title: Function of AtPGAP1 in GPI anchor lipid remodeling and transport to the cell surface of GPI-anchored proteins

abstract:
GPI-anchored proteins (GPI-APs) play an important role in a variety of plant biological processes including growth, stress response, morphogenesis, signalling and cell wall biosynthesis. The GPI-anchor contains a lipid-linked glycan backbone that is synthesized in the endoplasmic reticulum (ER) where it is subsequently transferred to the C-terminus of proteins containing a GPI signal peptide by a GPI transamidase. Once the GPI anchor is attached to the protein, the glycan and lipid moieties are remodelled. In mammals and yeast, this remodelling is required for GPI-APs to be included in Coat Protein II (COPII) coated vesicles for their ER export and subsequent transport to the cell surface. The first reaction of lipid remodelling is the removal of the acyl chain from the inositol group by Bst1p (yeast) and PGAP1 (mammals). In this work, we have used a loss-of-function approach to study the role of PGAP1/Bst1 like genes in plants. We have found that Arabidopsis PGAP1 localizes to the ER and probably functions as the GPI inositol-deacylase which cleaves the acyl chain from the inositol ring of the GPI anchor. In addition, we show that PGAP1 function is required for efficient ER export and transport to the cell surface of GPI-APs.

One sentence summaryGPI anchor lipid remodeling in GPI-anchored proteins is required for their transport to the cell surface in Arabidopsis.

category: cell biology


title: Dual regulation of the actin cytoskeleton by CARMIL-GAP

abstract:
CARMIL (Capping protein Arp2/3 Myosin I Linker) proteins are multi-domain scaffold proteins that regulate actin dynamics by regulating the activity of Capping Protein (CP). Here we characterize CARMIL-GAP, a Dictyostelium CARMIL isoform that contains a ~130 residue insert that, by homology, is a GTPase activating (GAP) domain for Rho-related GTPases. Consistently, this GAP domain binds Dictyostelium Rac1a and accelerates its rate of GTP hydrolysis. CARMIL-GAP concentrates with F-actin in phagocytic cups and at the leading edge of chemotaxing cells, and CARMIL-GAP null cells exhibit pronounced defects in phagocytosis and chemotactic streaming. Importantly, these defects are fully rescued by expressing GFP-tagged CARMIL-GAP in CARMIL-GAP null cells. Finally, rescue with versions of CARMIL-GAP that lack either GAP activity or the ability to regulate CP show that while both activities contribute significantly to CARMIL-GAP function, the GAP activity plays the bigger role. Together, our results add to the growing evidence that CARMIL proteins influence actin dynamics by regulating signaling molecules as well as CP, and that the continuous cycling of the Rho GTPases nucleotide state is often required to drive Rho-dependent biological processes.

SUMMARY STATEMENTThe assembly of actin filaments supports a wide array of fundamental cellular functions, including cell migration and phagocytosis. Actin assembly is controlled by a host of regulatory proteins, with Capping Protein being one of the most important. Capping Protein is in turn regulated by the CARMIL family of proteins. Actin assembly is also controlled by signaling pathways that often converge on Rho-related GTPases like Rac1. These GTPases cycle between an active, GTP-bound state and an inactive, GDP-bound state. Guanine nucleotide exchange factors (GEFs) and guanine nucleotide activating proteins (GAPs) drive Rho-related GTPases to their GTP-bound and GDP-bound states, respectively. Here we characterized a version of CARMIL that contains within it a GAP domain for Rac1. We show that CARMIL-GAP supports the actin-based processes of cell migration and phagocytosis. We also show that while CARMIL-GAPs ability to regulate Capping Protein and the nucleotide state of Rac1 are both important for its cellular functions, its ability to regulate Rac1 via its GAP domain plays the bigger role. Finally, our data support the emerging concept that the continuous cycling of Rho GTPases between their GTP- bound and GDP-bound states is often required to drive Rho-dependent biological processes.


title: A multi-phase multi-objective dynamic genome-scale model shows different redox balancing among yeast species in fermentation

abstract:
Yeasts constitute over 1500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts metabolic specificity in batch cultures. Here we propose a multi-phase multi-objective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic model describing the time-varying culture environment. Besides, we proposed a multi-phase multi-objective flux balance analysis to compute the dynamics of intracellular fluxes. We then compared the metabolism of S. cerevisiae and S. uvarum strains in a rich medium fermentation. The model successfully explained the experimental data and brought novel insights into how cryotolerant strains achieve redox balance. The proposed model (along with the corresponding code) provides a comprehensive picture of the main steps occurring inside the cell during batch cultures and offers a systematic approach to prospect or metabolically engineering novel yeast cell factories.

IMPORTANCENon-conventional yeast species hold the promise to provide novel metabolic routes to produce industrially relevant compounds and tolerate specific stressors, such as cold temperatures. This work presented and validated the first multi-phase multi-objective genome-scale dynamic model to describe carbon and nitrogen metabolism throughout batch fermentation. To test and illustrate its performance, we considered the comparative metabolism of three yeast strains of the Saccharomyces genus in rich medium fermentation. The study revealed that cryotolerant Saccharomyces species might use the GABA shunt and the production of reducing equivalents as alternative routes to achieve redox balance, a novel biological insight worth being explored further. The proposed model (along with the provided code) can be applied to a wide range of batch processes started with different yeast species and media, offering a systematic and rational approach to prospect non-conventional yeast species metabolism and engineering novel cell factories.

category: systems biology


title: Structure and dynamics of the SARS-CoV-2 envelope protein monomer

abstract: Coronaviruses, especially SARS-CoV-2, present an ongoing threat for human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic -helical transmembrane domain (TMD) and amphiphilic -helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43 and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the E protein both generates and senses the membrane curvature, preferably localizing with the C-terminus at the convex regions of the membrane. This may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate budding of the viral particles. The presented results may be helpful for better understanding of the function of coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.

category: biophysics


title: iEC7871 Quercus suber model: the first multi-tissue diel cycle genome-scale metabolic model of a woody tree

abstract: In the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behavior at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871), the first of a woody plant. The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyze the pathways associated with the synthesis of suberin monomers. Nevertheless, the models developed in this work can provide insights into other aspects of the metabolism of Q. suber, such as its secondary metabolism and cork formation.


title: The first multi-tissue diel genome-scale metabolic model of a woody plant highlights the suberin biosynthesis pathways in Quercus suber


title: A conversion from slow to fast memory in response to passive motion

abstract: When the same perturbation is experienced consecutively, learning is accelerated on the second attempt. This savings is a central property of sensorimotor adaptation. Current models suggest that these improvements in learning are due to changes in the brains sensitivity to error. Here, we tested whether these increases in error sensitivity could be facilitated by passive movement experiences. In each experimental group, the robot moved the arm passively in the direction that solved the upcoming rotation, but no visual feedback was provided. Then, following a break in time, participants adapted to a visuomotor rotation. Prior passive movements substantially improved motor learning, increasing total compensation in each group by approximately 30%. Similar to savings, a state-space model suggested that this improvement in learning was due to an increase in error sensitivity, but not memory retention. Thus, passive memories appeared to increase the motor learning systems sensitivity to error. However, some features in the observed behavior were not captured by this model, nor by similar empirical models, which assumed that learning was due a single exponential process. When we considered the possibility that learning was supported by parallel fast and slow adaptive processes, a striking pattern emerged; whereas initial improvements in learning were driven by a slower adaptive state, increases in error sensitivity gradually transferred to a faster learning system with the passage of time.

category: neuroscience


title: Location, location, location- choice of Voxel-Based Morphometry processing pipeline drives variability in the location of neuroanatomical brain markers

abstract: Fundamental and clinical neuroscience has benefited from the development of automated computational analyses of Magnetic Resonance Imaging (MRI) data, such as Voxel-based Morphometry (VBM). VBM determines regional gray matter variations with high spatial resolution and results are commonly interpreted in a regional-specific manner, for instance with respect to which specific brain regions differ in volume between women and men. In excess of 600 papers using VBM are now published every year and a number of different automated VBM processing pipelines are frequently used in analyses although it remains to be fully and systematically assessed whether they come up with the same answers. Here we have therefore examined variability between four commonly used VBM pipelines in two large brain structural datasets. Spatial similarity, reproducibility and reliability of the processed gray matter brain maps was generally low between pipelines. Examination of sex-differences and age-related changes in gray matter volumes revealed considerable differences between the pipelines in terms of the specific regions identified as well as meta-analytic characterization of their function. In contrast, applying machine learning-based multivariate analyses allowed an accurate prediction of sex or age based on the gray matter maps across pipelines, although prediction accuracy differed strongly between them. Together the findings suggest that the choice of pipeline alone leads to considerable variability in brain structural analyses which poses a serious challenge for reproducibility as well as interpretation.


title: Inner hair cell dysfunction in Klhl18 mutant mice leads to low frequency progressive hearing loss

abstract:
Age-related hearing loss in humans (presbycusis) typically involves impairment of high frequency sensitivity before becoming progressively more severe at lower frequencies. Pathologies initially affecting lower frequency regions of hearing are less common. Here we describe a progressive, predominantly low-frequency hearing impairment in two mutant mouse lines, carrying different mutant alleles of the Klhl18 gene: a spontaneous missense mutation (Klhl18lowf) and a targeted mutation (Klhl18tm1a(KOMP)Wtsi). Both males and females were studied, and the two mutant lines showed similar phenotypes. Auditory brainstem response (ABR) thresholds (a measure of auditory nerve and brainstem neural activity) were normal at 3 weeks old but showed progressive increases from 4 weeks onwards. In contrast, distortion product otoacoustic emission (DPOAE) sensitivity and amplitudes (a reflection of cochlear outer hair cell function) remained normal in mutants. Electrophysiological recordings from the round window of Klhl18lowf mutants at 6 weeks old revealed 1) raised compound action potential thresholds that were similar to ABR thresholds, 2) cochlear microphonic potentials that were normal compared with wildtype and heterozygous control mice and 3) summating potentials that were reduced in amplitude compared to control mice. Scanning electron microscopy showed that Klhl18lowf mutant mice had abnormally tapering inner hair cell stereocilia in the apical half of the cochlea while their synapses appeared normal. These results suggest that Klhl18 is necessary to maintain inner hair cell stereocilia and normal inner hair cell function at low frequencies. Klhl18 mutant mice exhibit an uncommon low frequency hearing impairment with physiological features consistent with Auditory Neuropathy Spectrum Disorder (ANSD).

SIGNIFICANCE STATEMENTWe describe a novel progressive hearing loss in Klhl18 mutant mice that affects the lower frequencies of its hearing range. Investigation of two mutant alleles of this gene revealed primary inner hair cell defects affecting the neural output of the cochlea while outer hair cell function appeared normal. The tallest stereocilia of inner hair cells showed an abnormal tapering shape, especially notable in the apical half of the cochlear duct corresponding to the low frequency hearing loss. Our finding of a primary inner hair cell defect associated with raised thresholds for auditory brainstem responses combined with normal outer hair cell function suggests that Klhl18 deficiency and inner hair cell pathology may contribute to Auditory Neuropathy Spectrum Disorder in humans.


title: Distinct foraging strategies generated by single-action behavioural flexibility

abstract: Animals with diverse diets must adapt their food priorities to a wide variety of environmental conditions. This diet optimization problem is especially complex for predators that compete with prey for food. Although predator-prey competition is widespread and ecologically critical, it remains difficult to disentangle predatory and competitive motivations for attacking competing prey. Here, we dissect the foraging decisions of the omnivorous nematode Pristionchus pacificus to reveal that its seemingly failed predatory attempts against Caenorhabditis elegans are actually motivated acts of efficacious territorial aggression. While P. pacificus easily kills and eats larval C. elegans with a single bite, adult C. elegans typically survives and escapes from bites. However, nonfatal biting can provide competitive benefits by reducing access of adult C. elegans and its progeny to bacterial food that P. pacificus also eats. We show that P. pacificus considers costs and benefits of both predatory and territorial outcomes to decide which food goal, prey or bacteria, should guide its motivation for biting. These predatory and territorial motivations impose different sets of rules for adjusting willingness to bite in response to changes in bacterial abundance. In addition to biting, predatory and territorial motivations also influence which search tactic P. pacificus uses to increase encounters with C. elegans. When treated with an octopamine receptor antagonist, P. pacificus switches from territorial to predatory motivation for both biting and search. Overall, we demonstrate that P. pacificus assesses alternate outcomes of attacking C. elegans and flexibly reprograms its foraging strategy to prioritize either prey or bacterial food.


category: animal behavior and cognition


title: Flexible reprogramming of Pristionchus pacificus motivation for attacking Caenorhabditis elegans in predator-prey competition


title: Task switching costs contribute to the apparent speeding of multisensory reaction times

abstract: Faster reaction times for the detection of multisensory compared to unisensory stimuli are considered a hallmark of multisensory integration. While this multisensory redundant signals effect (RSE) has been reproduced many times, it has also been repeatedly criticized as confounding multisensory integration and general task switching effects. When unisensory and multisensory conditions are presented in random order, some trials repeat the same sensory-motor association (e.g. an auditory followed by an auditory trial), while others switch this association (e.g. an auditory followed by a visual trial). This switch may slow down unisensory reaction times and inflate the observed RSE. Following this line of ideas, we used an audio-visual detection task and quantified the RSE for trials derived from pure unisensory blocks and trials from mixed blocks involving a repeat or switch of modalities. The RSE was largest for switch trials and smallest for unisensory trials. In fact, during unisensory blocks the multisensory reaction times did not differ from predictions by the race model, speaking against a genuine multisensory benefit. These results confirm that the observed multisensory RSE can be easily confounded by task switching costs, and suggest that the true benefit of multisensory stimuli for reaction speed may often be overestimated.


title: Nanoscopic dopamine transporter distribution and conformation are inversely regulated by excitatory drive and D2-autoreceptor activity

abstract: The nanoscopic organization and regulation of individual molecular components in presynaptic varicosities of neurons releasing modulatory volume neurotransmitters like dopamine (DA) remain largely elusive. Here we show by application of several single-molecule sensitive super-resolution microscopy techniques to cultured neurons and mouse striatal slices, that the dopamine transporter (DAT), a key protein in varicosities of dopaminergic neurons, exists in the membrane in dynamic equilibrium between an inward-facing nanodomain-localized and outward-facing unclustered configuration. The balance between these configurations is inversely regulated by excitatory drive and by DA D2-autoreceptor activation in a manner dependent on Ca2+-influx via N-type voltage-gated Ca2+-channels. The DAT nanodomains contain tens of transporters molecules and overlap with nanodomains of PIP2 (phosphatidylinositol-4,5-bisphosphate) but show little overlap with D2-autoreceptor, syntaxin-1 and clathrin nanodomains. Summarized, the data reveal a mechanism for rapid alterations in nanoscopic DAT distribution and show a striking link of this to the conformational state of the transporter.


title: Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

abstract: Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.

category: immunology


title: Naturally-acquired immunity in Syrian Golden Hamsters provides protection from re-exposure to emerging heterosubtypic SARS-CoV-2 variants B.1.1.7 and B.1.351

abstract: The ability of acquired immune responses against SARS-CoV-2 to protect after subsequent exposure to emerging variants of concern (VOC) such as B1.1.7 and B1.351 is currently of high significance. Here, we use a hamster model of COVID-19 to show that prior infection with a strain representative of the original circulating lineage B of SARS-CoV-2 induces protection from clinical signs upon subsequent challenge with either B1.1.7 or B1.351 viruses, which recently emerged in the UK and South Africa, respectively. The results indicate that these emergent VOC may be unlikely to cause disease in individuals that are already immune due to prior infection, and this has positive implications for overall levels of infection and COVID-19 disease.

category: microbiology


title: Structures and function of locked conformations of SARS-CoV-2 spike

abstract: The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct "S-R/x3" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.


title: Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike


title: Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations

abstract: DNA markers are an essential tool for the detection and evaluation of genetic variations, a central theme in genetics and biology. Effective markers must be highly reproducible, polymorphic, accurate and efficient to profile. We developed multiple dispersed nucleotide polymorphism (MNP) DNA marker and an efficient MNP genotyping method called MNP-Seq. The MNP marker was 17.48% more polymorphic than the highly polymorphic marker of microsatellites on a collection of hybrid rice plants. When applied to genotype more than 80,000 individual MNP markers of diploid rice and polyploidy hybrid cotton varieties which were notoriously difficult to genotype accurately, MNP-Seq finished in two days and achieved accuracies of 99.999% and 99.988%, respectively. We adopted MNP-Seq to reveal the ubiquitous, albeit subtle and neglected, genetic heterogeneities in homonyms of Nipponbare rice, a popular model organism for plant biology. This result raised a question on the consistency of the published results using the model plant. We also used MNP-Seq to accurately and efficiently determine the identities of plant varieties, a key but difficult problem for the protection of plant intellectual property rights. While being applied to plants in the current study, the MNP marker and MNP-Seq are general and readily applicable to similar problems in animals and micro-organisms.

category: molecular biology


title: Tumor protein D52 (TPD52) affects cancer cell metabolism by negatively regulating AMPK.

abstract: The AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis, with deregulation leading to cancer and other diseases. When intracellular ATP levels decrease during energy stress, AMPK is phosphorylated and activated through AMP binding. However, how this pathway is dysregulated in cancer remains unclear. Here, we find that tumor protein D52 (TPD52), initially identified to be overexpressed in many human cancers, forms a stable complex with AMPK in cancer cells. TPD52 directly interacts with AMPK and inhibits AMPK kinase activity in vitro and in vivo. We generated TPD52 transgenic mice, and found that overexpression of TPD52 leads to AMPK inhibition and multiple metabolic defects in mice. Together, our results shed new light on AMPK regulation and on our understanding of the etiology of cancers with TPD52 overexpression.


title: Five years of citizen science and standardized field surveys reveal a threatened urban Eden for wild bees in Brussels, Belgium

abstract:
O_LIUrbanisation is often put forward as an important driver of biodiversity loss, including for pollinators such as wild bees. However, recent evidence shows that the mosaics of urban green spaces, and in particular certain categories of informal urban green spaces (IGS), can play an important role to help native wild bees thrive in cities.
C_LIO_LIHere, we describe the results of five years of citizen science and standardised field surveys of wild bees conducted at the Friche Josaphat, a 24-ha urban wasteland in the Brussels-Capital Region (Belgium). These field surveys were initiated following the planned restructuring and partial destruction of this site by the regional authorities.
C_LIO_LIWe recorded a total of 2,507 specimens belonging to 127 species of wild bees, i.e. 60.5% of the 210 species recorded regionally, including nine that are threatened with extinction at national or European scales. The Friche Josaphat encompasses a significant share of the functional and phylogenetic diversity of wild bees known from the Brussels-Capital Region and is one of the most species-rich localities known to date for wild bees in Belgium.
C_LIO_LICollectively, our results highlight the strong complementarity of citizen science and academic approaches in biodiversity surveys, and they reaffirm that wastelands are essential components of urban biodiversity. Our study stresses the need to provide biodiverse IGS with a formal status within the mosaic of urban green spaces, but also to acknowledge and safeguard their natural capital and the multiple ecosystem services they provide.
C_LI

category: ecology


title: Multiple resource limitations explain biomass-precipitation relationships in grasslands

abstract: Interannual variability in grassland primary production is strongly driven by precipitation, nutrient availability and herbivory, but there is no general consensus on the mechanisms linking these variables. If grassland biomass is limited by the single most limiting resource at a given time, then we expect that nutrient addition will not affect biomass production at arid sites. We conducted a distributed experiment manipulating nutrients and herbivores at 44 grassland sites in 8 regions around the world, spanning a broad range in aridity. We estimated the effects of 5-11 years of nutrient addition and herbivore exclusion treatments on precipitation sensitivity of biomass (proportional change in biomass relative to proportional change in rainfall among years), and the biomass in the driest year (to measure treatment effects when water was most limiting) at each site. Grazer exclusion did not interact with nutrients to influence driest year biomass or sensitivity. Nutrient addition increased driest year biomass by 74% and sensitivity by 0.12 (proportional units), and that effect did not change across the range of aridity spanned by our sites. Grazer exclusion did not interact with nutrients to influence sensitivity or driest year biomass. At almost half of our sites, the previous year's rainfall explained as much variation in biomass as current year precipitation. Overall, our distributed fertilization experiment detected co-limitation between nutrients and water governing grasslands, with biomass sensitivity to precipitation being limited by nutrient availability irrespective of site aridity and herbivory. Our findings refute the classical ideas that grassland plant performance is limited by the single most limiting resource at a site. This suggests that nutrient eutrophication will destabilize grassland ecosystems through increased sensitivity to precipitation variation.


title: Variation in reflectance spectroscopy of European beech leaves captures phenology and biological hierarchies despite measurement uncertainties

abstract:
The measurement of leaf optical properties (LOP) using reflectance and scattering properties of light allows a continuous, time-resolved, and rapid characterization of many species traits including water status, chemical composition, and leaf structure. Variation in trait values expressed by individuals result from a combination of biological and environmental variations. Such species trait variations are increasingly recognized as drivers and responses of biodiversity and ecosystem properties. However, little has been done to comprehensively characterize or monitor such variation using leaf reflectance, where emphasis is more often on species average values. Furthermore, although a variety of platforms and protocols exist for the estimation of leaf reflectance, there is neither a standard method, nor a best practise of treating measurement uncertainty which has yet been collectively adopted. In this study, we investigate what level of uncertainty can be accepted when measuring leaf reflectance while ensuring the detection of species trait variation at several levels: within individuals, over time, between individuals, and between populations. As a study species, we use an economically and ecologically important dominant European tree species, namely Fagus sylvatica. We first use fabrics as standard material to quantify the measurement uncertainties associated with leaf clip (0.0001 to 0.4 reflectance units) and integrating sphere measurements (0.0001 to 0.01 reflectance units) via error propagation. We then quantify spectrally resolved variation in reflectance from F. sylvatica leaves. We show that the measurement uncertainty associated with leaf reflectance, estimated using a field spectroradiometer with attached leaf clip, represents on average a small portion of the spectral variation within a single individual sampled over time (2.7 {+/-} 1.7%), or between individuals (1.5 {+/-} 1.3% or 3.4 {+/-} 1.7%, respectively) in a set of monitored F. sylvatica trees located in Swiss and French forests. In all forests, the spectral variation between individuals exceeded the spectral variation of a single individual measured within one week. However, measurements of variation within an individual at different canopy positions over time indicate that sampling design (e.g., standardized sampling, and sample size) strongly impacts our ability to measure between-individual variation. We suggest best practice approaches towards a standardized protocol to allow for rigorous quantification of species trait variation using leaf reflectance.

HighlightsO_LIWe partition biological variation from measurement uncertainty for leaf spectra.
C_LIO_LIMeasurement uncertainty represents ca. 3% of spectral variation among beech trees.
C_LIO_LIBiological variation within an individual increases by 80% as leaves mature.
C_LIO_LIMaxima of uncertainty correspond to maxima of biological variation (water content).
C_LIO_LIWe recommend procedures to quantify biological variation in spectral measurements.
C_LI


title: Genome structure of Brachionus asplanchnoidis, a Eukaryote with intrapopulation variation in genome size

abstract: Eukaryotic genomes vary greatly in size due to variation in the proportion of non-coding DNA, a pattern that emerges both in comparisons at a larger taxonomic scale and at the level of individuals within a species. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of intraspecific genome size variation among Eukaryotes, displaying almost 2-fold variation within a geographic population. Here we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short-reads of 15 individuals from the same geographic population. We identified large, contiguous copy number variable regions (CNVs), which exhibited significant coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were mainly composed of tandemly repeated satellite DNA, with only few interspersed genes or other sequences, and were characterized by an elevated GC-content. Judging from their distributions across contigs, some CNVs are fragments of accessory (B-)chromosomes while others resemble large insertions to normal chromosomes. CNV patterns in offspring of two parents with divergent genome size, and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Our study provides unprecedented insights into genome size evolution at microevolutionary time scales and thus paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

category: evolutionary biology


title: Admixed Populations Improve Power for Variant Discovery and Portability in Genome-wide Association Studies

abstract: Genome-wide association studies (GWAS) are primarily conducted in single-ancestry settings. The low transferability of results has limited our understanding of human genetic architecture across a range of complex traits. In contrast to homogeneous populations, admixed populations provide an opportunity to capture genetic architecture contributed from multiple source populations and thus improve statistical power. Here, we provide a mechanistic simulation framework to investigate the statistical power and transferability of GWAS under directional polygenic selection or varying divergence. We focus on a two-way admixed population and show that GWAS in admixed populations can be enriched for power in discovery by up to 2-fold compared to the ancestral populations under similar sample size. Moreover, higher accuracy of cross-population polygenic score estimates is also observed if variants and weights are trained in the admixed group rather than in the ancestral groups. Common variant associations are also more likely to replicate if first discovered in the admixed group and then transferred to an ancestral population, than the other way around (across 50 iterations with 1,000 causal SNPs, training on 10,000 individuals, testing on 1,000 in each population, p=3.78e-6, 6.19e-101, ~0 for FST = 0.2, 0.5, 0.8, respectively). While some of these FST values may appear extreme, we demonstrate that they are found across the entire phenome in the GWAS catalog. This framework demonstrates that investigation of admixed populations harbors significant advantages over GWAS in single-ancestry cohorts for uncovering the genetic architecture of traits and will improve downstream applications such as personalized medicine across diverse populations.

category: genetics


title: A topological approach to DNA similarity analysis from 5-dimensional representation

abstract: In this paper, we propose another topological approach for DNA similarity analysis. For each DNA sequence, we transform it into a collection of vectors in 5-dimensional space in which all nucleotides of the same type, say A, C, G, T are on the same line in this 5D space. Based on this special geometric property, we combine this representation with tools in persistent homology to obtain only zeroth persistence diagrams as a topological representation of DNA sequences. Similarities between DNA sequences are signified via how close the representing zeroth persistence diagrams of the DNA sequences are, based on the Wasserstein distance of order zero, which provides a new method for analyzing similarities between DNA sequences. We test our methods on the datasets of Human rhinovirus (HRV) and Influenza A virus.

category: genomics


title: Genome features of common vetch (Vicia sativa) in natural habitats

abstract:
Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1,243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. These findings suggest that high heterozygosity at the population level would be required for wild plants to survive under natural conditions while allowing important gene loci to be fixed to adapt the conditions. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.

HighlightSequence analysis of the common vetch (Vicia sativa) genome and SNP genotyping across natural populations revealed nucleotide diversity levels associated with native population environments.


title: Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.

abstract: Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.


title: Automated video tracking and flight analysis show how bumblebees solve a pattern discrimination task using active vision

abstract:
Active vision, the ability of the visual system to actively sample and select relevant information out of a visual scene through eye and head movements, has been explored in a variety of animal species. Small-brained animals such as insects might rely even more on sequential acquisition of pattern features since there might be less parallel processing capacity in their brains than in vertebrates. To investigate how active vision strategies enable bees to solve visual tasks, here, we employed a simple visual discrimination task in which individual bees were presented with a multiplication symbol and a 45{degrees} rotated version of the same pattern ("plus sign"). High-speed videography of unrewarded tests and analysis of the bees flight paths shows that only a small region of the pattern is inspected before successfully accepting a target or rejecting a distractor. The bees scanning behaviour of the stimuli differed for plus signs and multiplication signs, but for each of these, the flight behaviour was consistent irrespective of whether the pattern was rewarding or unrewarding. Bees typically oriented themselves at ~{+/-}30{degrees} to the patterns such that only one eye had an unobscured view of stimuli. There was a significant preference for initially scanning the left side of the stimuli. Our results suggest that the bees movement may be an integral part of a strategy to efficiently analyse and encode their environment.

Summary statementAutomated video tracking and flight analysis is proposed as the next milestone in understanding mechanisms underpinning active vision and cognitive visual abilities of bees.


title: Movement patterns and activity levels are shaped by the neonatal environment in Antarctic fur seal pups

abstract: Tracking studies of juveniles are rare compared to those of adults, and consequently little is known about the influence of intrinsic and extrinsic factors on activity during this critical life stage. We used hourly GPS data, collected from 66 Antarctic fur seal pups from birth until moulting, to investigate the explanatory power of multiple individual-based and environmental variables on activity levels. Pups were sampled from two nearby breeding colonies of contrasting density during two subsequent years, and a two-state hidden Markov model was used to identify modalities in their movement behaviour, specifically  active and  inactive states. We found that movement was typified by central place exploration, with active movement away from and subsequent return to a location of inactivity. The probability of such directed exploration was unaffected by several factors known to influence marine mammal movement including sex, body condition, and temperature. Compared to pups born at the high-density colony, pups at low-density were more active, increased their activity with age, and transitioned earlier into the tussock grass, which offers protection from predators and extreme weather. Our study illustrates the importance of extrinsic factors, such as colony of birth, to early-life activity patterns and highlights the adaptive potential of movement.


title: Anomalous low impedance for small platinum microelectrodes

abstract:
ObjectiveElectrical measurement of the activity of individual neurons is a primary goal for many invasive neural electrodes. Making these "single unit" measurements requires that we fabricate electrodes small enough so that only a few neurons contribute to the signal, but not so small that the impedance of the electrode creates overwhelming noise or signal attenuation. Thus, neuroelectrode design often must strike a balance between electrode size and electrode impedance, where the impedance is often assumed to scale linearly with electrode area.

Approach and main resultsHere we study how impedance scales with neural electrode area and find that the 1 kHz impedance of Pt electrodes (but not Au electrodes) transitions from scaling with area (r-2) to scaling with perimeter (r-1) when the electrode radius falls below 10 microns. This effect can be explained by the transition from planar to spherical diffusion behavior previously reported for electrochemical microelectrodes. Significance: These results provide important intuition for designing small, single unit recording electrodes. Specifically, for materials where the impedance is dominated by a pseudo-capacitance that is associated with a diffusion limited process, the total impedance will scale with perimeter rather than area when the electrode size becomes comparable with the diffusion layer thickness. For Pt electrodes this transition occurs around 10 um radius electrodes. At even lower frequencies (1 Hz) impedance approaches a constant. This transition to r-1 scaling implies that electrodes with a pseudo-capacitance can be made smaller than one might expect before thermal noise or voltage division limits the ability to acquire high-quality single-unit recordings.

category: bioengineering


title: Impedance scaling for gold and platinum microelectrodes


title: All-polymeric transient neural probe for prolonged in-vivo electrophysiological recordings

abstract: Transient bioelectronics has grown fast, opening possibilities never thought before. In medicine, transient implantable devices are interesting because they could eliminate the risks related to surgical retrieval and reduce the chronic foreign body reaction. However, despite recent progress in this area, the short functional lifetime of devices due to short-lived transient metals, which is typically a few days or weeks, still limits the potential of transient medical devices. We report that a switch from transient metals to an entirely polymer-based approach allows for a slower degradation process and a longer lifetime of the transient probe, thus opening new possibilities for transient medical devices. As a proof-of-concept, we fabricated all-polymeric transient neural probes that can monitor brain activity in mice for a few months rather than a few days or weeks. Also, we extensively evaluated the foreign body reaction around the implant during the probes degradation. This kind of devices might pave the way for several applications in neuroprosthetics.


title: Mechanism of praziquantel action at a parasitic flatworm ion channel

abstract: Praziquantel (PZQ) is an essential medicine for treating parasitic flatworm infections such as schistosomiasis, which afflicts over 250 million people. However, PZQ is not universally effective, lacking activity against the liver fluke Fasciola. The reason for this insensitivity is unclear, as the mechanism of PZQ action is unknown. Here, we show PZQ activates a transient receptor potential melastatin ion channel (TRPMPZQ) in schistosomes by engaging a hydrophobic ligand binding pocket within the voltage-sensor like domain to cause Ca2+ entry and worm paralysis. PZQ activates TRPMPZQ homologues in other PZQ-sensitive flukes, but not Fasciola. However, a single amino acid change in the Fasciola TRPMPZQ binding pocket, to mimic schistosome TRPMPZQ, confers PZQ sensitivity. After decades of clinical use, the basis of PZQ action at a druggable TRP channel is resolved.

category: pharmacology and toxicology


title: Trophic transfer of microplastics enhances tissue accumulation of chemical additives in fish

abstract: Organisms ingest microplastics directly from environments and indirectly from food sources. Ingesting microplastics can lead to an organism accumulating plastic-derived chemicals. However, the relative contributions of the two exposure routes (direct ingestion vs. indirect ingestion) to plastic-derived chemical accumulation in an organism are unknown. Using microplastics containing different types of plastic additives, we performed exposure experiments to compare chemical accumulation patterns in fish (Myoxocephalus brandti) between the exposure from the water and prey (Neomysis spp.). We found significantly higher brominated flame retardant concentrations in fish fed microplastic-contaminated prey than fish exposed to microplastics suspended in the water. The results indicate that prey-mediated ingestion of microplastics can be a more significant route for organisms accumulating plastic-derived chemicals, suggesting that organisms at higher trophic levels are more exposed to microplastics and associated chemicals than organisms at lower trophic levels.


title: The nuclear ubiquitin ligase adaptor SPOP is a conserved regulator of C9orf72 dipeptide toxicity

abstract:
A hexanucleotide repeat expansion in the C9orf72 gene is the most common cause of inherited amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Unconventional translation of the C9orf72 repeat produces dipeptide repeat proteins (DPRs). Previously, we showed that the DPRs (PR)50 and (GR)50 are highly toxic when expressed in C. elegans and this toxicity depends on nuclear localization of the DPR. In an unbiased genome-wide RNAi screen for suppressors of (PR)50 toxicity, we identified 12 genes that consistently suppressed either the developmental arrest and/or paralysis phenotype evoked by (PR)50 expression. All of these genes have vertebrate homologs and 7/12 contain predicted nuclear localization signals. One of these genes was spop-1, the C. elegans homolog of SPOP, a nuclear localized E3 ubiquitin ligase adaptor only found in metazoans. SPOP is also required for (GR)50 toxicity and functions in a genetic pathway that includes cul-3, which is the canonical E3 ligase partner for SPOP. Genetic or pharmacological inhibition of SPOP in mammalian primary spinal cord motor neurons suppressed DPR toxicity without affecting DPR expression levels. Finally, we find that genetic inhibition of bet-1, the C. elegans homolog of the known SPOP ubiquitination targets BRD2/3/4, suppresses the protective effect of SPOP mutations. Together, these data suggest a model in which SPOP promotes the DPR-dependent ubiquitination and degradation of BRD proteins. We speculate the pharmacological manipulation of this pathway, which is currently underway for multiple cancer subtypes, could also represent a novel entry point for therapeutic intervention to treat C9 FTD/ALS.

Significance statementThe G4C2 repeat expansion in the C9orf72 gene is a major cause of Fronto-Temporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). Unusual translation of the repeat sequence produces two highly toxic dipeptide repeat proteins, PRX and GRX, which accumulate in the brain tissue of individuals with these diseases. Here, we show that PR and GR toxicity in both C. elegans and mammalian neurons depends on the E3 ubiquitin ligase adaptor SPOP. SPOP acts through the bromodomain protein BET-1 to mediate dipeptide toxicity. SPOP inhibitors, which are currently being developed to treat SPOP-dependent renal cancer, also protect neurons against DPR toxicity. Our findings identify a highly conserved and  druggable pathway that may represent a new strategy for treating these currently incurable diseases.


title: Electrophysiological signatures of hierarchical learning

abstract: Human perception and learning is thought to rely on a hierarchical generative model that is continuously updated via precision-weighted prediction errors (pwPEs). However, the neural basis of such cognitive process and how it unfolds during decision making, remain poorly understood. To investigate this question, we combined a hierarchical Bayesian model (i.e., Hierarchical Gaussian Filter, HGF) with electrophysiological (EEG) recording, while participants performed a probabilistic reversal learning task in alternatingly stable and volatile environments. Behaviorally, the HGF fitted significantly better than two control, non-hierarchical, models. Neurally, low-level and high-level pwPEs were independently encoded by the P300 component. Low-level pwPEs were reflected in the theta (4-8 Hz) frequency band, but high-level pwPEs were not. Furthermore, the expressions of high-level pwPEs were stronger for participants with better HGF fit. These results indicate that the brain employs hierarchical learning, and encodes both low- and high-level learning signals separately and adaptively.


title: A role for glial fibrillary acidic protein (GFAP)-expressing cells in the regulation of gonadotropin-releasing hormone (GnRH) but not arcuate kisspeptin neuron output

abstract: GnRH neurons are the final central neural output regulating fertility. Kisspeptin neurons in the hypothalamic arcuate nucleus (KNDy neurons) are considered the main regulator of GnRH output. GnRH and KNDy neurons are surrounded by astrocytes, which can modulate neuronal activity and communicate over distances. Prostaglandin E2 (PGE2), synthesized primarily by astrocytes, increases GnRH neuron activity and downstream pituitary release of luteinizing hormone (LH). We hypothesized GFAP-expressing astrocytes play a role regulating GnRH and/or KNDy neuron activity and LH release. We used adenoassociated viruses to target designer receptor exclusively activated by designer drugs (DREADDs) to GFAP-expressing cells to activate Gq or Gi-mediated signaling. Activating Gq signaling in the preoptic area, near GnRH neurons, but not in the arcuate, increases LH release in vivo and GnRH firing in vitro via a mechanism in part dependent upon PGE2. These data suggest astrocytes can activate GnRH/LH release in a manner independent of KNDy neurons.


title: Flow cytometry allows rapid detection of protein aggregates in cell culture and zebrafish models of spinocerebellar ataxia-3

abstract: Spinocerebellar ataxia-3 (SCA3, also known as Machado Joseph Disease), is a neurodegenerative disease caused by inheritance of a ATXN3 gene containing a CAG repeat expansion, resulting in presence of a polyglutamine (polyQ) repeat expansion within the encoded human ataxin-3 protein. SCA3 is characterized by the formation of ataxin-3 protein aggregates within neurons, neurodegeneration, and impaired movement. In this study we have identified protein aggregates in both neuronal-like (SHSY5Y) cells and in vivo (transgenic zebrafish) models expressing human ataxin-3 protein containing polyQ expansion. We have adapted a flow cytometric methodology, allowing rapid quantification of detergent insoluble forms of ataxin-3 fused to a green fluorescent protein. Flow cytometric analysis revealed an increased number of detergent-insoluble ataxin-3 particles in cells and zebrafish expressing polyQ expanded ataxin-3 when compared to cells and zebrafish expressing wildtype human ataxin-3. Interestingly, a protein aggregation phenotype could be detected as early as two days of age in transgenic zebrafish, prior to the onset of a detectable movement impairment at 6 days of age, suggesting protein aggregation may be an early disease phenotype in SCA3. Further, treatment of SCA3 cells and transgenic zebrafish with compounds known to modulate the activity of the autophagy protein quality control pathway altered the number of detergent-insoluble ataxin-3 particles detected by flow cytometry. We conclude that flow cytometry is a powerful tool that can be harnessed to rapidly quantify ataxin-3 aggregates, both in vitro and in vivo, and can be utilised to screen and compare potential protein aggregate targeting therapies.


title: Psychomotor impairments and therapeutic implications revealed by a mutation linked with Infantile Parkinsonism-Dystonia

abstract:
Parkinson disease (PD) is a progressive, neurodegenerative disorder affecting over 6.1 million people worldwide. Although the cause of PD remains unclear, studies of highly-penetrant mutations identified in early-onset familial parkinsonism have contributed to our understanding of the molecular mechanisms underlying disease pathology. Dopamine (DA) transporter (DAT) deficiency syndrome (DTDS) is a distinct type of infantile parkinsonism-dystonia that shares key clinical features with PD, including motor deficits (progressive bradykinesia, tremor, hypomimia) and altered DA neurotransmission. Here, we define structural, functional, and behavioral consequences of a Cys substitution at R445 in human DAT (hDAT R445C), identified in a patient with DTDS. We found that this R445 substitution disrupts a phylogenetically conserved intracellular (IC) network of interactions that compromise the hDAT IC gate. This is demonstrated by both Rosetta molecular modeling and fine-grained simulations using hDAT R445C, as well as EPR analysis and X-ray crystallography of the bacterial homolog leucine transporter. Notably, the disruption of this IC network of interactions supported a channel-like intermediate of hDAT and compromised hDAT function. We demonstrate that Drosophila melanogaster expressing hDAT R445C show impaired hDAT activity, which is associated with DA dysfunction in isolated brains and with abnormal behaviors monitored at high-speed time resolution.

We show that hDAT R445C Drosophila exhibit motor deficits, lack of motor coordination (i.e. flight coordination) and phenotypic heterogeneity in these behaviors that is typically associated with DTDS and PD. These behaviors are linked with altered dopaminergic signaling stemming from loss of DA neurons and decreased DA availability. We rescued flight coordination through enhanced DAT surface expression via the lysosomal inhibitor chloroquine. Together, these studies shed light on how a DTDS-linked DAT mutation underlies DA dysfunction and, more broadly, the clinical phenotypes shared by DTDS and PD.


title: Effect of chronic JUUL aerosol inhalation on inflammatory states of the brain, lung, heart and colon in mice

abstract:
While health effects of conventional tobacco are well defined, data on vaping devices, including the most popular e-cigarette JUUL, are less established. Prior acute e-cigarette studies demonstrated inflammatory and cardiopulmonary physiology changes while chronic studies demonstrated extra-pulmonary effects, including neurotransmitter alterations in reward pathways. In this study we investigated effects of chronic flavored JUUL aerosol inhalation on inflammatory markers in brain, lung, heart, and colon. JUUL induced upregulation of cytokine and chemokine gene expression and increased HMGB1 and RAGE in the nucleus accumbens. Inflammatory gene expression increased in colon, and cardiopulmonary inflammatory responses to acute lung injury with lipopolysaccharide were exacerbated in the heart. Flavor-dependent changes in several responses were also observed. Our findings raise concerns regarding long-term risks of e-cigarette use as neuroinflammation may contribute to behavioral changes and mood disorders, while gut inflammation has been tied to poor systemic health and cardiac inflammation to development of heart disease.

One Sentence SummaryChronic, daily inhalation of pod-based e-cigarette aerosols alters the inflammatory state across multiple organ systems in mice.


title: Ecophysiology of the cosmopolitan OM252 bacterioplankton (Gammaproteobacteria)

abstract:
Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus (Candidatus Halomarinus), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors, with subclade I genomes encoding the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance but a mesophilic temperature range for growth, with a maximum of 0.36 doublings/hr at 35{degrees}C. Cells were curved rod/spirillum-shaped, ~1.5 x 0.2 m. Growth on thiosulfate as the sole electron donor under autotrophic conditions was roughly one third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some Ca. Halomarinus organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur.

ImportanceMarine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic datasets, we examined the diversity within the OM252 clade, the distribution of these taxa in the worlds oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point towards the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.


title: The ubiquitous terpene geosmin is a warning chemical

abstract: Known as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis we found that geosmin and the related terpene 2-methylisoborneol reduced predation of Streptomyces coelicolor and Myxococcus xanthus by the bacteriophagous Caenorhabditis elegans. Predation was restored by the removal of both terpene biosynthetic pathways or deletion of the C. elegans ASE sensory neuron, and resulted in the death of the nematodes. Geosmin itself was non-toxic. This is the first warning chemical to be identified in bacteria or fungi, and suggests molecular signalling affects microbial predator-prey interactions in a manner similar to the well-studied visual markers of poisonous animal prey.


title: Bacteriophage inhibits murine norovirus replication after co-incubation in RAW 264.7 cells

abstract: Bacteriophages (phages) are viruses of bacteria. Despite the growing progress in research on phage interactions with eukaryotic cells, our understanding of the roles of phages and their potential implications remains incomplete. The objective of this study was to investigate the effects of the Staphylococcus aureus phage vB_SauM_JS25 on murine norovirus (MNV) replication. Experiments were performed using the RAW 264.7 cell line. After phage treatment, MNV multiplication was significantly inhibited, as indicated by real-time quantitative PCR (RT-qPCR) analysis, western blot, and immunofluorescence assay. Furthermore, we demonstrated the transcriptional changes in phage-MNV co-incubated RAW 264.7 cells through RNA sequencing (RNA-Seq) and bioinformatic analysis. Our subsequent analyses revealed that the innate immune response may play an important role in the restriction of MNV replication, such as the cellular response to IFN-{gamma} and response to IFN-{gamma}. In addition, the gene expression of IL-10, Arg-1, Ccl22, GBP2, GBP3, GBP5, and GBP7 was proven to increase significantly by RT-qPCR, showing a strong correlation between RT-qPCR and RNA-Seq results. Furthermore, phage treatment activated guanylate binding proteins (GBPs), as revealed by RT-qPCR analysis, western blotting, and confocal microscopy. Taken together, these data suggest that the phage affects the innate response (such as the IFN-inducible GTPases and GBPs), reflecting their direct antimicrobial effect on the membrane structure of the MNV replication complexes, and therefore, exerts an antiviral effect in vitro. Collectively, our findings provide insights into the interactions of immune cells and phages, which improve our understanding of the actual role and potential of phages.


title: A neural progenitor mitotic wave is required for asynchronous axon outgrowth and morphology

abstract: Spatiotemporal mechanisms generating neural diversity are fundamental for understanding neural processes. Here, we investigated how neural diversity arises from neurons coming from identical progenitors. In the dorsal thorax of Drosophila, rows of mechanosensory organs originate from the division of sensory organ progenitor (SOPs). We show that in each row of the notum, a central SOP divides first, then neighboring SOPs divide, and so on. This centrifugal wave of mitoses depends on cell-cell inhibitory interactions mediated by SOP cytoplasmic protrusions and Scabrous, a secreted protein interacting with the Delta/Notch complex. Furthermore, when the mitotic wave was abolished, axonal growth was more synchronous, axonal terminals had a complex branching pattern and fly behavior was impaired. We show that the temporal order of progenitor divisions influences the birth order of sensory neurons, axon branching and impact on grooming behavior. These data support the idea that developmental timing controls axon wiring neural diversity.

category: developmental biology


title: MinION barcodes: biodiversity discovery and identification by everyone, for everyone

abstract:
BackgroundDNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to <10 cents, and allows fast turnaround from specimen to sequence by using the portable, real-time sequencer MinION.

ResultsWe describe cost-effective and rapid procedures for barcoding individual specimens with MinION sequencing. We illustrate how tagged amplicons can be obtained and sequenced with the portable, real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for >10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (>99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018.

ConclusionsWe propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.


title: Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape

abstract: Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. Richness of the olfactory repertoire depends on the diversity of receptors coded by homologous genes classified into four families: OR, TAAR, VR1 and VR2. Herein, we focus on the OR gene repertoire. While independent large contractions of the OR gene repertoire associated with ecological transitions have been found in mammals, little is known about the diversity of the OR gene repertoire and its evolution within teleost fishes, a group that includes more than 34,000 living species. We analyzed genomes of 163 species representing diversity in this large group. We found a large range of variation in the number of functional OR genes, from 15 in Syngnathus typhle and Mola mola, to 429 in Mastacembelus armatus. The number of OR genes was higher in species with an extensively folded olfactory epithelium, that is, for example, when a multi-lamellar rosette was present in the olfactory organ. Moreover, the number of lamellae was correlated with the richness of the OR gene repertoire. While a slow and balanced birth-and-death process generally drives evolution of the OR gene repertoire, we inferred several episodes of high rates of gene loss, sometimes followed by large gains in the number of OR genes. These gains coincide with morphological changes of the olfactory organ and suggest a strong functional association between changes in the morphology and the evolution of the OR gene repertoire.


title: Dynamic sampling bias and overdispersion induced by skewed offspring distributions

abstract: Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions, leading to so-called  jackpot events. The resulting allele frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the dynamics forward in time, especially with selection. Here, we employ an exact asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law n-(1+). To demonstrate that this coarse-grained model captures a wide variety of non-equilibrium dynamics, we validate our results in traveling waves, where the phenomenon of  gene surfing can produce any exponent 1 <  < 2. We argue that the concept of a dynamic sampling bias is useful generally to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history.


title: Fungal Transcription factors: Markers of genetic innovation, network rewiring and conflict between genomics and transcriptomics.

abstract:
Gene Regulatory Networks (GRNs) are shaped by the democratic/hierarchical relationships among transcription factors (TFs) and associated proteins, together with the cis-regulatory sequences (CRSs) bound by these TFs at target promoters. GRNs control all cellular processes, including metabolism, stress-response, growth and development. Due to the ability to modify morphogenetic and developmental patterns, there is the consensus view that the reorganization of GRNs is a driving force of species evolution and differentiation. Duplication of TF-coding genes, their divergent sequence evolution and gain/loss/modification of CRSs are events rewiring GRNs. Fungi (mainly Saccharomycotina) have served as a reference kingdom for the study of GRN evolution. Here, I studied the genes predicted to encode TFs in the fungus Aspergillus nidulans (Pezizomycotina). The analysis of the expansion of different families of TFs suggests that duplication of TFs impacts the species level and that the expansion in Zn2Cys6 TFs is mainly due to dispersed duplication events. Comparison of genomic annotation and transcriptomic data suggests that a significant percentage of genes should be re-annotated while many others remain silent. Finally, a new regulator of growth and development is identified and characterized. Overall, this study establishes a novel theoretical framework in synthetic biology, since overexpression of silent TF forms would provide additional tools to assess how GRNs are rewired.

Impact StatementGRNs controlling fungal sexual and asexual development, stress response, carbon/nitrogen metabolism or secondary metabolism, have been widely characterized in the fungus A. nidulans and, in several cases, were characterized for the first time in this fungus. The functional and genetic relationships among the TFs of these networks are known. By comparing the genomes/proteomes of hundreds of fungal genomes available in public repositories, researchers can track the emergence of regulators of interest, and identify groups of paralog TFs. The present work uses basic bioinformatics tools and standard RNA-seq analysis tools to compare genomic annotation and transcriptomics data, find incorrectly annotated TFs, identify paralog clusters of TFs, track the trajectories of duplication events and expansion of bHLH-type TFs, and identify TFs with a role in the control of growth and development. The study of TFs and GRNs of A. nidulans offers the opportunity to dissect and analyze sequentially the contribution of each cis and trans regulatory element to network rewiring and the modification of developmental patterns.

Data SummaryThe data underlying this article are available in supplementary tables and supplementary figures. RNA-seq, genomic and proteomic data used is this article (and previously deposited by others; see references and accession numbers in Materials and Methods) were retrieved from sources (www.ebi.ac.uk/arrayexpress/; www.ncbi.nlm.nih.gov/bioproject/; https://www.ncbi.nlm.nih.gov/geo/) and databases (https://fungidb.org/fungidb/app) in the public domain. Aspergillus nidulans strains generated in this article will be shared on reasonable request to the corresponding author.

One-sentence summaryA study of the predicted set of transcriptional regulators in the fungus Aspergillus nidulans, their conservation patterns and the correlation between gene annotations and transcriptomic data


title: Transcription factors in the fungus Aspergillus nidulans: Markers of genetic innovation, network rewiring and conflict between genomics and transcriptomics


title: Identification of Cell-Free DNA Methylation Patterns Unique to the Human Left Ventricle as a Potential Indicator of Acute Cellular Rejection

abstract: Increased levels of donor-derived cell-free DNA (dd-cfDNA) in recipient plasma have been associated with rejection after transplantation. DNA sequence differences have been used to distinguish between donor and recipient but epigenetic differences could also potentially identify dd-cfDNA. This pilot study aimed to identify ventricle-specific differentially methylated regions of DNA (DMRs) that could be detected in cfDNA. We identified 24 ventricle-specific DMRs and chose two for further study, one on chromosome 9 and one on chromosome 12. The specificity of both DMRs for the left ventricle was confirmed using genomic DNA from multiple human tissues. Serial matched samples of myocardium (n=33) and plasma (n=24) were collected from stable adult heart transplant recipients undergoing routine endomyocardial biopsy for rejection surveillance. Plasma DMR levels increased with biopsy-proven rejection grade for individual patients. Mean cellular apoptosis in biopsy samples increased significantly with rejection severity (2.4%, 4.4% and 10.0% for ACR 0R, 1R and 2R, respectively) but did not show a consistent relationship with DMR levels. We identified multiple DNA methylation patterns unique to the human ventricle and conclude that epigenetic differences in cfDNA populations represent a promising alternative strategy for the non-invasive detection of rejection.


title: Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

abstract: AO_SCPLOWBSTRACTC_SCPLOWChromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.


title: Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus


title: Hierarchical semantic composition of biosimulation models using bond graphs

abstract:
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in biology and physiology are often not modular and therefore difficult to assemble into larger models. Even when this is possible, the resulting model may not be useful due to inconsistencies either with the laws of physics or the physiological behaviour of the system. Here, we propose a general methodology for composing models, combining the energy-based bond graph approach with semantics-based annotations. This approach improves model composition and ensures that a composite model is physically plausible. As an example, we demonstrate this approach to automated model composition using a model of human arterial circulation. The major benefit is that modellers can spend more time on understanding the behaviour of complex biological and physiological systems and less time wrangling with model composition.

Author summaryBiological and physiological systems usually involve multiple underlying processes, mechanisms, structures, and phenomena, referred to here as sub-systems. Modelling the whole system every time from scratch requires a huge amount of effort. An alternative is to model each sub-system in a modular fashion, i.e., containing meaningful interfaces for connecting to other modules. Such modules are readily combined to produce a whole-system model. For the combined model to be consistent, modules must be described using the same modelling scheme. One way to achieve this is to use energy-based models that are consistent with the conservation laws of physics. Here, we present an approach that achieves this using bond graphs, which allows modules to be combined faster and more efficiently. First, physically plausible modules are generated using a small number of template modules. Then a meaningful interface is added to each module to automate connection. This approach is illustrated by applying this method to an existing model of the circulatory system and verifying the results against the reference model.


title: Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples

abstract: Estimating cell type composition of blood and tissue samples is a biological challenge relevant in both laboratory studies and clinical care. In recent years, a number of computational tools have been developed to estimate cell type abundance using gene expression data. While these tools use a variety of approaches, they all leverage expression profiles from purified cell types to evaluate the cell type composition within samples. In this study, we compare ten deconvolution tools and evaluate their performance while using each of eleven separate reference profiles. Specifically, we have run deconvolution tools on over 4,000 samples with known cell type proportions, spanning both immune and stromal cell types. Twelve of these represent in vitro synthetic mixtures and 300 represent in silico synthetic mixtures prepared using single cell data. A final 3,728 clinical samples have been collected from the Framingham Cohort, for which cell populations have been quantified using electrical impedance cell counting. When tools are applied to the Framingham dataset, the tool EPIC produces the highest correlation while GEDIT produces the lowest error. The best tool for other datasets is varied, but CIBERSORT and GEDIT most consistently produce accurate results. In terms of reference choice, we find that the Human Primary Cell Atlas (HPCA) and references published by the EPIC authors produce accurate results for the largest number of tools and datasets. When applying deconvolution to blood samples, the leukocyte reference matrix LM22 is also a suitable choice, usually (but not always) outperforming HPCA and EPIC. Running time varies substantially across tools. For as many as 5052 samples, SaVanT and dtangle reliably finish in under one minute, while slower tools may require up to two hours. However, when using custom references, CIBERSORT can run very slowly, taking over 24 hours to complete for large datasets. We conclude that combining the best tools with optimal reference datasets can provide significant gains in accuracy when carrying out deconvolution tasks.

category: bioinformatics


title: ChexMix: A Literature Content Extraction Tool for Bioentities

abstract: Biomedical databases grow by more than a thousand new publications every day. The large volume of biomedical literature that is being published at an unprecedented rate hinders the discovery of relevant knowledge from keywords of interest to gather new insights and form hypotheses. A text-mining tool, PubTator, helps to automatically annotate bioentities, such as species, chemicals, genes, and diseases, from PubMed abstracts and full-text articles. However, the manual re-organization and analysis of bioentities is a non-trivial and highly time-consuming task. ChexMix was designed to extract the unique identifiers of bioentities from query results. Herein, ChexMix was used to construct a taxonomic tree with allied species among Korean native plants and to extract the medical subject headings unique identifier of the bioentities, which co-occurred with the keywords in the same literature. ChexMix discovered the allied species related to a keyword of interest and experimentally proved its usefulness for multi-species analysis.


title: End-to-end Learning of Evolutionary Models to Find Coding Regions in Genome Alignments

abstract:
1MotivationThe comparison of genomes using models of molecular evolution is a powerful approach for finding or towards understanding functional elements. In particular, comparative genomics is a fundamental building brick in building high-quality, complete and consistent annotations of ever larger sets of alignable genomes.

ResultsWe here present our new program ClaMSA that classifies multiple sequence alignments using a phylogenetic model. It uses a novel continuous-time Markov chain machine learning layer, named CTMC, that is learned end-to-end together with (recurrent) neural networks for a learning task. We trained ClaMSA discriminately to classify aligned codon sequences that are candidates of coding regions into coding or non-coding and obtained six times fewer false positives for this task on vertebrate and fly alignments than existing methods at the same true positive rate. ClaMSA and the CTMC layer are general tools that could be used for other machine learning tasks on tree-related sequence data.

AvailabilityFreely from https://github.com/Gaius-Augustus/clamsa.


title: CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data

abstract:
MotivationThe chromatin profile measured by ATAC-seq, ChIP-seq, or DNase-seq experiments can identify genomic regions critical in regulating gene expression and provide insights on biological processes such as diseases and development. However, quality control and processing chromatin profiling data involve many steps, and different bioinformatics tools are used at each step. It can be challenging to manage the analysis.

ResultsWe developed a Snakemake pipeline called CHIPS (CHromatin enrichment Processor) to streamline the processing of ChIP-seq, ATAC-seq, and DNase-seq data. The pipeline supports single- and paired-end data and is flexible to start with FASTQ or BAM files. It includes basic steps such as read trimming, mapping, and peak calling. In addition, it calculates quality control metrics such as contamination profiles, PCR bottleneck coefficient, the fraction of reads in peaks, percentage of peaks overlapping with the union of public DNaseI hypersensitivity sites, and conservation profile of the peaks. For downstream analysis, it carries out peak annotations, motif finding, and regulatory potential calculation for all genes. The pipeline ensures that the processing is robust and reproducible.

AvailabilityCHIPS is available at https://github.com/liulab-dfci/CHIPS


title: Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus

abstract: Gestational diabetes mellitus (GDM) is one of the metabolic diseases during pregnancy. The identification of the central molecular mechanisms liable for the disease pathogenesis might lead to the advancement of new therapeutic options. The current investigation aimed to identify central differentially expressed genes (DEGs) in GDM. The transcription profiling by array data (E-MTAB-6418) was obtained from the ArrayExpress database. The DEGs between GDM samples and non GDM samples were analyzed with limma package. Gene ontology (GO) and REACTOME enrichment analysis were performed using ToppGene. Then we constructed the protein-protein interaction (PPI) network of DEGs by the Search Tool for the Retrieval of Interacting Genes database (STRING) and module analysis was performed. Subsequently, we constructed the miRNA-hub gene network and TF-hub gene regulatory network by the miRNet database and NetworkAnalyst database. The validation of hub genes was performed through receiver operating characteristic curve (ROC). Finally, the candidate small molecules as potential drugs to treat GDM were predicted by using molecular docking. Through transcription profiling by array data, a total of 869 DEGs were detected including 439 up regulated and 430 down regulated genes. Biological process analysis of GO enrichment analysis showed these DEGs were mainly enriched in reproduction, nuclear outer membrane-endoplasmic reticulum membrane network, identical protein binding, cell adhesion, supramolecular complex and signaling receptor binding. Signaling pathway enrichment analysis indicated that these DEGs played a vital in cell surface interactions at the vascular wall and extracellular matrix organization. Ten genes, HSP90AA1, EGFR, RPS13, RBX1, PAK1, FYN, ABL1, SMAD3, STAT3, and PRKCA in the center of the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network were associated with GDM, according to ROC analysis. Finally, the most significant small molecules were predicted based on molecular docking. Our results indicated that HSP90AA1, EGFR, RPS13, RBX1, PAK1, FYN, ABL1, SMAD3, STAT3, and PRKCA could be the potential novel biomarkers for GDM diagnosis, prognosis and the promising therapeutic targets. The current might be essential to understanding the molecular mechanism of GDM initiation and development.


title: Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression.

abstract:
In single-cell RNA-sequencing (scRNA-seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation and regeneration, at unprecedented resolutions. In such dynamic biological systems, grouping cells into discrete groups is not reflective of the biology. Cellular states rather form a continuum, e.g., for the differentiation of stem cells into mature cell types. This process is often represented via a trajectory in a reduced-dimensional representation of the scRNA-seq dataset.

While many methods have been suggested for trajectory inference, it is often unclear how to handle multiple biological groups or conditions, e.g., inferring and comparing the differentiation trajectories of wild-type and knock-out stem cell populations.

In this manuscript, we present a method for the estimation and downstream interpretation of cell trajectories across multiple conditions. Our framework allows the interpretation of differences between conditions at the trajectory, cell population, and gene expression levels. We start by integrating datasets from multiple conditions into a single trajectory. By comparing the conditions along the trajectorys path, we can detect large-scale changes, indicative of differential progression. We also demonstrate how to detect subtler changes by finding genes that exhibit different behaviors between these conditions along a differentiation path.


title: A smoothed version of the Lassosum penalty for fitting integrated risk models

abstract: Polygenic risk scores are a popular means to predict the disease risk or disease susceptibility of an individual based on its genotype information. When adding other important epidemiological covariates such as age or sex, we speak of an integrated risk model. Methodological advances for fitting more accurate integrated risk models are of immediate importance to improve the precision of risk prediction, thereby potentially identifying patients at high risk early on when they are still able to benefit from preventive steps/interventions targeted at increasing their odds of survival, or at reducing their chance of getting a disease in the first place. This article proposes a smoothed version of the "Lassosum" penalty used to fit polygenic risk scores and integrated risk models. The smoothing allows one to obtain explicit gradients everywhere for efficient minimization of the Lassosum objective function while guaranteeing bounds on the accuracy of the fit. An experimental section on both Alzheimers disease and COPD (chronic obstructive pulmonary disease) demonstrates the increased accuracy of the proposed smoothed Lassosum penalty compared to the original Lassosum algorithm, allowing it to draw equal with state-of-the-art methodology such as LDpred2 when evaluated via the AUC (area under the ROC curve) metric.


title: Cancer type classification in liquid biopsies based on sparse mutational profiles enabled through data augmentation and integration

abstract:
Identifying the cell of origin of cancer is important to guide treatment decisions. However, in patients with  cancer of unknown primary (CUP), standard diagnostic tools often fail to identify the primary tumor. As an alternative, machine learning approaches have been proposed to classify the cell of origin based on somatic mutation profiles in the genome of solid tissue biopsies. However, solid biopsies can cause complications and certain tumors are not accessible. A promising alternative would be liquid biopsies, which contain ctDNA originating from the tumor. Problematically, somatic mutation profiles of tumors obtained from liquid biopsies are inherently extremely sparse and current machine learning models fail to perform in this setting.

Here we propose an improved machine learning method to deal with the sparse nature of liquid biopsy data. Firstly, we downsample the SNVs in the samples in order to mimic sparse data conditions. Then extensive data augmentation is performed to artificially increase the number of training samples in order to enhance model robustness under sparse data conditions. Finally, we employ data integration to merge information from i) somatic single nucleotide variant (SNV) density across the genome, ii) somatic SNVs in driver genes and iii) trinucleotide motifs. Our adapted method achieves an average accuracy of 0.88 on the data where only 70% of SNVs are retained, which is comparable to an average accuracy of 0.87 with the original model on the full SNV data. Even when only 2% of the data is retained, the average accuracy is 0.65 compared to 0.41 with the original model. The method and results presented here open the way for application of machine learning in the detection of the cell of origin of cancer from sparse liquid biopsy data.

Author SummaryThe identification of the  cell of origin of cancer is an important step towards more personalized cancer care, but this remains a challenge for patients with  cancer of unknown primary (CUP) where the source of the malignancy cannot be identified even after extensive clinical assessment with standard diagnostic methods. Somatic mutation profile-based  cell of origin classification has emerged in recent years as a promising alternative diagnostic tool that could circumvent the issues of standard CUP diagnostic. In this approach the somatic mutations are obtained from whole genome sequencing (WGS) of solid tissue biopsies from the tumor. However, needle biopsies from tumor tissue can be challenging, as accessibility to the tumor can be limited and taking a biopsy can cause further complications. For these reasons, liquid biopsies have been proposed as a safer alternative to solid tissue biopsies. Problematically, the circulating tumor DNA fragments available in e.g. blood typically represent a much scarcer tumor source than conventional solid tissue biopsies and therefore liquid biopsies give rise to sparse somatic mutation profiles. Therefore it is crucial to investigate the applicability of sparse somatic mutation profiles in the identification of  cell of origin and explore potential improvements of the data analysis and prediction models to overcome sparsity.