title: Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome

abstract:
BackgroundAntimicrobial Resistance (AMR) has a detrimental impact on human health on Earth and it is equally concerning in other environments such as space due to microgravity, radiation and confinement, especially for long-distance space travel. The International Space Station (ISS) is ideal for investigating microbial diversity and virulence. The shotgun metagenomics data of the ISS generated during the Microbial Tracking - 1 (MT-1) project and resulting metagenome-assembled genomes (MAGs) across three flights in eight different locations during 12 months were used in this study. The objective of this study was to identify the AMR genes associated with whole genomes of 227 cultivable strains, 21 shotgun metagenome sequences, and 24 MAGs retrieved from the ISS environmental samples that were treated with propidium monoazide (PMA; viable microbes).

ResultsWe have analyzed the data using a deep learning model, allowing us to go beyond traditional cut-offs based only on high DNA sequence similarity and extending the catalog of AMR genes. Our results in PMA treated samples revealed AMR dominance in the last flight for Kalamiella piersonii, a bacteria related to urinary tract infection in humans. The analysis of 227 pure strains isolated from the MT-1 project revealed hundreds of antibiotic resistance genes from many isolates, including two top-ranking species that corresponded to strains of Enterobacter bugandensis and Bacillus cereus. Computational predictions were experimentally validated by antibiotic resistance profiles in these two species, showing a high degree of concordance. Specifically, disc assay data confirmed the high resistance of these two pathogens to various beta-lactam antibiotics.

ConclusionOverall, our computational predictions and validation analyses demonstrate the advantages of machine learning to uncover concealed AMR determinants in metagenomics datasets, expanding the understanding of the ISS environmental microbiomes and their pathogenic potential in humans.


title: Differential CO2-fixation potentials and supporting roles of phagotrophy and proton pump among plankton lineages in a subtropical marginal sea

abstract:
Lineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites of South China Sea to investigate carbon fixation in different lineages. We catalogued 4.4 million unique genes, [~]37% being annotatable and mainly involved in microbial metabolism, photosynthesis, amino acid synthesis, oxidative phosphorylation, and two-component systems. With RuBisCO expression as proxy, Calvin carbon fixation (CCF) was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, Haptophyta and non-diatom Stramenopiles, which was differentially affected by environmental factors among lineages. CCF exhibited positive or negative correlations with phagotrophy gene expression depending on lineages, suggesting phagotrophy enhances (Bacillariophyta, Haptophyta, and Chlorophyta) or complements (Dinophyta) CCF. Our data reveal significant potential of non-Calvin carbon fixation (NCF), mainly contributed by Flavobacteriales, Alteromonadales, Oceanospirillales and Rhodobacterales. Furthermore, in Flavobacteriales, Alteromonadales, Pelagibacterales and Rhodobacterales, NCF potential was positively correlated with proteorhodopsin expression, suggesting that NCF is energetically supported by proteorhodopsin. The novel insights into lineage-dependent potential of carbon fixation, widespread mixotrophy, and proteorhodopsin as energy source for NCF lay a methodological and informational foundation for further research to understand the carbon fixation and trophic landscape in the ocean.

ImportanceLineage-dependent physiologies are very important for understanding the contributions of different lineages to the biogeochemical processes in the oceanic plankton, but it is hardly possible using classical ecological methods. Even though metatranscriptomic methods have now been increasingly used to investigate physiologies of marine plankton, lineage-specific contribution to carbon fixation and phagotrophy has not received due research effort. Using whole-assemblage (prokaryotes + eukaryotes) plankton metatranscriptomic approach, with RNA quantity-based calibration to allow comparison across separately sequenced samples, this study reveals differential capacities of carbon fixation among lineages, widespread mixotrophy, and the potential of proteorhodopsin as energy source for non-photosynthetic carbon fixation. With these novel insights this study lays a methodological and informational foundation for further research to understand the carbon fixation and trophic landscape in the ocean.

category: bioinformatics


title: RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

abstract:
Inferring gene co-expression networks is a useful process for understanding gene regulation and pathway activity. The networks are usually undirected graphs where genes are represented as nodes and an edge represents a significant co-expression relationship. When gene-expression data from multiple conditions (e.g., treatments, tissues, strains) are available, joint estimation of networks harnessing shared information across them can significantly increase the power of analysis. In addition, examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. Condition adaptive fused graphical lasso (CFGL) is an existing method that incorporates condition specificity in a fused graphical lasso (FGL) model for estimating multiple co-expression networks. However, the current implementation of CFGL is prohibitively slow even for a moderate number of genes and can only be used for a maximum of three conditions. In this paper, we propose a fast alternative of CFGL known as rapid condition adaptive fused graphical lasso (RCFGL). In RCFGL, we incorporate the condition specificity into another popular model for joint network estimation, known as fused multiple graphical lasso (FMGL). We use a more efficient algorithm in the iterative steps compared to CFGL, enabling faster computation and making it easily generalizable for more than three conditions. We also present a novel screening rule to determine if the full network estimation problem can be broken down into estimation of smaller disjoint sub-networks, thereby reducing the complexity further. We demonstrate the computational advantage and superior performance of our method compared to two non-condition adaptive methods, FGL and FMGL, and one condition adaptive method, CFGL in several simulation scenarios. We use RCFGL to jointly estimate the gene co-expression networks of different brain regions (conditions) using a cohort of heterogeneous stock rats. We also provide an accommodating C and Python based package that implements RCFGL.

Author summaryInferring gene co-expression networks can be useful for understanding pathway activity and gene regulation. While jointly estimating co-expression networks of multiple conditions, taking into account condition specificity such as information about an edge being present only in a specific condition, substantially increases the power. In this paper, a computationally rapid condition adaptive method for jointly estimating gene co-expression networks of multiple conditions is proposed. The novelty of the method is demonstrated through a broad range of simulation studies and a real data analysis with multiple brain regions from a genetically diverse cohort of rats.


title: Identification of Catechins Binding Pockets in Monomeric Aβ42 Through Ensemble Docking and MD Simulations

abstract: The assembly of the Amyloid-{beta} peptide (A{beta}) into toxic oligomers and fibrils is associated with Alzheimers disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the A{beta} monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of A{beta}, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline - in the framework of the ensemble docking strategy - to identify catechins binding pockets in monomeric A{beta}42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to A{beta}42. Also, it has been found that all the studied ligands, especially the EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of the A{beta}. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against A{beta}.

category: biophysics


title: Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers

abstract: The growth of a tissue, which depends on cell-cell interactions and biologically relevant process such as cell division and apoptosis, is regulated by a mechanical feedback mechanism. We account for these effects in a minimal two-dimensional model in order to investigate the consequences of mechanical feedback, which is controlled by a critical pressure, pc. A cell can only grow and divide if the pressure it experiences, due to interaction with its neighbors, is less than pc. Because temperature is an irrelevant variable in the model, the cell dynamics is driven by self-generated active forces (SGAFs) that are created by cell division. It is shown that even in the absence of intercellular interactions, cells undergo diffusive behavior. The SGAF-driven diffusion is indistinguishable from the well-known dynamics of a free Brownian particle at a fixed finite temperature. When intercellular interactions are taken into account, we find persistent temporal correlations in the force-force autocorrelation function (FAF) that extends over timescale of several cell division times. The time-dependence of the FAF reveals memory effects, which increases as pc increases. The observed non-Markovian effects emerge due to the interplay of cell division and mechanical feedback, and is inherently a non-equilibrium phenomenon.


title: Conformational change in the monomeric alpha-synuclein imparts fibril polymorphs

abstract: -Synuclein inclusion bodies are a pathological hallmark of several neurodegenerative diseases. Although it has been hypothesized a relationship between fibril polymorphism and different pathologies, the molecular origins of polymorphism are not understood. Here, employing biophysical approaches, we demonstrate that the conformational state of the monomeric Syn is responsible for fibril polymorphism: Syn can exist as a compact monomer that produces rod fibrils, and as extended monomers that generate twisted fibrils. Using NMR, we found that the compaction relies on a polar interaction between the initial part of the NAC region and a wide section of the C-terminus domain. The compaction can be commonly affected by changes in the chemical environment, like NaCl, the presence of Ca2+ or cellular components, like endotoxins, that alter the interaction NAC/C-terminus domain. Our compaction model also provides mechanistic insights that explain how the behavior of the C-terminus domain imparts the polymorphism during the fibril formation.


title: GFAP-directed Inactivation of Men1 Exploits Glial Cell Plasticity in Favor of Neuroendocrine Reprogramming

abstract:
BACKGROUND & AIMSEfforts to characterize the signaling mechanisms that underlie gastroenteropancreatic neoplasms (GEP-NENs) are precluded by a lack of comprehensive model systems that recapitulate pathogenesis. Investigation into a potential cell-of-origin for gastrin-secreting NENs revealed a role for enteric glia in neuroendocrine cell specification. Here we investigated the hypothesis that loss of menin in glial cells stimulated neuroendocrine differentiation and tumorigenesis.

METHODSUsing Cre-lox technology, we generated a conditional glial fibrillary acidic protein-directed Men1 knockout (GFAP{Delta}Men1) mouse model. Cre specificity was confirmed using a tdTomato reporter. GFAP{Delta}Men1 mice were evaluated for GEP-NEN development and neuroendocrine cell hyperplasia. siRNA-mediated Men1 silencing in a rat enteric glial cell line was performed in parallel.

RESULTSGFAP{Delta}Men1 mice developed pancreatic NENs, in addition to pituitary prolactinomas that phenocopied the human MEN1 syndrome. GFAP{Delta}Men1 mice exhibited gastric neuroendocrine hyperplasia that coincided with a significant loss of GFAP expression. Mechanistically, Men1 deletion induced reprogramming from a mature glial phenotype toward a neuroendocrine lineage. Furthermore, blockade of Hedgehog signaling in enteric glia attenuated neuroendocrine hyperplasia by restricting the neuroendocrine cell fate.

CONCLUSIONSGFAP-directed Men1 inactivation exploits glial cell plasticity in favor of neuroendocrine differentiation.

GRAPHICAL ABSTRACT

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category: cancer biology


title: High-Field Asymmetric Waveform Ion Mobility Spectrometry and Parallel Reaction Monitoring Increases Sensitivity for Clinical Biomarker Quantitation from Formalin-Fixed, Paraffin-Embedded Tumor Biopsies

abstract: Mass spectrometry-based targeted proteomics allows objective protein quantitation of clinical biomarkers from a single section of formalin-fixed, paraffin-embedded (FFPE) tumor tissue biopsies. We combined high-field asymmetric waveform ion mobility spectrometry (FAIMS) and parallel reaction monitoring (PRM) to increase assay sensitivity. The modular nature of the FAIMS source allowed direct comparison of the performance of FAIMS-PRM to PRM. Limits of quantitation were determined by spiking synthetic peptides into a human spleen matrix. In addition, 20 clinical samples were analyzed using FAIMS-PRM and the quantitation of HER2 was compared with that obtained with the Ventana immunohistochemistry assay. FAIMS-PRM improved the overall signal-to-noise ratio over that from PRM and increased assay sensitivity in FFPE tissue analysis for four (HER2, EGFR, cMET, and KRAS) of five proteins of clinical interest. FAIMS-PRM enabled sensitive quantitation of basal HER2 expression in breast cancer samples classified as HER2 negative by immunohistochemistry. Furthermore, we determined the degree of FAIMS-dependent background reduction and showed that this correlated with an improved lower limit of quantitation with FAIMS. FAIMS-PRM is anticipated to benefit clinical trials in which multiple biomarker questions must be addressed and the availability of tumor biopsy samples is limited.


title: The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies


title: Functional Characterization of lncRNA152 as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers

abstract:
AO_SCPLOWBSTRACTC_SCPLOWLong non-coding RNAs have been implicated in many of the hallmarks of cancer. Herein, we found that the expression of lncRNA152 (lnc152; a.k.a. DRAIC), which we annotated previously, is highly upregulated in luminal breast cancer (LBC) and downregulated in triple-negative breast cancer (TNBC). Knockdown of lnc152 promotes cell migration and invasion in LBC cell lines. In contrast, ectopic expression of lnc152 inhibits growth, migration, invasion, and angiogenesis in TNBC cell lines. In mice, lnc152 inhibited the growth of TNBC cell xenografts, as well as metastasis of TNBC cells in an intracardiac injection model. Transcriptome analysis of the xenografts indicated that lnc152 downregulates genes controlling angiogenesis. Using pull down assays coupled with LC-MS/MS, we identified RBM47, a known tumor suppressor in breast cancer, as a lnc152-interacting protein. The effects of lnc152 in TNBC cells are mediated, in part, by regulating the expression of RBM47. Collectively, our results demonstrate that lnc152 is an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC.

SO_SCPLOWTATEMENTC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWOFC_SCPLOW SO_SCPLOWIGNIFICANCEC_SCPLOWThis study identifies lncRNA152 as an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC by upregulating the expression of the tumor suppressor RBM47. As such, lncRNA152 may serve as a biomarker to track aggressiveness of breast cancer, as well as therapeutic target for treating TNBC.


title: Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin

abstract: Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts. Notably, transcripts encoding highly-cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were ~2-fold more abundant in M. sativa than in M. officinalis, and ~27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly-cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.

category: plant biology


title: Rapid evaporative ionisation mass spectrometry (REIMS): A potential and rapid tool for the identification of insecticide resistance in mosquito larvae.

abstract: Insecticide resistance is a significant challenge facing the successful control of mosquito vectors globally. Bioassays are currently the only method for phenotyping resistance. They require large numbers of mosquitoes for testing, the availability of a susceptible comparator strain and often insectary facilities. This study aimed to trial the novel use of rapid evaporative ionisation mass spectrometry (REIMS) for the identification of insecticide resistance in mosquitoes. No sample preparation is required for REIMS and analysis can be rapidly conducted within hours. Temephos resistant Aedes aegypti (Linnaeus) larvae from Cucuta, Colombia and temephos susceptible larvae from two origins (Bello, Colombia, and the lab reference strain New Orleans) were analysed using REIMS. We tested the ability of REIMS to differentiate three relevant variants: population source, lab versus field origin and response to insecticide. The classification of these data was undertaken using linear discriminant analysis (LDA) and random forest. Classification models built using REIMS data were able to differentiate between Ae. aegypti larvae from different populations with 82% ({+/-} 0.01) accuracy, between mosquitoes of field and lab origin with 89% ({+/-} 0.01) accuracy and between susceptible and resistant larvae with 85% ({+/-} 0.01) accuracy. LDA classifiers had higher efficiency than random forest with this data set. The high accuracy observed here identifies REIMS as a potential new tool for rapid identification of resistance in mosquitoes. We argue that REIMS and similar modern phenotyping alternatives should complement existing insecticide resistance management tools.

category: systems biology


title: Effects of substrate on shrimp growth, water quality and bacterial community in the biofloc system nursing Penaeus vannamei postlarvae at a salinity of 5{per thousand}

abstract: This study aimed to investigate the effects of substrate on water quality, shrimp growth and bacterial community in the biofloc system with a salinity of 5{per thousand}. Two treatments, biofloc system with (sB) or without (nB) addition of elastic solid packing filler (nylon) as substrate, were set up. Penaeus vannamei postlarvae (PL, [~] stage 15) were stocked at a density of 4000 PL m-3 in each treatment with triplicates for a 28-days culture experiment, taking glucose as carbon source (C:N 15:1). Results showed that the survival rate (96.3{+/-}3.6%), FCR (0.76{+/-}0.06) and productivity (1.54{+/-}0.12 kg m-3) in sB treatment were significantly better than those in nB treatment (81.0{+/-}7.1%, 0.98{+/-}0.08 and 1.14{+/-}0.09 kg m-3, P<0.05). All water parameters were in the recommended ranges. Substrate showed significant effect on TAN, TSS, turbidity, biofloc volume, pH and carbonate alkalinity (P < 0.05). Actinobacteria (4.0-22.7%), Bacteroidetes (10.4-33.5%), Firmicutes (0.2-11.2%), Planctomycetes (4.0-14.9%) and Proteobacteria (29.4-59.0%) were the most dominant phyla for both treatments. However, the bacterial community in sB treatment showed to be significantly different from that in nB treatment (Jaccard distance 0.94{+/-}0.01, P=0.001). Substrate showed significant effects on Shannon, Heip, Pielou and Simpson index, as well as relative abundances of Actinobacteria, Bacteroidetes and Planctomycetes (P < 0.05). The results suggested that addition of substrate affected the shrimp growth, water quality and bacterial community in the biofloc system nursing P. vannamei PL with a 5{per thousand} salinity.

category: zoology


title: Effects of substrate on shrimp growth, water quality and bacterial community in the biofloc system nursing Penaeus vannamei postlarvae


title: Impacts of Spaceflight Experience on Human Brain Structure

abstract: Spaceflight induces widespread changes in human brain morphology. It is unclear if these brain changes differ with varying mission durations or ones history of spaceflight experience (e.g., number of prior missions, time between missions). Here we addressed this issue by quantifying voxelwise post-flight changes in gray matter volume, white matter microstructure, extracellular free water (FW), and ventricular volume in a sample of 28 astronauts. We found that longer missions induced greater ventricular expansion and larger FW displacement at the top of the brain. A greater number of prior missions was associated with white matter microstructure declines in a tract supporting voluntary leg movement. Longer inter-mission intervals were associated with greater ventricle expansion, with compensatory ventricular expansion observed only in those crewmembers with inter-missions intervals of 3 years or longer. Longer missions therefore induce more extensive brain fluid shifts, and the ventricles may require at least 3 years to recover post-flight.

category: neuroscience


title: Not all noise-reduction methods for fMRI preprocessing are created equal

abstract:
Preprocessing fMRI data requires striking a fine balance between conserving signals of interest and removing noise. Typical steps of preprocessing include motion correction, slice timing correction, spatial smoothing, and high-pass filtering. However, these standard steps do not remove many sources of noise. Thus, noise-reduction techniques such as CompCor and FIX have been developed to further improve the ability to draw meaningful conclusions from the data. The ability of these techniques to minimize noise while conserving signals of interest has been tested almost exclusively in resting-state fMRI datasets and, only rarely, in task-related fMRI datasets. Application of noise-reduction techniques to task-related fMRI is particularly important given that such procedures have been shown to reduce false positive rates. However, little remains known about the impact of different noise reduction techniques on the retention of signal, particularly during tasks that may be associated with systemic physiological changes. In this paper, we compared two noise-reduction techniques, i.e. FIX and CompCor, in an fMRI dataset including noxious heat stimulation and non-noxious auditory stimulation.

Results show that preprocessing including FIX noise-reduction technique conserves significantly more signal than a preprocessing protocol including CompCor noise-reduction technique in both noxious heat and non-noxious auditory stimulations, while removing only slightly less noise. These results suggest that FIX might be the most appropriate technique to achieve the balance between conserving signals of interest and removing noise.


title: Express detection and discrimination of visual objects by primate superior colliculus neurons

abstract: Primate superior colliculus (SC) neurons exhibit rich visual feature tuning properties and are implicated in a subcortical network hypothesized to mediate fast threat and/or conspecific detection. However, the mechanisms through which generalized object detection may be mediated by SC neurons remain unclear. Here we explored whether, and how quickly, SC neurons detect and discriminate real-life object stimuli. We presented experimentally-controlled gray-scale images of seven different object categories within the response fields (RFs) of SC neurons, and we also presented a variety of luminance- and spectral-matched image controls. We found that all of our functionally-identified SC neuron types preferentially detected real-life objects even in their very first stimulus-evoked visual bursts (starting within approximately 50 ms from image onset). Intriguingly, even visually-responsive motor-related neurons exhibited such robust early object detection, and they also preferentially discriminated between object categories in their initial visual bursts. We further identified spatial frequency information in visual images as a critical source for early object detection and discrimination by SC neurons. Our results demonstrate rapid and robust SC processing of visual objects, and they underline how the visual processing capabilities of the primate SC support perception and action.


title: Single-cell multi-region dissection of brain vasculature in Alzheimer's Disease

abstract: Cerebrovascular breakdown occurs early in Alzheimers Disease (AD), but its cell-type-specific molecular basis remains uncharacterized. Here, we characterize single-cell transcriptomic differences in human cerebrovasculature across 220 AD and 208 control individuals and across 6 brain regions. We annotate 22,514 cerebrovascular cells in 11 subtypes of endothelial, pericyte, smooth muscle, perivascular fibroblast, and ependymal cells, and how they differ in abundance and gene expression between brain regions. We identify 2,676 AD-differential genes, including lower expression of PDGFRB in pericytes, and ABCB1 and ATP10A in endothelial cells. These AD-differential genes reveal common upstream regulators, including MECOM, EP300, and KLF4, whose targeting may help restore vasculature function. We find coordinated vasculature-glial-neuronal co-expressed gene modules supported by ligand-receptor pairs, involved in axon growth/degeneration and neurogenesis, suggesting mechanistic mediators of neurovascular unit dysregulation in AD. Integration with AD genetics reveals 125 AD-differential genes directly linked to AD-associated genetic variants (through vasculature-specific eQTLs, Hi-C, and correlation-based evidence), 559 targeted by AD-associated regulators, and 661 targeted by AD-associated ligand-receptor signaling. Lastly, we show that APOE4-genotype associated differences are significantly enriched among AD-associated genes in capillary and venule endothelial cells, and subsets of pericytes and fibroblasts, which underlie the vascular dysregulation in APOE4-associated cognitive decline. Overall, our multi-region molecular atlas of differential human cerebrovasculature genes and pathways in AD can help guide early-stage AD therapeutics.


title: Task-dependent and automatic tracking of hierarchical linguistic structure

abstract: Linguistic phrases are tracked in sentences even though there is no clear acoustic phrasal marker in the physical signal. This phenomenon suggests an automatic tracking of abstract linguistic structure that is endogenously generated by the brain. However, all studies investigating linguistic tracking compare conditions where either relevant information at linguistic timescales is available, or where this information is absent altogether (e.g., sentences versus word lists during passive listening). It is therefore unclear whether tracking at these phrasal timescales is related to the content of language, or rather, is a consequence of attending to the timescales that happen to match behaviourally-relevant information. To investigate this question, we presented participants with sentences and word lists while recording their brain activity with MEG. Participants performed passive, syllable, word, and word-combination tasks corresponding to attending to rates they would naturally attend to, syllable-rates, word-rates, and phrasal-rates, respectively. We replicated overall findings of stronger phrasal-rate tracking measured with mutual information (MI) for sentences compared to word lists across the classical language network. However, in the inferior frontal gyrus (IFG) we found a task-effect suggesting stronger phrasal-rate tracking during the word-combination task independent of the presence of linguistic structure, as well as stronger delta-band connectivity during this task. These results suggest that extracting linguistic information at phrasal-rates occurs automatically with or without the presence of an additional task, but also that that IFG might be important for temporal integration across various perceptual domains.


title: Direct Modulation Index: a measure of phase amplitude coupling for neurophysiology data

abstract:
Neural communication across different spatial and temporal scales is a topic of great interest in clinical and basic science. Phase-amplitude coupling (PAC) has attracted particular interest due to its functional role in a wide range of cognitive and motor functions. Here, we introduce a novel measure termed the direct modulation index (dMI). Based on the classical modulation index, dMI provides an estimate of PAC that is bound to an absolute interval between 0 and +1, resistant against noise, and reliable even for small amounts of data. To highlight the properties of this newly-proposed measure, we evaluated dMI by comparing it to the classical modulation index, mean vector length, and phase-locking value using simulated data. We ascertained that dMI provides a more accurate estimate of PAC than the existing methods and that is resilient to varying noise levels and signal lengths. As such, dMI permits a reliable investigation of PAC, which may reveal insights crucial to our understanding of functional brain architecture in key contexts such as behaviour and cognition. A Python toolbox that implements dMI and other measures of PAC is freely available at https://github.com/neurophysiological-analysis/FiNN.

Highlights- Neural coupling measures are sensitive to higher harmonics of the target oscillation.
- dMI achieves frequency-specificity by sine-fitting the phase-amplitude histogram.
- Increased robustness to noise and signal duration in comparison to other measures.
- dMI allows for reliable estimation of phase-amplitude coupling.


title: Brain aging differs with cognitive ability regardless of education

abstract: Higher general cognitive ability (GCA) is associated with lower risk of neurodegenerative disorders, but neural mechanisms are unknown. GCA could be associated with more cortical tissue, from young age, i.e. brain reserve, or less cortical atrophy in adulthood, i.e. brain maintenance. Controlling for education, we investigated the relative association of GCA with reserve and maintenance of cortical volume, -area and -thickness through the adult lifespan, using multiple longitudinal brain imaging cohorts (n = 3327, 7002 MRI scans, baseline age 20-88 years, followed-up up to 11 years). There were widespread positive relationships between GCA and cortical characteristics (level-level associations). In select regions, higher baseline GCA was associated with less atrophy over time (level-change associations). Relationships remained when controlling for polygenic scores for both GCA and education. Our findings suggest that higher GCA is associated with cortical volumes by both brain reserve and -maintenance mechanisms through the adult lifespan.


title: CD36 homologs determine microbial resistance to the Lyme disease spirochete

abstract:
Pattern recognition receptors sense pathogens in arthropods and mammals through distinct immune processes. Whether these molecules share a similar function and recognize the same microbe in evolutionarily distant species remain ill-defined. Here, we establish that the CD36 superfamily is required for Borrelia burgdorferi resistance in both the arthropod vector and humans. Using the blacklegged tick Ixodes scapularis and an electronic health record-linked biobank, we demonstrate that CD36 members elicit immunity to the Lyme disease spirochete. In ticks, the CD36-like protein Croquemort recognizes lipids and initiates the immune deficiency and jun N-terminal kinase pathways against B. burgdorferi. In humans, exome sequencing and clinical information reveal that individuals with CD36 loss-of-function variants have increased prevalence of Lyme disease. Altogether, we discovered a conserved mechanism of anti-bacterial immunity.

One Sentence SummaryLipid receptors belonging to the CD36 superfamily exhibit a shared immune function in both ticks and humans.

category: immunology


title: The Composition of Diesel Fuel Influences the Structure of Microbiological Assemblages in Contaminated Fuel Storage Tanks

abstract:
Microbiological contamination in diesel storage tanks is widespread and under-reported. The contaminating microorganisms can degrade components of the fuel, which contributes to fouling and corrosion. To better understand the connection between the microorganisms that are responsible for this contamination, the composition of affected fuels, and the resulting impact on fuel quality, we conducted a survey of 106 fuel tanks at 17 military bases across the continental United States. Fuel was sampled from each tank and the resident microbial communities were characterized using high throughput sequencing of small subunit ribosomal RNA gene libraries. Fatty acid methyl esters (FAME) and n-alkanes were characterized and quantified using GC-MS to determine their correlation with the presence of microbial taxa. Redundancy Analyses identified which microbial taxa were more prominent in contaminated fuels. Members of the fungal family Trichomaceae were found to be prominent in fuels containing more FAME. Members of the yeast family Debaryomycetaceae were found to be prominent in fuels containing more pentadecanoic and oleic acid methyl esters. These relationships between fungal taxa and fuel components were directly tested in growth experiments with representative isolates of the Trichocomaceae (Paecilomyces AF001) and Debaryomycetaceae (Wickerhamomyces SE3) families. Paecilomyces was capable of growth on linoleic acid methyl ester but unable to grow on pentadecanoic acid methyl ester, while Wickerhamomyces was able to grow on both substrates. Fuel composition may provide some insight into which microorganisms can proliferate but other factors like competition and symbiosis may also drive microbial proliferation, fouling, degradation, and corrosion in diesel fuels.

ImportanceBiodiesel, widely used as an additive or extender of ultra-low sulfur diesel, can increase the potential for microorganisms to proliferate in storage tanks. It is important to know how the composition of diesel fuels can influence the growth of organisms linked to fuel degradation and microbiologically influenced corrosion. This research describes how certain populations of fungi and bacteria can prevail in fuels of different composition, which can be helpful in predicting biodegradation and biocorrosion, and formulating fuels less susceptible to the growth of problematic organisms.

category: microbiology


title: Parallel Expansion and Divergence of the Hyr/Iff-like (Hil) Adhesin Family in Pathogenic Yeasts Including Candida auris

abstract: Opportunistic yeast pathogens evolved multiple times in the Saccharomycetes class. A recent example is Candida auris, a multidrug resistant pathogen associated with a high mortality rate and multiple hospital outbreaks. Genomic changes shared between independently evolved pathogens could reveal key factors that enable them to infect the host. One such change may be the expansion of cell wall adhesins, which mediate biofilm formation and adherence and are established virulence factors in Candida spp. Here we show that homologs of a known adhesin family in C. albicans, the Hyr/Iff-like (Hil) family, repeatedly expanded in divergent pathogenic Candida lineages including in C. auris. Evolutionary analyses reveal varying levels of selective constraint and a potential role of positive selection acting on the ligand-binding domain during the family expansion in C. auris. The repeat-rich central domain evolved rapidly after gene duplication, leading to large variation in protein length and {beta}-aggregation potential, both known to directly affect adhesive functions. Within C. auris, isolates from the less virulent Clade II lost five of the eight Hil homologs, while other clades show abundant tandem repeat copy number variation. We hypothesize that expansion and diversification of adhesin gene families are a key step towards the evolution of fungal pathogens and that variation in the adhesin repertoire could contribute to within and between species differences in the adhesive and virulence properties.


title: Actin remodelling controls proteasome homeostasis upon stress

abstract: When cells are stressed, bulk translation is often downregulated to reduce energy demands whilst stress-response proteins are simultaneously upregulated. 19S Regulatory Particle Assembly-Chaperones (RPACs) are selectively translated upon TORC1 inhibition to promote proteasome assembly and activity, maintaining cell viability. However, the molecular mechanism for such selective translational upregulation is unclear. Using yeast, we discover that remodelling of the actin cytoskeleton is important for RPAC translation following TORC1 inhibition. mRNA of the RPAC ADC17 travels along actin cables and is enriched at cortical actin patches under stress, dependent upon the early endocytic protein Ede1. ede1{Delta} cells failed to induce RPACs and proteasome assembly upon TORC1 inhibition. Conversely, artificially tethering ADC17 mRNA to cortical actin patches enhanced its translation upon stress. These findings suggest that actin dense structures such as cortical actin patches may serve as a translation platform for a subset of stress-induced mRNAs including regulators of proteasome homeostasis.

category: cell biology


title: Selective effects of a short transient environmental fluctuation on a natural population

abstract: Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short-term response to a sudden environmental change has in several cases been attributed to polygenic traits, but the underlying genomic dynamics and architecture are poorly understood. In this study, took advantage of a natural experiment in an insect population by monitoring genome-wide allele frequencies before and after a cold snap event. Whole genome pooled sequencing of time series samples revealed ten selected haplotypes carrying ancient polymorphisms, partially with signatures of balancing selection. By constantly cold exposing genetically variable individuals in the laboratory, we could demonstrate with whole genome resequencing i) among the survivors, the same alleles rose in frequency as in the wild and ii) that the identified variants additively predicted fitness (survival time) of its bearers. Finally, by simultaneously sequencing the genome and the transcriptome of cold exposed individuals we could tentatively link some of the selected SNPs to the cis- and trans-regulation of genes and pathways known to be involved in cold response of insects, like Cytochrome P450 and fatty acid metabolism. Altogether, our results shed light on the strength and speed of selection in natural populations and the genomic architecture of its underlying polygenic trait. Population genomic time series data thus appear as promising tool for measuring the selective tracking of fluctuating selection in natural populations.

category: evolutionary biology


title: Chimeric Inheritance and Crown-Group Acquisitions of Carbon Fixation Genes within Chlorobiales

abstract: The geological record of microbial metabolisms and ecologies primarily consists of stable isotope fractionations and the diagenetic products of biogenic lipids. Carotenoid lipid biomarkers are particularly useful proxies for reconstructing this record, providing information on microbial phototroph primary productivity, redox couples, and oxygenation. The biomarkers okenane, chlorobactane, and isorenieratene are generally considered to be evidence of anoxygenic phototrophs, and provide a record that extends to [~]1.64 Ga. The utility of the carotenoid biomarker record may be enhanced by examining the carbon isotopic ratios in these products, which are diagnostic for specific pathways of biological carbon fixation found today within different microbial groups. However, this joint inference assumes that microbes have conserved these pathways across the duration of the preserved biomarker record. Testing this hypothesis, we performed phylogenetic analyses of the enzymes constituting the reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of anoxygenic phototrophic bacteria usually implicated in the deposition of chlorobactane and isorenieretane. We find phylogenetically incongruent patterns of inheritance across all enzymes, indicative of horizontal gene transfers to both stem and crown Chlorobiales from multiple potential donor lineages. This indicates that a complete rTCA cycle was independently acquired at least twice within Chlorobiales and was not present in the last common ancestor. When combined with recent molecular clock analyses, these results predict that the Mesoproterzoic lipid biomarker record diagnostic for Chlorobiales should not preserve isotopic fractionations indicative of a full rTCA cycle. Furthermore, we conclude that coupling isotopic and biomarker records is insufficient for reliably reconstructing microbial paleoecologies in the absence of a complementary and consistent phylogenomic narrative.


title: Global determinants of the distribution of insect genetic diversity

abstract: Understanding global patterns of genetic diversity (GD) is essential to describe, monitor, and preserve the processes giving rise to life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrate groups that comprise a small fraction of Earths biodiversity. Here, we construct the first global map of predicted insect genetic diversity. We calculate the global distribution of GD mean (GDM) and evenness (GDE) of insect assemblages, identify the global environmental correlates of insect GD, and make predictions for undersampled regions. Based on the largest and most species-rich single-locus genetic dataset assembled to date, we find that both GD metrics follow a bimodal latitudinal gradient, where GDM and GDE correlate with contemporary climate variation. Our models explain 1/4 and 1/3 of the observed variation in GDM and GDE in insects, respectively, making an important step towards describing global biodiversity patterns in the most diverse animal taxon.


title: The interplay between developmental stage and environment determines the adaptive effect of a natural transposable element insertion

abstract:
Establishing causal links between adaptive mutations and their ecologically relevant phenotypes is key to understanding adaptation, a central goal in evolutionary biology. Although progress has been made, the number of causal adaptive mutations identified so far is still limited as gene by gene, and gene by environment interactions, among others, complicates linking genetic variation with its fitness-related effects. Transposable elements, often ignored in the quest for the genetic basis of adaptive evolution, are known to be a genome-wide source of regulatory elements across organisms that at times can lead to adaptive phenotypes. In this work, we combine gene expression, in vivo reporter assays, CRISPR/Cas9 genome editing and survival experiments to characterize in detail the molecular and phenotypic consequences of a natural Drosophila melanogaster transposable element insertion: the roo solo-LTR FBti0019985. This transposable element provides an alternative promoter to the transcription factor Lime, involved in cold- and immune-stress responses, and acts as an enhancer in response to immune-stress. We found that the effect of FBti0019985 on Lime expression depends on the interplay between the developmental stage and the environmental conditions. We further establish a causal link between the presence of FBti0019985 and increased survival to cold- and immune-stress. Our results exemplify how several developmental stages and environmental conditions need to be considered to characterize the molecular and functional effects of a genetic variant, and add to the growing body of evidence that transposable elements can induce complex mutations with ecologically relevant effects.

SIGNIFICANT STATEMENTTransposable elements (TEs) are repetitive DNA sequences with the ability to move along the genome. TEs are a genome-wide source of regulatory elements capable of regulating the expression of nearby genes. TEs can act as enhancers in specific tissues or developmental stages, and can also regulate the expression of nearby genes depending on the environmental context. In this work, we characterize a natural TE insertion whose effects on the expression of its nearby gene depends on the interplay between the developmental stage and the environmental conditions. A precise deletion of this TE insertion in natural populations using the CRISPR/Cas9 editing tool further proves that the insertion is the causal mutation leading to increased survival to cold- and immune-stress.


title: Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes

abstract: Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture -- once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization.

category: genetics


title: High sorbic acid resistance of Penicillium roqueforti is mediated by the SORBUS gene cluster

abstract:
Penicillium roqueforti is a major food-spoilage fungus known for its high resistance to the food preservative sorbic acid. Here, we demonstrate that the minimum inhibitory concentration of undissociated sorbic acid (MICu) ranges between 4.2 and 21.2 mM when 34 P. roqueforti strains were grown on malt extract broth. A genome-wide association study revealed that the six most resistant strains contained the 180 kbp gene cluster SORBUS, which was absent in the other 28 strains. In addition, a SNP analysis revealed five genes outside the SORBUS cluster that may be linked to sorbic acid resistance. A partial SORBUS knock-out (>100 of 180 kbp) in a resistant strain reduced sorbic acid resistance to similar levels as observed in the sensitive strains. Whole genome transcriptome analysis revealed a small set of genes present in both resistant and sensitive P. roqueforti strains that were differentially expressed in the presence of the weak acid. These genes could explain why P. roqueforti is more resistant to sorbic acid when compared to other fungi, even in the absence of the SORBUS cluster. Together, the MICu of 21.2 mM makes P. roqueforti among the most sorbic acid-resistant fungi, if not the most resistant fungus, which is mediated by the SORBUS gene cluster.

Author summaryChemical preservatives, such as sorbic acid, are often used in food to prevent spoilage by fungi, yet some fungi are particularly well-suited to deal with these preservatives. First, we investigated the resistance of 34 Penicillium roqueforti strains to various food preservatives. This revealed that some strains were highly resistant to sorbic acid, while others are more sensitive. Next, we used DNA sequencing to compare the genetic variation between these strains and discovered a specific genetic region (SORBUS) that is unique to the resistant strains. Through comparative analysis with other fungal species the SORBUS region was studied in more detail and with the use of genetic engineering tools we removed this unique region. Finally, the mutant lacking the SORBUS region was confirmed to have lost its sorbic acid resistance. This finding is of particular interest as it suggests that only some, not all, P. roqueforti strains are potent spoilers and that specific genetic markers could help in the identification of resistant strains.

category: genomics


title: A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

abstract:
Using adult zebrafish inner ears as a model for sensorineural regeneration, we performed a targeted ablation of the mechanosensory receptors in the utricle and saccule and characterized the single-cell epigenome and transcriptome at consecutive time-points following hair cell ablation. Using deep learning on the regeneration-induced open chromatin sequences, we were able to identify unique, cell-specific transcription factor (TF) motif patterns enriched in the raw data. We correlated enhancer activity with gene expression to identify gene regulatory networks. A clear pattern of overlapping Sox- and Six-family transcription factor gene expression and binding motifs was detected, suggesting a combinatorial program of TFs driving regeneration and cell identity. Pseudo-time analysis of single-cell transcriptomic data demonstrated that the support cells within the sensory epithelium changed cell identity to a more pluripotent "progenitor" cell population that could either differentiate into hair cells or return to a support cell identity. We showed that sox2 becomes enriched in the progenitor cells and is reduced again when the cells differentiate in either direction. Analysis of the scATAC-seq data identified a 2.6 kb DNA sequence element upstream of the sox2 promoter that dynamically changed in accessibility during hair cell regeneration. When deleted, the upstream regulator of sox2 showed a dominant phenotype that resulted in a hair cell regeneration-specific deficit in both the lateral line and adult inner ear.

HIGHLIGHTSIntegrated scRNA-seq and scATAC-seq of the adult zebrafish inner ear during hair cell regeneration.
Support cells transition to an intermediate cell type that can differentiate to hair cells. Coordinated expression of Sox and Six transcription factors are key to hearing regeneration.
Sox transcription factors trigger the regeneration response in the support cells while Sox and Six factors cooperate during hair cell differentiation.
Deletion of an upstream enhancer that controls the timing of sox2 expression causes regeneration-specific defects in hearing regeneration.


title: Multinuclear MRI reveals early efficacy of stem cell therapy in stroke

abstract: Compromised adult human mesenchymal stem cells (hMSC) can impair cell therapy efficacy and further reverse ischemic recovery. However, in vitro assays require extended passage to characterize cells, limiting rapid assessment for therapeutic potency. Multinuclear magnetic resonance imaging and spectroscopy (MRI/S) provides near real-time feedback on disease progression and tissue recovery. Applied to ischemic stroke, 23Na MRI evaluates treatment efficacy within 24 h after middle cerebral artery occlusion, showing recovery of sodium homeostasis and lesion reduction in specimens treated with hMSC while 1H MRS identifies reduction in lactate levels. This combined metric was confirmed by evaluating treatment groups receiving healthy or compromised hMSC versus control (sham saline injection) over 21 d. Behavioral tests to assess functional recovery and cell analysis for immunomodulatory and macrophage activity to detect hMSC potency confirm MR findings. Clinically, these MR metrics may prove critical to early evaluations of therapeutic efficacy and overall stroke recovery.

category: bioengineering


title: An evaluation of RNA-seq differential analysis methods

abstract:
RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A fundamental research question in most RNA-seq experiments is the identification of differentially expressed genes among experimental conditions or sample groups. Numerous statistical methods for RNA-seq differential analysis have been proposed since the emergence of the RNA-seq assay.

To evaluate popular differential analysis methods used in the open source R and Bioconductor packages, we conducted multiple simulation studies to compare the performance of eight RNA-seq differential analysis methods used in RNA-seq data analysis (edgeR, DESeq, DESeq2, baySeq, EBSeq, NOISeq, SAMSeq, Voom). The comparisons were across different scenarios with either equal or unequal library sizes, different distribution assumptions and sample sizes. We measured performance using false discovery rate (FDR) control, power, and stability. No significant differences were observed for FDR control, power, or stability across methods, whether with equal or unequal library sizes. For RNA-seq count data with negative binomial distribution, when sample size is 3 in each group, EBSeq performed better than the other methods as indicated by FDR control, power, and stability. When sample sizes increase to 6 or 12 in each group, DESeq2 performed slightly better than other methods. All methods have improved performance when sample size increases to 12 in each group except DESeq. For RNA-seq count data with log-normal distribution, both DESeq and DESeq2 methods performed better than other methods in terms of FDR control, power, and stability across all sample sizes. Real RNA-seq experimental data were also used to compare the total number of discoveries and stability of discoveries for each method.

For RNA-seq data analysis, the EBSeq method is recommended for studies with sample size as small as 3 in each group, and the DESeq2 method is recommended for sample size of 6 or higher in each group when the data follow the negative binomial distribution. Both DESeq and DESeq2 methods are recommended when the data follow the log-normal distribution.


title: The guardian of the genome meets a viral master gene regulator at a biomolecular condensate

abstract: As guardian of the genome, p53 exerts its tumor suppressor activity by modulating the expression of several hundreds of genes and by interacting with a large number of proteins. However, p53 can also repress viral replication and it is targeted by a variety of viral proteins to allow viral replication to proceed. p53 can repress human papillomavirus replication by binding to the viral E2 master gene regulator. Here we show how full-length p53 can spontaneously form phase separated liquid-like droplets that evolve to amyloid-like aggregates in a time-dependent manner, highlighting the fact that homotypic condensation is on the path to aggregation as observed in several protein aggregopathies. The DNA binding domain of HPV E2 (E2C) triggers heterotypic liquid-liquid phase separation with p53 with a precise 1 p53 : 2 E2C stoichiometry at the onset for demixing, yielding large regular spherical droplets that increase in size with E2C concentration. Moreover, E2C is able to slowly reshape time-evolved p53 aggregates into regular heterotypic liquid droplets. Using in situ sub-cellular fractionation, we show that E2 and wild-type p53 co-localize to the nucleus with a grainy pattern, and E2 can re-localize p53 into chromatin associated foci, a function independent of the DNA binding capacity of p53. A small DNA duplex containing the specific binding site for p53 deforms and dissolves both homotypic and heterotypic condensates at a 1 p53 : 1 DNA stoichiometry, whereas a [~]1000 base pair DNA fragment instead reshaped the condensates into distinct amorphous condensates containing p53, E2C and DNA, reminiscent of what we observe bound to chromatin. We conclude that p53 is a scaffold for liquid-liquid phase separation in line with its structural and functional features, in particular as a hub that binds multiple cellular protein partners as well as nucleic acids. Moreover, the capacity of E2C to rescue p53 from the amyloid aggregation route impacts on p53-rescuing drugs cancers where p53 mutation leads to loss of function.


title: Adipose cells and tissues soften with lipid accumulation while in diabetes adipose tissue stiffens

abstract: Adipose tissue expansion involves both differentiation of new precursors and size increase of mature adipocytes. While the two processes are well balanced in healthy tissues, obesity and diabetes type II are associated with abnormally enlarged adipocytes and excess lipid accumulation. We hypothesised that adipocyte shape and size changes with differentiation and lipid accumulation would be accompanied by changes in the mechanical phenotype at both the cell and tissue level. We quantified by optical diffraction tomography (ODT) that differentiating preadipocytes increased their volumes drastically. Atomic force microscopy (AFM)-indentation and -microrheology revealed that during the early phase of differentiation, human preadipocytes became more compliant and more fluid-like, concomitant with ROCK-mediated F-actin remodelling. Adipocytes that had accumulated large lipid droplets were more compliant, and further promoting lipid accumulation led to an even more compliant phenotype. In line with that, high fat diet-induced obesity was associated with more compliant adipose tissue compared to lean animals, both for drosophila fat bodies and murine gonadal adipose tissue. In contrast, adipose tissue of diabetic mice became significantly stiffer as shown not only by AFM but also magnetic resonance elastography (MRE). Altogether, we dissect relative contributions of the cytoskeleton and lipid droplets to cell and tissue mechanical changes across different functional states, such as differentiation, nutritional state and disease. Since preadipocytes are mechanosensitive, tissue stiffening in diabetes might be critical to the balance between hyperplasia and hypertrophy and moreover present a potential target in the prevention of metabolic disorders.


title: Single-cell molecular characterization to partition the human glioblastoma tumor microenvironment (TME) genetic background

abstract: Glioblastoma (GB) is a devastating primary brain malignancy. Recurrence of GB is inevitable despite the standard treatment of surgery, chemotherapy, and radiation, and the median survival is limited to around 15 months. Barriers to treatment include the complex interactions among the different cellular components inhabitant of the tumor microenvironment. These challenges are further compounded by extensive inter- and intra-tumor heterogeneity and by the dynamic plasticity of GB cells. The complex heterogeneous nature of GB cells is helped by the local inflammatory tumor microenvironment, which mostly induces tumor aggressiveness and drug resistance. More effective therapy development heavily depends on higher resolution molecular subtype signatures. All cellular components of a GB tumor are subjected to a continuous pressure inducing proliferation that might favor the accumulation of genetic mutations. Understanding the genetic background of several cellular component s belonging to a GB microenvironment could give insights into tumor behavior and progression. In the present study by using fluorescent multiple labeling and DEPArray cell separator, we recovered several single cells or groups of single cells from populations of different origins from IDH-WT GB samples. From each GB sample, we collected astrocytes (GFAP+), microglia (IBA+), stem cells (CD133+), and endothelial cells (CD105+) and performed Copy Number Aberration (CNA) analysis with a low sequencing depth. The same tumors were subjected to a bulk CNA analysis. The tumor partition in its single components allowed single-cell molecular subtyping which revealed new aspects of GB altered genetic background. Nowadays, single-cell approaches are leading to a new understanding of GB physiology and disease. Moreover, single-cell CNAs resource will permit new insights into genome heterogeneity, mutational processes, and clonal evolution in malignant tissues.


title: A new immunocompetent rectal cancer model to study radiation therapy

abstract: We describe a new mouse model of rectal cancer (RC) involving rapid tumor organoid engraftment via orthotopic transplantation; the resulting RC tumors invaded inward from the mucosal surface and metastasized to distant organs. Histologically the tumors closely resemble human RC and mirror remodeling of the tumor microenvirnoment (TME) in response to radiation. This murine RC model thus recapitulates the pathogenesis of human RC, thereby fulfilling the need for a physiologically accurate model for preclinical efficacy studies.


title: Recapitulation of Human Pathophysiology and Identification of Forensic Biomarkers in a Translational Swine Model of Chlorine Inhalation Injury

abstract:
RationaleChlorine gas (Cl2) has been repeatedly used as a chemical weapon, first in World War I and most recently in Syria. Life-threatening Cl2 exposures frequently occur in domestic and occupational environments, and in transportation accidents. There is a knowledge gap in large animal models of Cl2-induced acute lung injury (ALI) required to accurately model human etiology and for the development of targeted countermeasures

ObjectiveTo develop a translational model of Cl2-induced ALI in swine to study toxico-pathophysiology and identify biomarkers useful for forensic analysis.

MethodsSpecific pathogen-free Yorkshire swine (30-40 kg) of either sex were exposed to Cl2 gas ([≤] 240 ppm for 1 h) or filtered air under anesthesia and controlled mechanical ventilation.

ResultsExposure to Cl2 resulted in severe hypoxia and hypoxemia, increased airway resistance and peak inspiratory pressure, and decreased dynamic lung compliance. Chlorine exposure resulted in increased total BALF and neutrophil counts, vascular leakage, and edema compared to the control group. The model recapitulated all three key histopathological features of human ALI, such as neutrophilic alveolitis, deposition of hyaline membranes, and formation of microthrombi. Free and lipid-bound 2-chlorofatty acids and chlorotyrosine-modified proteins (3-chloro-L-tyrosine and 3,5-dichloro-L-tyrosine) were detected in plasma and lung after Cl2-exposure.

ConclusionsThe translational model developed in this study replicates key features of humans exposed to Cl2 and is suitable to test medical countermeasures. Specific biomarkers of Cl2 exposure have been identified in plasma and lung tissue samples.

Take home messageWe developed a swine model of chlorine gas-induced acute lung injury that exhibits several features of human acute respiratory distress syndrome. We validated chlorinated fatty acids and protein adducts in plasma and lung samples as forensic biomarkers.

category: pharmacology and toxicology


title: The dynamics of non-photochemical quenching and cyclic electron transport in A.thaliana exposed to harmonically oscillating light

abstract:
Plants are often exposed in nature to light fluctuations with characteristic periods of several seconds to minutes. Photosynthetically active irradiance fluctuates typically in the range of several hundreds of mol(photons){middle dot}m- 2{middle dot}s-1. The photosynthetic regulatory networks that are necessary for minimizing damage by the dynamic load between redox reactions in fluctuating light are poorly understood. Arbitrary light fluctuations can be represented by a sum of harmonic oscillations and, to resolve the elemental components of any complex light patterns, we aimed at characterizing photosynthetic reactions in light that oscillated as an elemental sinus function. Chlorophyll fluorescence yield and optical transmission proxies of P700, plastocyanin, and ferredoxin were measured in Arabidopsis thaliana under oscillating light of various frequencies and amplitudes. The role of non-photochemical quenching (NPQ) and of cyclic electron transport around Photosystem I (CET) was studied by comparing the dynamics in wild-type plants with mutants that were deficient in NPQ (npq1 and npq4) or CET (crr2-2 and pgrl1ab).

The study revealed a highly contrasting response in the mutants compared to wild type documenting relevance of non-photochemical quenching and cyclic electron transport for the functioning of plants in a dynamic light environment. The mutants deficient in the non-photochemical quenching constituents exhibited forced oscillations of much higher amplitude than those found in the wild types. The contrast was used to identify the range of frequencies (f < 1/60s) in which the non-photochemical quenching was highly effective. The frequency-domain analysis revealed complex resonance behaviors with the 1/30 s-1 and 1/60 s-1 frequencies that were absent in the npq4 mutant and reduced in the npq1 mutant. This contrast suggests an anomalous dynamic behavior of thylakoid acidification and PsbS-dependent feedback downregulation of Photosystem II light-harvesting at these frequencies.

The mutants incapacitated in the cyclic electron transport exhibited a distinct dynamic response. The crr2-2 mutant lacks the activity of photosynthetic NADH dehydrogenase-like complex and typically exhibits wild-type-like induction during a dark-light transition and differs in the light-to-dark relaxation in the time domain. It showed a distinct dynamic signature in oscillating light that involved both rising and declining light phases. The pgrl1ab mutant exhibited a contrasting anomalous response to oscillating light, particularly in the redox reactions involving plastocyanin, P700, and ferredoxin. These findings thus suggest a crucial role of cyclic electron transport in the dynamic properties and regulation of the plants in fluctuating irradiance.

The finding of contrasting frequency-dependent modes may explain the existence of multiple, seemingly redundant regulatory mechanisms, each presumably protecting the plant in a different frequency range. The study moreover documented that the harmonically oscillating light can serve, in addition to identifying the photosynthetic dynamics in natural fluctuating light, for revealing unique dynamic features in mutants, and, likely, for sensing plant stress. Furthermore, the sensing by harmonic forcing does not require dark-acclimation and may, thus, conveniently monitor the status of photosynthesis of plants in phenotyping platforms, in greenhouses, and in-field.

One sentence summaryOscillations in Chl fluorescence and redox states of plastocyanin, P700, and ferredoxin in A.thaliana induced by sinusoidal light reveal at least two distinct types of dynamic responses that depend on the non-photochemical quenching and cyclic electron transport.


title: Crowdsourced EEG Experiments: A proof of concept for remote EEG acquisition using EmotivPRO Builder and EmotivLABS

abstract: Online research platforms have enabled mass data collection enabling representative samples for cognitive behavioural studies. However, the benefits of online data collection have not been available for cognitive neuroscience fields such as electroencephalography (EEG). In this study, we introduce an approach for remote EEG data collection. We demonstrate how an experiment can be built via the EmotivPRO Builder and deployed to the EmotivLABS website where it can be completed by participants who own EMOTIV EEG headsets. To demonstrate the data collection technique, we collected EEG while participants engaged in a resting state task where participants sat with their eyes open and then eyes closed for two minutes each. We observed a significant difference in alpha power between the two conditions thereby demonstrating the well-known alpha suppression effect. Thus, we demonstrate that EEG data collection, particularly for frequency domain analysis, can be successfully conducted online with remote users.


title: A large-scale computational model to accurately predict early brain activity in response to written words

abstract: To better understand the computational steps that the brain performs during reading, we used a convolutional neural network as a computational model of visual word recognition, the first stage of reading. In contrast to traditional models of reading, our model directly operates on the pixel values of an image containing text, and has a large vocabulary of 10k Finnish words. The same stimuli can thus be presented unmodified to both the model and human volunteers in a magnetoencephalography (MEG) scanner. In a direct comparison between model and brain activity, we show that the model accurately predicts the amplitude of three evoked MEG response components commonly observed during reading. We conclude that the deep learning techniques that revolutionized models of object recognition can also create models of reading that can be straightforwardly compared to neuroimaging data, which will greatly facilitate testing and refining theories on language processing in the brain.


title: Inhibitory NPY neurons provide a large and heterotopic commissural projection in the inferior colliculus

abstract: Located in the midbrain, the inferior colliculus (IC) plays an essential role in many auditory computations, including speech processing and sound localization. The right and left side of the IC are interconnected by a dense fiber tract, the commissure of the IC (CoIC), that provides each IC with one its largest sources of input (i.e., the contralateral IC). Despite its prominence, the CoIC remains poorly understood. Previous studies using anterograde and retrograde tract-tracing showed that IC commissural projections are predominately homotopic and tonotopic, targeting mirror-image locations in the same frequency region in the contralateral IC. However, it is unknown whether specific classes of neurons, particularly inhibitory neurons which constitute [~]10-40% of the commissural projection, follow this pattern. We therefore examined the commissural projections of Neuropeptide Y (NPY) neurons, the first molecularly identifiable class of GABAergic neurons in the IC. Using retrograde tracing with Retrobeads in NPY-hrGFP mice of both sexes, we found that NPY neurons comprise [~]11% of the commissural projection. Moreover, focal injections of Retrobeads showed that NPY neurons in the central nucleus of the IC exhibit a more divergent and heterotopic commissural projection pattern than non-NPY neurons. Thus, commissural NPY neurons are positioned to provide cross-frequency, lateral inhibition to the contralateral IC. Through this circuit, sounds that drive activity in limited frequency bands on one side of the IC might suppress activity across a larger number of frequency bands in the contralateral IC.


title: CD8 memory precursor cells generation is a continuous process

abstract: In this work, we studied the generation of memory precursor cells following an acute infection by analyzing single-cell RNA-seq data that contained CD8 T cells collected during the postinfection expansion phase. We used different tools to reconstruct the developmental trajectory that CD8 T cells followed after activation. Cells that exhibited a memory precursor signature were identified and positioned on this trajectory. We found that memory precursors are generated continuously with increasing numbers being generated over time. Similarly, expression of genes associated with effector functions was also found to be raised in memory precursors at later time points. The ability of cells to enter quiescence to differentiate into memory cells was confirmed by BrdU pulse-chase experiment in vivo. Analysis of cell counts indicates that the vast majority of memory cells are generated at later time points from cells that have extensively divided.


title: Rose flavor compound β-damascone regulates dendritic cell-mediated immunoresponses by modulating the NRF2 pathway and ameliorates contact hypersensitivity

abstract: Numerous pharmacologically beneficial compounds have been isolated from natural products derived from plants, which are often characterized as phytochemicals and are used in flavors, spices, and fragrances. Here we show that {beta}-damascone, a major ingredient of rose fragrance, was selected from an aroma library as a candidate compound that suppresses antigen-dependent T cell activation. {beta}-Damascone inhibited dendritic cell (DC)-related responses, including DC-induced Th1 development, TLR ligand-induced production of inflammatory cytokines in DCs. {beta}-Damascone treatment increased the levels of NRF2 protein and Hmox1 mRNA in DCs. Nrf2-/- DCs possessed Th1-induction activity and higher IL-12p40 production activity even in the presence of {beta}-damascone in comparison with Nrf2+/- DCs. Finally, we found that {beta}-damascone intake suppressed ear swelling of contact hypersensitivity model mice. Taken together, we conclude that the rose aroma compound {beta}-damascone, which suppresses DC-mediated immunoresponses by activating the NRF2 pathway, could be useful to ameliorate immunorelated diseases.


title: Linear DNA amplicons as a novel cancer vaccine strategy

abstract: DNA-based vaccines represent a simple, safe and promising strategy for harnessing the immune system to fight infectious diseases as well as various forms of cancer and thus are considered an important tool in the cancer immunotherapy toolbox. Nonetheless, the manufacture of plasmid DNA vaccines has several drawbacks, including long lead times and the need to remove impurities from bacterial cultures. Here we report the development of polymerase chain reaction (PCR)-produced amplicon expression vectors as DNA vaccines and their in vivo application to elicit antigen-specific immune responses in animal cancer models. Amplicons encoding tumor-associated-antigens, such as telomerase reverse transcriptase or neoantigens expressed by murine tumor cell lines were able to elicit antigen-specific immune responses and proved to significantly impact tumor growth when administered in combination with immune-checkpoint inhibitors (ICIs). These results strongly support the further exploration of the use of PCR-based amplicons as an innovative immunotherapeutic approach to cancer treatment.


title: The Role of Notch Signaling in Endometrial Mesenchymal Stromal/Stem-like Cells Maintenance

abstract: Human endometrium undergoes cycles of regeneration in reproductive women. The endometrial mesenchymal stromal/stem cells (eMSC) contribute to this process. Notch signaling is essential for the homeostasis of somatic stem cells. However, its role in eMSC remains unclear. The gain and loss function shows that activation of Notch signaling promotes eMSC maintenance, while inhibition displays opposite effect. Activation of Notch pathway better maintains eMSC in a quiescent state. However, these quiescent eMSC can re-enter into the cell cycle depending on Notch and Wnt activity in the microenvironment, suggesting a crosstalk between two signaling pathways. In a mouse menstrual-like model, we observe that Notch signaling is highly involved in the dynamic endometrial remodeling event. Suppression of Notch signaling significantly reduces the proliferation of Notch1+ label-retaining stromal cells and consequently delays the endometrial repair. Our data demonstrate the importance of Notch signaling in regulating the endometrial stem/progenitor cells in vitro and in vivo.


title: Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean

abstract: Microbial assemblages under sea ice of Dease Strait, Canadian Arctic, were sequenced for metagenomes and metatranscriptomes of the small size fraction (0.2 to 3 {micro}m). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Towards summer, Bacteroidetes and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. Likely, this cheating ability of the Bacteroidetes contributed to their dominance in summer.

category: ecology


title: Protecting seabed sediment carbon for climate mitigation: a UK case study

abstract:
Protecting areas of seabed sediment would appear to be an important climate mitigation strategy, however carbon has not been considered in national management plans. Using spatial analyses we show, in the UK Exclusive Economic Zone (EEZ), high potential organic carbon loss due to mobile bottom fishing is likely to be geographically restricted. Currently designated seabed marine protected areas (MPAs) cover 32.9% of the EEZ, 30.0% of carbon stocks, but only 12.9% of fishing disturbance. If all MPAs were closed to mobile bottom fishing, we estimate a prevention of only 6.9% of potential organic carbon losses due to fishing disturbance across the EEZ. In contrast, areas identified as having largest climate change mitigation potential cover just 16.5% of the EEZ, contain 24.7% of OC stocks and closing these areas to mobile fishing could save 29.6% of potential carbon losses. We must re-evaluate current seabed management plans and incorporate evidence-based carbon considerations.

TeaserRestrictions on bottom trawling and dredging outside of MPA networks may be necessary to derive a climate mitigation benefit.


title: A simulation study of the ecological speciation conditions in the Galician marine snail Littorina saxatilis

abstract:
In the last years the interest on evolutionary divergence at small spatial scales has increased and so did the study of speciation caused by ecologically-based divergent natural selection. The evolutionary interplay between gene flow and local adaptation can lead to low-dispersal locally adapted specialists. When this occurs the evolutionary interplay between gene flow and local adaptation could eventually lead to speciation.

The L. saxatilis system consists of two ecotypes displaying a microhabitat-associated intraspecific dimorphism along the wave-exposed rocky shores of Galicia. In spite of being a well-known system, the dynamics of the ecotype formation remains unclear and cannot be studied from empirical evidence alone. In this study, individual-based simulations were used to incorporate relevant ecological, spatial and genetic information, to check different evolutionary scenarios that could evolve non-random mating preferences and finally may facilitate speciation.

As main results, we observed the evolution of intermediate values of choice which matches estimates from empirical data of L. saxatilis in Galician shores and coincides with previous theoretical outcomes. Also, the use of the mating correlation as a proxy for assortative mating led to spuriously inferring greater reproductive isolation in the middle habitat than in the others, which does not happen when directly considering the choice values from the simulations. We also corroborate the well-known fact that the occurrence of speciation is influenced by the strength of selection. Taken together, this means, also according to other L. saxatilis systems, that speciation is not an immediate consequence of local divergent selection and mating preferences, but a fine tuning among several factors including the ecological conditions in the shore levels, the selection strength, the mate choice stringency and cost to choosiness. The L. saxatilis system could correspond to a case of incomplete reproductive isolation, where choice intensity is intermediate and local adaptation within the habitat is strong. These results support previous interpretations of the L. saxatilis model system and indicate that further empirical studies would be interesting to test whether the mate choice mechanism functions as a similarity-like mechanism as has been shown in other littorinids.


title: Evidence for RNA or protein transport from somatic tissues to the male reproductive tract in mouse

abstract: The development of tools to manipulate the mouse genome, including knockout and transgenic technology, revolutionized our ability to explore gene function in mammals. Moreover, for genes that are expressed in multiple tissues or at multiple stages of development, the use of tissue-specific expression of the Cre recombinase allows gene function to be perturbed in specific cell types and/or at specific times. However, it is well known that putative tissue-specific promoters often drive unanticipated "off target" expression. In our efforts to explore the biology of the male reproductive tract, we unexpectedly found that expression of Cre in the central nervous system resulted in recombination in the epididymis, a tissue where sperm mature for ~1-2 weeks following the completion of testicular development. Remarkably, we not only observed reporter expression in the epididymis when Cre expression was driven from neuron-specific transgenes, but also when Cre expression in the brain was induced from an AAV vector carrying a Cre expression construct. A surprisingly wide range of Cre drivers - including six different neuronal promoters as well as the adipose-specific AdipoQ Cre promoter - exhibited off target recombination in the epididymis, with a subset of drivers also exhibiting unexpected activity in other tissues such as the reproductive accessory glands. Finally, using a combination of parabiosis and serum transfer experiments, we find evidence supporting the hypothesis that Cre may be trafficked from its cell of origin to the epididymis through the circulatory system. Together, our findings should motivate extreme caution when interpreting conditional alleles, and suggest the exciting possibility of inter-tissue RNA or protein trafficking in modulation of reproductive biology.


title: iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects

abstract: Single-cell RNA sequencing (scRNA-seq) enables assessment of transcriptome-wide changes at single-cell resolution. However, dominant subject effect in scRNA-seq datasets with multiple subjects severely confounds cell-type-specific differential expression (DE) analysis. We developed iDESC to separate subject effect from disease effect with consideration of dropouts to identify DE genes. iDESC was shown to have well-controlled type I error and high power compared to existing methods and obtained the best consistency between datasets and disease relevance in two scRNA-seq datasets from same disease, suggesting the importance of considering subject effect and dropouts in the DE analysis of scRNA-seq data with multiple subjects.


title: A Novel congenic Mouse Model to study Obesity, Diabetes and NAFLD

abstract: The genetic background of the mutant mouse strain plays an important role in disease development. We investigated whether Lepr mutation on different genetic background (WSB/EiJ) influences the development of obesity, diabetes and non-alcoholic fatty liver diseases (NAFLD). For this study heterozygote (db/+) mice were backcrossed with WSB/EiJ strain (that is resistant to obesity and NAFLD) for more than 10 generations and intercrossed for five generations having Lepr mutated gene incorporated in WSB/EiJ background. The newly derived congenic strain was assessed and related with the B6.db strain and WSB/EiJ strain for the development of obesity, diabetes and NAFLD. The Lepr mutated congenic strain on the WSB/EiJ background gained significant body weight and showed other characteristic features of obesity. However, the incidence of diabetes, NAFLD, and other kidney complications were not observed in this strain. The novel congenic mouse strain having Lepr gene on WSB/EiJ background would be a promising model for the study of obesity without diabetes and NAFLD and will also help to understand the various mechanisms involved in the development diabetes and NAFLD.

category: physiology


title: Inducible Nitric Oxide Synthase deficiency leads to early demyelination by altering the balance between pro- and anti-inflammatory responses against Murine-β-Coronavirus

abstract:
The neurological disease Multiple sclerosis (MS) is characterized by neuroinflammation and demyelination orchestrated by the activated glial cells, the CNS infiltrating leukocytes, and their reciprocal interaction through inflammatory signals. Inducible nitric oxide synthase (iNOS), an enzyme that catalyzes sustained nitric oxide production in response to an inflammatory stimulus, is a pro-inflammatory marker expressed particularly by the microglia/macrophages (MG/M{varphi}) during neuroinflammation. In MS, iNOS has been reportedly associated with the disease pathology; however, studies dissecting its role in the underlying mechanisms, specifically demyelination, are limited. Therefore, we studied the role of iNOS in a recombinant beta-coronavirus-MHV-RSA59-induced neuroinflammation, which is a prototypic animal model used to investigate the pathological hallmarks of MS, neuroinflammatory demyelination, and axonal degeneration. During the acute phase of infection with RSA59, wildtype C57BL/6 (WT) mice had significantly upregulated iNOS expression in macrophages, natural killer cells, and natural killer T cells suggesting a role for iNOS in RSA59-induced neuroinflammation. Studies comparing RSA59-infected WT and iNOS-deficient mice revealed that iNOS deficiency aggravated the disease with increased CNS infiltration of macrophages and neutrophils and enhanced mortality. As early as 9-10 days after the infection, the CNS of iNOS-deficient mice had substantially higher demyelination marked with morphologically defined MG/M{varphi} in the demyelinating regions. Transcript analysis confirmed the significant upregulation of type2 macrophage (M2) markers-Arginase 1, CD206, and TREM2-in the CNS of iNOS-deficient mice. Corroborating to the phenotype, the iNOS-deficient mice showed a significantly higher expression of TGF{beta}-an anti-inflammatory cytokine- and increased T regulatory (Treg) cell infiltration, indicating an anti-inflammatory milieu established early after the infection. These observations highlight a protective role of iNOS in virus-induced neuroinflammation whereas its absence leads to MG/M{varphi} polarization towards a phenotype that may be involved in the exacerbated demyelination pathology.

Author summaryContrary to the reported pathogenic role of inducible nitric oxide synthase (iNOS) in multiple sclerosis and related autoimmune animal models, we show that the mice deficient in iNOS show an exacerbated disease with accelerated demyelination accompanied by heightened production of an anti-inflammatory and phagocytic markers and more numbers of Tregs in a mouse model of a recombinant mouse hepatitis virus RSA59 infection. Therefore, iNOS may play protective and regulatory roles in this beta-coronavirus infection.


title: An automated pipeline for extracting quantitative histological metrics for voxelwise MRI-histology comparisons

abstract: The acquisition of MRI and histology in the same post-mortem tissue sample enables direct correlation between MRI and histologically-derived parameters. However, there still lacks a standardised automated pipeline to process histology data, with most studies relying on heavy manual intervention. Here, we introduce an automated pipeline to extract quantitative histology metrics (stained area fraction) from multiple immunohistochemical (IHC) stains. The pipeline is designed to directly address key IHC artefacts related to tissue staining and slide digitisation. This pipeline was applied to post-mortem human brain data from multiple subjects, relating MRI parameters (FA, MD, R2*, R1) to IHC slides stained for myelin, neurofilaments, microglia and activated microglia. Utilising high-quality MRI-IHC co-registrations, we then performed whole-slide voxelwise comparisons (simple correlation, partial correlation and multiple regression analyses) between multimodal MRI- and IHC-derived parameters. The pipeline was found to be reproducible, robust to some artefacts and generalisable across multiple IHC stains. Our partial correlation results suggest that some simple MRI-IHC correlations should be interpreted with caution, due to the colocalisation of certain tissue features (e.g. myelin and neurofilaments). Further, we find activated microglia to consistently be the strongest predictor of DTI FA, which may suggest sensitivity of diffusion MRI to neuroinflammation. Taken together, these results show the utility of this approach in carefully curating IHC data and performing multimodal analyses to better understand microstructural relationships with MRI.


title: A single dose of the catecholamine precursor Tyrosine reduces physiological arousal and decreases decision thresholds in reinforcement learning and temporal discounting

abstract: Supplementation with the catecholamine precursor L-Tyrosine might enhance cognitive performance, but overall findings are mixed. Here, we investigate the effect of a single dose of tyrosine (2g) vs. placebo on two key aspects of catecholamine-dependent decision-making: model-based reinforcement learning (2-step task) and temporal discounting, using a double-blind, placebo-controlled, within-subject design (n=28 healthy male participants). We leveraged drift diffusion models in a hierarchical Bayesian framework to jointly model participants choices and response times in both tasks. Furthermore, comprehensive autonomic monitoring (heart rate, heart rate variability, pupillometry, spontaneous eye-blink rate) was performed both pre- and post-supplementation, to explore potential physiological effects of supplementation. Across tasks, tyrosine consistently reduced participants RTs without deteriorating task-performance. Diffusion modeling linked this effect to attenuated decision-thresholds in both tasks and further revealed increased model-based control (2-step task) and (if anything) attenuated temporal discounting. On the physiological level, participants pupil dilation was predictive of the individual degree of temporal discounting. Tyrosine supplementation reduced physiological arousal as revealed by increases in pupil dilation variability and reductions in hear rate. Supplementation-related changes in physiological arousal predicted individual changes in temporal discounting. Our findings provide first evidence that tyrosine supplementation might impact psychophysiological parameters, and suggest that modeling approaches based on sequential sampling models can yield novel insights into latent cognitive processes modulated by amino-acid supplementation.


title: Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis

abstract: Autoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. Although this inflammation is often limited to specific target tissues, it remains yet to be explored whether distinct affected sites are infiltrated with the same, persistent T cell clones. Here we performed CyTOF analysis and T cell receptor (TCR) sequencing to study immune cell composition and (hyper-)expansion of circulating and joint-derived Tregs and non-Tregs in Juvenile Idiopathic Arthritis (JIA). We studied different joints affected at the same time, as well as over the course of relapsing-remitting disease. We found that the composition and functional characteristics of immune infiltrates are strikingly similar between joints within one patient, and observed a strong overlap between dominant T cell clones, especially Treg, of which some could also be detected in circulation and persisted over the course of relapsing remitting disease. Moreover, these T cell clones were characterized by a high degree of sequence similarity, indicating the presence of TCR clusters responding to the same antigens. These data suggest that in localized autoimmune disease there is auto-antigen driven expansion of both Teffector and Treg clones, that are highly persistent and are (re)circulating. These dominant clones might represent interesting therapeutic targets.


title: Staphylococcus aureus nt5 gene contributes to bacterial infection ability to form kidney abscess

abstract: Staphylococcus aureus (S. aureus) is a commonly conditional infection pathogen, in which several key virulence genes are responsible for bacterial infection ability. The S. aureus nt5 gene, encoding 5-nucleotidase, mediates bacterial nucleic acid pathway, yet it is nearly unknown of nt5 function for staphylococcal infection ability. Herein we have constructed S. aureus mutant with the gene nt5C166T silence (S. aureus {Delta}nt5) by a CRISPR RNA-guided base editing system to investigate bacterial infection ability in vitro and in vivo. As expected, several nt5-related genes are disturbed in S. aureus {Delta}nt5, in which gene transcription level of py is decreased compared with the wild-type S. aureus. Bacterial gene nt5 is downregulated and py/adk are upregulated when S. aureus is exposed to antibiotics daptomycin, which indicates nt5-mediated nucleic acid pathway is interfered upon with daptomycin treatment. Furthermore, the mutant {Delta}nt5 displays about a 40-fold reduction of bacterial loading in mouse kidney on a mouse sepsis model, and the infection ability of {Delta}nt5 is reduced than the wild-type bacteria. The gene nt5 contributes to S. aureus-infected abscess formation in mouse kidney, and the silence of nt5 gene promotes phagocytosis of S. aureus by mouse and human immunocytes. In general, our findings reveal nt5 silence impedes bacterial loading in kidney to form abscess but enhances S. aureus to be phagocytosed by host cell immune system in vitro and in vivo, which indicates that nt5 gene plays an important role in bacterial infection and immune evasion.


title: Nutrient-dependent regulation of β-cell KATP channels is controlled by the isoforms of pyruvate kinase and the source of phosphoenolpyruvate

abstract: Insulin release from pancreatic {beta}-cells is triggered by the metabolism-dependent closure of ATP-sensitive K+ (KATP) channels. Here, we used isoform-specific deletion of pyruvate kinase (PK) to identify the unique roles of PKm1 and PKm2 in the {beta}-cell nutrient response. In the absence of PK activity, cytosolic ATP/ADP was insufficient to close KATP channels. Both PK isoforms were found on the plasma membrane, where they endow KATP channels with nutrient sensitivity and specificity. Although PKm1 accounts for >90% of cellular activity, PKm2 controls glucosedependent KATP closure. Amino acids, which generate mitochondrial phosphoenolpyruvate (PEP) without allosterically activating PKm2, depend on PKm1 to raise ATP/ADP and close KATP channels. Shifting the {beta}-cell from PKm2 to PKm1 correspondingly increased amino acid sensitivity and boosted secretory output. In addition to these membrane depolarizing "on-switches," {beta}-cell deletion of PCK2 exposed a mitochondrial PEP-dependent "off-switch" that facilitates Ca2+ extrusion. Restricting PCK2 prolonged Ca2+ influx and increased insulin secretion. In summary, it is not the KATP channel alone, but the PK-KATP microcompartment that confers nutrient sensitivity to the {beta}-cell plasma membrane. The differential response of the PK isoforms to the glycolytic and mitochondrial sources of PEP influences {beta}-cell nutrient preference, and controls the oscillatory cycle regulating insulin secretion.


title: The isoforms of pyruvate kinase act as nutrient sensors for the β-cell KATP channel