title: Dependency of Lower Limb Joint Reaction Forces on Femoral Anteversion

abstract:
BackgroundMusculoskeletal (MSK) models based on literature data are meant to represent a generic anatomy and are a popular tool employed by biomechanists to estimate the internal loads occurring in the lower limb joints, such as joint reaction forces (JRFs). However, since these models are normally just linearly scaled to an individuals anthropometry, it is unclear how their estimations would be affected by the personalization of key features of the MSK anatomy, one of which is the femoral anteversion angle.

Research QuestionHow are the lower limb JRF magnitudes computed through a generic MSK model affected by changes in the femoral anteversion?

MethodsWe developed a bone-deformation tool in MATLAB (https://simtk.org/projects/bone_deformity) and used it to create a set of seven OpenSim models spanning from 2{degrees} femoral retroversion to 40{degrees} anteversion. We used these models to simulate the gait of an elderly individual with an instrumented prosthesis implanted at their knee joint (5th Grand Challenge dataset) and quantified both the changes in JRFs magnitude due to varying the skeletal anatomy and their accuracy against the correspondent in vivo measurements at the knee joint.

ResultsHip and knee JRF magnitudes were affected by the femoral anteversion with variations from the unmodified generic model up to 11.7{+/-}5.5% at the hip and 42.6{+/-}31.0% at the knee joint. The ankle joint was unaffected by the femoral geometry. The MSK models providing the most accurate knee JRFs (root mean squared error: 0.370{+/-}0.069 body weight, coefficient of determination: 0.764{+/-}0.104, largest peak error: 0.36{+/-}0.16 body weight) were those with the femoral anteversion angle closer to that measured on the segmented bone of the individual.

SignificanceFemoral anteversion substantially affects hip and knee JRFs estimated with generic MSK models, suggesting that personalizing key MSK anatomical features might be necessary for accurate estimation of JRFs with these models.


title: Effect of Initial pH and Organic Matter Concentration on Production of Volatile Organic Acids Through Acidogenesis of Sugarcane Vinasse

abstract: Sugarcane vinasse is an industrial liquid waste generated in great amounts in Brazilian ethanol industries. Nowadays its main use occurs at sugarcane crops, where vinasse is applied as a nutrient source for fertirrigation. However, continued use of vinasse in soil can cause several environmental impacts. So, aiming to provide a more environmentally friendly destination to the effluent, the goal of this work was to investigate the acidogenesis using a synthetic vinasse as substrate, focusing on the effects of initial pH and Chemical Oxygen Demand (COD) on short chain organic acids (SCOAs) concentrations. Synthetic vinasse was prepared at laboratory taking some real sugarcane vinasse composition given in previous works as references. So, major contribution presented here is the investigation on obtaining high added-value SCOAs from a simulated effluent. Cattle manure sludge was utilized as inoculum to promote the conversion of carbohydrate (sucrose, Suc) in synthetic vinasse into SCOAs in batch reactors during a total incubation time of 72 h. Acidogenesis profiles have shown that concentration of lactic acid (HLa) was prevailing among all metabolites, indicating that process followed through an essentially lactic route. Furthermore, considerable concentrations of propionic, acetic and isobutyric acids were also verified at some specific operation times, while solventogenesis was not detected at all. The greatest peak of lactate content was 4.96 g HLa L-1, observed under initial pH 6.0 and 25 g COD L-1, at 16 h. Maximum of lactate productivity was 332.10 g HLa L-1 h-1 at 8 h, associated to a yield of 189.14 g HLa (g Suc)-1, under initial pH 7.5 and 20 g COD L-1.

category: bioengineering


title: Bone mechanoregulation allows subject-specific load estimation based on time-lapsed micro-CT and HR-pQCT in vivo

abstract: Patients at high risk of fracture due to metabolic diseases frequently undergo long-term antiresorptive therapy. However, in some patients treatment is unsuccessful in preventing fractures or causes severe adverse health outcomes. Understanding load driven bone remodelling, i.e. mechanoregulation, is critical to understand which patients are at risk for progressive bone degeneration and may enable better patient selection or adaptive therapeutic intervention strategies. Bone microarchitecture assessment using high-resolution peripheral quantitative computed tomography (HR-pQCT) combined with computed mechanical loads has successfully been used to investigate bone mechanoregulation at the trabecular level. To obtain the required mechanical loads that induce local variances in mechanical strain and cause bone remodelling, estimation of physiological loading is essential. Yet, current models homogenise strain patterns throughout the bone to estimate load distribution in vivo, which may be a flawed assumption for investigating alterations in bone mechanoregulation. By further utilising available spatiotemporal information of time-lapsed bone imaging studies, we developed a mechanoregulation-based load estimation algorithm (MR). MR calculates organ scale loads by scaling and superimposing a set of predefined independent unit loads to optimise measured bone formation in high, quiescence in medium and resorption in low strain regions. We benchmarked our algorithm against a previously published load history algorithm (LH) using synthetic data, micro-CT images of murine vertebrae under defined experimental in vivo loadings and HR-pQCT images from seven patients. Our algorithm consistently outperformed LH in all three datasets. In silico generated time evolutions of distal radius geometries (n = 5) indicated significantly higher sensitivity, specificity, and accuracy for MR than LH (p < 0.01). This increased performance led to substantially better discrimination between physiological and extra-physiological loading in mice (n = 8). Moreover, a significantly (p < 0.01) higher association between remodelling events and computed local mechanical signals were found using MR (CCR = 0.42) than LH (CCR = 0.38) to estimate human distal radius loading. Future applications of MR may enable clinicians to link subtle changes in bone strength to changes in day-to-day loading, identifying weak spots in the bone micro-structure for local intervention and personalised treatment approaches.


title: Milk-Way Algorithm applied in Imbalanced Dataset

abstract: We wish to evaluate the algorithm Milk-Way, using a known dataset deposited in a public repository. The new algorithm, which converges various techniques from different areas of knowledge, can classify ligands and select potential new drugs. It was used a dataset of ligands, organized by 15 Bioassays and described by different fingerprints. Full details of the dataset architecture were already published in a public repository. Through the stratified feature selection, using the Milk-Way algorithm, the True Positive and False Positive Rates reached a higher performance compared to the published paper. Using all the features available for each Bioassay, we reached the lowest metrics in all of them. We demonstrated that adding more features have not made a significant impact on the performance. In all the Bioassays, the True Positives and False Positives reached 100% and 0%, respectively, only using 50% and 75% of the features available. The Milk-Way algorithm suggests a holistic approach, which will contribute to the machine-learning area, namely to classified ligands in the virtual screening.

category: bioinformatics


title: Designing of multiepitope-based vaccine against Leptospirosis using Immuno-Informatics approaches.

abstract: Leptospira is a zoonotic pathogen causing significant morbidity and mortality both in animals and humans. Although several surface proteins have been identified as vaccine candidate, they failed to induce sterilizing immunity and cross protection against different serovars. Thus, identification of highly immunogenic antigens that are conserved among pathogenic serovars would be first step towards development of universal vaccine for Leptospirosis. Here we used reverse vaccinology pipeline to screen core genome of pathogenic Leptospira spp.in order to identify suitable vaccine candidates. Based on properties like sub cellular localization, adhesin, homology to human proteins, antigenicity and allergenicity, 18 antigenic proteins were identified and were further investigated for immunological properties. Based on immunogenicity, Protegenicity, Antigenicity, B-cell and promiscuous T-cell epitopes, 6 Potential Vaccine Candidates (PVCs) were finally selected which covered most of the affected world population. For designing a Multi-Epitope Vaccine (MEV), 6 B-cell and 6 promiscuous MHC-I and MHC-II epitopes from each candidate were clustered with linkers in between and stitched along with a TLR4 adjuvant (APPHALS) at the N-terminal to form a construct of 361 amino acids. The physiochemical properties, secondary and tertiary structure analysis revealed that MEV was highly stable. Molecular docking analysis revealed the deep binding interactions of the MEV construct within the grooves of human TLR4 (4G8A). In-silico codon optimization and cloning of the vaccine construct assured good expression. Further, immune simulations have shown that MEV could induce strong and diverse B and T cell responses. Taken together our results indicate that the designed MEV could be a promising subunit vaccine candidate against Leptospirosis, however it requires experimental validation.


title: Protein-protein docking with large-scale backbone flexibility

abstract: Most of the protein-protein docking methods treat proteins as almost rigid objects. Only the side-chains flexibility is usually taken into account. The few approaches enabling docking with a flexible backbone typically work in two steps, in which the search for protein-protein orientations and structure flexibility are simulated separately. In this work, we propose a new straightforward approach for docking sampling. It consists of a single simulation step during which a protein undergoes large-scale backbone rearrangements, rotations, and translations. Simultaneously, the other protein exhibits small backbone fluctuations. Such extensive sampling was possible using the CABS coarse-grained protein model and Replica Exchange Monte Carlo dynamics at a reasonable computational cost. In our proof-of-concept simulations of 62 protein-protein complexes, we obtained acceptable quality models for a significant number of cases.


title: Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulations


title: Lipid type doping of the sponge (L3) mesophase

abstract: The polymorphism of lipid aggregates has long attracted detailed study due to the myriad factors that determine the final mesophase observed. This study is driven by the need to understand mesophase behaviour for a number of applications, such as drug delivery and membrane protein crystallography. In the case of the latter, the role of the so-called  sponge (L3) mesophase has been often noted, but not extensively studied by itself. The L3 mesophase can be formed in monoolein/water systems on the addition of butanediol to water, which partitions the headgroup region of the membrane, and decreases its elastic moduli. Like cubic mesophases, it is bicontinuous, but unlike them, has no long-range translational symmetry. In our present study, we show that the formation of the L3 phase can delicately depend on the addition of dopant lipids to the mesophase. While electrostatically neutral molecules similar in shape to monoolein (DOPE, cholesterol) have little effect on the general mesophase behaviour, others (DOPC, DDM) significantly reduce the region in which it can form. Additionally, we show that by combining cholesterol with the anionic lipid DOPG, it is possible to form the largest stable L3 mesophases observed to date, with correlation lengths over 220 [A].

category: biophysics


title: Chaperones Skp and SurA dynamically expand unfolded outer membrane protein X and synergistically disassemble oligomeric aggregates

abstract: Periplasmic chaperones Skp and SurA are essential players in outer membrane protein (OMP) biogenesis. They prevent unfolded OMPs from misfolding during their passage through the periplasmic space and aid in the disassembly of OMP aggregates under cellular stress conditions. However, functionally important links between interaction mechanisms, structural dynamics, and energetics that underpin both Skp and SurA association with OMPs have remained largely unresolved. Here, using single-molecule fluorescence spectroscopy, we dissect the conformational dynamics and thermodynamics of Skp and SurA binding to unfolded OmpX, and explore their disaggregase activities. We show that both chaperones expand unfolded OmpX distinctly and induce microsecond chain reconfigurations in the client OMP structure. We further reveal that Skp and SurA bind their substrate in a fine-tuned thermodynamic process via enthalpy-entropy compensation. Finally, we observed synergistic activity of both chaperones in the disaggregation of oligomeric OmpX aggregates. Our findings provide an intimate view into the multi-faceted functionalities of Skp and SurA and the fine-tuned balance between conformational flexibility and underlying energetics in aiding chaperone action during OMP biogenesis.


title: An evolutionarily conserved coreceptor gene is essential for CLAVATA signaling in Marchantia polymorpha

abstract: Growth and development of land plants are controlled by CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) family of peptide hormones. In contrast to the genetic diversity of CLE family in flowering plants, the liverwort Marchantia polymorpha possesses a minimal set of CLE, MpCLE1(TDIF homolog) and MpCLE2 (CLV3 homolog). MpCLE1 and MpCLE2 peptides exert distinct function at the apical meristem of M. polymorpha gametophyte via specific receptors, MpTDIF RECEPTOR (MpTDR) and MpCLAVATA1 (MpCLV1), respectively, both belonging to the subclass XI of leucine-rich repeat receptor-like kinases (LRR-RLKs). Biochemical and genetic studies in Arabidopsis have shown that TDR/PXY family and CLV1/BAM family recognize the CLE peptide ligand in a heterodimeric complex with a member of subclass-II coreceptors. Here we show that three LRR-RLK genes of M. polymorpha are classified into subclass II, representing three distinct subgroups evolutionarily conserved in land plants. To address the involvement of subclass-II coreceptors in M. polymorpha CLE signaling, we performed molecular genetic analysis on one of them, MpCLAVATA3 INSENSITIVE RECEPTOR KINASE (MpCIK). Two knockout alleles for MpCIK formed narrow apical meristems marked by promMpYUC2:GUS marker, which were not expanded by MpCLE2 peptide treatment, phenocopying Mpclv1. Loss of sensitivity to MpCLE2 peptide was also observed in gemma cup formation in both Mpclv1 and Mpcik. Biochemical analysis using a Nicotiana benthamiana transient expression system revealed weak association between MpCIK and MpCLV1, as well as MpCIK and MpTDR. While MpCIK may also participate in MpCLE1 signaling, our data show that the conserved CLV3-CLV1-CIK module functions in M. polymorpha, controlling meristem activity for development and organ formation for asexual reproduction.

category: plant biology


title: Clinically-Driven Design of Synthetic Gene Regulatory Programs in Human Cells

abstract: Synthetic biology seeks to enable the rational design of regulatory molecules and circuits to reprogram cellular behavior. The application of this approach to human cells could lead to powerful gene and cell-based therapies that provide transformative ways to combat complex diseases. To date, however, synthetic genetic circuits are challenging to implement in clinically-relevant cell types and their components often present translational incompatibilities, greatly limiting the feasibility, efficacy and safety of this approach. Here, using a clinically-driven design process, we developed a toolkit of programmable synthetic transcription regulators that feature a compact human protein-based design, enable precise genome-orthogonal regulation, and can be modulated by FDA-approved small molecules. We demonstrate the toolkit by engineering therapeutic human immune cells with genetic programs that enable titratable production of immunotherapeutics, drug-regulated control of tumor killing in vivo and in 3D spheroid models, and the first multi-channel synthetic switch for independent control of immunotherapeutic genes. Our work establishes a powerful platform for engineering custom gene expression programs in mammalian cells with the potential to accelerate clinical translation of synthetic systems.

category: synthetic biology


title: Rewritable Two-Dimensional DNA-Based Data Storage with Machine Learning Reconstruction

abstract: DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores high-density images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global errorcorrection redundancy.


title: Analysing variations in pelage patterning among European Felis silvestris silvestris populations

abstract:
The pelage pattern of wildcats from six regions within the distribution range of the species is analysed to test the hypothesis that clear differences between different regions exist. In total, 98 furs were used, but with different distribution from the Eifel (Germany), Harz Mountains (Germany), Caucasus, Western Spain, Switzerland/France and Greece. Specimens were at least seven months old, sex was not considered. The characteristics used were adapted from the literature and included typical wildcat features like the tail and stripes on the neck. Polychoric correlations, as a binary version of Spearmans rank correlation coefficient, were used as a measure of correlation between pelage characteristics. Pairwise tetrachoric correlations were computed with R 3.1.2., cluster analyses were conducted with SPSS 14.

No clear relationship between the pelage characteristics and the geographic distribution of the six studied wildcat populations were found, the hypothesis needs to be rejected. It is however suggested, that coat patterning of Caucasian wildcats to some degree differ from other European wildcat. The results, however, do not clearly corroborate this hypothesis as Caucasian wildcats were not grouped into closed clusters in all the cluster analyses. To a lesser extent, pelage characteristic differences may also exist between wildcats from Western Spain as well as South-Western Greece and other European regions, but the samples are too small to draw conclusions. To test these refined hypotheses, more specimens from the Caucasus, Western Spain and South-Western Greece (but also Switzerland/North-Eastern France) need to be collected and compared according to our protocol.

category: zoology


title: Functional modules within a distributed neural network control feeding in a model medusa

abstract: Jellyfish are free-swimming, radially symmetric organisms with complex behaviors that arise from coordinated interactions between distinct, autonomously functioning body parts. This behavioral complexity evolved without a corresponding cephalization of the nervous system. The systems-level neural mechanisms through which such decentralized control is achieved remain unclear. Here, we address this question using the jellyfish, Clytia, and present it as a new neuroscience model. We describe a coordinated, asymmetric behavior in which food is passed from the umbrellar margin to the central mouth via directed margin folding. Using newly developed transgenic jellyfish lines to ablate or image specific neuronal subpopulations, we find, unexpectedly, that margin folding reflects the local activation of neural subnetworks that tile the umbrella. Modeling suggests that this structured ensemble activity emerges from sparse, local connectivity rules. These findings reveal how an organismal behavior can emerge from local interactions between functional modules in the absence of a central brain.

category: neuroscience


title: The amyloid concentric β-barrel hypothesis: models of Synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels.

abstract: Amyloid beta (A{beta} of Alzheimers disease) and -synuclein (-Syn of Parkinsons disease) form large fibrils. Evidence is increasing however that much smaller oligomers are more toxic and that these oligomers can form transmembrane ion channels. We have proposed previously that A{beta}42 oligomers, annular protofibrils, and ion channels adopt concentric {beta}-barrel molecular structures. Here we extend that hypothesis to the superfamily of , {beta}, and {gamma}-synucleins. Our models of numerous Synuclein oligomers, annular protofibrils, tubular protofibrils, lipoproteins, and ion channels were developed to be consistent with sizes, shapes, molecular weights, and secondary structures of assemblies as determined by EM and other studies. The models have the following features: 1) all subunits have identical structures and interactions; 2) they are consistent with conventional {beta}-barrel theory; 3) the distance between walls of adjacent {beta}-barrels is between 0.6 and 1.2 nm; 4) hydrogen bonds, salt bridges, interactions among aromatic side-chains, burial and tight packing of hydrophobic side-chains, and aqueous solvent exposure of hydrophilic side-chains are relatively optimal; and 5) residues that are identical among distantly related homologous proteins cluster in the interior of most oligomers whereas residues that are hypervariable are exposed on protein surfaces. Atomic scale models of some assemblies were developed.


title: Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders

abstract: Recent neuroscience studies demonstrate that a deeper understanding of brain function requires a deeper understanding of behavior. Detailed behavioral measurements are now often collected using video cameras, resulting in an increased need for computer vision algorithms that extract useful information from video data. Here we introduce a new video analysis tool that combines the output of supervised pose estimation algorithms (e.g. DeepLabCut) with unsupervised dimensionality reduction methods to produce interpretable, low-dimensional representations of behavioral videos that extract more information than pose estimates alone. We demonstrate this tool by extracting interpretable behavioral features from videos of three different head-fixed mouse preparations, as well as a freely moving mouse in an open field arena, and show how these interpretable features can facilitate downstream behavioral and neural analyses. We also show how the behavioral features produced by our model improve the precision and interpretation of these downstream analyses compared to using the outputs of either fully supervised or fully unsupervised methods alone.


title: Unexpected false feelings of familiarity about faces are associated with increased pupil dilations

abstract: Our subjective sense that something we encounter is familiar to us is reflected by changes in pupil size. Although pupil dilation effects of familiarity have been well documented, familiarity is not the only, or even the strongest, contributing factor to pupil dilation. Changes in pupil dilation also reflect changes in brightness, affective or emotional responses, hormonal release, expected value or utility, and surprise, among others. Because many factors can affect pupil dilation, important questions remain about how pupil dilation changes reflect high-order cognitive processes, like attention and memory. For example, because surprise and familiarity are often difficult to fully distinguish (since new experiences can be surprising or unexpected), it can be difficult to tease apart pupil dilation effects of surprise versus familiarity. To better understand the effects of surprise and familiarity on pupil dilation, we examined pupil responses during a recognition memory task involving photographs of faces and outdoor scenes. When participants rated novel face images as "familiar," we observed a robust pupil dilation response.


title: Parallel processing of natural images by overlapping retinal neuronal ensembles

abstract: Even though the retinal microcircuit organization has been described in detail at the single-cell level, little is known about how groups of retinal cells coordinated activity encode and process parallel information representing the spatial and temporal structure of changing environmental conditions. To describe the population dynamics of retinal neuronal ensembles, we used microelectrode array recordings that describe hundreds of retinal ganglion cells simultaneous activity in response to a short movie captured in the natural environment where our subject develops their visual behaviors. The vectorization of population activity allowed the identification of retinal neuronal ensembles that synchronize to specific segments of natural stimuli. These synchronous retinal neuronal ensembles were reliably activated by the same stimuli at different trials, indicating a robust population response of retinal microcircuits. The generation of asynchronous events required integrating a physiologically meaningful time window larger than 80 ms, demonstrating that retinal neuronal ensembles time integration filters non-structured visual information. Interestingly, individual neurons could be part of several ensembles indicating that parallel circuits could encode environmental conditions changes. We conclude that parallel neuronal ensembles could represent the functional unit of retinal computations and propose that the further study of retinal neuronal ensembles could reveal emergent properties of retinal circuits that individual cells activity cannot explain.


title: Diffuse optical reconstructions of NIRS data using Maximum Entropy on the Mean

abstract:
Functional near-infrared spectroscopy (fNIRS) measures the hemoglobin concentration changes associated with neuronal activity. Diffuse optical tomography (DOT) consists of reconstructing the optical density changes measured from scalp channels to the oxy-/deoxy-hemoglobin (i.e., HbO/HbR) concentration changes within the cortical regions. In the present study, we adapted a nonlinear source localization method developed and validated in the context of Electro- and Magneto-Encephalography (EEG/MEG): the Maximum Entropy on the Mean (MEM), to solve the inverse problem of DOT reconstruction. We first introduced depth weighting strategy within the MEM framework for DOT reconstruction to avoid biasing the reconstruction results of DOT towards superficial regions. We also proposed a new initialization of the MEM model improving the temporal accuracy of the original MEM framework. To evaluate MEM performance and compare with widely used depth weighted Minimum Norm Estimate (MNE) inverse solution, we applied a realistic simulation scheme which contained 4000 simulations generated by 250 different seeds at different locations and 4 spatial extents ranging from 3 to 40cm2 along the cortical surface. Our results showed that overall MEM provided more accurate DOT reconstructions than MNE. Moreover, we found that MEM was remained particularly robust in low signal-to-noise ratio (SNR) conditions. The proposed method was further illustrated by comparing to functional Magnetic Resonance Imaging (fMRI) activation maps, on real data involving finger tapping tasks with two different montages. The results showed that MEM provided more accurate HbO and HbR reconstructions in spatial agreement with the main fMRI cluster, when compared to MNE.

HighlightsO_LIWe introduced a new fNIRS reconstruction method - Maximum Entropy on the Mean.
C_LIO_LIWe implemented depth weighting strategy within the MEM framework.
C_LIO_LIWe improved the temporal accuracy of the original MEM reconstruction.
C_LIO_LIPerformances of MEM and MNE were evaluated with realistic simulations and real data.
C_LIO_LIMEM provided more accurate and robust reconstructions than MNE.
C_LI


title: Suppression of alpha-band power underlies exogenous attention to emotional distractors

abstract:
Alpha-band oscillations (8-14 Hz) are essential for attention and perception processes by facilitating the selection of relevant information. Directing visuospatial endogenous (voluntary) attention to a given location consistently results in a power suppression of alpha activity over occipito-parietal areas contralateral to the attended visual field. In contrast, the neural oscillatory dynamics underlying the involuntary capture of attention, or exogenous attention, are currently under debate. By exploiting the inherent capacity of emotionally salient visual stimuli to capture attention, we aimed to investigate whether exogenous attention is characterized by either a reduction or an increase in alpha-band activity. Electroencephalographic activity was recorded while participants completed a Posner visuospatial cueing task, in which a lateralized image with either positive, negative, or neutral emotional content competed with a target stimulus presented in the opposite hemifield. Compared with trials with no distractors, alpha power was reduced over occipital regions contralateral to distracting images. This reduction of alpha activity turned out to be functionally relevant, as it correlated with impaired behavioural performance on the ongoing task and was enhanced for distractors with negative valence. Taken together, our results demonstrate that visuospatial exogenous attention is characterized by a suppression of alpha-band activity contralateral to distractor location, similar to the oscillatory underpinnings of endogenous attention. Further, these results highlight the key role of exogenous attention as an adaptive mechanism for the efficient detection of biologically salient stimuli.

HighlightsO_LIExogenous attention is indexed by alpha suppression contralateral to distractors.
C_LIO_LIAlpha power decrease is enhanced by distractors with negative emotional valence.
C_LIO_LILower levels of alpha power correlate with poorer task performance accuracy.
C_LIO_LIThe negativity bias in exogenous attention might reflect an adaptive mechanism.
C_LI


title: Hierarchical cross-scale analysis identifies parallel ventral striatal networks coding for dynamic and stabilized olfactory reward predictions

abstract: The unbiased identification of brain circuits responsible for behavior and their local cellular computations is a challenge for neuroscience. We establish here a hierarchical cross-scale approach from behavioral modeling and fMRI in task-performing mice to cellular network dynamics to identify how reward predictions are represented in the forebrain upon olfactory conditioning. fMRI identified functional segregation in reward prediction and error computations among olfactory cortices and subcortical circuits. Among them, the olfactory tubercle contributed both to dynamic reward predictions and prediction error. In this region, cellular recordings revealed two parallel neuronal populations for prediction coding. One population produced stabilized predictions as distributed stimulus-bound transient network activity; the other evolved during anticipatory waiting and fully reflected predicted value in single-units, dynamically integrating the recent cue-specific history of uncertain outcomes. Thus, the cross-scale approach revealed regional functional differentiation among the distributed forebrain circuits with a limbic hotspot for multiple non-redundant reward prediction coding.


title: improv: A flexible software platform for adaptive neuroscience experiments

abstract: Neuroscientists now routinely record the activity of large numbers of neurons at high temporal and spatial resolution. With these capabilities comes the promise of causally intervening during these recordings by perturbing neurons or changing experimental conditions, requiring tight integration between data acquisition, analysis, and manipulation. Unfortunately, solutions for real-time interventions are rare, difficult to design and implement, and remain largely unused. Here, we introduce improv, a software platform that allows users to flexibly specify and manage adaptive experiments to integrate data collection, preprocessing, visualization, and user-defined analytics. Using improv for streaming data analysis for two photon calcium imaging and behavior we demonstrate how access to online information can be used for automated, integrated experimentation.


title: Frequency of quorum sensing mutations in Pseudomonas aeruginosa strains isolated from different environments

abstract:
Pseudomonas aeruginosa uses quorum sensing (QS) to coordinate the expression of multiple genes necessary for establishing and maintaining infection. lasR QS mutations have been shown to frequently arise in cystic fibrosis (CF) lung infections, however, there has been far less emphasis on determining whether QS system mutations arise across other environments. To test this, we utilized 852 publicly available sequenced P. aeruginosa genomes from the Pseudomonas International Consortium Database (IPCD) to study P. aeruginosa QS mutational signatures. We found that across all isolates, LasR is the most variable protein sequence compared to other QS proteins. In order to study isolates by source, we focused on a subset of 654 isolates collected from CF, wounds, and non-infection environmental isolates, where we could clearly identify their source. Using this sub-set analysis, we found that LasR mutations are not specific to CF lungs, but are common across all environments. We then used amino acid length as a proxy for observing loss of function in LasR proteins among the strains. We found that truncated LasR proteins are more abundant in P. aeruginosa strains isolated from human infection than the environment. Overall, our findings suggest that the evolution of lasR QS mutations in P. aeruginosa are common and not limited to infection environments.

ImportancePseudomonas aeruginosa is an opportunistic pathogen which is often isolated from infection and environmental sources. P. aeruginosa uses quorum sensing (QS) to establish and adapt to infection environments. QS in P. aeruginosa is controlled by a complex hierarchical gene network in which the transcriptional regulator LasR has traditionally been thought to play a major controlling role. Despite this, lasR mutants are frequently isolated from chronic infection sites including the cystic fibrosis lung. Using an online P. aeruginosa strain database, we determined the frequency of mutation in key QS genes in multiple infection and non-infection environments and found that mutations and truncations in the lasR gene is more common than in other QS genes. Further, we found that lasR mutants are common in both infection and environmental strains. These findings further our understanding of QS in P. aeruginosa and have implications for the development of future therapies designed to inhibit QS.

category: microbiology


title: Protocol for mapping the spatial variability in cell wall mechanical bending behavior in living leaf pavement cells

abstract:
An integrated, experimental-computational approach is presented to analyze the variation of elastic bending behavior in the primary cell wall of living Arabidopsis thaliana pavement cells and to measure turgor pressure in the cells quantitatively under different osmotic conditions. Mechanical properties, size and geometry of cells and internal turgor pressure greatly influence their morphogenesis. Computational models of plant morphogenesis require values for wall elastic modulus and turgor pressure but very few experiments were designed to validate the results using measurements that deform the entire thickness of the cell wall. Because new wall material is deposited from inside the cell, full-thickness deformations are needed to quantify relevant changes associated with cell development. The approach here uses laser scanning confocal microscopy to measure the three-dimensional geometry of a single pavement cell, and indentation experiments equipped with high magnification objective lens to probe the local mechanical responses across the same cell wall. These experimental results are matched iteratively using a finite element model of the experiment to determine the local mechanical properties, turgor pressure, and cell height. The resulting modulus distribution along the periclinal wall is shown to be nonuniform. These results are consistent with the characteristics of plant cell walls which have a heterogeneous organization. This research and the resulting model will provide a reference for future work associated with the heterogeneity and anisotropy of mechanical properties of plant cell walls in order to understand morphogenesis of the primary cell walls during growth and to predict quantitatively the magnitudes/directions of cell wall forces.

One sentence summaryThe distribution of elastic modulus of the periclinal cell walls of living

Arabidopsis epidermis is nonuniform as measured by bending the entire thickness of the wall.

HighlightsO_LIExperimental characterization of the spatial distribution of elastic bending behavior across the periclinal wall
C_LIO_LIQuantification of the turgor pressure of the living plant epidermal cells validated with osmotic treatments
C_LIO_LIQuantification of the effect of cell geometry on the measured mechanical response
C_LI

Graphical abstract

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category: cell biology


title: The multidimensional nutritional niche of fungus-cultivar provisioning in free-ranging colonies of a neotropical leafcutter ant

abstract:
The foraging trails of Atta leafcutter colonies are among the most iconic scenes in Neotropical ecosystems, with thousands of ants carrying freshly cut plant fragments back to their nests where they are used to provision a fungal food crop. We tested a hypothesis that the fungal cultivars multidimensional requirements for macronutrients (protein and carbohydrates) and minerals (Al, Ca, Cu, Fe, K, Mg, Mn, Na, P and Zn) govern the foraging breadth of Atta colombica leafcutter ants in a Panamanian rainforest. Analyses of freshly cut plant fragments carried by leafcutter foragers showed that the combination of fruits, flowers, and leaves provide for a broad realized nutritional niche that can maximize cultivars performance. And, while the leaves that comprised the most harvested resource also delivered an intake target containing protein in excess of the amounts that can maximize cultivar growth, in vitro experiments showed that the minerals P, Al, and Fe can enhance the cultivars tolerance to protein-biased substrates, and potentially expand the ants foraging niche. Yet, the cultivar also exhibits narrow margins between mineral limitation and toxicity that may render plant fragments with seemingly optimal blends of macronutrients unsuitable for provisioning. Our approach highlights that optimal foraging is inherently multidimensional and links the foraging behavior of a generalist insect herbivore to the fundamental nutritional niche of its microbial symbiont.

Significance StatementColonies of Atta colombica leafcutter ants can contain millions of specialized workers exhibiting large-scale generalist herbivory. Yet, this generalist foraging niche also depends on the poorly understood physiological needs of the ants domesticated fungal cultivar. We show the cultivars fundamental nutritional niche is broad for carbohydrates but narrower for protein and a suite of minerals, but that the cultivars sensitivity to excess protein is also mediated by Al, Fe, and P. More generally, this study decouples the multidimensional foraging strategies that enable a generalist herbivore to navigate a complex nutritional landscape and mix many imbalanced foods to achieve balanced cultivar provisioning.

category: ecology


title: Variation in self-compatibility among genotypes and across ontogeny in a self-fertilizing vertebrate

abstract: Mixed mating strategies offer the benefits of both self-fertilizing ones own eggs (selfing) and outcrossing, while limiting the costs of both methods. The economics of mixed mating is further determined by individual self-compatibility. In gynodioecious (hermaphrodites, females) and androdioecious (hermaphrodites, males) species, the level of self-compatibility of the hermaphrodites also acts as a selection pressure on the fitness of the other sex. Mangrove rivulus fish populations are comprised of selfing hermaphrodites and males that result from hermaphrodites changing sex. Although hermaphrodites overwhelmingly reproduce through internal selfing, they occasionally oviposit unfertilized eggs. Males can externally fertilize these eggs. Here, we reveal that fecundity and self-compatibility varies within individuals across ontogeny until about 365 days post hatch, and among individuals derived from lineages that vary in their propensity to change sex. Hermaphrodites from high sex changing lineages were significantly less fecund and self-compatible than hermaphrodites from low sex changing lineages. These differences in self-compatibility and fecundity have the potential to drive evolutionary changes on mating strategy and the fitness of males in populations of the mangrove rivulus. This study also illustrates the importance of including lineage variation when estimating the costs and benefits of mixed mating strategies.

category: evolutionary biology


title: A more accurate method for colocalisation analysis allowing for multiple causal variants

abstract: In genome-wide association studies (GWAS) it is now common to search for, and find, multiple causal variants located in close proximity. It has also become standard to ask whether different traits share the same causal variants, but one of the popular methods to answer this question, coloc, makes the simplifying assumption that only a single causal variant exists for any given trait in any genomic region. Here, we examine the potential of the recently proposed Sum of Single Effects (SuSiE) regression framework, which can be used for fine-mapping genetic signals, for use with coloc. SuSiE is a novel approach that allows evidence for association at multiple causal variants to be evaluated simultaneously, whilst separating the statistical support for each variant conditional on the causal signal being considered. We show this results in more accurate coloc inference than other proposals to adapt coloc for multiple causal variants based on conditioning. We therefore recommend that coloc be used in combination with SuSiE to optimise accuracy of colocalisation analyses when multiple causal variants exist.

category: genetics


title: Male mate choice unresolved in the mangrove rivulus

abstract: Mate choice has the potential to drive phenotypic evolution because it can determine traits that increase an individuals likelihood to reproduce (courtship behaviors, elaborate ornamentation). These traits, however, can also be detrimental for health or survival, often antagonizing the evolution of extreme phenotypes. Mangrove rivulus fish (Kryptolebias marmoratus) develop as self-fertilizing simultaneous hermaphrodites. Hermaphrodites overwhelmingly self-fertilize their eggs internally, but occasionally oviposit unfertilized eggs. Some individuals change sex to male after sexual maturity, essentially forgoing the reproductive assurance of selfing. In a continuing effort to understand how sex change to male is maintained this species, I designed an experiment to determine whether males act as choosers to increase their likelihood of finding unfertilized eggs for reproduction. I hypothesized that males would prefer to associate with younger hermaphrodites when given a dichotomous choice, as they lay a greater proportion of unfertilized eggs compared to older hermaphrodites. The males in this study did not show a preference for either the younger or older hermaphrodite but exhibited greater within individual variance across subtrials than among individual variation. I discuss alternative hypotheses concerning male mate choice in mangrove rivulus, which may illuminate hypotheses to be tested in this and other hermaphroditic species.

category: animal behavior and cognition


title: Seven amino acid types suffice to reconstruct the core fold of RNA polymerase

abstract: AbstractThe extant complex proteins must have evolved from ancient short and simple ancestors. Nevertheless, how such prototype proteins emerged on the primitive earth remains enigmatic. The double-psi beta-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its evolutionary pathway started by "interlacing homo- dimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.

category: biochemistry


title: Chemoproteomics Enabled Discovery of Selective Probes for NuA4 Factor BRD8

abstract: Bromodomain-containing proteins frequently reside in multisubunit chromatin complexes with tissue or cell state-specific compositions. Recent studies have revealed tumor-specific dependencies on the BAF complex bromodomain subunit BRD9 that are a result of recurrent mutations afflicting the structure and composition of associated complex members. To enable the study of ligand engaged complex assemblies, we established a chemoproteomics approach using a functionalized derivative of the BRD9 ligand BI-9564 as an affinity matrix. Unexpectedly, in addition to known interactions with BRD9 and associated BAF complex proteins, we identify a previously unreported interaction with members of the NuA4 complex through the bromodomain-containing subunit BRD8. We apply this finding, alongside homology model guided design, to develop chemical biology approaches for the study of BRD8 inhibition, and to arrive at first-in-class selective and cellularly active probes for BRD8. These tools will empower further pharmacological studies of BRD9 and BRD8 within respective BAF and NuA4 complexes.


title: clusTCR: a Python interface for rapid clustering of large sets of CDR3 sequences

abstract:
The T-cell receptor (TCR) determines the specificity of a T-cell towards an epitope. As of yet, the rules for antigen recognition remain largely undetermined. Current methods for grouping TCRs according to their epitope specificity remain limited in performance and scalability. Multiple methodologies have been developed, but all of them fail to efficiently cluster large data sets exceeding 1 million sequences. To account for this limitation, we developed clusTCR, a rapid TCR clustering alternative that efficiently scales up to millions of CDR3 amino acid sequences. Benchmarking comparisons revealed similar accuracy of clusTCR with other TCR clustering methods. clusTCR offers a drastic improvement in clustering speed, which allows clustering of millions of TCR sequences in just a few minutes through efficient similarity searching and sequence hashing.

clusTCR was written in Python 3. It is available as an anaconda package (https://anaconda.org/svalkiers/clustcr) and on github (https://github.com/svalkiers/clusTCR).


title: DeepMotifSyn: a deep learning approach to synthesize heterodimeric DNA motifs

abstract:
MotivationThe cooperativity of transcription factors (TFs) is a widespread phenomenon in the gene regulation system. However, the interaction patterns between TF binding motifs remain elusive. The recent high-throughput assays, CAP-SELEX, have identified over 600 composite DNA sites (i.e. heterodimeric motifs) bound by cooperative TF pairs. However, there are over 25,000 inferentially effective heterodimeric TFs in human cell. It is not practically feasible to validate all heterodimeric motifs due to cost and labour. Therefore, it is highly demanding to develop a fast and accurate computational tool for heterodimeric motif synthesis.

ResultsWe introduce DeepMotifSyn, a deep-learning-based tool for synthesizing heterodimeric motifs from monomeric motif pairs. Specifically, DeepMotifSyn is composed of heterodimeric motif generator and evaluator. The generator is a U-Net-based neural network that can synthesize heterodimeric motifs from aligned motif pairs. The evaluator is a machine-learning-based model that can score the generated heterodimeric motif candidates based on the motif sequence features. Systematic evaluations on CAP-SELEX data illustrates that DeepMotif-Syn significantly outperforms the current state-of-the-art predictors. In addition, DeepMotifSyn can synthesize multiple heterodimeric motifs with different orientation and spacing settings. Such a feature can address the shortcomings of previous models. We believe Deep-MotifSyn is a more practical and reliable model than current predictors on heterodimeric motif synthesis.

Availability and implementationThe software is freely available at https://github.com/JasonLinjc/deepMotifSyn.


title: TP-MAP - an Integrated Software Package for the Analysis of 1D and 2D Thermal Profiling Data

abstract: Thermal profiling (TP) has emerged as a promising experimental methodology for elucidating the molecular targets of drugs and metabolites on a proteome-wide scale. Here, we present the Thermal Profiling Meltome Analysis Program (TP-MAP) software package for the analysis and ranking of 1D and 2D thermal profiling datasets. TP-MAP provides a user-friendly interface to quickly identify hit candidates and further explore targets of interest via intersection and crosslinking to public databases.


title: BiSEK: a platform for a reliable differential expression analysis

abstract: Differential Expression Analysis (DEA) of RNA-sequencing data is frequently performed for detecting key genes, affected across different conditions. Although DEA-workflows are well established, preceding reliability-testing of the input material, which is crucial for consistent and strong results, is challenging and less straightforward. Here we present Biological Sequence Expression Kit (BiSEK), a graphical user interface-based platform for DEA, dedicated to a reliable inquiry. BiSEK is based on a novel algorithm to track discrepancies between the data and the statistical model design. Moreover, BiSEK enables differential-expression analysis of groups of genes, to identify affected pathways, without relying on the significance of genes comprising them. Using BiSEK, we were able to improve previously conducted analysis, aimed to detect genes affected by FUBP1 depletion in chronic myeloid leukemia cells of mice bone-marrow. We found affected genes that are related to the regulation of apoptosis, supporting in-vivo experimental findings. We further tested the host response following SARS-CoV-2 infection. We identified a substantial interferon-I reaction and low expression levels of TLR3, an inducer of interferon-III (IFN-III) production, upon infection with SARS-CoV-2 compared to other respiratory viruses. This finding may explain the low IFN-III response upon SARS-CoV-2 infection. BiSEK is open-sourced, available as a web-interface.


title: Sulfur limitation increases duckweed starch accumulation without compromising growth

abstract:
Duckweeds contain relatively high levels of starch and are a potential biomass feedstock for biofuel production. Here, the biomass and starch yield of duckweed under three different nutrient-limited conditions were analyzed to investigate possible ways of further increasing the efficiency of starch production. The results showed that sulfur limitation resulted in the highest starch yield, which was 42% and 73% higher than in nitrogen or phosphorus limitation, respectively. The high yield of sulfur-limited duckweed is largely due to the combinations of little effects on biomass and high accumulations of starch. Although nitrogen limitation led to higher starch content (67.4%), it severely reduced biomass production. The photosynthetic performance indicator Fv/Fm was a simple and sensitive indicator of starch content in nutrient-limited duckweed. Taken together, this study demonstrates that sulfur limitation is a simple and efficient way to increase starch yield, highlighting the great potential of duckweed for biofuel production. We report that sulfur limitation is a practical approach to increase starch yields in duckweed without affecting growth or biomass.

HighlightsO_LISulfur limitation induces starch production in a duckweed specie.
C_LIO_LINitrogen limitation triggers the highest starch content, but limits growth.
C_LIO_LISulfur limitation results in the highest starch yield.
C_LIO_LIFv/Fm is a rapid and robust proxy of starch content in nutrient-limited duckweed.
C_LI


title: Modeling metallicity: low level visual features support robust material perception

abstract: The human visual system is able to rapidly and accurately infer the material properties of objects and surfaces in the world. Yet an inverse optics approach--estimating the bi-directional reflectance distribution function of a surface, given its geometry and environment, and relating this to the optical properties of materials--is both intractable and computationally unaffordable. Rather, previous studies have found that the visual system may exploit low-level spatio-chromatic statistics as heuristics for material judgment. Here, we present results from psychophysics and modelling that supports the use of image statistics heuristics in the judgement of metallicity--the quality of appearance that suggests an object is made from metal. Using computer graphics, we generated stimuli that varied along two physical dimensions: the smoothness of a metal object, and the evenness of its transparent coating. This allowed for the manipulation of low-level image statistics, whilst ensuring that each stimulus was a naturalistic, physically plausible image. A conjoint-measurement task decoupled the contributions of these dimensions to the perception of metallicity. Low-level image features, as represented in the activations of oriented linear filters at different spatial scales, were found to correlate with the dimensions of the stimulus space, and decision-making models using these activations replicated observer performance in judging metal smoothness, coating bumpiness, and metallicity. Importantly, the performance of these models did not deteriorate when objects were rotated within their simulated scene, with corresponding changes in image properties. We therefore conclude that low-level image features may provide reliable cues for the robust perception of metallicity.


title: Ultrafast large-scale simulations of biophysically realistic neurons using deep learning

abstract: Understanding the activity of the mammalian brain requires an integrative knowledge of circuits at distinct scales, ranging from ion channel gating to circuit connectomics. To understand how multiple parameters contribute synergistically to circuit behavior, neuronal computational models are regularly employed. However, traditional models containing anatomically and biophysically realistic neurons are computationally demanding even when scaled to model local circuits. To overcome this limitation, we trained several artificial neural net (ANN) architectures to model the activity of realistic, multicompartmental neurons. We identified a single ANN that accurately predicted both subthreshold and action potential firing and correctly generalized its responses to previously unobserved synaptic input. When scaled, processing times were orders of magnitude faster compared with traditional approaches, allowing for rapid parameter-space mapping in a circuit model of Rett syndrome. Thus, we present a novel ANN approach that allows for rapid, detailed network experiments using inexpensive, readily available computational resources.


title: Ultrafast Simulation of Large-Scale Neocortical Microcircuitry with Biophysically Realistic Neurons


title: Chelator sensing and lipopeptide interplay mediates molecular interspecies interactions between soil bacilli and pseudomonads

abstract: AbstractSome bacterial species are important members of the rhizosphere microbiome and confer protection to the host plant against pathogens. However, our knowledge of the multitrophic interactions determining the ecological fitness of these biocontrol bacteria in their highly competitive natural niche is still limited. In this work, we investigated the molecular mechanisms underlying interactions between B. velezensis, considered as model plant-associated and beneficial species in the Bacillus genus, and Pseudomonas as a rhizosphere-dwelling competitor. Our data show that B. velezensis boosts its arsenal of specialized antibacterials upon the perception of the secondary siderophore enantio-pyochelin produced by phylogenetically distinct pseudomonads and some other genera. We postulate that B. velezensis has developed some chelator sensing systems to learn about the identity of its surrounding competitors. Illustrating the multifaceted molecular response of Bacillus, surfactin is another crucial component of the secondary metabolome mobilized in interbacteria competition. Its accumulation not only enhances motility but, unexpectedly, the lipopeptide also acts as a chemical trap that reduces the toxicity of other lipopeptides released by Pseudomonas challengers. This in turn favors the persistence of Bacillus populations upon competitive root colonization. Our work thus highlights new ecological roles for bacterial secondary metabolites acting as key drivers of social interactions.


title: Dietary vitamin B12 reduces amyloid-β proteotoxicity by alleviating oxidative stress and mitochondrial dysfunction

abstract: Alzheimers disease (AD) is a devastating neurodegenerative disorder with no effective treatment. Diet, as a modifiable risk factor for AD, could potentially be targeted to slow disease onset and progression. However, complexity of the human diet and indirect effects of the microbiome make it challenging to identify protective nutrients. Multiple factors contribute to AD pathogenesis including amyloid beta (A{beta}) deposition, mitochondrial dysfunction, and oxidative stress. Here we used Caenorhabditis elegans to define the impact of diet on A{beta} proteotoxicity. We discovered that dietary vitamin B12 alleviated mitochondrial fragmentation, bioenergetic defects, and oxidative stress, delaying A{beta}-induced paralysis without affecting A{beta} accumulation. Vitamin B12 had this protective effect by acting as a cofactor for methionine synthase rather than as an antioxidant. Vitamin supplementation of B12 deficient adult A{beta} animals was beneficial, demonstrating potential for vitamin B12 as a therapy to target pathogenic features of AD triggered by both aging and proteotoxic stress.


title: Solving the Sample Size Problem for Resource Selection Analysis

abstract:
O_LISample size sufficiency is a critical consideration for conducting Resource-Selection Analyses (RSAs) from GPS-based animal telemetry. Cited thresholds for sufficiency include a number of captured animals M [≥] 30 and as many relocations per animal N as possible. These thresholds render many RSA-based studies misleading if large sample sizes were truly insufficient, or unpublishable if small sample sizes were sufficient but failed to meet reviewer expectations.
C_LIO_LIWe provide the first comprehensive solution for RSA sample size by deriving closed-form mathematical expressions for the number of animals M and the number of relocations per animal N required for model outputs to a given degree of precision. The sample sizes needed depend on just 2 biologically meaningful quantities: habitat selection strength and a novel measure of landscape complexity, which we define rigorously. The mathematical expressions are calculable for any environmental dataset at any spatial scale and are applicable to any study involving resource selection (including sessile organisms). We validate our analytical solutions using globally relevant empirical data including 5,678,623 GPS locations from 511 animals from 10 species (omnivores, carnivores, and herbivores living in boreal, temperate, and tropical forests, montane woodlands, swamps, and arctic tundra).
C_LIO_LIOur analytic expressions show that the required M and N must decline with increasing selection strength and increasing landscape complexity, and this decline is insensitive to the definition of availability used in the analysis. Our results contradict conventional wisdom by demonstrating that the most biologically relevant effects on the utilization distribution (i.e. those landscape conditions with the greatest absolute magnitude of resource selection) can often be estimated with far fewer data than is commonly assumed.
C_LIO_LIWe identify several critical steps in implementing these equations, including (i) a priori selection of expected model coefficients, and (ii) sampling intensity for background (absence/pseudo-absence) data within a given definition of availability. We show that random sampling of background data violates the underlying mathematics of RSA, leading to incorrect values for necessary M and N and potentially incorrect RSA model outputs. We argue that these equations should be a mandatory component for all future RSA studies.
C_LI


title: Beneficial cumulative effects of old parental age on offspring fitness

abstract: Old parental age is commonly associated with negative effects on offspring life-history traits. Such parental effect senescence is predicted to have a cumulative detrimental effect over successive generations. However, old parents may benefit from producing high-quality offspring when these compete for seasonal resources. Thus, old parents may choose to increase investment in their offspring, thereby producing fewer but larger and more competitive progeny. We show that Caenorhabditis elegans hermaphrodites increase parental investment with advancing age, resulting in fitter offspring who reach their reproductive peak earlier. Remarkably, these effects increased over six successive generations of breeding from old parents and were subsequently reversed following a single generation of breeding from a young parent. These results contradict the theory that old parents transfer a cumulative detrimental "ageing factor" to their offspring. Instead, our findings support the hypothesis that offspring of old parents receive more resources and convert them into increasingly faster life-histories.


title: Dominance shifts increase the likelihood of soft selective sweeps

abstract: Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from the standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.


title: A copper chaperone-mimetic polytherapy for SOD1-associated amyotrophic lateral sclerosis

abstract: Amyotrophic lateral sclerosis (ALS)-associated mutations in Cu/Zn superoxide dismutase (SOD1) reduce folding stability, resulting in misfolding, aggregation, and ultimately cellular toxicity. A great deal of effort has focused on preventing the misfolding and aggregation of SOD1 as a potential therapy for ALS, however, the results have been mixed. Here, we utilise a small-molecule polytherapy of CuATSM and ebselen to mimic the metal delivery and disulfide bond promoting activity of SOD1s cellular chaperone, the  copper chaperone for SOD1 (CCS). We find that polytherapy using CuATSM and ebselen is highly effective at reducing inclusion formation in a cell model of SOD1 aggregation, reduces mutant SOD1-associated cell death, and promotes effective maturation of SOD1 beyond either compound alone. Our data suggest that a polytherapy of CuATSM and ebselen may be an effective method of treating SOD1-associated ALS.


title: Hydrophobic-cationic peptides enhance RNA polymerase ribozyme activity by accretion

abstract: Accretion and the resulting increase in local concentration to enhance target stability and function is a widespread mechanism in biology (for example in the liquid-liquid demixing phases and coacervates). It is widely believed that such macromolecular aggregates (formed through ionic and hydrophobic interactions) may have played a role in the origin of life. Here, we report on the behaviour of a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) that forms insoluble aggregates, accrete RNA on their surfaces in a size-dependent manner, and thus enhance the activities of various ribozymes. At low Mg2+ concentrations ([Mg2+]: 25 mM MgCl2), the activity of a small ribozyme (hammerhead ribozyme) was enhanced by P43, while larger ribozymes (RNA polymerase ribozyme (RPR), RNase P, F1* ligase) were inhibited. In contrast, at high [Mg2+] ([≥]200 mM), the RPR activity was enhanced. Another hydrophobic-cationic peptide with a simpler sequence (K2V6: KKVVVVVV) also exhibited similar regulatory effects on the RPR activity. Furthermore, inactive RPR captured on P43 aggregates at low [Mg2+] could be reactivated in a high [Mg2+] buffer. Therefore, in marked contrast to previously studied purely cationic peptides (like K10) that enhance RPR only at low ionic strength, hydrophobic-cationic peptides can reversibly concentrate RNA and enhance the RPR activity even at high ionic strength conditions such as in eutectic ice phases. Such peptides could have aided the emergence of longer and functional RNAs in a fluctuating environment (e.g., dry-wet / freeze-thaw cycles) on the prebiotic earth.


title: Acidogenic Fermentation of Sugarcane Vinasse and Glucose Using Two Different Anaerobic Digestion Inocula

abstract: Vinasse is an agroindustrial wastewater obtained at large amounts in countries such as Brazil, which is one of the world greatest sugar and ethanol producers from sugarcane. Despite its most common use is as nutrient for fertirrigation in sugarcane crops nowadays, alternative processing has been intensely sought in last decades for vinasse aiming primarily the production of energy carriers and high-added value chemicals. One of these alternatives is the anaerobic digestion promoted by bacteria, which results in several products of economic importance. In view of these information, this work presents an investigation of acidogenic fermentation by C. acetobutylicum ATCC 824 and C. beijerinckii ATCC 25752 was conducted in batch reactors by using synthetic vinasse and aqueous glucose solution as substrates. Evaluation of effects of microorganism and carbon source was focused mainly on the production of short chain organic acids (SCOAs), although other metabolites, such as ethanol, were also detected. Carbohydrates were effectively consumed by bacteria, so remaining concentrations of sucrose and glucose (Suc and Glu) in both substrates were considerably low at the end of tests. Lactic acid (HLa) was the prevailing metabolite in all experiments, determining the trends observed for total SCOAs content as a function of incubation time, while other acids were generated in much lesser amounts. Moreover, ethanol (EtOH) attained notably higher concentrations in batch reactors containing glucose as substrate, which showed more relevant production of this chemical. Maximum of 14.1 g HLa L-1 was quantified for lactic acid at incubation time 96 h in reactor using synthetic vinasse and C. beijerinckii (VB), linked to a productivity P = 146.46 mg HLa L-1 h-1 and a yield Y = 1108.03 mg HLa (g Sue)-1. For ethanol, maximum was 1.6 g EtOH L-1, occurring in reactor containing glucose and C. acetobutylicum (GA) also at incubation time 90 h, resulting in P = 13.60 mg EtOH L-1 h-1 and Y = 73.04 mg EtOH (g Glu)-1. Finally, kinetic models were adjusted to experimental data of carbohydrate content, lactate concentration and optical density (indicative of microorganism growth), showing good prediction capability as suggested by values of fit quality parameters such as Residual Sum of Squares (RSS) and R2.


title: Visualizing multi-protein patterns at the synapse of neuronal tissue with DNA-assisted single-molecule localization microscopy

abstract: The development of super-resolution microscopy (SRM) has widened our understanding of biomolecular structure and function in biological materials. Imaging multiple targets within a single area would elucidate their spatial localization relative to the cell matrix and neighboring biomolecules, revealing multi-protein macromolecular structures and their functional co-dependencies. SRM methods are, however, limited to the number of suitable fluorophores that can be imaged during a single acquisition as well as the loss of antigens during antibody washing and restaining for organic dye multiplexing. We report the visualization of multiple protein targets within the pre- and postsynapse in 350-400 nm thick neuronal tissue sections using DNA-assisted single-molecule localization microscopy. Using antibodies labeled with short DNA oligonucleotides, multiple targets are visualized successively by sequential exchange of fluorophore-labeled complementary oligonucleotides present in the imaging buffer. The structural integrity of the tissue is maintained owing to only a single labelling step during sample preparation. Multiple targets are imaged using a single laser wavelength, minimizing chromatic aberration. This method proved robust for multi-target imaging in semi-thin tissue sections, paving the way towards structural cell biology with single-molecule super-resolution microscopy.


title: macroH2A2 shapes chromatin accessibility at enhancer elements in glioblastoma to modulate a targetable self-renewal epigenetic network

abstract:
Self-renewal is a crucial property of glioblastoma cells and is enabled by the choreographed function of chromatin regulators and transcription factors. Identifying targetable epigenetic mechanisms of self-renewal could represent an important step toward developing new and effective treatments for this universally lethal cancer. Here we uncover a targetable epigenetic axis of self-renewal mediated by the histone variant macroH2A2. Using patient-derived in vitro and in vivo models, we show that macroH2A2 has a direct role in shaping chromatin accessibility at enhancer elements to antagonize transcriptional programs of self-renewal. Pharmaceutical inhibition of the chromatin remodeler Menin increased macroH2A2 levels and repressed self- renewal. Our results reveal a targetable epigenetic mechanism of self-renewal controlled by macroH2A2 and suggest new treatment approaches for glioblastoma patients.

SIGNIFICANCEGlioblastoma is an incurable brain cancer. Malignant self-renewing cells have been shown to drive tumor growth, to be refractory to current treatment approaches and to seed relapses, which ultimately prove lethal. Identifying new and targetable mechanisms associated with self-renewal could be a fundamental first step in designing effective therapies that slow or prevent glioblastoma relapses. Using patient-derived models of glioblastoma, we deployed epigenomic approaches and functional assays to define the role of the histone variant macroH2A2 in repressing self-renewal. We identified compounds that increase macroH2A2 levels and repress self-renewal, including a Menin inhibitor. As Menin inhibitors are being tested in clinical trials, these compounds could be used in new therapeutic paradigms to target self-renewing cell populations in glioblastoma.

category: cancer biology


title: Systems approaches identify the consequences ofmonosomy in somatic human cells

abstract: Chromosome loss that results in monosomy is detrimental to viability, yet, it is frequently observed in cancers. How cancers survive with monosomy is unknown. Using p53 deficient monosomic cell lines, we found that chromosome loss impairs proliferation and genomic stability. Transcriptome and proteome analysis revealed a partial compensation of the gene dosage changes that mitigates the effects of chromosome loss. Monosomy triggers global gene expression changes that differ from the effects of trisomy. We show that ribosome biogenesis and translation were commonly downregulated in monosomic cells, likely due to haploinsufficiency of ribosomal genes. The ensuing ribosome biogenesis stress triggers the p53 pathway and G1 arrest when TP53 is reintroduced into monosomic cells. Accordingly, impaired ribosome biogenesis and p53 inactivation are associated with monosomy in cancer. Our first systematic study of monosomy in human cells explains why monosomy is so detrimental and how loss of p53 enables its incidence in cancer.

category: systems biology


title: A preliminary assessment of allostatic load in male mantled howler monkeys

abstract: Allostatic load refers to the wear and tear of the organism associated with the repeated activation of mechanisms that allow for homeostasis. Although allostasis (i.e., maintaining stability through change) is achieved through the orchestration of multiple systems, assessments of allostatic load in wildlife have usually relied on the measurement of single or few physiological mediators. In the present study, we aimed at constructing an allostatic load index (ALI) for male mantled howler monkeys (Alouatta palliata) based on seven physiological mediators (C-peptide, triiodothyronine, glucocorticoids, testosterone, amount of activity, foraging effort, and participation in agonistic interactions). We then examined if variation in this ALI was associated with social, ecological, and abiotic challenges. For five years, we studied ten adult males belonging to two groups. We assessed physiological mediators via behavioral observations (3,364 hours of samplings), and both urine (1,500 assayed samples) and fecal (1,500 assayed samples) sampling. We calculated an ALI based on mediator specific risk scores. Seasonality, encounters with extragroup males, mating, and centrality were positively related with male allostatic load, though only the first two had significant effects on ALI. ALI reflected the physiological and behavioral responses of males to social, ecological, and abiotic challenges. It remains for future research to determine if the observed trends correspond to normal fluctuations in mechanisms that allow male mantled howler monkeys to cope with their environment.


title: Broad influence of mutant ataxin-3 on the proteome of the adult brain, young neurons, and axons reveals central molecular processes and biomarkers in SCA3/MJD using knock-in mouse model

abstract: Spinocerebellar ataxia type 3 (SCA3/MJD) has a polyQ etiology but, the current knowledge on molecular processes and proteins involved in pathogenesis is not sufficient to fully determine the disease mechanism and find drug targets. Proteases and deubiquitinases, such as Ataxin-3, often have a profound impact on other proteins, yet the global model picture of SCA3 disease progression on the protein level, showing the most crucial proteins and pathways in the brain, and neurons, was not investigated previously. Here, we investigated molecular SCA3 mechanism using interdisciplinary research paradigm combining SCA3 knock-in model, behavior, MRI, brain proteomics, precise axonal proteomics, neuronal energy recordings, labeling of vesicles, and inclusions and focusing in axonal compartment. We have demonstrated that altered metabolic and mitochondrial proteins in the brain and the lack of weight gain in Ki91 SCA3/MJD mice is reflected by the failure of energy metabolism recorded in neonatal SCA3 cerebellar neurons. We have determined that further, during disease progression, proteins responsible for metabolism, cytoskeletal architecture, vesicular and axonal transport proteins are disturbed, revealing axons as one of the essential cell compartments in SCA3 pathogenesis. Therefore we focus on SCA3 pathogenesis in axonal and somatodendritic compartments revealing highly increased axonal localization of protein synthesis machinery, including ribosomes, translation factors, and RNA binding proteins, while the level of proteins responsible for cellular transport, and mitochondria was decreased. We demonstrate the accumulation of axonal vesicles in neonatal SCA3 cerebellar neurons and increased phosphorylation of SMI-312 positive adult cerebellar axons, which indicate axonal dysfunction in SCA3. In summary, the SCA3 disease mechanism is based on the broad influence of mutant ataxin-3 on the neuronal proteome. Processes central in our SCA3 model include disturbed localization of proteins between axonal and somatodendritic compartment, early neuronal energy deficit, altered neuronal cytoskeletal structure, an overabundance of protein synthetic machinery in axons.


title: Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription

abstract: Co-activator complexes dynamically deposit post-translational modifications (PTMs) on histones, or remove them, to regulate chromatin accessibility and/or to create/erase docking surfaces for proteins that recognize histone PTMs. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The deubiquitylation module (DUB) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and three adaptor proteins, ATXN7, ATXN7L3 and ENY2, which are all needed for the full activity of the USP22 enzyme to remove monoubiquitin (ub1) from histone H2B. Two additional USP22-related ubiquitin hydrolases (called USP27X or USP51) have been described to form alternative DUBs with ATXN7L3 and ENY2, which can also deubiquitylate H2Bub1. Here we report that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process, as Atxn7l3-/- embryos show developmental delay already at embryonic day (E) 7.5, while Usp22-/- embryos are normal at this stage, but die at E14.5. Global histone H2Bub1 levels were only slightly affected in Usp22 null embryos, in contrast H2Bub1 levels were strongly increased in Atxn7l3 null embryos and derived cell lines. Our transcriptomic analyses carried out from wild type and Atxn7l3-/- mouse embryonic stem cells (mESCs), or primary mouse embryonic fibroblasts (MEFs) suggest that the ATXN7L3-related DUB activity regulates only a subset of genes in both cell types. However, the gene sets and the extent of their deregulation were different in mESCs and MEFs. Interestingly, the strong increase of H2Bub1 levels observed in the Atxn7l3-/- mESCs, or Atxn7l3-/- MEFs, does not correlate with the modest changes in RNA Polymerase II (Pol II) occupancy and lack of changes in Pol II elongation observed in the two Atxn7l3-/- cellular systems. These observations together indicate that deubiquitylation of histone H2Bub1 does not directly regulate global Pol II transcription elongation.

category: molecular biology


title: Human basigin (CD147) does not directly interact with SARS-CoV-2 spike glycoprotein

abstract:
Basigin, or CD147, has been reported as a co-receptor used by SARS-CoV-2 to invade host cells. Basigin also has a well-established role in Plasmodium falciparum malaria infection of human erythrocytes where it is bound by one of the parasites invasion ligands, reticulocyte binding protein homolog 5 (RH5). Here, we sought to validate the claim that the receptor binding domain (RBD) of SARS-CoV-2 spike glycoprotein can form a complex with basigin, using RH5-basigin as a positive control. Using recombinantly expressed proteins, size exclusion chromatography and surface plasmon resonance, we show that neither RBD nor full-length spike glycoprotein bind to recombinant human basigin (either expressed in E. coli or mammalian cells). Given the immense interest in SARS-CoV-2 therapeutic targets, we would caution the inclusion of basigin in this list on the basis of its reported direct interaction with SARS-CoV-2 spike glycoprotein.

ImportanceReducing the mortality and morbidity associated with COVID-19 remains a global health priority. Critical to these efforts is the identification of host factors that are essential to viral entry and replication. Basigin, or CD147, was previously identified as a possible therapeutic target based on the observation that it may act as a co-receptor for SARS-COV-2, binding to the receptor binding domain of the spike protein. Here, we show that there is no direct interaction between the RBD and basigin, casting doubt on its role as a co-receptor and plausibility as a therapeutic target.


title: SARS-CoV-2 causes brain inflammation and induces Lewy body formation in macaques

abstract:
SARS-CoV-2 may cause acute respiratory disease, but the infection can also initiate neurological symptoms. Here we show that SARS-CoV-2 infection causes brain inflammation in the macaque model. An increased metabolic activity in the pituitary gland of two macaques was observed by longitudinal positron emission tomography-computed tomography (PET-CT). Post-mortem analysis demonstrated infiltration of T-cells and activated microglia in the brain, and viral RNA was detected in brain tissues from one animal. We observed Lewy bodies in brains of all rhesus macaques. These data emphasize the virus capability to induce neuropathology in this nonhuman primate model for SARS-CoV-2 infection. As in humans, Lewy body formation is an indication for the development of Parkinsons disease, this data represents a warning for potential long-term neurological effects after SARS-CoV-2 infection.

TeaserSARS-CoV-2 causes brain inflammation and Lewy bodies, a hallmark for Parkinson, after an asymptomatic infection in macaques.


title: Increased complement activation is a distinctive feature of severe SARS-CoV-2 infection.

abstract:
Complement activation has been implicated in the pathogenesis of severe SARS-CoV-2 infection. However, it remains to be determined whether increased complement activation is a broad indicator of critical illness (and thus, no different in COVID-19). It is also unclear which pathways are contributing to complement activation in COVID-19, and, if complement activation is associated with certain features of severe SARS-CoV-2 infection, such as endothelial injury and hypercoagulability. To address these questions, we investigated complement activation in the plasma from patients with COVID-19 prospectively enrolled at two tertiary care centers. We compared our patients to two non-COVID cohorts: (a) patients hospitalized with influenza, and (b) patients admitted to the intensive care unit (ICU) with acute respiratory failure requiring invasive mechanical ventilation (IMV). We demonstrate that circulating markers of complement activation (i.e., sC5b-9) are elevated in patients with COVID-19 compared to those with influenza and to patients with non-COVID-19 respiratory failure. Further, the results facilitate distinguishing those who are at higher risk of worse outcomes such as requiring ICU admission, or IMV. Moreover, the results indicate enhanced activation of the alternative complement pathway is most prevalent in patients with severe COVID-19 and is associated with markers of endothelial injury (i.e., Ang2) as well as hypercoagulability (i.e., thrombomodulin and von Willebrand factor). Our findings identify complement activation to be a distinctive feature of COVID-19, and provide specific targets that may be utilized for risk prognostication, drug discovery and personalized clinical trials.

SUMMMARYComplement has been implicated in COVID-19. However, whether this is distinctive of COVID-19 remains unanswered. Ma et al report increased complement activation in COVID-19 compared to influenza and non-COVID respiratory failure, and demonstrate alternative pathway activation as a key marker of multiorgan failure and death.

category: immunology


title: At the Intersection Between SARS-CoV-2, Macrophages and the Adaptive Immune Response: A Key Role for Antibody-Dependent Pathogenesis But Not Enhancement of Infection in COVID-19

abstract:
Since entering the world stage in December of 2019, SARS-CoV-2 has impacted every corner of the globe with over 1.48 million deaths and caused untold economic damage. Infections in humans range from asymptomatic to severe disease associated with dysregulation of the immune system leading to the development of acute respiratory distress syndrome (ARDs).

The distinct shift in peripheral monocyte activation and infiltration of these cells into the respiratory tract in ARDs patients suggests severe COVID-19 may largely result from damage to the respiratory epithelia by improperly activated macrophages. Here, we present evidence that dysregulation of the immune response in COVID-19 begins with activation of macrophages by non-neutralizing antibodies and induction of ACE2 expression, rendering these cells susceptible to killing by SARS-CoV-2. Death of macrophages occurs independently of viral replication and leads to the release of inflammatory mediators and modulation of the susceptibility of downstream epithelial cells to SARS-CoV-2.


title: A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem inflammatory syndrome in children (MIS-C) with severe myocarditis

abstract: SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often including myocarditis. To better understand these cases, we applied a multi-parametric approach to the study of blood cells of 56 children hospitalized with suspicion of SARS-CoV-2 infection. The most severe forms of MIS-C (multisystem inflammatory syndrome in children related to SARS-CoV-2), that resulted in myocarditis, were characterized by elevated levels of pro-angiogenesis cytokines and several chemokines. Single-cell transcriptomic analyses identified a unique monocyte/dendritic cell gene signature that correlated with the occurrence of severe myocarditis, characterized by sustained NF-{kappa}B activity, TNF- signaling, associated with decreased gene expression of NF-{kappa}B inhibitors. We also found a weak response to type-I and type-II interferons, hyperinflammation and response to oxidative stress related to increased HIF-1 and VEGF signaling. These results provide potential for a better understanding of disease pathophysiology.


title: Chromatin reader Dido3 regulates the genetic network of B cell differentiation

abstract: The development of hematopoietic lineages is based on a complex balance of transcription factors whose expression depends on the epigenetic signatures that characterize each differentiation step. The B cell lineage arises from hematopoietic stem cells through the stepwise silencing of stemness genes and balanced expression of mutually regulated transcription factors, as well as DNA rearrangement. Here we report the impact on B cell differentiation of the lack of DIDO3, a reader of chromatin status, in the mouse hematopoietic compartment. We found reduced DNA accessibility in hematopoietic precursors, leading to severe deficiency in the generation of successive B cell differentiation stages. The expression of essential transcription factors and differentiation markers is affected, as is the somatic recombination process.


title: Adult zebrafish anaesthesia: a study of efficacy and behavioural recovery of different anaesthetics

abstract:
The use of proper anaesthesia in zebrafish research is essential to ensure fish welfare and data reliability. However, anaesthesia long-term side effects remain poorly understood. The purpose of this study was to assess anaesthesia quality and recovery in adult zebrafish using different anaesthetic protocols and to determine possible long-term effects on the fish activity and anxiety-like behaviours after anaesthesia.

Mixed sex adult AB zebrafish were randomly assigned to 5 different groups (control, 175mg/L MS222, 45 mg/L clove oil, 2 mg/L etomidate and 5mg/L propofol combined with 150mg/L lidocaine) and placed in the respective anaesthetic bath. Time to lose the equilibrium, response to touch and to tail pinch stimuli, and recovery after anaesthesia administration were evaluated. In addition, after stopping anaesthesia, respiratory rate, activity and anxiety-like behaviours in the novel tank test were studied.

Overall, all protocols proved to be adequate for zebrafish anaesthesia research as they showed full recovery at 1h, and only etomidate had minor effects on fish behaviour in the novel tank, a validated test for anxiety.


title: Structural and functional characterization of SARS-CoV-2 RBD domains produced in mammalian cells

abstract: As the SARS-CoV-2 pandemic is still ongoing and dramatically influences our life, the need for recombinant proteins for diagnostics, vaccine development, and research is very high. The spike (S) protein, and particularly its receptor binding domain (RBD), mediates the interaction with the ACE2 receptor on host cells and may be modulated by its structural features. Therefore, well characterized recombinant RBDs are essential. We have performed an in-depth structural and functional characterization of RBDs expressed in Chinese hamster ovary (CHO) and human embryonic kidney (HEK293) cells. To structurally characterize the native RBDs (comprising N- and O-glycans and additional posttranslational modifications) a multilevel mass spectrometric approach was employed. Released glycan and glycopeptide analysis were integrated with intact mass analysis, glycan-enzymatic dissection and top-down sequencing for comprehensive annotation of RBD proteoforms. The data showed distinct glycosylation for CHO- and HEK293-RBD with the latter exhibiting antenna fucosylation, higher level of sialylation and a combination of core 1 and core 2 type O-glycans. Additionally, from both putative O-glycosylation sites, we could confirm that O-glycosylation was exclusively present at T323, which was previously unknown. For both RBDs, the binding to SARS-CoV-2 antibodies of positive patients and affinity to ACE2 receptor was addressed showing comparable results. This work not only offers insights into RBD structural and functional features but also provides a workflow for characterization of new RBDs and batch-to-batch comparison.


title: Mass cytometry reveals immunological response to radiation-induced cardiac fibrosis in mice

abstract:
BackgroundRadiation-induced cardiac injury results in complex clinical presentations, unique management issues, and increased morbidity and mortality. But the underlying mechanism of radiation-induced cardiac injury is still unclear. The aim of this study is to explain the compositional alterations of innate and adaptive cells after thoracic irradiation and the relationship of macrophage with other adaptive cells.

MethodsC57BL/6 mice were anesthetized and performed with 20Gy single dose cardiac irradiation. We carried out mice echocardiography to examine cardiac function. Masson and immunohistochemical staining were adopted to analyze cardiac fibrosis. Blood and cardiac tissue were collected 7 days, 4 weeks and 8 weeks after irradiation and sham-irradiated mice were set as a control group. Part of blood and tissue samples were analyzed with mass cytometry. We also used remaining blood samples to measure pro-fibrotic cytokines.

ResultsWe observed reduced cardiac diastolic function and pathologically confirmed cardiac fibrosis after thoracic irradiation. Through mass cytometry, we identified that the proportion of neutrophils, macrophages and monocytes elevated. The ratio of T and B cells decreased after irradiation in the blood samples. For tissue samples, the proportion of macrophages, monocytes and neutrophils increased, endothelial cells reduced, but T and B cells also increased. The level of TGF-{beta}, TNF-, IL-6 climbed considerably, all of them are closely associated with the evolution of macrophage function during recovering phase of cardiac injury. In the correlation plot, we also discovered that CD4+T and CD8+T cells were strongly positively correlated with macrophages.

ConclusionWe illustrated the immunological response after radiation-induced cardiac fibrosis, and macrophage may play a crucial role during the process. The results might have therapeutic potential for targeting macrophages in order to reduce radiation-induced cardiac fibrosis.


title: A new two-generation approach to the population dynamics of gregarious parasitoids

abstract: Parasitoids, as important natural enemies, help maintain balance in natural ecosystems. Their population dynamics is generally predicted from the number of individuals. Here, using gregarious parasitoids as models, we show that this traditional approach omits one important parameter: the mothers manipulation of offspring fertility due to the clutch size-body size- fertility correlation. As a result of this correlation, when females deliberately adjust the number of offspring laid in a host, they determine not only the number but also the body sizes and reproductive potentials of those offspring. For the first time in the model species Anaphes flavipes, we determined the parasitoids offspring fertility from clutch size. Using this, we experimentally clarified the advantage of specific clutch size combinations and we show that identical fertility in the F1 generation can lead to distinctly different fertility values in the F2 generation. Even with the same number of hosts, lower fertility in the F1 generation can cause higher fertility in the F2 generation. Based on these results, we propose a novel two-generation approach which includes the clutch size-body size-fertility correlation. Our novel approach provides a new perspective for determining the individual fitness levels of gregarious parasitoids with new options for the modelling of parasitoid population dynamics.


title: A novel two-generation approach to the population dynamics of gregarious parasitoids


title: Resting-state theta oscillations and reward sensitivity in risk taking

abstract: Females demonstrate greater risk aversion than males on a variety of tasks, but the underlying neurobiological basis is still unclear. We studied how theta (4-7 Hz) oscillations at rest related to three different measures of risk taking. Thirty-five participants (15 females) completed the Bomb Risk Elicitation Task (BRET), which allowed us to measure risk taking during an economic game. The Domain-Specific Risk-Taking Scale (DOSPERT) was used to measure self-assessed risk attitudes as well as reward and punishment sensitivities. In addition, the Barratt Impulsiveness Scale (BIS11) was included to quantify impulsiveness. To obtain measures of frontal theta asymmetry and frontal theta power, we used magnetoencephalography (MEG) acquired prior to task completion, while participants were at rest. Frontal theta asymmetry correlated with average risk taking during the game but only in the female sample. By contrast, frontal theta power correlated with risk taking as well as with measures of reward and punishment sensitivity in the joint sample. Importantly, we showed that reward sensitivity mediated a correlation between risk taking and the power of theta oscillations localized to the anterior cingulate cortex. In addition, we observed significant sex differences in source- and sensor-space theta power, risk taking during the game, and reward sensitivity. Our findings suggest that sensitivity to rewards, associated with resting-state theta oscillations in the anterior cingulate cortex, is a trait that potentially contributes to sex differences in risk taking.