title: ProxLogs: Miniaturised proximity loggers for monitoring association behaviour in small mammals

abstract:
O_LIThe ability to monitor associations between wild animals is essential for understanding the processes governing gene transfer, information transfer, competition, predation and disease transmission.
C_LIO_LIUntil recently, such insights have been confined to large, visible or captive animals. However, the rapid development of miniature sensors for consumer electronics is allowing ecologists to monitor the natural world in ways previously considered impossible.
C_LIO_LIHere we describe miniature (<1g) proximity loggers we have developed that use Bluetooth Low Energy transmission to register contacts between individuals. Our loggers are open source, low cost, rechargeable, able to store up to 2000 contacts, can be programmed in situ and can download data remotely or through a mobile phone application, increasing their utility in remote areas or with species which are challenging to recapture.
C_LIO_LIWe successfully trialled our loggers in a range of field realistic conditions, demonstrating that Bluetooth Low Energy is capable of logging associations in structurally complex habitats, and that changes in received signal strength can be equated to short range changes in distance between loggers. Furthermore, we tested the system on starlings (Sturnidae vulgaris).
C_LIO_LIThe ability to include other sensors is retained in our prototypes, allowing for the potential integration of physiological and behavioural inference into social networks derived from our approach. Due to its open source nature, small size, flexibility of use and the active research currently being undertaken with Bluetooth Low Energy, we believe that our approach is a valuable addition to the biologging toolkit.
C_LI


title: Small Directional Treadmill Perturbations Induce Differential Gait Stability Adaptation

abstract:
Introducing unexpected perturbations to challenge gait stability is an effective approach to investigate balance control strategies. Little is known about the extent to which people can respond to small perturbations during walking. This study aimed to determine how subjects adapted gait stability to multidirectional perturbations with small magnitudes applied on a stride-by-stride basis. Ten healthy young subjects walked on a treadmill that either briefly decelerated belt speed ("stick"), accelerated belt speed ("slip"), or shifted the platform medial-laterally at right leg mid-stance. We quantified gait stability adaptation in both anterior-posterior and medial-lateral directions using margin of stability and its components, base of support and extrapolated center of mass. Gait stability was disrupted upon initially experiencing the small perturbations as margin of stability decreased in the stick, slip, and medial shift perturbations and increased in the lateral shift perturbation. Gait stability metrics were generally disrupted more for perturbations in the coincident direction. Subjects employed both feedback and feedforward strategies in response to the small perturbations, but mostly use feedback strategies during adaptation. Subjects primarily used base of support (foot placement) control in the lateral shift perturbation and extrapolated center of mass control in the slip and medial shift perturbations. These findings provide new knowledge about the extent of gait stability adaptation to small magnitude perturbations applied on a stride-by-stride basis and reveal potential new approaches for balance training interventions to target foot placement and center of mass control.

NEW & NOTEWORTHYLittle is known about if and how humans can adapt to small magnitude perturbations experienced on a stride-by-stride basis during walking. Here, we show that even small perturbations disrupted gait stability and that subjects could still adapt their reactive balance control. Depending on the perturbation direction, subjects might prefer adjusting their foot placement over their center of mass and vice versa. These findings could help potentially tune balance training to target specific aspects of balance.

category: bioengineering


title: ksrates: positioning whole-genome duplications relative to speciation events using rate-adjusted mixed paralog-ortholog KS distributions

abstract:
SummaryWe present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication (WGD) events with respect to speciation events in a phylogeny by comparing paralog and ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved.

Availability and implementationksrates is implemented in Python 3 and as a Nextflow pipeline. The source code, Singularity and Docker containers, documentation and tutorial are available via https://github.com/VIB-PSB/ksrates.

Contactsteven.maere@ugent.vib.be, rolf.lohaus@ugent.vib.be

category: bioinformatics


title: ksrates: positioning whole-genome duplications relative to speciation events in KS distributions


title: Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata

abstract:
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.

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title: The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata


title: Are adaptive chemotherapy schedules robust? A three-strategy stochastic evolutionary game theory model

abstract:
We investigate the robustness of adaptive chemotherapy schedules over repeated cycles and a wide range of tumor sizes. We introduce a non-stationary stochastic three-component fitness-dependent Moran process to quantify the variance of the response to treatment associated with multidrug adaptive schedules that are designed to mitigate chemotherapeutic resistance in an idealized (well-mixed) setting. The finite cell (N tumor cells) stochastic process consists of populations of chemosensitive cells, chemoresistant cells to drug 1, and chemoresistant cells to drug 2, and the drug interactions can be synergistic, additive, or antagonistic. First, the adaptive chemoschedule is determined by using the N [->] {infty} limit of the finite-cell process (i.e. the adjusted replicator equations) which is constructed by finding closed treatment response loops (which we call evolutionary cycles) in the three component phase-space. The schedules that give rise to these cycles are designed to manage chemoresistance by avoiding competitive release of the resistant cell populations. To address the question of how these cycles are likely to perform in practice over large patient populations with tumors across a range of sizes, we then consider the statistical variances associated with the approximate stochastic cycles for finite N, repeating the idealized adaptive schedule over multiple periods. For finite cell populations, the error distributions remain approximately multi-Gaussian in the principal component coordinates through the first three cycles, with variances increasing exponentially with each cycle. As the number of cycles increases, the multi-Gaussian nature of the distribution breaks down due to the fact that one of the three subpopulations typically saturates the tumor (competitive release) resulting in treatment failure. This suggests that to design an effective and repeatable adaptive chemoschedule in practice will require a highly accurate tumor model and accurate measurements of the subpopulation frequencies or the errors will quickly (exponentially) degrade its effectiveness, particularly when the drug interactions are synergistic. Possible ways to extend the efficacy of the stochastic cycles in light of the computational simulations are discussed.

Prepared for Special IssueUnderstanding the Evolutionary Dynamics and Ecology of Cancer Treatment Resistance, Ed. D. Basanta, Cancers (2021)

category: biophysics


title: RHAMMB-mediated bifunctional nanotherapy targeting Bcl-xL and mitochondria for pancreatic neuroendocrine tumor treatment

abstract: The incidence of pancreatic neuroendocrine tumor (PNET) has continued to rise. Due to their indolent feature, PNET patients often present with incurable, metastatic diseases. Novel therapies are urgently needed. We have previously shown that Receptor for Hyaluronic Acid-Mediated Motility isoform B (RHAMMB) and Bcl-xL are upregulated in PNETs and both of them promote PNET metastasis. Because RHAMM protein is undetectable in most adult tissues, we hypothesized that RHAMMB could be a gateway for nanomedicine delivery into PNETs. To test this, we developed RHAMMB-targeting nanoparticle. Inside this nanoparticle, we assembled siRNA against Bcl-xL (siBcl-xL) and mitochondria-fusing peptide KLA. We demonstratsed that RHAMMB-positive PNETs picked up the RHAMMB-targeting nanoparticles. siBcl-xL or KLA alone only killed 30% of PNET cells. In contrast, a synergistic killing effect was achieved with the co-delivery of siBcl-xL and KLA peptide in vitro. Unexpectedly, siBcl-xL induced cell death before reducing Bcl-xL protein levels. The systemically-injected RHAMMB-targeting nanoparticles carrying siBcl-xL and KLA peptide significantly reduced tumor burden in mice bearing RHAMMB-positive PNETs. Together, these findings indicate that the RHAMMB-targeting nanotherapy serves as a promising drug delivery system for PNET and possibly other malignancies upregulating RHAMMB. The combination of siBcl-xL and KLA peptide can be a therapy for PNET treatment.

category: cancer biology


title: Dual Drug Targeting to Kill Colon Cancer Cells

abstract: Colorectal cancer (CRC) is driven by a small set of oncogenic and tumor suppressor mutations. However, different combinations of mutations often lead to poor tumor responses to individual anti-cancer drugs. We have investigated the anti-proliferative and in vitro cytotoxic activity of pair-wise combinations of inhibitors which target specific signalling pathways. Colon cancer cells in non-adherent cultures were killed more effectively by combinations of pyrvinium pamoate (a Wnt pathway inhibitor) and ABT263 (a pro-apoptotic Bcl-2 family inhibitor) or Ly29004 (a PI3kinase inhibitor). However, in a mouse xenograft model, the formulation and toxicity of the ABT737/PP combination prevent the use of these drugs for treatment of tumors. Fortunately, oral analogues of PP (pyrvinium phosphate, PPh) and ABT737(ABT263) have equivalent activity and can be used for treatment of mice carrying SW620 colorectal cancer xenografts. The PPh/ABT263 induced SW620 tumor cell apoptosis and reduced the rate of SW620 tumor growth. Combinations of Wnt signaling inhibitors and specific inhibitor of pro-survival proteins should be considered for the treatment of precancerous colon adenomas and advanced colorectal cancers with APC mutations.


title: Intravital imaging of real-time endogenous actin dysregulation in proximal and distal tubules at the onset of severe ischemia-reperfusion injury

abstract: Severe renal ischemia-reperfusion injury (IRI) can lead to acute and chronic kidney dysfunction. Cytoskeletal modifications are among the main effects of this condition. The majority of studies that have contributed to the current understanding of IRI have relied on histological analyses using exogenous probes after the fact. Here we report the successful real-time visualization of actin cytoskeletal alterations in live proximal and distal tubules that arise at the onset of severe IRI. To achieve this, we induced fluorescent actin expression in these segments in rats with hydrodynamic gene delivery (HGD). Using intravital two-photon microscopy we then tracked and quantified endogenous actin dysregulation that occurred by subjecting these animals to 60 minutes of bilateral renal ischemia. Rapid (by 1-hour post-reperfusion) and significant (up to 50%) declines in actin content were observed. The decline in fluorescence within proximal tubules was significantly greater than that observed in distal tubules. Actin-based fluorescence was not recovered during the measurement period extending 24 hours post-reperfusion. Such injury decimated the renal architecture, in particular, actin brush borders, and hampered the reabsorptive and filtrative capacities of these tubular compartments. Thus, for the first time, we show that the combination of HGD and intravital microscopy can serve as an experimental tool to better understand how IRI modifies the cytoskeleton in vivo and provide an extension to current histopathological techniques.

category: physiology


title: Gibberellins target shoot-root growth, morpho-physiological and molecular pathways to induce cadmium tolerance in mung bean

abstract: Cadmium (Cd) inhibits plant growth, perturb nutrient uptake and affect chloroplast ultra structure. Cd soil pollution is mainly contributed by excessive use of phosphate fertilizers, nickel Cd batteries, plating and sewage sludge. Research investigations deciphering role of Cd in affecting overall performance of mung bean is least understood. Likewise ameliorative effects of gibberellins (GAs) in Cd induced toxicity in mung bean are lesser known. In this context, effects of Cd stress (CdCl2, IC50 -500 {micro}M L-1) with or without GA3 application on mung bean (Vigna radiata L. Var. SML-668) plants were comprehensively investigated under controlled conditions. In brief, a total of 80 mung bean plants (15 days old of uniform height) were divided into four groups, with each group (n=20) subjected to four different treatments (Control, CdCl2, GA3, CdCl2+GA3), twice during the entire life cycle of mung bean plants (until harvest 85-90 days). Results revealed negative impacts of Cd stress on shoot morphometry (plant height, leaf surface area, stem diameter, shoot fresh weight, number of leaves, number of pods, length and diameter of pods), root morphometry (root length, root surface area, root dry weight, nodule number and nodule diameter), photosynthetic pigments and agronomic traits. GA3 ameliorated Cd stress by modulating shoot and root growth rates, improving overall plant metabolism, photosynthetic pigments, and shoot and root morphometry and transcript abundance of VgPCS1, VgPCS2, VgCdR and VgIRT1. Current study proposes GA3 application for the effective management of Cd induced phytotoxicity in mung bean plants.

category: plant biology


title: Transfer learning framework for cell segmentationwith incorporation of geometric features

abstract: With recent advances in multiplexed imaging and spatial transcriptomic and proteomic technologies, cell segmentation is becoming a crucial step in biomedical image analysis. In recent years, Fully Convolutional Networks (FCN) have achieved great success in nuclei segmentation in in vitro imaging. Nevertheless, it remains challenging to perform similar tasks on in situ tissue images with more cluttered cells of diverse shapes. To address this issue, we propose a novel transfer learning, cell segmentation framework incorporating shape-aware features in a deep learning model, with multi-level watershed and morphological post-processing steps. Our results show that incorporation of geometric features improves generalizability to segmenting cells in in situ tissue images, using solely in vitro images as training data.

category: systems biology


title: Transfer learning framework for cell segmentation with incorporation of geometric features


title: GPRuler: metabolic Gene-Protein-Reaction rules automatic reconstruction

abstract:
BackgroundMetabolic network models are increasingly being used in health care and industry. As a consequence, many tools have been released to automate their reconstruction process de novo. In order to enable gene deletion simulations and integration of gene expression data, these networks must include gene-protein-reaction (GPR) rules, which describe with a Boolean logic relationships between the gene products (e.g., enzyme isoforms or subunits) associated with the catalysis of a given reaction. Nevertheless, the reconstruction of GPRs still remains a largely manual and time consuming process. Aiming at fully automating the reconstruction process of GPRs for any organism, we propose the open-source python-based framework GPRuler.

ResultsBy mining text and data from 9 different biological databases, GPRuler can reconstruct GPRs starting either from just the name of the target organism or from an existing metabolic model. The performance of the developed tool is evaluated at small-scale level for a manually curated metabolic model, and at genome-scale level for three metabolic models related to Homo sapiens and Saccharomyces cerevisiae organisms. By exploiting these models as benchmarks, the proposed tool shown its ability to reproduce the original GPR rules with a high level of accuracy. In all the tested scenarios, after a manual investigation of the mismatches between the rules proposed by GPRuler and the original ones, the proposed approach revealed to be in many cases more accurate than the original models.

ConclusionsBy complementing existing tools for metabolic network reconstruction with the possibility to reconstruct GPRs quickly and with a few resources, GPRuler paves the way to the study of context-specific metabolic networks, representing the active portion of the complete network in given conditions, for organisms of industrial or biomedical interest that have not been characterized metabolically yet.


title: Savings in human force field learning supported by feedback adaptation

abstract:
Savings have been described as the ability of healthy humans to relearn a previously acquired motor skill faster than the first time, which in the context of motor adaptation suggests that the learning rate in the brain could be adjusted when a perturbation is recognized. Alternatively, it has been argued that apparent savings were the consequence of a distinct process that instead of reflecting a change in the learning rate, revealed an explicit re-aiming strategy. Based on recent evidence that feedback adaptation may be central to both planning and control, we hypothesized that this component could genuinely accelerate relearning in human adaptation to force fields during reaching. Consistent with our hypothesis, we observed that upon re-exposure to a previously learned force field, the very first movement performed by healthy volunteers in the relearning context was better adapted to the external disturbance, and this occurred without any anticipation or cognitive strategy because the relearning session was started unexpectedly. We conclude that feedback adaptation is a medium by which the nervous system can genuinely accelerate learning across movements.

Significance StatementSavings describe the ability of healthy humans to faster relearn a previously acquired motor skill. It is debated whether savings result from implicit changes in the learning rate or an explicit strategy. Given recent evidence that feedback control plays a key role in movement adaptation, we hypothesized that this component also contributed to savings in the context of force field adaptation. We confirm that relearning was faster and demonstrate that the very first relearning movement was better adapted to the external disturbance, i.e., the online corrections in the first re-exposure trial carried imprints of feedback adaptation from the previous sessions in the absence of any explicit strategy. We conclude that this non-explicit feedback component can genuinely accelerate motor learning.

category: neuroscience


title: Brain Dynamics of Spatial Reference Frame Proclivity in Active Navigation

abstract: Recent research into navigation strategy of different spatial reference frame proclivities (RFPs) has revealed that the parietal cortex plays an important role in processing allocentric information to provide a translation function between egocentric and allocentric spatial reference frames. However, most studies merely focused on a passive experimental environment, which is not truly representative of our daily spatial learning/navigation tasks. This study investigated the factor associated with brain dynamics that causes people to switch their preferred spatial strategy in different environments in virtual reality (VR) based active navigation task to bridge the gap. High-resolution electroencephalography (EEG) signals were recorded to monitor spectral perturbations on transitions between egocentric and allocentric frames during a path integration task. Our brain dynamics results showed navigation involved areas including the parietal cortex with modulation in the alpha band, the occipital cortex with beta and low gamma band perturbations, and the frontal cortex with theta perturbation. Differences were found between two different turning-angle paths in the alpha band in parietal cluster event-related spectral perturbations (ERSPs). In small turning-angle paths, allocentric participants showed stronger alpha desynchronization than egocentric participants; in large turning-angle paths, participants for two reference frames had a smaller difference in the alpha frequency band. Behavior results of homing errors also corresponded to brain dynamic results, indicating that a larger angle path caused the allocentric to have a higher tendency to become egocentric navigators in the active navigation environment.


title: Selective attention and decision-making have separable neural bases in space and time

abstract: Attention and decision-making processes are fundamental to cognition. However, they are usually experimentally confounded, making it impossible to link neural observations to specific processes. Here we separated the effects of selective attention from the effects of decision-making in human observers using a two-stage task where the attended stimulus and decision were orthogonal and separated in time. Multivariate pattern analyses of multimodal neuroimaging data revealed the dynamics of perceptual and decision-related information coding through time (magnetoencephalography (MEG)), space (functional Magnetic Resonance Imaging (fMRI)), and their combination (MEG-fMRI fusion). Our MEG results showed an effect of attention before decision-making could begin, and fMRI results showed an attention effect in early visual and frontoparietal regions. Model-based MEG-fMRI fusion suggested that attention boosted stimulus information in frontoparietal and early visual regions before decision-making was possible. Together, our results suggest that attention affects neural stimulus representations in frontoparietal regions independent of decision-making.


title: A structural analysis of amyloid polymorphism in disease: clues for selective vulnerability?

abstract: The increasing amount of amyloid structures offers an opportunity to investigate the general principles determining amyloid stability and polymorphism in disease. We find that amyloid stability is dominated by about 30% of residues localized in few segments interspersed with regions that are often structurally frustrated in the cross-{beta} conformation. These stable segments correspond to known aggregation-nucleating regions and constitute a cross-{beta} structural framework that is shared among polymorphs. Alternative tertiary packing of these segments within the protofibril results in conformationally different but energetically similar polymorphs. This combination of a conserved structural framework along the axis and energetic ambiguity across the axis results in polymorphic plasticity that explains a number of fundamental amyloid properties, including fibril defects and brittleness but also the polymorphic instability of amyloids in simple aqueous buffers. Together these findings suggest a structural model for in vivo polymorphic bias and selective cellular vulnerability whereby (1) polymorphic bias is induced by particular templating interactions in susceptible cells, (2) once formed specific polymorphs are entropically primed to selectively bind similar targets in neighbouring cells, (3) conservation of polymorphic bias during pathological spreading implies the continued presence of similar templating interactions in successive susceptible cells and (4) absence of templating interactions relaxes polymorphic bias possibly allowing for the modification of cellular susceptibilities during disease progression by novel templating interactions.


title: VISUAL CORTICAL AREA MT IS REQUIRED FOR DEVELOPMENT OF THE DORSAL STREAM AND ASSOCIATED VISUOMOTOR BEHAVIOURS

abstract:
The middle temporal (MT) area of the extrastriate visual cortex has long been studied in adulthood for its distinctive physiological properties and function as a part of the dorsal stream, yet interestingly possesses a similar maturation profile as the primary visual cortex (V1). Here we examined whether an early-life lesion of MT altered the dorsal stream development and the behavioural precision of reaching to grasp sequences. We observed permanent changes in the anatomy of cortices associated with both reaching (PE and MIP) and grasping (AIP), as well as in reaching and grasping behaviours. In addition, we observed a significant impact on the anatomy of V1 and the direction sensitivity of V1 neurons in the lesion projection zone. These findings indicate that area MT is a crucial node for the development of the primate vision, impacting both V1 and areas in the dorsal visual pathway known to mediate visually guided manual behaviours.

TeaserThe early life loss of visual area MT leads to significant anatomical, physiological and behavioural changes.


title: Visual Cortical Area MT is Required For Development of the Dorsal Stream and Associated Visuomotor Behaviours


title: Beyond colour gamuts: Novel metrics for thereproduction of photoreceptor signals

abstract: Colour gamuts describe the chromaticity reproduction capabilities of a display, i.e. its ability to reproduce the relative cone excitations from real-world radiance spectra. While the cones dominate "canonical" visual function (i.e. perception of colour, space, and motion) under photopic light levels, they are not the only photoreceptors in the human retina. Rods and melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) also respond to light and contribute to both visual and non-visual light responses, including circadian rhythms, sleep-wake control, mood, pupil size, and alertness. Three-primary display technologies, with their focus on reproducing colour, are not designed to reproduce the rod and melanopsin excitations. Moreover, conventional display metrics used to characterize three-primary displays fail to describe the displays ability (or inability) to reproduce rod and melanopsin excitations, and thus do not capture the displays ability to reproduce the full human physiological response to light. In this paper, three novel physiologically relevant metrics are proposed for quantifying the reproduction and distortion of the photoreceptor signals by visual displays. A novel equal-luminance photoreceptor excitation diagram is proposed, extending the well-known MacLeod-Boynton chromaticity diagram, to allow visualizations of the five-dimensional photoreceptor signal space in a three-dimensional projection.


title: Synergistic positive feedback underlying seizure initiation

abstract:
Seizure onset is a critically important brain state transition that has proved very difficult to predict accurately from recordings of brain activity. Here we show that an intermittent, optogenetic, stimulation paradigm reveals a latent change in dendritic excitability that is tightly correlated to the onset of seizure activity. Our data show how the precipitous nature of the transition can be understood in terms of multiple, synergistic positive feedback mechanisms: raised intracellular Cl- and extracellular K+, coupled to a reduced threshold for dendritic plateau potentials, and which in turn leads to a switch to pyramidal burst firing. Notably, the stimulation paradigm also delays the evolving epileptic activity, meaning that not only can one monitor seizure risk safely, it may even have an additional anti-epileptic benefit.

One Sentence SummaryRapid transitions into seizures arise from mutually accelerating feedback loops, involving changes in dendritic excitability


title: A BCI-based vibrotactile neurofeedback training improves motor cortical excitability during motor imagery

abstract: In this study, we address the issue of whether vibrotactile feedback can enhance the motor cortex excitability translated into the plastic changes in local cortical areas during motor imagery (MI) BCI-based training. For this purpose, we focused on two of the most notable neurophysiological effects of MI - the event-related-desynchronization (ERD) level and the increase in cortical excitability assessed with navigated transcranial magnetic stimulation (nTMS). For TMS navigation, we used individual high-resolution 3D brain MRIs. Ten BCI-naive and healthy adults participated in this study. The MI (rest or left/right hand imagery using Graz-BCI paradigm) tasks were performed separately in the presence and absence of feedback. To investigate how much the presence/absence of vibrotactile feedback in MI BCI-based training could contribute to the sensorimotor cortical activations, we compared the MEPs amplitude during MI after training with and without feedback. In addition, the ERD levels during MI BCI-based training were investigated. Our findings provide evidence that applying vibrotactile feedback during MI training leads to (i) an enhancement of the desynchronization level of mu-rhythm EEG patterns over the contralateral motor cortex area corresponding to the MI of the non-dominant hand; (ii) an increase in motor cortical excitability in hand muscle representation corresponding to a muscle engaged by the MI.


title: Antibody response patterns to Helicobacter pylori infection in a rural Ugandan population cohort.

abstract:
BackgroundHelicobacter pylori (H. pylori) establishes life-long infection in humans in the absence of treatment and has been associated with a variety of gastrointestinal conditions including peptic ulcer and gastric cancer. Antibody responses to H. pylori antigens are found to be associated with disease risk, however, data from Africa are scarce.

MethodsTo assess the seroprevalence of H. pylori and characterise antibody response patterns, we measured serum IgG antibody levels to 14 antigens among 7,211 individuals in a rural Ugandan population cohort. Multivariate-adjusted linear regression models were fitted to investigate the influence of age, sex, and co-infection on antibody seroreactivity levels.

ResultsH. pylori seroprevalence was 95% in our study population, with 94% of individuals seropositive in childhood (<15 years). In H. pylori positive individuals, we found a markedly high seroprevalence (~99%) and antibody levels to the high-risk antigens CagA and VacA, in addition to Cag{delta}. HSV-2 co-infection was significantly associated with higher IgG levels of CagA and VacA (OR=1.10, 95% C. I=1.05-1.16). HIV infection was associated with lowered IgG levels to CagA (OR=0.86, 95% C.I.=0.80-0.93), and HPV infection was associated with increased IgG levels to VacA (OR=1.16, 95% C.I.=1.11-1.21).

ConclusionsH. pylori in this population is ubiquitous from childhood, with a high prevalence and high seroreactivity levels of high-risk antigens, suggesting chronic active inflammatory responses in individuals that are indicative of risk of disease. Further investigation is warranted to fully understand the relationship between host, immunogenicity, and clinical outcomes to better stratify by risk and improve treatment.

Key MessagesO_LIAntibody responses to H. pylori antigens are found to be associated with risk of gastric cancer, however, despite the high seroprevalence in African populations, data from Africa are scarce. This is the first study of antibody response patterns and their determinants from an African population.
C_LIO_LIOur study shows a population where H. pylori is ubiquitous from childhood, and seroprevalence of virulent antigens is distinctively high suggesting an increased of disease compared to other populations.
C_LIO_LIWe observe inter-individual variation in virulent antibody responses partly influenced by co-infection.
C_LIO_LIWe highlight crucial insights into antibody-based biomarkers of disease risk and reinforce the need for population-based H. pylori screening and treatment programmes for gastric cancer control.
C_LI

category: immunology


title: Infusion of CCR5 Gene-Edited T Cells Allows Immune Reconstitution, HIV Reservoir Decay, and Long-Term Virological Control

abstract: Antiretroviral therapy (ART) fails to fully restore immune function and is not curative. A single infusion of CCR5 gene-edited autologous CD4+ T cells (SB-728-T) led to sustained increases in CD4+ T cell counts, improved T cell homeostasis, and reduced the estimated size of the HIV reservoir. These outcomes were associated with the expansion and long-term persistence of a novel CCR5 gene-edited CD4+ T memory stem cell (CD45RAintROint TSCM) subset that can replenish the pool of more differentiated memory cells. We showed that novel CD45RAintROint TSCM cells are transcriptionally distinct from the previously described CD45RA+ TSCM and are minimally differentiated cells uncommitted to a specific Th-lineage. Subsequently, we showed in an independent trial that infusion of the SB-728-T cell product resulted in partial control of viral replication upon cessation of ART which was correlated with the frequencies of CCR5 gene-edited TSCM and their TEM progeny. Interestingly, one participant that remained off ART to this date demonstrated long-term maintenance of CCR5 gene-edited cells and increased frequency of polyfunctional HIV-specific CD4+ and CD8+ T cells, contributing to low levels of viral load 5 years post-infusion. Consequently, the generation of HIV protected memory CD4+ T cells by CCR5 disruption can contribute toward novel interventions aimed at achieving a sustained ART-free viral remission of HIV disease.


title: Therapeutic immunization against Helicobacter pylori infection in BALB/c mice induced by a multi-epitope vaccine based on computer-aided design

abstract:
BackgroundCombined antibiotic regimens have caused problems such as increasing antimicrobial resistance to H. pylori and intestinal flora disturbance. Vaccination is a great alternative approach, but also faces the limited immune response induced by monovalent vaccines. Therefore, the development of multi-epitope vaccines is promising immunotherapy to control H. pylori infection.

ObjectiveTo develop a multi-epitope vaccine and evaluate its therapeutic efficacy against H. pylori infection.

Materials and MethodsThe B and T cell epitopes from UreB, FlaA, AlpB, SabA, and HpaA were linked for producing 2 multi-epitope vaccines (CTB-S3 and CTB-S5) by a structural evaluation based on computer-aided design. The abilities to produce antigen-specific antibodies and neutralizing antibodies of CTB-S3 and CTB-S5 were evaluated in BALB/c mice. After that, their therapeutic efficacy was explored in H. pylori-infected mice.

ResultsCTB-S3 or CTB-S5 could induce high levels of specific antibodies against UreB, FlaA, AlpB, SabA, HpaA, and neutralizing antibodies against H. pylori urease and adhesion. Also, oral therapeutic immunization with CTB-S3 or CTB-S5 could decrease H. pylori colonization and reduce stomach damage; the protection was correlated with H. pylori-specific IgG, SIgA antibodies, and CD4+ T cell immune response.

ConclusionsOur study developed a multi-epitope vaccine based on a computer-aided design. The CTB-S3 and CTB-S5 vaccines may be promising therapeutic candidate vaccines against H. pylori infection and provide a reference for vaccine design of other pathogens.


title: The component parts of bacteriophage virions accurately defined by a machine-learning approach built on evolutionary features.

abstract:
Antimicrobial resistance (AMR) continues to evolve as a major threat to human health and new strategies are required for the treatment of AMR infections. Bacteriophages (phages) that kill bacterial pathogens are being identified for use in phage therapies, with the intention to apply these bactericidal viruses directly into the infection sites in bespoke phage cocktails. Despite the great unsampled phage diversity for this purpose, an issue hampering the roll out of phage therapy is the poor quality annotation of many of the phage genomes, particularly for those from infrequently sampled environmental sources. We developed a computational tool called STEP3 to use the "evolutionary features" that can be recognized in genome sequences of diverse phages. These features, when integrated into an ensemble framework, achieved a stable and robust prediction performance when benchmarked against other prediction tools using phages from diverse sources. Validation of the prediction accuracy of STEP3 was conducted with high-resolution mass spectrometry analysis of two novel phages, isolated from a watercourse in the Southern Hemisphere. STEP3 provides a robust computational approach to distinguish specific and universal features in phages to improve the quality of phage cocktails, and is available for use at http://step3.erc.monash.edu/.

IMPORTANCEIn response to the global problem of antimicrobial resistance there are moves to use bacteriophages (phages) as therapeutic agents. Selecting which phages will be effective therapeutics relies on interpreting features contributing to shelf-life and applicability to diagnosed infections. However, the protein components of the phage virions that dictate these properties vary so much in sequence that best estimates suggest failure to recognize up to 90% of them. We have utilised this diversity in evolutionary features as an advantage, to apply machine learning for prediction accuracy for diverse components in phage virions. We benchmark this new tool showing the accurate recognition and evaluation of phage components parts using genome sequence data of phages from under-sampled environments, where the richest diversity of phage still lies.

category: microbiology


title: Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonisation potential of bacterial pathogens and commensals.

abstract: Located at the tip of cell surface glycoconjugates, sialic acids are at the forefront of host-microbe interactions and, being easily liberated by sialidase enzymes, are used as metabolites by numerous bacteria, particularly by pathogens and commensals living on or near diverse mucosal surfaces. These bacteria rely on specific transporters for the acquisition of host-derived sialic acids. Here, we present the first comprehensive genomic and phylogenetic analysis of bacterial sialic acid transporters, leading to the identification of multiple new families and subfamilies. Our phylogenetic analysis suggests that sialic acid-specific transport has evolved independently at least 8 times during the evolution of bacteria, from within 4 of the major families/superfamilies of bacterial transporters, and we propose a robust classification scheme to bring together a myriad of different nomenclatures that exist to date. The new transporters discovered occur in diverse bacteria including Spirochaetes, Bacteroidetes, Planctomycetes, and Verrucomicrobia, many of which are species that have not been previously recognised to have sialometabolic capacities. Two subfamilies of transporters stand out in being fused to the sialic acid mutarotase enzyme, NanM, and these transporter fusions are enriched in bacteria present in gut microbial communities. We also provide evidence for a possible function of a sialic acid transporter component in chemotaxis that is independent of transport. Our analysis supports the increasing experimental evidence that competition for host-derived sialic acid is a key phenotype for successful colonisation of complex mucosal microbiomes, such that a strong evolutionary selection has occurred for the emergence of sialic acid specificity within existing transporter architectures.


title: Development of a chemiluminescence immunoassay to accurately detect African swine fever virus antibodies in serum

abstract: The outbreak of African swine fever (ASF) has caused significant economic losses to animal husbandry worldwide. Currently, there is no effective vaccine or treatment available to control the disease, and therefore, efficient disease control is dependent on early detection and diagnosis of ASF virus (ASFV). In this study, a chemiluminescent immunoassay (CLIA) was developed using the ASFV protein p54 as a serum diagnostic antigen and an anti-p54 monoclonal antibody. After optimizing the working parameters of the CLIA, the sensitivity of the established CLIA was 1:128, ASFV-specific serum antibody was identified, and there was no cross-reaction with other swine virus antibodies. After testing 49 clinical serum samples, the consistency rate between the CLIA and the World Organization for Animal Health (OIE) recommended commercial kit was 100%. Thus, this CLIA had a high degree of specificity, sensitivity, and reliability, and could be used as a rapid detection method for epidemiological investigations of ASFV infection.


title: The establishment of variant surface glycoprotein monoallelic expression revealed by single-cell RNA-seq of Trypanosoma brucei in the tsetse fly salivary glands.

abstract: The long and complex Trypanosoma brucei development in the tsetse fly vector culminates when parasites gain mammalian infectivity in the salivary glands. A key step in this process is the establishment of monoallelic variant surface glycoprotein (VSG) expression and the formation of the VSG coat. The establishment of VSG monoallelic expression is complex and poorly understood, due to the multiple parasite stages present in the salivary glands. Therefore, we sought to further our understanding of this phenomenon by performing single-cell RNA-sequencing (scRNA-seq) on these trypanosome populations. We were able to capture the developmental program of trypanosomes in the salivary glands, identifying populations of epimastigote, gamete, pre-metacyclic and metacyclic cells. Our results show that parasite metabolism is dramatically remodeled during development in the salivary glands, with a shift in transcript abundance from tricarboxylic acid metabolism to glycolytic metabolism. Analysis of VSG gene expression in pre-metacyclic and metacyclic cells revealed a dynamic VSG gene activation program. Strikingly, we found that pre-metacyclic cells contain transcripts from multiple VSG genes, which resolves to singular VSG gene expression in mature metacyclic cells. Single molecule RNA fluorescence in situ hybridisation (smRNA-FISH) of VSG gene expression following in vitro metacyclogenesis confirmed this finding. Our data demonstrate that multiple VSG genes are transcribed before a single gene is chosen. We propose a transcriptional race model governs the initiation of monoallelic expression.

category: molecular biology


title: The Mechanism of Neurite Outgrowth Induction by Novel Synthetic Retinobenzoic Acids

abstract: Retinoids are a family of vitamin A-derived molecules and include the biologically active metabolite, retinoic acid (RA). RA acts as a specific modulator of neuronal differentiation and proliferation. However, teratogenicity and a large excess of RA have been found in animal studies. Thus, development of effective and stable retinoids is desirable. In this study, we showed that treatment with novel synthetic retinobenzoic acids promotes neurite outgrowth in a selected subpopulation of the human neuroblastoma cell line SK-N-SH. Furthermore, we found that, although acting via a different mechanism, retinobenzoic acids have the same neurite outgrowth-inducing effect as RA. Retinoids, including RA, bind to nuclear retinoic acid receptors (RARs). Therefore, we examined the expression of RARs in retinobenzoic acid-treated cells. Similar to already known retinoids, novel synthetic retinobenzoic acids promote the upregulation of RAR{beta} and have no effect on RAR or {gamma}. These results suggest that retinobenzoic acids act via RAR{beta} during neurite outgrowth. Moreover, stimulation with RA or retinobenzoic acids significantly increased the phosphorylation levels of both ERK1/2 and mTOR. ERK1/2 and mTOR inhibition blocked the retinobenzoic acid-induced increase in neurite outgrowth, suggesting that retinobenzoic acids promoted neurite outgrowth by activating the ERK1/2 and mTOR signaling pathways. Notably, the RA-induced increase in neurite outgrowth was blocked by the ERK1/2 inhibitor U0126, but not by the mTOR inhibitor rapamycin. In addition, ERK1/2 inhibition blocked the upregulation of RAR{beta} promoted by RA and retinobenzoic acids. In contrast, mTOR inhibition had no effect on upregulation of RAR{beta}. Our results show that novel synthetic retinobenzoic acids induce neurite outgrowth by a different mechanism than RA. These findings suggest that activation of both ERK1/2, which results in downstream regulation of RAR{beta}, and mTOR, are responsible for the novel synthetic retinobenzoic acid-induced neurite outgrowth in human neuroblastoma cells.

category: cell biology


title: Human iPSC-derived renal cells change their immunogenic properties during maturation: Implications for regenerative therapies

abstract: Therapeutic success of human induced pluripotent stem cell (hiPSC)-based therapies critically depends on immunological compatibility of the hiPSC-derived transplant. As grafted hiPSC-derived cells are often immature, we hypothesized that their immunologic properties may change due to post-grafting maturation. Subsequently, this will affect their interaction with the host immune system and may compromise graft tolerance. In the present study allogeneic and autologous cellular immunity of primary cells, therof reprogrammed hiPSC, hiPSC-derived progenitor and terminally differentiated cells was investigated in vitro by using renal cells as a model system. In contrast to allogeneic primary cells, hiPSC-derived early renal progenitors and mature renal epithelial cells were both tolerated not only by autologous but also by allogeneic T cells. These immune-privileged properties resulted from active immune-modulation and low immune visibility, which declined during the process of cell maturation. However, autologous and allogeneic natural killer (NK) cell responses were not suppressed by hiPSC-derived renal cells and efficiently changed NK cell activation status. These findings clearly show a dynamic stage-specific dependency of autologous and allogeneic T- and NK cell responses to the hiPSC-derived renal cell lineage with consequences for effective cell therapies. The study suggests that hiPSC-derived early progenitors may provide advantageous immune suppressive properties when applied in cell therapy. The data furthermore indicate a need to suppress NK cell activation in allogeneic as well as autologous settings.


title: CAMSAP2 organizes a γ-tubulin-independent microtubule nucleation centre

abstract: Microtubules are dynamic polymers consisting of {beta}-tubulin heterodimers. The initial polymerization process, called microtubule nucleation, occurs spontaneously via {beta}-tubulin. Since a large energy barrier prevents microtubule nucleation in cells, the {gamma}-tubulin ring complex is recruited to the centrosome to overcome the nucleation barrier. However, detachment of a considerable number of microtubules from the centrosome is known to contribute to fundamental processes in cells. Here, we present evidence that minus-end-binding calmodulin-regulated spectrin-associated protein 2 (CAMSAP2) serves as a strong nucleator for microtubule formation from soluble {beta}-tubulin independent of {gamma}-tubulin. CAMSAP2 significantly reduces the nucleation barrier close to the critical concentration for microtubule polymerization by stabilizing the longitudinal contacts among {beta}-tubulins. CAMSAP2 clusters together with {beta}-tubulin to generate nucleation intermediates, from which numerous microtubules radiate, forming aster-like structures. Our findings suggest that CAMSAP2 supports microtubule growth by organizing a nucleation centre as well as by stabilizing microtubule nucleation intermediates.


title: Kinesin-4 Motor Teams Effectively Navigate Dendritic Microtubule Arrays Through Track Switching and Regulation of Microtubule Dynamics

abstract: Microtubules establish the directionality of intracellular transport by kinesins and dynein through their polarized assembly, but it remains unclear how directed transport occurs along microtubules organized with mixed polarity. We investigated the ability of the plus-end directed kinesin-4 motor KIF21B to navigate mixed polarity microtubules in mammalian dendrites. Reconstitution assays with recombinant KIF21B and engineered microtubule bundles or extracted neuronal cytoskeletons indicate that nucleotide- independent microtubule binding regions of KIF21B modulate microtubule dynamics and promote directional switching on antiparallel microtubules. Optogenetic recruitment of KIF21B to organelles in live neurons resulted in unidirectional transport in axons but bi-directional transport with a net retrograde bias in dendrites; microtubule dynamics and the secondary microtubule binding regions are required for this net directional bias. We propose a model in which cargo-bound KIF21B motors coordinate nucleotide- sensitive and insensitive microtubule binding sites to achieve net retrograde movement along the dynamic mixed polarity microtubule arrays of dendrites.


title: BMP signaling is necessary and sufficient for osteoarthritis and a target for disease modifying therapy

abstract:
Osteoarthritis (OA) is a prominent musculoskeletal disorder with no effective therapy. Moreover, molecular aetiology of OA and the development and maintenance of articular cartilage are poorly understood. During OA, articular cartilage undergoes cellular and molecular changes reminiscent of transient cartilage, the embryonic precursor of endochondral bone. Previous studies from our lab suggest that during embryonic development, a precise spatio-temporally regulated WNT-BMP signaling interplay dictates differentiation of a common progenitor pool to either articular or transient cartilage fate in adjacent domains. While Wnt signaling promotes articular cartilage fate, transient cartilage differentiation is critically BMP signaling dependent. Moreover, any ectopic activation of BMP signalling embryonically, leads to ectopic transient cartilage differentiation at the expense of articular cartilage. In this study, we show that BMP signaling is sufficient and necessary for pathogenesis of OA by ectopically activating BMP signaling and depleting BMP ligands in adult mice articular cartilage, respectively. Similarly, human osteoarthritic specimens show upregulation of BMP signaling in the articular cartilage. A recent study based on our work (1), suggests that pharmacological inhibition of BMP signaling allows maintenance of hMSC derived chondrocytes, implanted in mice, for longer time duration (2). Similarly, we observe in vivo local pharmacological inhibition of BMP signaling resulted in delayed onset and reduced severity of OA in a mouse model of OA as well as long term protection from OA like changes. Therefore, pharmacological inhibition of BMP signaling and consequent block of transient cartilage differentiation of joint cartilage cells can be a potential disease modifying therapy for OA.

Significance statementThis manuscript provides new insights into the mechanistic basis for the maintenance of articular cartilage in adults. Here we demonstrate the role of BMP signaling in the pathogenesis of osteoarthritis in mice and humans. To the best of our understanding, this is the first (3)study investigating the relationship between molecular histological changes observed in the articular cartilage during osteoarthritis and inflammation. Moreover, we demonstrate that local inhibition of BMP signaling can be a potential disease modifying therapy for osteoarthritis which is among the most prominent musculoskeletal disorders.

category: developmental biology


title: Molecular diet analysis in zebra and quagga mussels (Dreissena spp.) and an assessment of the utility of aquatic filter feeders as biological eDNA filters

abstract: Molecular gut content analysis is a popular tool to study food web interactions and was recently also suggested as an alternative source for DNA based biomonitoring. However, the overabundant consumers DNA often outcompetes that of its diet during PCR. Blocking approaches are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. We here designed an assay to monitor the eukaryotic diet of mussels and test their utility as biological eDNA filters to monitor planktonic communities. We designed several rDNA primer sets with a broad taxonomic suitability for eukaryotes, which suppress the amplification of mussels. The primers were tested using mussel DNA extracts and the results were compared to eDNA water samples collected next to the mussel colonies. Taxonomic recovery, as well as patterns of alpha and beta diversity, were compared between mussels and water samples. In addition, we analyzed time series samples of mussel samples from different German rivers. Our primer sets efficiently block the amplification of various mussel genera. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also recover various taxa of possible commensals and parasites, associated with the mussels. Our protocol will enable large scale dietary analysis in mussels, facilitate aquatic food web analysis, elucidate the ecological impact of invasive bivalves and the rapid survey of mussel aquacultures for pathogens. Moreover, we show that mussels could serve as an interesting complementary DNA source for biomonitoring.

category: ecology


title: Combined effects of salinity and temperature on grazing activity of invasive Gammarus tigrinus on charophytes

abstract: Charophytes are a refuge for zooplankton and stabilize sediments, but they are also a food source for various animal species (water birds, fishes, invertebrates). Especially the introduction of new species, like Gammarus tigrinus, into the Baltic Sea led to yet not understood changes in the food web. Furthermore, future projections point to increased water temperatures at lowered salinity levels affecting species capacity to acclimatize to changing abiotic factors. In this study we investigated the influence of temperature and salinity on the grazing pressure of Gammarus tigrinus on two charophyte species: Chara aspera and Chara tomentosa. The grazing experiments were conducted in a full factorial design with the factors salinity (3 - 13 g kg-1), temperature (5 - 30 {degrees}C), and charophyte species. Grazing rates were determined as mass deviation within 48 hours considering biomass changes in the presence and absence of gammarids. Grazing rate were further used to calculate charophyte losses in two coastal lagoons with different salinity concentrations for recent and future time periods. The potential grazing peak of about 24 {degrees}C is not yet reached in these coastal waters but may be reached in the near future as shown by our future projection results. However, the temperature increase, and desalination will cause a shift in seasonal individual grazing patterns from summer to spring and autumn. Desalination and temperature increase can lead to a shift in optimal habitats for G. tigrinus in the future.


title: Desalination and temperature increase will shift seasonal grazing patterns of invasive Gammarus tigrinus on charophytes


title: The status of current and tentative marine natural World Heritage areas

abstract: The 1972 World Heritage Convention (WHC), along with the 1994 Global Strategy, aim to preserve the outstanding universal value of internationally important cultural and natural sites within a "representative, balanced and credible" network of highly-protected areas. Increasing human pressures and shortfalls in representation have been documented across the World Heritage network, particularly in terrestrial and cultural sites, threatening the integrity and primary goals of the WHC. However, the conservation status of current and tentative (i.e., proposed) marine natural World Heritage areas remains relatively unknown. We assessed the extent of recent (2013) and historical (2008-2013) cumulative human impacts and several metrics of representation (country, continent, ecoregion, wilderness, and threatened species) within existing and tentative marine natural World Heritage areas. We found moderate yet increasing cumulative human impacts across most existing sites, and high or very high impacts across the majority of tentative sites. Climate change impacts comprised nearly 75% of impact scores, on average, and differences in land and marine impacts across sites could help prioritise management decisions. Over 75% of marine ecoregions and 85% of threatened species considered in this study have no representation within the existing marine natural World Heritage network. We outline examples of how prioritizing representation across tentative sites for future World Heritage listing could greatly increase these measures. We urge the WHC to adopt quantitative, systematic and transparent evaluations of how current and tentative sites contribute to the overarching goals of maintaining a representative World Heritage network and preserving their outstanding universal values for future generations.


title: Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing among full-sibs

abstract: Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most wild animal populations. Using estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci, we estimated quantitative genetic parameters for traits known to be under directional natural selection in nine-spined sticklebacks (Pungitius pungitius) and compared these to traditional pedigree-based estimators. Using four different datasets, with varying sample sizes and pedigree complexity, we further assessed the performance of different Genomic Relationship Matrices (GRM) to estimate additive and dominance variance components. Large variance in IBD relationships allowed accurate estimation of genetic variance components, and revealed significant heritability for all measured traits, with negligible dominance contributions. Genome-partitioning analyses revealed that all traits have a polygenic basis and are controlled by genes at multiple chromosomes. The results demonstrate how large full-sib families of highly fecund vertebrates can be used to obtain accurate estimates quantitative genetic parameters to provide insights on genetic architecture of quantitative traits in non-model organisms from the wild. This approach should be particularly useful for studies requiring estimates of genetic variance components from multiple populations as for instance when aiming to infer the role of natural selection as a cause for population differentiation in quantitative traits.

category: evolutionary biology


title: Playing soft with cooperators emerges as a moral norm and promotes cooperation in evolutionary games

abstract: In many biological populations, individuals face a complex strategic setting, where they need to make strategic decisions over a diverse set of issues. To study evolution in such a complex strategic context, here we introduce evolutionary models where individuals play two games with different structures. Individuals decide upon their strategy in a second game based on their knowledge of their opponents strategy in the first game. By considering a case where the first game is a social dilemma, we show that, as long as the second game has an asymmetric Nash equilibrium, the system possesses a spontaneous symmetry-breaking phase transition above which the symmetry between cooperation and defection breaks. A set of cooperation supporting moral norms emerges according to which cooperation stands out as a valuable trait. Notably, the moral system also brings a more efficient allocation of resources in the second game. This observation suggests a moral system has two different roles: Promotion of cooperation, which is against individuals self-interest but beneficial for the population, and promotion of organization and order, which is at both the populations and the individuals self-interest. Interestingly, the latter acts like a Trojan horse: Once established out of individuals self-interest, it brings the former with itself. Furthermore, we show that in structured populations, recognition noise can have a surprisingly positive effect on the evolution of moral norms and facilitates cooperation in the Snow Drift game.


title: Lantern shark Etmopterus use coelenterazine as substrate for their luciferin-luciferase bioluminescence system

abstract: The lantern shark genus Etmopterus is a group of deep-sea bioluminescent fishes. They emit blue light mainly from the ventral body surface, and the primary biological function is considered to be for camouflage by counterillumination. In this study, we detected both coelenterazine and coelenterazine-specific luciferase activity in the ventral photophore tissues. The results suggested that bioluminescence in lantern sharks is produced using coelenterazine as the substrate for the luciferin-luciferase reaction.

category: biochemistry


title: Etmopterus lantern sharks use coelenterazine as the substrate for their luciferin-luciferase bioluminescence system


title: MXtrodes: MXene-infused bioelectronic interfaces for multiscale electrophysiology and stimulation

abstract: Soft bioelectronic interfaces for mapping and modulating excitable networks at high resolution and at large scale can enable paradigm-shifting diagnostics, monitoring, and treatment strategies. Yet, current technologies largely rely on materials and fabrication schemes that are expensive, do not scale, and critically limit the maximum attainable resolution and coverage. Solution processing is a cost-effective manufacturing alternative, but biocompatible conductive inks matching the performance of conventional metals are lacking. Here, we introduce MXtrodes, a novel class of soft, high-resolution, large-scale bioelectronic interfaces enabled by Ti3C2 MXene and scalable solution processing. We show that the electrochemical properties of MXtrodes exceed those of conventional materials, and do not require conductive gels when used in epidermal electronics. Furthermore, we validate MXtrodes in a number of applications ranging from mapping large scale neuromuscular networks in humans to delivering cortical microstimulation in small animal models. Finally, we demonstrate that MXtrodes are compatible with standard clinical neuroimaging modalities.


title: The openCARP Simulation Environment for Cardiac Electrophysiology

abstract:
Background and ObjectiveCardiac electrophysiology is a medical specialty with a long and rich tradition of computational modeling. Nevertheless, no community standard for cardiac electrophysiology simulation software has evolved yet. Here, we present the openCARP simulation environment as one solution that could foster the needs of large parts of this community.

Methods and ResultsopenCARP and the Python-based carputils framework allow developing and sharing simulation pipelines which automate in silico experiments including all modeling and simulation steps to increase reproducibility and productivity. The continuously expanding openCARP user community is supported by tailored infrastructure. Documentation and training material facilitate access to this complementary research tool for new users. After a brief historic review, this paper summarizes requirements for a high-usability electrophysiology simulator and describes how openCARP fulfills them. We introduce the openCARP modeling workflow in a multi-scale example of atrial fibrillation simulations on single cell, tissue, organ and body level and finally outline future development potential.

ConclusionAs an open simulator, openCARP can advance the computational cardiac electrophysiology field by making state-of-the-art simulations accessible. In combination with the carputils framework, it offers a tailored software solution for the scientific community and contributes towards increasing use, transparency, standardization and reproducibility of in silico experiments.


title: The global carrier frequency and genetic prevalence of Upshaw-Schulman syndrome

abstract:
PurposeUpshaw-Schulman syndrome (USS) is an autosomal recessive disease of thrombotic microangiopathy, caused by pathogenic variants in ADAMTS13. We aimed to (1) perform data mining pathogenicity of ADAMTS13 variants, (2) estimate carrier frequency and genetic prevalence of USS from gnomAD data, and (3) curated ADAMTS13 gene pathogenic variants dataset.

MethodsPubMed and Scopus were comprehensive retrieved. All previously reported pathogenic ADAMTS13 variants were compiled and annotated with gnomAD allele frequencies. Pooled global and population-specific carrier frequency and genetic prevalence for USS were calculated using Hardy-Weinberg equation.

Resultswe mined reported disease-causing variants, of these were present in gnomAD exomes v2.1.1, filtering by allele frequency, pathogenicity of variants were classified by American College of Medical Genetics and Genomics criteria. The genetic prevalence and carrier frequency of USS was 0.43 per 1 million (95% CI: [0.36, 0.55]) and 1.31 per thousand, respectively. Combining known with novel pathogenic/likely pathogenic variants, the genetic prevalence and carrier frequency are 1.1 per 1 million (95% CI: [0.89, 1.37]) and 2.1 per thousand, respectively.

Conclusionthe genetic prevalence and carrier frequency of Upshaw-Schulman syndrome are within range of previously rough estimated.


title: MetaFetcheR: An R package for complete mapping of small compound data

abstract:
MotivationSmall-compound databases contain large amount of information for metabolites and metabolic pathways. However, the plethora of such databases and the redundancy of their information lead to major issues with analysis and standardization. Lack of preventive establishment of means of data access at the infant stages of a project might lead to mislabelled compounds, reduced statistical power and large delays in delivery of results.

ResultsWe developed MetaFetcheR, an open-source R package that links metabolite data from several small-compound databases, resolves inconsistencies and covers a variety of use-cases of data fetching. We showed that the performance of MetaFetcheR was superior to existing approaches and databases by benchmarking the performance of the algorithm in two independent case studies based on two published datasets.

AvailabilityMetaFetcheR is available at https://github.com/komorowskilab/MetaFetcheR/.


title: Placental uptake and metabolism as determinants of pregnancy vitamin D status

abstract: Pregnancy 25-hydroxyvitamin D (25(OH)D) concentrations are associated with maternal and fetal health outcomes. Using physiological human placental perfusion and villous explants, we investigate the role of the placenta in regulating the relationships between maternal 25(OH)D and fetal physiology. We demonstrate active placental uptake of 25(OH)D3 by endocytosis, placental metabolism of 25(OH)D3 into 24,25-dihydroxyvitamin D3 and active 1,25-dihydroxyvitamin D [1,25(OH)2D3], with subsequent release of these metabolites into both the maternal and fetal circulations. Active placental transport of 25(OH)D3 and synthesis of 1,25(OH)2D3 demonstrate that fetal supply is dependent on placental function rather than simply the availability of maternal 25(OH)D3. We demonstrate that 25(OH)D3 exposure induces rapid effects on the placental transcriptome and proteome. These map to multiple pathways central to placental function and thereby fetal development, independent of vitamin D transfer. Our data suggest that the underlying epigenetic landscape helps dictate the transcriptional response to vitamin D treatment. This is the first quantitative study demonstrating vitamin D transfer and metabolism by the human placenta, with widespread effects on the placenta itself. These data demonstrate a complex interplay between vitamin D and the placenta and will inform future interventions using vitamin D to support fetal development and maternal adaptations to pregnancy.


title: Placental uptake and metabolism of 25(OH)Vitamin D determines its activity within the fetoplacental unit


title: Direct cochlear recordings show human hearing nerve activity is modulated by selective attention

abstract:
The architecture of the efferent auditory system enables prioritization of strongly overlapping spatiotemporal cochlear activation patterns elicited by relevant and irrelevant inputs. So far, attempts at finding such attentional modulations of cochlear activity delivered indirect insights in humans or required direct recordings in animals. The extent to which spiral ganglion cells forming the human auditory nerve are sensitive to selective attention remains largely unknown. We investigated this question by testing the effects of attending to either the auditory or visual modality in human cochlear implant (CI) users (3 female, 13 male). Auditory nerve activity was directly recorded with standard CIs during a silent (anticipatory) cue-target interval. When attending the upcoming auditory input, ongoing auditory nerve activity within the theta range (5-8 Hz) was enhanced. Crucially, using the broadband signal (4-25 Hz), a classifier was even able to decode the attended modality from single-trial data. Follow-up analysis showed that the effect was not driven by a narrow frequency in particular. Using direct cochlear recordings from deaf individuals, our findings suggest that cochlear spiral ganglion cells are sensitive to top-down attentional modulations. Given the putatively broad hair-cell degeneration of these individuals, the effects are likely mediated by alternative efferent pathways as compared to previous studies using otoacoustic emissions. Successful classification of single-trial data could additionally have a significant impact on future closed-loop CI developments that incorporate real-time optimization of CI parameters based on the current mental state of the user.

Significance StatementThe efferent auditory system in principle allows top-down modulation of auditory nerve activity, however evidence for this is lacking in humans. Using cochlear recordings in participants performing an audiovisual attention task, we show that ongoing auditory nerve activity in the silent cue-target period is directly modulated by selective attention. Specifically, ongoing auditory nerve activity is enhanced within the theta range when attending upcoming auditory input. Furthermore, over a broader frequency range, the attended modality can be decoded from single-trial data. Demonstrating this direct top-down influence on auditory nerve activity substantially extends previous works that focus on outer hair cell activity. Generally, our work could promote the use of standard cochlear implant electrodes to study cognitive neuroscientific questions.


title: Direct cochlear recordings in humans show a theta rhythmic modulation of the auditory nerve by selective attention


title: Dynamic signatures of the Eureka effect: An EEG study

abstract: The Eureka effect refers to the common experience of suddenly solving a problem. Here we study this effect in a pattern recognition paradigm that requires the segmentation of complex scenes and recognition of objects on the basis of Gestalt rules and prior knowledge. In the experiments both sensory evidence and prior knowledge were manipulated in order to obtain trials that do or do not converge towards a perceptual solution. Subjects had to detect objects in blurred scenes and signal recognition with manual responses. Neural dynamics were analyzed with high-density Electroencephalography (EEG) recordings. The results show significant changes of neural dynamics with respect to spectral distribution, coherence, phase locking, and fractal dimensionality. The Eureka effect was associated with increased coherence of oscillations in the alpha and theta band over widely distributed regions of the cortical mantle predominantly in the right hemisphere. This increase in coherence was associated with a decrease of beta band activity over parietal and central regions, and with a decrease of alpha power over frontal and occipital areas. In addition, there was a lateralized reduction of fractal dimensionality for activity recorded from the right hemisphere. These results suggest that the transition towards the solution of a perceptual task is mainly associated with a change of network dynamics in the right hemisphere that is characterized by enhanced coherence and reduced complexity. We propose that the Eureka effect requires cooperation of cortical regions involved in working memory, creative thinking, and the control of attention.


title: Bayesian MEG time courses with fMRI priors

abstract: Magnetoencephalography (MEG) records brain activity with excellent temporal and good spatial resolution, while functional magnetic resonance imaging (fMRI) offers good temporal and excellent spatial resolution. The aim of this study is to implement a Bayesian framework to use fMRI data as spatial priors for MEG inverse solutions. We used simulated MEG data with both evoked and induced activity and experimental MEG data from sixteen participants to examine the effectiveness of using fMRI spatial priors in MEG source reconstruction. Our results provide empirical evidence that the use of fMRI spatial priors improves the accuracy of MEG source reconstruction.


title: miRNA-dependent poly(A) length control in uncoupling transcription and translation of haploid male germ cells

abstract: As one of the post-transcriptional regulatory mechanisms, transcription and translations uncoupling plays an essential role in development and adulthood physiology. However, it remains elusive how thousands of mRNAs get translationally silenced while stability is maintained for up to hours or even days before translation. In addition to oocytes and neurons, developing spermatids have significant uncoupling of transcription and translation for delayed translation. Therefore, spermiogenesis represents an excellent in vivo model for investigating the mechanism underlying uncoupled transcription and translation. Through full-length poly(A) deep sequencing, we discovered dynamic changes in poly(A) length through deadenylation and re-polyadenylation. Deadenylation appeared to be mediated by microRNAs (miRNAs), and transcripts with shorter poly(A) tails tend to be sequestered into ribonucleoproteins (RNPs) for translational repression and stabilization. In contrast, re-polyadenylation allows for translocation of the translationally repressed transcripts from RNPs to polysomes for translation. Overall, our data suggest that miRNA-dependent poly(A) length control represents a novel mechanism underlying uncoupled translation and transcription in haploid male germ cells.


title: Butterfly eyespots evolved via co-option of the antennal gene-regulatory network

abstract: Butterfly eyespots are beautiful novel traits with an unknown developmental origin. Here we show that eyespots likely originated via co-option of the antennal gene-regulatory network (GRN) to novel locations on the wing. Using comparative transcriptome analysis, we show that eyespots cluster with antennae relative to multiple other tissues. Furthermore, three genes essential for eyespot development (Distal-less (Dll), spalt (sal), and Antennapedia (Antp)) share similar regulatory connections as those observed in the antennal GRN. CRISPR knockout of cis-regulatory elements (CREs) for Dll and sal led to the loss of eyespots and antennae, and also legs and wings, demonstrating that these CREs are highly pleiotropic. We conclude that eyespots likely re-used the ancient antennal GRN, a network previously implicated also in the development of legs and wings.


title: Serotonin signaling modulates aging-associated metabolic network integrity in response to nutrient choice

abstract: Aging arises from complex interactions among multiple biochemical and metabolic products. Systems-level analyses of biological networks may provide insights into the causes and consequences of aging that evade single-gene or single-pathway studies. We have shown that dietary choice per se is sufficient to modulate aging and metabolic health in the vinegar fly, Drosophila melanogaster. In other words, how each meal is presented, or the way in which it is eaten, is influential, independent of the amount or type of nutrients that are consumed. For example, when major macronutrients were presented separately, male flies exhibited a rapid and significant increase in mortality rate and a reduced overall lifespan relative to those fed a single medium containing both sugar and yeast. These effects are mediated by specific components of serotonin signaling, as a mutation in serotonin receptor 2A (5-HT2A) eliminated the effects of dietary choice. Here we show that dietary choice influenced several measures of metabolic network integrity, including connectivity, average shortest distance, community structure, and robustness, with the effects of the latter two restricted to tissues in the head. These changes in network structure were associated with organism resilience and increased susceptibility to genetic perturbation, as measured by starvation survival. Our data suggest that the behavioral or perceptual consequences of exposure to individual macronutrients, involving serotonin signaling through 5-HT2A, qualitatively change the state of metabolic networks throughout the organism from one that is highly connected and robust to one that is fragmented, fragile, and vulnerable to perturbations.

category: genetics


title: A Universal Chemical Method for Rational Design of Protein-based Nanoreactors

abstract: Self-assembly of a monomeric protease to form a multi-subunit protein complex "proteasome" enables targeted protein degradation in living cells. The naturally occurring proteasomes serve as an inspiration and blueprint for the design of artificial protein-based nanoreactors. Here we disclose a general chemical strategy for the design of proteasome-like nanoreactors. Micelle-assisted protein labeling (MAPLab) technology along with the N-terminal bioconjugation strategy is utilized for the synthesis of a well-defined monodisperse self-assembling semi-synthetic protease. The designer protein is programmed to self-assemble into a proteasome-like nanostructure which preserves the functional properties of native protease.

category: synthetic biology


title: Biological networks with singular Jacobians: their origins and adaptation criteria

abstract: This work is focused on Ordinary Differential Equations(ODE)-based models of biochemical systems that possess a singular Jacobian manifesting in non-hyperbolic equilibria. We show that there are several classes of systems that exhibit this behavior: a)systems with monomial-type interaction terms and b)systems with linear or nonlinear conservation laws. While models derived from mass-action principles often present with linear conservation laws stemming from the underlying biologic rationale, nonlinear conservation laws are more subtle and harder to detect. Nevertheless, in both situations the corresponding ODE system will contain non-hyperbolic equilibria. While having a potentially more complex dynamics and falling outside of the scope of existing theoretical frameworks, this class of systems can still exhibit adapting behavior associated with certain nodes and inputs. We derive a generalized adaptation condition that extends to singular systems and is compatible with both single-input/single-output and multiple-input/multiple-output settings. The approach explored herein, based on the notion of Moore-Penrose pseudoinverse, is tested on several synthetic systems that are shown to exhibit homeostatic behavior but are not covered by existing methods. These results highlight the role of the network structure and modeling assumptions when understanding system response to input and can be helpful in discovering intrinsic relationships between the nodes.


title: Mice immunized with the vaccine candidate HexaPro spike produce neutralizing antibodies against SARS-CoV-2

abstract: Updated and revised versions of COVID-19 vaccines are vital due to genetic variations of the SARS-CoV-2 spike antigen. Furthermore, vaccines that are safe, cost-effective, and logistically friendly are critically needed for global equity, especially for middle to low income countries. Recombinant protein-based subunit vaccines against SARS-CoV-2 have been reported with the use of the receptor binding domain (RBD) and the prefusion spike trimers (S-2P). Recently, a new version of prefusion spike trimers, so called "HexaPro", has been shown for its physical property to possess two RBD in the "up" conformation, as opposed to just one exposed RBD found in S-2P. Importantly, this HexaPro spike antigen is more stable than S-2P, raising its feasibility for global logistics and supply chain. Here, we report that the spike protein HexaPro offers a promising candidate for SARS-CoV-2 vaccine. Mice immunized by the recombinant HexaPro adjuvanted with aluminium hydroxide using a prime-boost regimen produced high-titer neutralizing antibodies for up to 56 days after initial immunization against live SARS-CoV-2 infection. In addition, the level of neutralization activity is comparable to that of convalescence sera. Our results indicate that the HexaPro subunit vaccine confers neutralization activity in sera collected from mice receiving the prime-boost regimen.


title: Effect of SARS-CoV-2 proteins on vascular permeability

abstract: SARS-CoV-2 infection leads to severe disease associated with cytokine storm, vascular dysfunction, coagulation, and progressive lung damage. It affects several vital organs, seemingly through a pathological effect on endothelial cells. The SARS-CoV-2 genome encodes 29 proteins, whose contribution to the disease manifestations, and especially endothelial complications, is unknown. We cloned and expressed 26 of these proteins in human cells and characterized the endothelial response to overexpression of each, individually. Whereas most proteins induced significant changes in endothelial permeability, nsp2, nsp5_c145a (catalytic dead mutant of nsp5) and nsp7 also reduced CD31, and increased von Willebrand factor expression and IL-6, suggesting endothelial dysfunction. Using propagation-based analysis of a protein-protein interaction (PPI) network, we predicted the endothelial proteins affected by the viral proteins that potentially mediate these effects. We further applied our PPI model to identify the role of each SARS-CoV-2 protein in other tissues affected by COVID-19. Overall, this work identifies the SARS-CoV-2 proteins that might be most detrimental in terms of endothelial dysfunction, thereby shedding light on vascular aspects of COVID-19.


title: A novel splice variant of human TGF-β type II receptor encodes a soluble protein and its Fc-tagged version prevents liver fibrosis in vivo.

abstract: We describe, for the first time, a new splice variant of the human TGF-{beta} type II receptor (T{beta}RII). The new transcript lacks 149 nucleotides, causing a frameshift with the appearance of an early stop codon, rendering a truncated mature protein of 57 amino acids. The predicted protein, lacking the transmembrane domain and with a distinctive 13 amino acid stretch in the C-terminus, was named T{beta}RII-Soluble Endogenous (T{beta}RII-SE). Binding predictions indicated that the novel 13 amino acid stretch interacts with all three TGF-{beta} cognate ligands and generate a more extensive protein-protein interface than T{beta}RII. T{beta}RII-SE and human IgG1 Fc-domain, were fused in frame in a lentiviral vector (Lv) for further characterization. With this vector, we transduced 293T cells and purified T{beta}RII-SE/Fc by A/G protein chromatography from conditioned medium. Immunoblotting revealed homogeneous bands of approximately 37 kDa (reduced) and 75 kD (non-reduced), indicating that T{beta}RII-SE/Fc is secreted as a disulphide-linked homodimer. Moreover, high affinity binding of T{beta}RII-SE to the three TGF-{beta} isoforms was confirmed by Surface Plasmon Resonance (SPR) analysis. Also, intrahepatic delivery of Lv.T{beta}RII-SE/Fc in a carbon tetrachloride-induced liver fibrosis model revealed amelioration of liver injury and fibrosis. Our results indicate that T{beta}RII-SE is a novel member of the TGF-{beta} signaling pathway with distinctive characteristics. This novel protein offers an alternative for the prevention and treatment of pathologies caused by the overproduction of TGF-{beta} ligands.


title: A ciliopathy complex builds distal appendages to initiate ciliogenesis

abstract:
Cells inherit two centrioles, the older of which is uniquely capable of generating a cilium. Using proteomics and super-resolved imaging, we identified a module which we term DISCO (DIStal centriole COmplex). DISCO components CEP90, MNR and OFD1 underlie human ciliopathies. This complex localized to both distal centrioles and centriolar satellites, proteinaceous granules surrounding centrioles. Cells and mice lacking CEP90 or MNR did not generate cilia, failed to assemble distal appendages, and did not transduce Hedgehog signals. Disrupting the satellite pools did not affect distal appendage assembly, indicating that it is the centriolar populations of MNR and CEP90 that are critical for ciliogenesis. CEP90 recruited the most proximal known distal appendage component, CEP83, to root distal appendages formation, an early step in ciliogenesis. In addition, MNR, but not CEP90, restricted centriolar length by recruiting OFD1. We conclude that DISCO acts at the distal centriole to support ciliogenesis by restraining centriole length and assembling distal appendages, defects in which cause human ciliopathies.

eTOC summaryKumar et al. identifies a multi-protein complex called DISCO (DIStal centriole COmplex) required to nucleate distal appendages and restrain centriole elongation, essential for the initiation of cilium assembly. Without DISCO, cells fail to ciliate and transduce Hedgehog signals, critical for mammalian development.


title: Delineating the complex mechanistic interplay between autophagy and monocyte to macrophage differentiation: a functional perspective

abstract:
Autophagy is an extremely essential cellular process aimed to clear redundant and damaged materials. In this study, we demonstrated that mTOR dependent classical autophagy is ubiquitously triggered in differentiating monocytes. Moreover, autophagy plays a decisive role in sustaining the process of monocyte to macrophage differentiation. We have delved deeper into understanding the underlying mechanistic complexities that trigger autophagy during differentiation. We have also shown that autophagy directs monocyte differentiation via protein degradation. Further, we delineated the complex cross-talk between autophagy and cell-cycle arrest in differentiating monocytes. This study also inspects the contribution of adhesion on various steps of autophagy and its ultimate impact on monocyte differentiation. Our study reveals new mechanistic insights into the process of autophagy associated with monocyte differentiation and would undoubtedly help to understand the intricacies of the process better for the effective design of therapeutics as autophagy and autophagy-related processes have enormous importance in human patho-physiology.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Immunoglobulin superfamily receptor Junctional adhesion molecule 3 (Jam3) requirement for melanophore survival and patterning during formation of zebrafish stripes

abstract: Adhesive interactions are essential for tissue patterning and morphogenesis yet difficult to study owing to functional redundancies across genes and gene families. A useful system in which to dissect roles for cell adhesion and adhesion-dependent signaling is the pattern formed by pigment cells in skin of adult zebrafish, in which stripes represent the arrangement of neural crest derived melanophores, cells homologous to melanocytes. In a forward genetic screen for adult pattern defects, we isolated the pissarro (psr) mutant, having a variegated phenotype of spots, as well as defects in adult fin and lens. We show that psr corresponds to junctional adhesion protein 3b (jam3b) encoding a zebrafish orthologue of the two immunoglobulin-like domain receptor JAM3 (JAM-C), known for roles in adhesion and signaling in other developing tissues, and for promoting metastatic behavior of human and murine melanoma cells. We found that zebrafish jam3b is expressed post-embryonically in a variety of cells including melanophores, and that jam3b mutants have defects in melanophore survival. Jam3b supported aggregation of cells in vitro and was required autonomously by melanophores for an adherent phenotype in vivo. Genetic analyses further indicated both overlapping and non-overlapping functions with the related receptor, Immunoglobulin superfamily 11 (Igsf11) and Kit receptor tyrosine kinase. These findings suggest a model for Jam3b function in zebrafish melanophores and hint at the complexity of adhesive interactions underlying pattern formation.


title: Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving C. elegans

abstract: The force-induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existence in vivo. Prominently, stretch-induced unfolding is postulated to be the activation mechanism of the twitchin/titin family of autoinhibited sarcomeric kinases linked to the mechanical stress response of muscle. To test the occurrence of mechanical kinase activation in living working muscle, we generated transgenic C. elegans expressing twitchin containing FRET moieties flanking the kinase domain and developed a quantitative technique for extracting FRET signals in freely moving C. elegans, using tracking and simultaneous imaging of animals in three channels (donor fluorescence, acceptor fluorescence, and transmitted light). Computer vision algorithms were used to extract fluorescence signals and muscle contraction states in each frame, in order to obtain fluorescence and body curvature measurements with spatial and temporal precision in vivo. The data revealed statistically significant periodic changes in FRET signals during muscle activity, consistent with a periodic change in the conformation of twitchin kinase. We conclude that stretch-unfolding of twitchin kinase occurs in the active muscle, whereby mechanical activity titrates the signalling pathway of this cytoskeletal kinase. We anticipate that the methods we have developed here could be applied to obtaining in vivo evidence for force-induced conformational changes or elastic behavior of other proteins not only in C. elegans but in other animals in which there is optical transparency (e.g zebrafish).


title: REDUCED ER-MITOCHONDRIA CONNECTIVITY PROMOTES NEUROBLASTOMA MULTIDRUG RESISTANCE

abstract: Most cancer deaths result from progression of therapy resistant disease, yet our understanding of this phenotype is limited. Cancer therapies generate stress signals that act upon mitochondria to initiate apoptotic programs. We isolated mitochondria from neuroblastoma cell lines obtained from children at diagnosis and after relapse following failed therapy, and profiled responses to tBid and Bim, death effectors activated by therapeutic stress. Mitochondria from post-relapse models had markedly attenuated cytochrome c release (surrogate for apoptotic commitment) in comparison with patient-matched diagnostic models. Mitochondrial DNA content, size, and shape did not differ consistently. However, we used electron microscopy to identify reduced endoplasmic reticulum-mitochondria contacts (ERMCs) as correlated with therapy resistance. ERMCs form microdomains for the transfer of Ca2+ to mitochondria. We confirmed reduced Ca2+ transfer in resistant cells, with restoration by re-opposing ERMCs via genetically-encoded linkers. However, reduced Ca2+ transfer was not present in all ERMC-reduced cancers with therapy resistance, supporting Ca2+-independent mechanisms. Genetically or biochemically reducing ERMCs in therapy sensitive tumors phenocopied resistance, validating these inter-organelle contacts as physiologic regulators of apoptosis. Our work confirms the importance of ERMCs in stress signaling and provides a previously unrecognized mechanism for cancer cell resistance that is not exclusive to other contributors.


title: In vitro screening of herbal medicinal products for their supportive curing potential in the context of SARS-CoV-2

abstract:
BackgroundHerbal medicinal products have a long-standing history of use in the therapy of common respiratory infections. In the COVID-19 pandemic, they may have the potential for symptom relief in non-severe or moderate disease cases. Here we describe the results derived by in vitro screening of five herbal medicinal products with regard to their potential to i) interfere with the binding of the human Angiotensin-converting enzyme 2 (ACE2) receptor with the SARS-CoV-2 Spike S1 protein, ii) modulate the release of the human defensin HBD1 and cathelicidin LL-37 from human A549 lung cells upon Spike S1 protein stimulation and iii) modulate the release of IFN-{gamma} from activated human peripheral blood mononuclear cells (PBMC). The investigated extracts were: Sinupret extract (SINx), Bronchipret thyme-ivy (BRO TE), Bronchipret thyme-primrose (BRO TP), Imupret (IMU), and Tonsipret (TOP).

MethodsThe inhibitory effect of the herbal medicinal products on the binding interaction of Spike S1 protein and the human ACE2 receptor was measured by ELISA. The effects on intracellular IFN-{gamma} expression in stimulated human PBMCs were measured by flow cytometry. Regulation on HBD1 and LL-37 expression and secretion was assessed in 25d long-term cultured human lung A549 epithelial cells by RT-PCR and ELISA.

ResultsIMU and BRO TE concentration-dependently inhibited the interaction between spike protein and the ACE2 Receptor. However, this effect was only observed in the cell-free assay at a concentration range which was later on determined as cytotoxic to human PBMC. SINx, TOP and BRO TP significantly upregulated the intracellular expression of antiviral IFN{gamma} from stimulated PBMC. Co-treatment of A549 cells with IMU or BRO TP together with SARS-CoV-2 spike protein significantly upregulated mRNA expression (IMU) and release (IMU and BRO TP) of HBD1 and LL-37 (BRO TP).

ConclusionsThe in vitro screening results provide first evidence for an immune activating potential of some of the tested herbal medicinal extracts in the context of SARS-CoV-2. Whether these could be helpful in prevention of SARS-CoV-2 invasion or supportive in recovery from SARS-CoV-2 infection needs deeper understanding of the observations.

category: pharmacology and toxicology