title: Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.

abstract:
Yanocomp is a tool for predicting the positions and stoichiometries of RNA modifications in Nanopore direct RNA sequencing data. It uses general mixture models to identify differentially modified sites between two conditions, with good support for replicates. Yanocomp models across adjacent kmers and uses a uniform component to account for outliers, improving the accuracy of single molecule predictions. Consequently, Yanocomp can be used to measure modification stoichiometry, and correlate modifications with other RNA processing events.

AvailabilityYanocomp is available under an MIT license at www.github.com/bartongroup/yanocomp.


title: Accurate and fast cell marker gene identification with COSG

abstract: Accurate cell classification is the groundwork for downstream analysis of single-cell sequencing data, yet how to identify marker genes to distinguish different cell types still remains as a big challenge. We developed COSG as a cosine similarity-based method for more accurate and scalable marker gene identification. COSG is applicable to single-cell RNA sequencing data, single-cell ATAC sequencing data and spatially resolved transcriptome data. COSG is fast and scalable for ultra-large datasets of million-scale cells. Application on both simulated and real experimental datasets demonstrates the superior performance of COSG in terms of both accuracy and efficiency as compared with other available methods. Marker genes or genomic regions identified by COSG are more indicative and with greater cell-type specificity.

category: bioinformatics


title: HKG: An open genetic variant database of 205 Hong Kong Cantonese exomes

abstract: HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long been a research gap in the understanding of the genetic architecture of southern Chinese subgroups, including Hong Kong Cantonese. HKG detected 196,325 high-quality variants with 5.93% being novel, and 25,472 variants were found to be unique in HKG compared to other Chinese populations (CHN). PCA illustrates the uniqueness of HKG in CHN, and IBD analysis revealed that it is related mostly to southern Chinese with a similar effective population size. An admixture study estimated the ancestral composition of HKG and CHN, with a gradient change from north to south, consistent with their geological distribution. ClinVar, CIViC and PharmGKB annotated 599 clinically significant variants and 360 putative loss-of-function variants, substantiating our understanding of population characteristics for future medical development. Among the novel variants, 96.57% were singleton and 6.85% were of high impact. With a good representation of Hong Kong Cantonese, we demonstrated better variant imputation using reference with the addition of HKG data, thus successfully filling the data gap in southern Chinese to facilitate the regional and global development of population genetics.


title: DOPAL initiates αSynuclein-mediated impaired proteostasis in neuronal projections leading to enhanced vulnerability in Parkinson's disease.

abstract: Dopamine dyshomeostasis has been acknowledged to be among the determinants of nigrostriatal neuron degeneration in Parkinsons disease (PD). Several studies in experimental models and postmortem PD patients underlined increasing levels of the aldehydic dopamine metabolite 3,4-dihydroxyphenylacetaldehyde (DOPAL), which is highly reactive towards proteins. DOPAL has been shown to covalently modify the presynaptic protein Synuclein (Syn), whose misfolding and aggregation represent a major trait of PD pathology, triggering Syn oligomerization in dopaminergic neurons. Here, we demonstrated that DOPAL elicits Syn neuronal accumulation and hampers Syn clearance at synapses and the soma. By combining cellular and in vivo models, we provided evidence that DOPAL-induced Syn buildup lessens neuronal resilience, compromises synaptic integrity, and overwhelms protein quality control pathways, specifically at neuronal projections. The resulting progressive decline of neuronal homeostasis leads to dopaminergic neuron loss and motor impairment, corroborating the Syn-DOPAL interplay as an early event in PD neurodegeneration.

category: neuroscience


title: Whole-brain studies of spontaneous behavior in head-fixed rats enabled by zero echo time MB-SWIFT fMRI

abstract: Understanding the link between the brain activity and behavior is a key challenge in modern neuroscience. Behavioral neuroscience, however, lacks tools to record whole-brain activity in complex behavioral settings. Here we demonstrate that a novel Multi-Band SWeep Imaging with Fourier Transformation (MB-SWIFT) functional magnetic resonance imaging (fMRI) approach enables whole-brain studies in spontaneously behaving head-fixed rats. First, we show anatomically relevant functional parcellation. Second, we show sensory, motor, exploration, and stress-related brain activity in relevant networks during corresponding spontaneous behavior. Third, we show odor-induced activation of olfactory system with high correlation between the fMRI and behavioral responses. We conclude that the applied methodology enables novel behavioral study designs in rodents focusing on tasks, cognition, emotions, physical exercise, and social interaction. Importantly, novel zero echo time and large bandwidth approaches, such as MB-SWIFT, can be applied for human behavioral studies, allowing more freedom as body movement is dramatically less restricting factor.


title: Does an artistic representation of brand logos increase their effect on customers?

abstract:
BackgroundIn numerous fMRI studies, brands strongly confound the customers economic decisions on a neural level by modulating cortical activity in reward-related areas.

ObjectiveTo test the hypothesis that the effect of logos can be increased by artistic logo representations, we presented logos in original and artistically changed versions during fMRI.

MethodsFollowing a pre-study survey on the familiarity of original brand logos, 15 logos rated as "familiar" and 10 logos rated as "unfamiliar" were selected for fMRI experiment. During fMRI, 15 healthy subjects were presented with original and artistically changed logos out of the familiar/unfamiliar categories. A whole-brain and ROI analysis for reward-related areas were performed. Moreover, logo-induced valence and arousal were measured with the self-assessment manikin.

ResultsWhole-brain analysis revealed activation in bilateral visual cortex for artistically changed logos (familiar/unfamiliar) compared to original logos. No significant effect could be detected for the ROI analysis. On average, the logos caused neutral emotions. However, when analyzing valence and arousal for familiar/unfamiliar and original/artistically changed logos separately, familiar original logos evoked stronger positive emotions than familiar artistically changed logos. Artistically changed logos (familiar/unfamiliar) excited participants significantly more than original logos.

ConclusionArtistically changed logos elicit activation in the bilateral visual cortex but not in reward-related areas.


title: Conservation of endangered galaxiid fishes in the Falkland Islands requires urgent action on invasive brown trout

abstract: Non-native salmonids are protected in the Southern hemisphere where they sustain aquaculture and valuable sport fisheries, but also impact on native galaxiid fishes, which poses a conservation conundrum. Legal protection and human-assisted secondary releases may have helped salmonids to spread, but this has seldom been tested. We reconstructed the introduction of brown trout (Salmo trutta) to the Falkland Islands using historical records and modelled its dispersal. Our results indicate that establishment success was [~]88%, and that dispersal was facilitated by proximity to introduction sites and density of stream-road crossings, suggesting it was human assisted. Brown trout has already invaded 54% of Falkland rivers, which are 2.9-4.5 times less likely to contain native galaxiids than uninvaded streams. Without strong containment we predict brown trout will invade nearly all suitable freshwater habitats in the Falklands within the next [~]70 years, which might put native freshwater fishes at a high risk of extinction.

category: ecology


title: Unsupervised Spatial Embedded Deep Representation of Spatial Transcriptomics

abstract: Spatial transcriptomics enable us to dissect tissue heterogeneity and map out inter-cellular communications. Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting the data. We present SEDR, an unsupervised spatially embedded deep representation of both transcript and spatial information. The SEDR pipeline uses a deep autoencoder to construct a low-dimensional latent representation of gene expression, which is then simultaneously embedded with the corresponding spatial information through a variational graph autoencoder. We applied SEDR on human dorsolateral prefrontal cortex data and achieved better clustering accuracy, and correctly retraced the prenatal cortex development order with trajectory analysis. We also found the SEDR representation to be eminently suited for batch integration. Applying SEDR to human breast cancer data, we discerned heterogeneous sub-regions within a visually homogenous tumor region, identifying a tumor core with pro-inflammatory microenvironment and an outer ring region enriched with tumor associated macrophages which drives an immune suppressive microenvironment.


title: Reference-free cell-type deconvolution of pixel-resolution spatially resolved transcriptomics data

abstract: Recent technological advancements have enabled spatially resolved transcriptomic profiling but at multi-cellular pixel resolution, thereby hindering the identification of cell-type-specific spatial patterns and gene expression variation. To address this challenge, we developed STdeconvolve as a reference-free approach to deconvolve underlying cell-types comprising such multi-cellular pixel resolution spatial transcriptomics (ST) datasets. Using simulated as well as real ST datasets from diverse spatial transcriptomics technologies comprising a variety of spatial resolutions such as Spatial Transcriptomics, 10X Visium, DBiT-seq, and Slide-seq, we show that STdeconvolve can effectively recover cell-type transcriptional profiles and their proportional representation within pixels without reliance on external single-cell transcriptomics references. STdeconvolve provides comparable performance to existing reference-based methods when suitable single-cell references are available, as well as potentially superior performance when suitable single-cell references are not available. STdeconvolve is available as an open-source R software package with the source code available at https://github.com/JEFworks-Lab/STdeconvolve.


title: Reference-free cell-type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data


title: Mapping Activity-Dependent Quasi-Stationary States of Mitochondrial Membranes with Graphene-Induced Energy Transfer Imaging

abstract: Graphene-induced energy transfer (GIET) was recently introduced for the precise localization of fluorescent molecules along the optical axis of a microscope. GIET is based on near-field energy transfer from an optically excited fluorophore to a single sheet of graphene. As a proof-of-concept, we demonstrated its potential by determining the distance between the two leaflets of supported lipid bilayers (SLBs) with sub-nanometer accuracy. Here, we use GIET imaging for three-dimensional reconstruction of the mitochondrial membrane architecture. We map two quasi-stationary states of the inner and outer mitochondrial membranes before and during adenosine tri-phosphate (ATP) synthesis. We trigger the ATP synthesis state in vitro by activating mitochondria with precursor molecules. Our results demonstrate that the inner membrane (IM) approaches the outer membrane (OM) while the outer membrane (OM) does not show a measurable change in average axial position upon activation. As a result, the inter-membrane space (IM-OM distance) is reduced by [~]2 nm upon activation of the mitochondria. This direct experimental observation of the subtle dynamics of mitochondrial membranes and the change in inter-membrane distance induced by ATP synthesis is relevant for our understanding of the physical functioning of mitochondria.

category: biophysics


title: Rapid homeostatic modulation of transsynaptic nanocolumn rings

abstract:
Robust neural information transfer relies on a delicate molecular nano-architecture of chemical synapses. Neurotransmitter release is controlled by a specific arrangement of proteins within presynaptic active zones. How the specific presynaptic molecular architecture relates to postsynaptic organization, and how synaptic nano-architecture is transsynaptically regulated to achieve stable synaptic transmission remains enigmatic. Using time-gated stimulated emission depletion (gSTED) microscopy at the Drosophila neuromuscular junction, we here find that presynaptic nano-rings formed by the active-zone scaffold Bruchpilot (Brp) precisely align with postsynaptic glutamate receptor (GluR) rings. Individual rings harbor ~5 transsynaptically-aligned Brp-GluR  nanocolumns. Intriguingly, acute GluR impairment rapidly triggers the formation of new transsynaptic nanocolumns on the minute time scale during homeostatic plasticity. We reveal distinct phases of structural transsynaptic homeostatic plasticity, with postsynaptic reorganization preceding presynaptic modulation. Finally, the auxiliary GluR subunit Neto-{beta} promotes structural and functional homeostatic plasticity. Thus, transsynaptic nanocolumns arrange in stereotypic rings that are rapidly modulated during homeostatic plasticity to stabilize synaptic efficacy.

One Sentence SummaryRapid changes of transsynaptic nanocolumn rings during homeostatic plasticity.


title: Comprehensive Phenotyping of Cutaneous Afferents Reveals Rapid-Onset Alterations in Nociceptor Response Properties Following Spinal Cord Injury

abstract: Spinal cord injury (SCI) is a complex syndrome that has profound effects on patient well-being, including the development of medically-resistant chronic pain. The mechanisms underlying SCI pain have been the subject of thorough investigation but remain poorly understood. While the majority of the research has focused on changes occurring within and surrounding the site of injury in the spinal cord, there is now a consensus that alterations within the peripheral nervous system, namely sensitization of nociceptors, contribute to the development and maintenance of chronic SCI pain. Here we demonstrate that thoracic spinal contusion injury results in the emergence of autotomy and spasticity, both indicators of spontaneous pain, in areas below the level of the injury within 24 hr of SCI. These behaviors were associated with hindpaw edema and elevated cutaneous calcitonin gene-related peptide (CGRP) concentration. Electrophysiological recordings using an ex vivo skin/nerve/DRG/spinal cord preparation demonstrated that SCI increased mechanical and thermal sensitivity, as well as the incidence of spontaneous activity (SA) and afterdischarge (AD), in below-level C-fiber nociceptors 24 hr following injury. Interestingly, the distribution of nociceptors that exhibit SA and AD are not identical, and the development of SA was observed more frequently in nociceptors with low thermal thresholds, while AD was found more frequently in nociceptors with high thermal thresholds. These results demonstrate that SCI causes the rapid-onset of peripheral inflammation-like processes that sensitize nociceptors, which may contribute to the early emergence and persistence of chronic SCI pain.


title: Vision is required for the formation of binocular neurons prior to the classical critical period

abstract: Depth perception emerges from the development of binocular neurons in primary visual cortex. Vision is required for these neurons to acquire their mature responses to visual stimuli. The prevailing view is that vision does not influence binocular circuitry until the onset of the critical period, about a week after eye opening, and that plasticity of visual responses is triggered by increased inhibition. Here, we show that vision is required to form binocular neurons and to improve binocular tuning and matching from eye opening until critical period closure. Enhancing inhibition does not accelerate this process. Vision soon after eye opening improves the tuning properties of binocular neurons by strengthening and sharpening ipsilateral-eye cortical responses. This progressively changes the population of neurons in the binocular pool and this plasticity is sensitive to interocular differences prior to critical period onset. Thus, vision establishes binocular circuitry and guides binocular plasticity from eye opening.


title: A molecular census of midbrain dopaminergic neurons in Parkinson's disease

abstract: Midbrain dopamine (DA) neurons in the substantia nigra pars compacta (SNpc) project widely throughout the central nervous system, playing critical roles in voluntary movements, reward processing, and working memory. Many of these neurons are highly sensitive to neurodegeneration in Parkinsons Disease (PD), and their loss correlates strongly with the pathognomonic symptoms. To characterize these populations molecularly, we developed a protocol to enrich and transcriptionally profile DA neuron nuclei from postmortem human SNpc of both PD patients and matched controls. We identified a total of ten distinct populations, including one that was primate-specific. A single subtype, marked by the gene AGTR1, was highly susceptible to degeneration, and was enriched for expression of genes associated with PD in genetic studies, suggesting many risk loci act within this subtype to influence its neurodegeneration. The AGTR1 subtype also showed the strongest upregulation of TP53 and its downstream targets, nominating a potential pathway of degeneration in vivo. The transcriptional characterization of differentially disease-vulnerable DA neurons in the SNpc will inform the development of laboratory models, enable the nomination of novel disease biomarkers, and guide further studies of pathogenic disease mechanisms.


title: Structure of mycobacterial cytochrome bcc in complex with Q203 and TB47, two anti-TB drug candidates

abstract: Pathogenic mycobacteria pose a sustained threat to global human health. Recently, cytochrome bcc complexes have gained interest as targets for antibiotic drug development. However, there is currently no structural information for the cytochrome bcc complex from these pathogenic mycobacteria. Here, we report the structures of M. tuberculosis cytochrome bcc alone (2.68 [A] resolution) and in complex with clinical drug candidates Q203 (2.67 [A] resolution) and TB47 (2.93 [A] resolution) determined by single-particle cryo-electron microscopy. M. tuberculosis cytochrome bcc forms a dimeric assembly with endogenous menaquinone/menaquinol bound at the quinone/quinol binding pockets. Q203 and TB47 are bound to the quinol-binding site. Hydrogen bonds are formed between the inhibitor and the side chains of QcrBThr313 and QcrBGlu314, residues that are conserved across pathogenic mycobacteria. These high-resolution structures provide a basis for the design of new mycobacterial cytochrome bcc inhibitors that could be developed into broad spectrum drugs to treat mycobacterial infections.

category: microbiology


title: Single-cell transcriptome analysis of embryonic and adult endothelial cells allows to rank the hemogenic potential of post-natal endothelium

abstract: Hematopoietic stem cells are crucial for the continuous production of blood cells during life. The transplantation of these cells is one of the most common treatments to cure patient suffering of blood diseases. However, the lack of suitable donors is a major limitation. One option to get hematopoietic stem cells matching perfectly a patient is cellular reprogramming. Hematopoietic stem cells emerge from endothelial cells in blood vessels during embryogenesis through the endothelial to hematopoietic transition. Here, we used single-cell transcriptomics analysis to compare embryonic and post-natal endothelial cells to investigate the potential of adult vasculature to be reprogrammed in hematopoietic stem cells. Although transcriptional similarities have been found between embryonic and adult endothelial cells, we found some key differences in term of transcription factors expression. There is a deficit of expression of Runx1, Tal1, Lyl1 and Cbfb in adult endothelial cells compared to their embryonic counterparts. Using a combination of gene expression profiling and gene regulatory network analysis, we found that endothelial cells from the pancreas, brain, kidney and liver appear to be the most suitable targets for cellular reprogramming into hematopoietic stem cells. Overall, our work provides an important resource for the rational design of a reprogramming strategy for the generation of hematopoietic stem cells.

category: developmental biology


title: The respiratory supercomplex from C. glutamicum

abstract: Corynebacterium glutamicum is a preferentially aerobic Gram-positive bacterium belonging to the Actinobacteria phylum, which also includes the pathogen Mycobacterium tuberculosis. In the respiratory chain of these bacteria, complexes III (CIII) and IV (CIV) form a CIII2CIV2 supercomplex that catalyzes oxidation of menaquinol and reduction of dioxygen to water. Electron transfer within the CIII2CIV2 supercomplex is linked to transmembrane proton translocation, which maintains an electrochemical proton gradient that drives ATP synthesis and transport processes. We isolated the C. glutamicum supercomplex and used cryo-EM to determine its structure at 2.9 [A] resolution. The structure shows a central CIII2 dimer flanked by a CIV on each side. One menaquinone is bound in each of the QN and QP sites in each CIII, near the cytoplasmic and periplasmic sides, respectively. In addition, we identified a menaquinone positioned ~14 [A] from heme bL on the periplasmic side. A di-heme cyt. cc subunit provides an electronic connection between each CIII monomer and the adjacent CIV. In CIII2, the Rieske iron-sulfur (FeS) proteins are positioned with the iron near heme bL. Multiple subunits interact to form a convoluted sub-structure at the cytoplasmic side of the supercomplex, which defines a novel path that conducts protons into CIV.

category: biochemistry


title: Machine Learning Identification of Capsid Mutations to Improve AAV Production Fitness

abstract: The adeno-associated virus (AAV) holds great potential for gene therapy efforts by providing a viable vector. However, current efforts are constrained by a lack of AAV variants that exhibit specific tropisms or immunogenicity and a lack of sustainable industrial projection. Departing from experimental approaches to addressing these issues, we built a model to predict residue mutations to improve AAV production fitness. Our model leverages the evolutionary paradigm and microenvironment characteristics by analyzing structural AAV data without needing domain knowledge or experimental fitness data for AAV as inputs. When testing our model's predictions for AAV2 residue mutations, we found a threefold increase in the percent of mutations yielding variants with better production fitness than wild type compared to random mutations, achieving a p-value of 7.46x10-12. Given these results, our machine learning approach of using structural data to approximate fitness data has the potential to accelerate AAV development.


title: Mineral crystal thickness in calcified cartilage and subchondral bone in healthy and osteoarthritic knees

abstract:
Osteoarthritis (OA) is the most common joint disease globally. In OA, articular cartilage degradation is often accompanied with sclerosis of the subchondral bone. However, the association between OA and tissue mineralization at the nanostructural level is currently not understood. Especially, it is technically challenging to identify calcified cartilage, where relevant but poorly understood pathological processes like tidemark multiplication and advancement occur. Here, we used state-of-the-art micro-focus small-angle X-ray scattering with high 5{micro}m spatial resolution to determine mineral crystal thickness in human subchondral bone and calcified cartilage. Specimens with a wide spectrum of OA severities were acquired from the medial and lateral compartments of medial compartment knee OA patients (n=15) and cadaver knees (n=10). For the first time, we identified a well-defined layer of calcified cartilage associated with pathological tidemark multiplication, containing 0.32nm thicker crystals compared to the rest of calcified cartilage. In addition, we found 0.2nm thicker mineral crystals in both tissues of the lateral compartment in OA compared with healthy knees, indicating a loading-related disease process since the lateral compartment is typically less loaded in medial compartment knee OA. Furthermore, the crystal thickness of the subchondral bone was lower with increasing histopathological OA severity. In summary, we report novel changes in mineral crystal thickness during OA. Our data suggest that unloading in the knee is associated with the growth of mineral crystals, which is especially evident in the calcified cartilage. In the subchondral bone, mineral crystals become thinner with increasing OA severity, which indicates new bone formation with sclerosis.

One Sentence SummaryMineral crystal thickness increases with osteoarthritis in the lateral condyle that is typically unloaded.


title: Inhibitory and Stimulatory Micropeptides Preferentially Bind to Different Conformations of the Cardiac Calcium Pump

abstract:
The ATP-dependent ion pump SERCA sequesters Ca2+ in the endoplasmic reticulum to establish a reservoir for cell signaling. Because of its central importance in physiology, this transporter is tightly controlled by physical interactions with tissue-specific regulatory micropeptides that tune SERCA function to match changing physiological conditions. In the heart, phospholamban (PLB) inhibits SERCA, while dwarf open reading frame (DWORF) stimulates SERCA. These competing interactions determine cardiac performance by modulating the amplitude of Ca2+ signals that drive the contraction/relaxation cycle. The distinct functions of these peptides may relate to their reciprocal preferences for SERCA binding. While SERCA binds PLB more avidly at low cytoplasmic Ca2+, it binds DWORF better at high Ca2+. In the present study, we determined that this opposing Ca2+ sensitivity is due to preferential binding of DWORF and PLB to different intermediate conformations that the pump samples during the Ca2+ transport cycle. The results suggest a mechanistic basis for inhibitory and stimulatory micropeptide function. In addition, fluorescence resonance energy transfer (FRET) measurements revealed dynamic shifts in SERCA-micropeptide binding equilibria during cellular Ca2+ elevations. The data suggest Ca2+-dependent dynamic exchange of inhibitory and stimulatory micropeptides from SERCA during the cardiac cycle. Together, these mechanisms provide beat-to-beat modulation of cardiac Ca2+ handling and contribute to the hearts adaptation to the increased physiological demands of exercise.

O_TEXTBOXSignificance

Interactions between SERCA and its regulatory micropeptides modulate cardiac performance. A previous study demonstrated that while the SERCA inhibitor, phospholamban, loses affinity during intracellular Ca2+ elevations, its competitor DWORF stimulates SERCA and binds better at elevated Ca2+. Here, we found this Ca2+-dependent difference in affinity is driven by preferential micropeptide binding to different SERCA conformations sampled during its enzymatic cycle. Tight binding to different conformations of the pump may underly the distinct mechanistic functions of these regulators. Lower affinity during alternating phases of the cardiac cycle may drive dynamic exchange of inhibitory and stimulatory micropeptides during contraction and relaxation. Our results reveal mechanisms that modulate cardiac Ca2+ handling on a beat-to-beat basis and help the heart adapt to exercise.

C_TEXTBOX


title: Fungi anaesthesia

abstract: Electrical activity of fungus Pleurotus ostreatus is characterised by slow (hours) irregular waves of baseline potential drift and fast (minutes) action potential likes spikes of the electrical potential. An exposure of the mycelium colonised substrate to a chloroform vapour lead to several fold decrease of the baseline potential waves and increase of their duration. The chloroform vapour also causes either complete cessation of spiking activity or substantial reduction of the spiking frequency. Removal of the chloroform vapour from the growth containers leads to a gradual restoration of the mycelium electrical activity.


title: Frequency chasing of individual megadalton ions in an Orbitrap analyzer improves precision of analysis in single molecule mass spectrometry

abstract: To enhance the performance of charge detection mass spectrometry, we investigated the behavior of macromolecular single ions on their paths towards and within the Orbitrap analyzer. We discovered that ions in mass beyond one megadalton reach a plateau of stability and can be successfully trapped for seconds, travelling a path length of multiple kilometers, thereby enabling precise mass analysis with an effective resolution of greater than 100,000 at m/z 35,000. Through monitoring the frequency of individual ions, we show that these high mass ions, rather than being lost from the trap, can gradually lose residual solvent molecules and, in rare cases, a single elementary charge. Our observations highlight the importance of efficient desolvation for optimal charge detection mass spectrometry and inspired us to implement multiple improved data acquisition strategies. We demonstrate that the frequency drift of single ions due to desolvation and charge stripping can be corrected, which improves the effective ion sampling 23-fold and gives a two-fold improvement in mass precision and resolution, as demonstrated in the analysis of various viral particles.


title: Universal and Programmable Thinning and Thickening of Topologically-Active DNA Fluids

abstract: Understanding and controlling the rheology of polymeric fluids that are out-of-equilibrium is a fundamental problem in biology and industry. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this impressive feat, we combine experiments with theory and simulations to show that complex fluids of entangled DNA display a rich range of non-equilibrium material properties when undergoing enzymatic reactions that alter their topology and size. We reveal that while enzymatically-active fluids of linear DNA display universal viscous thinning, circular DNA fluids - undergoing the same non-equilibrium process - display thickening with a rate and degree that can be tuned by the DNA and enzyme concentrations. Our results open the way for the topological functionalization of DNA-based materials via naturally occurring enzymes to create a new class of  topologically-active materials that can autonomously alter their rheological properties in a programmable manner.


title: Lipid nanodiscs facilitate the identification of a fragment compound inhibiting the enzymatic activity of the bacterial membrane protein MsbA.

abstract: Membrane proteins are critical elements of numerous therapeutic approaches ranging from cancer to bacterial infections. MsbA is a bacterial membrane protein that has received increasing attention as an antibacterial target for its role in the processing of Lipid A, a key precursor of lipopolysaccharide that is essential for bacterial growth. When employing nanodiscs it is possible to stabilize MsbA by providing a membrane-like environment that enhances its enzymatic activity. Taking advantage of this property we have carried out a fragment screening using the biophysical method of surface plasmon resonance. This approach identified several compounds that bind specifically to MsbA. In particular, one of these fragment molecules not only binds to the target, but also inhibits the ATPase activity of the MsbA protein. The similarity of this fragment to the adenine moiety of ATP points at a route to generate stronger and more potent inhibitors for MsbA and even other proteins of its family of ABC transporters. Collectively, our study reveals biophysical approaches that facilitate the identification of fragment candidates inhibiting the activity of membrane proteins.


title: 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves

abstract: Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.

category: plant biology


title: Honey bees cannot sense harmful concentrations of metal pollutants in food

abstract: Whether animals can actively avoid food contaminated with harmful compounds through taste is key to understand their ecotoxicological risks. Here, we investigated the ability of honey bees to perceive and avoid food resources contaminated with common metal pollutants known to impair their cognition at low concentrations (lead, zinc and arsenic). In behavioural assays, bees did not discriminate food contaminated with field-realistic concentrations of these metals. Bees only reduced their food consumption and displayed aversive behaviours at very high, unrealistic concentrations of lead and zinc that they perceived through their antennae and proboscis. Electrophysiological analyses confirmed that high concentrations of the three metals in sucrose solution induced a reduced neural response to sucrose in their antennae. Our results thus show that honey bees can avoid metal pollutants in their food, but only at very high concentrations above regulatory levels. Their inability to detect lower, yet harmful, concentrations in a field-realistic range suggests that metal pollution is a major threat for pollinators.


title: NEST Desktop - An educational application for neuroscience

abstract:
Simulation software for spiking neuronal network models matured in the past decades regarding performance and flexibility. But the entry barrier remains high for students and early career scientists in computational neuroscience since these simulators typically require programming skills and a complex installation. Here, we describe an installation-free Graphical User Interface (GUI) running in the web browser, which is distinct from the simulation engine running anywhere, on the students laptop or on a supercomputer. This architecture provides robustness against technological changes in the software stack and simplifies deployment for self-education and for teachers. Our new open source tool, NEST Desktop, comprises graphical elements for creating and configuring network models, running simulations, and visualizing and analyzing the results. NEST Desktop allows students to explore important concepts in computational neuroscience without the need to learn a simulator control language before. Our experiences so far highlight that NEST Desktop helps advancing both quality and intensity of teaching in computational neuroscience in regular university courses. We view the availability of the tool on public resources like the European ICT infrastructure for neuroscience EBRAINS as a contribution to equal opportunities.

Significance StatementThe graphical user interface NEST Desktop makes neuronal network simulations accessible to non-programmers. It facilitates the interactive exploration of neuronal network models by integrating the whole workflow of wiring up the setup, simulating the neuronal dynamics, and analyzing the recorded activity data into a single tool. NEST Desktop effectively supports teaching the concepts and methods of computational neuroscience. Due to its installation-free web-based implementation, it is in particularly suitable for online courses.


title: Validating marker-less pose estimation with 3D x-ray radiography

abstract:
To reveal the neurophysiological underpinnings of natural movement, neural recordings must be paired with accurate tracking of limbs and postures. Here we validate the accuracy of DeepLabCut (DLC) by comparing it to a 3D x-ray video radiography system that tracks markers placed under the skin (XROMM). We record behavioral data simultaneously with XROMM and high-speed video for DLC as marmosets engage in naturalistic foraging and reconstruct three-dimensional kinematics in a shared coordinate system. We find that DLC tracks position and velocity of 12 markers on the forelimb and torso with low median error (0.272 cm and 1.76 cm/s, respectively) corresponding to 2.9% of the full range of marker positions and 5.9% of the range of speeds. For studies that can accept this relatively small degree of error, DLC and similar marker-less pose estimation tools enable the study of more naturalistic, unconstrained behaviors in many fields including non-human primate motor control.

Summary StatementWe validate the accuracy of DeepLabCut, a widely used marker-less pose estimation tool, using a marker-based 3D x-ray radiography system (XROMM).

category: animal behavior and cognition


title: Spatial dynamics of feedback and feedforward regulation in cell lineages

abstract: Feedback mechanisms within cell lineages are thought to be important for maintaining tissue homeostasis. Mathematical models that assume well-mixed cell populations, together with experimental data, have suggested that negative feedback from differentiated cells on the stem cell self-renewal probability can maintain a stable equilibrium and hence homeostasis. Cell lineage dynamics, however, are characterized by spatial structure, which can lead to different properties. Here, we investigate these dynamics using spatially explicit computational models, including cell division, differentiation, death, and migration / diffusion processes. According to these models, the negative feedback loop on stem cell self-renewal fails to maintain homeostasis, both under the assumption of strong spatial restrictions and fast migration / diffusion. Although homeostasis cannot be maintained, this feedback can regulate cell density and promote the formation of spatial structures in the model. Tissue homeostasis, however, can be achieved if spatially restricted negative feedback on self-renewal is combined with an experimentally documented spatial feedforward loop in which stem cells regulate the fate of transit amplifying cells. This indicates that the dynamics of feedback regulation in tissue cell lineages are more complex than previously thought, and that combinations of spatially explicit control mechanisms are likely instrumental.

category: systems biology


title: A new adaptive procedure for estimating perceptual thresholds: the effects of observer bias and its correction.

abstract:
Adaptive threshold estimation procedures sample close to a subjects perceptual threshold by dynamically adapting the stimulation based on the subjects performance. Yet, perceptual thresholds not only depend on the observers sensory capabilities but also on any bias in terms of their expectations and response preferences, thus distorting the precision of the threshold estimates. Using the framework of signal detection theory (SDT), independent estimates of both, an observers sensitivity and internal processing bias can be delineated from threshold estimates. While this approach is commonly available for estimation procedures engaging the method of constant stimuli (MCS), correction procedures for adaptive methods (AM) are only scarcely applied. In this article, we introduce a new AM that takes individual biases into account, and that allows for a bias-corrected assessment of subjects sensitivity. This novel AM is validated with simulations and compared to a typical MCS-procedure, for which the implementation of bias correction has been previously demonstrated.

Comparing AM and MCS demonstrates the viability of the presented AM. Besides its feasibility, the results of the simulation reveal both, advantages, and limitations of the proposed AM. The procedure has considerable practical implications, in particular for the design of shaping procedures in sensory training experiments, in which task difficulty has to be constantly adapted to an observers performance, to improve training efficiency.


title: Stopping vs Resting state during motor imagery paradigm

abstract: Current non-invasive Brain Machine interfaces commonly rely on the decoding of sustained motor imagery activity (MI). This approach enables a user to control brain-actuated devices by triggering predetermined motor actions. One major drawback of such strategy is that users are not trained to stop their actions. Indeed, the termination process involved in BMI is poorly understood with most of the studies assuming that the end of an MI action is similar to the resting state. Here we hypothesize that the process of stopping MI (MI termination) and resting state are two different processes that should be decoded independently due to the exhibition of different neural pattens. We compared the detection of both states transitions of an imagined movement, i.e. rest-to-movement (onset) and movement-to-rest (offset). Our results shows that both decoders show significant differences in term of performances and latency (N=17 Subjects) with the offset decoder able to detect faster and better MI termination. While studying this difference, we found that the offset decoder is primarily based on the use of features in Beta band which appears earlier. Based on this finding, we also proposed a Random Forrest based decoder which enable to distinguish three classes (MI, MI termination and REST).


title: Multivariate associations between dopamine receptor availability and risky investment decision making across adulthood

abstract: Pharmacological manipulations have revealed that enhancing dopamine increases financial risk taking across adulthood. However, it is unclear whether baseline individual differences in dopamine function, assessed using PET imaging, are related to performance on risky financial decision making tasks. Here, thirty-five healthy adults completed an incentive-compatible learning-based risky investment decision task and a PET scan at rest using [11C]FLB457 to assess dopamine D2-like receptor availability. In the task, participants made choices between a safe asset (bond) and a risky asset (stock) with either an expected value less than the bond ("bad stock") or expected value greater than the bond ("good stock"). Five measures of behavioral performance (choice inflexibility, risk seeking, suboptimal investment) and beliefs (absolute error, optimism) were extracted from the task data and average non-displaceable dopamine D2-like binding potential was extracted from four brain regions of interest (midbrain, amygdala, anterior cingulate, insula) from the PET imaging data. Given the presence of multiple independent and dependent variables, we used canonical correlation analysis (CCA) to evaluate multivariate associations between learning-based decision making and dopamine function controlling for age. Decomposition of the first dimension (r = .76) revealed that the strongest associations were between measures of choice inflexibility, incorrect choice, optimism, amygdala binding potential, and age. Follow-up univariate analyses revealed that amygdala binding potential and age were both independently associated with choice inflexibility. The findings reveal latent associations between baseline neural and behavioral measures suggesting that individual differences in dopamine function may be associated with learning-based financial risk taking in healthy adults.


title: Sexual dimorphism in a neuronal mechanism of spinal hyperexcitability across rodent and human models of pathological pain

abstract: The prevalence and severity of many chronic pain syndromes differ across sex, and recent studies have identified differences in immune signalling within spinal nociceptive circuits as a potential mediator. Although it has been proposed that sex-specific pain mechanisms converge once they reach neurons within the superficial dorsal horn (SDH), direct investigations using rodent and human preclinical pain models have been lacking. Here, we discovered that in the Freunds Adjuvant in vivo model of inflammatory pain, where both male and female rats display tactile allodynia, a pathological coupling between KCC2-dependent disinhibition and NMDA receptor potentiation within SDH neurons was observed in male but not female rats. Unlike males, the neuroimmune mediator, BDNF, failed to downregulate inhibitory signalling elements (KCC2 and STEP61) and upregulate excitatory elements (pFyn, GluN2B, and pGluN2B) in female rats, resulting in no effect of ex vivo BDNF on synaptic NMDA receptor responses in female lamina I neurons. Importantly, this sex difference in spinal pain processing was conserved from rodents to humans. As in rodents, ex vivo spinal treatment with BDNF downregulated markers of disinhibition and upregulated markers of facilitated excitation in SDH neurons from male but not female human organ donors. Ovariectomy in female rats recapitulated the male pathological pain neuronal phenotype, with BDNF driving a coupling between disinhibition and NMDA receptor potentiation in adult lamina I neurons following the prepubescent elimination of sex hormones in females. This discovery of sexual dimorphism in a central neuronal mechanism of chronic pain across species provides a foundational step towards a better understanding and treatment for pain in both sexes.


title: A need for time-varying models to suppress artefacts of tACS in the M/EEG

abstract: Rhythmic modulation of brain activity by transcranial alternating current stimulation (tACS) can entrain neural oscillations in a frequency- and phase-specific manner. However, large stimulation artefacts contaminate concurrent  online neuroimaging measures, including magneto- and electro-encephalography (M/EEG)--restricting most analyses to periods free from stimulation ( offline aftereffects). While many published methods exist for removing artefacts of tACS from M/EEG recordings, they universally assume linear artefacts: either time-invariance (i.e., an artefact is a scaled version of itself from cycle to cycle) or sensor-invariance (i.e., artefacts are scaled versions of one another from sensor to sensor). However, heartbeat and respiration both nonlinearly modulate the amplitude and phase of these artefacts, predominantly via changes in scalp impedance. The spectral symmetry this introduces to the M/EEG spectra may lead to false-positive evidence for entrainment around the frequency of tACS, if not adequately suppressed. Good electrophysiological evidence for entrainment therefore requires that tACS artefacts are fully accounted for before comparing online spectra to a control (e.g., as might be observed during sham stimulation). Here I outline an approach to linearly solve templates for tACS artefacts, and demonstrate how event-locked perturbations to amplitude and phase can be introduced from simultaneous recordings of heartbeat and respiration--effectively forming time-varying models of tACS artefacts. These models are constructed for individual sensors, and can therefore be used in contexts with few EEG sensors and with no assumption of artefact collinearity. I also discuss the feasibility of this approach in the absence of simultaneous recordings of heartbeat and respiration traces.


title: Restoring statistical validity in group analyses of motion-corrupted MRI data

abstract: Motion during the acquisition of magnetic resonance imaging (MRI) data degrades image quality, hindering our capacity to characterize disease in patient populations. Quality control procedures allow the exclusion of the most affected images from analysis. However, the criterion for exclusion is difficult to determine objectively and exclusion can lead to a suboptimal compromise between image quality and sample size. We provide an alternative, data-driven solution that assigns weights to each image, computed from an index of image quality using restricted maximum likelihood. We illustrate this method through the analysis of brain MRI data. The proposed method restores the validity of statistical tests, and performs near optimally in all brain regions, despite local effects of head motion. This method is amenable to the analysis of a broad type of MRI data and can accommodate any measure of image quality.


title: Attrition Rate in Infant fNIRS Research: A Meta-Analysis

abstract:
Understanding the trends and predictors of attrition rate, or the proportion of collected data that is excluded from the final analyses, is important for accurate research planning, assessing data integrity, and ensuring generalizability. In this pre-registered meta-analysis, we reviewed 182 publications in infant (0-24 months) functional near-infrared spectroscopy (fNIRS) research published from 1998 to April 9, 2020 and investigated the trends and predictors of attrition. The average attrition rate was 34.23% among 272 experiments across all 182 publications. Among a subset of 136 experiments which reported the specific reasons of subject exclusion, 21.50% of the attrition were infant-driven while 14.21% were signal-driven. Subject characteristics (e.g., age) and study design (e.g., fNIRS cap configuration, block/trial design, and stimulus type) predicted the total and subject-driven attrition rates, suggesting that modifying the recruitment pool or the study design can meaningfully reduce the attrition rate in infant fNIRS research. Based on the findings, we established guidelines on reporting the attrition rate for scientific transparency and made recommendations to minimize the attrition rates. We also launched an attrition rate calculator (LINK) to aid with research planning. This research can facilitate developmental cognitive neuroscientists in their quest toward increasingly rigorous and representative research.

HighlightsO_LIAverage attrition rate in infant fNIRS research is 34.23%
C_LIO_LI21.50% of the attrition are infant-driven (e.g., inattentiveness) while 14.21% are signal-driven (e.g., poor optical contact)
C_LIO_LISubject characteristics (e.g., age) and study design (e.g., fNIRS cap configuration, block/trial design, and stimulus type) predict the total and infant-driven attrition rates
C_LIO_LIModifying the recruitment pool or the study design can meaningfully reduce the attrition rate in infant fNIRS research
C_LI


title: Macrophages stimulate epicardial VEGFaa to trigger cardiomyocyte proliferation in larval zebrafish heart regeneration

abstract: Cardiac injury induces a sustained macrophage response in both zebrafish and mammals. Macrophages perform a range of both beneficial and detrimental functions during mammalian cardiac repair, yet their precise roles in zebrafish cardiac regeneration are not fully understood. Here we characterise cardiac regeneration in the rapidly regenerating larval zebrafish laser injury model and use macrophage ablation and macrophage-null irf8 mutants to define the role of macrophages in key stages of regeneration. Live heartbeat-synchronised imaging and RNA sequencing revealed an early proinflammatory phase, marked by tnfa+ macrophages, which then resolved to an anti-inflammatory, profibrotic phase. Macrophages were required for cardiomyocyte proliferation but not for functional or structural recovery following injury. Importantly, we found that macrophages are specifically recruited to the epicardial-myocardial niche, triggering the expansion of the epicardium which upregulates VEGFaa expression to induce cardiomyocyte proliferation. Hence, revealing a novel mechanism by which macrophages facilitate cardiac regeneration.

category: immunology


title: Macrophages stimulate epicardial VEGFaa expression to trigger cardiomyocyte proliferation in larval zebrafish heart regeneration


title: APRIL drives a co-ordinated but diverse response as a foundation for plasma cell longevity.

abstract: Antibody secreting cells (ASCs) survive in niche microenvironments, but cellular responses driven by particular niche signals are incompletely defined. The TNF superfamily member APRIL provides a niche signal that can support the transition of transitory plasmablasts into long-lived plasma cells. Here we explore how APRIL helps to establish the biological programs that promote life in the niche, by studying the initial response of primary human plasmablast to APRIL. Under conditions allowing the maturation of ex vivo or in vitro generated plasmablasts, we find that APRIL drives activation of ERK, p38 and JNK. This is accompanied by a classical NF{kappa}B response. Under these conditions induction of AKT phosphorylation is also observed with similar kinetics, paralleled by FOXO1 phosphorylation and nuclear exclusion. Time course gene expression data resolve the downstream co-ordinated transcriptional response. The APRIL-signal propagates via immediate early genes and classical NF{kappa}B responsive targets to converge onto modules of MYC- and OCT2-regulated gene expression linked to cell growth, as well as leading to enhanced expression of ICAM1 and SQSTM1 associated with adhesion and metabolic/stress responses. Thus, APRIL drives a combination of multiple transcriptional programs that co-ordinate cell growth, stress response and adhesion in human ASCs, providing a broad foundation to support plasma cell longevity.


title: Multiple RSV strains infecting HEp-2 and A549 cells reveal cell line-dependent differences in resistance to RSV infection.

abstract:
Respiratory syncytial virus (RSV) is a leading cause of pediatric acute respiratory infection worldwide. There are currently no approved vaccines or antivirals to combat RSV disease. A few transformed cell lines and two historic strains have been extensively used to study RSV. Here we report a thorough molecular and cell biological characterization of HEp-2 and A549 cells infected with four strains of RSV representing both major subgroups as well as historic and more contemporaneous genotypes -- [RSV/A/Tracy (GA1), RSV/A/Ontario (ON), RSV/B/18537 (GB1), RSV/B/Buenos Aires (BA)] -- via measurements of viral replication kinetics and viral gene expression, immunofluorescence-based imaging of gross cellular morphology and cell-associated RSV, and measurements of host response including transcriptional changes and levels of secreted cytokines and growth factors. Our findings strongly suggest 1) the existence of a conserved difference in gene expression between RSV subgroups A and B; 2) the A549 cell line is a more stringent and natural host of replicating RSV than the HEp-2 cell line; and 3) consistent with previous studies, determining the full effects of viral genetic variation in RSV pathogenesis requires model systems as tractable as transformed cell lines but better representative of the human host.

IMPORTANCEInfection with respiratory syncytial virus (RSV) early in life is essentially guaranteed and can lead to severe disease. In vitro data from two historic RSV/A strains and two cell lines, HEp-2 and A549, constitute most of our knowledge; but RSV contains ample variation from two evolving subgroups (A and B) showing recent convergent evolution. Here we measure viral action and host response in HEp-2 and A549 cells infected with four RSV strains from both subgroups and representing both historic and more contemporaneous strains. We discover a subgroup-dependent difference in viral gene expression and find A549 cells are more potently antiviral and more sensitive, albeit subtly, to viral variation. Our findings reveal important differences between RSV subgroups and two widely used cell lines and provide baseline data for experiments with model systems better representative of natural RSV infection.


title: The use of autologous skeletal muscle-derived cells as a sling in the treatment of induced stress urinary incontinence, an experimental study

abstract:
Introduction & hypothesisThis is an experimental pre-clinical study testing for the applicability of autologous skeletal muscle derived cells as a seeded sling for the treatment of SUI in the canine model

Methods10 Mongrel dogs: In 4, skeletal muscle biopsy was harvested from Biceps Femoris. 1 month later, incontinence was induced in 8 dogs through surgical disruption of the pubourethral ligaments. Muscle biopsy was incubated in DMEM medium and after expansion for 8 weeks, MDCs were collected. PGA scaffold was immersed in culture medium, coated with matrigel and cells were seeded. The sling was placed suburethrally in 8 dogs; 2 of which were cell-seeded and 4 had the scaffold only.

Urethral pressure (UP) measurement was done at baseline and 2 weeks alter insertion of the sling.

The urethra with its surrounding was harvested 4 weeks after sling insertion for histopathology. 2 dogs were considered as control, in which no urethrolysis or insertion of slings were carried out

ResultsUP show increase of maximum urethral pressure during static measurement in all dogs with a scaffold inserted. The increase ranged from 5-40 cmH20 (Median 23 cmH20)

Histopathology shows significant periurethral proliferation of skeletal muscles in 4 dogs with cell-seeded scaffold, as demonstrated by Desmin. This was maximum in dogs # 1& 2. This was not the case in the 4 dogs that had PGA sling only.

ConclusionThe use of skeletal muscle -seeded PGA scaffold is a practical technique with preserved integrity of histological differentiation in canine model at short term.

Brief SummaryAutologous Skeletal muscle-derived cells could be propagated in vitro and seeded to PGS scaffolds and used as slings


title: Forest loss and fire in the Dominican Republic during the 21st Century

abstract: Forest loss is an environmental issue that threatens valuable ecosystems in the Dominican Republic (the DR). Although shifting agriculture by slash-and-burn methods is thought to be the main driver of forest loss in the DR, empirical evidence of this relationship is still lacking. Since remotely sensed data on fire occurrence is a suitable proxy for estimating the spread of shifting agriculture, here I explore the association between forest loss and fire during the first 18 years of the 21st Century using zonal statistics and spatial autoregressive models on different spatio-temporal layouts. First, I found that both forest loss and fire were spatially autocorrelated and statistically associated with each other at a country scale over the study period. The hotspots were concentrated mainly in Cordillera Central, Sierra de Bahoruco, Los Haitises/Samana Peninsula, and the northwestern and easternmost regions. Second, from regional scale analysis, I found no statistical association between forest loss and fire in the eastern half of the country, a region that hosts a large international tourism hub. Third, deforestation and fire showed a joint cyclical variation pattern of approximately four years up to 2013, and from 2014 onwards deforestation alone followed a worrying upward trend, while at the same time fire activity declined significantly. Fourth, I found no significant differences between the deforested area of small (<1 ha) and large (>1 ha) clearings of forest. I propose these findings hold potential to inform land management policies that help reduce forest loss, particularly in protected areas, mountain areas, and the vicinity of tourism hubs.


title: Diel population dynamics and mortality of Prochlorococcus in the North Pacific Subtropical Gyre

abstract: Marine ecosystem models often consider temporal dynamics on the order of months to years, and spatial dynamics over regional and global scales as a means to understand the ecology, evolution, and biogeochemical impacts of marine life. Large-scale dynamics are themselves driven over diel scales as a result of light-driven forcing, feedback, and interactions. Motivated by high-frequency measurements taken by Lagrangian sampling in the North Pacific Subtropical Gyre, we develop a hierarchical set of multitrophic community ecology models to investigate and understand daily ecological dynamics in the near-surface ocean including impacts of light-driven growth, infection, grazing, and phytoplankton size structure. Using these models, we investigate the relative impacts of viral-induced and grazing mortality for Prochlorococcus; and more broadly compare in silico dynamics with in situ observations. Via model-data fitting, we show that a multi-trophic model with size structure can jointly explain diel changes in cyanobacterial abundances, cyanobacterial size structure, viral abundance, viral infection rates, and grazer abundances. In doing so, we find that a significant component (between 5% to 55%) of estimated Prochlorococcus mortality is not attributed to either viral lysis (by T4- or T7-like cyanophage) or grazing by heterotrophic nanoflagellates. Instead, model-data integration suggests a heightened ecological relevance of other mortality mechanisms - including grazing by other predators, particle aggregation, and stress-induced loss mechanisms. Altogether, linking mechanistic multitrophic models with high-resolution measurements provides a route for understanding of diel origins of large-scale marine microbial community and ecosystem dynamics.


title: Noninvasive genetic sampling of two flying fox species provides a high rate of genotyping success and a low error rate during amplification

abstract: Noninvasive genetic sampling techniques are useful tools for providing genetic data that are crucially needed for determining suitable conservation actions. Yet these methods may be highly unreliable in certain situations for instance, when working with faecal samples of frugivorous species in tropical areas. In this study, we tested the applicability of noninvasive genetic sampling on two Comoro Islands flying fox species: Pteropus livingstonii and P.seychellensis comorensis in order to optimize the sampling and laboratory process. Both mitochondrial (mtDNA) and microsatellite markers were tested using two common faeces conservation protocols (ethanol and silica gel), and the polymerase chain reaction (PCR) success and genotyping error rates were assessed. The average proportion of mtDNA PCRs positive results was 55% for P.livingstonii and 38% for P.s.comorensis, and higher amplification success was obtained for samples preserved in ethanol as compared to silica gel. The average genotyping success rate was high (74% for P.livingstonii and 95% for P.s.comorensis) and the genotyping error rate was low for both species. Despite our results confirm the effectiveness of using noninvasive genetic sampling methods to study flying fox species, the protocol we used can be optimized to provide higher efficiency. Some recommendations related to field sampling protocols and laboratory methods are proposed in order to optimize amplification rate and minimize genotyping errors.


title: Coexistence patterns and diversity in a trait-based metacommunity on an environmental gradient

abstract: The dynamics of trait-based metacommunities have attracted much attention, but not much is known about how dispersal and spatial environmental variability mutually interact with each other to drive coexistence patterns and diversity. Here, we present a spatially-explicit model of resource competition in a metacommunity on a one-dimensional environmental gradient. We find that both the strength of dispersal and the range of spatial environmental variability affect coexistence patterns, spatial structure, trait distribution and local and regional diversity. Without dispersal, species are sorted according to their optimal growth conditions on the gradient. With the onset of dispersal source-sink effects are initiated, which increases the effects of environmental filtering and interspecific competition and generates trait lumping, so that only a few species from an environment-defined trait range can survive. Interestingly, for very large dispersal rates the system becomes spatially homogeneous, but nevertheless two species at the extreme ends of the trait-off curve can coexist for large environmental variability. Local species richness follows a classic hump-shaped dependence on dispersal rate, while local and regional diversity exhibit a pronounced peak for intermediate values of the environmental variability. Our findings provide important insights into the factors that shape the structure of trait-based metacommunities.


title: Incorporating evolutionary and threat processes into crop wild relatives conservation

abstract: Biodiversity conservation calls for spatial explicit approaches to maximize the representation and persistence of genetic diversity given species idiosyncratic threats in mosaic landscapes, but conservation planning methodologies seldom account for this. Here, we introduce a novel approach that uses proxies of genetic diversity to identify conservation areas, applying systematic conservation planning tools to produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa specific tolerance to human-modified habitats and their extinction risk status. We illustrate our approach with crop wild relatives (CWR) because their intra- and interspecific diversity is important for crop breeding and food security. Although we focus on Mesoamerican CWR within Mexico, our methodology offers new opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.


title: Sticking around: plant persistence strategies on edaphic islands

abstract:
O_LISpecies extinction risk at local scales can be partially offset by strategies promoting in-situ persistence. We explored how persistence-related traits of clonal and non-clonal plants in temperate dry grasslands respond intra- and interspecifically to variation in environmental conditions (soil, climate) and insularity.
C_LIO_LIWe focused on edaphic island specialist species, hypothesizing that plants experiencing harsh soil environments and strong insularity are distinguished by traits supporting enhanced persistence, such as small stature, long lifespan and resource-conservative strategies. We used linear mixed-effect models and bivariate ordinary least squares linear models to explore the response of species triats to environmental and biogeographic predictors.
C_LIO_LIWe found general support for this hypothesis. Soil properties and insularity emerged as the most important drivers of trait patterns. However, clonal species showed more consistent responses to variation in environmental conditions and insularity than non-clonal plants, which were characterized by distinct species-specific responses.
C_LIO_LISoil properties and insularity confirmed their major role in shaping the persistence strategies of edaphic island plant species. These drivers may exert their effect on specific functions (e.g. belowground resource conservation captured by BDMC). Additionally, we unambiguously identified that clonal species had different persistence strategies than non-clonal ones.
C_LI


title: Musculoskeletal modelling of sprawling and parasagittal forelimbs provides insight into synapsid postural transition

abstract: The sprawling-parasagittal postural shift was a major transition during synapsid evolution and is considered key to mammalian ecological diversity. Despite a good fossil record, debate remains over when the shift to parasagittal posture occurred, primarily due to limited comparative biomechanical data on extant species. Here, we built forelimb musculoskeletal models of three extant taxa that bracket the sprawling-parasagittal transition: a tegu lizard, an echidna, and an opossum. We measured shoulder joint range of motion (ROM) about all three degrees of rotational freedom and characterized shoulder muscle moment arms (MMAs) across the entire pose space. Our results show that both the opossum and the tegu had high shoulder joint ROM, and both were substantially higher than the echidna. However, the opossum occupied a distinct region of pose space characterized by high humeral retraction angles. There are clear interspecific differences in MMAs related to posture, with the sprawling tegu and echidna emphasizing humeral depression, and the parasagittal opossum emphasizing humeral elevation. There are also notable differences between our sprawling taxa, with the echidna possessing much greater moment arms for humeral pronation than the tegu. We demonstrate clear functional variation between locomotor grades and use these data to hypothesize major shifts in forelimb function and posture along the mammalian stem.

category: evolutionary biology


title: Seascape genomics reveals population structure and local adaptation in a widespread coral reef snail, Coralliophila violacea (Kiener, 1836)

abstract: Local adaptation to different environments may reinforce neutral evolutionary divergence, especially in populations in the periphery of a species geographic range. Seascape genomics (high-throughput genomics coupled with ocean climate databases) facilitates the exploration of neutral and adaptive variation in concert, developing a clearer picture of processes driving local adaptation in marine populations. This study used a seascape genomics approach to test the relative roles of neutral and adaptive processes shaping population divergence of a widespread coral reef snail, Coralliophila violacea. We collected C. violacea from colonies of their coral host (Porites spp.) at ten locations spanning a large portion of their geographic range. We used RAD-seq to investigate possible local adaptation via genetic-environmental associations with five ocean climate variables. Four genetic partitions were concordant with regions previously observed in mtDNA (Indian Ocean, Coral Triangle, and Hawaiian Islands), with the addition of Vietnam and varying isolation and admixture levels. We identified outlier loci (FDR = 0.10, N = 72) among individual localities and between regions (FDR = 0.10, N = 34), suggesting that some loci are putatively under divergent selection. Association analyses showed that the two strongest drivers of local adaptation were the annual range and mean of sea surface temperature. Populations that experience lower sea surface temperatures at the periphery of C. violaceas geographic range drive these associations. Our results show that local adaptation to different environments likely reinforces neutral divergence, especially in peripheral populations.


title: Beta-Catenin Limits Osteogenesis on Regenerative Materials in a Stiffness-Dependent Manner

abstract:
Targeted refinement of regenerative materials requires mechanistic understanding of cell-material interactions. The nanoparticulate mineralized collagen glycosaminoglycan (MC-GAG) scaffold is a porous biomaterial that promotes regenerative healing of calvaria defects in vivo without addition of exogenous growth factors or progenitor cells, suggesting its potential as an off-the-shelf implant for reconstructing skull defects. In this work, we evaluate the relationship between material stiffness, a tunable MC-GAG property, and activation of the canonical Wnt (cWnt) signaling pathway. Primary human bone marrow-derived mesenchymal stem cells (hMSCs) were differentiated on two MC-GAG scaffolds varying by stiffness (non- crosslinked, NX-MC, 0.3 kPa vs. conventionally crosslinked, MC, 3.9 kPa). hMSCs exhibited increased expression of activated {beta}-catenin, the major cWnt intracellular mediator, and the mechanosensitive YAP protein with near complete subcellular colocalization in stiffer MC scaffolds. Small molecule Wnt pathway inhibitors reduced activated {beta}-catenin and YAP protein quantities and colocalization, osteogenic differentiation, and mineralization on MC, with no effects on NX-MC. Concomitantly, Wnt inhibitors increased BMP4 and phosphorylated Smad1/5 (p-Smad1/5) expression on MC, but not NX-MC. Unlike non-specific Wnt pathway downregulation, isolated canonical Wnt inhibition with {beta}-catenin knockdown increased osteogenic gene expression and mineralization specifically on the stiffer MC. {beta}-catenin knockdown also increased p-Smad1/5, Runx2, and BMP4 expression only on the stiffer MC material. Our data indicates stiffness-induced activation of the Wnt and mechanotransduction pathways promotes osteogenesis in MC-GAG scaffolds. However, activated {beta}-catenin is a limiting agent and may serve as a useful target or readout for optimal modulation of stiffness in skeletal regenerative materials.

One Sentence Summary{beta}-Catenin limits stiffness-induced osteogenenic differentiation on nanoparticulate mineralized collagen glycosaminoglycan materials

category: bioengineering


title: Raman Needle Arthroscopy for In Vivo Molecular Assessment of Cartilage

abstract: The development of treatments for osteoarthritis (OA) is burdened by the lack of standardized biomarkers of cartilage health that can be applied in clinical trials. We present a novel arthroscopic Raman probe that can "optically biopsy" cartilage and quantify key ECM biomarkers for determining cartilage composition, structure, and material properties in health and disease. Technological and analytical innovations to optimize Raman analysis include: 1) multivariate decomposition of cartilage Raman spectra into ECM-constituent-specific biomarkers (glycosaminoglycan [GAG], collagen [COL], water [H2O] scores), and 2) multiplexed polarized Raman spectroscopy to quantify superficial zone collagen anisotropy via a PLS-DA-derived Raman collagen alignment factor (RCAF). Raman measurements were performed on a series of ex vivo cartilage models: 1) chemically GAG-depleted bovine cartilage explants (n=40), 2) mechanically abraded bovine cartilage explants (n=30), 3) aging human cartilage explants (n=14), and 4) anatomical-site-varied ovine osteochondral explants (n=6). Derived Raman GAG score biomarkers predicted 95%, 66%, and 96% of the variation in GAG content of GAG-depleted bovine explants, human explants, and ovine explants, respectively (p<0.001). RCAF values were significantly different for explants with abrasion-induced superficial zone collagen loss (p<0.001). The multivariate linear regression of Raman-derived ECM biomarkers (GAG and H2O scores) predicted 94% of the variation in elastic modulus of ovine explants (p<0.001). Finally, we demonstrated the first in vivo Raman arthroscopy assessment of an ovine femoral condyle through intraarticular entry into the synovial capsule. This work advances Raman arthroscopy towards a transformative low cost, minimally invasive diagnostic platform for objective monitoring of treatment outcomes from emerging OA therapies.


title: GIP: An open-source computational pipeline for mapping genomic instability from protists to cancer cells

abstract:
Genome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many human pathologies. Even though genome instability encompasses different types of genomic alterations, most available genome analysis software are limited to just one kind mutation or analytical step. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida, and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our analysis tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline allowed us to uncover the convergent amplification of erythrocyte binding proteins and to identify a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.

One Sentence SummaryGIP - a novel pipeline for detecting, comparing and visualizing genome instability.


title: Active feature selection discovers minimal gene-sets for classifying cell-types and disease states in single-cell mRNA-seq data

abstract: Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological information with a minimal number of genes. Here, we introduce an active learning method (ActiveSVM) that identifies minimal but highly-informative gene sets that enable the identification of cell-types, physiological states, and genetic perturbations in single-cell data using a small number of genes. Our active feature selection procedure generates minimal gene sets from single-cell data through an iterative cell-type classification task where misclassified cells are examined at each round of analysis to identify maximally informative genes through an  active support vector machine (ActiveSVM) classifier. By focusing computational resources on misclassified cells, ActiveSVM scales to analyze data sets with over a million single cells. We demonstrate that ActiveSVM feature selection identifies gene sets that enable 90% cell-type classification accuracy across a variety of data sets including cell atlas and disease characterization data sets. The method generalizes to reveal genes that respond to genetic perturbations and to identify region specific gene expression patterns in spatial transcriptomics data. The discovery of small but highly informative gene sets should enable substantial reductions in the number of measurements necessary for application of single-cell mRNA-seq to clinical tests, therapeutic discovery, and genetic screens.


title: Active feature selection discovers minimal gene sets for classifying cell types and disease states with single-cell mRNA-seq data


title: Prediction of biological age by morphological staging of sarcopenia in Caenorhabditis elegans

abstract: Sarcopenia encompasses a progressive decline in allover muscle quantity and quality. Given its close association with aging, it may represent a valuable healthspan marker. Given the strong commonalities with human muscle structure and the facile visualization possibilities, C. elegans represents an attractive model for studying the relationship between sarcopenia and healthspan. However, classical assessment relies on visual scoring of muscle architecture, which is subjective and inaccurate. To resolve this, we have developed an automated image analysis pipeline for the detailed quantification and classification of muscle integrity in confocal microscopy images from a cohort of aging myosin::GFP reporter strains. We then extracted a variety of morphological descriptors and found a subset to scale linearly with age. This allowed us to establish a general linear model that predicts biological age from a morphological muscle signature. To validate the model, we evaluated muscle architecture in long-lived worms that are known to experience delayed sarcopenia by targeted RNAi-mediated knockdown of the daf-2 gene. We conclude that quantitative microscopy allows for staging sarcopenia in C. elegans and will be of use for systematic screening for pharmacological or genetic modulators that mitigate age-related muscle frailty and thus improve healthspan in C. elegans.


title: Transcriptional reprogramming and constitutive PD-L1 expression in melanoma are associated with dedifferentiation and activation of interferon and tumor necrosis factor signaling pathways

abstract:
Melanoma is the most aggressive type of skin cancer, with increasing incidence worldwide. Advances in targeted therapy and immunotherapy have improved the survival of melanoma patients experiencing recurrent disease, but unfortunately treatment resistance frequently reduces patient survival. Resistance to targeted therapy is associated with transcriptomic changes, and has also been shown to be accompanied by increased expression of programmed death ligand 1 (PD-L1), a potent inhibitor of immune response. Intrinsic upregulation of PD-L1 is associated with genome-wide DNA hypomethylation and widespread alterations in gene expression in melanoma cell lines. However, an in-depth analysis of the transcriptomic landscape of melanoma cells with intrinsically upregulated PD-L1 expression is lacking. To determine the transcriptomic landscape of intrinsically upregulated PD-L1 expression in melanoma, we investigated transcriptomes in melanomas with constitutive versus inducible PD-L1 expression (referred to as PD-L1CON and PD-L1IND). RNA-Seq analysis was performed on seven PD-L1CON melanoma cell lines and ten melanoma cell lines with low inducible PD-L1IND expression. We observed that PD-L1CON melanoma cells had a reprogrammed transcriptome with a characteristic pattern of dedifferentiated gene expression, together with active interferon (IFN) and tumor necrosis factor (TNF) signalling pathways. Furthermore, we identified key transcription factors that were also differentially expressed in PD-L1CON versus PD-L1IND melanoma cell lines. Overall, our studies describe transcriptomic reprogramming of melanomas with PD-L1CON expression.

Simple SummaryMelanoma, an aggressive form of skin cancer, is frequently associated with drug resistance in the advanced stages. For instance, frequently resistance is observed to sequential treatment of melanoma with targeted therapy and immunotherapy. In this research, the authors investigated whether potential transcriptional mechanisms and pathways associated with PD-L1 protein expression could underlie targeted therapy drug resistance in melanoma. The authors found a PD-L1 expression transcriptional pattern underlies resistance to targeted therapy in a subgroup of melanomas. These melanomas were markedly dedifferentiated, as compared to melanomas that were not drug resistant. Understanding changes in transcription and molecular pathways that lead to drug resistance could allow researchers to develop interventions to prevent drug resistance from occurring in melanoma, which could also be relevant to other cancer types.

category: cancer biology


title: Sirtuin 5 levels are limiting in preserving cardiac function and suppressing fibrosis in response to pressure overload

abstract: Heart failure (HF) is defined as an inability of the heart to pump blood adequately to meet the bodys metabolic demands. HF with reduced systolic function is characterized by cardiac hypertrophy, ventricular fibrosis and remodeling, and decreased cardiac contractility, leading to cardiac functional impairment and death. Transverse aortic constriction (TAC) is a well-established model for inducing hypertrophy and HF in rodents. Mice globally deficient in sirtuin 5 (SIRT5), a NAD+-dependent deacylase, are hypersensitive to cardiac stress and display increased mortality after TAC. Prior studies assessing SIRT5 functions in the heart have all employed loss-of-function approaches. In this study, we generated SIRT5 overexpressing (SIRT5OE) mice, and evaluated their response to chronic pressure overload induced by TAC. Compared to littermate controls, SIRT5OE mice were protected from left ventricular dilation and impaired ejection fraction, adverse functional consequences of TAC. Transcriptomic analyses revealed that SIRT5 suppresses key HF sequelae, including the metabolic switch from fatty acid oxidation to glycolysis, immune activation, and increased fibrotic signaling. We conclude that SIRT5 is a limiting factor in the preservation of cardiac function in response to experimental pressure overload.

category: pathology


title: Nitrates increase abscisic acid levels to regulate haustoria formation in the parasitic plant Phtheirospermum japonicum

abstract: Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. Some, the obligate parasites are entirely dependent on their hosts for survival, whereas others, the facultative parasites, are independent of their hosts and infect depending on environmental conditions and the presence of the host. How parasitic plants regulate their haustoria in response to their environment is largely unknown. Using the facultative root parasite Phtheirospermum japonicum, we found that external nutrient levels modified haustorial numbers. This effect was independent of phosphate and potassium but nitrates were sufficient and necessary to block haustoria formation. Elevated nitrate levels prevented the activation of hundreds of genes associated with haustoria formation, downregulated genes associated with xylem development and increased levels of abscisic acid (ABA). Enhancing ABA levels independently of nitrates blocked haustoria formation whereas reducing ABA biosynthesis allowed haustoria to form in the presence of nitrates suggesting that nitrates mediated haustorial regulation in part via ABA production. Nitrates also inhibited haustoria formation and reduced infectivity of the obligate root parasite Striga hermonthica, suggesting a more widely conserved mechanism by which parasitic plants adapt their extent of parasitism according to nitrogen availability in the external environment.


title: Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research

abstract: Inspired by well-established material and pedagogy provided by The Carpentries (Wilson 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al. 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.

category: scientific communication and education


title: Emergent properties of coupled bistable switches

abstract: Understanding the dynamical hallmarks of network motifs is one of the fundamental aspects of systems biology. Positive feedback loops constituting one or two nodes - self-activation, toggle switch, and double activation loops - are commonly observed motifs in regulatory networks underlying cell-fate decision systems. Their individual dynamics are well-studied; they are capable of exhibiting bistability. However, studies across various biological systems suggest that such positive feedback loops are interconnected with one another, and design principles of coupled bistable motifs remain unclear. We wanted to ask what happens to bistability or multistability traits and the phenotypic space (collection of phenotypes exhibited by a system) due to the couplings. In this study, we explore a set of such interactions using discrete and continuous simulation methods. Our results suggest that couplings that do not connect the bistable switches in a way that contradicts the connections within individual bistable switches lead to a steady state space that is strictly a subset of the set of possible combinations of steady states of bistable switches. Furthermore, adding direct and indirect self-activations to these coupled networks can increase the frequency of multistability. Thus, our observations reveal specific dynamical traits exhibited by various coupled bistable motifs.


title: Validating the Representational Space of DeepReinforcement Learning Models of Behavior withNeural Data

abstract: Deep Reinforcement Learning (Deep RL) agents have in recent years emerged as successful models of animal behavior in a variety of complex learning tasks, as exemplified by Song et al. [2017]. As agents are typically trained to mimic an animal subject, the emphasis in past studies on behavior as a means of evaluating the fitness of models to experimental data is only natural. But the true power of Deep RL agents lies in their ability to learn neural computations and codes that generate a particular behavior--factors that are also of great relevance and interest to computational neuroscience. On that basis, we believe that model evaluation should include an examination of neural representations and validation against neural recordings from animal subjects. In this paper, we introduce a procedure to test hypotheses about the relationship between internal representations of Deep RL agents and those in animal neural recordings. Taking a sequential learning task as a running example, we apply our method and show that the geometry of representations learnt by artificial agents is similar to that of the biological subjects, and that such similarities are driven by shared information in some latent space. Our method is applicable to any Deep RL agent that learns a Markov Decision Process, and as such enables researchers to assess the suitability of more advanced Deep Learning modules, or map hierarchies of representations to different parts of a circuit in the brain, and help shed light on their function. To demonstrate that point, we conduct an ablation study to deduce that, in the sequential task under consideration, temporal information plays a key role in molding a correct representation of the task.


title: Freely-moving mice visually pursue prey using a retinal area with least optic flow

abstract: Mice have a large visual field that is constantly stabilized by vestibular ocular reflex driven eye rotations that counter head-rotations. While maintaining their extensive visual coverage is advantageous for predator detection, mice also track and capture prey using vision. However, in the freely moving animal quantifying object location in the field of view is challenging. Here, we developed a method to digitally reconstruct and quantify the visual scene of freely moving mice performing a visually based prey capture task. By isolating the visual sense and combining amouse eye optic model with the head and eye rotations, the detailed reconstruction of the digital environment and retinal features were projected onto the corneal surface for comparison, and updated throughout the behavior. By quantifying the spatial location of objects in the visual scene and their motion throughout the behavior, we show that the image of the prey is maintained within a small area, the functional focus, in the upper-temporal part of the retina. This functional focus coincides with a region of minimal optic flow in the visual field and consequently minimal motion-induced image blur during pursuit, as well as the reported high density-region of Alpha-ON sustained retinal ganglion cells.


title: Epigenetic Conditioning Induces Intergenerational Resilience to Dementia in a Mouse Model of Vascular Cognitive Impairment

abstract:
BackgroundVascular cognitive impairment and dementia (VCID), which occurs immediately or in delayed fashion in 25-30% of stroke survivors, or secondary to chronic cerebral hypoperfusion, is the second leading cause of dementia following Alzheimers disease. To date, efficacious therapies are unavailable. We have shown previously in mice that repetitive hypoxic preconditioning (RHC) induces a long-lasting resilience to acute stroke (Stowe et al., 2011). More recently, we documented that untreated, first-generation adult progeny of mice exposed to RHC prior to mating are protected from retinal ischemic injury (Harman et al., 2020), consistent with accumulating evidence supporting the concept that long-lasting phenotypes induced epigenetically by intermittent stressors may be heritable. We undertook the present study to test the hypothesis that RHC will induce resilience to VCID, and that such RHC-induced resilience can also be inherited.

MethodsChronic cerebral hypoperfusion (CCH) was induced in C57BL/6J mice secondary to bilateral carotid artery stenosis with microcoils in both the parental (F0) generation, and in their untreated first-generation (F1) offspring. Cohorts of F0 mice were directly exposed to either 8 wks of RHC (1 h of systemic hypoxia [11% oxygen] 3x/week) or normoxia prior to CCH. Cohorts of F1 mice were derived from F0 mice treated with RHC prior to mating, and untreated, normoxic controls that were age-matched at the time of stenosis induction. Demyelination in the corpus callosum of F0 mice was assessed following 3 months of CCH by immunohistochemistry. Mice from both generations were assessed for short-term recognition memory in vivo by novel object preference (NOP) testing following 3 months of CCH, and a month thereafter, ex vivo measurements of CA1 hippocampal long-term potentiation (LTP) were recorded from the same animals as a metric of long-lasting changes in synaptic plasticity.

ResultsThree months of CCH caused demyelination and concomitant impairments in recognition memory in control mice from both generations. However, these CCH-induced memory impairments were prevented in F0 animals directly treated with RHC, as well as in their untreated adult F1 progeny. Similarly, hippocampal LTP was preserved in the 4-month CCH cohorts of mice directly treated with RHC, and in their untreated offspring with CCH.

ConclusionsOur findings demonstrate that RHC or other repetitively-presented, epigenetic-based therapeutics may hold promise for inducing a long-lasting resilience to VCID in treated individuals, and in their first-generation adult progeny.


title: The anatomical logic of smell

abstract: The sense of smell helps us navigate the environment, but its molecular architecture and underlying logic remain unknown. The spatial location of odorant receptor genes (Olfrs) in the nose is widely thought to be independent of the structural diversity of the odorants they detect. Using spatial transcriptomics, we created a genome-wide 3D atlas of the mouse olfactory mucosa (OM). Topographic maps of genes differentially expressed in space reveal that both Olfrs and non-Olfrs are distributed in a continuous and overlapping fashion over five broad zones in the OM. The spatial locations of Olfrs correlate with the mucus solubility of the odorants they recognize, providing direct evidence for the chromatographic theory of olfaction. This resource resolved the molecular architecture of the mouse OM, and will inform future studies on mechanisms underlying Olfr gene choice, axonal pathfinding, patterning of the nervous system, and basic logic for the peripheral representation of smell.


title: A 3D transcriptomics atlas of the mouse olfactory mucosa