title: Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy

abstract: Single cell RNA-Seq (scRNA-seq) and other profiling assays have opened new windows into understanding the properties, regulation, dynamics, and function of cells at unprecedented resolution and scale. However, these assays are inherently destructive, precluding us from tracking the temporal dynamics of live cells, in cell culture or whole organisms. Raman microscopy offers a unique opportunity to comprehensively report on the vibrational energy levels of molecules in a label-free and non-destructive manner at a subcellular spatial resolution, but it lacks in genetic and molecular interpretability. Here, we developed Raman2RNA (R2R), an experimental and computational framework to infer single-cell expression profiles in live cells through label-free hyperspectral Raman microscopy images and multi-modal data integration and domain translation. We used spatially resolved single-molecule RNA-FISH (smFISH) data as anchors to link scRNA-seq profiles to the paired spatial hyperspectral Raman images, and trained machine learning models to infer expression profiles from Raman spectra at the single-cell level. In reprogramming of mouse fibroblasts into induced pluripotent stem cells (iPSCs), R2R accurately (r>0.96) inferred from Raman images the expression profiles of various cell states and fates, including iPSCs, mesenchymal-epithelial transition (MET) cells, stromal cells, epithelial cells, and fibroblasts. R2R outperformed inference from brightfield images, showing the importance of spectroscopic content afforded by Raman microscopy. Raman2RNA lays a foundation for future investigations into exploring single-cell genome-wide molecular dynamics through imaging data, in vitro and in vivo.

category: genomics


title: MuDCoD: Multi-Subject Community Detection in Personalized Dynamic Gene Networks from Single Cell RNA Sequencing

abstract: Developments in single-cell RNA sequencing (scRNA-seq) advanced our understanding of transcriptional programs of different cell types and cellular stages at the individual cell level. Single-cell RNA-seq datasets across multiple individuals and time points are now routinely generated for different conditions. Analysis of personalized dynamic gene networks constructed from these datasets could unravel subject-specific network-level variation critical for phenotypic differences. While there have been developments in the gene module discovery methods on networks estimated from scRNA-seq data, these have mostly focused on static gene networks. In this work, we develop MuDCoD to cluster genes in personalized dynamic gene networks and identify gene modules that vary not only across time but also among subjects. To this end, MuDCoD extends the global spectral clustering framework of the previously developed method, PisCES, to promote information sharing among the subject as well as the time domain. Our computational experiments across a wide variety of settings indicate that, when present, MuDCoD leverages shared signals among networks of the subjects, and performs robustly when subjects do not share any apparent information. An application to human-induced pluripotent stem cell scRNA-seq data during dopaminergic neuron differentiation indicates that MuDCoD enables robust inference for identifying time-varying personalized gene modules. Our results illustrate how personalized dynamic community detection can aid the exploration of subject-specific biological processes that vary across time. MuDCoD is publicly available at https://github.com/bo1929/MuDCoD.


title: Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in South Central Coast, Vietnam

abstract: Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin, and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South-Central Coast of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. Pulsed-field gel electrophoresis identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and single-nucleotide polymorphism (SNP) genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0-2 SNPs). There was no association between geographic origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 217 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55-7.96 Mbp in size, have an average G+C content of 68.2%, and encode 7,602-7,958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into N. seriolae epidemiology and pathogenicity and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.


title: Benefits of living closer to kin vary by genealogical relationship in a territorial mammal

abstract: While cooperative interactions among kin are a key building block in the societies of group-living mammals, their importance for species with more variable social environments is unclear. North American red squirrels (Tamiasciurus hudsonicus) defend individual territories in dynamic neighbourhoods and are known to benefit from living among familiar conspecifics, but not relatives. However, kin-directed behaviours may be restricted to specific genealogical relationships or strongly mediated by geographic distance, masking their influence at broader scales. Using distance between territories as a proxy for the ability of individuals to interact, we estimated the influence of primary kin (parents, offspring, siblings) on the annual survival and reproductive success of red squirrels. Contrary to previous work, this approach revealed large fitness effects of living closer to kin, but only for certain genealogical relationships and fitness components. For example, females had enhanced annual survival when living closer to their daughters, though the reverse was not true. Most surprising was the finding that males had higher annual reproductive success when living closer to their father, raising new questions about cooperation among fathers and sons. Together, these findings reveal unexpected nuance in the fitness consequences of kinship dynamics for a species that is territorial and largely solitary.

category: animal behavior and cognition


title: A generalized distribution interpolated between the exponential and power law distributions and applied to the walking data of the pill bug (Armadillidium vulgare)

abstract: To determine whether the walking pattern of an organism is a Levy walk or a Brownian walk, it has been compared whether the frequency distribution of linear step lengths follows a power law distribution or an exponential distribution. However, there are many cases where actual data cannot be classified into either of these categories. In this paper, we propose a general distribution that includes the power law and exponential distributions as special cases. This distribution has two parameters: One represents the exponent, similar to the power law and exponential distributions, and the other is a shape parameter representing the shape of the distribution. By introducing this distribution, an intermediate distribution model can be interpolated between the power law and exponential distributions. In this study, the proposed distribution was fitted to the frequency distribution of the step length calculated from the walking data of pill bugs. The autocorrelation coefficients were also calculated from the time-series data of the step length, and the relationship between the shape parameter and time dependency was investigated. The results showed that individuals whose step-length frequency distributions were closer to the power law distribution had stronger time dependence.


title: A Resident State Allows Influenza Polymerase to Smoothly Switch between Transcription and Replication Cycles

abstract: Influenza polymerase (FluPol) transcripts viral mRNA and switches to replicate viral genome after transcription. However, it remains unknown how FluPol switches between transcription and replication cycles, especially when considering that the structural basis of these two functions is fundamentally different. Here, we proposed a mechanism that FluPol achieves the functional switching between these two cycles through an unreported intermediate conformation, termed as resident state. We obtained a resident state structure of H5N1 FluPol at 3.7 [A] using cryo-EM, which is characterized by a blocked Cap-binding domain and a contracted core region, distinct from the structures of either transcription or replication states. Structural analysis results suggest that the resident state structure is feasible to smoothly transit into structures of both transcription and replication states. Furthermore, we show that formation of the resident state is required for both transcription and replication activities of FluPol. Together, the transcription and replication cycles of FluPol are connected via a resident state.

category: biochemistry


title: Heterogeneous Tissue Modulus Improved Prediction of Mechanical Behavior in Osteoporotic Vertebral Cancellous Bone

abstract: The structural integrity of cancellous bone, which is essential to skeletal load-bearing capacity, is governed chiefly by apparent density, trabecular architecture, and tissue material properties. Metabolic bone disorders like osteoporosis can affect each of these factors separately, resulting in compromised load-bearing function. While the impact of apparent density and architecture on bone structural behavior has been well-documented, much less is known about the influence of tissue material properties, particularly in osteoporotic bone. The goal of this study was to isolate the influence of tissue material properties on normal and osteoporotic cancellous bone structural integrity, indicated by the apparent elastic modulus under uniaxial compression, using finite element (FE) models derived from 3D microcomputed tomography images. Three sets of models with increasing material detail were studied: 1) universal tissue elastic modulus, 2) specimen-specific average tissue modulus, and 3) heterogeneous tissue modulus. FE results were compared to matched parameters from physical testing. Increasing material detail did not significantly affect model predictions for normal bone. For osteoporotic bone, incorporating a specimen-specific tissue modulus significantly improved the ability of FE models to predict the apparent elastic modulus of physical specimens compared to using a universal tissue modulus. Incorporating material heterogeneity also improved model performance compared to models with a universal tissue modulus but did not afford significant improvement over models with specimen-specific average properties. We conclude that, while the influence of bone apparent density and trabecular architecture on structural integrity are dominant in healthy bone, average material properties also play a role in osteoporotic bone. Osteoporosis is diagnosed based primarily on apparent density, so these results highlight the need to consider other patient-specific differences that may affect average material properties, such as bone remodeling rate, in clinical assessments of osteoporotic bone structural integrity.

category: bioengineering


title: Genetic Encoding of A Nonhydrolyzable Phosphotyrosine Analog in Mammalian Cells

abstract: Protein tyrosine phosphorylation plays a critical role in signal transduction and the regulation of many cellular processes. It is of great significance to understand the underlying regulatory mechanism of particular tyrosine phosphorylation events. Here we report the genetic incorporation of a phosphotyrosine (pTyr) analog, p-carboxymethyl-L-phenylalanine (CMF), into proteins in mammalian cells. This nonhydrolyzable pTyr analog can facilitate biological studies by removing complications caused by the dynamic interconversion between the phosphorylated and non-phosphorylated isoforms of a protein. The developed methodology was demonstrated by using the human signal transducer and activator of transcription-1 (STAT1) as a model protein for homogeneous and defined incorporation of CMF. This tool will greatly enhance ones capability to study protein tyrosine phosphorylation-associated biomolecular and cellular events, and enhance biomedical research that target protein tyrosine phosphorylation, which will have a broad impact to both fundamental studies and practical applications.


title: Optogenetic operated probiotics to regulate host metabolism by mimicking enteroendocrine

abstract: The enteroendocrine system plays an important role in metabolism. The gut microbiome regulates enteroendocrine in an extensive way, arousing attention in biomedicine. However, conventional strategies of enteroendocrine regulation via gut microbiome are usually non-specific or imprecise. Here, an optogenetic operated probiotics system was developed combining synthetic biology and flexible electronics to achieve in situ controllable secretion to mimic enteroendocrine. Firstly, optogenetic engineered Lactococcus lactis (L. lactis) were administrated in the intestinal tract. A wearable optogenetic device was designed to control optical signals remotely. Then, L. lactis could secrete enteroendocrine hormone according to optical signals. As an example, optogenetic L. lactis could secrete glucagon-like peptide-1(GLP-1) under the control of the wearable optogenetic device. To improve the half-life of GLP-1 in vivo, the Fc domain from immunoglobulin was fused. Treated with this strategy, blood glucose, weight and other features were relatively well controlled in rats and mice models. Furthermore, up-conversion microcapsules were introduced to increase the excitation wavelength of the optogenetic system for better penetrability. This strategy has biomedical potential in metabolic diseases therapy by mimicking enteroendocrine.


title: Euler method can outperform more complex ODE solvers in the numerical implementation of the Izhikevich artificial Spiking Neuron Model given the allocated FLOPS

abstract: The Izhikevich artificial spiking neuron model is among the most employed models in neuromorphic engineering and computational neuroscience, due to the affordable computational effort to discretize it and its biological plausibility. It has been adopted also for applications with limited computational resources in embedded systems. It is important therefore to realize a compromise between error and computational expense to solve numerically the models equations. Here we investigate the effects of discretization and we study the solver that realizes the best compromise between accuracy and computational cost, given an available amount of Floating Point Operations per Second (FLOPS). We considered three fixed-step solvers for Ordinary Differential Equations (ODE), commonly used in computational neuroscience: Euler method, the Runge-Kutta 2 method and the Runge-Kutta 4 method. To quantify the error produced by the solvers, we used the Victor Purpura spike train Distance from an ideal solution of the ODE. Counterintuitively, we found that simple methods such as Euler and Runge Kutta 2 can outperform more complex ones (i.e. Runge Kutta 4) in the numerical solution of the Izhikevich model if the same FLOPS are allocated in the comparison. Moreover, we quantified the neuron rest time (with input under threshold resulting in no output spikes) necessary for the numerical solution to converge to the ideal solution and therefore to cancel the error accumulated during the spike train; in this analysis we found that the required rest time is independent from the firing rate and the spike train duration. Our results can generalize in a straightforward manner to other spiking neuron models and provide a systematic analysis of fixed step neural ODE solvers towards an accuracy-computational cost tradeoff.


title: Therapeutic downregulation of neuronal PAS domain 2 (Npas2) promotes surgical skin wound healing

abstract: Attempts to minimize scarring remain among the most difficult challenges facing surgeons, despite the use of optimal wound closure techniques. Previously, we reported improved healing of dermal excisional wounds in circadian clock neuronal PAS domain 2 (Npas2)-null mice. In this study, we performed high-throughput drug screening to identify a compound that downregulates Npas2 activity. The hit compound (Dwn1) suppressed circadian Npas2 expression, increased murine dermal fibroblast cell migration, and decreased collagen synthesis in vitro. Based on the in vitro results, Dwn1 was topically applied to iatrogenic full-thickness dorsal cutaneous wounds in a murine model. The Dwn1-treated dermal wounds healed faster with favorable mechanical strength and developed less granulation tissue than the controls. The expression of type I collagen, Tgf{beta}1, and -smooth muscle actin was significantly decreased in Dwn1-treated wounds, suggesting that hypertrophic scarring and myofibroblast differentiation are attenuated by Dwn1 treatment. NPAS2 may represent an important target for therapeutic approaches to optimal surgical wound management.


title: Image recognition based on deep learning in Haemonchus contortus motility assays

abstract: Poor efficacy of some anthelmintics and rising concerns about the widespread drug resistance have highlighted the need for new drug discovery. The parasitic nematode Haemonchus contortus is an important model organism widely used for studies of drug resistance and drug screening with the current gold standard being the motility assay. We applied a deep learning approach Mask R-CNN for analysing motility videos containing varying rates of motile worms and compared it to other commonly used algorithms with different levels of complexity, namely the Wiggle Index and the Wide Field-of-View Nematode Tracking Platform. Mask R-CNN consistently outperformed the other algorithms in terms of the detection of worms as well as the precision of motility forecasts, having a mean absolute percentage error of 7.6% and a mean absolute error of 5.6% for the detection and motility forecasts, respectively. Using Mask R-CNN for motility assays confirmed the common problem with algorithms that use non-maximum suppression in detecting overlapping objects, which negatively impacts the overall precision. The use of intersect over union as a measure of the classification of motile / non-motile instances had an overall accuracy of 89%, indicating that it is a viable alternative to previously used methods based on movement characteristics, such as body bends. In comparison to the existing methods evaluated here, Mask R-CNN performed better and we anticipate that this method will broaden the number of possible approaches to video analysis of worm motility.

category: bioinformatics


title: R code and downstream analysis objects for the scRNA-seq atlas of human breast spanning normal, preneoplastic and tumorigenic states

abstract: Breast cancer is a common and highly heterogeneous disease. Understanding the cellular diversity in the mammary gland and its surrounding micro-environment across different states can provide insight into the cancer development in human breast. Recently, a large-scale single-cell RNA expression atlas was constructed of the human breast spanning normal, preneoplastic and tumorigenic states. Single-cell expression profiles of nearly 430,000 cells were obtained from 69 distinct surgical tissue specimens from 55 patients. This article extends the study by providing downstream processed R data objects, complete cell annotation and R code to reproduce all the analyses. Details of all the bioinformatic analyses that produced the results described in the study are provided.


title: Prediction of drug targets for specific diseases leveraging gene perturbation data: A machine learning approach

abstract:
Identification of the correct targets is a key element for successful drug development. However, there are limited approaches for predicting drug targets for specific diseases using omics data, and few have leveraged expression profiles from gene perturbations.

We present a novel computational target discovery approach based on machine learning(ML) models. ML models are first trained on drug-induced expression profiles, with outcomes defined as whether the drug treats the studied disease. The goal is to "learn" expression patterns associated with treatment. The fitted ML models were then applied to expression profiles from gene perturbations(over-expression[OE]/knockdown[KD]). We prioritized targets based on predicted probabilities from the ML model, which reflects treatment potential.

The methodology was applied to predict targets for hypertension, diabetes mellitus(DM), rheumatoid arthritis(RA) and schizophrenia(SCZ). We validated our approach by evaluating whether the identified targets may  re-discover known drug targets from an external database(OpenTargets). We indeed found evidence of significant enrichment across all diseases under study. Further literature search revealed that many candidates were supported by previous studies. For example, we predicted PSMB8 inhibition to be associated with treatment of RA, which was supported by a study showing PSMB8 inhibitors(PR-957) ameliorated experimental RA in mice.

In conclusion, we propose a new ML approach to integrate expression profiles from drugs and gene perturbations and validated the framework. Our approach is flexible and may provide an independent source of information when prioritizing targets.


title: Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections

abstract: Atomistic molecular dynamics (MD) simulations represent established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development of efficient enhanced sampling techniques is important for two reasons. First, they allow to overcome the sampling limitations and, second, they can be used to quantify ff imbalances provided they reach a sufficient convergence. Here, we study two RNA tetraloops (TLs), namely the GAGA and UUCG motifs. We perform extensive folding simulations and calculate folding free energies ({Delta}Gfold) with the aim to compare different enhanced sampling techniques and to test several modifications of the nonbonded terms extending the AMBER OL3 RNA ff. We demonstrate that replica exchange solute tempering (REST2) simulations with 12-16 replicas do not show any sign of convergence even when extended to time scale of 120 s per replica. However, combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a time-scale of 5-10 s per replica, improving the sampling efficiency by at least two orders of magnitude. Effects of ff modifications on {Delta}Gfold energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manually-prepared variants of gHBfix potential which improve stability of the native state of both TLs by up to ~2 kcal/mol. This is sufficient to conveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van der Waals parameters for C-H...O5 base-phosphate interaction are also shown to be capable of further stabilizing the native states of both TLs by ~0.6 kcal/mol.

category: biophysics


title: Ligand-induced changes in dynamics mediate long-range allostery in the lac repressor

abstract: Allostery, broadly defined as a proteins functional response to distal perturbations, is fundamental to biological regulation. In classical models, allosteric ligand binding produces a defined set of structural changes in the protein, resulting in a different low-energy conformation. Proteins that undergo ligand-induced allostery with few observable structural changes therefore frustrate interpretations by classical models. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map the allosteric effects in a paradigm ligand-responsive allosteric transcription factor, the lac repressor (LacI). X-ray crystal structures of the core domain of LacI bound to different small molecule ligands, or the DNA operator, show less than 1.5 [A] difference in the protein all-atom root-mean-square-deviation (RMSD) between any two structures. Despite this high degree of similarity among static structures, our HDX/MS experiments reveal widespread and unexpected differences in the flexibility of secondary structures in the LacI core domain in each functional state. We propose a model in which ligand binding allosterically switches the functional response of the repressor by selectively changing the dynamics of particular secondary structure elements relative to each other, shifting the conformational ensemble of the protein between mutually incompatible DNA-bound and inducer-bound states. Our model also provides a mechanistic context for the altered functions of thousands of documented LacI mutants. Furthermore, our approach provides a platform for characterizing and engineering allosteric responses in proteins.


title: Uveal Melanoma: a miR-16 disease?

abstract: Uveal melanoma (UM), the most common primary intraocular tumor in adults, has been extensively characterized by omics technologies during the last 5 years. Despite the discovery of gene signatures, the molecular actors driving the cancer aggressiveness are not fully understood and UM is still associated to a dismal overall survival at metastatic stage. Here, we showed that microRNA-16 (miR-16) is involved in uveal melanoma by an unexpected mechanism. By defining the miR-16-interactome, we revealed that miR-16 mainly interacts via non-canonical base-pairing to a subset of RNAs, promoting their expression levels (sponge RNAs). Consequently, the canonical miR-16 activity, involved in the RNA decay of oncogenes such as cyclin D1 and D3, is impaired. This miR-16 non-canonical base-pairing to sponge RNAs can explain both the derepression of miR-16 targets and the promotion of oncogenes expression observed for patients with poor overall survival in two cohorts. miR-16 activity assessment using our sponge-signature discriminates the patients overall survival as efficiently as the current method based on copy number variations and driver mutations detection. To conclude, miRNA loss of function due to miRNA sequestration seems to promote cancer burden by two combined events - "loss of brake and an acceleration". Our results highlight the oncogenic role of the non-canonical base-pairing between miRNAs/mRNAs in uveal melanoma.

category: cancer biology


title: MK2 Expression Promotes Non-Small Cell Lung Cancer Cell Death and Predicts Survival

abstract: Non-small cell lung cancers demonstrate intrinsic resistance to cell death even in response to chemotherapy. Previous work suggested that defective nuclear translocation of active caspase 3 may play a role in resistance to cell death. Separately, our group has identified that mitogen activated protein kinase activated protein kinase 2 (MK2) is required for nuclear translocation of active caspase 3 in the execution of apoptosis. This study demonstrates a relatively low expression of MK2 in non-small cell lung carcinoma cell lines compared to small cell carcinoma cell lines. Further, overexpression of MK2 in non-small cell lung carcinoma cell lines results in increased caspase 3 activity and caspase 3 mediated cell death. Higher MK2 transcript levels were observed in patients with earlier-stage non-small cell lung cancer. Higher expression of MK2 is associated with better survival in patients with early stage non-small cell lung cancer across two independent clinical datasets. Using data sets spanning multiple cancer types, we observed improved survival with higher MK2 expression was unique to lung adenocarcinoma. Mechanistically, MK2 promotes nuclear translocation of caspase 3 leading to PARP1 cleavage and execution of cell death. While MK2 can directly phosphorylate caspase 3, neither phosphorylation status of caspase 3 nor the kinase activity of MK2 impacts caspase 3 activation, nuclear translocation and execution of cell death. Rather, a non-kinase function of MK2, specifically trafficking via its nuclear localization sequence, is required for caspase 3 mediated cell death. In summary this study highlights the importance of a non-enzymatic function of MK2 in the execution of apoptosis, which may be leveraged in the adjunctive treatment of NSCLC or other conditions where regulation of apoptosis is crucial.


title: Insights into energy balance dysregulation from a mouse model of methylmalonic aciduria

abstract: Inherited disorders of mitochondrial metabolism, including isolated methylmalonic aciduria (MMAuria), present unique challenges to energetic homeostasis by disrupting energy producing pathways. To better understand global responses to energy shortage, we investigated a hemizygous mouse model of methylmalonyl-CoA mutase (Mmut) type MMAuria. We found Mmut mutant mice to have reduced appetite, energy expenditure and body mass compared to littermate controls, along with a relative reduction in lean mass but increase in fat mass. Brown adipose tissue showed a process of whitening, in line with lower body surface temperature and lesser ability to cope with cold challenge. Mutant mice had dysregulated plasma glucose, delayed glucose clearance and a lesser ability to regulate energy sources when switching from the fed to fasted state, while liver investigations indicated metabolite accumulation and altered expression of peroxisome proliferator-activated receptor and Fgf21-controlled pathways. Together, these indicate hypometabolism, energetic inflexibility and increased stores at the expense of active tissue as energy shortage consequences.

category: physiology


title: Elucidating the acid-base mechanisms underlying otolith overgrowth in fish exposed to ocean acidification

abstract: Over a decade ago, ocean acidification (OA) exposure was reported to induce otolith overgrowth in teleost fish. This phenomenon was subsequently confirmed in multiple species; however, the underlying physiological causes remain unknown. Here, we report that splitnose rockfish (Sebastes diploproa) exposed to ~1,600 atm pCO2 (pH ~7.5) were able to fully regulated the pH of both blood and endolymph (the fluid that surrounds the otolith within the inner ear). However, while blood was regulated around pH 7.80, the endolymph was regulated around pH ~8.30. These different pH setpoints result in increased pCO2 diffusion into the endolymph, which in turn leads to proportional increases in endolymph [HCO3-] and [CO32-]. Endolymph pH regulation despite the increased pCO2 suggests enhanced H+ removal. However, a lack of differences in inner ear bulk and cell-specific Na+/K+-ATPase and vacuolar type H+-ATPase protein abundance localization pointed out to activation of preexisting ATPases, non-bicarbonate pH buffering, or both, as the mechanism for endolymph pH-regulation. These results provide the first direct evidence showcasing the acid-base chemistry of the endolymph of OA-exposed fish favors otolith overgrowth, and suggests that this phenomenon will be more pronounced in species that count with more robust blood and endolymph pH regulatory mechanisms.


title: Skeletal muscle releases extracellular vesicles with distinct protein and miRNA signatures that accumulate and function within the muscle microenvironment

abstract: Extracellular vesicles (EVs) contain various regulatory molecules and mediate intercellular communications. Although EVs are secreted from various cell types, including skeletal muscle cells, and present in the blood, their identity is poorly characterized in vivo, limiting the identification of their origin in the blood. Since the skeletal muscle is the largest organ in the body, it could substantially contribute to circulating EVs as their source. However, due to the lack of defined markers that distinguish SkM-EVs from others, whether the skeletal muscle releases EVs in vivo and how much the skeletal muscle-derived EVs (SkM-EVs) account for plasma EVs remain poorly understood. In this work, we perform quantitative proteomic analyses on EVs released from C2C12 cells and human iPS cell-derived myocytes and identify potential marker proteins that mark SkM-EVs. These markers we identified apply to in vivo tracking of SkM-EVs. The results show that skeletal muscle makes only a subtle contribution to plasma EVs as their source in both control and exercise conditions in mice. On the other hand, we demonstrate that SkM-EVs are concentrated in the skeletal muscle interstitium. Furthermore, we show that interstitium EVs are highly enriched with the muscle-specific miRNAs and repress the expression of the paired box transcription factor Pax7, a master regulator for myogenesis. Taken together, our findings reveal that the skeletal muscle releases exosome-like small EVs with distinct protein and miRNA profiles in vivo and that SkM-EVs mainly play a role within the muscle microenvironment where they accumulate.


title: Dual role of strigolactone receptor signaling partner in inhibiting substrate hydrolysis

abstract: Plant branch and root growth relies on metabolism of the strigolactone (SL) hormone. The interaction between the SL molecule, Oryza sativa DWARF14 (D14) SL receptor, and D3 F-box protein has been shown to play a critical role in SL perception. Previously, it was believed that D3 only interacts with the closed form of D14 to induce downstream signaling, but recent experiments indicate that D3, as well as its C-terminal helix (CTH), can interact with the open form as well to inhibit strigolactone signaling. Two hypotheses for the CTH induced inhibition are that either the CTH affects the conformational ensemble of D14 by stabilizing catalytically inactive states, or the CTH interacts with SLs in a way that prevents them from entering the binding pocket. In this study, we have performed molecular dynamics (MD) simulations to assess the validity of these hypotheses. We used an apo system with only D14 and the CTH to test the active site conformational stability and a holo system with D14, the CTH, and an SL molecule to test the interaction between the SL and CTH. Our simulations show that the CTH affects both active site conformation and the ability of SLs to move into the binding pocket. In the apo system, the CTH allosterically stabilized catalytic residues into their inactive conformation. In the holo system, significant interactions between SLs and the CTH hindered the ability of SLs to enter the D14 binding pocket. These two mechanisms account for the observed decrease in SL binding to D14 and subsequent ligand hydrolysis in the presence of the CTH.

category: plant biology


title: 15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector

abstract: Metabolic labeling using stable isotopes is widely used for the relative quantification of proteins in proteomic studies. In plants, metabolic labeling using 15N has great potential, but the associated complexity of data analysis has limited its usage. Here, we present the 15N stable-isotope labeled protein quantification workflow utilizing open-access web-based software Protein Prospector. Further, we discuss several important features of 15N labeling required to make reliable and precise protein quantification. These features include ratio adjustment based on labeling efficiency, median and interquartile range for protein ratios, isotope cluster pattern matching to flag incorrect monoisotopic peak assignment, and caching of quantification results for fast retrieval.


title: A novel PSII photosynthetic control is activated in anoxic cultures of green algae

abstract: Photosynthetic green algae face an ever-changing environment of fluctuating light as well as unstable oxygen levels, which via the production of free radicals constantly challenges the integrity of the photosynthetic complexes. To face such challenges, a complex photosynthetic control network monitors and tightly control the membrane redox potential. Here, we show that not only that the photosynthetic control set the rate limiting step of photosynthetic linear electron flow, but also, upon its ultimate dissipation, it triggers intrinsic alternations in the activity of the photosynthetic complexes. These changes have a grave and prolonged effect on the activity of photosystem II, leading to a massive 3-fold decrease in its electron output. We came into this conclusion via studying a variety of green algae species and applying advance mass-spectrometry and diverse spectroscopic techniques. Our results shed new light on the mechanism of photosynthetic regulation, and provide new target for improving photosynthesis.


title: Simulation of pedigree vs. fully-informative marker based relationships matrices in a loblolly pine breeding population

abstract: Computer simulations of breeding strategies are an essential resource for tree breeders because they allow exploratory analyses into potential long-term impacts on genetic gain and inbreeding consequences without bearing the cost, time, or resource requirements of field experiments. Previous work has modeled the potential long-term implications on inbreeding and genetic gain using random mating and phenotypic selection. Reduction in sequencing costs has enabled the use of DNA marker-based relationship matrices in addition to or in place of pedigree-based allele sharing estimates; this has been shown to provide a significant increase in the accuracy of progeny breeding value prediction. A potential pitfall of genomic selection using genetic relationship matrices is increased coancestry among selections, leading to the accumulation of deleterious alleles and inbreeding depression. We used simulation to compare the relative genetic gain and risk of inbreeding depression within a breeding program similar to loblolly pine, utilizing pedigree-based or marker-based relationships over ten generations. We saw a faster rate of purging deleterious alleles when using a genomic relationship matrix based on markers that track identity-by-descent of segments of the genome. Additionally, we observed an increase in the rate of genetic gain when using a genomic relationship matrix instead of a pedigree-based relationship matrix. While the genetic variance of populations decreased more rapidly when using genomic-based relationship matrices as opposed to pedigree-based, there appeared to be no long-term consequences on the accumulation of deleterious alleles within the simulated breeding strategy.


title: Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits

abstract: Genetic feedback loops can be used by cells as a means to regulate internal processes or keep track of time. It is often thought that, for a genetic circuit to display self-sustained oscillations, a degree of cooperativity is needed in the binding and unbinding of actor species. This cooperativity is usually modeled using a Hill function, regardless of the actual promoter architecture. Moreover, genetic circuits do not operate in isolation and often transcription factors are shared between different promoters. In this work we show how mathematical modelling of genetic feedback loops can be facilitated with a mechanistic fold-change function that takes into account the titration effect caused by competing binding sites for transcription factors. The model shows how the titration effect aids self-sustained oscillations in a minimal genetic feedback loop: a gene that produces its own repressor directly -- without cooperative transcription factor binding. The use of delay-differential equations leads to a stability contour that predicts whether a genetic feedback loop will show self-sustained oscillations, even when taking the bursty nature of transcription into account.

category: systems biology


title: Spatiotemporal NF-κB dynamics encodes the position, amplitude and duration of local immune inputs

abstract: Infected cells communicate through secreted signaling molecules like cytokines, which inform nearby cells about the type, severity and location of pathogens. How differences in cytokine secretion affect inflammatory signaling over space and time, and how responding cells decode information from propagating cytokine signals are not understood. By computationally and experimentally studying NF-{kappa}B dynamics in co-cultures of signal sending cells (macrophages) and receiving cells (fibroblasts), we found that cytokine signals are transmitted by wave-like propagation of NF-{kappa}B activity and create well-defined cellular activation zones in a responding cell population. Remarkably, NF-{kappa}B dynamics in responding cells can simultaneously encode information about cytokine dose, duration, and distance to the cytokine source. Spatially-resolved transcriptional analysis revealed that responding cells transmit local cytokine information to distance specific pro-inflammatory gene expression patterns, creating "gene expression zones" in the population. Despite single-cell variability, the size and duration of the signaling zone is tightly controlled by the macrophage cytokine secretion profile. Our results highlight how macrophages tune their cytokine secretion dynamics to control signal transmission distance, and how NF-{kappa}B interprets these signals to coordinate inflammatory response in space and time.


title: Black-box testing in motor sequence learning

abstract: During learning of novel motor sequences, practice leads to the consolidation of hierarchical structures, namely motor chunks, facilitating the accurate execution of sequences at increasing speeds. Recent studies show that such hierarchical structures are largely represented upstream of the primary motor cortex in the motor network, suggesting their function to be more related to the encoding, storage, and retrieval of sequences rather than their sole execution. We isolated different components of motor skill acquisition related to the consolidation of spatiotemporal features and followed their evolution over training. We found that optimal motor skill acquisition relies on the storage of the spatial features of the sequence in memory, followed by the optimization of its execution and increased execution speeds (i.e., a shift in the speed-accuracy trade-off) early in training, supporting the model proposed by Hikosaka in 1999. Contrasting the dynamics of these components during ageing, we identified less-than-optimal mechanisms in older adults explaining the observed differences in performance. We applied noninvasive brain stimulation in an attempt to support the aging brain to compensate for these deficits. The present study found that anodal direct current stimulation applied over the motor cortex restored the mechanisms involved in the consolidation of spatial features, without directly affecting the speed of execution of the sequence. This led older adults to sharply improve their accuracy, resulting in an earlier yet gradual emergence of motor chunks. The results suggest the early storage of the sequence in memory, largely independent of motor practice, is crucial for an optimal motor acquisition and retrieval of this motor behavior. Nevertheless, the consolidation of optimal temporal patterns, detected as motor chunks at a behavioral level, is not a direct consequence of storing the sequence elements, but rather of motor practice.

category: neuroscience


title: Topological conditions for propagation of spatially-distributed neural activity

abstract: An important task of the nervous system is to transmit information faithfully and reliably across brain regions, a process that involves the coordinated activity of a relatively large population of neurons. In topographically organized networks, where the entering and exiting axons of neurons terminate in confined areas, successful propagation depends on the spatial patterns of activity: the firing neurons in a presynaptic or source layer must be located sufficiently close to each other to ensure that cells in the postsynaptic or target layer receive the requisite number of convergent inputs to fire. Here, we use principles of topology to define the conditions for transmitting information across layers. We show that simplicial complexes formed by source neurons can be used to: 1) determine whether target neurons receive suprathreshold inputs; 2) identify neurons within the active population that contribute to firing; and 3) discriminate between single and multiple active clusters of neurons.


title: Modelling the effect of ephaptic coupling on spike propagation in peripheral nerve fibres

abstract: Experimental and theoretical studies have shown that ephaptic coupling leads to the synchronisation and slowing down of spikes propagating along the axons within peripheral nerve bundles. However, the main focus thus far has been on a small number of identical axons, whereas realistic peripheral nerve bundles contain numerous axons with different diameters. Here, we present a computationally efficient spike propagation model, which captures the essential features of propagating spikes and their ephaptic interaction, and facilitates the theoretical investigation of spike volleys in large, heterogeneous fibre bundles. The spike propagation model describes an action potential, or spike, by its position on the axon, and its velocity. The velocity is primarily defined by intrinsic features of the axons, such as diameter and myelination status, but it is also modulated by changes in the extracellular potential. These changes are due to transmembrane currents that occur during the generation of action potentials. The resulting change in the velocity is appropriately described by a linearised coupling function, which is calibrated with a biophysical model. We first lay out the theoretical basis to describe how the spike in an active axon changes the membrane potential of a passive axon. These insights are then incorporated into the spike propagation model, which is calibrated with a biophysically realistic model based on Hodgkin-Huxley dynamics. The fully calibrated model is then applied to fibre bundles with a large number of axons and different types of axon diameter distributions. One key insight of this study is that the heterogeneity of the axonal diameters has a dispersive effect, and that with increasing level of heterogeneity the ephaptic coupling strength has to increase to achieve full synchronisation between spikes. Another result of this study is that in the absence of full synchronisation, a subset of spikes on axons with similar diameter can form synchronised clusters. These findings may help interpret the results of noninvasive experiments on the electrophysiology of peripheral nerves.


title: The Long Noncoding RNA FEDORA is a Cell-Type- and Sex-Specific Regulator of Depression

abstract: Women suffer from depression at twice the rate of men, but the underlying molecular mechanisms are poorly understood. Here, we identify dramatic baseline sex differences in expression of long noncoding RNAs (lncRNAs) in human postmortem brain tissue that are profoundly lost in depression. One such lncRNA, RP11-298D21.1 (which we termed FEDORA), is enriched in oligodendrocytes and neurons and upregulated in several cortical regions of depressed females but not males. We found that virally-expressing FEDORA selectively either in neurons or in oligodendrocytes of prefrontal cortex promoted depression-like behavioral abnormalities in female mice only, changes associated with cell-type-specific regulation of synaptic properties, myelin thickness, and gene expression. We also found that blood FEDORA levels have diagnostic significance for depressed women. These findings demonstrate the important role played by lncRNAs, and FEDORA in particular, in shaping the sex-specific landscape of the brain and contributing to sex differences in depression.


title: Discovering tumor-reactive T-cell receptors through single-cell sequencing of tumor-infiltrating lymphocytes

abstract:
We evaluated the utility of single-cell sequencing of tumor-infiltrating lymphocytes (TIL) for tumor-reactive T-cell receptor (TCR) discovery. Using the MC38 cell line as our tumor model in mice, we show that expression of exogenous TCRs via mRNA electroporation in human T cells provides an easy and quick path to validating tumor-specific candidate TCRs. We detail the identification and validation of four novel MC38-reactive mouse TCRs with varying levels of reactivity to the target cells. Validating our process, one of the MC38 TCRs is specific against a previously reported neoantigen (ASMTNMELM in the Adpgk gene). Consideration of these methodologies may aid in the development of rapid TCR-based therapies for the treatment of cancer and human disease.

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category: immunology


title: Metabolite Damage and Damage-Control in a Minimal Genome

abstract: Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes with known metabolite damage repair or preemption functions were identified and experimentally validated, including 5-formyltetrahydrofolate cyclo-ligase, CoA disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage-control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.

category: microbiology


title: Label-free characterisation of amyloids and alpha-Synuclein polymorphs by exploiting their intrinsic fluorescence property

abstract: Conventional in vitro aggregation assays often involve tagging with extrinsic fluorophores which can interfere with aggregation. We propose the use of intrinsic amyloid fluorescence lifetime probed using two-photon excitation and represented by model-free phasor plots, as a label-free assay to characterise amyloid structure. Intrinsic amyloid fluorescence arises from structured packing of {beta}-sheets in amyloids and is independent of aromatic-based fluorescence. We show that different amyloids (i.e., -Synuclein (S), {beta}-Lactoglobulin and TasA) and different polymorphic populations of S (induced by aggregation in salt-free and salt buffers mimicking the intra-/extracellular environments) can be differentiated by their unique fluorescence lifetimes. Moreover, we observe that disaggregation of pre-formed fibrils of S and {beta}LG leads to increased fluorescence lifetimes, distinct to those of their fibrillar counterpart. Our assay presents a medium-throughput method for rapid classification of amyloids and their polymorphs (the latter of which recent studies have shown lead to different disease pathology), and for testing small molecule inhibitory compounds.

category: molecular biology


title: TWISTED DWARF1 regulates Arabidopsis stamen development by differential activation of ABCB-mediated auxin transport

abstract:
Despite clear evidence that a local accumulation of auxin is likewise critical for male fertility, much less is known about the components that regulate auxin-controlled stamen development.

In this study, we analyzed physiological and morphological parameters in mutants of key players of ABCB-mediated auxin transport and spatially and temporally dissected their expression on the protein level as well as auxin fluxes in the Arabidopsis stamens. Our analyses revealed that the FKBP42, TWISTED DWARF1 (TWD1), promotes stamen elongation and, to a lesser extent, anther dehiscence, as well as pollen maturation and thus is required for seed development. Most of the described developmental defects in twd1 are shared with the abcb1 abcb19 mutant, which can be attributed to the fact that TWD1 - as a described ABCB chaperon - is a positive regulator of ABCB1 and ABCB19-mediated auxin transport. However, reduced stamen number was dependent on TWD1 but not on investigated ABCBs, suggesting additional actors down-stream of TWD1. We predict an overall housekeeping function for ABCB1 during earlier stages, while ABCB19 seems to be responsible for the key event of rapid elongation at later stages of stamen development. Our data indicate that TWD1 controls stamen development by differential activation of ABCB-mediated auxin transport in the stamen.

HighlightBy using a mix of phenotypical and imaging analyses, we here identify and functionally characterize a new master regulator of flower development.

category: developmental biology


title: Invertebrate-induced priority effects and secondary metabolites control fungal community composition in dead wood

abstract: During decomposition of organic matter, microbial communities may follow different successional trajectories depending on the initial environment and colonizers. The timing and order of the assembly history can lead to divergent communities through priority effects. We explored how assembly history and resource quality affected fungal dead wood communities and decomposition, 1.5 and 4.5 years after tree felling. Additionally, we investigated the effect of invertebrate exclusion during the first two summers. For aspen (Populus tremula) logs, we measured initial resource quality of bark and wood, and surveyed the fungal communities by DNA metabarcoding at different time points during succession. We found that a gradient in fungal community composition was related to resource quality and discuss how this may reflect tolerance-dominance trade-offs in fungal life history strategies. As with previous studies, the initial amount of bark tannins was negatively correlated with wood decomposition rate over 4.5 years. The initial fungal community explained variation in community composition after 1.5, but not 4.5 years, of succession. Although the assembly history of initial colonizers may cause alternate trajectories in successional communities, our results indicate that the communities may easily converge with the arrival of secondary colonizers. We also identified a strong invertebrate-induced priority effect of fungal communities, even after 4.5 years of succession, thereby adding crucial knowledge to the importance of invertebrates in affecting fungal community development. By measuring and manipulating aspects of assembly history and resource quality that have rarely been studied, we expand our understanding of the complexity of fungal community dynamics.

category: ecology


title: Contrasting adaptation and optimization of stomatal traits across communities at continental-scale

abstract: The maximum stomatal conductance (g), a major anatomical constraint on plant productivity, is a function of the stomatal area fraction (f) and stomatal space-use efficiency (e). However, f and g have been considered as equivalents, with e rarely considered, and their adaptation to the environment and their regulation of ecosystem productivity are unclear. Here, we analyzed the community-weighted mean, variance, skewness, and kurtosis of stomatal traits from tropical to cold-temperature forests. The variance of g and f was higher for arid sites, indicating greater functional niche differentiation, whereas that for e was lower, indicating convergence in efficiency. Besides, when other stomatal trait distributions remained unchanged, increasing kurtosis but decreasing skewness of g would improve ecosystem productivity, and f showed the opposite patterns. These findings highlight how the relative importance and equivalence of inter-related traits can differ at community scale.


title: Does heat tolerance actually predict geographic thermal limits of animal species?

abstract:
To understand species' climatic vulnerability, our measures of species thermal tolerance should predict their geographic thermal limits. Yet, this assumption is ungranted. We tested if animals' heat tolerance restrict the warmest temperatures they can live at (Tmax), distinguishing among species differently challenged by their thermal environment. For that, we compiled 2350 measurements of species heat tolerance indexes and corresponding Tmax, measured at different microhabitats. We show that reptiles, a flagship for climatic vulnerability studies, are particularly unbounded by their heat tolerance. Contrarily, tolerance restricted marine fish geography in a non-linear fashion which contrasts with terrestrial taxa. Behavioral tolerance indexes, widely used to predict vulnerability, predicted Tmax inconsistently across Tmax indexes, or were inversely related to it. Animals heat tolerance restricts geographic limits more strongly for more thermally challenged species. In turn, factors uncoupling heat tolerance and Tmax (plasticity, thermoregulation, adaptation) should be more important for less thermally challenged species.

Significance StatementTo identify climatic vulnerability, heat tolerance indices need to predict species' thermal limits to geographic distribution. Yet, we show that heat tolerance predicts geographic limits quite heterogeneously, depending on taxa, the type of measure of heat tolerance and how challenged are species at their hottest known location. Particularly, reptiles, a flagship of vulnerability studies, were less bounded by tolerance than taxa regarded as more capable to evade high temperatures, due to their capacity to evaporate water, find refuge, or migrate (Ex. amphibians, arthropods, birds and mammals). Measures of species behavioral heat tolerance may still need to improve. Factors thought to uncouple thermal tolerance and geographic limits should be stronger for less thermally challenged species.


title: Emergent multilevel selection in a simple spatial model of the evolution of altruism

abstract: Theories on the evolutionary origins of altruistic behavior have a long history and have become a canonical part of the theory of evolution. Nevertheless, the mechanisms that allow altruism to appear and persist are still incompletely understood. The spatial structure of populations is known to be an important determinant. In both theoretical and experimental studies, much attention has been devoted to populations that are subdivided into discrete groups. Such studies typically imposed the structure and dynamics of the groups by hand. Here, we instead present a simple individual-based model in which organisms spontaneously self-organize into spatially separated colonies that themselves reproduce by binary fission and hence behave as Darwinian entities in their own right. Using software to automatically track the rise and fall of colonies, we are able to apply formal theory on multilevel selection and thus quantify the within- and among-group dynamics. This reveals that individual colonies inevitably succumb to defectors, resulting in within-colony "tragedies of the commons". Even so, altruism persists in the population because more altruistic colonies reproduce more frequently. The emergence of the colonies themselves depends crucially on the length scales of motility, altruism, and competition. This reconfirms the general relevance of these scales for social evolution, but also stresses that their impact can only be understood fully in the light of the emergent eco-evolutionary spatial patterns. The results also demonstrate that emergent spatial population patterns can function as a starting point for transitions of individuality.

category: evolutionary biology


title: Interplay between PML NBs and HIRA for H3.3 deposition on transcriptionally active interferon-stimulated genes

abstract: Promyelocytic Leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. Here, by using specific siRNAs and protein Affimers, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. In addition, we demonstrate that HIRA localization in the nuclear bodies is intimately linked to the presence of a soluble pool of H3.3-H4 dimers inside PML NBs, that is not found in cancer cells. Transcription inhibition prevents HIRA accumulation in PML NBs underscoring the importance of transcriptional activity to drive HIRA through PML NBs. Finally, in the context of inflammatory responses, HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of interferon-stimulated genes (ISGs), well beyond the peak of transcription. We thus propose that HIRA partitioning in PML NBs is essential to regulate H3.3 deposition on transcriptionally active regions.

category: genetics


title: Inverse PI by NMR: Analysis of Ligand 1H-Chemical Shifts in the Protein-Bound State

abstract: The study of protein-ligand interactions via protein-based NMR generally relies on the detection of chemical-shift changes induced by ligand binding. However, the chemical shift of the ligand when bound to the protein is rarely discussed, since it is not readily detectable. In this work we use protein deuteration in combination with [1H-1H]-NOESY NMR to extract 1H chemical shift values of the ligand in the bound state. The chemical shift perturbations (CSPs) experienced by the proton ligand resonances (free vs bound) are an extremely rich source of information on protein-ligand complexes. Besides allowing for the detection of intermolecular CH-{pi} interactions and elucidation of the protein-bound ligand conformation, the CSP information can be used to analyse (de)solvation effects in a site-specific manner. In conjunction with crystal structure information, it is possible to distinguish protons whose desolvation penalty is compensated for upon protein-binding, from those that are not. Combined with the previously reported PI by NMR technique for the protein-based detection of intermolecular CH-{pi} interactions, this method represents another important step towards the ultimate goal of Interaction-Based Drug Discovery.


title: De Novo Pyrimidine Synthesis is a Targetable Vulnerability in IDH Mutant Glioma

abstract: Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they appear less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1 mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH mutant gliomas. Mechanistically, this vulnerability selectively applies to de novo pyrimidine, but not purine, synthesis because glioma cells engage disparate programs to produce these nucleotide species and because IDH oncogenes increase DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.


title: SR Ca2+ handling in unbranched, immediately post-necrotic fast-twitch mdx fibres is similar to wt littermates

abstract:
There is a lack of consensus in the literature regarding the effects of dystrophin deficiency on the Ca2+-handling properties of the SR in mdx mice, an animal model of Duchenne muscular dystrophy. One possible reason for this is that only a few studies control for the presence of branched fibres. Fibre branching, a consequence of degenerative-regenerative processes such as muscular dystrophy, has in itself a significant influence on the function of the SR. In our present study we attempt to detect early effects of dystrophin deficiency on SR Ca2+ handling by using unbranched fibres from the immediate post-necrotic stage in mdx mice (just regenerated following massive necrosis). Using kinetically-corrected Fura-2 fluorescence signals measured during twitch and tetanus, we analysed the amplitude, rise time and decay time of {Delta}[Ca2+]i in unfatigued and fatigued fibres. Decay was also resolved into SR pump and SR leak components. Fibres from mdx mice were similar in all respects to fibres from wt littermates apart from: (i) a longer rise time and slower rate of rise of [Ca2+]i during a tetanus; and (ii) a mitigation of the fall in {Delta}[Ca2+]i amplitude during the course of fatigue. Our findings suggest that the early effects of a loss of dystrophin on SR Ca2+ handling are only slight, and differ from the widely held view that there is significant Ca2+ pathology in mdx mice. It may be that Ca2+ pathology is magnified by progressive branching and degeneration.

New findingsCentral question: What are the early effects of dystrophin deficiency on SR Ca2+ handling in the mdx mouse?

Main finding: In the mdx mouse, Ca2+ handling by the SR is little affected by the absence of dystrophin when looking at fibres without branches that have just regenerated following massive myonecrosis. This has important implications for the traditional view that Ca2+ pathology is significant in the mdx mouse.


title: Chitin-induced systemic disease resistance in rice requires both OsCERK1 and OsCEBiP and is mediated via perturbation of cell-wall biogenesis in leaves

abstract:
O_LIChitin is a well-known elicitor of disease resistance whose recognition by plants is crucial to perceive fungal infections. Chitin can induce both a local immune response and a systemic disease resistance when provided as a supplement in soils. Unlike local immune responses, how chitin-induced systemic disease resistance is deployed has not been studied in detail.
C_LIO_LIIn this study, we evaluated systemic disease resistance against the fungal pathogen Bipolaris oryzae by performing a transcriptome analysis and monitoring cell-wall composition in rice plants grown in chitin-supplemented soils. We also examined the local immune response to chitin by measuring the production of reactive oxygen species in leaves.
C_LIO_LIChitins induced both local immune response and systemic disease resistance with differing requirements for the receptors OsCERK1 and OsCEBiP. Transcriptome analysis suggested that a perturbation in cell-wall biogenesis is involved in the induction of systemic disease resistance, an idea which was supported by the induction of disease resistance by treatment with a cellulose biosynthesis inhibitor and alterations of cell-wall composition.
C_LIO_LIThese findings suggest that chitin-induced systemic disease resistance in rice is caused by a perturbation of cell-wall biogenesis in leaves through long-distance signalling after recognition of chitins by OsCERK1 and OsCEBiP.
C_LI


title: AP2/ERF transcription factor NbERF-IX-33 is involved in the regulation of phytoalexin production for the resistance of Nicotiana benthamiana to Phytophthora infestans.

abstract: Plants recognize molecular patterns unique to a certain group of microbes to induce effective resistance mechanisms. Elicitins are secretory proteins produced by plant pathogenic oomycete genera including Phytophthora and Pythium. Treatment of INF1 (an elicitin produced by P. infestans) induces a series of defense responses in Nicotiana species, including reactive oxygen species (ROS) production, transient induction of ethylene production, hypersensitive cell death and accumulation of the sesquiterpenoid phytoalexin capsidiol. In this study, we analyzed the expression profiles of N. benthamiana genes after INF1 treatment by RNAseq analysis. Based on their expression patterns, N. benthamiana genes were categorized into 20 clusters and 4,761 (8.3%) out of 57,140 genes were assigned to the clusters for INF1-induced genes. All genes encoding enzymes dedicated to capsidiol production, 5-epi-aristolochene (EA) synthase (NbEAS, 10 copies) and EA dehydrogenase (NbEAH, 6 copies), and some genes for ethylene production, such as 1-aminocyclopropane 1-carboxylate (ACC) synthase (NbACS) and ACC oxidase (NbACO), were significantly upregulated by INF1 treatment. Analysis of NbEAS1 and NbEAS4 promoters revealed that AGACGCC (GCC box-like motif) is the essential cis-element required for INF1-induced expression of NbEAS genes. Given that the GCC box is known to be targeted by ERF (ethylene-responsive factor) transcription factors, we created a complete list of N. benthamiana genes encoding AP2/ERF family transcription factors, and identified 45 out of 337 AP2/ERF genes in the clusters for INF1-induced genes. Among INF1-induced NbERF genes, silencing of NbERF-IX-33 compromised resistance against P. infestans and INF1-induced production of capsidiol. Recombinant NbERF-IX-33 protein can bind to the promoter sequence of NbEAS4, suggesting that NbERF-IX-33 is a transcription factor directly regulating the expression of genes for phytoalexin production.


title: Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor

abstract: Synthetic directed evolution via localized sequence diversification and the simultaneous application of selection pressure is a promising method for producing new, beneficial alleles that affect traits of interest in diverse species; however, this technique has rarely been applied in plants. Developing systems to induce localized sequence diversification at high efficiency will expand our ability to evolve traits of interest that improve global food security. In this study, we designed, built, and tested a chimeric fusion of T7 RNA Polymerase (RNAP) and deaminase to enable the localized sequence diversification of a target sequence of interest. We tested our T7 RNAP-DNA base editor in Nicotiana benthamiana transient assays to target a transgene expressing GFP under the control of the T7 promoter. More than 7% of C nucleotides were converted to T in long segments of the GFP sequence. We then targeted the T7 promoter-driven ACETOLACTATE SYNTHASE (ALS) sequence that had been stably integrated in the rice (Oryza sativa) genome and generated C-to-T and G-to-A transitions. We used herbicide treatment as selection pressure for the evolution of the ALS sequence, resulting in the enrichment of herbicide-responsive residues. We then targeted these herbicide-responsive regions in the rice genome using a CRISPR-directed evolution platform and identified herbicide-resistant ALS variants. Thus, our system could be used for the continuous synthetic evolution of gene functions to produce variants with improved herbicide resistance, as well as for other trait engineering applications.

category: synthetic biology


title: Emergence of planar cell polarity from the interplay of asymmetric interaction and tissue-level gradients

abstract: Planar cell polarity (PCP) - asymmetric localization of proteins at cell-cell interface - is essential for embryonic development and physiological functions. Abnormalities in PCP can lead to neural tube closure defects, misalignment in hair follicles etc. Thus, decoding the mechanism responsible for PCP establishment and maintenance remains an open fundamental question. While various molecules - broadly classified into "global" and "local" modules - have been well investigated, their necessity and sufficiency in explaining PCP and connecting their perturbations and defects in experimentally observed patterns has not been examined. Here, we develop a minimal model that captures the proposed features of these two modules- a global tissue level gradient and local asymmetric distribution of protein complexes. Our model results suggest that while polarity can emerge in absence of a gradient, the gradient can provide the direction of polarity as well as offer robustness for maintenance of PCP in presence of stochastic perturbations. We also recapitulated swirling patterns (seen experimentally) and the features of non-domineering autonomy, using only three free parameters in the model - protein binding rate, concentration of proteins forming heterodimer across cell boundaries and steepness of gradient. Our results explain how self-stabilizing asymmetric localisations in presence of tissue-level gradient can lead to robust PCP patterns in diverse biological systems and reveals the minimal design principles for a polarized system.


title: Stimulus dependence of theta rhythmic activity in primate V1 and its potential relevance for visual perception

abstract: A growing body of psychophysical research reports theta (3-8 Hz) rhythmic fluctuations in visual perception that are often attributed to an attentional sampling mechanism arising from theta rhythmic neural activity in mid- to high-level cortical association areas. However, it remains unclear to what extent such neuronal theta oscillations might already emerge at early sensory cortex like the primary visual cortex (V1), e.g. from the stimulus filter properties of neurons. To address this question, we recorded multi-unit neural activity from V1 of two macaque monkeys viewing a static visual stimulus with variable sizes, orientations and contrasts. We found that among the visually responsive electrode sites, more than 50 % showed a spectral peak at theta frequencies. Theta power varied with varying basic stimulus properties. Within each of these stimulus property domains (e.g. size), there was usually a single stimulus value that induced the strongest theta activity. In addition to these variations in theta power, the peak frequency of theta oscillations increased with increasing stimulus size and also changed depending on the stimulus position in the visual field. Further analysis confirmed that this neural theta rhythm was indeed stimulus-induced and did not arise from small fixational eye movements (microsaccades). When the monkeys performed a detection task of a target embedded in a theta-generating visual stimulus, reaction times also tended to fluctuate at the same theta frequency as the one observed in the neural activity. The present study shows that a highly stimulus-dependent neuronal theta oscillation can be elicited in V1 that appears to influence the temporal dynamics of visual perception.


title: Capturing cognitive events embedded in the real-world using mobile EEG and Eye-Tracking

abstract: The study of cognitive processes underlying natural behaviours implies to depart from computerized paradigms and artificial experimental probes. The aim of the present study is to assess the feasibility of capturing neural markers of visual attention (P300 Event-Related Potentials) in response to objects embedded in a real-world environment. To this end, electroencephalography and eye-tracking data were recorded while participants attended stimuli presented on a tablet and while they searched for books in a library. Initial analyses of the library data revealed P300-like features shifted in time. A Dynamic Time Warping analysis confirmed the presence of P300 ERP in the library condition. Library data were then lag-corrected based on cross-correlation co-efficients. Together these approaches uncovered P300 ERP responses in the library recordings. These findings high-light the relevance of scalable experimental designs, joint brain and body recordings and template-matching analyses to capture cognitive events during natural behaviours.


title: Tertiary lymphoid structures induced by CXCL13-producing CD4+ T cells increase tumor infiltrating CD8+ T cells and B cells in ovarian cancer

abstract:
BackgroundTertiary lymphoid structures (TLSs) are transient ectopic lymphoid aggregates whose formation might be caused by chronic inflammation states, such as cancer. The presence of TLS is associated with a favorable prognosis in most solid malignancies. The recognition of the relevance of TLS to cancer has led to a growing interest in TLS as an immunomodulatory target to enhance tumor immunity, although how TLSs are induced in the tumor microenvironment (TME) and how they affect patient survival are not well understood.

MethodsTLS distribution in relation to tumor infiltrating lymphocytes (TILs) and related gene expression were investigated in high grade serous ovarian cancer (HGSC) specimens. CXCL13 expression, which is strongly associated with TLS, and its localization in immune cells, were examined. We explored the tumor microenvironment for CXCL13 secretion by adding various inflammatory cytokines in vitro. The induction of TLS by CXCL13 was examined in a mouse model of ovarian cancer.

ResultsCXCL13 gene expression correlated with TLS formation and the infiltration of T cells and B cells, and was a favorable prognostic factor for HGSC patients. The coexistence of CD8+ T cells and B-cell lineages in the TME was associated with a better prognosis of HGSC and was closely related to the presence of TLSs. CXCL13 expression was predominantly coincident with CD4+ T cells in TLSs and CD8+ T cells in TILs, and shifted from CD4+ T cells to CD21+ follicular dendritic cells as the TLS matured. Although TGF-{beta} was reported to stimulate CXCL13 production, our in vitro results revealed that CXCL13 secretion was promoted in CD4+ T cells under TGF-{beta} + IL-2-restricted conditions and in CD8+ T cells under TGF-{beta} + IL-12-rich conditions. In a mouse model of ovarian cancer, recombinant CXCL13 induced TLSs and enhanced survival by the infiltration of CD8+ T cells.

ConclusionsTLS formation was promoted by CXCL13-producing CD4+ T cells and TLSs facilitated the coordinated antitumor responses of cellular and humoral immunity in ovarian cancer.


title: CADHERIN mediated AMIS localisation

abstract: Individual cells within de novo polarising tubes and cavities must integrate their forming apical domains into a centralised apical membrane initiation site (AMIS). This is necessary to enable organised lumen formation within multi-cellular tissue. Despite the well documented importance of cell division in localising the AMIS, we have found a division-independent mechanism of AMIS localisation that relies instead on Cadherin-mediated cell-cell adhesion. Our study of de novo polarising mouse embryonic stem cells (mESCs) cultured in 3D suggest that cell-cell adhesion directs the localisation of apical proteins such as PAR-6 to a centralised AMIS. Unexpectedly, we also found that mESC cell clusters lacking functional E-Cadherin were still able to form a lumen-like cavity in the absence of AMIS localisation and did so at a later stage of development via a  closure mechanism, instead of via hollowing. This work suggests that there are two, interrelated mechanisms of apical polarity localisation: cell adhesion and cell division. Alignment of these mechanisms in space allows for redundancy in the system and ensures the development of a coherent epithelial structure within a growing organ.


title: E-Cadherin mediated AMIS localisation


title: Repeated genetic adaptation to high altitude in two tropical butterflies

abstract: Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to high altitude in two divergent tropical butterflies, H. erato and H. melpomene, which have repeatedly and independently adapted to high elevations on either side of the Andean mountains. We sequenced 518 whole genomes from elevational transects and found many regions under selection at high altitude, with repeated genetic differentiation across multiple replicates, including allopatric comparisons. In contrast, there is little  molecular parallelism between H. erato and H. melpomene. With a further 85 whole genomes of five close relatives, we find that a large proportion divergent regions have arisen from standing variation and putative adaptive introgression from high-altitude specialist species. Taken together our study supports a key role of standing genetic variation and gene flow from pre-adapted species in promoting parallel genetic local adaptation to the environment.


title: Evolutionary history of sexual differentiation mechanism in insects

abstract: Gain of alternative splicing gives rise to functional diversity in proteins and underlies the complexity and diversity of biological aspects. However, it is still not fully understood how alternatively spliced genes develop the functional novelty. To this end, we infer the evolutionary history of the doublesex gene, the key transcriptional factor in the sexual differentiation of arthropods. doublesex is controlled by sex-specific splicing and promotes both male and female differentiation in some holometabolan insects. In contrast, doublesex promotes only male differentiation in some hemimetabolan insects. Here, we investigate ancestral states of doublesex using Thermobia domestica belonging to Zygentoma, the sister group of winged insects. We find that doublesex of T. domestica expresses sex-specific isoforms but is only necessary for male differentiation of sexual morphology. This result ensures the hypothesis that doublesex was initially only used to promote male differentiation during insect evolution. However, T. domestica doublesex has a short female-specific region and upregulates the expression of vitellogenin homologs in females, suggesting that doublesex may have already controlled some aspects of feminization in the common ancestor of winged insects. Reconstruction of the ancestral sequence and prediction of the protein structure show that the female-specific isoform of doublesex has a long C-terminal disordered region in holometabolan insects, but not in non-holometabolan species. We propose that doublesex acquired a female-specific isoform and then underwent a change in the protein motif structure, which became essential for female differentiation in sexual dimorphisms.


title: Interpreting dN/dS under different selective regimes in cancer evolution

abstract: The standard relationship between the dN/dS statistic and the selection coefficient is contingent upon the computation of the rate of fixation of non-synonymous and synonymous mutations among divergent lineages (substitutions). In cancer genomics, however, dN/dS is typically calculated by including mutations that are still segregating in the cell population. The interpretation of dN/dS within sexual populations has been shown to be problematic. Here we used a simple model of somatic evolution to study the relationship between dN/dS and the selection coefficient in the presence of deleterious, neutral, and beneficial mutations in cancer. We found that dN/dS can be used to distinguish cancer genes under positive or negative selection, but it is not always informative about the magnitude of the selection coefficient. In particular, under the asexual scenario simulated, dN/dS is insensitive to negative selection strength. Furthermore, the relationship between dN/dS and the positive selection coefficient depends on the mutation detection threshold, and, in particular scenarios, it can become non-linear. Our results warn about the necessary caution when interpreting the results drawn from dN/dS estimates in cancer.


title: Comparative proteogenomics deciphers the origin and evolution of eukaryotic chromatin

abstract: Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.


title: A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution


title: Ambiguous Body Ownership Experience Caused by Feeling-judgement Conflict: Evidence from Subjective Measurement in Rubber Hand Illusion using Integrated Information Theory

abstract:
AO_SCPLOWBSTRACTC_SCPLOWHuman body awareness is malleable and adaptive to changing contexts. The illusory sense of body-ownership has been studied since the publication of the rubber hand illusion, where ambiguous body ownership feeling, expressed as "the dummy hand is my hand even though that is not true", was first defined. Phenomenologically, the ambiguous body ownership is attributed to a conflict between feeling and judgement; in other words, it characterises a discrepancy between first-person (i.e. bottom-up) and third-person (i.e. top-down) processes. Although Bayesian inference can explain this malleability of body image sufficiently, the theory does not provide a good illustration of why we have different experiences to the same stimuli - the difficulty lies in the uncertainty regarding the concept of judgement in their theory.

This study attempts to explain subjective experience during rubber hand illusions using integrated information theory (IIT). The integrated information {Phi} in IIT measures the difference between the entire system and its subsystems. This concept agrees with the phenomenological interpretation - that is, there is conflict between judgement and feeling. By analysing the seven nodes of a small body- brain system, we demonstrate that the integrity of the entire system during the illusion decreases with increasing integrity of its subsystems. These general tendencies agree well with many brain-image analyses and subjective reports; furthermore, we found that subjective ratings were associated with the {Phi}s. Our result suggests that IIT can explain the general tendency of the sense of ownership illusions and individual differences in subjective experience during the illusions.

category: animal behavior and cognition


title: Strength-frequency curve for micromagnetic neurostimulation through EPSPs on rat hippocampal neurons and numerical modeling of magnetic microcoil (μcoil)

abstract:
ObjectiveThe objective of this study was to measure the effect of micromagnetic stimulation (MS) on hippocampal neurons, by using single microcoil (coil) prototype, Magnetic Pen (MagPen). MagPen will be used to stimulate the CA3 region magnetically and excitatory post synaptic potential (EPSP) response measurements will be made from the CA1 region. The threshold for micromagnetic neurostimulation as a function of stimulation frequency of the current driving the coil will be demonstrated. Finally, the optimal stimulation frequency of the current driving the coil to minimize power will be estimated.

ApproachA biocompatible, watertight, non-corrosive prototype, MagPen was built, and customized such that it is easy to adjust the orientation of the coil and its distance over the hippocampal tissue in an in vitro recording setting. Finite element modeling (FEM) of the coil design was performed to estimate the spatial profiles of the magnetic flux density (in T) and the induced electric fields (in V/m). The induced electric field profiles generated at different values of current applied to the coil can elicit a neuron response, which was validated by numerical modeling. The modeling settings for the coil were replicated in experiments on rat hippocampal neurons.

Main resultsThe preferred orientation of MagPen over the Schaffer Collateral fibers was demonstrated such that they elicit a neuron response. The recorded EPSPs from CA1 region due to MS at CA3 region were validated by applying tetrodotoxin (TTX). Application of TTX to the hippocampal slice blocked the EPSPs from MS while after prolonged TTX washout, a partial recovery of the EPSP from MS was observed. Finally, it was interpreted through numerical analysis that increasing frequency of the current driving the coil, led to a decrease in the current amplitude threshold for micromagnetic neurostimulation.

SignificanceThis work reports that micromagnetic neurostimulation can be used to evoke population EPSP responses in the CA1 region of the hippocampus. It demonstrates the strengthfrequency curve for MS and its unique features related to orientation dependence of the coils, spatial selectivity and stimulation threshold related to distance dependence. Finally, the challenges related to MS experiments were studied including ways to overcome them.

category: bioengineering


title: Rice leaves undergo a rapid metabolic reconfiguration during a specific stage of primordium development

abstract:
Leaf development is crucial to establish the photosynthetic competency of plants. It is a process that requires coordinated changes in cell number and differentiation, transcriptomes, metabolomes and physiology. However, despite the importance of leaf formation for our major crops, early developmental processes for rice have not been comprehensively described. Here we detail the temporal developmental trajectory of early rice leaf development and connect morphological changes to metabolism. In particular, a developmental index based on the patterning of epidermal differentiation visualised by electron microscopy enabled high resolution staging of early growth for single primordium metabolite profiling. These data demonstrate that a switch in the constellation of tricarboxylic acid (TCA) cycle metabolites defines a narrow window towards the end of the P3 stage of leaf development. Taken in the context of other data in the literature, our results substantiate that this phase of rice leaf growth, equivalent to a change of primordium length from around 5 to 7.5 mm, defines a major shift in rice leaf determination towards a photosynthetically defined structure. We speculate that efforts to engineer rice leaf structure should focus on the developmental window prior to these determining events.

HighlightRice leaves undergo a shift in fundamental metabolism during a very early and narrow developmental window which co-incides with them acquiring the ability to capture light for photosynthesis


title: Neural basis for anxiety and anxiety-related physiological responses during simulated driving: An fMRI study

abstract: While the exteroceptive and interoceptive prediction of a negative event increases a persons anxiety in daily life situations, the relationship between the brain mechanism of anxiety and the anxiety-related autonomic response has not been fully understood. In this fMRI study, we examined the neural basis of anxiety and anxiety-related autonomic responses in a daily driving situation. Participants viewed a driving video clip in the first-person perspective. During the video clip, participants were presented with a cue to indicate whether a subsequent crash could occur (attention condition) or not (safe condition). Enhanced activities in the anterior insula, bed nucleus of the stria terminalis, thalamus, and periaqueductal gray, and higher sympathetic nerve responses (pupil dilation and peripheral arterial stiffness) were triggered by the attention condition but not with the safe condition. Autonomic response-related functional connectivity was detected in the visual cortex, cerebellum, brainstem, and MCC/PCC with the right anterior insula and its adjacent regions as seed regions. Thus, the right anterior insula and adjacent regions, in collaboration with other regions play a role in eliciting anxiety based on the prediction of negative events, by mediating anxiety-related autonomic responses according to interoceptive information.


title: Neural basis for anxiety and anxiety-related physiological responses during a driving situation: An fMRI study


title: Multiscale and extended retrieval of associative memory structures in a cortical model of local-global inhibition balance

abstract: Inhibitory neurons take on many forms and functions. How this diversity contributes to memory function is not completely known. Previous formal studies indicate inhibition differentiated by local and global connectivity in associative memory networks functions to rescale the level of retrieval of excitatory assemblies. However, such studies lack biological details such as a distinction between types of neurons (excitatory and inhibitory), unrealistic connection schemas, and non-sparse assemblies. In this study, we present a rate-based cortical model where neurons are distinguished (as excitatory, local inhibitory, or global inhibitory), connected more realistically, and where memory items correspond to sparse excitatory assemblies. We use this model to study how local-global inhibition balance can alter memory retrieval in associative memory structures, including naturalistic and artificial structures. Experimental studies have reported inhibitory neurons and their sub-types uniquely respond to specific stimuli and can form sophisticated, joint excitatory-inhibitory assemblies. Our model suggests such joint assemblies, as well as a distribution and rebalancing of overall inhibition between two inhibitory sub-populations - one connected to excitatory assemblies locally and the other connected globally - can quadruple the range of retrieval across related memories. We identify a possible functional role for local-global inhibitory balance to, in the context of choice or preference of relationships, permit and maintain a broader range of memory items when local inhibition is dominant and conversely consolidate and strengthen a smaller range of memory items when global inhibition is dominant. This model therefore highlights a biologically-plausible and behaviourally-useful function of inhibitory diversity in memory.


title: Human ventromedial prefrontal cortex lesions enhance expectation-related pain modulation

abstract:
Pain is strongly modulated by expectations and beliefs. Research across species indicates that subregions of the ventromedial prefrontal cortex (VMPFC) play a fundamental role in learning and generating predictions about valued outcomes. Consistent with this overarching framework, neuroimaging studies of experimental pain indicate that VMPFC activation tracks expectations of pain relief and statistically mediates expectation-related reductions in responses to painful stimuli across a distributed pain processing network. However, lesion studies in preclinical models and in humans with refractory chronic pain suggest that VMPFC may play a more general role in representing the affective and motivational qualities of pain that contribute to its strong aversive drive. To test whether VMPFC is necessary for pain processing in general, or instead plays a more specific role in the modulation of pain by expectations, we studied responses to experimental heat pain in five adults with bilateral surgical lesions of VMPFC and twenty healthy adults without brain damage.

All participants underwent quantitative sensory testing (QST) to characterize pain sensitivity, followed by a pain expectancy task. Participants were instructed that auditory cues would be followed by heat calibrated to elicit low or high pain. Following a conditioning phase, each cue was intermittently paired with a single temperature calibrated to elicit moderate pain. We compared ratings of moderate heat stimuli and subjective expectancy ratings as a function of cue to evaluate whether VMPFC lesions impact cue-based expectancy and expectancy effects on pain intensity and unpleasantness. We also analyzed QST measures to evaluate whether VMPFC lesions were associated with overall shifts in pain sensitivity.

Compared to adults without brain damage, individuals with VMPFC lesions reported larger differences in expectations as a function of pain-predictive cues, and stronger cue-based modulation of pain ratings, particularly for ratings of pain unpleasantness. There were no group differences in pain sensitivity, nor in the relationship between pain and autonomic arousal, indicating that the impact of VMPFC lesions is specific to expectancy-based modulation of pain unpleasantness.

Our findings suggest that the VMPFC is not essential for basic subjective and physiological responses to painful stimuli. Rather, our findings of significantly enhanced cue- related expectancy effects may suggest that VMPFC plays an important role in updating expectations or integrating sensory information with expectations to guide subjective judgements about pain. Taken together, these results expand our understanding VMPFCs contribution to pain and highlight the role of VMPFC in integrating cognitive representations with sensory information to yield affective responses.