title: Capturing scientific knowledge in computable form

abstract:
Technological advances in computing provide major opportunities to accelerate scientific discovery. The wide availability of structured knowledge would allow us to take full advantage of these by enabling efficient human-computer interaction. Traditionally, biological knowledge is captured in publications and knowledge bases, however, the information in articles is not directly accessible to computers, and knowledge bases are constrained by finite resources available for manual curation. To accelerate knowledge capture and communication and to keep pace with the rapid growth of scientific reports, we developed the Biofactoid (biofactoid.org) software suite, which crowdsources structured knowledge in articles from authors. Biofactoid is a web-based system that lets scientists draw a network of interactions between genes, their products, and chemical compounds and employs smart-automation to translate user input into a structured language using the expressive power of a formal ontology. The resulting data is shared via public information resources, enabling author-curated knowledge to be appreciated in the context of all existing computable knowledge. Authors of recently published papers across a range of journals have already contributed their pathway information, much of which is novel and extends existing pathway databases into new biological areas. We envision the adoption of Biofactoid for crowdsourced curation by scientists and publishers as part of an ecosystem of tools that accelerate scientific communication and discovery.

AvailabilityBiofactoid server at https://biofactoid.org

category: bioinformatics


title: Phylogeography, codon usage, and DNA barcoding of lesser short nosed fruit bat (Cynopterus brachyotis Muller, 1838) populations in Indonesia

abstract: Fruit bat (Pteropodidae) is one of the mammals that is common in environments and widely distributed from subtropical to tropical Asia. Whereas the information on phylogeography of fruit bat Cynopterus brachyotis is still limited. From this situation, this paper aims to assess the phylogeography, codon usage, and DNA barcoding of C. brachyotis populations in Indonesia. Phylogeography was developed based on 657 bp of the mtDNA COI gene for all bat individuals and Bayesian inference to construct the phylogeny tree. The C. brachyotis populations in Indonesia are different to the populations from the Asias continent. The results show that C. brachyotis populations in Indonesia were divided into 3 distinct clades. A putative geographical barrier, recent, and rapid range expansion in the Sunda lineage associated with changes in sea levels, possibly coupled with related ecological differences, may have driven population divergence, allopatric, and sympatric speciation. Codon usage and high frequency were also contributing to the dispersal of C. brachyotis forming a distinct population.

category: ecology


title: Cooperative herbivory between two important pests of rice

abstract: Normally, when different species of herbivorous arthropods feed on the same plant this leads to fitness reducing competition. We found this to be uniquely different for two of Asias most destructive rice pests, the brown planthopper and the rice striped stem borer. Both insects directly and indirectly benefit from jointly attacking the same host plant. Double infestation improved plant quality, particularly for the stemborer because the planthopper fully suppresses caterpillar-induced production of proteinase inhibitors. It also drastically reduced the risk of egg parasitism, due to diminished parasitoid attraction. Females of both pests have adapted their oviposition behaviour accordingly. Their strong preference for plants infested by the other species even overrides their avoidance of plants already attacked by conspecifics. This uncovered cooperation between herbivores is telling of the exceptional adaptations resulting from the evolution of plant-insect interactions, and points out mechanistic vulnerabilities that can be targeted to control two major pests.


title: Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European range

abstract: The application of demographic history modeling and inference to the study of divergence between species is becoming a cornerstone of speciation genomics. The demographic history is usually reconstructed by analysing a single population from each species, assuming that the divergence history inferred between these populations represents the actual speciation history. However, this assumption is rarely explicitly tested, and it may not be met when species diverge with gene flow. For instance, secondary contact between two species after a range expansion may be confined into a specific geographic region. In this study, we tested to what extent the divergence history inferred from two heterospecific populations would vary depending on their geographic locations, using mound-building red wood ants. The wood ant species Formica polyctena and F. aquilonia have contrasting distributions in Europe and naturally hybridize in Finland. We first performed whole-genome resequencing of 20 individuals sampled in multiple populations across both species ranges. We then reconstructed the divergence histories of distinct heterospecific population pairs using a coalescent-based approach. We found that the analysis of these different population pairs always supported a scenario of divergence with gene flow, suggesting that species divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration stopped (2-19 kya, depending on the population pair considered). However, we found support for contemporary gene flow in the sympatric population pair from Finland, where hybrids have been described. Overall, our results suggest that divergence histories reconstructed from a few individuals may be reliable and applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is heterogeneous across their geographical ranges.

category: evolutionary biology


title: Corticosterone differentially modulates time-dependent fear generalization following mild or moderate fear conditioning training in rats

abstract:
Stressful and emotionally arousing experiences create strong memories that seem to lose specificity over time. It is uncertain, however, how the stress system contributes to the phenomenon of time-dependent fear generalization. Here, we investigated whether post-training corticosterone (CORT-HBC) injections, given after different training intensities, affect contextual fear memory specificity at several time points. We trained male Wistar rats on the contextual fear conditioning (CFC) task using two footshock intensities (mild CFC, 3 footshocks of 0.3 mA, or moderate CFC, 3x 0.6 mA) and immediately after the training session we administered CORT-HBC systemically. We first tested the animals in a novel context and then in the training context at different intervals following training (2, 14, 28 or 42 days). By measuring freezing in the novel context and then contrasting freezing times shown in both contexts, we inferred contextual fear generalization for each rat, classifying them into Generalizers or Discriminators. Following mild CFC training, the glucocorticoid injection promoted an accurate contextual memory at the recent time point (2 days), and increase the contextual memory accuracy 28 days after training. In contrast, after the moderate CFC training, CORT-HBC facilitated contextual generalization at 14 days, compared to the control group that maintained contextual discrimination at this timepoint. For this training intensity, however, CORT-HBC did not have any effect on recent memory specificity. These findings indicate that treatment with CORT-HBC immediately after the encoding of mild or moderately arousing experiences may differentially modulate memory consolidation and time-dependent fear generalization.

HIGHLIGHTS- Rats were trained in a contextual fear task and tested for fear generalization.
- Corticosterone (CORT) injected after a mild training promoted accuracy up to 28 days.
- CORT injected after a moderate training facilitated time-dependent fear generalization.

category: animal behavior and cognition


title: Low-Cost, Modular Modification to a Desktop 3D Printer for General Purpose Gel/Paste Extrusion & Direct Ink Writing

abstract: We propose a design for a simple paste extruder modification that can be used for the selective deposition and patterning of gels and pastes, using a desktop 3D printer as the primary platform. This technology has found use with a variety of materials in seemingly disparate fields, including the printing of ceramics, food and biological materials, each with a variety of material-specific solutions to enhance printability. However, we focus on a syringe-pump driven system that is simple, low-cost, modular, easily assembled and highly modifiable with a low barrier of entry in order to maximise the generalisability and range of printable materials.

category: bioengineering


title: A Comparative Analysis of Novel Deep Learning Models and Ensemble Learning Models to Predict the Allergenicity of Food Allergens

abstract: Traditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned two drawbacks and is becoming an efficient auxiliary tool. Aiming to overcome the limitations of lower accuracy of traditional machine learning models in predicting the allergenicity of food proteins, this work proposed to introduce deep learning model - transformer with self-attention mechanism, ensemble learning models (representative as Light Gradient Boosting Machine (LightGBM) eXtreme Gradient Boosting (XGBoost)) to solve the problem. In order to highlight the superiority of the proposed novel method, the study also selected various commonly used machine learning models as the baseline classifiers. The results of 5-fold cross-validation showed that the AUC of the deep model was the highest (0.9578), which was better than the ensemble learning and baseline algorithms. But the deep model need to be pre-trained, and the training cost is the highest. By comparing the characteristics of the transformer model and boosting models, it can be analyzed that, each model has its own advantage, which provides novel clues and inspiration for the rapid prediction of food allergens in the future.


title: A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins


title: New opabiniid diversifies the weirdest wonders of the euarthropod lower stem group

abstract:
Once considered  weird wonders of the Cambrian, the emblematic Burgess Shale animals Anomalocaris and Opabinia are now recognized as lower stem-group euarthropods. Anomalocaris and its relatives (radiodonts) had a worldwide distribution and survived until at least the Devonian, whereas - despite intense study - Opabinia remains the only formally described opabiniid to date. Here we reinterpret a fossil from the Wheeler Formation of Utah as a new opabiniid, KUMIP 314087. By visualizing the sample of phylogenetic topologies in treespace, our results fortify support for the position of KUMIP 314087 beyond the nodal support traditionally applied. Our phylogenetic evidence expands opabiniids to multiple Cambrian Stages spanning approximately five million years. Our results underscore the power of treespace visualization for resolving imperfectly preserved fossils and expanding the known diversity and spatiotemporal ranges within the euarthropod lower stem group.

Additional noteThis work contains a new biological name. New names in preprints are not considered available by the ICZN. To avoid ambiguity, the new biological name is not included in this preprint, and the specimen number (KUMIP 314087) is used as a placeholder.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/434726v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@e770aaorg.highwire.dtl.DTLVardef@95bbd3org.highwire.dtl.DTLVardef@5e460eorg.highwire.dtl.DTLVardef@1494152_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOCover image.C_FLOATNO Artistic reconstruction of the new opabiniid from the Wheeler Formation, Utah, USA (Cambrian: Drumian). Artwork by F. Anthony.

C_FIG

category: paleontology


title: The rise and fall of the photoinhibition-related energy dissipation qI

abstract:
Photosynthesis converts sunlight into chemical energy, sustaining the vast majority of the biosphere. Photosystem II (PSII), the oxygen-forming enzyme that initiates photosynthesis, is however particularly prone to light-induced damage in a process known as photoinhibition, which limits the productivity of both aquatic and land photosynthesis. Photoinhibition is associated with an energy dissipation process of unknown origin, termed qI. Here, we present a detailed biophysical and biochemical in vivo study of qI in model green alga Chlamydomonas reinhardtii. Time-resolved fluorescence measurements demonstrate the origin of qI, and indicate the PSII reaction centre as the site of the quencher. Oxygen-dependence of quenching site formation, but not photoinhibition itself, is shown, suggesting that two types of PSII damage - donor and acceptor-side impairment - can be separated. We then demonstrate that the quenching loss takes place in the absence of PSII repair, and is mediated by the degradation of photoinhibited PSII cores by the FtsH protease. Finally, we integrate data ranging from picoseconds to hours in the context of structure-function excitation energy-transferring membrane patches, revealing the extent of PSII heterogeneity from the onset of photoinhibition until the breakdown of damaged PSII.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/434601v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@d7c64dorg.highwire.dtl.DTLVardef@1c2943org.highwire.dtl.DTLVardef@d90b83org.highwire.dtl.DTLVardef@182cd12_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIUpon photoinhibition, oxygen sensitization results in an irreversible formation of quenching (qI) and inactivation of Photosystem II
C_LIO_LIqI takes place in the PSII reaction centre
C_LIO_LIPhotoinhibition-induced D1 cleavage is much slower than qI formation
C_LIO_LIFtsH metalloprotease is required to degrade quenching PSII reaction centres
C_LIO_LIA multiscale energy transfer model describes heterogeneity of PSII during photoinhibition
C_LI

category: plant biology


title: Predicting the fitness costs of complex mutations

abstract: The fitness cost of complex pleiotropic mutations is generally difficult to assess. On the one hand, it is necessary to identify which molecular properties are directly altered by the mutation. On the other, this alteration modifies the activity of many genetic targets with uncertain consequences. Here, we examine the possibility of addressing these challenges by identifying unique predictors of these costs. To this aim, we consider mutations in the RNA polymerase (RNAP) in Escherichia coli as a model of complex mutations. Changes in RNAP modify the global program of transcriptional regulation, with many consequences. Among others is the difficulty to decouple the direct effect of the mutation from the response of the whole system to such mutation. A problem that we solve quantitatively with data of a set of constitutive genes, which better read the global program. We provide a statistical framework that incorporates the direct effects and other molecular variables linked to this program as predictors, which leads to the identification that some genes are more suitable predictors than others. Therefore, we not only identified which molecular properties best anticipate costs in fitness, but we also present the paradoxical result that, despite pleiotropy, specific genes serve as better predictors. These results have connotations for the understanding of the architecture of robustness in biological systems.

category: systems biology


title: Excitatory postsynaptic calcium transients at Aplysia sensory-motor neuron synapses allow for quantal examination of synaptic strength over multiple days in culture

abstract: The ability to monitor changes in strength at individual synaptic contacts is required to test the hypothesis that specialized synapses maintain changes in synaptic strength that underlie memory. Measuring excitatory post-synaptic calcium transients through calcium permeable AMPA receptors is one way to monitor synaptic strength at individual synaptic contacts. Using a membrane targeted genetic calcium sensor, we demonstrate that one can measure synaptic events at individual synaptic contacts in Aplysia sensory-motor neuron synapses. These results show that synaptic strength is not evenly distributed between all contacts in these cultures, but dominated by multiquantal sites of synaptic contact. The probability, quantal size and quantal content can be measured over days at individual synaptic contacts using this technique. Surprisingly, most synaptic contacts were not found opposite presynaptic varicosities, but instead at areas of pre- and post-synaptic contact with no visible thickening of membranes. This technique shows promise in being able to address whether specialized synapses maintain synaptic strength underlying memory.

category: neuroscience


title: Distinct generation of subjective vividness and confidence during naturalistic memory retrieval in angular gyrus

abstract: Our subjective experience of remembering guides and monitors the reconstruction of past and simulation of the future, which enables us to identify mistakes and adjust our behavior accordingly. However, it remains incompletely understood what underlies the process of subjective mnemonic experience. Here, we combined behavior, repetitive transcranial magnetic stimulation (rTMS), and functional neuroimaging to probe whether vividness and confidence are generated differently during retrieval. We found that preretrieval rTMS targeting the left angular gyrus (AnG) selectively attenuated the vividness efficiency compared to control stimulation while keeping metacognitive efficiency and objective memory accuracy unaffected. Using trial-wise data, we showed that AnG stimulation altered the mediating role of vividness in confidence in the accuracy of memory judgment. Moreover, resting-state functional connectivity of hippocampus and AnG was specifically associated with vividness efficiency, but not metacognitive efficiency across individuals. Together, these results identify the causal involvement of AnG in gauging the vividness, but not the confidence, of memory, thereby suggesting a differentiation account of conscious assessment of memory by functionally and anatomically dissociating the monitoring of vividness from confidence.


title: Diversify your workflow! - An inconvenient suggestion to analyze spike data from intracranial recordings

abstract: An important challenge of neuroscience research and future brain machine interfacing is the reliable assignment of spikes to putative neurons. By means of extracellular recordings, researchers try to match different types action potentials with their putative neuronal source and timing. Unfortunately, this procedure is by far not standardized and reliable, leading to many different suggestions and as many differing results. It appears that sharing of data is thus hampered by different processing pipelines in different labs, thus playing along the reproducibility crisis in neurosciences. To systematically shed light on this issue, we present preliminary results of several easy event detection schemes on one data set, meant to illustrate the inconsistencies arising from different processing pipelines already in its initial step. The results indicate that thresholding choices alter findings due to a lack of a ground truth for spike sorting. We suggest to increase reliability in findings by only accepting and further processing events accepted by more than one processing pipeline.


title: Neural Basis of the Delayed Gratification

abstract:
Balancing instant gratification versus delayed, but better gratification is important for optimizing survival and reproductive success. Although psychologists and neuroscientists have long attempted to study delayed gratification through human psychological and brain activity monitoring, and animal research, little is known about its neural basis. We successfully trained mice to perform a waiting-and-water-reward delayed gratification task and used these animals in physiological recording and optical manipulation of neuronal activity during the task to explore its neural basis. Our results showed that the activity of DA neurons in ventral tegmental area (VTA) increases steadily during the waiting period. Optical activation vs. silencing of these neurons, respectively, extends or reduces the duration of waiting. To interpret this data, we developed a reinforcement learning (RL) model that reproduces our experimental observations. In this model, steady increases in DAergic activity signal the value of waiting and support the hypothesis that delayed gratification involves real-time deliberation.

TEASERSustained ramping dopaminergic activation helps individuals to resist impulsivity and wait for laerger but later return.


title: The Neural Basis of Delayed Gratification


title: Low intensity repetitive transcranial magnetic stimulation drives structural synaptic plasticity in the young and aged motor cortex.

abstract:
BackgroundRepetitive transcranial magnetic stimulation (rTMS) is a non-invasive tool commonly used to drive neural plasticity in the young adult and aged brain. Recent data from mouse models have shown that even at subthreshold intensities (0.12 Tesla), rTMS can drive neuronal and glial plasticity in the motor cortex. However, the physiological mechanisms underlying subthreshold rTMS induced plasticity and whether these are altered with normal ageing are unclear.

ObjectiveTo assess the effect of subthreshold rTMS, using the intermittent theta burst stimulation (iTBS) protocol on structural synaptic plasticity in the mouse motor cortex of young and aged mice.

MethodsLongitudinal in vivo 2-photon microscopy was used to measure changes to the structural plasticity of pyramidal neuron dendritic spines in the motor cortex following a single train of subthreshold rTMS (in young adult and aged animals) or the same rTMS train administered on 4 consecutive days (in young adult animals only). Data were analysed with Bayesian hierarchical generalized linear regression models and interpreted with the aid of Bayes Factors (BF).

ResultsWe found strong evidence (BF>10) that subthreshold rTMS altered the rate of dendritic spine losses and gains, dependent on the number of stimulation sessions and that a single session of subthreshold rTMS was effective in driving structural synaptic plasticity in both young adult and aged mice.

ConclusionThese findings provide further evidence that rTMS drives synaptic plasticity in the brain and uncovers structural synaptic plasticity as a key mechanism of subthreshold rTMS induced plasticity.


title: Subthreshold repetitive transcranial magnetic stimulation drives structural synaptic plasticity in the young and aged motor cortex.


title: The feedback regulator Nord controls Dpp/BMP signaling via extracellular interaction with Dally in the Drosophila wing

abstract:
The Drosophila BMP 2/4 homologue Decapentaplegic (Dpp) acts as a morphogen to regulate diverse developmental processes, including wing morphogenesis. Transcriptional feedback regulation of this pathway ensures tightly controlled signaling outputs to generate the precise pattern of the adult wing. Nevertheless, few direct Dpp target genes have been explored and our understanding of feedback regulation remains incomplete. Here, we employ transcriptional profiling following dpp conditional knockout to identify nord, a novel Dpp/BMP feedback regulator. Nord mutants generated by CRISPR/Cas9 mutagenesis produce a smaller wing and display low penetrance venation defects. At the molecular level, nord encodes a heparin-binding protein and we show that its overexpression is sufficient to antagonize Dpp/BMP signaling. Further, we demonstrate that Nord physically and genetically interacts with the Dpp/BMP co-receptor Dally. In sum we propose that Nord acts with Dally to fine tune Dpp/BMP signaling, with implications for both developmental and disease models.

Impact statementFunctional analyses of the Drosophila homologue of Neuron Derived Neurotrophic Factor reveal a new mode of extracellular heparan sulfate proteoglycan regulation required for proper morphogen action.

category: developmental biology


title: Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte

abstract:
Histone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) oocytes using ultra-low input ChIP-seq, with comparisons to DNA methylation and gene expression analyses. H3K4me3 was redistributed in Setd1b cKO oocytes showing losses at active gene promoters associated with downregulated gene expression. Remarkably, many regions also gained H3K4me3, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich, which are hallmarks of MLL2 targets. Consequently, loss of SETD1B disrupts the balance between MLL2 and de novo DNA methyltransferases in determining the epigenetic landscape during oogenesis. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression and MLL2 to CpG content.

Graphical AbstractIn oogenesis, SETD1B and CXXC1 target H3K4me3 to actively transcribed gene promoters, while MLL2 targets transcriptionally inactive regions based on underlying CpG composition (upper panel). When SETD1B is ablated, H3K4me3 is lost at a subset of active promoters, resulting in downregulation of transcription (lower panel). Loss of SETD1B alters the activity of MLL2, permitting MLL2 to deposit H3K4me3 at CpG-rich regions, many of which should otherwise be DNA methylated. Thus, it is evident that MLL2 and de novo DNMTs compete for genomic occupancy late in oogenesis, and loss of SETD1B disrupts the balance of these mechanisms.

O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation


title: The zebrafish presomitic mesoderm elongates through compression-extension

abstract: In vertebrate embryos the presomitic mesoderm become progressively segmented into somites at the anterior end while extending along the anterior-posterior axis. A commonly adopted model to explain how this tissue elongates is that of posterior growth, driven in part by the addition of new cells from uncommitted progenitor populations in the tailbud. However, in zebrafish, much of somitogenesis is associated with an absence of overall volume increase and posterior progenitors do not contribute new cells until the final stages of somitogenesis. Here, we perform a comprehensive 3D morphometric analysis of the paraxial mesoderm and reveal that extension is linked to a volumetric decrease, compression in both dorsal-ventral and medio-lateral axes, and an increase in cell density. We also find that individual cells decrease in their cell volume over successive somite stages. Live cell tracking confirms that much of this tissue deformation occurs within the presomitic mesoderm progenitor zone and is associated with non-directional rearrangement. Furthermore, unlike the trunk somites that are laid down during gastrulation, tail somites develop from a tissue that can continue to elongate in the absence of functional PCP signalling. Taken together, we propose a compression-extension mechanism of tissue elongation that highlights the need to better understand the role of tissue intrinsic and extrinsic forces play in regulating morphogenesis.


title: Beyond residence time: quantifying factors that drive the spatially explicit filtration services of a 'pristine' oyster population

abstract: The Guana-Tolomato-Matanzas (GTM) system is a relatively pristine and well-flushed estuary in Northeastern Florida, USA and characterized as having an extraordinarily high abundance of oysters. Historically, dense populations of oysters, such as those found in GTM, are believed to play an important role in water filtration; however, few biofiltration studies have had access to such pristine populations. To quantify the filtration service (FS) of Eastern oysters (Crassostrea virginica) in GTM at several spatial scales (i.e. reef, watershed, estuary), we implemented a model that solves for the hydrodynamics and depletion of particulate matter passing over model oyster populations, the latter of which were derived from detailed bay-wide surveys. The model results suggested that oyster reefs populating the GTM play an important role in water quality by filtering ~60% of the estuarys volume within its residence time. Our approach teases apart the role of reef size, residence time, particle concentration, and other physical factors on the generation of FS at different spatial scales. Downstream effects were found to be very important for estuary FS, which depend on the spatial distribution of the reefs in the GTM and local and estuarine-scale hydrodynamics. Therefore, the difference between "realized" FS and the "potential" FS of a given reef may be substantial when considering the complex hydrodynamic and connectivity among populations at several scales. Our model results provide clear and actionable information for management of these oyster populations and conservation of their ecosystem services.


title: Pool choice in a vertical landscape: tadpole rearing site flexibility in phytotelm-breeding frogs

abstract: Many species of Neotropical frogs have evolved to deposit their tadpoles in small water bodies inside plant structures called phytotelmata. These pools are small enough to exclude large predators but have limited nutrients and high desiccation risk. Here, we explore phytotelm use by three common Neotropical species: Osteocephalus oophagus, an arboreal frog that periodically feeds eggs to its tadpoles; Dendrobates tinctorius, a tadpole-transporting poison frog with cannibalistic tadpoles; and Allobates femoralis, a terrestrial tadpole-transporting poison frog with omnivorous tadpoles. We found that D. tinctorius occupies pools across the chemical and vertical gradient, whereas A. femoralis and O. oophagus appear to have narrower niches that are restricted primarily by pool height, water capacity, alkalinity, and salinity. Dendrobates tinctorius tadpoles are particularly flexible, and can survive in a wide range of chemical, physical, and biological conditions, whereas O. oophagus seems to prefer small, clear pools and A. femoralis occupies medium-sized pools with abundant leaf litter and low salinity. Together, these results show the possible niche partitioning of phytotelmata among frogs, and provide insight into stressors and resilience of phytotelm breeders.


title: Complex landscapes partially mitigate negative pesticide effects on tropical pollinator communities

abstract:
Land-use change and pesticides have been identified as two of the main causes behind pollinator decline. Understanding how these factors affect crop pollinator communities is crucial to inform practices that generate optimal pollination and ensure sustainable food production. In this study, we investigated the effects of landscape composition and pesticide residues on bee communities and their pollination services in Solanum quitoense "lulo" crops in Colombia. On 10 farms, located along a gradient of landscape complexity that varied from 0.15 to 0.62 in their natural habitat proportion, we characterized the bee community visiting the crop, and carried out pollination experiments with bagged and open inflorescences to later estimate fruit set, weight, and diameter at every site. Additionally, we performed pesticide analysis on collected anthers through liquid chromatography to estimate pesticide risk coming from the crop fields using hazard quotients (HQ). Bee abundance and species richness decreased with increased HQ, but these negative pesticide effects were less detrimental in farms with higher natural habitat proportions. However, this buffer effect was lost at sites with very high HQs. Imidacloprid was frequently found in the anthers and there were extremely high concentrations in some farms (0.6 to 13063 g/kg), representing the molecule of greater risk for bees in this context. Pollinators importance to crop yield was demonstrated in the exclusion experiments, where we found a reduction in fruit set (51%), weight (39%), and diameter (25%). We found a significant effect of bee richness on fruit set, while landscape composition and HQ had no significant effect on fruit set, suggesting that the last two factors do not affect yield directly, but indirectly through a decrease in pollinator diversity. Our results provide novel evidence that the natural habitat loss due to the expansion of pastures for cattle ranching and pesticide residues in anthers reduce bee diversity and abundance in this Andean cropping system, but strategies to protect and restore natural habitat can help to buffer, until certain levels, these negative effects.

Highlights- We explored how landscape composition and pesticide residues impact bee communities and pollination services in Solanum quitoense crops.
- As the proportion of natural habitat in the landscape increased, bee richness also increased. While as pesticide hazard quotients in S. quitoense anthers increased, bee diversity and abundance decreased.
- The natural habitat surrounding farms mitigates the negative pesticide effects on bees when hazard quotients are low/medium, but not when they are high.
- S. quitoense crops are highly dependent on bees for optimum yield.


title: Genomic heterogeneity affects the response to Daylight Saving Time

abstract: Circadian rhythms drive the timing of many physiological events in the 24-hour day. When individuals undergo an abrupt external shift (e.g., change in work schedule or travel across multiple time zones), circadian rhythms become misaligned with the new time and may take several days to adjust. Chronic circadian misalignment, e.g., as a result of shift work, has been shown to lead to several physical and mental health problems. Despite the serious health implications of circadian misalignment, relatively little is known about how genetic variation affects an individuals ability to shift to abrupt external changes. Accordingly, we use the one-hour advance from the onset of daylight saving time (DST) as a natural experiment to comprehensively study how individual heterogeneity affects the shift of sleep-wake rhythms in response to an abrupt external time change. We find that individuals genetically predisposed to a morning tendency adjust to the advance in a few days, while genetically predisposed evening-inclined individuals have not shifted. Observing differential effects by genetic disposition after a one-hour advance underscores the importance of heterogeneity in adaptation to external schedule shifts, and these genetic differences may affect how individuals adjust to jet lag or shift work as well.

category: genomics


title: Generalized Hierarchical Mixed Model Association Analysis

abstract: In genome-wide association analysis for complex diseases, we partitioned the genomic generalized linear mixed model (GLMM) into two hierarchies--the GLMM regarding genomic breeding values (GBVs) and a generalized linear regression of the GBVs to the tested marker effects. In the first hierarchy, the GBVs were predicted by solving for the genomic best linear unbiased prediction for GLMM, and in the second hierarchy, association tests were performed using the generalized least square (GLS) method. The so-called Hi-GLMM method exhibited advantages over existing methods in terms of both genomic control for complex population structure and statistical power to detect quantitative trait nucleotides (QTNs), especially when the GBVs were estimated precisely, and using joint association analysis for QTN candidates obtained from a test at once.


title: Efficient Genomic Control for Mixed Model Associationsin Large-scale Population

abstract: Among linear mixed model-based association methods, GRAMMAR has the lowest computing complexity for association tests, but it produces a high false-negative rate due to the deflation of test statistics for complex population structure. Here, we present an optimized GRAMMAR method by efficient genomic control, Optim-GRAMMAR, that estimates the phenotype residuals by regulating downward genomic heritability in the genomic best linear unbiased prediction. Even though using the fewer sampling markers to evaluate genomic relationship matrices and genomic controls, Optim-GRAMMAR retains a similar statistical power to the exact mixed model association analysis, which infers an extremely efficient approach to handle large-scale data. Moreover, joint association analysis significantly improved statistical power over existing methods.


title: GRAMMAR-Lambda: An Extreme Simplification for Genome-wide Mixed Model Association Analysis

abstract: A highly efficient genome-wide association method, GRAMMAR-Lambda is proposed to make simple genomic control for the test statistics deflated by GRAMMAR, producing statistical power as high as exact mixed model association method. Using the simulated and real phenotypes, we show that at a moderate or above genomic heritability, polygenic effects can be estimated using a small number of randomly selected markers, which extremely simplify genome-wide association analysis with an approximate computational complexity to naive method in large-scale complex population. Upon a test at once, joint association analysis offers significant increase in statistical power over existing methods.


title: Structured illumination microscopy with noise-controlled image reconstructions

abstract: Super-resolution structured illumination microscopy (SIM) has become a widely used method for biological imaging. Standard reconstruction algorithms, however, are prone to generate noise-specific artefacts that limit their applicability for lower signal-to-noise data. Here, we present a physically realistic noise model that explains the structured noise artefact and that is used to motivate new complementary reconstruction approaches. True Wiener-filtered SIM optimizes contrast given the available signal-to-noise ratio, flat-noise SIM fully overcomes the structured noise artefact while maintaining resolving power. Both methods eliminate ad-hoc user adjustable reconstruction parameters in favour of physical parameters, enhancing objectivity. The new reconstructions point to a trade-off between contrast and a natural noise appearance. This trade-off can be partly overcome by additional notch filtering, but at the expense of a decrease in signal-to-noise ratio. The benefits of the proposed approaches are demonstrated on focal adhesion and tubulin samples in 2D and 3D, and on nano-fabricated fluorescent test patterns.

category: biophysics


title: DFT and Raman study of all-trans astaxanthin optical isomers

abstract:
Astaxanthin (AST) is a xanthophyll carotenoid widely distributed in aquatic animals, which has many physiological functions such as antioxidant, anti-inflammatory, anti-hypertensive and anti-diabetic activities. Astaxanthin has three optical isomers, including a pair of enantiomers (3S,3  S and 3R,3  R) and a meso form (3R,3  S). Different optical isomers have differences in a variety of physiological functions. Traditionally, High Performance Liquid Chromatography (HPLC) can be used to distinguish these isomers. In this work, its found that Raman spectroscopy can be employed to distinguish the three optical isomers. Because the intensities of two Raman bands at 1190 cm-1 and 1215 cm-1 of three isomers are different. DFT calculations are performed and used to analyze the spectral differences. The calculation results show that the structures of these chiral isomers are not strictly mirror-symmetrical to each other, which leads to the difference in their Raman spectra.

HighlightsO_LIRaman spectroscopy can be utilized to distinguish three optical isomers of all-trans astaxanthin.
C_LIO_LIThe DFT-calculated spectrum is used to explain why the Raman bands of optical isomers at 1190 and 1215 cm-1 are different.
C_LIO_LIThe structural parameters of the three optical isomers have been identified.
C_LI


title: A New Type of Satellite associated with Cassava Mosaic Begomoviruses

abstract:
Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated as SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is co-inoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus resistant Arabidopsis accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in Arabidopsis. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of a SEGS-2 encoded protein that may also be encoded in the cassava genome.

IMPORTANCECassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the worlds cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.


title: An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

abstract: Mucins are present in mucosal membranes throughout the body and play a key role in the microbe clearance and infection prevention. Understanding the metabolic responses of pathogens to mucins will further enable the development of protective approaches against infections. We update the genome-scale metabolic network reconstruction (GENRE) of one such pathogen, Pseudomonas aeruginosa PA14, through metabolic coverage expansion, format update, extensive annotation addition, and literature-based curation to produce iPau21. We then validate iPau21 through MEMOTE, growth rate, carbon source utilization, and gene essentiality testing to demonstrate its improved quality and predictive capabilities. We then integrate the GENRE with transcriptomic data in order to generate context-specific models of P. aeruginosa metabolism. The contextualized models recapitulated known phenotypes of unaltered growth and a differential utilization of fumarate metabolism, while also revealing an increased utilization of propionate metabolism upon MUC5B exposure. This work serves to validate iPau21 and demonstrate its utility for providing biological insights.


title: CD36 family members are TCR-independent ligands for CD1 antigen-presentingmolecules

abstract:
CD1c presents lipid-based antigens to CD1c-restricted T cells which are thought to be a major component of the human T cell pool. The study of CD1c-restricted T cells, however, is hampered by the presence of an abundantly expressed CD1c-binding partner on blood cells distinct to the T cell receptor (TCR), confounding analysis of TCR-mediated CD1c tetramer staining. Here, we identify the CD36 family (CD36, CD36-L1 and CD36-L2) as novel ligands for CD1c, CD1b and CD1d proteins, and show that CD36 is the receptor responsible for non-TCR-mediated CD1c tetramer staining of blood cells. Moreover, CD36-blockade enables tetramer-based identification of CD1c-restricted T cells and clarifies identification of CD1b- and CD1d-restricted T cells. We use this technique to characterise CD1c-restricted T cells ex vivo and show diverse phenotypic features, TCR repertoire and antigen-specific subsets. Accordingly, this work will enable further studies into the biology of CD1 and human CD1-restricted T cells.

One Sentence SummaryCD1 molecules bind CD36 family members and blockade of this interaction facilitates the study of CD1-restricted T cells.

category: immunology


title: Reconstituting the genus Mycobacterium

abstract:
The definition of a genus has wide ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus Mycobacterium has been debated due to the proposed split of this genus into five new genera (Mycolicibacterium, Mycolicibacter, Mycolicibacillus, Mycobacteroides and an emended Mycobacterium). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species is does not cause confusion in clinical treatment as outlined by the nomen periculosum rule (56a) of the Prokaryotic Code.

In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus Mycobacterium is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera used as sub-genus complex names.

category: microbiology


title: Additive and synergistic effects of arbuscular mycorrhizal fungi, insect pollination and nutrient availability in a perennial fruit crop

abstract: Managing ecosystem services may reduce the dependence of modern agriculture on external inputs and increase the sustainability of agricultural production. Insect pollinators and arbuscular mycorrhizal fungi (AMF) provide vital ecosystem services for crop production, but it has not been tested whether their effects on crop yield interact and how their effects are influenced by nutrient availability. Here we use potted raspberry (Rubus idaeus L.) plants in a full-factorial randomized block design to assess the interacting effects of insect pollination, AMF inoculation and four levels of fertilizer application. AMF inoculation increased the per-plant flower number by 33% and fruit number by 35%, independently from insect pollination and fertilizer application. Single berry weight furthermore increased more strongly with fertilizer application rates in AMF inoculated plants than in non-inoculated plants. As a consequence, AMF inoculation boosted raspberry yield by 43% compared to non-inoculated plants. AMF inoculation increased pollinator visitation rate under intermediate fertilizer levels, suggesting additional indirect effects of AMF on yield. Fruit yield of pollinated plants increased more strongly with fertilizer application rate than the yield of plants from which pollinators had been excluded. At maximum nutrient availability, the combined benefits of both ecosystem services resulted in a 135% higher yield than that of fertilizer-only treatments. Our results suggest that benefits of ecosystem services on yield can be additive or synergistic to the effects of conventional management practices. Intensive, high-input farming systems that do not consider the potential adverse effects of management on ecosystem service providing species may risk becoming limited by delivery of ecosystem services. Pro-actively managing ecosystem services, on the other hand, has the potential to increase crop yield at the same level of external inputs.


title: Sampling of Structure and Sequence Space of Small Protein Folds

abstract: Nature only samples a small fraction in sequence space, yet many more amino acid combinations can fold into stable proteins. Furthermore, small structural variations in a single fold, which may only be a few amino acids different from the next homolog, define their molecular function. Hence, to design proteins with novel molecular functionalities, such as molecular recognition, methods to control and sample shape diversity are necessary. To explore this space, we developed and experimentally validated a computational platform that can design a wide variety of small protein folds while sampling high shape diversity. We designed and evaluated about 30,000 de novo protein designs of 7 different folds. Among these designs, about 6,200 stable proteins were identified, with predicted structures having first-of-its-kind minimalized thioredoxin. Obtained data revealed more protein folding rules, such as helix connecting loops, which were in nature. Beyond providing a resource database for protein engineering, our data presents a large training data set for machine learning. We developed a high-accuracy classifier to predict the stability of our designed proteins. The methods and the wide range of new protein shapes provide a basis for the design of new protein function without compromising stability.


title: PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools

abstract:
SummaryPhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments. It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF/GTF files using precomputed tracks or computes and scores multiple sequence alignments on the fly with MMseqs2.

AvailabilityPhyloCSF++ is released under the AGPLv3 license. Binaries and source code are available at https://github.com/cpockrandt/PhyloCSFpp. The software can be installed through bioconda. A variety of tracks can be accessed through ftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/.

Contactpockrandt@jhu.edu, martin.steinegger@snu.ac.kr


title: Handling of intracellular K + determines voltage dependence of plasmalemmal monoamine transporter function

abstract: The concentrative power of the transporters for dopamine (DAT), norepinephrine (NET) and serotonin (SERT) is thought to be fueled by the transmembrane Na+ gradient, but it is conceivable that they can also tap other energy sources, e.g. membrane voltage and/or the transmembrane K+ gradient. We address this by recording uptake of endogenous substrates or the fluorescent substrate APP+ ((4-(4-dimethylamino)phenyl-1-methylpyridinium) under voltage control in cells expressing DAT, NET or SERT. We show that DAT and NET differ from SERT in intracellular handling of K+. In DAT and NET, substrate uptake was voltage-dependent due to the transient nature of intracellular K+ binding, which precluded K+ antiport. SERT, however, antiports K+ and achieves voltage-independent transport. Thus, there is a trade-off between maintaining constant uptake and harvesting membrane potential for concentrative power, which we conclude to occur due to subtle differences in the kinetics of co-substrate ion binding in closely related transporters.


title: Different issue types have different signal intensity on b=0 images and its implication on intravoxel incoherent motion (IVIM) analysis: examples of liver MRI

abstract: Intravoxel incoherent motion (IVIM) theory in MRI was proposed to account for the effect of vessel/capillary perfusion on the aggregate diffusion weighted MR signal. The prevalent IVIM modeling is based on equation-1: SI(b)/SI(0) = (1 -PF) x exp(-b x Dslow) + PF x exp(-b x Dfast) [1] where SI(b) and SI(0) denote the signal intensity of images acquired with the b-factor value of b and b=0 s/mm2, respectively. We recently reported that, for the liver and likely for other organs as well, IVIM modeling of the perfusion component is constrained by the diffusion component, with a reduced Dslow measure leading to artificially higher PF and Dfast measures. With higher b-value associated lower image signal of the targeted tissue, Euqation-1 is focused on describing the signal decay pattern along increasingly higher b-values by three IVIM parameters. Signal intensity at each b-value (i.e., SI(b)) is normalised by the signal intensity of b=0 image (i.e., SI(0)). We noted an apparent problem for Euqation-1. For example, if we want to compare the IVIM parameters of the normal liver parenchyma and a liver tumor, following Euqation-1 we will take the assumption that the SI(0) of the normal parenchyma and the tumor are the same and considered equally as 1 (or 100) for the biexponential decay modelling. However, this assumption is invalid for many scenarios. From our liver IVIM database of 27 healthy female subjects, we chose six of the youngest subjects (20-27 yrs) and six of the oldest subjects (58-71 yrs) and measured the signals of the liver and left erector spinae muscle on b=0 and 2 s/mm2 images. The results show, while there was no apparent difference of left erector spinae muscle signal among the young and elderly groups, the elderly groups liver SI(0) is approximately 20 % lower than that of young group. This difference skewed the ratios of various SI(b)/SI(0) and the followed IVIM parameter determination. The general trend is that lower liver SI(0) is associated with lower Dslow and higher PF and Dfast. If IVIM bi-exponential decay fitting starts from a very low non-zero b images (such as b=2 s/mm2 images), this problem persists. We performed an additional analysis of our IVIM database of five cirrhotic livers and the results show SI(b=2) of cirrhotic right liver is positively associated Dslow (Pearson r=0.687), and negatively associated with PF (Pearson r=-0.733). Though the examples we used in this letter are on liver aging and liver fibrosis, the points discussed are expected to be generalisable to other pathologies and to other organs.


title: Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

abstract:
Accessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43 and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. The number of UMRs and ACRs that can be identified is more accurate when chromatin data is aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are substantially enriched within shared regions, as determined by chromosomal alignments. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only a small number being polymorphic between genotypes. However, the majority of UMRs between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.

Article summaryRegions of the genome that have accessible chromatin or unmethylated DNA are often associated with cis-regulatory elements. We assessed chromatin accessibility and DNA methylation in four structurally diverse maize genomes. There are accessible or unmethylated regions within the non-shared portions of the genomes but these features are depleted within these regions. Evaluating the dynamics of methylation and accessibility between genotypes reveals conservation of features, albeit with variable boundaries suggesting some instability of the precise edges of unmethylated regions.


title: A general model of multivalent binding with ligands of heterotypic subunits and multiple surface receptors

abstract: Multivalent cell surface receptor binding is a ubiquitous biological phenomenon with functional and therapeutic significance. Predicting the amount of ligand binding for a cell remains an important question in computational biology as it can provide great insight into cell-to-cell communication and rational drug design toward specific targets. In this study, we extend a mechanistic, two-step multivalent binding model. This model predicts the behavior of a mixture of different multivalent ligand complexes binding to cells expressing various types of receptors. It accounts for the combinatorially large number of interactions between multiple ligands and receptors, optionally allowing a mixture of complexes with different valencies and complexes that contain heterogeneous ligand units. We derive the macroscopic predictions and demonstrate how this model enables large-scale predictions on mixture binding and the binding space of a ligand. This model thus provides an elegant and computationally efficient framework for analyzing multivalent binding.


title: Distinct profiles of spatio-temporal brain dynamics along symptoms dimensions in autism

abstract: Autism Spectrum Disorders are accompanied by atypical brain activity and impairments in brain connectivity. In particular, dynamic functional connectivity approaches highlighted aberrant brain fluctuations at rest in individuals with autism compared to a group composed of typically developed individuals, matched in age and gender. However, the characterization of these variations remains unclear. Here, we quantified the spatio-temporal network dynamics using two novel dynamic group-based measures, namely system diversity and spatio-temporal diversity. Using the public database ABIDE 1, we explored the differences between individuals with autism and typically developed individuals. Our results show evidence that individuals with autism have atypical connectivity patterns over time characterized by a lower integration of heterogeneous cognitive processes and unstable functional activity, except for the default mode network presenting its own specific dynamic pattern. Within the autism group, we find this pattern of results to be stronger in more severely affected patients with a predominance of symptoms in the social affect domain. However, patients with prominently restricted and repetitive behaviours demonstrate a more conservative profile of brain dynamics characterized by a lower spatio-temporal diversity of the default mode network.


title: Aβ promotes amyloidogenic processing of APP through a Go/Gβγ signaling

abstract: Alzheimers disease (AD) is characterized by a cognitive impairment associated to amyloid beta (A{beta}) aggregation and deposition in the brain. A{beta} is generated by sequential cleavage of the amyloid precursor protein (APP) by {beta}-site APP cleaving enzyme 1 (BACE1) and {gamma}-secretase complex. The mechanisms that underlie exacerbated production of A{beta}, favoring its deposition in the brain, is largely unknown. In vitro studies have shown that A{beta} aggregates trigger enhanced production of A{beta} by a yet non described mechanism. Here, we show that in different cell types, including human neurons derived from induced pluripotent stem cells (iPSC), oligomers and fibrils of A{beta} enhance the convergence and interaction of APP and BACE1 in endosomal compartments. We demonstrated a key role of A{beta}-APP/Go/G{beta}{gamma} signaling on the amyloidogenic processing of APP. We show that APP mutants with impaired capacity to bind A{beta} or to activate Go protein, are unable to exacerbate APP and BACE1 colocalization in the presence of A{beta}. Moreover, pharmacological inhibition of G{beta}{gamma} subunits signaling with gallein, abrogate A{beta}-dependent interaction of APP and BACE1 in endosomes preventing {beta}-processing of APP. Collectively, these findings uncover a feed-forward mechanism of amyloidogenesis that might contribute to A{beta} pathology in early stages of AD and suggest that gallein might have clinical relevance.


title: Antibody responses to SARS-CoV-2 mRNA vaccines are detectable in saliva

abstract: Vaccines are critical for curtailing the COVID-19 pandemic (1, 2). In the USA, two highly protective mRNA vaccines are available: BNT162b2 from Pfizer/BioNTech and mRNA-1273 from Moderna (3, 4). These vaccines induce antibodies to the SARS-CoV-2 S-protein, including neutralizing antibodies (NAbs) predominantly directed against the Receptor Binding Domain (RBD) (1-4). Serum NAbs are induced at modest levels within [~]1 week of the first dose, but their titers are strongly boosted by a second dose at 3 (BNT162b2) or 4 weeks (mRNA-1273) (3, 4). SARS-CoV-2 is most commonly transmitted nasally or orally and infects cells in the mucosae of the respiratory and to some extent also the gastrointestinal tract (5). Although serum NAbs may be a correlate of protection against COVID-19, mucosal antibodies might directly prevent or limit virus acquisition by the nasal, oral and conjunctival routes (5). Whether the mRNA vaccines induce mucosal immunity has not been studied. Here, we report that antibodies to the S-protein and its RBD are present in saliva samples from mRNA-vaccinated healthcare workers (HCW). Within 1-2 weeks after their second dose, 37/37 and 8/8 recipients of the Pfizer and Moderna vaccines, respectively, had S-protein IgG antibodies in their saliva, while IgA was detected in a substantial proportion. These observations may be relevant to vaccine-mediated protection from SARS-CoV-2 infection and disease.


title: SARS-CoV-2 comprehensive receptor profiling: mechanistic insight to drive new therapeutic strategies

abstract: Here we describe a hypothesis free approach to screen for interactions of SARS-CoV-2 spike (S) protein with human cell surface receptors. We used a library screening approach to detect binding interactions across one of the largest known panels of membrane-bound and soluble receptors, comprising 5845 targets, expressed recombinantly in human cells. We were able confirm and replicate SARS-CoV-2 binding to ACE2 and other putative coreceptors such as CD209 and CLEC4M. More significantly, we identified interactions with a number of novel SARS-CoV-2 S binding proteins. Three of these novel receptors, NID1, CNTN1 and APOA4 were specific to SARS-CoV-2, and not SARS-COV, with APOA4 binding the S-protein with equal affinity as ACE2. With this knowledge we may further understand the disease pathogenesis of COVID-19 patients and how infection by SARS-CoV-2 may lead to differences in pathology in specific organs or indeed the virulence observed in different ethnicities. Importantly we illustrate a methodology which can be used for rapid, unbiassed identification of cell surface receptors, to support drug screening and drug repurposing approaches for this and future pandemics.

category: cell biology


title: Novel inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives

abstract: The global emergence of SARS-CoV-2 has triggered numerous efforts to develop therapeutic options for COVID-19 pandemic. The main protease of SARS-CoV-2 (Mpro), which is a critical enzyme for transcription and replication of SARS-CoV-2, is a key target for therapeutic development against COVID-19. An organoselenium drug called ebselen has recently been demonstrated to have strong inhibition against Mpro and antiviral activity but its molecular mode of action is unknown preventing further development. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of ebselen derivatives. A free selenium atom bound with cysteine 145 of Mpro catalytic dyad has been revealed by crystallographic studies of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct, formation of a phenolic by-product is confirmed by mass spectrometry. The target engagement of these compounds with an unprecedented mechanism of SARS-CoV-2 Mpro inhibition suggests wider therapeutic applications of organo-selenium compounds in SARS-CoV-2 and other zoonotic beta-corona viruses.


title: Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants

abstract: High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called  Tiled-ClickSeq, which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.

category: molecular biology


title: Telencephalic outputs from the medial entorhinal cortex are copied directly to the hippocampus

abstract: Complementary actions of the neocortex and the hippocampus enable encoding and long-term storage of experience dependent memories. Standard models for memory storage assume that sensory signals reach the hippocampus from superficial layers of the entorhinal cortex (EC). Deep layers of the EC on the other hand relay hippocampal outputs to the telencephalic structures including many parts of the neocortex. Here we show that cells in Layer 5a of the medial EC send a copy of their telencephalic outputs back to the CA1 region of the hippocampus. Combining cell-type specific anatomical tracing, high-throughput RNA-sequencing based projection mapping and optogenetics aided circuit mapping, we show that these projections have a unique topography and target hippocampal pyramidal cells and interneurons. Our results suggest that rather than serving as a relay, deep EC may coordinate hippocampal-neocortical interactions in spatial cognition and memory.


title: Seasonal dynamics and repeatability of gastrointestinal parasite burdens in wild Soay sheep

abstract: Seasonality is a ubiquitous feature of wildlife disease ecology, but is determined by a complex interplay of environmental, parasitological and host factors. Gastrointestinal parasites often exhibit strong seasonal dynamics in wild vertebrate populations due to, for example, environmental influences on free-living or vectored life stages, and variation in the physiological and immune status of hosts across their annual cycle. At the same time, wild populations are typically infected with multiple parasites. The seasonal dynamics of co-infecting parasites may differ depending on age and reproductive status, and associations among parasites may be driven by short-term within-individual changes or longer-term interactions that are consistent among hosts. Here, we used faecal samples and egg counts collected repeatedly from individually marked and monitored wild Soay sheep that were part of a long-term study to investigate seasonal dynamics of six gastrointestinal parasite groups (strongyle nematodes, coccidian protozoa, Capillaria, Strongyloides, Nematodirus, and Moniezia). Prevalence and abundance generally tended to be higher spring and summer, and burdens were higher in lambs than adults. Within the highly prevalent strongyle nematode group, we found differences in seasonality of egg counts depending on adult reproductive status. Reproductive ewes had increased counts in spring around the time of birth followed by a drop in abundance in summer, while barren ewes showed little evidence of seasonality. Males showed a sustained rise in egg counts through spring and summer, and sex differences were only strongly apparent in summer. In contrast, in similarly prevalent coccidia we found a peak in faecal oocyst counts in spring but no differences in seasonality among males, barren and pregnant ewes. Using multivariate mixed-effects models, we went on to show that both strongyle and coccidia counts are moderately repeatable across seasons among individuals. We further show that apparent positive correlation between strongyle and coccidia counts was driven by short-term within-individual changes in both parasite burdens rather than long-term among-individual covariation. Overall, our results demonstrate that seasonality varies across demographic and parasite groups and highlight the value of investigating fluctuating susceptibility and exposure over time for understanding epidemiology of a population.


title: The Genetic Basis of Differential Autodiploidization in Evolving Yeast Populations

abstract: Spontaneous whole-genome duplication, or autodiploidization, is a common route to adaptation in experimental evolution of haploid budding yeast populations. The rate at which autodiploids fix in these populations appears to vary across strain backgrounds, but the genetic basis of these differences remains poorly characterized. Here we show that the frequency of autodiploidization differs dramatically between two closely related laboratory strains of Saccharomyces cerevisiae, BY4741 and W303. To investigate the genetic basis of this difference, we crossed these strains to generate hundreds of unique F1 segregants and tested the tendency of each segregant to autodiplodize across hundreds of generations of laboratory evolution. We find that variants in the SSD1 gene are the primary genetic determinant of differences in autodiploidization. We then used multiple laboratory and wild strains of S. cerevisiae to show that clonal populations of strains with a functional copy of SSD1 autodiploidize more frequently in evolution experiments, while knocking out this gene or replacing it with the W303 allele reduces autodiploidization propensity across all genetic backgrounds tested. These results suggest a potential strategy for modifying rates of spontaneous whole-genome duplications in laboratory evolution experiments in haploid budding yeast. They may also have relevance to other settings in which eukaryotic genome stability plays an important role, such as biomanufacturing and the treatment of pathogenic fungal diseases and cancers.


title: SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies

abstract: With the vast improvements in sequencing technologies and increased number of protocols, sequencing is finding more applications to answer complex biological problems. Thus, the amount of publicly available sequencing data has tremendously increased in repositories such as SRA, EGA, and ENCODE. With any large online database, there is a critical need to accurately document study metadata, such as the source protocol and organism. In some cases, this metadata may not be systematically verified by the hosting sites and may result in a negative influence on future studies. Here we present SeqWho, a program designed to heuristically assess the quality of sequencing files and reliably classify the organism and protocol type. This is done in an alignment-free algorithm that leverages a Random Forest classifier to learn from native biases in k-mer frequencies and repeat sequence identities between different sequencing technologies and species. Here, we show that our method can accurately and rapidly distinguish between human and mouse, nine different sequencing technologies, and both together, 98.32%, 97.86%, and 96.38% of the time in high confidence calls respectively. This demonstrates that SeqWho is a powerful method for reliably checking the identity of the sequencing files used in any pipeline and illustrates the programs ability to leverage k-mer biases.


title: Single-Cell Spatial Proteomics Analyses of Head and Neck Squamous Cell Carcinoma Reveal Tumor Heterogeneity and Immune Architectures Associated with Clinical Outcome

abstract: There is increasing evidence that the spatial organization of cells within the tumor-immune microenvironment (TiME) of solid tumors influences survival and response to therapy in numerous cancer types. Here, we report results and demonstrate the applicability of quantitative single-cell spatial proteomics analyses in the TiME of primary and recurrent human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) tumors. Single-cell compositions of a nine patient, primary and recurrent (n=18), HNSCC cohort is presented, followed by deeper investigation into the spatial architecture of the TiME and its relationship with clinical variables and progression free survival (PFS). Multiple spatial algorithms were used to quantify the spatial landscapes of immune cells within TiMEs and demonstrate that neoplastic tumor-immune cell spatial compartmentalization, rather than mixing, is associated with longer PFS. Mesenchymal (SMA+) cellular neighborhoods describe distinct immune landscapes associated with neoplastic tumor-immune compartmentalization and improved patient outcomes. Results from this investigation are concordant with studies in other tumor types, suggesting that trends in TiME cellular heterogeneity and spatial organization may be shared across cancers and may provide prognostic value in multiple cancer types.

category: cancer biology


title: In vitro profiling of orphan G protein coupled receptor (GPCR) constitutive activity

abstract:
Background and PurposeMembers of the G protein coupled receptor (GPCR) family are targeted by a significant fraction of the available FDA-approved drugs. However, the physiological role and pharmacological properties of many GPCRs remain unknown, representing untapped potential in drug design. Of particular interest are ~100 less-studied GPCRs known as orphans because their endogenous ligands are unknown. Intriguingly, disease-causing mutations identified in patients, together with animal studies, have demonstrated that many orphan receptors play crucial physiological roles, and thus, represent attractive drug targets.

Experimental ApproachThe majority of deorphanized GPCRs demonstrate coupling to Gi/o, however a limited number of techniques allow the detection of intrinsically small constitutive activity associated with Gi/o protein activation which represents a significant barrier in our ability to study orphan GPCR signaling. Using luciferase reporter assays, we effectively detected constitutive Gs, Gq, and G12/13 protein signaling by unliganded receptors, and introducing various G protein chimeras, we provide a novel, highly-sensitive tool capable of identifying Gi/o coupling in unliganded orphan GPCRs.

Key ResultsUsing this approach, we measured the constitutive activity of the entire class C GPCR family that includes 8 orphan receptors, and a subset of 20 prototypical class A GPCR members, including 11 orphans. Excitingly, this approach illuminated the G protein coupling profile of 8 orphan GPCRs (GPR22, GPR137b, GPR88, GPR156, GPR158, GPR179, GPRC5D, and GPRC6A) previously linked to pathophysiological processes.

Conclusion and ImplicationsWe provide a new platform that could be utilized in ongoing studies in orphan receptor signaling and deorphanization efforts.

What is already knownO_LIA large group of understudied orphan GPCRs controls a variety of physiological process.
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What this study addsO_LIA new strategy to identify G protein signaling associated with orphan GPCRs.
C_LIO_LIIdentification of Gi/o coupling for 8 orphan GPCRs.
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What is the clinical significanceO_LIMany orphan GPCRs are associated with pathological conditions and represent promising druggable targets.
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category: pharmacology and toxicology


title: Insulin-stimulated adiponectin secretion in pregnancy is mediated by inhibition of adiponectin ubiquitination and degradation and is impaired in obesity

abstract: In pregnancy, adiponectin serves as an endocrine link between maternal adipose tissue, placental function and fetal growth, with low adiponectin promoting placental function and fetal growth. Circulating adiponectin levels are decreased in obese pregnant women and in gestational diabetes, which is believed to contribute to the insulin resistance and increased risk of fetal overgrowth associated with these conditions. However, the molecular mechanisms governing adiponectin secretion from maternal adipose tissues in pregnancy are poorly understood. Using visceral adipose tissue from lean and obese pregnant mice, we show that obesity in pregnancy is associated with adipose tissue inflammation, ER stress, insulin resistance, increased adiponectin ubiquitination and decreased total abundance of adiponectin. Moreover, adiponectin ubiquitination was increased in visceral fat of obese pregnant women as compared to lean pregnant women. We further observed that insulin prevents, whereas ER stress and inflammation promote, adiponectin ubiquitination and degradation in differentiated 3T3-L1 adipocytes. We have identified key molecular pathways regulating adiponectin secretion in pregnancy. This information will help us better understand the mechanisms controlling maternal insulin resistance and fetal growth in pregnancy and may provide a foundation for the development of strategies aimed at improving adiponectin production in pregnant women with obesity or gestational diabetes.

category: physiology


title: The optimal spatial arrangement of ON and OFF receptive fields

abstract:
Many sensory systems utilize parallel ON and OFF pathways that signal stimulus increments and decrements, respectively. These pathways consist of ensembles or grids of ON and OFF detectors spanning sensory space. Yet encoding by opponent pathways raises a question: How should grids of ON and OFF detectors be arranged to optimally encode natural stimuli? We investigated this question using a model of the retina guided by efficient coding theory. Specifically, we optimized spatial receptive fields and contrast response functions to encode natural images given noise and constrained firing rates. We find that the optimal arrangement of ON and OFF receptive fields exhibits a transition between aligned and anti-aligned grids. The preferred phase depends on detector noise and the statistical structure of the natural stimuli. These results reveal that noise and stimulus statistics produce qualitative shifts in neural coding strategies and provide novel theoretical predictions for the configuration of opponent pathways in the nervous system.

Significance StatementAcross a wide variety of species, cells in the retina specialized for signaling either increases (ON) or decreases (OFF) in light represent one of the most basic building blocks of visual computation. These cells coordinate to form mosaics, with each cell responsible for a small, minimally-overlapping portion of visual space, but the ways in which these mosaics could be spatially coordinated with each other are relatively unknown. Here, we show how efficient coding theory, which hypothesizes that the nervous system minimizes the amount of redundant information it encodes, can predict the relative spatial arrangement of ON and OFF mosaics. The most information-efficient arrangements are determined both by levels of noise in the system and the statistics of natural images.


title: Behavior emerges from unstructured muscle activity in response to neuromodulation

abstract: Identifying neural substrates of behavior requires defining actions in terms that map onto brain activity. Brain and muscle activity naturally correlate via the output of motor neurons, but apart from simple movements it has been difficult to define behavior in terms of muscle contractions. By mapping the musculature of the pupal fruit fly and comprehensively imaging muscle activation at single cell resolution, we here describe a multiphasic behavioral sequence in Drosophila. Our characterization identifies a previously undescribed behavioral phase and permits extraction of major movements by a convolutional neural network. We deconstruct movements into a syllabary of co-active muscles and identify specific syllables that are sensitive to neuromodulatory manipulations. We find that muscle activity shows considerable variability, which reduces upon neuromodulation. Our work provides a platform for studying whole-animal behavior, quantifying its variability across multiple spatiotemporal scales, and analyzing its neuromodulatory regulation at cellular resolution.


title: Female fruitflies use gustatory cues to exhibit reproductive plasticity in response to the social environment

abstract: Animals can exhibit remarkable reproductive plasticity in response to their social surroundings, with profound fitness consequences. The study of such plasticity in females, particularly in same-sex interactions, has been severely neglected. Here we measured the impact of variation in the pre-mating social environment on reproductive success in females and tested the underlying mechanisms involved. We used the Drosophila melanogaster model system to test the effect of varying female group size prior to mating and deployed physical and genetic methods to manipulate the perception of different social cues and sensory pathways. We found that socially isolated females were significantly more likely to retain unfertilised eggs before mating, but to show the opposite pattern and lay significantly more fertilised eggs in the 24h after mating, in comparison to grouped females. More than 48h of exposure to other females was necessary for this socially-induced plasticity to be expressed. Neither olfactory nor visual cues were involved in mediating these responses. Instead, we found that females detected other females through direct contact with the deposits they leave behind, even in the absence of eggs. The results demonstrate that females show striking reproductive plasticity in response to their social surroundings and that the nature of their plastic reproductive responses, and the cues they use, differ markedly from those of males. The results emphasise the stark contrasts in how each sex realises reproductive success.

category: evolutionary biology


title: The fast-slow continuum is not the end-game of life history evolution, human or otherwise

abstract: Life history human evolution places a strong emphasis on the fast-slow continuum and pace-of-life continuum. Papers in this area frequently make a call for more integrative research to explore the relationships between the fast-slow continuum (population-level variation in traits) and pace-of-life continuum (ditto at the individual level). Here, using high-resolution demographic models from natural populations of 41 modern human populations, and hundreds of non-human animal populations and plant populations, I show that the fast-slow continuum, while of interest to explore variation in human strategies, should not be the sole focus of attention. Using a phylogenetically corrected principal component analysis, I show that other axes of life history variation show great promise. Specifically, understanding of the mechanisms of inter-specific and intra-specific differences in senescence rates in reproduction and survival, and how species respond to stochastic variation, I argue, should become the focus of my interdisciplinary research. The proposed new axis of demographic buffering-lability emerges as an important one to explain over 20% of variation in human and non-human populations. I show that these axes help predict demographic resilience, and also correlates with human nation per capita GDP and population growth rates.


title: Bromodomain and Extraterminal Protein Inhibitor, Apabetalone (RVX-208), Reduces ACE2 Expression and Attenuates SARS-CoV-2 Infection in vitro

abstract:
Effective therapeutics are urgently needed to counter infection and improve outcomes for patients suffering from COVID-19 and to combat this pandemic. Manipulation of epigenetic machinery to influence viral infectivity of host cells is a relatively unexplored area. The bromodomain and extraterminal (BET) family of epigenetic readers have been reported to modulate SARS-CoV-2 infection. Herein, we demonstrate apabetalone, the most clinical advanced BET inhibitor, downregulates expression of cell surface receptors involved in SARS-CoV-2 entry, including angiotensin-converting enzyme 2 (ACE2) and dipeptidyl-peptidase 4 (DPP4 or CD26) in SARS-CoV-2 permissive cells. Moreover, we show that apabetalone inhibits SARS-CoV-2 infection in vitro to levels comparable to antiviral agents. Taken together, our study supports further evaluation of apabetalone to treat COVID-19, either alone or in combination with emerging therapeutics.

Graphical Abstract

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title: Beyond Turing: Far-from-equilibrium patterns and mechano-chemical feedback

abstract: Turing patterns are commonly understood as specific instabilities of a spatially homogeneous steady state, resulting from activator-inhibitor interaction destabilised by diffusion. We argue that this view is restrictive and its agreement with biological observations is problematic. We present two alternative to the  classical Turing analysis of patterns. First, we employ the abstract framework of evolution equations to enable the study of far-from-equilibrium patterns. Second, we introduce a mechano-chemical model, with the surface on which the pattern forms being dynamic and playing an active role in the pattern formation, effectively replacing the inhibitor. We highlight the advantages of these two alternatives vis-a-vis the  classical Turing analysis, and give an overview of recent results and future challenges for both approaches.


title: Alphaproteobacteria facilitate Trichodesmium community trimethylamine utilization

abstract: In the surface waters of the warm oligotrophic ocean, filaments and aggregated colonies of the nitrogen (N)-fixing cyanobacterium Trichodesmium create microscale nutrient-rich oases. These hotspots fuel primary productivity and harbor a diverse consortium of heterotrophs. Interactions with associated microbiota can affect the physiology of Trichodesmium, often in ways that have been predicted to support its growth. Recently, it was found that trimethylamine (TMA), a globally-abundant organic N compound, inhibits N2 fixation in cultures of Trichodesmium without impairing growth rate, suggesting that Trichodesmium receives nitrogen from TMA. In this study, 15N-TMA DNA stable isotope probing (SIP) of a Trichodesmium enrichment was employed to further investigate TMA metabolism and determine if TMA-N is incorporated directly or secondarily via cross-feeding facilitated by microbial associates. Herein we identify two members of the marine Roseobacter clade (MRC) of Alphaproteobacteria as the likely metabolizers of TMA and provide genomic evidence that they converted TMA into a more readily available form of N, e.g., NH4+, which was subsequently used by Trichodesmium and the rest of the community. The results implicate microbiome-mediated carbon (C) and N transformations in modulating N2 fixation, and thus highlight the involvement of host-associated heterotrophs in global biogeochemical cycling.


title: Low ozone concentration and negative ions for rapid SARS-CoV-2 inactivation

abstract:
Ozone is a powerful anti-bacterial, anti-fungal and anti-viral agent, yet exposure to high levels of ozone can pose risks to human/animal health and, in the long term, corrode certain objects. In order to overcome these risks, we evaluated the potential of using a relatively short exposure of a low concentration of ozone to disinfect an indoor environment in the absence of individuals and animals. ICON3 by O3ZONO/M2L, a new disinfection device generating both ozone and negative ions, was selected to assess the potential of this strategy to inactivate different viral isolates of SARS-CoV-2.

Tests under controlled laboratory conditions were performed in a system consisting of an ozone-proof airtight plastic box inside a biological safety cabinet, where suspensions of two strains of SARS-CoV-2 were exposed to ozone and negative ions and virucidal activity was measured by means of two complementary methodologies: viral replication capacity and viral titer determination.

These studies revealed that low concentration ozone (average 3.18 ppm after the peak) inactivated up to >99% of SARS-CoV-2 within 20 minutes of exposure. Under controlled conditions, similar ozone exposure was recreated with ICON3 in different volume rooms (15, 30, 60 m3) where a linear relationship was observed between the room volume and the time of continuous ozone/ions flow required to reach and maintain the desired ozone levels used in the laboratory studies.

These studies suggest that ICON3 may have the potential for use in the disinfection of SARS-CoV-2 in indoor environments in the absence of individuals and animals, under properly controlled and monitored safety conditions.


title: Bacterial filamentation drives colony chirality

abstract: Chirality is ubiquitous in nature, with consequences at the cellular and tissue scales. As Escherichia coli colonies expand radially, an orthogonal component of growth creates a pinwheel-like pattern that can be revealed by fluorescent markers. To elucidate the mechanistic basis of this colony chirality, we investigated its link to left-handed, single-cell twisting during E. coli elongation. While chemical and genetic manipulation of cell width altered single-cell twisting handedness, colonies ceased to be chiral rather than switching handedness, and anaerobic growth altered colony chirality without affecting single-cell twisting. Chiral angle increased with increasing temperature even when growth rate decreased. Unifying these findings, we discovered that colony chirality was associated with the propensity for cell filamentation. Inhibition of cell division accentuated chirality under aerobic growth and generated chirality under anaerobic growth. Thus, regulation of cell division is intrinsically coupled to colony chirality, providing a mechanism for tuning macroscale spatial patterning.


title: Membrane-Tethered Mucin 1 is Stimulated by Interferon in Multiple Cell Types and Antagonizes Influenza A Virus Infection in Human Airway Epithelium

abstract:
Influenza A virus (IAV) causes seasonal epidemics and periodic pandemics, resulting in significant morbidity and mortality in the human population. Tethered mucin 1 (MUC1) is highly expressed in airway epithelium, the primary site of IAV replication, and also by other cell types that influence IAV infection, including macrophages. MUC1 has the potential to influence infection dynamics through physical interactions and/or signaling activity, and recent work suggests MUC1 acts as a releasable decoy receptor and anti-inflammatory molecule during IAV infection. Still, the modulation of MUC1 and its impact during viral pathogenesis remains unclear. Thus, we sought to further investigate the interplay between MUC1 and IAV in an in vitro model of primary human airway epithelium (HAE). Our data indicate that a recombinant IAV hemagglutinin (H3) and H3N2 virus can bind endogenous HAE MUC1. We find that infection of HAE cultures with H1N1 or H3N2 IAV strains does not trigger enhanced MUC1 shedding, but instead stimulates an increase in cell-associated MUC1 protein. We observed a similar increase after stimulation with either type I or type III interferon (IFN); however, inhibition of IFN signaling during H1N1 infection only partially abrogated this increase, indicating multiple soluble factors contribute to MUC1 upregulation during the antiviral response. We expanded these findings and demonstrate that in addition to HAE, primary human monocyte-derived macrophages also upregulate MUC1 protein in response to both IFN treatment and conditioned media from IAV-infected HAE cultures. We then developed HAE genetically depleted for MUC1 to determine its impact on IAV pathogenesis, finding that MUC1 knock-out cultures exhibited enhanced viral growth compared to control cultures for several IAV strains. Together, our data support a model whereby MUC1 antagonizes productive uptake of IAV in HAE. Infection then stimulates MUC1 expression on multiple cell types through IFN-dependent and -independent mechanisms that may further impact infection dynamics.

Author SummaryThe mucosal surface of the respiratory epithelium is an important site of first contact for viral respiratory pathogens. Large and heavily glycosylated molecules known as tethered mucins extend from the cell surface and may physically restrict access to underlying cells. Recently, one of these tethered mucins, MUC1, has also been shown to influence cell signaling and inflammation. Still, despite its abundance in the airway and multifunctional capability, the role of MUC1 during influenza virus infection in the human respiratory tract remains unclear. Here, we demonstrate that influenza virus directly interacts with MUC1 in a physiologically-relevant model of human airway epithelium and find that MUC1 protein expression is elevated throughout the epithelium and in primary human monocyte-derived macrophages in response to important antiviral signals produced during infection. Using genetically-modified human airway cultures lacking MUC1, we then provide evidence of more efficient influenza virus infection in the absence of this mucin. Our data suggest that MUC1 not only physically restricts influenza virus uptake, but also represents a dynamic component of the host response that acts to further stem viral spread.


title: In vitro and in vivo preclinical studies predict REGEN-COV protection against emergence of viral escape in humans

abstract: Monoclonal antibodies against SARS-CoV-2 are a clinically validated therapeutic option against COVID-19. As rapidly emerging virus mutants are becoming the next major concern in the fight against the global pandemic, it is imperative that these therapeutic treatments provide coverage against circulating variants and do not contribute to development of treatment emergent resistance. To this end, we investigated the sequence diversity of the spike protein and monitored emergence of minor virus variants in SARS-COV-2 isolates found in COVID-19 patients or identified from preclinical in vitro and in vivo studies. This study demonstrates that a combination of non-competing antibodies, REGEN-COV, not only provides full coverage against current variants of concern/interest but also protects against emergence of new such variants and their potential seeding into the population in a clinical setting.


title: REGEN-COV protects against viral escape in preclinical and human studies