these unassociated sounds was related to the TMR benefit. Altogether, our data suggest that, depending on their precise temporal coordination during post learning sleep, slow and sigma oscillations play a crucial role in either memory reinstatement or protection against irrelevant information; two processes that critically contribute to motor memory consolidation.


title: The eyes have it: The pupillary light response as a physiological index of aphantasia, sensory and phenomenological imagery strength

abstract: The pupillary light response is an important automatic physiological response that optimises light reaching the retina. Recent work has shown that the pupil also adjusts in response to illusory brightness and a range of cognitive functions, however, it remains unclear what exactly drives these endogenous changes. Here we show that the imagery pupillary light response correlates with objective measures of sensory imagery strength. Further, the trial-by-trial phenomenological vividness of visual imagery is tracked by the imagery pupillary light response. We also demonstrated that there was no evidence for an imagery pupillary light response in a group of individuals without visual imagery (aphantasia), however, they did show perceptual pupil light responses and pupil dilation with larger cognitive load. Our results provide evidence that the pupillary light response indexes the sensory strength of visual imagery and also provides the first physiological validation of aphantasia.


title: The role of V3 neurons in speed-dependent interlimb coordination during locomotion in mice

abstract: Speed-dependent interlimb coordination allows animals to maintain stable locomotion under different circumstances. We have previously demonstrated that a subset of spinal V3 neurons contributes to stable locomotion by mediating mutual excitation between left and right lumbar rhythm generators (RGs). Here, we expanded our investigation to the V3 neurons involved in ascending long propriospinal interactions (aLPNs). Using retrograde tracing, we revealed a subpopulation of lumbar V3 aLPNs with contralateral cervical projections. V3OFF mice, in which all V3 neurons were silenced, had a significantly reduced maximal locomotor speed, were unable to move using stable trot, gallop, or bound, and predominantly used lateral-sequence walk. To understand the functional roles of V3 aLPNs, we adapted our previous model of spinal circuitry controlling quadrupedal locomotion (Danner et al., 2017), by incorporating diagonal V3 aLPNs mediating inputs from each lumbar RG to the contralateral cervical RG. The updated model reproduces our experimental results and suggests that locally projecting V3 neurons, mediating left-right interactions within lumbar and cervical cords, promote left-right synchronization necessary for gallop and bound, whereas the V3 aLPNs promote synchronization between diagonal fore and hind RGs necessary for trot. The model proposes the organization of spinal circuits available for future experimental testing.


title: Characterization of Mayer wave oscillations in functional near-infrared spectroscopy using a physiologically informed model of the neural power spectra

abstract:
OverviewO_ST_ABSSignificanceC_ST_ABSMayer waves are spontaneous oscillations in arterial blood pressure that can mask cortical hemodynamic responses associated with neural activity of interest.

AimTo characterize the properties of oscillations in the fNIRS signal generated by Mayer waves in a large sample of fNIRS recordings. Further, we aim to determine the impact of short-channel correction for the attenuation of these unwanted signal components.

ApproachMayer wave oscillation parameters were extracted from 310 fNIRS measurements using the Fitting Oscillations & One-Over-F (FOOOF) method to compute normative values. The effect of short-channel correction on Mayer wave oscillation power was quantified on 222 measurements. The practical benefit of the short-channel correction approach for reducing Mayer waves and improving response detection was also evaluated on a subgroup of 17 fNIRS measurements collected during a passive auditory speech detection experiment.

ResultsMayer-wave oscillations had a mean frequency of 0.108 Hz, bandwidth of 0.04 Hz, and power of 3.5 M2/Hz. The distribution of oscillation signal power was positively skewed, with some measurements containing large Mayer waves. Short-channel correction significantly reduced the amplitude of these undesired signals; greater attenuation was observed for measurements containing larger Mayer-wave oscillations.

ConclusionsA robust method for quantifying Mayer-wave oscillations in the fNIRS signal spectrum was presented and used to provide normative parameterization. Short-channel correction is recommended as an approach for attenuating Mayer waves, particularly in participants with large oscillations.


title: Systems-level analysis of patients treated for acute P. falciparum malaria reveals a role for the humoral response and cytokine milieu in limiting γδ T cell expansion

abstract:
The mechanism of acquisition and maintenance of natural immunity against Plasmodium falciparum malaria remains unclear. Although, clinical immunity develops over time with repeated malaria episodes, disease tolerance is more rapidly acquired compared to protective immunity. It remains unclear, how pre-existing immune responses impacts the mechanism responsible for disease tolerance. Here, we investigated a cohort of returning travelers treated for acute symptomatic P. falciparum malaria, either infected for the first time, or with a previous history of malaria. Through repeated sampling over one year in a malaria free setting, we were able to study the acute and longitudinal effects of the infection. We combined comprehensive immune cell and plasma protein profiling with integrated and data driven analysis, describing the immune landscape from acute disease to one year after infection. We identified a strong association between pro-inflammatory signatures and {gamma}{delta} T cell expansion. The association was significantly impacted by previous exposure to malaria, resulting in a dampened pro-inflammatory response, which translated to reduced V{delta}2+ {gamma}{delta} T cell expansion compared to primary infected individuals. The dampened inflammatory signal was associated with early expansion of Fc{gamma}RIII+ monocytes and parasite-specific antibodies of IgG1 and IgG3 isotypes.

Our data suggest that the interplay of Fc{gamma}RIII+ monocytes and a cytophilic parasite-specific IgG during the early blood stage infection lead to lower parasitemia and a dampened pro-inflammatory response with reduced {gamma}{delta} T cell expansion. This enhanced control and reduced inflammation points to a potential mechanism on how tolerance is established following repeated malaria exposure.

One Sentence SummaryA systems immunology analysis on natural malaria sheds light on disease tolerance mechanism associated with gamma delta T cell expansion

category: immunology


title: Systems analysis shows a role of cytophilic antibodies in shaping innate tolerance to malaria


title: Freshwater dissolved oxygen dynamics: changes due to glyphosate, 2,4-D and their mixture, both under clear and turbid-organic conditions.

abstract: We performed two independent outdoor mesocosm experiments where we measured the variation of DO saturation (DO%) in freshwater after a single input of Roundup Max(R) (G) (glyphosate-based formulation), AsiMax 50(R) (2,4-D) (2,4-D-based formulation) and their mixture (M). Two concentration levels were tested; 0.3 mg/L G and 0.135 mg/L 2,4-D (Low; L) and 3 mg/L G and 1.35 mg/L 2,4-D (High; H). We assayed consolidated microbial communities coming from a system in organic turbid eutrophic status and a system in clear mesotrophic status during 21 and 23 days, respectively. A sample of phytoplankton (micro+nano, pico-eukaryotes, pico-cyanobacteria), mixotrophic algae and heterotrophic bacteria was collected to determine abundances at each of four sampling dates. The clear and turbid systems showed similar, but not synchronized, patterns of daily DO% changes in relation to the controls (DO%v), after exposure to both single and combined formulations. Under glyphosate scenarios (GL, GH, ML and MH), the two types of systems showed similar DO%v but different microbial abundances, being associated to an increase in the micro+nano and pico-eukaryotic phytoplankton fractions for the clear system. In contrast, in the turbid system changes were associated with increased pico-cyanobacteria and decreased mixotrophic algae. Effects of 2,4-D were only observed in the turbid system, leading to decreased micro+nano phytoplankton abundances. Under the turbid scenario, the herbicide mixture at high concentration had a synergistic effect on DO%v and recovery was not detected by the end of the experiment. Our results revealed that herbicides inputs induced changes in phytoplankton abundances that leads to measurable DO variations.


title: Genomic signatures of sexual selection on pollen-expressed genes in Arabis alpina

abstract: Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.


title: Ether Lipid Biosynthesis Promotes Lifespan Extension and Enables Diverse Prolongevity Paradigms

abstract:
Biguanides, including the worlds most commonly prescribed drug for type 2 diabetes, metformin, not only lower blood sugar, but also promote longevity in preclinical models. Epidemiologic studies in humans parallel these findings, indicating favorable effects of metformin on longevity and on reducing the incidence and morbidity associated with aging-related diseases, such as cancer. In spite of these promising observations, the full spectrum of the molecular effectors responsible for these health benefits remains elusive. Through unbiased genetic screening in C. elegans, we uncovered a novel role for genes necessary for ether lipid biosynthesis in the favorable effects of biguanides. We demonstrate that biguanides govern lifespan extension via a complex effect on the ether lipid landscape requires enzymes responsible for both ether lipid biogenesis and polyunsaturated fatty acid synthesis. Remarkably, loss of the ether lipid biosynthetic machinery also mitigates lifespan extension attributable to dietary restriction, target of rapamycin (TOR) inhibition, and mitochondrial electron transport chain inhibition. Furthermore, overexpression of a single, key ether lipid biosynthetic enzyme, fard-1/FAR1, is sufficient to promote lifespan extension. These findings illuminate the ether lipid biosynthetic machinery as a novel therapeutic target to promote healthy aging.

Significance StatementMetformin is the most widely used drug to treat patients with type 2 diabetes and extends lifespan in multiple species, yet the molecular targets responsible for these prolongevity benefits remain incompletely understood. To this end, we demonstrate that a subset of lipids, known as ether lipids, are necessary for biguanides anti-aging effects and various other paradigms of lifespan extension. Strikingly, modulation of the machinery responsible for ether lipid biosynthesis is sufficient to stimulate lifespan extension, illuminating the possibility of using these lipids as therapeutic targets to promote healthy aging.


title: Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica

abstract: The gray short-tailed opossum is an established laboratory-bred marsupial model for biomedical research. It serves as a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs. ancestral states of genomic/epigenomic characteristics for all eutherian mammal lineages. To characterize the current genetic profile of this laboratory marsupial, we examined 79 individuals from eight established laboratory strains. Double digest restriction-site associated DNA sequencing (ddRAD-seq) and whole-genome resequencing experiments were performed to investigate the genetic architecture in these strains. A total of 66,640 high-quality single nucleotide polymorphisms (SNPs) were identified. We analyzed SNP density, average heterozygosity, nucleotide diversity, and population differentiation parameter Fst within and between the eight strains. Principal component and population structure analysis clearly resolve the strains at the level of their ancestral founder populations, and the genetic architecture of these strains correctly reflects their breeding history. We confirmed the successful establishment of the first inbred laboratory opossum strain LSD (inbreeding coefficient F > 0.99) and a nearly inbred strain FD2M1 (0.98 < F < 0.99), each derived from a different ancestral background. These strains are suitable for various experimental protocols requiring controlled genetic backgrounds and for intercrosses and backcrosses that can generate offspring with informative SNPs for studying a variety of genetic and epigenetic processes. Together with recent advances in reproductive manipulation and CRISPR/Cas9 techniques for M. domestica, the existence of distinctive inbred strains will enable genome editing on different genetic backgrounds, greatly expanding the utility of this marsupial model for biomedical research.


title: Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

abstract: Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on their associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.), in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.


title: Green synthesis of silver nanoparticles using psychrotolerant strains of Tulasnella albida from South Orkney Islands (Antarctica)

abstract: Nanoparticles are widely studied due to their possible uses in biological and technological systems. Four psychrotolerant strains of Tulasnella albida isolated from Antarctica were tested and compared in their ability to synthesize silver nanoparticles. The four strains were capable of synthesizing silver nanoparticles with the addition of AgNO3 (final concentration of 0.5 mM), showing similar results under the same conditions: 28{degrees}C, 200 rpm, pH 9. Additionally, we registered the synthesis of nanoparticles at 6{degrees}C using biomass generated at the same temperature. For the characterization of synthesized nanoparticles, TEM and SEM microscopy analyses were performed. The images obtained showed the existence of spherically shaped silver nanoparticles with a log-normal size distribution centered at 2 nm diameter for 28{degrees}C. The largest ones showed a capping shell around them, appearing associated with the formation of small silver nanoparticles. Theoretical calculations of optical absorption based on core-shell Ag-Ag2O nanoparticles were used to characterize the experimental absorption spectra of silver nanoparticles colloids. This work contributes to expanding the studies and possible technological applications of psychrotolerant organisms in the industry, particularly in the green synthesis of nanoparticles at suboptimal conditions.

category: bioengineering


title: Clinically Relevant Mathematical Model for the BCG-based Treatment Of Type 1 Diabetes

abstract:
This work introduces a model of immunotherapy treatment, namely the Bacillus Calmette-Guerin (BCG) vaccine, of type 1 diabetes (T1D). The model takes into consideration a clinically relevant interaction network between multiple immune cells and compartments. A set of ordinary differential equations (ODEs) is introduced to capture the connectivity between these variables and clinical presentation of the disease. Four subsets of the T1D patients and healthy controls that exhibit normal and high-level glucose consumption are evaluated. The results that obtained for mice, suggest that BCG treatment of the T1D patients that follow healthy eating habits normalizes glucose to levels observed in non-diabetic controls. Furthermore, glucose consumption profoundly influences disease progression. The stable equilibrium state with constant glucose levels is not attainable without repeated BCG treatment. This outcome suggests that immunotherapy may modulate molecular and cellular manifestations of the disease but it does not eliminate T1D. Of note, our data indicate that the BCG immunotherapy treatment may benefit healthy controls on a high-glucose diet. One may speculate the preventive BCG treatment to provide long-term health benefits in this specific cohort.

Author summaryWe proposed a clinically relevant mathematical model of Bacillus Calmette-Guerin (BCG) based immunotherapy for type 1 diabetes (T1D) treatment. The model shows that BCG treatment is able to delay the T1D effects and to provide long-term health benefits while it may modulate molecular and cellular manifestations of the disease but it does not eliminate T1D. The main advantage of the proposed model is the ability to personalize the treatment protocol according to the patients metabolism and diet.


title: MrParse: Finding homologues in the PDB and the EBI AlphaFold database for Molecular Replacement and more

abstract: Crystallographers have an array of search model options for structure solution by Molecular Replacement (MR). Well-established options of homologous experimental structures and regular secondary structure elements or motifs are increasingly supplemented by computational modelling. Such modelling may be carried out locally or use pre-calculated predictions retrieved from databases such as the EBI AlphaFold database. MrParse is a new pipeline to help streamline the decision process in MR by consolidating bioinformatic predictions in one place. When reflection data are provided, MrParse can rank any homologues found using eLLG which indicates the likelihood that a given search model will work in MR. In-built displays of predicted secondary structure, coiled-coil and transmembrane regions further inform the choice of MR protocol. MrParse can also identify and rank homologues in the EBI AlphaFold database, a function that will also interest other structural biologists and bioinformaticians.


title: Extensive germline-somatic interplay drives prostate cancer through HNF1B co-option of TMPRSS2-ERG

abstract: Genome-wide association studies have identified 270 loci conferring risk for prostate cancer (PCa), yet the underlying biology and clinical impact remain to be investigated. Here we observe an enrichment of transcription factor genes including HNF1B within PCa risk-associated regions. While focused on the 17q12/HNF1B locus, we find a strong eQTL for HNF1B and multiple potential causal variants involved in the regulation of HNF1B expression in PCa. An unbiased genome-wide co-expression analysis reveals PCa-specific somatic TMPRSS2-ERG fusion as a transcriptional mediator of this locus and the HNF1B eQTL signal is ERG fusion status dependent. We investigate the role of HNF1B and find its involvement in several pathways related to cell cycle progression and PCa severity. Furthermore, HNF1B interacts with TMPRSS2-ERG to co-occupy large proportion of genomic regions with a remarkable enrichment of additional PCa risk alleles. We finally show that HNF1B co-opts ERG fusion to mediate mechanistic and biological effects of the PCa risk-associated locus 17p13.3/VPS53/FAM57A/GEMIN4. Taken together, we report an extensive germline-somatic interaction between TMPRSS2-ERG fusion and genetic variations underpinning PCa risk association and progression.


title: Simultaneous Dissection of Grain Carotenoid Levels and Kernel Color in Biparental Maize Populations with Yellow-to-Orange Grain

abstract: Maize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the U.S. maize nested association mapping population that have yellow to orange grain. Quantitative trait loci (QTL) were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color QTL ranging from 2.4 to 17.5%. These QTL were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized [~]27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the - or {beta}-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with {beta}-branch and total carotenoids and negligible correlations with -branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.


title: Pubertal sex hormones control transcriptional trajectories in the medial preoptic area

abstract: Pubertal maturation aids development of emotion, cognition, and reproduction. We investigated transcriptional dynamics in the medial preoptic area (MPOA), a hypothalamic center for reproductive behaviors, in male and female mice at single-cell resolution (scRNAseq) during puberty. Defined subsets of neurons expressing Slc32a1 and Esr1 (Vgat+ Esr1+) were the most transcriptionally dynamic compared to other cell types throughout puberty. These cell type specific transcriptional progressions towards adulthood were bidirectionally controlled by the levels of circulating testosterone and estradiol. Selective deletion of Esr1 in Slc32a1-expressing cells in the MPOA prior to puberty arrested transcriptional progression and revealed a sexually dimorphic gene-regulatory network governed by Esr1. Deletion of Esr1 in Vgat+ cells prevented the development of mating behavior in both sexes. These analyses reveal both sexually common and dimorphic transcriptional progressions during puberty as well as their regulatory mechanisms, which have important implications towards understanding adaptative and maladaptive processes governing adolescent brain development.


title: Central hormone-sensitive lipase is located at synapses and is necessary for normal memory performance in mice

abstract: Hormone-sensitive lipase (HSL) is mainly present in the adipose tissue where it hydrolyses diacylglycerol. Although brain expression of HSL has been reported, its presence in different cellular compartments is uncertain, and its role in regulating brain lipid metabolism remains hitherto unexplored. We propose that HSL has a role in regulating the availability of bioactive lipids necessary for adequate neuronal function. Therefore, we tested the hypothesis that dampening HSL activity leads to brain dysfunction. We found HSL protein and activity throughout all the mouse brain, localised in neurons and especially enriched in synapses. HSL null mice were then analysed using a battery of behavioural tests. Relative to wild-type littermates, HSL null mice showed impaired short- and long-term memory, but preserved exploratory behaviours. Molecular analysis of the cortex and hippocampus showed increased expression of genes involved in glucose utilization in the hippocampus but not cortex of HSL null mice compared to controls. Lipidomics analyses indicated an impact of HSL deletion on the profile of bioactive lipids, including endocannabinoids and eicosanoids that are known to modulate neuronal activity, cerebral blood blow and inflammation processes. Accordingly, mild increases in expression of pro-inflammatory cytokines suggest low grade inflammation in HSL null mice compared to littermates. We conclude that HSL has a homeostatic role in maintaining pools of lipids that are needed for brain function. It remains to be tested, however, whether the recruitment of HSL for the synthesis of these lipids occurs during increased neuronal activity, or whether HSL participates in neuroinflammatory responses.


title: Chronic exposure to odors at naturally occurring concentrations triggers limited plasticity in early stages of Drosophila olfactory processing

abstract: In insects and mammals, chronic exposure to odors at high concentrations in early life alters olfactory function, but the role of odor experience-dependent plasticity in more naturalistic contexts is less clear. We investigated olfactory plasticity in the Drosophila antennal lobe by exposing flies to odors at concentrations that are typically encountered in natural odor sources. These stimuli also strongly and selectively activated only a single class of olfactory receptor neuron (ORN) input, facilitating the investigation of input-specific plasticity. Overall, chronic exposure to three such odors elicited limited plasticity in the odor responses of second-order projection neurons (PNs). Exposure to some odors elicited mild increases in PN responses to weak stimuli, extending the lower bound of the dynamic range of PN signaling. When present, plasticity was observed broadly in multiple PN types and thus was not selective for PNs receiving direct input from the chronically active ORNs. Chronic E2-hexenal exposure did not affect PN intrinsic properties, local inhibitory innervation, ORN responses, or ORN-PN synaptic strength, but modestly increased broad lateral excitation evoked by some odors. These results show that PN odor coding is only mildly affected by strong persistent activation of a single olfactory input and highlight the stability of early stages of insect olfactory processing to significant perturbations in the sensory environment.


title: Coding of social odors in the hippocampal CA2 region as a substrate for social memory

abstract: The ability to encode and update information about individuals is critical for lasting social relationships. Although the hippocampus is important for social recognition memory, its underlying neural representations remain elusive. Here we investigate the neural codes mediating social recognition and learning by examining social odor recognition and associative odor-reward learning in mice. We performed high-resolution calcium imaging from the hippocampal CA2 region of awake head-fixed mice, as CA2 is necessary for social recognition memory. We find that CA2 encodes specific neural representations of novel social odors that are further refined during associative odor-reward learning. Optogenetic silencing of CA2 impairs the formation of reward associations. Furthermore, CA2 population activity represents odors in a geometry that enables abstract representations of social versus non-social odors. Thus, CA2 distinguishes multiple forms of olfactory stimuli to enhance the learning of social odors and associations, which are poised to serve as substrates of social memory.


title: Characterization of SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.618 on cell entry, host range, and sensitivity to convalescent plasma and ACE2 decoy receptor

abstract: Recently, highly transmissible SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.618 were identified in India with mutations within the spike proteins. The spike protein of Kappa contains four mutations E154K, L452R, E484Q and P681R, and Delta contains L452R, T478K and P681R, while B.1.618 spike harbors mutations {Delta}145-146 and E484K. However, it remains unknown whether these variants have altered in their entry efficiency, host tropism, and sensitivity to neutralizing antibodies as well as entry inhibitors. In this study, we found that Kappa, Delta or B.1.618 spike uses human ACE2 with no or slightly increased efficiency, while gains a significantly increased binding affinity with mouse, marmoset and koala ACE2 orthologs, which exhibits limited binding with WT spike. Furthermore, the P618R mutation leads to enhanced spike cleavage, which could facilitate viral entry. In addition, Kappa, Delta and B.1.618 exhibits a reduced sensitivity to neutralization by convalescent sera owning to the mutation of E484Q, T478K, {Delta}145-146 or E484K, but remains sensitive to entry inhibitors-ACE2-lg decoy receptor. Collectively, our study revealed that enhanced human and mouse ACE2 receptor engagement, increased spike cleavage and reduced sensitivity to neutralization antibodies of Kappa, Delta and B.1.618 may contribute to the rapid spread of these variants and expanded host range. Furthermore, our result also highlighted that ACE2-lg could be developed as broad-spectrum antiviral strategy against SARS-CoV-2 variants.

category: microbiology


title: SARS-CoV-2 infection activates dendritic cells via cytosolic receptors rather than extracellular TLRs

abstract:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), an infectious disease characterized by strong induction of inflammatory cytokines, progressive lung inflammation and potentially multi-organ dysfunction. It remains unclear whether SARS-CoV-2 is sensed by pattern recognition receptors (PRRs) leading to immune activation. Several studies suggest that the Spike (S) protein of SARS-CoV-2 might interact with Toll-like receptor 4 (TLR4) and thereby activate immunity. Here we have investigated the role of TLR4 in SARS-CoV-2 infection and immunity. Neither exposure of isolated S protein, SARS-CoV-2 pseudovirus nor a primary SARS-CoV-2 isolate induced TLR4 activation in a TLR4-expressing cell line. Human monocyte-derived dendritic cells (DCs) express TLR4 but not ACE2, and DCs were not infected by a primary SARS-CoV-2 isolate. Notably, neither S protein nor the primary SARS-CoV-2 isolate induced DC maturation or cytokines, indicating that both S protein and SARS-CoV-2 virus particles do not trigger extracellular TLRs, including TLR4. Ectopic expression of ACE2 in DCs led to efficient infection by SARS-CoV-2. Strikingly, infection of ACE2-positive DCs induced type I IFN and cytokine responses, which was inhibited by antibodies against ACE2. These data strongly suggest that not extracellular TLRs but intracellular viral sensors are key players in sensing SARS-CoV-2. These data imply that SARS-CoV-2 escapes direct sensing by TLRs, which might underlie the lack of efficient immunity to SARS-CoV-2 early during infection.

Author summaryThe immune system needs to recognize pathogens such as SARS-CoV-2 to initiate antiviral immunity. Dendritic cells (DCs) are crucial for inducing antiviral immunity and are therefore equipped with both extracellular and intracellular pattern recognition receptors to sense pathogens. However, it is unknown if and how SARS-CoV-2 activates DCs. Recent research suggests that SARS-CoV-2 is sensed by extracellular Toll-like receptor 4 (TLR4). We have previously shown that DCs do not express ACE2, and are therefore not infected by SARS-CoV-2. Here we show that DCs do not become activated by exposure to viral Spike proteins or SARS-CoV-2 virus particles. These findings suggest that TLR4 and other extracellular TLRs do not sense SARS-CoV-2. Next, we expressed ACE2 in DCs and SARS-CoV-2 efficiently infected these ACE2-positive DCs. Notably, infection of ACE2-positive DCs induced an antiviral immune response. Thus, our study suggests that infection of DCs is required for induction of immunity, and thus that intracellular viral sensors rather than extracellular TLRs are important in sensing SARS-CoV-2. Lack of sensing by extracellular TLRs might be an escape mechanism of SARS-CoV-2 and could contribute to the aberrant immune responses observed during COVID-19.


title: Wildlife in Cameroon harbor diverse coronaviruses including many isolates closely related to human coronavirus 229E

abstract:
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. SARS-CoV-2 highlights the global impact emergence events can have. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations.

We sampled and tested wildlife in the central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection.

Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n=8) and beta (n=9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human derived HCoV-229E isolates closest to those from camels in terms of the S and N genes, but closest to isolates from bats for the E, M, and RdRp genes. The CoV RNA positivity rate in bats varied significantly (p<0.001) between the wet (8.2%) and dry season (4.5%). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found.

Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.


title: Excitatory neurotransmission activates compartmentalized calcium transients in Müller glia without affecting lateral process motility

abstract: Neural activity has been implicated in the motility and outgrowth of glial cell processes throughout the central nervous system. Here we explore this phenomenon in Muller glia, which are specialized radial astroglia that are the predominant glial type of the vertebrate retina. Muller glia extend fine filopodia-like processes into retinal synaptic layers, in similar fashion to brain astrocytes and radial glia which exhibit perisynaptic processes. Using two-photon volumetric imaging, we found that during the second postnatal week, Muller glial processes were highly dynamic, with rapid extensions and retractions that were mediated by cytoskeletal rearrangements. During this same stage of development, retinal waves led to increases in cytosolic calcium within Muller glial lateral processes and stalks. These comprised distinct calcium compartments, distinguished by variable participation in waves, timing, and sensitivity to an M1 muscarinic acetylcholine receptor antagonist. However, we found that motility of lateral processes was unaffected by the presence of pharmacological agents that enhanced or blocked wave-associated calcium transients. Finally, we found that mice lacking normal cholinergic waves in the first postnatal week also exhibited normal Muller glial process morphology. Hence, outgrowth of Muller glial lateral processes into synaptic layers is determined by factors that are independent of neuronal activity.


title: Top-down identification of keystone species in the microbiome

abstract: Keystone species in ecological communities are native species that play an especially important role in the stability of their ecosystem and can also be potentially used as its main drivers. However, we still lack an effective framework for identifying these species from the available metagenomic data without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the species. Our method does not assume pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real metagenomic data of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module - multiple candidate keystones species with correlated occurrence. The keystones analysis of single-time-point cross-sectional data is also later verified by evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.


title: Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs

abstract:
Significant alterations in signaling pathways and transcriptional regulatory programs together represent major hallmarks of many cancers. These, among all, include the reactivation of stemness, which is registered by the expression of pathways that are active in the embryonic stem cells (ESCs). Here, we assembled gene sets that reflect the stemness and proliferation signatures and used them to analyze a large panel of RNA-seq data from The Cancer Genome Atlas (TCGA) Consortium in order to specifically assess the expression of stemness-related and proliferation-related genes across a collection of different tumor types. We introduced a metric that captures the collective similarity of the expression profile of a tumor to that of ESCs, which showed that stemness and proliferation signatures vary greatly between different tumor types. We also observed a high degree of intertumoral heterogeneity in the expression of stemness- and proliferation-related genes, which was associated with increased hazard ratios in a fraction of tumors and mirrored by high intratumoral heterogeneity across cancer cells in single cell RNA-seq datasets. Taken together, these results indicate that the expression of stemness signatures is highly heterogeneous and cannot be used as a universal determinant of cancer. This calls into question the universal validity of diagnostic tests that are based on stem cell markers.

Author summaryCancer is a deadly human disease which is characterized by uncontrolled proliferation of abnormal cells. Stemness, or the expression of stem cell markers, has been identified as a key feature for cancer progression and in many cases correlates with patient survival. In this work, we reanalyzed a large cohort of cancers from TCGA (The Cancer Genome Atlas) collection and single-cell cancer data, and found that the degree of stemness reactivation varies greatly between different tumor types, between different tumors of the same type, and also different cells within a tumor. The observed stemness heterogeneity implies that the expression of stemness markers cannot be used as a universal determinant of cancer and calls into question the validity of stemness-based tests that are frequently used for cancer diagnostics.


title: Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites

abstract: The prevalent one-dimensional alignment of genomic signals to a reference landmark is a cornerstone of current methods to study transcription and its DNA-dependent processes but it is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. We analyzed transcription in human and uncovered a complex dependence on the relative position of neighboring transcription start sites (TSSs) that is consistently conserved among cell types. The dependence ranges from enhancement to suppression of transcription depending on the relative distances to the TSSs, their intragenic position, and the transcriptional activity of the gene. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.


title: Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data

abstract:
BackgroundBiomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize schema.org or other biomedical schema projects.

ResultsOur browser-based tool includes features which can help address many of the barriers towards schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema--a large multi-class schema for harmonizing various COVID-19 related resources.

ConclusionsWe have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR.


title: XSTREME: Comprehensive motif analysis of biological sequence datasets

abstract: XSTREME is a web-based tool for performing comprehensive motif discovery and analysis in DNA, RNA or protein sequences, as well as in sequences in user-defined alphabets. It is designed for both very large and very small datasets. XSTREME is similar to the MEME-ChIP tool, but expands upon its capabilities in several ways. Like MEME-ChIP, XSTREME performs two types of de novo motif discovery, and also performs motif enrichment analysis of the input sequences using databases of known motifs. Unlike MEME-ChIP, which ranks motifs based on their enrichment in the centers of the input sequences, XSTREME uses enrichment anywhere in the sequences for this purpose. Consequently, XSTREME is more appropriate for motif-based analysis of sequences regardless of how the motifs are distributed within the sequences. XSTREME uses the MEME and STREME algorithms for motif discovery, and the recently developed SEA algorithm for motif enrichment analysis. The interactive HTML output produced by XSTREME includes highly accurate motif significance estimates, plots of the positional distribution of each motif, and histograms of the number of motif matches in each sequences. XSTREME is easy to use via its web server at https://meme-suite.org, and is fully integrated with the widely-used MEME Suite of sequence analysis tools, which can be freely downloaded at the same web site for non-commercial use.


title: PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface

abstract: Peptide docking can be perceived as a subproblem of protein-protein docking. However, due to the short length and flexible nature of peptides, many do not adopt one defined conformation prior to binding. Therefore, to tackle a peptide docking problem, not only the relative orientation between the two partners, but also the bound conformation of the peptide needs to be modeled. Traditional peptide-centered approaches use information about the peptide sequence to generate a representative conformer ensemble, which can then be rigid body docked to the receptor. Alternatively, one may look at this problem from the viewpoint of the receptor, namely that the protein surface defines the peptide bound conformation.We present PatchMAN (Patch-Motif AligNments), a novel peptide docking approach which uses structural motifs to map the receptor surface with backbone scaffolds extracted from protein structures. On a non-redundant set of protein-peptide complexes, starting from free receptor structures, PatchMAN successfully models and identifies near-native peptide-protein complexes in 62% / 81% within 2.5[A] / 5[A] RMSD, with corresponding sampling in 81% / 100% of the cases, outperforming other approaches. PatchMAN leverages the observation that structural units of peptides with their binding pocket can be found not only within interfaces, but also within monomers. We show that the conformation of the bound peptide is sampled based on the structural context of the receptor only, without taking into account any sequence information. Beyond peptide docking, this approach opens exciting new avenues to study principles of peptide-protein association, and to the design of new peptide binders.