title: DENSS-Multiple: A Structure Reconstruction Method using Multiple Contrast Variation of Small-Angle Neutron Scattering Based on the DENSS Algorithm

abstract: Small-angle neutron scattering (SANS) provides easily manipulable neutron contrast variation that has been widely exploited to study the structure and function of biological macromolecules and their complex in solution. Here, we developed a method called DENSS-Multiple based on the DENSS (DENsity from Solution Scattering) algorithm to provide ab initio structure reconstruction with SANS contrast variation data. This new tool can exploit additional information in different SANS contrasts for improved ab initio reconstruction results.


title: Creating a 'Timeline' of ductal carcinoma in situ to identify processes and biomarkers for progression towards invasive ductal carcinoma

abstract: Ductal carcinoma in situ (DCIS) is considered a non-invasive precursor to breast cancer, and although associated with an increased risk of developing invasive disease, many women with DCIS will never progress beyond their in situ diagnosis. The path from normal duct to invasive disease is not well understood, and efforts to do so are hampered by the substantial heterogeneity that exists between patients and even within patients. Using gene expression analysis, we have generated a  Timeline of disease progression, utilising the variability within patients and combining >2,000 individually micro-dissected ductal lesions from 145 patients into one continuous trajectory. Using this Timeline we show there is a progressive loss in basal layer integrity, coupled with two epithelial to mesenchymal transitions (EMT), one early in the timeline and a second just prior to cells leaving the duct. We identify early processes and potential biomarkers, including CAMK2N1, MNX1, ADCY5, HOXC11 and ANKRD22, whose reduced expression is associated with the progression of DCIS to invasive breast cancer.

category: cancer biology


title: Spatial patterning and immunosuppression of glioblastoma immune contexture in hypoxic niches

abstract: Glioblastoma (GBM), a highly lethal brain cancer, is notorious for its immunosuppressive microenvironment, yet current immunotherapies are ineffective. Thus, understanding the immune contexture and governing factors of immunosuppression is crucial. Here, we identified a highly dynamic temporospatial patterning of tumor-associated macrophages (TAMs) corresponding to vascular changes in GBM: as tumor vessels transition from an initial dense regular network to later scant engorged vasculature, CD68+ TAMs shift away from perivascular regions to poorly vascularized areas. Remarkably, this process is heavily influenced by the immunocompetency of host animal, as tumor vessels in immunodeficient hosts remained dense and regular while TAMs evenly distributed. Utilizing a sensitive fluorescent reporter to track tumor hypoxia, we revealed that hypoxic niche controls immunosuppression by at least two mechanisms: first, attracting and sequestering activated TAMs in hypoxic zones, and second, reprograming entrapped TAMs towards an immunotolerant state. Indeed, entrapped TAMs also experience hypoxia and upregulate phagocytic marker Cd68 and immunotolerant genes Mrc1 and Arg1, thereby facilitating debris clearing, inflammatory containment, and immunosuppression in hypoxic zones. Mechanistically, we identified Ccl8 and IL-1{beta} as two hypoxic niche factors released by TAMs in response to cues from hypoxic GBM cells, functioning to reinforce TAM retainment. Reciprocally, niche factors also shape the transcriptional responses of hypoxic tumor cells that exhibit quiescence and mesenchymal shift. Moreover, hypoxic niche factors are highly enriched in human GBMs, particularly mesenchymal subtype, and predict poor survival. Importantly, perturbing hypoxic niches resulted in reduced TAM sequestration and better tumor control. Together, understanding the mutual influence of immune contexture and metabolic landscape has important ramifications for improving efficacy of immunotherapies against GBM.


title: Loss of LGR5 through plasticity or gene ablation is associated with therapy resistance and enhanced MET-STAT3 signaling in colorectal cancer cells

abstract:
Plasticity plays a significant role in colorectal tumor initiation, progression, and drug resistance. LGR5 is highly expressed in colorectal cancer (CRC) and marks functional cancer stem cells (CSCs). While LGR5+ CSCs are tumor-initiating, the majority of CRC cells that disseminate to seed metastases are LGR5-; however, reemergence of LGR5+ CSCs is required to drive metastatic outgrowth. LGR5+ CSCs have been shown to convert to LGR5- CRC cells in response to chemotherapies and this loss of LGR5 promotes a more drug-resistant phenotype. However, the molecular mechanisms that mediate plasticity remain elusive. In this study, we demonstrate conversion of LGR5+ CRC cells to an LGR5- state in response to chemotherapy, LGR5-targeted antibody-drug conjugates (ADCs), or LGR5 gene ablation, led to activation of STAT3. Further investigation revealed increased STAT3 activation occurred a result of increased MET activity. LGR5 overexpression decreased MET-STAT3 activity and sensitized CRC cells to therapy. STAT3 inhibition suppressed MET phosphorylation, while constitutively active STAT3 reduced LGR5 levels and increased MET activity, suggesting a potential feedback mechanism. Combination treatment of MET-STAT3 inhibitors with irinotecan or ADCs substantiated synergistic effects in vitro. In CRC xenografts, STAT3 inhibition combined with irinotecan enhanced tumor growth suppression and prolonged survival. These findings suggest a mechanism by which drug-resistant LGR5- CRC cells acquire a survival advantage through activation of MET-STAT3 and provide rationale for new treatment strategies that target CRC cell plasticity.

SignificanceThis study reveals that transition of highly plastic LGR5+ CRC cells to a more drug-resistant LGR5- state involves activation of MET-STAT3 signaling and provides new insight into therapeutic strategies to combat plasticity.


title: A primary patient-derived model for investigating functional heterogeneity within the human Leukemic Stem Cell Compartment

abstract: The ability of leukemic stem cells (LSC) to evade therapy and fuel leukemic progression causing relapse impedes therapeutic success in acute myeloid leukemia (AML). The LSC pool within a patient sample is not homogenous but comprises distinct LSC subsets that vary in self-renewal and propagation properties. The stemness programs that underlie LSC types are poorly understood since human LSC studies require primary patient samples where LSC numbers are low and isolation methods impure. To overcome these challenges, we developed a patient-derived AML model system (OCI-AML22) displaying a functionally, transcriptionally and epigenetically defined cellular hierarchy driven by functional LSCs that can be immunophenotypically identified and isolated. Through single cell and functional approaches, the OCI-AML22 LSC fraction was found to contain distinct LSCs that vary in proliferative and differentiation properties. OCI-AML22 represents a valuable resource to decipher mechanisms driving stemness and the multiple layers of heterogeneity within LSCs.


title: Remodelling of potassium currents underlies arrhythmic action potential prolongation under beta-adrenergic stimulation in hypertrophic cardiomyopathy

abstract: Hypertrophic cardiomyopathy (HCM) patients often present an enhanced arrhythmogenicity that can lead to lethal arrhythmias, especially during exercise. Recent studies have indicated an abnormal response of HCM cardiomyocytes to {beta}-adrenergic receptor stimulation ({beta}-ARS), with prolongation of their action potential rather than shortening. The mechanisms underlying this aberrant response to sympathetic stimulation and its possible proarrhythmic role remain unknown. The aims of this study are to investigate the key ionic mechanisms underlying the HCM abnormal response to {beta}-ARS and the resultant repolarisation abnormalities using human-based experimental and computational methodologies. We integrated and calibrated the latest models of human ventricular electrophysiology and {beta}-ARS using experimental measurements of human adult cardiomyocytes from control and HCM patients. Our major findings include: (1) the developed in silico models of {beta}-ARS capture the behaviour observed in the experimental data, including the aberrant response of HCM cardiomyocytes to {beta}-ARS; (2) the reduced increase of potassium currents under {beta}-ARS was identified as the main mechanism of action potential prolongation in HCM, rather than a more sustained inward calcium current; (3) dispersion of repolarisation between healthy and HCM tissue was increased upon {beta}-ARS, while transmural dispersion in HCM tissue was reduced; (4) models presenting repolarisation abnormalities were characterised by downregulation of the rapid delayed rectifier potassium current and the sodium-potassium pump, while inward currents were upregulated. In conclusion, our results identify causal relationships between the HCM phenotype and its arrhythmogenic response to {beta}-ARS through the downregulation of potassium currents.

category: physiology


title: Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain

abstract: Cognitive decline is a common pathological outcome during aging, with an ill-defined cellular or molecular basis. Among the cellular changes observed with age are alterations to neuronal plasticity, changes in the glial compartment and the decline of the neurogenic niche. In the recent years, the concept of inflammaging, defined as a low-grade inflammation increasing with age, has emerged as a nexus for age-related diseases. This increase of basal inflammation is also observed in the central nervous system. While not classically considered a neurological cell type, infiltrating T cells increase in the brain with age, and may be responsible for amplification of inflammatory cascades and disruptions to the neurogenic niche. Recently, a small resident population of regulatory T cells has been identified in the brain, and the capacity of IL2-mediated expansion of this population to counter neuroinflammatory disease has been demonstrated. Here we test a brain-specific IL2 delivery system for the prevention of neurological decline in aging mice. We identify the molecular hallmarks of aging in the brain glial compartments, and identify partial restoration of this signature through IL2 treatment. At a behavioral level, brain IL2 delivery prevented the age-induced defect in spatial learning, without improving the general decline in motor skill or arousal. These results identify immune modulation as a potential path to preserving cognitive function for healthy ageing.

category: neuroscience


title: Visual Perception of 3D Space and Shape In Time - Part IV: 3D Shape Recognition by 3D Rotation

abstract:
Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear at any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size upfront at the object center, the direct comparison between the one-sized memory and an incoming new image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly as we experience it in our daily lives?

This paper specifically addresses the recognition of human faces with arbitrary 3D orientation in the [Roll, Yaw, Pitch] axes. According to our new model of NHT (Neural Holography Tomography), space is represented by time utilizing the phase of the alpha brainwave. This principle should be applicable to any mental rotation in 3D; thus, it predicts that extra time is required to perceive a rotated face to revolve it back to upright by the constant-speed alpha wave.

To assess this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of upright unfamiliar faces. Following the memorization phase, similar stimuli with a wide range of rotating faces in 3D were presented, and RTs were recorded. As expected, the memorized upfront face was the fastest RT. The excess of the RT was observed proportional to the rotating angle in all [Roll, Yaw, Pitch] axes. Roll had the flattest slope, whereas upper Pitch was the steepest. We suspect that Roll is the swiftest mental operation because it can be conducted by the linear frame translation on the log-polar retinotopy of the visual cortex.


title: Deep networks may capture biological behaviour for shallow, but not deep, empirical characterizations

abstract: We assess whether deep convolutional networks (DCN) can account for a most fundamental property of human vision: detection/discrimination of elementary image elements (bars) at different contrast levels. The human visual process can be characterized to varying degrees of  depth, ranging from percentage of correct detections to detailed tuning and operating characteristics of the underlying perceptual mechanism. We challenge deep networks with the same stimuli/tasks used with human observers and apply equivalent characterization of the stimulus-response coupling. In general, we find that popular DCN architectures do not account for signature properties of the human process. For shallow depth of characterization, some variants of network-architecture/training-protocol produce human-like trends; however, richer empirical descriptors expose glaring discrepancies. These results urge caution in assessing whether neural networks do or do not capture human behaviour: ultimately, our ability to assess  success in this area can only be as good as afforded by the depth of behavioural characterization against which the network is evaluated. We propose a novel set of metrics/protocols that impose stringent constraints on the evaluation of DCN behaviour as adequate approximation of biological processes.


title: A critical contribution of a sparse neuronal ensemble in the amygdala central nucleus to extinction

abstract: Adaptive behaviour critically depends on the delicate and dynamic balance between acquisition and extinction memories. Disruption of this balance, particularly when the extinction memory loses control over behaviour, is the root of treatment failure of maladaptive behaviours such as substance abuse or anxiety disorders. Understanding this balance requires a better understanding of the underlying neurobiology and its contribution to behavioural regulation. Here, we used Daun02 in Fos-lacZ transgenic rats to delete extinction-recruited neuronal ensembles in BLA and CN and examine their contribution to behaviour in an appetitive Pavlovian task. Deletion of extinction-activated ensembles in CN but not BLA impaired the retrieval of extinction and increased activity in the BLA. The disruptive effect of deleting these CN ensembles was enduring as it hindered further extinction learning, and promoted greater levels of behavioural restoration across opposing levels of the response scale seen in spontaneous recovery and reinstatement. Our data indicate that the initial extinction-recruited CN ensemble is critical to the acquisition-extinction balance, and that greater behavioural restoration does not mean weaker extinction contribution. These findings provide a novel avenue for thinking about the neural mechanisms of extinction and in developing treatments for cue-triggered appetitive behaviours.


title: The influence of movement-related costs when searching to act and acting to search

abstract:
Real world search behaviour often involves limb movements, either during search or following search. Here we investigated whether movement-related costs influence search behaviour in two kinds of search tasks. In our visual search tasks, participants made saccades to find a target object among distractors and then moved a cursor, controlled by the handle of a robotic manipulandum, to the target. In our manual search tasks, participants moved the cursor to perform the search, placing it onto objects to reveal their identity as either a target or a distractor. Across experiments, we manipulated either the effort or time costs associated with movement such that these costs varied across the search space. We varied effort by applying different resistive forces to the handle and we varied time costs by altering the speed of the cursor. Our analysis of cursor and eye movements during manual and visual search, respectively, showed that effort influenced manual search but did not influence visual search. In contrast, time costs influenced both visual and manual search. Our results demonstrate that, in addition to perceptual and cognitive factors, movement-related costs can also influence search behaviour.

Public Significance StatementMany of the tasks we perform on a daily basis involve searching for targets. Numerous studies have investigated perceptual and cognitive factors that influence decisions about where to search. However, few studies have examined how search is influenced by movement-related costs associated with manual search (e.g., opening drawers to find a corkscrew) or acting on an object once it has been located (e.g., reaching for a particular bottle of wine once it has been spied in a rack). We show that movement effort and time costs associated with manual search, and time costs associated with moving after visual search, can influence decision-making about where to search over time.


title: Intracranial EEG spectral feature analysis and focal brain stimulation reveal affective specialization within dorsal anterior cingulate cortex

abstract: Emotion is represented in several limbic and prefrontal cortical brain areas herein referred to as the Affective Salience Network (ASN). Within this network, less is known about how valence and intensity are processed in the dorsal anterior cingulate (dACC), and how affective processes in dACC compare to activity in other nodes within the ASN. Using a novel spectral feature approach to analyze intracranial electrophysiological data, we discover hemispheric specialization in the dACC such that the right hemisphere is sensitive to intensity while the left hemisphere is sensitive to valence and negative affective bias. We further applied 130 Hz continuous stimulation to the anterior cingulum bundle while patients viewed emotional faces. Faces were rated happier in all patients, an effect modulated by baseline affective bias, suggesting a causal role for the dACC during the processing of external affective stimuli.


title: Dopaminergic modulation of dynamic emotion perception

abstract:
Emotion recognition abilities are fundamental to our everyday social interaction. A large number of clinical populations show impairments in this domain, with emotion recognition atypicalities being particularly prevalent among disorders exhibiting a dopamine system disruption (e.g., Parkinsons disease). Although this suggests a role for dopamine in emotion recognition, studies employing dopamine manipulation in healthy volunteers have exhibited mixed neural findings and no behavioural modulation. Interestingly, whilst a dependence of dopaminergic drug effects on individual baseline dopamine function has been well established in other cognitive domains, the emotion recognition literature so far has failed to account for these possible interindividual differences. The present within-subjects study therefore tested the effects of the dopamine D2 antagonist haloperidol on emotion recognition from dynamic, whole-body stimuli while accounting for interindividual differences in baseline dopamine. 33 healthy male and female adults rated emotional point-light walkers (PLWs) once after ingestion of 2.5 mg haloperidol and once after placebo. To evaluate potential mechanistic pathways of the dopaminergic modulation of emotion recognition, participants also performed motoric and counting-based indices of temporal processing. Confirming our hypotheses, effects of haloperidol on emotion recognition depended on baseline dopamine function, where individuals with low baseline dopamine showed enhanced, and those with high baseline dopamine decreased emotion recognition. Drug effects on emotion recognition were related to drug effects on movement-based and explicit timing mechanisms, indicating possible mediating effects of temporal processing. Results highlight the need for future studies to account for baseline dopamine and suggest putative mechanisms underlying the dopaminergic modulation of emotion recognition.

Significance statementA high prevalence of emotion recognition difficulties amongst clinical conditions where the dopamine system is affected suggests an involvement of dopamine in emotion recognition processes. However, previous psychopharmacological studies seeking to confirm this role in healthy volunteers thus far have failed to establish whether dopamine affects emotion recognition and lack mechanistic insights. The present study uncovered effects of dopamine on emotion recognition in healthy individuals by controlling for interindividual differences in baseline dopamine function and investigated potential mechanistic pathways via which dopamine may modulate emotion recognition. Our findings suggest that dopamine may influence emotion recognition via its effects on temporal processing, providing new directions for future research on typical and atypical emotion recognition.


title: Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays

abstract: Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1,779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.


title: A New Power Law Linking the Speed to the Geometry of Tool-Tip Orientation in Teleoperation of a Robot Assisted Surgical System

abstract: Fine manipulation is important in dexterous tasks executed via teleoperation, including in robot-assisted surgery. Discovering fundamental laws of human movement can benefit the design and control of teleoperated systems, and the training of their users. These laws are formulated as motor invariants, such as the well-studied speed-curvature power law. However, while the majority of these laws characterise translational movements, fine manipulation requires controlling the orientation of objects. This subject has received little attention in human motor control studies. Here, we report a new power law linking the speed to the geometry in orientation control - humans rotate their hands with an angular speed that is exponentially related to the local change in rotation direction. We demonstrate this law in a teleoperated task performed by surgeons with a surgical robotics research platform. Additionally, we show that the laws parameters change slowly with the surgeons training, and are robust within participants across task segments and repetitions. The fact that this power law is a robust motor invariant suggests that it may be an outcome of sensorimotor control. It also opens questions about the nature of this control and how it can be harnessed for better control of human-teleoperated robotic systems.


title: Sub-harmonic Entrainment of Cortical Gamma Oscillations to Deep Brain Stimulation in Parkinson's Disease: Predictions and Validation of a Patient-Specific Non-Linear Model

abstract:
BackgroundEntrainment of brain oscillations has been hypothesised as a potential mechanism of neuromodulation. While neuromodulation has been shown to be an effective therapy for a variety of pathologies, there is no algorithmic approach to programming neurostimulators for specific neurological disorders. This is due in part to the lack of understanding of the effects of stimulation on neuronal rhythms. Counterintuitively, cortical finely-tuned gamma oscillations around 75Hz have been reported to be entrained at 65Hz during 130Hz deep brain stimulation (DBS) in patients with Parkinsons disease (PD).

Objective/MethodsHere, we demonstrate that these observations are consistent with 1:2 entrainment, which is a special case of sub-harmonic entrainment predicted by synchronisation theory. We fit a coupled neuronal population model to selected features characterising a PD patients off-stimulation finely-tuned gamma rhythm recorded through electrocorticography.

ResultsOur model predicts the patient-specific regions of entrainment (Arnold tongues) in the stimulation frequency/amplitude space. We show that the resulting patient-specific neural circuit model exhibits 1:2 entrainment when stimulation is provided at 130Hz. Furthermore, we verify keys features of the 1:2 Arnold tongue with follow-up recordings from the same patient, such as the loss of 1:2 entrainment beyond a certain stimulation amplitude.

ConclusionOur results reveal that periodic DBS in patients can lead to counter-intuitive patterns of neuronal entrainment across stimulation parameters, and that these responses can be predicted by modelling. Should entrainment prove to be an important mechanism of therapeutic stimulation, our modelling framework may reduce the parameter space that clinicians must consider when programming devices for optimal benefit.

HighlightsO_LIEntrainment of cortical gamma oscillation at half stimulation frequency in patients with Parkinsons disease is predicted by synchronisation theory.
C_LIO_LIA Wilson-Cowan model, fitted to off-stimulation patient data, predicts a 1:2 synchronisation region biased towards lower stimulation frequencies where 1:2 entrainment will be lost at increased stimulation amplitudes.
C_LIO_LIThe fitted model also predicts that power spectral density of the 1:2 entrained frequency will be largest at lower stimulation frequencies and amplitudes.
C_LIO_LIObservations of 1:2 entrainment at variable stimulation parameters for the same patient as the model was fitted to, are in line with the predictions from the model.
C_LI


title: Cross-comparison of state of the art neuromorphological simulators on modern CPUs and GPUs using the Brain Scaffold Builder

abstract: A variety of software simulators exist for neuronal networks, and a subset of these tools allow the scientist to model neurons in high morphological detail. The scalability of such simulation tools over a wide range in neuronal networks sizes and cell complexities is predominantly limited by effective allocation of components of such simulations over computational nodes, and the overhead in communication between them. In order to have more scalable simulation software, it is therefore important to develop a robust benchmarking strategy that allows insight into specific computational bottlenecks for models of realistic size and complexity. In this study, we demonstrate the use of the Brain Scaffold Builder (BSB; De Schepper et al., 2021) as a framework for performing such benchmarks. We perform a comparison between the well-known neuromorphological simulator NEURON (Carnevale and Hines, 2006), and Arbor (Abi Akar et al., 2019), a new simulation library developed within the framework of the Human Brain Project. The BSB can construct identical neuromorphological and network setups of highly spatially and biophysically detailed networks for each simulator. This ensures good coverage of feature support in each simulator, and realistic workloads. After validating the outputs of the BSB generated models, we execute the simulations on a variety of hardware configurations consisting of two types of nodes (GPU and CPU). We investigate performance of two different network models, one suited for a single machine, and one for distributed simulation. We investigate performance across different mechanisms, mechanism classes, mechanism combinations, and cell types. Our benchmarks show that, depending on the distribution scheme deployed by Arbor, a speed-up with respect to NEURON of between 60 and 400 can be achieved. Additionally Arbor can be up to two orders of magnitude more energy efficient.


title: Visual Perception of 3D Space and Shape in Time - Part III: 2D Shape Recognition by Log-Scaling

abstract:
Human vision has a remarkable ability to recognize complex 3D objects such as faces that appear with any size and 3D orientations at any 3D location. If we initially memorize a face only with a normalized size and viewed from directly head on, the direct comparison between the one-sized memory and a new incoming image would demand tremendous mental frame translations in 7D. How can we perform such a demanding task so promptly and reliably as we experience the objects in the world around us?

Intriguingly, our primary visual cortex exhibits a 2D retinotopy with a log-polar coordinate system, where scaling up/down of shape is converted to linear frame translation. As a result, mental scaling can be performed by linearly translating the memory or the perceptual image until they overlap with each other. According to our new model of NHT (Neural Holography Tomography), alpha brainwaves traveling at a constant speed can conduct this linear translation. With this scheme, every scaling up/down by a factor of two should take the same amount of extra mental time to recognize a smaller/larger face.

To test this hypothesis, we designed a reaction time (RT) experiment, where participants were first asked to memorize sets of unfamiliar faces with a given specific size (4{degrees} or 8{degrees}). Following the memorization phase, similar stimuli with a wide range of sizes (from 1{degrees} to 32{degrees}) were presented, and RTs were recorded. As predicted, the increase in RT was proportional to the scaling factor in the log scale. Furthermore, we observed that RTs were fastest for 8{degrees} faces even if the memorized face was 4{degrees}. This supports our hypothesis that we always memorize faces at the exact size of ~8 {degrees}. To our surprise, the increases in RT were also consistent with the mentally-estimated depth sensation, which indicates that the apparent size of the recognized face can create a proper depth sensation.


title: NAC1 Modulates Autoimmunity by Suppressing Regulatory T Cell- Mediated Tolerance

abstract: FoxP3+ regulatory T cells (Tregs) are a distinct subset of CD4+ T cells integral to the maintenance of the balance of the immune system, and their dysregulation is a trigger of autoimmunity. We report here that nucleus accumbens-associated protein-1 (NAC1), a nuclear factor of the broad complex, tramtrack, bric-a-brac / poxvirus and zinc finger (BTB/POZ) gene family, is a negative regulator of FoxP3 in Tregs and a critical determinant of immune tolerance. Phenotypically, NAC1-/- mice show substantial tolerance to the induction of autoimmunity, as evidenced by the significantly decreased occurrences of autoimmune arthritis and colitis. Analysis of T cells from the wild-type (WT) or NAC1 knockout (-/-) mice found that NAC1 is crucially involved in the early stage of T cell development. NAC1 positively affects CD8+ T cell differentiation, but negatively regulates Treg development. Compared with WT animals, NAC1-/- mice displayed defects in CD8+ T cell development but generated a larger amount of CD4+ regulatory Tregs that exhibit a higher metabolic profile and immune suppressive activity, increased acetylation, and expression of FoxP3, and slower turnover of this transcriptional factor. Furthermore, treatment of Tregs with the pro-inflammatory cytokines IL-1{beta} or TNF- induced a robust upregulation of NAC1 but an evident downregulation of FoxP3 as well as the acetylated FoxP3, suggesting that the reduction of FoxP3 by the NAC1-mediated deacetylation and destabilization of this lineage-specific transcriptional factor contributes considerably to break of immune tolerance. These findings imply that the pro-inflammatory cytokines-stimulated upregulation of NAC1 acts as a trigger of the immune response through destabilization of Tregs and suppression of tolerance induction, and that therapeutic targeting of NAC1 warrants further exploration as a potential tolerogenic strategy for treatment of autoimmune disorders.

category: immunology


title: The Grainyhead/LSF transcription factor GRH-1 is rhythmically required for molting

abstract: Molting, that is, the synthesis and shedding of a cuticular exoskeleton, is a defining characteristic of ecdysozoa. In nematodes such as C. elegans, molts rhythmically terminate each of four larval stages. The molting cycle is tightly coupled to the rhythmic expression of thousands of genes. The mechanisms that support the regular molting cycle and oscillatory gene expression have remained largely elusive. Here, we performed an RNAi-based screen for transcription factors required for molting to identify potential components of a molting clock. We find that depletion of GRH-1, BLMP-1, NHR-23, NHR-25, MYRF-1 or BED-3 impairs progression through the molting cycle. We characterize GRH-1, a Grainyhead/LSF transcription factor whose functions in C. elegans development have remained largely unexplored, but whose orthologues in other animals are known to be key epithelial cell fate regulators. We show that GRH-1 depletion causes a dose-dependent extension of molt duration, with severe depletion causing defects in cuticle formation and shedding, and larval death. GRH-1 is required repetitively, during a specific time window prior to each larval molt. This rhythmic activity is consistent with the rhythmic accumulation of GRH-1 protein. These features are consistent with GRH-1 functioning as a key component, or high-level output, of the a gene regulatory network that controls molting. As its mammalian orthologues, as well as those of BLMP-1 and NHR-23, have been implicated in rhythmic homeostatic skin regeneration in mouse, the mechanisms underlying rhythmic C. elegans molting may be conserved beyond nematodes.

category: developmental biology


title: In vivo assessment of mechanical properties during axolotl development and regeneration using confocal Brillouin microscopy

abstract: In processes such as development and regeneration, where large cellular and tissue rearrangements occur, cell fate and behavior are strongly influenced by tissue mechanics. While most well-established tools probing mechanical properties require an invasive sample preparation, confocal Brillouin microscopy captures mechanical parameters optically with high resolution in a contact-free and label-free fashion. In this work, we took advantage of this tool and the transparency of the highly regenerative axolotl to probe its mechanical properties in vivo for the first time. We mapped the Brillouin frequency shift with high resolution in developing limbs and regenerating digits, the most studied structures in the axolotl. We detected a gradual increase in the cartilage Brillouin frequency shift, suggesting decreasing tissue compressibility during both development and regeneration. Moreover, we were able to correlate such increase with the regeneration stage, which was undetected with fluorescence microscopy imaging. The present work evidences the potential of Brillouin microscopy to unravel the mechanical changes occurring in vivo in axolotls, setting the basis to apply this technique in the growing field of epimorphic regeneration.


title: Developmentally programmed epigenome regulates cellular plasticity at the parental-to-zygote transition

abstract:
During metazoan development, the dramatic potency change from germline to embryos raises an important question regarding how the new life cycle is reset. Here, we report a tightly regulated epigenome landscape change from the parental germline to embryos in C. elegans. The epigenome is enriched with histone H3 in early-stage germ cells but switches to a histone variant H3.3-enriched epigenome in the mature egg. This H3.3-dominant epigenome persists in early-stage embryos until gastrulation, when the epigenome becomes H3 abundant again. We further demonstrate that this developmentally programmed H3 [->] H3.3 [->] H3 epigenome landscape change is regulated through differential expression of distinct histone gene clusters and is required for both germline integrity and early embryonic cellular plasticity. Together, this study reveals that a bimodal expression of H3 versus H3.3 is important for epigenetic reprogramming during gametogenesis and embryonic plasticity.

One Sentence SummaryDevelopmentally programmed epigenome resets cellular plasticity at the parental-to-zygote transition in C. elegans.


title: An initial assessment of the sustainability of waterbird harvest in the United Kingdom

abstract:
O_LIThere is a need to assess the sustainability of current harvest levels of wild birds in the United Kingdom (UK), and more widely, across Europe. Yet data on population and harvest size, as well as population demographics of many species are limited.
C_LIO_LIWe used a Demographic Invariant Method (DIM) to estimate Potential Excess Growth (PEG) for populations of waterbirds wintering in the UK and calculated a Sustainable Harvest Index (SHI) for each species or population. We compared this with population trends and conservation classifications (e.g. Birds of Conservation Concern) to assess the sustainability of harvests and the utility of these classifications.
C_LIO_LIOur approach found no evidence for overharvest of any duck or wader species, except potentially for gadwall Mareca strepera. We estimated that Canada geese Branta canadensis and both British and Icelandic greylag geese Anser anser are potentially overharvested in the UK. With the exception of Icelandic greylag geese, all of the goose populations predicted to be experiencing overharvest show strong population growth. This conflicting result raises concern about current population size estimates, harvest estimates or both.
C_LIO_LIWe found no relationship between sustainable harvest indices and short-term or long-term wintering trends in harvested species, or conservation classification under the UKs Birds of Conservation Concern framework.
Policy Implications: Our results suggest that UK based harvest is unlikely to be a major determinant of population trends for overwintering waterbirds in the UK. Additionally, the lack of a relationship between conservation classifications and SHI strongly suggests that these are not an appropriate tool for making decisions about harvest management. Our assessment provides the basis for a framework to make evidence-based decisions on sustainable harvest levels in the UK in the face of incomplete data. Investment in data collection for European waterbird population size and harvest is long overdue.
C_LI

category: ecology


title: Macrosystem community change in lake phytoplankton and its implications for diversity and function

abstract: The combined effects of eutrophication, land-use and climate change are major threats to aquatic ecosystems, their biodiversity and integrity in sustaining ecosystem functions. Disentangling the mechanisms by which environmental change contributes to community assembly processes and species niches remains challenging, especially at macro-ecological scales. Here, we collated phytoplankton community data including 853 lakes along a 1200km latitudinal gradient, monitored over four decades, to quantify the spatio-temporal and scale-dependent environmental impacts on species niches and assembly processes while accounting for species traits and phylogenetic constraints. Our results demonstrate the emergence of novel and widespread community composition clusters in previously more uniform communities. While total species richness remained relatively stable, changes in community weighted mean traits of the clusters indicate functional differences. A robust phylogenetic signal of species responses to the environment indicates strong niche conservatism and low taxonomic dispersion. Our findings imply profound spatio-temporal structuring of species co-occurrence patterns and highlight emerging functional differences of lake phytoplankton communities to environmental change over space and time.


title: Robust Inference of Bi-Directional Causal Relationships in Presence of Correlated Pleiotropy with GWAS Summary Data

abstract: To infer a causal relationship between two traits, several correlation-based causal direction (CD) methods have been proposed with the use of SNPs as instrumental variables (IVs) based on GWAS summary data for the two traits; however, none of the existing CD methods can deal with SNPs with correlated pleiotropy. Alternatively, reciprocal Mendelian randomization (MR) can be applied, which however may perform poorly in the presence of (unknown) invalid IVs, especially for bi-directional causal relationships. In this paper, first, we propose a CD method that performs better than existing methods regardless of the presence of correlated pleiotropy. Second, along with a simple but yet effective IV screening rule, we propose applying a closely related and state-of-the-art MR method in reciprocal MR, showing its almost identical performance to that of the new CD method when their model assumptions hold; however, if the modeling assumptions are violated, the new CD method is expected to better control type I errors. Notably bi-directional causal relationships impose some unique challenges beyond those for uni-directional ones, and thus requiring special treatments. For example, we point out for the first time several scenarios where a bi-directional relationship, but not a uni-directional one, can unexpectedly cause the violation of some weak modeling assumptions commonly required by many robust MR methods. Finally we applied the proposed methods to 12 risk factors and 4 common diseases, confirming mostly well-known uni-directional causal relationships, while identifying some novel and plausible bi-directional ones such as between BMI and T2D, and between BMI and CAD.

category: genetics


title: Deciphering of Somatic Mutational Signatures of Cancer

abstract: Somatic mutational signatures (MSs) identified by genome sequencing play important roles in exploring the cause and development of cancer. Thus far, many such signatures have been identified, and some of them do imply causes of cancer. However, a major bottleneck is that we do not know the potential meanings (i.e., cancer causal or biological functions) and contributing genes for most of them. Here we presented a computational framework, Gene Somatic Genome Pattern (GSGP), which can decipher the molecular mechanisms of the MSs. More importantly, it is the first time, GSGP is able to process MSs from RNA sequencing, which greatly extended the applications of both MS analysis and RNA sequencing. As a result, GSGP analysis matches consistently with previous reports and identify the aetiologies for a number of novel signatures. Notably, we applied GSGP to RNA sequencing data and revealed an RNA-derived MS involved in deficient DNA mismatch repair (dMMR) and microsatellite instability (MSI) in colorectal cancer (CRC).

category: genomics


title: A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

abstract: Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explore chromosome evolutionary patterns in the order. Whole genome resequencing of six males and six females enabled the identification of 41 fixed allelic variants in the follicle stimulating hormone receptor (fshr) gene, homozygous in females and heterozygous in males, consistent with an XX / XY chromosome system. The observed association between fshr SNPs and sex was confirmed at the species level in a broad sample, which allowed tuning up a molecular sexing tool. Fshr demonstrated differential gene expression between male and female gonads since 86 days post-fertilization, when the gonad was still an undifferentiated primordium, concomitant with the activation of other testis and ovary marker genes, such as amh and cyp19a1a genes, respectively. Interestingly, the Y-linked fshr allele, which included 24 non-synonymous variants, expressed to a higher level than the X-linked allele at all stages. We hypothesize a molecular mechanism hampering the action of the follicle stimulating hormone that would drive the undifferentiated gonad toward testis.


title: Improved target capture with lower hybridization temperatures for invertebrate loci with different baiting strategies: a case study of the leaf-footed bugs and allies (Hemiptera: Coreoidea)

abstract: Target capture approaches are widely used in phylogenomic studies, yet few experimental comparisons of critical parameters, e.g. hybridization temperature, have been published. Even fewer studies have focused on invertebrates where bait-target divergences may be high. Most capture studies use a fixed hybridization temperature of 65{degrees}C to maximize the proportion of on-target data, but lower temperatures, which might improve locus recovery, are not commonly employed. We used fresh and degraded specimens of leaf-footed bugs and relatives (Hemiptera: Coreoidea) to investigate the effect of hybridization temperature on capture success of previously published ultraconserved elements (UCE) targeted by baits derived from divergent hemipteran genomes and other loci targeted by newly designed baits derived from less divergent coreoid transcriptomes. We found touchdown capture approaches with lower hybridization temperatures generally resulted in lower proportions of on-target reads and lower coverage but were associated with more assembled contigs and improved recovery of targeted UCE loci. Low hybridization temperatures were also associated with increased numbers of putative paralogs of targeted UCE loci and recovery of well-known loci (from off-target reads) with historical uses in Sanger-based molecular phylogenetic studies. Hybridization temperatures did not generally affect recovery of newly targeted loci, which we attributed to lower bait-target divergences (compared to higher divergences between UCE baits and targets) and greater bait tiling density. Thus, optimizing in vitro target capture conditions to accommodate low hybridization temperatures can provide a cost-effective, widely applicable solution to improve recovery of protein-coding loci in invertebrates, while retrieving other potentially useful data for downstream comparative analyses.


title: Ascorbic acid derived carbon dots promote circadian rhythm and contribute to attention deficit hyperactivity disorder

abstract:
Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent psychiatric disorders in children, and ADHD patients always display circadian abnormalities. While, the ADHD drugs currently used in clinic have strong side effects, such as psychosis, allergic reactions and heart problems. Here, we demonstrated carbon dots derived from the ascorbic acid (VCDs) could strongly rescue the hyperactive and impulsive behaviour of a zebrafish ADHD disease model caused by per1b mutation. VCDs prolonged the circadian period of zebrafish for more than half an hour. In addition, the amplitude and circadian phase were also changed. The dopamine level was specifically increased, which may be caused by stimulation of the dopaminergic neuron development in the midbrain. Notably, it was found that the serotonin level was not altered by VCDs treatments. Also, the gene transcriptome effects of VCDs were discussed in present work. Our results provided the dynamic interactions of carbon dots with circadian system and dopamine signaling pathway, which illustrates a potential application of degradable and bio-safe VCDs for the treatment of the attention deficient and hyperactive disorder through circadian intervention.

Brief summary

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category: animal behavior and cognition


title: Uneven terrain treadmill walking in younger and older adults

abstract: We developed a method for altering terrain unevenness on a treadmill to study gait kinematics. We attached rigid polyurethane disks (12.7 cm diameter, 1.3-3.8 cm tall) to the treadmill belt using hook-and-loop fasteners. We tested four terrain unevenness conditions: Flat, Low, Medium, and High. The main objective was to test the hypothesis that increasing the unevenness of the terrain would result in greater gait kinematic variability. We tested 17 younger adults (age 20-40 years), 25 higher-functioning older adults (age 65+ years), and 29 lower-functioning older adults (age 65+ years, Short Physical Performance Battery score < 10). We customized the treadmill speed to each participants walking ability, keeping the speed constant across all four terrain conditions. Participants completed two 3-minute walking trials per condition. Using an inertial measurement unit placed over the sacrum and pressure sensors in the shoes, we calculated the stride-to-stride variability in step duration and sacral excursion (coefficient of variation; standard deviation expressed as percentage of the mean). Participants also self-reported their perceived stability for each condition. Terrain was a significant predictor of step duration variability, which roughly doubled from Flat to High terrain for all participant groups: younger adults (Flat 4.0%, High 8.2%), higher-functioning older adults (Flat 5.0%, High 8.9%), lower-functioning older adults (Flat 7.0%, High 14.1%). Similarly, all groups exhibited significant increases in sacral excursion variability for all three uneven terrain conditions compared to Flat. Participants were also significantly more likely to report feeling less stable walking over all three uneven terrain conditions compared to Flat. These findings support the hypothesis that altering terrain unevenness on a treadmill will increase gait kinematic variability and reduce perceived stability in younger and older adults.

category: bioengineering


title: Mini-IsoQLR: a pipeline for isoform quantification using long-reads sequencing data for single locus analysis

abstract:
MotivationDNA variants altering the pre-mRNA splicing process represent an underestimated cause of human genetic diseases. Their association to disease traits needs to be confirmed by means of functional assays from patient cell lines or other models to detect the formation of aberrant mRNAs. Long-read sequencing is a suitable technique to identify and quantify splicing isoforms. Available tools for isoform clusterization and/or quantification are not designed for the analysis of a single locus without previous information of splice sites.

ResultsMini-IsoQLR identifies and quantifies known and novel isoforms using long-read sequencing data from the mRNA expression and maturation of single-locus splicing assays. This pipeline uses GMAP aligner to generate a GFF3 file that is used to extract the consensus splice sites, define, and quantify all isoforms present.

Availability and implementationMini-IsoQLR requires GMAP, R (version 3.6), and R packages ggplot, plyr and optparse. It is freely available in GitHub (https://github.com/TBLabFJD/Mini-IsoQLR). This software is provided under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).

category: bioinformatics


title: Comparing Machine Learning Architectures for the Prediction of Peptide Collisional Cross Section

abstract: 1Mass spectrometry is the method of choice in large-scale proteomics studies. One common method is data-independent acquisition (DIA), which allows for high-throughput analysis of biological samples, but also produces complex data. Methods of peptide separation, in addition to retention time, improve data analysis and there has been increasing interest in separating peptides based on collisional cross section (CCS), which is a measure of the size of a peptide. However, existing libraries that are used during data analysis lack CCS measurements, and this data is expensive and time-consuming to acquire. This has led to the desire to predict library values for mass spectrometry analysis. Here we compare three deep learning architectures, LSTM, CNN, and transformer, for the tasks of retention time and collisional cross section prediction. We show that the LSTM and CNN models perform similarly and that the transformer has a lower performance than expected.


title: Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

abstract:
Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterized the proteome and transcriptome in-depth alongside genetic and ex-vivo drug response profiling in a clinically well annotated CLL discovery cohort (n= 68). Unsupervised clustering of the proteome data revealed six subgroups. Five of these proteomic groups were associated with genetic features, while one group was only detectable at the proteome level. This new group was characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). We developed classifiers to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n= 165, n= 169) and confirmed that ASB-CLL comprises about 20 % of CLL patients. The inferior overall survival observed in ASB-CLL was independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.

Single sentence summaryWe performed the largest proteogenomic analysis of CLL, linked proteomic profiles to clinical outcomes, and discovered a new poor outcome subgroup (ASB-CLL).


title: Target isoforms are an overlooked challenge and opportunity in chimeric antigen receptor cell therapy

abstract: The development of novel chimeric antigen receptor (CAR) cell therapies is rapidly growing, with 299 new agents being reported and 109 new clinical trials initiated so far this year. One critical lesson from approved CD19-specific CAR therapies is that target isoform switching has been shown to cause tumor relapse, but little is known about the isoforms of CAR targets in solid cancers. Here we assess the protein isoform landscape and identify both the challenges and opportunities protein isoform switching present as CAR therapy is applied to solid cancers.


title: A comprehensive single-cell expression atlas of human AML leukemia-initiating cells unravels the contribution of HIF pathway and its therapeutic potential

abstract: Relapse remains a major challenge in the clinical management of acute myeloid leukemia (AML), and is driven by rare therapy-resistant leukemia-initiating stem cells (LSCs) that reside in specific bone marrow niches. Hypoxia signaling keeps cells in a quiescent and metabolically relaxed state, desensitizing them to chemotherapy. This suggests the hypothesis that hypoxia contributes to AML-LSC function and chemoresistance and is a therapeutic target to sensitize AML-LSCs to chemotherapy. Here, we provide a comprehensive single-cell expression atlas (119,000 cells) of AML cells and AML-LSCs in paired diagnostic-relapse samples from risk-stratified patients with AML. The HIF/hypoxia pathway is attenuated in AML-LSCs compared with differentiated AML cells, but is enhanced when compared with healthy hematopoietic cells. Accordingly, chemical inhibition cooperates with standard-of-care chemotherapy to impair leukemogenesis, substantially eliminating AML-LSCs. These findings support the HIF pathway as a stem cell regulator in human AML, and reveal avenues for combinatorial targeted and chemotherapy-based approaches to specifically eliminate AML-LSCs.


title: Class-Controlled Copy-Paste Based Cell Segmentation for CoNIC Challenge

abstract: Muti-class cell segmentation in histopathology images is a challenging task. Here, we propose a copy-paste augmentation-based method for CoNIC challenge. As the challenge train data is severely class imbalanced. To deal with it, we copy all cell objects of train data and paste them to the train image on the fly while training model. The paste strategy is that we paste more cell objects of the insufficient classes and paste less cell objects for the sufficient classes. We experimented the method by stratified splitting train data in 4:1 ratio, the result shows the copy paste method can reach PQ 64.84 and mPQ 53.72, which improved and 0.66 compared to without copy pasted. Moreover, the improvements in those insufficient classes is more obvious.

category: pathology


title: Motion of the Cochlear Reticular Lamina Varies Radially Across Outer-Hair-Cell Rows

abstract: The basilar membrane (BM) is connected to the reticular lamina (RL) through three rows of Y-shaped structures consisting of an outer hair cell (OHC) and a Deiters cell (DC) with a phalangeal process (PhP) that forms part of the RL mosaic surface. Morphological differences in the anatomy of the Y-shaped structures across the three OHC rows suggest differences in motion across the rows. Here we report OoC transverse motions measured across several radial locations for the gerbil basal region corresponding to ~45 kHz. Cross-sectional imaging and vibrometry measurements were made using a high-resolution (2.23 um axially in water) spectral-domain optical-coherence-tomography (SD-OCT) system. The stimuli were pure tones (2-63 kHz) at ear-canal sound pressure levels (SPLs) of 30-95 dB SPL in anesthetized gerbils (N=9) with healthy cochleae. We report displacements at the RL regions of OHC rows 1-3 (RL1-3), at the OHC-DC junctions of OHC rows 1-3 (OHC-DC-junction1-3), and at the arcuate zone, arcuate-pectinate junction, and pectinate zone of the BM (BMAZ, BMAPJ, and BMPZ, respectively). The in vivo BM displacements showed classic compressive nonlinearity and traveling-wave delays. The RL gain was similar to the BM gain at low frequencies (<20 kHz), but increased with frequency. Near the best frequency (BF), the RL gain was greater than the high-level BM gain by 40 {+/-}5 dB (mean{+/-}std), and had greater compressive nonlinearity. RL motion varied radially, and the RL3 gain was significantly greater than that of RL1 by 10 {+/-}1 dB (p<0.001). In contrast, the OHC-DC-junction gain varied little radially across OHCs. At low frequencies the OHC-DC-junction gain was constant across SPLs, and 14 {+/-} 3 dB greater than the BM gain. As the frequency increased, the OHC-DC-junction gain decreased to a level similar to the BM gain at BF. The RL2, 3 phase was advanced by 0.25-0.375 cycles relative to the BM phase at low frequencies, but the RL2, 3 phase lead decreased as the frequency increased, became similar to the BM phase at BF, and lagged behind the BM phase by 0.25-0.5 cycles above BF. The OHC-DC-junction phases were mostly similar to the BM phase at low frequencies, but became delayed relative to the BM as the frequency increased, typically by 0.25-0.5 cycles near BF and by up to 1 cycle above BF. Our results show the most detailed picture of motion around the three OHC rows yet published, indicating that RL motion varied radially. Surprisingly, there was little motion difference across the three OHC rows in the OHC-DC-junction region, indicating that the tops of the DCs move in unison. Our data show a rich array of OoC amplitude and phase variations that are not explained by current theories.


title: Connectomic Analysis of the Drosophila Lateral Neuron Clock Cells Reveals the Synaptic Basis of Functional Pacemaker Classes.

abstract: The circadian clock orchestrates daily changes in physiology and behavior to ensure internal temporal order and optimal timing across the day. In animals, a central brain clock coordinates circadian rhythms throughout the body and is characterized by a remarkable robustness that depends on synaptic connections between constituent neurons. The clock neuron network of Drosophila, which shares network motifs with clock networks in the mammalian brain yet is built of many fewer neurons, offers a powerful model for understanding the network properties of circadian timekeeping. Here we report an assessment of synaptic connectivity within a clock network, focusing on the critical lateral neuron (LN) clock neuron classes. Our results reveal that previously identified anatomical and functional subclasses of LNs represent distinct connectomic types. Moreover, we identify a small number of clock cell subtypes representing highly synaptically coupled nodes within the clock neuron network. This suggests that neurons lacking molecular timekeeping likely play integral roles within the circadian timekeeping network. To our knowledge, this represents the first comprehensive connectomic analysis of a circadian neuronal network.


title: A structural atlas of the developing zebrafish telencephalon based on spatially-restricted transgene expression

abstract: 1.Zebrafish telencephalon acquires an everted morphology by a two-step process that occurs from 1 to 5 days post-fertilization (dpf). Little is known about how this process affects the positioning of discrete telencephalic cell populations, hindering our understanding of how eversion impacts telencephalic structural organisation. In this study, we characterise the neurochemistry, cycle state and morphology of an EGFP positive (+) cell population in the telencephalon of Et(gata2:EGFP)bi105 transgenic fish during eversion and up to 20dpf. We map the transgene insertion to the early-growth-response-gene-3 (egr3) locus and show that EGFP expression recapitulates endogenous egr3 expression throughout much of the pallial telencephalon. Using the gata2:EGFPbi105 transgene, in combination with other well-characterised transgenes and structural markers, we track the development of various cell populations in the zebrafish telencephalon as it undergoes the morphological changes underlying eversion. These datasets were registered to reference brains to form an atlas of telencephalic development at key stages of the eversion process (1dpf, 2dpf and 5dpf) and compared to expression in adulthood. Finally, we registered gata2:EGFPbi105 expression to the Zebrafish Brain Browser 6dpf reference brain (ZBB, see Marquart et al., 2015, 2017; Tabor et al. 2019), to allow comparison of this expression pattern with anatomical data already in ZBB.


title: Early life pain experience changes adult functional pain connectivity in the rat somatosensory and the medial prefrontal cortex

abstract:
Early life pain experience (ELP) alters adult pain behaviour and increases injury induced pain hypersensitivity, but the effect of ELP upon adult functional brain connectivity is not known. We have performed continuous local field potential (LFP) recording in the awake adult male rats to test the effect of ELP upon functional cortical connectivity related to pain behaviour. Somatosensory cortex (S1) and medial prefrontal cortex (mPFC) LFPs evoked by mechanical hindpaw stimulation were recorded simultaneously with pain reflex behaviour for 10 days after adult skin injury. We show that, post adult injury, S1 LFP delta and gamma energy and S1 LFP delta/gamma frequency modulation are significantly increased in ELP rats compared to controls. Adult injury also induces increases in S1-mPFC functional connectivity which is significantly prolonged in ELP rats, lasting 4 days compared to 1 day in controls. Importantly, the increases in LFP energy and connectivity in ELP rats were directly correlated with increased behavioural pain hypersensitivity. Thus, early life pain (ELP) alters adult brain functional connectivity, both within and between cortical areas involved in sensory and affective dimensions of pain. The results reveal altered brain connectivity as a mechanism underlying the effects of early life pain upon adult pain perception.

Significance StatementPain and stress in early life has a lasting impact upon pain behaviour and may increase vulnerability to chronic pain in adults. Here we record pain-related cortical activity and simultaneous pain behaviour in awake adult male rats previously exposed to pain in early life. We show that functional connectivity within and between the somatosensory cortex and the medial prefrontal cortex is increased in these rats and that these increases are correlated with their behavioural pain hypersensitivity. The results reveal that early life pain alters adult brain connectivity, which may explain the impact of childhood pain upon adult chronic pain vulnerability.


title: Chemo-architecture of area prostriata in adult and developing mice: comparison with presubiculum and parasubiculum

abstract: Retrosplenial area 29e, which was a cortical region described mostly in earlier rodent literature, is often included in the dorsal presubiculum (PrSd) or postsubiculum (PoS) in modern literature and commonly used brain atlases. Recent anatomical and molecular studies have revealed that retrosplenial area 29e belongs to the superficial layers of area prostriata, which in primates is found to be important in fast analysis of quickly moving objects in far peripheral visual field. As in primates, the prostriata in rodents adjoins area 29 (granular retrosplenial area), area 30 (agranular retrosplenial area), medial visual cortex, PrSd-PoS, parasubiculum (PaS) and postrhinal cortex (PoR). The present study aims to reveal the chemo-architecture of the prostriata versus PrSd-PoS or PaS by means of a systematic survey of gene expression patterns in adult and developing mouse brains. First, we find many genes that display differential expression across the prostriata, PrSd-PoS and PaS and that show obvious laminar expression patterns. Second, we reveal subsets of genes that selectively express in the dorsal or ventral parts of the prostriata, suggesting the existence of at least two subdivisions. Third, we detect some genes that shows differential expression in the prostriata of postnatal mouse brains from adjoining regions, thus enabling identification of the developing area prostriata. Fourth, gene expression difference of the prostriata from the medial visual cortex and PoR is also observed. Finally, molecular and connectional features of the prostriata in rodents and non-human primates are discussed and compared.


title: Manipulating prior beliefs causally induces under- and overconfidence

abstract: Making a decision is invariably accompanied by a sense of confidence in that decision. There is widespread variability in the exact level of confidence, even for tasks that do not differ in objective difficulty. Such expressions of under- and overconfidence are of vital importance, as they are related to fundamental life outcomes. Yet, a clear account regarding the computational mechanisms underlying under- and overconfidence is currently missing. In the current work, we propose that prior beliefs in the ability to perform a task can explain why confidence can differ dramatically despite similar task performance. In two experiments, we provide evidence for this hypothesis by showing that manipulating prior beliefs about task performance in an induction phase causally influences reported levels of confidence in a testing phase, while leaving actual performance unaffected. This is true both when prior beliefs are influenced via manipulated feedback and by manipulating the difficulty of the task during the training phase. These results are accounted for within an accumulation-to-bound model by assuming an additional parameter controlling prior beliefs about task performance. Our results provide a fundamental mechanistic insight into the computations underlying over- and underconfidence.


title: The dynamics of protein localisation to restricted zones within Drosophila mechanosensory cilia

abstract: The Drosophila chordotonal neuron cilium is the site of mechanosensory transduction. The cilium has a 9+0 axoneme structure and is highly sub-compartmentalised, with proximal and distal zones harbouring different TRP channels and the proximal zone axoneme also being decorated with axonemal dynein motor complexes. The activity of the dynein complexes is essential for mechanotransduction. We investigate the localisation of TRP channels and dynein motor complexes during ciliogenesis. Differences in timing of TRP channel localisation correlate with order of construction of the two ciliary zones. Dynein motor complexes are initially not confined to their target proximal zone, but complexes beyond the proximal zone are later cleared, perhaps by retrograde transport. Differences in transient distal localisation of ODAs and IDAs are consistent with previous suggestions from unicellular eukaryotes of differences in processivity during intraflagellar transport. Stable localisation depends on the targeting of their docking proteins in the proximal zone. For outer dynein arm (ODA) complexes, we characterise an ODA docking complex (ODA-DC) that is targeted directly to the proximal zone. Interestingly, the subunit composition of the ODA-DC in chordotonal neuron cilia appears to be different from the predicted ODA-DC in Drosophila sperm.

category: cell biology


title: Neovascularization and the recruitment of CD31+ cells from the bone marrow are unique under regenerative but not wound repair conditions

abstract: The long-noted observation that endostatin is a potent inhibitor of tumor vasculature but has little or no effect on wound repair or pregnancy remains an "as of yet unexplained but remarkable phenomenon"(1). However, there is another path to wound healing, epimorphic regeneration, and here we present data in mice demonstrating that endostatin is, in fact, a potent inhibitor of epimorphic regeneration. In this study, we show that a rege nerative response seen in the spontaneously regenerating MRL mouse involves CD31+ endothelial precursors that migrate from the bone marrow into the wound site and form new vessels, unlike that seen in the non-regenerating C57BL/6 mouse injury site. Furthermore, this appears to relate to the induction of HIF-1a, an inducer of regeneration (2). Inducing epimorphic regeneration in otherwise non-regenerating mice via an enhanced HIF-1a response by employing the PHD inhibitor 1,4-DPCA/hydrogel, a HIF-1a stabilizer, results in the same increased bone marrow-derived CD31+ endothelial precursor response and increased vasculogenesis. This regenerative response is completely blocked by endostatin, supporting the notion that vascularization induced during regeneration shares similarities to the tumor vasculature.


title: Rpadrino: an R package to access and use PADRINO, an open access database of Integral Projection Models

abstract:
O_LIDiscrete time structured population projection models are an important tool for studying population dynamics. Within this field, Integral Projection Models (IPMs) have become a popular method for studying populations structured by continuously distributed traits (e.g. height, weight). Databases of discrete time, discrete state structured population models, for example DATLife (life tables) and COMPADRE & COMADRE (matrix population models), have made quantitative syntheses straightforward to implement. These efforts allow researchers to address questions in both basic and applied ecology and evolutionary biology. There are now over 300 peer-reviewed publications containing IPMs. We describe a novel framework to quickly reconstruct these models for subsequent analyses using Rpadrino R package, which serves as an interface to PADRINO, a new database of structured population models.
C_LIO_LIWe introduce an R package, Rpadrino, which enables users to download, subset, reconstruct, and extend published IPMs. Rpadrino makes use of recently created software, ipmr, to provide an engine to reconstruct a wide array of IPMs from their symbolic representations and conduct subsequent analyses. Rpadrino and ipmr are extensively documented to help users learn their usage.
C_LIO_LIRpadrino currently enables users to reconstruct 280 IPMs from 40 publications that describe the demography of 14 animal and 26 plant species. All of these IPMs are tested to ensure they reproduce published estimates. Rpadrino provides an interface to augment PADRINO with external data and modify parameter values, creating a platform to extend models beyond their original purpose while retaining full reproducibility.
C_LIO_LIPADRINO and Rpadrino provide a toolbox for asking new questions and conducting syntheses with peer-reviewed published IPMs. Rpadrino provides a user-friendly interface so researchers do not need to worry about the database structure or syntax, and can focus on their research questions and analyses. Additionally, Rpadrino is thoroughly documented, and provides numerous examples of how to perform analyses which are not included in the packages functionality.
C_LI


title: Large haploblocks underlie rapid adaptation in an invasive weed

abstract:
Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. We leverage extensive contemporary and historical collections of Ambrosia artemisiifolia--an aggressively invasive weed and primary cause of pollen-induced hayfever--to track the phenotypic and genetic causes of adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks--indicative of chromosomal inversions--contain a disproportionate share of genomic regions conferring parallel adaptation between ranges (18%), are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of structural and large-effect variants in rapid adaptation, which have been critical to A. artemisiifolias global spread.

One Sentence SummaryParallel evolution between native and invasive ranges of Ambrosia artemisiifolia is aided by putative chromosomal inversions.

category: evolutionary biology


title: Regulation associated modules reflect 3D genome modularity associated with chromatin activity

abstract: The 3D genome has been shown to be organized into modules including topologically associating domains (TADs) and compartments that are primarily defined by spatial contacts from Hi-C or other experiments. There exists a gap to investigate whether and how the spatial modularity of the chromatin is related to the functional modularity resulting from the chromatin activity. Increasing evidence shows a tight interplay between histone modifications and 3D chromatin organization. As the histone modifications reflect the chromatin activity, it is tempting to infer the spatial modularity of the genome directly from the histone modification patterns, which would establish the connection between the spatial and functional modularity of the genome. However, uncovering the 3D genomic modules using histone modifications has not been well explored. Here, we report that the histone modifications show a modular pattern (referred to as regulation associated modules, RAMs) that reflects the spatial modularity of the chromatin structure. We found that enhancer-promoter interactions and extrachromosomal DNAs (ecDNAs) occur more often within the same RAMs than within the same TADs, indicating stronger insulation of the RAM boundaries and a modularization of the 3D genome at a scale better aligned with the chromatin activity. Consistently, compared to the TAD boundaries, in silico predictions showed that deletions of RAM boundaries perturb the chromatin structure more severely and somatic variants in the cancer samples are more enriched in the RAM boundaries. These observations suggest that RAMs reflect a modular organization of the 3D genome at a scale better aligned with chromatin activity, providing a bridge connecting the structural and functional modularity of the genome.


title: Relationship among evolutionary distance, variance-covariance matrix and principal component analysis

abstract: Principal component analyses (PCAs) are often used to visualize patterns of genetic variation in human populations. Previous studies showed a close correspondence between genetic and geographic distances. In such PCAs, the principal components are eigenvectors of the datas variance-covariance matrix, which is obtained by a genetic relationship matrix (GRM). However, it is difficult to apply GRM to multiallelic sites. In this paper, I showed that a PCA from GRM is equivalent to multidimensional scaling (MDS) from nucleotide differences. Therefore, a PCA can be conducted using nucleotide differences. The new method provided in this study provides a straightforward method to predict the effects of different demographic processes on genetic diversity.


title: Optimization of dynamic soaring in a flap-gliding seabird and its impacts on large-scale distribution at sea

abstract:
Dynamic soaring harvests energy from a spatiotemporal wind gradient, allowing albatrosses to glide over vast distances. However, its use is challenging to demonstrate empirically, and has yet to be confirmed in other seabirds. Here we investigate how flap-gliding Manx Shearwaters optimise their flight for dynamic soaring. We do so by deriving a new metric, the horizontal wind effectiveness, that quantifies how effectively flight harvests energy from a shear layer. We evaluate this metric empirically for fine-scale trajectories reconstructed from bird-borne video data using a simplified flight dynamics model. We find that the birds undulations are phased with their horizontal turning to optimise energy harvesting. We also assess the opportunity for energy harvesting in long-range, GPS-logged foraging trajectories, and find that Manx Shearwaters optimise their flight to increase the opportunity for dynamic soaring during favourable wind conditions. Our results show how small-scale dynamic soaring impacts large-scale Manx Shearwater distribution at sea.

TeaserFlap-gliding shearwaters harvest wind energy by fine-scale trajectory optimization and this impacts their large-scale distribution at sea.


title: Rapid quantification of polyhydroxyalkanoates accumulated in living cells based on green fluorescence protein labeled phasin: The qPHA method

abstract: Polyhydroxyalkanoates (PHA), are microbial polyesters with possibility to replace non-biodegradable petro-plastics. No rapid in situ PHA quantitation method has been available for the past 40 years to replace the traditional method which is complicated, time and labor consuming. Quantification of PHA in living cells were finally developed from fluorescence intensities generated from green fluorescence protein (GFP) fused with the Halomonas bluephagenesis phasin proteins attached on the PHA granules. Phasins PhaP1 and PhaP2 were used to fuse with GFP which reflects PHA accumulation with an R-square over 0.9, respectively. Also, a standard correlation was established to calculate PHA contents based on the fluorescence and cell density recorded via a microplate reader with R-square over 0.95 when grown on various substrates, respectively. The PhaP2-GFP containing H. bluephagenesis was applied successfully to quantify PHA synthesis in a 7.5 L fermenter with high precision. The method is named qPHA.


title: Single-cell data analysis in the browser

abstract: We present kana, a web application for interactive single-cell RNA-seq (scRNA-seq) data analysis in the browser. Like, literally, in the browser: kana leverages web technologies such as WebAssembly to efficiently perform the relevant computations on the users machine, avoiding the need to provision and maintain a backend service. The application provides a streamlined one-click workflow for all steps in a typical scRNA-seq analysis, starting from a count matrix and finishing with marker detection. Results are presented in an intuitive web interface for further exploration and iterative analysis. Testing on public datasets shows that kana can analyze over 100,000 cells within 5 minutes on a typical laptop.


title: Defining cellular population dynamics at single cell resolution during prostate cancer progression

abstract: Advanced prostate malignancies are a leading cause of cancer-related deaths in men, in large part due to our incomplete understanding of cellular drivers of disease progression. We investigated prostate cancer cell dynamics at single-cell resolution from disease onset to the development of androgen independence in vivo. We observe a dramatic expansion of a castration-resistant intermediate luminal cell type that correlates with treatment resistance and poor prognosis in human patients. Moreover, transformed epithelial cells and associated fibroblasts create a microenvironment conducive to pro-tumorigenic immune infiltration, which is in part androgen responsive. Androgen independent prostate cancer leads to significant diversification of intermediate luminal cell populations characterized by a range of androgen signaling activity inversely correlated with proliferation and mRNA translation. Accordingly, distinct epithelial populations are exquisitely sensitive to translation inhibition which leads to epithelial cell death, loss of pro-tumorigenic signaling, and decreased tumor heterogeneity. Our findings reveal a complex tumor environment largely dominated by castration-resistant luminal cells and immunosuppressive infiltrates.


title: Universality of distribution of tumor mutation burden - a biomarker for the tumor evolution and disease risk

abstract: Cancers, resulting in uncontrolled cell proliferation, are driven by accumulation of somatic mutations. Genome-wide sequencing has produced a catalogue of millions of somatic mutations, which contain the evolutionary history of the cancers. However, the connection between the mutation accumulation and disease development and risks is poorly understood. Here, we analyzed more than 1,200,000 mutations from 5,000 cancer patients with whole-exome sequencing, and discovered two novel signatures for 16 cancer types in The Cancer Genome Atlas (TCGA) database. A clock-like mutational process, a strong correlation between Tumor Mutation Burden (TMB) and the Patient Age at Diagnosis (PAD), is observed for cancers with low TMB (mean value less than 3 mutations per million base pairs) but is absent in cancers with high TMB. We also validate this finding using whole-genome sequencing data from more than 2,000 patients for 24 cancer types. Surprisingly, we discovered that the distribution of TMB are universal. At low TMB it exhibits a Gaussian distribution and transitions to a power law at hight TMB. The differences in cancer risk between the sexes are also mainly driven by the disparity in mutation burden. The TMB variations, imprinted at the chromosome level, also reflect accumulation of mutation clusters within small chromosome segments in high TMB cancers. By analyzing the characteristics of mutations based on multi-region sequencing, we found that a combination of TMB and intratumor heterogeneity could be a potential biomarker for predicting the patient survival and response to treatment.


title: Gene Expression and Tracer-Based Metabolic Flux Analysis Reveals Tissue-Specific Metabolic Scaling in vitro, ex vivo, and in vivo

abstract: Metabolic scaling, the inverse correlation of metabolic rates to body mass, has been appreciated for more than 80 years. Studies of metabolic scaling have almost exclusively been restricted to mathematical modeling of oxygen consumption. The possibility that other metabolic processes scale with body size has not been studied. To address this gap in knowledge, we employed a systems approach spanning from transcriptomics to in vitro and in vivo tracer-based flux. Gene expression in livers of five species spanning a 30,000-fold range in mass revealed differential expression of genes related to cytosolic and mitochondrial metabolic processes, in addition to detoxication of oxidative damage. This suggests that transcriptional scaling of damage control mechanisms accommodates increased oxidative metabolism in smaller species. To determine whether flux through key implicated metabolic pathways scaled, we applied stable isotope tracer methodology to study multiple cellular compartments, tissues, and species. Comparing mice and rats, we demonstrate that while scaling of metabolic fluxes is not observed in the cell-autonomous setting, it is present in liver slices and in vivo. Together, these data reveal that metabolic scaling extends beyond oxygen consumption to numerous other metabolic pathways, and is likely regulated at the level of gene expression and substrate supply.


title: Engineering bacterial blight-resistant plants through CRISPR/Cas9-targeted editing of the MeSWEET10a promoter in cassava

abstract: Editing of the promoter in the disease-susceptibility gene MeSWEET10a of SC8 cassava confers resistance to CBB. All mutated cassava lines had normal morphological and yield-related traits as the wild type. The results lay a research foundation for breeding cassava resistant to bacterial blight.

category: plant biology


title: PIF4/HEMERA-mediated daytime thermosensory growth requires the Mediator subunit MED14

abstract:
While moderately elevated ambient temperatures do not trigger stress responses in plants, they do significantly stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis thaliana. Although it is well known that PIF4 promotes plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. Our previous studies demonstrated that HEMERA (HMR), a transcriptional co-activator of PIF4, promotes the thermo-induced expression of PIF4 target genes through its nine-amino-acid transactivation domain (9aaTAD). In this report, we investigate the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 is identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 is required for the thermal induction of PIF4 target genes but has a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirm that the expression of numerous PIF4/HMR-dependent, auxin-related genes requires MED14 at warm temperatures. Moreover, PIF4 and HMR physically interact with MED14 and both are indispensable for the association of MED14 with the promoters of these thermoresponsive genes. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature.

One-sentence summaryThe Mediator subunit MED14 promotes thermomorphogenesis by interacting with PHYTOCHROME-INTERACTING FACTOR 4 and HEMERA to induce the expression of growth-promoting genes at elevated temperatures.


title: A Genome-Scale Metabolic Model for the Smut-Fungus Ustilago maydis

abstract: Ustilago maydis is an important plant pathogen causing corn-smut disease and an effective biotechnological production host. The lack of a comprehensive metabolic overview hinders a full understanding of environmental adaptation and a full use of the organisms metabolic potential. Here, we report the first genome scale metabolic model (GSMM) of Ustilago maydis (iUma22) for the simulation of metabolic activities. iUma22 was reconstructed from sequencing and annotation using PathwayTools, the biomass equation was derived from literature values and from the codon composition. The final model contains over 25% of annotated genes in the sequenced genome. Substrate utilization was corrected by Biolog-Phenotype arrays and exponential batch cultivations were used to test growth predictions. A pan-genome of four different U. maydis strains revealed missing metabolic pathways in iUma22. The majority of metabolic differences between iUma22 and the pangenome occurs in the inositol, purine and starch metabolic pathways. The new model allows studies of metabolic adaptations to different environmental niches as well as for biotechnological applications.

category: systems biology


title: The order Axinellida (Porifera: Demospongiae) in California

abstract: Sponges are common and diverse in California, but they have received little study in the region, and the identities of many common species remain unclear. Here we combine fresh collections and museum vouchers to revise the order Axinellida for California. Seven new species are described, including representatives from one family and four genera that previously had no described species in the state. One new combination is also described, and two names are placed in synonymy with existing names, resulting in a total of 13 species; a dichotomous key to differentiate them is provided. DNA data from 10 of the 13 species is combined with publicly available data to produce updated global phylogenies for the order.

category: zoology


title: Precocious sperm exchange in the simultaneously hermaphroditic nudibranch, Berghia stephanieae

abstract: Sexual systems vary greatly across molluscs. This diversity includes simultaneous hermaphroditism, with both sexes functional at the same time. Most nudibranch molluscs are thought to be simultaneous hermaphrodites, but detailed studies of reproductive development and timing remain rare as most species cannot be cultured in the lab. The aeolid nudibranch, Berghia stephanieae, is one such species that can be cultured through multiple generations on the benchtop. We studied B. stephanieae reproductive timing to establish when animals first exchange sperm and how long sperm can be stored. We isolated age- and size-matched individuals at sequential timepoints to learn how early individuals exchange sperm. Individuals isolated at 13 weeks post laying (wpl) can produce fertilized eggs. This is 6 weeks before animals first lay egg masses, indicating that sperm exchange occurs well before individuals are capable of laying eggs. Our results indicate that male gonads become functional for animals between 6 mm (~9 wpl) and 9 mm (~15 wpl) in length. That is much smaller (and sooner) than the size (and age) of individuals at first laying (12-19 mm; ~19 wpl), indicating that male and female functions do not develop simultaneously. We also tracked the number of fertilized eggs in each egg mass, which remained steady for the first 10-15 egg masses, followed by a decline to near-to-no fertilization. This large, novel dataset provides insights into precise timing of the onset of functionality of the male and female reproductive systems in B. stephanieae. These data contribute to a broader understanding of reproductive development and the potential for understanding evolution of diverse sexual systems in molluscs.


title: Repressor element 1-silencing transcription factor deficiency yields profound hearing loss through Kv7.4 channel upsurge in auditory neurons and hair cells

abstract:
Repressor element 1-silencing transcription factor (REST) is a transcriptional repressor that recognizes neuron-restrictive silencer elements in the mammalian genomes in a tissue- and cell-specific manner. The identity of REST target genes and molecular details of how REST regulates them are emerging. We performed conditional null deletion of Rest (cKO) in murine hair cells (HCs) and auditory neurons, spiral ganglion neurons (SGNs). Null-deletion of full-length REST resulted in normal HCs and SGNs development but manifested with progressive hearing loss in adulthood. We found that deletion of REST results in an increased abundance of Kv7.4 channels at the transcript, protein, and function levels. Specifically, we found that SGNs and HCs from Rest cKO mice displayed increased Kv7.4 expression and augmented Kv7 currents; SGNs excitability was also significantly reduced. Administration of Kv7.4 channel activator, fasudil, recapitulated progressive hearing loss in mice.

In contrast, inhibition of the Kv7.4 channel by XE991 rescued the auditory phenotype of Rest cKO mice. Previous studies identified some loss-of-function mutations within the Kv7.4-coding gene, Kcnq4, as a causative factor for progressive hearing loss in mice and humans. Thus, the present findings revealed that a critical homeostatic Kv7.4 channel level is required for proper auditory functions.


title: Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades

abstract: Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime--within alpha cycles--to the amplification regime--across a few alpha cycles--that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events--a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the "waxing and waning" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the "waxing and waning" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.


title: Subgroups of eating behavior traits independent of obesity defined using functional connectivity and feature representation learning

abstract: AO_SCPLOWBSTRACTC_SCPLOWEating behavior is highly heterogeneous across individuals, and thus, it cannot be fully explained using only the degree of obesity. We utilized unsupervised machine learning and functional connectivity measures to explore the heterogeneity of eating behaviors. This study was conducted on 424 healthy adults. We generated low-dimensional representations of functional connectivity defined using the resting-state functional magnetic resonance imaging, and calculated latent features using the feature representation capabilities of an autoencoder by nonlinearly compressing the functional connectivity information. The clustering approaches applied to latent features identified three distinct subgroups. The subgroups exhibited different disinhibition and hunger traits; however, their body mass indices were comparable. The model interpretation technique of integrated gradients revealed that these distinctions were associated with the functional reorganization in higher-order associations and limbic networks and reward-related subcortical structures. The cognitive decoding analysis revealed that these systems are associated with reward- and emotion-related systems. We replicated our findings using an independent dataset, thereby suggesting generalizability. Our findings provide insights into the macroscopic brain organization of eating behavior-related subgroups independent of obesity.