title: Organization of thalamocortical structural covariance and a corresponding 3D atlas of the mouse thalamus

abstract:
For information from sensory organs to be processed by the brain, it is usually passed to appropriate areas of the cerebral cortex. Almost all of this information passes through the thalamus, a relay structure that reciprocally connects to the vast majority of the cortex. The thalamus facilitates this information transfer through a set of thalamocortical connections that vary in cellular structure, molecular profiles, innervation patterns, and firing rates. Additionally, corticothalamic connections allow for intracortical information transfer through the thalamus. These efferent and afferent connections between the thalamus and cortex have been the focus of many studies, and the importance of cortical connectivity in defining thalamus anatomy is demonstrated by multiple studies that parcellate the thalamus based on cortical connectivity profiles.

Here, we examine correlated morphological variation between the thalamus and cortex, or thalamocortical structural covariance. For each voxel in the thalamus as a seed, we construct a cortical structural covariance map that represents correlated cortical volume variation, and examine whether high structural covariance is observed in cortical areas that are functionally relevant to the seed. Then, using these cortical structural covariance maps as features, we subdivide the thalamus into six non-overlapping regions (clusters of voxels), and assess whether cortical structural covariance is associated with cortical connectivity that specifically originates from these regions.

We show that cortical structural covariance is high in areas of the cortex that are functionally related to the seed voxel, cortical structural covariance varies along cortical depth, and sharp transitions in cortical structural covariance profiles are observed when varying seed locations in the thalamus. Subdividing the thalamus based on structural covariance, we additionally demonstrate that the six thalamic clusters of voxels stratify cortical structural covariance along the dorsal-ventral, medial-lateral, and anterior-posterior axes. These cluster-associated structural covariance patterns are prominently detected in cortical regions innervated by fibers projecting out of their related thalamic subdivisions.

Together, these results advance our understanding of how the thalamus and the cortex couple in their volumes. Our results indicate that these volume correlations reflect functional organization and structural connectivity, and further provides a novel segmentation of the mouse thalamus that can be used to examine thalamic structural variation and thalamocortical structural covariation in disease models.


title: Neuromodulation of striatal D1 cells shapes BOLD fluctuations in anatomically connected thalamic and cortical regions

abstract: Understanding how the brains macroscale dynamics are shaped by underlying microscale mechanisms is a key problem in neuroscience. In animal models, we can now investigate this relationship in unprecedented detail by directly manipulating cellular-level properties while measuring the whole-brain response using resting-state fMRI. Here we focused on understanding how blood-oxygen-level-dependent (BOLD) dynamics, measured within a structurally well-defined striato-thalamo-cortical circuit, are shaped by chemogenetically exciting or inhibiting D1 medium spiny neurons (MSNs) of the right dorsomedial striatum (CPdm). We characterize changes in both the BOLD dynamics of individual cortical and subcortical brain areas, and patterns of inter-regional coupling (functional connectivity) between pairs of areas. Using a classification approach based on a large and diverse set of time-series properties, we found that CPdm neuromodulation alters BOLD dynamics within thalamic subregions that project back to dorsomedial striatum. In the cortex, the strongest changes in local dynamics were observed in unimodal regions, i.e., regions that process information from a single sensory modality, while changes in the local dynamics weakened along a putative cortical hierarchical gradient towards transmodal regions. In contrast, a decrease in functional connectivity was observed only for cortico-striatal connections after D1 excitation. Our results provide a comprehensive understanding of how targeted cellular-level manipulations affect local BOLD dynamics at the macroscale, including the role of a circuits structural characteristics and hierarchical cortical level in shaping those dynamics. These findings contribute to ongoing attempts to understand the influence of structure-function relationships in shaping inter-regional communication at subcortical and cortical levels.

category: neuroscience


title: Development of a PET radioligand for α2δ-1 subunit of calcium channels for imaging neuropathic pain

abstract: Neuropathic pain affects 7-10% of the adult population. Being able to accurately monitor biological changes underlying neuropathic pain will improve our understanding of neuropathic pain mechanisms and facilitate the development of novel therapeutics. Positron emission tomography (PET) is a noninvasive molecular imaging technique that can provide quantitative information of biochemical changes at the whole-body level by using radiolabeled ligands. One important biological change underlying the development of neuropathic pain is the overexpression of 2{delta}-1 subunit of voltage-dependent calcium channels (the target of gabapentin). Thus, we hypothesized that a radiolabeled form of gabapentin may allow imaging changes in 2{delta}-1 for monitoring the underlying pathophysiology of neuropathic pain. Here, we report the development of two 18F-labeled derivatives of gabapentin (trans-4-[18F]fluorogabapentin and cis-4-[18F]fluorogabapentin) and their evaluation in healthy rats and a rat model of neuropathic pain (spinal nerve ligation model). Both isomers were found to selectively bind to the 2{delta}-1 receptor with trans-4-[18F]fluorogabapentin having a higher affinity. Both tracers displayed around 1.5- to 2-fold increased uptake in injured nerves over the contralateral uninjured nerves when measured by gamma counting ex vivo. Although the small size of the nerves and the signal from surrounding muscle prevented visualizing these changes using PET, this work demonstrates that fluorinated derivatives of gabapentin retain binding to 2{delta}-1 and that their radiolabeled forms can be used to detect pathological changes in vitro and ex vivo. Furthermore, this work confirms that 2{delta}-1 is a promising target for imaging specific features of neuropathic pain.


title: Electroencephalographic dynamics of rhythmicbreath-based meditation

abstract: Meditation has been practised for millennia but the neuroscientific understanding of the dynamics is still lacking. Sudarshan Kriya Yoga (SKY) is an evidence based breathing based meditation technique that utilizes rhythmic breathing to induce a deep state of relaxation and calm. Multiple studies have found benefits of the SKY technique from genetic, physiological, psychological to behaviour levels. We collected Electroencephalographic (EEG) data in 43 subjects who underwent the SKY technique and analysed the brain rhythms at different stages of the technique namely preparatory breathing (Pranayama), rhythmic breathing (Kriya) and meditation (Yoga Nidra) using newly developed methods to analyse periodic and aperiodic components. Alpha waves amplitude in the parieto-occipital region decreased as the rhythmic breathing progressed and dropped sharply during the meditation period. Theta amplitudes and peak frequency increased in the centro-frontal region during the rhythmic breathing period but were marked by sustained low theta waves during the meditation period. The delta wave amplitude was not affected by breathing but both delta band power and peak frequency increased during the meditation period in the centro-frontal region. We also saw a decrease in the 1/f aperiodic signal across the brain during the meditation period suggesting a modification of excitation-inhibition balance. We see an overall slowing down of brain oscillations from alpha to theta to delta as the meditation progressed. The paper studies in depth the transitional dynamics of the SKY technique analysing the alpha, theta, delta waves and aperiodic signals and demonstrates that each phase in a breathing based meditation has a unique electrophysiological signature.


title: Alpha-1-antitrypsin binds to the glucocorticoid receptor with biological significance in macrophages

abstract: Alpha-1-antitrypsin (AAT), a serine protease inhibitor produced mainly by the liver, is the third most abundant protein in plasma. While a canonical receptor for AAT has not been identified, AAT can be internalized into the cytoplasm and is known to affect gene regulation. Since AAT has significant anti-inflammatory properties affecting many cell types including macrophages, we examined whether AAT binds the cytoplasmic glucocorticoid receptor (GR) in macrophages. We report the novel finding that AAT binds to GR in macrophages using several approaches, including co-immunoprecipitation, mass spectrometry, microscale thermophoresis, and molecular modeling. The mass spectrometry data are available via ProteomeXchange with identifier PXD030989. We further demonstrate that AAT induction of angiopoietin-like 4 protein and AAT inhibition of lipopolysaccharide-induced nuclear factor-kappa B activation and interleukin-8 production are mediated, in part, through AAT-GR interaction. Furthermore, this interaction contributes to a host-protective role against mycobacteria in macrophages. The interaction of AAT and GR described in this study identifies a mechanism for the antiinflammatory and host-defense properties of AAT.

category: immunology


title: The role of Staphylococcus agnetis and Staphylococcus hyicus in the pathogenesis of buffalo fly skin lesions in cattle

abstract: Buffalo flies (Haematobia irritans exigua) are hematophagous ectoparasites of cattle causing production and welfare impacts in northern Australian herds. Skin lesions associated with buffalo fly infestation and Stephanofilaria nematode infection are manifested as focal dermatitis or ulcerated areas most commonly on the medial canthus of the eye, along the lateral and ventral neck and on the abdomen of cattle. For closely related horn flies (Haematobia irritans irritans), Staphylococcus aureus have been suggested as a contributing factor in the development of lesions. To investigate the potential role of bacterial infection in the pathogenesis of buffalo fly lesions, swabs were taken from lesions and normal skin, and bacteria were also isolated from surface washings of buffalo flies and surface-sterilised homogenized flies. Bacterial identification was conducted by MALDI-TOF, strain typing by rep-PCR and DNA sequencing to determine species similarity and virulence factors. Of 49 bacterial isolates collected from lesions, 37 were identified as Staphylococcus agnetis and 12 as Staphylococcus hyicus, whereas from normal skin four isolates were S. hyicus and one was Staphylococcus sciuri. Of the Staphylococcus isolates isolated from buffalo flies, five were identified as S. agnetis and three as S. hyicus. Fifty percent of the buffalo fly isolates had rep-PCR genotypic patterns identical to the lesion isolates. Genome sequencing of 16 S. agnetis and four S. hyicus isolates revealed closely similar virulence factor profiles, with all isolates possessing exfoliative toxin A and C genes. The findings from this study suggest the involvement of S. agnetis and S. hyicus in buffalo fly lesion pathogenesis. This should be taken into account in the development of effective treatment and control strategies for lesions.

category: microbiology


title: Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence

abstract: Acute Respiratory Distress Syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, has no cure. Hypoxemia is a defining feature, yet its impact on inflammation is often neglected. Patients with ARDS are monocytopenic early in the onset of the disease. Endotoxin or Streptococcus pneumoniae acute lung injury (ALI) in the context of hypoxia replicates this finding, through hypoxia-driven suppression of type I interferon signalling. This results in failed lung monocyte-derived interstitial macrophages (IM) niche expansion and unchecked neutrophilic inflammation. Administration of colony stimulating factor 1 (CSF1) rescues the monocytopenia, alters the circulating classical monocyte phenotype in hypoxic endotoxin-driven ALI and enables lung IM population expansion, thus limiting lung injury in endotoxin- and virally-induced hypoxic ALI. Hypoxia directly alters immune dynamics to the detriment of the host and manipulation of this aberrant response offers new therapeutic strategies for ARDS.

category: cell biology


title: Automated classification of estrous stage in rodents using deep learning

abstract: The rodent estrous cycle modulates a range of biological functions, from gene expression to behavior. The cycle is typically divided into four stages, each characterized by distinct hormone concentration profiles. Given the difficulty of repeatedly sampling plasma steroid hormones from rodents, the primary method for classifying estrous stage is by identifying vaginal epithelial cell types. However, manual classification of epithelial cell samples is time-intensive and variable, even amongst expert investigators. Here, we use a deep learning approach to achieve classification accuracy at expert levels in a matter of seconds. Due to the heterogeneity and breadth of our input dataset, our deep learning approach ("EstrousNet") is highly generalizable across rodent species, stains, and subjects. The EstrousNet algorithm exploits the temporal dimension of the hormonal cycle by fitting classifications to an archetypal estrous cycle, highlighting possible misclassifications and flagging anestrus phases (e.g., pseudopregnancy). EstrousNet allows for rapid estrous cycle staging, improving the ability of investigators to consider endocrine state in their rodent studies.


title: ID1 and CEBPA Coordinate Epidermal Progenitor Cell Differentiation

abstract: The regulatory circuits that coordinate epidermal differentiation during development are still not fully understood. Here we report that the transcriptional regulator ID1 is enriched in basal epidermal progenitor cells and find ID1 expression to be diminished upon differentiation. In utero silencing of Id1 impairs progenitor cell proliferation, leads to precocious delamination of targeted progenitor cells and enables differentiated keratinocytes to retain progenitor markers and characteristics. Transcriptional profiling suggests ID1 acts by mediating adhesion to the basement membrane while inhibiting spinous layer differentiation. Co-immunoprecipitation reveals ID1 binding to transcriptional regulators of the class I bHLH family. We localize bHLH Tcf3, Tcf4 and Tcf12 to epidermal progenitor cells during epidermal stratification and established TCF3 as a downstream effector of ID1-mediated epidermal proliferation. Finally, we identify crosstalk between CEBPA, a known mediator of epidermal differentiation, and Id1 and demonstrate that CEBPA antagonizes BMP-induced activation of Id1. Our work establishes ID1 as a key coordinator of epidermal development, acting to balance progenitor proliferation with differentiation and unveils how functional crosstalk between CEBPA and Id1 orchestrates epidermal lineage progression.

category: developmental biology


title: Estimating contemporary migration numbers of adults based on kinship relationships in iteroparous species

abstract: In this paper, we describe the development of estimators for the contemporary migration number and rate of adults between two populations in iteroparous species. The proposed estimators are based on known half-sibling (HS) and/or parent-offspring (PO) relationships observed between the populations across breeding seasons. The rationale is that the HS and PO pairs exhibit information about the occurrence frequency of parental movements during the breeding interval. The proposed method allows for variance in the average number of off-spring per parent both within and between populations. In addition, coupled with the PO pairs found within the population, the estimators can be obtained from only genetic data. Generally, a sample size representing the square root of the population size is required to obtain meaningful information regarding migration. We describe a detailed evaluation of the performance of the estimators by running an individual-based model, and the results provide guidance regarding sample sizes to ensure the required accuracy and precision. Furthermore, given that there are few effective methods to estimate adult movement (especially when populations cannot be genetically distinct), we discuss the usefulness of this proposed kinship assignment method in terms of conservation biology and wildlife management.

category: ecology


title: Effects of disease emergence on invasive grass impacts

abstract: Invasive species impact ecosystems through their large abundances and strong per capita effects. Enemies can regulate abundances and per capita effects, but are notably absent for many new invaders. However, invaders acquire enemies over time and as they spread; processes hypothesized to mitigate negative invader impacts by reducing abundance or per capita effects. Alternatively, properties of invaders or acquired enemies, such as an enemys ability to attack multiple species, may hinder enemy mitigation of invader impacts. We used field experiments to evaluate disease mitigation of invader impacts using the invasive grass Microstegium vimineum, which hosts an emerging fungal disease, and a native grass competitor, Elymus virginicus. We manipulated competition through density gradients of each plant species, and we reduced ambient foliar diseases with fungicide and autoclaving. We then modeled long-term population dynamics with field-estimated parameters. In the field, disease did not reduce invader abundance or per capita effects. The invader amplified disease on itself and the competitor, and disease reduced invader and competitor fitness components (e.g., germination). The dynamical model predicted that disease impacts on the competitor are greater than on the invader, such that disease will reduce invader abundance by 18%, and competitor abundance by 88%, over time. Our study suggests that enemies acquired by invaders will not necessarily mitigate invader impacts if the invader amplifies the enemy and the enemy attacks and suppresses competitor species.


title: Analysis of synthetic genetic interactions of non-coding RNAs in Saccharomyces cerevisiae

abstract: Recent studies identified non-coding RNAs (ncRNAs) with unknown function that are responsible for major fitness changes in yeast. To understand ncRNA interplay and aid their functional assignment, the synthetic genetic array (SGA) methodology was employed to create >15,000 double mutants and to score their epistasis in different environments. Unlike the protein network, ncRNAs mostly displayed positive epistasis in rich medium. Interestingly, the negative interactions significantly increased under stressors, showing environmental-dependent functions for ncRNAs. No correlation was found between the network of ncRNAs and that of their neighbouring genes, suggesting functional independence. The U3 paralogs, SNR17A and SNR17B, share the majority of genetic interactions in rich medium as expected. For example, SUT480 interacted with both paralogs and its function was linked to 18S rRNA processing. However, under stressors, a large number of unique epistatic interactions were observed, supporting the notion that SNR17A and SNR17B have diverged and sub-functionalised after genome duplication.

category: genetics


title: Genome-wide analysis of the non-coding RNA synthetic genetic network reveals extensive plasticity and unique phenotypes in yeast


title: Oxytocin and Emotional Tear in Dogs

abstract: In humans, tear volume increases in emotional arousal. No studies have investigated the relationship of emotional arousal and tear volume in animals. We measured tear volume in dogs before and after reunion with their owners. Tear volume increased significantly during owner, but not familiar non-owner, reunions but not during reunions with familiar non-owners. When oxytocin instillation was applied to dogs, the tear volume increased, suggesting that oxytocin can mediate the emotion-induced tear secretion in dogs. When the photos of dogs face in which artificial tear was applied to the dogs eyes, the positive impression of these photo increased. These suggest that emotional tear can facilitate human-dog emotional connection.

category: animal behavior and cognition


title: Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development

abstract: The SARS-CoV-2 non-structural protein 14 (NSP14) is a dual function enzyme containing an N-terminal exonuclease domain (ExoN) and C-terminal Guanine-N7-methyltransferase (N7-MTase) domain. Both enzymatic activities appear to be essential for the viral life cycle and thus may be targeted for anti-viral therapeutics. NSP14 forms a stable complex with the SARS-CoV-2 zinc binding protein NSP10, and this interaction greatly enhances the nuclease but not the methyltransferase activity. In this study, we have determined the crystal structure of SARS-CoV-2 NSP14 in the absence of NSP10 to 1.7 [A] resolution. Comparisons of this structure with the structure of NSP14/NSP10 complexes solved to date reveal significant conformational changes that occur within the NSP14 ExoN domain upon binding of NSP10, including significant movements and helix to coil transitions that facilitate the formation of the ExoN active site and provide an explanation of the stimulation of nuclease activity by NSP10. Conformational changes are also seen in the MTase active site within a SAM/SAH interacting loop that plays a key role in viral mRNA capping. We have also determined the structure of NSP14 in complex with cap analogue 7MeGpppG, offering new insights into MTase enzymatic activity. We have used our high resolution crystals to perform X-ray fragment screening of NSP14, revealing 72 hits bound to potential sites of inhibition of the ExoN and MTase domains. These structures serve as excellent starting point tools for structure guided development and optimization of NSP14 inhibitors that may be used to treat COVID-19 and potentially other future viral threats.

category: biochemistry


title: Double NPY motifs at the N-terminus of Sso2 synergistically bind Sec3 to promote membrane fusion

abstract:
Exocytosis is an active vesicle trafficking process by which eukaryotes secrete materials to the extracellular environment and insert membrane proteins into the plasma membrane. The final step of exocytosis in yeast involves the assembly of two t-SNAREs, Sso1/2 and Sec9, with the v-SNARE, Snc1/2, on secretory vesicles. The rate-limiting step in this process is the formation of a binary complex of the two t-SNAREs. Despite of the previous report for how the binary complex assembly is accelerated by Sec3, it remains unknown how Sso2 is efficiently recruited to the vesicle-docking site marked by Sec3. Here we report a crystal structure of the pleckstrin homology (PH) domain of Sec3 in complex with a nearly full-length version of Sso2 only lacking its C-terminal transmembrane helix. The structure shows an uncharacterized binding site for Sec3 at the N-terminus of Sso2, consisting of two highly conserved triple residue motifs (NPY: Asn-Pro-Tyr). We further reveal that the two NPY motifs bind Sec3 synergistically and play an essential role in the fusion of secretory vesicles at target sites on the plasma membrane.

SignificanceSNARE assembly, which involves one v-SNARE with two t-SNARE proteins, drives the fusion of vesicles to target compartments. The rate-limiting step in SNARE assembly is the assembly of the two t-SNARE proteins on the target membrane. Previous studies showed that in yeast Sec3, a component of the exocyst vesicle tethering complex, directly interacts with the t-SNARE protein Sso2 to promote fast assembly of an Sso2-Sec9 binary t-SNARE complex. This paper presents a new crystal structure of the Sec3 PH domain in complex with a nearly full-length version of Sso2, which reveals a previously unknown binding site for Sec3 at the N-terminus of Sso2. Our work demonstrates that the interaction between Sso2 and Sec3 plays an essential role in promoting the fusion of secretory vesicles at target sites on the plasma membrane.


title: Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg

abstract: MINORg is an offline gRNA design tool that generates the smallest possible combination of gRNA capable of covering all desired targets in multiple non-reference genomes. As interest in pangenomic research grows, so does the workload required for large screens in multiple individuals. MINORg aims to lessen this workload by capitalising on sequence homology to favour multi-target gRNA while simultaneously screening multiple genetic backgrounds in order to generate reusable gRNA panels. We demonstrated the practical application of MINORg by knocking out a 11 homologous genes tandemly arrayed in a multigene cluster in two Arabidopsis thaliana lineages using three gRNA output by MINORg. Source code is freely available at https://github.com/rlrq/MINORg.

category: bioinformatics


title: Mechanical stress driven by rigidity sensing governs epithelial stability

abstract: Epithelia act as a barrier against environmental stress and abrasion and in vivo they are continuously exposed to environments of various mechanical properties. The impact of this environment on epithelial integrity remains elusive. By culturing epithelial cells on 2D hydrogels, we observe a loss of epithelial monolayer integrity through spontaneous hole formation when grown on soft substrates. Substrate stiffness triggers an unanticipated mechanical switch of epithelial monolayers from tensile on soft to compressive on stiff substrates. Through active nematic modelling, we find unique patterns of cell shape texture called nematic topological defects that underpin large isotropic stress fluctuations at certain locations thereby triggering mechanical failure of the monolayer and hole opening. Our results show that substrate stiffness provides feedback on monolayer mechanical state and that topological defects can trigger stochastic mechanical failure, with potential application towards a mechanistic understanding of compromised epithelial integrity in bacterial infection, tumor progression and morphogenesis.

category: biophysics


title: Direct measurement of the aerotactic response in a bacterial suspension

abstract: Aerotaxis is the ability of motile cells to navigate towards oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterise the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment and present in living organisms. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band travelling towards the oxygen source. We compute the aerotactic response{chi} (c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law{chi} {propto} c-2, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.


title: Evaluating the "cost of generating force" hypothesis across frequency in human running and hopping

abstract: The volume of active muscle and duration of extensor muscle force well-explain the associated metabolic energy expenditure across body mass and speed during level-ground running and hopping. However, if these parameters fundamentally drive metabolic energy expenditure, then they should pertain to multiple modes of locomotion and provide a simple framework for relating biomechanics to metabolic energy expenditure in bouncing gaits. Therefore, we evaluated the ability of the  cost of generating force hypothesis to link biomechanics and metabolic energy expenditure during human running and hopping across step frequencies. We asked participants to run and hop at 0%, {+/-}8% and {+/-}15% of preferred step frequency. We calculated changes in active muscle volume, force duration, and metabolic energy expenditure. Overall, as step frequency increased, active muscle volume decreased due to postural changes via effective mechanical advantage (EMA) or duty factor. Accounting for changes in EMA and muscle volume better related to metabolic energy expenditure during running and hopping at different step frequencies than assuming a constant EMA and muscle volume. Thus, to ultimately develop muscle mechanics models that can explain metabolic energy expenditure across different modes of locomotion, we suggest more precise measures of muscle force production that include the effects of EMA.

category: physiology


title: Robust high-throughput phenotyping with deep segmentation enabled by a web-based annotator

abstract: The abilities of plant biologists and breeders to characterize the genetic basis of physio-logical traits is limited by their abilities to obtain quantitative data representing precise details of trait variation, and particularly to collect this data at a high-throughput scale at low cost. Although deep learning methods have demonstrated unprecedented potential to automate plant phenotyping, these methods commonly rely on large training sets that can be time-consuming to generate. Intelligent algorithms have therefore been proposed to enhance the productivity of these annotations and reduce human efforts. We propose a high-throughput phenotyping system which features a Graphical User Interface (GUI) and a novel interactive segmentation algorithm: Semantic-Guided Interactive Object Segmentation (SGIOS). By providing a user-friendly interface and intelligent assistance with annotation, this system offers potential to streamline and accelerate the generation of training sets, reducing the effort required by the user. Our evaluation shows that our proposed SGIOS model requires fewer user inputs compared to the state-of-art models for interactive segmentation. As a case study in the use of the GUI applied for genetic discovery in plants, we present an example of results from a preliminary genome-wide association study (GWAS) of in planta regeneration in Populus trichocarpa (poplar). We further demonstrate that the inclusion of semantic prior map with SGIOS can accelerate the training process for future GWAS, using a sample of a dataset extracted from a poplar GWAS of in vitro regeneration. The capabilities of our phenotyping system surpass those of humans unassisted to rapidly and precisely phenotype our traits of interest. The scalability of this system enables large-scale phenomic screens that would otherwise be time-prohibitive, thereby providing increased power for GWAS, mutant screens, and other studies relying on large sample sizes to characterize the genetic basis of trait variation. Our user-friendly system can be used by researchers lacking a computational background, thus helping to democratize the use of deep segmentation as a tool for plant phenotyping.

category: plant biology


title: Characterization of dengue virus 3UTR RNA binding proteins in mosquitoes reveals that AeStaufen reduces subgenomic flaviviral RNA in saliva

abstract:
Dengue viruses (DENV) are expanding global pathogens that are transmitted through the bite of mosquitoes, mostly Aedes aegypti. As RNA viruses, DENV rely on RNA-binding proteins (RBPs) to complete their life cycle. Alternatively, RBPs can act as restriction factors that prevent DENV multiplication. While the importance of RBPs is well-supported in humans, there is a dearth of information about their influence on DENV transmission by mosquitoes. Such knowledge could be harnessed to design novel, effective interventions against DENV. Here, we successfully adapted RNA-affinity chromatography coupled with mass spectrometry - a technique initially developed in mammalian cells - to identify RBPs in Ae. aegypti cells. We identified fourteen RBPs interacting with DENV serotype 2 3UTR, which is involved in the viral multiplication and produces subgenomic flaviviral RNA (sfRNA). We validated the RNA affinity results for two RBPs by confirming that AePur binds the 3UTR, whereas AeStaufen interacts with both 3UTR and sfRNA. Using in vivo functional evaluation, we determined that RBPs like AeRan, AeExoRNase, and AeRNase have pro-viral functions, whereas AeGTPase, AeAtu, and AePur have anti-viral functions in mosquitoes. Furthermore, we showed that human and mosquito Pur homologs have a shared affinity to DENV2 RNA, although the anti-viral effect is specific to the mosquito protein. Importantly, we revealed that AeStaufen mediates a reduction of gRNA and sfRNA copies in several mosquito tissues, including the salivary glands and that AeStaufen-mediated sfRNA reduction diminishes the concentration of transmission-enhancing sfRNA in saliva, thereby revealing AeStaufens role in DENV transmission. By characterizing the first RBPs that bind to DENV2 3UTR in mosquitoes, our study unravels new pro- and anti-viral targets for the design of novel therapeutic interventions as well as provides foundation for studying the role of RBPs in virus-vector interactions.

Author abstractDengue viruses are important human pathogens transmitted by mosquitoes. Currently, there are no effective control measures for dengue. The RNA-binding proteins (RBPs) in mosquitoes, which bind to the dengue virus genome to regulate viral multiplication, could serve as new targets for developing therapeutic interventions. In this study, we pioneered the use of RNA-affinity chromatography - a technique that identifies proteins binding to specific RNA sequences - in mosquito cells. This led to the detection of fourteen RBPs that bind to the 3UTR of dengue virus serotype 2. We validated our results using immunoprecipitation method. Furthermore, we demonstrated that 6 of the 14 RBPs influence viral multiplication in mosquitoes. Among these six RBPs, we showed that the AePur mosquito and human homologs share an affinity to dengue virus RNA, whereas the anti-viral function is specific to the mosquito homolog. Importantly, we revealed that AeStaufen mediates a reduction of genomic and subgenomic flaviviral RNAs in multiple mosquito tissues. We also showed that the reduction of subgenomic flaviviral RNA in salivary glands diminishes the secretion of salivary subgenomic RNA, which facilitates infection at the bite site, thereby unveiling the function of AeStaufen in the virus transmission. By characterizing the first mosquito RBPs that bind to dengue virus genome, our study paves the way for leveraging these proteins as potential targets to block virus transmission.

category: zoology


title: The role of UBE3A in the autism and epilepsy-related Dup15q syndrome using patient-derived, CRISPR-corrected neurons

abstract: Chromosome 15q11-q13 duplication syndrome (Dup15q) is a neurodevelopmental disorder caused by maternal duplications of this region. Autism and epilepsy are key features of Dup15q, but affected individuals also exhibit intellectual disability and developmental delay. UBE3A, the gene encoding the ubiquitin protein ligase E3A, is likely a major driver of Dup15q because individuals with maternal, but not paternal 15q duplications have the disorder, and UBE3A is the only imprinted gene expressed solely from the maternal allele in mature neurons. Nevertheless, the exact role of UBE3A is yet to be determined. To establish whether UBE3A overexpression is required for Dup15q neuronal deficits, UBE3A expression was manipulated in patient-derived induced pluripotent stem cell (iPSC) lines using antisense oligonucleotides. Dup15q neurons exhibited hyperexcitability features compared to genome-edited isogenic control neurons, and this phenotype was generally prevented by normalizing UBE3A levels throughout in vitro development. Overexpression of UBE3A in an iPSC line with a paternal duplication resulted in a profile similar to that of Dup15q neurons except for synaptic phenotypes. These results indicate that UBE3A overexpression is necessary for most Dup15q cellular phenotypes. However, the inability of UBE3A overexpression to recapitulate synaptic phenotypes suggests an important role for non-imprinted genes in the disorder.


title: Pan-phylum In Silico Analyses of Nematode Endocannabinoid Signalling Systems Highlight Novel Opportunities for Parasite Drug Target Discovery

abstract:
The endocannabinoid signalling (ECS) system is a complex lipid signalling pathway that modulates diverse physiological processes in both vertebrate and invertebrate systems. In nematodes, knowledge of endocannabinoid (EC) biology is derived primarily from the free-living model species Caenorhabditis elegans, where ECS has been linked to key aspects of nematode biology. The conservation and complexity of nematode ECS beyond C. elegans is largely uncharacterised, undermining the understanding of ECS biology in nematodes including species with key importance to human, veterinary and plant health. In this study we exploited publicly available omics datasets, in silico bioinformatics and phylogenetic analyses to examine the presence, conservation and life-stage expression profiles of EC-effectors across phylum Nematoda. Our data demonstrate that: (i) ECS is broadly conserved across phylum Nematoda, including in therapeutically and agriculturally relevant species; (ii) EC-effectors appear to display clade and lifestyle-specific conservation patterns; (iii) filarial species possess a reduced EC-effector complement; (iv) there are key differences between nematode and vertebrate EC-effectors; (v) life stage-, tissue- and sex-specific EC-effector expression profiles suggest a role for ECS in therapeutically relevant parasitic nematodes. These data also highlight putative novel targets for anthelmintic therapies. To our knowledge, this study represents the most comprehensive characterisation of ECS pathways in phylum Nematoda and inform our understanding of nematode ECS complexity. Fundamental knowledge of nematode ECS systems will seed follow-on functional studies in key nematode parasites to underpin novel drug target discovery efforts.

CONTRIBUTION TO THE FIELDThis manuscript reports the in silico characterisation of endocannabinoid (EC) signalling pathways across the nematode phylum. The physiological relevance and therapeutic potential of EC signalling in higher organisms has received significant attention. In contrast much of our knowledge on EC signalling in nematodes has been derived from the free-living nematode Caenorhabditis elegans where the EC signalling system appears to play key roles in nematode biology and features GPCRs distinct from vertebrate cannabinoid receptors. Unfortunately, the configuration and broader biological significance of EC signalling pathways across the nematode phylum, including in parasites of agricultural, veterinary and medical significance, remains unknown. The in silico exploration of the nematode EC signalling system reported here will provide baseline data on novel neuronal signalling pathways to seed future drug target discovery pipelines for parasites.


title: Domain-general and domain-specific functional networks of Broca's area underlying language processing

abstract: Despite abundant research on the role of Brocas area in language processing, there is still no consensus on language specificity of this region and its connectivity network. The present study employed the meta-analytic connectivity modeling procedure to identify and compare domain-specific (language-related) and domain-general (non-language) functional connectivity patterns of three subdivisions within the broadly defined Brocas area: pars opercularis (IFGop), pars triangularis (IFGtri) and pars orbitalis (IFGorb) of the left inferior frontal gyrus. The findings revealed a left-lateralized frontotemporal network for all regions of interest underlying domain-specific linguistic functions. The domain-general network and its conjunction with the domain-specific network, however, spanned frontoparietal regions that overlap with the multiple-demand network. The findings suggest that language-specificity of Brocas area emerges within a left-lateralized frontotemporal network, and that domain-general resources are garnered from the frontoparietal network when required by task demands.


title: The maternal X chromosome impairs cognition and accelerates brain aging through epigenetic modulation in female mice

abstract: Female mammalian cells harbor two X chromosomes, one of maternal and one of paternal origin. During development, one X randomly inactivates1-4. This renders either the maternal or paternal X active, causing X mosaicism that varies among individual females, with some showing considerable or complete skew in the general female population5-7. Parent-of-X-origin can modify epigenetics via DNA methylation8, 9 and possibly gene expression; thus, mosaicism could buffer dysregulated processes in aging and disease. However, whether X skewing - or its mosaicism - alters functions in females is largely unknown. Here we tested whether skew toward the maternal X (Xm) influences key functions of the body. Among cardiac, bone, metabolic, and brain functions, Xm selectively impaired cognition in female mice throughout the lifespan. Cognitive deficits were accompanied by Xm-mediated acceleration of biologic or epigenetic aging of the female hippocampus, a key center for learning and memory. Xm showed epigenetic imprinting of several genes within hippocampal neurons, suggesting silenced cognitive loci. Thus, the maternal X chromosome impaired cognition, accelerated brain aging, and silenced genes. Understanding how the maternal X impairs brain function could lead to new understanding of female heterogeneity in cognitive heath and to X chromosome-derived pathways against cognitive deficits and brain aging.


title: Influenza A Virus Compromises anti-Streptococcal Innate Immunity

abstract: Seasonal influenza epidemics pose a considerable hazard for global health. In the past decades, accumulating evidence revealed that influenza A virus (IAV) renders the host vulnerable to bacterial superinfections which in turn are a major cause for morbidity and mortality. However, whether the impact of influenza on anti-bacterial innate immunity is restricted to the vicinity of the lung or systemically extends to remote sites is underexplored. We therefore sought to investigate intranasal infection of adult C57BL/6J mice with IAV H1N1 in combination with bacteremia elicited by intravenous application of Group A Streptococcus (GAS). Co-infection in vivo was supplemented in vitro by challenging murine bone marrow derived macrophages and exploring gene expression and cytokine secretion. Our results show that viral infection of mice caused mild disease, led to persistent pulmonary immune response in the lung and induced the depletion of CCL2 in the periphery. Influenza preceding GAS infection promoted the unopposed dissemination of bacteria and their invasion into remote tissues like lung and joints and was accompanied by exacerbated sepsis. In vitro co-infection of macrophages led to significantly elevated expression of TLR2 and CD80 compared to bacterial mono-infection, whereas CD163 and CD206 were downregulated. The GAS-inducible upregulation of inflammatory genes, such as Nos2, as well as the secretion of TNF and IL-1{beta} were notably reduced or even abrogated following co-infection. Our results indicate that IAV primes an innate immune layout that is inadequately equipped for bacterial clearance.


title: IFN-induced protein with tetratricopeptide repeats 2 (Ifit2) limits autoimmune inflammation by regulating myeloid cell activation and metabolic activity

abstract: Besides anti-viral functions, Type I IFN expresses potent anti-inflammatory properties and is being widely used to treat certain autoimmune conditions, such as multiple sclerosis (MS). In murine model of MS, experimental autoimmune encephalomyelitis (EAE), administration of IFN{beta} effectively attenuates the disease development. However, the precise mechanisms underlying the treatment remain elusive. In this study, we report that IFN-induced protein with tetratricopeptide repeats 2 (Ifit2), a type I and type III IFN-stimulated gene, plays a previously unrecognized immune regulatory role during autoimmune neuroinflammation. Mice deficient in Ifit2 display greater susceptibility to EAE and escalated immune cell infiltration in the central nervous system. Ifit2 deficiency is also associated with microglial activation and increased myeloid cell infiltration. Unexpectedly, myelin debris clearance and the subsequent remyelination is impaired in Ifit2-/- CNS tissues. Clearing myelin debris is an important property of reparative M2 type myeloid cells to promote remyelination. Indeed, we observed that bone marrow derived macrophages, CNS infiltrating myeloid cells, and microglia from Ifit2-/- mice express cytokine and metabolic genes associated with proinflammatory M1 type subsets. Taken together, our findings uncover a novel regulatory function of Ifit2 in autoimmune inflammation in part by modulating myeloid cell function and metabolic activity.


title: Functional entry of Members of Venezuelan Equine Encephalitis Complex into host cells is dependent on clathrin-mediated endocytosis, in a pH-Dependent Manner

abstract: Pixuna virus (PIXV) and Rio Negro virus (RNV) are mosquito-borne alphaviruses belonging to the Venezuelan Equine Encephalitis (VEE) complex, which includes pathogenic epizootic and enzootic subtypes responsible for life-threatening diseases in equines. Considering that the first steps in viral infection are crucial for the efficient production of new progeny, the aim of this study was to elucidate early events of the replication cycle of these two viruses. To this end, we used chemical inhibitors and the expression of dominant-negative constructs to study the dependence of clathrin and endosomal pH on PIXV and RNV internalization mechanism. We demonstrated that both viruses are internalized primarily via clathrin-mediated endocytosis, where the low pH of endosomes is crucial for viral replication. Contributing knowledge the entry route of VEE complex members is important to understand the pathogenesis of these viruses and to develop new antiviral strategies.


title: Optical photothermal infrared spectroscopy can differentiate equine osteoarthritic plasma extracellular vesicles from healthy controls

abstract:
BackgroundEquine osteoarthritis is a chronic degenerative disease of the articular joint, characterised by cartilage degradation resulting in pain and reduced mobility and thus is a prominent equine welfare concern. Diagnosis is usually at a late stage through radiographic examination, whilst treatment is symptomatic not curative. Extracellular vesicles are small nanoparticles that are involved in intercellular communication. The objective of this study was to investigate the feasibility of Raman and optical photothermal infrared spectroscopy to detect osteoarthritis using plasma-derived extracellular vesicles.

MethodsPlasma samples were derived from thoroughbred racehorses. A total of 14 samples were selected (control; n= 6 and diseased; n=8). Extracellular vesicles were isolated using differential ultracentrifugation and characterised using nanoparticle tracking analysis, transmission electron microscopy, and human tetraspanin chips. Samples were then analysed using Raman and optical photothermal infrared spectroscopy.

ResultsInfrared spectra were analysed between 950-1800 cm-1. Raman spectra had bands between the wavelengths of 900-1800 cm-1 analysed. Bands below 900 cm-1. Spectral data for both Raman and optical photothermal infrared spectroscopy was used to obtain a classification model and confusion matrices, characterising the techniques ability to distinguish diseased samples. Optical photothermal infrared spectroscopy could differentiate osteoarthritic extracellular vesicles from healthy with good classification (93.4%) whereas Raman displayed poor classification (64.3%). Plasma-derived extracellular vesicles from osteoarthritic horses contained increased signal for proteins, lipids and nucleic acids.

Discussion/ conclusionFor the first time we demonstrated the ability to use optical photothermal infrared spectroscopy to interrogate extracellular vesicles and osteoarthritis-related samples. Optical photothermal infrared spectroscopy was superior to Raman in this study, and could distinguish osteoarthritis samples, suggestive of its potential use diagnostically to identify osteoarthritis in equine patients. This study demonstrates the potential of Raman and optical photothermal infrared spectroscopy to be used as a diagnostic tool in clinical practice, with the capacity to detect changes in extracellular vesicles from clinically derived samples.

category: molecular biology


title: Alveolar regeneration following viral infection is independent of tuft cells

abstract: Severe injuries following viral infection cause lung epithelial destruction with the presence of ectopic basal progenitor cells (EBCs), although the exact function of EBCs remains controversial. We and others previously showed the presence of ectopic tuft cells in the disrupted alveolar region following severe influenza infection. Here, we further revealed that the ectopic tuft cells are derived from EBCs. This process is amplified by Wnt signaling inhibition but suppressed by Notch inhibition. Further analysis revealed that p63-CreER labeled population de novo arising during regeneration includes alveolar epithelial cells when Tamoxifen was administrated after viral infection. The generation of the p63-CreER labeled alveolar cells is independent of tuft cells, demonstrating segregated differentiation paths of EBCs in lung repair. EBCs and ectopic tuft cells can also be found in the lung parenchyma post SARS-CoV-2 infection, suggesting a similar response to severe injuries in humans.


title: An easily modifiable conjugative plasmid for studying horizontal gene transfer

abstract: Horizontal gene transfer is an important mechanism in bacterial evolution and can occur at striking frequencies when mediated by mobile genetic elements. Conjugative plasmids are mobile genetic elements that are main drivers of horizontal transfer and a major facilitator in the spread of antibiotic resistance genes. However, conjugative plasmid models that readily can be genetically modified with the aim to study horizontal transfer are not currently available. The aim of this study was to develop a conjugative plasmid model where the insertion of gene cassettes such as reporter genes (e.g., fluorescent proteins) or antibiotic resistance genes would be efficient and convenient. For that, we introduced a single attTn7 site into the conjugative broad-host-range IncP-1 plasmid pKJK5 in a non-disruptive manner. Furthermore, a version with lower transfer rate and a non-conjugative version of pKJK5-attTn7 were also constructed. The advantage of having the attTn7 sites is that genes of interest can be introduced in a single step with very high success rate using the Tn7 transposition system. In addition, larger genetic fragments can be inserted. To illustrate the efficacy of the constructed pKJK5 plasmids, they were complimented with sfgfp in addition to seven different {beta}-lactamase genes representing the four known classes of {beta}-lactamases.

category: evolutionary biology


title: Using Local Genetic Correlation Improves Polygenic Score Prediction Across Traits

abstract:
IntroductionThe predictive utility of polygenic scores (PGS) is steadily increasing as genome-wide association studies (GWAS) increase in sample size and diversity, and as PGS methodology is further developed. Multivariate PGS approaches incorporate GWAS results for secondary phenotypes which are genetically correlated with the target phenotype. These improve prediction over using PGS for only the target phenotype. However, previous methods have only considered the genome-wide estimates of SNP-based heritability (h2SNP) and genetic correlation (rg) between target and secondary phenotypes. In this study, we assess the impact of local h2SNP and rg within specific loci on cross-trait prediction.

MethodsWe evaluate PGS using three target phenotypes (depression, intelligence, BMI) in the UK Biobank, with GWAS summary statistics matching the target phenotypes and 14 genetically correlated secondary phenotypes. PGS SNP-weights were derived using MegaPRS. Local h2SNP and rg were estimated using LAVA. We then evaluated PGS after reweighting SNP-weights according to local h2SNP and rg estimates between the target and secondary phenotypes. Elastic net models containing PGS for multiple phenotypes were evaluated using nested 10-fold cross validation.

ResultsModelling target and secondary PGS significantly improved target phenotype prediction over the target PGS alone, with relative improvements ranging from 0.8-12.2%. Furthermore, we show reweighting PGS by local h2SNP and rg estimates can enhance the predictive utility of PGS across phenotypes, with additional relative improvements of 0.2%-2.8%. Reweighting PGS by local h2SNP and rg improved target phenotype prediction most when there was a mixture of positive and negative local rg estimates between target and secondary phenotypes.

ConclusionModelling PGS for secondary phenotypes consistently improves prediction of target phenotypes, and this approach can be further enhanced by incorporating local h2SNP and rg estimates to highlight relevant genetic effects across phenotypes.

category: genomics


title: Floating EMG Sensors and Stimulators Wirelessly Powered and Operated by Volume Conduction for Networked Neuroprosthetics

abstract:
BackgroundImplantable neuroprostheses consisting of a central electronic unit wired to electrodes benefit thousands of patients worldwide. However, they present limitations that restrict their use. Those limitations, which are more adverse in motor neuroprostheses, mostly arise from their bulkiness and the need to perform complex surgical implantation procedures. Alternatively, it has been proposed the development of distributed networks of intramuscular wireless microsensors and microstimulators that communicate with external systems for analyzing neuromuscular activity and performing stimulation or controlling external devices. This paradigm requires the development of miniaturized implants that can be wirelessly powered and operated by an external system. To accomplish this, we propose a wireless power transfer (WPT) and communications approach based on volume conduction of innocuous high frequency (HF) current bursts. The currents are applied through external textile electrodes and are collected by the wireless devices through two electrodes for powering and bidirectional digital communications. As these devices do not require bulky components for obtaining power, they may have a flexible threadlike conformation, facilitating deep implantation by injection.

MethodsWe report the design and evaluation of advanced prototypes based on the above approach. The system consists of an external unit, floating semi-implantable devices for sensing and stimulation, and a bidirectional communications protocol. The devices are intended for their future use in acute human trials to demonstrate the distributed paradigm. The technology is assayed in vitro using an agar phantom, and in vivo in hindlimbs of anesthetized rabbits.

ResultsThe semi-implantable devices were able to power and bidirectionally communicate with the external unit. Using 13 commands modulated in innocuous 3 MHz HF current bursts, the external unit configured the sensing and stimulation parameters, and controlled their execution. Raw EMG was successfully acquired by the wireless devices at 1 ksps.

ConclusionsThe demonstrated approach overcomes key limitations of existing neuroprostheses, paving the way to the development of distributed flexible threadlike sensors and stimulators. To the best of our knowledge, these devices are the first based on WPT by volume conduction that can work as EMG sensors and as electrical stimulators in a network of wireless devices.

category: bioengineering


title: Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

abstract:
BackgroundEukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with shotgun sequencing techniques, since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not yet incorporate strategies to handle presence of unknown eukaryotes.

ResultsHere we present CORALE (for Clustering of Reference Alignments), a tool for identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate, but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel species and strains. We finally deploy CORALE on our MicrobiomeDB.org resource, demonstrating adequate reliability and throughput.

ConclusionCORALE allows eukaryotic detection to be automated and carried out at scale. Since our approach is independent of the reference used, it is applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as identification of novel bacterial strains or taxonomic classification of viral reads.


title: Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning

abstract: Exome sequencing has been widely used in genetic studies of human diseases and clinical genetic diagnosis. Accurate detection of copy number variants (CNVs) is important to fully utilize exome sequencing data. However, due to the nature of noisy data, none of the existing methods can achieve high precision and high recall rate at the same time. A common practice is to perform filtration with quality metrics followed by manual inspection of read depth of candidate CNV regions. This approach does not scale in large studies. To address this issue, we present a deep transfer learning method, CNV-espresso, for confirming rare CNVs from exome sequencing data in silico. CNV-espresso encodes candidate CNV regions from exome sequencing data as images and uses convolutional neural networks to classify the image into different copy numbers. We trained and evaluated CNV-espresso on a large-scale offspring-parents trio exome sequencing dataset, using inherited CNVs in probands as positives and CNVs with mendelian errors as negatives. We further tested the performance using samples that have both exome and whole genome sequencing (WGS) data. Assuming the CNVs detected from WGS data as proxy of ground truth, CNV-espresso significantly improves precision while keeping recall almost intact, especially for CNVs that span small number of exons in exome data. We conclude that CNV-espresso is an effective method to replace most of manual inspection of CNVs in large-scale exome sequencing studies.


title: Web-based Histology Reference Atlas for the Freshwater Crustacean Daphnia magna

abstract: Daphnia, an important model system for the study of evolution, development, phenotypic plasticity, and environmental health, lacks a modern reference atlas for microanatomy. To facilitate the comprehensive assessment of phenotypic effects of genes and environment, we created the Daphnia histology reference atlas (http://daphnia.io/anatomy/), a tractable, interactive web-based tool that provides insight into normal phenotype through vectorized annotations overlaid onto digital histology sections imaged at 40X magnification. Guided by our expert-curated and multimodal informed hierarchical anatomical ontology, we show that this resource can be used to elucidate sex-specific differences between female and male Daphnia magna in each of 3 orthogonal planes, providing new insight for the study of sex-specific traits. This atlas is a new, open-source resource for the Daphnia community to facilitate education and research collaboration, and as a precursor for the 3D atlas. It is also our intention that this atlas aids in phenotypic anchoring of large-scale biomolecular (multi-omics) data from comparative toxicological studies. Greater access to high-quality histological data may clarify cross-correlations between microanatomic and multi-omic phenotypes caused by genetic variation, environment, and disease across phylogeny.


title: A connectomics-based taxonomy of mammals

abstract: Mammalian taxonomies are conventionally defined by morphological traits and genetics. How species differ in terms of neural circuits and whether inter-species differences in neural circuit organization conform to these taxonomies is unknown. The main obstacle for the comparison of neural architectures have been differences in network reconstruction techniques, yielding species-specific connectomes that are not directly comparable to one another. Here we comprehensively chart connectome organization across the mammalian phylogenetic spectrum using a common reconstruction protocol. We analyze the mammalian MRI (MaMI) data set, a database that encompasses high-resolution ex vivo structural and diffusion magnetic resonance imaging (MRI) scans of 124 species across 12 taxonomic orders and 5 superorders, collected using a single protocol on a single scanner. We assess similarity between species connectomes using two methods: similarity of Laplacian eigenspectra and similarity of multiscale topological features. We find greater inter-species similarities among species within the same taxonomic order, suggesting the connectome organization recapitulates traditional taxonomies defined by morphology and genetics. While all connectomes retain hallmark global features and relative proportions of connection classes, inter-species variation is driven by local regional connectivity profiles. By encoding connectomes into a common frame of reference, these findings establish a foundation for investigating how neural circuits change over phylogeny, forging a link from genes to circuits to behaviour.

category: neuroscience


title: Genetic mapping of APP and amyloid-β biology modulation by trisomy 21

abstract: Individuals who have Down syndrome frequently develop early onset Alzheimers disease, a neurodegenerative condition caused by the build-up of aggregated amyloid-{beta} and tau proteins in the brain. Amyloid-{beta} is produced by APP, a gene located on chromosome 21. People who have Down syndrome have three copies of chromosome 21 and thus also an additional copy of APP; this genetic change drives the early development of Alzheimers disease in these individuals. Here we use a combination of next-generation mouse models of Down syndrome (Tc1, Dp3Tyb, Dp(10)2Yey and Dp(17)3Yey) and a knockin mouse model of amyloid-{beta} accumulation (AppNL-F) to determine how chromosome 21 genes other than APP modulate APP/amyloid-{beta} in the brain when in three copies. We demonstrate that three copies of other chromosome 21 genes are sufficient to partially ameliorate amyloid-{beta} accumulation in the brain. We go on to identify a subregion of chromosome 21 that contains the gene/genes causing this decrease in amyloid-{beta} accumulation and investigate the role of two lead candidate genes Dyrk1a and Bace2. Thus an additional copy of chromosome 21 genes, other than APP, can modulate APP/amyloid-{beta} in the brain under physiological conditions. This work provides critical mechanistic insight into the development of disease and an explanation for the typically later age of onset of dementia in people who have AD-DS compared to those who have familial AD caused by triplication of APP.


title: In vitro susceptibility to beta-lactam antibiotics and viability of Neisseria gonorrhoeae strains producing plasmid-mediated broad- and extended-spectrum beta-lactamases

abstract: N. gonorrhoeae strains producing plasmid-mediated broad- and extended-spectrum {beta}-lactamases (ESBLs) have been obtained in vitro and studied for their viability and susceptibility to {beta}-lactam antibiotics. The artificial pblaTEM-1 and pblaTEM-20 plasmids were constructed by site-directed mutagenesis from a pblaTEM-135 plasmid of the Toronto/Rio type, which was extracted from the clinical isolate. MIC values were determined for a series of {beta}-lactam antibiotics, including benzylpenicillin, ampicillin, cefuroxime, ceftriaxone, cefixime, cefotaxime, cefepime, meropenem, imipenem, and doripenem. The N. gonorrhoeae strain carrying the pblaTEM-20 plasmid exhibited a high level of resistance to penicillins and II-IV generation cephalosporins (MIC [≥] 2 mg/L) but not to carbapenems (MIC [≤] 0.008 mg/L). However, this strain stopped growing after 6 hours of cultivation. The reduced viability was not associated with the plasmid loss but can be explained by the following factors: the presence of the plasmid itself, which requires additional costs for its reproduction, and the expression of ESBL, which can affect the structure of the peptidoglycan layer in the cell membrane. The cell growth was mathematically modeled using the generalized Verhulst equation. The parameter, characterizing the maximum possible number of cells grown under given conditions, decreased within the wild type (without plasmids) - pblaTEM-135 - pblaTEM-1 - pblaTEM-20 series, i.e., the plasmid-bearing strains had reduced viability compared to that of the wild-type strain. The kinetics for the cell death of N. gonorrhoeae strains without the pblaTEM-20 plasmid in the presence of ceftriaxone can be described by a modified Chick-Watson law. For the N. gonorrhoeae strain that harbors the pblaTEM-20 plasmid, the kinetics for cell number changes with time reflected several processes: the hydrolysis of ceftriaxone by TEM-20 {beta}-lactamase, growth and gradual death of cells. The demonstrated reduced viability of N. gonorrhoeae strains with the pblaTEM-20 plasmid probably explains the absence of clinical isolates of N. gonorrhoeae that produce ESBL.

category: microbiology


title: In vitro susceptibility to β-lactam antibiotics and viability of Neisseria gonorrhoeae strains producing plasmid-mediated broad- and extended-spectrum β-lactamases


title: The role of Cycloastragenol at the intersection of Nrf-2/ARE, telomerase, and proteasome activity

abstract: Aging is well-characterized by the gradual decline of cellular functionality. As redox balance, proteostasis, and telomerase systems have been found to be associated with aging and age-related diseases, targeting these systems by small compounds has been considered as a promising therapeutic approach. Cycloastragenol (CA), a small molecule telomerase activator obtained from Astragalus species, has been reported to have positive effects on several age-related pathophysiologies, including ischemia, glucose intolerance, diabetes, and neurodegenerative diseases. Although CA has received intense attention as a promising compound for aging and age-related diseases, the mechanisms underlying CA activity related to redox balance, proteasome, and telomerase has not yet been reported. Here, we presented that CA increased Nrf-2 activity leading to upregulation of cytoprotective enzymes and attenuation of oxidative stress-induced ROS levels. Furthermore, CA enhanced telomerase activity by increasing not only the expression of hTERT but also its nuclear localization via the Hsp90-chaperon complex. CA alleviated the oxidative stress-induced mitochondrial hTERT levels while increasing the nuclear hTERT levels. Additionally, the proteasome activity and assembly were increased by CA. Strikingly, our data revealed that CA-mediated neuroprotection requires both Nrf-2 and hTERT induction. In conclusion, this study is the first report describing the effect of CA on these aging-related three major cellular pathways and their interrelationships. As the proteasome activator effect of CA is dependent on induction of telomerase activity, which is mediated by Nrf-2 system, CA has a great potential for healthier aging and prevention or treatment of age-related diseases by positively affecting these three cellular pathways.

category: cell biology


title: Novel pathogen introduction rapidly alters evolved movement strategies, restructuring animal societies

abstract: Animal social interactions are the outcomes of evolved strategies that integrate the costs and benefits of being sociable. Using a novel mechanistic, evolutionary, individual-based simulation model, we examine how animals balance the risk of pathogen transmission against the benefits of social information about resource patches, and how this determines the emergent structure of socio-spatial networks. We study a scenario in which a fitness-reducing infectious pathogen is introduced into a population which has initially evolved movement strategies in its absence. Within only a few generations, pathogen introduction provokes a rapid evolutionary shift in animals social movement strategies, and the importance of social cues in movement decisions increases. Individuals undertake a dynamic social distancing approach, trading more movement (and less intake) for lower infection risk. Pathogen-adapted populations disperse more widely over the landscape, and thus have less clustered social networks than their pre-introduction, pathogen-naive ancestors. Running epidemiological simulations on these emergent social networks, we show that diseases do indeed spread more slowly through pathogen-adapted animal societies. Finally, the mix of post-introduction strategies is strongly influenced by a combination of landscape productivity, the usefulness of social information, and disease cost. Our model suggests that the introduction of an infectious pathogen into a population can trigger a rapid eco-evolutionary cascade, rapidly changing animals social movement strategies, which alters movement decisions and encounters between individuals. In turn, this changes emergent social structures, and our model informs how such change can make populations more resilient to future disease outbreaks. Overall, we offer both a modelling framework and initial predictions for the evolutionary and ecological consequences of wildlife pathogen spillover scenarios.


title: Optimized high-throughput screening of non-coding variants identified from genome-wide association studies

abstract: The vast majority of disease-associated single nucleotide polymorphisms identified from genome-wide association study (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and number of variants tested per loci. Using this strategy, we interrogated 70 of 140 known prostate cancer (PCa) risk-associated loci and demonstrated that 26 (37%) of them harbor 36 SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.


title: Observation of a single protein by ultrafast X-ray diffraction

abstract: The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory1, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes2. This was first demonstrated on biological samples a decade ago on the giant mimivirus3. Since then a large collaboration4 has been pushing the limit of the smallest sample that can be imaged5,6. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter7 is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.


title: Calcium-induced environmental adaptability of the blood protein vitronectin

abstract:
The adaptability of proteins to their work environments is fundamental for cellular life. Here we describe how the hemopexin-like (HX) domain of the multifunctional blood glycoprotein vitronectin (Vn) binds Ca2+ to adapt to excursions of temperature and shear stress. Using X-ray crystallography and molecular dynamics (MD) simulations, nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSF), we describe how Ca2+ and its flexible hydration shell enable the protein to perform conformational changes, that relay beyond the Ca2+ binding site to alter the number of polar contacts and confer conformational stability. By means of mutagenesis, we identify key residues that cooperate with Ca2+ to promote protein stability, and we show that Ca2+ association confers protection against shear stress, a property that provides conformational advantage for proteins that circulate in the vasculature like Vn. The data reveal a mechanism of adaptation.

Significance StatementThe protein vitronectin (Vn) plays important roles in cell adhesion and migration, bone remodeling and immunity. It circulates in blood, but it is also found in the extracellular matrix, and it accumulates with plaques associated with age-related macular degeneration, Alzheimers disease, atherosclerosis and other degenerative disorders. Vn is a calcium-binding protein, and here, we show that calcium helps Vn alter its structure in response to diverse environmental conditions. The results shed light on the way in which Vn adapts to its surroundings. This structural knowledge is important for the development of diagnostic, preventive or therapeutic approaches.


title: Field and experimental data together with computational models reveal how cleaner fish adjust decisions in a biological market

abstract:
While it is generally straightforward to quantify individual performance in cognitive experiments, identifying the underlying cognitive processes remains a major challenge. Often, different mechanistic underpinnings yield similar performances, and Lloyd Morgans cannon warrants acceptance of the simpler explanation. Alternatively, when the different mechanisms interact with environmental conditions, variation in performance across environments might allow to statistically infer the mechanism responsible. We illustrate this point by fitting computational models to experimental data on performance by wild-caught cleaner fish Labroides dimidiatus in an ephemeral reward task, as well as cleaner and client fish densities from the locations of capture. Using Bayesian statistics to fit the model parameters to performance data revealed that cleaner fish most likely estimate future consequences of an action, while it appears unlikely that the removal of the ephemeral reward acts as psychological punishment (negative reinforcement). Incorporating future consequences also yields performances that can be considered the result of locally optimal decision-rules, in contrast to the negative reinforcement mechanism. We argue that the combination of computational models with data is a powerful tool to infer the mechanistic underpinnings of cognitive performance.

Author summaryPerformance in behavioural experiments is often used to assess the cognitive abilities of animals. However, animals can get to the same outcome in alternative ways. Thus, the outcome of the experiments does not tell us how animals achieve their performance. In order to overcome this limitation, we used a set of computational models, which provide predictions on how alternative cognitive mechanisms perform in the face of varying environmental conditions, and compare their predictions to performance data from individuals that experienced different conditions throughout their life. Our study system is the cleaner fish Labroides dimidiatus, a coral reef fish that feeds off ectoparasites and dead tissue from the skin of other reef fishes. Cleaner fish often have to choose among alternative clients seeking their cleaning service, and the optimal choice is often hard to achieve. Our performance experiments mimic the natural choices the cleaner fish make. The combination of experiments and computational models points to cleaner fish abilities to account for the future effect of their choices by estimating the long term expected value of those choices. Estimating long term value is a mechanism involved in human foresight.


title: Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

abstract: AO_SCPLOWBSTRACTC_SCPLOWMolecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant-calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate to what extent the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find greatest topological accuracy when filtering sites for minor allele count >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with minor allele count >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, indicating that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that care needs to be taken when choosing parameters for assembling and filtering large genomic data sets from short read data.


title: Blockade of redox second messengers inhibits JAK/STAT and MEK/ERK signaling sensitizing FLT3-mutant acute myeloid leukemia to targeted therapies

abstract:
FLT3-mutations are diagnosed in 25-30% of patients with acute myeloid leukemia (AML) and are associated with a poor prognosis. AML is associated with the overproduction of reactive oxygen species (ROS), which drives genomic instability through the oxidation of DNA bases, promoting clonal evolution, treatment resistance and poor outcomes. ROS are also important second messengers, triggering cysteine oxidation in redox sensitive signaling proteins, however, the specific pathways influenced by ROS in AML remain enigmatic. Here we have surveyed the posttranslational architecture of primary AML patient samples and assessed oncogenic second messenger signaling. Signaling proteins responsible for growth and proliferation were differentially oxidized and phosphorylated between patient subtypes either harboring recuring mutation in FLT3 compared to patients expressing the wildtype-FLT3 receptor, particularly those mapping to the Src family kinases (SFKs). Patients harboring FLT3-mutations also showed increased oxidative posttranslational modifications in the GTPase Rac activated-NADPH oxidase-2 (NOX2) complex to drive autocratic ROS production. Pharmacological and molecular inhibition of NOX2 was cytotoxic specifically to FLT3-mutant AMLs, and reduced phosphorylation of the critical hematopoietic transcription factor STAT5 and MAPK/ERK to synergistically increase sensitivity to FLT3-inhibitors. NOX2 inhibition also reduced phosphorylation and cysteine oxidation of FLT3 in patient derived xenograft mouse models in vivo, highlighting an important link between oxidative stress and oncogenic signaling. Together, these data raise the promising possibility of targeting NOX2 in combination with FLT3-inhibitors to improve treatment of FLT3-mutant AML.

One Sentence SummaryFLT3-precision therapies have entered the clinic for AML however, their durability is limited. Here we identify the Rac-NOX2 complex as the major driver of redox second messenger signaling in FLT3-mutant AML. Molecular and pharmacological inhibition of NOX2 decreased FLT3, STAT5 and MEK/ERK signaling to delay leukemia progression, and synergistically combined with FLT3 inhibitors.

category: cancer biology


title: Triosephosphate export from chloroplasts regulates flavonoid biosynthesis and permits high light acclimation through the inactivation of SnRK1

abstract: Plants evolved multiple strategies to cope with rapid changes in the environment. During high light acclimation, biosynthesis of photoprotective flavonoids, such as anthocyanins, is induced. However, the exact nature of the signal and downstream factors for high light induction of flavonoid biosynthesis (FB) are still under debate. Here we show that carbon-fixation in chloroplasts, subsequent export of photosynthates by TRIOSEPHOSPHATE/PHOSPHATE TRANSLOCATOR (TPT), and the rapid increase in cellular sugar contents permit the transcriptional activation of FB during high light acclimation. In combination with genetic and physiological analysis, targeted and whole transcriptome gene expression studies showed that reactive oxygen species and phytohormones play only a minor role for rapid HL-induction of the anthocyanin branch of FB. In addition to FB, sugar-responsive genes were late-repressed or induced in tpt-2 in the course of the high light treatment and a significant overlap with transcripts regulated by SNF1-RELATED PROTEIN KINASE 1 (SnRK1) was found. Analysis of mutants with increased and repressed SnRK1 activity revealed that inactivation of SnRK1 is required for the rapid induction of FB during high light acclimation. Our study underlines the central role of chloroplasts as sensors for environmental changes and emphasizes the vital function of sugar-signalling in plant acclimation, even beyond the regulation of FB.


title: Syntaxin-1A modulates vesicle fusion in mammalian neurons via juxtamembrane domain dependent palmitoylation of its transmembrane domain

abstract: SNAREs are undoubtedly one of the core elements of synaptic transmission. On the contrary to the well characterized function of their SNARE domains bringing the plasma and vesicular membranes together, the level of contribution of their juxtamembrane domain (JMD) and the transmembrane domain (TMD) to the vesicle fusion is still under debate. To elucidate this issue, we analyzed three groups of STX1A mutations: 1) elongation of STX1As JMD by three amino acid insertions in the junction of SNARE-JMD or JMD-TMD; 2) charge reversal mutations in STX1As JMD; and 3) palmitoylation deficiency mutations in STX1As TMD. We found that both JMD elongations and charge reversal mutations have position dependent differential effects on Ca2+-evoked and spontaneous neurotransmitter release in cultured murine hippocampal neurons. Importantly, we show that STX1As JMD regulates the palmitoylation of STX1As TMD and loss of STX1A palmitoylation either through charge reversal mutation K260E or by loss of TMD cysteines particularly inhibits spontaneous vesicle fusion. Interestingly, the retinal ribbon specific STX3B has a glutamate in the position corresponding to the K260E mutation in STX1A and mutating it with E259K acts as a molecular on-switch. Furthermore, palmitoylation of post-synaptic STX3A can be induced by the exchange of its JMD with STX1As JMD together with the incorporation of two cysteines into its TMD. Forced palmitoylation of STX3A dramatically enhances spontaneous vesicle fusion suggesting that STX1A regulates spontaneous release through two distinct mechanisms: one through the C-terminal half of its SNARE domain and the other through the palmitoylation of its TMD.


title: Modelling the modulation of cortical Up-Down state switching by astrocytes

abstract: Converging experimental reports have shown that the firing dynamics of neural networks in several cortical brain areas can exhibit Up-Down synchronization regimes, spontaneously alternating between long periods of high collective firing activity (Up state) and long periods of relative silence (Down state). The molecular or cellular mechanisms that support the emergence of these reversible transitions are still uncertain. In addition to intrinsic mechanisms supported by the local neurons of the network, recent experimental studies have suggested that the astrocytes of the local network can actually control the emergence of Up-Down regimes. Here we propose and study a neural network model to explore the implication of astrocytes in this dynamical phenomenon. We consider three populations of cells: excitatory neurons, inhibitory neurons and astrocytes, interconnected by gliotransmission events, from neurons to astrocytes and back. We derive two models for this three-population system: a rate model and a stochastic spiking neural network with thousands of neurons and astrocytes. In numerical simulations of these three-population models, the presence of astrocytes is indeed observed to promote the emergence of Up-Down regimes with realistic characteristics. Linear stability analysis reveals that astrocytes in these models do not change the bifurcation structure of these systems, but change the localization of the bifurcations in the parameter space. Accordingly, with the addition of astrocytes, the network can enter a bistability region of the dynamics, where the Up-Down dynamical regime emerges. Simulations of the stochastic network model further evidence that astrocytes provide a stationary and stable background of gliotransmission events to the neurons, that triggers spontaneous transitions between synchronized Up and Down phases of neuronal firing. Taken together, our work provides a theoretical framework to test scenarios and hypotheses on the modulation of Up-Down dynamics by gliotransmission from astrocytes.


title: Age- and sex-dependent effects of DNA glycosylase Neil3 on amyloid pathology, adult neurogenesis, and memory in a mouse model of Alzheimer's disease

abstract: Oxidative stress generating DNA damage has been shown to be a key characteristic in Alzheimers disease (AD). However, how it affects the pathogenesis of AD is not yet fully understood. Neil3 is a DNA glycosylase initiating repair of oxidative DNA base lesions and with a distinct expression pattern in proliferating cells. In brain, its function has been linked to hippocampal-dependent memory and to induction of neurogenesis after stroke and in prion disease. Here, we generated a novel AD mouse model deficient for Neil3 to study the impact of impaired oxidative base lesion repair on the pathogenesis of AD. Our results demonstrate an age-dependent decrease in amyloid-{beta} (A{beta}) plaque deposition in female Neil3-deficient AD mice, whereas no significant difference was observed in male mice. Furthermore, male but not female Neil3-deficient AD mice show reduced neural stem cell proliferation in the adult hippocampus and impaired working memory compared to controls. These effects seem to be independent of DNA repair as both sexes show increased level of oxidative base lesions in the hippocampus upon loss of Neil3. Thus, our findings suggest an age- and sex-dependent role of Neil3 in the progression of AD by altering cerebral A{beta} accumulation and promoting adult hippocampal neurogenesis to maintain cognitive function.


title: Placental inflammation leads to abnormal embryonic heart development

abstract: Placental and embryonic heart development occurs in parallel, and these organs have been proposed to exert reciprocal regulation during gestation. Poor placentation has been associated with congenital heart disease (CHD), an important cause of infant mortality. However, the mechanisms by which altered placental development can lead to CHD remain unresolved. In the current study we show that neutrophil-driven placental inflammation leads to inadequate placental development and loss of barrier function. Consequently, placental inflammatory monocytes of maternal origin become capable to migrate to the embryonic heart and alter the normal composition of resident cardiac macrophages and cardiac tissue structure. This cardiac impairment continues into postnatal life, hindering normal tissue architecture and function. Finally, we demonstrate that tempering placental inflammation can rescue this fetal cardiac defect and is sufficient to promote normal cardiac function in postnatal life. Taken together, our observations provide a mechanistic paradigm whereby neutrophil-driven inflammation in pregnancy can preclude normal embryonic heart development as a direct consequence of poor placental development.

category: immunology


title: Prokaryotic phospholipid translocation by ubiquitous PplT domain proteins

abstract: Flippase proteins exchanging phospholipids between the cytoplasmic membrane leaflets have been identified in Eukaryotes but remained largely unknown in Prokaryotes. Only MprF proteins that synthesize aminoacyl phospholipids in some bacteria have been found to contain a domain that translocates the produced lipids. We show here that this domain, which we named  prokaryotic phospholipid translocator (PplT), is widespread in Bacteria and Archaea, encoded as a separate protein or fused to different types of enzymes. We also demonstrate that the Escherichia coli PplT protein interacts with many phospholipid-synthetic enzymes and deletion of pplT impaired bacterial growth and membrane fluidity. Thus, PplT domain proteins appear to be general prokaryotic lipid flippases with critical roles in cellular homeostasis.


title: Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing

abstract: Wool traits of rabbits are important in fiber production and model organism research on hair growth, while the genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a well-known fiber breed. Balancing genotyping cost and variant detection, we proposed low-coverage whole genome sequencing (LCS) followed by genotype imputation for genotyping. Different genotype imputation strategies, sequencing coverages and sample sizes were compared, and we found by BaseVar + STITCH, genotyping reached high accuracy (>0.97) at a depth of 1.0X and a sample size > 300. Multivariate GWAS followed by conditional GWAS and confidence interval estimation of QTLs were used to reveal the genetic architecture of wool traits. Six QTLs were detected with phenotypic variation contribution ranging from 0.42% to 7.50%. Gene-level mapping implicated FGF10 associated with fiber growth and diameter, which supported previous function research on fibroblast growth factor family in other species and provided genetic information for wool rabbit breeding. We suggest LCS as a cost-effective alternative for assessing common variants. GWAS combined with LCS can excavate QTLs and fine-map genes associated with quantitative traits. This study provides a powerful analysis mentality for investigating complex traits, which lays the foundation for genomic breeding.

category: genetics


title: Resolving clonal substructure from single cell genomic data using CopyKit

abstract: High-throughput methods for single cell copy number sequencing have enabled the profiling of thousands of cells in parallel, yet there remains a significant bottleneck for data analysis. Here we present CopyKit, a comprehensive set of computational methods for the pre-processing and analysis of single cell copy number data to resolve clonal substructure and reconstruct genetic lineages in tumors. We performed single cell DNA sequencing of 2977 cells from multiple spatial regions in two liver metastasis and 7365 cells from three primary tumors with matched metastatic tissues. In the liver metastases, CopyKit resolved clonal substructure in different spatial regions, which revealed both clonal intermixing and spatial segregation in the tumor mass. In the matched metastatic colorectal and breast cancers, CopyKit resolved metastatic lineages and identified subclones and genomic events that were associated with metastases. These applications show that CopyKit is comprehensive tool for resolving copy number substructure in tumors.


title: Structural and biochemical insights into lipid transport by VPS13 proteins.

abstract: VPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral or integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into, respectively, the cytosolic leaflet of donor and acceptor organelles in the course of protein-mediated transport.


title: Deep learning in human neurons predicts mechanistic subtypes of Parkinson's

abstract: Parkinsons disease (PD) is a common, devastating, and incurable neurodegenerative disorder. Several molecular mechanisms have been proposed to drive PD, with genetic and pathological evidence pointing towards aberrant protein homeostasis and mitochondrial dysfunction. PD is clinically highly heterogeneous, it is likely that different mechanisms underlie the pathology in different individuals, each requiring a specific targeted treatment. Recent advances in stem cell technology and fluorescent live-cell imaging have enabled the generation of patient-derived neurons with different mechanistic subtypes of PD. Here, we performed multi-dimensional fluorescent labelling of organelles in iPSC-derived neurons, in healthy control cells, and in four different disease subclasses. We generated a machine learning-based model that can simultaneously predict the presence of disease, and its primary mechanistic subtype. We independently trained a series of classifiers using both quantitative single-cell fluorescence variables and images to build deep neural networks. Quantitative cellular profile-based classifiers achieve an accuracy of 82%, whilst image based deep neural networks predict control, and four distinct disease subtypes with an accuracy of 95%. The classifiers achieve their accuracy across all subtypes primarily utilizing the organellar features of the mitochondria, with additional contribution of the lysosomes, confirming their biological importance in PD. Taken together, we show that machine learning approaches applied to patient-derived cells are able to predict disease subtypes, demonstrating that this approach may be used to guide personalized treatment approaches in the future.