title: Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction

abstract: Among a wide variety of mass spectrometry (MS) methodologies available for structural characterizations of proteins, ion mobility (IM) provides structural information about protein shape and size in the form of an orientationally averaged collision cross-section (CCS). While IM data have been predominantly employed for the structural assessment of protein complexes, CCS data from IM experiments have not yet been used to predict tertiary structure from sequence. Here, we are showing that IM data can significantly improve protein structure determination using the modeling suite Rosetta. The Rosetta Projection Approximation using Rough Circular Shapes (PARCS) algorithm was developed that allows for fast and accurate prediction of CCS from structure. Following successful rigorous testing for accuracy, speed, and convergence of PARCS, an integrative modelling approach was developed in Rosetta to use CCS data from IM experiments. Using this method, we predicted protein structures from sequence for a benchmark set of 23 proteins. When using IM data, the predicted structure improved or remained unchanged for all 23 proteins, compared to the predicted models in the absence of CCS data. For 15/23 proteins, the RMSD (root-mean-square deviation) of the predicted model was less than 5.50 [A], compared to only 10/23 without IM data. We also developed a confidence metric that successfully identified near-native models in the absence of a native structure. These results demonstrate the ability of IM data in de novo structure determination.


title: Histone acetyltransferase activity of CREB-binding protein is essential for synaptic plasticity in 	Lymnaea

abstract: In eukaryotes, CREB-binding protein (CBP), a coactivator of CREB, functions both as a platform for recruiting other components of the transcriptional machinery and as a histone acetyltransferase (HAT) that alters chromatin structure. We previously showed that the transcriptional activity of cAMP-responsive element binding protein (CREB) plays a crucial role in neuronal plasticity in the pond snail Lymnaea stagnalis. However, there is no information on the role CBP plays in CREB-initiated plastic changes in Lymnaea. In this study, we characterized the Lymnaea CBP (LymCBP) gene and investigated the roles it plays in synaptic plasticity involved in regulating feeding behaviors. Similar to CBPs of other species, LymCBP possesses functional domains, such as KIX domain, which is essential for interaction with CREB and was shown to regulate long-term memory (LTM). In situ hybridization showed that the staining patterns of LymCBP mRNA in the central nervous system were very similar to those of Lymnaea CREB1 (LymCREB1). A particularly strong LymCBP mRNA signal was observed in the Cerebral Giant Cell (CGC), an identified extrinsic modulatory interneuron of the feeding circuit, key to both appetitive and aversive LTM for taste. Biochemical experiments using the recombinant protein of LymCBP HAT domain showed that its enzymatic activity was blocked by classical HAT inhibitors such as curcumin, anacardic acid and garcinol. Preincubation of Lymnaea CNSs with these HAT inhibitors blocked cAMP-induced long-term potentiation between the CGC and the follower B1 motoneuron. We therefore suggest that HAT activity of LymCBP in the CGCs is a key factor in synaptic plasticity contributing to LTM after classical conditioning.

category: neuroscience


title: Establishment, verification and application of rapid detection of baculovirus infectious titer by flow cytometry

abstract: Titer detection of baculovirus usually is time-consuming.It is important to establish a rapid detection method for baculovirus titer. In this report, Staining of cells with a fluorescently labeled anti-gp64 antibody allows for identification of infected insect cells. By inoculating cultures with a series of log dilutions of virus, and staining of the cultures 13-22 hours post inoculation, the ratio of infected to un-infected insect cells can be determined by flow cytometry. Statistical analysis of the percentage of infected cells in the virus dilution series enables accurate infectious titer determination. The culture time, cell growth state, the concentration of GP64-APC antibody and the concentration of inactivated FBS in diluent were optimized.The generality, repeatability and intermediate precision of the method were verified. The FCM method has the advantages of simplicity, accuracy, low cost and good repeatability.

category: immunology


title: Phage-Derived Depolymerase as an Antibiotic Adjuvant Against Multidrug-Resistant Acinetobacter Baumannii

abstract: Bacteriophage-encoded depolymerases are responsible for degrading capsular polysaccharides (CPS), lipopolysaccharides (LPS) and exopolysachcharides (EPS) of the host bacteria during phage invasion. They have been considered as promising antivirulence agents in controlling bacterial infections, including those caused by drug-resistant bacteria. This feature inspires a hope of utilizing these enzymes to disarm the polysaccharide capsid of the bacterial cells, which then strengthens the action of antibiotics. Here we have identified, cloned, and expressed a depolymerase Dpo71 from a bacteriophage specific for the gram-negative (G-ve) bacterium Acinetobacter baumannii in the heterologous host E. coli. Dpo71 sensitizes the multidrug-resistant (MDR) A. baumannii to the host immune attack, and also acts as an adjuvant to assist or boost the action of antibiotics, for example colistin. Specifically, Dpo71 at 10 {micro}g/ml enables a complete bacterial eradication by human serum at 50% volume ratio. Dpo71 inhibits biofilm formation and disrupts the pre-formed biofilm. Combination of Dpo71 could significantly enhance the antibiofilm activity of colistin, and improve the survival rate of A. baumannii infected Galleria mellonella. Dpo71 retains the strain-specificity of the parent phage from which Dpo71 is derived: the phage-sensitive A. baumannii strains respond to Dpo71 treatment, whereas the phage-insensitive strains do not. This indicates that Dpo71 indeed is responsible for the host specificity of bacteriophages. In summary, our work demonstrates the feasibility of using recombinant depolymerases as an antibiotic adjuvants to supplement the development of new antibacterials and to battle against MDR pathogens.

category: microbiology


title: TCAB1 is necessary for telomerase assembly

abstract: Localization of a wide variety of RNAs to non-membrane bound cellular compartments such as nucleoli, Cajal bodies, and stress-granules is critical for their function and stability. The molecular mechanisms that underly the recruitment and exclusion of specific RNAs from these phase-separated organelles is poorly understood. Telomerase is a ribonucleoprotein (RNP), that is composed of the reverse transcriptase protein TERT, the telomerase RNA (TR), and several auxiliary proteins that associate with TR, including TCAB1. Here we show that, that in the absence of TCAB1, TR is sequestered in the nucleolus, while TERT localizes to the nucleoplasm and is excluded from the nucleolus, which prevents telomerase assembly. Thus, nuclear compartmentalization by the non-membrane bound nucleolus counteracts telomerase assembly and TCAB1 is required to exclude the telomerase RNA from the nucleolus. Our work provides general insight into the mechanism and functional consequences of RNA recruitment to organelles formed by phase-separation and proposes a new model explaining the critical role of TCAB1 in telomerase function.

category: cell biology


title: TCAB1 prevents nucleolar accumulation of the telomerase RNA to promote telomerase assembly


title: Fur4 mediated uracil-scavenging to screen for surface protein regulators

abstract: Cell surface membrane proteins perform diverse and critical functions and are spatially and temporally regulated by membrane trafficking pathways. Although perturbations in these pathways underlie many pathologies, our understanding of these pathways at a mechanistic level remains incomplete. Using yeast as a model, we have developed an assay that reports on the surface activity of the Fur4 uracil permease in uracil auxotroph strains grown in the presence of limited uracil. This assay was used to screen a haploid deletion library that identified mutants with both diminished and enhanced comparative growth in restricted uracil media. Factors identified, including various multi-subunit complexes, were enriched for membrane trafficking and transcriptional functions, in addition to various uncharacterised genes. Bioinformatic analysis of expression profiles from many strains lacking identified transcription factors required for efficient uracil-scavenging revealed they control expression of other uracil-scavenging factors, in addition to membrane trafficking genes essential for viability, and therefore not represented in the screen. Finally, we performed a secondary mating factor secretion screen to functionally categorise factors implicated in uracil-scavenging, most of which are conserved throughout evolution.


title: Genomic signatures of recent adaptation in a wild bumblebee

abstract: Behavioral experiments and analyses of observation records have shown that environmental changes threaten insect pollinators, creating risks for agriculture and ecosystem stability. Despite their importance, we know little about how wild insects or other animals can adapt in response to environmental pressures. To understand the genomic bases of adaptation in an ecologically important pollinator, we analyzed genomes of Bombus terrestris bumblebees collected across Great Britain. We reveal extensive genetic diversity within this population, and strong signatures of recent adaptation throughout the genome. More specifically, we find that selection recently affected key processes underpinning environmental interactions, including neurobiology, wing development, and response to xenobiotics. We also discover unusual features of the genome, including a 53-gene region that lacks genetic diversity in many bee species, and a horizontal gene transfer from a Wolbachia bacteria. The genetic diversity and gene flow we observe for this species could support its resilience to ongoing and future challenges. Overall, we provide important insight on the genetic health of an ecologically and economically important pollinator and reveal mechanisms by which it has recently adapted. The approach we used could help to understand how species differ in their adaptive potential, and to develop conservation strategies for those most at risk.

category: evolutionary biology


title: A novel class of human milk oligosaccharides based on 6-galactosyllactose and containing N-acetylglucosamine branches extended by oligogalactoses

abstract: Human milk oligosaccharides (HMOs) have attracted much attention in recent years not only as a prebiotic factor, but in particular as an essential component in infant nutrition related to their impact in innate immunity. The backbone structures of complex HMOs generally contain single or repetitive lacto-N-biose (type 1) or lactosamine (type 2) units in either linear or branched chains extending from a lactose core. While all known branched structures originate from 3,6-substitution of the lactosyl core galactose, we here describe a new class of HMOs that tentatively branch at terminal galactose of 6-galactosyllactose. Another novel feature of this class of HMOs was found in linear oligo-galactosyl chains linked to one of the N-acetylglucosamine (GlcNAc) branches. The novel structures exhibit general formulas with hexose vs. hexosamine contents of 5/2 to 8/2 and can be designated as high-galactose (HG)-HMOs. In addition, up to three fucosyl residues are linked to the octa- to dodecasaccharides, which were detected in two human milk samples from Lewis blood group defined donors. Structural analyses of methylated glycans and their alditols comprised MALDI mass spectrometry, ESI-(CID)MS and linkage analyses by GC-MS of the derived partially methylated alditol acetates. Enzymatic degradation by application of {beta}1-3,4-specific galactosidase supported the presence of terminal galactose linked {beta}1-6 to one of the two GlcNAc branches.

category: biochemistry


title: Structural mechanisms for gating and ion selectivity of the human polyamine transporter ATP13A2

abstract:
Mutations in ATP13A2, also known as PARK9, cause a rare monogenic form of juvenile onset Parkinsons disease named Kufor-Rakeb syndrome and other neurodegenerative diseases. ATP13A2 encodes a neuroprotective P5B P-type ATPase highly enriched in the brain that mediates selective import of spermine ions from lysosomes into the cytosol via an unknown mechanism. Here we present three structures of human ATP13A2 bound to an ATP analogue or to spermine in the presence of phosphomimetics determined by electron cryo-microscopy. ATP13A2 autophosphorylation opens a lysosome luminal gate to reveal a narrow lumen access channel that holds a spermine ion in its entrance. ATP13A2s architecture establishes physical principles underlying selective polyamine transport and anticipates a "pump-channel" intermediate that could function as a counter-cation conduit to facilitate lysosome acidification. Our findings establish a firm foundation to understand ATP13A2 mutations associated with disease and bring us closer to realizing ATP13A2s potential in neuroprotective therapy.

HighlightsO_LIStructures of the Parkinsons disease-associated polyamine transporter ATP13A2
C_LIO_LIStructures of three transport cycle intermediates reveal the gating mechanism
C_LIO_LIArchitecture of the polyamine binding site reveals mechanisms for ion selectivity
C_LIO_LIThe polyamine binding sites location anticipates an ion channel-like mechanism
C_LI

category: biophysics


title: Interactions of surfactants with the bacterial cell wall and inner membrane: Revealing the link between aggregation and antimicrobial activity

abstract: Surfactants with their intrinsic ability to solubilize lipids are widely used as antibacterial agents. Interaction of surfactants with the bacterial cell envelope is complicated due to their propensity to aggregate. It is important to discern the interactions of micellar aggregates and single surfactants on the various components of the cell envelope to improve selectivity and augment the efficacy of surfactant-based products. In this study, we present a combined experimental and molecular dynamics investigation to unravel the molecular basis for the superior kill efficacy of laurate over oleate observed in contact time assays with live E. coli. To gain a molecular understanding of these differences, we performed all-atom molecular dynamics simulations to observe the interactions of surfactants with the periplasmic peptidoglycan layer and the inner membrane of Gram-negative bacteria. The peptidoglycan layer allows a greater number of translocation events for laurate when compared with oleate molecules. More interestingly, aggregates did not translocate the peptidoglycan layer, thereby revealing an intrinsic sieving property of the bacterial cell wall to effectively modulate the surfactant concentration at the inner membrane. The molecular dynamics simulations exhibit greater thinning of the inner membrane in the presence of laurate when compared with oleate, and laurate induced greater disorder and decreased the bending modulus of the inner membrane to a greater extent. The enhanced antimicrobial efficacy of laurate over oleate was further verified by experiments with giant unilamellar vesicles, which revealed that laurate induced vesicle rupture at lower concentrations in contrast to oleate. The novel molecular insights gained from our study uncovers hitherto unexplored pathways to rationalize the development of antimicrobial formulations and therapeutics.


title: Actin dynamics as a multiscale integrator of cellular guidance cues

abstract:
Cells are able to integrate multiple, and potentially competing, cues to determine a migration direction. For instance, in wound healing, cells follow chemical signals or electric fields to reach the wound edge, regardless of any local guidance cues. To investigate this integration of guidance cues, we monitor the actin-polymerization dynamics of immune cells in response to cues on a subcellular scale (nanotopography) and on the cellular scale (electric fields, EFs). In the fast, amoeboid-type migration, commonly observed in immune cells, actin polymerization at the cells leading edge is the driver of motion. The excitable systems character of actin polymerization leads to self-propagating, two-dimensional wavefronts that enable persistent cell motion. We show that EFs guide these wavefronts, leading to turning of cells when the direction of the EF changes. When nanoridges promote one-dimensional (1D) waves of actin polymerization that move along the ridges (esotaxis), EF guidance along that direction is amplified. 1D actin waves cannot turn or change direction, so cells respond to a change in EF direction by generating new 1D actin waves. At the cellular scale, the emergent response is a turning of the cell. For nanoridges perpendicular to the direction of the EF, the 1D actin waves are guided by the nanotopography, but both the average location of new actin waves and the whole cell motion are guided by the EF. Thus, actin waves respond to each cue on its intrinsic length scale, allowing cells to exhibit versatile responses to the physical microenvironment.

Significance StatementEffective cell migration requires the integration of multiple, and sometimes competing, guidance cues. For instance, in wound healing, immune cells are guided towards a wound edge by long-range electrical and chemical cues that may conflict with guidance cues from the local environment. How cells combine and respond to such cues is not well understood. We demonstrate that multiple guidance mechanisms can act simultaneously, but on different scales. Nanotopography, a local mechanical cue, guides individual waves of actin polymerization, thereby biasing the direction cell motion on the time scale of these waves. An external electric field applied at the same time biases the locations of new waves of actin polymerization, leading to overall directed migration over long distance scales.


title: Distinct REV-ERBα Conformational State Predicted by GaMD Simulations Leads to the Structure-Based Discovery of Novel REV-ERBα Antagonist

abstract: REV-ERB is a nuclear hormone receptor that plays important role in the regulation of many physiological processes such as circadian clock regulation, inflammation, and metabolism. Despite its importance, few chemical tools are available to study this receptor. In addition, there is no available X-ray crystal structures of REV-ERB bound with synthetic ligands, hampering the development of targeted therapeutics. SR8278 is the only identified synthetic antagonist of REV-ERB. We have performed Gaussian accelerated molecular dynamics (GaMD) simulations to sample the binding pathway of SR8278 and associated conformational changes to REV-ERB. The simulations revealed a novel and more energetically favorable conformational state than the starting conformation. The new conformation allows ligand binding to the orthosteric binding site in a specific orientation. This state is reached after a tryptophan (Trp436) rotameric switch coupled with H3-H6 distance change. We used the newly identified GaMD conformational state in structure-based virtual screening of one million compounds library which led to the identification of novel REV-ERB antagonist. This study is the first that demonstrates a synthetic ligand binding pathway to REV-ERB, which provided important insights into the REV-ERB functional mechanism and lead to the discovery of novel REV-ERB antagonists. This study further emphasizes the power of computational chemistry methods in advancing drug discovery research.


title: Antibody structure prediction using interpretable deep learning

abstract:
Therapeutic antibodies make up a rapidly growing segment of the biologics market. However, rational design of antibodies is hindered by reliance on experimental methods for determining antibody structures. In recent years, deep learning methods have driven significant advances in general protein structure prediction. Here, we present DeepAb, a deep learning method for predicting accurate antibody FV structures from sequence. We evaluate DeepAb on two benchmark sets - one balanced for structural diversity and the other composed of clinical-stage therapeutic antibodies - and find that our method consistently outperforms the leading alternatives. Previous deep learning methods have operated as "black boxes" and offered few insights into their predictions. By introducing a directly interpretable attention mechanism, we show that our network attends to physically important residue pairs. For example, in prediction of one CDR H3 residue conformation, the network attends to proximal aromatics and a key hydrogen bonding interaction that constrain the loop conformation. Finally, we present a novel mutant scoring metric derived from network confidence and show that for a particular antibody, all eight of the top-ranked mutations improve binding affinity. These results suggest that this model will be useful for a broad range of antibody prediction and design tasks.

SignificanceAccurate structure models are critical for understanding the properties of potential therapeutic antibodies. Conventional methods for protein structure determination require significant investments of time and resources and may fail. Although greatly improved, methods for general protein structure prediction still cannot consistently provide the accuracy necessary to understand or design antibodies. We present a deep learning method for antibody structure prediction and demonstrate improvement over alternatives on diverse, therapeutically relevant benchmarks. In addition to its improved accuracy, our method reveals interpretable outputs about specific amino acids and residue interactions that should facilitate design of novel therapeutic antibodies.


title: Maximally predictive ensemble dynamics from data

abstract:
We leverage the interplay between microscopic variability and macroscopic order to connect physical descriptions across scales directly from data, without underlying equations. We reconstruct a state space by concatenating measurements in time, building a maximum entropy partition of the resulting sequences, and choosing the sequence length to maximize predictive information. Trading non-linear trajectories for linear, ensemble evolution, we analyze reconstructed dynamics through transfer operators. The evolution is parameterized by a transition time{tau} : capturing the source entropy rate at small{tau} and revealing timescale separation with collective, coherent states through the operator spectrum at larger{tau} . Applicable to both deterministic and stochastic systems, we illustrate our approach through the Langevin dynamics of a particle in a double-well potential and the Lorenz system. Applied to the behavior of the nematode worm C. elegans, we derive a "run-and-pirouette" navigation strategy directly from posture dynamics. We demonstrate how sequences simulated from the ensemble evolution capture both fine scale posture dynamics and large scale effective diffusion in the worms centroid trajectories and introduce a top-down, operator-based clustering which reveals subtle subdivisions of the "run" behavior.

POPULAR SUMMARYComplex structure is often composed from a limited set of relatively simple building blocks; such as novels from letters or proteins from amino acids. In musical composition, e.g., sounds and silences combine to form longer time scale structures; motifs form passages which in turn form movements. The challenge we address is how to identify collective variables which distinguish structures across such disparate time scales. We introduce a principled framework for learning effective descriptions directly from observations. Just as a musical piece transitions from one movement to the next, the collective dynamics we infer consists of transitions between macroscopic states, like jumps between metastable states in an effective potential landscape.

The statistics of these transitions are captured compactly by transfer operators. These operators play a central role, guiding the construction of maximally-predictive short-time states from incomplete measurements and identifying collective modes via eigenvalue decomposition. We demonstrate our analysis in both stochastic and deterministic systems, and with an application to the movement dynamics of an entire organism, unravelling new insight in long time scale behavioral states directly from measurements of posture dynamics. We can, in principle, also make connections to both longer or shorter timescales. Microscopically, postural dynamics result from the fine scale interactions of actin and myosin in the muscles, and from electrical impulses in the brain and nervous system. Macroscopically, behavioral dynamics may be extended to longer time scales, to moods or dispositions, including changes during aging, or over generations due to ecological or evolutionary adaptation. The generality of our approach provides opportunity for insights on long term dynamics within a wide variety of complex systems.


title: Confounds of using the unc-58 selection marker highlights the importance of genotyping co-CRISPR genes

abstract: Multiple advances have been made to increase the efficiency of CRISPR/Cas9 editing using the model genetic organism Caenorhabditis elegans (C. elegans). Here we report on the use of co-CRISPR  marker genes: worms in which co-CRISPR events have occurred have overt, visible phenotypes which facilitates the selection of worms that harbour CRISPR events in the target gene. Mutation in the co-CRISPR gene is then removed by outcrossing to wild type but this can be challenging if the CRISPR and co-CRISPR gene are hard to segregate. However, outcrossing can be avoided by selecting worms of wild type appearance from a  jackpot brood. These are broods in which a high proportion of the progeny of a single injected worm display the co-CRISPR phenotype suggesting high CRISPR efficiency. This can deliver worms that harbour the desired mutation in the target gene locus without the co-CRISPR mutation. We have successfully generated a discrete mutation in the C. elegans nlg-1 gene using this method. However, in the process of sequencing to authenticate editing in the nlg-1 gene we discovered genomic rearrangements that arise at the co-CRISPR gene unc-58 that by visual observation were phenotypically silent but nonetheless resulted in a significant reduction in motility scored by thrashing behaviour. This highlights that careful consideration of the hidden consequences of co-CRISPR mediated genetic changes should be taken before downstream analysis of gene function. Given this, we suggest sequencing of co-CRISPR genes following CRISPR procedures that utilise phenotypic selection as part of the pipeline.

category: genetics


title: Biological Constraints Can Improve Prediction inPrecision Oncology

abstract:
Machine learning (ML) algorithms are used to build predictive models or classifiers for specific disease outcomes using transcriptomic data. However, some of these models show deteriorating performance when tested on unseen data which undermines their clinical utility.

In this study, we show the importance of directly embedding prior biological knowledge into the classifier decision rules to build simple and interpretable gene signatures. We tested this in two important classification examples-- a) progression in non-muscle invasive bladder cancer; and b) response to neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC) - using different ML algorithms. For each algorithm, we developed two sets of classifiers: agnostic, trained using either individual gene expression values or the corresponding pairwise ranks without biological consideration; and mechanistic, trained by restricting the search to a set of gene pairs capturing important biological relations. Both types were trained on the same training data and their performance was evaluated on unseen testing data using different methodologies and multiple evaluation metrics.

Our analysis shows that mechanistic models outperform their agnostic counterparts when tested on independent data and show more consistency to their performance in the training with enhanced interpretability. These findings suggest that using biological constraints in the training process can yield more robust and interpretable gene signatures with high translational potential.

category: bioinformatics


title: Mechanosensitive Osteogenesis on Native Cellulose Scaffolds for Bone Tissue Engineering.

abstract: In recent years, plant-derived cellulosic biomaterials have become a popular way to create scaffolds for a variety of tissue engineering applications. Moreover, such scaffolds possess similar physical properties (porosity, stiffness) that resemble bone tissues and have been explored as potential biomaterials for tissue engineering applications. Here, plant-derived cellulose scaffolds were seeded with MC3T3-E1 pre-osteoblast cells. Moreover, to assess the potential of these biomaterials, we also applied cyclic hydrostatic pressure (HP) to the cells and scaffolds over time to mimic a bone-like environment more closely. After one week of proliferation, cell-seeded scaffolds were exposed to HP up to 270 KPa at a frequency of 1Hz, once per day, for up to two weeks. Scaffolds were incubated in osteogenic inducing media (OM) or regular culture media (CM). The effect of cyclic HP combined with OM on cell-seeded scaffolds resulted in an increase of differentiated cells. This corresponded to an upregulation of alkaline phosphatase activity and scaffold mineralization. Importantly, the results reveal that well known mechanosensitive pathways cells which regulate osteogenesis appear to remain functional even on novel plant-derived cellulosic biomaterials.


title: Sorption of neuropsychopharmaca in microfluidic materials for in-vitro studies

abstract: Sorption (i.e., ad- & ab-sorption) of small-molecule compounds to polydimethylsiloxane (PDMS) is widely acknowledged. However, studies to date have largely been conducted under atypical conditions for microfluidic applications (lack of perfusion, lack of biological fluids); especially considering the biological studies such as Organs-on-Chips where small-molecule sorption poses the largest concern. Here, we present the first study of small-molecule sorption under relevant conditions for microphysiological systems, focusing on a standard geometry for biological barrier studies that find application in pharmacokinetics. We specifically assess the sorption of a compound panel including 15 neuropsychopharmaca at in-vivo concentration levels. We consider devices constructed from PDMS as well as two material alternatives (off-stoichiometry thiol-ene-epoxy, or tape/polycarbonate laminates). Moreover, we study the much-neglected impact of peristaltic pump tubing, an essential component of the recirculating systems required to achieve in-vivo-like perfusion shear stresses. We find that choice of device material does not significantly impact sorption behavior in our barrier-on-chip-type system. Our PDMS observations in particular suggest that excessive compound sorption observed in prior studies is not sufficiently described by compound hydrophobicity or other suggested predictors. Critically, we show that sorption by peristaltic tubing, including the commonly-utilized PharMed BPT, dominates over device sorption even on an area-normalized basis, let alone at the typically much larger tubing surface areas. Our findings highlight the importance of validating compound dosages in Organ-on-Chip studies, as well as the need for considering tubing materials with equal or higher care than device materials.

category: bioengineering


title: Distinct internal states interact to shape food choice by modulating sensorimotor processing at global and local scales

abstract: When deciding what to eat, animals evaluate sensory information about food quality alongside multiple ongoing internal states. How internal states interact to alter sensorimotor processing and shape decisions such as food choice remains poorly understood. Here, we use pan-neuronal volumetric activity imaging in the Drosophila brain to investigate the neuronal basis of internal state dependent nutrient appetites. We created a functional atlas of the ventral fly brain and find that metabolic state shapes sensorimotor processing across large sections of the neuropil. Reproductive state, in contrast, acts locally to define how sensory information is translated into feeding motor output. Thereby, these two states synergistically modulate protein-specific food intake and thus food choice. Finally, using a novel computational strategy, we identify driver lines innervating state-modulated regions and show that the newly identified borboleta region is sufficient to direct food choice towards protein-rich food. We therefore identify a generalizable principle by which distinct internal states are integrated to shape decision-making and propose a strategy to uncover and functionally validate how internal states shape behavior.


title: Neural activation in the olfactory epithelium of East African cichlid in response to odorant exposure

abstract: Fish use olfaction to gain various information. To know what they receive and how they receive is vital for understanding the diversity of fish. However, studies on fish olfactory or pheromone receptors are still insufficient, and most of them are on a model organism. Here, we established an experimental system to detect a biological-derived neural response from the olfactory epithelium of East African cichlid, the most diversified fish lineage, by in situ hybridizations of c-fos. We first tested the response of microvillous neurons, which are expected to be dominated by V2R-expressing neurons, to several odorants. We showed that microvillous neurons responded to amino acids and food extraction, suggesting that fish receive amino acids via V2R receptors as food-related odorants. We next tested the response of each of the four subfamilies of V2R receptors, showing that two of four subfamilies responded to proteinogenic amino acids. Notably, individual paralogs in subfamily 14, which responded to arginine, had variability in receptivity to arginine, indicating the ligand differentiation in the cichlid-specifically expanded subfamily. Finally, we established a noninvasive method to collect urine and tested the response of putative pheromone receptor V1R to male urine, and we showed two V1R receptors responded to male urine. Furthermore, we showed V1R2 receptor responded to 4-hydroxyphenyl acetate and lithocholic acid. This study provides an experimental basis for the study of olfaction in East African cichlids related to its ecology and speciation.


title: Neural Activation in the Olfactory Epithelium of East African Cichlid in Response to Odorant Exposure


title: Differences in nanoscale organization of DNase I hypersensitive and insensitive chromatin in single human cells

abstract: Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. By using a combination of high throughput super-resolution microscopy and coarse-grained modelling we investigated properties of active and inactive chromatin in interphase nuclei. Using DNase I hypersensitivity as a criterion, we have selected prototypic active and inactive regions from ENCODE data that are representative for K-562 and more than 150 other cell types. By using oligoFISH and automated STED microscopy we systematically measured physical distances of the endpoints of 5kb DNA segments in these regions. These measurements result in high-resolution distance distributions which are right-tailed and range from very compact to almost elongated configurations of more than 200 nm length for both the active and inactive regions. Coarse-grained modeling of the respective DNA segments suggests that in regions with high DNase I hypersensitivity cell-to-cell differences in nucleosome occupancy determine the histogram shape. Simulations of the inactive region cannot sufficiently describe the compaction measured by microscopy, although internucleosomal interactions were elevated and the linker histone H1 was included in the model. These findings hint at further organizational mechanisms while the microscopy-based distance distribution indicates high cell-to-cell differences also in inactive chromatin regions. The analysis of the distance distributions suggests that direct enhancer-promoter contacts, which most models of enhancer action assume, happen for proximal regulatory elements in a probabilistic manner due to chromatin flexibility.


title: Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9

abstract: The zebra finch is a powerful model for several biological fields, particularly neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. Here we describe a cell line, CFS414, generated from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we demonstrated a stress-dependent localization response of the zebra finch song nuclei specialized gene, SAP30L, and disrupted endogenous gene sequences using S.aureus Cas9. The utility of this cell line enhances the molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.


title: In vitro hepatotoxicity assessment of Lippia javanica (Burm.f.) Spreng. aqueous leaf extract

abstract:
Ethnopharmacological relevanceLippia javanica leaves are popular in traditional food, medicine and for insecticidal uses in various Africa countries and North-East India. Anecdotal evidence suggests that it is safe to use but limited animal studies suggested potential toxicity at high dosages, including hepatotoxicity.

Aim of the studyTo screen for potential hepatotoxicity of L. javanica leaf extracts in vitro, thereby contributing to its toxicological profile for safe use in food and topical applications.

Materials and methodsHigh content analysis techniques and fluorescent dyes were used to monitor C3A hepatocarcinoma cells for changes in morphological features that are associated with development of mitotoxicity, steatosis, oxidative stress, and lysosomal dysfunction.

ResultsNo changes were observed in cell viability, reactive oxygen species or lysosomal content at concentrations up to 200 {micro}g/ml in C3A cells. Mitochondrial membrane potential was reduced by approximately 10% but this effect was not dose-dependent nor was it accompanied by a reduction in mitochondrial content. A dose-dependent decrease was observed in neutral lipid content.

ConclusionThe results from this in vitro study suggest that L. javanica leaf extracts is not anticipated to be hepatotoxic at concentrations in the range that is assumed for food or topical use.


title: ERK1/2 is an ancestral organising signal in spiral cleavage

abstract: Animal development is classified as conditional or autonomous based on whether cell fates are specified through inductive signals or maternal determinants, respectively. Yet how these two major developmental modes evolved remains unclear. During spiral cleavage--a stereotypic embryogenesis ancestral to 15 invertebrate groups, including molluscs and annelids--most lineages specify cell fates conditionally, while some define the primary axial fates autonomously. To identify the mechanisms driving this change, we studied Owenia fusiformis, an early-branching, conditional annelid. In Owenia, ERK1/2-mediated FGF receptor signalling specifies the endomesodermal progenitor. This cell likely acts as an organiser, inducing mesodermal and posterodorsal fates in neighbouring cells and repressing anteriorising signals. The organising role of ERK1/2 in Owenia is shared with molluscs, but not with autonomous annelids. Together, these findings suggest that conditional specification of an ERK1/2+ embryonic organiser is ancestral in spiral cleavage and was repeatedly lost in annelid lineages with autonomous development.

category: developmental biology


title: Neuron-radial glial cell communication via BMP/Id1 signaling maintains the regenerative capacity of the adult zebrafish telencephalon

abstract: The mechanisms of the management of the neural stem cell (NSC) pool underlying the regenerative capacity of the adult zebrafish brain are not understood. We show that Bone Morphogenetic Proteins (BMPs) which are exclusively expressed by neurons in the adult telencephalon and the helix-loop-helix (HLH) transcription co-regulator, Inhibitor of differentiation 1 (Id1), control quiescence of NSCs. Upon injury, lack of id1 function leads to an initial over-proliferation and subsequent loss of NSCs and the regenerative capacity. BMP/Id1 signaling up-regulates the transcription factor her4.1 which is also a target of Notch signaling mediating short-range control of NSC quiescence. Hence, the two signaling systems converge onto Her4.1. Our data show that neurons feedback on NSC proliferation. BMP1/Id1 signaling appears as the predominant safeguard of the NSC pool under regenerative conditions while Notch signaling is sufficient to maintain NSCs under homeostatic baseline neurogenesis in the uninjured animal.


title: How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

abstract: Quantifying the diversity of species in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, the reliability of biodiversity detection from eDNA samples can be low in marine environments because eDNA density is low and certainly patchy in this vast, heterogenous and dynamic environment. So, the number of sampling replicates and filtered volume necessary to obtain accurate estimates of biodiversity in rich tropical marine environments using eDNA metabarcoding is still unknown. Here, we used a paired sampling design of 30L per replicate on 68 reef transects from 8 sites in three tropical regions and identified fish Molecular Taxonomic Units (MOTUs) using a 12S marker. We quantified local biodiversity variation as MOTU richness, compositional turnover and compositional nestedness between replicated pairs of seawater samples. We report strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one-another. As a result, localised diversity accumulation curves showed that even 6 replicates (180L) in the same location underestimated local diversity (for an area <1km). However, sampling of regional diversity using [~]25 replicates in variable locations (often covering 10s of km) achieved saturation of biodiversity accumulation curves. Our results demonstrate high variability of diversity estimates perhaps arising from heterogeneous and local distribution of eDNA distribution in seawater or highly skewed frequencies of eDNA traces. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes of local assemblages. Future biomonitoring efforts could be strongly undermined by a high level of false-negative detections under low replication protocols. We reveal the need to increase replicates or increase sampled water volume to better inform management of marine biodiversity using eDNA.

category: ecology


title: A different type of tolerance: selection for and phenotypic characteristics of antibiotic tolerance evaluated at the single cell level under recurring antibiotic exposure in Escherichia coli.

abstract:
Non-heritable drug resistance, such as tolerance and persistence towards antibiotics, is little characterized compared to genetic resistance. Tolerance and persistence allow cells to survive application of antibiotics that are bactericidal to non-tolerant cells. Non-heritable drug resistance challenges antibiotic treatment, particularly of recurrent infections, and have implications towards heritable resistance evolution. Tolerant cells have commonly been characterized as growth arrested cells prior and during antibiotic application that quickly resume growth post-application. Here, we explore characteristic of tolerant and susceptible E. coli single bacteria cells to different levels of recurrent antibiotic exposure and quantify their occurrence. In using a high throughput single-cell microfluidic device, we find that tolerant cells reduce their growth rate by about 50%, but contrary to previous findings do not go into growth arrest or near growth arrest. The growth reduction is induced by antibiotic exposure and not caused by a stochastic switch or predetermined state as previously described. Cells exhibiting constant intermediate growth survived best under antibiotic exposure and selection did not primarily act on fast growing cells, as expected for a {beta}-lactam antibiotic. Control experiments on population cultures confirmed and challenged scaling of single cell findings to population level processes. Our findings suggest a prevalent type of tolerance that differs from previously described tolerance and persister characteristics. Our described characteristics and its high frequency of occurrence supports acclaims of an underappreciated role of tolerant cells towards resistance evolution.

Author SummaryResistance to antibiotics is a major cause of treatment failure in modern medicine. In addition to genetic resistance, bacterial cells can sustain periods of bactericidal application in a so-called tolerant state. Previously tolerant cells were characterized by growth arrest prior and during exposure to antibiotics. Here, we show a distinctive type of tolerance that arises out of normally growing cells, where during antibiotic exposure, cell growth is slowed but does not go into growth arrest. Cells with an intermediate growth have the best survival, which is contrary to the assumptions of exposure to a {beta}-lactam antibiotic where selection is assumed to act against the fastest growing cells and the least against non-growing cells. The novel characteristics of tolerance that we have uncovered provides bacteria with another route to evade antibiotics and that could be a considerable threat to the efficiency of antibiotic treatment.


title: Single-cell phenotypic characteristics of tolerance under recurring antibiotic exposure in Escherichia coli.


title: A new method to study genome mutations using the information entropy

abstract: We report a non-clinical, mathematical method of studying genetic sequences based on the information theory. Our method involves calculating the information entropy spectrum of genomes by splitting them into "windows" containing a fixed number of nucleotides. The information entropy value of each window is computed using the m-block information entropy formula. We show that the information entropy spectrum of genomes contains sufficient information to allow detection of genetic mutations, as well as possibly predicting future ones. Our study indicates that the best m-block size is 2 and the optimal window size should contain more than 9, and less than 33 nucleotides. In order to implement the proposed technique, we created specialized software, which is freely available. Here we report the successful test of this method on the reference RNA sequence of the SARS-CoV-2 virus collected in Wuhan, Dec. 2019 (MN908947) and one of its randomly selected variants from Taiwan, Feb. 2020 (MT370518), displaying 7 mutations.


title: Deep Learning-based Subcellular Phenotyping of Protrusion Dynamics Reveals Fine Differential Drug Responses at Subcellular and Single-Cell Levels

abstract: Intracellular processes such as cytoskeletal organization and organelle dynamics exhibit massive subcellular heterogeneity. Although recent advances in fluorescence microscopy allow researchers to acquire an unprecedented amount of live cell image data at high spatiotemporal resolutions, the traditional ensemble-averaging of uncharacterized subcellular heterogeneity could mask important activities. Moreover, the curse of dimensionality of these complex dynamic datasets prevents access to critical mechanistic details of subcellular processes. Here, we establish an unsupervised machine learning framework called DeepHACKS (Deep phenotyping of Heterogeneous Activities in the Coordination of cytosKeleton at the Subcellular level) for "deep phenotyping," which identifies rare subcellular phenotypes specifically sensitive to molecular perturbations. DeepHACKS dissects the heterogeneity of subcellular time-series datasets by allowing bi-directional LSTM (Long-Short Term Memory) neural networks to extract fine-grained temporal features by integrating autoencoders with conventional machine learning outcomes. We applied DeepHACKS to subcellular protrusion dynamics in pharmacologically perturbed epithelial cells, revealing fine differential responses of leading edge dynamics specific to each perturbation. Particularly, DeepHACKS in conjunction with blebistantin treatment revealed the emergence of rare subcellular and single-cell phenotypes driven by "bursting" protrusion. This suggests that the temporal features directly learned from leading edge dynamics enable fine-grained identification of drug-related phenotypes, which may not be accessible from static cell images. In summary, our study provides an analytical framework for detailed and quantitative understandings of molecular mechanisms hidden in their heterogeneity. DeepHACKS can be potentially applied to analyze various time-series data measured from other subcellular processes.


title: Deep learning-based risk stratification for HER2-negative breast cancer patients

abstract: In this paper, we present our analysis of the tumor microenvironment in digital pathology images to stratify risk in HER2-negative breast cancer patients using clinicopathological, spatial image, and cell-based features in a Coxs proportional hazard model. We start the analysis by processing a set of 304 training pathology images using our in-house pan-cancer trained tumor, stroma, and lymphocyte region identification convolutional neural networks. The next step is computation of spatial regions of interest, namely: lymphocytes within (and adjacent to) tumor, lymphocytes within (and adjacent to) stroma, and stroma within (and adjacent to) tumor areas. Various cell-level information in these regions are then summarized, augmented to clinicopathological data, and linked to patients survival to train a Coxs proportional hazards model. The proposed model outperformed a baseline model based on clinicopathological features only in analysis of an untouched test set of 202 whole slide images with p 8.49E-08 (HR = 0.4273).

category: pathology


title: Dissociating the impact of movement time and energy costs on decision-making and action initiation in humans

abstract: Recent theories and data suggest that adapted behavior involves economic computations during which multiple trade-offs between reward value, accuracy requirement, energy expenditure and elapsing time are solved so as to obtain rewards as soon as possible while spending the least possible amount of energy. However, the relative impact of movement energy and duration costs on perceptual decision-making and movement initiation is poorly understood. Here, we tested 31 healthy subjects on a perceptual decision-making task in which they executed reaching movements to report probabilistic choices. In three distinct blocks of trials, the reaching time and energy costs were independently varied while decision difficulty was maintained similar at the block level. Participants also performed a fully instructed delayed-reaching (DR) task in each motor condition. Results in that DR task show that time-consuming movements extended reaction times (RTs) in most subjects, whereas energy-consuming movements led to mixed effects on RTs. In the choice task, about half of the subjects decreased their decision durations (DDs) in the time consuming condition, while the impact of energy costs on DDs were again mixed across subjects. Decision accuracy was overall similar across motor conditions. These results indicate that movement duration and, to a lesser extent, energy expenditure, idiosyncratically affect perceptual decision-making and action initiation. We propose that subjects who shortened their decisions in the time consuming condition of the choice task did so to limit a drop of their rate of reward.


title: Effective interferon (IFN)-lambda treatment regimen to control lethal MERS-CoV infection in mice

abstract: Effective broad-spectrum antivirals are critical to prevent and control emerging human coronavirus (hCoV) infections. Despite considerable progress made towards identifying and evaluating several synthetic broad-spectrum antivirals against hCoV infections, a narrow therapeutic window has limited their success. Enhancing the endogenous interferon (IFN) and interferon-stimulated gene (ISG) response is another antiviral strategy known for decades. However, the side effects of pegylated type-I IFNs (IFN-Is) and the pro-inflammatory response detected after delayed IFN-I therapy have discouraged their clinical use. In contrast to IFN-Is, IFN-{lambda}, a dominant IFN at the epithelial surface, is shown to be less pro-inflammatory. Consequently, we evaluated the prophylactic and therapeutic efficacy of IFN-{lambda} in hCoV infected airway epithelial cells and mice. Human primary airway epithelial cells treated with a single dose of IFN-I (IFN-) and IFN-{lambda} showed similar ISG expression, whereas cells treated with two doses of IFN-{lambda} expressed elevated levels of ISG compared to IFN-a treated cells. Similarly, mice treated with two dose IFN-{lambda} were better protected compared to mice receiving a single dose, and a combination of prophylactic and delayed therapeutic regimens completely protected mice from lethal MERS-CoV-infection. A two dose IFN-{lambda} regimen significantly reduced lung viral RNA and inflammatory cytokine levels with marked improvement in lung inflammation. Collectively, we identify an ideal regimen for IFN-{lambda} use and demonstrate the protective efficacy of IFN-{lambda} in MERS-CoV infected mice.


title: Environment, rather than Hematodinium parasitization, determines collateral disease contraction in a crustacean host

abstract: Host, pathogen, and environment are determinants of the disease triangle, the latter being a key driver of disease outcomes and persistence within a community. The dinoflagellate genus Hematodinium is detrimental to crustaceans globally - considered to suppress the innate defences of hosts, making them more susceptible to co-infections. Evidence supporting immune-suppression is largely anecdotal and sourced from diffuse accounts of compromised decapods. We used a population of shore crabs (Carcinus maenas), where Hematodinium sp. is endemic, to determine the extent of collateral infections across two distinct environments (open water, semi- closed dock). Using a multi-resource approach (PCR, histology, haematology, population genetics, eDNA), we identified 162 Hematodinium-positive crabs and size/sex-matched these to 162 Hematodinium-free crabs out of 1,191 analysed. Crabs were interrogated for additional disease-causing agents; haplosporidians, microsporidians, mikrocytids, Vibrio spp., fungi, Sacculina, trematodes, and haemolymph bacterial loads. We found no significant differences in occurrence, severity or composition of collateral infections between Hematodinium-positive and Hematodinium-free crabs at either site, but crucially, we recorded site-restricted blends of pathogens. We found no gross signs of host cell immune reactivity toward Hematodinium in the presence or absence of other pathogens. We contend Hematodinium sp. is an immune-evader rather than immune-suppressor, which suggests an evolutionary drive toward latency in this environmentally plastic host.


title: SARS-CoV-2 inactivation by human defensin HNP1 and retrocyclin RC-101

abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is an enveloped virus responsible for the COVID-19 respiratory disease pandemic. While induction of adaptive antiviral immunity via vaccination holds promise for combatting the pandemic, the emergence of new potentially more transmissible and vaccine-resistant variants of SARS-CoV-2 is an ever-present threat. Thus, it remains essential to better understand innate immune mechanisms that are active against the virus. One component of the innate immune system with broad anti-pathogen, including antiviral, activity is a group of cationic immune peptides termed defensins. The defensins ability to neutralize enveloped and non-enveloped viruses and to inactivate numerous bacterial toxins correlate with their ability to promote the unfolding of thermodynamically pliable proteins. Accordingly, we found that human neutrophil a-defensin HNP1 and retrocyclin RC-101 destabilize SARS-CoV-2 Spike protein and interfere with Spike-mediated membrane fusion and SARS-CoV-2 infection in cell culture. We show that HNP1 binds to Spike with submicromolar affinity. Although binding of HNP1 to serum albumin is more than 20-fold weaker, serum reduces the anti-SARS-CoV-2 activity of HNP1. At high concentrations of HNP1, its ability to inactivate the virus was preserved even in the presence of serum. These results suggest that specific a- and 8-defensins may be valuable tools in developing SARS-CoV-2 infection prevention strategies.


title: Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals

abstract: The SARS-CoV-2 B.1.617 lineage emerged in October 2020 in India1-6. It has since then become dominant in some indian regions and further spread to many countries. The lineage includes three main subtypes (B1.617.1, B.1617.2 and B.1.617.3), which harbour diverse Spike mutations in the N-terminal domain (NTD) and the receptor binding domain (RBD) which may increase their immune evasion potential. B.1.617.2 is believed to spread faster than the other versions. Here, we isolated infectious B.1.617.2 from a traveller returning from India. We examined its sensitivity to monoclonal antibodies (mAbs) and to antibodies present in sera from COVID-19 convalescent individuals or vaccine recipients, in comparison to other viral lineages. B.1.617.2 was resistant to neutralization by some anti-NTD and anti-RBD mAbs, including Bamlanivimab, which were impaired in binding to the B.1.617.2 Spike. Sera from convalescent patients collected up to 12 months post symptoms and from Pfizer Comirnaty vaccine recipients were 3 to 6 fold less potent against B.1.617.2, relative to B.1.1.7. Sera from individuals having received one dose of AstraZeneca Vaxzevria barely inhibited B.1.617.2. Thus, B.1.617.2 spread is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes.


title: Polyelectrolyte Coating of Ferumoxytol Differentially Impacts on Labeling of Inflammatory and Steady-State Dendritic Cell Subtypes

abstract: Engineered magnetic nanoparticles (MNPs) are emerging as advanced tools for medical applications. The coating of MNPs using polyelectrolytes (PEs) is a versatile means to tailor MNP properties and is used to optimize MNP functionality. Dendritic cells (DCs) are critical regulators of adaptive immune responses. Functional distinct DC subsets exist either under steady-state or inflammatory conditions, which are explored for the specific treatment of various diseases, such as cancer, autoimmunity or transplant rejection. Here, the impact of PE coating of ferumoxytol for uptake into both inflammatory and steady-state DCs and cellular responses to the MNP labeling is addressed. Labeling efficiency by uncoated and PE-coated ferumoxytol is highly variable in different DC subsets, and PE coating significantly improves the labeling of steady-state DCs. Uncoated ferumoxytol results in increased cytotoxicity of steady-state DCs after labeling that is abolished by the PE coating, while no increased cell death is observed in inflammatory DCs. Furthermore, uncoated and PE-coated ferumoxytol appears immunologically inert in inflammatory DCs but induces activation of steady-state DCs. These results show that PE coating of MNPs can be applied to endow particles with desired properties for enhanced uptake and cell type-specific responses in distinct target DC populations.


title: The Hox gene Antennapedia regulates wing development through 20-hydroxyecdysone in insect

abstract: A long-standing view in the field of evo-devo is that insect forewings develop without any Hox gene input. The Hox gene Antennapedia (Antp), despite being expressed in the thoracic segments of insects, has no effect on wing development. This view has been obtained from studies in two main model species, Drosophila and Tribolium. Here, we show that partial loss of function of Antp resulted in reduced and malformed adult wings in Bombyx, Drosophila, and Tribolium. Antp mediates wing growth in Bombyx by directly regulating the ecdysteriod biosynthesis enzyme gene (shade) in the wing tissue, which leads to local production of the growth hormone 20E. In turn, 20E signaling also up-regulates Antp. Additional targets of Antp are wing cuticular protein genes CPG24, CPH28, and CPG9, essential for wing development. We propose, thus, that insect wing development occurs in an Antp-dependent manner.


title: Actin-related protein 5 functions as a novel modulator of MyoD and MyoG in skeletal muscle and in rhabdomyosarcoma

abstract: Myogenic regulatory factors (MRFs) are pivotal transcription factors in myogenic differentiation. MyoD commits cells to the skeletal muscle lineage by inducing myogenic genes through recruitment of chromatin remodelers to its target loci. This study showed that Actin-related protein 5 (Arp5) acts as an inhibitory regulator of MyoD and MyoG by binding to their cysteine-rich (CR) region, which overlaps with the region essential for their epigenetic functions. Arp5 expression was faint in skeletal muscle tissues. Excessive Arp5 in mouse hind limbs caused skeletal muscle fiber atrophy. Further, Arp5 overexpression in myoblasts inhibited myotube formation by diminishing myogenic gene expression, whereas Arp5 depletion augmented myogenic gene expression. Arp5 disturbed MyoD-mediated chromatin remodeling through competition with the three-amino-acid-loop-extension-class homeodomain transcription factors the Pbx1-Meis1 heterodimer for binding to the CR region. This antimyogenic function was independent of the INO80 chromatin remodeling complex, although Arp5 is an important component of that. In rhabdomyosarcoma (RMS) cells, Arp5 expression was significantly higher than in normal myoblasts and skeletal muscle tissue, probably contributing to MyoD and MyoG activity dysregulation. Arp5 depletion in RMS partially restored myogenic properties while inhibiting tumorigenic properties. Thus, Arp5 is a novel modulator of MRFs in skeletal muscle differentiation.


title: Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity

abstract: Spinal motor neurons (MNs) constitute cellular substrates for several movement disorders. Although their early development has received much attention, how spinal MNs become and remain terminally differentiated is poorly understood. Here, we determined the transcriptome of mouse brachial MNs at embryonic and postnatal stages. We found that genes encoding homeodomain (HOX, LIM) transcription factors (TFs), previously implicated in early MN development, continue to be expressed postnatally, suggesting later functions. To test this, we inactivated Hoxc8 at successive stages of MN development. We found that Hoxc8 is not only required to establish but also maintain expression of several MN terminal differentiation markers. Furthermore, we uncovered novel TFs with continuous MN expression, a Hoxc8 dependency for maintained expression of Iroquois (Irx) homeodomain TFs, and a new role for Irx2 in MN development. Our findings dovetail recent observations in C. elegans MNs, pointing toward an evolutionarily conserved role for Hox in neuronal terminal differentiation.


title: Measuring the exposure of primate reservoir hosts to mosquito vectors in Malaysian Borneo

abstract: Several vector-borne pathogens of primates have potential for human spillover. An example is the simian malaria Plasmodium knowlesi which is now a major public health problem in Malaysia. Characterization of exposure to mosquito vectors is essential for assessment of the force of infection within wild primate populations, however few methods exist to do so. Here we demonstrate the use of thermal imaging and Mosquito Magnet Independence Traps (MMIT) to assess the abundance, diversity and infection rates in mosquitoes host seeking near long-tailed macaque (Macaca fasicularis) sleeping sites in the Lower Kinabatangan Wildlife Sanctuary, Malaysian Borneo. The primary Plasmodium knowlesi vector, Anopheles balabacensis, was trapped at higher abundance near sleeping sites than control trees. Although none of the An. balabacensis collected (n=15) were positive for P. knowlesi, two were infected with another primate malaria Plasmodium inui. Analysis of macaque stools from sleeping sites confirmed a high prevalence of Plasmodium infection, suspected to be P. inui. Plasmodium inui infections have not yet been reported in humans, but its presence in An. balabacensis here and previously in human-biting collections highlight its potential for spillover. We advocate the use of MMITs for non-invasive sampling of mosquito vectors that host seek on wild primate populations.


title: How do symbiotic associations in lecideoid lichens respond to different environmental conditions along the Transantarctic Mountains, Ross Sea region, Antarctica?

abstract:
Lecideoid lichens as dominant vegetation-forming organisms in the climatically harsh areas of the southern part of continental Antarctica show clear preferences in relation to environmental conditions (i.e. macroclimate). 306 lichen samples were included in the study, collected along the Ross Sea coast (78{degrees}S-85.5{degrees}S) at six climatically different sites. The species compositions as well as the associations of their two dominant symbiotic partners (myco- and photobiont) were set in context with environmental conditions along the latitudinal gradient. Diversity values were nonlinear with respect to latitude, with the highest alpha diversity in the milder areas of the McMurdo Dry Valleys (78{degrees}S) and the most southern areas (Durham Point, 85.5{degrees}S; Garden Spur, 84.5{degrees}S), and lowest in the especially arid and cold Darwin Area (~79.8{degrees}S). Furthermore, the specificity of mycobiont species towards their photobionts decreased under more severe climate conditions. The generalist lichen species Lecanora fuscobrunnea and Lecidea cancriformis were present in almost all habitats, but were dominant in climatically extreme areas. Carbonea vorticosa, Lecidella greenii and Rhizoplaca macleanii were confined to milder areas.

In summary, the macroclimate is considered to be the main driver of species distribution, making certain species useful as bioindicators of climate conditions and, consequently, for detecting climate change.


title: Collation of indigenous and local knowledge as evidence base for herpetofauna conservation outside protected areas: Case study from an agricultural landscape in Eastern India

abstract: Systematic appraisal of communitys knowledge as evidence for biodiversity conservation has been widely recognized. For conserving the rich biodiversity in the rural landscape outside the protected areas, it is important to document the knowledge and perception of the farming community. Although such appraisal is available for different taxa, no such systematic study is available for herpetofauna-one of the most vulnerable faunal groups. Our study attempts to document the impact of agricultural intensification on herpetofauna in an agricultural landscape through knowledge and perception appraisal of the farming community. A semi-structured questionnaire survey and validation was conducted in areas of low, medium, and high agricultural intensification. In all areas, farmers indicated an overall decrease in herpetofauna abundance. Farmers at the mid and high agricultural intensification zones reported a more significant decrease in herpetofauna sightings specifically for amphibians and snakes compared to those under low intensification regions. Farmers at low intensification area recognized significantly more herpetofauna. Farmers attributed five major threats to herpetofauna and ranked pesticide as the most significant reason, especially those in higher intensification. The majority were aware of the importance of herpetofauna as a biological pest control agent. Level of education or farming experience did not seem to have any influence on the farmers knowledge. Our findings integrated with other quantitative studies will facilitate future community-driven conservation in the studied agricultural landscapes.


title: Genome-wide evolutionary response of European oakssince the Little Ice Age

abstract: The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of convergent linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last three hundred years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. Our results therefore provide evidence of selection operating on long-lived species during recent climatic changes.


title: Genetic diversity of the pathogenic banana Fusarium wilt in northern Viet Nam

abstract: Fusarium is one of the most important fungal genera of plant pathogens that affect the cultivation of a wide range of crops. Agricultural losses caused by Fusarium oxysporum f. sp. cubense (Foc) have a direct effect on the income, subsistence and nourishment of thousands of smallholder farmers worldwide. In addition, also commercial growers are strongly affected. For Viet Nam, predictions on the impact of Foc for the future are dramatic with an estimated loss in banana production area of 8% within the next 5 years and up to 71% within the next 25 years. In the current study we applied a combined morphological - molecular approach to assess the taxonomic identity and phylogenetic position of the different Foc isolates that were collected in northern Viet Nam. In addition, we aim to estimate the proportion of the different Fusarium races that are infecting bananas in northern Viet Nam. The morphology of the isolates was investigated by growing the collected Fusarium isolates on four distinct nutritious media (PDA, SNA, CLA, and OMA). Molecular phylogenetic relationships were inferred by sequencing partial rpb1, rpb2 and tef1a genes and adding the obtained sequences into a large phylogenetic framework. The present study showed that Foc Race 1 is the most common strain in northern Viet Nam, causing 74% of all the infections. A more in-depth molecular characterization shows that of the Foc Race 1 infections, 92% are caused by Fusarium tardichlamydosporum and 8% by F. duoseptatum. Compared to Foc Race 1, Foc TR4 (represented by F. odoratissimum) account for only 10.5% of the Fusarium wilting in northern Viet Nam demonstrating that Foc TR4 is not yet a dominant strain in the region. Foc Race 2 infections of Vietnamese bananas also account for 10.5% of the Fusarium wilting in northern Viet Nam. One of the isolates cultured from diseased bananas collected in northern Viet Nam was phylogenetically not positioned within the F. oxysporum species complex (FOSC), but in contrast fell within the Fusarium fujikuroi species complex (FFSC). As a result, it is possible that a new pathogen for bananas has been found. Besides being present on several ABB  Tay banana, Foc Race 1 was also found as pathogen on wild Musa lutea, showing the importance of wild bananas as possible sink for Foc.


title: Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin

abstract: The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an "Out-of-Italy" expansion following the Messinian salinity crisis (~5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flow have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.


title: Rigorous estimation of post-translational proteasomal splicing in the immunopeptidome

abstract: Recently, de novo peptide sequencing has made it possible to gain new insights into the human immunopeptidome without relying on peptide databases, while identifying peptides of unknown origin. Many recent studies have attributed post-translational proteasomal splicing as the origin of those peptides. Here, we describe a peptide source assignment workflow to rigorously assign the source of de novo sequenced peptides and find that the estimated extent of post-translational splicing in the immunopeptidome is much lower than previously reported. Our approach demonstrates that many peptides that were thought to be post-translationally spliced are likely linear peptides, and many peptides that were thought to be trans-spliced could be cis-spliced. We believe our approach furthers the understanding of post-translationally spliced peptides and thus improves the characterization of immunopeptidome which plays a critical role in the immune response to antigens in cancer, autoimmune disease, and infections.


title: TIGER: The gene expression regulatory variation landscape of human pancreatic islets

abstract: GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.


title: Learned deconvolution using physics priors for structured light-sheet microscopy

abstract: Deconvolution is a challenging inverse problem, particularly in techniques that employ complex engineered point-spread functions, such as microscopy with propagation-invariant beams. Here, we present a deep learning method that uses known physics priors, in lieu of any ground truths, to rapidly and robustly deconvolve and super-resolve these microscopy images. Specifically, we constrain a generative adversarial network with images generated with the known point-spread function of the system, and combine this with unpaired experimental data that preserves perceptual content. Our network overcomes a major present barrier to deep learning adoption, namely, the need for 1,000-10,000s of paired training images. It is experimentally unsupervised and can be trained solely on a few hundred regions of interest. We demonstrate its performance on light-sheet microscopy with propagation-invariant Airy beams, including in calibration beads, oocytes, preimplantation embryos, and excised brain tissue, as well as illustrate its utility for Bessel-beam LSM. This method aims to democratise learned methods for deconvolution, as it does not require data acquisition outwith the conventional imaging protocol.


title: Learned deconvolution using physics priors for light-sheet microscopy with propagation-invariant beams


title: Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway

abstract: We previously discovered that deletion of c-Rel in the E-Myc mouse model of lymphoma results in earlier onset of disease, a finding that contrasted with the expected function of this NF-{kappa}B subunit in B-cell malignancies. Here we report that c-rel -/- E{micro}-Myc cells have an unexpected and major defect in the CHK1 pathway, with almost undetectable levels of CHK1 and CLSPN protein leading to therapeutic resistance to the highly specific CHK1 inhibitor (CHK1i) CCT244747. Similar downregulation of CHK1 levels was also seen in CCT244747 resistant U20S osteosarcoma cells. Further investigation revealed that downregulation of the deubiquitinase USP1 is responsible, at least in part, for these effects. Importantly, we demonstrate that c-rel -/- E{micro}-Myc lymphoma cells survive though upregulation of compensatory PI3K/AKT pathway activity. Moreover, targeting this pathway with Pictilisib (GDC-0941) effectively killed c-rel -/- E{micro}-Myc in vivo, while having no effect on wild type E-Myc cells. This data reveals an NF-{kappa}B regulated pathway controlling CHK1 activity in cancer cells and identifies a potential mechanism for both acquiring and overcoming CHK1i resistance in cancer patients.

category: cancer biology


title: Dysregulated heparan sulfate proteoglycan metabolism promotes Ewing sarcoma tumor growth

abstract: The Ewing sarcoma family of tumors is a group of malignant small round blue cell tumors (SRBCTs) that affects children, adolescents and young adults. The tumors are characterized by reciprocal chromosomal translocations that generate chimeric fusion oncogenes, the most common of which is EWSR1-FLI1. Survival is extremely poor for patients with metastatic or relapsed disease, and no molecularly-targeted therapy for this disease currently exists. The absence of a reliable genetic animal model of Ewing sarcoma has impaired investigation of tumor cell/microenvironmental interactions in vivo. We have developed a new genetic model of Ewing sarcoma based on Cre-inducible expression of human EWSR1-FLI1 in wild type zebrafish, which causes rapid onset of SRBCTs at high penetrance. The tumors express canonical EWSR1-FLI1 target genes and stain for known Ewing sarcoma markers including CD99. Growth of tumors is associated with activation of the MAPK/ERK pathway, which we link to dysregulated extracellular matrix metabolism in general and heparan sulfate catabolism in particular. Targeting heparan sulfate proteoglycans with the specific heparan sulfate antagonist Surfen reduces ERK1/2 signaling and decreases tumorigenicity of Ewing sarcoma cells in vitro and in vivo. These results highlight the important role of the extracellular matrix in Ewing sarcoma tumor growth and the potential of agents targeting proteoglycan metabolism as novel therapies for this disease.


title: A ratiometric dual color luciferase reporter for fast characterization of transcriptional regulatory elements

abstract:
Plant synthetic biology requires precise characterization of genetic elements to construct complex genetic circuits that can improve plant traits or confer them new characteristics. Transcriptional reporter assays are essential to quantify the effect of gene expression regulator elements. Therefore, transcriptional reporter systems are a key tool in understanding control of gene expression in biology.

In this work we construct and characterize a dual-color luciferase ratiometric reporter system that possesses several advantages over currently used reporters. It is ratiometric, reducing variability and increasing consistency between experiments; it is fast, as both reporters can be measured at the same time in a single reaction, and it is cheaper to perform than current dual-luciferase reporter assays. We have validated our system quantifying the transcriptional capability of a panel of promoters and terminators commonly used in synthetic biology with a broad range of expression magnitudes, and in a biologically relevant system, nitrate response.

category: synthetic biology


title: Early beta oscillations in multisensory association areas underlie crossmodal performance enhancement

abstract:
The combination of signals from different sensory modalities can enhance perception and facilitate behavioral responses. While previous research described crossmodal influences in a wide range of tasks, it remains unclear how such influences drive performance enhancements. In particular, the neural mechanisms underlying performance-relevant crossmodal influences, as well as the latency and spatial profile of such influences are not well understood. Here, we examined data from high-density electroencephalography (N = 30) and electrocorticography (N = 4) recordings to characterize the oscillatory signatures of crossmodal facilitation of response speed, as manifested in the speeding of visual responses by concurrent task-irrelevant auditory information. Using a data-driven analysis approach, we found that individual gains in response speed correlated with reduced beta power (13-25 Hz) in the audiovisual compared with the visual condition, starting within 80 ms after stimulus onset in multisensory association and secondary visual areas. In addition, the electrocorticography data revealed a beta power suppression in audiovisual compared with visual trials in the superior temporal gyrus (STG). Our data suggest that the crossmodal facilitation of response speed is associated with early beta power in multisensory association and secondary visual areas, presumably reflecting the enhancement of early sensory processing through selective attention. This finding furthers our understanding of the neural correlates underlying crossmodal response speed facilitation and highlights the critical role of beta oscillations in mediating behaviorally relevant audiovisual processing.

Significance StatementThe use of complementary information across multiple senses can enhance perception. Previous research established a central role of neuronal oscillations in multisensory perception, but it remains poorly understood how they relate to multisensory performance enhancement. To address this question, we recorded electrophysiological signals from scalp and intracranial electrodes (implanted for presurgical monitoring) in response to simple visual and audiovisual stimuli. We then associated the difference in oscillatory power between the two conditions with the speeding of responses in the audiovisual trials. We demonstrate, that the crossmodal facilitation of response speed is associated with beta power in multisensory association areas during early stages of sensory processing. This finding highlights the importance of beta oscillations in mediating behaviorally relevant audiovisual processing.


title: Expansion and contraction of resource allocation in sensory bottlenecks

abstract: Topographic sensory representations often do not scale proportionally to the size of their input regions, with some expanded and others contracted. In vision, the foveal representation is magnified cortically, as are the fingertips in touch. What principles drive this allocation, and how should receptor density, e.g. the high innervation of the fovea or the fingertips, and stimulus statistics, e.g. the higher contact frequencies on the fingertips, contribute? Building on work in efficient coding, we address this problem using linear models that maximize information transmission through decorrelation. We introduce a sensory bottleneck to impose constraints on resource allocation and derive the optimal neural allocation. We find that bottleneck width is a crucial factor in resource allocation, inducing either expansion or contraction. Both receptor density and stimulus statistics affect allocation and jointly determine convergence for wider bottlenecks. Furthermore, we show a close match between the predicted and empirical cortical allocations in a well-studied model system, the star-nosed mole. Overall, our results suggest that the strength of cortical magnification depends on resource limits.


title: Using OPMs to measure neural activity in standing, mobile participants

abstract: Optically pumped magnetometer-based magnetoencephalography (OP-MEG) can be used to measure neuromagnetic fields while participants move in a magnetically shielded room. Head movements in previous OP-MEG studies have been up to 20 cm translation and [~]30{degrees} rotation in a sitting position. While this represents a step-change over stationary MEG systems, naturalistic head movement is likely to exceed these limits, particularly when participants are standing up. In this proof-of-concept study, we sought to push the movement limits of OP-MEG even further. Using a 90 channel (45-sensor) whole-head OP-MEG system and concurrent motion capture, we recorded auditory evoked fields while participants were: (i) sitting still, (ii) standing up and still, and (iii) standing up and making large natural head movements continuously throughout the recording - maximum translation 120 cm, maximum rotation 198{degrees}. Following pre-processing, movement artefacts were substantially reduced but not eliminated. However, upon utilisation of a beamformer, the M100 event-related field localised to primary auditory regions. Furthermore, the event-related fields from auditory cortex were remarkably consistent across the three conditions. These results suggest that a wide range of movement is possible with current OP-MEG systems. This in turn underscores the exciting potential of OP-MEG for recording neural activity during naturalistic paradigms that involve movement (e.g. navigation), and for scanning populations who are difficult to study with stationary MEG (e.g. young children).


title: Development of the visual white matter pathways mediates development of electrophysiological responses in visual cortex

abstract: The latency of neural responses in the visual cortex changes systematically across the lifespan. Here we test the hypothesis that development of visual white matter pathways mediates maturational changes in the latency of visual signals. Thirty-eight children participated in a cross-sectional study including diffusion MRI and MEG sessions. During the MEG acquisition, participants performed a lexical decision and a fixation task on words presented at varying levels of contrast and noise. For all stimuli and tasks, early evoked fields were observed around 100 ms after stimulus onset (M100), with slower and lower amplitude responses for low as compared to high contrast stimuli. The optic radiations and optic tracts were identified in each individuals brain based on diffusion MRI tractography. The diffusion properties of the optic radiations predicted M100 responses, especially for high contrast stimuli. Higher optic radiation fractional anisotropy (FA) values were associated with faster and larger M100 responses. Over this developmental window, the M100 responses to high contrast stimuli became faster with age and the optic radiation FA mediated this effect. These findings suggest that the maturation of the optic radiations over childhood accounts for individual variations observed in the developmental trajectory of visual cortex responses.


title: The sensory and motor components of the cortical hierarchy are coupled to the rhythm of the stomach during rest

abstract:
Bodily rhythms appear as novel scaffolding mechanisms orchestrating the spatio-temporal organization of spontaneous brain activity. Here, we follow up on the discovery of the gastric resting-state network (Rebollo et al, 2018), composed of brain regions in which the fMRI signal is phase-synchronized to the slow (0.05 Hz) electrical rhythm of the stomach. Using a larger sample size (n=63 human participants), we further characterize the anatomy and effect sizes of gastric-brain coupling across resting-state networks, a fine grained cortical parcellation, as well as along the main gradients of cortical organization. Most (67%) of the gastric network is included in the somato-motor-auditory (38%) and visual (29%) resting state networks. Gastric brain coupling also occurs in the granular insula and, to a lesser extent, in the piriform cortex. Thus, all sensory and motor cortices corresponding to both exteroceptive and interoceptive modalities are coupled to the gastric rhythm during rest. Conversely, little gastric-brain coupling occurs in cognitive networks and transmodal regions. These results suggest not only that gastric rhythm and sensory-motor processes are likely to interact, but also that gastric-brain coupling might be a mechanism of sensory and motor integration that mostly bypasses cognition, complementing the classical hierarchical organization of the human brain.

Significance statementWhile there is growing interest for brain-body communication in general and brain-viscera communication in particular, little is known about how the brain interacts with the gastric rhythm, the slow electrical rhythm continuously produced in the stomach. Here, we show in human participants at rest that the gastric network, composed of brain regions synchronized with delays to the gastric rhythm, includes all motor and sensory (vision, audition, touch and interoception, olfaction) regions, but only few of the transmodal regions associated with higher-level cognition. Such results prompt for a reconsideration of the classical view of cortical organization, where the different sensory modalities are considered as relatively independent modules.


title: Plasmodium falciparum and helminth coinfections increase IgE and parasite-specific IgG responses

abstract:
Coinfection with Plasmodium falciparum and helminths may impact the immune response to these parasites since they induce different immune profiles. We studied the effects of coinfections on the antibody profile in a cohort of 715 Mozambican children and adults using the Luminex technology with a panel of 16 antigens from P. falciparum and 11 antigens from helminths (Ascaris lumbricoides, hookworm, Trichuris trichiura, Strongyloides stercoralis and Schistosoma spp.) and measured antigen-specific IgG and total IgE responses. We compared the antibody profile between groups defined by P. falciparum and helminth previous exposure (based on serology) and/or current infection (determined by microscopy and/or qPCR). In multivariable regression models adjusted by demographic, socioeconomic, water and sanitation variables, individuals exposed/infected with P. falciparum and helminths had significantly higher total IgE and antigen-specific IgG levels, magnitude (sum of all levels) and breadth of response to both types of parasites compared to individuals exposed/infected with only one type of parasite (p[≤] 0.05). There was a positive association between exposure/infection to P. falciparum and exposure/infection to helminths or the number of helminth species, and vice versa (p[≤] 0.001). In addition, children coexposed/coinfected tended (p= 0.062) to have higher P. falciparum parasitemia than those single exposed/infected. Our results suggest that an increase in the antibody responses in coexposed/coinfected individuals may reflect higher exposure and be due to a more permissive immune environment to infection in the host.

GRAPHICAL ABSTRACT

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title: The P5-ATPase ATP13A1 modulates MR1-mediated antigen presentation

abstract: The monomorphic antigen presenting molecule MHC-I-related protein 1 (MR1) presents small molecule metabolites to mucosal-associated invariant T (MAIT) cells. The MR1-MAIT cell axis has been implicated in a variety of infectious and non-communicable diseases and recent studies have begun to develop an understanding of the molecular mechanisms underlying this specialised antigen presentation pathway. Yet, the proteins regulating MR1 folding, loading, stability, and surface expression remain to be identified. Here, we performed a gene trap screen to discover novel modulators of MR1 surface expression through insertional mutagenesis of an MR1-overexpressing clone derived from the near-haploid human cell line HAP1 (HAP1.MR1). The most significant positive regulators identified included {beta}2-microglobulin, a known regulator of MR1 surface expression, and ATP13A1, a P5-ATPase in the endoplasmic reticulum (ER) with putative transporter function not previously associated with MR1-mediated antigen presentation. CRISPR/Cas9-mediated knock-out of ATP13A1 in both HAP1.MR1 and THP-1 cell lines revealed a profound reduction in MR1 protein levels and a concomitant functional defect specific to MR1-mediated antigen presentation. Collectively, these data are consistent with the ER-resident ATP13A1 as a key post-transcriptional determinant of MR1 surface expression.