title: Injectable hydrogels with phase-separated structures that can encapsulate live cells

abstract: Injectable hydrogels are biomaterials that can be administered minimally invasively in liquid form, and are considered promising artificial extracellular matrix (ECM) materials. However, ordinary injectable hydrogels are synthesized from water-soluble molecules to ensure injectability, resulting in nonphase-separated structures, making them structurally different from natural ECMs with phase-separated insoluble structural proteins, such as collagen and elastin. Here, we propose a simple material design approach to impart phase-separated structures to injectable hydrogels by adding inorganic salts. Injecting a gelling solution of mutually crosslinkable tetra-arm poly(ethylene glycol)s with potassium sulfate at optimal concentrations results in the formation of a hydrogel with phase-separated structures in situ. These phase-separated structures provide up to an 8-fold increase in fracture toughness while allowing the encapsulation of live mouse chondrogenic cells without compromising their proliferative activity. Our findings highlight that the concentration of inorganic salts is an important design parameter in injectable hydrogels for artificial ECMs.


title: QSMRim-Net: Imbalance-Aware Learning for Identification of Chronic Active Multiple Sclerosis Lesions on Quantitative Susceptibility Maps

abstract:
Background and PurposeChronic active multiple sclerosis (MS) lesions are characterized by a paramagnetic rim at the edge of the lesion and are associated with increased disability in patients. Quantitative susceptibility mapping (QSM) is an MRI technique that is sensitive to chronic active lesions, termed rim+ lesions on the QSM. We present QSMRim-Net, a data imbalance-aware deep neural network that fuses lesion-level radiomic and convolutional image features for automated identification of rim+ lesions on QSM.

MethodsQSM and T2-weighted-Fluid-Attenuated Inversion Recovery (T2-FLAIR) MRI of the brain were collected at 3T for 172 MS patients. Rim+ lesions were manually annotated by two human experts, followed by consensus from a third expert, for a total of 177 rim+ and 3986 rim negative (rim-) lesions. Our automated rim+ detection algorithm, QSMRim-Net, consists of a two-branch feature extraction network and a synthetic minority oversampling network to classify rim+ lesions. The first network branch is for image feature extraction from the QSM and T2-FLAIR, and the second network branch is a fully connected network for QSM lesion-level radiomic feature extraction. The oversampling network is designed to increase classification performance with imbalanced data.

ResultsOn a lesion-level, in a five-fold cross validation framework, the proposed QSMRim-Net detected rim+ lesions with a partial area under the receiver operating characteristic curve (pROC AUC) of 0.760, where clinically relevant false positive rates of less than 0.1 were considered. The method attained an area under the precision recall curve (PR AUC) of 0.704. QSMRim-Net out-performed other state-of-the-art methods applied to the QSM on both pROC AUC and PR AUC. On a subject-level, comparing the predicted rim+ lesion count and the human expert annotated count, QSMRim-Net achieved the lowest mean square error of 0.98 and the highest correlation of 0.89 (95% CI: 0.86, 0.92).

ConclusionThis study develops a novel automated deep neural network for rim+ MS lesion identification using T2-FLAIR and QSM images.

category: bioinformatics


title: CRISPR-based multi-locus real-time tracking reveals single chromosome dynamics and compaction

abstract: In eukaryotic nuclei, individual chromosomes occupy discrete three-dimensional spaces with little overlap. Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin anchoring to nuclear landmarks often leads to massive reorganization and motion changes. Chromatin dynamics has been reported to be locally confined but contributes to the large-scale coherent chromatin motion across the entire nucleus. However, the dynamics and compaction of chromosomal sub-regions along a single chromosome are not well-understood. In this study, we combined quantitative real-time single-molecule fluorescence microscopy, CRISPR-based genomic labeling, biophysical analysis and polymer models to characterize the dynamics of specific genomic loci and chromatin-nuclear landmark interactions on human chromosome 19 in living cells. Precise genomic labeling allows us to dissect loci motions and chromatin elasticity on a single chromosome basis. We found that the dynamics of genomic loci were all subdiffusive but varied at different regions along the chromosome. The mobility of genomic loci was similar among interior chromosomal loci but deviated for the loci at pericentromeric and near-telomeric regions. Tighter compaction on chromosome 19 long arm, compared to the short arm was observed, which may correlate to more active genes on the short arm than the long arm, shown by our RNA-seq analysis. The strong tethering interaction was found for loci at the pericentromeric region, suggesting a higher degree of local condensation, perhaps through stronger interactions or association between pericentromeric regions and their microenvironments, such as chromatin-nuclear body association through sequence-specific domains on DNA.

category: biophysics


title: Selective inhibitors of JAK1 targeting a subtype-restricted allosteric cysteine

abstract: The JAK family of non-receptor tyrosine kinases includes four subtypes (JAK1, JAK2, JAK3, and TYK2) and is responsible for signal transduction downstream of diverse cytokine receptors. JAK inhibitors have emerged as important therapies for immuno(onc)ological disorders, but their use is limited by undesirable side effects presumed to arise from poor subtype selectivity, a common challenge for inhibitors targeting the ATP-binding pocket of kinases. Here, we describe the chemical proteomic discovery of a druggable allosteric cysteine present in the non-catalytic pseudokinase domain of JAK1 (C817) and TYK2 (C838), but absent from JAK2 or JAK3. Electrophilic compounds selectively engaging this site block JAK1-dependent transphosphorylation and cytokine signaling, while appearing to act largely as "silent" ligands for TYK2. Importantly, the allosteric JAK1 inhibitors do not impair JAK2-dependent cytokine signaling and are inactive in cells expressing a C817A JAK1 mutant. Our findings thus reveal an allosteric approach for inhibiting JAK1 with unprecedented subtype selectivity.

category: pharmacology and toxicology


title: The effect of treatment of auxin producing bacterial culture supernatant in combination with organic and inorganic fertilizers

abstract: Bacteria that secret plant growth promoting substances are good candidate for field application to improve crop yield. Especially, bacteria that excrete auxin can enhance root growth and settlement of crops to help adapting new soil environment when transplanted. In this study, we applied culture supernatant of an auxin producing bacteria Ignatzschineria sp. CG20001. The bacterial culture supernatant (BCS) was applied in combination with chicken manure and liquid chemical fertilizer. The treatment of bacterial culture supernatant enhanced growth of red kohlrabi, Brassica oleraceae var. gongyloides, especially in combination with chicken manure. To understand mechanisms related higher growth, we compared photosynthetic efficiency by measuring chlorophyll fluorescence and light harvesting antenna pigments composition. The performance index PS II was higher in BCS treated plants, and recovered faster after leaf harvest. Photoprotective mechanism was also increased in BCS treated plants, however, and DTT infiltration, non-photochemical quenching (NPQ) reduced to similar level, implying higher xanthophyll cycle dependent NPQ induction mechanism in BCS treated plants. However, in liquid chemical fertilized plants, BCS treated and non-treated plants showed the opposite pattern in the change of NPQ. The chlorophyll a/b ratio was highest in no-fertilized non-treated control, and lowest in chicken manure and BCS combination, implying impact of nutrition availability between the two groups. Through these results, we conclude that the appropriate combination of organic fertilizer and plant growth promoting bacterial metabolite can improve plant growth more than chemical fertilizers. This study also provides physiological understanding for strategic fertilization regime of organic fertilizer and biofertilizer combination.

category: plant biology


title: Deep proteome analysis of plasma reveals novel biomarkers of mild cognitive impairment and Alzheimer's disease: A longitudinal study

abstract: Ageing is the primary risk factor for AD; however, there is a poor understanding of the biological mechanisms by which the ageing process contributes to the development of AD in some individuals, while others progress to advanced age with relatively little AD neuropathology. To halt the progression of AD, the preclinical stage of neurodegeneration (before the onset of clinical symptoms) is anticipated to be the more effective time point for applying potentially disease-modifying interventions in AD. The main objective of this study was to understand the age and disease related proteomic changes are detectable in plasma, based on retrospective analysis of longitudinal data and cross-sectional analyses of clinically diagnosed cases. We conducted an in-depth plasma proteomics analysis using intensive depletion of high-abundant plasma proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 14 (Hu14) followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE) technique. In this study, we have begun to address the following questions; (1) differences in plasma proteomic profiles between normal ageing, vs ageing with progress to cognitive decline (MCI) or disease (dementia, probable AD), (2) cross-sectional analysis of baseline data, when all subjects are clinically identified as cognitively normal, provides insight into the preclinical changes which precede subsequent progression to AD and potentially provide early biomarkers, and (3) comparison of plasma at the point of progression to clinically diagnosed onset of cognitive decline or AD, can provide potential plasma biomarkers to facilitate clinical diagnosis. Furthermore, our findings also identified some proteins previously discovered in AD CSF and brain proteomics signatures that could provide clinically meaningful information. We identified differentially expressed proteins which were associated with several biological and molecular processes that may serve as therapeutic targets and fluid biomarkers for the disease.

category: neuroscience


title: New efficient intercellular spread mode of respiratory syncytial virus contributes to neutralization escape and persistence

abstract: There is no licensed vaccine or therapeutic antibody for respiratory syncytial virus (RSV). The induction of high-titer, potent neutralizing antibodies cannot completely inhibit breakthrough infection and enhanced respiratory disease (ERD), encouraging a focus on the relationship between virus intercellular spread and neutralizing antibodies. By blocking the known intercellular spread modes and with the aid of ultrahigh-resolution imaging, we observed a new efficient mode of intercellular spread in which RSV-infected cells directly transfer viral materials (including viral replication factories) to neighboring cells through protruding open-ended microfilament-rich intercellular nanotubes. The new mode is virion-independent and antibody-insensitive, beginning as early as 3 h post infection. Furthermore, replication-defective viral genomes (DVGs) might also utilize the new mode, facilitating the establishment of latent viral infections. Therefore, our data provide a new perspective on RSV cell-to-cell spread and might help to explain the immune escape and latent persistence of paramyxoviruses.

category: microbiology


title: Engineering SARS-CoV-2 cocktail antibodies into a bispecific format improves neutralizing potency and breadth

abstract: One major limitation of neutralizing antibody-based COVID-19 therapy is the requirement of costly cocktails to reduce antibody resistance. We engineered two bispecific antibodies (bsAbs) using distinct designs and compared them with parental antibodies and their cocktail. Single molecules of both bsAbs block the two epitopes targeted by parental antibodies on the receptor-binding domain (RBD). However, bsAb with the IgG-(scFv)2 design (14-H-06) but not the CrossMAb design (14-crs-06) increases antigen-binding and virus-neutralizing activities and spectrum against multiple SARS-CoV-2 variants including the Omicron, than the cocktail. X-ray crystallography and computational simulations reveal distinct neutralizing mechanisms for individual cocktail antibodies and suggest higher inter-spike crosslinking potentials by 14-H-06 than 14-crs-06. In mouse models of infections by SARS-CoV-2 and the Beta, Gamma, and Delta variants, 14-H-06 exhibits higher or equivalent therapeutic efficacy than the cocktail. Rationally engineered bsAbs represent a cost-effective alternative to antibody cocktails and a promising strategy to improve potency and breadth.


title: Understanding Chicks' Emotions: Are Eye Blinks & Facial Temperatures Reliable Indicators?

abstract: In commercial farming systems, chicks are reared without a mother. This absence of maternal influence can cause welfare problems when the chicks become older. Chicks imprint on their mothers they are young, and this mediates their stress and fear response. It is important to recognise problems early in the development of chicks to avoid welfare issues when they are older. One way to assess welfare is by measuring affective states. Research has shown chickens can display empathy, both towards their offspring and towards conspecifics. Measures of negative and positive affective states, either behavioural or physiological, could be good welfare indicators. This study employed non-invasive methods to measure affective states in laying hen chicks. Using video and thermal imaging, it analysed temperature changes in the peripheral areas and head region as well as changes in blinking behaviour before and after exposure to a stressor. The prediction was that the temperature would decrease in the eye and peripheral regions in response to a stressor and that the blinking rate would decrease. These changes would be indicative of a negative affective state. The results showed that the eye temperature as well as the blinking rate both decreased, whereas the temperature in the head region and the beak area increased. These results could be indicative of a negative affective state.

category: animal behavior and cognition


title: Mesenchymal stem cells support human vascular endothelial cells to form vascular sprouts in human platelet lysate-based matrices.

abstract:
During tissue regeneration, mesenchymal stem cells can support endothelial cells in the process of new vessel formation. For a functional interaction of endothelial cells with mesenchymal stem cells a vascular inductive microenvironment is required. Using a cellular model for neo-vessel formation, we could show that newly formed vascular structures emanated from the embedded aggregates, consisting of mesenchymal stem cells co-cultured with human umbilical vein endothelial cells, into the avascular HPL-based matrices bridging distances up to 5 mm to join with adjacent aggregates with the same morphology forming an interconnected network. These newly formed vascular sprouts showed branch points and generated a lumen as sign of mature vascular development. Mesenchymal stem cells in fluid phase could bind to and interact with adherent human umbilical vein endothelial cells when a shear-force of 2 dyne/mm2 was applied in the flow chamber using a Bioflux(R)200 device. Under these conditions, mesenchymal stem cells bind to human umbilical vein endothelial cells previously damaged by laser beam irradiation to interact and shed particles.

In conclusion, we observed that mesenchymal stem cells support human umbilical vein endothelial cells to form new vessels in HPL-based matrices when co-cultured in spherical aggregates to generate complex vascular networks in a primarily avascular scaffold and bind to the damaged cells under shear-force to eventually aid in their regeneration.

category: bioengineering


title: Gene Expression Meta-Analysis of Colon Rectal Cancer Tumour Cells Reveals Genes in Association With Tumorogenesis.

abstract:
BackgroundEvery year, more than 12 million people are diagnosed with colorectal cancer(CRC), and more than 600,000 people die from it, making it second most deadly form of cancer.This work analyzes differential gene expression across CRC and other glandular tumour samples to identify expression changes potentially contributing to the development of CRC tumorogenesis.

MethodsThis work defines 13 gene signatures representing four CRC tumour and 10 other glandular tumours that are colonic by origin.Gene Set Enrichment Analysis (GSEA) is used to define positive and negative CRC gene panels from GSEA-identified leading-edge genes using two CRC signatures. GSEA then is used to verify enrichment and leading-edge gene membership of CRC panels in two independent CRC gene signatures. Analysis is then extended to four individual and 10 glandular tumour signatures. Genes most associated with CRC tumorogenesis are predicted by intersecting membership of GSEA-identified leading-edges across signatures.

ResultsSignificant enrichment is observed between CRC gene identification signatures, from which the positive (55 genes) and negative (77 genes) CRC panels are defined. Non-random significant enrichment is observed between CRC gene panels and verification signatures, from which 54 over- and 72 under-expressed genes are shared across leading-edges. Considering other glandular tumour samples individually and in combination with CRC, significant non-random enrichment is observed across these signatures. Eight solute carrier family genes such as (SLC25A32, SLC22A3, SLC25A20, SLC36A1, SLC26A3,SLC9A2, SLC4A4 and SLC26A2) from the CRC panel were shared commonly across all the gene signatures leading-edges, regardless of the colonic tumour type.

ConclusionThis meta-analysis identifies gene expression changes associated with the process of CRC tumorogenesis. These changes may contribute to developing therapeutic treatments available for CRC patients.


title: VeChat: Correcting errors in long reads using variation graphs

abstract:
Error correction is the canonical first step in long-read sequencing data analysis. The current standard is to make use of a consensus sequence as a template. However, in mixed samples, such as metagenomes or organisms of higher ploidy, consensus induced biases can mask true variants affecting haplotypes of lower frequencies, because they are mistaken as errors.

The novelty presented here is to use graph based, instead of sequence based consensus as a template for identifying errors. The advantage is that graph based reference systems also capture variants of lower frequencies, so do not mistakenly mask them as errors. We present VeChat, as a novel approach to implement this idea: VeChat distinguishes errors from haplotype-specific true variants based on variation graphs, which reflect a popular type of data structure for pangenome reference systems. Upon initial construction of an ad-hoc variation graph from the raw input reads, nodes and edges that are due to errors are pruned from that graph by way of an iterative procedure that is based on principles from frequent itemset mining. Upon termination, the graph exclusively contains nodes and edges reflecting true sequential phenomena. Final re-alignments of the raw reads indicate where and how reads need to be corrected.

Extensive benchmarking experiments demonstrate that PacBio and ONT reads corrected by VeChat contain 4 to 15, or, respectively, 2 to 10 times less errors than when corrected state of the art approaches. VeChat is implemented in an easy-to-use open-source tool and publicly available at https://github.com/HaploKit/vechat.


title: The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context

abstract: Mitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterised by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It however lacked functions aimed at integrating mitochondria in the cellular context and thus, identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade we implemented two novel integrative functions, Network Analysis and the transcription factor- (TF-) Enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualisation, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species as well as an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in 3 specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.


title: A Deep Learning solution for triaging patient with cancer from their predicted mutational status using histopathological images

abstract: The presence of mutation in cancer can be associated with a response to a targeted cancer therapy. Therefore it has become an important information while it helps giving a more specialized and more efficient treatment for each patient. Detection of mutation is routinely made by DNA-sequencing diagnostic tests. Recently, a new strategy of deep learning based method of prediction of mutation from histopathological images has shown promising results. However it is still unknown whether these methods can be useful as screening tests aside from sequencing methods for efficient population diagnosis. Here we developed our own deep learning based prediction pipeline for the detection of mutation in breast, lung, colon and ovarian cancer and find clinically relevant genes that have easy-to-detect mutational status, and especially TP53 which can be detected in these four tumors. We then propose 3 potential screening strategies and show the effectiveness of our deep learning pipeline for optimizing diagnosis in the patient population.


title: Cilia stimulatory and antibacterial activities of bitter receptor agonist diphenhydramine: insights into potential complimentary strategies for CF nasal infections

abstract:
BACKGROUNDBitter compounds increase ciliary beating and nitric oxide (NO) production in nasal epithelial cells through T2Rs in motile cilia. We examined expression of cilia T2Rs and both host and bacterial responses to T2R14 agonist diphenhydramine.

METHODUsing cultured human nasal epithelial cells grown at air liquid interface, we measured expression of T2Rs via qPCR. We measured effects of diphenhydramine on ciliary beat frequency via high-speed imaging and nitric oxide production via fluorescent dye DAF-FM. We measured effects of diphenhydramine on growth of lab and clinical strains of Pseudomonas aeruginosa. We measured biofilm formation of P. aeruginosa using crystal violet staining and surface attachment of P. aeruginosa to cystic fibrosis bronchial epithelial (CBFE41o-) cells using CFU counting.

RESULTST2R expression increased with mucocilliary differentiation and did not vary between CF and non-CF ALIs. Treatment with P. aeruginosa flagellin decreased expression of diphenhydramine-responsive T2R14 and 40, among other isoforms. Diphenhydramine increased both NO and CBF. Increases in CBF were disrupted after flagellin treatment. Diphenhydramine impaired growth, biofilm production, and surface attachment of P. aeruginosa.

CONCLUSIONST2R expression is similar between normal and CF cells but decreases with flagellin treatment. Utilizing T2R agonists as therapeutics within the context of CF, P. aeruginosa infections may require co-treatment with anti-inflammatories to prevent the reduction of T2R expression with TLR activation. T2R agonist diphenhydramine increases NO production and CBF while also decreasing bacterial growth and biofilm production, and thus diphenhydramine or derivate compounds may have potential clinical usefulness in CF infections as a topical therapy.

HIGHLIGHTSO_LIT2R14 agonist diphenhydramine increases nitric oxide production and cilia beating
C_LIO_LIFlagellin decreases T2R14 expression in primary airway epithelial cells
C_LIO_LIT2R14 agonist Diphenhydramine inhibits Pseudomonas growth and biofilm formation
C_LI

category: physiology


title: Stable Potassium Isotopes (41K/39K) Track Transcellular and Paracellular Potassium Transport in Biological Systems

abstract: Here we present measurements of the stable isotope ratios of potassium (41K/39K) in three biological systems. We show that the ratio of 41K to 39K varies systematically: between the single-celled green alga Chlamydomonas reinhardtii and growth medium; between muscles of both euryhaline and stenohaline marine teleosts and seawater; and between blood plasma and red blood cells, muscles, cerebrospinal fluid, brain tissues, and urine in the terrestrial mammal Rattus norvegicus. Considered in the context of our current understanding of K+ transport in these biological systems, our results provide evidence that the fractionation of K isotopes depends on transport pathway and transmembrane transport machinery: K+ channels and paracellular transport through tight-junctions favor 39K whereas K+ pumps and co-transporters exhibit less isotopic fractionation. These results indicate that stable K isotopes can provide unique quantitative insights into the machinery and dynamics of K+ homeostasis in biological systems.


title: Psychedelics and schizophrenia: Distinct alterations to Bayesian inference

abstract: Schizophrenia and states induced by certain psychotomimetic drugs may share some physiological and phenomenological properties, but they differ in fundamental ways: one is a crippling chronic mental disease, while the others are temporary, pharmacologically-induced states presently being explored as treatments for mental illnesses. Building towards a deeper understanding of these different alterations of normal consciousness, here we compare the changes in neural dynamics induced by LSD and ketamine (in healthy volunteers) against those associated with schizophrenia, as observed in resting-state M/EEG recordings. While both conditions exhibit increased neural signal diversity, our findings reveal that this is accompanied by an increased transfer entropy from the front to the back of the brain in schizophrenia, versus an overall reduction under the two drugs. Furthermore, we show that these effects can be reproduced via different alterations of standard Bayesian inference applied on a computational model based on the predictive processing framework. In particular, the effects observed under the drugs are modelled as a reduction of the precision of the priors, while the effects of schizophrenia correspond to an increased precision of sensory information. These findings shed new light on the similarities and differences between schizophrenia and two psychotomimetic drug states, and have potential implications for the study of consciousness and future mental health treatments.


title: Non-self RNA rewires IFNβ signaling: A mathematical model of the innate immune response

abstract: Viral RNA-activated transcription factors IRF3 and NF-{kappa}B trigger synthesis of interferons and interleukins. In non-infected bystander cells, the innate immune response is reinforced by secreted interferon {beta} (IFN{beta}), which induces the expression of interferon-activated genes (ISGs) through activation of STAT1/2. Here, we show that in cells transfected with an analog of viral RNA, poly(I:C), transcriptional activity of STAT1/2 is terminated due to depletion of the IFN{beta} receptor, IFNAR. We demonstrate that two ISGs, RNase L and PKR, not only hinder replenishment of IFNAR, but also suppress negative regulators of IRF3 and NF-{kappa}B, consequently promoting their transcriptional activity. We incorporated these findings into a comprehensive mathematical model of innate immunity. By coupling signaling through the IRF3/NF-{kappa}B and the STAT1/2 pathways with activity of RNase L and PKR, the model explains how poly(I:C) switches the transcriptional program from STAT1/2-induced to IRF3/NF-{kappa}B-induced, transforming IFN{beta}-responding cells into IFN{beta}-secreting cells. Using an ample set of experiments on wild-type and knock-out A549 cell lines for fitting the model, we managed to achieve parameter identifiability.

category: immunology


title: Inside-out tracking and projection mapping for robot-assisted transcranial magnetic stimulation

abstract: Transcranial Magnetic Stimulation (TMS) is a neurostimulation technique based on the principle of electromagnetic induction of an electric field in the brain with both research and clinical applications. To produce an optimal neuro-modulatory effect, the TMS coil must be placed on the head and oriented accurately with respect to the region of interest within the brain. A robotic method can enhance the accuracy and facilitate the procedure for TMS coil placement. This work presents two system improvements for robot-assisted TMS (RA-TMS) application. Previous systems have used outside-in tracking method where a stationary external infrared (IR) tracker is used as a reference point to track the head and TMS coil position. This method is prone to losing track of the coil or the head if the IR camera is blocked by the robotic arm during its motion. To address this issue, we implemented an inside-out tracking method by mounting a portable IR camera on the robot end-effector. This method guarantees that the line of sight of the IR camera is not obscured by the robotic arm at any time during its motion. We also integrated a portable projection mapping device (PPMD) into the RA-TMS system to provide visual guidance during TMS application. PPMD can track the head via an IR tracker, and can project a planned contact point of the TMS coil on the head or overlay the underlying brain anatomy in real-time.


title: Genetic diversity analysis and characterization of Ugandan sorghum

abstract: The National Genebank of Uganda houses diverse and rich Sorghum bicolor germplasm collection. This genetic diversity resource is untapped, under-utilized and has not been systematically incorporated into sorghum breeding programs. In this study, we characterized the germplasm collection using whole genome SNP markers. Discriminant analysis of principal components (DAPC) was implemented to study racial ancestry of the accessions in comparison to a global sorghum diversity set and characterize sub-groups and admixture in the Ugandan germplasm. Genetic structure and phylogenetic analysis was conducted to identify distinct genotypes in the Ugandan collection and relationships among groups. Furthermore, in a case study for identification of potentially useful adaptive trait variation for breeding, we performed genome-wide association studies for juvenile cold tolerance. Genomic regions potentially involved in adaptation of Ugandan sorghum varieties to cooler climatic conditions were identified that could be of interest for expansion of sorghum production into temperate latitudes. The study demonstrates how genebank genomics can potentially facilitate effective and efficient usage of valuable, untapped germplasm collections for agronomic trait evaluation and subsequent allele mining.


title: Oscillations without cortex: Working memory modulates brainwaves in the endbrain of crows

abstract:
Complex cognition requires coordinated neuronal activity at the network level. In mammals, this coordination results in distinct dynamics of local field potentials (LFP) that have been central in many models of higher cognition. Because these models are based on mammalian data, they often implicitly assume a cortical organization. Higher associative regions of the brains of birds do not have cortical layering, yet these regions have neuronal single-cell correlates of higher cognition that are very similar to those found in mammals. Here we recorded LFP in the avian equivalent of prefrontal cortex while crows performed a highly controlled and cognitively demanding working memory task, adapted from monkeys. To further ensure that recordings reflected only cognitive processes detached from motor-related activities we trained and monitored the animals to keep their head still. We found signatures in local field potentials, modulated by working memory. Frequencies of a narrow gamma (30-59 Hz) and the beta band (13-19 Hz) contained information about the location of the target items on the screen and were modulated by working memory load. This indicates a critical involvement of these bands in ongoing cognitive processing. We also observed bursts in the beta and gamma frequencies, similar to those observed in monkeys. Such bursts are a vital part of  activity silent models of working memory. Thus, despite the lack of a cortical organization the avian associative pallium can create LFP signatures reminiscent of those observed in primates. This points towards a critical cognitive function of oscillatory dynamics evolved through convergence in species capable of complex cognition.

Relevance statementContemporary models of higher cognition, like those of working memory, often include temporal dynamics of neural activity such as gamma oscillations. Birds and mammals convergently evolved these cognitive functions and here we show that, despite the large evolutionary distance and largely different brain organization, crows share many of the oscillatory fingerprints reported in primates. This indicates that neural networks required for such LFP phenomena have evolved in parallel and may be critical to higher cognition.


title: Dissociable neural correlates of multisensory coherence and selective attention

abstract: Previous work has demonstrated that performance in an auditory selective attention task can be enhanced or impaired, depending on whether a task-irrelevant visual stimulus is temporally coherent with a target auditory stream or with a competing distractor. However, it remains unclear how audiovisual (AV) temporal coherence and auditory selective attention interact at the neurophysiological level. Here, we measured neural activity using electroencephalography (EEG) while participants performed an auditory selective attention task, detecting deviants in a target audio stream. The amplitude envelope of the two competing auditory streams changed independently, while the radius of a visual disc was manipulated to control the audiovisual coherence. Analysis of the neural responses to the sound envelope demonstrated that auditory responses were enhanced independently of the attentional condition: both target and masker stream responses were enhanced when temporally coherent with the visual stimulus. In contrast, attention enhanced the event-related response (ERP) evoked by the transient deviants, independently of AV coherence. Finally, we identified a spatiotemporal component of the ERP, likely originating from the superior temporal gyrus and the frontoparietal network, in which both attention and coherence synergistically modulated ERP amplitude. These results provide evidence for dissociable neural signatures of bottom-up (coherence) and top-down (attention) effects in the AV object formation.


title: A multi-omics approach to visualize early neuronal differentiation in 4D

abstract:
Neuronal differentiation of pluripotent stem cells is an established method to study physiology, disease and medication safety. However, the sequence of events in human neuronal differentiation and the ability of in vitro models to recapitulate early brain development are poorly understood. We developed a protocol optimized for the study of early human brain development and neuropharmacological applications. We comprehensively characterized gene expression and epigenetic profiles at four timepoints, as the cells differentiate from embryonic stem cells towards a heterogenous population of progenitors, immature and mature neurons bearing telencephalic signatures. A multi-omics roadmap of neuronal differentiation, combined with searchable interactive gene analysis tools, allows for extensive exploration of early neuronal development and the effect of medications.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/478732v1_ufig1.gif" ALT="Figure 1">
View larger version (55K):
org.highwire.dtl.DTLVardef@163539forg.highwire.dtl.DTLVardef@72c09org.highwire.dtl.DTLVardef@dc04eforg.highwire.dtl.DTLVardef@c821d2_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIMulti-omics charting a new neuronal differentiation protocol for human ES cells
C_LIO_LISingle-cell analyses reveals marker genes during neuronal differentiation
C_LIO_LIIdentified transcriptional waves similar to early human brain development
C_LIO_LISearchable tools to visualize single-cell gene expression and chromatin state
C_LI

In BriefWe have developed a novel protocol for human embryonic stem cells to study neural induction and early neuronal differentiation. Multi-omics analyses uncovered cell populations, genes and transcriptional waves defining cell fate commitment. We comprehensively describe epigenetic landscapes and gene expression and provide searchable analysis tools for exploration of the data.

category: cell biology


title: A cell fate decision map reveals abundant direct neurogenesis in the human developing neocortex

abstract: The human neocortex has undergone strong evolutionary expansion, largely due to an increased progenitor population, the basal radial glial (bRG) cells. These cells are responsible for the production of a diversity of cell types, but the successive cell fate decisions taken by individual progenitors remains unknown. Here, we developed a semi-automated live/fixed correlative imaging method to generate a map of bRG cell division modes in early fetal tissue and cerebral organoids. Through the analysis of over 1,000 dividing progenitors, we show that bRG cells undergo abundant symmetric amplifying divisions, followed by frequent direct neurogenic divisions, bypassing intermediate progenitors. These direct neurogenic divisions are more abundant in the upper part of the subventricular zone. We furthermore demonstrate asymmetric Notch activation in the self-renewing daughter cells, independently of basal fiber inheritance. Our results reveal a remarkable conservation of fate decisions in cerebral organoids, supporting their value as models of early human neurogenesis.

category: developmental biology


title: The transformability of genotype-phenotype landscapes

abstract:
The mapping from genotype to phenotype to fitness typically involves multiple nonlinearities that can transform the effects of mutations. For example, mutations may contribute additively to a phenotype, but their effects on fitness may combine non-additively because selection favors a low or intermediate value of that phenotype. This can cause incongruence between the topographical properties of a fitness landscape and its underlying genotype-phenotype landscape. Yet, genotype-phenotype landscapes are often used as a proxy for fitness landscapes to study the dynamics and predictability of evolution. Here, we use theoretical models and empirical data on transcription factor-DNA interactions to systematically study the incongruence of genotype-phenotype and fitness landscapes when selection favors a low or intermediate phenotypic value. Using the theoretical models, we prove a number of fundamental results. For example, selection for low or intermediate phenotypic values does not change simple sign epistasis into reciprocal sign epistasis, yet it changes reciprocal sign epistasis into simple sign epistasis and no sign epistasis with equal probability. More broadly, we show that such selection tends to create fitness landscapes that are more rugged than the underlying genotype-phenotype landscape, but this increased ruggedness typically does not frustrate adaptive evolution because the local adaptive peaks in the fitness landscape tend to be nearly as tall as the global peak. Many of these results carry forward to the empirical genotype-phenotype landscapes, which may help to explain why low- and intermediate-affinity transcription factor-DNA interactions are so prevalent in eukaryotic gene regulation.

AUTHOR SUMMARYHow do mutations change phenotypic traits and organismal fitness? This question is often addressed in the context of a classic metaphor of evolutionary theory -- the fitness landscape. A fitness landscape is akin to a physical landscape, in which genotypes define spatial coordinates, and fitness defines the elevation of each coordinate. Evolution then acts like a hill-climbing process, in which populations ascend fitness peaks as a consequence of mutation and selection. It is becoming increasingly common to construct such landscapes using experimental data from high-throughput sequencing technologies and phenotypic assays, in systems such as macromolecules and gene regulatory circuits. Although these landscapes are typically defined by molecular phenotypes, and are therefore more appropriately referred to as genotype-phenotype landscapes, they are often used to study evolutionary dynamics. This requires the assumption that the molecular phenotype is a reasonable proxy for fitness, which need not be the case. For example, selection may favor a low or intermediate phenotypic value, causing incongruence between a fitness landscape and its underlying genotype-phenotype landscape. Here, we study such incongruence using a diversity of theoretical models and experimental data from gene regulatory systems. We regularly find incongruence, in that fitness landscapes tend to comprise more peaks than their underlying genotype-phenotype landscapes. However, using evolutionary simulations, we show that this increased ruggedness need not impede adaptation.

category: evolutionary biology


title: On the incongruence of genotype-phenotype and fitness landscapes


title: Cellular genome wide association study identifies common genetic variation influencing lithium induced neural progenitor proliferation

abstract: Lithium is used in the treatment of bipolar disorder (BD) and is known to increase neural progenitor cell (NPC) proliferation. Though the mechanism of lithiums therapeutic effect is not understood, evidence suggests that genetic variation influences response to treatment. Here, we used a library of genetically diverse human NPCs to identify common genetic variants that modulate lithium induced proliferation. We identified a locus on chr3p21.1 associated with lithium induced proliferation that colocalizes with BD risk. One lithium responsive gene, GNL3, was detected within the locus. The allele associated with increased baseline and lithium-induced GNL3 expression was also associated with increased lithium-induced NPC proliferation. Experimental manipulation of GNL3 expression using CRISPRa/i in NPCs showed that GNL3 was necessary for lithiums full proliferative effects, and sufficient to induce proliferation without lithium treatment. In all, our data suggest that GNL3 expression sensitizes NPCs for a stronger proliferative response to lithium.

category: genetics


title: Molecular mechanisms involved in Atlantic halibut (Hippoglossus hippoglossus) egg quality: impairments at transcription and protein folding levels induce inefficient protein and energy homeostasis during early development

abstract:
BackgroundReproductive success and normal development in all animals are dependent on egg quality and developmental competence of the produced embryo. This study employed tandem mass tags labeling based liquid chromatography tandem mass spectrometry for egg proteomic profiling to investigate differences in the global proteome of good versus poor quality Atlantic halibut eggs at 1-cell stage post fertilization.

ResultsA total of 115 proteins were found to be differentially abundant between good and poor quality eggs. Frequency distribution of these proteins revealed higher protein folding activity in good quality eggs in comparison to higher transcription and protein degradation activities in poor quality eggs (p < 0.05). Poor quality halibut eggs were significantly enriched with additional proteins related to mitochondrial structure and biogenesis (p < 0.05). The differential abundance of a selection of proteins was first confirmed at gene expression level using a transcriptomic approach followed by a targeted proteomic approach (parallel reaction monitoring based mass spectrometry) in biological samples obtained from two consecutive reproductive seasons. The findings of global proteome profiling, together with the validation of differential abundance of targeted proteins and their related genes, suggest impairments in protein and energy homeostasis which might be related to unfolded protein response and mitochondrial stress in poor quality eggs. Additional transmission electron microscopy studies were taken to assess potential differences in abundance and morphological integrity of mitochondria between good and poor quality eggs. Observations reveal poor quality eggs to contain significantly higher number of mitochondria with higher number of cristae. These mitochondria, however, are significantly smaller and have a more irregular shape than those found in high-quality eggs. Therewithal difference in mtDNA levels represented by mt-nd5 and mt-atp6 genomic DNA abundance in this study, were found to be not statistically significant (p > 0.05) between good and bad quality eggs at both 1 hpf and 24 hpf stages.

ConclusionOverall evidence from this study indicate that poor quality eggs undergo impairments at both transcription and translation level leading to endoplasmic reticulum and mitochondrial deficiencies. Additional research may be required to expediate the details and the potential of these impairments occurring in different species. Nonetheless, this study will pave the way for future research and will help in acceleration of recent advances in the field of embryonic developmental competence of living organisms.

category: molecular biology


title: A pseudotyped lentivirus-based assay to titer SARS-CoV-2 neutralizing antibodies in Mexico

abstract:
Measuring the neutralizing potential of SARS-CoV-2 antigens-exposed sera informs on effective humoral immunity. This is relevant to 1-monitor levels of protection within an asymptomatic population, 2-evaluate the efficacy of existing and novel vaccines against emerging variants, 3-test prospective therapeutic monoclonal neutralizing antibodies (NAbs) and, overall, to contribute to understand SARS-CoV-2 immunity. However, the gold-standard method to titer NAbs is a functional assay of virus-mediated infection, which requires biosafety level 3 (BSL-3) facilities. As these facilities are insufficient in Latin American countries, including Mexico, scant information has been obtained about NAb in these countries during the COVID-19 pandemic. An alternative solution to acquire NAb information locally is to use non-replicative viral particles that display the SARS-CoV-2 Spike (S) protein on their surface, and deliver a reporter gene into target cells upon transduction. Here we present the development of a NAb-measuring assay based on Nanoluc-mediated luminescence measurements from SARS-CoV-2 S-pseudotyped lentiviral particle-infected cells. The successive steps of development are presented, including lentiviral particles production, target cell selection, and TCID50 determination. We applied the optimized assay in a BSL-2 facility to measure NAbs in 15 pre-pandemic, 18 COVID-19 convalescent and 32 BNT162b2 vaccinated serum samples, which evidenced the assay with 100% sensitivity, 86.6% specificity and 96% accuracy. The assay highlighted heterogeneity in neutralization curves which are relevant in discussing neutralization potency dynamics. Overall, this is the first report of a BSL-2 safe functional assay to measure SARS-CoV-2 in Mexico and a cornerstone methodology necessary to measure NAb with a functional assay in the context of limited resources settings.

ImportanceEvaluating effective humoral immunity against SARS-CoV-2 requires a functional assay with infectious virus. Handling the authentic SARS-CoV-2 virus requires specialized facilities that are not readily available in Latin America, including Mexico. Here we produce non-replicative viral particles pseudotyped with the SARS-CoV-2 S protein that are used as safe surrogate viral particles in an optimized BSL-2 ready neutralization assay. The establishment of this assay is critical to allow the evaluation of effective humoral immunity to SARS-CoV-2 post-infection and to monitor the efficacy of existing or novel vaccines against emerging variants in the Mexican population.


title: Three Distinct Transcriptional Profiles of Monocytes Correlate with Disease Activity in SSc Patients

abstract:
Background/PurposePatients with systemic sclerosis (SSc) display a complex clinical phenotype. There are numerous studies that relate transcriptional signatures from PBMC or whole skin of SSc patients to disease activity. However, analyses of whole tissue RNA-sequencing studies are subjected to changes in cellular composition that can drive gene expression signatures and a loss of the ability to detect biologically important transcriptional changes within minority cell populations. Here, we focused on circulating monocytes, which have been shown to exist as two central populations classical (CM) and non-classical (NCM).

MethodsSSc patients were recruited from four different sites that form PRESS: Northwestern University, University of Texas, University of Michigan and University of Utah. Comprehensive clinical data was collected for all patients. We isolated CM and NCM from these patients and age, sex, and race-matched healthy volunteers were used as controls. RNA-seq was performed on CM and NCM populations as well as on isolated bulk macrophages from skin.

ResultsWe first performed RNA-seq on CM, which are the predominant population in circulation. In order to capture the variability across the SSc cohort, we defined 1790 differentially expressed genes in each patient. We then used these genes to cluster patients into 3 subgroups: Groups A-C. Group A exhibited the strongest interferon signature and innate immune pathways. Group B patients expressed genes in the same pathways but was also enriched for response to cAMP and corticosteroids. Both Group B and Group C exhibited upregulation of genes associated with vasculature development and blood vessel formation. Group C uniquely upregulated TGFB pathways. Next, we performed RNA-seq on NCM isolated from the same patients. When NCM were clustered based on the same 1790 genes as CM, we found that Groups A and C were recapitulated, while Group B was less cohesive. Our analysis stratified SSc patients based on their transcriptional profiles in monocytes but was agnostic to their clinical presentation. We found that Group B and C patients exhibited significantly worsened lung function at the time of monocyte isolation than Group A patients. However, there were no significant differences in skin disease. We then isolated macrophages from skin biopsies of SSc patients and showed that the transcriptional profile of Group A and C in SSc patients was conserved. We also used gene expression data from another study on monocytes which stratified patients based on disease presentation. We found that Group A accurately distinguished dcSSc and ncSSc patients from controls, but not lcSSc.

ConclusionWe are the first to show that transcriptomic analysis of classical and non-classical circulating monocytes can unbiasedly stratify SSc patients and correlate with disease activity outcome measures.

category: genomics


title: Temporal and spatial auxin responsive networks in maize primary roots

abstract: Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin regulated networks underlying maize root development we have characterized auxin responsive transcription across two time points (30 and 120 minutes) and four regions of the primary root: the meristematic zone, elongation zone, cortex, and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin regulated genes are region unique and are predominantly observed in differentiated tissues compared to the root meristem. Auxin gene regulatory networks (GRNs) were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin Response Factor (ARF) subnetworks were generated to identify target genes which exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.


title: Autosomal monoallelic genes are differentially regulated based on parental origin

abstract: The mammalian diploid nucleus contains two copies of its genome, one copy derived from each parent and thus each autosomal gene is represented by two alleles. A small number of recent studies have emphasized sex-biased gene expression and chromosomal arrangement in mammals1-4. Yet, no insights have been made to explore allele-specific regulatory mechanisms of autosomes. Here we used allele-specific single cell transcriptomic analysis to elucidate the establishment of monoallelic gene expression in the cardiac lineage. We revealed that pluripotent and cardiac lineage specific monoallelically expressed genes are regulated by different epigenetic mechanisms based upon their genetic background and parental origin. In addition, we observed epigenetic differences between deterministic and random autosomal monoallelic genes. Deterministic monoallelic genes are highly enriched in processes of cardiac musculature and cell physiology, whereas random autosomal monoallelic genes encode basic cellular processes. Moreover, we also found a greater contribution of the maternal versus paternal allele to the development and homeostasis of cardiac tissue and in cardiac health, highlighting the importance of maternal influence in male cardiac tissue homeostasis. Our findings emphasize the significance of allele-specific insights into gene regulation in development, homeostasis and disease.


title: Increased academic performance and prolonged career duration among Taiwanese academic faculty in ecology and evolutionary biology

abstract: Academic job markets have become increasingly challenging worldwide, yet it remains poorly characterized how competitively-successful candidates should be and what the underlying determinants of their success are. Focusing on ecology and evolutionary biology, we analyzed the academic performance (measured as h-index) as well as the duration for landing a faculty position and promotion to full professor of 145 principal investigators (PI) over the past 34 years in Taiwan. We found that faculty members had higher performance and longer duration before recruitment as a new PI in recent years. Performance before promotion remained stable, whereas the duration increased over time. The origin and prestige of PhD university had no effect on the performance or duration neither for recruitment nor promotion. Our findings highlight the increasingly crucial role of academic performance, rather than PhD degree itself, in determining academic success.

category: scientific communication and education


title: GLMsingle: a toolbox for improving single-trial fMRI response estimates

abstract: Advances in modern artificial intelligence (AI) have inspired a paradigm shift in human neuroscience, yielding large-scale functional magnetic resonance imaging (fMRI) datasets that provide high-resolution brain responses to tens of thousands of naturalistic visual stimuli. Because such experiments necessarily involve brief stimulus durations and few repetitions of each stimulus, achieving sufficient signal-to-noise ratio can be a major challenge. We address this challenge by introducing GLMsingle, a scalable, user-friendly toolbox available in MATLAB and Python that enables accurate estimation of single-trial fMRI responses (glmsingle.org). Requiring only fMRI time-series data and a design matrix as inputs, GLMsingle integrates three techniques for improving the accuracy of trial-wise general linear model (GLM) beta estimates. First, for each voxel, a custom hemodynamic response function (HRF) is identified from a library of candidate functions. Second, cross-validation is used to derive a set of noise regressors from voxels unrelated to the experimental paradigm. Third, to improve the stability of beta estimates for closely spaced trials, betas are regularized on a voxel-wise basis using ridge regression. Applying GLMsingle to the Natural Scenes Dataset and BOLD5000, we find that GLMsingle substantially improves the reliability of beta estimates across visually-responsive cortex in all subjects. Furthermore, these improvements translate into tangible benefits for higher-level analyses relevant to systems and cognitive neuroscience. Specifically, we demonstrate that GLMsingle: (i) improves the decorrelation of response estimates between trials that are nearby in time; (ii) enhances representational similarity between subjects both within and across datasets; and (iii) boosts one-versus-many decoding of visual stimuli. GLMsingle is a publicly available tool that can significantly improve the quality of past, present, and future neuroimaging datasets that sample brain activity across many experimental conditions.


title: Generating spatiotemporal patterns of linearly polarised light at high frame rates for insect vision research

abstract: Polarisation vision is commonplace among invertebrates; however, most experiments focus on determining behavioural and/or neurophysiological responses to static polarised light sources rather than moving patterns of polarised light. To this end, we designed a polarisation stimulation device based on superimposing polarised and non-polarised images from two projectors, which can display moving patterns at frame rates exceeding invertebrate flicker fusion frequencies. A linear polariser fitted to one projector enables moving patterns of polarised light to be displayed, whilst the other projector contributes arbitrary intensities of non-polarised light to yield moving patterns with a defined polarisation and intensity contrast. To test the device, we measured receptive fields of polarisation sensitive Argynnis paphia butterfly photoreceptors for both non-polarised and polarised light. We then measured local motion sensitivities of the optic flow-sensitive lobula plate tangential cell H1 in Calliphora vicina blowflies under both polarised and non-polarised light, finding no polarisation sensitivity in this neuron.


title: Anatomical variability, multi-modal coordinate systems, and precision targeting in the marmoset brain

abstract:
Localising accurate brain regions needs careful evaluation in each experimental species due to their individual variability. However, the function and connectivity of brain areas is commonly studied using a single-subject cranial landmark-based stereotactic atlas in animal neuroscience. Here, we address this issue in a small primate, the common marmoset, which is increasingly widely used in systems neuroscience. We developed a non-invasive multi-modal neuroimaging-based targeting pipeline, which accounts for intersubject anatomical variability in cranial and cortical landmarks in marmosets. This methodology allowed creation of multi-modal templates (MarmosetRIKEN20) including head CT and brain MR images, embedded in coordinate systems of anterior and posterior commissures (AC-PC) and CIFTI grayordinates. We found that the horizontal plane of the stereotactic coordinate was significantly rotated in pitch relative to the AC-PC coordinate system (10 degrees, frontal downwards), and had a significant bias and uncertainty due to positioning procedures. We also found that many common cranial and brain landmarks (e.g., bregma, intraparietal sulcus) vary in location across subjects and are substantial relative to average marmoset cortical area dimensions. Combining the neuroimaging-based targeting pipeline with robot-guided surgery enabled proof-of-concept targeting of deep brain structures with an accuracy of 0.2 mm. Altogether, our findings demonstrate substantial intersubject variability in marmoset brain and cranial landmarks, implying that subject-specific neuroimaging-based localization is needed for precision targeting in marmosets. The population-based templates and atlases in grayordinates, created for the first time in marmoset monkeys, should help bridging between macroscale and microscale analyses.

HighlightsO_LIAchieved sub-millimeter localization accuracy of subject-wise brain region
C_LIO_LIPropose a dedicated non-invasive multi-modal subject-specific registration pipeline
C_LIO_LIConstruct brain coordinate system in AC-PC and grayordinate spaces
C_LIO_LIEstablish multi-modal MRI and CT brain and cortical templates, MarmosetRIKEN20
C_LIO_LIQuantify intersubject variabilities in marmoset brain
C_LIO_LISignificant bias and uncertainty exist in marmoset stereotactic positioning
C_LI


title: A hardware system for real-time decoding of in-vivo calcium imaging data

abstract: Epifluorescence miniature microscopes ("miniscopes") are widely used for in vivo calcium imaging of neural population activity. Imaging data is usually collected while subjects are engaged in a task and stored for later offline analysis, but emerging techniques for online imaging offer potential for novel real-time experiments in which closed-loop interventions (such as neurostimulation or sensory feedback) are triggered at short latencies in response to neural population activity. Here we introduce DeCalciOn, a plug-and-play hardware device for online population decoding of in vivo calcium signals that can trigger closed-loop feedback at millisecond latencies, and is compatible with miniscopes that use the UCLA Data Acquisition (DAQ) interface. In performance tests, the position of rats (n=13) on a linear track was decoded in real time from hippocampal CA1 population activity by 24 linear classifiers. DeCalciOn required <2.5 ms after each end-of-frame to decode up to 1,024 calcium traces and trigger TTL control outputs. Decoding was most efficient using a  contour-free method of extracting traces from ROIs that were unaligned with neurons in the image, but  contour-based extraction from neuronal ROIs is also supported. DeCalciOn is an easy-to-use system for real-time decoding of calcium fluorescence that enables closed-loop feedback experiments in behaving animals.


title: RT-DeCal: A hardware system for real-time decoding of in-vivo calcium imaging data


title: DeCalciOn: A hardware system for real-time decoding of in-vivo calcium imaging data


title: Embodiment of Supernumerary Robotic Limbs in Virtual Reality

abstract: The supernumerary robotic limb system expands the motor function of human users by adding extra artificially designed limbs. It is important for us to embody the system as if it is a part of ones own body and to maintain cognitive transparency in which the cognitive load is suppressed. Embodiment studies have been conducted with an expansion of bodily functions through a "substitution" and "extension." However, there have been few studies on the "addition" of supernumerary body parts. In this study, we developed a supernumerary robotic limb system that operates in a virtual environment, and then evaluated whether the extra limb can be regarded as a part of ones own body using a questionnaire and whether the perception of peripersonal space changes with a visuotactile crossmodal congruency task. We found that the participants can embody the extra-limbs after using the supernumerary robotic limb system. We also found a positive correlation between the perceptual change in the crossmodal congruency task and the subjective feeling that the number of ones arms had increased (supernumerary limb sensation). These results suggest that the addition of an extra body part may cause the participants to feel that they had acquired a new body part that differs from their original body part through a functional expansion.


title: Seasonal IVIG contains high infectivity neutralizing and hemagglutination inhibition activity against seasonal flu virus strains selected for vaccines (2020-22)

abstract: IVIG solutions (10%) were tested for infectivity neutralization and hemagglutination inhibition against the influenza strains (two A and two B) recommended by the WHO for inclusion in vaccines for Northern and Southern hemispheres 2020-2022. The IVIG batches used were manufactured (June 2020) from plasma pools collected in the US. Potent neutralization and inhibition of hemagglutination were seen with these IVIG batches. This raises the possibility that IVIG could be added to existing therapies, especially in immunocompromised patients, to fight serious influenza infections. Further study of the potential of IVIG in influenza is warranted.


title: The extinction time under mutational meltdown

abstract: AO_SCPLOWBSTRACTC_SCPLOWMutational meltdown describes an eco-evolutionary process in which the accumulation of deleterious mutations causes a fitness decline that eventually leads to the extinction of a population. Possible applications of this concept include medical treatment of RNA virus infections based on mutagenic drugs that increase the mutation rate of the pathogen. To determine the usefulness and expected success of such an antiviral treatment, estimates of the expected time to mutational meltdown are necessary. Here, we compute the extinction time of a population under high mutation rates, using both analytical approaches and stochastic simulations. Extinction is the result of three consecutive processes: (1) initial accumulation of deleterious mutations due to the increased mutation pressure; (2) consecutive loss of the fittest haplotype due to Mullers ratchet; (3) rapid population decline towards extinction. We find accurate analytical results for the mean extinction time, which show that the deleterious mutation rate has the strongest effect on the extinction time. We confirm that intermediatesized deleterious selection coefficients minimize the extinction time. Finally, our simulations show that the variation in extinction time, given a set of parameters, is surprisingly small.


title: A high-quality genome assembly and annotation of the European earwig Forficula auricularia.

abstract: The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ~90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. A phylogenetic analysis revealed the isolate used in our genomic analysis belongs to Subspecies B, one of the two known genetic subspecies of F. auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.


title: Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer

abstract: Recent efforts to sequence the genomes of thousands of matched normal-tumor samples have led to the identification of millions of somatic mutations, the majority of which are non-coding. Most of these mutations are believed to be passengers, but a small number of non-coding mutations could contribute to tumor initiation or progression, e.g. by leading to dysregulation of gene expression. Efforts to identify putative regulatory drivers rely primarily on information about the recurrence of mutations across tumor samples. However, in regulatory regions of the genome, individual mutations are rarely seen in more than one donor. Instead of using recurrence information, here we present a method to identify putative regulatory driver mutations based on the magnitude of their effects on transcription factor-DNA binding. For each gene, we integrate the effects of mutations across all its regulatory regions, and we ask whether these effects are larger than expected by chance, given the mutation spectra observed in regulatory DNA in the cohort of interest. We applied our approach to analyze mutations in a liver cancer data set with ample somatic mutation and gene expression data available. By combining the effects of mutations across all regulatory regions of each gene, we identified dozens of genes whose regulation in tumor cells is likely to be significantly perturbed by non-coding mutations. Overall, our results show that focusing on the functional effects of non-coding mutations, rather than their recurrence, has the potential to identify putative regulatory drivers and the genes they dysregulate in tumor cells.


title: Physiological stress responses to non-mimetic model brood parasite eggs: leukocyte profiles and heat-shock protein Hsp70 levels

abstract: Obligate avian brood parasites lay their eggs in the nest of other bird species (hosts). Brood parasitism often imposes severe fitness costs on hosts, which selects for the evolution of effective anti-parasitic defences, such as recognition and rejection of brood parasite eggs. Glucocorticoids have been recently found to mediate host physiological and behavioural adjustments in response to brood parasite eggs; however, it remains unclear whether brood parasitism triggers a general response involving multiple physiological elements. In this study, we experimentally investigated whether a salient brood parasitic stimulus (the presence of a non-mimetic model egg in the nest) causes physiological adjustments in adult Eurasian blackbirds (Turdus merula) at immune (leukocyte profiles) and cellular (heat-shock protein Hsp70 synthesis) level. Also, we explored whether these physiological changes are mediated by variations in corticosterone levels. We found that experimental brood parasitism caused an increase in heterophils and a decrease in lymphocytes, leading to higher H/L ratios in parasitized birds. Nevertheless, we did not find trade-offs between immune function and corticosterone levels. Hsp70 synthesis was not affected by our experimental manipulation. Our findings provide evidence that brood parasite eggs trigger a general stress response in egg-rejecter hosts, including changes in cellular immune profiles.


title: Gut-liver-axis microphysiological system for studying cellular fluidic shear stress and inter-tissue interaction

abstract: Gut-liver-axis (GLA) is a fundamental interaction between the gut and liver for maintaining human health. To clarify the physiological and pathological roles of GLA in the human body, a GLA microphysiological system (GLA-MPS) holds great potential. However, in current GLA-MPS, the importance of a physiologically relevant flow for gut and liver cells cultivation is not fully addressed. In addition, the integration of individual organ perfusion, circulation flow, and organ tissue functions in a single device has not been achieved. Here, we introduce a GLA-MPS by integrating two cell culture chambers with individually applied perfusion flows and a circulation channel with an on-chip pneumatic micropump under cell culture chambers via a porous membrane for interconnecting them. We analyzed the fluid shear stress (FSS) with computational fluid dynamics simulations and confirmed that the physiologically relevant FSS (i.e., 8 x 10-3 and 1.2 x 10-7 dyne cm-2) could be applied for the gut (Caco-2) and liver (HepG2) cells, respectively. Under physiologically relevant flow, the Caco-2 and HepG2 cells in the GLA-MPS maintained a cell survival rate of 95% and 92%, respectively; further, they enhanced the expression of functional proteins such as zonula occludens 1 (ZO-1) and albumin (ALB), respectively. Thus, the presented GLA-MPS can be adapted as an advanced in vitro model in a wide range of applications for disease modeling associated with inter-tissue interactions, such as fatty liver diseases.


title: Surface engineering enhances the therapeutic potential of extracellular vesicles following acute myocardial infarction

abstract:
Structured AbstractO_ST_ABSObjectivesC_ST_ABSThe objective of the study was to assess the therapeutic efficacy of targeting remote zone cardiomyocytes with cardiosphere-derived cell (CDC) extracellular vesicles (EVs) in acute myocardial infarction.

BackgroundCardiomyocyte (CM) cell death plays a significant role in left ventricular (LV) remodeling and cardiac dysfunction following myocardial infarction (MI). While EVs secreted by CDCs have shown efficacy in promoting cardiac repair in preclinical models of MI, their translational potential is limited by their biodistribution. We hypothesized that targeting therapeutic EVs to CMs would result in further reduction of cardiomyocyte (CM) cell death in vivo and improvement in cardiac function post-MI.

MethodsCDC-derived EVs were engineered to express a CM-specific binding peptide (CMP) on their surface and characterized for size, morphology, and protein expression. Mice with acute MI underwent delivery of human CDC EVs, CMP-EVs and placebo in a double-blind study. LVEF was assessed by echo at 1- and 28-days post-MI and tissue samples processed for assessment of EV biodistribution and histological endpoints.

ResultsCMP-EVs demonstrated superior cardiac targeting and retention when compared with control EVs 24 hours post MI. While intramyocardial administered CDC-EVs improved LVEF compared with placebo at 4 weeks, mice treated with CMP-EVs demonstrated a significant improvement in LVEF compared with non-targeted EVs. Likely accounting for their augmented therapeutic efficacy, CMP-EVs demonstrated enhanced reduction of remote zone cardiomyocyte apoptosis.

ConclusionsTargeting CMP-EVs to CMs post-MI improved cardiac function compared with unmodified EVs demonstrating a strategy to further optimize therapeutic EV delivery to increase efficacy and decease off-target effects.

Condensed AbstractExtracellular vesicles (EVs) offer several potential advantages over small molecule therapeutics for cardiovascular disease (CVD). However, their potential is limited by their biodistribution and lack of specificity. We engineered cardiosphere-derived cells (CDCs) to express Lamp2b fused to a cardiomyocyte specific peptide (CMP), generating EVs with increased cardiomyocyte uptake and cardiac retention. CMP-EVs enhanced cardiac function following acute MI and further reduced remote zone apoptosis when compared with unmodified CDC-EVs. This work highlights a role for targeting therapeutic EVs to cardiomyocytes following injury and serves as a proof-of-concept study for the utility of EV surface engineering in the treatment of CVD.


title: NetMix2: Unifying network propagation andaltered subnetworks

abstract: A standard paradigm in computational biology is to use interaction networks to analyze high-throughput biological data. Two common approaches for leveraging interaction networks are: (1) network ranking, where one ranks vertices in the network according to both vertex scores and network topology; (2) altered subnetwork identification, where one identifies one or more subnetworks in an interaction network using both vertex scores and network topology. The dominant approach in network ranking is network propagation which smooths vertex scores over the network using a random walk or diffusion process, thus utilizing the global structure of the network. For altered subnetwork identification, existing algorithms either restrict solutions to subnetworks in subnetwork families with simple topological constraints, such as connected subnetworks, or utilize ad hoc heuristics that lack a rigorous statistical foundation. In this work, we unify the network propagation and altered subnetwork approaches. We derive a subnetwork family which we call the propagation family that approximates the subnetworks ranked highly by network propagation. We introduce NetMix2, a principled algorithm for identifying altered subnetworks from a wide range of subnetwork families, including the propagation family, thus combining the advantages of the network propagation and altered subnetwork approaches. We show that NetMix2 outperforms network propagation on data simulated using the propagation family. Furthermore, NetMix2 outperforms other methods at recovering known disease genes in pan-cancer somatic mutation data and in genome-wide association data from multiple human diseases. NetMix2 is publicly available at https://github.com/raphael-group/netmix2.

category: bioinformatics


title: ClustAssess: tools for assessing the robustness of single-cell clustering

abstract:
The transition from bulk to single-cell analyses refocused the computational challenges for high-throughput sequencing data-processing. The core of single-cell pipelines is partitioning cells and assigning cell-identities; extensive consequences derive from this step; generating robust and reproducible outputs is essential. From benchmarking established single-cell pipelines, we observed that clustering results critically depend on algorithmic choices (e.g. method, parameters) and technical details (e.g. random seeds).

We present ClustAssess, a suite of tools for quantifying clustering robustness both within and across methods. The tools provide fine-grained information enabling (a) the detection of optimal number of clusters, (b) identification of regions of similarity (and divergence) across methods, (c) a data driven assessment of optimal parameter ranges. The aim is to assist practitioners in evaluating the robustness of cell-identity inference based on the partitioning, and provide information for choosing robust clustering methods and parameters.

We illustrate its use on three case studies: a single-cell dataset of in-vivo hematopoietic stem and progenitors (10x Genomics scRNA-seq), in-vitro endoderm differentiation (SMART-seq), and multimodal in-vivo peripheral blood (10x RNA+ATAC). The additional checks offer novel viewpoints on clustering stability, and provide a framework for consistent decision-making on preprocessing, method choice, and parameters for clustering.


title: A New Classification Method Based on Dynamic Ensemble Selection and its Application to Predict Variance Patterns in HIV-1 Env

abstract: Therapeutics that target the envelope glycoproteins (Envs) of human immunodeficiency virus type 1 (HIV-1) effectively reduce virus levels in patients. However, due to mutations, new Env variants are frequently generated, which may be resistant to the treatments. The appearance of such sequence variance at any Env position is seemingly random. A better understanding of the spatiotemporal patterns of variance across Env may lead to the development of new therapeutic strategies. We hypothesized that, at any time point in a patient, positions with sequence variance are clustered on the three-dimensional structure of Env. To test this hypothesis, we examined whether variance at any Env position can be predicted by the variance measured at adjacent positions. Sequences from 300 HIV-infected patients were applied to a new algorithm we developed. The k-best classifiers (KBC) method is a dynamic ensemble selection technique that identifies the best classifier(s) within the neighborhood of a new observation. It applies bootstrap resampling to generate out-of-bag samples that are used with the resampled set to evaluate each classifier. For many positions of Env, primarily in the CD4-binding site, KBC accurately predicted variance based on the variance at their adjacent positions. KBC improved performance compared to the initial learners, static ensemble, and other baseline models. KBC also outperformed other algorithms for predicting variance at multi-position footprints of therapeutics on Env. These understandings can be applied to refine models that predict future changes in HIV-1 Env. More generally, we propose KBC as a new high-performance dynamic ensemble selection technique.


title: The Human "Contaminome": Bacterial, Viral, and Computational Contamination in Whole Genome Sequences from 1,000 Families

abstract:
BackgroundThe unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1,000 families and 5,000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies.

ResultsWe present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes.

ConclusionBoth experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.

genomics WGS contamination


title: Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets

abstract: AO_SCPLOWBSTRACTC_SCPLOWLong-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic profiling. The development of long-read specific tools for taxonomic profiling is accelerating, yet there is a lack of consensus regarding their relative performance. Here, we perform a critical benchmarking study using five long-read methods and four popular short-read methods. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology (ONT) sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates. Our results show that long-read methods generally outperformed short-read methods. Short-read methods (including Kraken2, Bracken, Centrifuge, and MetaPhlAn3) produced many false positives (particularly at lower abundances), required heavy filtering to achieve acceptable precision (at the cost of reduced recall), and produced inaccurate abundance estimates. By contrast, several long-read methods displayed very high precision and acceptable recall without any filtering required, including BugSeq, MEGAN-LR using translation alignments (DIAMOND to NCBI nr) or nucleotide alignments (minimap2 to NCBI nt). Furthermore, in the PacBio HiFi datasets these long-read methods detected all species down to the 0.1% abundance level with high precision. Other long-read methods, such as MetaMaps and MMseqs2, required moderate filtering to reduce false positives to achieve a suitable balance between precision and recall. We found read quality affected performance for methods relying on protein prediction or exact kmer matching, and these methods performed better with PacBio HiFi datasets. We also found that long-read datasets with a large proportion of shorter reads (<2kb length) resulted in lower precision and worse abundance estimates, relative to length-filtered datasets. Finally, for a given mock community we found that the long-read datasets produced significantly better results than short-read datasets, demonstrating clear advantages for long-read metagenomic sequencing. Our critical assessment of available methods provides recommendations for current research using long reads and establishes a baseline for future benchmarking studies.


title: Identification of significant molecules and signaling pathways between 2D and 3D culture methods of renal cancer cells

abstract: The majority of cancer studies are conducted with the two-dimensional (2D) culture method, which does not reflect tumor in vivo structure. The 3D culture method can form free bundles of cancer cells and spheroid, which mimics the tumor microenvironment in vivo. However, the molecules and signaling pathways between the 2D and 3D culture methods are still unknown. In this study, we aim to identify the key molecules and signaling pathways by analyzing the RNA-seq data. The GSE190296 was created by the BGISEQ-500 (Homo sapiens). The KEGG and GO analyses indicated sulfur compound metabolic process and regulation of leukocyte mediated immunity are the major differences between 2D and 3D renal cancer cell cultures. Moreover, we figured out several interactive genes including MYC, EGF, VEGFA, STAT3, NOTCH1, CAT, CCND1, HSPA8, DLG4, and HSPA5. Our study may provide new knowledge on the differences between 2D and 3D cancer cell cultures.


title: Designing a Multi-Epitope Vaccine Candidate against Salmonella Typhi Using Immunoinformatics Approach

abstract: Salmonella enterica subsp. enterica serovar Typhi (Salmonella Typhi) is the causative agent of typhoid. A large population living in developing and under-developed countries are mainly susceptible to the infection of this pathogen. The use of an effective vaccine targeting the highest-risk populations could be an extremely useful approach in the prevention of typhoid. The currently licenced and widely used typhoid conjugate vaccine (Vi-TCV) can promote emergence of Vi antigen negative strains, necessitating the design of alternative vaccine candidates. Vaccine consisting of multiple epitopes from different surface proteins can serve as a solution to this problem. In this study, 10 Salmonella Typhi whole genome sequences were retrieved from NCBI database. From the proteomes of these organisms, epitopes from four surface proteins such as peptidoglycan-associated lipoprotein (Accession No. AYU85048.1), outer membrane protein S1 (Accession No. AYU86170.1), outer membrane protein F (Accession No. AYU85220.1 and outer membrane porin L (Accession No. AYU87629.1) returned better results than some other surface proteins in terms of antigenicity, promiscuity to interact with MHC alleles, non-allergenicity, non-similarity with human proteins, conservation and population coverage. These epitopes were joined together using suitable adjuvant and linkers, resulting in a vaccine candidate comprising 201 amino acids. This multi epitope vaccine candidate exhibited promising results in molecular docking, molecular dynamics simulation and immune simulation. BLAST search revealed that the chosen epitopes for vaccine development against Salmonella Typhi are 100% identical with corresponding epitopes of Salmonella Paratyphi A, Salmonella Typhimurium and Salmonella Enteritidis, indicating that the proposed vaccine might give cross protection against major Salmonella pathogenic serovars. The prospective results in this dry laboratory work demonstrates potential positive outcomes in the future for in vivo animal model testing and clinical analyses.


title: Soil amendments and suppresssion of Phytophthora root rot in avocado (Persea indica)

abstract: The ability of microbial or mineral-based soil additives to suppress root rot caused by Phytophthora cinnamomi was assessed. Phosphite and metalaxyl treatments for the control of disease, and glyphosate for weed control were also assessed. A treatment simulating avocado orchard conditions had chicken manure, wood mulch, and mulch from beneath trees in an avocado orchard added to the pots. Soil treatments (three probiotic and two mineral-based) were applied to 9-month-old saplings growing in containers in a glasshouse. After one-month, half of the plants of each treatment were inoculated with the pathogen. Three months after inoculation, plants were harvested and plant growth and root damage were measured. In the first experiment infestation with P. cinnamomi significantly reduced fine root dry weight in all plants except those in soil treated with one silicon-based mineral mulch. Visible root damage was higher in plants treated with probiotics. In this experiment, and in a repeat experiment the reduction of fine root damage achieved by spraying plants with phosphite or addition of a silica based mineral mulch was similar. Phosphite was preferable to metalaxyl as a chemical treatment, as the latter reduced shoot and root growth of non-infected plants. Glyphosate treatment of wheat seedlings growing in the pots with the avocados reduced shoot and fine root growth of both non-infected and infected plants. These observations need to be confirmed under field conditions.


title: Robust deep learning object recognition models rely on low frequency information in natural images

abstract: Machine learning models have difficulty generalizing to data outside of the distribution they were trained on. In particular, vision models are usually vulnerable to adversarial attacks or common corruptions, to which the human visual system is robust. Recent studies have found that regularizing machine learning models to favor brain-like representations can improve model robustness, but it is unclear why. We hypothesize that the increased model robustness is partly due to the low spatial frequency preference inherited from the neural representation. We tested this simple hypothesis with several frequency-oriented analyses, including the design and use of hybrid images to probe model frequency sensitivity directly. We also examined many other publicly available robust models that were trained on adversarial images or with data augmentation, and found that all these robust models showed a greater preference to low spatial frequency information. We show that preprocessing by blurring can serve as a defense mechanism against both adversarial attacks and common corruptions, further confirming our hypothesis and demonstrating the utility of low spatial frequency information in robust object recognition.


title: Statistical learning of successor representations is related to on-task replay

abstract: Humans automatically infer higher-order relationships between events in the environment from their statistical co-occurrence, often without conscious awareness. Neural replay of task representations, which has been described as sampling from a learned transition structure of the environment, is a candidate mechanism by which the brain could use or even learn such relational information in the service of adaptive behavior. Human participants viewed sequences of images that followed probabilistic transitions determined by ring-like graph structures. Behavioral modeling revealed that participants acquired multi-step transition knowledge through gradual updating of an internal successor representation (SR) model, although half of participants did not indicate any knowledge about the sequential task structure. To investigate neural replay, we analyzed dynamics of multivariate functional magnetic resonance imaging (fMRI) patterns during short pauses from the ongoing statistical learning task. Evidence for sequential replay consistent with the probabilistic task structure was found in occipito-temporal and sensorimotor cortices during short on-task intervals. These findings indicate that implicit learning of higher-order relationships establishes an internal SR-based map of the task, and is accompanied by cortical on-task replay.


title: Different dopaminergic neurons signal absolute and relative aversive value in the Drosophila mushroom body.

abstract: Animals use prior experience to assign absolute (good or bad) and also relative (better or worse) value to new experience. These learned values guide appropriate later decision-making. While our understanding of how the dopaminergic system computes absolute value is relatively advanced, the mechanistic underpinnings of relative valuation are unclear. Here we reveal mechanisms of absolute and relative aversive valuation in Drosophila. Three types of punishment-sensitive dopaminergic neurons (DANs) drive intensity-scaled plasticity at their respective mushroom body output neuron (MBON) connections to code absolute aversive value. In contrast, by comparing current and previous aversive experiences the MBON-DAN network can code relative aversive value by recruiting a specific subtype of reward-coding dopaminergic neurons which assigns a  better than value to the lesser of two aversive experiences. This study therefore provides an important functional consequence of having opposing populations of DANs and illustrates how these can operate together as a system within the MB network to code and compare sequential aversive experience to learn relative aversive value.


title: Activity and state dependent modulation of salt taste behavior in Drosophila melanogaster

abstract: Sodium present in NaCl is a fundamental nutrient required for many physiological processes. In animals including Drosophila low-salt concentrations induce attraction and high-salt concentrations evoke aversive behavior. Although high salt detection pathways have been studied in great details but mechanisms that regulate high salt consumption in animals are largely undetermined. We looked into the neural mechanisms of high NaCl consumption in adult Drosophila by which flies modify their acceptance of high salt as a function of diet where a long-term high-salt exposure increases taste sensitivity of pharyngeal LSO neurons and enhance high salt intake. Exposing flies to high NaCl diet for three days show decline in high salt aversion under starvation. Additionally, genetic suppression of LSO pharyngeal neurons in high NaCl fed flies inhibit excessive salt intake. We observed this modulation requires functional LSO neurons and a starvation state or dopamine. Multiple independent taste receptor neurons and pathways are involved in such a modulation. Silencing any one of multiple LSO neuronal types inhibits excessive salt intake. Our study suggests flies can adapt to the amount of salt ingested over several days, indicating the presence of a critical mechanism to reset the salt appetite and related neural circuits.


title: JUN Regulation of Injury-induced Enhancers in Schwann Cells

abstract:
Schwann cells play a critical role after peripheral nerve injury by clearing myelin debris, forming axon-guiding Bands of Bungner, and re-myelinating regenerating axons. Schwann cells undergo epigenomic remodeling to differentiate into a repair state that expresses unique genes, some of which are not expressed at other stages of Schwann cell development. We previously identified a set of enhancers that are activated in Schwann cells after nerve injury, and we determined if these enhancers are pre-programmed into the Schwann cell epigenome as poised enhancers prior to injury. Poised enhancers share many attributes of active enhancers, such as open chromatin, but are marked by repressive H3K27 trimethylation (H3K27me3) rather than H3K27ac. We find that most injury-induced enhancers are not marked as poised enhancers prior to injury indicating that injury-induced enhancers are not pre-programmed in the Schwann cell epigenome. Injury-induced enhancers are enriched with AP-1 binding motifs, and the c-JUN subunit of AP-1 had been shown to be critical to drive the transcriptional response of Schwann cells after injury. Using in vivo ChIP-seq analysis we find that c-JUN binds to a subset of injury-induced enhancers. To test the role of specific injury-induced enhancers, we focused on c-JUN-binding enhancers upstream of the Sonic Hedgehog (Shh) gene, which is only upregulated in repair Schwann cells compared to other stages of Schwann cell development. We confirm that c-JUN regulates these enhancers and also show that the enhancers are required for robust induction of the Shh gene after injury.

Significance StatementThe pro-regenerative actions of Schwann cells after nerve injury depends on upon profound reprogramming of the epigenome. The repair state is directed by injury-induced transcription factors, like JUN, which is uniquely required after nerve injury. In this study, we test whether the injury program is pre-programmed into the epigenome as poised enhancers and define which enhancers bind JUN. Finally, we test the roles of these enhancers by performing CRISPR-mediated deletion of JUN-bound injury enhancers in the Sonic hedgehog gene. While many long range enhancers drive expression of Sonic hedgehog at different developmental stages of specific tissues, these studies identify an entirely new set of enhancers that are required for Sonic hedgehog induction in Schwann cells after injury.