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bioRxiv2017

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of Comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria ({beta}-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.\n\nComammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to {beta}-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to {beta}-AOB.\n\n{beta}-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from {beta}-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from {beta}-AOB to comammox Nitrospira is predicted - followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.\n\nSignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

microbiology↗

bioRxiv2017

The Nonlinear Relationship Between Sensory And Motor Primitives During Reaching Movements

The stabilizing role of sensory feedback in relation to realistic 3-dimensional movement dynamics remains poorly understood. The objective of this study was to quantify how primary afferent activity contributes to shaping muscle activity patterns during reaching movements. To achieve this objective, we designed a virtual reality task that guided healthy human subjects through a set of planar reaching movements with controlled kinematic and dynamic conditions that minimized inter-subject variability. Next, we integrated human upper-limb models of musculoskeletal dynamics and proprioception to analyze motion and major muscle activation patterns during these tasks. We recorded electromyographic and motion-capture data and used the integrated model to simulate joint kinematics, joint torques due to muscle contractions, muscle length changes, and simulated primary afferent feedback. The parameters of the primary afferent model were altered systematically to evaluate the effect of fusimotor drive. The experimental and simulated data were analyzed with hierarchical clustering. We found that the muscle activity patterns contained flexible task-dependent groups that consisted of co-activating agonistic and antagonistic muscles that changed with the dynamics of the task. The activity of muscles spanning only the shoulder generally grouped into a proximal cluster, while the muscles spanning the wrist grouped into a distal cluster. The bifunctional muscle spanning the shoulder and elbow were flexibly grouped with either proximal or distal cluster based on the dynamical requirements of the task. The composition and activation of these groups reflected the relative contribution of active and passive forces to each motion. In contrast, the simulated primary afferent feedback was most related to joint kinematics rather than dynamics, even though the primary afferent models had nonlinear dynamical components and variable fusimotor drive. Simulated physiological changes to the fusimotor drive were not sufficient to reproduce the dynamical features in muscle activity pattern. Altogether, these results suggest that sensory feedback signals are in a different domain from that of muscle activation signals. This indicates that to solve the neuromechanical problem, the central nervous system controls limb dynamics through task-dependent co-activation of muscles and non-linear modulation of monosynaptic primary afferent feedback. New & NoteworthyHere we answered the fundamental question in sensorimotor transformation of how primary afferent signals can contribute to the compensation for limb dynamics evident in muscle activity. We combined computational and experimental approaches to create a new experimental paradigm that challenges the nervous system with passive limb dynamics that either assists or resists the desired movement. We found that the active dynamical features present in muscle activity are unlikely to arise from direct feedback from primary afferents.

neuroscience↗

bioRxiv2017

Body Size Shifts Influence Effects Of Increasing Temperatures On Ectotherm Metabolism

INTRODUCTION INTRODUCTION METHODS RESULTS DATA ACCESSIBILITY BIOSKETCH REFERENCES Environmental temperature influences organisms in many ways; temperature increases or decreases rates of physiological processes (Brown et al., 2012), determines timing of reproduction (Olive, 1995), and even directly affects mortality (Pauly, 1980). Because of the far-reaching influence of temperature, projected increases in global temperatures due to climate change are expected to substantially alter diverse species characteristics. Increased temperatures have already been implicated in shifts in species geographic distributions (e.g., Buckley et al., 2010), and in the phenology of species life history and development (e.g., Wolkovich ...

ecology↗

bioRxiv2017

The Structure Of Small Beta Barrels

0.The small {beta}-barrel is an ancient protein structural domain characterized by extremes: It features an extremely broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of biomolecular pathways and physiological functions. These and related features of this domain are described and analyzed herein. Specifically, we present a comprehensive, survey-based analysis of the structural properties of small {beta}-barrels (SBBs). We first consider the defining characteristics of the SBB fold, as well as the various systems of nomenclature used to describe it. In order to begin elucidating how such vast functional diversity is achieved by a relatively simple protein domain, we then explore the anatomy of the SBB fold and some of its representative structural variants. Many types of SBB proteins assemble into cyclic oligomers that act as the biologically-functional entity. These oligomers exhibit a great deal of plasticity even at the quaternary structural level--including homomeric and heteromeric assemblies, rings of variable subunit stoichiometries (pentamer, hexamer, etc.), as well as higher-order oligomers (e.g., double-rings) and fibrillar polymers. We conclude with three themes that emerge from the SBBs unique structure{leftrightarrow}function versatility.

bioinformatics↗

bioRxiv2017

Assigning Function To Natural Allelic Variation Via Dynamic Modeling Of Gene Network Induction

More and more natural DNA variants are being linked to physiological traits. Yet, understanding what differences they make on molecular regulations remains challenging. Important properties of gene regulatory networks can be captured by computational models. If model parameters can be personalized according to the genotype, their variation may then reveal how DNA variants operate in the network. Here, we combined experiments and computations to visualize natural alleles of the yeast GAL3 gene in a space of model parameters describing the galactose response network. Alleles altering the activation of Gal3p by galactose were discriminated from those affecting its activity (production/degradation or efficiency of the activated protein). The approach allowed us to correctly predict that a non-synonymous SNP would change the binding affinity of Gal3p with the Gal80p transcriptional repressor. Our results illustrate how personalizing gene regulatory models can be used for the mechanistic interpretation of genetic variants.

systems biology↗

bioRxiv2017

Dynamic blue light-inducible T7 RNA polymerases (Opto-T7RNAPs) for precise spatiotemporal gene expression control

Light has emerged as control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark-state, high expression strength when induced with blue light, or an inducible range of more than 300-fold. Following optimization of the system to reduce expression variability, we have created a variant, which returns to the inactive dark-state within minutes, once blue light is turned off. This allows for precise dynamic control of gene expression, which is a key aspect for most applications using optogenetic regulation. The regulators were developed and tested in the bacterium Escherichia coli, which is a crucial cell factory for biotechnology due to its fast and inexpensive cultivation and well understood physiology and genetics. However, minor alterations should be sufficient to allow their use in other species in which the T7 RNAP polymerase and the light-inducible Vivid regulator were shown to be functional, which comprises other bacterial species and eukaryotes such as mammalian cells or yeast. We anticipate that our approach will expand the applicability of using light as an inducer for gene expression independent from cellular regulation, and allow for a more reliable dynamic control of synthetic and natural gene networks.

synthetic biology↗

bioRxiv2017

Low-Level Carbon Monoxide Exposure Affects BOLD FMRI

Blood Oxygen Level Dependent (BOLD) FMRI is a common technique for measuring brain activation that could be affected by low-level carbon monoxide (CO) exposure from e.g. smoking. This study aimed to probe the vulnerability of BOLD FMRI to CO and determine whether it constitutes a significant confound in neuroimaging and clinical trials. Low-level (6ppm exhaled) CO effects on BOLD signal were assessed in 12 healthy never-smokers on two separate experimental days (CO and air control). FMRI tasks were breath-holds (hypercapnia), visual stimulation and fingertapping. CO significantly dampened global BOLD FMRI signal during hypercapnia and visual cortex activation during visual stimulation. During fingertapping, CO reduced visual cortex activation but increased premotor cortex activation. Behavioural and physiological measures remained unchanged. We conclude that BOLD FMRI is vulnerable to CO, possibly through baseline increases in CBF, and suggest exercising caution when imaging populations exposed to elevated CO levels, e.g. with high smoking prevalence.

neuroscience↗

bioRxiv2017

Disruption Of Ankyrin B And Caveolin-1 Interaction Sites Alters Na+,K+-ATPase Lateral Diffusion In HEK293 Cell Plasma Membranes

The Na+,K+-ATPase is a plasma membrane ion transporter of high physiological importance for ion homeostasis and cellular excitability in electrically active tissues. Mutations in the genes coding for Na+,K+-ATPase -subunit isoforms lead to severe human pathologies including Familial Hemiplegic Migraine type 2 (FHM2), Alternating Hemiplegia of Childhood (AHC), Rapid Dystonia Parkinsonism (RDP) or epilepsy. Many of the reported mutations lead to change- or loss-of-function effects, whereas others do not alter the functional properties, but lead to e.g. reduced protein stability, reduced protein expression or defective plasma membrane targeting. Na+,K+-ATPase frequently assembles with other membrane transporters or cellular matrix proteins in specialized plasma membrane microdomains, but the effects of these interactions on targeting or protein mobility are elusive so far. Mutational disruption of established interaction motifs of the Na+,K+-ATPase with ankyrin B and caveolin-1 are expected to result in changes in plasma membrane targeting, changes of the localization pattern, and of the diffusion behavior of the enzyme. We studied the consequences of mutations in these binding sites by monitoring diffusion of eGFP-labeled Na+,K+-ATPase constructs in the plasma membrane of living HEK293T cells by fluorescence correlation spectroscopy (FCS) as well as fluorescence recovery after photobleaching (FRAP) or photoswitching (FRAS) and observed significant differences compared to the wild-type enzyme, with synergistic effects for combinations of interaction site mutations. These measurements expand the possibilities to study the consequences of Na+,K+-ATPase mutations and provide information about the interaction of Na+,K+-ATPase 2-isoform with cellular matrix proteins, the cytoskeleton or other membrane protein complexes.

biophysics↗

bioRxiv2017

Extended Synaptotagmin Is A Presynaptic ER Ca2+ Sensor That Promotes Neurotransmission And Synaptic Growth In Drosophila

The endoplasmic reticulum (ER) is an extensive presynaptic organelle, exerting important influences at synapses by responding to Ca2+ and modulating transmission, growth, lipid metabolism, and membrane trafficking. Despite intriguing evidence for these crucial functions, how presynaptic ER influences synaptic physiology remains enigmatic. To gain insight into this question, we have generated and characterized mutations in the single Extended Synaptotagmin (Esyt) ortholog in Drosophila. Esyts are evolutionarily conserved ER proteins with Ca2+ sensing domains that have recently been shown to orchestrate membrane tethering and lipid exchange between the ER and plasma membrane. We first demonstrate that Esyt localizes to an extensive ER structure that invades presynaptic terminals at the neuromuscular junction. Next, we show that synaptic growth, structure, function, and plasticity are surprisingly unperturbed at synapses lacking Esyt expression. However, presynaptic overexpression of Esyt leads to enhanced synaptic growth, neurotransmission, and sustainment of the vesicle pool during intense levels of activity, suggesting that elevated Esyt at the ER promotes constitutive membrane trafficking or lipid exchange with the plasma membrane. Finally, we find that Esyt mutants fail to maintain basal neurotransmission and short term plasticity at elevated extracellular Ca2+, consistent with Esyt functioning as an ER Ca2+ sensor that modulates synaptic activity. Thus, we identify Esyt as a presynaptic ER Ca2+ sensor that can promote neurotransmission and synaptic growth, revealing the first in vivo neuronal functions of this conserved gene family.

neuroscience↗

bioRxiv2017

Drosophila CaV2 Channels Harboring Human Migraine Mutations Cause Synapse Hyperexcitability That Can Be Suppressed By Inhibition Of A Ca2+ Store Release Pathway

Gain-of-function mutations in the human CaV2.1 gene CACNA1A cause familial hemiplegic migraine type 1 (FHM1). To characterize cellular problems potentially triggered by CaV2.1 gains of function, we engineered mutations encoding FHM1 amino-acid substitutions S218L (SL) and R192Q (RQ) into transgenes of Drosophila melanogaster CaV2/cacophony. We expressed the transgenes pan-neuronally. Phenotypes were mild for RQ-expressing animals. By contrast, single mutant SL- and complex allele RQ,SL-expressing animals showed overt phenotypes, including sharply decreased viability. By electrophysiology, SL- and RQ,SL-expressing neuromuscular junctions (NMJs) exhibited enhanced evoked discharges, supernumerary discharges, and an increase in the amplitudes and frequencies of spontaneous events. Some spontaneous events were gigantic (10-40 mV), multi-quantal events. Gigantic spontaneous events were eliminated by application of TTX - or by lowered or chelated Ca2+ - suggesting that gigantic events were elicited by spontaneous nerve firing. A follow-up genetic approach revealed that some neuronal hyperexcitability phenotypes were reversed after knockdown or mutation of Drosophila homologs of phospholipase C{beta} (PLC{beta}), IP3 receptor, or ryanodine receptor (RyR) - all factors known to mediate Ca2+ release from intracellular stores. Pharmacological inhibitors of intracellular Ca2+ store release produced similar effects. Interestingly, however, the decreased viability phenotype was not reversed by genetic impairment of intracellular Ca2+ release factors. On a cellular level, our data suggest inhibition of signaling that triggers intracellular Ca2+ release could counteract hyperexcitability induced by gains of CaV2.1 function.\n\nAUTHOR SUMMARYPrior research has demonstrated that gain-of-function mutations in a gene important for neurotransmission (CACNA1A) are known to cause migraine in humans. We attempted to mimic some of those gain-of-function mutations in a simple genetic model organism and to examine neurotransmission by electrophysiology. Our findings yield potential clues as to how particular migraine-causing mutations may impact neurophysiology on a cellular level. We used the fruit fly Drosophila melanogaster and its model synapse, the neuromuscular junction (NMJ) to perform our studies. We document three main advances: 1) characterization of fruit fly models harboring gain-of-function calcium channel alterations known to cause human familial hemiplegic migraine type 1 (FHM1); 2) characterization of hyperactive neurotransmission caused by one of these alterations; and 3) an ability to quell hyperactive neurotransmission by impairing intracellular Ca2+ store release, through both genetic and pharmacological means. Our work contributes to a broader understanding of how pathological mutations could impact cellular physiology. More generally, the utilization of genetic model organisms promises to uncover potential ways to reverse those impacts.

neuroscience↗

bioRxiv2017

Rob And MarA Alter Susceptibility Of Escherichia coli To Antibiotics In Presence Of Salicylate

When exposed to stress, bacterial cells launch a diverse response to enhance their chances of survival. This response involves modulation of expression of a large number of proteins which help the cell counter stress. This modulation is facilitated by several transcription factors in bacteria and in E. coli three homologous regulators, MarA, Sox, and Rob are known to launch a coordinated response to combat various stress environments. MarA and SoxS are known to control multiple antibiotic resistance and superoxide regulon respectively. Rob has been observed to control similar downstream targets as MarA and SoxS. However, physiological relevance of Rob in not understood. We show that Rob along with MarA, in presence of inducer salicylate, can help cell survive in presence of lethal concentration of wide range of antibiotics.

microbiology↗

bioRxiv2017

Sequential Eviction Of Crowded Nucleoprotein Complexes By The RecBCD Molecular Motor

In physiological settings, all nucleic acids motor proteins must travel along substrates that are crowded with other proteins. However, the physical basis for how motor proteins behave in these highly crowded environments remains unknown. Here we use real-time single molecule imaging, kinetic Monte Carlo simulations, and Molecular dynamics simulations to determine how the ATP-dependent translocase RecBCD travels along DNA occupied by tandem arrays of high affinity DNA-binding proteins. We demonstrate that RecBCD forces each protein into its nearest adjacent neighbor, causing rapid disruption of the underlying protein-nucleic acid interface. This mechanism is not simply the same way that RecBCD disrupts isolated nucleoprotein complexes on otherwise naked DNA. Instead, molecular crowding itself completely alters the mechanism by which RecBCD removes tightly bound protein obstacles from DNA.\n\nSignificance statementChromosomes are crowded places, and any nucleic acid motor proteins that act upon DNA must function within these crowded environments. How crowded environments affect motor protein behaviors remains largely unexplored. Here, we use single molecule fluorescence microscopy visualize the ATP-dependent motor protein RecBCD as it travels along crowded DNA molecules bearing long tandem arrays of DNA-binding proteins. Our findings show that RecBCD can push through highly crowded protein arrays while evicting the proteins from DNA. Molecular dynamics simulations suggest that RecBCD forces the proteins into once another, causing rapid disruption of the protein-DNA interface. These findings may provide insights into how other types of motor proteins travel along crowded nucleic acids.

biophysics↗

bioRxiv2017

Olfactory Receptors Are Required For Social Behavior And Neural Plasticity In Ants, As Evidenced By CRISPR-Mediated Gene Knockout

The chemosensory system is key to establishing and maintaining social structure in eusocial insects. Ants exhibit cooperative colonial behaviors reflective of an advanced form of sociality with an extensive dependency on communication. Cuticular hydrocarbons (CHCs) serve as pheromones and cues that regulate multiple aspects of social interactions and behaviors in ants. The perception of CHCs entails odorant receptor neurons (ORNs) that express specific odorant receptors (ORs) encoded by a dramatically expanded Or gene family in ants. Until recently, studies of the biological functions of ORs in eusocial insects were stymied by the lack of genetic tools. In most eusocial insect species, only one or a few queens in a colony can transmit the genetic information to their progeny. In contrast, any worker in the ant Harpegnathos saltator can be converted into a gamergate (pseudo-queen), and used as a foundress to engender an entire new colony and be crossed for genetic experiments. This feature facilitated CRISPR-Cas9 gene targeting to generate a germline mutation in the orco gene that encodes the obligate co-receptor whose mutation should significantly impact ant olfaction. Our results show that Orco exhibits a conserved role in the perception of general odorants but also a role in reproductive physiology and social behavior plasticity in ants. Surprisingly, and in contrast to other insect systems, the loss of OR functionality also dramatically reduces the development of the ant antennal lobe where ORNs project. Taken together, these findings open the possibility of studying the genetics of eusociality and provide inroads towards understanding the function of the expanded ORs family in eusocial insects in regulating caste determination, social communication and neuronal plasticity.

neuroscience↗

bioRxiv2017

Wireless Implantable Sensor For Non-Invasive, Longitudinal Quantification Of Axial Strain Across Rodent Long Bone Defects

Bone development, maintenance, and regeneration are remarkably sensitive to mechanical cues. Consequently, mechanical stimulation has long been sought as a putative target to promote endogenous healing after fracture. Given the transient nature of bone repair, tissue-level mechanical cues evolve rapidly over time after injury and are challenging to measure non-invasively. The objective of this work was to develop and characterize an implantable strain sensor for non-invasive monitoring of axial strain across a rodent femoral defect during functional activity. Herein, we present the design, characterization, and in vivo demonstration of the devices capabilities for quantitatively interrogating physiological dynamic strains during bone regeneration. Ex vivo experimental characterization of the device showed that it exceeded the technical requirements for sensitivity, signal resolution, and electromechanical stability. The digital telemetry minimized power consumption, enabling long-term intermittent data collection. Devices were implanted in a rat 6 mm femoral segmental defect model and after three days, data were acquired wirelessly during ambulation and synchronized to corresponding radiographic videos, validating the ability of the sensor to non-invasively measure strain in real-time. Lastly, in vivo strain measurements were utilized in a finite element model to estimate the strain distribution within the defect region. Together, these data indicate the sensor is a promising technology to quantify local tissue mechanics in a specimen specific manner, facilitating more detailed investigations into the role of the mechanical environment in dynamic skeletal healing and remodeling.

bioengineering↗

bioRxiv2017

Polycystic Ovary Syndrome As An Endogenous Alcoholic Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is a growing worldwide public health problem that affects millions of women in their reproductive age. Despite being a very common disorder among women, there are still gaps regarding knowledge of disease mechanisms. In this respect, it was recently reported that acetaldehyde (ACD) is endogenously formed during normal ovarian steroidogenesis. The researchers demonstrated that in physiological concentrations ACD caused no detrimental effect on ovarian tissue. Contrariwise, in supraphysiological levels, ACD impairs granulosa cell differentiation, reduces ovulation, and decreases oocyte quality. Gut microbiota of patients with nonalcoholic fatty liver disease (NAFLD) produces significant quantities of endogenous ethanol (EE) and ACD. Because PCOS is closely linked to NAFLD, an ethanol-producing disorder, we hypothesize that it can be an endogenous alcoholic polycystic ovary syndrome (EAPCOS). The main findings of this study were that (i) the odds ratio of having polycystic ovaries is 30-fold greater in alcohol-exposed women than among unexposed controls; (ii) NAFLD/PCOS patients produce gonadotoxic quantities of EE; (iii) NAFLD/PCOS and alcoholic hepatitis individuals share similar liver expression levels of genes regulating high-km ethanol-metabolizing enzymes; (iv) NAFLD/PCOS and alcohol-tolerant drinkers share similar high-capacity to metabolize ethanol in the gut-liver axis; and (v) low blood alcohol concentration (BAC) in NAFLD/PCOS and alcohol-tolerant individuals stem from extensive alcohol degradation in gut-liver axis and significant fecal loss of ethanol. In summary, we provide mechanistic insights supporting the hypothesis that PCOS can be indeed an EAPCOS.

molecular biology↗

bioRxiv2017

Local Signal Processing In Mouse Horizontal Cell Dendrites

The mouse retina contains a single type of horizontal cell, a GABAergic interneuron that samples from all cone photoreceptors within reach and modulates their glutamatergic output via parallel feedback mechanisms. Because horizontal cells form an electrically-coupled network, they have been implicated in global signal processing, such as large scale contrast enhancement. Recently, it has been proposed that horizontal cells can also act locally at the level of individual cone photoreceptors. To test this possibility physiologically, we used two-photon microscopy to record light stimulus-evoked Ca2+ signals in cone axon terminals and horizontal cell dendrites as well as glutamate release in the outer plexiform layer. By selectively stimulating the two mouse cone opsins with green and UV light, we assessed whether signals from individual cones remain \"isolated\" within horizontal cell dendritic tips, or whether they spread across the dendritic arbour. Consistent with the mouse s opsin expression gradient, we found that the Ca2+ signals recorded from dendrites of dorsal horizontal cells were dominated by M- and those of ventral horizontal cells by S-opsin activation. The signals measured in neighbouring horizontal cell dendritic tips varied markedly in their chromatic preference, arguing against global processing. Rather, our experimental data and results from biophysically realistic modelling support the idea that horizontal cells can process cone input locally, extending the \"classical\" view of horizontal cells function. Pharmacologically removing horizontal cells from the circuitry reduced the sensitivity of the cone signal to low frequencies, suggesting that local horizontal cell feedback shapes the temporal properties of cone output.\n\nHighlightsO_LILight-evoked Ca2+ signals in horizontal cell dendrites reflect opsin gradient\nC_LIO_LIChromatic preferences in neighbouring dendritic tips vary markedly\nC_LIO_LIMouse horizontal cells process cone photoreceptor input locally\nC_LIO_LILocal horizontal cell feedback shapes the temporal properties of cone output\nC_LI\n\neTOC BlurbChapot et al. show that local light responses in mouse horizontal cell dendrites inherit properties, including chromatic preference, from the presynaptic cone photoreceptor, suggesting that their dendrites can provide \"private\" feedback to cones, for instance, to shape the temporal filtering properties of the cone synapse.

neuroscience↗

bioRxiv2017

Coupling Of Tactile LFP Signals Between Mouse Cortex And Olfactory Bulb

Local field potentials are an important measure of brain activity and have been used to address various mechanistic and behavioral questions. We revealed a prominent whisker evoked local field potential signal in the olfactory bulb and investigated its physiology. This signal, dependent on barrel cortex activation and highly correlated with its local activity, represented a pure volume conductance signal that was sourced back to the activity in the ventro-lateral orbitofrontal cortex, located a few millimeters away. Thus, we suggest that special care should be taken when acquiring and interpreting LFP data.

neuroscience↗

bioRxiv2018

Different alleles of the same gene vary in pleiotropy, often mediated through currency metabolite production

A major obstacle to the mapping of genotype-phenotype relationships is pleiotropy, the tendency of mutations to affect seemingly unrelated traits. Pleiotropy has major implications for evolution, development, ageing, and disease. Except for disease data, pleiotropy is almost exclusively estimated from full gene knockouts. However, most deleterious alleles segregating in natural populations do not fully abolish gene function, and the degree to which a polymorphism reduces protein function may influence the number of traits it affects. Utilizing genome-scale metabolic models for Escherichia coli and the bakers yeast Saccharomyces cerevisiae, we show that most fitness-reducing full gene knockouts of metabolic genes have pleiotropic effects, i.e., they compromise the production of multiple biomass components. Alleles of the same gene with increasingly reduced enzyme function typically affect an increasing number of biomass components. This increasing pleiotropy is often mediated through effects on the generation of currency metabolites such as ATP or NADPH. We conclude that the physiological effects observed in full gene knockouts will in most cases not be representative for alleles with only partially reduced enzyme capacity or expression level.

systems biology↗