title: The species-specificity of energy landscapes for soaring birds, and its consequences for transferring suitability models across species

abstract:
O_LISoaring birds use the energy available in the environment in the form of atmospheric uplifts, to subsidize their flight. Their dependence on soaring opportunities makes them extremely sensitive to anthropogenic wind energy development. Predictive modelling is now considered instrumental to forecast the impact of wind farms on single species of concern. However, as multiple species often coexist in the same area, there is clear need to overcome the limitations of single species approaches.
C_LIO_LIWe looked for converging patterns in the way two obligate soaring species use the energy available in the landscape to soar, using movement data from 57 white storks, Ciconia ciconia, and 27 griffon vultures, Gyps fulvus. We first compared the soaring efficiency of the two species. We then tested the accuracy of topographic features, important correlates of collision risk in soaring birds, in predicting their soaring behaviour. We finally tested the transferability of soaring suitability models across species.
C_LIO_LITopography alone can predict and map the soaring opportunities available to storks across Europe, but not as efficiently in vultures. Only 20.5% of the study area was suitable to both species to soar, suggesting the existence of species-specific requirements in the use of the landscape for soaring. Storks relied on uplift occurrence while vultures on uplift quality, needing stronger uplifts to support their higher body mass and wing loading.
C_LIO_LISynthesis and applications: Our results indicate that the flight of highly specialized soaring species is more dependent on atmospheric conditions than on static features, and that more knowledge is required to accurately predict their behaviour. Despite the superficially similar soaring behaviour, the two species have different environmental requirements, suggesting that energy landscapes are species-specific. Our models provide a base to explore the effects that changes in the landscape have on the flight behaviour of different soaring species and suggest that there is no reliable and responsible way to shortcut risk assessment in areas where multiple species might be at risk by anthropogenic structures.
C_LI


title: gen3sis: the general engine for eco-evolutionary simulations on the origins of biodiversity

abstract: Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially-explicit, eco-evolutionary engine with a modular implementation that enables the modelling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatio-temporally dynamic landscapes. Modelled processes can include environmental filtering, biotic interactions, dispersal, speciation and evolution of ecological traits. Commonly observed biodiversity patterns, such as , {beta} and {gamma} diversity, species ranges, ecological traits and phylogenies, emerge as simulations proceed. As a case study, we examined alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earths Cenozoic era. We found that a carrying capacity linked with energy was the only model variant that could simultaneously produce a realistic LDG, species range size frequencies, and phylogenetic tree balance. The model engine is open source and available as an R-package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a step towards a numeric and mechanistic understanding of the physical and biological processes that shape Earths biodiversity.

category: evolutionary biology


title: Honeybee dance-followers respond similarly to dances regardless of their spatial information content

abstract: Honeybees famously use waggle dances to communicate foraging locations to nestmates in the hive, thereby recruiting them to those sites. The decision to dance is governed by rules that, when operating collectively, are assumed to direct foragers to the most profitable locations with little input from potential recruits, who are presumed to respond similarly to any dance regardless of its information content. Yet variation in receiver responses can qualitatively alter collective outcomes. Here, we use network-based diffusion analysis to compare the collective influence of dance information during recruitment to feeders at different distances. We further assess how any such effects might be achieved at the individual level by dance-followers either persisting with known sites when novel targets are distant and/or seeking more accurate spatial information to guide long-distance searches. Contrary to predictions, we found no evidence that dance-followers responses depended on target distance. While dance information was always key to feeder discovery, its importance did not vary with feeder distance, and bees were in fact quicker to abandon previously rewarding sites for distant alternatives. These findings provide empirical support for the longstanding assumption that self-organized foraging by honeybee colonies relies heavily on signal performance rules with limited input from recipients.

category: animal behavior and cognition


title: Deep learning-based chest X-ray age serves as a novel biomarker for cardiovascular aging

abstract: Chest X-ray (CXR) is one of the most commonly performed medical imaging tests. Although aging, sex and disease status have been known to cause changes in CXR findings, the extent of these effects has not been fully characterized. Here, we present a deep neural network (DNN) model trained using more than 100,000 CXRs to estimate the patients age and sex solely from CXRs. Our DNN exhibited high performance in terms of estimating age and sex, with Pearsons correlation coefficient between the actual and estimated age of above 0.9 and an area under the ROC curve of 0.98 for sex estimation. The difference between the actual and estimated age is large in CXRs with abnormal findings, suggesting that the estimated age ("CXR age") can be a biomarker for disease status. Furthermore, by applying our DNN to CXRs of consecutive 1,562 hospitalized heart failure patients, we demonstrated that an elevated CXR age is not only associated with aging-related diseases, such as hypertension and atrial fibrillation, but also a worse outcome of heart failure. Given these results, our new concept "CXR age" serves as a novel biomarker for cardiovascular aging and can help clinicians to predict, prevent, and manage cardiovascular diseases.

category: bioinformatics


title: Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes

abstract:
In order to advance the mission of in silico cell biology, modeling the interactions of large and complex biological systems becomes increasingly relevant. The combination of molecular dynamics (MD) and Markov state models (MSMs) have enabled the construction of simplified models of molecular kinetics on long timescales. Despite its success, this approach is inherently limited by the size of the molecular system. With increasing size of macromolecular complexes, the number of independent or weakly coupled subsystems increases, and the number of global system states increase exponentially, making the sampling of all distinct global states unfeasible. In this work, we present a technique called Independent Markov Decomposition (IMD) that leverages weak coupling between subsystems in order to compute a global kinetic model without requiring to sample all combinatorial states of subsystems. We give a theoretical basis for IMD and propose an approach for finding and validating such a decomposition. Using empirical few-state MSMs of ion channel models that are well established in electrophysiology, we demonstrate that IMD can reproduce experimental conductance measurements with a major reduction in sampling compared with a standard MSM approach. We further show how to find the optimal partition of all-atom protein simulations into weakly coupled subunits.

Significance StatementMolecular simulations of proteins are often interpreted using Markov state models (MSMs), in which each protein configuration is assigned to a global state. As we explore larger and more complex biological systems, the size of this global state space will face a combinatorial explosion, rendering it impossible to gather sufficient sampling data. In this work, we introduce an approach to decompose a system of interest into separable subsystems. We show that MSMs built for each subsystem can be later coupled to reproduce the behaviors of the global system. To aid in the choice of decomposition we also describe a score to quantify its goodness. This decomposition strategy has the promise to enable robust modeling of complex biomolecular systems.

category: biophysics


title: Correction of multiple-blinking artefacts in photoactivated localisation microscopy

abstract: Photoactivated localisation microscopy (PALM) produces an array of localisation coordinates by means of photoactivatable fluorescent proteins. However, observations are subject to fluorophore multiple-blinking and each protein is included in the dataset an unknown number of times at different positions, due to localisation error. This causes artificial clustering to be observed in the data. We present a workflow using calibration-free estimation of blinking dynamics and model-based clustering, to produce a corrected set of localisation coordinates now representing the true underlying fluorophore locations with enhanced localisation precision. These can be reliably tested for spatial randomness or analysed by other clustering approaches, and previously inestimable descriptors such as the absolute number of fluorophores per cluster are now quantifiable, which we validate with simulated data. Using experimental data, we confirm that the adaptor protein, LAT, is clustered at the T cell immunological synapse, with its nanoscale clustering properties depending on location and intracellular phosphorylatable tyrosine residues.


title: Bacterial Rdl2 dsRNA increased the insecticidal activity of GABAR blockers and allosteric modulators against Plutella xylostella

abstract:
BACKGROUNDThe application of RNAi to control pests has attracted the attention of researchers. Our results indicated that knockout of PxRdl2 can decrease resistance to fipronil in Plutella xylostella, providing a suitable target gene for RNAi-based pest control.

RESULTSThe differences in the sensitivity of two established homozygous knockout strains of P. xylostella. (Rdl1KO and Rdl2KO) and susceptible P. xylostella to a series of compounds were evaluated. Quinazolines and isoxazolines both showed stronger efficacy in the Rdl2KO strain. Therefore, we proposed a method based on the knockdown of the P. xylostella Rdl2 gene as a tactic to enhance the toxicity of quinazolines and isoxazolines. To reduce costs and protect dsRNA against degradation, we applied a bacterial expression system using the L4440 vector to express PxRdl2 dsRNA in HT115 Escherichia coli. Transformed bacteria (dsRNA-Bac) fed through leaves combined with quinazoline and isoxazolines proved to be more effective in both the susceptible and fipronil-resistant P. xylostella.

CONCLUSIONOur results provide a strategy for the development of novel insecticide spray formulations containing dsRNA-Bac, which synergize with insecticide toxins by suppressing PxRdl2, reducing the use of pesticides in the field.

category: pharmacology and toxicology


title: Investigations on regulation of miRNAs in rice reveal cyt signal transduction regulated miRNAs

abstract: MicroRNAs are critical components of the multi-dimensional regulatory networks in eukaryotic systems. They regulate a spectrum of developmental and metabolic processes in both plants and animals. Thus, it is quite apparent that the transcription, processing as well as activity of the miRNAs themselves is very dynamically regulated. One of the most important and universally implicated signalling molecule is [Ca2+]cyt. It is known to regulate a plethora of developmental and metabolic processes in both plants and animals, however their impact on the regulation of miRNA expression is relatively less explored. The current study employed a combination of internal and external calcium channel inhibitors, to establish that [Ca2+]cyt signatures actively regulate miRNA expression in rice. Involvement of [Ca2+]cyt in regulation of miRNA expression was further confirmed by treatment with calcimycin, the calcium ionophore. Modulation of the cytosolic calcium levels was also found to regulate the drought responsive expression as well as ABA mediated response of miRNA genes in rice seedlings. The study further establishes the role of calmodulins and Calmodulin-binding Transcription Activators (CAMTAs) as important components of the signal transduction schema that regulates miRNA expression. Yeast-one-hybrid assay established that OsCAMTA4 & 6 are involved in the transcriptional regulation of miR156a and miR167h. Thus, the study was able to clearly establish that [Ca2+]cyt is actively involved in regulating expression of miRNA genes both under control and stress conditions.

category: plant biology


title: A stochastic oscillator model simulates the entrainment of vertebrate cellular clocks by light

abstract:
The circadian clock is a cellular mechanism that synchronizes various biological processes with respect to the time of the day. While much progress has been made characterizing the molecular mechanisms underlying this clock, it is less clear how external light cues influence the dynamics of the core clock mechanism and thereby entrain it with the light-dark cycle. Zebrafish-derived cell cultures possess clocks that are directly light-entrainable, thus providing an attractive laboratory model for circadian entrainment. Here, we have developed a stochastic oscillator model of the zebrafish circadian clock, which accounts for the core clock negative feedback loop, light input, and the proliferation of single-cell oscillator noise into population-level luminescence recordings. The model accurately predicts the entrainment dynamics observed in bioluminescent clock reporter assays upon exposure to a wide range of lighting conditions. Furthermore, we have applied the model to obtain refitted parameter sets for cell cultures exposed to a variety of pharmacological treatments and predict changes in single-cell oscillator parameters. Our work paves the way for model-based, large-scale screens for genetic or pharmacologically-induced modifications to the entrainment of circadian clock function.

Author summaryThe circadian clock is a key, cell-autonomous timing mechanism that is encountered in most organisms. It is entrained by environmental lighting conditions and in turn temporally coordinates most aspects of physiology according to the time of day. Cell lines derived from zebrafish are attractive experimental models for studying how clocks are entrained by light since they possess clocks that respond directly to light stimuli. Here we describe a mathematical model for the behavior of the circadian clock in zebrafish cell lines during exposure to a range of lighting conditions. Using this model, we can determine how different pharmacological treatments may affect the entrainment dynamics of the clock and the degree of synchronization of individual cells circadian clocks in bioluminescent clock reporter assays. Our current model is mathematically simple and thus easy to apply and extend in future studies.

category: systems biology


title: A search-engine for single-cell epigenome profiles for multi-purpose applications

abstract: The true benefits of large data-sets of single-cell epigenome and transcriptome profiles can be availed only when they are searchable to annotate individual unannotated cells. Matching a single-cell epigenome profile to a large pool of reference cells remains as a challenge and largely unexplored. Here, we introduce scEpiSearch, which enables a user to query single-cell open-chromatin read-count matrices for comparison against a large pool of single-cell expression and open-chromatin profiles from human and mouse cells ([~] 3.5 million cells). Besides providing accurate search in a short time and scalable visualization of results for multiple query cells, scEpisearch also provides a low-dimensional representation of single-cell open-chromatin profiles. It outperformed many other methods in terms of correct low-dimensional embedding of single-cell open-chromatin profiles originating from different platforms and species. Here we show how scEpiSearch is unique in providing several facilities to assist researchers in the analysis of single-cell open-chromatin profiles to infer cellular state, lineage, potency and representative genes.


title: Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data.

abstract: Renewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and applications of such models in biotechnology and synthetic biology. In particular, genome-scale models of cellular metabolism beyond the steady state are required in order to represent transient and dynamic regulatory properties of the system. Development of such whole-cell models requires new modelling approaches. Here we propose the energy-based bond graph methodology, which integrates stoichiometric models with thermo-dynamic principles and kinetic modelling. We demonstrate how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems. The approach is illustrated using a well-established stoichiometric model of Escherichia coli (E. coli) and published experimental data.


title: Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data.


title: Role of ventral subiculum neuronal ensembles in incubation of oxycodone craving after electric barrier-induced voluntary abstinence

abstract:
We recently developed a rat model of incubation of oxycodone craving where opioid seeking progressively increases after voluntary suppression of drug self-administration by adverse consequences of drug seeking. Here, we studied the role of ventral subiculum (vSub) neuronal ensembles in this incubation, using the activity marker Fos, muscimol-baclofen (GABAergic agonists) inactivation, and Daun02 chemogenetic inactivation.

We trained Sprague-Dawley or Fos-lacZ transgenic male and female rats to self-administer oxycodone (0.1 mg/kg/infusion, 6-h/d) for 14 days. The rats were then exposed for 14 days to an electric barrier of increasing intensity (0.1 to 0.4 mA) near the drug-paired lever that caused voluntary abstinence or were exposed to 14 days of forced abstinence. We tested Sprague-Dawley rats for relapse to oxycodone seeking without shock and drug on abstinence day 15 and extracted their brains for Fos-immunohistochemistry, or tested them after vSub vehicle or muscimol-baclofen injections on abstinence days 1 and 15. We performed Daun02 inactivation of relapse-activated vSub Fos neurons in Fos-lacZ transgenic rats on abstinence day 15 and then tested them for relapse on abstinence day 18.

Relapse after electric barrier-induced abstinence increased Fos expression in vSub. Muscimol-baclofen inactivation or Daun02 selective inactivation of vSub Fos-expressing neuronal ensembles decreased "incubated" oxycodone seeking after voluntary abstinence. Muscimol-baclofen vSub inactivation had no effect on non-incubated opioid seeking on abstinence day 1 or incubation after forced abstinence.

Our results demonstrate a selective role of vSub neuronal ensembles in incubation of opioid craving after cessation of drug self-administration by adverse consequences of drug seeking.

Significance statementHigh relapse rate is a cardinal feature of opioid addiction and a major impediment for successful treatment. In humans, abstinence is often self-imposed, and relapse typically involves a conflict situation between the desire to experience the drugs rewarding effects and negative consequences of drug seeking. To mimic this human condition, we recently introduced a rat model of incubation of oxycodone craving after electric barrier-induced voluntary abstinence. Here, we used the activity marker Fos, muscimol-baclofen (GABAergic agonists) inactivation, and Daun02 chemogenetic inactivation to demonstrate a selective role of vSub neuronal ensembles in incubation of oxycodone craving after electric barrier-induced voluntary abstinence, but not in incubation of opioid craving after forced abstinence or non-incubated opioid seeking during early abstinence.

category: neuroscience


title: Anisotropy Measure from Three Diffusion-Encoding Gradient Directions

abstract:
PurposeWe propose a method that can provide information about the anisotropy and orientation of diffusion in the brain from only 3 orthogonal gradient directions without imposing additional assumptions.

MethodsThe method is based on the Diffusion Anisotropy (DiA) that measures the distance from a diffusion signal to its isotropic equivalent. The original formulation based on a Spherical Harmonics basis allows to go down to only 3 orthogonal directions in order to estimate the measure. In addition, an alternative simplification and a color-coding representation are also proposed.

ResultsAcquisitions from a publicly available database are used to test the viability of the proposal. The DiA succeeded in providing anisotropy information from the white matter using only 3 diffusion-encoding directions. The price to pay for such reduced acquisition is an increment in the variability of the data and a subestimation of the metric.

ConclusionsThe calculation of anisotropy information from DMRI is feasible using fewer than 6 gradient directions by using DiA. The method is totally compatible with existing acquisition protocols and it may provide complementary information about orientation in fast diffusion acquisitions.


title: Extremely Fast pRF Mapping for Real-Time Applications

abstract: Population receptive field (pRF) mapping is a popular tool in computational neuroimaging that allows for the investigation of receptive field properties, their topography and interrelations in health and disease. Furthermore, the possibility to invert population receptive fields provides a decoding model for constructing stimuli from observed cortical activation patterns. This has been suggested to pave the road towards pRF-based brain-computer interface (BCI) communication systems, which would be able to directly decode internally visualized letters from topographically organized brain activity. A major stumbling block for such an application is, however, that the pRF mapping procedure is computationally heavy and time consuming. To address this, we propose a novel and fast pRF mapping procedure that is suitable for real-time applications. The method is build upon hashed-Gaussian encoding of the stimulus, which significantly reduces computational resources. After the stimulus is encoded, mapping can be performed using either ridge regression for fast offline analyses or gradient descent for real-time applications. We validate our model-agnostic approach in silico, as well as on empirical fMRI data obtained from 3T and 7T MRI scanners. Our approach is capable of estimating receptive fields and their parameters for millions of voxels in mere seconds. This method thus facilitates real-time applications of population receptive field mapping.


title: Definition, modeling and detection of saccades in the face of post-saccadic oscillations

abstract: When analyzing eye tracking data, one of the central tasks is the detection of saccades. Although many automatic saccade detection algorithms exist, the field still debates how to deal with brief periods of instability around saccade offset, so-called post-saccadic oscillations (PSOs), which are especially prominent in todays widely used video-based eye tracking techniques. There is good evidence that PSOs are caused by inertial forces that act on the elastic components of the eye, such as the iris or the lens. As this relative movement can greatly distort estimates of saccade metrics, especially saccade duration and peak velocity, video-based eye tracking has recurrently been considered unsuitable for measuring saccade kinematics. In this chapter, we review recent biophysical models that describe the relationship between pupil motion and eyeball motion. We found that these models were well capable of accurately reproducing saccade trajectories and implemented a framework for the simulation of saccades, PSOs, and fixations, which can be used - just like datasets hand-labelled by human experts - to evaluate detection algorithms and train statistical models. Moreover, as only pupil and corneal-reflection signals are observable in video-based eye tracking, one may also be able to use these models to predict the unobservable motion of the eyeball. Testing these predictions by analyzing saccade data that was registered with video-based and search-coil eye tracking techniques revealed strong relationships between the two types of measurements, especially when saccade offset is defined as the onset of the PSO. To enable eye tracking researchers to make use of this definition, we present and evaluate two novel algorithms - one based on eye-movement direction inversion, one based on linear classifiers previously trained on simulation data. These algorithms allow for the detection of PSO onset with high fidelity. Even though PSOs may still pose problems for a range of eye tracking applications, the techniques described here may help to alleviate these.


title: Transthyretin promotes axon growth via regulation of microtubule dynamics and tubulin acetylation

abstract: Transthyretin (TTR), a plasma and cerebrospinal fluid protein, increases axon growth and organelle transport in sensory neurons. These TTR functions were suggested to underlie its activity in promoting nerve regeneration. While neurons extend their axons, the microtubule (MT) cytoskeleton is crucial for the segregation of functional compartments and axonal outgrowth. Herein, we investigated the hypothesis that TTR promotes axon elongation and regeneration by modulating MT dynamics. Indeed, we found that TTR KO mice have an intrinsic increase in dynamic MTs and reduced levels of acetylated -tubulin in uninjured peripheral axons, and fail to modulate microtubule dynamics in response to sciatic nerve injury. Importantly, restoring acetylated -tubulin levels of TTR KO DRG neurons using an HDAC6 inhibitor was sufficient to completely revert defective MT dynamics and neurite outgrowth. In summary, our results revealed a new role for TTR in the modulation of MT dynamics by regulating -tubulin acetylation and support that this activity underlies TTR neuritogenic function.


title: A new chemoenzymatic semisynthetic approach provides novel insight into the role of phosphorylation beyond exon1 of Huntingtin and reveals N-terminal fragment length-dependent distinct mechanisms of aggregation

abstract:
Huntingtons disease is a neurodegenerative disorder caused by the expansion of a polyglutamine (poly Q) repeat (>36Q) in the N-terminal domain of the huntingtin protein (Htt), which renders the protein or fragments thereof more prone to aggregate and form inclusions. Although several Htt N-terminal fragments of different lengths have been identified within Htt inclusions, most studies on the mechanisms, sequence, and structural determinants of Htt aggregation have focused on the Htt exon1 (Httex1). Herein, we investigated the aggregation properties of mutant N-terminal Htt fragments of various lengths (Htt171, Htt140, and Htt104) in comparison to mutant Httex1. We also present a new chemoenzymatic semisynthetic strategy that enables site-specific phosphorylation of Htt beyond Httex1. These advances yielded novel insights into how PTMs and structured domains beyond Httex1 influence aggregation mechanisms, kinetics, and fibril morphology of longer N-terminal Htt fragments. We demonstrate that phosphorylation at T107 significantly slowed its aggregation, whereases phosphorylation at T107 and S116 accelerated the aggregation of Htt171, underscoring the importance of crosstalk between different PTMs. We demonstrate that mutant Htt171 proteins aggregate via a different mechanism and form oligomers and fibrillar aggregates with morphological properties that are distinct from that of mutant Httex1. These observations suggest that different N-terminal fragments could have distinct mechanisms of aggregation and that a single polyQ-targeting anti-aggregation strategy may not effectively inhibit the aggregation of all N-terminal Htt fragments. Finally, our results underscore the importance of further studies to investigate the aggregation mechanisms of Htt fragments and how the various fragments interact with each other and influence Htt toxicity, pathology formation, and disease progression.

Table of content

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title: Modelling nonlinear dendritic processing of facilitation in a dragonfly target-tracking neuron

abstract: Dragonflies are highly skilled and successful aerial predators that are even capable of selectively attending to one target within a swarm. Detection and tracking prey is likely to be driven by small target motion detector (STMD) neurons identified from several insect groups. Prior work has shown that dragonfly STMD responses are facilitated by targets moving on a continuous path, enhancing the response gain at the present and predicted future location of targets. In this study, we combined detailed morphological data with computational modelling to test whether a combination of dendritic morphology combined with the nonlinear properties of NMDA receptors could explain these observations. We developed a hybrid neuronal model of neurons within the dragonfly optic lobe, which integrates numerical and morphological components. The model was able to generate potent facilitation for targets moving on continuous trajectories, including a localized spotlight of maximal sensitivity close to the last seen target location, as also measured during in vivo recordings. The model did not, however, include a mechanism capable of producing a traveling or spreading wave of facilitation. Our data support a strong role for the high dendritic density seen in the dragonfly neuron in enhancing non-linear facilitation. An alternative model based on morphology of an unrelated type of motion processing neuron from a dipteran fly required more than 3 times higher synaptic gain in order to elicit similar levels of facilitation, despite having only 20% fewer synapses. Our data supports a potential role for NMDA receptors in target tracking and also demonstrates the feasibility of combining biologically plausible dendritic computations with more abstract computational models for basic processing as used in earlier studies.


title: Transcriptional and cellular signatures of cortical morphometric similarity remodelling in chronic pain

abstract: Chronic pain is a highly debilitating and poorly understood condition. Here, we attempt to advance our understanding of the brain mechanisms driving chronic pain by investigating alterations in morphometric similarity (MS) and corresponding transcriptomic and cellular signatures, in three cohorts of patients with distinct chronic pain syndromes (knee osteoarthritis, low back pain and fibromyalgia). We uncover a novel pattern of cortical MS remodelling involving mostly MS increases in the insula and limbic cortex, which cuts across the boundaries of specific pain syndromes. We show that cortical MS remodelling in chronic pain spatially correlates with the brain-wide expression of genes involved in the glial immune response and neuronal plasticity. Cortical remodelling in chronic pain might involve a disruption of multiple elements of the cellular architecture of the brain. Therefore, multi-target therapeutic approaches tackling both glial activation and neuronal hyperexcitability might better encompass the full neurobiology of chronic pain.


title: The use of non-functional clonotypes as a natural spike-in for multiplex PCR bias correction in immune receptor repertoire profiling

abstract: High-throughput sequencing of immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful methods for TCR/BCR repertoire reconstruction and analysis have been developed in the past decade. However, detection and correction of the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: Immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5 RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches. The developed tool can be used to increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.

category: immunology


title: A folder mechanism ensures size uniformity among C. elegans individuals by coupling growth and development

abstract:
Animals increase by orders of magnitude in their volume during development. Hence, even small differences in the growth rates between individuals could generate large differences in their adult body size. Yet, such volume divergence among individuals is usually not observed in nature.

We combined theory and experiment to understand the mechanisms of body size uniformity. Using live imaging, we measured the volume growth of hundreds of individuals of C. elegans over the entire span of their postembryonic development. We find that C. elegans grows exponentially in volume with a coefficient of variation of the growth rate of [~]7%, but that individuals diverge much less in volume than expected from this heterogeneity. The mechanism counteracting size divergence does not involve size thresholds for developmental milestones. Instead, an inverse coupling of the growth rate and the duration of development produces a constant volume fold change per larval stage.

The duration of larval stages of C. elegans is determined by the period of a developmental oscillator. Using mathematical modelling, we show that an anti-correlation between the growth rate and the oscillatory period emerges as an intrinsic property of a genetic oscillator. We propose that the robustness of body volume fold change is a hard-wired characteristic of the oscillatory circuit and does not require elaborate mechanisms of size control by cellular signalling. Indeed, the coupling of growth and development was unaltered by mutation of canonical pathways of growth control. This novel concept of size homeostasis may broadly apply to other multicellular systems controlled by genetic oscillators.

category: developmental biology


title: Histological analysis of implantation embryos in large Japanese field mouse (Apodemus speciosus) and estimation of developmental stage.

abstract: The large Japanese field mice (Apodemus speciosus) are small rodent specie endemic to Japan. The genetic characteristics of A. speciosus is different chromosome numbers within one species. Furthermore, A. speciosus is used for research in radiation and genetics. In this present study, a pregnant A. speciosus was obtained, and histochemical analysis of the implanted embryos was performed and compared with developmental stages of the mouse. Although there were some differences, the structures of the implanted embryos including the primitive streak and placenta of A. speciosus were similar to that of the mouse. Our study will be important report in the construction of a developmental atlas of A. speciosus.


title: Negative effects of agricultural intensification on energetic gain rates of a declining aerial insectivore

abstract: The historical rise of intensive agricultural practices is hypothesized to be related to declines of grassland and aerial insectivorous birds. Drivers of declines may also influence the overall abundance and spatial distribution of insects within agricultural landscapes. Subsequently, the food provisioning rate of birds breeding within more agro-intensive landscapes may be impacted. Lower provisioning rates in agro-intensive landscapes may lead to reduced growth rate, body condition or fledging success of nestlings but also to diminished body condition of food provisioning adults. Results from a previous study supported this hypothesis as the fledging success and proxies of nestling body condition were lowest for an aerial insectivore breeding in more agro intensive landscapes. Of the multiple hypotheses put forward to explain these correlations, one mechanism may act through variation in food provisioning rates. In this study, we expounded on this hypothesis using data derived from the aforementioned study system and assessed if provisioning rates to nestlings and food provisioning behavior of adults varied across a gradient of agricultural intensification in a declining aerial insectivore, the Tree Swallow (Tachycineta bicolor). We found that the hourly provisioning rate was lower in agro-intensive landscapes, and yet travel distances were longest within less agro-intensive landscapes. Our results highlight that, in order to maximize long term average gain rates, Tree Swallows breeding within agro-intensive landscapes must forage with greater intensity, perhaps at a cost to themselves, or else costs will transfer to growing broods. Our work provides further evidence that agricultural intensification on the breeding grounds can contribute to the declines of aerial insectivores in part through a trophic pathway.

category: ecology


title: Survey data on European organic multi-species livestock farms

abstract: While there is increasing evidence of the sustainability benefits of diversified systems in the organic cropping sector, this has been much less investigated with organic livestock farming. To fill this knowledge gap, we surveyed a sample of 128 European organic multi-species livestock farms located across seven countries - Austria, Belgium, France, Germany, Italy, Sweden and Switzerland - and covering a large range of livestock species combinations. We recorded 1574 variables as raw data out of which we calculated 107 indicators describing farm structure, management and several sustainability dimensions: resource use efficiency and conservation, animal, land and work productivities, animal and human welfare. After technical validation of the data, we withdrew 26 farms and the database covers 102 farms. This database is well suited to unveil relationships between various dimensions of organic multi-species livestock farm sustainability and their structure and management. It can help reveal sustainable strategies for organic multi-species livestock farming systems and understand levers or barriers to their development.


title: Taking full advantage of modelling to better assess environmental risk due to xenobiotics

abstract:
In the European Union, more than 100,000 man-made chemical substances are awaiting an environmental risk assessment (ERA). Simultaneously, ERA of chemicals has now entered a new era. Indeed, recent recommendations from regulatory bodies underline a crucial need for the use of mechanistic effect models, allowing assessments that are not only ecologically relevant, but also more integrative, consistent and efficient. At the individual level, toxicokinetic-toxicodynamic (TKTD) models are particularly encouraged for the regulatory assessment of pesticide-related risks on aquatic organisms. In this paper, we first propose a brief review of classical dose-response models to put into light the on-line MOSAIC tool offering all necessary services in a turnkey web platform whatever the type of data to analyze. Then, we focus on the necessity to account for the time-dimension of the exposure by illustrating how MOSAIC can support a robust calculation of bioaccumulation factors. At last, we show how MOSAIC can be of valuable help to fully complete the EFSA workflow regarding the use of TKTD models, especially with GUTS models, providing a user-friendly interface for calibrating, validating and predicting survival over time under any time-variable exposure scenario of interest. Our conclusion proposes a few lines of thought for an even easier use of modelling in ERA.

Graphical art

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title: Extracellular Matrix Hydrogels Promote Expression of Paxillin, a Muscle-Tendon Junction Marker

abstract:
Muscle and tendon injuries are prevalent and range from minor sprains and strains to traumatic, debilitating injuries. However, the interactions between these tissues during injury and recovery remain unclear. Three-dimensional tissue models that incorporate both tissues and a physiologically relevant junction between muscle and tendon may help understand how the two tissues interact. Here, we use tissue specific extracellular matrix (ECM) derived from muscle and tendon to determine how cells of each tissue interact with the microenvironment of the opposite tissue resulting in junction specific features. ECM materials were derived from the Achilles tendon and gastrocnemius muscle, decellularized, and processed to form tissue specific pre-hydrogel digests. ECM materials were unique in respect to protein composition and included many types of ECM proteins, not just collagens. After digestion and gelation, ECM hydrogels had similar complex viscosities which were less than type I collagen hydrogels at the same concentration. C2C12 myoblasts and tendon fibroblasts were cultured in tissuespecific ECM conditioned media or encapsulated in tissue-specific ECM hydrogels to determine cell-matrix interactions and the effects on a muscle-tendon junction marker, paxillin. ECM conditioned media had only a minor effect on upregulation of paxillin in cells cultured in monolayer. However, cells cultured within ECM hydrogels had 50-70% higher paxillin expression than cells cultured in type I collagen hydrogels. Contraction of the ECM hydrogels varied by the type of ECM used. Subsequent experiments with varying density of type I collagen (and thus contraction) showed no correlation between paxillin expression and the amount of gel contraction, suggesting that a constituent of the ECM was the driver of paxillin expression in the ECM hydrogels. In addition, the extracellular matrix protein type XXII collagen had similar expression patterns as paxillin, with smaller effect sizes. Using tissue specific ECM allowed for the de-construction of the cell-matrix interactions similar to muscletendon junctions to study the expression of MTJ specific proteins.

Impact StatementThe muscle-tendon junction is an important feature of muscle-tendon units; however, despite crosstalk between the two tissue types, it is overlooked in current research. Deconstructing the cell-matrix interactions will provide the opportunity to study significant junction specific features and markers that should be included in tissue models of the muscletendon unit, while gaining a deeper understanding of the natural junction. This research aims to inform future methods to engineer a more relevant multi-tissue platform to study the muscletendon unit.

category: bioengineering


title: Extracellular Matrix Hydrogels Promote Expression of Muscle-Tendon Junction Proteins


title: Degradable endovascular neural interface for minimally invasive neural recording and stimulation

abstract: Neural recording and stimulation have been widely used to mitigate traumatic injuries, neurodegenerative diseases or mental disorders. Most neural interfaces commonly require invasive surgery, potentially entailing both transient and permanent complications. A promising strategy designed to overcome these risks involves exploiting the cerebrovascular system as an access route to the neural tissue. Here we present a novel endovascular neural interface for neural recording and stimulation, fully polymeric and degradable. This concept might allow for better integration of the device in the body, reduced inflammatory reaction, the possibility of replacing the implant after degradation, and avoiding removal surgeries. The vasculatures strategic distribution and the use of soft polymers for the devices fabrication will permit targeting both the brain vasculature and the peripheral system. Therefore, this novel endovascular neural interface will broaden the range of applications from neurological diseases and mental disorders to bioelectronics medicine.


title: Evaluation of solvents used for fabrication of microphysiological systems

abstract: Microphysiological systems (MPSs) have shown great promise for the advancement of drug discovery and toxicological tests, and as an alternative to animal models. However, although several chips and systems have been reported, some important issues are yet to be addressed, such as the use of polydimethylsiloxane (PDMS). Cyclo olefin polymers (COPs) have advantages over other thermoplastic materials, but most COP-based MPSs use solvent bonding during fabrication, which can affect any cells they are used to culture. This study uses a photobonding process with vacuum ultraviolet (UVU) to produce MPSs without the need for solvents such as cyclohexane, dichloromethane, and toluene. This is then used for comparison to investigate the effects of solvents on cell cultures. Quantitative immunofluorescent assays show that the coating efficiencies of extracellular matrix proteins, such as Matrigel and collagen I, are reduced on solvent-treated COP surfaces, compared with those prepared using VUV photobonding. Furthermore, SH-SY5Y neuroblastoma cells are used to evaluate cytotoxicity. This shows that solvent-MPSs induce apoptosis, but VUV-MPSs do not. These results provide insights into solvent bonding for MPS fabrication so that undesirable reactions can be avoided. Moreover, this work may be used to standardize MPS protocols and establish good manufacturing practices.


title: Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages

abstract: Single-cell RNA-sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue where collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nuclei extraction is often much more efficient and therefore single-nuclei RNA-sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We demonstrate that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, and how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we demonstrate successful integration of scRNA-seq and snRNA-seq datasets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for characterization of cellular diversity in the adipose tissue.


title: Autism_genepheno: Text mining of gene-phenotypeassociations reveals new phenotypic profiles ofautism-associated genes

abstract: Autism is a spectrum disorder with wide variation in type and severity of symptoms. Understanding gene-phenotype associations is vital to unravel the disease mechanisms and advance its diagnosis and treatment. To date, several databases have stored a large portion of gene-phenotype associations which are mainly obtained from genetic experiments. However, a large proportion of gene-phenotype associations are still buried in the autism-related literature and there are limited resources to investigate autism-associated gene-phenotype associations. Given the abundance of the autism-related literature, we were thus motivated to develop Autism_genepheno, a text mining pipeline to identify sentence-level mentions of autism-associated genes and phenotypes in literature through natural language processing methods. We have generated a comprehensive database of gene-phenotype associations in the last five years autism-related literature that can be easily updated as new literature becomes available. We have evaluated our pipeline through several different approaches, and we are able to rank and select top autism-associated genes through their unique and wide spectrum of phenotypic profiles, which could provide a unique resource for the diagnosis and treatment of autism. The data resources and the Autism_genpheno pipeline are available at: https://github.com/maiziezhoulab/Autism_genepheno.


title: minicore: Fast scRNA-seq clustering with various distance measures

abstract:
Single-cell RNA-sequencing (scRNA-seq) analyses typically begin by clustering a gene-by-cell expression matrix to empirically define groups of cells with similar expression profiles. We describe new methods and a new open source library, minicore, for efficient k-means++ center finding and k-means clustering of scRNA-seq data. Minicore works with sparse count data, as it emerges from typical scRNA-seq experiments, as well as with dense data from after dimensionality reduction. Minicores novel vectorized weighted reservoir sampling algorithm allows it to find initial k-means++ centers for a 4-million cell dataset in 1.5 minutes using 20 threads. Minicore can cluster using Euclidean distance, but also supports a wider class of measures like Jensen-Shannon Divergence, Kullback-Leibler Divergence, and the Bhattacharyya distance, which can be directly applied to count data and probability distributions.

Further, minicore produces lower-cost centerings more efficiently than scikit-learn for scRNA-seq datasets with millions of cells. With careful handling of priors, minicore implements these distance measures with only minor (<2-fold) speed differences among all distances. We show that a minicore pipeline consisting of k-means++, localsearch++ and minibatch k-means can cluster a 4-million cell dataset in minutes, using less than 10GiB of RAM. This memory-efficiency enables atlas-scale clustering on laptops and other commodity hardware. Finally, we report findings on which distance measures give clusterings that are most consistent with known cell type labels.

AvailabilityThe open source library is at https://github.com/dnbaker/minicore. Code used for experiments is at https://github.com/dnbaker/minicore-experiments.


title: Mesenchymal-like glioma cells are enriched in the gelatin methacrylate hydrogels

abstract: Glioblastoma is the most lethal primary malignant brain tumor in adults. Simplified two-dimensional (2D) cell culture and neurospheres in vitro models fail to recapitulate the complexity of the tumor microenvironment, limiting its ability to predict therapeutic response. Three-dimensional (3D) scaffold-based models have emerged as a promising alternative for addressing these concerns. One such 3D system is gelatin methacrylate (GelMA) hydrogels, which can be used for modeling the glioblastoma microenvironment. We characterized the phenotype of patient-derived glioma cells cultured in GelMA hydrogels (3D-GMH) for their tumorigenic properties using invasion and chemoresponse assays. In addition, we used integrated single-cell and spatial transcriptome analysis to compare cells cultured in 3D-GMH to cells in vivo. Finally, we assessed tumor-immune cell interactions with a macrophage infiltration assay and a cytokine array. We show that cells cultured in 3D-GMH develop a mesenchymal-like cellular phenotype found in perivascular and hypoxic regions present in the core of the tumor, and recruit macrophages by secreting cytokines in contrast to the cells grown as neurospheres that match the phenotype of cells of the infiltrative edge of the tumor.

category: cancer biology


title: Stress is basic: ABA alkalinizes both the xylem sap and the cytosol of Arabidopsis vascular bundle sheath cellsby inhibiting their P-type H+-ATPaseand stimulating their V-type H+-ATPase

abstract:
BACKGROUND AND HYPOTHESIS* Under water deprivation, in many perennial species, the stress hormone, ABA, appears in the xylem sap in the shoot (including leaf) veins and the xylem sap pH (pHEXT) increases. This study aimed to test the hypothesis that ABA is the signal for an altered proton balance of the leaf-vein-enwrapping bundle sheath cells (BSCs).

METHODS* Plant Material. We used a few Arabidopsis thaliana (L.) Heynh. genotypes: wildtype (WT) of two accessions, Landsberg erecta (Ler) and Columbia (Col), and a few mutants and transformants in these backgrounds.
* H+-Pumps activities. We monitored ABA effects on the H+-pump activities in the BSCs cytosol-delimiting membranes (plasma membrane and tonoplast) by monitoring the cytosol and the xylem pH, and the membrane potential (EM), by imaging the fluorescence of pH- and membrane potential (EM)-reporting probes: (a) the BSCs pHEXT - with the ratiometric fluorescent dye FITC-dextran petiole-fed into detached leaves in unbuffered xylem perfusion solution (XPS), (b) the BSCs pHCYT - with the ratiometric dye SNARF1 loaded into BSCs isolated protoplasts, and (c) the BSCs EM - with the ratiometric dye di- 8-ANEPPS.

RESULTS* ABA increased the pHEXT; this response was abolished in an abi1-1 mutant with impaired signaling via a PP2C (ABI1) and in an aha2-4 mutant with knocked-down AHA2;
* ABA depolarized the WT BSCs;
* ABA increased pHCYT irrespective of AHA2 activity (i.e., whether or not AHA was inhibited by vanadate, or in the aha2-4 mutant);
* The ABA-induced cytosol alkalinization was abolished in the absence of VHA activity (i.e., when VHA was inhibited by bafilomycin A1, or in the vha-a2 vha-a3 double mutant with inactive VHA);
* All these results resemble the ABA effect on GCs;
* In contrast to GCs, AHA2 and not AHA1 is the ABA major target in BSCs;
* Blue light (BL) enabled the response of the BSCs VHA to ABA;
* The ABA- and BL-signaling pathways acting on both BSCs pumps, AHA2 and VHA, are likely to be BSCs autonomous, based on (a) the presence in the BSCs of many genes of the ABA- and BL-signaling pathways and (b) ABA responses (depolarization and pHCYT elevation) demonstrated under BL in isolated protoplasts.

SIGNIFICANCE STATEMENTWe reveal here an alkalinizing effect of the plant drought-stress hormone ABA on the pH on both sides of the plasmalemma of the vein-enwrapping bundle sheath cells (BSCs), due to ABA inhibition of the BSCs AHA2, the plasmalemma H+- ATPase and stimulation of VHA, their vacuolar H+-ATPase. Since pH affects the BSCs selective regulation of solute and water fluxes into the leaf, these H+- pumps may be attractive targets for manipulations aiming to improve plant drought response.


title: Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

abstract:
White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled inline (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid-{beta} (A{beta}) plaques.

HighlightsO_LIX-ray phase-contrast tomography (XPCT) enables myelin mapping of the whole brain
C_LIO_LIXPCT detects and quantifies white-matter injuries in a range of diseases
C_LIO_LIFiber directions and anisotropy metrics can be retrieved from XPCT data
C_LIO_LIXPCT is compatible with subsequent conventional histology of brain samples
C_LIO_LIXPCT is a powerful virtual histology tool that requires minimal sample preparation
C_LI

Graphical Abstract

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title: A computational probe into the behavioral and neural markers of atypical facial emotion processing in autism.

abstract: Despite ample behavioral evidence of atypical facial emotion processing in individuals with autism (IwA), the neural underpinnings of such behavioral heterogeneities remain unclear. Here, I have used brain-tissue mapped artificial neural network (ANN) models of primate vision to probe candidate neural and behavior markers of atypical facial emotion recognition in IwA at an image-by-image level. Interestingly, the ANNs image-level behavioral patterns better matched the neurotypical subjects behavior than those measured in IwA. This behavioral mismatch was most remarkable when the ANN behavior was decoded from units that correspond to the primate inferior temporal (IT) cortex. ANN-IT responses also explained a significant fraction of the image-level behavioral predictivity associated with neural activity in the human amygdala -- strongly suggesting that the previously reported facial emotion intensity encodes in the human amygdala could be primarily driven by projections from the IT cortex. Furthermore, in silico experiments revealed how learning under noisy sensory representations could lead to atypical facial emotion processing that better matches the image-level behavior observed in IwA. In sum, these results identify primate IT activity as a candidate neural marker and demonstrate how ANN models of vision can be used to generate neural circuit-level hypotheses and guide future human and non-human primate studies in autism.


title: Interhemispheric Connectivity Supports Load-Dependent Working Memory Maintenance for Complex Visual Stimuli

abstract: A critical manipulation used to study the neural basis of working memory (WM) is to vary the information load at encoding followed by measurements of activity and connectivity during maintenance in the subsequent delay period. The hallmark finding is that delay period activity and connectivity increases between frontal and parietal brain regions as load is increased. Most WM studies, however, employ simple stimuli (e.g., simple shapes or letters) during encoding and utilize unfilled intervals (e.g., a blank screen or fixation cross) during the delays. In the present study, we asked how delay period activity and connectivity change during low and high load maintenance of complex stimuli. Twenty-two participants completed a modified Sternberg WM task with two or five naturalistic scenes as stimuli while scalp EEG was recorded. In each trial, the delay interval was filled with phase scrambled scenes to provide a visual perceptual control with color and spatial frequency similar to the non-scrambled scenes presented during encoding. The results showed that theta and alpha delay activity amplitude was reduced during high compared to low WM load across frontal, central, and parietal sources. Functional connectivity during the delay was assessed by phase-locking value (PLV) and revealed a network with higher connectivity during low WM load consisting of increased PLV between 1) left frontal and right posterior temporal sources in the theta and alpha bands, 2) right anterior temporal and left central sources in the alpha and lower beta bands, and 3) left anterior temporal and posterior temporal sources in the theta, alpha, and lower beta bands. These findings demonstrate a role for interhemispheric connectivity during WM maintenance of complex stimuli. We discuss significance with respect to allocation of limited attentional resources and the filtering of interference.


title: A viral toolbox for conditional and transneuronal gene expression in zebrafish

abstract: The zebrafish is an important model in systems neuroscience but a key limitation is the lack of viral tools to dissect the structure and function of neuronal circuitry. We developed methods for efficient gene transfer and retrograde tracing in adult and larval zebrafish by herpes simplex viruses (HSV1). HSV1 can be combined with the Gal4/UAS system to target cell types with high spatial, temporal and molecular specificity. We also established methods for efficient transneuronal tracing by modified rabies viruses in zebrafish. We demonstrate that HSV1 and rabies viruses can be used to visualize and manipulate genetically or anatomically identified neurons within and across different brain areas of adult and larval zebrafish. An expandable library of viruses is provided to express fluorescent proteins, calcium indicators, optogenetic probes, toxins and other molecular tools. This toolbox creates new opportunities to interrogate neuronal circuits in zebrafish through combinations of genetic and viral approaches.


title: Neural circuitry for maternal oxytocin release induced by infant cries

abstract: Oxytocin is a neuropeptide important for maternal physiology and childcare, including parturition and milk ejection during nursing. Suckling triggers oxytocin release, but other sensory cues- specifically infant cries- can elevate oxytocin levels in new human mothers, indicating that cries can activate hypothalamic oxytocin neurons. Here we describe a neural circuit routing auditory information about infant vocalizations to the oxytocin system of the mouse brain. We performed in vivo electrophysiological recordings and photometry from identified oxytocin neurons in awake maternal mice presented with pup calls. We found that oxytocin neurons responded to pup vocalizations via input from the posterior intralaminar thalamus, and repetitive thalamic stimulation induced lasting disinhibition of oxytocin neurons. Suppression of this pathway impaired maternal behavior and playing pup calls led to central oxytocin release in vivo. This circuit provides a mechanism for transforming acoustic input into hormonal output to ensure modulation of brain state required for successful parenting.


title: Electrophysiological and Transcriptomic Features Reveal a Circular Taxonomy of Cortical Neurons

abstract:
The complete understanding of the mammalian brain requires exact knowledge of the function of each of the neurons composing its parts. To achieve this goal, an exhaustive, precise, reproducible, and robust neuronal taxonomy should be defined. In this paper, a new circular taxonomy based on transcriptomic features and novel electrophysiological features is proposed. The approach is validated by analysing more than 1850 electrophysiological signals of different mouse visual cortex neurons proceeding from the Allen Cell Types Database.

The study is conducted on two different levels: neurons and their cell-type aggregation into Cre Lines. At the neuronal level, electrophysiological features have been extracted with a promising model that has already proved its worth in neuronal dynamics. At the Cre Line level, electrophysiological and transcriptomic features are joined on cell types with available genetic information. A taxonomy with a circular order is revealed by a simple transformation of the first two principal components that allow the characterization of the different Cre Lines. Moreover, the proposed methodology locates other Cre Lines in the taxonomy that do not have transcriptomic features available. Finally, the taxonomy is validated by Machine Learning methods which are able to discriminate the different neuron types with the proposed electrophysiological features.


title: Hunger improves reinforcement-driven but not planned action

abstract:
Human decisions can be reflexive or planned, being governed respectively by model-free and model-based learning systems. These two systems might differ in their responsiveness to our needs. Hunger drives us to specifically seek food rewards, but here we ask whether it might have more general effects on these two decision systems. On one hand, the model-based system is often considered flexible and context-sensitive, and might therefore be modulated by metabolic needs. On the other hand, the model-free systems primitive reinforcement mechanisms may have closer ties to biological drives. Here, we tested participants on a well-established two-stage sequential decision-making task that dissociates the contribution of model-based and model-free control. Hunger enhanced overall performance by increasing model-free control, without affecting model-based control. These results demonstrate a generalised effect of hunger on decision-making that enhances reliance on primitive reinforcement learning, which in some situations translates into adaptive benefits.

Significance statementThe prevalence of obesity and eating disorder is steadily increasing. To counteract problems related to eating, people need to make rational decisions. However, appetite may switch us to a different decision mode, making it harder to achieve long-term goals. Here we show that planned and reinforcement-driven actions are differentially sensitive to hunger. Hunger specifically affected reinforcement-driven actions, and did not affect the planning of actions. Our data shows that people behave differently when they are hungry. We also provide a computational model of how the behavioural changes might arise.


title: Mugs and Plants: Object Semantic Knowledge Alters Perceptual Processing with Behavioral Ramifications

abstract:
Neural processing of objects with action associations recruits dorsal visual regions more than objects without such associations. We hypothesized that because the dorsal and ventral visual pathways have differing proportions of magno- and parvo-cellular input, there should be behavioral differences in perceptual tasks between manipulable and non-manipulable objects. This hypothesis was tested in adults across five experiments (Ns = 26, 26, 30, 25, 25) using a gap detection task, suited to the spatial resolution of parvocellular processing, and an object flicker discrimination task, suited to the temporal resolution of magnocellular processing. Directly predicted from the cellular composition of each pathway, a strong non-manipulable object advantage was observed in gap detection, and a small manipulable object advantage in flicker discrimination. Additionally, these effects are modulated by reducing object recognition through inversion and by suppressing magnocellular processing using red light. These results establish perceptual differences between objects dependent on semantic knowledge.

Statement of RelevanceWhen we perceive an object, our knowledge of that object is brought to mind. Previous work has shown specifically that knowledge of object manipulability biases neural processing to areas of the brain in the parietal lobe which are relevant to motor processing. In this study we show that this neural bias, caused by knowledge of the object, has an effect on object perception. Using behavioral paradigms designed to take advantage of the specific response properties of neurons in the parietal and temporal object processing areas, we found that manipulable objects are perceived with higher temporal resolution while non-manipulable objects are perceived with higher spatial resolution. Our results demonstrate a specific neural mechanism by which prior knowledge affects current perception.


title: Fast and statistically robust cell extraction from large-scale neural calcium imaging datasets

abstract: State-of-the-art Ca2+ imaging studies that monitor large-scale neural dynamics can produce video datasets ~10 terabytes or more in total size, roughly comparable to ~10,000 Hollywood films. Processing such data volumes requires automated, general-purpose and fast computational methods for cell identification that are robust to a wide variety of noise sources. We introduce EXTRACT, an algorithm that is based on robust estimation theory and uses graphical processing units (GPUs) to extract neural dynamics in computing times up to 10-times faster than imaging durations. We validated EXTRACT on simulated and experimental data and processed 94 public datasets from the Allen Institute Brain Observatory in one day. Showcasing its superiority over past cell-sorting methods at removing noise contaminants, neural activity traces from EXTRACT allow more accurate decoding of animal behavior. Overall, EXTRACT provides neuroscientists with a powerful computational tool matched to the present challenges of neural Ca2+ imaging studies in behaving animals.


title: Lack of sex differences in gonadotropin-releasing hormone (GnRH) neuron potassium currents and excitability

abstract:
Gonadotropin-releasing hormone (GnRH) drives pituitary secretion of luteinizing hormone (LH) and follicle-stimulating hormone, which in turn regulate gonadal functions including steroidogenesis. The pattern of GnRH release and thus fertility depend on gonadal steroid feedback. Under homeostatic (negative) feedback conditions, removal of the gonads from either females or males increases the amplitude and frequency of GnRH release and alters the long-term firing pattern of these neurons in brain slices. The neurobiological mechanisms intrinsic to GnRH neurons that are altered by homeostatic feedback are not well studied and have not been compared between sexes. During estradiol positive feedback, which is unique to females, there are correlated changes in voltage-gated potassium currents and neuronal excitability. We thus hypothesized these same mechanisms would be engaged in homeostatic negative feedback. Voltage-gated potassium channels play a direct role in setting excitability and action potential properties. Whole-cell patch-clamp recordings of GFP-identified GnRH neurons in brain slices from sham-operated and castrated adult female and male mice were made to assess fast (IA) and slow (IK) inactivating potassium currents as well as action potential properties. Surprisingly, no changes were observed in most potassium current properties, input resistance or capacitance and this was reflected in a lack of differences in excitability and specific action potential properties. These results support the concept that, in contrast to positive feedback, steroid negative feedback regulation of GnRH neurons in both sexes is likely conveyed to GnRH neurons via mechanisms that do not induce major changes in the biophysical properties of these cells.

Significance StatementThe pattern of activity of gonadotropin-releasing hormone (GnRH) neurons is crucial to reproductive success in both males and females. Direct comparison of GnRH neurons from mice of both sexes during negative feedback and after gonadectomy revealed few differences in potassium currents, excitability, and action potential properties. These results support the hypothesis that neurons presynaptic to GnRH neurons communicate negative feedback to these cells in a manner that does not alter their intrinsic biophysical properties.


title: Neural Activity Classification with Machine Learning Models Trained on Interspike Interval Time-Series Data

abstract: Modern well-performing approaches to neural decoding are based on machine learning models such as decision tree ensembles and deep neural networks. The wide range of algorithms that can be utilized to learn from neural spike trains, which are essentially time-series data, results in the need for diverse and challenging benchmarks for neural decoding, similar to the ones in the fields of computer vision and natural language processing. In this work, we propose a spike train classification benchmark, based on open-access neural activity datasets and consisting of several learning tasks such as stimulus type classification, animals behavioral state prediction and neuron type identification. We demonstrate that an approach based on hand-crafted time-series feature engineering establishes a strong baseline performing on par with state-of-the-art deep learning based models for neural decoding. We release the code allowing to reproduce the reported results 1.


title: A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants

abstract:
The emergence of antigenically distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility is a public health threat. Some of these variants show substantial resistance to neutralization by SARS-CoV-2 infection- or vaccination-induced antibodies, which principally target the receptor binding domain (RBD) on the virus spike glycoprotein. Here, we describe 2C08, a SARS-CoV-2 mRNA vaccine-induced germinal center B cell-derived human monoclonal antibody that binds to the receptor binding motif within the RBD. 2C08 broadly neutralizes SARS-CoV-2 variants with remarkable potency and reduces lung inflammation, viral load, and morbidity in hamsters challenged with either an ancestral SARS-CoV-2 strain or a recent variant of concern. Clonal analysis identified 2C08-like public clonotypes among B cell clones responding to SARS-CoV-2 infection or vaccination in at least 20 out of 78 individuals. Thus, 2C08-like antibodies can be readily induced by SARS-CoV-2 vaccines and mitigate resistance by circulating variants of concern.

One Sentence SummaryProtection against SARS-CoV-2 variants by a potently neutralizing vaccine-induced human monoclonal antibody.


title: Whole genome sequencing evidences higher rates of relapse in Clostridioides difficile infection caused by PCR ribotype 106

abstract: Increasing prevalence and widespread of Clostridioides difficile infection (CDI) caused by the epidemic DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or the higher resistance rates found in some strains. Previous studies have also attributed higher recurrence rates to RT106 as compared to others. This study describes the genetic analysis by whole genome sequencing (WGS) of primary and recurrent isolates of RT106 to determine if the higher rate of recurrence associated to RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. The whole-genome sequences of ten primaries and fourteen recurrent RT106 isolates from ten patients were obtained to determine MLST profiles, resistance mutations and phylogenetic relatedness between the different isolates by comparative single nucleotide variants (SNV) analysis using the C. difficile DH/NAP11/106/ST-42 genome as reference (GenBank accession: GCA_002234355.1). All isolates were classified as ST42 and SNVs comparative analysis showed that those belonging to the same patient were isogenic (differed by [≤]3 SNVs), with one exception (6 SNVs); while strains belonging to different patients were not (differing by 4 to 43 SNVs) with two exceptions of isogenic isolates from different patients, suggesting putative transmission events. Phylogenetic analysis suggested the presence of similar local epidemic lineages, except for one patient whose isolates clustered with different US isolates. All the isolates, except those clustering with the US lineage, were also associated to moxifloxacin resistant since all of them were resistant by agar diffusion (MIC >32) and contained the Thr82Ile mutation in gyrA. Our results evidence that recurrent Clostridioides difficile infections caused by RT06/ST42 are mainly due to relapses, caused by primary strains, showing the great capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes.

category: microbiology


title: Identification of enzymes that are required for Rhodoquinone-dependent metabolism as targets for new species-specific inhibitors

abstract: Soil transmitted helminths (STHs) are major human pathogens that infect over a billion people. Resistance to current anthelmintics is rising and new drugs are needed. Here we combine multiple approaches to find druggable targets that are essential for RQ-dependent metabolism, an unusual form of anaerobic metabolism which STHs need to survive in their host. We identified 25 genes predicted to act in RQ-dependent metabolism from sensing hypoxia to RQ synthesis -- this includes components of the kynurenine pathway we previously showed to be essential for RQ synthesis (Del Borrello et al., 2019). We found 9 genes to be required -- since all have host orthologues, we used comparative genomics and structural modeling to identify those with helminth-specific active sites and found 4 such targets. These 4 high confidence targets open up the possibility of in silico screens to identify STH-specific inhibitors of these enzymes as new anthelmintics.

category: molecular biology


title: Germ plasm anchors at tight junctions in the early zebrafish embryo

abstract: The zebrafish germline is specified during early embryogenesis by inherited maternal RNAs and proteins collectively called germ plasm. Only the cells containing germ plasm will become part of the germline, whereas other cells will commit to somatic cell fates. Therefore, proper localization of germ plasm is key for germ cell specification and its removal is critical for the development of soma. The molecular mechanism underlying this process in vertebrates is largely unknown. Here we show that germ plasm localization in zebrafish is similar to Xenopus and amniotes but distinct from Drosophila. We identified non muscle myosin II (NMII) and tight junction (TJ) components as interaction candidates of Bucky ball (Buc), which is the germ plasm organizer in zebrafish. Remarkably, we also found that TJ protein ZO1 colocalizes with germ plasm and electron microscopy (EM) of zebrafish embryos uncovered TJ like structures at early cleavage furrows. In addition, injection of the TJ-receptor Claudin-d (Cldn-d) produced extra germ plasm aggregates. Our findings discover for the first time a role of TJs in germ plasm localization.


title: Duox generated reactive oxygen species activate ATR/Chk1 to induce G2 arrest in Drosophila tracheoblasts

abstract: Progenitors of the thoracic tracheal system of adult Drosophila (tracheoblasts) arrest in G2 during larval life and rekindle a mitotic program subsequently. G2 arrest is dependent on ATR-dependent phosphorylation of Chk1 that is actuated in the absence of detectable DNA damage. We are interested in the mechanisms that activate ATR/Chk1 (Kizhedathu et al., 2018, 2020). Here we report that levels of reactive oxygen species (ROS) are high in arrested tracheoblasts and decrease upon mitotic re-entry. High ROS is dependent on expression of Duox, an H2O2 generating-Dual Oxidase. ROS quenching by overexpression of Superoxide Dismutase 1, or by knockdown of Duox, abolishes Chk1 phosphorylation and results in precocious proliferation. Tracheae deficient in Duox, or deficient in both Duox and regulators of DNA damage-dependent ATR/Chk1 activation (Claspin/ATRIP/TOPBP1), can induce phosphorylation of Chk1 in response to micromolar concentrations of H2O2 in minutes. The findings presented reveal that H2O2 activates ATR/Chk1 in tracheoblasts by a non-canonical, potentially direct, mechanism.


title: Metacommunities from bacteria to birds: stronger environmental effects in Mediterranean than in tropical ponds.

abstract:
The metacommunity concept provides a theoretical framework that aims at explaining organism distributions by a combination of environmental filtering, dispersal and drift. With the development of statistical tools to quantify and partially isolate the role of each of these processes, empirical metacommunity studies have multiplied worldwide. However, few works attempt a multi-taxon approach and even fewer compare two distant biogeographical regions using the same methodology. Under this framework, we tested the expectation that temperate (mediterranean-climate) pond metacommunities would be more influenced by environmental and spatial processes than tropical ones, because of stronger environmental gradients and greater isolation of waterbodies.

We surveyed 30 tropical and 32 mediterranean temporary ponds from Costa Rica and Spain, respectively, and obtained data on 49 environmental variables (including limnological, hydrogeomorphological, biotic, climatic, and landscape variables). We characterized the biological communities of Bacteria and Archaea (from both the water column and the sediments), phytoplankton, zooplankton, benthic invertebrates, amphibians and birds, and estimated the relative role of space and environment on metacommunity organization for each group and region, by means of variation partitioning using Generalized Additive Models (GAMs).

Environmental selection was important in both tropical and mediterranean ponds, but markedly stronger in the latter, probably due to their larger limnological heterogeneity. Spatialized environment and pure spatial effects were greater in the tropics, related to higher climatic heterogeneity and dispersal processes (e.g. restriction, surplus) acting at different scales. The variability between taxonomic groups in spatial and environmental contributions was very wide. Effects on passive and active dispersers were similar within regions but different across regions, with higher environmental effects in mediterranean active dispersers. The residual (unexplained) variation was larger in tropical pond metacommunities, suggesting a higher role for stochastic processes and/or effects of biotic interactions in the tropics. Overall, these results provide support, for a wide variety of organisms related to aquatic habitats, for the classical view of stronger abiotic niche constraints in temperate areas compared to the tropics.


title: Metacommunities from bacteria to birds: stronger environmental effects in mediterranean than in tropical ponds.


title: Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance

abstract: Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination events. Thus, the evolutionary history of each gene should be represented by its own phylogenetic tree which may display different evolutionary patterns from the species tree that accounts for the main patterns of vertical descent. The output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree. Here, we describe a new efficient method for inferring multiple alternative consensus trees and supertrees to best represent the most important evolutionary patterns of a given set of phylogenetic trees (i.e. additive trees or X-trees). We show how a specific version of the popular k-means clustering algorithm, based on some interesting properties of the Robinson and Foulds topological distance, can be used to partition a given set of trees into one (when the data are homogeneous) or multiple (when the data are heterogeneous) cluster(s) of trees. We adapt the popular Cali[n]ski-Harabasz, Silhouette, Ball and Hall, and Gap cluster validity indices to tree clustering with k-means. A special attention is paid to the relevant but very challenging problem of inferring alternative supertrees, built from phylogenies constructed for different, but mutually overlapping, sets of taxa. The use of the Euclidean approximation in the objective function of the method makes it faster than the existing tree clustering techniques, and thus perfectly suitable for the analysis of large genomic datasets. In this study, we apply it to discover alternative supertrees characterizing the main patterns of evolution of SARS-CoV-2 and the related betacoronaviruses.


title: Mitogenomic analyses provide further evidence for multiple miniaturization events during the evolution of Seychelles caecilian amphibians

abstract: Whole mitochondrial genomes have been helpful in estimating phylogenetic relationships in many organismal groups, including caecilian amphibians. Despite the increasing ease of obtaining mitochondrial genome sequences from high-throughput sequencing, several species of caecilian lack this important molecular resource. As part of a targeted-sequence capture project of nuclear ultraconserved elements for a small but substantially diverse radiation of caecilian amphibians found on the granitic Seychelles, we examined off-target sequences to determine if we captured enough mitochondrial fragments to reconstruct mitogenomes. We reconstructed (near-)complete mitogenomes for six of the eight species of Seychelles caecilians and completed 14 independent phylogenetic analyses (Bayesian inference and maximum likelihood) on different mitochondrial datasets assembled using different alignment techniques. As with other studies, we were unable to fully resolve internal phylogenetic relationships of the group. However, we found strong support in most analyses that a recently described miniaturized species, Hypogeophis pti, and another similarly-sized miniaturized species, H. brevis are not sister taxa. Our study suggests that miniature species of caecilians likely evolved at least twice on the Seychelles and highlights the need to revise genus-level taxonomy of Seychelles caecilians while providing further evidence that off-target sequences often contain enough mitochondrial fragments to reconstruct mitogenomes.


title: The role of the Andean uplift as an asymmetrical barrier to gene flow in the Neotropical leaf-cutting ant Atta cephalotes

abstract: Neotropical diversification by the Andean uplift is typically addressed on a large evolutionary scale (e.g. speciation), even though many species are still distributed in both sides of the mountains. The three parallel mountain ranges in the northern Andes (Colombia) impose a major geographical barrier to species migration from South to Central America. How important these barriers are for conspecific diversification of cross-Andean species such as the leaf-cutting ants remains largely unknown. To answer this question, we studied the mtCOI gene of Atta cephalotes, the most widely distributed leaf-cutting ant species. Our hierarchical analyzes evidenced substantial genetic structure among regions and populations, suggesting a more complex biogeographical history of Andean populations than previously thought. These mountains seem to isolate Central American and Western Colombian populations from the rest of A. cephalotes in South America. Population and migration modelling are consistent with the origin of this species in South America and a major role of the Eastern cordillera as a geographical barrier to historical gene flow, restricting dispersion from north to south. These findings provide insights into the role of the Andean uplift as barrier to gene flow and, eventually, implications for monitoring and designing management strategies for leaf-cutting ants.

category: genetics


title: Base editing using CRISPR/Cas9 in Drosophila

abstract: Cas9 and a guide RNA function to target specific genomic loci for generation of a double stranded break. Catalytic dead versions of Cas9 (dCas9) no longer cause double stranded breaks and instead can serve as molecular scaffolds to target additional enzymatic proteins to specific genomic loci. To generate mutations in selected genomic residues, dCas9 can be used for genomic base editing by fusing a cytidine deaminase to induce C>T (or G>A) mutations at targeted sites. Here, we test base editing in Drosophila by expressing a transgenic Drosophila base editor (DBE2, based on the mammalian BE2) which consists of a fusion protein of cytidine deaminase, dCas9, and uracil glycosylase inhibitor. We utilized transgenic lines expressing gRNAs along with pan-tissue expression of the Drosophila Base Editor (Actin5C-DBE2) and found high rates of base editing at multiple targeted loci in the 20 bp target sequence. Highest rates of conversion of C>T were found in positions 3-9 of the gRNA targeted site, with conversion reaching nearly 100% of targeted DNA is somatic tissues. The simultaneous use of two gRNA targeting a genomic region spaced [~]50 bps apart led to mutations between the two gRNA targets, implicating a method to broaden the available sites accessible to targeting. These results indicate base editing is efficient in Drosophila, and could be used to induce point mutations at select loci.


title: Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

abstract: To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated 451,886 single-cell chromatin accessibility profiles and 208,557 single-cell transcriptomes from 48 polyps, 27 normal tissues, and 6 CRCs collected from patients with and without germline APC mutations. A large fraction of polyp and CRC cells exhibit a stem-like phenotype, and we define a continuum of epigenetic and transcriptional changes occurring in these stem-like cells as they progress from normal to CRC. Advanced polyps contain increasing numbers of stem-like cells, regulatory T-cells, and a subtype of FOX-regulated pre-cancer associated fibroblasts. In the cancerous state, we observe T-cell exhaustion, RUNX1-regulated cancer associated fibroblasts, and increasing accessibility associated with HNF4A motifs in epithelia. Methylation changes in sporadic CRC are strongly anti-correlated with accessibility changes along this continuum, further identifying regulatory markers for molecular staging of polyps.

category: genomics


title: Effect of Inoculum Pretreatment on Alcohol Production from Volatile Fatty Acids through an Anaerobic Solventogenic Process

abstract: 1This work evaluates four different physicochemical pretreatments (acidic, thermal, acidic-thermal and thermal-acidic) on an anaerobic inoculum used for alcohol production from acetate and butyrate. All experiments were conducted in single batches using acetate and butyrate as substrates at 30 {degrees}C and with a pressurized headspace of pure H2 at 2.15 atm (218.2 MPa). Thermal and acidic-thermal pretreatments lead to higher production of both ethanol and butanol. Mathematical modelling shows that the highest attainable concentrations of ethanol and butanol produced were 122 mg L-1 and 97 mg L-1 for the thermal pretreatment (after 17.5 days) and 87 mg L-1 and 143 mg L-1 for the acidic-thermal pretreatment (after 18.9 days). Acetate was produced in all assays. Thermodynamic data indicated that a high H2 partial pressure favoured solventogenic metabolic pathways. Finally, sequencing data showed that both thermal and acidic-thermal pretreatments selected mainly the bacterial genera Pseudomonas, Brevundimonas and Clostridium. The acidic-thermal pretreatment selected a bacterial community more adapted to the conversion of acetate and butyrate into ethanol and butanol, respectively. Thermal-acidic pretreatment was unstable, showing significant variability between replicates. Acidic pretreatment showed the lowest alcohol production.


title: Microorganisms Characterization in Anaerobic Solventogenic Processing of Volatile Fatty Acids


title: Microbial Communities Performing Hydrogen Solventogenic Metabolism of Volatile Fatty Acids


title: Novel cancer subtyping method based on patient-specific gene regulatory network

abstract: The identification of cancer subtypes is important for the understanding of tumor heterogeneity. In recent years, numerous computational methods have been proposed for this problem based on the multi-omics data of patients. It is widely accepted that different cancer subtypes are induced by different molecular regulatory networks. However, only a few incorporate the differences between their molecular systems into the classification processes. In this study, we present a novel method to classify cancer subtypes based on patient-specific molecular systems. Our method quantifies patient-specific gene networks, which are estimated from their transcriptome data. By clustering their quantified networks, our method allows for cancer subtyping, taking into consideration the differences in the molecular systems of patients. Comprehensive analyses of The Cancer Genome Atlas (TCGA) datasets applied to our method confirmed that they were able to identify more clinically meaningful cancer subtypes than the existing subtypes and found that the identified subtypes comprised different molecular features. Our findings show that the proposed method, based on a simple classification using the patient-specific molecular systems, can identify cancer subtypes even with single omics data, which cannot otherwise be captured by existing methods using multi-omics data.


title: High-throughput screen using fluorescence lifetime detects compounds that modulate myosin-binding protein C interactions with actin

abstract:
Cardiac myosin-binding protein C (cMyBP-C) interacts with actin and myosin to modulate cardiac contractility. These interactions are regulated by cMyBP-C phosphorylation. Heart failure patients often have decreased cMyBP-C phosphorylation and phosphorylation in model systems appears to be cardioprotective for heart failure. Therefore, cMyBP-C is a potential target for heart failure drugs that mimic phosphorylation and/or perturb its interactions with actin/myosin.

We have used a novel fluorescence lifetime-based assay to identify small-molecule inhibitors of actin-cMyBP-C binding. Actin was labeled with a fluorescent dye (Alexa Fluor 568, AF568) near its cMyBP-C binding sites. When combined with cMyBP-C N-terminal fragment, C0-C2, the fluorescence lifetime of AF568-actin decreases. Using this reduction in lifetime as a readout of actin binding, a high-throughput screen of a 1280-compound library identified 3 reproducible Hit compounds that reduced C0-C2 binding to actin in the micromolar range. Binding of phosphorylated C0-C2 was also blocked by these compounds. That they specifically block binding was confirmed by a novel actin-C0-C2 time-resolved FRET (TR-FRET) binding assay. Isothermal titration calorimetry (ITC) and transient phosphorescence anisotropy (TPA) confirmed that the Hit compounds bind to cMyBP-C but not to actin. TPA results were also consistent with these compounds inhibiting C0-C2 binding to actin. We conclude that the actin-cMyBP-C lifetime assay permits detection of pharmacologically active compounds that affect cMyBP-Cs actin binding function. TPA, TR-FRET, and ITC can then be used to understand the mechanism by which the compounds alter cMyBP-C interactions with actin.