title: Geographic Name Resolution Service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling

abstract:
Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data and analysis of erroneous observations can lead to flawed results.

Here, we present the Geographic Name Resolution Service (GNRS), an application for the correction, standardization and indexing of world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In an assessment of geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a major data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and can be accessed via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.


title: Great-tailed Grackles (Quiscalus mexicanus) as a tolerant host of avian malaria parasites

abstract: Great-tailed Grackles (Quiscalus mexicanus) are a social, polygamous bird species whose populations have rapidly expanded their geographic range across North America over the past century. Before 1865, Great-tailed Grackles were only documented in Central America, Mexico, and southern Texas in the USA. Given the rapid northern expansion of this species, it is relevant to study its role in the dynamics of avian blood parasites. Here, 87 Great-tailed grackles in Arizona (a population in the new center of the range) were screened for haemosporidian parasites using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene. Individuals were caught in the wild from January 2018 until February 2020. Haemosporidian parasite prevalence was 60.9% (53/87). A high Plasmodium prevalence was found (59.8%, 52/87), and one grackle was infected with Haemoproteus (Parahaemoproteus) sp. (lineage SIAMEX01). Twenty-one grackles were infected with P. cathemerium, sixteen with P. homopolare, four with P. relictum (strain GRW04), and eleven with three different genetic lineages of Plasmodium spp. that have not been characterized to species level (MOLATE01, PHPAT01, and ZEMAC01). Gametocytes were observed in birds infected with three different Plasmodium lineages, revealing that grackles are competent hosts for some parasite species. This study also suggests that grackles are highly susceptible and develop chronic infections consistent with parasite tolerance, making them competent to transmit some generalist haemosporidian lineages. It can be hypothesized that, as the Great-tailed Grackle expands its geographic range, it may affect local bird communities by increasing the transmission of local parasites but not introducing new species into the parasite species pool.

category: zoology


title: GlycoVHH: Introducing N-glycans on the camelid VHH antibody scaffold - Optimal sites and use for macrophage delivery

abstract: As small and stable high-affinity antigen binders, VHHs boast attractive characteristics both for therapeutic use in various disease indications, and as versatile reagents in research and diagnostics. To further increase the versatility of VHHs, we explored the VHH scaffold in a structure-guided approach to select regions where the introduction of an N-glycosylation N-X-T sequon and its associated glycan should not interfere with protein folding or epitope recognition. We expressed variants of such glycoengineered VHHs in the Pichia pastoris GlycoSwitchM5 strain, allowing us to pinpoint preferred sites at which Man5GlcNAc2-glycans can be introduced at high site occupancy without affecting antigen binding. A VHH carrying predominantly a Man5GlcNAc2 N-glycan at one of these preferred sites showed highly efficient, glycan-dependent uptake by Mf4/4 macrophages in vitro and by alveolar lung macrophages in vivo, illustrating one potential application of glyco-engineered VHHs: a glycan-based targeting approach for lung macrophage endolysosomal system delivery. The set of optimal artificial VHH N-glycosylation sites identified in this study can serve as a blueprint for targeted glyco-engineering of other VHHs, enabling site-specific functionalization through the rapidly expanding toolbox of synthetic glycobiology.

category: molecular biology


title: CircEML1 facilitates the steroid synthesis in follicular granulosa cells of chicken through sponging gga-miR-449a to release IGF2BP3 expression

abstract: Non-coding RNAs (ncRNAs) induced competing endogenous RNAs (ceRNA) play crucial roles in various biological process by regulating target gene expression. However, the studies of ceRNA networks in the regulation of ovarian ovulation process of chicken remains deficient compared to that in mammals. In the present study, it was revealed that circEML1 was differential expressed in hens ovarian tissue at different ages (15W, 20W, 30W and 68W) and identified as a loop structure from EML1 pre-mRNA, which promoted the expressions of CYP19A1 and StAR and the production of E2 and P4 in follicular granulosa cells (GCs) using qRT-PCR and ELISA. Furthermore, circEML1 was proved to serve as a sponge of gga-miR-449a to participate in the steroidogenesis using the dual luciferase reporter, RNA FISH assays, qRT-PCR and ELISA assays. In addition, we evaluated several potential target genes of gga-miR-449a and found that IGF2BP3 was targeted by gga-miR-449a and promoted steroidogenesis and E2/P4 secretions in GCs, which may act the regulatory role via mTOR/p38MAPK pathways. Meanwhile, we implemented a rescue experiment and demonstrated that gga-miR-449a reversed the promoting role of circEML1 on IGF2BP3 expression and steroidogenesis. Eventually, this study suggested that circEML1/gga-miR-449a/IGF2BP3 axis exerted an important role in the regulation of steroidogenesis and steroid hormones production possibly through mTOR/p38MAPK pathways in follicular GCs of chicken and may contribute a better understanding of ceRNA network in the modulatory mechanism of hens ovarian development and ovulation cycle.


title: The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)

abstract: Understanding how populations adapt to local environments is increasingly important to prevent biodiversity loss due to climate change. Here we examined whole-genome variation of 12 Atlantic horse mackerel pool samples from the North Sea to north Africa, and the western Mediterranean Sea. This marine migratory benthopelagic fish is one of the most widely distributed and commercially important species in the eastern Atlantic. We found low population structure at neutral loci, but high differentiation at adaptive loci distinguishing the western Mediterranean and the North Seas from other Atlantic locations. Candidate genes distinctive of the Mediterranean include a green-sensitive-opsin harbouring two missense mutations that might fine-tune the spectral sensitivity to blue-green light conditions. Candidate genes characteristic of the North Sea could play a critical role in cold tolerance (energy metabolism and cell membrane structure) and increased sensitivity to odours, presumably to compensate reduced visibility in turbid waters. We also discovered a massive chromosomal inversion (9.9 Mb) that underlies a climate-related latitudinal cline with a break near mid Portugal. Genome-environment association analysis indicated that sea water dissolved oxygen concentration and temperature are likely the main environmental drivers of local adaptation. Our genomic data broadly supports the current ICES stock divisions, but recommends revision of the western and southern stock boundaries. We developed a reduced SNP panel that genetically discriminate the North Sea from neighbouring populations. Our study highlights the importance of life history and chromosomal inversions in adaptation with gene flow, and the complexity of evolutionary and ecological processes involved in local adaptation.

category: genomics


title: Changes in prefrontal GABA and glutamate through adolescence supports excitation/inhibition balance

abstract: Animal and human postmortem studies provide evidence for changes in gamma-aminobutyric acid (GABA) and glutamate in prefrontal cortex (PFC) during adolescence, suggesting shifts in excitation and inhibition balance consistent with critical period plasticity. However, how GABA and glutamate change through adolescence and how the balance of these inhibitory and excitatory neurotransmitters changes is not well understood in vivo in humans. High field (7 Tesla) Magnetic Resonance Spectroscopic Imaging was used to investigate age-related changes in the balance of GABA/creatine (Cr) and glutamate/Cr in multiple developmentally-relevant regions of PFC in 144 10 to 30-year-olds. Results indicated a homogenous pattern of age-related Glu/Cr decreases across PFC regions, while age-related changes in GABA/Cr were heterogenous, with a mix of stable and decreasing age effects. Importantly, balance between glutamate/Cr and GABA/Cr in areas of prefrontal cortex increased through adolescence, suggesting the presence of critical period plasticity in PFC at this significant time of development when adult trajectories are established.

category: neuroscience


title: Predicting individual skill learning, a cautionary tale

abstract: People show vast variability in skill learning. What determines a persons individual learning ability? In this study we explored the possibility to predict participants future learning, based on their behavior during initial skill acquisition. We recruited a large online multi-session sample of participants performing a sequential tapping skill learning task. We trained machine learning models to predict future skill learning from raw data acquired during initial skill acquisition, and from engineered features calculated from the raw data. While the models did not explain learning, strong correlations were observed between initial and final performance. In addition, the results suggest that in correspondence with other empirical fields testing human behavior, canonical experimental tasks developed and selected to detect average effects may constrain insights regarding individual variability, relevant for real-life scenarios. Overall, implementing machine learning tools on large-scale data sets may provide a powerful approach towards revealing what differentiates between high and low innate learning abilities, paving the way for learning optimization techniques which may generalize beyond motor skill learning to broad learning abilities.


title: Preterm infants voice processing is mediated by voice familiarity

abstract:
Understanding how prematurity and language or voice familiarity impact on language perception at birth becomes crucial to determine which brain regions support language processing at this age, and how an atypical early sensory experience affects language-related brain areas. However, the time-frequency correlates of maternal voice processing remain to date unknown.

Ten preterm and ten full-term newborns underwent EEG recordings during the presentation of their mothers or a strangers speech. The speech could be naturalistic (presented in the forward order) or non-naturalistic (in the backward order). Time-frequency decomposition was performed and task-related responses were analyzed following a topographical data driven clustering using General Linear Mixed model approaches.

Differential responses were observed in left and right temporal areas. In the left-temporal areas, a specific processing of the naturalistic mother compared to stranger speech was observed in low-frequency bands (theta and alpha bands), but taking antagonistic forms in the two groups i.e. a power increase for full-term and a power decrease (theta) or maintenance (alpha) in preterm babies. Left-temporal low-beta activity presents, in full-term babies, in the forward condition, a power increase for the maternal voice and a power decrease for the stranger voice, which were not observed in preterm babies. In the right-temporal scalp area, we observed in the low-beta and low-gamma bands a mother forward specific power-decrease in the preterm population specifically, with higher values for the mother backward, while terms were mostly activated by the most unfamiliar stimulus, the stranger backward voice.

The current study shows, through complex time-frequency patterns, that the naturalistic mother voice elicits expected brain responses in the full-term newborns, which were different from the preterms ones, both in the left and right temporal areas.


title: Huntington's Disease Produces Multiplexed Transcriptional Vulnerabilities of StriatalD1-D2 and Striosome-Matrix Neurons

abstract: Striatal cell-type-specific vulnerability in Huntingtons disease (HD) preferentially affects dopamine D2R-expressing projection neurons (SPNs), compatible with manifest motor symptomatology in HD. Transcriptional studies of striatal striosome-matrix compartmentalization in HD are, however, limited, despite pathologic evidence for striosome vulnerability aligning with early mood symptomatology. We used single-nucleus RNA-sequencing on striatal samples from two murine models, and rare Grade 1 HD patient tissues, to examine striosome and matrix sub-clusters within parent D1 and D2 SPN clusters. In human HD, striosomal SPNs were the most depleted SPN population. Surprisingly, for both mouse models, transcriptomic distinctiveness was diminished more for striosome-matrix SPNs than for D1-D2 SPNs. Compartmental markers were dysregulated so as to cancel endogenous identities as striosomal or matrix SPNs, but markers for D1-D2 exhibited less identity obscuring. The canonical striosome-matrix as well as D1-D2 organizations of the striatum thus are both strongly, but differentially, compromised in HD and are targets for therapeutics.


title: Next-generation matrices for marine metapopulations: the case of sea lice on salmon farms

abstract: Classifying habitat patches as sources or sinks and determining metapopulation persistence requires coupling connectivity between habitat patches with local demographic rates. In this paper we show how next-generation matrices, originally popularized in epidemiology to calculate new infections after one generation, can be used in an ecological context to couple connectivity with local demography to calculate sources and sinks as well as metapopulation persistence in marine metapopulations. To demonstrate the utility of the method, we construct a next-generation matrix for a network of sea lice populations on salmon farms in the Broughton Archipelago, BC, an intensive salmon farming region on the west coast of Canada where certain salmon farms are currently being removed under an agreement between local First Nations and the provincial government. We identify the salmon farms which are acting as the largest sources of sea lice and show that in this region the most productive sea lice populations are also the most connected. We find that the farms which are the largest sources of sea lice have not yet been removed from the Broughton Archipelago, and that warming temperatures could lead to increased sea louse growth.

category: ecology


title: Long-term imaging reveals behavioral plasticity during C. elegans dauer exit

abstract: During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to adjust through dynamic expression of neurotransmitters and receptors but also through growth, spatial reorganization and connectivity while integrating external stimuli. For instance, despite having a fixed neuronal cell lineage, the nematode Caenorhabditis elegans nervous system remains plastic throughout its development. Here, we focus on a specific example of nervous system plasticity, the C. elegans dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive dauer stage and adapt their behavior to cope with a new environment. Upon improved conditions, this stress resistant developmental stage is actively reversed to resume reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larvas behavioral change is unknown. To fill this gap, we developed a new open hardware method for long-term imaging (12h) of C. elegans larvae. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments to identify key decision points. Combining long-term behavioral imaging with transcriptomics, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior. Taken together, we show how a developing nervous system can robustly integrate environmental changes, activate a developmental switch and adapt the organisms behavior to a new environment.

category: animal behavior and cognition


title: Rapid biomechanical imaging at low irradiation level via dual line-scanning Brillouin microscopy

abstract: Brillouin microscopy is a promising all-optical technique for biomechanics but is limited by slow acquisition speed and/or large irradiation doses. Here, we introduce multiplexed Brillouin microscopy that overcomes both these limits by over one order of magnitude with selective illumination and single-shot analysis of hundreds of points along the incident beam axis. We demonstrate the enabling capabilities of this method probing rapid response to perturbations and long-term mechanical evolution of tumor spheroids.

category: bioengineering


title: Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

abstract: Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of communities of multiple species. Metatranscriptomics in particular offers an understanding of real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. However, these approaches are rarely validated. A systematic validation of metatranscriptome assembly and annotation methods is necessary to appropriately assess (1) the fidelity of our community composition measurements and (2) the confidence of novel taxonomic and functional content discovered with metatranscriptomics. Here, we present euk rhythmic, an automated and customizable multi-assembler workflow for eukaryotic metatranscriptome assembly, annotation, and analysis, and validate the ability of the pipeline to recapitulate simulated eukaryotic community-level expression data treated as a gold standard. Finally, we apply this pipeline to two previously published metatranscriptomic datasets, showing both recapitulation of previous results as well as enhanced taxonomic and functional gene discovery.

category: bioinformatics


title: Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference

abstract: Identifying the causal interactions in gene-regulatory networks requires an accurate understanding of the time-lagged relationships between transcription factors and their target genes. Here we describe DELAY, a convolutional neural network for the inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. We show that combining supervised deep learning with joint-probability matrices of pseudotime-lagged trajectories allows the network to overcome important limitations of ordinary Granger causality-based methods, such as the inability to infer cyclic relationships such as feedback loops. Our network outperforms several common methods for inferring gene regulation and predicts novel regulatory networks from scRNA-seq and scATAC-seq datasets given partial ground-truth labels. To validate this approach, we used DELAY to identify important genes and modules in the regulatory network of auditory hair cells, as well as likely DNA-binding partners for two hair cell cofactors (Hist1h1c and Ccnd1) and a novel binding sequence for the hair cell-specific transcription factor Fiz1. We provide an open-source implementation of DELAY at https://github.com/calebclayreagor/DELAY.


title: In silico modelling demonstrates that user variability during tumour measurement can affect in vivo therapeutic efficacy outcomes

abstract:
User measurement bias during subcutaneous tumor measurement is a source of variation in preclinical in vivo studies. We investigated whether this user variability could impact efficacy study outcomes, in the form of the false negative result rate when comparing treated and control groups.

Two tumor measurement methods were compared; calipers which rely on manual measurement, and an automatic 3D and thermal imaging device. Tumor growth curve data were used to create an in silico efficacy study with control and treated groups. Before applying user variability, treatment group tumor volumes were statistically different to the control group. Utilizing data collected from 15 different users across 9 in vivo studies, user measurement variability was computed for both methods and simulation was used to investigate its impact on the in silico study outcome.

User variability produced a false negative result in 3.5% to 19.5% of simulated studies when using calipers, depending on treatment efficacy. When using an imaging device with lower user variability this was reduced to 0.0% to 2.4%, demonstrating that user variability impacts study outcomes and the ability to detect treatment effect.

Reducing variability in efficacy studies can increase confidence in efficacy study outcomes without altering group sizes. By using a measurement device with lower user variability, the chance of missing a therapeutic effect can be reduced and time and resources spent pursuing false results could be saved. This improvement in data quality is of particular interest in discovery and dosing studies, where being able to detect small differences between groups is crucial.


title: Ancestral Body Plan and Adaptive Radiation of Sauropterygian Marine Reptiles

abstract: Mesozoic was the age of reptiles that not only occupied the land and sky but also adapted to the sea. Sauropterygia, from turtle-like placodonts, lizard-like pachypleurosaurs, and predatory nothosaurs to long-necked pistosaurs including plesiosaurs, is one of the most predominant lineages among secondarily aquatic reptiles. However, we know little about the early evolution of sauropterygians involving the morphological gaps among aforementioned sub-groups and their ancestral body-plan, because the Early Triassic fossil remains are scarce shortly after their origin. Here we report a skeleton from the Early Triassic in South China, representing the oldest known complete specimen related to Sauropterygia. It can be referred to Hanosaurus hupehensis and shows a mosaic morphology combining the characters of multiple sauropterygian sub-lineages. We constructed an updated character matrix obtaining the hitherto most comprehensive phylogeny of Triassic sauropterygians, and Hanosaurus hupehensis is stably resolved as the basal-most member of the Sauropterygiformes (clade nov.). Sauropterygians were previously considered using limb propulsion for the movement that is distinguishable from ichthyosaurs and other marine reptiles, but this skeleton reflects an ancestral body plan of sauropterygians unexpectedly developing an elongate trunk and four short limbs, being different from most sauropterygians but more convergently similar to the basal members of other marine reptilian lineages in body shape. After this convergence, we confirm the rapid adaptive radiation of sauropterygiform reptiles following the end-Permian mass extinction. Our results provide an evolutionary framework of sauropterygian marine reptiles and highlight the integrations of both convergences and divergences when an emerging animal lineage arises.

category: paleontology


title: A comparison of ImageJ and machine learning based image analysis methods to measure cassava bacterial blight disease severity

abstract:
BackgroundMethods to accurately quantify disease severity are fundamental to plant pathogen interaction studies. Commonly used methods include visual scoring of disease symptoms, tracking pathogen growth in planta over time, and various assays that detect plant defense responses. Several image-based methods for phenotyping of plant disease symptoms have also been developed. Each of these methods has different advantages and limitations which should be carefully considered when choosing an approach and interpreting the results.

ResultsIn this paper, we developed two image analysis methods and tested their ability to quantify different aspects of disease lesions in the cassava-Xanthomonas pathosystem. The first method uses ImageJ, an open-source platform widely used in the biological sciences. The second method is a few-shot support vector machine learning tool that uses a classifier file trained with five representative infected leaf images for lesion recognition. Cassava leaves were syringe infiltrated with wildtype Xanthomonas, a Xanthomonas mutant with decreased virulence, and mock treatments. Digital images of infected leaves were captured overtime using a Raspberry Pi camera. The image analysis methods were analyzed and compared for the ability to segment the lesion from the background and accurately capture and measure differences between the treatment types.

ConclusionsBoth image analysis methods presented in this paper allow for accurate segmentation of disease lesions from the non-infected plant. Specifically, at 4-, 6-, and 9-days post inoculation (DPI), both methods provided quantitative differences in disease symptoms between different treatment types. Thus, either method could be applied to extract information about disease severity. Strengths and weaknesses of each approach are discussed.

category: plant biology


title: From retina to motoneurons: a substrate for visuomotor transformation in salamanders

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe transformation of visual input into motor output is essential to approach a target or avoid a predator. In salamanders, visually-guided orientation behaviors have been extensively studied during prey capture. However, the neural circuitry involved is not resolved. Using salamander brain preparations, calcium imaging and tracing experiments, we describe a neural substrate through which retinal input is transformed into spinal motor output. We found that retina stimulation evoked responses in reticulospinal neurons of the middle reticular nucleus, known to control steering movements in salamanders. Microinjection of glutamatergic antagonists in the optic tectum (superior colliculus in mammals) decreased the reticulospinal responses. Using tracing we found that retina projected to the dorsal layers of the contralateral tectum, where the dendrites of neurons projecting to the middle reticular nucleus were located. In slices, stimulation of the tectal dorsal layers evoked glutamatergic responses in deep tectal neurons retrogradely labelled from the middle reticular nucleus. We then examined how tectum activation translated into spinal motor output. Tectum stimulation evoked motoneuronal responses, which were decreased by microinjections of glutamatergic antagonists in the contralateral middle reticular nucleus. Reticulospinal fibers anterogradely labelled from tracer injection in the middle reticular nucleus were preferentially distributed in proximity with the dendrites of ipsilateral motoneurons. Our work establishes a neural substrate linking visual and motor centers in salamanders. This retino-tecto-reticulo-spinal circuitry is well positioned to control orienting behaviors. Our study bridges the gap between the behavioral studies and the neural mechanisms involved in the transformation of visual input into motor output in salamanders.


title: Transcranial Direct Current Stimulation Alters the Waveform Shape of Cortical Gamma Oscillations

abstract: Neuronal oscillations in different frequency bands have been linked to a wide variety of cognitive functions, and may even be a fundamental mechanism of inter-regional communication. For this reason, manipulation of oscillatory activity via brain stimulation is a central goal in neuroscience research. However, the vast majority of studies characterise oscillatory activity solely in terms of amplitude and frequency. Oscillations can also be characterised by their waveform shape; the degree to which they resemble or deviate from sinusoids. Here we exploit Empirical Mode Decomposition (EMD), a novel method that allows quantification of oscillatory waveform shape. We show for the first time that transcranial direct current stimulation (tDCS) alters the waveform shape of gamma oscillatory activity in the visual cortex. Notably, changes in waveform shape were limited to one half of the phase cycle; anodal stimulation led to a relatively slower, and cathodal to a relatively faster, descending half-wave. tDCS is generally believed to affect cortical excitability via alteration of resting membrane potential. Interestingly, simulations of altered cortical excitability in a gamma-generating neuronal population indicated the waveform shape changes observed experimentally likely stem from stimulation of pyramidal neurons. These findings have implications for understanding the neural consequences of tDCS at the level of neuronal population phenomena such as cortical oscillations and underscore the importance of waveform shape as an important feature of neuronal oscillations.


title: Histone H2A serine-1 phosphorylation is a chaperone-dependent signal for dimerization with H2B and for enhanced deposition

abstract: Multiple histone chaperones and histone modifications are involved in the folding, transport, and re-lease of histones onto newly replicated DNA. Little is known about histone H2A-H2B pre-deposition his-tone modifications and their regulation of histone deposition. We previously showed that H2A serine 1 phosphorylation (H2AS1ph) is enriched on the soluble egg histones and on zygotic chromatin in Xenopus embryos. Here, we demonstrate that H2AS1 phosphorylation is required for a timely incorporation of H2A-H2B into the pronuclear chromatin. Our analysis revealed that exogenous H2AS1A-H2B dimers were poorly incorporated into pronuclei in egg extract compared with wildtype and H2AS1E-H2B dimers. Chaperone-mediated deposition using histones purified from pronuclei showed that neither Nap1 nor Nucleoplasmin (Npm2) histone deposition was directly affected by endogenous histone posttranslational modification. We further demonstrate that H2AS1 phosphorylation was dependent on Npm2 and required H2B. Surprisingly, Nap1 was incapable of promoting H2AS1 phosphorylation. These results suggest that serine 1 phosphorylation signals a specific state of H2A-H2B dimer bound by Nucleoplasmin. Neither Npm2 nor Nap1 exhibited preference for binding H2AS1A or H2AS1E mutant histones or dimers with H2B in vitro. We propose that H2AS1 phosphorylation is a pre-deposition modification that signals for the proper dimerization of H2A-H2B, which in turn activates downstream effectors leading to H2A-H2B deposition.


title: A generic risk assessment model for animal disease incursion through wildlife

abstract: Animal diseases can be introduced into countries or regions through wildlife. A generic risk model would allow to quantify this incursion risk for different diseases and wildlife species, despite the vast variety in both. Here, we propose such a generic risk assessment model and illustrate its workings by assessing the incursion risk of African swine fever (ASF) through wild boar and highly pathogenic avian influenza (HPAI) through wild birds for the Netherlands between 2014-2021. We used disease outbreak data and abstracted movement patterns to populate a stochastic risk model. We found that the incursion risk of HPAI fluctuated between the years with a peak in 2021. In that year, we estimated the number of infected birds to reach the Dutch border by wild bird migration at 261 (95% uncertainty interval: 248-278). The probability that ASF outbreaks that occurred between 2014 and 2021, reached the Dutch border through wild boar movement was very low throughout the whole period; only the upper confidence bound indicated a small incursion risk. On a yearly scale, the predicted incursion risk for HPAI correlated well with the number of observed outbreaks. In conclusion, we present a generic and flexible framework to assess the incursion risk of disease through wildlife. The model allows rapid and transparent estimation of the incursion risk for diverse diseases and wildlife species. The modular structure of the model allows to add nuance and complexity, when required or when more data becomes available.


title: Mating strategy predicts gene presence/absence patterns in a genus of simultaneously hermaphroditic flatworms

abstract: Gene repertoire turnover is a characteristic of genome evolution. However, we lack well-replicated analyses of presence/absence patterns associated with different selection contexts. Here, we study [~]100 transcriptome assemblies across Macrostomum, a genus of simultaneously hermaphroditic flatworms exhibiting multiple convergent shifts in mating strategy and associated reproductive morphologies. Many species mate reciprocally, with partners donating and receiving sperm at the same time. Other species convergently evolved to mate by hypodermic injection of sperm into the partner. We find that for orthologous genes annotated as expressed in the body region containing the testes, sequences from hypodermically inseminating species diverge more rapidly from the model species, M. lignano, and have a lower probability of being observed in other species. For other genes, simpler models with a constant rate of similarity decay with increasing genetic distance from M. lignano match the observed patterns well. Thus, faster rates of sequence evolution for hypodermically inseminating species in testis-region genes result in higher rates of homology detection failure, yielding a signal of rapid evolution in gene presence/absence patterns. Our results highlight the utility of considering appropriate null models for unobserved genes, as well as associating patterns of gene presence/absence with replicated evolutionary events in a phylogenetic context.

category: evolutionary biology


title: High-resolution line-scan Brillouin microscopy for live-imaging of mechanical properties during embryo development

abstract: Brillouin microscopy (BM) can be used to assess the mechanical properties of biological samples in a 3D, all-optical, and hence non-contact fashion, but its weak signals require long imaging times and illumination dosages harmful to living organisms. Here, we present a line-scanning Brillouin microscope optimized for fast and high-resolution live-imaging of dynamic biological processes with low photo-toxicity. In combination with fluorescence light-sheet imaging, we demonstrate the capabilities of our microscope to visualize the mechanical properties of cells and tissues over space and time in living model organisms such as fruit flies, ascidians, and mouse embryos.


title: Mixture Margin Random-effects Copula Models for Inferring Temporally Conserved Microbial Co-variation Networks from Longitudinal Data

abstract:
Longitudinal microbiome studies, in which data on a single subject is collected repeatedly over time, are becoming increasingly common in biomedical research. Such studies provide an opportunity to study the inherently dynamic nature of a microbiome in a way that cannot be done using cross-sectional studies. In this paper, we develop random-effects copula models with mixed zero-beta margins to identify biologically meaningful temporally conserved co-variation between two bacterial taxa, while accounting for the excessive zeros seen in 16S rRNA and metagenomic sequencing data. The model assumes a random-effects model for the dependence parameter in the copulas, which captures the conserved microbial co-variation while allowing for a time-specific dependence parameters. We develop a Monte Carlo EM algorithm for efficient estimation of model parameters and a corresponding Monte Carlo likelihood ratio test for the mean dependence parameter. Simulation studies show that our test controls the Type I error rate and provides an unbiased estimate of the mean dependence parameter. Additionally, we apply our method to a longitudinal pediatric cohort and identify changes in both local and global patterns of microbial co-variation networks in infants treated with antibiotics. Our analysis shows that the no antibiotics network is less dependent on individual taxon, thus making it more stable than the antibiotics network and more robust to both targeted and random attacks.

Author summaryIdentification of co-variation between two microbes in microbial communities provides important insights into the community structure and stability. The commonly used measures of co-variation do not handle excessive zeros observed in the data and cannot be applied to longitudinal microbiome data directly. In this paper, we develop random-effects copula models with mixed zero-beta margins to identify biologically meaningful temporally conserved co-variation between two bacterial taxa, while accounting for the excessive zeros seen in 16S rRNA and metagenomic sequencing data. The model captures the conserved microbial co-variations while allowing for a time-specific dependence parameters. We develop an efficient Monte Carlo-based algorithm for parameter estimation and statistical inference. We analyze the data from a pediatric longitudinal cohort and identify changes in both local and global patterns of microbial co-variation networks in infants treated with antibiotics.


title: Spatial Transcriptomics Prediction from Histology jointly through Transformer and Graph Neural Networks

abstract: The rapid development of spatial transcriptomics allows for the measurement of RNA abundance at a high spatial resolution, making it possible to simultaneously profile gene expression, spatial locations, and the corresponding hematoxylin and eosin-stained histology images. Since histology images are relatively easy and cheap to obtain, it is promising to leverage histology images for predicting gene expression. Though several methods have been devised to predict gene expression using histology images, they dont simultaneously include the 2D vision features and the spatial dependency, limiting their performances. Here, we have developed Hist2ST, a deep learning-based model using histology images to predict RNA-seq expression. At each sequenced spot, the corresponding histology image is cropped into an image patch, from which 2D vision features are learned through convolutional operations. Meanwhile, the spatial relations with the whole image and neighbored patches are captured through Transformer and graph neural network modules, respectively. These learned features are then used to predict the gene expression by following the zero-inflated negative binomial (ZINB) distribution. To alleviate the impact by the small spatial transcriptomics data, a self-distillation mechanism is employed for efficient learning of the model. Hist2ST was tested on the HER2-positive breast cancer and the cutaneous squamous cell carcinoma datasets, and shown to outperform existing methods in terms of both gene expression prediction and following spatial region identification. Further pathway analyses indicated that our model could reserve biological information. Thus, Hist2ST enables generating spatial transcriptomics data from histology images for elucidating molecular signatures of tissues.


title: Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation

abstract: Microsurgical techniques, such as those used in the early 1900s by Mangold and Spemann, were not only foundational for experimental embryology, but are still in use today. Here, we build on these classic techniques by introducing a user-friendly robotic microsurgery platform that allows precise mechanical manipulation of soft tissues in zebrafish embryos. As a proof of principle, we investigated the contribution of different embryonic tissues to vertebrate anteroposterior (AP) axis elongation and segmentation. Using our platform, we reproducibly targeted precise regions of tail explants, and quantified the response in real-time by following notochord and presomitic mesoderm (PSM) morphogenesis and segmentation clock dynamics. We find an extension force generated through the posterior notochord, independent of notochord cell vacuolation, that is strong enough to buckle the structure. Our data suggest that this force generates a unidirectional notochord extension towards the tailbud because PSM tissue around the posterior notochord does not let it slide anteriorly. These results complement existing biomechanical models of axis elongation, revealing a critical coupling between the posterior notochord, the tailbud, and the PSM, and show that somite patterning is robust against structural perturbations.

category: biophysics


title: Localization of chemical synapses and modulatory release sites in the cardiac ganglion of the crab, Cancer borealis

abstract: The crustacean cardiac ganglion (CG) comprises nine neurons that provide rhythmic drive to the heart. The CG is the direct target of multiple modulators. Synapsin-like immunoreactivity was found clustered around the somata of the large cells (LC) and in a neuropil at the anterior branch of the CG trunk. This implicates the soma as a key site of synaptic integration, an unusual configuration in invertebrates. Proctolin is an excitatory neuromodulator of the CG and proctolin-like immunoreactivity exhibited partial overlap with putative chemical synapses near the LCs and at the neuropil. A proctolin-like projection was also found in a pair of excitatory nerves entering the CG. GABA-like immunoreactivity was nearly completely colocalized with chemical synapses near the LCs but absent at the anterior branch neuropil. GABA-like projections were found in a pair of inhibitory nerves entering the CG. Cancer borealis Allatostatin B1 (CbAST-B1), red pigment concentrating hormone (RPCH) and FLMRFamide-like immunoreactivity each had a unique pattern of staining and co-localization with putative chemical synapses. These results provide morphological evidence that synaptic input is integrated at LC somata in the CG. Our findings provide a topographical organization for some of the multiple inhibitory and excitatory modulators that alter the rhythmic output of this semi-autonomous motor circuit.


title: The limited place in cognitive space

abstract: The idea that objects can be represented within multi-dimensional  cognitive spaces remains popular within psychology and neuroscience, and yet the restrictive topology of such spaces is seldom considered. Here, we show that it is possible, even within a simple set of items, to break such models by imposing neighbourhood relations that are incompatible with a purely spatial representation. These results highlight the fundamental limits of cognitive space as a representational format for complex cognition.


title: Astrocyte calcium dysfunction causes early network hyperactivity in Alzheimer's Disease

abstract: Dysfunctions of network activity and functional connectivity (FC) represent early events in Alzheimers disease (AD), but the underlying mechanisms remain unclear. Astrocytes regulate neuronal activity in the healthy brain, but their involvement in early network hyperactivity in AD is unknown. We show increased FC in the human cingulate cortex, several years before amyloid deposition. We found the same early cingulate FC disruption and neuronal hyperactivity in AppNL-F mice. Crucially, these network disruptions are accompanied by decreased astrocyte calcium signaling. Recovery of astroglial calcium activity normalizes neuronal hyperactivity and FC, as well as seizure susceptibility and day/night behavioral hyperactivity. In conclusion, we show for the first time that astrocytes mediate initial features of AD and drive clinically relevant phenotypes.


title: Transfer of weight information depends differently on used hand and handedness for perception and action

abstract: When lifting an object sequentially with the two hands, information about object weight can be transferred from one hand to the other. This information can be used to predictively scale fingertip forces and to form a perceptual estimation about the objects weight. This study investigated how weight information can be transferred between the two hands and how this depends on the used hand and handedness of the participant. Right- and left-handed participants lifted light and heavy objects with the right or left hand in a pseudorandomized order and estimated the objects weight. Results showed that predictive force scaling depended on the previously lifted object, with higher forces rates if a previous object was heavy. This known effect of sensorimotor memory was mostly independent of the used hand and handedness, indicating that weight information could be transferred for fingertip force scaling. Furthermore, a perceptual bias depending on the previous lifted object was found, with lower weight estimations when the previous object was heavy compared to light. In contrast to the results on force scaling, a transfer of this perceptual bias was only found in left-handed participants. In addition, right-handers only showed a bias when they used their dominant hand. These findings indicate that the transfer of weight information depends differently on the used hand and handedness for perceptual estimations and predictive force scaling.


title: Scientific opportunities for developing essential biodiversity variables from satellite remote sensing in the context of the post-2020 global biodiversity framework

abstract: Satellite remote sensing (SRS) provides huge potential for tracking progress towards achieving global conservation targets and goals. To make a transformative impact, SRS workflows should be tailored towards the requirements of ecological users and policymakers. Here, we assess requirements from the post-2020 global biodiversity framework of the Convention of Biological Diversity (CBD) by ranking the use of SRS products in biodiversity indicator workflows. Fifty unique indicators were identified for tracking the state of terrestrial biodiversity, spanning two goals and six targets across seventeen target components. Twentynine indicators shared enough information to analyse workflows and to classify underlying (spatial information) products into the Essential Biodiversity Variable (EBV) framework. We further quantified the policy relevance of EBVs by counting EBV usage across the CBD goals and targets. Combined with scores on the technical feasibility, accuracy, and immaturity of SRS products, we then identified which EBVs offer promising opportunities for workflow development from SRS. Top priority SRS products included the fraction of vegetation cover, plant area index profile, above-ground biomass, foliar N/P/K content, land cover (vegetation type), leaf area index, carbon cycle (above-ground biomass), chlorophyll content & flux, ecosystem fragmentation, ecosystem structural variance, and gross primary productivity. Our results showed that spatial information products related to ecosystem distribution, live cover fraction and species distribution EBVs are currently most widely used in the CBD context, while primary production and physiology EBVs remain under-used. To advance the monitoring of ecosystem distributions, harmonized and high resolution SRS products with higher thematic detail on specific ecosystems and habitat types are needed. Likewise, live cover fraction EBVs (e.g. fraction of vegetation cover and plant area index profile) would require developing and harmonizing ecosystem taxonomies and relating the fraction of vegetation (functional) types to a desired ecosystem reference state. Finally, to enable the monitoring of plant species phenology, stoichiometry and alien invasive species (impact), novel workflows need to combine very high resolution and multi-spectral satellite observations for mapping and monitoring the physiological traits of plant species (e.g. leaf area index, chlorophyll content & flux, and foliar N/P/K content). Capitalizing on these opportunities for SRS-enabled EBVs could improve the tracking of CBD goals and targets, e.g. in the context of ecosystem restoration, productivity and sustainability of agricultural and forested ecosystems, effective management of protected areas, reduction of species extinction rates, or a better management of the impact of alien invasive species.


title: Optimizing Oscillators for Specific Tasks Predicts Preferred Biochemical Implementations

abstract:
Oscillatory processes are used throughout cell biology to control time-varying physiology including the cell cycle, circadian rhythms, and developmental patterning. It has long been understood that free-running oscillations require feedback loops where the activity of one component depends on the concentration of another. Oscillator motifs have been classified by the positive or negative net logic of these loops. However, each feedback loop can be implemented by regulation of either the production step or the removal step. These possibilities are not equivalent because of the underlying structure of biochemical kinetics. By computationally searching over these possibilities, we find that certain molecular implementations are much more likely to produce stable oscillations. These preferred molecular implementations are found in many natural systems, but not typically in artificial oscillators, suggesting a design principle for future synthetic biology. Finally, we develop an approach to oscillator function across different reaction networks by evaluating the biosynthetic cost needed to achieve a given phase coherence. This analysis predicts that phase drift is most efficiently suppressed by delayed negative feedback loop architectures that operate without positive feedback.

PACS numbers47.15.-x

category: systems biology


title: Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

abstract: Single-cell RNA sequencing has the potential to unravel the differences in metabolism across cell types and cell states in both the healthy and diseased human body. The use of existing knowledge in the form of genome-scale metabolic models (GEMs) holds promise to strengthen such analyses, but the combined use of these two methods requires new computational methods. Here, we present a method for generating cell-type-specific genome-scale models from clusters of single-cell RNA-Seq profiles. Specifically, we developed a method to estimate the number of cells required to pool to obtain stable models, a bootstrapping strategy for estimating statistical inference, and a faster version of the tINIT algorithm for generating context-specific GEMs. In addition, we evaluated the effect of different RNA-Seq normalization methods on model topology and differences in models generated from single-cell and bulk RNA-Seq data. We applied our methods on data from mouse cortex neurons and cells from the tumor microenvironment of lung cancer and in both cases found that almost every cell subtype had a unique metabolic profile, emphasizing the need to study them separately rather than to build models from bulk RNA-Seq data. In addition, our approach was able to detect cancer-associated metabolic differences between cancer cells and healthy cells, showcasing its utility. With the ever-increasing availability of single-cell RNA-Seq datasets and continuously improved GEMs, their combination holds promise to become an important approach in the study of human metabolism.


title: In vitro longitudinal lumbar spinal cord preparations to study sensory and recurrent motor microcircuits of juvenile mice

abstract:
In vitro spinal cord preparations have been extensively used to study microcircuits involved in the control of movement. By allowing precise control of experimental conditions coupled with state-of-the-art genetics, imaging and electrophysiological techniques, isolated spinal cords from mice have been an essential tool in detailing the identity, connectivity and function of spinal networks. The majority of the research has arisen from in vitro spinal cords of neonatal mice, which are still undergoing important postnatal maturation. Studies from adults have been attempted in transverse slices, however, these have been quite challenging due to the poor motoneuron accessibility and viability, as well as to the extensive damage to the motoneuron dendritic trees. In this work, we describe two types of coronal spinal cord preparations with either the ventral or the dorsal horn ablated, obtained from mice of different postnatal ages, spanning from pre-weaned to one month old. These semiintact preparations allow recordings of sensory-afferent and motor-efferent responses from lumbar motoneurons using whole cell patch-clamp electrophysiology. We provide details of the slicing procedure and discuss the feasibility of whole-cell recordings. The in vitro dorsal and ventral horn-ablated spinal cord preparations described here are an useful tool to study spinal motor circuits in young mice that have reached the adult stages of locomotor development.

New & NoteworthyIn the past 20 years, most of the research into the mammalian spinal circuitry has been limited to in vitro preparations from embryonic and neonatal mice. We describe two in vitro longitudinal lumbar spinal cord preparations from juvenile mice, that allow the study of motoneuron properties and respective afferent or efferent spinal circuits through whole-cell patch-clamp. These preparations will be useful to those interested in the study of microcircuits at mature stages of motor development.


title: Early dosage compensation of zygotically-expressed genes in Drosophila melanogaster is mediated through a post-transcriptional regulatory mechanism

abstract: Many key regulators of early embryogenesis in Drosophila melanogaster are X-linked. However, the canonical, MSL-mediated dosage compensation, which involves hyper-transcription of the genes on the single X chromosome in males, is not active until the post-syncytial stage of development. A separate MSL-independent dosage compensation system active earlier in development has been described, though the mechanism through which the process functions remain unclear. In this study, we quantified transcription in living embryos at single-locus resolution to determine if early dosage compensation of the X-linked genes buttonhead and giant is sensitive to X chromosome dose. We found no evidence for a transcriptionally regulated mechanism of early dosage compensation, suggesting that the previously observed compensation of mRNA levels for these genes is achieved via a post-transcriptional regulatory mechanism.


title: Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

abstract: While a rich set of putative cis-regulatory sequences involved in mouse fetal development has been annotated recently based on chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, we mapped chromatin contacts between gene promoters and distal sequences genome-wide in seven mouse fetal tissues, and for one of them, across six developmental stages. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations as well as developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers, and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

category: developmental biology


title: Legacy of past exposure to hypoxia and warming regulates ecosystem service provided by oysters

abstract:
Climate change is having substantial impacts on organism fitness and ability to deliver critical ecosystem services, but these effects are often examined only in response to current environments. Past exposure to stress can also affect individuals via carryover effects, and whether these effects scale from individuals to influence ecosystem function and services is unclear. We explored carryover effects of two coastal climate change stressors - hypoxia and warming - on oyster (Crassostrea virginica) growth and nitrogen bioassimilation, an important ecosystem service. Oysters were exposed to a factorial combination of two temperature and two diel-cycling dissolved oxygen treatments at three-months-old and again one year later. Carryover effects of hypoxia and warming influenced oyster growth and nitrogen storage, with early life stress generally reducing nitrogen storage and relative tissue growth, particularly in warm environments. When extrapolated to the reef scale, carryover effects reduced estimated nitrogen storage by a restored oyster reef by as much as 41%, a substantial decline in a critical ecosystem service. Even brief exposure to climate change stressors early in life has persistent, negative effects on an ecosystem service one year later. Carryover effects on individuals impact processes at the ecological scale and must be considered in assessments of and management plans for species and ecosystems threatened by anthropogenic change.

Significance StatementAnthropogenic change threatens organisms ability to provide ecosystem services through effects on individual phenotypes. Past experiences with anthropogenic stress can have delayed, persistent impacts on organisms via carryover effects, but how carryover effects scale to influence ecosystem function and services is not yet established. In marine systems, foundation species such as oysters mitigate effects of eutrophication by storing nutrients like nitrogen in their tissue and shell. We show that past exposure to two interacting climate change stressors (hypoxia and warming) reduces nitrogen stored by oysters by as much as 41% one year after initial exposure. Our results reveal carryover effects as a novel pathway through which climate change affects ecosystem processes that should be incorporated into conservation and management plans.


title: Computational modeling of posteroanterior lumbar traction by an automated massage bed: predicting intervertebral disc stresses and deformation

abstract: Spinal traction is a physical intervention that provides constant or intermittent stretching axial force to the lumbar vertebrae to gradually distract spinal tissues into better alignment, reduce intervertebral disc (IVD) pressure, and manage lower back pain (LBP). However, such axial traction may change the normal lordotic curvature, and result in unwanted side effects and/or inefficient reduction of the IVD pressure. An alternative to axial traction has been recently tested, consisting of posteroanterior (PA) traction in supine posture, which was recently shown effective to increase the intervertebral space and lordotic angle using MRI. PA traction aims to maintain the lumbar lordosis curvature throughout the spinal traction therapy while reducing the intradiscal pressure. In this study, we developed finite element simulations of mechanical therapy produced by a commercial thermo-mechanical massage bed capable of spinal PA traction. The stress relief produced on the lumbar discs by the posteroanterior traction system was investigated on human subject models with different BMI (normal, overweight, moderate obese and extreme obese BMI cases). We predict typical traction levels lead to significant distraction stresses in the lumbar discs, thus producing a stress relief by reducing the compression stresses normally experienced by these tissues. Also, the stress relief experienced by the lumbar discs was effective in all BMI models, and it was found maximal in the normal BMI model. These results are consistent with prior observations of therapeutic benefits derived from spinal AP traction.


title: Predicting coordinates of peptide features in raw timsTOF data with machine learning for targeted extraction reduces missing values in label-free DDA LC-MS/MS proteomics experiments

abstract:
1The determination of relative protein abundance in label-free data dependant acquisition (DDA) LC-MS/MS proteomics experiments is hindered by the stochastic nature of peptide detection and identification. Peptides with an abundance near the limit of detection are particularly effected. The possible causes of missing values are numerous, including; sample preparation, variation in sample composition and the corresponding matrix effects, instrument and analysis software settings, instrument and LC variability, and the tolerances used for database searching.

There have been many approaches proposed to computationally address the missing values problem, predominantly based on transferring identifications from one run to another by data realignment, as in MaxQuants matching between runs (MBR) method, and/or statistical imputation. Imputation transfers identifications by statistical estimation of the likelihood the peptide is present based on its presence in other technical replicates but without probing the raw data for evidence.

Here we present a targeted extraction approach to resolving missing values without modifying or realigning the raw data. Our method, which forms part of an end-to-end timsTOF processing pipeline we developed called Targeted Feature Detection and Extraction (TFD/E), predicts the coordinates of peptides using machine learning models that learn the delta of each peptides coordinates from a reference library. The models learn the variability of a peptides location in 3D space from the variability of known peptide locations around it. Rather than realigning or altering the raw data, we create a run-specific  lens through which to observe the data, targeting a location for each peptide of interest and extracting it. By also creating a method for extracting decoys, we can estimate the false discovery rate (FDR). Our method outperforms MaxQuant and MSFragger by achieving substantially fewer missing values across an experiment of technical replicates. The software has been developed in Python using Numpy and Pandas and open sourced with an MIT license (DOI 10.5281/zenodo.6513126) to provide the opportunity for further improvement and experimentation by the community. Data are available via ProteomeXchange with identifier PXD030706.

2 Author SummaryMissed identifications of peptides in data-dependent acquisition (DDA) proteomics experiments are an obstacle to the precise determination of which proteins are present in a sample and their relative abundance. Efforts to address the problem in popular analysis workflows include realigning the raw data to transfer a peptide identification from one run to another. Another approach is statistically analysing peptide identifications across an experiment to impute peptide identifications in runs in which they were missing.

We propose a targeted extraction technique that uses machine learning models to construct a run-specific lens through which to examine the raw data and predict the coordinates of a peptide in a run. The models are trained on differences between observations of confidently identified peptides in a run and a reference library of peptide observations collated from multiple experiments. To minimise the risk of drawing unsound experimental conclusions based on an unknown rate of false discoveries, our method provides a mechanism for estimating the false discovery rate (FDR) based on the misclassification of decoys as target features. Our approach outperforms the popular analysis tool suites MaxQuant and MSFragger/IonQuant, and we believe it will be a valuable contribution to the proteomics toolbox for protein quantification.


title: IDENTIFICATION OF DYNAMIC MICROBIAL SIGNATURES IN LONGITUDINAL STUDIES

abstract:
The study of microbiome dynamics is key for unveiling the role of the microbiome in human health. Addressing the compositional structure of microbiome data is particularly critical in longitudinal studies where compositions measured at different times can yield to different subcompositions.

We propose a new compositional data analysis (CoDA) algorithm for inferring dynamic microbial signatures. The algorithm performs penalized regression over the summary of the log-ratio trajectories (the area under these trajectories) and the inferred microbial signature is expressed as a log-contrast model. Graphical representations of the results are provided to facilitate the interpretation of the analysis: plot of the log-ratio trajectories, plot of the signature and plot of the prediction accuracy of the model. The new proposal is illustrated with data on the developing microbiome of infants.

The algorithm is implemented in the R package "code4microbiome" (https://cran.r-project.org/web/packages/coda4microbiome/) that is accompanied with a vignette with a detailed description of the functions. The website of the project contains several tutorials: https://malucalle.github.io/coda4microbiome/


title: Mechanochemical signal transduction in synthetic cells

abstract: Mechanotransduction determines the adaptive response of natural cells via transmem-brane proteins1. The incorporation of membrane-spanning structures to guide cellular function and to enable transmembrane signalling is therefore a critical aim for bottom-up synthetic biology2,3,4. Here, we design membrane-spanning DNA origami signalling units (DOSUs) and mechanically couple them to DNA cytoskeletons5 encapsulated within giant unilamellar vesicles (GUVs). We verify the assembly and incorporation of the DOSUs into the GUV membranes and achieve their clustering upon external stimulation. The transmembrane-spanning DOSUs act as a pore to allow for the transport of single-stranded DNA into the GUVs. We employ this to externally trigger the reconfiguration of DNA cytoskeletons within GUVs using strand displacement reactions. In addition to chemical signalling, we achieve the mechanical coupling of the externally added DOSUs and the internal DNA cytoskeletons. We induce clustering of the DOSUs, which triggers a symmetry break in the organization of the DNA cytoskeleton which is mechanically coupled to the DOSU.Our work thus provides a mechanical and chemical transmembrane signaling module towards the assembly of stimuli-responsive and adaptive synthetic cells.


title: Mechanical confinement and DDR1 signalling synergise to regulate collagen-induced apoptosis in rhabdomyosarcoma cells

abstract:
Fibrillar collagens promote cell proliferation, migration, and survival in various epithelial cancers and are generally associated with tumour aggressiveness. However, the impact of fibrillar collagens on soft tissue sarcoma behaviour remains poorly understood.

Unexpectedly, we find here that fibrillar collagen-related gene expression is associated with favourable patient prognosis in rhabdomyosarcoma. By developing and using collagen matrices with distinct stiffness and in vivo-like microarchitectures, we uncover that the activation of DDR1 has pro-apoptotic and integrin {beta}1 pro-survival function, specifically in 3D rhabdomyosarcoma cell cultures. We demonstrate that rhabdomyosarcoma cell-intrinsic or extrinsic matrix remodelling promotes cell survival. Mechanistically, we find that the 3D-specific collagen-induced apoptosis results from a dual DDR1-independent and a synergistic DDR1-dependent TRPV4-mediated response to mechanical confinement. Altogether, our results indicate that dense microfibrillar collagen-rich microenvironments are detrimental to rhabdomyosarcoma cells through an apoptotic response orchestrated by the induction of DDR1 signalling and mechanical confinement. This mechanism helps to explain the preference of rhabdomyosarcoma cells to grow in and metastasise to low fibrillar collagen microenvironments such as the lung.

category: cancer biology


title: Salivary Proinflammatory Cytokines IL-1β, IL-6 And TNF Decrease With Age.

abstract:
Objectiveto analyze salivary concentrations interleukin-1{beta} (IL-1{beta}), 6 (IL-6) and tumor necrosis factor (TNF) according to age in healthy subjects to determine baseline inflammatory state of the oral mucosa in elderly subjects, who are at higher risk of developing inflammation-related diseases.

Materials and methodssixty-four healthy volunteers were divided into groups according to age: 20-39 (G1; n=20); 40-59 (G2; n=24); 60-80 years (G3; n=20). Their stomatognathic system and periodontal status were assessed; consumption of food sources of fatty acids (FA) was evaluated using a validated food frequency questionnaire. IL-1{beta}, IL-6, and TNF salivary levels were determined (ELISA) in mixed unstimulated saliva. Kruskal Wallis and Spearmans correlation tests were applied (p<0.05).

Resultssalivary IL-1{beta} and TNF levels were lower in G2 (p=0.001) and G3 (p<0.001) than in G1; IL-6 levels were lower in G3 than in G2 and G1 (p= <0.001). IL-1{beta} showed the highest concentration in all groups (p<0.001). No statistically significant differences in salivary cytokine levels were observed on sex in any of the groups. Associations were observed between salivary cytokines and consumption of some foods containing FA.

Conclusionsalivary concentration of proinflammatory cytokines decreased with age. It could be influenced by ageing-related changes. In addtition, the baseline inflammatory state of the oral mucosa would appear to be influenced by dietary intake of sources of anti-inflammatory FA.

Clinical relevancethe knowledge about inflammatory state of the oral mucosa, as determined by salivary cytokine concentrations, could be useful for understanding and prevention of developing inflammation-related diseases.

category: pathology


title: Hydroquinone, a cigarette smoke compound, affects cartilage homeostasis through activation of the aryl hydrocarbon receptor pathway.

abstract: Exposure to cigarette smoke has a proven detrimental impact on different aspects of human health. Increasing evidences link smoking to degeneration of joint tissues. However, the toxic mechanisms elicited by the different components of cigarette smoke have not been fully elucidated yet. We have previously shown that exposure to hydroquinone (HQ), a pro-oxidant chemical present in cigarette smoke, can promote joint tissue degradation in murine models of rheumatoid arthritis through the activation of the aryl hydrocarbon receptor (AhR) pathway. Osteoarthritis (OA) is a chronic debilitating articular disease characterized by progressive degradation of the articular cartilage, whose onset and progression have also been associated with smoking. In this work we aimed to investigate the effect of HQ exposure on articular chondrocytes and how it affects cartilage homeostasis. Cell viability, gene expression, oxidative stress and inflammatory parameters were quantified in primary articular chondrocytes exposed to HQ in presence or absence of IL-1{beta} pre-stimulation. HQ stimulation downregulated phenotypic markers genes such as SOX-9 and Col2a1, whereas upregulated the expression of the catabolic enzymes MMP-3 and ADAMTS5. HQ also promoted oxidative stress and reduced proteoglycan content. HQ exacerbated the pro-inflammatory effects mediated by the IL-1{beta} co-stimulation. Finally, we showed that HQ-degenerative effects were mediated by the activation of AhR. Together, our findings address the harmful effects of HQ in the articular cartilage health, providing novel evidence surrounding the toxic mechanisms of environmental pollutants underlying the onset of articular diseases.

category: pharmacology and toxicology


title: Spatially-enhanced clusterwise inference for testing and localizing intermodal correspondence

abstract: With the increasing availability of neuroimaging data from multiple modalities--each providing a different lens through which to study brain structure or function--new techniques for comparing, integrating, and interpreting information within and across modalities have emerged. Recent developments include hypothesis tests of associations between neuroimaging modalities, which can be used to determine the statistical significance of intermodal associations either throughout the entire brain or within anatomical subregions or functional networks. While these methods provide a crucial foundation for inference on intermodal relationships, they cannot be used to answer questions about where in the brain these associations are most pronounced. In this paper, we introduce a new method, called CLEAN-R, that can be used both to test intermodal correspondence throughout the brain and also to localize this correspondence. Our method involves first adjusting for the underlying spatial autocorrelation structure within each modality before aggregating information within small clusters to construct a map of spatially enhanced test statistics. Using structural and functional magnetic resonance imaging data from a subsample of children and adolescents from the Philadelphia Neurodevelopmental Cohort, we conduct simulations and data analyses where we illustrate the high statistical power and nominal type I error levels of our method. By constructing an interpretable map of group-level correspondence using spatially-enhanced test statistics, our method offers insights beyond those provided by earlier methods.


title: High precision magnetoencephalography reveals increased right-inferior frontal gyrus beta power during response conflict

abstract:
Flexibility of behavior and the ability to rapidly switch actions is critical for adaptive living in humans. It is well established that the right-inferior frontal gyrus (R-IFG) is recruited during outright action-stopping, relating to increased beta (12-30 Hz) power. Additionally, pre-supplementary motor area (pre-SMA) is plausibly recruited during response conflict/switching, relating to increased theta (4-8 Hz) power. It has been posited that inhibiting incorrect response tendencies is central to motor flexibility. However, it is not known if the commonly reported R-IFG beta signature of response inhibition in action-stopping is also recruited during response conflict, which would suggest overlapping networks for stopping and switching. In the current study, we analyzed high precision magnetoencephalography (hpMEG) data recorded with very high trial numbers (total n > 10,000) from 8 subjects during different levels of response conflict. We hypothesized that a R-IFG-triggered network for response inhibition is domain general and also involved in mediating response conflict. We therefore tested whether R-IFG showed increased beta power dependent on the level of response conflict. We also hypothesized that pre-SMA is an important node in response conflict processing, and tested whether pre-SMA theta power increased for response conflict trials. Using event-related spectral perturbations and linear mixed modeling, we found that both R-IFG beta and pre-SMA theta increased for response conflict trials, with the R-IFG beta increase specific to trials with strong response conflict. This result supports a more generalized role for R-IFG beta in response inhibition, beyond simple stopping behavior towards response switching.

Significance StatementResponse inhibition is a core component of cognitive control. Neural mechanisms of response inhibition are typically studied using stopping paradigms. However, there is an unresolved debate regarding whether the response inhibition network is specific to stopping or generalizes to switching between tasks and overcoming conflict between competing response tendencies. Increased beta (12-30 Hz) in R-IFG has historically been interpreted as a marker of successful response inhibition in the stop-signal task. Here, we investigated the presence of this electrophysiological marker of response inhibition specifically during response conflict (switching). We found R-IFG beta power increased for trials with strong response conflict, and not for weak or no response conflict, thereby supporting a generalized role for R-IFG beta in response inhibition and switching.


title: Sex-limited diversification of the eye in Heliconius butterflies

abstract: Butterflies have evolved an immense diversity in eye organization to support a range of vision-based behaviors including courtship, oviposition, and foraging. This diversity has been surveyed extensively across the butterfly phylogeny, and here we take a complementary approach to characterize the eye within a group of closely related Heliconius butterflies. Using a combination of immunostaining for different opsins and eyeshine for determining the distribution of light-filtering screening pigments, we identified several sexually dimorphic features of eye organization where male eyes varied and female eyes did not. Ultraviolet (UV) sensitive photoreceptors varied in which of two UV opsins were expressed, including co-expression of both within single photoreceptors, and these differences were consistent with a role in courtship and conspecific identification. Additional differences across species and sex included the distribution of three ommatidial types defined by the expression pattern of UV and blue opsins, the distribution of a red screening pigment, and which ommatidial types expressed the red screening pigment. We hypothesize that female eyes are optimized for a dimorphic behavior such as oviposition, while male eyes adapt to other selective pressures such as the local light environment.


title: ILC3s select for RORγt+ Tregs and establish tolerance to intestinal microbiota

abstract: Microbial colonization of the mammalian intestine elicits inflammatory or tolerogenic T cell responses, but the mechanisms controlling these distinct outcomes remain poorly understood and accumulating evidence indicates that aberrant immunity to intestinal microbiota is causally associated with infectious, inflammatory, and malignant diseases1-8. Here, we define a critical pathway controlling the fate of inflammatory versus tolerogenic T cells that are specific for the microbiota and express the transcription factor ROR{gamma}t. We profiled all ROR{gamma}t+ immune cells at single cell resolution from the intestine-draining lymph nodes of mice and reveal a dominant presence of Tregs and lymphoid tissue-induced (LTi)-like group 3 innate lymphoid cells (ILC3s), which co-localize at interfollicular regions. These ILC3s have interconverting potential with ROR{gamma}t+ extrathymic Aire-expressing cells, abundantly express major histocompatibility complex class II, and are necessary and sufficient to promote microbiota-specific ROR{gamma}t+ Tregs and prevent their expansion as inflammatory T helper (Th)17 cells. This occurs through ILC3-mediated antigen-presentation, interleukin-2 gradients, and v integrin. Finally, single-cell analyses demonstrate that ILC3 and ROR{gamma}t+ Treg interactions are impaired in inflammatory bowel disease. Our results define a novel paradigm whereby ILC3s positively select for antigen specific ROR{gamma}t+ Tregs, and against Th17 cells, to establish immune tolerance to the microbiota and intestinal health.

category: immunology


title: Mobile Laser Scanner understory characterization: an exploratory study on hazel grouse in Italian Alps

abstract: Forest vegetation structure assessment is a time expensive effort with traditional methods. The Mobile Laser Scanner (MLS) technology can greatly speed up field works, achieve detailed quantification of three-dimensional forest structure at detailed resolution and drive forest management to increase the conservation status of forests-specialist bird species. In this study, using Mobile hand-held Laser Scanner (MLS), we calculated a fine-scale vegetation density index (namely the Plant Density Index, PDI) to characterize the vertical structure of forest subcanopy (0-10 m). The collected MLS point clouds were used to estimate the abundance of Potential Hiding Refuges (PHR) for the hazel grouse (Tetrastes bonasia), a sedentary bird extremely sensitive to forest structure and composition. The study was carried out in 10 plots located in the Adamello Brenta Geopark (Southern Alps, Italy). The species was detected in 8 out of 18 transects in an uneven-aged spruce forest with a discontinuous tree cover. The PDI decreases as the height increases, showing greater value in the shrub and herbaceous layer while the upper values are represented by trees stems, and branches. Visibility analysis of lower understory, highlighted PHR mean value of 73.2% (sd = 9.2%). In our area, PDI and PHR revealed that the environmental factors for hazel grouse occurrence are forests with open habitats, understory vegetation, and good hiding opportunities. Our study is the first application that uses MLS derived parameters to describe the ecological niche of a grouse and we presented the surveyed area as "case report" of hazel grouse habitat.


title: Genetic and peripheral visual system changes underlie evolving butterfly mate preference

abstract:
Many studies have linked genetic variation to behavior, but less is known about how that variation alters the neural circuits that drive behavior. We investigated the genetic and neurobiological basis of courtship preference variation in Heliconius butterflies, which use vision to identify appropriate mates based on wing color patterns. We found that Heliconius cydno preference variation was strongly associated with genetic variation and differential expression of senseless-2, a gene predominantly expressed in the eye. Further measurements of photoreceptor sensitivities revealed differences in inter-photoreceptor inhibition of ultraviolet-sensitive cells corresponding to courtship preference variation. Our results reveal a genetic basis for preference/cue co-evolution, suggest a link between sens-2 and visual system variation, and support the idea that changing peripheral neural computations can significantly alter essential behaviors.

SummaryGenetic and expression variation of senseless-2 and inter-photoreceptor inhibition predict visual mate preference in a clade of diverse butterflies.


title: Regulation of human trophoblast gene expression by endogenous retroviruses

abstract: The placenta is a fast-evolving organ with large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programmes. Here, we assessed the contribution of transposable elements to human trophoblast gene expression as enhancers or promoters. Using epigenomic data from primary human trophoblast and trophoblast stem cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential expression in trophoblast. These largely primate-specific elements are associated with inter-species gene expression differences, and are bound by transcription factors with key roles in placental development. Using genetic editing we demonstrated that several elements act as transcriptional enhancers of important placental genes, such as CSF1R and PSG5. We also identified an LTR10A element that regulates ENG expression, affecting secretion of soluble ENG, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.

category: genetics


title: satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect

abstract:
BackgroundThe impact of thousands of individual genetic variants on molecular phenotypes for disease-relevant genes remains unknown. Multiplexed assays for variant effect (MAVEs) are highly scalable methods to annotate the relevant variants. However, current software methods for analyzing MAVEs lack standardized annotation, can require cumbersome configuration, and do not easily scale to large target regions.

ResultsHere, we present satmut_utils as a flexible solution for 1) simulation of saturation mutagenesis data; and 2) quantification of variants across four orders of magnitude from multiplexed assay data. Improvements of satmut_utils over existing solutions include support for multiple experimental strategies, unique molecular identifier-based consensus deduplication, and machine learning-based error correction. We developed a rigorous simulation workflow to validate the performance of satmut_utils and carried out the first benchmarking of existing software for variant calling. Finally, we used satmut_utils to determine the mRNA abundance of thousands of coding variants in cystathionine beta-synthase (CBS) by two library preparation methods. We identified an association between variants near chemical cofactor binding sites and decreased mRNA abundance. We also found a correlation between codon optimality and the magnitude of variant effects, emphasizing the potential of single-nucleotide variants to alter mRNA abundance.

Conclusionssatmut_utils enables high-performance analysis of saturation mutagenesis data, achieves unprecedented specificity through novel error correction approaches, and reveals the capability of single-codon variants to alter mRNA abundance in native coding sequences.

category: genomics


title: The regulation of circadian rhythm by insulin signaling in Drosophila

abstract:
Circadian rhythm is well conserved across species and relates to numerous biological functions. Circadian misalignment impairs metabolic function. Insulin signaling is a key modulator of metabolism in the fruit fly as well as mammals and its defects cause metabolic disease. Daily diet timing affects both circadian rhythmicities of behavior and metabolism. However, the relationship between circadian clock and insulin signaling is still elusive. Here, we report that insulin signaling regulates circadian rhythm in Drosophila melanogaster. We found the insulin receptor substrate mutant, chico1, showed a shorter free-running circadian period. The knockdown of insulin receptor (InR), or another signaling molecule downstream of InR, dp110, or the expression of a dominant-negative form of InR resulted in the shortening of the circadian period and diminished its amplitude. The impairment of insulin signaling both in all neurons and restricted circadian clock neurons altered circadian period length, indicating the insulin signaling plays a role in the regulation of circadian rhythm in clock cells. Among 3 insulin-like ligands expressed in the brain, dilp5 showed the largest effect on circadian phenotype when deleted. These results suggested that insulin signaling contributes to the robustness of the circadian oscillation and coordinates metabolism and behavior.

HighlightsO_LIInsulin receptor substrate mutant, chico1, displayed circadian rhythm phenotype.
C_LIO_LIPan-neuronal inhibition of insulin receptor signaling shortened circadian cycle.
C_LIO_LIInhibition of insulin signaling only in clock neurons altered circadian cycle.
C_LIO_LIDilp5 is a major insulin receptor ligand for circadian effects.
C_LI


title: SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors

abstract: The position of the nucleosome and chromatin packaging in eukaryotic genomes govern gene regulation and cellular functions. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. However, there is no method that is specifically designed for detecting differential chromatin accessibility using ATAC-seq datasets. In this study, we developed a bioinformatics tool called SeATAC, that used a conditional variational autoencoder (CVAE) model to learn the latent representation of ATAC-seq V-plots, and to estimate the statistically differential chromatin accessibility. We demonstrated that SeATAC outperformed MACS2 and NucleoATAC on four separate tasks including: (1) detection of differential V-plots; (2) definition of nucleosome positions; (3) detection of nucleosome changes and (4) designation of transcriptional factor binding sites (TFBS) with differential chromatin accessibility. By applying SeATAC to several pioneer factor induced differentiation or reprogramming ATAC-seq datasets, we found that induction of these pioneer factors not only relaxed the closed chromatin but also decreased the chromatin accessibility of 20% - 30% of their target sites. These two groups of TF binding sites were characterized by different genomic distribution and histone marks. Here, we present SeATAC as a novel tool to accurately reveal the genomic regions with differential chromatin accessibility from ATAC-seq data.


title: FebRNA: an automated fragment-ensemble-based model for building RNA 3D structures

abstract: Knowledge of RNA 3-dimensional (3D) structures is critical to understanding the important biological functions of RNAs. Although various structure prediction models have been developed, high accuracy of predicted RNA 3D structures is still limited to the RNAs with short length or with simple topology. In this work, we proposed a new model, namely FebRNA, for building RNA 3D structures through fragment assembly based on coarse-grained (CG) fragment ensembles. Specifically, FebRNA is composed of four processes: establishing the library of different types of CG fragment ensembles, building CG 3D structure ensemble through fragment assembly, identifying top-1 CG structure through a CG scoring function, and rebuilding the all-atom structure from the top-1 CG one. Extensive examination on different types of RNA structures indicates that FebRNA gives consistently reliable predictions on RNA 3D structures including pseudoknots, 3-way junction, 4-way and 5-way junctions, and RNAs in the RNA-Puzzles. FebRNA is available at website: https://github.com/Tan-group/FebRNA.


title: Real-time feeding behavior monitoring by electrical penetration graph rapidly reveals host plant susceptibility to crapemyrtle bark scale (Hemiptera: Eriococcidae)

abstract:
Host range confirmation of invasive hemipterans relies on the evaluation of plant susceptibility though greenhouse or field trials, which are inefficient and time-consuming. When the green industry faces the fast-spreading threat of invasive pests such as crapemyrtle bark scale (Acanthococcus lagerstroemiae), it is imperative to timely identify potential host plants and evaluate plant resistance/susceptibility to pest infestation. In this study, we developed an alternative technology to complement the conventional host confirmation methods. We used electrical penetration graph (EPG) based technology to monitor the A. lagerstroemiae stylet-tip position when it was feeding on different plant tissues in real-time. The frequency and relative amplitude of insect feeding waveforms (recorded by EPG) were extracted by an R programming-based software written to generate eleven feeding parameters for comparative analysis between plant species. The results demonstrated that the occurrences of phloem phase and xylem phase offered conclusive evidence for host plant evaluation. Furthermore, parameters including the percentage of insects capable of accessing phloem tissue, time duration spent on initiating phloem phase and ingesting phloem sap, provided insight into why host plant susceptibility differs among similar plant species. In summary, this study developed a novel real-time diagnostic tool for quick A. lagerstroemiae host confirmation, which laid the essential foundation for effective pest management.

Simple SummaryCrapemyrtle bark scale (CMBS; Acanthococcus lagerstroemiae), an invasive polyphagous sap feeder in the United States, has spread across 16 U.S. states in less than two decades, posing potential risks to the Green Industry. Confirming the host range is crucial for effective pest management of invasive insects. However, host range confirmation relying on greenhouse or field trials is often inefficient and time-consuming. In this study, we used the electrical penetration graph (EPG) to monitor the stylet penetration of CMBS in plant tissue in real-time. An R programming-based application was developed to better characterize the insect feeding waveforms recorded by EPG. By analyzing EPG-based feeding parameters, we demonstrated that CMBS have difficulty accessing the phloem tissue (salivation and ingestion) of a resistant plant compared to a susceptible plant. Importantly, we hereby present CMBS typical feeding behaviors on susceptible and non-susceptible plants comparatively, which provides direct evidence for revealing unknown hosts rapidly.


title: If Research is Not the Evidence, What is it? Explanations of the Lack of Research Citations in their Health Vlogs

abstract: Doctor-influencers have the knowledge needed to understand scientific research, and they have the social media popularity to share it with large audiences. In this article, I explore the treatment of evidence in vlogs by Egyptian doctor-influencers: how they present it and what they use instead of it. I answer the following questions: 1) How do doctor-influencers present evidence on social media? 2) If evidence is not the research, then what is it? The data was collected through in-depth interviews with 12 Egyptian doctor-influencers from different specializations; two focus groups; and a critical discourse analysis of 48 of the influencers most popular and most engaging videos. I found that the doctor-influencers cited academic research only in the videos about medical controversies, new treatments, misinformation, or common medical mistakes. In most of their videos, the Egyptian doctor-influencers scarcely referred to medical research. This is because they believe that their audiences would not understand evidence due to their low educational attainment, weak research skills, and the language barrier (as most medical research is published in English rather than Arabic). These findings highlight the challenges of communicating science in societies with a low level of education. In these settings, communicators may need to move beyond mediating research studies on social media and instead focus on simplifying, translating, and connecting evidence-based information to the cultural context.

category: scientific communication and education


title: If Research is Not the Evidence, What is it? The Lack of Research Citations in Health Vlogs