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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 487 records · Page 27Linked to original sources

bioRxiv2020

Bioengineered model of the human motor unit with physiologically functional neuromuscular junctions

Investigations of the human neuromuscular junction (NMJ) have predominately utilised experimental animals and model organisms. Consequently, there remains a paucity of data regarding the development of the human NMJ and a lack of systems that enable temporal investigation of the motor unit. This work addresses this need, providing the methodologies to bioengineer 3D models of the human motor unit. Separate maturation of primary human skeletal muscle and iPSC derived motor neurons seeks to accurately represent neuromuscular development via controlled addition of motor axons following primary myogenesis. Spheroid cultures of motor neuron progenitors augmented the transcription of OLIG2, ISLET1 and SMI32 motor neuron mRNAs [~]400, [~]150 and [~]200-fold respectively. Axon projections of adhered motor neuron spheroids exceeded 1000m in monolayer, with transcription of SMI32 and VACHT mRNAs further enhanced in a concentration dependent manner within optimised 3D type I collagen extracellular matrices. Bioengineered skeletal muscles produce functional forces, demonstrate increased acetylcholine receptor (AChR) clustering, and transcription of MUSK and LRP4 mRNAs indicating enhanced organisation of the post-synaptic membrane. Dosed integration of motor neuron spheroids outlined the motor pool required to functionally innervate muscle tissues in 3D, generating physiologically functional human NMJs that evidence pre- and post-synaptic membrane and motor nerve terminal co-localisation. Spontaneous firing was significantly elevated in 3D motor units, confirmed to be driven by the motor nerve via antagonistic inhibition of the AChR. Finally, functional analyses outlined decreased time to peak twitch and half relaxation times, indicating enhanced physiology of excitation contraction coupling of NMJs within innervated motor units.

bioengineering↗

bioRxiv2020

Testing for context-dependent effects of maternal thyroid hormones on offspring survival and physiology: an experimental approach manipulating temperature in a wild bird species

Maternal effects via hormonal transfer from the mother to the offspring provide a tool to translate environmental cues to the offspring. Experimental manipulations of maternally transferred hormones have yielded increasingly contradictory results, which may be explained by environment-dependent effects of hormones. Yet context-dependent effects have rarely been experimentally tested. We therefore studied whether maternally transferred thyroid hormones (THs) exert context-dependent effects on offspring survival and physiology by manipulating both egg TH levels and post-hatching nest temperature in wild pied flycatchers (Ficedula hypoleuca) using a full factorial design. We found no clear evidence for context-dependent effects of prenatal THs related to postnatal temperature on growth, survival and potential underlying physiological responses (plasma TH levels, oxidative stress and mitochondrial density). We conclude that future studies should test for other key environmental conditions, such as food availability, to understand potential context-dependent effects of maternally transmitted hormones on offspring, and their role in adapting to changing environments.

ecology↗

bioRxiv2020

Physiologic RNA Targets and Refined Sequence Specificity of Coronavirus EndoU

Coronavirus EndoU inhibits dsRNA-activated antiviral responses; however, the physiologic RNA substrates of EndoU are unknown. In this study, we used mouse hepatitis virus (MHV)-infected bone-marrow-derived macrophage (BMM) and cyclic phosphate cDNA sequencing to identify the RNA targets of EndoU. EndoU targeted viral RNA, cleaving the 3' side of pyrimidines with a strong preference for UA and CA sequences (endoYA). EndoU-dependent cleavage was detected in every region of MHV RNA, from the 5' NTR to the 3' NTR, including transcriptional regulatory sequences (TRS). Cleavage at two CA dinucleotides immediately adjacent to the MHV poly(A) tail suggest a mechanism to suppress negative-strand RNA synthesis and the accumulation of viral dsRNA. MHV with EndoU (EndoUmut) or 2'-5' phosphodiesterase (PDEmut) mutations provoked the activation of RNase L in BMM, with corresponding cleavage of RNAs by RNase L. The physiologic targets of EndoU are viral RNA templates required for negative-strand RNA synthesis and dsRNA accumulation. ImpactCoronavirus EndoU cleaves UA and CA sequences (endoYA) within viral (+) strand RNA to evade dsRNA-activated host responses.

microbiology↗

bioRxiv2020

Effect of leaf temperature on estimating physiological traits of wheat leaves from hyperspectral reflectance

A growing number of leaf traits can be predicted from hyperspectral reflectance data. These include structural and compositional traits, such as leaf mass per area, nitrogen and chlorophyll content, but also physiological traits such a Rubisco carboxylation activity, electron transport rate and respiration rate. Since physiological traits vary with leaf temperature, how does this impact on predictions made from reflectance measurements? We investigated this with two wheat varieties, by repeatedly measuring each leaf through a sequence of temperatures imposed by varying the air temperature in a growth room. The function predicting Rubisco capacity normalised to 25 {degrees}C predicted the same value, regardless of leaf temperatures ranging from 20 to 35{degrees}C. Leaf temperature affected none of the predicted traits: Vcmax25, J, chlorophyll content, LMA, N content per unit leaf area or Vcmax25/N. However, as others have derived models to predict Rubisco activity that includes variation associated with leaf temperature, we discuss whether these functions may include a temperature signal within the reflectance spectra.

plant biology↗

bioRxiv2020

Physiological noise modeling in fMRI based on the pulsatile component of photoplethysmograph

The blood oxygenation level-dependent (BOLD) contrast mechanism allows the noninvasive monitoring of changes in deoxyhemoglobin content. As such, it is commonly used in functional magnetic resonance imaging (fMRI) to study brain activity since levels of deoxyhemoglobin are indirectly related to local neuronal activity through neurovascular coupling mechanisms. However, the BOLD signal is severely affected by physiological processes as well as motion. Due to this, several noise correction techniques have been developed to correct for the associated confounds. The present study focuses on cardiac pulsatility fMRI confounds, aiming to refine model-based techniques that utilize the photoplethysmograph (PPG) signal. Specifically, we propose a new technique based on convolution filtering, termed cardiac pulsatility model (CPM) and compare its performance with the cardiac-related RETROICOR (Card-RETROICOR), which is a technique commonly used to model fMRI fluctuations due to cardiac pulsatility. Further, we investigate whether variations in the amplitude of the PPG pulses (PPG-Amp) covary with variations in amplitude of pulse-related fMRI fluctuations, as well as with the systemic low frequency oscillations (SLFOs) component of the fMRI global signal (GS - defined as the mean signal across all gray matter voxels). Capitalizing on 3T fMRI data from the Human Connectome Project, CPM was found to explain a significantly larger fraction of the fMRI signal variance compared to Card-RETROICOR, particularly for subjects with larger heart rate variability during the scan. The amplitude of the fMRI pulse-related fluctuations did not covary with PPG-Amp; however, PPG-Amp explained significant variance in the GS that was not attributed to variations in heart rate or breathing patterns. Our results suggest that the proposed approach can model high-frequency fluctuations due to pulsation as well as low-frequency physiological fluctuations more accurately compared to model-based techniques commonly employed in fMRI studies.

neuroscience↗

bioRxiv2020

A physiological role for GABAA receptor desensitization - induction of long-term potentiation at inhibitory synapses

GABAA receptors (GABAARs) are pentameric ligand-gated ion channels distributed throughout the brain where they mediate synaptic and tonic inhibition. Following activation, these receptors undergo desensitization which involves entry into long-lived agonist-bound closed states. Although the kinetic effects of this state are recognised and its structural basis has been uncovered, the physiological impact of desensitization on inhibitory neurotransmission remains unknown. Here we describe an enduring new form of long-term potentiation at inhibitory synapses that elevates synaptic current amplitude for 24 hrs following desensitization of GABAARs in response to prolonged agonist exposure or allosteric modulation. Using receptor mutants and allosteric modulators we demonstrate that desensitization of GABAARs facilitates their phosphorylation by PKC, which increases the number of receptors at inhibitory synapses. These observations provide a new physiological relevance to the desensitized state of GABAARs, acting as a signal to regulate the efficacy of inhibitory synapses during prolonged periods of inhibitory neurotransmission.

neuroscience↗

bioRxiv2020

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification

The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Furthermore, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 {approx} 0.036 {micro}M), but a higher nitrite affinity (Km(app)_NO2- {approx} 13.8 {micro}M), indicating an adaptation to highly oligotrophic environments. Counterintuitively for a nitrifying microorganism, we also observed an inhibition of ammonia oxidation at ammonium concentrations as low as 25 {micro}M. This substrate inhibition of "Ca. N. kreftii" indicate that differences in ammonium tolerance rather than affinity can be a niche determining factor for different comammox Nitrospira.

microbiology↗

bioRxiv2020

Methionine synthase is essential for cancer cell proliferation in physiological folate environments

Targeting folate metabolism can be an effective way to treat cancer. The enzyme methionine synthase catalyzes a key reaction in both folate and methionine metabolism. Early work suggested that inhibiting methionine synthase might restrain tumor growth, though the mechanism remains unclear. We find that due to its specific role in processing folates, methionine synthase is required for cancer proliferation. However, widely used cell culture conditions obscure the proliferative and metabolic consequences of methionine synthase inhibition. Complete dependence on methionine synthase only arises when 5-methyl tetrahydrofolate, the major folate found in circulation, is the predominant folate source provided to cells. In these physiological folate conditions, methionine synthase activity is necessary to maintain intracellular levels of nucleotides, but not methionine. These data reveal that the extracellular environment can alter the essentiality of methionine synthase and suggest that this enzyme plays a crucial cell-autonomous role in supporting nucleotide synthesis and cell proliferation in physiological contexts.

cancer biology↗

bioRxiv2020

Parabrachial Opioidergic Projections to Preoptic Hypothalamus Mediate Behavioral and Physiological Thermal Defenses

Maintaining stable body temperature through environmental thermal stressors requires detection of temperature changes, relay of information, and coordination of physiological and behavioral responses. Studies have implicated areas in the preoptic hypothalamic area (POA) and the parabrachial nucleus (PBN) as nodes in the thermosensory neural circuitry and indicate the opioid system within the POA is vital in regulating body temperate. In the present study we identify neurons projecting to the POA from PBN expressing the opioid peptides Dynorphin (Dyn) and Enkephalin (Enk). We determine that warm-activated PBN neuronal populations overlap with both Dyn and Enk expressing PBN populations. We demonstrate that Dyn and Enk expressing neurons are partially overlapping subsets of a glutamatergic population in the PBN. Using optogenetic approaches we selectively activate projections in the POA from PBN Dyn, Enk, and VGLUT2 expressing neurons. Our findings demonstrate that Dyn, Enk, and VGLUT2 expressing PBN neurons are critical for physiological and behavioral heat defense.

neuroscience↗

bioRxiv2020

Transgressive segregation for salt tolerance in rice due to physiological coupling and uncoupling and genetic network rewiring

Transgressive segregation is common in plant breeding populations, where a small minority of recombinants are outliers relative to parental phenotypes. While this phenomenon has been attributed to complementation and epistatic effects, the physiological, biochemical, and molecular bases have not been fully illuminated. By systems-level scrutiny of the IR29 x Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salt tolerance phenotypes are created by positive or negative coupling or uncoupling effects and novel regulatory networks. Hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. The large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits, while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The mechanisms elucidated in this study are consistent with the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study supports a breeding paradigm based on genomic modeling to create the novel adaptive phenotypes for the crops of the 21st century.

genetics↗

bioRxiv2020

Monoterpenes alter TAR1-driven physiology in Drosophila species

Monoterpenes are molecules with insecticide properties whose mechanism of action is however not completely elucidated. Furthermore, they seem to be able to modulate the monoaminergic system and several behavioural aspects in insects. In particular, tyramine (TA) and octopamine (OA) and their associated receptors orchestrate physiological processes such as feeding, locomotion and metabolism. Here we show that monoterpenes not only act as biopesticides in Drosophila species but can cause complex behavioural alterations that require a functional type 1 tyramine receptors (TAR1s). Variations in metabolic traits as well as locomotory activity were evaluated in both Drosophila suzukii and Drosophila melanogaster after treatment with three monoterpenes. A TAR1-/- D. melanogaster strain was used to better understand the relationships between the receptor and monoterpenes-related behavioural changes. Immunohistochemistry analysis revealed that, in the D. melanogaster brain, TAR1 appeared to be expressed in areas controlling metabolism. In comparison to the D. melanogaster wild type, the TAR-/- flies showed a phenotype characterized by higher triglyceride levels and food intake as well as lower locomotory activity. The monoterpenes, tested at sublethal concentrations, were able to induce a downregulation of the TAR1 coding gene in both Drosophila species. Furthermore, monoterpenes also altered the behaviour in D. suzukii and D. melanogaster wild types 24 h after a continuous monoterpene exposure. Interestingly, they were ineffective in modifying the physiological performances of TAR1-/- flies. In conclusion, it appears that monoterpenes not only act as biopesticides for Drosophila but they can also interfere with its behaviour and metabolism in a TAR1-dependent fashion.

animal behavior and cognition↗

bioRxiv2020

Inducing highly physiologically relevant phenotypes of human vascular smooth muscle cells via 3D printing

Vascular smooth muscle cells (vSMCs) are one of the essential cell types in blood vessel walls. A significant vSMC phenotype characteristic is that they collectively wrap around the outer layer of the healthy blood vessels with spindle-like morphology and help maintain the vascular tones and regulate the blood flow. Both physiological and biomedical research are impeded by the standard 2D cell culture approaches which do not create in vivo like microenvironment. Here, we systematically investigated the vSMCs culturing within 3D printed geometrical constraints and on printed microfilaments. Based on these models, we demonstrate a simple bioprinting approach for fast manufacturing vessel architectures with micro-grooved surfaces for vSMCs alignment. We validated that the vSMCs cultured on the printed vessel with microfilaments (VWMF) present a more physiologically relevant morphological phenotype and gene expression profile, and they are considerably more active in wound healing and ischemia than conventional planarly cultured vSMCs.

bioengineering↗

bioRxiv2020

Diploid hepatocytes drive physiological liver renewal in adult humans

Physiological liver cell replacement is central to maintaining the organs high metabolic activity, although its characteristics are difficult to study in humans. Using retrospective 14C birth dating of cells, we report that human hepatocytes show continuous and lifelong turnover, maintaining the liver a young organ (average age < 3 years). Hepatocyte renewal is highly dependent on the ploidy level. Diploid hepatocytes show an seven-fold higher annual exchange rate than polyploid hepatocytes. These observations support the view that physiological liver cell renewal in humans is mainly dependent on diploid hepatocytes, whereas polyploid cells are compromised in their ability to divide. Moreover, cellular transitions between these two subpopulations are limited, with minimal contribution to the respective other ploidy class under homeostatic conditions. With these findings, we present a new integrated model of homeostatic liver cell generation in humans that provides fundamental insights into liver cell turnover dynamics.

cell biology↗

bioRxiv2020

A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations

It has been long known that bacteria coordinate their physiology with environmental nutrient, yet our current understanding offers little intuition for how bacteria respond to the second-to-minute scale fluctuations in nutrient concentration characteristic of many microbial habitats. To investigate the effects of rapid nutrient fluctuations on bacterial growth, we coupled custom microfluidics with single-cell microscopy to quantify the growth rate of E. coli experiencing 30 s to 60 min nutrient fluctuations. Compared to steady environments of equal average concentration, fluctuating environments reduced growth rate by up to 50%. However, measured reductions in growth rate were only 38% of the growth loss predicted from single nutrient shifts -- an enhancement produced by the distinct growth response of cells grown in environments that fluctuate rather than shift once. We report an unexpected physiology adapted for growth in nutrient fluctuations and implicate nutrient timescale as a critical environmental parameter beyond nutrient concentration and source.

microbiology↗

bioRxiv2020

Low Physiological Arousal in Mental Fatigue: Analysis of Heart Rate Variability during Time-on-task, Recovery, and Reactivity

Heart Rate Variability (HRV) has been suggested as a useful tool to assess fatigue-sensitive psychological operations. The present study uses between and within-subject design to examine the temporal profile of HRV including the changes related to reactivity, time-on-task (ToT), and recovery on a cognitively demanding task. In the fatigue group, participants worked on a bimodal 2-back task with a game-like character (the gatekeeper task) for about 1.5 hours, followed by a 12-minute break, and a post-break block of performance (about 18 min). In the control group, participants watched documentaries. We hypothesized that mental fatigue is associated with low physiological arousal and increasing vagal-mediated HRV as a function of ToT. We also analysed the trial-based post-response cardiac activity as a physiological indicator of task-related motivation. Relative to the control, ToT was associated with an elevated level of subjective fatigue, decreased heart rate, and increased HRV most robustly in the vagal-mediated components. Based on fatigued participants post-error cardiac slowing, and post-error reaction time analyses, we found no evidence for motivation deficit in association with increasing HRV and ToT. The present findings support the low arousal state of mental fatigue and suggest that primarily the vagal components of the HRV spectrum are indicative of fatigue. In addition, the study provides evidence that many HRV indices might be changed not only in a fatiguing condition but also if individuals are engaged in a prolonged non-fatiguing activity. This finding emphasizes the relevance of control conditions in ToT experiments.

neuroscience↗

bioRxiv2020

Transcriptional and morpho-physiological responses of Marchantia polymorpha upon phosphate starvation

Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (eg. PHR1-SPX1 and STOP1-ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes and MpMYB14, an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting preference for citrate exudation. Analysis of MpPHR1 binding sequences (P1BS) shows enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability. Significance StatementThis study unravels the transcriptional and morphophysiological mechanisms executed by the non-vascular, and rootless, plant Marchantia polymorpha upon phosphate starvation conditions. The findings in this study shed light on the mechanisms that early land plants may have developed for the conquest of substrates poor in available phosphate, some of which are still conserved by current-day plants. Moreover, our results open several working hypotheses and novel perspectives for the study of Pi-starvation responses along plant evolution.

plant biology↗

bioRxiv2020

The impact of water deficit and heat stress combination on the molecular response, physiology and seed production of soybean

A combination of drought and heat stress, occurring at the vegetative or reproductive growth phase of many different crops, can have a devastating impact on yield. In soybean (Glycine max), a considerable effort has been made to develop genotypes with enhanced yield production under conditions of drought or heat stress. However, how these genotypes perform in terms of growth, physiological responses and most importantly seed production, under conditions of drought and heat combination is mostly unknown. Here, we studied the impact of water deficit and heat stress combination on the physiology, seed production and yield per plant of two soybean genotypes, Magellan and Plant Introduction (PI) 548313, that differ in their reproductive responses to heat stress. Our findings reveal that although PI 548313 produced more seeds than Magellan under conditions of heat stress, under conditions of water deficit and heat stress combination its seed production decreased. Because number of flowers and pollen germination of PI 548313 remained high under heat or water deficit and heat combination, the reduced seed production exhibited by PI 548313 under the stress combination could be a result of processes that occur at the stigma, ovaries and/or other parts of the flower following pollen germination. HighlightTolerance to heat stress was found not to confer tolerance to a combination of water deficit and heat stress in soybean, highlighting the need for breeding strategies targeting the stress combination.

plant biology↗

bioRxiv2020

FANCD2 Alleviates Physiologic Replication Stress in Fetal Liver HSC

Bone marrow failure (BMF) in Fanconi Anemia (FA) results from exhaustion of hematopoietic stem cells (HSC), but the physiological role of FA proteins in HSC pool integrity remains unknown. Herein we demonstrate that FANCD2, a core component of the FA pathway, counters replication stress during developmental HSC expansion in the fetal liver (FL). Rapid rates of proliferation and FANCD2 deficient result in excess RPA-coated ssDNA, and provoke pChk1 activation and Cdkn1a(p21) nuclear localization in fetal Fancd2-/- HSC. Checkpoint mediated S-phase delays induced by Cdkn1a(p21) are rescued by Tgf-{beta} inhibition, but pChk1 activation is further aggravated. Our observations reveal the mechanism and physiological context by which FANCD2 safeguards HSC pool formation during development.

developmental biology↗