title: Fission of megamitochondria into multiple smaller well-defined mitochondria in the ageing zebrafish retina

abstract: Mitochondria are essential adenosine triphosphate (ATP)-generating cellular organelles. In the retina, they are highly numerous in the photoreceptors and retinal pigment epithelium (RPE) due to their high energetic requirements. Fission and fusion of the mitochondria within these cells allow them to adapt to changing demands over the lifespan of the organism. Using transmission electron microscopy, we examined the mitochondrial ultrastructure of zebrafish photoreceptors and RPE from 5 days post fertilisation (dpf) through to late adulthood (3 years). Notably, mitochondria in the youngest animals were large and irregular shaped with a loose cristae architecture, but by 8 dpf they had reduced in size and expanded in number with more defined cristae. When investigating temporal gene expression of several mitochondrial-related markers, they indicated fission as the dominant mechanism contributing to these changes observed over time. This is likely to be due to continued mitochondrial stress resulting from the oxidative environment of the retina and prolonged light exposure. We have characterised retinal mitochondrial ageing in a key vertebrate model organism, that provides a basis for future studies of retinal diseases that are linked to mitochondrial dysfunction.


title: Manipulating the microbiome alters regenerative outcomes in Xenopus laevis tadpoles vis lipopolysaccharide signalling

abstract: Xenopus laevis tadpoles can regenerate functional tails, containing spinal cord, notochord, muscle, fin, blood vessels and nerves, except for a brief refractory period at around one week of age. At this stage, amputation of the tadpoles tail may either result in scarless wound healing, or the activation of a regeneration programme, which replaces the lost tissues. We recently demonstrated a link between bacterial lipopolysaccharides and successful tail regeneration in refractory stage tadpoles, and proposed that this could result from lipopolysaccharides binding to Toll-like receptor 4 (TLR4). Here, we have used 16S rRNA sequencing to show that the tadpole skin microbiome is highly variable between sibships and that the community can be altered by raising embryos in the antibiotic gentamicin. Six gram-negative genera, including Delftia and Chryseobacterium, were over-represented in tadpoles that underwent tail regeneration. Lipopolysaccharides purified from a commensal Chryseobacterium spp. XDS4, an exogenous Delftia spp. or Escherichia coli could significantly increase the number of antibiotic-raised tadpoles that attempted regeneration. Conversely, the quality of regeneration was impaired in native-raised tadpoles exposed to the antagonistic lipopolysaccharide of Rhodobacter sphaeroides. Editing TLR4 using CRISPR/Cas9 also reduced regeneration quality, but not quantity, at the level of the cohort. However, we found that the editing level of individual tadpoles was a poor predictor of regenerative outcome. In conclusion, our results suggest that variable regeneration in refractory stage tadpoles depends at least in part on the skin microbiome and lipopolysaccharide signalling, but that signalling via TLR4 cannot account for all of this effect.

category: developmental biology


title: Manipulating the microbiome alters regenerative outcomes in Xenopus laevis tadpoles via lipopolysaccharide signalling


title: A chemically defined biomimetic surface for enhanced isolation efficiency of high-quality human mesenchymal stromal cells under xeno-/serum-free conditions

abstract: Mesenchymal stromal cells (MSCs) are one of the most frequently used cell types in regenerative medicine and cell therapy. Generating sufficient cell numbers for MSC-based therapies is constrained by: 1) their low abundance in tissues of origin, which imposes the need for significant ex vivo cell amplification, 2) donor-specific characteristics including MSC frequency/quality that decline with disease state and increasing age, 3) cellular senescence, which is promoted by extensive cell expansion and results in decreased therapeutic functionality. The final yield of a manufacturing process is therefore primarily determined by the applied isolation procedure and its efficiency in isolating therapeutically active cells from donor tissue. To date, MSCs are predominantly isolated using media supplemented with either serum or its derivatives, which pose safety and consistency issues. To overcome those limitations while enabling robust MSC production with constant high yield and quality, we developed a chemically defined biomimetic surface coating, called isoMATRIX, that facilitates the isolation of significantly higher numbers of MSCs in xeno-/serum-free and chemically defined conditions. The isolated cells display a smaller cell size and higher proliferation rate than those derived from a serum-containing isolation procedure and a strong immunomodulatory capacity. In sum, the isoMATRIX promotes enhanced xeno-, serum-free, or chemically defined isolation of human MSCs and supports consistent and reliable cell performance for improved stem cell-based therapies.

category: cell biology


title: OSBP-mediated cholesterol transfer determines epithelial polarity and associated cargo secretion

abstract: Golgi lipid environment regulates sorting and cargo secretion. However, the mechanisms that spatiotemporally control the lipid composition of the secretory membranes to drive cargo trafficking are poorly understood. Lipid transfer proteins regulate the concentration of specific lipids at membrane contact sites. We hypothesised that by catalysing cholesterol/PI(4)P exchange at ER-trans-Golgi membrane contact sites the lipid transfer protein oxysterol binding protein (OSBP) affects the secretion of a subset of cargoes. Here, we report that OSBP is a major epithelial protein as its inhibition leads to complete loss of apico-basal polarity. By mapping the OSBP proximity proteome with the biotin ligase TurboID, we found that OSBP controls the secretion of multiple membrane associated proteins, including key polarity determinants such as E-cadherin. Mechanistically, we established that OSBP contributes to E-cadherin secretion by supplying cholesterol to post-Golgi membranes. Importantly, when cells downregulate cell-cell junctions upon epithelial-to-mesenchymal transition, they re-wire their lipid homeostasis and downregulate OSBP as well, thus altering the trafficking of the OSBP-dependent secretory cargoes.


title: No support for a meiosis suppressor in Daphnia pulex: Comparison of linkage maps reveals normal recombination in males of obligate parthenogenetic lineages.

abstract: It is often assumed that obligate parthenogenesis (OP) evolves by a disruption of meiosis and recombination. One emblematic example that appears to support this view is the crustacean Daphnia pulex. Here, by constructing high-density linkage maps, we estimate genome-wide recombination rates in males that are occasionally produced by OP lineages, as well as in males and females of cyclical parthenogenetic (CP) lineages. The results show no significant differences in recombination rates and patterns between CP and OP males nor between CP male and CP females. The observation that recombination is not suppressed in OP males invalidates the hypothesis of a general meiosis suppressor responsible for OP. Rather, our findings suggest that in D. pulex, as in other species where OP evolves from CP ancestors, the CP to OP transition evolves through a re-use of the parthenogenesis pathways already present in CP and through their extension to the entire life cycle, at least in females. In addition to the implications for the evolution of OP, the genetic maps produced by this study constitute an important genomic resource for the model species Daphnia.

category: evolutionary biology


title: Visual Interpretation of the Meaning of kcat/KM in Enzyme Kinetics

abstract: kcat and kcat/KM are the two fundamental kinetic parameters in enzyme kinetics. kcat is the first-order rate constant that determines the reaction rate when the enzyme is fully occupied at a saturating concentration of the substrate. kcat/KM is the second-order rate constant that determines the reaction rate when the enzyme is mostly free at a very low concentration of the substrate. Both parameters provide critical information on how the enzyme lowers the energy barriers along the reaction pathway for catalysis. However, it is surprising how often kcat/KM is used inappropriately as a composite parameter derived by dividing kcat with KM to assess both catalytic power and affinity to the substrate of the enzyme. The main challenge in explaining the true meaning of kcat/KM is the difficulty to demonstrate how the reaction energetics of enzyme catalysis determines kcat/KM in a simple way. Here, I report a step-by-step demonstration on how to visualize the meaning of kcat/KM on the reaction energy diagram. By using the reciprocal form of the expression of kcat/KM with the elementary rate constants in kinetic models, I show that kcat/KM is a harmonic sum of several kinetic terms that correspond to the heights of the transition states relative to the free enzyme. Then, I demonstrate that the height of the highest transition state has the dominant influence on kcat/KM, i. e. the step with the highest transition state is the limiting step for kcat/KM. The visualization of the meaning of kcat/KM on the reaction energy diagram offers an intuitive way to understand all the known properties of kcat/KM, including the Haldane relationship.

category: biochemistry


title: Predicting genes associated with RNA methylation pathways using machine learning

abstract: RNA methylation plays an important role in functional regulation of RNAs, and has thus attracted an increasing interest in biology and drug discovery. Here, we collected and collated transcriptomic, proteomic, structural and physical interaction data from the Harmonizome database, and applied supervised machine learning to predict novel genes associated with RNA methylation pathways in human. We selected five types of classifiers, which we trained and evaluated using cross-validation on multiple training sets. The best models reached 88% accuracy based on cross-validation, and an average 91% accuracy on the test set. Using protein-protein interaction data, we propose six molecular sub-networks linking model predictions to previously known RNA methylation genes, with roles in mRNA methylation, tRNA processing, rRNA processing, but also protein and chromatin modifications. Our study exemplifies how access to large omics datasets joined by machine learning methods can be used to predict gene function.

category: bioinformatics


title: Influence of effective polarization on ion and water interactions within a biomimetic nanopore

abstract: Interactions between ions and water at hydrophobic interfaces within ion channels and nanopores are suggested to play a key role in the movement of ions across biological membranes. Previous molecular dynamics (MD) simulations have shown that the affinity of polarizable anions to aqueous/hydrophobic interfaces can be markedly influenced by including polarization effects through an electronic continuum correction (ECC). Here, we designed a model biomimetic nanopore to imitate the polar pore openings and hydrophobic gating regions found in pentameric ligand-gated ion channels. MD simulations were then performed using both a non-polarizable force field and the ECC method to investigate the behavior of water, Na+ and Cl- ions confined within the hydrophobic region of the nanopore. Number density distributions revealed preferential Cl- adsorption to the hydrophobic pore walls, with this interfacial layer largely devoid of Na+. Free energy profiles for Na+ and Cl- permeating the pore also display an energy barrier reduction associated with the localization of Cl- to this hydrophobic interface, and the hydration number profiles reflect a corresponding reduction in the first hydration shell of Cl-. Crucially, these ion effects were only observed through inclusion of effective polarization which therefore suggests that polarizability may be essential for an accurate description for the behavior of ions and water within hydrophobic nanoscale pores, especially those that conduct Cl-.

category: biophysics


title: Lipidomic analysis of adipose-derived extracellular vesicles reveals their potential as lipid mediators of obesity-associated metabolic complications

abstract:
Adipose extracellular vesicles (AdEV) transport lipids that could participate to the development of obesity-related metabolic dysfunctions. This study aimed to define mice AdEV lipid signature in either healthy or obesity context by a targeted LC-MS/MS approach.

Distinct clustering of AdEV and visceral adipose tissue (VAT) lipidomes by principal component analysis reveals specific lipid composition of AdEV compared to source VAT. Comprehensive analysis identifies enrichment of ceramides and phosphatidylglycerols in AdEV compared to VAT in lean conditions. Lipid subspecies commonly enriched in AdEV highlight specific AdEV-lipid sorting. Obesity impacts AdEV lipidome, driving triacylglycerols and sphingomyelins enrichment in obese versus lean conditions. Obese mice AdEV also display elevated phosphatidylglycerols and acid arachidonic subspecies contents highlighting novel biomarkers and/or mediators of metabolic dysfunctions.

Our study identifies specific lipid-fingerprints for plasma, VAT and AdEV that are informative of the metabolic status and underline the signaling capacity of lipids transported by AdEV in obesity-associated complications.

category: physiology


title: Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

abstract:
Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sub-lethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analyzed the phenotypic responses of 1782 individuals across these stresses and different developmental stages.

Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analyzed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses.

Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sub-lethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.

category: plant biology


title: Tomato SlBES1.8 influences leaf morphogenesis by mediating gibberellin metabolism and signaling

abstract:
Leaf morphogenetic activity determines its shape diversity. However, our knowledge to the regulatory mechanism in maintaining leaf morphogenetic capacity is still limited. In tomato, gibberellin (GA) negatively regulates leaf complexity by shortening the morphogenetic window. We here reported a tomato BRI1-EMS-SUPPRESSOR 1 (BES1) transcription factor, SlBES1.8, that promoted the simplification of leaf pattern in a similar manner as GA functions. Enhanced level of SlBES1.8 dramatically decreased the sensibility of tomato to GA whereas increased the sensibility to the GA biosynthesis inhibitor, PAC. In line with the phenotypic observation, the endogenous bioactive GA contents were increased in OE-SlBES1.8 lines, which certainly promoted the degradation of the GA signaling negative regulator, SlDELLA. Moreover, transcriptomic analysis uncovered a set of overlapping genomic targets of SlBES1.8 and GA, and most of them were regulated in the same way. Expression studies showed the repression of SlBES1.8 to the transcriptions of two GA deactivated genes, SlGA2ox2 and SlGA2ox6, and one GA receptor, SlGID1b-1. Further experiments confirmed the direct regulation of SlBES1.8 to their promoters. On the other hand, SlDELLA physically interacted with SlBES1.8 and further inhibited its transcriptional regulation activity by abolishing SlBES1.8-DNA binding. Conclusively, by mediating GA deactivation and signaling, SlBES1.8 greatly influenced tomato leaf morphogenesis.

HighlightThe BRI1-EMS-SUPPRESSOR 1 (BES1) family protein SlBES1.8 promotes leaf simplification by inhibiting gibberellin deactivation and physically interacting with DELLA protein in tomato.


title: Iron treatment induces defense responses and disease resistance against Magnaporthe oryzae in rice

abstract:
BackgroundIron is an essential micronutrient required for plant growth and development. The impact of iron in plant-pathogen interactions is also well recognized. However, the molecular basis underlying the effect of plant iron status and immune function in plants is poorly understood. Here, we investigated the impact of treatment with high iron in rice immunity at the cellular and molecular level.

ResultsWe show that treatment with high iron confers resistance to infection by the blast fungus M. oryzae in rice. Histochemical staining of M. oryzae-infected leaves revealed that iron and Reactive Oxygen Species (ROS) accumulate at high levels in cells in the vicinity of the infection site. During pathogen infection, a stronger induction of defense-related genes occurs in leaves of iron-treated plants. Notably, a superinduction of phytoalexin biosynthetic genes, both diterpene phytoalexins and sakuranetin, is observed in iron-treated plants during pathogen infection. As a consequence, phytoalexin accumulation was higher in iron-treated plants compared with control plants. Transcriptional alterations of iron homeostasis-related genes and a reduction in apoplastic iron content were observed in leaves of Fe-treated rice plants.

ConclusionsThese results illustrate that the iron status plays a key role in the response of rice plants to pathogen infection, while reinforcing the notion that iron signaling and defense signaling must operate in a coordinated manner in controlling disease resistance in plants. This information provides a basis to better understand the molecular mechanisms involved in rice immunity.


title: Probing the segregation of evoked and spontaneous neurotransmission via photobleaching and recovery of a fluorescent glutamate sensor

abstract: Synapses maintain both action potential-evoked and spontaneous neurotransmitter release, however, organization of these two forms of release within an individual synapse remains unclear. Here, we used photobleaching properties of iGluSnFR, a fluorescent probe that detects glutamate, to investigate the subsynaptic organization of evoked and spontaneous release. In non-neuronal cells and neuronal dendrites, iGluSnFR fluorescence is intensely photobleached and recovers via diffusion of non-photobleached probes within 10-seconds. After photobleaching, while evoked iGluSnFR events could be rapidly suppressed, their recovery required several hours. In contrast, iGluSnFR responses to spontaneous release were comparatively resilient to photobleaching, unless the complete pool of iGluSnFR was activated by glutamate perfusion. This differential effect of photobleaching on different modes of neurotransmission is consistent with a subsynaptic organization where sites of evoked glutamate release are clustered and corresponding iGluSnFR probes are diffusion restricted, while spontaneous release sites are broadly spread across a synapse with readily diffusible iGluSnFR probes.

category: neuroscience


title: Topologically controlled circuits of human iPSC-derived neurons for electrophysiology recordings

abstract: Bottom-up neuroscience, which consists of building and studying controlled networks of neurons in vitro, is a promising method to investigate information processing at the neuronal level. However, in vitro studies tend to use cells of animal origin rather than human neurons, leading to conclusions that might not be generalizable to humans and limiting the possibilities for relevant studies on neurological disorders. Here we present a method to build arrays of topologically controlled circuits of human induced pluripotent stem cell (iPSC)-derived neurons. The circuits consist of 4 to 50 neurons with mostly unidirectional connections, confined by microfabricated polydimethylsiloxane (PDMS) membranes. Such circuits were characterized using optical imaging and microelectrode arrays (MEAs). Electrophysiology recordings were performed on circuits of human iPSC-derived neurons for at least 4.5 months. We believe that the capacity to build small and controlled circuits of human iPSC-derived neurons holds great promise to better understand the fundamental principles of information processing and storing in the brain.


title: Speech Sound Discrimination by Mongolian Gerbils

abstract:
The present study establishes the Mongolian gerbil (Meriones unguiculatus) as a model for investigating the perception of human speech sounds. We report data on the discrimination of logatomes (CVCs1 - consonant-vowel-consonant combinations with outer consonants /b/, /d/, /s/ and /t/ and central vowels /a/, /a:/, /{varepsilon}/, /e:/, /I/, /i:/, /[o]/, /o:/, /[mho]/ and /u:/, VCVs2 - vowel-consonant-vowel combinations with outer vowels /a/, /I/ and /[mho]/ and central consonants /b/, /d/, /f/, /g/, /k/, /l/, /m/, /n/, /p/, /s/, /t/ and /v/) by young gerbils. Four young gerbils were trained to perform an oddball target detection paradigm in which they were required to discriminate a deviant CVC or VCV in a sequence of CVC or VCV standards, respectively. The experiments were performed with an ICRA-1 noise masker with speech-like spectral properties, and logatomes of multiple speakers were presented at various signal-to-noise ratios. Response latencies were measured to generate perceptual maps employing multidimensional scaling, which visualize the gerbils internal representations of the sounds. The dimensions of the perceptual maps were correlated to multiple phonetic features of the speech sounds for evaluating which features of vowels and consonants are most important for the discrimination. The perceptual representation of vowels and consonants in gerbils was similar to that of humans, although gerbils needed higher signal-to-noise ratios for the discrimination of speech sounds than humans. The gerbils discrimination of vowels depended on differences in the frequencies of the first and second formant determined by tongue height and position. Consonants were discriminated based on differences in combinations of their articulatory features. The similarities in the perception of logatomes by gerbils and humans renders the gerbil a suitable model for human speech sound discrimination.

HighlightsO_LIPerceptual maps of vowels and consonants in Mongolian gerbils are derived
C_LIO_LIGerbils perceive vowels and consonants in the same way as humans
C_LIO_LIGerbils discriminate vowels based on frequency differences of the formants
C_LIO_LIGerbils discriminate consonants based on differences in articulatory features
C_LI


title: Systematic analysis of C. elegans embryo behavior reveals a stereotyped developmental progression and a rhythmic pattern of behavioral quiescence

abstract: Systematic analysis of rich behavioral recordings is being used to uncover how circuits encode complex behaviors. Here we apply the approach to embryos. What are the first embryonic behaviors and how do they evolve as early neurodevelopment ensues? To address these questions, we present a systematic description of behavioral maturation for Caenorhabditis elegans embryos. Posture libraries were derived from a genetically encoded motion capture suit imaged with light-sheet microscopy and annotated using custom semi-automated tracking software (Multiple Hypothesis Hypergraph Tracking; MHHT). Analysis of cell trajectories, postures, and behavioral motifs revealed a stereotyped developmental progression. Early movement is dominated by flipping between dorsal and ventral coiling, which gradually slows into a period of reduced motility. Late-stage embryos exhibit sinusoidal waves of dorsoventral bends, prolonged bouts of directed motion, and a rhythmic pattern of pausing, which we designate slow wave twitch (SWT). Synaptic transmission is required for late-stage motion but not for early flipping or the intervening inactive phase. A high-throughput behavioral assay and calcium imaging revealed that SWT is elicited by the rhythmic activity of a quiescence-promoting neuron (RIS). Similar periodic quiescent states are seen prenatally in divergent animals and may play an important role in promoting normal developmental outcomes.


title: Targeting targeted memory reactivation: characteristics of cued reactivation in sleep

abstract: Targeted memory reactivation (TMR) is a technique in which sensory cues associated with memories during wake are used to trigger memory reactivation during subsequent sleep. The characteristics of such cued reactivation, and the optimal placement of TMR cues, remain to be determined. We built an EEG classification pipeline that discriminated reactivation of right- and left-handed movements and found that cues which fall on the up-going transition of the slow oscillation (SO) are more likely to elicit a classifiable reactivation. We also used a novel machine learning pipeline to predict the likelihood of eliciting a classifiable reactivation after each TMR cue using the presence of spindles and features of SOs. Finally, we found that reactivations occurred either immediately after the cue or one second later. These findings greatly extend our understanding of memory reactivation and pave the way for development of wearable technologies to efficiently enhance memory through cueing in sleep.


title: Leaders are made: Learning acquisition of consistent leader-follower relationships depends on implicit haptic interactions.

abstract: Are leaders made or born? Leader-follower roles have been well characterized in social science, but they remain somewhat obscure in sensory-motor coordination. Furthermore, it is unknown how and why leader-follower relationships are acquired, including innate versus acquired controversies. We developed a novel asymmetrical coordination task in which two participants (dyad) need to collaborate in transporting a simulated beam while maintaining its horizontal attitude. This experimental paradigm was implemented by twin robotic manipulanda, simulated beam dynamics, haptic interactions, and a projection screen. Clear leader-follower relationships were learned despite participants not being informed that they were interacting with each other, but only when strong haptic feedback was introduced. For the first time, we demonstrate the emergence of consistent leader-follower relationships in sensory-motor coordination, and further show that haptic interaction is essential for dyadic co-adaptation. These results provide insights into neural mechanisms responsible for the formation of leader-follower relationships in our society.


title: Multi-taskLearning and Ensemble Approach to Predict Cognitive Scores for Patients with Alzheimer's Disease

abstract: The objective of this research was to explore the efficacy of integrating 1) using multi-task learning, 2) neuroimaging data and common risk factors to predict the ADAS-cog 11 score in Alzheimers patients. We applied heavy augmentations to magnetic resonance imaging (MRI) scans of 798 participants ranging between 0 and 96 months from the initial diagnosis. This enabled us to exploit the benefits of the U-Net architecture, a structure historically known to perform well on medical imaging tasks using limited data with heavy image augmentations. The multi-task model simultaneously performed segmentation of white matter, gray matter, and cerebrospinal fluid on the MRI input and regression to predict the ADAS-cog 11 score. There is a body of literature highlighting the independent relationships between gray and white matter volumes and dementia severity; the trajectory was to explore if the multi-task model structure for these interrelated tasks would boost performance for each individual task. The final model integrates the deep learning results with a Gradient Boosting model trained on demographic data. A considerable performance improvement from the initial multi-task U-Net on the ADAS-cog 11 prediction task was achieved across our experiments.


title: Seeing the future: predictive control in neural models of ocular accommodation

abstract: Ocular accommodation is the process of adjusting the eyes crystalline lens so as to bring the retinal image into sharp focus. The major stimulus to accommodation is therefore retinal defocus, and in essence, the job of accommodative control is to send a signal to the ciliary muscle which will minimize the magnitude of defocus. In this paper, we first provide a tutorial introduction to control theory to aid vision scientists without this background. We then present a unified model of accommodative control that explains properties of the accommodative response for a wide range of accommodative stimuli. Following previous work, we conclude that most aspects of accommodation are well explained by dual integral control, with a "fast" or "phasic" integrator enabling response to rapid changes in demand, which hands over control to a "slow" or "tonic" integrator which maintains the response to steady demand. Control is complicated by the sensorimotor latencies within the system, which delay both information about defocus and the accommodation changes made in response, and by the sluggish response of the motor plant. These can be overcome by incorporating a Smith predictor, whereby the system predicts the delayed sensory consequences of its own motor actions. For the first time, we show that critically-damped dual integral control with a Smith predictor accounts for adaptation effects as well as for the gain and phase for sinusoidal oscillations in demand. In addition, we propose a novel proportional-control signal to account for the power spectrum of accommodative microfluctuations during steady fixation, which may be important in hunting for optimal focus, and for the nonlinear resonance observed for low-amplitude, high-frequency input. Complete Matlab/Simulink code implementing the model is provided at https://doi.org/10.25405/data.ncl.14945550.


title: Rewarded extinction increases amygdalar connectivity and stabilizes long-term memory traces in the vmPFC

abstract:
Neurobiological evidence in rodents indicates that threat extinction incorporates reward neurocircuitry. Consequently, incorporating reward associations with an extinction memory may be an effective strategy to persistently attenuate threat responses. Moreover, while there is considerable research on the short-term effects of extinction strategies in humans, the long-term effects of extinction are rarely considered. In a within-subjects fMRI study, we compared counterconditioning (a form of rewarded-extinction) to standard extinction, at recent (24 hours) and remote ([~]1 month) retrieval tests. Relative to standard extinction, counterconditioning diminished 24-hour relapse of arousal and threat expectancy, and reduced activity in brain regions associated with the appraisal and expression of threat (e.g., thalamus, insula, periaqueductal gray). The retrieval of reward-associated extinction memory was accompanied by functional connectivity between the amygdala and the ventral striatum, whereas the retrieval of standard-extinction memories was associated with connectivity between the amygdala and ventromedial prefrontal cortex (vmPFC). One-month later, the retrieval of both standard- and rewarded-extinction was associated with amygdala-vmPFC connectivity. However, only rewarded extinction created a stable memory trace in the vmPFC, identified through overlapping multivariate patterns of fMRI activity from extinction to 24-hour and 1-month retrieval. These findings provide new evidence that reward may generate a more stable and enduring memory trace of attenuated threat in humans.

Significance StatementPrevalent treatments for pathological fear and anxiety are based on the principles of Pavlovian extinction. Unfortunately, extinction forms weak memories that only temporarily inhibit the retrieval of threat associations. Thus, to increase the translational relevance of extinction research, it is critical to investigate whether extinction can be augmented to form a more enduring memory, especially after long intervals. Here, we used a multi-day fMRI paradigm in humans to compare the short- and long-term neurobehavioral effects of aversive-to-appetitive counterconditioning, a form of augmented extinction. Our results provide novel evidence that including an appetitive stimulus during extinction can reduce short-term threat relapse and stabilize the memory trace of extinction in the vmPFC, for at least one month after learning.


title: Engineered biological neural networks on high density CMOS micro electrode arrays

abstract: In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatiotemporal resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatiotemporal resolution of the CMOS MEA enabled us to show that we can guide action potentials using the unidirectional topology of our circular multi-node microstructure.


title: Integration of visual motion and pursuit signals in areas V3A and V6+ across cortical depth using 9.4T fMRI

abstract:
Neural mechanisms underlying a stable perception of the world during pursuit eye movements are not fully understood. Both, perceptual stability as well as perception of real (i.e. objective) motion are the product of integration between motion signals on the retina and efference copies of eye movements. Human areas V3A and V6 have previously been shown to have strong objective ( real) motion responses. Here we used high-resolution laminar fMRI at ultra-high magnetic field (9.4T) in human subjects to examine motion integration across cortical depths in these areas. We found an increased preference for objective motion in areas V3A and V6+ i.e. V6 and possibly V6A towards the upper layers. When laminar responses were detrended to remove the upper-layer bias present in all responses, we found a unique, condition-specific laminar profile in V6+, showing reduced mid-layer responses for retinal motion only. The results provide evidence for differential, motion-type dependent laminar processing in area V6+. Mechanistically, the mid-layer dip suggests a special contribution of retinal motion to integration, either in the form of a subtractive (inhibitory) mid-layer input, or in the form of feedback into extragranular or infragranular layers. The results show that differential laminar signals can be measured in high-level motion areas in the human occipitoparietal cortex, opening the prospect of new mechanistic insights using non-invasive brain imaging.

Significance StatementVisual stability and our ability to differentiate between self-induced and real motion are central to our visual sense. Both require the integration of two signals - retinal motion and copies of muscle commands used for eye movements (efference copies). A reasonable assumption is that either the efference copy or the result of integration will be conveyed to high-level visual regions along with visual retinal input, possibly differentially across cortical depth as the input sources differ. Our ultra-high field recordings present the first laminar evidence of differential signal processing of retinal and objective motion signals in area V6+, and present a first window into a mechanistic understanding of visual high-level motion processing.


title: Performance During Whole Body Reaching Movements Is Impaired In Hypergravity While Preserved In Microgravity

abstract: While recent findings demonstrated the importance of initial state estimates about gravity for optimized motor control, it remains unclear whether novel initial states are rapidly implemented movement planning (and control) in the same way when gravity is removed or increased. Here, we investigated the effect of microgravity and hypergravity exposure on whole-body reaching movements performed by standing subjects during parabolic flights. Reaching movements were analyzed regarding spatial accuracy (finger endpoint deviation), arm kinematics (arm angular displacement), whole-body kinematics (body bending) and EMG activity (muscular activation and synergies) of eight muscles. Results showed that kinematics and muscular activity are adjusted in microgravity allowing accurate whole-body reaching, thus confirming the perfectly scaled sensorimotor reorganization reported in previous recent studies. Contrasting with these observations, participants hardly reached the targets in 1.8g (systematic undershot). Strikingly, whole-body kinematics remained unchanged in hypergravity compared to 1g observations. Finally, while the analysis of synergies highlighted a comparable muscular organization in all gravitational contexts, our main findings revealed local muscular adjustments leading to accurate motor responses in microgravity, but not in hypergravity.


title: People with nicotine dependence use-disorder exhibit more prefrontal activity during preparatory control but reduced anterior cingulate activity during reactive control

abstract: Reduced inhibitory control and a hypersensitivity to reward are key deficits in drug-dependents, however, they tend to be studied in isolation. Here we seek to understand the neural processes underlying control over reward and how this is different in people with a nicotine use disorder (pNUD). A novel variant of the monetary incentive delay task was performed by pNUD (n = 20) and non-smokers (n = 20), where we added a stop-signal component such that participants had to inhibit prepotent responses to earn a larger monetary reward. Brain activity was recorded using functional magnetic resonance imaging (fMRI). We estimated stop signal reaction times (SSRT), an indicator of impulsivity, and correlated these with brain activity. Inhibitory accuracy scores did not differ between the control group and pNUD. However, pNUD had slower SSRTs, suggesting that they may find it harder to inhibit responses. Brain data revealed that pNUD had greater preparatory control activity in the middle frontal gyrus and inferior frontal gyrus prior to successful inhibitions over reward. In contrast, non-smokers had greater reactive control associated with more activity in the anterior cingulate cortex during these successful inhibitions. SSRT-brain activity correlations revealed that pNUD engaged more control related prefrontal brain regions when SSRTs are slower. Overall, whilst the inhibition accuracy scores were similar between groups, differential neural processes and strategies were used to successfully inhibit a prepotent response. The findings suggest that increasing preparatory control in pNUD may be one possible treatment target in order to increase inhibitory control over reward.


title: D-amphetamine maintenance therapy reduces cocaine use in female rats

abstract: Currently, there are no approved medications to treat cocaine addiction. In this context, d-amphetamine maintenance therapy is a promising pharmacological strategy to reduce cocaine use. In both male rats and human cocaine users, d-amphetamine treatment reduces cocaine taking and seeking. However, this has not been examined systematically in female animals, even though cocaine addiction afflicts both women and men, and the sexes can differ in their response to cocaine. Here, we determined how d-amphetamine maintenance therapy during cocaine self-administration influences cocaine use in female rats. In experiment 1, two groups of female rats received 14 intermittent access (IntA) cocaine self-administration sessions. One group received concomitant d-amphetamine maintenance treatment (COC + A rats; 5 mg/kg/day, via minipump), the other group did not (COC rats). After discontinuing d-amphetamine treatment, we measured responding for cocaine under a progressive ratio schedule, responding under extinction and cocaine-primed reinstatement of drug seeking. In experiment 2, we assessed the effects of d-amphetamine maintenance on these measures in already cocaine-experienced rats. To this end, rats first received 14 IntA cocaine self-administration sessions without d-amphetamine. They then received 14 more sessions now either with (COC/COC + A rats) or without (COC/COC rats) concomitant d-amphetamine treatment. In both experiments, d-amphetamine treatment did not influence cocaine-primed reinstatement of cocaine seeking. However, after d-amphetamine treatment, rats responded less for cocaine both under progressive ratio and extinction conditions. Thus, d-amphetamine treatment can both prevent and reverse increases in the motivation to take and seek cocaine in female animals.


title: Extracellular release of two peptidases dominates generation of the trypanosome quorum-sensing signal

abstract:
Trypanosomes causing African sleeping sickness use quorum-sensing (QS) to generate transmission-competent stumpy forms in their mammalian hosts. This density-dependent process is signalled by oligopeptides that stimulate the signal transduction pathway leading to stumpy formation. Using mass spectrometry analysis, peptidases released by trypanosomes were identified and, for 12 peptidases, their extracellular delivery was confirmed. Thereafter, the contribution of each peptidase to QS signal production was determined using systematic inducible overexpression in vivo, activity being confirmed to operate through the physiological QS signalling pathway. Gene knockout of the QS-active peptidases identified two enzymes, oligopeptidase B and metallocarboxypeptidase I, that significantly reduced QS when ablated individually. Further, a combinatorial gene knockout of both peptidases confirmed their dominance in the generation of the QS signal, with peptidase release of oligopeptidase B mediated via an unconventional protein secretion pathway. This identifies how the QS signal driving trypanosome virulence and transmission is generated in mammalian hosts.

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category: microbiology


title: A conserved viral amphipathic helix governs the replication site-specific membrane association

abstract: Positive-strand RNA viruses assemble their viral replication complexes (VRCs) on specific host organelle membranes, yet it is unclear how viral replication proteins recognize and what motifs or domains in viral replication proteins determine their localizations. We show here that an amphipathic helix, helix B in replication protein 1a of brome mosaic virus (BMV), is necessary for 1as localization to the nuclear endoplasmic reticulum (ER) membrane where BMV assembles its VRCs. Helix B is also sufficient to target soluble proteins to the nuclear ER membrane in yeast and plant cells. We further show that an equivalent helix in several plant- and human-infecting viruses of the alphavirus-like superfamily targets fluorescent proteins to the organelle membranes where they form their VRCs, including ER, vacuole, and Golgi membranes. Our work reveals a conserved helix that governs the localization of VRCs among a group of viruses and points to a possible target for developing broad-spectrum antiviral strategies.


title: BrnQ-type Branched-chain Amino Acid Transporters Influence Bacillus anthracis Growth and Virulence

abstract:
Bacillus anthracis, the anthrax agent, exhibits robust proliferation in diverse niches of mammalian hosts. Metabolic attributes of B. anthracis that permit rapid growth in multiple mammalian tissues have not been established. We posit that branched-chain amino acid (BCAA: Isoleucine, leucine and valine) metabolism is key to B. anthracis pathogenesis. Increasing evidence indicates relationships between B. anthracis virulence and expression of BCAA-related genes. Expression of some BCAA-related genes is altered during culture in bovine blood in vitro and the bacterium exhibits valine auxotrophy in a blood serum mimic medium. Transcriptome analyses have revealed that the virulence regulator AtxA, that positively affects expression of the anthrax toxin and capsule genes, negatively regulates genes predicted to be associated with BCAA biosynthesis and transport. Here, we show that B. anthracis growth in defined media is severely restricted in the absence of exogenous BCAAs, indicating that BCAA transport is required for optimal growth in vitro. We demonstrate functional redundancy among multiple BrnQ-type BCAA transporters. Three transporters are associated with isoleucine and valine transport, and deletion of one, BrnQ3, attenuates virulence in a murine model for anthrax. Interestingly, an ilvD-null mutant lacking dihydroxy-acid dehydratase, an enzyme essential for BCAAs synthesis, exhibits unperturbed growth when cultured in media containing BCAAs, but is highly attenuated in the murine model. Finally, our data show that BCAAs enhance AtxA activity in a dose-dependent manner, suggesting a model in which BCAAs serve as a signal for virulence gene expression.

IMPORTANCEInfection with B. anthracis can result in systemic disease with large numbers of the bacterium in multiple tissues. We found that BCAA synthesis is insufficient for robust growth of B. anthracis; access to branched-chain amino acids (BCAAs) is necessary for proliferation of the pathogen during culture and during infection in a murine model for anthrax. B. anthracis produces an unusually large repertoire of BCAA-related transporters. We identified three isoleucine/valine transporters with partial functional redundancy during culture. Deletion of one of these transporters, BrnQ3, resulted in attenuated virulence. Interestingly, a BCAA biosynthesis mutant grew well in medium containing BCAAs, but like BrnQ3, was attenuated for virulence. These results suggest that BCAAs are limiting in multiple niches during infection and furthers understanding of nutritional requirements of this important pathogen.


title: Salmonella Typhimurium induces NAIP/NLRC4- and NLRP3/ASC-independent, caspase-1/4-dependent inflammasome activation in human intestinal epithelial cells

abstract: Salmonella enterica serovar Typhimurium is a gram-negative pathogen that causes diseases ranging from gastroenteritis to systemic infection and sepsis. Salmonella uses type III secretion systems (T3SSs) to inject effectors into host cells. While these effectors are necessary for bacterial invasion and intracellular survival, intracellular delivery of T3SS products also enables detection of Salmonella by cytosolic immune sensors. Upon detecting translocated Salmonella ligands, these sensors form multimeric complexes called inflammasomes, which activate caspases that lead to proinflammatory cytokine release and pyroptosis. In particular, the Salmonella T3SS needle, inner rod, and flagellin proteins activate the NAIP/NLRC4 inflammasome in murine intestinal epithelial cells (IECs), which leads to restriction of bacterial replication and extrusion of infected IECs into the intestinal lumen, thereby preventing systemic dissemination of Salmonella. While these processes are studied quite well in mice, the role of the NAIP/NLRC4 inflammasome in human IECs remains unknown. Unexpectedly, we found the NAIP/NLRC4 inflammasome is dispensable for early inflammasome responses to Salmonella in both human intestinal epithelial cell lines and organoids. Additionally, the NLRP3 inflammasome and the adaptor protein ASC are not required for inflammasome activation in Caco-2 cells. Instead, we observed a partial requirement for caspase-1, and a necessity for caspase-4 and GSDMD pore-forming activity in mediating inflammasome responses to Salmonella in Caco-2 cells. These findings suggest that unlike murine IECs, human IECs do not rely on NAIP/NLRC4, and also do not use NLRP3/ASC. Instead, they primarily use caspases-1 and -4 to mediate early inflammasome responses to SPI-1-expressing Salmonella.


title: Cell cycle-dependent recruitment of FtsN to the divisome in Escherichia coli

abstract:
Cell division in Escherichia coli starts with the formation of an FtsZ protofilament network in the middle of the cell, the Z ring. However, only after a considerable lag period do the cells start to form a midcell constriction. The basis of this cell cycle checkpoint is yet unclear. The onset of constriction is dependent upon the arrival of so-called late divisome proteins, among which, FtsN is the last arriving essential one. The timing and dependency of FtsN arrival to the divisome, along with genetic evidence, suggests it triggers cell division. In this study, we used high throughput fluorescence microscopy to quantitatively determine the arrival of FtsN and the early divisome protein ZapA to midcell at a single-cell level during the cell cycle. Our data show that recruitment of FtsN coincides with the initiation of constriction within experimental uncertainties and that the relative fraction of ZapA/FtsZ reaches its highest value at this event. We also find that FtsN is recruited to midcell in two distinct temporal stages with septal peptidoglycan synthesis starting in the first stage and accelerating in the second stage, during which the amount of ZapA/FtsZ in the midcell decreases. In the presence of FtsA*, recruitment of FtsN becomes concurrent with the formation of the Z-ring, but constriction is still delayed indicating FtsN recruitment is not rate limiting, at least under these conditions. Finally, our data support the recently proposed idea that ZapA/FtsZ and FtsN are part of physically separate complexes in midcell throughout the whole septation process.

ImportanceIn E. coli, FtsN has been considered a trigger for septal wall synthesis and the onset of constriction. While FtsN is critical for cell division, its recruitment kinetics to midcell has not been characterized. Using quantitative high throughput microscopy, we find that FtsN is recruited to midcell in two temporal stages. The septal cell wall synthesis starts at the first stage and accelerates in the second stage. In the presence of an FtsA mutant defective in self-interaction, recruitment of FtsN to midcell is enhanced, but constriction is still delayed. Our results shed new light on an essential but not rate-limiting role of FtsN in E. coli cell division and also support the view that ZapA/FtsZ and FtsN are part of physically separate complexes in midcell throughout the division process.


title: Colorimetric and fluorescent TRAP assays for visualising and quantifying fish osteoclast activity

abstract: Histochemical detection of tartrate-resistant acid phosphatase (TRAP) activity is a fundamental technique for visualizing osteoclastic bone resorption and assessing osteoclast activity status in tissues. This approach has mostly employed colorimetric detection, which has limited quantification of activity in situ and co-labelling with other skeletal markers. Here we report simple colorimetric and fluorescent TRAP assays in zebrafish and medaka, two important model organisms for investigating the pathogenesis of bone disorders. We show fluorescent TRAP staining, utilising the ELF97 substrate, is a rapid, robust and stable system to visualise and quantify osteoclast activity in zebrafish, and is compatible with other fluorescence stains, transgenic lines and antibody approaches. Using this approach, we show that TRAP activity is predominantly found around the base of the zebrafish pharyngeal teeth, where osteoclast activity state appears to be heterogeneous.


title: North and East African mitochondrial genetic variation needs further characterization towards precision medicine

abstract:
Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This requires a comprehensive catalogue of commonly observed genetic variations in the mitochondria for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. Towards this, we have created the most comprehensive quality-controlled North and East African mitochondrial dataset to date by compiling 11 published cohorts with novel data of mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n=2,504) and the Human Genome Diversity Project (n=828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination. Using a subset of high-coverage mitochondrial sequences we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. This demonstrates common hitherto unexplored variants in mitochondrial genomes of the North and East African region that lead to novel phylogenetic relationships, calling for further in-depth population genetic studies in that region.

Author summaryDoes currently available human mitochondrial genetic data sufficiently cover North and East African diversity to investigate precision medicine for mitochondria-related diseases? To address this question, we have integrated and compared novel with existing sequence data from that region and world-wide. We find that variant profiles, i.e. haplogroups, carried by North and East Africans are shared with or related to those observed in Europe, Africa and Asia alike. Nonetheless, for a few haplogroups, world-wide data is inaccurate and incomplete for North and East Africans. Thus, we call for additional, future studies to more comprehensively represent human mitochondrial genetic diversity towards implementing precision medicine.

category: genetics


title: A single-cell genomic strategy for alternative transcript start sites identification

abstract: Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-{beta} stimulated mouse embryonic fibroblasts (MEFs). We quantify the performance of our method and find it as accurate as other single cell methods for the detection of TSSs. Our data are also clearly discriminate two IFN-{beta} stimulated MEFs. Moreover, our results indicate 82% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on CAGE (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.

category: genomics


title: DeepPlnc: Discovering plant lncRNAs through multimodal deep learning on sequential data

abstract: Plant lncRNAs differ a lot from animals even in the mode of transcription and display poor sequence conservation. Scarce resources exist to reliably annotate the plant lncRNAs. Here, we present a bi-modal Convolution Neural Nets deep-learning system, DeepPlnc, to accurately identify plant lncRNAs. This biomodal deep-learning system parallely learns from sequence and structural encoding of the given RNA sequences. Unlike most of the existing software, it can accurately work even in conditions with ambiguity of boundaries like de novo assembled and incomplete sequences. It scored high on all the considered performance metrics while breaching the accuracy of >98% when tested across different validated datasets. Four different bench-marking datasets were used to ensure a clear picture. The software was comprehensively benchmarked against some of the recently published tools to identify the plant lncRNAs where it consistently and significantly outperformed them while maintaining a lead in the range of ~4%-8.5% from the second best performing tool. Finally, it was used to annotate a de novo assembled transcriptome to showcase its practical application. Here also it significantly outperformed the compared tools with almost half false positive rate than the compared tools, clearly displaying the kind of impact DeepPlnc could have in getting a much superior annotation. A pioneer deep-learning approach to detect plant lncRNAs, DeepPlnc will be a reliable resource for de novo identification of lncRNAs in plants. DeepPlnc has been made freely available as a web-server and GitHub stand-alone program at https://scbb.ihbt.res.in/DeepPlnc/.


title: Identification of functional residues using machine learning provides insights into the evolution of odorant receptor gene families in solitary and social insects

abstract: The gene family of insect odorant receptors (ORs) has greatly expanded in the course of evolution. ORs allow insects to detect volatile chemicals and therefore play an important role in social interactions, the detection of enemies and preys, and during foraging. The sequences of several thousand ORs are known, but their specific function or ligands have been identified only for very few of them. To advance the functional characterization of ORs, we compiled, curated and aligned the sequences of 3,902 ORs from 21 insect species. We identified the amino acid positions that best predict the response to ligands using machine learning on sets of functionally characterized proteins from the fly Drosophila melanogaster, the mosquito Anopheles gambiae and the ant Harpegnathos saltator. We studied the conservation of these predicted relevant residues across all OR subfamilies and show that the subfamilies that expanded strongly in social insects exhibit high levels of conservation in their binding sites. This indicates that ORs of social insect families are typically finely tuned and exhibit a sensitivity to very similar odorants. Our novel approach provides a powerful tool to use functional information from a limited number of genes to investigate the functional evolution of large gene families.


title: Isolation and characterization of fucosylated extracellular vesicles based on a novel GlyExo-Capture technique

abstract: Extracellular vesicles (EVs) derived from tumor cells have recently garnered great interest due to their diagnostic and therapeutic potential. The presence of different glycosylation at the EVs surface potentiates the need for efficient glycosylated-EVs isolation. Here, we developed a GlyExo-Capture technique for capturing fucosylated-EVs from serum and cell supernatants robustly. Lens culinaris lectin (LCA)-immobilized beads were found to capture approximately 60% of the total EVs from HepG2 cells. The capture efficiency was reduced to lower than 40% in non-tumorigenic MIHA cells. Notably, the cellular uptake pattern of highly fucosylated-EVs was markedly different from EVs with low fucosylation. The disclosure of enriched fucosylated-EVs miRNA cargos by next-generation deep sequencing revealed 75 differentially expressed miRNAs in hepatocellular carcinoma (HCC). Among them, a 4-miRNA panel was chosen and yielded an area under the ROC curve (AUC) of 0.86 and 0.84 for the detection of HCC from non-HCC controls in testing sample and an independent validation sample, respectively. The 4-miRNA signature was independent of AFP and a combined model with AFP yielded an increased AUC of 0.92. In conclusion, we developed a high-throughput method for capturing fucosylated-EVs efficiently and shed light on using fucosylated-EVs as potential sources of miRNA for cancer biomarker detection.

category: cancer biology


title: Quantification of microbial robustness

abstract:
Stable cell performance in a fluctuating environment is essential for sustainable bioproduction and synthetic cell functionality; however, microbial robustness is rarely quantified. Here, we describe a high-throughput strategy for quantifying robustness of multiple cellular functions and strains in a perturbation space. We evaluated quantifications theory on experimental data and concluded that the mean-normalized Fano factor allowed accurate, reliable, and standardized quantification. Our methodology applied to perturbations related to lignocellulosic bioethanol production showed that Saccharomyces cerevisiae Ethanol Red exhibited both higher and more robust growth rates than CEN.PK and PE-2, while a more robust product yield traded off for lower mean levels. The methodology validated that robustness is function-specific and characterized by positive and negative function-specific trade-offs. Systematic quantification of robustness to end-use perturbations will be important to analyze and construct robust strains with more predictable functions.

Graphical Abstract

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category: synthetic biology


title: Identification of genome-wide distribution of cyanobacterial group 2 sigma factor SigE accountable for its regulon

abstract:
Sigma factors are the subunits of bacterial RNA polymerase that govern the expression of genes by recognizing the promoter sequence. Cyanobacteria, which are oxygenic phototrophic eubacteria, have multiple alternative sigma factors that respond to various environmental stresses. The subgroup highly homologous to the primary sigma factor (SigA) is called the group 2 sigma factor. The model cyanobacterium, Synechocystis sp. PCC 6803, has four group 2 sigma factors (SigB-E) conserved within the phylum Cyanobacteria. Among the group 2 sigma factors in Synechocystis sp. PCC 6803, SigE is unique because it alters metabolism by inducing the expression of genes related to sugar catabolism and nitrogen metabolism. However, the features of promoter sequence of the SigE regulon remains elusive. Here, we identified the direct targets of SigA and SigE by chromatin immunoprecipitation sequencing (ChIP-seq). We then showed that the binding sites of SigE and SigA overlapped substantially, but SigE exclusively localized to SigE-dependent promoters. We also found consensus sequences from SigE-dependent promoters and confirmed their importance. ChIP-seq analysis showed both the redundancy and specificity of SigE compared with SigA, integrating information obtained from a previously adopted genetic approach and in vitro assays. The features of SigE elucidated in our study indicate its similarity with group 2 sigma factors of other bacteria, even though they are evolutionally irrelevant. Our approach is also applicable to other organisms and organelles, such as plant plastids, which have multiple group 2 sigma factors.

ImportanceGroup 2 sigma factors are alternative sigma factors highly homologous to primary sigma factors. Cyanobacteria, which are photosynthetic eubacteria, are unique because they have multiple group 2 sigma factors. Although each sigma factor induces the expression of specific genes, the redundancy and complicated network of the primary and group 2 sigma factors hinder the identification of their regulons via a genetic approach. Here, we identified the binding sites of SigE (group 2 sigma factor) and SigA (primary sigma factor) using chromatin immunoprecipitation sequencing and identified the minimal element of SigE-dependent promoters by subsequent promoter assays. Our study provides insights into the common features of group 2 sigma factors, which, though evolutionarily irrelevant, are widespread among eubacteria and plant plastids.

category: molecular biology


title: A nanobody-based toolset to monitor and modify the mitochondrial GTPase Miro1

abstract: The mitochondrial outer membrane (MOM)-anchored GTPase Miro1, is a central player in mitochondrial transport and homeostasis. The dysregulation of Miro1 in amyotrophic lateral sclerosis (ALS) and Parkinsons disease (PD) suggests that Miro1 may be a potential biomarker or drug target in neuronal disorders. However, the molecular functionality of Miro1 under (patho-) physiological conditions is poorly known. For a more comprehensive understanding of the molecular functions of Miro1, we have developed Miro1-specific nanobodies (Nbs) as novel research tools. We identified seven Nbs that bind either the N- or C-terminal GTPase domain of Miro1 and demonstrate their application as research tools for proteomic and imaging approaches. To visualize the dynamics of Miro1 in real time, we selected intracellularly functional Nbs, which we reformatted into chromobodies (Cbs) for time- lapse imaging of Miro1. By genetic fusion to an Fbox domain, these Nbs were further converted into Miro1-specific degrons and applied for targeted degradation of Miro1 in live cells. In summary, this study presents a collection of novel Nbs that serve as a toolkit for advanced biochemical and intracellular studies and modulations of Miro1, thereby contributing to the understanding of the functional role of Miro1 in disease-derived model systems.


title: Radiation Exposure Determination in a Secure, Cloud-based Online Environment

abstract:
BackgroundIn a major radiation incident, the speed of sample processing and interpretation of estimated exposures will be critical for triaging individuals. The Automated Dicentric Chromosome (DC) Identifier and Dose Estimator System (ADCI) selects and processes images to identify DCs and determines radiation dose without manual review. The goal of this study was to broaden accessibility and speed of this system with data parallelization while protecting data and software integrity.

MethodsADCI_Online is a secure web-streaming platform that can be accessed worldwide from distributed local nodes. Data and software are separated until they are linked for estimation of radiation exposures. Performance is assessed with data from multiple biodosimetry laboratories.

ResultsDose estimates from ADCI_Online are identical to ADCI running on dedicated GPU-accelerated hardware. Metaphase image processing, automated image selection, calibration curve generation, and radiation dose estimation of a typical set of samples of unknown exposures were completed in <2 days. Parallelized processing and analyses using cloned software instances on different hardware configurations of samples at the scale of an intermediate-sized radiation accident (54,595 metaphase images) accelerated estimation of radiation doses to within clinically-relevant time frames.

ConclusionsThe ADCI_Online streaming platform is intended for on-demand, standardized radiation research assessment, biodosimetry proficiency testing, inter-laboratory comparisons, and training. The platform has the capacity to handle analytic bottlenecks in intermediate to large radiation accidents or events.


title: Promising or problematic? Perceptions of active learning from STEM students with ADHD and specific learning disabilities

abstract: STEM instructors are encouraged to adopt active learning in their courses, yet our understanding of how active learning affects different groups of students is still developing. One group often overlooked in higher education research is students with disabilities. Two of the most commonly occurring disabilities on college campuses are attention-deficit/hyperactivity disorder (ADHD) and specific learning disorders (SLD). We investigated how the incorporation of active-learning practices influences the learning and self-advocacy experiences of students with ADHD and/or SLD (ADHD/SLD) in undergraduate STEM courses. Semi-structured interviews with 25 STEM majors with ADHD/SLD were conducted and data were analyzed using qualitative methods. Most participants perceived themselves to learn best in a STEM course with at least some elements of active learning. Participants described how they perceived active learning to support or hinder their learning and how active learning affected their self-advocacy. Active-learning barriers could be attributed to a combination of instructional factors. These factors included how a particular active-learning practice was implemented within a STEM course and limited awareness of universal design for learning. Defining the supports and barriers perceived by students with ADHD/SLD is a crucial first step in developing more inclusive active-learning STEM courses. Suggestions for research and teaching are provided.

category: scientific communication and education


title: Towards Biophysical Markers of Depression Vulnerability

abstract: A major difficulty with treating psychiatric disorders is their heterogeneity: different neural causes can lead to the same phenotype. To address this, we propose describing the underlying pathophysiology in terms of interpretable, biophysical parameters of a neural model derived from the electroencephalogram. We analyzed data from a small patient cohort of patients with depression and controls. We constructed biophysical models that describe neural dynamics in a cortical network activated during a task that is used to assess depression state. We show that biophysical model parameters are biomarkers, that is, variables that allow subtyping of depression at a biological level. They yield a low dimensional, interpretable feature space that allowed description of differences between individual patients with depressive symptoms. They capture internal heterogeneity/variance of depression state and achieve significantly better classification than commonly used EEG features. Our work is a proof of concept that a combination of biophysical models and machine learning may outperform earlier approaches based on classical statistics and raw brain data.


title: Whole-brain optical access in small adult vertebrates with two- and three-photon microscopy

abstract: Although optical microscopy has allowed us to study the entire brain in early developmental stages, access to the brains of live, adult vertebrates has been limited. Danionella, a genus of miniature, transparent fish closely related to zebrafish has been introduced as a neuroscience model to study the entire adult vertebrate brain. However, the extent of optically accessible depth in these animals has not been quantitatively characterized. Here, we show that two- and three-photon microscopy can be used to access the entire depth of the adult wild type Danionella dracula brain without any modifications to the animal other than mechanical stabilization. Three-photon microscopy provides high signal to background ratio and optical sectioning through the deepest part of the brain. While vasculature can be observed with two-photon microscopy, the deeper regions have low contrast. We show that multiphoton microscopy is ideal for readily penetrating the entire adult brain within the geometry of these animals head structures and without the need for pigment removal. With multiphoton microscopy enabling optical access to the entire adult brain and a repertoire of methods that allow observation of the larval brain, Danionella provides a model system for readily studying the entire brain over the lifetime of a vertebrate.


title: Using marine cargo traffic to identify countries in Africa with greatest risk of invasion by Anopheles stephensi

abstract: Anopheles stephensi is an efficient malaria vector commonly found in South Asia and the Arabian Peninsula, but in recent years it has established as an invasive species in the Horn of Africa (HoA). In this region, An. stephensi was first detected in a livestock quarantine station near a major seaport in Djibouti in 2012, in Ethiopia in 2016, in Sudan in 2018 and Somalia in 2019. Anopheles stephensi often uses artificial containers as larval habitats, which may facilitate introduction through maritime trade as has been seen with other invasive container breeding mosquitoes. If An. stephensi is being introduced through maritime traffic, prioritization exercises are needed to identify locations at greatest risk of An. stephensi introduction for early detection and rapid response, limiting further invasion opportunities. Here, we use UNCTAD maritime trade data to 1) identify coastal African countries which were most highly connected to select An. stephensi endemic countries in 2011, prior to initial detection in Africa, 2) develop a ranked prioritization list of countries based on likelihood of An. stephensi introduction for 2016 and 2020 based on maritime trade alone and maritime trade and habitat suitability, and 3) use network analysis to describe intracontinental maritime trade and eigenvector centrality to determine likely paths of further introduction on the continent if An. stephensi is detected in a new location. Our results show that in 2011, Sudan and Djibouti were ranked as the top two countries with likelihood of An. stephensi introduction based on maritime trade alone, and these were indeed the first two coastal countries in the HoA where An. stephensi was detected. Trade data from 2020 with Djibouti and Sudan included as source populations identify Egypt, Kenya, Mauritius, Tanzania, and Morocco as the top five countries with likelihood of An. stephensi introduction. When factoring in habitat suitability, Egypt, Kenya, Tanzania, Morocco, and Libya are ranked highest. Network analysis revealed that the countries with the highest eigenvector centrality scores, and therefore highest degrees of connectivity with other coastal African nations were South Africa (0.175), Mauritius (0.159), Ghana (0.159), Togo (0.157), and Morocco (0.044) and therefore detection of An. stephensi in any one of these locations has a higher potential to cascade further across the continent via maritime trade than those with lower eigenvector centrality scores. Taken together, these data could serve as tools to prioritize efforts for An. stephensi surveillance and control in Africa. Surveillance in seaports of countries at greatest risk of introduction may serve as an early warning system for the detection of An. stephensi, providing opportunities to limit further introduction and expansion of this invasive malaria vector in Africa.

category: ecology


title: Using ultraconserved elements to reconstruct the termite tree of life

abstract: The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: https://github.com/oist/TER-UCE-DB/.


title: Awake mouse brain photoacoustic and optical imaging through a transparent ultrasound cranial window

abstract: Optical resolution photoacoustic microscopy (OR-PAM) can map the cerebral vasculature at capillary level resolution. However, the OR-PAM setups bulky imaging head makes awake mouse brain imaging challenging and inhibits its integration with other optical neuroimaging modalities. Moreover, the glass cranial windows used for optical microscopy are unsuitable for OR-PAM due to the acoustic impedance mismatch between the glass plate and the tissue. To overcome these challenges, we propose a lithium niobate based transparent ultrasound trans-ducer (TUT) as a cranial window on a thinned mouse skull. The TUT cranial window simplifies the imaging head considerably due to its dual functionality as an optical window and ultrasound transducer. The window remains stable for six weeks, with no noticeable inflammation and minimal bone regrowth. The TUT windows potential is demonstrated by imaging the awake mouse cerebral vasculature using OR-PAM, intrinsic optical signal imaging and two-photon microscopy. The TUT cranial window can potentially also be used for ultrasound stimulation and simultaneous multimodal imaging of the awake mouse brain.

category: bioengineering


title: New insights into colorectal cancer liver metastasis carcinogenesis and its effect with moxibustion

abstract:
BackgroundChemotherapeutic drugs creates severe adverse reactions for colorectal cancer. Moxibustion confers clinical benefits for postoperative patients undergoing chemotherapy, it will fill the blank period of western medicine treatment and provide useful help for tumor patients to prevent recurrence and metastasis, but the physiological mechanisms behind the antitumor effects are unclear. This study was aimed to determine the effect and characterize the differential cytokines and gene expression profiles in intrasplenic transplanted GFP-HCT-116 cells-induced tumors model by Pre-Mox, Post-Mox and Pre-Post-Mox intervention.

MethodsHuman CRC cells with GFP fluorescence were implanted via intrasplenic injection into Balb/c nude mice spleens. Moxibustion stimulation was applied to the BL18 and ST36 acupoints. The model control (MC) group were given no treatment. Pre-Mox mice were received moxibustion for 2 weeks before HCT-116 cell injection. Post-Mox mice received moxibustion for 3 weeks after CRC cell injection. Pre-Post-Mox mice received moxibustion for 5 weeks (2 weeks before and 3 weeks after CRC cell injection). Peripheral bloods were collected, pooled and assayed using a RayBio(R) mouse inflammation antibody array. Multi-Analyte Suspension Array was opted for verification. RNA isolated from liver paracancerous tissues from the control group and the experimental groups was subjected to RNA-seq, and then screened out significant differences for in-depth verification.

RESULTSThe results showed that moxibustion stimulation increased the survival rate and decreased CRC liver metastasis. With the help of Multi-Analyte Suspension Array and RNA-seq, we screened significant differential expression of cytokines and RNA, then further verified them. The metastasis rate decreased significantly from 100% (10/10, MC group) to 50% (6/12, Pre-Mox group), to 46% (6/13, Post-Mox group), and further to 25% (3/12, Pre-Post-Mox group). Cytokine chips were used significant differences were found in MIP-3, MDC, IL-6, and IL-1a. Transcriptomic analysis suggested that the low-dose combination of Pre-Mox and Post-Mox modulated larger gene sets than the single treatment. We identified a small subset of genes, like APOA4, IGFBP5, IGFBP6, TIMP1, and MGP, as potential molecular targets involved in the preventive action of the combination of Pre-Mox and Post-Mox.

ConclusionsTaken together, the current results provide the first evidence in support of the chemopreventive effect of a combination of Pre-Mox and Post-Mox in CRC. Moreover, the cytokines and transcriptional profile obtained in our study may provide a framework for identifying the mechanisms underlying the carcinogenesis process from colonic cancer to liver metastasis as well as the cancer inhibitory effects and potential molecular targets of Pre-Post-Mox.


title: Rule-based and stimulus-based cues bias auditory decisions via different computational and physiological mechanisms

abstract:
Expectations, such as those arising from either learned rules or recent stimulus regularities, can bias subsequent auditory perception in diverse ways. However, it is not well understood if and how those diverse effects depend on the source of the expectations. Further, it is unknown whether these different sources of bias use the same or different computational and physiological mechanisms. We examined how rule-based and stimulus-based expectations influenced behavior and pupil-linked arousal, a marker of certain forms of expectation-based processing, of human subjects performing an auditory frequency-discrimination task. Rule-based cues biased choices and response times (RTs) toward the more-probable stimulus. In contrast, stimulus-based cues had a complex combination of effects, including choice and RT biases toward and away from the frequency of recently presented stimuli. These different behavioral patterns also had: 1) distinct computational signatures, including different modulations of key components of a novel form of a drift-diffusion decision model and 2) distinct physiological signatures, including substantial bias-dependent modulations of pupil size in response to rule-based but not stimulus-based cues. These results imply that different sources of expectations can modulate auditory processing via distinct mechanisms: one that uses arousal-linked, rule-based information and another that uses arousal-independent, stimulus-based information to bias the speed and accuracy of auditory perceptual decisions.

Author summaryPrior information about upcoming stimuli can bias our perception of those stimuli. Whether different sources of prior information bias perception in similar or distinct ways is not well understood. We compared the influence of two kinds of prior information on tone-frequency discrimination: rule-based cues, in the form of explicit information about the most-likely identity of the upcoming tone; and stimulus-based cues, in the form of sequences of tones presented before the to-be-discriminated tone. While both types of prior information biased auditory decision-making, they demonstrated distinct behavioral, computational, and physiological signatures. Our results suggest that the brain processes prior information in a form-specific manner rather than utilizing a general-purpose prior. Such form-specific processing has implications for understanding decision biases real-world contexts, in which prior information comes from many different sources and modalities.


title: Analysis of single-cell RNA-sequencing data to identify quiescent and proliferating neural cell populations in Glioblastoma

abstract:
BackgroundDiffuse Glioblastoma (GBM) has high mortality and remains one of the most challenging type of cancer to treat. Identifying and characterizing the cells populations driving tumor growth and therapy resistance has been particularly difficult owing to marked inter and intra tumoral heterogeneity observed in these tumors. These tumorigenic populations contain long lived cells associated with latency, immune evasion and metastasis.

MethodsHere, we analyzed the single-cell RNA-sequencing data of high grade glioblastomas from four different studies using integrated analysis of gene expression patterns, cell cycle stages and copy number variation to identify gene expression signatures associated with quiescent and cycling neuronal tumorigenic cells.

ResultsThe results show that while cycling and quiescent cells are present in GBM of all age groups, they exist in a much larger proportion in pediatric glioblastomas. These cells show similarities in their expression patterns of a number of pluripotency and proliferation related genes. Upon unbiased clustering, these cells explicitly clustered on their cell cycle stage. Quiescent cells in both the groups specifically overexpressed a number of genes for ribosomal protein, while the cycling cells were enriched in the expression of high-mobility group and heterogeneous nuclear ribonucleoprotein group genes. A number of well-known markers of quiescence and proliferation in neurogenesis showed preferential expression in the quiescent and cycling populations identified in our analysis. Through our analysis, we identify ribosomal proteins as key constituents of quiescence in glioblastoma stem cells.

ConclusionsThis study identifies gene signatures common to adult and pediatric glioblastoma quiescent and cycling stem cell niches. Further research elucidating their role in controlling quiescence and proliferation in tumorigenic cells in high grade glioblastoma will open avenues in more effective treatment strategies for glioblastoma patients.


title: Direct and latent effects of ocean acidification on the transition of a sea urchin from planktonic larva to benthic juvenile

abstract: AO_SCPLOWBSTRACTC_SCPLOWOngoing ocean acidification (OA) is expected to affect marine organisms and ecosystems. While sea urchins can survive a wide range of pH, this comes at a high energetic cost, and early life stages are particularly vulnerable. Information on how OA affects transitions between life-history stages is scarce. We evaluated the direct and indirect effects of pH (pHT 8.0, 7.6 and 7.2) on the development and transition between life-history stages of the sea urchin Strongylocentrotus droebachiensis, from fertilization to early juvenile. Continuous exposure to low pH negatively affected larval mortality and growth. At pH 7.2, formation of the rudiment (the primordial juvenile) was delayed by two days. Larvae raised at pH 8.0 and transferred to 7.2 after competency had mortality rates five to six times lower than those kept at 8.0, indicating that pH also has a direct effect on older, competent larvae. Latent effects were visible on the larvae raised at pH 7.6: they were more successful in settling (45%) and metamorphosing (30%) than larvae raised at 8.0 (17 and 1% respectively). These direct and indirect effects of OA on settlement and metamorphosis have important implications for population survival.

category: developmental biology


title: Digital restoration of the pectoral girdles of two Early Cretaceous birds, and implications for early flight evolution

abstract: Pectoral girdle morphology is a key determinant of flight capability, but in some respects is poorly known among stem birds. Here, we reconstruct the pectoral girdles of the Early Cretaceous birds Sapeornis and Piscivorenantiornis based on computed tomography and three-dimensional visualization, revealing key morphological details. Enantiornithines such as Piscivorenantiornis have a uniquely localized scapula-coracoid joint, with only one area of articulation. This single articulation contrasts with the double articulation widely present in non-enantiornithine pennaraptoran theropods, including Sapeornis and crown birds, which comprises main and subsidiary articular contacts. A partially closed triosseal canal occurs in non-euornithine birds, representing a transitional stage in flight apparatus evolution. Numerous modifications of the pectoral girdle along the line to crown birds, and lineage-specific pectoral girdle variations, produced diverse pectoral girdle morphologies among Mesozoic birds, which ensured that a commensurate range of capability levels and modes emerged during the early evolution of flight.

category: evolutionary biology


title: Urine proteomics as a non-invasive approach to monitor exertional rhabdomyolysis during military training

abstract: Exertional rhabdomyolysis (ERM), a condition often associated with strenuous exercise, a common practice in the military activities, can be defined as the process of injury and rupture of muscle cell membranes, with leakage of its components into the blood stream. Creatine kinase (CK) has been extensively used for ERM diagnosis, albeit several studies reported the discrepancy between CK levels and clinical signs or symptoms. In this study, we analyzed the biochemical profile of the blood, and the urinary proteome of ten marine soldiers in a special training course. The samples were collected in two periods, M1 and M2, which correspond to the lowest and highest CK levels during training, respectively. Quantitative urinary proteome profile of M1 and M2 was determined showing changes with highest significance in immune system and cell adhesion-related pathways after strenuous physical exercise. Changes in the abundance of several proteins was observed in individuals carrying genetic polymorphisms related to greater risk for muscle damage. Remarkably, we identified a panel of proteins (CTSH, PIK3IP1, DEFB1, ITGB1, BCAN, and TNFRSF10C) that present high correlation with three classical blood biochemical markers of ERM and AGT MET235Thr and ACE I/D polymorphisms. These proteins represent potential urine markers of muscle damage due to intense physical conditions such as military training activities.

category: biochemistry


title: Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers

abstract: Supported lipid bilayers are a well-developed model system for the study of membranes and their associated proteins, such as membrane channels, enzymes, and receptors. These versatile model membranes can be made from various components, ranging from simple synthetic phospholipids to complex mixtures of constituents, mimicking the cell membrane with its relevant physiochemical and molecular phenomena. In addition, the high stability of supported lipid bilayers allows for their study via a wide array of experimental probes. In this work, we describe a platform for supported lipid bilayers that is accessible both electrically and optically. We show that the polarization of the supported membrane can be electrically controlled and optically probed using voltage-sensitive dyes. Membrane polarization dynamics is understood through electrochemical impedance spectroscopy and the analysis of the equivalent electrical circuit. We also describe the effect of the conducting electrode layer on the fluorescence of the optical probe through metal-induced energy transfer. We conclude with a discussion on possible applications of this platform for the study of voltage-dependent membrane proteins and other processes in membrane biology and surface science.


title: RAS mutation patterns arise from tissue-specific responses to distinct oncogenic signaling

abstract: Despite multiple possible oncogenic mutations in the proto-oncogene KRAS, unique subsets of these mutations are detected in different cancer types. As KRAS mutations occur early, if not being initiating, these mutational biases are ostensibly a product of how normal cells respond to the encoded oncoprotein. Oncogenic mutations can impact not only the level of active oncoprotein, but also engagement with effectors and other proteins. To separate these two effects, we generated four novel inducible Kras alleles encoded by the biochemically distinct mutations G12D versus Q61R encoded by native (nat) rare versus common (com) codons to produce either low or high protein levels. Each allele induced a distinct transcriptional response in normal cells. At one end of the spectrum, the KrasnatG12D allele induced transcriptional hallmarks suggestive of an expansion of multipotent cells, while at the other end, the KrascomQ61R allele exhibited all the hallmarks of oncogenic stress and inflammation. Further, this dramatic difference in the transcriptomes of normal cells appears to be a product of signaling differences due to increased protein expression as well as the specific mutation. To determine the impact of these distinct responses on RAS mutational patterning in vivo, all four alleles were globally activated, revealing that hematolymphopoietic lesions were sensitive to the level of active oncoprotein, squamous tumors were sensitive to the G12D mutant, while carcinomas were sensitive to both these features. Thus, we identify how specific KRAS mutations uniquely signal to promote the conversion of normal hematopoietic, epithelial, or squamous cells towards a tumorigenic state.


title: Cognitive experience alters cortical involvement in navigation decisions

abstract: The neural correlates of decision-making have been investigated extensively, and recent work aims to identify under what conditions cortex is actually necessary for making accurate decisions. We discovered that mice with distinct cognitive experiences, beyond sensory and motor learning, use different cortical areas and neural activity patterns to solve the same task, revealing past learning as a critical determinant of whether cortex is necessary for decision-making. We used optogenetics and calcium imaging to study the necessity and neural activity of multiple cortical areas in mice with different training histories. Posterior parietal cortex and retrosplenial cortex were mostly dispensable for accurate decision-making in mice performing a simple navigation-based decision task. In contrast, these areas were essential for the same simple task when mice were previously trained on complex tasks with delay periods or association switches. Multi-area calcium imaging showed that, in mice with complex-task experience, single-neuron activity had higher selectivity and neuron-neuron correlations were weaker, leading to codes with higher task information. Therefore, past experience sets the landscape for how future tasks are solved by the brain and is a key factor in determining whether cortical areas have a causal role in decision-making.


title: Commanding or being a simple intermediary: how does it affect moral behavior and related brain mechanisms?

abstract: History has shown that fractioning operations between several individuals along a hierarchical chain allows diffusing responsibility between components of the chain, which has the potential to disinhibit antisocial actions. Here, we present two studies, one using fMRI (Study 1) and one using EEG (Study 2), designed to help understand how commanding or being in an intermediary position impacts the sense of agency and empathy for pain. In the age of military drones, we also explored whether commanding a human or robot agent influences these measures. This was done within a single behavioral paradigm in which participants could freely decide whether or not to send painful shocks to another participant in exchange for money. In Study 1, fMRI reveals that activation in social cognition and empathy-related brain regions was equally low when witnessing a victim receive a painful shock while participants were either commander or simple intermediary transmitting an order, compared to being the agent directly delivering the shock. In Study 2, results indicated that the sense of agency did not differ between commanders and intermediary, no matter if the executing agent was a robot or a human. However, we observed that the neural response over P3 was higher when the executing agent was a robot compared to a human. Source reconstruction of the EEG signal revealed that this effect was mediated by areas including the insula and ACC. Results are discussed regarding the interplay between the sense of agency and empathy for pain for decision-making.