title: Evidence Accumulates for Individual Attributes during Value-Based Decisions

abstract: When choosing between different options, we tend to consider specific attribute qualities rather than deliberating over some general sense of the options overall values. The importance of each attribute together with its quality will determine our preference rankings over the available alternatives. Here, we test the hypothesis that the most prominent class of model for simple decisions - sequential sampling or evidence accumulation to bound - can be bolstered by explicitly incorporating variables related to individual attributes in addition to the standard usage of overall value estimates. We examine six datasets in which participants evaluated snack foods both in terms of overall value and individual attributes, then chose between pairs of the same snacks, and show that only models that explicitly incorporate information about the individual attributes are able to reproduce fundamental patterns in the choice data, such as the influence of attribute disparity on decisions, and such models provide quantitatively better fits to the choice outcomes, response times, and confidence ratings compared to models based on overall value alone. Our results provide important evidence that incorporating attribute-level information into computational models helps us to better understand the cognitive processes involved in value-based decision-making.


title: The relative importance of individual attributes varies across preference elicitation methods

category: neuroscience


title: RIG-I-induced innate antiviral immunity protects mice from lethal SARS-CoV-2 infection

abstract: The SARS-CoV-2 pandemic has underscored the need for rapidly employable prophylactic and antiviral treatments against emerging viruses. Nucleic acid agonists of the innate immune system can be administered to activate an effective antiviral program for prophylaxis in exposed populations, a measure of particular relevance for SARS-CoV-2 infection due to its efficient evasion of the host antiviral response. In this study, we utilized the K18-hACE2 mouse model of COVID-19 to examine whether prophylactic activation of the antiviral receptor RIG-I protects mice from SARS-CoV-2 infection. Systemic treatment of mice with a specific RIG-I ligand one to seven days prior to infection with a lethal dose of SARS-CoV-2 improved their survival of by up to 50 %. Improved survival was associated with lower viral load in oropharyngeal swabs and in the lungs and brain of RIG-I-treated mice. Moreover, despite antiviral protection, the surviving mice that were treated with RIG-I ligand developed adaptive SARS-CoV-2-specific immunity. These results reveal that prophylactic RIG-I activation by synthetic RNA oligonucleotides is a promising strategy to convey short-term, unspecific antiviral protection against SARS-CoV-2 infection and may be a suitable broad-spectrum approach to constraining the spread of newly emerging viruses until virus-specific therapies and vaccines become available.

category: immunology


title: Nontypeable Haemophilus influenzae infection impedes Pseduomonas aeruginosa colonization and persistence in mouse respiratory tract

abstract:
Patients with cystic fibrosis (CF) experience lifelong respiratory infections which are a significant cause of morbidity and mortality. These infections are polymicrobial in nature, and the predominant bacterial species undergo a predictable series of changes as patients age. Young patients have populations dominated by opportunists that are typically found within the microbiome of the human nasopharynx, such as nontypeable Haemophilus influenzae (NTHi); these are eventually supplanted and the population within the CF lung is later dominated by pathogens such as Pseudomonas aeruginosa (Pa). In this study, we investigated how initial colonization with NTHi impacts colonization and persistence of Pa in the respiratory tract.

Analysis of polymicrobial biofilms in vitro by confocal microscopy revealed that NTHi promoted greater levels of Pa biofilm volume and diffusion. However, sequential respiratory infection of mice with NTHi followed by Pa resulted in significantly lower Pa as compared to infection with Pa alone. Coinfected mice also had reduced airway tissue damage and lower levels of inflammatory cytokines as compared with Pa infected mice. Similar results were observed after instillation of heat-inactivated NTHi bacteria or purified NTHi lipooligosaccharide (LOS) endotoxin prior to Pa introduction. Based on these results, we conclude that NTHi significantly reduces susceptibility to subsequent Pa infection, most likely due to priming of host innate immunity rather than a direct competitive interaction between species. These findings have potential significance with regard to therapeutic management of early life infections in patients with CF.

category: microbiology


title: Nontypeable Haemophilus influenzae infection impedes Pseudomonas aeruginosa colonization and persistence in mouse respiratory tract


title: Division of Labor between SOS and PafBC in Mycobacterial DNA Repair and Mutagenesis

abstract: DNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as M. tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.


title: Quantitation of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes

abstract:
We investigated the potential use and quantitation of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA and RNA enteric viruses, as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantitated in the extracted samples via quantitative PCR using TaqMan assays.

The average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.0547 and 0.7986) than the average gene copies assessed in the effluents for Adenovirus and crAssphage (DNA viruses), Pepper Mild Mottle Virus (RNA virus), and uidA in terms of both volume and biomass. A significant reduction of these enteric viruses was observed consistently in activated sludge samples compared with those for raw sewage. Corresponding reductions in gene copies per volume and gene copies per biomass were also seen for uidA but were not statistically significant (p-value = 0.8769 and p-value = 0.6353, respectively). The higher gene copy numbers of enteric viruses and E. coli observed in the effluents may be associated with the 12-hour hydraulic retention time in the facility. Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA. This indicate that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used as complementary viral indicators of human fecal pollution.


title: Establishment of a prognosis prediction model based on pyroptosis-related signatures associated with the immune microenvironment and molecular heterogeneity in clear cell renal carcinoma

abstract:
BackgroundPytoptosis is essential for tumorigenesis and progression of clear cell renal cell carcinoma (ccRCC). However, the heterogeneity of pyroposis and its relationship with the tumor microenvironment (TME) remain unclear. The aim of the present study was to identify proptosis-related subtypes and construct a prognosis prediction model based on pyroptosis signatures.

MethodsFirst, heterogenous pyroptosis subgroups were explored based on 33 pyroptosis-related genes and ccRCC samples from TCGA, and the model establsihed by LASSO regression was verified by ICGC database. Then, the clinical significance, functional status, immune infiltration, cell-cell communication, genomic alteration and drug sensitivity of different subgroups were further analyzed. Finally, the LASSO-Cox algorithm was applied to narrow down the candidate genes to develop a robust and concise prognostic model.

ResultsTwo heterogenous pyroptosis subgroups were identified: pyroptosis-low immunity-low C1 subtype, and pyroptosis-high immunity-high C2 subtype. Compared with C1, C2 was associated with a higher clinical stage or grade and a worse prognosis. More immune cell infiltration was observed in C2 than that in C1, while the response rate in C2 subgroup was lower than that in C1 subgroup. Pyroptosis related genes were mainly expressed in myeloid cells, and T cells and epithelial cells might influence other cell clusters via Pyroptosis related pathway. In addition, C1 was characterized by MTOR and ATM mutation, while C2 was characterized by more significant alterations in SPEN and ROS1 mutation. Finally, we constructed and validated a robust and promising signature based on the pyroptosis-related risk score for assessing the prognosis in ccRCC.

ConclusionWe identified two heterogeneous pyroptosis subtypes and 5 reliable risk signatures to establish a prognosis prediction model. Our findings may help better understand the role of pyroptosis in ccRCC progression and provide a new perspective in the management of ccRCC patients.

category: molecular biology


title: Vinculin recruitment to α-catenin halts the differentiation and maturation of enterocyte progenitors to maintain homeostasis of the Drosophila intestine.

abstract: Mechanisms communicating changes in tissue stiffness and size are particularly relevant in the intestine, because it is subject to constant mechanical stresses caused by peristalsis of its variable content. Using the Drosophila intestinal epithelium, we investigate the role of vinculin, one of the best characterised mechanoeffectors, which functions in both cadherin and integrin adhesion complexes. We discovered that vinculin regulates cell fate decisions, by preventing precocious activation and differentiation of intestinal progenitors into absorptive cells. It achieves this in concert with -catenin at sites of cadherin adhesion, rather than as part of integrin function. Following asymmetric division of the stem cell into a stem cell and an enteroblast, the two cells initially remain connected by adherens junctions, where vinculin is required, only on the enteroblast side, to maintain the enteroblast in a quiescent state and inhibit further divisions of the stem cell. Removing vinculin increases enteroblast differentiation and numbers, resulting in an enlarged gut with improved ability to recover after starvation. Thus, mechanical regulation at the contact between stem cells and their progeny is used to control tissue cell number.

category: developmental biology


title: Evolution of andrenine bees reveals a long and complex history of faunal interchanges between the Americas during the Mesozoic and Cenozoic

abstract: Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Among the main groups of bees, Andreninae sensu lato comprise about 3000 species widely distributed with greatest and disjunct diversity in arid areas of North America, South America, and the Palearctic region. Here, we present the first comprehensive dated phylogeny and historical biogeographic analysis for andrenine bees, including representatives of all currently recognized tribes. Our analyses rely on a dataset of 106 taxa and 7952 aligned nucleotide positions from one mitochondrial and six nuclear loci. Andreninae is strongly supported as a monophyletic group and the recovered phylogeny corroborates the commonly recognized clades for the group. Thus, we propose a revised tribal classification that is congruent with our phylogenetic results. The time-calibrated phylogeny and ancestral range reconstructions of Andreninae reveal a fascinating evolutionary history with Gondwana patterns that are unlike those observed in other subfamilies of bees. Andreninae arose in South America during the Late Cretaceous around 90 Million years ago (Ma) and the origin of tribes occurred through a relatively long time-window from this age to the Miocene. The early evolution of the main lineages took place in South America until the beginning of Paleocene with North American fauna origin from it and Palearctic from North America as results of multiple lineage interchanges between these areas by long-distance dispersal or hopping through landmass chains. Overall, our analyses provide strong evidence of amphitropical distributional pattern currently observed in Andreninae in the American continent as result at least three periods of possible land connections between the two American landmasses, much prior to the Panama Isthmus closure. The andrenine lineages reached the Palearctic region through four dispersal events from North America during the Eocene, late Oligocene and early Miocene, most probably via the Thulean Bridge. The few lineages with Afrotropical distribution likely originated from a Palearctic ancestral in the Miocene around 10 Ma when these regions were contiguous, and the Sahara Desert was mostly vegetated making feasible the passage by several organisms. Incursions of andrenine bees to North America and then onto the Old World are chronological congruent with distinct periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.

category: evolutionary biology


title: An Intrinsically Disordered Peptide Tag that Confers an Unusual Solubility to Aggregation-Prone Proteins

abstract:
There is a high demand for the production of recombinant proteins in Escherichia coli for biotechnological applications but their production is still limited by their insolubility. Fusion tags have been successfully used to enhance the solubility of aggregation-prone proteins; however, smaller and more powerful tags are desired for increasing the yield and quality of target proteins. Herein, NEXT tag, a 53 amino acid-length solubility enhancer, is described. The NEXT tag showed outstanding ability to improve both in vivo and in vitro solubilities with minimal effect on passenger proteins. The C-terminal region of the tag was mostly responsible for in vitro solubility, while the N-terminal region was essential for in vivo soluble expression. The NEXT tag appeared to be intrinsically disordered and seemed to exclude neighboring molecules and prevent protein aggregation by acting as an entropic bristle. This novel peptide tag should have general use as a fusion partner to increase the yield and quality of difficult-to-express proteins.

IMPORTANCEProduction of recombinant protein in Escherichia coli still suffers from the insolubility problem. Conventional solubility enhancers with large sizes represented by maltose-binding protein (MBP) have remained as the first-choice tags, however, the success in the soluble expression of tagged protein is largely unpredictable. In addition, the large tags can negatively affect the function of target proteins. In this work, NEXT tag, an intrinsically disordered peptide, was introduced as a small but powerful alternative to MBP. The NEXT tag could significantly improve both expression level and solubility of target proteins including a thermostable carbonic anhydrase and a polyethylene terephthalate (PET)-degrading enzyme that are remarkable enzymes for environmental bioremediation.

category: bioengineering


title: Analysis of Gene Expression Profiles to study Malaria Vaccine Dose Efficacy & Immune Response Modulation.

abstract: Malaria is a life-threatening disease, and the Africa is still one of the most affected endemic regions despite years of policy to limit infection and transmission rates. Further, studies into the variable efficacy of the vaccine are needed to provide a better understanding of protective immunity. Thus, the current study is designed to delineate the effect of the different vaccination doses on the transcriptional profiles of subjects to determine its efficacy and understand the molecular mechanisms underlying the protection this vaccine provides. Here, we used gene expression profiles of pre and post-vaccination patients after various doses of RTS,S based on 275 and 583 samples collected from the GEO datasets. At first, exploratory data analysis based Principal component analysis (PCA) shown the distinct pattern of different doses. Subsequently, differential gene expression analysis using edgeR revealed the significantly (FDR <0.005) 158 down-regulated and 61 upregulated genes between control vs. Controlled Human Malaria Infection (CHMI) samples. Further, enrichment analysis of significant genes using Annotation and GAGE tools delineate the involvement of CCL8, CXCL10, CXCL11, XCR1, CSF3, IFNB1, IFNE, IL12B, IL22, IL6, IL27, etc.,genes which found to be upregulated after earlier doses but downregulated after the 3rd dose in cytokine-chemokine pathways. Notably, we identified 13 cytokine genes whose expression significantly varied during three doses. Eventually, these findings give insight to the dual role of cytokine responses in malaria pathogenesis and variations in their expression patterns after various doses of vaccination involved in protection.

category: bioinformatics


title: DBpred: A deep learning method for the prediction of DNA interacting residues in protein sequences

abstract: DNA-protein interaction is one of the most crucial interactions in the biological system, which decide the fate of many processes such as transcription, regulation of gene expression, splicing, and many more. Though many computational approaches exist that can predict the DNA interacting residues from the protein sequences, there is still a significant opportunity for improvement in terms of performance and accessibility. In this study, we have downloaded the benchmark dataset from method hybridNAP and recently published method ProNA2020, for training and validation purposes, that comprise 864 and 308 proteins, respectively. We have implemented CD-HIT software to handle the redundancy with 30% identity, and left with 646 proteins for training and 46 proteins for validation purposes, in which the validation dataset do not share more than 30% of sequence identity with the training dataset. We have generated amino acid binary profiles, physicochemical-properties based binary profiles, PSSM profiles, and a combination of all profiles described as hybrid feature. 1D-CNN based model performed best as compared to other models for each set of features. The model developed using amino acid binary profile achieved AUROC of 0.83 and 0.74 for training and validation dataset. Using physicochemical properties based binary profile, model attained AUROC of 0.86 and 0.73 for training and validation dataset. Model generated using PSSM profile resulted in the better performance with AUROC 0.91 and 0.74 for training and validation dataset. And, model developed using hybrid of all features performed best with AUROC of 0.91, and 0.79 for training and validation dataset, respectively. We have compared our methods performance with the current approach and shown improvements. We have included the best-performing models in the standalone and web server accessible at https://webs.iiitd.edu.in/raghava/dbpred. DBPred is an effective approach to predict the DNA interacting residues in the protein using its primary structure.


title: MorphData: Automating the data extraction process of morphological features of microglial cells in ImageJ

abstract: Microglial cells are the first line of defense within the central nervous system, with morphological characterization being widely used to define their activation status. Most methods to evaluate microglia status are manual, and, therefore, often biased, inaccurate, and time consuming. In fact, the process to collect morphological data starts with the acquisition of photomicrographs from where images of single cells are extracted. Then, the researcher collects the morphological features that characterize each cell. However, a manual data collection process from single cells can take weeks to complete. This work describes an open-source ImageJ plugin, MorphData, which automatizes the data extraction process of morphological features of single microglial cells. The plugin collects, processes, and organizes features associated with cell complexity and ramification. In a computer with limited computing power, MorphData was able to handle 699 single cells in less than 14 minutes. The same process, if performed manually, would take almost 19 working days. Overall, MorphData significantly reduces the time taken to collect morphological data from microglial cells, which can then be used to study, understand, and characterize microglia behavior in the brain of human patients or of animal models of neurological and psychiatric diseases.


title: Synaptic and membrane conductance underlie phase transition in a simple half-center oscillator

abstract: Reciprocally inhibitory modules that form half-center oscillators require mechanisms for escaping or being released from inhibition. The central pattern generator (CPG) underlying swimming by the nudibranch mollusc, Dendronotus iris, is composed of only four neurons that are organized into two competing modules of a half center oscillator. In this system, bursting activity in left-right alternation is not driven by any of the neurons but is an emergent property of the network as a whole. We found that the unique synaptic actions and membrane properties of the two neurons in each module (Si2 and Si3) play complementary roles in generating stable bursting in this network oscillator. Only Si2 evokes fast and strong inhibition of its contralateral counterpart, the termination of which initiates post-inhibitory rebound in the Si3 of that module. Only Si3 is responsible for the rebound excitation because it has a hyperpolarization-activated inward current. Within each module, the synaptic actions and membrane properties of the two neurons complement each other: Si3 excites Si2, which then feeds back slow inhibition to Si3, terminating the burst. Using dynamic clamp, we showed that the magnitude of the slow inhibition sets the period of the oscillator. Thus, the synaptic actions of Si2 provide the hyperpolarization needed for the other module to rebound stably, whereas the membrane properties of Si3 in each module cause it to rebound first and excite Si2 and maintain the burst until the cycle repeats and the other module becomes active.


title: Bursting emerges from the complementary roles of neurons in a four-cell network


title: Impaired dynamics of brain precapillary sphincters and first order capillaries explains reduced neurovascular functions in aging

abstract: The microvascular inflow tract (MIT), comprising the penetrating arterioles, precapillary sphincters, and first order capillaries, is the bottleneck for brain blood flow and energy supply. However, the exact structural and functional alterations of the MIT during aging remain elusive. In vivo 4-dimensional two-photon imaging showed an age-dependent decrease in vaso-responsivity, with reduced sensitivity of the MIT to pinacidil and papaverine, vasoconstrictor endothelin-1, and nitric oxide synthase inhibitor L-NAME. This was accompanied by an age-dependent decrease in capillary density close to the arterioles and loss of pericyte processes, though the number of pericyte somas and pericyte SMA density were preserved. The age-related reduction in vascular reactivity was most pronounced at precapillary sphincters, highlighting their crucial role in capillary blood flow regulation. Mathematical modeling revealed dysregulated but preserved pressure and flow in aged mice during vasoconstriction. Preventing reduced responsivity of the MIT may ameliorate the blood flow decrease associated with aging-related brain frailty.


title: Translational modeling of non-traumatic raised intracranial pressure in rodents; the impact of diet-induced obesity on cephalic hypersensitivity and retinal degeneration

abstract:
Elevated intracranial pressure (ICP) is observed in many brain disorders. Obesity has been linked to ICP pathogenesis in disorders such as idiopathic intracranial pressure (IIH). We investigated the effect of diet induced obesity (DIO) on ICP and clinically relevant sequelae.

Rats were fed either a control or high fat diet. Following weight gain long term ICP, headache behavior, body composition and retinal outcome were examined. Post-hoc analysis of retinal histology and molecular analysis of choroid plexus and trigeminal ganglion (TG) were performed.

DIO rats demonstrated raised ICP by 55% which correlated with the abdominal fat percentage and increased non-respiratory slow waves, suggestive of altered cerebral compliance. Concurrently, DIO rats demonstrated a specific cephalic cutaneous allodynia which negatively correlated with the abdominal fat percentage. This sensitivity was associated with increased expression of headache markers in TG. Additionally, DIO rats had an in vivo increased retinal nerve fiber layer thickness associated with raised ICP with a subsequent post-hoc demonstration of neuroretinal degeneration.

This study demonstrates for the first time that DIO leads to raised ICP and subsequent clinically relevant symptom development. This novel model of non-traumatic raised ICP could expand the knowledge regarding disorders with elevated ICP such as IIH.


title: The impact of obesity; key features of raised intracranial pressure and clinical sequalae in rodents


title: Synaptic and mitochondrial plasticity associated with fear memory revealed by deep learning-based 3D reconstruction

abstract: Serial section electron microscopy (ssEM) can provide comprehensive 3D ultrastructural information of the brain with exceptional computational cost. Targeted reconstruction of subcellular structures from ssEM datasets is less computationally demanding but still highly informative. We thus developed a Region-CNN-based deep learning method to identify, segment, and reconstruct synapses and mitochondria to explore the structural plasticity of synapses and mitochondria in the auditory cortex of mice subjected to fear conditioning. Upon reconstructing over 135,000 mitochondria and 160,000 synapses, we found that fear conditioning significantly increases the number of mitochondria but decreases their size, and promotes the formation of multi-contact synapses comprising a single axonal bouton and multiple postsynaptic sites from different dendrites. Modeling indicates that such multi-contact configuration increases the information storage capacity of new synapses by over 50%. With high accuracy and speed in reconstruction, our method yields structural and functional insight into cellular plasticity associated with fear learning.


title: Fear memory-associated synaptic and mitochondrial changes revealed by deep learning-based processing of electron microscopy data


title: Epithelial Immunomodulation by Aerosolized Toll-like Receptor Agonists Attenuates Allergic Responsiveness in Mice

abstract:
Allergic asthma is a chronic inflammatory respiratory disease associated with eosinophilic infiltration, increased mucus production, airway hyperresponsiveness (AHR), and airway remodeling. Epidemiologic data has revealed that the prevalence of allergic sensitization and associated diseases has increased in the twentieth century. This has been hypothesized to be partly due to reduced contact with microbial organisms (the hygiene hypothesis) in industrialized society. Airway epithelial cells, once considered a static physical barrier between the body and the external world, are now widely recognized as immunologically active cells that can initiate, maintain, and restrain inflammatory responses, such as those that mediate allergic disease. Airway epithelial cells can sense allergens via myriad expression of Toll-like receptors (TLRs) and other pattern-recognition receptors (PRRs). We sought to determine whether the innate immune response stimulated by a combination of Pam2CSK4 ("Pam2", TLR2/6 ligand) and a class C oligodeoxynucleotide ODN362 ("ODN", TLR9 ligand) when delivered together by aerosol ("Pam2ODN"), can modulate the allergic immune response to allergens. Treatment with Pam2ODN 7 days before sensitization to House Dust Mite (HDM) extract resulted in a strong reduction in eosinophilic and lymphocytic inflammation. This Pam2ODN immunomodulatory effect was also seen using Ovalbumin (OVA) and A. oryzae (Ao) mouse models. The immunomodulatory effect was observed as much as 30 days before sensitization to HDM, but ineffective just 2 days after sensitization, suggesting that Pam2ODN immunomodulation lowers the allergic responsiveness of airway epithelial cells. Furthermore, Pam2 and ODN cooperated synergistically suggesting that this treatment is superior to any single agonist in the setting of allergen immunotherapy.

One Sentence SummaryA synergistic combination of Toll-like Receptor agonists, delivered directly into the lung mucosa, can attenuate allergic responsiveness of airway epithelial cells and prevent host sensitization to aeroallergens.

What is already knownO_LIAllergic sensitization has increased in the 20th century due to reduced contact with microbial organisms in industrialized society (ie. hygiene hypothesis)
C_LIO_LIWe have previously identified a pharmacological means to stimulate innate immunity of lung epithelial cells.
C_LI

What this study addsO_LIActivation of innate immunity in lung epithelial cells attenuates the allergic responsiveness of mice.
C_LIO_LISynergistic cooperation of pattern recognition receptors induces stronger immunomodulatory responses
C_LI

What is the clinical significanceO_LIAerosolized Toll-like Receptor agonists have been demonstrated as safe in human clinical trials
C_LIO_LIThis study provides proof-of-principle that aerosolized toll-like receptor agonists could have clinical efficacy in the setting of the allergen immunotherapy
C_LI


title: Learning torus PCA based classification for multiscale RNA backbone structure correction with application to SARS-CoV-2

abstract:
MotivationReconstructions of structure of biomolecules, for instance via X-ray crystallography or cryo-EM frequently contain clashes of atomic centers. Correction methods are usually based on simulations approximating biophysical chemistry, making them computationally expensive and often not correcting all clashes.

ResultsWe propose a computationally fast data-driven statistical method yielding suites free from within-suite clashes: From such a clash free training data set, devising mode hunting after torus PCA on adaptive cutting average linkage tree clustering (MINTAGE), we learn RNA suite shapes. With classification based on multiscale structure enhancement (CLEAN), for a given clash suite we determine its neighborhood on a mesoscopic scale involving several suites. As corrected suite we propose the Frechet mean on a torus of the largest classes in this neighborhood. We validate CLEAN MINTAGE on a benchmark data set, compare it to a state of the art correction method and apply it, as proof of concept, to two exemplary suites adjacent to helical pieces of the frameshift stimulation element of SARS-CoV-2 which are difficult to reconstruct. In contrast to a recent reconstruction proposing several different structure models, CLEAN MINTAGE unanimously proposes structure corrections within the same clash free class for all suites.

Code Availabilityhttps://gitlab.gwdg.de/henrik.wiechers1/clean-mintage-code


title: Knockout of circRNAs by base editing back-splice sites of circularized exons

abstract: A large number of circular RNAs (circRNAs) are produced from back-splicing of exon(s) of precursor mRNAs and generally co-expressed with their cognate linear RNAs from the same gene loci. Methods for circRNA-specific knockout are lacking, largely due to complete sequence-overlaps between circular and cognate linear RNAs. Here, we report to use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress both circular and linear RNAs expression, which confirms the requirement of canonical splice site signals for back-splice. Importantly, by targeting back-splice sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular, but not linear cognate RNAs. As hundreds of exons were found to be predominantly back-spliced to produce circRNAs, this study provides an efficient method to deplete circRNAs for function study.


title: Global change affects differently at local scales animal populations: why Starlings still expands to the south while other temperate species go to the north?

abstract:
Global change, which regroups global warming, landscape transformations and other anthropic modifications of ecosystems, has effects on populations and communities and produces modifications in the expansion area of species. While some species disappear, other ones are beneficiated by the new conditions and some of them evolve in new adapted forms or leave their ancient distribution area.

As climate change tends to increase the temperature in several regions of the world, some species have been seen to leave areas in equatorial regions in order to join colder areas either towards the north of the northern hemisphere or towards the south of the southern one.

Many birds as have moved geographically in direction to the poles and in many cases they have anticipated their laying dates. Actually, two tit species that use to lay their eggs in a period that their fledging dates synchronize with the emerging dates of caterpillars are now evolving to reproductive in periods earlier than before the climate change. Several species are reacting like that and other ones are moving to the north in Europe for example. Nevertheless, and very curiously, European starling, Sturnus vulgaris, populations are behaving on the contrary: their laying dates are moving towards later spring and their distribution area is moving towards the south. In this study we explore and discuss about different factors that may explain this difference from other birds.

category: ecology


title: Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion

abstract: The development of a tractable small animal model faithfully reproducing human COVID-19 pathogenesis would arguably meet a pressing need in biomedical research. Thus far, most investigators have used transgenic mice expressing the human ACE2 in epithelial cells (K18-hACE2 transgenic mice) that are intranasally instilled with a liquid SARS-CoV-2 suspension under deep anesthesia. Unfortunately, this experimental approach results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this models usefulness. Here, we describe the use of an inhalation tower system that allows exposure of unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in SARS-CoV-2- infected patients. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.


title: Multispecies phase diagram reveals biophysical principles of bacterial biofilm architectures

abstract: Bacterial biofilms are among the most abundant multicellular communities on Earth and play essential roles in a wide range of ecological, medical, and industrial processes. Recently developed imaging techniques offer unprecedented insights into the three-dimensional internal structure and external morphology of growing biofilms, but general ordering principles that govern the emergence of biofilm architecture across species remain unknown. Here, we combine experiments, simulations, and topological analysis to identify universal mechanical interaction properties that determine early-stage biofilm architectures of different bacterial species. Performing single-cell resolution imaging of Vibrio cholerae, Escherichia coli, Salmonella enterica, and Pseudomonas aeruginosa biofilms, we dis-covered that biofilm architectures up to a few thousand cells can be described by a two-dimensional phase diagram similar to nematic liquid crystals. Mechanistic simulations and experiments using single-species mutants for which the cell aspect ratio and the cell-cell adhesion are systematically varied, show that tuning these parameters reproduces biofilm architectures of different species. A topological analysis of biofilm architectures across species further reveals that cell neighborhood motifs can be described by a universal Tracy-Widom distribution. More generally, due to its generic mathematical formulation, the topological analysis framework enables a structural comparisons and classification of a wide range of multicellular life forms. Early-stage biofilm architectures of different species therefore display a universal topological structure, and their development is determined by conserved mechanical cell-cell interactions.


title: Functional roles of multiple Ton complex genes in a Sphingobium degrader of lignin-derived aromatic compounds

abstract: TonB-dependent transporters (TBDTs) mediate outer membrane transport of nutrients using the energy derived from proton motive force transmitted from the TonB-ExbB-ExbD complex localized in the inner membrane. Recently, we discovered ddvT encoding a TBDT responsible for the uptake of a 5,5-type lignin-derived dimer in Sphingobium sp. strain SYK-6. Furthermore, overexpression of ddvT in an SYK-6-derivative strain enhanced its uptake capacity, improving the rate of platform chemical production. Thus, understanding the uptake system of lignin-derived aromatics is fundamental for microbial conversion-based lignin valorization. Here we examined whether multiple tonB-, exbB-, and exbD-like genes in SYK-6 contribute to the outer membrane transport of lignin-derived aromatics. The disruption of tonB2-6 and exbB3 did not reduce the capacity of SYK-6 to convert or grow on lignin-derived aromatics. In contrast, the introduction of the tonB1-exbB1-exbD1-exbD2 operon genes into SYK-6, which could not be disrupted, promoted the conversion of {beta}-O-4-, {beta}-5-, {beta}-1-, {beta}-{beta}-, and 5,5-type dimers and monomers, such as ferulate, vanillate, syringate, and protocatechuate. These results suggest that TonB-dependent uptake involving the tonB1 operon genes is responsible for the outer membrane transport of the above aromatics. Additionally, exbB2/tolQ and exbD3/tolR were suggested to constitute the Tol-Pal system that maintains the outer membrane integrity.


title: Scaffolding protein GspB/OutB facilitates assembly of the Dickeya dadantii type 2 secretion system by anchoring the outer membrane secretin pore to the inner membrane and to the peptidoglycan cell wall.

abstract:
The phytopathogenic proteobacterium Dickeya dadantii secretes an array of plant cell wall degrading enzymes and other virulence factors via the type 2 secretion system (T2SS). T2SSs are widespread among important plant, animal and human bacterial pathogens. This multi-protein complex spans the double membrane cell envelope and secretes fully folded proteins through a large outer membrane pore formed by 15 subunits of the secretin GspD. Secretins are also found in the type 3 secretion system and the type 4 pili. Usually, specialized lipoproteins termed as pilotins assist the targeting and assembly of secretins into the outer membrane. Here, we show that in Dickeya, the pilotin acts in concert with the scaffolding protein GspB. Deletion of gspB profoundly impacts secretin assembly, pectinase secretion, and virulence. Structural studies reveal that GspB possesses a conserved periplasmic Homology Region domain that interacts directly with the N-terminal secretin domain. Site-specific photo cross-linking unravels molecular details of the GspB-GspD complex in vivo. We show that GspB facilitates outer membrane targeting and assembly of the secretin pores and anchors them to the inner membrane while the C-terminal extension of GspB scaffolds the secretin channel in the peptidoglycan cell wall. Phylogenetic analysis shows that in other bacteria, GspB homologs vary in length and domain composition and act in concert with either a cognate ATPase GspA or a pilotin GspS.

ImportanceGram-negative bacteria have two cell membranes sandwiching a peptidoglycan net that form together a robust protective cell envelope. To translocate effector proteins across this multilayer envelope, bacteria have evolved several specialized secretion systems. In the type 2 secretion system and some other bacterial machineries, secretins form large multimeric pores that allow transport of effector proteins or filaments across the outer membrane. The secretins are essential for nutrient acquisition and pathogenicity and constitute a target for development of new antibacterials. Targeting of secretin subunits into the outer membrane is often facilitated by a special class of lipoproteins called pilotins. Here, we show that in Dickeya and some other bacteria, the scaffolding protein GspB acts in concert with pilotin, facilitating the assembly of the secretin pore and its anchoring to both the inner membrane and the bacterial cell wall. GspB homologs of varied domain composition are present in many other T2SSs.


title: Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples

abstract: Effective monitoring of antibiotic resistance genes and their dissemination in environmental ecosystems has been hindered by the cost and efficiency of methods available for the task. We developed a method entitled the Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), a system implementing high-throughput sequencing to simultaneously sequence thousands of antibiotic resistant genes representing a full-spectrum of antibiotic resistance classes commonly seen in environmental systems. In this study, we demonstrated DARTE-QM by screening 662 antibiotic resistance genes within environmental samples originated from manure, soil, and animal feces, in addition to a mock-community used as a control to test performance. DARTE-QM offers a new approach to studying antibiotic resistance in environmental microbiomes, showing advantages in efficiency and the ability to scale for many samples. This method provides a means of data acquisition that will alleviate the obstacles that many researchers in this area currently face.


title: In vivo capture of bacterial cells by remote guiding

abstract: Recently, it has been shown that several bacterial strains can be very efficient in cancer treatment since they possess many important properties such as self-targeting, ease of detection, sensing and toxicity against tumors. However, there are only a few relevant "candidates" for such an approach, as targeting and detection one of the biggest challenges as well as there are many limitations in the use of genetic approaches. Here, it is proposed the solution that enables surface modification of alive bacterial cells without interfering with their genetic material and potentially reduces their toxic side effect. By the electrostatic interaction fluorescently labeled polyelectrolytes (PEs) and magnetite nanoparticles (NPs) were deposited on the bacterial cell surface to control the cell growth, distribution and detection of bacteria. According to the results obtained in vivo, by the magnet entrapment of the modified bacteria the local concentration of the cells was increased more than 5 times, keeping the high concentrations even when the magnet is removed. Since the PEs create a strong barrier, in vitro it was shown that the division time of the cells can be regulated for better immune presentation.


title: Assessment of native cadmium-resistant bacteria in cacao (Theobroma cacao L.) - cultivated soils

abstract: Traces of cadmium (Cd) have been reported in some chocolate products due to soils with Cd and the high ability of cacao plants to extract, transport, and accumulate it in their tissues. An agronomic strategy to minimize the uptake of Cd by plants is the use of cadmium-resistant bacteria (Cd-RB). However, knowledge about Cd-RB associated with cacao soils is scarce. This study was aimed to isolate and characterize Cd-RB associated with cacao-cultivated soils in Colombia that may be used in the bioremediation of Cd-polluted soils. Diversity of culturable Cd-RB, qualitative functional analysis related to nitrogen, phosphorous, carbon, and Cd were performed. Thirty different Cd-RB morphotypes were isolated from soils with medium (NC, Y1, Y2) and high (Y3) Cd concentrations using culture media with 6 mg Kg-1 Cd. Cd-RB were identified based on morphological and molecular analyses. The most abundant morphotypes (90%) were gram-negative belong to Phylum Proteobacteria and almost half of them showed the capacity to fix nitrogen, solubilize phosphates and degrade cellulose. Unique morphotypes were isolated from Y3 soils where Burkholderia and Pseudomonas were the dominant genera indicating their capacity to resist high Cd concentrations. P. putida GB78, P. aeruginosa NB2, and Burkholderia sp. NB10 were the only morphotypes that grew on 18 up to 90 (GB78) and 140 mg Kg-1 Cd (NB2-NB10); however, GB78 showed the highest Cd bioaccumulation (5.92 mg g-1). This study provides novel information about culturable Cd-RB soil diversity with the potential to develop biotechnology-based strategies.


title: Immunomodulatory properties of umbilical cord blood-derived small extracellular vesicles and their therapeutic potential for inflammatory skin disorders

abstract: Umbilical cord blood (UCB) has long been seen as a rich source of naive cells with strong regenerative potential, likely mediated by small extracellular vesicles (sEV). More recently, small extracellular vesicles (sEV), such as exosomes, have been shown to play essential roles in cell-to-cell communication, via the transport of numerous molecules, including small RNAs. Often explored for their potential as biomarkers, sEV are now known to have regenerative and immunomodulating characteristics, particularly if isolated from stem cell-rich tissues. In this study, we aim to characterize the immunomodulating properties of umbilical cord blood mononuclear cell sEV (herein referred as Exo-101), and explore their therapeutic potential for inflammatory skin diseases. Exo-101 was shown to shift macrophages toward an anti-inflammatory phenotype, which in turn exert paracrine effects on fibroblasts, despite previous inflammatory stimuli. Additionally, the incubation of PBMC with Exo-101 resulted in an reduction of total CD4+ and CD8+ T-cell proliferation and cytokine release, while specifically supporting the development of regulatory T-cells (Treg), by influencing FOXP3 expression. In a 3D model of psoriatic skin, Exo-101 reduced the expression of inflammatory and psoriatic markers IL-6, IL-8, CXCL10, COX-2, S100A7 and DEFB4. In vivo, Exo-101 significantly prevented or reversed acanthosis in imiquimod-induced psoriasis, and tendentially increased the number of Treg in skin, without having an overall impact on disease burden. This work provides evidence for the anti-inflammatory and tolerogenic effect of Exo-101, which may be harnessed for the treatment of Th17-driven inflammatory skin diseases, such as psoriasis.


title: An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans

abstract:
The auxin-inducible degradation system in C. elegans allows for spatial and temporal control of protein degradation via heterologous expression of a single Arabidopsis thaliana F-box protein, transport inhibitor response 1 (AtTIR1). In this system, exogenous auxin (Indole-3-acetic acid; IAA) enhances the ability of AtTIR1 to function as a substrate recognition component that adapts engineered degron-tagged proteins to the endogenous C. elegans E3 ubiquitin ligases complex (SKR-1/2-CUL-1-F-box (SCF)), targeting them for degradation by the proteosome. While this system has been employed to dissect the developmental functions of many C. elegans proteins, we have found that several auxin-inducible degron (AID)-tagged proteins are constitutively degraded by AtTIR1 in the absence of auxin, leading to undesired loss-of-function phenotypes. In this manuscript, we adapt an orthogonal auxin-derivative/mutant AtTIR1 pair (C. elegans AID version 2 (C.e.AIDv2)) that transforms the specificity of allosteric regulation of TIR1 from IAA to one that is dependent on an auxin derivative harboring a bulky aryl group (5-Ph-IAA). We find that a mutant AtTIR1(F79G) allele that alters the ligand binding interface of TIR1 dramatically reduces ligand-independent degradation of multiple AID*-tagged proteins. In addition to solving the ectopic degradation problem for some AID targets, addition of 5-Ph-IAA to culture media of animals expressing AtTIR1(F79G) leads to more penetrant loss-of-function phenotypes for AID*-tagged proteins than those elicited by the AtTIR1-IAA pairing at similar auxin analog concentrations. The improved specificity and efficacy afforded by the mutant AtTIR1(F79G) allele expands the utility of the AID system and broadens the number of proteins that can be effectively targeted with it.

ARITCLE SUMMARYImplementation of the auxin induced degradation (AID) system has increased the power if the C. elegans model through its ability to rapidly degrade target proteins in the presence of the plant hormone auxin (IAA). The current C.e.AID system is limited in that a substantial level of target degradation occurs in the absence of ligand and full levels of target protein degradation require high levels of auxin inducer. In this manuscript, we modify the AID system to solve these problems.


title: Structural characterization of a Thorarchaeota profilin indicates eukaryotic-like features but with an extended N-terminus

abstract: The emergence of the first eukaryotic cell was preceded by evolutionary events which are still highly debatable. Recently, comprehensive metagenomics analysis has uncovered that the Asgard super-phylum is the closest yet known archaea host of eukaryotes. However, it remains to be established if a large number of eukaryotic signature proteins predicated to be encoded by the Asgard super-phylum are functional at least, in the context of a eukaryotic cell. Here, we determined the three-dimensional structure of profilin from Thorarchaeota by nuclear magnetic resonance spectroscopy and show that this profilin has a rigid core with a flexible N-terminus which was previously implicated in polyproline binding. In addition, we also show that thorProfilin co-localizes with eukaryotic actin in cultured HeLa cells. This finding reaffirm the notion that Asgardean encoded proteins possess eukaryotic-like characteristics and strengthen likely existence of a complex cytoskeleton already in a last eukaryotic common ancestor.


title: CRISPR-Cas9-mediated Large Cluster Deletion and Multiplex Genome Editing in Paenibacillus polymyxa

abstract: The use of molecular tools based on the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems has rapidly advanced genetic engineering. These molecular biological tools have been applied for different genetic engineering purposes in multiple organisms, including the quite rarely explored Paenibacillus polymyxa. However, only limited studies on large cluster deletion and multiplex genome editing have been described for this highly interesting and versatile bacterium. Here, we demonstrate the utilization of a Cas9-based system to realize targeted deletions of four biosynthetic gene clusters in the range of 12 kb to 41 kb by the use of a single targeting sgRNA. Furthermore, we also harness the system for multiplex editing of genes and large genomic regions. Multiplex deletion was achieved with more than 80 % efficiency, while simultaneous integration at two distantly located sites was obtained with 58 % efficiency. The findings reported in this study are anticipated to accelerate future research in P. polymyxa and related species.

category: synthetic biology


title: Rotavirus pre-symptomatically downregulates ileum-innervating sympathetic nerves concomitant with increased intestinal transit and altered brain activity

abstract: While diarrhea, the hallmark symptom of rotavirus infection, has been considered to occur only due to intrinsic intestinal effects, we show evidence for central control underlying the symptomology. With large-scale 3D volumetric tissue imaging a mouse model, we show that rotavirus infection disrupts the autonomic balance by downregulating the noradrenergic sympathetic nervous system in ileum, concomitant with increased intestinal transit. A most interesting observation was that nervous response from CNS occurs pre-symptomatically, an observation that bring new understanding to how virus give raise to clinical symptoms. In the CNS of infected animals, we found increased pS6 immunoreactivity in the area postrema and decreased phosphorylated STAT5-immunoreactive neurons in the bed nucleus of the stria terminalis, which are associated with autonomic control including stress response. Our observations bring new and important knowledge of how rotavirus virus infection induce gut-nerve-brain crosstalk giving raise to sickness symptoms.


title: The darkest place is under the candlestick - healthy urogenital tract as a source of UTI-related Escherichia coli lineages

abstract:
Since the discovery of the urinary microbiome, including identification of Escherichia coli in healthy hosts, its involvement in UTI development is a subject of high interest.

We explored population diversity and antimicrobial resistance of E. coli from urogenital microbiome of asymptomatic and recurrent UTI (rUTI) women. We also evaluated the genomic relationship between extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, particularly of the ST131 lineage.

E. coli was highly prevalent in asymptomatic women (48%) with slightly higher prevalence in vaginal samples comparing to urine, and occasionally with multiclonal population in the same individual. B2 was the most frequent phylogenetic group, with most strains classified as ExPEC. We demonstrated that virulence associated genes profile does not allow to distinguish strains isolated from healthy and rUTI host. We identified E. coli widespread lineages e.g., sequence types (ST) 127, ST131 (asymptomatic cohort) and ST73, ST131 (rUTI), frequently resistant to at least one antibiotic. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness between healthy and diseased host.

These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including globally spread E. coli lineages causing UTI including ST131.


title: Environmental DNA from a small sample of reservoir water can tell volumes about its biodiversity.

abstract: We evaluated the potential of metabarcoding in assessing the environmental DNA (eDNA) biodiversity profile in the water column of an hydroelectric power plant reservoir in southeast Brazil. Samples were obtained in three technical replicates at 1 km from the dam at 1, 13 and 25 m depths. For each minibarcodes -- COI, 12S and 16S -- 1.5 million paired-reads (150 base pairs) were sequenced. A total of 44 unique taxa were found. COI identified most of the taxa (34 taxa; 77.2 %) followed by 16S (14; 31.8 %) and 12S (10; 22.7 %). All minibarcodes identified fishes (13 taxa), however, COI detected other aquatic macro-invertebrates (18), algae (3) and amoebas (2). Richness was the same across the three depths (35 taxa), although, beta diversity suggested slightly divergent profiles. In just one location we identified 15 taxa never reported previously, 50% of the fish species identified in the last year of fishery monitoring and 13% of the species in biodiversity surveys performed from 2012 to 2021. Clustering into Amplicon Sequence Variants (ASV) showed that 12S and 16S are able to detect predominant haplotypes of fishes, suggesting they are suitable to study population genetics of this group. In this study we reviewed the species occurring within the Tres Irmaos reservoir according to previous conventional surveys and demonstrated that eDNA metabarcoding can be applied to monitor its biodiversity.


title: Single-cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and stellate cell activation phenotypes with human liver

abstract:
Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated (1). The mechanisms of fibrogenesis are multi-faceted and remain elusive with no approved antifibrotic treatments available (2). Here we use single-cell RNA sequencing (scRNA-seq) of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single-cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA-seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA-seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells (HSCs), the driver cell in liver fibrosis (3), specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel, conserved marker for zebrafish HSCs. To demonstrate the power of scRNA-seq to study liver fibrosis, we performed scRNA-seq on our zebrafish model of a pediatric liver disease with characteristic early, progressive liver fibrosis caused by mutation in mannose phosphate isomerase (MPI) (4-6). Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor-ligand interactions within normal and fibrotic states. This study establishes the first scRNA-seq atlas of the adult zebrafish liver, highlights the high degree of similarity to the human liver, and strengthens its value as a model to study liver fibrosis.

Significance StatementTo our knowledge, this is the first single-cell characterization of the adult zebrafish liver, both in a normal physiologic state and in the setting of liver fibrosis. We identify transcriptionally distinct zebrafish liver cell populations and a high degree of transcriptional conservation between human and zebrafish cells across the majority of hepatic cell types. Furthermore, using this scRNA transcriptome, we identify key signaling pathways in zebrafish HSCs that are replicated in human HSCs and implicated in the regulation of liver fibrosis. Our work provides a useful resource that can be used to aid research using the zebrafish liver and asserts the usefulness of the adult zebrafish to study liver fibrosis.

category: cell biology


title: Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA

abstract: Integrity of mitochondrial DNA (mtDNA), encoding several subunits of the respiratory chain, is essential to maintain mitochondrial fitness. Mitochondria, as a central hub for metabolism, are affected in a wide variety of human diseases but also during normal ageing, where mtDNA integrity is compromised. Mitochondrial quality control mechanisms work at different levels, and mitophagy and its variants are critical to remove dysfunctional mitochondria together with mtDNA to maintain cellular homeostasis. Understanding the mechanisms governing a selective turnover of mutation-bearing mtDNA without affecting the entire mitochondrial pool is fundamental to design therapeutic strategies against mtDNA diseases and ageing. Here we show that mtDNA depletion after expressing a dominant negative version of the mitochondrial helicase Twinkle, or by chemical means, is due to an exacerbated mtDNA turnover. Targeting of nucleoids is controlled by Twinkle which, together with the mitochondrial transmembrane proteins ATAD3 and SAMM50, orchestrate mitochondrial membrane remodeling to form extrusions. mtDNA removal depends on autophagy and requires the vesicular trafficking protein VPS35 which binds to Twinkle-enriched mitochondrial subcompartments upon mtDNA damage. Stimulation of autophagy by rapamycin selectively removes mtDNA deletions which accumulated during muscle regeneration in vivo, but without affecting mtDNA copy number. With these results we unveil a new complex mechanism specifically targeting and removing mutant mtDNA which occurs outside the mitochondrial network. We reveal the molecular targets involved in a process with multiple potential benefits against human mtDNA related diseases, either inherited, acquired or due to normal ageing.


title: Differential Expression of Alkaline Phosphatase and PHOSPHO1 in Bone from a Murine Model of Chronic Kidney Disease

abstract: Patients with advanced chronic kidney disease (CKD) often present with skeletal abnormalities; a condition known as renal osteodystrophy (ROD). While Tissue-nonspecific alkaline phosphatase (TNAP) and PHOSPHO1 are recognized to be critical for bone mineralization, their role in the etiology of ROD is unclear. To address this, ROD was induced in both wild-type and Phospho1 knockout (P1KO) mice using dietary adenine supplementation. The mice presented with hyperphosphatemia, hyperparathyroidism, and elevated levels of FGF23 and bone turnover markers. In particular, we noted that in CKD mice, bone mineral density (BMD) was increased in cortical bone (p < 0.05) but decreased in trabecular bone (p < 0.05). These changes were accompanied by decreased TNAP (p < 0.01) and increased PHOSPHO1 (p < 0.001) expression in wild-type CKD bones. In P1KO CKD mice, the cortical BMD phenotype was rescued, suggesting that the increased cortical BMD of CKD mice was driven by increased PHOSPHO1 expression. Other structural parameters were also improved in P1KO CKD mice. We further investigated the driver of the mineralization defects, by studying the effects of FGF23, PTH, and phosphate administration on PHOSPHO1 and TNAP expression by primary murine osteoblasts. We found both PHOSPHO1 and TNAP expression to be down-regulated in response to phosphate and PTH. While matrix mineralization was increased with phosphate (Pi), it decreased with PTH and FGF23 had no effect. The in vitro data suggest that the TNAP reduction in CKD-MBD is driven by the hyperphosphatemia and/or hyperparathyroidism noted in these mice, while the higher PHOSPHO1 expression may be a compensatory mechanism in an attempt to protect the bone from hypomineralization. We propose that increased PHOSPHO1 expression in ROD may contribute to the disordered skeletal mineralization characteristic of this progressive disorder.


title: Increased PHOSPHO1 expression mediates cortical bone mineral density in renal osteodystrophy


title: Early megakaryocyte lineage-committed progenitors in adult mouse bone marrow

abstract: Hematopoietic stem cells (HSCs) have been considered to progressively lose their self-renewal and differentiation potentials prior to the commitment to each blood lineage. However, recent studies have suggested that megakaryocyte progenitors are generated at the level of HSCs. In this study, we newly identified early megakaryocyte lineage-committed progenitors (MgPs) in CD201-CD48- cells and CD48+ cells separated from the CD150+CD34-Kit+Sca-1+Lin- HSC population of the bone marrow in C57BL/6 mice. Single-cell transplantation and single-cell colony assay showed that MgPs, unlike platelet-biased HSCs, had little repopulating potential in vivo, but formed larger megakaryocyte colonies in vitro (on average eight megakaryocytes per colony) than did previously reported megakaryocyte progenitors (MkPs). Single-cell RNA-sequencing supported that these MgPs lie between HSCs and MkPs along the megakaryocyte differentiation pathway. Single-cell colony assay and single-cell RT-PCR analysis suggested the coexpression of CD41 and Pf4 is associated with megakaryocyte colony-forming activity. Single-cell colony assay of a small number of cells generated from single HSCs in culture suggested that MgPs are not direct progeny of HSCs. In this study, we propose a differentiation model in which HSCs give rise to MkPs through MgPs.


title: A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

abstract:
In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation.

Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation.

Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.


title: Association of the malate dehydrogenase-citrate synthase metabolon is modulated by intermediates of the Krebs tricarboxylic acid cycle

abstract: Mitochondrial malate dehydrogenase (MDH)-citrate synthase (CS) multi-enzyme complex is a part of the Krebs tricarboxylic acid (TCA) cycle  metabolon which is enzyme machinery catalyzing sequential reactions without diffusion of reaction intermediates into a bulk matrix. This complex is assumed to be a dynamic structure involved in the regulation of the cycle by enhancing metabolic flux. Microscale Thermophoresis analysis of the porcine heart MDH-CS complex revealed that substrates of the MDH and CS reactions, NAD+ and acetyl-CoA, enhance complex association while products of the reactions, NADH and citrate, weaken the affinity of the complex. Oxaloacetate enhanced the interaction only when it was presented together with acetyl-CoA. Structural modeling using published CS structures suggested that the binding of these substrates can stabilize the closed format of CS which favors the MDH-CS association. Two other TCA cycle intermediates, ATP, and low pH also enhanced the association of the complex. These results suggest that dynamic formation of the MDH-CS multi-enzyme complex is modulated by metabolic factors responding to respiratory metabolism, and it may function in the feedback regulation of the cycle and adjacent metabolic pathways.

category: biochemistry


title: In vitro tau aggregation inducer molecules influence the effects of MAPT mutations on aggregation dynamics

abstract: Alzheimers disease (AD) and Alzheimers disease related dementias (ADRDs) affect 6 million Americans and they are projected to have an estimated health care cost of $355 billion for 2021. A histopathological hallmark of AD and many ADRDs is the aberrant intracellular accumulation of the microtubule associated protein tau. These neurodegenerative disorders that contain tau aggregates are collectively known as tauopathies and recent structural studies have shown that different tauopathies are characterized by different "strains" of tau filaments. In addition, mutations in the gene that encodes for tau protein expression have been associated with a group of tauopathies known as frontotemporal dementias with Parkinsonism linked to chromosome 17 (FTDP-17 or familial frontotemporal dementia). In vitro studies often use small molecules to induce tau aggregation as tau is extremely soluble and does not spontaneously aggregate in typical lab conditions and the use of authentic filaments to conduct in vitro studies is not feasible. This study highlights how different inducer molecules can have fundamental disparities to how disease related mutations effect the aggregation dynamics of tau. Using three different classes of tau aggregation inducer molecules we characterized disease relevant mutations in taus PGGG motifs at positions P301S, P332S, and P364S. When comparing these mutations to wild type tau, we found that depending on the type of inducer molecule used we saw fundamental differences in total aggregation, aggregation kinetics, immunoreactivity, and filament morphology. These data support the hypothesis that different tau aggregation inducer molecules make different polymorphs and perhaps structurally distinct strains.


title: Paracrine granules are cytoplasmic RNP granules distinct from stress granules assembling in response to viral infection.

abstract:
To rapidly respond and adapt to stresses, such as viral infections, cells have evolved several mechanisms, which include the activation of stress response pathways and the innate immune response. These stress responses result in the rapid inhibition of translation and condensation of stalled mRNAs, together with RNA-binding proteins and signalling components, into cytoplasmic biocondensates called stress granules. Increasing evidence suggests that stress granules contribute to antiviral defense and thus viruses need to evade these response pathways to propagate. In addition, the stress granule pathway is proposed to be dynamic and adaptable to specific stresses. We previously showed that Feline Calicivirus (FCV) impairs SGs assembly by cleaving the scaffolding protein G3BP1. We also observed that uninfected bystander cells assembled G3BP1-granules, suggesting a paracrine response trigged by the infection. We now present evidence that virus-free supernatant generated from infected cells can induce the formation of paracrine granules. They are different from canonical stress granules and exhibit specific kinetics of assembly-disassembly, protein and RNA composition and are linked to antiviral activity. We propose that this paracrine induction reflects a novel cellular defence mechanism to limit viral propagation and promote stress responses in bystander cells.

Summary statementWe describe a novel type of paracrine induced RNA granules associated with viruses, highlighting how different stresses results in heterogeneous stress granule-like condensates with specific cellular functions.


title: Membrane Fusion can be Driven by Sec18/NSF, Sec17/αSNAP, and trans-SNARE complex without HOPS

abstract: Yeast vacuolar membrane fusion has been reconstituted with R, Qa, Qb, and Qc-family SNAREs, Sec17/SNAP, Sec18/NSF, and the hexameric HOPS complex. HOPS tethers membranes and catalyzes SNARE assembly into RQaQbQc trans-complexes which zipper through their SNARE domains to promote fusion. Previously, we demonstrated that Sec17 and Sec18 can bypass the requirement of complete zippering for fusion (Song et al., 2021), but it has been unclear whether this activity of Sec17 and Sec18 is directly coupled to HOPS. HOPS can be replaced for fusion by a synthetic tether when the three Q-SNAREs are pre-assembled. We now report that SNARE zippering-arrested fusion intermediates that are formed without HOPS support Sec17/Sec18-triggered fusion. This zippering-bypass fusion is thus a direct result of Sec17 and Sec18 interactions: with each other, with the platform of partially zippered SNAREs, and with the apposed tethered membranes. As these fusion elements are shared among all exocytic and endocytic traffic, Sec17 and Sec18 may have a general role in directly promoting fusion.


title: Disc and Actin-Associated Protein 1 Influence Host Attachment in the Intestinal Parasite Giardia lamblia

abstract:
The deep-branching eukaryote Giardia lamblia is an extracellular parasite that attaches to the host intestine via a microtubule-based structure called the ventral disc. Control of attachment is mediated in part by the movement of two regions of the ventral disc that either permit or exclude the passage of fluid under the disc. Several known disc-associated proteins (DAPs) contribute to disc structure and function, but no force-generating protein has been identified among them. We recently identified several Giardia actin (GlActin) interacting proteins at the ventral disc, which could potentially employ actin polymerization for force generation and disc conformational changes. One of these proteins, Disc and Actin Associated Protein 1 (DAAP1), is highly enriched at the two regions of the disc previously shown to be important for fluid flow during attachment. In this study, we investigate the role of both GlActin and DAAP1 in ventral disc morphology and function. We confirmed interaction between GlActin and DAAP1 through coimmunoprecipitation, and used immunofluorescence to localize both proteins throughout the cell cycle and during trophozoite attachment. Similar to other DAPs, the association of DAAP1 with the disc is stable, except during cell division when the disc disassembles. Depletion of GlActin by translation-blocking antisense morpholinos resulted in both impaired attachment and defects in the ventral disc, indicating that GlActin contributes to disc-mediated attachment. Depletion of DAAP1 through CRISPR interference resulted in intact discs but impaired attachment, gating, and flow under the disc. As attachment is essential for infection, elucidation of these and other molecular mediators is a promising area for development of new therapeutics against a ubiquitous parasite.

Author SummaryGiardia lamblia is a single-celled organism and one of the most common gastrointestinal parasites worldwide. In developing countries, recurrent Giardia infections are common, due to lack of access to clean water. Giardia infections can lead to diarrhea, vomiting, dehydration, disruption of the intestinal microbiome, and chronic infections can lead to irritable bowel syndrome. Because existing drug treatments have side effects and Giardias resistance to drugs is increasing, new treatment strategies are needed. The parasites attachment to the hosts intestine is mediated by a Giardia-specific structure that resembles a suction cup and is called the ventral adhesive disc. We previously identified DAAP1, a protein which interacts with Giardia actin and localizes to the ventral disc. Here, we explore the relationship between these two proteins and investigate their role in disc-based attachment. Most disc proteins, including DAAP1, are unrelated to any human proteins, making them appealing drug targets to inhibit parasite attachment and infection.


title: Disc and Actin-Associated Protein 1 Influence Attachment in the Intestinal Parasite Giardia lamblia


title: The mouse bone metabolome is sexually dimorphic and is associated with whole bone strength

abstract: Cortical bone quality, which is sexually dimorphic, depends on bone turnover and therefore the activities of remodeling bone cells. However, sex differences in cortical bone metabolism are not yet defined. Adding to the uncertainty about cortical bone metabolism, the metabolomes of whole bone, isolated cortical bone without marrow, and bone marrow have not been compared. We hypothesized that the metabolome of isolated cortical bone would be distinct from that of bone marrow and would reveal sex differences. Metabolite profiles from LC-MS of whole bone, isolated cortical bone, and bone marrow were generated from humeri from 20-week-old female C57Bl/6J mice. The cortical bone metabolomes were then compared for 20-week-old female and male C57Bl/6J mice. Femurs from male and female mice were evaluated for flexural material properties and were then categorized into bone strength groups. The metabolome of isolated cortical bone was distinct from both whole bone and bone marrow. We also found sex differences in the isolated cortical bone metabolome. Based on metabolite pathway analysis, females had higher lipid metabolism, and males had higher amino acid metabolism. High-strength bones, regardless of sex, had greater tryptophan and purine metabolism. For males, high strength bones had upregulated nucleotide metabolism, whereas lower strength bones had greater pentose phosphate pathway metabolism. Since the higher strength groups (females compared with males, high strength males compared with lower strength males) had higher serum CTX1/P1NP, we estimate that the metabolomic signature of bone strength in our study at least partially reflects differences in bone turnover. These data provide novel insight into bone bioenergetics and the sexual dimorphic nature of bone material properties in C57Bl/6 mice.


title: The cortical bone metabolome of C57BL/6J mice is sexually dimorphic


title: Resistance to amitraz in the parasitic honey bee mite Varroa destructor is associated with mutations in the β-adrenergic-like octopamine receptor

abstract:
Varroa destructor is considered a major reason for high loss rate of Western honey bee (Apis mellifera) colonies. To prevent colony losses caused by V. destructor it is necessary to actively manage the mite population. Beekeepers, particularly commercial beekeepers, have few alternative treatments other than synthetic acaricides to control the parasite, resulting in intensive treatment regimens that led to the evolution of resistance in mite populations.

To investigate the mechanism of the resistance to amitraz detected in V. destructor mites from French and U.S. apiaries, we identified and characterized octopamine and tyramine receptors (the known targets of amitraz) in this species. The comparison of sequences obtained from mites collected from different apiaries with different treatment regimens, showed that the amino acid substitutions N87S or Y215H in the Oct{beta}R were associated with treatment failures reported in French or U.S. apiaries, respectively. Based on our findings, we have developed and tested two high throughput diagnostic assays based on TaqMan(R) able to accurately detect mites carrying the mutations in this receptor. This valuable information may be of help for beekeepers when selecting the most suitable acaricide to manage V. destructor.

category: genetics


title: Visual modulation of spectrotemporal receptive fields in mouse auditory cortex

abstract:
Recent studies have established significant anatomical and functional connections between visual areas and primary auditory cortex (A1), which may be important for perceptual processes such as communication and spatial perception. However, much remains unknown about the microcircuit structure of these interactions, including how visual context may affect different cell types across cortical layers, each with diverse responses to sound. The present study examined activity in putative excitatory and inhibitory neurons across cortical layers of A1 in awake male and female mice during auditory, visual, and audiovisual stimulation. We observed a subpopulation of A1 neurons responsive to visual stimuli alone, which were overwhelmingly found in the deep cortical layers and included both excitatory and inhibitory cells. Other neurons for which responses to sound were modulated by visual context were similarly excitatory or inhibitory but were less concentrated within the deepest cortical layers. Important distinctions in visual context sensitivity were observed among different spike rate and timing responses to sound. Spike rate responses were themselves heterogeneous, with stronger responses evoked by sound alone at stimulus onset, but greater sensitivity to visual context by sustained firing activity following transient onset responses. Minimal overlap was observed between units with visual-modulated firing rate responses and spectrotemporal receptive fields (STRFs) which are sensitive to both spike rate and timing changes. Together, our results suggest visual information in A1 is predominantly carried by deep layer inputs and influences sound encoding across cortical layers, and that these influences independently impact qualitatively distinct responses to sound.

Significance statementMultisensory integration is ubiquitous throughout the brain, including primary sensory cortices. The present study examined visual responses in primary auditory cortex, which were found in both putative excitatory and inhibitory neurons and concentrated in the deep cortical layers. Visual-modulated responses to sound were similarly observed in excitatory and inhibitory neurons but were more evenly distributed throughout cortical layers. Visual modulation moreover differed substantially across distinct sound response types. Transient stimulus onset spike rate changes were far less sensitive to visual context than sustained spike rate changes during the remainder of the stimulus. Spike timing changes were often modulated independently of spike rate changes. Audiovisual integration in auditory cortex is thus diversely expressed among cell types, cortical layers, and response types.


title: Spatiotemporal dynamics of human microglia are linked with brain developmental processes across the lifespan

abstract: Microglia, the brains resident macrophages, shape neural development and wiring, and are key neuroimmune hubs in the pathological signature of neurodevelopmental disorders. In the human brain, microglial development has not been carefully examined yet, and most of our knowledge derives from rodents. We established an unprecedented collection of 97 postmortem tissues enabling quantitative, sex-matched, detailed analysis of microglial across the human lifespan. We identify the dynamics of these cells in the human telencephalon, describing novel waves in microglial density across gestation and infancy, controlled by a balance of proliferation and apoptosis, which track key neurodevelopmental milestones. These profound changes in microglia are also observed in bulk RNAseq and single-cell RNAseq datasets. This study provides unparalleled insight and detail into the spatiotemporal dynamics of microglia across the human lifespan. Our findings serve as a solid foundation for elucidating how microglia contribute to shaping neurodevelopment in humans.


title: Homeobox transcription factor MNX1 is crucial for restraining the expression of pan-neuronal genes in motor neurons

abstract: Motor neurons (MNs) control muscle movement and are essential for breathing, walking and fine motor skills. Motor Neuron and Pancreas Homeobox 1 (MNX1) has long been recognized as a key marker of the MN lineage. Deficiency of the Mnx1 gene in mice results in early postnatal lethality - likely by causing abnormal MN development and respiratory malfunction. However, the genome-wide targets and exact regulatory function of Mnx1 in MNs remains unresolved. Using an in vitro model for efficient MN induction from mouse embryonic stem cells, we identified about six thousand MNX1-bound loci, of which half are conserved enhancers co-bound by the core MN-inducing factors ISL1 and LHX3, while the other half are promoters for housekeeping-like genes. Despite its widespread binding, disruption of Mnx1 affects the activity of only a few dozen MNX1-bound loci, and causes mis-regulation of about one hundred genes, the majority of which are up-regulated pan-neuronal genes with relatively higher expression in the brain compared to MNs. Integration of genome-wide binding, transcriptomic and epigenomic data in the wild-type and Mnx1-disrupted MNs predicts that Pbx3 and Pou6f2 are two putative direct targets of MNX1, and both are homeobox transcription factors highly expressed in the central nervous system. Our results suggest that MNX1 is crucial for restraining the expression of many pan-neuronal genes in MNs, likely in an indirect fashion. Further, the rarity of direct targets in contrast to the widespread binding of MNX1 reflects a distinctive mode of transcriptional regulation by homeobox transcriptional factors.


title: DAAM mediates the assembly of long-lived, treadmilling stress fibers in collectively migrating epithelial cells in Drosophila

abstract: Stress fibers (SFs) are actomyosin bundles commonly found in individually migrating cells in culture. However, whether and how cells use SFs to migrate in vivo or collectively is largely unknown. Studying the collective migration of the follicular epithelial cells in Drosophila, we found that the SFs in these cells show a novel treadmilling behavior that allows them to persist as the cells migrate over multiple cell lengths. Treadmilling SFs grow at their fronts by adding new integrin-based adhesions and actomyosin segments over time. This causes the SFs to have many internal adhesions along their lengths, instead of adhesions only at the ends. The front-forming adhesions remain stationary relative to the substrate and typically disassemble as the cell rear approaches. By contrast, a different type of adhesion forms at the SFs terminus that slides with the cells trailing edge as the actomyosin ahead of it shortens. We further show that SF treadmilling depends on cell movement and identify a developmental switch in the formins that mediate SF assembly, with DAAM acting during migratory stages and Diaphanous acting during post-migratory stages. We propose that treadmilling SFs keep each cell on a linear trajectory, thereby promoting the collective motility required for epithelial migration.


title: Cryo-EM Structures of Prestin and the Molecular Basis of Outer Hair Cell Electromotility

abstract: The voltage-dependent motor protein, Prestin (SLC26A5) is responsible for the electromotive behavior of outer hair cells (OHCs). Here, we determined the structure of dolphin Prestin in six distinct states using single particle cryo-electron microscopy. Structural and functional data suggest that Prestin adopts a unique and complex set of states, tunable by the identity of bound anions. Complexes with the inhibitor salicylate show that it competes for the anion-binding site of Prestin. These conformations reveal a novel mechanism of area expansion that depends on the helix flexibility and conformational transitions at the membrane protein interface and putatively affects the physical state of the surrounding membrane. These observations illuminate the structural basis of Prestin electromotility, a key component of the mammalian cochlear amplifier.


title: Continuous sensing of nutrients and growth factors by the mTORC1-TFEB axis

abstract: mTORC1 senses nutrient and growth factor status and phosphorylates downstream targets, including the transcription factor TFEB, to coordinate metabolic supply and demand. The molecular mechanisms of mTORC1 activation are thought to enforce a strict requirement for simultaneous amino acid and growth factor stimuli, but this model has not been evaluated with quantitative or single-cell methods. Here, we develop a series of fluorescent protein-TFEB fusions and investigate how combinations of stimuli jointly regulate signaling from mTORC1 to TFEB at the single-cell level. Live-cell imaging of individual cells revealed that mTORC1-TFEB signaling responds with graded changes to individual amino acid and growth factor inputs, rather than behaving as a logical "AND" gate. We find that mTORC1 inputs can be sequentially sensed, with responses that vary between mTORC1 substrates and are amplified by input from other kinases, including GSK3{beta}. In physiologically relevant concentrations of amino acids, we observe fluctuations in mTORC1-TFEB signaling that indicate continuous responsiveness to nutrient availability. Our results clarify how the molecular regulation of mTORC1 enables homeostatic processes at the cellular level and provide a more precise understanding of its behavior as an integrator of multiple inputs.


title: Cross-Individual Affective Detection Using EEG Signals with Audio-Visual Embedding

abstract: EEG signals have been successfully used in affective detection applications, which could directly capture brain dynamics and reflect emotional changes at a high temporal resolution. However, the generalized ability of the model across individuals has not been thoroughly developed yet. An involvement of other data modality, such as audio-visual information which are usually used for emotion eliciting, could be beneficial to estimate intrinsic emotions in video content and solve the individual differences problem. In this paper, we propose a novel deep affective detection model, named as EEG with audio-visual embedding (EEG-AVE), for cross-individual affective detection. Here, EEG signals are exploited to identify the individualized emotional patterns and contribute the individual preferences in affective detection; while audio-visual information is leveraged to estimate the intrinsic emotions involved in the video content and enhance the reliability of the affective detection performance. Specifically, EEG-AVE is composed of two parts. For EEG-based individual preferences prediction, a multi-scale domain adversarial neural network is developed to explore the shared dynamic, informative, and domain-invariant EEG features across individuals. For video-based intrinsic emotions estimation, a deep audio-visual feature based hypergraph clustering method is proposed to examine the latent relationship between semantic audio-visual features and emotions. Through an embedding model, both estimated individual preferences and intrinsic emotions are incorporated with shared weights and further are used together to contribute to affective detection across individuals. We conduct cross-individual affective detection experiments on two well-known emotional databases for model evaluation and comparison. The results show our proposed EEG-AVE model achieves a better performance under a leave-one-individual-out cross-validation individual-independent evaluation protocol. EEG-AVE is demonstrated as an effective model with good generalizability, which makes it a power tool for cross-individual emotion detection in real-life applications.


title: Deep learning based kcat prediction enables improved enzyme constrained model reconstruction

abstract: Enzyme turnover numbers (kcat values) are key parameters to understand cell metabolism, proteome allocation and physiological diversity, but experimentally measured kcat data are sparse and noisy. Here we provide a deep learning approach to predict kcat values for metabolic enzymes in a high-throughput manner with the input of substrate structures and protein sequences. Our approach can capture kcat changes for mutated enzymes and identify amino acid residues with great impact on kcat values. Furthermore, we applied the approach to predict genome scale kcat values for over 300 yeast species, demonstrating that the predicted kcat values are consistent with current evolutional understanding. Additionally, we designed an automatic pipeline using the predicted kcat values to parameterize enzyme-constrained genome scale metabolic models (ecGEMs) facilitated by a Bayesian approach, which outperformed the default ecGEMs in predicting phenotypes and proteomes and enabled to explain phenotype differences among yeast species. The deep learning kcat prediction approach and automatic ecGEM construction pipeline would thus be a valuable tool to uncover the global trend of enzyme kinetics and physiological diversity, and to further elucidate cell metabolism on a large scale.

category: systems biology


title: Overlapping influences shape motor activity during hasty sensorimotor decisions

abstract: Humans and other animals are able to adjust their speed-accuracy tradeoff (SAT) at will depending on the urge to act, favoring either cautious or hasty decision policies in different contexts. An emerging view is that SAT regulation relies on influences exerting broad changes on the motor system, tuning its activity up globally when hastiness is at premium. The present study aimed to test this hypothesis. Fifty subjects performed a task involving choices between left and right index fingers, in which incorrect choices led either to a high or to a low penalty in two contexts, inciting them to emphasize either cautious or hasty policies. We applied transcranial magnetic stimulation on multiple motor representations, eliciting motor evoked potentials (MEP) in nine finger and leg muscles. MEP amplitudes allowed us to probe activity changes in the corresponding finger and leg representations, while subjects were deliberating about which index to choose. Our data indicate that hastiness entails a broad amplification of motor activity, though this amplification was limited to the chosen side. On top of this effect, we identified a local suppression of motor activity, surrounding the chosen index representation. Hence, a decision policy favoring speed over accuracy appears to rely on overlapping processes producing a broad (but not global) amplification and a surround suppression of motor activity. The latter effect may help to increase the signal-to-noise ratio of the chosen representation, as supported by single-trial correlation analyses indicating a stronger differentiation of activity changes in finger representations in the hasty context.


title: Hasty sensorimotor decisions rely on an overlap of broad and selective changes in motor activity


title: Measuring the double-drift illusion with hand tracking

abstract: If a gabor pattern drifts in one direction while its internal texture drifts in the orthogonal direction, its perceived position deviates further and further away from its true path. We first evaluated the illusion using manual tracking. Participants followed the gabor with a stylus on a drawing tablet that coincided optically with the horizontal monitor surface. Their hand and the stylus were not visible during the tracking. The magnitude of the tracking illusion corresponded closely to previous perceptual and pointing measures indicating that manual tracking is a valid measure for the illusion. This allowed us to use it in a second experiment to capture the behavior of the illusion as it eventually degrades and breaks down in single trials. Specifically, the deviation of the gabor stops accumulating at some point and either stays at a fixed offset or resets toward the veridical position. To report the perceived trajectory of the gabor, participants drew it after the gabor was removed from the monitor. Resets were detected and analyzed and their distribution matches neither a temporal nor a spatial limit, but rather a broad gamma distribution over time. This suggests that resets are triggered randomly, about once per 1.3 s, possible by extraneous distractions or eye movements.


title: Measuring the double-drift illusion with hand trajectories


title: Measuring the double-drift illusion and its resets with hand trajectories