title: Stress deceleration theory: chronic adolescent stress exposure results in decelerated neurobehavioral maturation

abstract: Normative development in adolescence indicates that the prefrontal cortex is still under development thereby unable to exert efficient top-down inhibitory control on subcortical regions such as the basolateral amygdala and the nucleus accumbens. This imbalance in the developmental trajectory between cortical and subcortical regions is implicated in expression of the prototypical impulsive, compulsive, reward seeking and risk-taking adolescent behavior. Here we demonstrate that a chronic mild unpredictable stress procedure during adolescence in male Wistar rats arrests the normal behavioral maturation such that they continue to express adolescent-like impulsive, hyperactive, and compulsive behaviors into late adulthood. This arrest in behavioral maturation is associated with the hypoexcitability of prelimbic cortex (PLC) pyramidal neurons and reduced PLC-mediated synaptic glutamatergic control of BLA and nucleus accumbens core (NAcC) neurons that lasts late into adulthood. At the same time stress exposure in adolescence results in the hyperexcitability of the BLA pyramidal neurons sending stronger glutamatergic projections to the NAcC. Chemogenetic reversal of the PLC hypoexcitability decreased compulsivity and improved the expression of goal-directed behavior in rats exposed to stress during adolescence, suggesting a causal role for PLC hypoexcitability in this stress-induced arrested behavioral development.


title: Motor plans under uncertainty reflect a trade-off between maximizing reward and success

abstract: When faced with multiple potential movement options, individuals either reach directly to one of the options, or initiate a reach intermediate between the options. It remains unclear why people generate these two types of behaviors. Using the go-before-you-know task (commonly used to study behavior under choice uncertainty), we examined two key questions. First, do these two types of responses reflect distinct movement strategies, or are they simply examples of a more general response to choice uncertainty? If the former, the relative desirability (i.e., weighing the likelihood of successfully hitting the target versus the attainable reward) of the two target options might be computed differently for direct versus intermediate reaches. We showed that indeed, when exogenous reward and success likelihood (i.e., endogenous reward) differ between the two options, direct reaches were more strongly biased by likelihood whereas intermediate movements were more strongly biased by reward. Second, what drives individual differences in how people respond under uncertainty? We found that risk/reward-seeking individuals generated a larger proportion of intermediate reaches and were more sensitive to trial-to-trial changes in reward, suggesting these movements reflect a strategy to maximize reward. In contrast, risk-adverse individuals tended to generate more direct reaches in an attempt to maximize success. Together, these findings suggest that when faced with choice uncertainty, individuals adopt movement strategies consistent with their risk/reward-seeking tendency, preferentially biasing behavior toward exogenous rewards or endogenous success and consequently modulating the relative desirability of the available options.

category: neuroscience


title: Optimizing transcranial direct current stimulation (tDCS) electrode position, size, and distance doubles the on-target cortical electric field: Evidence from 3000 Human Connectome Project models

abstract: Transcranial direct current stimulation (tDCS) is a widely used noninvasive brain stimulation technique with mixed results and no FDA-approved therapeutic indication to date. So far, thousands of published tDCS studies have placed large scalp electrodes directly over the intended brain target and delivered the same stimulation intensity to each person. Inconsistent therapeutic results may be due to insufficient cortical activation in some individuals and the inability to determine an optimal dose. Here, we computed 3000 MRI-based electric field models in 200 Human Connectome Project (HCP) participants, finding that the largely unexamined variables of electrode position, size, and between-electrode distance significantly impact the delivered cortical electric field magnitude. At the same scalp stimulation intensity, smaller electrodes surrounding the neural target deliver more than double the on-target cortical electric field while stimulating only a fraction of the off-target brain regions. This new optimized tDCS method can ensure sufficient cortical activation in each person and could produce larger and more consistent behavioral effects in every prospective research and transdiagnostic clinical application of tDCS.


title: Exploration of the antimicrobial synergy between selected natural substances on Streptococcus mutans to identify candidates for the control of dental caries

abstract:
Dental caries is caused by dental plaque, a community of micro-organisms embedded in an extracellular polymer matrix as a biofilm on the tooth surface. Natural products that are widely available could be used as an alternative or adjunctive anti-caries therapy. Sometimes, when two products are used together, they yield a more powerful antimicrobial effect than the anticipated additive effect. These synergistic combinations are often better treatment options because individual agents may not have sufficient antimicrobial action to be effective when used alone. Cranberries contain phenolic compounds like proanthocyanidins (PAC) that disrupt biofilm formation. Manuka honey has high concentrations of the agent methylglyoxal, which is cariostatic. Because these agents have varied modes of antimicrobial action, they show potential for possible synergistic effects when paired.

Various cranberry extracts were tested pairwise with manuka honey or methylglyoxal by well-diffusion assays and 96-well checkerboard assays in the presence of Streptococcus mutans to test for synergy. Synergy was demonstrated in two of the cranberry extracts paired with manuka honey. The synergistic combinations found in this research thus can be considered as candidates for the formulation of a dentifrice that could be used to inhibit the formation of dental plaque and thereby avoid the development of caries.

Significance and ImpactThe emergence of bacteria resistant to antimicrobial agents has led to a shortage of options when choosing effective treatment agents. Further, some antibiotics used at therapeutic doses can produce undesired side effects. However, by utilizing synergistic combinations of antimicrobial agents, the desired antimicrobial effects can often be produced without subjecting the patient to toxic or irritating doses of individual agents. Streptococcus mutans growth and biofilm formation is a major contributor towards dental caries. In this study, a synergistic combination of Manuka honey and cranberry extracts gives evidence that it can be used as an alternative or adjunctive anti-caries therapy.

category: microbiology


title: Alu repeats at the boundaries of regulatory elements shape the epigenetic environment of immune genes in T cells

abstract: Promoters and enhancers are sites of transcription initiation (TSSs) and carry active histone modifications, including H3K4me1, H3K4me3, and H3K27ac. Yet, the principles governing the boundaries of such regulatory elements are still poorly characterized. Alu elements are good candidates for a boundary function, being highly abundant in gene-rich regions, while essentially excluded from regulatory elements. Here, we show that the interval from the TSS to the first upstream Alu accommodates all H3K4me3 and most H3K27ac marks, while excluding DNA methylation. Remarkably, the average length of this intervals greatly varies in-between tissues, being longer in stem-and shorter in immune-cells. The very shortest TSS-to-Alu intervals were observed at promoters active in T cells, particularly at immune genes, correlating with RNA polymerase II transcription through the first Alu and accumulation of H3K4me1 signal on this first Alu. Finally, DNA methylation at first-Alus was found to evolved with age, regressing from young to middle-aged, then recovering later in life. Thus, the first Alus upstream of TSSs appear as dynamic boundaries marking the transition from DNA methylation to active histone modifications at regulatory elements, while also participating in the recording of immune gene transcriptional events by positioning H3K4me1-modified nucleosomes.

category: molecular biology


title: The "Alu-ome" shapes the epigenetic environment of regulatory elements controlling cellular defense


title: Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

abstract: Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Cienegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent modern analogs of ancient microbial mats where functions were preserved over time, whereas composition was subject to diversification in the face of local and planetary perturbations.

category: ecology


title: Unravelling the regulation pathway of photosynthetic AB-GAPDH

abstract:
Oxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme of the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant formed by hetero-tetramers of A and B-subunits, and the homo-tetramer A4. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and for this reason is strictly regulated. While A4-GAPDH is regulated by CP12, AB-GAPDH is autonomously regulated through the C-terminal extension (CTE) of B-subunits. Reversible inactivation of AB-GAPDH occurs via oxidation of a cysteine pair located in the CTE, and substitution of NADP(H) with NAD(H) in the cofactor binding domain. These combined conditions lead to a change in the oligomerization state and enzyme inactivation. SEC-SAXS and single-particle cryoEM analysis disclosed the structural basis of this regulatory mechanism. Both approaches revealed that (A2B2)n-GAPDH oligomers with n=1, 2, 4 and 5 co-exist in a dynamic system. B-subunits mediate the contacts between adjacent A2B2 tetramers in A4B4 and A8B8 oligomers. The CTE of each B-subunit penetrates into the active site of a B-subunit of the adjacent tetramer, while the CTE of this subunit moves in the opposite direction, effectively preventing the binding of the substrate 1,3-bisphosphoglycerate in the B-subunits. The whole mechanism is made possible, and eventually controlled, by pyridine nucleotides. In fact, NAD(H) by removing NADP(H) from A-subunits allows the entrance of the CTE in B-subunits active sites and hence inactive oligomer stabilization.

Significance StatementIn land plants, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) unique sink of reducing power of the entire Calvin-Benson cycle, is finely regulated. Based on the redox state and substrates concentration, its heteromeric form AB-GAPDH oscillates between a fully active heterotetramer (A2B2) and inactive oligomers. Experimental evidence demonstrates that GAPDH inactivation depends on the formation of dimers, tetramers or pentamers of A2B2-modules, linked together by C-terminal extensions (CTE) of B-subunits that extrude from one modular tetramer and occupy two active sites of the adjacent one. This molecular mechanism along with the unexpected observed dynamism of the system, shed light on how the Calvin-Benson cycle is modulated in function of the light environmental changes.

category: biochemistry


title: Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning

abstract: The identification of xenobiotics in nontargeted metabolomic analyses is a vital step in understanding human exposure. Xenobiotic metabolism, excretion, and co-existence with other endogenous molecules however greatly complicate nontargeted studies. While mass spectrometry (MS)-based platforms are commonly used in metabolomic measurements, deconvoluting endogenous metabolites and xenobiotics is often challenged by the lack of xenobiotic parent and metabolite standards as well as the numerous isomers possible for each small molecule m/z feature. Here, we evaluate the use of ion mobility spectrometry coupled with MS (IMS-MS) and mass defect filtering in a xenobiotic structural annotation workflow to reduce large metabolomic feature lists and uncover potential xenobiotic classes and species detected in the metabolomic studies. To evaluate the workflow, xenobiotics having known high toxicities including per- and polyfluoroalkyl substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) were examined. Initially, to address the lack of available IMS collision cross section (CCS) values for per- and polyfluoroalkyl substances (PFAS), 88 PFAS standards were evaluated with IMS-MS to both develop a targeted PFAS CCS library and for use in machine learning predictions. The CCS values for biomolecules and xenobiotics were then plotted versus m/z, clearly distinguishing the biomolecules and halogenated xenobiotics. The xenobiotic structural annotation workflow was then used to annotate potential PFAS features in NIST human serum. The workflow reduced the 2,423 detected LC-IMS-MS features to 80 possible PFAS with 17 confidently identified through targeted analyses and 48 additional features correlating with possible CompTox entries.


title: Genotyping strategies for detecting CRISPR mutations in polyploid species: a case study-based approach in hexaploid wheat

abstract: As a versatile tool for genome engineering, CRISPR-Cas9 has been revolutionizing the field of molecular biology, biotechnology, and crop improvement. By precisely targeting pre-selected genomic sites, CRISPR-Cas9 primarily induces insertions or deletions (indels) of variable size. Despite the significant advance in the technology per se, detecting these indels is the major and difficult part of the CRISPR program in polyploid species, like wheat, with relatively low mutation rates. A plethora of methods are available for detecting mutations, but no method is perfect for all mutation types. In this case study, we demonstrated a new, protocol for capturing length polymorphism from small indels using a nested PCR approach. This new method is tractable, efficient, and cost-effective in detecting and genotyping indels >3-bp. We also discussed the major genotyping platforms used in our wheat CRISPR projects, such as mismatch cleavage assay, restriction enzyme assay, ribonucleoprotein assay, and Sanger sequencing, for their advantages and pitfalls in wheat CRISPR mutation detection.

category: bioengineering


title: Biomechanics of aging and osteoarthritic human knee ligaments

abstract:
BackgroundLigaments work to stabilize the human knee joint and prevent excessive movement. Whilst ligaments are known to decline in structure and function with aging, there has been no systematic effort to study changes in gross mechanical properties in the four major human knee ligaments due to osteoarthritis (OA). This study aims to collate material properties for the anterior (ACL) and posterior (PCL) cruciate ligaments, medial (MCL) and lateral (LCL) collateral ligaments. Our cadaveric samples come from a diverse demographic from which the effects of aging and OA on bone and cartilage material properties have already been quantified. Therefore, by combining our previous bone and cartilage data with the new ligament data from this study we are facilitating subject-specific whole-joint modelling studies.

MethodsThe demographics of the collected cadaveric knee joints were diverse with age range between 31 to 88 years old, and OA International Cartilage Repair Society grade 0 to 4. Twelve cadaveric human knee joints were dissected, and bone-ligament-bone specimens were extracted for mechanical loading to failure. Ligament material properties were determined from the load-extension curves, namely: linear and ultimate (failure) stress and strain, secant modulus, tangent modulus, and stiffness.

ResultsThere were significant negative correlations between age and ACL linear force (p=0.01), stress (p=0.03) and extension (p=0.05), ACL failure force (p=0.02), stress (p=0.02) and extension (p=0.02), PCL secant (p=0.02) and tangent (p=0.02) modulus, and LCL stiffness (p=0.05). Significant negative correlations were also found between OA grades and ACL linear force (p=0.05), stress (p=0.02), extension (p=0.01) and strain (p=0.03), and LCL failure stress (p=0.05). However, changes in age or OA grade did not show a statistically significant correlation with the MCL tensile parameters. Trends showed that almost all the tensile parameters of the ACL and PCLs decreased with increasing age and progression of OA. Due to small sample size, the combined effect of age and presence of OA could not be statistically derived.

ConclusionsThis research is the first to correlate changes in tensile properties of the four major human knee ligaments to aging and OA. The current ligament study when combined with our previous findings on bone and cartilage for the same twelve knee cadavers, supports conceptualization of OA as a whole-joint disease that impairs the integrity of many peri-articular tissues within the knee. The subject-specific data pool consisting of the material properties of the four major knee ligaments, subchondral and trabecular bones and articular cartilage will aid reconstruction and graft replacements and advance knee joint finite element models, whilst knowledge of aged or diseased mechanics may direct future therapeutic interventions.


title: pISA-tree - a data management framework for life science research projects using a standardised directory tree

abstract: We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) via a series of sequential batch files in a standardised manner based on the ISA metadata framework. The system supports reproducible research and is in accordance with the Open Science initiative and FAIR principles. Compared with similar frameworks, it does not require any systems administration and maintenance as it can be run on a personal computer or network drive. It is complemented with two R packages, pisar and seekr, where the former facilitates integration of the pISA-tree datasets into bioinformatic pipelines and the latter enables synchronisation with the FAIRDOMHub public repository using the SEEK API. Source code and detailed documentation of pISA-tree and its supporting R packages are available from https://github.com/NIB-SI/pISA-tree.

category: bioinformatics


title: Artificial Intelligence Guided Conformational Mining of Intrinsically Disordered Proteins

abstract: Artificial intelligence recently achieved the breakthrough of predicting the three-dimensional structures of proteins. The next frontier is presented by intrinsically disordered proteins (IDPs), which, representing 30% to 50% of proteomes, readily access vast conformational space. Molecular dynamics (MD) simulations are promising in sampling IDP conformations, but only at extremely high computational cost. Here, we developed generative autoencoders that learn from short MD simulations and generate full conformational ensembles. An encoder represents IDP conformations as vectors in a reduced-dimensional latent space. The mean vector and covariance matrix of the training dataset are calculated to define a multivariate Gaussian distribution, from which vectors are sampled and fed to a decoder to generate new conformations. The ensembles of generated conformations cover those sampled by long MD simulations and are validated by small-angle X-ray scattering profile and NMR chemical shifts. This work illustrates the vast potential of artificial intelligence in conformational mining of IDPs.

category: biophysics


title: A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution

abstract: In many brain areas, neural populations act as a coordinated network whose state is tied to behavior on a moment-by-moment basis and millisecond timescale. Two-photon (2p) calcium imaging is a powerful tool to probe network-scale computation, as it can measure the activity of many individual neurons, monitor multiple layers simultaneously, and sample from identified cell types. However, estimating network states and dynamics from 2p measurements has proven challenging because of noise, inherent nonlinearities, and limitations on temporal resolution. Here we describe RADICaL, a deep learning method to overcome these limitations at the population level. RADICaL extends methods that exploit dynamics in spiking activity for application to deconvolved calcium signals, whose statistics and temporal dynamics are quite distinct from electrophysiologically-recorded spikes. It incorporates a novel network training strategy that exploits the timing of 2p sampling to recover network dynamics with high temporal precision. In synthetic tests, RADICaL infers network states more accurately than previous methods, particularly for high-frequency components. In real 2p recordings from sensorimotor areas in mice performing a "water grab" task, RADICaL infers network states with close correspondence to single-trial variations in behavior, and maintains high-quality inference even when neuronal populations are substantially reduced.


title: Computational Compensatory Mutation Discovery Approach: Predicting a PARP1 Variant Rescue Mutation

abstract:
The prediction of protein mutations that affect function may be exploited for multiple uses. In the context of disease variants, the prediction of compensatory mutations that reestablish functional phenotypes could aid in the development of genetic therapies. In this work, we present an integrated approach that combines coevolutionary analysis and molecular dynamics (MD) simulations to discover functional compensatory mutations. This approach is employed to investigate possible rescue mutations of a poly(ADP-ribose) polymerase 1 (PARP1) variant, PARP1 V762A, associated with lung cancer and follicular lymphoma. MD simulations show PARP1 V762A exhibits noticeable changes in structural and dynamical behavior compared with wild type PARP1. Our integrated approach predicts A755E as a possible compensatory mutation based on coevolutionary information, and molecular simulations indicate that the PARP1 A755E/V762A double mutant exhibits similar structural and dynamical behavior to WT PARP1. Our methodology can be broadly applied to a large number of systems where single nucleotide polymorphisms (SNPs) have been identified as connected to disease and can shed light on the biophysical effects of such changes as well as provide a way to discover potential mutants that could restore wild type-like functionality. This can in turn be further utilized in the design of molecular therapeutics that aim to mimic such compensatory effect.

Significance StatementDiscovering protein mutations with desired phenotypes can be challenging due to its combinatorial nature. Herein we employ a methodology combining gene SNP association to disease, direct coupling analysis and molecular dynamics simulations to systematically predict rescue mutations. Our workflow identifies A755E as a potential rescue for the PARP1 V762A mutation, which has been associated with cancer. This methodology is general and can be applied broadly.


title: The Effect of COVID-19 on the Postdoctoral Experience: a comparison of pre-pandemic and pandemic surveys.

abstract:
In the interest of advocating for the postdoctoral community in the United States, we present results from survey data collected before and during the COVID-19 pandemic on the same population of postdocs. In 2019, 5,929 postdocs in the US completed a comprehensive survey, and in 2020, a subset completed a follow-up survey several months into the pandemic. The results show that the pandemic has substantially impacted postdocs mental health and wellness irrespective of gender, race, citizenship, or other identities. Postdocs also reported a significant impact on their career trajectories and progression, reduced confidence in achieving career goals, and negative perceptions of the job market compared to pre-COVID-19. International postdocs also reported experiencing distinct stressors due to the changes in immigration policy. Notably, having access to Postdoctoral Associations and Postdoctoral Offices positively impacted postdocs overall well-being and helped mitigate the personal and professional stresses and career uncertainties caused by the pandemic.

Graphical Abstract

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category: scientific communication and education


title: Zinc finger protein Zfp335 controls early T cell development and survival through beta-selection-dependent and -independent mechanisms

abstract: T cell development in the thymus undergoes the process of differentiation, selective proliferation and survival from CD4-CD8- double negative (DN) stage to CD4+CD8+ double positive (DP) stage prior to the formation of CD4+ helper and CD8+ cytolytic T cells ready for circulation. Each developmental stage is tightly regulated by sequentially-operating molecular networks, of which only limited numbers of transcription regulators have been deciphered. Here we identified Zfp335 transcription factor as a new player in the regulatory network controlling thymocyte development. We demonstrate that Zfp335 intrinsically controls DN to DP transition, as T cell-specific deficiency in Zfp335 leads to a substantial accumulation of DN3 along with reduction of DP, CD4+ and CD8+ thymocytes. This developmental blockade at DN stage results from the impaired intracellular TCR{beta} expression as well as increased susceptibility to apoptosis in thymocytes. Transcriptomic and ChIP-seq analyses revealed a direct regulation of transcription factors Bcl6 and Rorc by Zfp335. Importantly, enhanced expression of TCR{beta} and Bcl6/Ror{gamma}T restores the developmental defect during DN3 to DN4 transition and improves thymocytes survival, respectively. These findings identify a critical role of Zfp335 in controlling T cell development by maintaining intracellular TCR{beta} expression-mediated {beta}- selection and independently activating cell survival signaling.

category: immunology


title: Atlas of Inhibitory Neurons in the Mouse Brain

abstract:
The mouse brain contains a rich diversity of inhibitory interneuron types that have been characterized by their patterns of gene expression. However, it is still unclear how these cell types are distributed across the mouse brain. We developed a computational method to estimate the densities of different interneuron types across the mouse brain. Our method allows the unbiased integration of diverse and disparate datasets into one framework to predict interneuron densities for uncharted brain regions. We constrained our estimates based on previously computed brain-wide neuron densities, gene expression data from in situ hybridization image stacks together with a wide range of values reported in the literature. Using constrained optimization, we derived coherent estimates of cell densities for the different interneuron types. We estimate that 20.3% of all neurons in the mouse brain are inhibitory. Among all inhibitory neurons, 18% predominantly express parvalbumin (PV), 16% express somatostatin (SST), 3% express vasoactive intestinal peptide (VIP), and the remainder 63% belong to the residual GABAergic population. We find that our density estimations improve as more literature values are integrated. Our pipeline is extensible, allowing new cell types or data to be integrated as they become available. The data, algorithms, software, and results of our pipeline are publicly available and update the Blue Brain Cell Atlas. This work therefore leverages the research community to collectively converge on the numbers of each cell type in each brain region.

Author summaryObtaining a global understanding of the cellular composition of the brain is a very complex task, not only because of the great variability that exists between reports of similar counts but also because of the numerous brain regions and cell types that make up the brain. Previously, we presented a model of a cell atlas, which provided an estimate of the densities of neurons, glia and their subtypes for each region in the mouse brain. Here, we describe an extension of this model to include more inhibitory neuron types. We collected estimates of inhibitory neuron counts from literature and built a framework to combine them into a consistent cell atlas. Using brain slice images, we also estimated inhibitory neuron density in regions where no literature data are available. We estimated that in the mouse brain 20.3% of all neurons are inhibitory. Among all inhibitory neurons, 18% predominantly express parvalbumin (PV), 16% express somatostatin (SST), 3% express vasoactive intestinal peptide (VIP), and the remainder 63% belong to the residual GABAergic population Our approach can be further extended to any other cell type and provides a resource to build tissue-level models of the rodent brain.


title: A method to estimate the cellular composition of the mouse brain from heterogeneous datasets


title: Reconstructing essential active zone functions within a synapse

abstract: Active zones are molecular machines that control neurotransmitter release through synaptic vesicle docking and priming, and through coupling of these vesicles to Ca2+ entry. The complexity of active zone machinery has made it challenging to determine which mechanisms drive these roles in release. Here, we induce RIM+ELKS knockout to eliminate active zone scaffolding networks, and then reconstruct each active zone function. Re-expression of RIM1-Zn fingers positioned Munc13 on undocked vesicles and rendered them release-competent. Reconstitution of release-triggering required docking of these vesicles to Ca2+ channels. Fusing RIM1-Zn to CaV{beta}4-subunits sufficed to restore docking, priming and release-triggering without reinstating active zone scaffolds. Hence, exocytotic activities of the 80 kDa CaV{beta}4-Zn fusion protein bypassed the need for megadalton-sized secretory machines. These data define key mechanisms of active zone function, establish that fusion competence and docking are mechanistically separable, and reveal that active zone scaffolding networks are not required for release.


title: Nrf2 mediated ER-phagy protects against oxidative damage in intervertebral disc degeneration

abstract:
Intervertebral disc degeneration (IDD) increases the risk of low back pain (LBP). Oxidative stress may induce cellular damage and contribute to various diseases including IDD. Endoplasmic reticulum autophagy (ER-phagy) is a specific type of autophagy, its role in oxidative stress induced damage as well as in IDD is unknown. This study explores the role of ER-phagy in oxidative damage in intervertebral disc nucleus pulposus cells (NPCs), as well as the Nrf2/FAM134B axis in ER-phagy regulation and IDD therapy. We found ER-phagy was decreased in NPCs during oxidative stress; while FAM134B may promote ER-phagy and alleviate oxidative stress induced ER-stress and apoptosis. In addition, the nuclear transcription factor Nrf2 may promote the expression of FAM134B as well as ER-phagy, and suppress ER-stress and apoptosis in NPCs. Furthermore, overexpression of FAM134B and Nrf2 could effectively attenuate the progression of IDD in rats in vivo. These results suggest Nrf2/FAM134B mediated ER-phagy may combat oxidative damage in cells; meanwhile, ER-phagy as well as Nrf2 could be potential therapeutic targets for IDD.

Graphical abstract

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category: cell biology


title: A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data

abstract: Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of the clonal substructure of tumors from single cell data. It uses a multichannel segmentation algorithm exploiting the assumption that all the cells in a given copy number clone share the same breakpoints. Thus, the smoothed expression profile of every individual cell constitutes part of the evidence of the copy number profile in each subclone. SCEVAN can automatically and accurately discriminate between malignant and non-malignant cells, resulting in a practical framework to analyze tumors and their microenvironment. We apply SCEVAN to several datasets encompassing 106 samples and 93,322 cells from different tumors types and technologies. We demonstrate its application to characterize the intratumor heterogeneity and geographic evolution of malignant brain tumors.


title: Laser Ablation and Fluid Flows Show a Single Force Mechanism Governs Spindle Positioning

abstract: Few techniques are available for elucidating the nature of forces that drive subcellular behaviors. Here we develop two complementary ones: 1) femtosecond stereotactic laser ablation (FESLA), which rapidly creates complex cuts of subcellular structures, thereby allowing precise dissection of when, where, and in what direction forces are generated; and 2) assessment of subcellular fluid flows, by comparing direct flow measurements, using microinjected fluorescent nanodiamonds, to large-scale fluid-structure simulations of different models of force transduction. We apply these to study centrosomes in Caenorhabditis elegans early embryos, and use the data to construct a biophysically-based model of centrosome dynamics. Taken together, we demonstrate that cortical pulling forces provide a general explanation for many behaviors mediated by centrosomes, including pronuclear migration/centration and rotation, metaphase spindle positioning, asymmetric spindle elongation and spindle oscillations. In sum, this work establishes new methodologies for disentangling the forces responsible for cell biological phenomena.


title: Robust and Efficient Assessment of Potency (REAP): A Quantitative Tool for Dose-response Curve Estimation

abstract: The median-effect equation has been widely used to describe the dose-response relationship and identify compounds that activate or inhibit specific disease targets in contemporary drug discovery. However, the experimental data often contain extreme responses, which may significantly impair the estimation accuracy and impede valid quantitative assessment in the standard estimation procedure. To improve the quantitative estimation of the dose-response relationship, we introduce a novel approach based on robust beta regression. Substantive simulation studies under various scenarios demonstrate solid evidence that the proposed approach consistently provides robust estimation for the median-effect equation, particularly when there are extreme outcome observations. Moreover, simulation studies illustrate that the proposed approach also provides a narrower confidence interval, suggesting a higher power in statistical testing. Finally, to efficiently and conveniently perform common lab data analyses, we develop a freely accessible web-based analytic tool to facilitate the quantitative implementation of the proposed approach for the scientific community.

category: pharmacology and toxicology


title: Post-translational modification patterns on β-myosin heavy chain are altered in ischemic and non-ischemic human hearts

abstract: Phosphorylation and acetylation of sarcomeric proteins are important for fine-tuning myocardial contractility. Here, we used bottom-up proteomics and label-free quantification to identify novel post-translational modifications (PTMs) on beta-myosin heavy chain ({beta}-MHC) in normal and failing human heart tissues. We report six acetylated lysines and two phosphorylated residues: K34-Ac, K58-Ac, S210-P, K213-Ac, T215-P, K429-Ac, K951-Ac, and K1195-Ac. K951-Ac was significantly reduced in both ischemic and non-ischemic failing hearts compared to non-diseased hearts. Molecular dynamics simulations show that K951-Ac may impact stability of thick filament tail interactions and ultimately myosin head positioning. K58-Ac altered the solvent exposed SH3 domain surface - known for protein-protein interactions - but did not appreciably change motor domain conformation or dynamics under conditions studied. Together, K213-Ac/T215-P altered loop 1s structure and dynamics - known to regulate ADP-release, ATPase activity, and sliding velocity. Our study suggests that {beta}-MHC acetylation levels may be influenced more by the PTM location than the type of heart disease since less protected acetylation sites are reduced in both heart failure groups. Additionally, these PTMs have potential to modulate interactions between {beta}-MHC and other regulatory sarcomeric proteins, ADP-release rate of myosin, flexibility of the S2 region, and cardiac myofilament contractility in normal and heart failure hearts.

category: physiology


title: Population Imaging of Central Sensitization

abstract:
Capsaicin applied locally to the skin causes central sensitization that results in allodynia, a state in which pain is elicited by innocuous stimuli. Here, we used two-photon calcium imaging of neurons in the dorsal spinal cord to visualize central sensitization across excitatory interneurons and spinal projection neurons. To distinguish among excitatory neuron subtypes, we developed CICADA, a cell profiling approach that leverages the expression of distinct Gq-coupled receptors. We then identified capsaicin-responsive and capsaicin-sensitized neuronal populations. Capsaicin-sensitized neurons showed emergent responses to low threshold input and increased receptive field sizes consistent with the psychophysical phenomenon that allodynia is observed across an extended secondary zone. Finally, we identified spinal projection neurons that showed a shift in tuning toward low threshold input. These experiments provide a population-level view of central sensitization and a framework with which to model somatosensory integration in the dorsal horn.

HighlightWarwick et al. use two-photon calcium imaging coupled with pharmacological profiling to identify neuronal populations in the spinal dorsal horn that mediate capsaicin-induced central sensitization.


title: Cryo-EM structures of the channelrhodopsin ChRmine in lipid nanodiscs

abstract: Microbial channelrhodopsins are light-gated ion channels widely used for optogenetic manipulation of neuronal activity. ChRmine is a bacteriorhodopsin-like cation channelrhodopsin (BCCR) more closely related to ion pump rhodopsins than other channelrhodopsins. ChRmine displays unique properties favorable for optogenetics including high light sensitivity, a red-shifted activation spectrum, cation selectivity, and large photocurrents while its slow closing kinetics impede some applications. The structural basis for ChRmine function, or that of any other BCCR, is unknown. Here, we present cryo-EM structures of ChRmine in lipid nanodiscs in apo (opsin) and retinal-bound (rhodopsin) forms. The structures reveal an unprecedented trimeric architecture with a lipid filled central pore. Large electronegative cavities on either side of the membrane facilitate high conductance and selectivity for cations over protons. The retinal binding pocket structure suggests spectral and kinetic properties could be tuned with mutations and we identify ChRmine variants with two-fold increased and ten-fold decreased closing rates. These results provide insight into structural features that generate an ultra-potent microbial opsin and provide a platform for rational engineering of channelrhodopsins with improved properties that could expand the scale, depth, and precision of optogenetic manipulations.


title: Red backgrounds have different effects on electrophysiological responses to fearful faces in groups with low and high autistic tendency

abstract: Visual processing differences in the magnocellular pathway have been reported across the autistic spectrum. On the basis that the firing of primate Type IV magnocellular cells is suppressed by diffuse red backgrounds, several groups have used red backgrounds as a means to investigate magnocellular contributions to visual processing in humans. Here, we measured emotional identification accuracy, and compared the P100 and N170 responses from groups with low (n=21; AQ<11) and high (n=22; AQ>22) Autism Spectrum Quotient (AQ) scores, in response to low (LSF) and high (HSF) spatially filtered fearful and neutral face stimuli presented on red and green backgrounds. For the LSF stimuli, the low AQ group correctly identified fearful expressions more often when presented on a red compared to a green background. The low AQ group also showed red backgrounds reduced the effect of LSF fearful expressions on P100 amplitudes. In contrast, the high AQ group showed that background colour did not significantly alter P100 responses to LSF stimuli. Interestingly, red background reduced the effects of HSF stimuli for the high AQ group. The effects of background color on LSF and HSF facial emotion responses were not evident for the N170 component. Our findings suggest that presenting face stimuli on a red background alters both magnocellular and parvocellular contributions to the P100 waveform, and that these effects differ for groups with low and high autistic tendencies. In addition, a theoretical model for explaining the temporal differences in facial emotion processing for low and high AQ groups is proposed.


title: A dual voltage clamp technique to study gap junction hemichannels in astrocytes cultured from neonatal rodent spinal cords

abstract: Astrocytes express surface channels involved in purinergic signaling, and among these channels, pannexin-1 (Px1) and connexin-43 (Cx43) hemichannels (HCs) mediate ATP release that acts directly, or through its derivatives, on neurons and glia via purinergic receptors. Although HCs are functional, i.e., open and close, under physiological and pathological conditions, single channel conductance of Px1 HCs is not well defined. Here, we developed a dual voltage clamp technique in HeLa cells overexpressing human Px1-YFP, and then applied this system to rodent spinal astrocytes. Single channels were recorded in cell attached patches and evoked with ramp cycles of 2 s duration and -/+ 80-100 mV amplitude through another pipette in whole cell clamp. Conductance of Px1 HC openings recorded during ramp stimuli ranged 25-110 pS. Based on their single channel conductances, Px1 HCs could be distinguished from Cx43 HCs and P2X7 receptors (P2X7Rs) in spinal astrocytes during dual voltage clamp experiments. Furthermore, we found that single channel activity of Cx43 HCs and P2X7Rs was increased, and that of Px1 HCs was decreased, in spinal astrocytes treated for 7 h with FGF-1, a growth factor implicated in neurodevelopment, repair and inflammation.


title: Dissociating experience-dependent and maturational changes in fine motor function during adolescence

abstract: Adolescence is a sensitive period in motor development but little is known about how long-term learning dependent processes shape hand function in tasks of different complexity. We mapped two fundamental aspects of hand function: simple repetitive and complex sequential finger movements, as a function of the length of musical instrumental training. We controlled maturational factors such as chronological and biological age of adolescent female participants (11 to 15 years of age, n=114). We demonstrated that experience improves performance as a function of task complexity, the more complex task being more susceptible for experience driven performance changes. Overall, these results suggest that fine motor skills involving cognitive control and relying on long-range functional brain networks are substantially shaped by experience. On the other hand, performance in a simple repetitive task that explains fine motor speed is primarily shaped by white matter development driven by maturational factors.


title: Macrophage network dynamics depend on haptokinesis for optimal local surveillance

abstract: Macrophages are key immune cells with important roles for tissue surveillance in almost all mammalian organs. Cellular networks made up of many individual macrophages allow for optimal removal of dead cell material and pathogens in tissues. However, the critical determinants that underlie these population responses have not been systematically studied. Here, we investigated how cell shape and the motility of individual cells influences macrophage network responses in 3D culture settings and in mouse tissues. We show that surveying macrophage populations can tolerate lowered actomyosin contractility, but cannot easily compensate for a lack of integrin-mediated adhesion. Although integrins were dispensable for macrophage chemotactic responses, they were crucial to control cell movement and protrusiveness for optimal surveillance by a macrophage population. Our study reveals that {beta}1 integrins are important for maintaining macrophage shape and network sampling efficiency in mammalian tissues, and sets macrophage motility strategies apart from the integrin-independent 3D migration modes of many other immune cell subsets.


title: Bovine serum albumin as a resuscitation promoting factor for viable but non-culturable Mycobacterium tuberculosis via the activation of protein kinase A-dependent cellular processes

abstract:
ObjectiveMycobacterium tuberculosis (Mtb) H37Ra strain has been reported to rapidly enter the viable but non-culturable (VBNC) state following treatment with an NADH oxidase inhibitor (diphenyleneiodonium [DPI]) and to be resuscitated by fetal bovine serum (FBS). However, the mechanism underlying FBS-induced resuscitation is currently unclear. We tried to reveal the underlying mechanism of FBS-induced resuscitation using M. tuberculosis H37Rv. Methods: First, we evaluated the effect of DPI on culturability, viability and changes of cellular phenotypes toward H37Rv. Secondly, we measured the resuscitation-promoting effects of human serum albumin, egg-white albumin, N-acetyl-L-cysteine, and D-mannitol in DPI-induced VBNC cells, as antioxidative agents have been reported to be key molecules for resuscitation of other microbes. We also evaluated the effect of inhibition of cAMP production and protein kinase A on BSA-induced resuscitation.

ResultsDPI treatment successfully induced a VBNC state in H37Rv, resulting in a low proportion of culturable cells, loss of acid-fastness and lipid-accumulation but a high proportion of viable cells. Not only FBS but also bovine serum albumin (BSA) alone could resuscitate H37Rv. Contrary to our expectation, only human serum albumin had a similar resuscitative effect to BSA. The inhibition of adenylyl cyclase by SQ22536 did not have a significant effect on resuscitation; however, the inhibition of protein kinase A by H89 strongly suppressed the BSA-induced resuscitation.

ConclusionDPI-induced VBNC Mtb cells may be resuscitated via the activation of protein kinase A-dependent processes through interaction with BSA.


title: Mitotic Outcomes in Fibrous Environments

abstract: During mitosis, cells round up and generate outward forces to create space and orient the mitotic spindles. Here, using suspended ECM-mimicking nanofiber networks, we recapitulate in vivo adhesion organization and confinement to interrogate mitotic outcomes for various interphase cell shapes. Elongated cells attached to single fibers through two focal adhesion clusters (FACs) at their extremities result in perfect spherical mitotic cell bodies that undergo large 3D displacement while being held by retraction fibers. Increasing the number of parallel fibers increases cellular extremity FACs and retraction fiber-driven stability, leading to reduced 3D cell-body movement, metaphase plate rotations, and significantly faster division times. Interestingly, interphase kite shapes on a crosshatch pattern of four fibers undergo mitosis resembling single-fiber outcomes due to rounded bodies being primarily held in position by retraction fibers from two perpendicular suspended fibers. We develop a cortex-astral microtubule analytical friction and force model to capture retraction-fiber-driven stability of the metaphase plate rotations. We report that reduced orientational stability results in increased monopolar mitotic defects. In the case of cells attached to two parallel fibers, rounded mitotic cells can get confined between the suspended fibers, allowing estimation of the mitotic forces through measurement of the outward deflection of the fibers. Interestingly, confinement causes rotated mitotic spindles similar to those reported in dense tissues. Overall, we establish dynamics of mitosis in fibrous environments governed by fiber arrangement and architecture-driven differences in interphase cell shapes, adhesion geometries, and varying levels of mechanical confinement.


title: Human Biopsies in Nanofibrillar Cellulose Hydrogel - A Novel Method for Long-term Tissue Culture

abstract:
Advanced 3D in vitro models are laborious to prepare and susceptible to unintentional design errors due to culture adaptations, cell immaturity, xenofactors or yet incomplete knowledge of the dynamics within tissues or materials. In order to acquire cost-efficient research material with intact in vivo composition, we developed novel tissue culture method with plant-derived scaffolding.

Human skin-, foreskin- and glioblastoma multiforme biopsies were dissected mechanically and cultivated for 28 days in plant-derived nanofibrillar cellulose hydrogel. Comparative cultures were done using mouse sarcoma tumor -derived Matrigel. Long-term preservation of cultivated tissues was evaluated against typical immunohistochemical biomarkers for each tissue type: skin tissues for cytokeratins 5/6, E-cadherin and vimentin for sustained tissue structures, and brain neoplasia for Olig2, S100, Nestin, NOTCH1, MAP2 and GFAP for preserved disease profile.

Histological analysis from both culture conditions showed that until day 28, all cultivated biopsy types were able to sustain their characteristic protein expressions without signs of necrosis. We here conclude a novel tissue culture model in xeno-free 3D scaffolding, that can enable long-term sample storage in vitro, studies of human tumor tissues and their non-neoplastic microenvironment, and innovations in personalized medicine research.


title: Large scale PVA modelling of insects in cultivated grasslands: the role of dispersal in mitigating the effects of management schedules under climate change

abstract: In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on severity of climate change in sub regions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m2) scale in 107 sub regions, altogether encompassing a range of different grassland cover, climate change projections and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many sub regions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions, but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.


title: Heterosis Related to Fitness and Phenotypic Variance in the Evolution of Diploid Gene Regulatory Network

abstract:
Heterosis describes the phenomenon whereby a hybrid population has higher fitness than an inbred population, and has previously been explained by either Mendelian dominance or overdominance, where it is generally assumed that one gene controls one trait. How-ever, recent studies have demonstrated that genes interact through a complex gene regulatory network (GRN). Furthermore, phenotypic variance due to noise is reportedly lower for heterozygotes, whereas the origin of such variance-related heterosis remains elusive. There-fore, a theoretical analysis linking heterosis to GRN evolution and stochastic gene expression dynamics is required. Here, we investigate heterosis related to fitness and phenotypic variance in a system with interacting genes, by numerically evolving diploid GRNs. According to the results, the heterozygote population exhibited higher fitness than the homozygote population, that is, fitness-related heterosis resulting from evolution. In addition, the heterozygote population expressed lower noise-related phenotypic variance in expression levels than the homozygous population, implying that the heterozygote population is more robust to noise. Furthermore, the distribution of the ratio of heterozygote phenotypic variance to homozygote phenotypic variance exhibited quantitative agreement with previous experimental results. By applying dominance and over-dominance to the gene expression pattern rather than only a single gene expression, we confirmed the correlation between heterosis and overdominance. We explain our results by proposing that the convex high-fitness region is evolutionarily shaped in the genetic space to gain noise robustness under genetic mixing through sexual reproduction.

Significance StatementHeterosis, that is higher fitness in hybrid populations than inbred populations, is a long-standing problem in genetics, evolution, and breeding studies. Heterosis is not necessarily the result of a trait uniquely determined by a single gene, but likely involves stochasticity and interactions among genes. Through numerical evolution of the gene regulatory network, we demonstrate that heterosis is shaped by evolution to achieve robustness against noise and genetic mixing by sexual recombination in gene expression dynamics. That is, a mixed population is more robust to noise than inbred populations, as revealed experimentally by reduced phenotypic variance. The observed link between heterosis and phenotypic robustness, Mendelian dominance, and the convex single-humped fitness landscape represents a novel avenue in evolution and genetics research.

category: evolutionary biology


title: Reduction in population size and not a shift in parasite community affect evolution of immune genes in island birds.

abstract: Shared ecological conditions encountered by species that colonize islands often lead to the evolution of convergent phenotypes, commonly referred to as "island syndrome". Reduced immune functions have been previously proposed to be part of the island syndrome, as a consequence of the reduced diversity of pathogens on island ecosystems. According to this hypothesis, immune genes are expected to exhibit genomic signatures of relaxed selection pressure in island species. In this study, we used comparative genomic methods to study immune genes in island species (N = 20) and their mainland relatives (N = 14). We gathered public data as well as generated new data on innate (Toll-Like Receptors, Beta Defensins) and acquired immune genes (Major Histocompatibility Complex classes I and II), but also on hundreds of genes annotated as involved in various immune functions. As a control, we used a set of 97 genes not involved in immune functions, to account for the lower effective population sizes in island species. We used synonymous and non-synonymous variations to estimate the selection pressure acting on immune genes. For the genes evolving under balancing selection, we used simulation to estimate the impact of population size variation. We found a significant effect of drift on immune genes of island species leading to a reduction in genetic diversity and efficacy of selection. However, the intensity of relaxed selection was not significantly different from control genes, except for MHC class II genes. These genes exhibit a significantly higher level of non-synonymous loss of polymorphism than expected assuming only drift and an evolution under frequency dependent selection, possibly due to a reduction of extracellular parasite communities on islands. Overall, our results showed that demographic effects lead to a decrease in the immune functions of island species, but the relaxed selection caused by a reduced parasite pressure may only occur in some immune genes categories.


title: CAMO: A molecular congruence analysis framework for evaluating model organisms

abstract: CAMO provides a rigorous and user-friendly solution for quantification and mechanistic exploration of omics congruence in model organisms and humans. It performs threshold-free differential analysis, quantitative concordance/discordance scoring, pathway-centric investigation, and topological subnetwork detection. Instead of dichotomous claims of "poorly" or "greatly" mimicking humans, CAMO facilitates discovery and visualization of specific molecular mechanisms that are best or least mimicked, providing foundations for hypothesis generation and subsequent translational investigations.

category: genomics


title: reComBat: Batch effect removal in large-scale, multi-source omics data integration

abstract:
MotivationWith the steadily increasing abundance of omics data produced all over the world under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch-effect removal for entire databases lies in the large number of batches and biological variation which can result in design matrix singularity. This problem can currently not be solved satisfactorily by any common batch-correction algorithm.

ResultsWe present reComBat, a regularized version of the empirical Bayes method to overcome this limitation and benchmark it against popular approaches for the harmonization of public gene expression data (both microarray and bulkRNAsq) of the human opportunistic pathogen Pseudomonas aeruginosa. Batch-effects are successfully mitigated while biologically meaningful gene expression variation is retained. reComBat fills the gap in batch-correction approaches applicable to large-scale, public omics databases and opens up new avenues for data-driven analysis of complex biological processes beyond the scope of a single study.

Contactmichael.adamer@bsse.ethz.ch

AvailabilityThe code is available at https://github.com/BorgwardtLab/reComBat, all data and evaluation code can be found at https://github.com/BorgwardtLab/batchCorrectionPublicData


title: Long-lasting and responsive DNA/enzyme-based programs in serum-supplemented extracellular media

abstract: DNA molecular programs are emerging as promising pharmaceutical approaches due to their versatility for biomolecular sensing and actuation. However, the implementation of DNA programs has been mainly limited to serum-deprived in vitro assays due to the fast deterioration of the DNA reaction networks by the nucleases present in the serum. Here, we show that DNA/enzyme programs are functional in serum for 24h but are latter disrupted by nucleases that give rise to parasitic amplification. To overcome this, we implement 3-letter code networks that suppress autocatalytic parasites while still conserving the functionality of DNA/enzyme programs for at least 3 days in the presence of 10% serum. In addition, we define a new buffer that further increases the biocompatibility and conserves responsiveness to changes in molecular composition across time. Finally, we demonstrate how serum-supplemented extracellular DNA molecular programs remain responsive to molecular inputs in the presence of living cells, having responses 6-fold faster than cellular division rate and are sustainable for at least 3 cellular divisions. This demonstrates the possibility of implementing in situ biomolecular characterization tools for serum-demanding in vitro models. We foresee that the coupling of chemical reactivity to our DNA programs by aptamers or oligonucleotide conjugations will allow the implementation of extracellular synthetic biology tools, which will offer new biomolecular pharmaceutical approaches and the emergence of complex and autonomous in vitro models.


title: A corticothalamic circuit trades off speed for safety during decision-making under motivational conflict

abstract: Decisions to act while pursuing goals in the presence of danger must be made quickly but safely. Premature decisions risk injury or death whereas postponing decisions risk goal loss. Here we show how mice resolve these competing demands. Using microstructural behavioral analyses, we identified the spatiotemporal dynamics of approach-avoidance decisions under motivational conflict. Then we used cognitive modelling to show that these dynamics reflect the speeded decision-making mechanisms used by humans and non-human primates, with mice trading off decision speed for safety of choice when danger loomed. Using calcium imaging and functional circuit analyses, we show that this speed-safety trade off occurs because increases in paraventricular thalamus (PVT) activity increase decision caution, thereby increasing approach-avoid decision times in the presence of danger. Our findings demonstrate that a discrete brain circuit involving the PVT and its prefrontal cortical input dynamically adjusts decision caution during motivational conflict, trading off decision speed for decision safety when danger is close. They identify the corticothalamic pathway as central to cognitive control during decision-making under conflict.


title: Lasting effects of low-calorie sweeteners on glucose regulation, sugar intake, and memory

abstract: Low-calorie sweetener (LCS) consumption in children has increased due to widespread LCS presence in the food environment and efforts to mitigate obesity through sugar replacement. However, mechanistic studies on the impact of early-life LCS consumption are lacking. Therefore, we developed a rodent model to evaluate the effects of daily LCS consumption (acesulfame potassium, saccharin, or stevia) during adolescence on adult metabolic, gut microbiome, neural, and behavioral outcomes. Results reveal that habitual early-life LCS consumption disrupts post-oral glucose tolerance and impairs hippocampal-dependent memory in the absence of weight gain. Furthermore, LCS consumption reduces lingual sweet taste receptor expression and alters sugar-motivated appetitive and consummatory responses. RNA sequencing analyses reveal that LCS also impacts collagen- and synaptic signaling-related gene pathways in the hippocampus and nucleus accumbens, respectively, in a sex-dependent manner. Collectively, these results suggest that regular early-life LCS consumption yields long-lasting impairments in metabolism, sugar-motivated behavior, and hippocampal-dependent memory.


title: Activity-dependent circuitry plasticity via the regulation of the histamine receptor level in the Drosophila visual system

abstract: Activity-dependent synaptic plasticity is crucial for responses to the environment. Although the plasticity mechanisms of presynaptic photoreceptor neurons in the Drosophila visual system have been well studied, postsynaptic modifications remain elusive. In addition, further studies on the adaption of the visual system to different light experiences at a circuitry scale are required. Using the modified transcriptional reporter of intracellular Ca2+ method, we describe a way to visualize circuitry changes according to different light experiences. We found enhanced postsynaptic neuronal activity responses in lamina monopolar neuron L2 after prolonged light treatment. Although L1 also has connections with photoreceptors, there were no enhanced activity responses in L1. We also report in this study that activity-dependent transcriptional downregulation of inhibitory histamine receptors (HRs) occurs in postsynaptic neuron L2, but not in L1, during continuous light conditions. We expressed exogenous HR proteins in L2 neurons and found that it attenuated the enhanced activity response caused by constant light exposure. These findings, together with the fact that histamine is the main inhibitory neurotransmitter released by photoreceptors in the Drosophila visual system, confirmed our hypothesis that the activity-dependent transcriptional downregulation of HRs is responsible for the constant light exposure-induced circuitry response changes in L2. The results successfully demonstrated the selective circuit change after synaptic remodeling evoked by long-term activation and provided in vivo evidence of circuitry plasticity upon long-term environmental stimulation.


title: The different brain areas occupied for integrating information of hierarchical linguistic units: a study based on EEG and TMS

abstract: Human linguistic units are hierarchical, and our brain responds differently when processing linguistic units during sentence comprehension, especially when the modality of the received signal is different (auditory, visual, or audio-visual). However, it is unclear how the brain processes and integrates language information at different linguistic units (words, phrases, and sentences) provided simultaneously in audio and visual modalities. To address the issue, we presented participants with sequences of short Chinese sentences through auditory or visual or combined audio- visual modalities, while electroencephalographic responses were recorded. With a frequency tagging approach, we analyzed the neural representations of basic linguistic units (i.e., characters/monosyllabic words) and higher-level linguistic structures (i.e., phrases and sentences) across the three modalities separately. We found that audio-visual integration occurs at all linguistic units, and the brain areas involved in the integration varied across different linguistic levels. In particular, the integration of sentences activated the local left prefrontal area. Therefore, we used continuous theta-burst stimulation (cTBS) to verify that the left prefrontal cortex plays a vital role in the audio-visual integration of sentence information. Our findings suggest the advantage of bimodal language comprehension at hierarchical stages in language-related information processing and provide evidence for the causal role of the left prefrontal regions in processing information of audio-visual sentences.


title: Signaling by the integrated stress response kinase PKR is fine-tuned by dynamic clustering

abstract: The double-stranded RNA sensor kinase PKR is one of four integrated stress response (ISR) sensor kinases that phosphorylate the alpha subunit of the eukaryotic initiation factor 2 (eIF2) in response to stress. The current model of PKR activation considers the formation of back-to-back PKR dimers as a prerequisite for signal propagation. Here we show that PKR signaling involves the assembly of dynamic PKR clusters. PKR clustering is driven by ligand binding to PKRs sensor domain and by front-to-front interfaces between PKRs kinase domains. PKR clusters are discrete, heterogeneous, autonomous coalescences that share some protein components with processing bodies. Strikingly, eIF2 is not recruited to PKR clusters, and PKR cluster disruption enhances eIF2 phosphorylation. Together, these results support a model in which PKR clustering buffers downstream signaling, which may enable proofreading the ISR.


title: Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

abstract:
O_LIAssessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics and can help distinguish between anthropogenic and natural causes for population decline.
C_LIO_LIJapanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. Here we assess the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods.
C_LIO_LIThe analyses indicate a reduction in effective population size (Ne) from 38 000 to 10 000 individuals between 4 and 1 Ma, followed by an increase to 80 000 individuals, between 1 Ma and 22-30 kya. Approximately 22-30 kya there is evidence for a reduction in Ne to approximately 60 000 individuals. These events are likely due to changes in environmental conditions, such as sea level and oceanic currents, especially around the last glacial maximum (19-33 kya).
C_LIO_LIThe results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. This pattern of demographic history may make Japanese eel sensitive to current and future population declines. Conservation management of Japanese eel should focus on practical ways to prevent further population decline and the loss of genetic diversity that is essential for the species to adapt to changing environmental conditions such as climate change.
C_LI


title: Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species

abstract: The response of coral reef ecosystems to anthropogenic climate change is driven by a complex interaction between location, stress history, species composition, and genetic background of the reef system. The latter two factors are particularly relevant when considering the different reproductive strategies used by coral species. We studied the stress resistant coral Montipora capitata and the more stress sensitive Pocillopora acuta from K[a]neohe Bay, Oahu, Hawaii. High-quality genome assemblies were generated for both species with the M. capitata assembly at chromosome-level resolution and the P. acuta assembly derived from a triploid colony, representing the first non-diploid genome generated from a coral. We report significant differences in the reproductive strategies of these coral species that not only affect the genetic structure of their populations in K[a]neohe Bay, but also impact algal symbiont composition. Single-nucleotide polymorphism analysis shows that P. acuta comprises at least nine distinct genotypes in the bay with ancestral diploid and derived triploid lineages. In contrast, M. capitata colonies are diploids with nearly all being genotypically distinct. Genotype has a strong effect on gene expression profiles in these species, largely outweighing the effects of environmental stress. Our insights advance understanding of how reproductive strategy and ploidy can vary between different coral species and among local populations, how these factors constrain coral holobiont genetic diversity, and how genotype constrains genome-wide gene expression.


title: Antitumor Effects Of Phytochemicals Of Hot Three Plants On Gastric Adenocarcinoma

abstract:
BACKGROUNDThymoquinone (TQ) and beta-sitosterol (BS), the bioactive constituents derived from the medicinal plant Atragene sibirica L, Ranunculus repens L, Pulsatilla Bungeana have been used for anti-cancer treatment in Traditional Mongolian Medicine. Recent studies reported that TQ, BS exhibited anti-proliferative effects on several cancer cell lines. This study was performed to investigate the antitumor effects of phytochemicals on gastric adenocarcinoma in vitro.

METHODSTo this aim, we performed a cell apoptosis assay WST1 and several cancer-related gene expressions (Bcl, BIRC5, p53, BAX). NCI-N87, MKN74 cells were seeded at a density of 5x104 cells per well in 96-well culture plates. After overnight incubation, the fresh medium containing different concentrations of TQ (20, 40, 60, 80, and 100 mM/ml) and beta-sitosterol (10, 1, 0.1, 0.001, 0.001 mM/ml) were applied. Following a 24-h incubation, the cell viability was determined by WST-1 assay. We also quantified the expression levels of mRNAs of these genes through qRT-PCR experiments.

RESULTSOur results showed that TQ induced a higher percentage of cell apoptosis in the human gastric adenocarcinoma cell lines compared to that of control. We observed a significant 4.8-fold change in BAX/BCL2 ratio. These increases were highly correlated with a concentration-dependent manner (p=0.00178). Moreover, the expression of p53 and BIRC5 was downregulated in MKN74 cells after treatment with TQ.

CONCLUSIONSOur results demonstrate that TQ effectively inhibits cell proliferation through several gene expressions in vitro. Moreover, inhibition of the downstream molecule of these genes would explain the underlying mechanism of the antitumor activity in cancer cell lines.

category: cancer biology


title: Stress Resistance Heat Shock Protein 70 (HSP70) Analysis in Sorghum (Sorghum bicolor L.) at Genome-Wide Level

abstract: Heat shock proteins (HSP70) play an important role in many biological processes. However, as typical in Sorghum bicolor, the systematic identification of the HSP70 gene is very limited, and the role of the Hsp70 gene in the evolution of Sorghum bicolor has not been described systematically a lot. To overcome the gap, Insilco analysis of HSP70 gene family was conducted.The investigation was utilizing the bioinformatics method to analyze the HSP70 gene family and it has been identified that 30 HSP70 genes from the genome sequence of Sorghum bicolor. A comprehensive analysis of these 30 identified genes undertaking the analysis of gene structure, phylogeny, and physicochemical properties, subcellular localization, and promoter region analysis. The gene structure visualization analyses revealed that 22 genes contains both 5 and 3 UTRS and one 5 and one 3 gene and 6 genes without UTR. The highest number of introns was recorded as 12 and those genes have shown that without in any intron. In the promoter region analysis, ten protein motifs are identified and characterized and 2219 cis-acting elements are identified. Among those, the promoter enhancer elements share the highest number (1411) and light-responsive elements share the next value (335). The physicochemical properties analysis revealed that 23 families have an acidic nature while four families are basic and the rests are neutral. In general, the different analyses performed disclosed their structural organization, subcellular localization, physicochemical properties, cis-acting elements, phylogenetic, and understress conditions. This study provides further information for the functional characterization of HSP70 and helps to understand the mechanisms of abiotic stress tolerance under diverse stress conditions in Sorghum bicolor.

category: plant biology


title: A structured scaffold underlies activity in the hippocampus

abstract: Place cells are believed to organize memory across space and time, inspiring the idea of the cognitive map. Yet unlike the structured activity in the associated grid and head-direction cells, they remain an enigma: their responses have been difficult to predict and are complex enough to be statistically well-described by a random process. Here we report one step toward the ultimate goal of understanding place cells well enough to predict their fields. Within a theoretical framework in which place fields are derived as a conjunction of external cues with internal grid cell inputs, we predict that even apparently random place cell responses should reflect the structure of their grid inputs and that this structure can be unmasked if probed in sufficiently large neural populations and large environments. To test the theory, we design experiments in long, locally featureless spaces to demonstrate that structured scaffolds undergird place cell responses. Our findings, together with other theoretical and experimental results, suggest that place cells build memories of external inputs by attaching them to a largely prespecified grid scaffold.

category: neuroscience


title: Humans can track but fail to predict accelerating objects

abstract: Objects in our visual environment often move unpredictably and can suddenly speed up or slow down. The ability to account for acceleration when interacting with moving objects can be critical for survival. Here, we investigate how human observers track an accelerating target with their eyes and predict its time of reappearance after a temporal occlusion by making an interceptive hand movement. Before occlusion, the target was initially visible and accelerated for a brief period. We tested how observers integrated target motion information by comparing three alternative models that predicted time-to-contact (TTC) based on the (1) final target velocity sample before occlusion, (2) average target velocity before occlusion, or (3) target acceleration. We show that visually-guided smooth pursuit eye movements reliably reflect target acceleration prior to occlusion. However, systematic saccade and manual interception timing errors reveal an inability to consider acceleration when predicting TTC. Interception timing is best described by the final velocity model that relies on extrapolating the last available velocity sample before occlusion. These findings provide compelling evidence for differential acceleration integration mechanisms in vision-guided eye movements and prediction-guided interception and a mechanistic explanation for the function and failure of interactions with accelerating objects.


title: Missing genetic links between general factors of brain resting-state functional magnetic resonance imaging, cognition and psychopathology

abstract: General factors capturing the shared genetics in psychiatric (genomic p-factor) and cognitive traits (genomic g-factor), and more recently in resting-state functional magnetic resonance imaging-derived brain networks, have contributed to our increased understanding of the etiologies in their respective domains. Yet it remains unclear whether general factors can capture the three-way genetic overlap of psychopathology, cognition and brain function. Here we tested for the presence of this genetic overlap via genetic correlation analyses using summary statistics of genome-wide association studies of the p-factor (N = 162,151 cases and 276,846 controls), the g-factor (N = 269,867), and the two genomic factors estimated from the amplitude in resting-state functional magnetic resonance imaging-derived brain networks (N = 31,688). Unlike hypothesized, only the genetic correlation between the p-factor and the g-factor was significant. We conclude that specific functional brain network constructs may have more potential than their derived general dimensions to capture relevant genetic variation for cognition and psychopathology.


title: Anxiety attenuates learning advantages conferred by statistical stability and induces loss of volatility-attuning in brain activity

abstract: Anxiety can alter an individuals perception of their external sensory environment. Previous studies suggest that anxiety can increase the magnitude of neural responses to unexpected (or surprising) stimuli. Additionally, surprise responses are reported to be boosted during stable compared to volatile environments. Few studies, however, have examined how learning is impacted by both threat and volatility. To investigate these effects, we used threat-of-shock to transiently increase subjective anxiety in healthy adults during an auditory oddball task, in which the regularity could be stable or volatile, while undergoing functional Magnetic Resonance Imaging (fMRI) scanning. We then used Bayesian Model Selection (BMS) mapping to pinpoint the brain areas where different models of anxiety displayed the highest evidence. Behaviourally, we found that threat-of-shock eliminated the accuracy advantage conferred by environmental stability over volatility in the task at hand. Neurally, we found that threat-of-shock led to both attenuation and loss of volatility-attuning of neural activity evoked by surprising sounds across most subcortical and limbic brain regions including the thalamus, basal ganglia, claustrum, insula, anterior cingulate, hippocampal gyrus and also the superior temporal gyrus. Conversely, within two small clusters in the left medial frontal gyrus and extrastriate area, threat-of-shock boosted the neural activity (relative to the safe and volatile condition) to the levels observed during the safe and stable condition, while also inducing a loss of volatility-attuning. Taken together, our findings suggest that threat eliminates the learning advantage conferred by statistical stability compared to volatility. Thus, we propose that anxiety disrupts behavioural adaptation to environmental statistics, and that multiple subcortical and limbic regions are implicated in this process.


title: Miniscope-LFOV: A large field of view, single cell resolution, miniature microscope for wired and wire-free imaging of neural dynamics in freely behaving animals

abstract: We present a large field of view (FOV) open-source miniature microscope (MiniLFOV) designed to extend the capabilities of the UCLA Miniscope platform to large-scale, single cell resolution neural imaging in freely behaving large rodents and head-fixed mice. This system is capable of multiple imaging configurations, including deep brain imaging using implanted optical probes and cortical imaging through cranial windows. The MiniLFOV interfaces with existing open-source UCLA Miniscope DAQ hardware and software, can achieve single cell resolution imaging across a 3.6 x 2.7 mm field of view at 23 frames per second, has an electrically adjustable working distance of up to 3.5 mm{+/-}150 {micro}m using an onboard electrowetting lens, incorporates an absolute head-orientation sensor, and weighs under 14 grams. The MiniLFOV provides a 30-fold larger FOV and yields 20-fold better sensitivity than Miniscope V3, and a 12-fold larger FOV with 2-fold better sensitivity than Miniscope V4. Power and data transmission are handled through a single, flexible coaxial cable down to 0.3 mm in diameter facilitating naturalistic behavior. We validated the MiniLFOV in freely behaving rats by simultaneously imaging >1000 GCaMP7s expressing neurons in the CA1 layer of the hippocampus and in head-fixed mice by simultaneously imaging [~]2000 neurons in the mouse dorsal cortex through a 4 x 4 mm cranial window. For freely behaving experiments, the MiniLFOV supports optional wire-free operation using a 3.5 g wire-free data acquisition expansion board which enables close to 1-hour of wire-free recording with a 400 mAh (7.5 g) on-board single-cell lithium-polymer battery and expands wire-free imaging techniques to larger animal models. We expect this new open-source implementation of the UCLA Miniscope platform will enable researchers to address novel hypotheses concerning brain function in freely behaving animals.


title: Clonal hematopoiesis in individuals with ANKRD26 or ETV6 germline mutations

abstract:
Currently, there are at least a dozen recognized hereditary hematopoietic malignancies (HHMs), some of which phenocopy others. Among these, three HHMs driven by germline mutations in ANKRD26, ETV6, or RUNX1 share a phenotype of thrombocytopenia, qualitative platelet defects, and an increased lifetime risk of hematopoietic malignancies (HMs). Prior work has demonstrated that RUNX1 germline mutation carriers experience an elevated lifetime risk (66%) for developing clonal hematopoiesis (CH) prior to age 50. Germline mutations in ANKRD26 or ETV6 phenocopy RUNX1 germline mutations, but no studies have focused on the risk of CH in individuals with germline mutations in ANKRD26 or ETV6.

To determine the prevalence of CH in individuals with germline mutations in ANKRD26 or ETV6, we performed next generation sequencing on hematopoietic tissue from twelve individuals with either germline ANKRD26 or germline ETV6 mutations. Each patient had thrombocytopenia but had not developed HMs. Among the seven individuals with germline ANKRD26 mutations, one patient had a CH clone driven by a somatic SF3B1 mutation (p.Lys700Glu). This mutation increased from a variant allele frequency (VAF) of 9.4% at age 56 to 17.4% at age 60. None of the germline ETV6 mutation carriers had evidence of CH at the limits of detection of the NGS assay (5% VAF). Unlike individuals with germline mutations in RUNX1, no individuals under the age of 50 with germline mutations in ANKRD26 or ETV6 had detectable CH. This work demonstrates that ANKRD26 germline mutation carriers, but not ETV6 mutation carriers, experience elevated risk for CH.

category: genetics


title: Substrate stiffness modulates integrin α5 expression and ECM-associated gene expression in fibroblasts

abstract: Biomaterials, like polydimethylsiloxane (PDMS), are soft, biocompatible, and tuneable, which makes them useful to delineate specific substrate factors that regulate the complex landscape of cell-substrate interactions. We used a commercial formulation of PDMS to fabricate substrates with moduli 40 kPa, 300 kPa, and 1.5 MPa, and cultured HMF3S fibroblasts on them. Gene expression analysis was performed by RT-PCR and Western blotting. Cellular and nuclear morphologies were analyzed using confocal imaging, and MMP-2 and MMP-9 activities were determined with gelatin zymography. Results, comparing mechanotransduction on PDMS substrates with control petridishes, show that substrate stiffness modulates cell morphologies and proliferations. Cell nuclei were rounded on compliant substrates and correlated with increased tubulin expression. Proliferations were higher on stiffer substrates with cell cycle arrest on softer substrates. Integrin 5 expression decreased on lower stiffness substrates, and correlated with inefficient TGF-{beta} activation. Changes to the activated state of the fibroblast on higher stiffness substrates were linked to altered TGF-{beta} secretion. Collagen I, collagen III, and MMP-2 expression levels were lower on compliant PDMS substrates as compared to stiffer ones; there was little MMP-9 activity on substrates. These results demonstrate critical feedback mechanisms between substrate stiffness and ECM regulation by fibroblasts which is highly relevant in diseases like tissue fibrosis.


title: Systematic assessment of the accuracy of subunit counting in biomolecular complexes using automated single molecule brightness analysis

abstract: Analysis of single molecule brightness allows subunit counting of high-order oligomeric biomolecular complexes. Although the theory behind the method has been extensively assessed, systematic analysis of the experimental conditions required to accurately quantify the stoichiometry of biological complexes remains challenging. In this work, we develop a high-throughput, automated computational pipeline for single molecule brightness analysis that requires minimal human input. We use this strategy to systematically quantify the accuracy of counting under a wide range of experimental conditions in simulated ground-truth data and then validate its use on experimentally obtained data. Our approach defines a set of conditions under which subunit counting by brightness analysis is designed to work optimally and helps establishing the experimental limits in quantifying the number of subunits in a complex of interest. Finally, we combine these features into a powerful, yet simple, software that can be easily used for the stoichiometry analysis of such complexes.


title: Re-introduction of endogenous pathways for propionyl-CoA, 1-propanol and propionate formation in Escherichia coli

abstract: In a previous study, we found that 2-ketobutyrate (2-KB) was seriously degraded in Escherichia coli. In the present investigation, we tried to clarify the products of that degradation process, and intriguingly reconfirmed that 2-KB is chopped up to form propionyl-CoA, 1-propanol and propionate. This short commentary re-introduces efficient endogenous pathways for production of value-added odd-chain compounds such as propionyl-CoA-derived chemicals.

category: synthetic biology


title: Estradiol and oxytocin modulate sex differences in hippocampal reactivity and episodic memory

abstract: Considerable evidence supports sex differences in episodic memory, which may translate to heightened vulnerability to stress- and trauma-related disorders in women. The hormones estradiol and oxytocin both affect episodic memory, but possible underlying hormonal interactions have not been systemically tested in humans. To this end, healthy women (n = 111) and men (n = 115) received estradiol gel (2 mg) or placebo before the administration of intranasal oxytocin (24 IU) or placebo in a randomized, placebo-controlled, parallel-group functional magnetic resonance imaging (fMRI) study. In the fMRI session, participants viewed positive, neutral, and negative scenes. A surprise recognition task was conducted three days later. Under placebo, women showed a significantly better recognition memory and increased hippocampal responses to subsequently remembered items independent of the emotional valence compared to men. The separate treatments with either hormone significantly diminished this mnemonic sex difference and reversed the hippocampal activation pattern. However, the combined treatments led to a memory performance comparable to that of the placebo group. Collectively, the results suggest that both hormones play a crucial role in modulating sex differences in episodic memory. Furthermore, possible antagonistic interactions between estradiol and oxytocin could explain previously observed opposing hormonal effects in women and men.


title: Exogenous estradiol and oxytocin modulate sex differences in hippocampal reactivity and episodic memory


title: Do naps benefit novel word learning? Developmental differences and white matter correlates

abstract: Behavioural and neuroimaging data suggest that memory representations of newly learned words undergo changes during nocturnal sleep, including improvements in explicit recall and lexical integration (i.e., after sleep, novel words compete with existing words during online word recognition). Some studies have revealed larger sleep-benefits in children relative to adults. However, whether daytime naps play a similar facilitatory role is unclear. We investigated the effect of a daytime nap (relative to wake) on explicit memory (recall/recognition) and lexical integration (lexical competition) of newly learned novel words in young adults and children aged 10-12 years, also exploring white matter correlates of the pre- and post-nap effects of word learning in the child group with diffusion weighted MRI. In both age groups, a nap maintained explicit memory of novel words and wake led to forgetting. However, there was an age group interaction when comparing change in recall over the nap: children showed a slight improvement whereas adults showed a slight decline. There was no evidence of lexical integration at any point. Although children spent proportionally more time in slow-wave sleep (SWS) than adults, neither SWS nor spindle parameters correlated with over-nap changes in word learning. For children, increased fractional anisotropy (FA) in the uncinate fasciculus and arcuate fasciculus were associated with the recognition of novel words immediately after learning, and FA in the right arcuate fasciculus was further associated with changes in recall of novel words over a nap, supporting the importance of these tracts in the word learning and consolidation process. These findings point to a protective role of naps in word learning, and emphasize the need to advance theories of word learning by better understanding both the active and passive roles that sleep plays in supporting vocabulary consolidation over development.


title: Multimodal Gradient Mapping of Rodent Hippocampus

abstract: The hippocampus plays a central role in supporting our coherent and enduring sense of self and our place in the world. Understanding its functional organisation is central to understanding this complex role. Previous studies suggest function varies along a long hippocampal axis, but there is disagreement about the presence of sharp discontinuities or gradual change along that axis. Other open questions relate to the underlying drivers of this variation and the conservation of organisational principles across species. Here, we delineate the primary organisational principles underlying patterns of hippocampal functional connectivity (FC) in the mouse using gradient analysis on resting state fMRI data. We further applied gradient analysis to mouse gene co-expression data to examine the relationship between variation in genomic anatomy and functional organisation. Two principal FC gradients along a hippocampal axis were revealed. The principal gradient exhibited a sharp discontinuity that divided the hippocampus into dorsal and ventral compartments. The second, more continuous, gradient followed the long axis of the ventral compartment. Dorsal regions were more strongly connected to areas involved in spatial navigation while ventral regions were more strongly connected to areas involved in emotion, recapitulating patterns seen in humans. In contrast, gene co-expression gradients showed a more segregated and discrete organisation. Our findings suggest that hippocampal functional organisation exhibits both sharp and gradual transitions and that hippocampal genomic anatomy exerts a subtle influence on this organisation.


title: Immunogenomic, single-cell and spatial dissection of CD8+T cell exhaustion reveals critical determinants of cancer immunotherapy

abstract: Tumoural-CD8+T cells exhibit exhausted or dysfunctional states. Contrary to immunotherapy-responsive exhausted-CD8+T cells, the clinical features of dysfunctional-CD8+T cells are disputed. Hence, we conducted large-scale multi-omics and multi-dimensional mapping of CD8+T cell-states across multiple cancer patient-cohorts. This identified tumour-specific continuum of CD8+T cell-states across 6 human cancers, partly imprinted by organ-specific immuno-modulatory niches. Herein, melanoma and glioblastoma enriched prototypical exhausted (CD8+TEXT) and severely-dysfunctional (CD8+TSDF) states, respectively. Contrary to CD8+TEXT, CD8+TSDF displayed transcriptomic and epigenetic effector/cytolytic dysfunctions, and dysregulated effector/memory single-cell trajectories, culminating into maladaptive prodeath stress and cell-cycle defects. Suboptimal antigen-priming underscored CD8+TSDF, which was distinct from immune-checkpoints "rich" CD8+TEXT, reflecting chronic antigen-stimulation. Continuum variation also existed on tumour spatial-level, with convergent (CD8+TEXT-supportive vascular regions) and divergent features (dysfunctional CD4+T::CD8+TSDFcell-to-cell interactions) between melanoma and glioblastoma. Globally, IFN{gamma}-IL2 disparities, paucity of intra-tumoural CD4+/CD8+T cells, and myeloid TGF{beta}/wound healing responses, distinguished CD8+TSDF-landscape. Within immuno-oncology clinical-trials, anti-PD1 immunotherapy failed to "reinvigorate" CD8+TSDF-landscape, and instead facilitated effector-dysfunction and TGF{beta}/wound healing. However, cellular immunotherapies (dendritic cell-vaccines, adoptive T-cell therapy) ameliorated assorted CD8+TSDF-landscape disparities, highlighting a roadmap for anti-glioblastoma multimodal-immunotherapy. Collectively, our study comprehensively expands clinical-knowledge on CD8+T cell-exhaustion and suggests that tumour-specific, pre-existing CD8+TEXT/TSDF-states, determine immunotherapy-responses.