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bioRxiv2019

Hypotonic stress induces fast, reversible degradation of the vimentin cytoskeleton via intracellular calcium release

The dynamic response of the cell to osmotic changes is critical to its physiology and has been widely exploited for cell manipulation. Using 3D-STORM super-resolution microscopy, here we examine the hypotonic stress-induced ultrastructural changes of the cytoskeleton of a common fibroblast cell type. Unexpectedly, we observe a fast, yet reversible dissolution of the vimentin intermediate filament system that precedes ultrastructural changes of the supposedly more dynamic actin and tubulin cytoskeletal systems, as well as changes in cell morphology. In combination with calcium imaging and biochemical analysis, we next show that the vimentin-specific fast cytoskeletal degradation under hypotonic stress is due to proteolysis by the calcium-dependent protease calpain. We find the process to be activated by the hypotonic stress-induced calcium release from intracellular stores, and so is efficiently suppressed by inhibiting any part of the IP3-Ca2+-calpain pathway we establish. Together, our findings highlight an unexpected, fast degradation mechanism for the vimentin cytoskeleton in response to the external stimuli, and point to the significant, yet previously overlooked physiological impacts of hypotonic stress-induced intracellular calcium release on cell ultrastructure and function.

cell biology↗

bioRxiv2019

The Michaelis-Menten paradox: Km is not an equilibrium constant but a steady-state constant.

Often, in vitro or in vivo enzyme-mediated catalytic events occur far from equilibrium and, therefore, substrate affinity measured as the inverse of ES {rightleftarrows} E+S dissociation equilibrium constant (Kd) has a doubtful physiological meaning; in practice it is almost impossible to determine Kd (except using stopped-flow or other sophisticated methodologies). The Michaelis-Menten constant (Km), the concentration of substrate ([S]) providing half of enzyme maximal activity, is not the (Kd). In the simple E+S {rightleftarrows} ES [->] E+P or in more complex models describing S conversion into P, Km must be considered the constant defining the steady state at any substrate concentration. Enzyme kinetics is based on initial rate determination, i.e. in the linear part of the S to P conversion when the concentration of [ES] remains constant while steady state occurs. We also show that Systems Biology issues such as the time required to respond to a system perturbation, is more dependent on k1, the kinetic constant defining substrateenzyme association, than on Km. Whereas Km is instrumental for biochemical basic and applied approaches, in any physiological condition, an important parameter to be considered is the substrate association rate (k1).

biochemistry↗

bioRxiv2019

Directional and frequency characteristics of auditory neurons in Culex male mosquitoes

The paired auditory organ of mosquito, the Johnstons organ (JO), being the receiver of particle velocity component of sound, is directional by its structure. However, to date almost no direct physiological measurements of its directionality was done. In addition, the recent finding on the grouping of the JO auditory neurons into the antiphase pairs demanded confirmation by different methods. Using the vector superposition of the signals produced by two orthogonally oriented speakers, we measured the directional characteristics of individual units as well as their relations in physiologically distinguishable groups - pairs or triplets. The feedback stimulation method allowed to discriminate responses of the two simultaneously recorded units, and to show that they indeed responded in antiphase. We also show that ratios between the individual tuning frequencies in pairs and triplets are non-random and follow the principle of harmonic synchronization, remarkably similar to the one known from the observations of mosquito behavior. Units of different tuning and sensitivity are evenly distributed around the axis of the JO, providing the mosquito with the ability to produce complex auditory behaviors.\n\nSummary statementAuditory neurons of mosquito are grouped into pairs or triplets, each unit tuned to a specific frequency. Within the pair units respond to opposite directions of the sound. Units of different tuning and sensitivity are evenly distributed around the axis of the Johnstons organ.

neuroscience↗

bioRxiv2019

A dynamical model of the laminar BOLD response

High-resolution functional magnetic resonance imaging (fMRI) using blood oxygenation dependent level-dependent (BOLD) signal is an increasingly popular tool to non-invasively examine neuronal processes at the mesoscopic level. However, as the BOLD signal stems from hemodynamic changes, its temporal and spatial properties do not match those of the underlying neuronal activity. In particular, the laminar BOLD response (LBR), commonly measured with gradient-echo (GE) MRI sequence, is confounded by non-local changes in deoxygenated hemoglobin and cerebral blood volume propagated within intracortical ascending veins, leading to a unidirectional blurring of the neuronal activity distribution towards the cortical surface. Here, we present a new cortical depth-dependent model of the BOLD response based on the principle of mass conservation, which takes the effect of ascending (and pial) veins on the cortical BOLD responses explicitly into account. It can be used to dynamically model cortical depth profiles of the BOLD signal as a function of various baseline- and activity-related physiological parameters for any spatiotemporal distribution of neuronal changes. We demonstrate that the commonly observed spatial increase of LBR is mainly due to baseline blood volume increase towards the surface. In contrast, an occasionally observed local maximum in the LBR (i.e. the so-called \"bump\") is mainly due to spatially inhomogeneous neuronal changes rather than locally higher baseline blood volume. In addition, we show that the GE-BOLD signal laminar point-spread functions, representing the signal leakage towards the surface, depend on several physiological parameters and on the level of neuronal activity. Furthermore, even in the case of simultaneous neuronal changes at each depth, inter-laminar delays of LBR transients are present due to the ascending vein. In summary, the model provides a conceptual framework for the biophysical interpretation of common experimental observations in high-resolution fMRI data. In the future, the model will allow for deconvolution of the spatiotemporal hemodynamic bias of the LBR and provide an estimate of the underlying laminar excitatory and inhibitory neuronal activity.

neuroscience↗

bioRxiv2019

Scale-free Vertical Tracking Microscopy: Towards Bridging Scales in Biological Oceanography

Understanding key biophysical phenomena in the ocean often requires one to simultaneously focus on microscale entities, such as motile plankton and sedimenting particles, while maintaining the macroscale context of vertical transport in a highly stratified environment. This poses a conundrum: How to measure single organisms, at microscale resolution, in the lab, while allowing them to freely move hundreds of meters in the vertical direction? We present a solution in the form of a scale-free, vertical tracking microscope based on a circular \"hydrodynamic-treadmill\". Our technology allows us to transcend physiological and ecological scales, tracking organisms from marine zooplankton to single-cells over vertical scales of meters while resolving microflows and behavioral processes. We demonstrate measurements of sinking particles, including marine snow as they sediment tens of meters while capturing sub-particle-scale phenomena. We also demonstrate depth-patterned virtual-reality environments for novel behavioral analyses of microscale plankton. This technique offers a new experimental paradigm in microscale ocean biophysics by combining physiological-scale imaging with free movement in an ecological-scale patterned environment.\n\nOne sentence summaryScale-free vertical tracking microscopy captures, for the first time, untethered behavioral dynamics at cellular resolution for marine plankton.

biophysics↗

bioRxiv2019

The conserved metalloprotease invadolysin is present in invertebrate haemolymph and vertebrate blood

We identified invadolysin, a novel essential metalloprotease, for functions in chromosome structure, cell proliferation and migration. Invadolysin also plays an important metabolic role in insulin signaling and is the only protease known to localise to lipid droplets, the main lipid storage organelle in the cell. In silico examination of the protein sequence of invadolysin predicts not only protease and lipase catalytic motifs, but also post-translational modifications and the secretion of invadolysin. Here we show that the protease motif of invadolysin is important for its role in lipid accumulation, but not in glycogen accumulation. The lipase motif does not appear to be functionally important for accumulation of lipids or glycogen. Post-translational modifications likely contribute to modulating the level, localisation or activity of invadolysin. We identified a secreted form of invadolysin in the soluble fraction of invertebrate hemolymph (where we observe sexually dimorphic forms) and also vertebrate plasma, including in the extracellular vesicle fraction. Biochemical analysis for various post-translational modifications demonstrated that secreted invadolysin is both N-and O-glycosylated, but not apparently GPI-linked. The discovery of invadolysin in the extracellular milieu suggests a role for invadolysin in normal organismal physiology.\n\nSummary StatementIn this study, we show that the conserved metalloprotease invadolysin is present in invertebrate hemolymph and vertebrate blood, suggesting the protein may function in organismal physiology.

cell biology↗

bioRxiv2019

Low Dose Ionizing Radiation Strongly Stimulates Insertional Mutagenesis in a γH2AX Dependent Manner

Extrachromosomal DNA can integrate into the genome with no sequence specificity producing an insertional mutation. This process, which is referred to as random integration (RI), requires a double stranded break (DSB) in the genome. Inducing DSBs by various means, including ionizing radiation, increases the frequency of integration. Here we report that non-lethal physiologically relevant doses of ionizing radiation (10-100 mGy), within the range produced by medical imaging equipment, stimulate RI of transfected and viral episomal DNA in human and mouse cells with an extremely high efficiency. Genetic analysis of stimulated RI (S-RI) revealed that it is distinct from the background RI, requires histone H2AX S139 phosphorylation ({gamma}H2AX) and is not reduced by DNA polymerase {theta} (Polq) inactivation. S-RI efficiency was unaffected by the main DSB repair pathway (homologous recombination and non-homologous end joining) disruptions, but double deficiency in MDC1 and 53BP1 phenocopies {gamma}H2AX inactivation. The robust responsiveness of S-RI to physiological amounts of DSBs has implications for radiation risk assessment and can be exploited for extremely sensitive, macroscopic and direct detection of DSB-induced mutations.

molecular biology↗

bioRxiv2019

Macrophage plasticity is Rac signalling and MMP9 dependant

In vitro, depending on extracellular matrix (ECM) architecture, macrophages migrate either in amoeboid or mesenchymal mode; while the first is a general trait of leukocytes, the latter is associated with tissue remodelling via Matrix Metalloproteinases (MMPs). To assess whether these stereotyped migrations could be also observed in a physiological context, we used the zebrafish embryo and monitored macrophage morphology, behaviour and capacity to mobilisation haematopoietic stem/progenitor cells (HSPCs), as a final functional readout. Morphometric analysis identified 4 different cell shapes. Live imaging revealed that macrophages successively adopt all four shapes as they migrate through ECM. Treatment with inhibitors of MMPs or Rac GTPase to abolish mesenchymal migration, suppresses both ECM degradation and HSPC mobilisation while differently affecting macrophage behaviour. This study depicts real time macrophage behaviour in a physiological context and reveals extreme reactivity of these cells constantly adapting and switching migratory shapes to achieve HSPCs proper mobilisation.

cell biology↗

bioRxiv2019

Mapping interactions of microbial metabolites and human receptors

Despite evidence linking the human microbiome to health and disease, the mechanistic details of how the microbiota affects human physiology remain largely unknown. Metabolites encoded by bacteria are expected to play an integral role in the microbiotas effect on its human host. Assigning function to these metabolites is therefore critical to determining the molecular underpinnings of the host-microbe relationship and ultimately developing microbiota inspired therapies. Here we use large-scale functional screening of small molecules produced by individual members of a simplified human microbiota to identify bacterial metabolites that agonize G-protein coupled receptors (GPCR). This analysis revealed a complex network of metabolite host receptor interactions and guided our identification of multiple microbiota derived agonists of GPCRs associated with diverse biological functions within the nervous and immune systems, among others. Collectively, the metabolite-receptor pairs we uncovered indicate that diverse aspects of human health are potentially modulated by structurally simple metabolites arising from primary bacterial metabolism.\n\nStatement of SignificanceBacteria residing within the human body have been shown to influence human health. It is likely that physiological responses to the human microbiota are mediated by the collection of small molecules encoded within these bacteria. In this study we use direct functional screening of small molecules produced by individual members of a simplified human microbiota to identify new G protein coupled receptor-metabolite interactions that seek to explain the molecular underpinnings of the microbiotas influence on its human host.

microbiology↗

bioRxiv2019

Analysis of the testis transcriptome of the Chagas’ disease vector Rhodnius prolixus

Rhodnius prolixus is amongst the most important vectors of Trypanosoma cruzi in the Americas, putting thousands of people at risk of contracting Chagas Disease. This insect is also one of the most important models in insect physiology, especially regarding the blood-feeding process. However, studies on R. prolixus genetics lagged, and our understanding on the regulation of gene expression is incipient. Transcriptomes have the power to study the expression of thousands of genes in a single experiment. A comprehensive R. prolixus transcriptome was performed in 2014, sequencing RNA from different tissues (anterior gut, midgut, posterior gut, rectum, ovaries, fat body, maphigian tubules, and testicles). However, on that occasion, only the gut transcriptome was deeply analysed. Here we evaluated the results of the testicles transcriptome of R. prolixus with the objective to find and understand genes that could have an important role in male reproduction. We found, that from the 25,673 transcripts assembled in the whole transcriptome, 5,365 have a testicle specific expression pattern. As expected, amongst the most abundant families of transcripts, are those related to spermatogenesis and male fertility, such as myosins, actins, and dyneins. To our surprise, lipocalins, serine protease inhibitors (serpins), and lysozymes also were highly abundant in testicles. The role of these classes of genes are well known in other tissues, such as salivary glands and gut, but very little is known on their role in male reproduction (and we proposed here a few hypothesis that could be tested to address the role of these genes in male fertility). It would be interesting to study further the role of these genes on R. prolixus male fertility. Finally, as a reflection of the lack of knowledge on triatomine genetics, we found that almost half of the transcripts in R. prolixus testicles have no similarities to any other genes on reference databases. Our study shows that we still have a lot to know and to understand about reproduction in triatomine, especially in males. Besides the large number of genes without described function (possibly novel genes), there are those in which the function is known for other tissues, and we can only guess, at best, the role and importance of such genes for triatomine male fertility. Author SummaryThe understanding of the biology of insects vectors of parasitic diseases is key to the development of strategies of public health. For decades, the studies on the biology of male insects vectors of diseases was neglected, since in many cases female insects are those with relevant role in the spread of diseases. With the development of genomics, large scale studies to compare differential gene expression (transcriptomics) among different tissues, developmental stages, and sex became accessible. In this study, we looked at the physiology of the male reproductive organs of the vector of Chagas disease Rhodnius prolixus. This is a first glimpse, from a perspective of genes differentially expressed in male gonads, in such insects. We also performed an effort to link all identified genes with the insect genome published in 2015. We found ~14,000 genes expressed in the testicles, from which 5,635 genes are expressed exclusively in male reproductive organs. From the ~14,000 genes, we were able to attribute putative biological functions to 6,372 genes, which allowed us to draw a bigger picture on how these genes contribute to male fertility. This study now opens the door for further in-depth studies to find key genes for R. prolixus reproductive biology.

genomics↗

bioRxiv2019

From 3D to 3D: isolation of mesenchymal stem/stromal cells into a three-dimensional human platelet lysate matrix

Mesenchymal stem/stromal cells (MSCs) are considered an important candidate in cell therapy and tissue engineering approaches. The culture of stem cells in a 3D environment is known to better resemble the in vivo situation and to promote therapeutically relevant effects in isolated cells. Therefore, the aim of this study was to develop an approach for the isolation of MSCs from adipose tissue into a 3D environment. Furthermore, the use of cryoprotective medium for cryopreservation of whole adipose tissue was evaluated. For the isolation of MSCs, a novel human platelet lysate-based hydrogel was used as matrix and the migration, yield, viability and metabolic activity of cells from the 3D matrix were compared to cells from 2D explant culture. Also, the surface marker profile and differentiation capacity of MSCs from the 3D matrix were evaluated and compared to MSCs from isolation by enzymatic treatment. We found that cryopreservation of whole adipose tissue is feasible, and therefore adipose tissue can be stored and is available for MSC isolation on demand. Also, we demonstrate the isolation of MSCs into the 3D matrix and that cells from this condition display a similar phenotype and differentiation capacity like MSCs derived by traditional isolation procedure. The presented approach allows, for the first time, to isolate MSCs directly into a soft 3D hydrogel environment, avoiding any contact to a 2D plastic culture surface.\n\nSignificance StatementIn this paper we present a new method for the isolation of mesenchymal stem cells. Usually, these cells grow on two-dimensional plastic surfaces which is far away from their physiologic environment. Our new method allows for the first time the direct outgrowth of cells from primary tissue into a three-dimensional environment, avoiding any contact to a two-dimensional plastic surface. In future, this will allow an entirely three-dimensional in vitro cultivation of stem cells. Using 3D isolated cells will probably also increase the physiologic relevance of in vitro models.

cell biology↗

bioRxiv2019

HIV chromatin is a preferred target for drugs that bind in the DNA minor groove

The HIV genome is rich in A but not G or U and deficient in C. This nucleotide bias controls HIV phenotype by determining the highly unusual composition of all majors HIV proteins. Since drugs that bind in the DNA minor groove disrupt nucleosomes on sequences that contain closely spaced oligo-A tracts which are prevalent in HIV DNA because of this bias, it was of interest to determine if these drugs exert this selective inhibitory effect on HIV chromatin. To test this possibility, nucleosomes were reconstituted onto five double-stranded DNA fragments from the HIV-1 pol gene in the presence and in the absence of several minor groove binding drugs (MGBDs). The results demonstrated that the MGBDs inhibited the assembly of nucleosomes onto all of the HIV-1 segments in a manner that was proportional to the A-bias, but had no detectable effect on the formation of nucleosomes on control cloned fragments or genomic DNA from chicken and human. Nucleosomes preassembled onto HIV DNA were also preferentially destabilized by the drugs as evidenced by enhanced nuclease accessibility in physiological ionic strength and by the preferential loss of the histone octamer in hyper-physiological salt solutions. The drugs also selectively disrupted HIV-containing nucleosomes in yeast as revealed by enhanced nuclease accessibility of the in vivo assembled HIV chromatin and reductions in superhelical densities of plasmid chromatin containing HIV sequences. A comparison of these results to the density of A-tracts in the HIV genome indicates that a large fraction of the nucleosomes that make up HIV chromatin should be preferred in vitro targets for the MGBDs. These results show that the MGBDs preferentially disrupt HIV-1 chromatin in vitro and in vivo and raise the possibility that non-toxic derivatives of certain MGBD might serve as a novel class of anti-HIV agents.

molecular biology↗

bioRxiv2019

Origin of a novel CYP20A1 lncRNA through 23 Alu exaptations in the human lineage creates a potential multi-miRNA sponge

BackgroundPrimate-specific Alus contribute to transcriptional novelties in conserved gene regulatory networks. Alu RNAs are present at elevated levels in stress conditions and consequently leads to transcript isoform specific functional role modulating the physiological outcome. One of the possible mechanisms could be Alu nucleated mRNA-miRNA interplay. ResultUsing combination of bioinformatics and experiments, we report a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) through exaptation of 23 Alus in its 9kb 3UTR. CYP20A1_Alu-LT, confirmed by 3RACE, is an outlier in length and expressed in multiple cell lines. We demonstrate its presence in single nucleus RNA-seq of [~]16000 human cortical neurons (including rosehip neurons). Its expression is restricted to the higher primates. Most strikingly, miRanda predicts [~]4700 miRNA recognition elements (MREs; with threshold< -25kcal/mol) for [~]1000 miRNAs, which have majorly originated within the 3UTR-Alus post exaptation. We hypothesized that differential expression of this transcript could modulate mRNA-miRNA networks and tested it in primary human neurons where CYP20A1_Alu-LT is downregulated during heat shock response and upregulated upon HIV1-Tat treatment. CYP20A1_Alu-LT could possibly function as a miRNA sponge as it exhibits features of a sponge RNA such as cytosolic localization and [≥]10 MREs for 140 miRNAs. Small RNA-seq revealed expression of nine miRNAs that can potentially be sponged by CYP20A1_Alu-LT in neurons. Additionally, CYP20A1_Alu-LT expression was positively correlated (low in heat shock and high in Tat) with 380 differentially expressed genes that contain cognate MREs for these nine miRNAs. This set is enriched in genes involved in neuronal development and hemostasis pathways. ConclusionWe demonstrate a potential role for CYP20A1_Alu-LT as miRNA sponge through preferential presence of MREs within Alus in a transcript isoform specific manner. This highlights a novel component of Alu-miRNA mediated transcriptional modulation leading to physiological homeostasis.

evolutionary biology↗

bioRxiv2019

Unicellular Cyanobacteria Exhibit Light-Driven, Oxygen-Tolerant, Constitutive Nitrogenase Activity Under Continuous Illumination

Cyanobacteria have played a profound role in shaping the biosphere, most notably through the Great Oxygenation Event (GOE) with the advent of photosynthesis1. Cyanobacteria also contribute to global primary production through biological nitrogen fixation (BNF) using nitrogenase2,3, an oxygen-labile enzyme complex that evolutionarily predates the GOE4. Current literature reports nitrogenase activity in unicellular cyanobacteria is protected from oxygen through diurnal separation of photosynthesis and BNF5. However, historic conditions of continuous-light and warm temperature at polar latitudes during the Triassic and Cretaceous may have created a selective advantage amongst unicellular cyanobacteria for non-temporal mechanisms of maintaining nitrogenase activity in the presence of oxygen. Here we report constitutive nitrogenase activity concurrent with a net-gain of oxygen through photosynthesis in a continuous-light adapted culture of the unicellular cyanobacteria, Cyanothece sp. ATCC 51142. Nitrogenase activity in the adapted culture exhibited dependence on light and an increased resilience to artificially raised oxygen-tension compared to traditional culture. We predict cyanobacteria closely related to Cyanothece sp. ATCC 51142 also possess this physiology and found an accessory predicted proteome with functional relevance. This work provides a model of light-driven, oxygen-tolerant, constitutive nitrogenase activity and suggests this physiology may be conserved in closely related unicellular diazotrophic cyanobacteria with implications for primary production in polar ecosystems and potential biotechnological application in sustainable agriculture production.

microbiology↗

bioRxiv2019

Epigenetic bookmarking of H2S exposure in Caenorhabditis elegans

Physiological memories of environmental stress can serve to predict future environmental changes, allowing the organism to initiate protective mechanisms and survive. Although physiological memories, or bookmarks, of environmental stress have been described in a wide range of organisms, from bacteria to plants to humans, the mechanism by which these memories persist in the absence of stress is still largely unknown. We have discovered that C. elegans transiently exposed to low doses of hydrogen sulfide (H2S) survive subsequent exposure to otherwise lethal H2S concentrations and induce H2S-responsive transcripts more robustly than naive controls. H2S bookmarking can occur at any developmental stage and persists through cell divisions and development but is erased by fasting. We show that maintenance of the H2S bookmark requires the SET-2 histone methyltransferase and the CoREST-like demethylase complex. We propose a model in which exposure to low doses of H2S generates a long-lasting, epigenetic memory by modulating H3K4me2 modifications at specific promoters. Understanding the fundamental aspects of H2S bookmarking in this tractable system can provide mechanistic insight into how environmental exposures are translated into the epigenetic landscape in animals.

genetics↗

bioRxiv2019

An Electrophysiological Marker of Arousal Level in Humans

Deep non-rapid eye movement sleep (NREM) - also called slow wave sleep (SWS) - and general anesthesia are prominent states of reduced arousal linked to the occurrence of slow oscillations in the electroencephalogram (EEG). Rapid eye movement (REM) sleep, however, is also associated with a diminished arousal level, but is characterized by a desynchronized, wake-like EEG. This observation challenges the notion of oscillations as the main physiological mediator of reduced arousal. Using intracranial and surface EEG recordings in four independent data sets, we establish the 1/f spectral slope as an electrophysiological marker that accurately delineates wakefulness from anesthesia, SWS and REM sleep. The spectral slope reflects the non-oscillatory, scale-free measure of neural activity and has been proposed to index the local balance between excitation and inhibition. Taken together, these findings reconcile the long-standing paradox of reduced arousal in both REM and NREM sleep and provide a common unifying physiological principle -- a shift in local Excitation/ Inhibition balance -- to explain states of reduced arousal such as sleep and anesthesia in humans.\n\nSignificance StatementThe clinical assessment of arousal levels in humans depends on subjective measures such as responsiveness to verbal commands. While non-rapid eye movement (NREM) sleep and general anesthesia share some electrophysiological markers, rapid eye movement sleep (REM) is characterized by a wake-like electroencephalogram. Here, we demonstrate that non-oscillatory, scale-free electrical brain activity -- recorded from both scalp electroencephalogram and intracranial recordings in humans -- reliably tracks arousal levels during both NREM and REM sleep as well as under general anesthesia with propofol. Our findings suggest that non-oscillatory brain activity can be used effectively to monitor vigilance states.

neuroscience↗

bioRxiv2019

Application of extracellular flux analysis for determining mitochondrial function in mammalian oocytes and early embryos

1.BackgroundMitochondria provide the major source of ATP for mammalian oocyte maturation and early embryo development. Oxygen Consumption Rate (OCR) is an established measure of mitochondrial function. OCR by mammalian oocytes and embryos has generally been restricted to overall uptake and detailed understanding of the components of OCR dedicated to specific molecular events remains lacking.\n\nResultsHere, extracellular flux analysis (EFA) was applied to small groups of bovine, equine, mouse and human oocytes and bovine early embryos to measure OCR. Using EFA, we report the changes in mitochondrial activity during the processes of oocyte maturation, fertilization, and pre-implantation development to blastocyst stage in response to physiological demands in mammalian embryos. Crucially, we describe the real time partitioning of overall OCR to spare capacity, proton leak, non-mitochondrial and coupled respiration - showing that while there are alterations in activity over the course of development to respond to physiological demand, the overall efficiency is unchanged.\n\nConclusionEFA is shown to be able to measure mitochondrial function in small groups of mammalian oocytes and embryos in a manner which is robust, rapid and easy to use. EFA is non-invasive and allows real-time determination of the impact of compounds on OCR, facilitating an assessment of the parameters of mitochondrial activity. This provides proof-of-concept for EFA as an accessible system with which to study oocyte and embryo metabolism.

developmental biology↗

bioRxiv2019

Surprise response as a probe for compressed memory states

The limited capacity of recent memory inevitably leads to partial memory of past stimuli. There is also evidence that behavioral and neural responses to novel or rare stimuli are dependent on ones memory of past stimuli. Thus, these responses may serve as a probe of different individuals remembering and forgetting characteristics. Here, we utilize two lossy compression models of stimulus sequences that inherently involve forgetting, which in addition to being a necessity under many conditions, also has theoretical and behavioral advantages. One model is based on a simple stimulus counter and the other on the Information Bottleneck (IB) framework. These models are applied to analyze a novelty-detection event-related potential commonly known as the P300. The trial-by-trial variations of the P300 response, recorded in an auditory oddball paradigm, were subjected to each model to extract two stimulus-compression parameters for each subject: memory length and representation accuracy. These parameters were then utilized to estimate the subjects recent memory capacity limit under the task conditions. The results, along with recently published findings on single neurons on the IB model, underscore how a lossy compression framework can be utilized to account for trial-by-trial variability of neural responses at different spatial scales and in different individuals, while at the same time providing estimates of individual memory characteristics at different levels of representation using a theoretically-based parsimonious model.\n\nAuthor summarySurprise responses reflect expectations based on preceding stimuli representations, and hence can be used to infer the characteristics of memory utilized for a task. We suggest a quantitative method for extracting an individual estimate of effective memory capacity dedicated for a task based on the correspondence between a theoretical surprise model and electrophysiological single-trial surprise responses. We demonstrate this method on EEG responses recorded while participants were performing a simple auditory task; we show the correspondence between the theoretical and physiological surprise, and calculate an estimate of the utilized memory. The generality of this framework allows it to be applied to different EEG features that reflect different modes and levels of the processing hierarchy, as well as other physiological measures of surprise responses. Future studies may use this framework to construct a handy diagnostic tool for a quantitative, individualized characterization of memory-related disorders.

neuroscience↗