title: Optimising expression quantitative trait locus mapping workflows for single-cell studies

abstract: Single-cell RNA-sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for sample multiplexing improving, population-scale scRNA-seq, and thus single-cell expression quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping of sc-eQTL provides additional resolution to study the regulatory role of common genetic variants on gene expression across a plethora of cell types and states, and promises to improve our understanding of genetic regulation across tissues in both health and disease. While previously established methods for bulk eQTL mapping can, in principle, be applied to sc-eQTL mapping, there are a number of open questions about how best to process scRNA-seq data and adapt bulk methods to optimise sc-eQTL mapping. Here, we evaluate the role of different normalisation and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines. We use both real and simulated datasets across single-cell technologies to systematically assess the impact of these different statistical approaches and provide recommendations for future single-cell eQTL studies that can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.

category: genetics


title: Shape Recovery of Deformed Biomolecular Droplets: Dependence on Condensate Viscoelasticity

abstract: A theoretical study on the shape dynamics of phase-separated biomolecular droplets is presented, highlighting the importance of condensate viscoelasticity. Previous studies on shape dynamics have modeled biomolecular condensates as purely viscous, but recent data have shown them to be viscoelastic. Here we present an exact analytical solution for the shape recovery dynamics of deformed biomolecular droplets. The shape recovery of viscous droplets has an exponential time dependence, with the time constant given by the "viscocapillary" ratio, i.e., viscosity over interfacial tension. In contrast, the shape recovery dynamics of viscoelastic droplets is multi-exponential, with shear relaxation yielding additional time constants. During shape recovery, viscoelastic droplets exhibit shear thickening (increase in apparent viscosity) at fast shear relaxation rates but shear thinning (decrease in apparent viscosity) at slow shear relaxation rates. These results highlight the importance of viscoelasticity and expand our understanding of how material properties affect condensate dynamics in general, including aging.

category: biophysics


title: A method for detection of permeation events in Molecular Dynamics simulations of lipid bilayers

abstract: The cell membrane is one of the most important structures of life. Understanding its functioning is essential for several human knowledge areas, mainly how it controls the efflux of substances between the cytoplasm and the environment. Being a complex structure, composed of several classes of compounds such as lipids, proteins, sugars, etc., a convenient way to mimic it is through a phospholipid bilayer. The Molecular Dynamics simulation of lipid bilayers in solution is the main computational approach to model the cell membrane. In this work, we present a method to detect permeation events of molecules through the lipid bilayer, characterizing its crossing time and trajectory. By splitting the simulation box into well-defined regions, the method distinguishes the passage of molecules through the bilayer from artifacts produced by crossing molecules through the simulation box edges when using periodic boundary conditions. We apply the method to study the spontaneous permeation of water molecules through bilayers with different lipid compositions and modeled with different force fields. Our method successfully characterizes the permeation events, and the results obtained show that the frequency and time of permeation are independent of the force field used to model the phospholipids. Besides, it is observed that the increase in the concentration of cholesterol molecules in lipid bilayers induces the reduction of permeation events due to its compacting action on the bilayer, making it denser and, therefore, hindering the diffusion of water molecules inside it. The computational tool to perform the method discussed here is available on https://github.com/crobertocamilo/MD-permeation.

category: bioinformatics


title: Experimental evidence for the benefits of higher X-ray energies for macromolecular crystallography

abstract: X-ray induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete datasets for structure solution of challenging samples. Increasing the X-ray energy beyond the typical 10-15 keV range promises to provide an extension of crystal lifetime via an increase in diffraction efficiency. To date however hardware limitations have negated any possible gains. Through the first use of a Cadmium Telluride Eiger2 detector and a beamline optimised for high energy data collection, we show that at higher energies fewer crystals will be required to obtain complete data, as the diffracted intensity per unit dose increases by a factor of more than 3 between 12.4 and 25 keV. Additionally, those higher energy data provide more information, evidenced by an increase in high-resolution limit of up to 0.3 [A], pointing to a high energy future for synchrotron-based macromolecular crystallography.

category: biochemistry


title: Taxonomic, ecological and morphological diversity of Ponto-Caspian gammaridean amphipods: a review

abstract: Thanks to its dynamic geological history the Ponto-Caspian region harbors a unique and unusually adaptable fauna, notorious for its invasive species. Gammarid amphipods attained considerable diversity, becoming the worlds second most speciose ancient-lake amphipod radiation. Nonetheless, apart from a few invasive species, this group remains poorly studied. Herein, we review and quantify the taxonomic, morphological and ecological diversity, as well as phylogenetic context of Ponto-Caspian gammarids within the adaptive radiation framework. Published molecular phylogenies indicate that this radiation has a monophyletic mid-Miocene Paratethyan origin, and is nested within the morphologically-conserved Atlanto-Mediterranean genus Echinogammarus. We find extensive disparity in body shape, size, ornamentation and appendage length, along a broad ecological gradient from mountain springs to depths exceeding 500 m, on virtually all substrate types (including symbiosis). We propose four putative ecomorphs that appear convergent with distantly related oceanic and Baikal Lake taxa. Thus, the identified patterns support the adaptive radiation model, although extensive further research is needed. A checklist and provisional key to all known endemic species are provided to facilitate taxonomic research. Ponto-Caspian gammarids could be a potentially powerful model for studying adaptive radiations and invasive species evolution.

category: zoology


title: Coupled myovascular expansion directs growth and regeneration of the neonatal mouse heart

abstract:
BackgroundHeart regeneration requires multiple cell types to enable cardiomyocyte (CM) proliferation. How these cells interact to create growth niches is unclear. Here we profile proliferation kinetics of cardiac endothelial cells (CECs) and CMs in the neonatal mouse heart and find that they are spatiotemporally coupled.

Methods and ResultsWe show that coupled myovascular expansion during cardiac growth or regeneration is dependent upon VEGF-VEGFR2 signaling, as genetic deletion of Vegfr2 from CECs or inhibition of VEGFA abrogates both CEC and CM proliferation. Repair of cryoinjury displays poor spatial coupling of CEC and CM proliferation. Boosting CEC density after cryoinjury with virus encoding Vegfa enhances regeneration. Using Mendelian randomization, we demonstrate that circulating VEGFA levels are positively linked with human myocardial mass, suggesting that Vegfa can stimulate human cardiac growth.

ConclusionsOur work demonstrates the importance of coupled CEC and CM expansion and reveals a myovascular niche that may be therapeutically targeted for heart regeneration.

category: developmental biology


title: Coupled myovascular expansion directs cardiac growth and regeneration


title: Braiding Braak and Braak: Staging patterns and model selection in network neurodegeneration

abstract:
A hallmark of Alzheimers disease is the aggregation of insoluble amyloid-beta plaques and tau protein neurofibrillary tangles. A key histopathological observation is that tau protein aggregates follow a structured progression pattern through the brain. Mathematical network models of prion-like propagation have the ability to capture such patterns but a number of factors impact the observed staging result, thus introducing questions regarding model selection. Here, we introduce a novel approach, based on braid diagrams, for studying the structured progression of a marker evolving on a network. We apply this approach to a six-stage  Braak patternof tau proteins, in Alzheimers disease, motivated by a recent observation that seed-competent tau precedes tau aggregation. We show that the different modeling choices, from the model parameters to the connectome resolution, play a significant role in the landscape of observable staging patterns. Our approach provides a systematic way to approach model selection for network propagation of neurodegenerative diseases that ensures both reproducibility and optimal parameter fitting.

Author summaryNetwork diffusion models of neurodegenerative diseases are a class of dynamical systems that simulate the evolution of toxic proteins on the connectome. These models predict, from an initial seed, a pattern of invasion called staging. The generalized staging problem seeks to systematically study the effect of various model choices on staging. We introduce methods based on braid diagrams to test the possible staging landscape of a model and how it depends on the choice of connectome, as well as the model parameters. Our primary finding is that connectome construction, the choice of the graph Laplacian, and transport models all have an impact on staging that should be taken into account in any study.

category: neuroscience


title: Tristetraprolin prevents gastric metaplasia in mice by suppressing pathogenic inflammation

abstract: Aberrant immune activation is associated with numerous inflammatory and autoimmune diseases and contributes to cancer development and progression. Within the stomach, inflammation drives a well-established sequence from gastritis to metaplasia, eventually resulting in adenocarcinoma. Unfortunately, the processes that regulate gastric inflammation and prevent carcinogenesis remain unknown. Tristetraprolin (TTP) is an RNA-binding protein that promotes the turnover of numerous pro-inflammatory and oncogenic mRNAs. Here, we utilized a TTP-overexpressing model, the TTP{Delta}ARE mouse, to examine whether TTP can protect the stomach from adrenalectomy (ADX)-induced gastric inflammation and spasmolytic polypeptide-expressing metaplasia (SPEM). We found that TTP{Delta}ARE mice were completely protected from ADX-induced gastric inflammation and SPEM. RNA sequencing revealed that TTP overexpression suppressed the expression of genes associated with the innate immune response. Finally, we show that protection from gastric inflammation was only partially due to suppression of Tnf, a well-known TTP target. Our results demonstrate that TTP exerts broad anti-inflammatory effects in the stomach and suggest that therapies that increase TTP expression may be effective treatments of pro-neoplastic gastric inflammation.

category: immunology


title: Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes

abstract:
SEDS family peptidoglycan (PG) glycosyltransferases RodA and FtsW require their cognate transpeptidases PBP2 and FtsI (class B penicillin binding proteins) to synthesize PG along the cell cylinder and at the septum, respectively. The activities of these SEDS-bPBPs complexes are tightly regulated to ensure proper cell elongation and division. In Escherichia coli FtsN switches FtsA and FtsQLB to the active forms that synergize to stimulate FtsWI, but the exact mechanism is not well understood. Previously, we isolated an activation mutation in ftsW (M269I) that allows cell division with reduced FtsN function. To try and understand the basis for activation we isolated additional substitutions at this position and found that only the original substitution produced an active mutant whereas drastic changes resulted in an inactive mutant. In another approach we isolated suppressors of an inactive FtsL mutant and obtained FtsWE289G and FtsIK211I and found they bypassed FtsN. Epistatic analysis of these mutations and others confirmed that the FtsN-triggered activation signal goes from FtsQLB to FtsI to FtsW. Mapping these mutations and others affecting the activities of FtsWI on the RodA-PBP2 structure revealed they are located at the interaction interface between the extracellular loop 4 (ECL4) of FtsW and the pedestal domain of FtsI (PBP3). This supports a model in which the interaction between the ECL4 of SEDS proteins and the pedestal domain of their cognate bPBPs plays a critical role in the activation mechanism.

Author summaryBacterial cell division requires the synthesis of septal peptidoglycan by the widely conserved SEDS-bPBP protein complex FtsWI, but how the complex is activated during cell division is still poorly understood. Previous studies suggest that FtsN initiates a signaling cascade in the periplasm to activate FtsW. Here we isolated and characterized activated FtsW and FtsI mutants and confirmed that the signaling cascade for FtsW activation goes from FtsN to FtsQLB to FtsI and then to FtsW. The residues corresponding to mutations affecting FtsWI activation are clustered to a small region of the interaction interface between the pedestal domain of FtsI and the extracellular loop 4 of FtsW, suggesting that this interaction mediates activation of FtsW. This is strikingly similar to the proposed activation mechanism for the RodA-PBP2 complex, another SEDS-bPBP complex required for cell elongation. Thus, the two homologous SEDS-bPBP complexes are activated similarly by completely unrelated activators that modulate the interaction interface between the SEDS proteins and the bPBPs.

category: microbiology


title: A brief report of sleep and circadian rhythm quotas in a population of dog owners in North Carolina, USA

abstract:
ObjectivesTo characterize sleep and circadian rhythms of a sample population of healthy, dog-owning adults from North Carolina, USA.

MethodsActigraphy was used to analyze sleep-wake patterns in forty-two dog owners from the Raleigh area in North Carolina. Sleep quotas, including sleep duration, efficiency, and fragmentation were measured alongside a Non-parametric Circadian Rhythms Analysis (NPCRA) to quantify strength, consistency, and fragmentation of rhythms.

ResultsCompared to females, males demonstrated later sleep onset and sleep end (p<0.01), greater wake after sleep onset and sleep fragmentation (P<0.001), and lower sleep efficiency (p<0.001). The NPCRA revealed comparable relative amplitude (strength) and interdaily stability (consistency), yet less intra-daily variability (fragmentation), than previously reported post-industrial samples.

ConclusionsThis study adds to the current data available on sleep and circadian rhythms in discrete human populations and highlights the need for more research characterizing cross-cultural sleep and circadian rhythmicity.

category: evolutionary biology


title: Indian genetic heritage in Southeast Asian populations

abstract:
The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Deeply divergent East Eurasian hunter-gatherers were the first anatomically modern human population known to migrate to the region. Agriculturalists from South China migrated to the region and admixed with the local hunter-gatherers during the Neolithic period. During the Bronze and Iron Ages, the genetic makeup of people in MSEA changed again, indicating an additional influx of populations from South China. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, and this cultural influence is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA, we generated genome-wide SNP data (the HumanOrigins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data from MSEA using the PCA, ADMIXTURE, f3-statistics, qpAdm, and qpGraph methods. We found South Asian low-level admixture in various MSEA populations which are probably descendants of people from the ancient Indian-influenced states, but failed to find a South Asian genetic component in present-day hunter-gatherer groups and relatively isolated groups from highlands in Northern Thailand. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.

Author SummaryMainland Southeast Asia is a region with great ethnolinguistic diversity and complex population history. We studied genetic population history of present-day mainland Southeast Asian populations using genome-wide SNP data (the HumanOrigins array). We generated new data for 10 present-day ethnic groups from Thailand, which we further combined with published data from mainland and island Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various mainland Southeast Asian ethnic groups which are highly influenced by Indian culture, but failed to find it in groups who remained culturally isolated until recently. Our finding suggests that a massive migration of Indian people in the past was responsible for the spread of Indian culture in mainland Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesianspeaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.


title: HLA-G gene editing: a novel therapeutic alternative in cancer immunotherapy

abstract: Cancer immunotherapies based mainly on the blockade of immune-checkpoint (IC) molecules by anti-IC antibodies offer new alternatives for treatment in oncological diseases. However, a considerable proportion of patients remain unresponsive to them. Hence, the development of novel clinical immunotherapeutic approaches and/or targets are crucial. In this context, targeting the immune-checkpoint HLA-G/ILT2/ILT4 has caused great interest since it is abnormally expressed in several malignancies generating a tolerogenic microenvironment. Here, we used CRISPR/Cas9 gene editing to block the HLA-G expression in two tumor cell lines expressing HLA-G, including a renal cell carcinoma (RCC7) and a choriocarcinoma (JEG-3). Different sgRNA/Cas9 plasmids targeting HLA-G exon 1 and 2 were transfected in both cell lines. Downregulation of HLA-G was reached to different degrees, including complete silencing. Most importantly, HLA-G - cells triggered a higher in vitro response of immune cells with respect to HLA-G + wild type cells. Altogether, we demonstrated for the first time the HLA-G downregulation through gene editing. We propose this approach as a first step to develop novel clinical immunotherapeutic approaches in cancer.

category: cancer biology


title: IMPAIRED OLFACTORY NETWORK FUNCTIONAL CONNECTIVITY IN PARKINSON'S DISEASE: A NOVEL MARKER FOR DISEASE PROGRESSION

abstract:
ObjectiveDetermine the neural basis of olfactory impairment in akinetic-rigid (PDAR) and tremor predominant (PDT) Parkinsons disease subtypes.

MethodsWe combined resting-state fMRI (rs-fMRI) with seed based functional connectivity (FC) in order to delineate the olfactory networks functional connectivity (ON FC) between PDAR and PDT patients. We then contrasted their ON FC patterns with cognitively normal (CN) subjects. All three groups were closely matched in age, demographic variables, and adjusted for relative cognitive performance. Olfactory function was measured using the University of Pennsylvania Smell Identification Test (UPSIT).

ResultsUPSIT scores were lower in akinetic-rigid vs tremor subtypes; ON FC values were lower in PDAR compared to PDT and CN, and followed the trend observed in UPSIT scores. UPSIT scores and ON FC values were significantly correlated, reflecting the effects of PD pathologies.

ConclusionsThe results show that olfactory function differs between PDAR and PDT suggesting a correlation between PD-related motor symptoms and olfactory deficits. ON FC differences accounts for the impaired olfactory functions observed between PDAR and PDT. PDAR is known to have worse clinical outcomes and faster cognitive decline compared to PDT; therefore, PD-related olfactory dysfunction may serve as a novel metric for enhancing PD prognosis.


title: Structure of an Hsp90-immunophilin complex reveals cochaperone recognition of the client-maturation state

abstract: The Hsp90 chaperone promotes the folding and activation of hundreds of client proteins in the cell through an ATP-dependent conformational cycle guided by distinct cochaperone regulators. The FKBP51 immunophilin binds Hsp90 with its tetratricopeptide repeat (TPR) domain and catalyzes peptidyl-prolyl isomerase (PPIase) activity during the folding of kinases, nuclear receptors and tau. Here we have determined the cryo-EM structure of the human Hsp90:FKBP51:p23 complex to 3.3 [A] that, together with mutagenesis and crosslinking analysis, reveals the basis for cochaperone binding to Hsp90 during client maturation. A helix extension in the TPR functions as a key recognition element, interacting across the Hsp90 C-terminal dimer interface presented in the closed, ATP conformation. The PPIase domain is positioned along the middle domain, adjacent Hsp90 client binding sites, while a single p23 makes stabilizing interactions with the N-terminal dimer. With this architecture, FKBP51 could thereby act on specific client residues presented during Hsp90-catalyzed remodeling.


title: A Single Cell Atlas of Lung Development

abstract: Lung organogenesis requires precisely timed shifts in the spatial organization and function of parenchymal cells, especially during the later stages of lung development. To investigate the mechanisms governing lung parenchymal dynamics during development, we performed a single cell RNA sequencing (scRNA-seq) time-series yielding 92,238 epithelial, endothelial, and mesenchymal cells across 8 time points from embryonic day 12 (E12) to postnatal day 14 (P14) in mice. We combined new computational analyses with RNA in situ hybridization to explore transcriptional velocity, fate likelihood prediction, and spatiotemporal localization of cell populations during the transition between the saccular and alveolar stages. We interrogated this atlas to illustrate the complexity of type 1 pneumocyte function during the saccular and alveolar stages, and we demonstrate an integrated view of the cellular dynamics during lung development.


title: A Simple Ultrafast Multicolor Immunolabelling and Clearing Approach for Whole-Organ and Large Tissue 3D Imaging

abstract: High-resolution whole-organ imaging of cleared tissues captures cellular and molecular insights within the intact tissue and tumour microenvironments. However, current immunolabelling and clearing methods are complicated and time-consuming; extending to several weeks. Here, we developed Simple Ultrafast Multicolor Immunolabelling and Clearing or SUMIC, a method that enables multicolor immunolabelling and clearing of whole murine organs and human tissues within 2 to 2.5 days. Moreover, SUMIC is simple, robust, non-hazardous and versatile comprising antigen retrieval, permeabilization, collagenase-based digestion, immunolabelling, dehydration, and clearing. SUMIC permits quantitative and singlecell resolution analysis and detection of rare cells in whole organs, for example, round SMA positive cells in the thymus. Upon volumetric imaging, SUMIC-processed samples retain normal tissue architecture and can be used for paraffin-embedding and histology. We employed the SUMIC method for whole-organ mapping of lymphatic vessels across different ages and organs. This analysis revealed the expansion of lymphatic vessels in endocrine tissues but not in any other organs with aging. Hence, SUMIC will accelerate discoveries compared to other whole organ imaging pipelines.

category: physiology


title: Bispecific antibody prevents SARS-CoV-2 escape and protects mice from disease

abstract: Neutralizing antibodies targeting the receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) are among the most promising approaches against coronavirus disease 2019 (COVID-19)1,2. We developed a bispecific, IgG1-like molecule (CoV-X2) based on two antibodies derived from COVID-19 convalescent donors, C121 and C1353. CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable S binding to Angiotensin-Converting Enzyme 2 (ACE2), the virus cellular receptor. Furthermore, CoV-X2 neutralizes SARS-CoV-2 and its variants of concern, as well as the escape mutants generated by the parental monoclonals. In a novel animal model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, combining into a single molecule the advantages of antibody cocktails.


title: Bispecific antibody neutralizes circulating SARS-CoV-2 variants, prevents escape and protects mice from disease


title: Different resource allocation in a Bacillus subtilis population displaying bimodal motility

abstract:
To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so-called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to the continuous increase in cell volume, it is difficult for these activators to reach an activation threshold concentration when cells are growing exponentially. This is one reason why bimodal differentiation is primarily observed from the onset of the stationary phase when exponential growth ceases. An exception is the bimodal induction of motility in Bacillus subtilis, which occurs early during exponential growth. Several mechanisms have been put forward to explain this, including double negative-feedback regulation and the stability of the mRNA molecules involved. In this study, we used fluorescence-assisted cell sorting to compare the transcriptome of motile and non-motile cells and noted that expression of ribosomal genes is lower in motile cells. This was confirmed using an unstable GFP reporter fused to the strong ribosomal rpsD promoter. We propose that the reduction in ribosomal gene expression in motile cells is the result of a diversion of cellular resources to the synthesis of the chemotaxis and motility systems. In agreement, single-cell microscopic analysis showed that motile cells are slightly shorter than non-motile cells, an indication of slower growth. We speculate that this growth rate reduction can contribute to the bimodal induction of motility during exponential growth.

IMPORTANCETo cope with sudden environmental changes, bacteria can use a bet-hedging strategy and generate different types of cells within a population, so called bimodal differentiation. For example, a Bacillus subtilis culture can contain both motile and non-motile cells. In this study we compared the gene expression between motile and non-motile cells. It appeared that motile cells express less ribosomes. To confirm this, we constructed a ribosomal promoter fusion that enabled us to measure expression of this promoter in individual cells. This reporter fusion confirmed our initial finding. The re-allocation of cellular resources from ribosome synthesis towards synthesis of the motility apparatus results in a reduction in growth. Interestingly, this growth reduction has been shown to stimulate bimodal differentiation.


title: Evolution of recombination landscapes in diverging populations of bread wheat.

abstract: Reciprocal exchanges of DNA (crossovers) that occur during meiosis are mandatory to ensure the production of fertile gametes in sexually reproducing species. They also contribute to shuffle parental alleles into new combinations thereby fuelling genetic variation and evolution. However, due to biological constraints, the recombination landscape is highly heterogenous along the genome which limits the range of allelic combinations and the adaptability of populations. An approach to better understand the constraints on the recombination process is to study how it evolved in the past. In this work we tackled this question by constructing recombination profiles in four diverging bread wheat (Triticum aestivum L.) populations established from 371 landraces genotyped at 200,062 SNPs. We used linkage disequilibrium (LD) patterns to estimate in each population the past distribution of recombination along the genome and characterize its fine-scale heterogeneity. At the megabase scale, recombination rates derived from LD patterns were consistent with family-based estimates obtained from a population of 406 recombinant inbred lines. Among the four populations, recombination landscapes were significantly positively correlated between each other and shared a statistically significant proportion of highly recombinant intervals. However, this comparison also highlighted that the similarity in recombination landscapes between populations was significantly decreasing with their genetic differentiation in most regions of the genome. This observation was found to be robust to SNP ascertainment and demography and suggests a relatively rapid evolution of factors determining the fine-scale localization of recombination in bread wheat.


title: Improvements in the Sequencing and Assembly of Plant Genomes

abstract:
BackgroundAdvances in DNA sequencing have reduced the difficulty of sequencing and assembling plant genomes. A range of methods for long read sequencing and assembly have been recently compared and we now extend the earlier study and report a comparison with more recent methods.

ResultsUpdated Oxford Nanopore Technology software supported improved assemblies. The use of more accurate sequences produced by repeated sequencing of the same molecule (PacBio HiFi) resulted in much less fragmented assembly of sequencing reads. The use of more data to give increased genome coverage resulted in longer contigs (higher N50) but reduced the total length of the assemblies and improved genome completeness (BUSCO). The original model species, Macadamia jansenii, a basal eudicot, was also compared with the 3 other Macadamia species and with avocado (Persea americana), a magnoliid, and jojoba (Simmondsia chinensis) a core eudicot. In these phylogenetically diverse angiosperms, increasing sequence data volumes also caused a highly linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity apparently influenced the success of assembly from these different species.

ConclusionsAdvances in long read sequencing technology have continued to significantly improve the results of sequencing and assembly of plant genomes. However, results were consistently improved by greater genome coverage (using an increased number of reads) with the amount needed to achieve a particular level of assembly being species dependant.

category: genomics


title: The Arabidopsis immune receptor EFR increases resistance to the bacterial pathogens Xanthomonas and Xylella in transgenic sweet orange

abstract: Plants employ cell surface receptors to recognize pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs), which are crucial for immune system activation. The well-studied Arabidopsis thaliana ELONGATION FACTOR-TU RECEPTOR (EFR) recognizes the conserved bacterial PAMP EF-Tu, and the derived peptides elf18 and elf26. The interfamily transfer of EFR has been shown to increase disease resistance in several crops, such as tomato, rice, wheat, and potato. Here, we generated sweet orange (Citrus sinensis) transgenic lines expressing EFR to test if it would confer broad-spectrum resistance against two important citrus bacterial diseases: citrus canker and citrus variegated chlorosis (CVC). Independent EFR transgenic lines gained responsiveness to elf18 and elf26 peptides from Xanthomonas citri and Xylella fastidiosa, as measured by reactive oxygen species (ROS) production, mitogen-activated protein kinase (MAPK) activation and defense gene expression. Consistently, infection assays showed that Citrus-EFR transgenic plants were more resistant to citrus canker and CVC. Our results show that the EFR immune receptor can improve plant immunity in a perennial crop against bacterial pathogens, opening perspectives to engineer durable broad-spectrum disease resistance under field conditions.

category: plant biology


title: Burkholderia from fungus gardens of fungus-growing ants produce antifungals that inhibit the specialized parasite Escovopsis

abstract:
Within animal associated microbiomes, the functional roles of specific microbial taxa are often uncharacterized. Here, we use the fungus-growing ant system, a model for microbial symbiosis, to determine the potential defensive roles of key bacterial taxa present in the ants fungus gardens. Fungus gardens serve as an external digestive system for the ants, with mutualistic fungi in the genus Leucoagaricus spp. converting plant substrate into energy for the ants. The fungus garden is host to specialized parasitic fungi in the genus Escovopsis. Here, we examine the potential role of Burkholderia spp. that occur within ant fungus gardens in inhibiting Escovopsis. We isolated members of the bacterial genera Burkholderia spp. and Paraburkholderia spp. from 50% of the 52 colonies sampled, indicating that the family Burkholderiaceae are common fungus garden inhabitants of a diverse range of fungus-growing ant genera. Using antimicrobial inhibition bioassays, we found that 28 out of 32 isolates inhibited at least one Escovopsis strain with a zone of inhibition greater than 1 cm. Genomic assessment of Burkholderiaceae isolates indicated that isolates with strong inhibition all belonged to the genus Burkholderia and contained biosynthetic gene clusters that encoded the production of two antifungals: burkholdine1213 and pyrrolnitrin. Organic extracts of cultured isolates confirmed these compounds as responsible for antifungal activity that inhibit Escovopsis but, at low concentrations, not Leucoagaricus spp. Overall, these new findings, combined with previous evidence, suggest that members of the fungus garden microbiome play an important role in maintaining the health and function of the fungus-farming ant colony.

IMPORTANCEMany organisms partner with microbes to defend themselves against parasites and pathogens. Fungus-growing ants must protect Leucoagaricus spp., the fungal mutualist that provides sustenance for the ants, from a specialized fungal parasite, Escovopsis spp. The ants take multiple approaches, including weeding their fungus gardens to remove Escovopsis spores, as well as harboring Pseudonocardia that produce antifungals that inhibit Escovopsis. In addition, a genus of bacteria commonly found in fungus gardens, Burkholderia spp., is known to produce secondary metabolites that inhibit Escovopsis spp. In this study, we isolated Burkholderia spp. from fungus-growing ants, assessed the isolates ability to inhibit Escovopsis spp., and identified two compounds responsible for inhibition. Our findings suggest that Burkholderia spp. are often found in fungus gardens, adding another possible mechanism within the fungus-growing ant system to suppress the growth of the specialized parasite Escovopsis.


title: Fine-scale Population Structure of North American  Arabidopsis thaliana  Reveals Multiple Sources of Introduction from Across Eurasia

abstract: Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can contribute to observed patterns of genetic diversity and our understanding of the adaptive spread of alleles. While human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of non-native species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present here the most comprehensive view of population structure of North American Arabidopsis thaliana by studying a set of 500 (whole-genome sequenced) and over 2800 (RAD-seq genotyped) individuals in the context of global diversity represented by Afro-Eurasian genomes. We use haplotype-sharing, phylogenetic modeling and rare-allele sharing based methods to identify putative sources of introductions of extant N. American A. thaliana from the native range of Afro-Eurasia. We find evidence of admixture among the introduced lineages that has resulted in the increased haplotype diversity and reduced mutational load. Further, we also present signals of selection in the immune-system related genes that impart qualitative disease resistance to pathogens of bacterial and oomycete origins. Thus, multiple introductions to a non-native range can quickly increase adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. The results presented here lay the foundation for further investigations into the functional significance of admixture.


title: Binaural (pre)processing for contralateral sound field attenuation and improved speech-in-noise recognition

abstract: Understanding speech presented in competition with other sound sources can be challenging. Here, we reason that this task can be facilitated by improving the signal-to-noise ratio (SNR) in either of the two ears and that in free-field listening scenarios, this can be achieved by attenuating contralateral sounds. We present a binaural (pre)processing algorithm that improves the SNR in the ear ipsilateral to the target sound source by linear subtraction of the weighted contralateral stimulus. Although the weight is regarded as a free parameter, we justify setting it equal to the ratio of ipsilateral to contralateral head-related transfer functions averaged over an appropriate azimuth range. The algorithm is implemented in the frequency domain and evaluated technically and experimentally for normal-hearing listeners in simulated free-field conditions. Results show that (1) it can substantially improve the SNR (up to 20 dB) and the short-term intelligibility metric in the ear ipsilateral to the target source, particularly for speech-like maskers; (2) it can improve speech reception thresholds for sentences in competition with speech-shaped noise by up to 8.5 dB in bilateral listening and 10.0 dB in unilateral listening; (3) it hardly affects sound-source localization; and (4) the improvements, and the algorithms directivity pattern depend on the weights. The algorithm accounts qualitatively for binaural unmasking for speech in competition with multiple maskers and for multiple target-masker spatial arrangements, an unexpected property that can inspire binaural intelligibility models.

category: bioengineering


title: Temporal Self-Compression: Behavioral and neural evidence that past and future selves are compressed as they move away from the present

abstract:
Although it is well-known that people feel disconnected from their past and future selves, the underlying mechanism supporting this phenomenon is unknown. To help fill this gap, we considered a basic principle of perception. As objects increase in distance from an observer, they also become logarithmically compressed in perception (i.e., not differentiated from one another), making them hard to distinguish. Here, we report four studies that suggest we may feel disconnected from distant selves, in part, because they are increasingly indiscriminable with temporal distance from the present self. In Studies 1-3, participants made trait ratings across various time points in the past and future. We found that participants compressed their past and future selves, relative to their present self. This effect was preferential to the self and could not be explained by the alternative possibility that individuals simply perceive arbitrary self-change with time irrespective of temporal distance. In Study 4, we tested for neural evidence of temporal self-compression by having participants complete trait ratings across time points while undergoing functional magnetic resonance imaging (fMRI). Representational similarity analysis (RSA) was used to determine if neural self-representations are compressed with temporal distance, as well. We found evidence of temporal self-compression in areas of the default network, including medial prefrontal cortex (MPFC) and posterior cingulate cortex (PCC). Specifically, neural pattern similarity between self-representations was logarithmically compressed with temporal distance. Taken together, these findings reveal a "temporal self-compression" effect, with temporal selves becoming increasingly indiscriminable with distance from the present.

Significance StatementFor centuries, great thinkers have struggled to understand why we feel disconnected from our past and future selves. Insight may come from a basic principle of perception: as objects become distant, they also become less discriminable, or  compressed. In Studies 1-3, we demonstrate that peoples ratings of their own personality become increasingly less differentiated as they consider more distant past and future selves. In Study 4, we found neural evidence that the brain compresses self-representations with time, as well. When we peer out a window, objects close to us are in clear view whereas distant objects are hard to tell apart. We provide novel evidence that self-perception may operate similarly, with the nuance of distant selves increasingly harder to perceive.


title: Multiparametric Profiling of Single Nanoscale Extracellular Vesicles by Combined Atomic Force and Fluorescence Microscopy: Correlation and Heterogeneity in Their Molecular and Biophysical Features

abstract: Being a key player in intercellular communications, nanoscale extracellular vesicles (EVs) offer unique opportunities for both diagnostics and therapeutics. However, their cellular origin and functional identity remain elusive due to the high heterogeneity in their molecular and physical features. Here, for the first time, multiple EV parameters involving membrane protein composition, size and mechanical properties on single small EVs (sEVs) are simultaneously studied by combined fluorescence and atomic force microscopy. Furthermore, their correlation and heterogeneity in different cellular sources are investigated. The study, performed on sEVs derived from Human Embryonic Kidney 293, Cord Blood Mesenchymal Stromal and Human Acute Monocytic Leukemia cell lines, identifies both common and cell line-specific sEV subpopulations bearing distinct distributions of the common tetraspanins (CD9, CD63 and CD81) and biophysical properties. Although the tetraspanin abundances of individual sEVs are independent of their sizes, the expression levels of CD9 and CD63 are strongly correlated. A sEV population co-expressing all the three tetraspanins in relatively high abundance, however, having on average diameters <100 nm and relatively low Young moduli, is also found in all cell lines. Such a multiparametric approach is expected to provide new insights regarding EV biology and functions, potentially deciphering unsolved questions in this field.


title: ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIVE containing protein that controls root growth angle in barley and wheat

abstract:
The root growth angle defines how roots grow towards the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience and as a consequence yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin independent higher responsiveness to gravity compared to wild type plants. We cloned the EGT2 gene by a combination of bulked segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. Subcellular localization experiments revealed that EGT2 localizes to the nucleus and cytoplasm. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA-seq, we observed that seven expansin genes were transcriptionally downregulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals.

Significance StatementTo date the potential of utilizing root traits in plant breeding remains largely untapped. In this study we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain containing protein. We demonstrated that EGT2 is a key gene of root growth angle regulation in response to gravity which is conserved in barley and wheat and could be a promising target for crop improvement in cereals.


title: Moderately pathogenic maternal influenza A virus infection disrupts placental integrity but spares the fetal brain

abstract:
Maternal infection during pregnancy is a known risk factor for offspring mental health disorders. Animal models of maternal immune activation (MIA) have implicated specific cellular and molecular etiologies of psychiatric illness, but most rely on pathogen mimetics. Here, we developed a mouse model of live H3N2 influenza A virus (IAV) infection during pregnancy that induces a robust inflammatory response but is sublethal to both dams and offspring. We observed lung inflammatory cytokine production and severely diminished weight gain in IAV-infected dams. This was accompanied by immune cell infiltration in the placenta and partial breakdown of placental integrity. However, indications of IL-17A signaling and fetal neuroinflammation, which are hallmarks of mimetic-induced MIA, were not detected. Our results suggest that mild or moderately pathogenic IAV infection during pregnancy does not inflame the developing fetal brain, and highlight the importance of live pathogen infection models for the study of MIA.

HighlightsO_LIA mouse model of influenza A virus (IAV) infection during pregnancy was established
C_LIO_LIModerate IAV infection induced lung inflammation and blunted weight gain in dams
C_LIO_LIMaternal IAV infection caused mild pathology in the placenta without pup loss
C_LIO_LIModerate gestational IAV infection did not induce fetal brain inflammation
C_LIO_LIAn IAV infection severity threshold may exist for inducing fetal neuroinflammation
C_LI


title: REM: An Integrative Rule Extraction Methodology for Explainable Data Analysis in Healthcare

abstract: Deep learning models are receiving increasing attention in clinical decision-making, however the lack of explainability impedes their deployment in day-to-day clinical practice. We propose REM, an explainable methodology for extracting rules from deep neural networks and combining them with rules from non-deep learning models. This allows integrating machine learning and reasoning for investigating basic and applied biological research questions. We evaluate the utility of REM in two case studies for the predictive tasks of classifying histological and immunohistochemical breast cancer subtypes from genotype and phenotype data. We demonstrate that REM efficiently extracts accurate, comprehensible rulesets from deep neural networks that can be readily integrated with rulesets obtained from tree-based approaches. REM provides explanation facilities for predictions and enables the clinicians to validate and calibrate the extracted rulesets with their domain knowledge. With these functionalities, REM caters for a novel and direct human-in-the-loop approach in clinical decision-making.


title: Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars

abstract:
BackgroundAmyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite lack of apparent sequence homology. They are hard to detect in large sequence databases either with the alignment-based profile methods (due to short length and diversity) or with generic amyloid- and prion-finding tools (due to insufficient discriminative power). We propose to address the challenge with a machine learning grammatical model capable of generalizing over diverse collections of unaligned yet related motifs.

ResultsFirst, we introduce and test improvements to our probabilistic context-free grammar framework for protein sequences that allow for inferring more sophisticated models achieving high sensitivity at low false positive rates. Then, we infer universal grammars for a collection of recently identified bacterial amyloid signaling motifs and demonstrate that the method is capable of generalizing by successfully searching for related motifs in fungi. The results are compared to available alternative methods. Finally, we conduct spectroscopy analyses of selected peptides to verify their structural and functional relationship.

ConclusionsWhile the profile HMMs remain the method of choice for modeling homologous sets of sequences, PCFGs seem more suitable for building meta-family descriptors and extrapolating beyond the seed sample.


title: Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

abstract: Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 695 novel, full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night in cyanobacteria but not in other phyla, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.


title: FIVEx: an interactive multi-tissue eQTL browser

abstract:
SummaryExpression quantitative trait loci (eQTLs) characterize the associations between genetic variation and gene expression to provide insights into tissue-specific gene regulation. Interactive visualization of tissue-specific eQTLs can facilitate our understanding of functional variants relevant to disease-related traits. However, combining the multi-dimensional nature of eQTLs into a concise and informative visualization is challenging. Existing eQTL visualization tools provide useful ways to summarize the unprecedented scale of transcriptomic data but are not necessarily tailored to answer questions about the functional interpretations of trait-associated variants or other variants of interest. We developed FIVEx, an interactive eQTL browser with an intuitive interface tailored to the functional interpretation of associated variants. It features the ability to navigate seamlessly between different data views while providing relevant tissue- and locus-specific information to offer users a better understanding of population-scale multi-tissue transcriptomic profiles. Our implementation of the FIVEx browser on the Gene-Tissue Expression (GTEx) dataset provides important insights for understanding potential tissue-specific regulatory mechanisms underlying trait-associated signals.

Availability and implementationA FIVEx instance visualizing GTEx v8 data can be found at https://eqtl.pheweb.org. The FIVEx source code is open source under an MIT license at https://github.com/statgen/fivex.


title: mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants

abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative infection of a global pandemic that has led to more than 2 million deaths worldwide. The Moderna mRNA-1273 vaccine has demonstrated ~94% efficacy in a Phase 3 study and has been approved under Emergency Use Authorization. The emergence of SARS-CoV-2 variants with mutations in the spike protein, most recently circulating isolates from the United Kingdom (B.1.1.7) and Republic of South Africa (B.1.351), has led to lower neutralization from convalescent serum by pseudovirus neutralization (PsVN) assays and resistance to certain monoclonal antibodies. Here, using two orthogonal VSV and lentivirus PsVN assays expressing spike variants of 20E (EU1), 20A.EU2, D614G-N439, mink cluster 5, B.1.1.7, and B.1.351 variants, we assessed the neutralizing capacity of sera from human subjects or non-human primates (NHPs) that received mRNA-1273. No significant impact on neutralization against the B.1.1.7 variant was detected in either case, however reduced neutralization was measured against the mutations present in B.1.351. Geometric mean titer (GMT) of human sera from clinical trial participants in VSV PsVN assay using D614G spike was 1/1852. VSV pseudoviruses with spike containing K417N-E484K-N501Y-D614G and full B.1.351 mutations resulted in 2.7 and 6.4-fold GMT reduction, respectively, when compared to the D614G VSV pseudovirus. Importantly, the VSV PsVN GMT of these human sera to the full B.1.351 spike variant was still 1/290, with all evaluated sera able to fully neutralize. Similarly, sera from NHPs immunized with 30 or 100g of mRNA-1273 had VSV PsVN GMTs of ~ 1/323 or 1/404, respectively, against the full B.1.351 spike variant with a ~ 5 to 10-fold reduction compared to D614G. Individual mutations that are characteristic of the B.1.1.7 and B.1.351 variants had a similar impact on neutralization when tested in VSV or in lentivirus PsVN assays. Despite the observed decreases, the GMT of VSV PsVN titers in human vaccinee sera against the B.1.351 variant remained at ~1/300. Taken together these data demonstrate reduced but still significant neutralization against the full B.1.351 variant following mRNA-1273 vaccination.


title: mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge

abstract: The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.


title: An efficient algorithm for estimating population history from genetic data

abstract: The Legofit statistical package uses genetic data to estimate parameters describing population history. Previous versions used computer simulations to estimate probabilities, an approach that limited both speed and accuracy. This article describes a new deterministic algorithm, which makes Legofit faster and more accurate. The speed of this algorithm declines as model complexity increases. With very complex models, the deterministic algorithm is slower than the stochastic one. In an application to simulated data sets, the estimates produced by the deterministic and stochastic algorithms were essentially identical. Reanalysis of a human data set replicated the findings of a previous study and provided increased support for the hypotheses that (a) early modern humans contributed genes to Neanderthals, and (b) a "superarchaic" population (which separated from all other humans early in the Pleistocene) was either large or deeply subdivided.


title: From zero to infinity: minimum to maximum diversity of the planet by spatio-parametric Rao's quadratic entropy

abstract:
AimThe majority of work done to gather information on Earth diversity has been carried out by in-situ data, with known issues related to epistemology (e.g., species determination and taxonomy), spatial uncertainty, logistics (time and costs), among others. An alternative way to gather information about spatial ecosystem variability is the use of satellite remote sensing. It works as a powerful tool for attaining rapid and standardized information. Several metrics used to calculate remotely sensed diversity of ecosystems are based on Shannons Information Theory, namely on the differences in relative abundance of pixel reflectances in a certain area. Additional metrics like the Raos quadratic entropy allow the use of spectral distance beside abundance, but they are point descriptors of diversity, namely they can account only for a part of the whole diversity continuum. The aim of this paper is thus to generalize the Raos quadratic entropy by proposing its parameterization for the first time.

InnovationThe parametric Raos quadratic entropy, coded in R, i) allows to represent the whole continuum of potential diversity indices in one formula, and ii) starting from the Raos quadratic entropy, allows to explicitly make use of distances among pixel reflectance values, together with relative abundances.

Main conclusionsThe proposed unifying measure is an integration between abundance- and distance-based algorithms to map the continuum of diversity given a satellite image at any spatial scale.

category: ecology


title: Linked supergenes underlie split sex ratio and social organization in an ant

abstract:
Sexually reproducing organisms usually invest equally in male and female offspring. Deviations from this pattern have led researchers to new discoveries in the study of parent-offspring conflict, genomic conflict, and cooperation. Some social insect species exhibit the unusual population-level pattern of split sex ratio, wherein some colonies specialize in the production of future queens and others specialize in the production of males. Theoretical work focused on the relatedness asymmetries emerging from haplodiploid inheritance, whereby queens are equally related to daughters and sons, but their daughter workers are more closely related to sisters than to brothers, led to a series of testable predictions and spawned many empirical studies of this phenomenon. However, not all empirical systems follow predicted patterns, so questions remain about how split sex ratio emerges. Here, we sequence the genomes of 138 Formica glacialis workers from 34 male-producing and 34 gyne-producing colonies to determine whether split sex ratio is under genetic control. We identify a supergene spanning 5.5 Mbp that is closely associated with sex allocation in this system. Strikingly, this supergene is adjacent to another supergene spanning 5 Mbp that is associated with variation in colony queen number. We identify a similar pattern in a second related species, Formica podzolica. The discovery that split sex ratio is determined, at least in part, by a supergene in two species opens a new line of research on the evolutionary drivers of split sex ratio.

Significance StatementSome social insects exhibit split sex ratio, wherein some colonies produce future queens and others produce males. This phenomenon spawned many influential theoretical studies and empirical tests, both of which have advanced our understanding of parent-offspring conflicts and cooperation. However, some empirical systems did not follow theoretical predictions, indicating that researchers lack a comprehensive understanding of the drivers of split sex ratio. Here, we show that split sex ratio is associated with a large genomic region in two ant species. The discovery of a genetic basis for sex allocation in ants provides a novel explanation for this phenomenon, particularly in systems where empirical observations deviate from theoretical predictions.


title: LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life

abstract:
SummaryThere are now more than two million RNA sequencing experiments for plants, animals, bacteria and fungi publicly available, allowing us to study gene expression within and across species and kingdoms. However, the tools allowing the download, quality control and annotation of this data for more than one species at a time are currently missing. To remedy this, we present the Large-Scale Transcriptomic Analysis Pipeline in Kingdom of Life (LSTrAP-Kingdom) pipeline, which we used to process 134,521 RNA-seq samples, achieving ~12,000 processed samples per day. Our pipeline generated quality-controlled, annotated gene expression matrices that rival the manually curated gene expression data in identifying functionally-related genes.

Availability and implementationLSTrAP-Kingdom is available from: https://github.com/wirriamm/plants-pipeline and is fully implemented in Python and Bash.


title: Gaining Insight into the Deformation of Achilles Tendon Entheses in Mice

abstract: Understanding the biomechanics of tendon entheses is fundamental for surgical repair and tissue engineering, but also relevant in biomimetics and palaeontology. 3D imaging is becoming increasingly important in the examination of soft tissue deformation. But entheses are particularly difficult objects for micro-computed tomography because they exhibit extreme differences in X-ray attenuation. In this article, the ex vivo examination of Achilles tendon entheses from mice using a combination of tensile tests and synchrotron radiation-based micro-computed tomography is reported. Two groups of specimens with different water content are compared with regard to strains and volume changes in the more proximal free tendon and the distal tendon that wraps around the Tuber calcanei. Tomograms of relaxed and deformed entheses are recorded with propagation-based phase contrast. The tissue structure is rendered in sufficient detail to enable manual tracking of patterns along the tendon, as well as 3D optical flow analysis in a suitable pair of tomograms. High water content is found to increase strain and to change the strain distribution among proximal and distal tendon. In both groups, the volume changes are higher in the distal than in the proximal tendon. These results support the existence of a compliant zone near the insertion. They also show that the humidity of the specimen environment has to be controlled. Necessary steps to extend the automatic tracking of tissue displacements to all force steps are discussed.


title: Comparison of Two Illumina Whole Transcriptome RNA Sequencing Library Preparation Methods Using Human FFPE Specimens

abstract: RNA extraction and library preparation from formalin-fixed, paraffin-embedded (FFPE) samples are crucial pre-analytical steps towards achieving optimal downstream RNA Sequencing (RNASeq) results. We assessed the Illumina TruSeq Stranded Total RNA library preparation method and the Illumina TruSeq RNA Access library preparation method for RNA-Seq analysis using 25 FFPE samples from human cancer indications (NSCLC, CRC, RC, BC and HCC) at two independent vendors. These FFPE samples covered a wide range of sample storage durations (3-25 years-old), sample qualities, and specimen types (resection vs. core needle biopsy). Our data showed that TruSeq RNA Access libraries yield over 80% exonic reads across different quality samples, indicating higher selectivity of the exome pull down by the capture approach compared to the random priming of the TruSeq Stranded Total kit. The overall QC data for FFPE RNA extraction, library preparation, and sequencing generated by the two vendors are comparable, and downstream gene expression quantification results show high concordance as well. With the TruSeq Stranded Total kit, the average Spearman correlation between vendors was 0.87 and the average Pearson correlation was 0.76. With the TruSeq RNA Access kit, the average Spearman correlation between vendors was 0.89 and the average Pearson correlation was 0.73. Interestingly, examination of the crossvendor correlations compared to various common QC statistics suggested that library concentration is better correlated with consistency between vendors than is the RNA quantity. Our analyses provide evidence to guide selection of sequencing methods for FFPE samples in which the sample quality may be severely compromised.


title: Induction of a colitogenic phenotype in Th1 cells depends on IL-23R signaling

abstract: The cytokine receptor IL-23R plays a fundamental role in inflammation and autoimmunity. However, several observations have been difficult to reconcile under the assumption that only Th17 cells critically depend on IL-23 to acquire a pathogenic phenotype. Here, we report that Th1 cells differentiated in vitro with IL-12 + IL-21 show similar levels of IL-23R expression as in pathogenic Th17 cells. We demonstrate that IL-23R is required for Th1 cells to acquire a highly colitogenic phenotype. scRNAseq analysis of intestinal T cells enabled us to identify novel regulators induced by IL-23R-signaling in Th1 cells which differed from those expressed in Th17 cells. The perturbation of one of these regulators (CD160) in Th1 cells inhibited induction of colitis. In this process, we were able to uncouple IL-23R as a purely Th17 cell-specific factor and implicate IL-23R signaling as a pathogenic driver of Th1 cell-mediated tissue inflammation and disease.


title: Dynamic posttranslational modifications of cytoskeletal proteins unveil hot spots under nitroxidative stress

abstract: The cytoskeleton is a supramolecular structure consisting of interacting protein networks that support cell dynamics in essential processes such as migration and division, as well as in responses to stress. Fast cytoskeletal remodeling is achieved with the participation of regulatory proteins and posttranslational modifications (PTMs). Redox-related PTMs are emerging as critical players in cytoskeletal regulation. Here we used a cellular model of mild nitroxidative stress in which a peroxynitrite donor induced transient changes in the organization of three key cytoskeletal proteins, i.e., vimentin, actin and tubulin. Nitroxidative stress-induced reconfiguration of intermediate filaments, microtubules and actin structures were further correlated with their PTM profiles and dynamics of the PTM landscape. Using high-resolution mass spectrometry, 62 different PTMs were identified and relatively quantified in vimentin, actin and tubulin proteins, including 12 enzymatic, 13 oxidative and 2 nitric oxide-derived modifications as well as 35 modifications by carbonylated lipid peroxidation products, thus evidencing the occurrence of a chain reaction with formation of reactive species and the activation of multiple signaling pathways. Our results unveil the presence of certain modifications under basal conditions and their modulation in response to stress in a target-, residue- and reactive species-dependent manner. Moreover, we identified protein PTM "hot spots", such as the single cysteine residue of vimentin, supporting its role in PTM cross-talk and redox sensing. Finally, identification of novel PTMs in these proteins may pave the way for unveiling novel cytoskeleton regulatory mechanisms.

category: cell biology


title: Mild impacts do not subsidize aquatic insect communities in an Atlantic Forest stream.

abstract:
Odums perturbation theory hypothesizes that toxic pollutants cause damage to ecosystems early in the course of contamination. In contrast, organic pollutants enrich the ecosystem until it exceeds their carrying capacity, an effect known as the subsidy-stress gradient. Understanding this dynamic can improve the efficiency of river restoration programs and bring significant benefits to society by providing ecosystem services that were lost. However, the initial effects of the most common human-induced disturbances in Atlantic Forest streams are not well known, indicating the necessity to evaluate the subsidy-stress gradient in these vulnerable and diverse ecosystems.

AimWe evaluated the composition and abundance of the community of aquatic insects from leaf litter of headwater streams in three conditions: a fully forested area (reference stream), a low-intensity urban settlement (urban stream), and a region with small farms dedicated to the cultivation of fruits and vegetables (agricultural stream).

MethodsWe used alpha and beta diversity metrics and a specific biotic index to test the subsidy-stress gradient prediction.

ResultsThe agricultural stream showed the most degraded ecological condition. The urban stream and the reference stream showed similarity in alpha diversity metrics. According to the biotic index, the streams showed a gradient of environmental quality, with the reference stream showing the best quality and the agricultural stream the worst quality.

ConclusionsThe agricultural stream showed a decrease in the environmental quality consistent with the effect predicted by the subsidy-stress gradient due to toxic pollutants contribution. However, the low-intensity enrichment of organic matter from the urban settlement causes a disorder in the ecosystem that reduces its environmental quality, contrary to the predicted by the subsidy-stress gradient.


title: Representation and inference of size control laws by neural network aided point processes

abstract: The regulation and coordination of cell growth and division is a long-standing problem in cell physiology. Recent single-cell measurements using microfluidic devices provide quantitative time-series data of various physiological parameters of cells. To clarify the regulatory laws and associated relevant parameters such as cell size, mathematical models have been constructed based on physical insights over the phenomena and tested by their capabilities to reproduce the measured data. However, such a conventional model construction by abduction faces a constant risk that we may overlook important parameters and factors especially when complicated time series data is concerned. In addition, comparing a model and data for validation is not trivial when we work on noisy multi-dimensional data. Using cell size control as an example, we demonstrate that this problem can be addressed by employing a neural network (NN) method, originally developed for history-dependent temporal point processes. The NN can effectively segregate history-dependent deterministic factors and unexplainable noise from a given data by flexibly representing functional forms of the deterministic relation and noise distribution. With this method, we represent and infer birth and division cell size distributions of bacteria and fission yeast. The known size control mechanisms such as adder model are revealed as the conditional dependence of the size distributions on history and their Markovian properties are shown sufficient. In addition, the inferred NN model provides a better data representation for the abductive model searching than descriptive statistics. Thus, the NN method can work as a powerful tool to process the noisy data for uncovering hidden dynamic laws.

category: systems biology


title: Extended applicability of causal inference to compositional data by reciprocal logarithmic ratio transformation

abstract:
Understanding state transition caused by several intrinsic and extrinsic factors such as environmental change and increased stress of human activities has been a significant focus in ecological studies. Analysis of time-series data is indispensable to identify a causal relationship between the possible factors and community change. Among several time-series analysis, a nonlinear time series analysis method called empirical dynamic modeling (EDM) has been recently applied to infer causality of community change that arose from intraspecies interactions. EDM allows model-free analysis to estimate the degree of action strength of intraspecific and interspecific interactions at the population level. Convergent cross-mapping (CCM) is an empirical dynamic analysis method used to suggest the existence of causality by reconstructing the state space of a dynamical system from a time series of observations without assuming any explicit mathematical equations. Although CCM allows for inferring directional interpretation of causal relationships from multivariate time series data, one of the major challenges is its non-applicability to compositional data, a common representation of next generation sequencing data such as microbiome. This study aimed to explore a practical approach applied explicitly to compositional data analysis. More specifically, we propose a heuristic but useful transformation that enables CCM to be applied to compositional data. The proposed transformation has demonstrated its applicability to compositional data equivalent to the conventional CCM to untransformed data. Application of the proposed transformation to sequence-based microbial community profiling data provides reasonable implication to the possible causal relationship during state transition.

Author summarySeveral types of ecological studies such as trophic changes in lakes, marine plankton communities, forest ecosystems, terrestrial ecosystems, and interactions between plants and soils have employed time-series analyses for identifying the factors that might cause state changes. With the rise of next-generation sequencing, our understanding of these ecosystems is expanding to analyze sequence data. A nonlinear time series analysis method, termed empirical dynamic modeling, has been recently applied for analyzing time-series data. Among different empirical dynamic modeling methods, convergent cross-mapping (CCM) is frequently used to infer a causal relationship. Although CCM enables the directional interpretation of causal relationships, it cannot be applied to compositional data analysis. This study proposes a novel type of transformation, Reciprocal Logarithmic Ratio (RLR) transformation, that enables CCM to be applied to compositional data. With RLR-transformation, CCM results for compositional data are comparable to those for absolute data, and it is confirmed that the transformation is applicable to sequence data as well. The RLR-transformation is expected to provide a better understanding of ecological interactions by estimating causal relationships in compositional data.


title: 6mer Seed Toxicity and Platinum Resistance in Ovarian Cancer

abstract: Numerous micro(mi)RNAs (short noncoding RNAs that negatively regulate gene expression) have been linked to platinum (Pt) sensitivity and resistance in ovarian cancer (OC). miRNA activity occurs when the guide strand of the miRNA, with its seed sequence (pos. 2-7/8), is loaded into the RNA induced silencing complex (RISC) and targets complementary short seed matches in the 3 untranslated region of mRNAs. Toxic seeds, targeting genes critical for cancer cell survival, have been found in tumor suppressive miRNAs. Many si- and shRNAs can also kill cancer cells via toxic seeds, the most toxic carrying G-rich 6mer seed sequences. We now show that treatment of OC cells with Pt leads to an increase in RISC-bound miRNAs carrying toxic 6mer seeds and a decrease in miRNAs with nontoxic seeds. Pt-resistant cells did not exhibit this toxicity shift but retained sensitivity to cell death mediated by siRNAs carrying toxic 6mer seeds. Analysis of RISC-bound miRNAs in OC patients revealed that the ratio between miRNAs with toxic versus miRNAs with nontoxic seeds was predictive of treatment outcome. Application of the 6mer seed toxicity concept to cancer relevant miRNAs provides a new framework for understanding and predicting cancer therapy responses.


title: The balance between toxic versus nontoxic microRNAs determines platinum sensitivity in ovarian cancer


title: Trophic position derived from amino-acid nitrogen isotopes reflect physiological status of both predator and prey over four decades

abstract:
Nitrogen isotope analyses of amino-acids ({delta}15N-AA) are increasingly used to decipher food webs. Interpretation of {delta}15N-AA in consumers relies on the assumption that physiological status has a negligible influence on the trophic enrichment factor (TEF). Recent experiments have shown that this is not always the case and there is a need to validate derived trophic position (TP) estimates using ecological data. We analyzed {delta}15N-AA in cod and herring (1980-2019) from the Baltic Sea, a species-poor system where dramatic reduction in condition status of cod has occurred. We expected that TEFcod-herring in trophic AAs would increase during periods of poor cod growth, resulting in inflated TP estimates. We found that TEF and TP estimates were negatively linked to individual condition status, prey fat content and the hypoxic state of the ecosystem. Statistically adjusting for these variables resulted in lower cod TP, highlighting the importance of including ecological knowledge when interpreting TP.

Scientific Significance StatementNitrogen stable isotope analyses in amino acids are increasingly used in ecology to understand how environmental change impacts food-webs. Specifically, it is used to more accurately calculate trophic position (TP) of consumers. Controlled experiments have shown that physiological status can alter amino acid isotope composition and TP interpretation, but field studies are lacking. We use 40 years of archived material to demonstrate that TP estimates in Baltic Sea cod and its prey herring are directly related to physiological status. This has important implications for interpreting the real trophic ecology of consumers under environmental stress. By simultaneously measuring condition status in both predator and prey it is possible to adjust for them as confounding variables and decipher actual consumer TP.


title: RegEnrich: An R package for gene regulator enrichment analysis reveals key role of ETS transcription factor family in interferon signaling

abstract: Changes in a few key transcriptional regulators can lead to different biological states, including cell activation and differentiation, and diseases. Extracting the key gene regulators governing a biological state allows us to gain mechanistic insights and can further help in translational research. Most current tools perform pathway/GO enrichment analysis to identify key genes and regulators but tend to overlook the regulatory interactions between genes and proteins. Here we present RegEnrich, an open-source Bioconductor R package, which combines differential expression analysis, data-driven gene regulatory network inference, enrichment analysis, and gene regulator ranking to identify key regulators using gene/protein expression profiling data. By benchmarking using multiple gene expression datasets of gene silencing studies, we found that RegEnrich using the GSEA method to rank the regulators performed the best to retrieve the key regulators. Further, RegEnrich was applied to 21 publicly available datasets on in vitro interferon-stimulation of different cell types. We found that not only IRF and STAT transcription factor families played an important role in cells responding to IFN, but also several ETS transcription factor family members, such as ELF1 and ETV7, are highly associated with IFN stimulations. Collectively, RegEnrich can accurately identify key gene regulators from the cells under different biological states in a data-driven manner, which can be valuable in mechanistically studying cell differentiation, cell response to drug stimulation, disease development, and ultimately drug development.


title: Large Organellar Changes occur during Mild Heat Shock in Yeast

abstract:
When the temperature is increased, the heat shock response is activated to protect the cellular environment. The transcriptomics and proteomics of this process are intensively studied, while information about how the cell responds structurally to heat stress is mostly lacking. Here, Saccharomyces cerevisiae were subjected to a mild continuous heat shock and intermittently cryo-immobilized for electron microscopy. Through measuring changes in all distinguishable organelle numbers, sizes, and morphologies in over 2400 electron micrographs a major restructuring of the cells internal architecture during the progressive heat shock was revealed. The cell grew larger but most organelles within it expanded even more. Organelles responded to heat shock at different times, both in terms of size and number, and adaptations of certain organelles morphology were observed. Multivesicular bodies grew to almost 170% in size, indicating a previously unknown involvement in the heat shock response. A previously undescribed electron translucent structure accumulated close to the plasma membrane during the entire time course. This all-encompassing approach provides a detailed chronological progression of organelle adaptation throughout the cellular stress response.

Summary statementExposure to mild heat shock leads to large quantifiable changes in the cellular ultrastructure of yeast, shows involvement of MVBs in the heat shock response and the apparition of novel structures.


title: Hydrodynamic stress and phenotypic plasticity of the zebrafish regenerating fin

abstract: Understanding how extrinsic factors modulate genetically encoded information to produce a specific phenotype is of prime scientific interest. In particular, the feedback mechanism between abiotic forces and locomotory organs during morphogenesis to achieve efficient movement is a highly relevant example of such modulation. The study of this developmental process can provide unique insights on the transduction of cues at the interface between physics and biology. Here, we take advantage of the natural ability of adult zebrafish to regenerate their amputated fins to assess its morphogenic plasticity upon external modulations. Using a variety of surgical and chemical treatments, we are able to induce phenotypic responses to the structure of the fin. In particular, fin cleft depth and the bifurcation of the bony rays are modulated by the surface area of the stump. To dissect the role of mechanotransduction in this process, we investigate the patterns of hydrodynamic forces acting on the surface of a zebrafish fin during regeneration by using particle tracking velocimetry on a range of biomimetic hydrofoils. This experimental approach enables us to quantitatively compare hydrodynamic stress distributions over flapping fins of varying sizes and shapes. As a result, viscous shear stress acting on the tip of the fin and the resulting internal tension are proposed as suitable signals for guiding the regulation of ray growth dynamics and branching pattern. Our findings suggest that mechanical forces are involved in the fine-tuning of the locomotory organ during fin morphogenesis.

category: biophysics


title: Disrupting D2-NMDA receptor heteromerization blocks the rewarding effects of cocaine but preserves natural reward processing

abstract: Addictive drugs increase dopamine in the nucleus accumbens (NAc), where it persistently shapes excitatory glutamate transmission and hijacks natural reward processing. Herein, we provide evidence, from mice to human, that an underlying mechanism relies on drug-evoked heteromerization of glutamate NMDA receptors (NMDAR) with dopamine receptor 1 (D1R) or 2 (D2R). Using temporally-controlled inhibition of D1R-NMDAR heteromerization, we unraveled their selective implication in early developmental phases of cocaine-mediated synaptic, morphological and behavioral responses. In contrast, preventing D2R-NMDAR heteromerization blocked the persistence of these adaptations. Importantly, interfering with these heteromers spared natural reward processing. Strikingly, we established that D2R-NMDAR complexes exist in human samples and showed that, despite a decreased D2R protein expression in the NAc, psychostimulant-addicts display a higher proportion of D2R forming heteromers with NMDAR. These findings contribute to a better understanding of molecular mechanisms underlying addiction and uncover D2R-NMDAR heteromers as targets with potential therapeutic value.


title: RBD11, a bioengineered Rab11-binding module for visualizing and analyzing endogenous Rab11

abstract: The small GTPase Rab11 plays pivotal roles in diverse physiological phenomena, including the recycling of membrane proteins, cytokinesis, neurite outgrowth, and epithelial morphogenesis. One effective method of analyzing the function of endogenous Rab11 is to overexpress a Rab11-binding domain of one of its effectors, e.g., the C-terminal domain of Rab11-FIP2 (Rab11-FIP2-C), as a dominant-negative construct. However, the drawback of this method is the broader Rab binding specificity of the effector domain, because Rab11-FIP2-C binds to Rabs other than Rab11, e.g., to Rab14 and Rab25. In this study, we bioengineered an artificial Rab11-specific binding domain, named RBD11. Expression of RBD11 visualized endogenous Rab11 without affecting its localization or function, whereas expression of a tandem RBD11, named 2xRBD11, inhibited epithelial morphogenesis and induced a multi-lumen phenotype characteristic of Rab11-deficient cysts. We also developed two tools for temporally and reversibly analyzing Rab11-dependent membrane trafficking: tetracycline-inducible 2xRBD11 and an artificially oligomerized domain (FM)-tagged RBD11.


title: Antifungal effects of alantolactone on Candida albicans: an in vitro study

abstract: The human fungal pathogen Candida albicans can cause many kinds of infections, including biofilm infections on medical devices, while the available antifungal drugs are limited to only a few. In this study, alantolactone (Ala) demonstrated antifungal activities against C. albicans, as well as other Candida species, with a MIC of 72 g/mL. Ala could also inhibit the adhesion, yeast-to-hyphal transition, biofilm formation and development of C. albicans. The exopolysaccharide of biofilm matrix and extracellular phospholipase production could also be reduced by Ala treatment. Ala could increase permeability of C. albicans cell membrane and ROS contribute to the antifungal activity of Ala. Overall, the present study suggests that Ala may provide a promising candidate for developing antifungal drugs against C. albicans infections.


title: Structural and functional studies of the first tripartite protein complex at the Trypanosoma brucei flagellar pocket collar

abstract:
The flagellar pocket (FP) is the only endo- and exocytic organelle in most trypanosomes and, as such, is essential throughout the life cycle of the parasite. The neck of the FP is maintained enclosed around the flagellum via the flagellar pocket collar (FPC). The FPC is a macromolecular cytoskeletal structure and is essential for the formation of the FP and cytokinesis. FPC biogenesis and structure are poorly understood, mainly due to the lack of information on FPC composition. To date, only two FPC proteins, BILBO1 and FPC4, have been characterized. BILBO1 forms a molecular skeleton upon which other FPC proteins can, theoretically, dock onto. We previously identified FPC4 as the first BILBO1 interacting partner and demonstrated that its C-terminal domain interacts with the BILBO1 N-terminal domain (NTD). Here, we report the characterization of a new FPC component and BILBO1 partner protein, BILBO2 (Tb927.6.3240) by yeast two-hybrid screen, bioinformatics, functional and structural studies. We show that BILBO2 colocalizes with BILBO1 and can modulate the shape of the BILBO1 filament by interacting with the BILBO1 EF-hand domains. Further, we demonstrate that BILBO1 and BILBO2 share a homologous NTD domain and that both domains interact with FPC4. We have determined a 1.9 [A] resolution crystal structure of the BILBO2 NTD in complex with the FPC4 BILBO1-binding domain. Together with mutational analyses, our studies reveal key residues for the function of the BILBO2 NTD and its interaction with FPC4 and evidenced a tripartite interaction between BILBO1, BILBO2, and FPC4. Our work sheds light on the first atomic structure of an FPC protein complex and represents a significant step in deciphering the FPC function in Trypanosoma brucei and other pathogenic kinetoplastids.

Author summaryTrypanosomes belong to a group of zoonotic, protist, parasites that are found in Africa, Asia, South America, and Europe and are responsible for severe human and animal diseases. They all have a common structure called the flagellar pocket (FP). In most trypanosomes, all macromolecular exchanges between the trypanosome and the environment occur via the FP. The FP is thus essential for cell viability and evading the host immune response. We have been studying the flagellar pocket collar (FPC), an enigmatic macromolecular structure at the neck of the FP, and demonstrated its essentiality for the biogenesis of the FP. We demonstrated that BILBO1 is an essential protein of the FPC that interacts with other proteins including a microtubule-binding protein FPC4.

Here we identify another bona fide FPC protein, BILBO2, so named because of close similarity with BILBO1 in protein organization and functional domains. We demonstrate that BILBO1 and BILBO2 share a common N-terminal domain involved in the interaction with FPC4, and illustrate a tripartite interaction between BILBO1, BILBO2, and FPC4. Our study also provides the first atomic view of two FPC components. These data represent an additional step in deciphering the FPC structure and function in T. brucei.


title: Mapping biochemical states associated with HP1 target recognition at sites of heterochromatin formation in living cells

abstract: HP1 proteins bind with low affinity but high specificity to histone H3 lysine 9 methylation (H3K9me), forming transcriptionally inactive genomic compartments referred to as heterochromatin. How HP1 proteins traverse a complex and crowded chromatin landscape on the millisecond timescale and yet recognize H3K9me with high specificity remains paradoxical. Here, we visualize the single-molecule dynamics of an HP1 homolog, the fission yeast Swi6, in its native chromatin environment. By analyzing the motions of individual Swi6 molecules, we identify mobility states that map to discrete biochemical intermediates. Using mutants that perturb Swi6 H3K9me recognition, oligomerization, or nucleic acid binding, we parse the mechanism by which each biochemical property affects protein dynamics. We find that rather than enhancing chromatin binding, nucleic acid interactions, compete with and titrates Swi6 away from heterochromatin. However, as few as four tandem Swi6 chromodomains are necessary and sufficient to restore H3K9me-dependent localization. Our studies propose propose that HP1 oligomerization stabilizes higher-order protein configurations of a defined stoichiometry that facilitates high-specificity H3K9me recognition and outcompetes the inhibitory effects of nucleic acid-binding.


title: HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization


title: Training Data: How can we best prepare instructors to teach data science in undergraduate biology and environmental science courses?

abstract: There is a clear and concrete need for greater quantitative literacy in the biological and environmental sciences. Data science training for students in higher education necessitates well-equipped and confident instructors across curricula. However, not all instructors are versed in data science skills or research-based teaching practices. Our study sought to survey the state of data science education across institutions of higher learning, identify instructor needs, and illuminate barriers to teaching data science in the classroom. We distributed a survey to instructors around the world, focused on the United States, and received 106 complete responses. Our results indicate that instructors across institutions use, teach, and view data management, analysis, and visualization as important for students to learn. Code, modeling, and reproducibility were less valued by instructors, although there were differences by institution type (doctoral, masters, or baccalaureate), and career stage (time since terminal degree). While there were a variety of barriers highlighted by respondents, instructor background, student background, and space in the curriculum were the greatest barriers of note. Interestingly, instructors were most interested in receiving training for how to teach code and data analysis in the undergraduate classroom. Our study provides an important window into how data science is taught in higher education as well as suggestions for how we can best move forward with empowering instructors across disciplines.

category: scientific communication and education


title: Adolescent predatory stress increases peripheral TNFα response to LPS regardless of sex

abstract: Chronic adolescent stress has been shown to cause increased adverse effects in response to an immune stressor later in life including the development of anxiety and PTSD. Following stress, the production of inflammatory cytokines including IL-1{beta} and TNF is expected to increase in response to an immune challenge such as LPS. Male and female mice underwent fifteen consecutive days of predatory stress. Chronic adolescent stress was shown to increase both anxiety-like behavior (F(1, 28) = 19.82, p = 0.0001) and TNF levels within the periphery (F(1, 19) = 4.748, p = 0.0421).


title: Inhalable textile microplastic fibers impair airway epithelial growth

abstract:
Synthetic textiles shed fibers that accumulate indoors and this results in continuous exposure when indoors. High exposure to microplastic fibers in nylon flock workers has been linked to the development of airway and interstitial lung disease, but the exact health effects of microplastic fibers on the lungs are unknown. Here we determined effects of polyester and nylon textile microplastic fibers on airway and alveolar epithelial cells using human and murine lung organoids. We observed that particularly nylon microfibers had a negative impact on the growth and development of airway organoids. We demonstrated that this effect was mediated by components leaking from nylon. Moreover, our data suggested that microplastic textile fibers may especially harm the developing airways or airways undergoing repair. Our results call for a need to assess exposure and inhalation levels in indoor environments to accurately determine the actual risk of these fibers to human health.

TeaserAirborne fibers shed from synthetic textiles, in particular nylon, can inhibit repair of the cells coating the airways

category: pharmacology and toxicology