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bioRxiv2021

A Novel Swine Model of the Acute Respiratory Distress Syndrome Using Clinically-Relevant Injury Exposures

To date, existing animal models of the acute respiratory distress syndrome (ARDS) have failed to translate preclinical discoveries into effective pharmacotherapy or diagnostic biomarkers. To address this translational gap, we developed a high-fidelity swine model of ARDS utilizing clinically-relevant lung injury exposures. Fourteen male swine were anesthetized, mechanically ventilated, and surgically instrumented for hemodynamic monitoring, blood, and tissue sampling. Animals were allocated to one of three groups: 1) Indirect lung injury only: animals were inoculated by direct injection of E. coli into the kidney parenchyma, provoking systemic inflammation and distributive shock physiology; 2) Direct lung injury only: animals received volutrauma, hyperoxia, and bronchoscope-delivered gastric particles; 3) Combined indirect and direct lung injury: animals were administered both above-described indirect and direct lung injury exposures. Animals were monitored for up to 12 hours, with serial collection of physiologic data, blood samples, and radiographic imaging. Lung tissue was acquired post-mortem for pathological examination. In contrast to indirect lung injury only and direct lung injury only groups, animals in the combined indirect and direct lung injury group exhibited all of the physiological, radiographic, and histopathologic hallmarks of human ARDS: impaired gas exchange (mean PaO2/FiO2 ratio 124.8 {+/-} 63.8), diffuse bilateral opacities on chest radiographs, and extensive pathologic evidence of diffuse alveolar damage. Our novel porcine model of ARDS, built on clinically-relevant lung injury exposures, faithfully recapitulates the physiologic, radiographic, and histopathologic features of human ARDS, and fills a crucial gap in the translational study of human lung injury.

pathology↗

bioRxiv2021

Water levels affect photosynthesis and nutrient use more than salinity in a scrub Red Mangrove forest of the southeastern Florida Everglades

We investigated how mangrove-island micro-elevation (i.e., habitat: center vs. edge) affects tree physiology in a scrub mangrove forest of the southeastern Everglades. We measured leaf gas exchange rates of scrub Rhizophora mangle L. trees monthly during 2019, hypothesizing that CO2 assimilation (Anet) and stomatal conductance (gsw) would decline with increasing water levels and salinity, expecting more-considerable differences at mangrove-island edges than centers, where physiological stress is greatest. Water levels varied between 0 and 60 cm from the soil surface, rising during the wet season (May-October) relative to the dry season (November-April). Porewater salinity ranged from 15 to 30 ppt, being higher at mangrove-island edges than centers. Anet maximized at 15.1 {micro}mol m-2 s-1, and gsw was typically <0.2 mol m-2 s-1, both of which were greater in the dry than the wet season and greater at island centers than edges, with seasonal variability being roughly equal to variation between habitats. After accounting for season and habitat, water level positively affected Anet in both seasons but did not affect gsw. Our findings suggest that inundation stress (i.e., water level) is the primary driver of variation in leaf gas exchange rates of scrub mangroves in the Florida Everglades, while also constraining Anet more than gsw. The interaction between inundation stress due to permanent flooding and habitat varies with season as physiological stress is alleviated at higher-elevation mangrove-island center habitats during the dry season. Freshwater inflows during the wet season, increase water levels and inundation stress at higher-elevation mangrove-island centers, but also potentially alleviate salt and sulfide stress in soils. Thus, habitat heterogeneity leads to differences in nutrient and water acquisition and use between trees growing in island centers versus edges, creating distinct physiological controls on photosynthesis, which likely affect carbon flux dynamics of scrub mangroves in the Everglades.

plant biology↗

bioRxiv2021

The seasonal dynamics of bud dormancy in grapevine suggest a regulated checkpoint prior to acclimation

Grapevine (Vitis vinifera L.) displays wide plasticity to climate and seasonality, ranging from strongly deciduous to evergreen. Understanding the physiology of decisions to grow or quiesce is critical for improved crop management, prediction, and the adaptability of production to alternative climate scenarios. The perenniating bud (N+2) is a major economic unit and focus of study. Here we investigated the physiology and transcriptome of cv. Merlot buds grown in a temperate maritime climate from summer to spring in two consecutive years. The changes in bud respiration, hydration and internal tissue oxygen data were consistent with the transcriptome data. ABA-responsive gene processes prevailed upon the transition to a deep metabolic and cellular quiescence in the bud during autumn. Light, together with hypoxia and redox signalling presided over the resumption of nuclear and cellular growth in the transition to spring. Comparisons with transcriptome data from bud burst studies revealed a number of regulatory candidates for the orderly resumption of growth in spring, including components that may integrate light and temperature signalling. Importantly however, the bud burst forcing data, which is widely used as a measure of bud dormancy, were not consistent with the physiological and transcription data. We hypothesise the existence of a physiological checkpoint following bud set in summer, which if not met results in extreme quiescence. Collectively this is the most integrated developmental dataset of the latent bud of cultivated grapevine, and establishes a platform for systems approaches to study seasonal plasticity. One sentence summaryPhysiology and transcriptome data provide strong evidence of a regulatory checkpoint prior to acclimation and dormancy in latent grapevine buds.

plant biology↗

bioRxiv2021

A preliminary assessment of allostatic load in male mantled howler monkeys

Allostatic load refers to the wear and tear of the organism associated with the repeated activation of mechanisms that allow for homeostasis. Although allostasis (i.e., maintaining stability through change) is achieved through the orchestration of multiple systems, assessments of allostatic load in wildlife have usually relied on the measurement of single or few physiological mediators. In the present study, we aimed at constructing an allostatic load index (ALI) for male mantled howler monkeys (Alouatta palliata) based on seven physiological mediators (C-peptide, triiodothyronine, glucocorticoids, testosterone, amount of activity, foraging effort, and participation in agonistic interactions). We then examined if variation in this ALI was associated with social, ecological, and abiotic challenges. For five years, we studied ten adult males belonging to two groups. We assessed physiological mediators via behavioral observations (3,364 hours of samplings), and both urine (1,500 assayed samples) and fecal (1,500 assayed samples) sampling. We calculated an ALI based on mediator specific risk scores. Seasonality, encounters with extragroup males, mating, and centrality were positively related with male allostatic load, though only the first two had significant effects on ALI. ALI reflected the physiological and behavioral responses of males to social, ecological, and abiotic challenges. It remains for future research to determine if the observed trends correspond to normal fluctuations in mechanisms that allow male mantled howler monkeys to cope with their environment.

zoology↗

bioRxiv2021

Genetic variation in haemoglobin regulates breathing in high-altitude deer mice

Physiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated the in vivo effects on respiratory physiology of genetic variants in haemoglobin (Hb) that contribute to hypoxia adaptation in high-altitude deer mice (Peromyscus maniculatus). We created F2 inter-population hybrids of highland and lowland deer mice to test the phenotypic effects of - and {beta}-globin variants on a mixed genetic background. High-altitude genotypes were associated with breathing phenotypes that enhance O2 uptake in hypoxia, including a deeper more effective breathing pattern and an augmented hypoxic ventilatory response. These effects could not be explained by erythrocyte Hb-O2 affinity or globin gene expression in the brainstem. Therefore, adaptive variation in haemoglobin can have unexpected effects on physiology that are distinct from the canonical function of this protein in circulatory O2 transport.

evolutionary biology↗

bioRxiv2021

High and low expression of the hyperpolarization activated current (Ih) in mouse CA1 stratum oriens interneurons.

Inhibitory interneurons are among the most diverse cell types in the brain; the hippocampus itself contains more than 28 different inhibitory interneurons. Interneurons are typically classified using a combination of physiological, morphological and biochemical observations. One broad separator is action potential firing: low threshold, regular spiking vs. higher threshold, fast spiking. We found that spike frequency adaptation (SFA) was highly heterogeneous in low threshold interneurons in the mouse stratum oriens region of area CA1. Analysis with a k-means clustering algorithm parsed the data set into two distinct clusters based on a constellation of physiological parameters and reliably sorted strong and weak SFA cells into different groups. Interneurons with strong SFA fired fewer action potentials across a range of current inputs and had lower input resistance compared to cells with weak SFA. Strong SFA cells also had higher sag and rebound in response to hyperpolarizing current injections. Morphological analysis shows no difference between the two cell types and the cell types did not segregate along the dorsal-ventral axis of the hippocampus. Strong and weak SFA cells were labeled in hippocampal slices from SST:cre Ai14 mice suggesting both cells express somatostatin. Voltage-clamp recordings showed hyperpolarization activated current Ih was significantly larger in strong SFA cells compared to weak SFA cells. We suggest that the strong SFA cell represents a previously uncharacterized type of CA1 stratum oriens interneuron. Due to the combination of physiological parameters of these cells, we will refer to them as Low Threshold High Ih (LTH) cells. Key PointsO_LISpike frequency adaptation (SFA) was highly variable among stratum oriens interneurons C_LIO_LIAdapting stratum oriens interneurons were separated into two cell groups using multiple subthreshold and action potential parameters by cluster analysis C_LIO_LICells with strong SFA fired fewer action potentials for a given current injection, had lower input resistance and more sag and rebound compared to weak SFA cells C_LIO_LIThe physiological differences were not correlated with neuron morphology, location in stratum oriens, or anatomical location along the dorsal-ventral axis of the hippocampus C_LIO_LIVoltage-clamp recordings revealed that strong SFA cells had higher density of the hyperpolarization activated current Ih compared to weak SFA cells C_LI

neuroscience↗

bioRxiv2021

Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis

Tsetse flies (Glossina spp.) house a population-dependent assortment of microorganisms that can include pathogenic African trypanosomes and maternally transmitted endosymbiotic bacteria, the latter of which mediate numerous aspects of their hosts metabolic, reproductive, and immune physiologies. One of these endosymbionts, Spiroplasma, was recently discovered to reside within multiple tissues of field captured and laboratory colonized tsetse flies grouped in the Palpalis subgenera. In various arthropods, Spiroplasma induces reproductive abnormalities and pathogen protective phenotypes. In tsetse, Spiroplasma infections also induce a protective phenotype by enhancing the flys resistance to infection with trypanosomes. However, the potential impact of Spiroplasma on tsetses viviparous reproductive physiology remains unknown. Herein we employed high-throughput RNA sequencing and laboratory-based functional assays to better characterize the association between Spiroplasma and the metabolic and reproductive physiologies of G. fuscipes fuscipes (Gff), a prominent vector of human disease. Using field-captured Gff, we discovered that Spiroplasma infection induces changes of sex-biased gene expression in reproductive tissues that may be critical for tsetses reproductive fitness. Using a Gff line composed of individuals heterogeneously infected with Spiroplasma, we observed that the bacterium and tsetse host compete for finite nutrients, which negatively impact female fecundity by increasing the length of intrauterine larval development. Additionally, we found that when males are infected with Spiroplasma, the motility of their sperm is compromised following transfer to the female spermatheca. As such, Spiroplasma infections appear to adversely impact male reproductive fitness by decreasing the competitiveness of their sperm. Finally, we determined that the bacterium is maternally transmitted to intrauterine larva at a high frequency, while paternal transmission was also noted in a small number of matings. Taken together, our findings indicate that Spiroplasma exerts a negative impact on tsetse fecundity, an outcome that could be exploited for reducing tsetse population size and thus disease transmission. Author SummaryEndosymbiotic bacteria regulate numerous aspects of their hosts reproductive physiology. Natural populations of the tsetse fly, Glossina fuscipes fuscipes (Gff), house heterogeneous infections with the bacterium Spiroplasma glossinidia. Infection with the bacterium results in the presentation of several phenotypes in both male and female Gff that would put them at a significant reproductive disadvantage when compared to their counterparts that do not house the bacterium. These Spiroplasma induced phenotypes include changes in sex-biased gene expression in the reproductive organs, a depletion in the availability of metabolically critical lipids in pregnant females that results in delayed larval development, and compromised sperm fitness. These findings indicate that Spiroplasma exerts an overall negative impact on both male and female reproductive fitness and thus likely has a profound effect on fly population structure. This outcome, in conjunction with the fact that Spiroplasma infected tsetse are unusually refractory to infection with pathogenic African trypanosomes, indicates that the bacterium could be experimentally exploited to reduce disease transmission through the fly.

microbiology↗

bioRxiv2021

Functional degeneracy in translationally active Nitrospira populations confers resilience to out-selection in partial nitritation activated sludge

Managing and engineering activated sludge wastewater treatment microbiomes for low-energy nitrogen removal requires process control strategies to stop the oxidation of ammonium at nitrite. Our ability to out-select nitrite oxidizing bacteria (NOB) from activated sludge is challenged by their metabolic and physiological diversity, warranting measurements of their in situ physiology and activity under selective growth pressures. Here, we examined the stability of nitrite oxidation in activated sludge during a press disturbance induced by treating a portion of return activated sludge with a sidestream flow containing free ammonia (FA) at 200 mg NH3-N/L. The nitrite accumulation ratio peaked at 42% by day 40 in the experimental bioreactor with the press disturbance, while it did not increase in the control bioreactor. A subsequent decrease in nitrite accumulation within the experimental bioreactor coincided with shifts in dominant Nitrospira 16S rRNA amplicon sequence variants (ASVs). We applied bioorthogonal non-canonical amino acid tagging (BONCAT) coupled with fluorescence activated cell sorting (FACS) to investigate changes in the translational activity of NOB populations throughout batch exposure to FA. BONCAT-FACS confirmed that the single Nitrospira ASV washed-out of the experimental bioreactor had reduced translational activity following exposure to FA, whereas the two Nitrospira ASVs that emerged after process acclimation were not impacted by FA. Thus, the coexistence of functionally degenerate and physiologically resistant Nitrospira populations provided resilience to the nitrite-oxidizing function during the press disturbance. These results highlight how BONCAT-FACS can resolve ecological niche differentiations within activated sludge and inform strategies to engineer and control microbiome function. ImportanceNitrogen removal from activated sludge wastewater treatment systems is an energy-intensive process due to the large aeration requirement for nitrification. This energy footprint could be minimized with engineering control strategies that wash-out nitrite oxidizing bacteria (NOB) to limit oxygen demands. However, NOB populations can have a high degree of physiological diversity, and it is currently difficult to decipher the behavior of individual taxa during applied selective pressures. Here, we utilized a new substrate analog probing approach to measure the activity of NOB at the cellular translational level in the face of an applied press disturbance to the activated sludge process. Substrate analog probing corroborated the time-series reactor sampling, showing that coexisting and functionally redundant Nitrospira provided resilience to the nitrite oxidation process. Taken together, these results highlight how substrate analog approaches can illuminate in situ ecophysiologies within shared niches, and can inform strategies to improve microbiome engineering and management.

microbiology↗

bioRxiv2021

A Hypoxia Sensitive to Hypoxia Resistant Transformation in Long-Lived Germline Mutants

Signals from the germline play a significant role in determining longevity in numerous animal models. In C. elegans, ablation of the germline leads to long life span and various other types of stress resistance. It has been reported that mutations that block oogenesis or an upstream step in germline development confer strong resistance to hypoxia. We report here that the hypoxia resistance of sterile mutants is dependent on developmental stage and age. In just a 12-hour period, sterile animals transform from hypoxia sensitive L4 larvae into highly hypoxia resistant adults. Since this transformation occurs in animals with no germline, the physiological programs that determine hypoxia sensitivity must occur independently of germline signals and instead rely on developmental signals from somatic tissues. Furthermore, we found two distinct mechanisms of hypoxia resistance in long-lived germline deficient animals. First, a DAF-16/FoxO independent mechanism that occurs in all hypoxia resistant sterile adults and, second, a DAF-16/FoxO dependent mechanism that confers an added layer of resistance, or "super-resistance", to animals with no germline as they age past day 1 of adulthood. RNAseq data showed that nearly all genes involved in both cytosolic and mitochondrial protein translation, as well as in mitochondrial protein import, are repressed in germline deficient adults and further repressed as they age. The hypoxia super-resistance of aging germline deficient animals was suppressed by dual mutation of ncl-1 and larp-1, two regulators of nucleolar biology and protein translation, demonstrating that the hypoxia super-resistance mechanism involves reduced protein translation. These studies provide novel insight into a profound physiological transformation that takes place in germline mutants during development, showing that some of the unique physiological properties of these long-lived animals are dependent on developmental repression of genes involved in protein translation, which operate independently of germline signals. AUTHOR SUMMARYIn addition to being extremely long lived, germline deficient animals have other extraordinary properties, such as robust resistance to oxygen deprivation. Here we provide new insight into the mechanisms of hypoxia resistance in germline deficient animals. We demonstrate that, in just a 12-hour period, germline mutants transform from hypoxia sensitive larvae into highly hypoxia resistant adults. Therefore, hypoxia resistance is not a general property of germline ablated animals, but is instead "switched on" only in adult animals. We have found two distinct mechanisms of hypoxia resistance in germline deficient animals and both mechanisms are mediated by signals from somatic tissues and do not require the germline. We have determined that reduced transcription of genes involved in protein translation is one of the mechanisms of hypoxia resistance. Like hypoxia resistance, repression of protein translation genes only occurs in adults. Our findings establish that the unique physiological properties of germline-deficient animals are "switched" on in adults and therefore must be mediated by developmental signals from somatic tissues. We conclude that the L4/adult developmental switch in germline ablated animals presents an excellent system for investigating the longevity and hypoxia resistance of germline deficient animals.

genetics↗

bioRxiv2021

Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi

BackgroundKra monkeys (Macaca fascicularis), a natural host of Plasmodium knowlesi, control parasitaemia caused by this parasite species and escape death without treatment. Knowledge of the disease progression and resilience in kra monkeys will aid the effective use of this species to study mechanisms of resilience to malaria. This longitudinal study aimed to define clinical, physiological and pathological changes in kra monkeys infected with P. knowlesi, which could explain their resilient phenotype. MethodsKra monkeys (n = 15, male, young adults) were infected intravenously with cryopreserved P. knowlesi sporozoites and the resulting parasitaemias were monitored daily. Complete blood counts, reticulocyte counts, blood chemistry and physiological telemetry data (n = 7) were acquired as described prior to infection to establish baseline values and then daily after inoculation for up to 50 days. Bone marrow aspirates, plasma samples, and 22 tissue samples were collected at specific time points to evaluate longitudinal clinical, physiological and pathological effects of P. knowlesi infections. ResultsAs expected, the kra monkeys controlled parasitaemia and remained with low-level, persistent parasitaemias without antimalarial intervention. Unexpectedly, early in the infection, fevers developed, which ultimately returned to baseline, as well as mild to moderate thrombocytopaenia, and moderate to severe anaemia. Mathematical modeling and the reticulocyte production index indicated that the anaemia was largely due to the removal of uninfected erythrocytes and not impaired production of erythrocytes. Mild tissue damage was observed, and tissue parasite load was associated with tissue damage even though parasite accumulation in the tissues was generally low. ConclusionsKra monkeys experimentally infected with P. knowlesi sporozoites presented with multiple clinical signs of malaria that varied in severity among individuals. Overall, the animals shared common mechanisms of resilience characterized by controlling parasitaemia 3-5 days after patency, and controlling fever, coupled with physiological and bone marrow responses to compensate for anaemia. Together, these responses likely minimized tissue damage while supporting the establishment of chronic infections, which may be important for transmission in natural endemic settings. These results provide new foundational insights into malaria pathogenesis and resilience in kra monkeys, which may improve understanding of human infections.

pathology↗

bioRxiv2021

Effect of artificial light at night on sleep and metabolism in weaver birds

Artificial light at night is constantly minimizing the span of dark nights from the natural light-dark cycle of earth. Over the past century, the lightscape of earth has completely changed owing to technological advancements which subsequently changed the lifestyle of human as well as the nearby animal species. This motivated the present study, wherein we investigated the impact of light at night (LAN) on behavior and physiology of a diurnal passerine finch, baya weaver (Ploceus philippinus). A group of bird (N=10) exposed to 12L:12D photoperiod was initially subjected to dark nights (0 lux) for a period of 10 days followed by 5 lux; night light for a span of 4 weeks. First week in LAN served as acute treatment with respect to fourth week (chronic). Acute exposure had more pronounced impact on the behavioral and physiological observations when compared with chronic treatment. The results reveal significant increase in nighttime activity, sleep loss, significant inclusion of drowsiness behavior during the day in response to LAN. Beside these behavioral alterations, changes in physiological parameters such as; reduction in body mass, loss of gradient between pre- and post-prandial blood glucose levels, elevation in plasma corticosterone levels were more prominent during acute exposure of LAN. Plasma metabolites such as triglycerides, total protein, serum glutamic-oxaloacetic transaminase (SGOT) and creatinine concentrations also hiked in response to LAN treatment. Thus, the study broadly enumerates the impact of acute and chronic exposure of LAN on behavior (rest/sleep) and physiology (metabolism) of birds.

zoology↗

bioRxiv2021

Trichoderma asperellum: First report in Bangladesh

The experiment was conducted at four laboratory, Bangladesh Agricultural University, Mymensingh to identify T. asperellum and its characterization was obtained from the rhizosphere of 49 different crops in 109 different locations of 36 districts in Bangladesh. Fifteen isolates of 88 isolates in T. asperellum were characterized on morphological and physiological features. All of the isolates were produced at 35 {degrees}C, but only TR27 and TR45 were grown and sporulate at 40 {degrees}C. Mycelial growth of all the isolates was reduced with the increasing of pH value. Molecular characterization in four isolates of TR27, TR45, TR70 and TR85 were studied at ITS and TEF region nucleotide sequencing among 15 isolates of T. asperellum and the morphological characterization at ITS and tef1 nucleotide sequencing was assimilated with molecular characterization. The isolates of TR45, TR70 and TR85 were found with 98% homology and TR27 exhibited 88% against their respective closest isolate. The isolates of TR27 and TR85 marked their respective nearest homology at 96%, while TR45 showed 99%, and 93% homology was signified with TR70 in TEF sequences. Three isolates (TR45, TR70 and TR85) were identified as T. asperellum of 100% bootstrap value and TR27 isolate was also recognized with 72% bootstrap value in phylogenetic tree. In phylogenetic analysis, tef1 extended better differentiation among the Trichoderma isolates within and among the groups of closely related species than the rDNA of the ITS region in reflecting wider variability in the isolates while a higher transversion ratio and evolutionary divergence were defined. Moreover the exploring of scientific and useful diversification of Trichoderma isolates on physiological and molecular traits has deemed in research fields. IMPORTANCETrichoderma is an important genus in different aspect of uses as biofertilizer and bioremediation in agriculture. Specific identification in physiological and molecular characterization has also foremost attention with genome sequences as stored in databases. The diversity and genetic distances were ascertained among the isolates in phylogenetic analysis with the sequence data of the ITS region and tef1 of known Trichoderma strains was found in GenBank. Consequently, the databases of Trichoderma asperellum in molecular characterization can be frequently studied in the beneficial scope of agriculture. Trichoderma isolates of Rhizosphere soil in 4 locations with crops of (TR27) Sadar, Moulvibazar (Rice), (TR45) Sadar, Mymensingh (Sweet gourd), (TR70) Chapra, Chapai Nawabganj (Sesame) and (TR85) Nayanpur, Lalmonirhat (Maize) were found to be substantiated as Trichoderma asperellum strain in Bangladesh that were confirmed on physiological and molecular characters, and utilization of this strain can run faster in invasive technologies to control crop diseases.

molecular biology↗

bioRxiv2021

Comparison of Plaque Size, Thermal Stability, and Replication Rate among SARS-CoV-2 Variants of Concern

SARS-CoV-2, like other RNA viruses, has a propensity for genetic evolution owing to the low fidelity of its viral polymerase. This evolution results in the emergence of novel variants with different characteristics than their ancestral strain. Several recent reports have described a series of novel SARS-CoV-2 variants. Some of these have been identified as variants of concern (VOCs), including alpha (B.1.1.7, Clade GRY), beta (B.1.351, Clade GH), gamma (P.1, Clade GR), and delta (B.1.617.2, Clade G). VOCs are likely to have some effect on transmissibility, antibody evasion, and changes in therapeutic or vaccine effectiveness. However, the physiological and virological understanding of these variants remains poor. We demonstrated that these four VOCs exhibited differences in plaque size, thermal stability at physiological temperature, and replication rates. The mean plaque size of beta was the largest, followed by those of gamma, delta, and alpha. Thermal stability, evaluated by measuring infectivity and half-life after prolonged incubation at physiological temperature, was correlated with plaque size in all variants except alpha. However, despite its relatively high thermal stability, alphas small plaque size resulted in lower replication rates and fewer progeny viruses. Our findings may inform further virological studies of SARS-CoV-2 variant characteristics, VOCs, and variants of interest. These studies are important for the effective management of the COVID-19 pandemic. IMPORTANCEThe global pandemic caused by SARS-CoV-2 continues to persist, due in part to mutations that have resulted in the emergence of different variants. Many of these variants have become more virulent and infectious than their ancestral strain, resulting in an ever-increasing spread. However, our virological understanding of these variants remains poor. Here, we directly compared the plaque size, stability, and replication kinetics of four SARS-CoV-2 variants of concern following prolonged incubation at physiological temperatures. Our observations may help to characterize each variant in terms of their interactions with host factors and responses to environmental conditions. We also believe that our evaluations will improve understanding of the emergence of new variants and contribute to controlling their spread.

microbiology↗

bioRxiv2021

Bottom-up and top-down effects of temperature on body growth, population size spectra and yield in a size-structured food web

Resolving the combined effect of climate warming and exploitation in a food web context is key for predicting future biomass production, size-structure, and potential yields of marine fishes. Previous studies based on mechanistic size-based food web models have found that bottom-up processes are important drivers of size-structure and fisheries yield in changing climates. However, we know less about the joint effects of bottom-up and physiological effects of temperature; how do temperature effects propagate from individual-level physiology through food webs and alter the size-structure of exploited species in a community? Here we assess how a species-resolved size-based food web is affected by warming through both these pathways, and by exploitation. We parameterize a dynamic size spectrum food web model inspired by the offshore Baltic Sea food web, and investigate how individual growth rates, size-structure, relative abundances of species and yields are affected by warming. The magnitude of warming is based on projections by the regional coupled model system RCA4-NEMO and the RCP 8.5 emission scenario, and we evaluate different scenarios of temperature dependence on fish physiology and resource productivity. When accounting for temperature-effects on physiology in addition to on basal productivity, projected size-at-age in 2050 increases on average for all fish species, mainly for young fish, compared to scenarios without warming. In contrast, size-at-age decreases when temperature affects resource dynamics only, and the decline is largest for young fish. Faster growth rates due to warming, however, do not always translate to larger yields, as lower resource carrying capacities with increasing temperature tend to result in declines in the abundance of larger fish and hence spawning stock biomass. These results suggest that to understand how global warming affects the size structure of fish communities, both direct metabolic effects and indirect effects of temperature via basal resources must be accounted for.

ecology↗

bioRxiv2021

Genome-scale modeling specifies the metabolic capabilities of Rhizophagus irregularis

Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here we used all published genomics, transcriptomics, and metabolomics resources to gain insights in the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to: (1) accurately predict increased growth of R. irregularis on myristate with minimal medium; (2) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation ({rho}S = 0.74) to measured hyphal dry weight; and (3) simulated growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance. ImportanceMounting evidence points at the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; yet, the molecular mechanisms underlying the physiological responses of this fungus to different host plants and environments remain largely unknown. We present a manually curated, enzyme-constrained genome-scale metabolic model of R. irregularis that can accurately predict experimentally observed phenotypes. We show that this high-quality model provides an entry point into better understanding the metabolic and physiological responses of this fungus to changing environments due to the availability of different nutrients. The model can be used to design metabolic engineering strategies to tailor R. irregularis metabolism towards improving the performance of host plants.

systems biology↗

bioRxiv2021

Pupillometry and electroencephalography in the digit span task

This dataset consists of raw 64-channel EEG, cardiovascular (electrocardiography and photoplethysmography), and pupillometry data from 86 human participants recorded during 4 minutes of eyes-closed resting and during performance of a classic working memory task - digit span task with serial recall. The participants either memorized or just listened to sequences of 5, 9, or 13 digits presented auditorily every 2 seconds. The dataset can be used for (1) developing algorithms for cognitive load discrimination and detection of cognitive overload; (2) studying neural (event-related potentials and brain oscillations) and peripheral (electrocardiography, photoplethysmography, and pupillometry) physiological signals during encoding and maintenance of each sequentially presented memory item; (3) correlating cognitive load and individual differences in working memory to neural and peripheral physiology, and studying the relationship between the physiological signals; (4) integration of the physiological findings with the vast knowledge coming from behavioral studies of verbal working memory in simple span paradigms. The data are shared in Brain Imaging Data Structure (BIDS) format and freely available on OpenNeuro (https://openneuro.org/datasets/ds003838).

neuroscience↗

bioRxiv2021

Investigating the genetic and environmental basis of head micromovements during MRI

IntroductionHead motion during magnetic resonance imaging is heritable. Further, it shares phenotypical and genetic variance with body mass index (BMI) and impulsivity. Yet, to what extent this trait is related to single genetic variants and physiological or behavioral features is unknown. We investigated the genetic basis of head motion in a meta-analysis of genome-wide association studies. Further, we tested whether physiological or psychological measures, such as respiratory rate or impulsivity, mediated the relationship between BMI and head motion. MethodsWe conducted a genome-wide association meta-analysis for mean and maximal framewise head displacement (FD) in seven population neuroimaging cohorts (UK Biobank, LIFE-Adult, Rotterdam Study cohort 1-3, Austrian Stroke Prevention Family Study, Study of Health in Pomerania; total N = 35.109). We performed a pre-registered analysis to test whether respiratory rate, respiratory volume, self-reported impulsivity and heart rate mediated the relationship between BMI and mean FD in LIFE-Adult. ResultsNo variant reached genome-wide significance for neither mean nor maximal FD. Neither physiological nor psychological measures mediated the relationship between BMI and head motion. ConclusionBased on these findings from a large meta-GWAS and pre-registered follow-up study, we conclude that the previously reported genetic correlation between BMI and head motion relies on polygenic variation, and that neither psychological nor simple physiological parameters explain a substantial amount of variance in the association of BMI and head motion. Future imaging studies should thus rigorously control for head motion at acquisition and during preprocessing.

neuroscience↗

bioRxiv2021

Paradoxical excitation of lateral habenula neurons by propofol involves enhanced presynaptic release of glutamate

Sleep is a fundamental physiological process conserved across most species. As such, deficits in sleep can result in a myriad of psychological and physical health issues. However, the mechanisms underlying the induction of sleep are relatively unknown. Interestingly, general anesthetics cause unconsciousness by positively modulating GABA-A receptors (GABAARs). Based on this observation, it is hypothesized that GABAARs play a critical role in modulating circuits involved in sleep to promote unconsciousness. Recently, the lateral habenula (LHb) has been demonstrated to play a role in sleep physiology and sedation. Specifically, propofol has been shown to excite LHb neurons to promote sedation. However, the mechanism by which this occurs is unknown. Here, we utilize whole-cell voltage and current clamp recordings from LHb neurons obtained from 8-10 week old male mice to determine the physiological mechanisms for this phenomenon. We show that bath application of 1.5M propofol is sufficient to increase LHb neuronal excitability involving synaptic transmission, but not through modulation of intrinsic properties. Additionally, although there is increased LHb neuronal excitability, GABAARs localized postsynaptically on LHb neurons are still responsive to propofol, as indicated by an increase in the decay time. Lastly, we find that propofol increases the synaptic drive onto LHb neurons involving enhanced presynaptic release of both glutamate and GABA. However, the greatest contributor to the potentiated synaptic drive is the increased release of glutamate which shifts the balance of synaptic transmission towards greater excitation. Taken together, this study is the first to identify the physiological basis for why LHb neurons are excited by propofol, rather than inhibited, and as a result promote sedation.

neuroscience↗