bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant growers’ environmental consciousness may not be enough to mitigate pollinator declines: a questionnaire-based case study in Hungary
Authors: Varga-Szilay Zsófia , Pozsgai Gábor
Published: April 2022

BACKGROUND

Pesticides are one of the most important anthropogenic-related stressors. In times of global pollinator decline, the role of integrated farming and that of urban gardens in supporting wild pollinators is becoming increasingly important. We circulated an online questionnaire to survey the plant protection practices among Hungarian farmers and garden owners with a particular emphasis on pollinator protection.

RESULTS

We found that plant growers heavily rely on pesticide use, and pesticides are widely used in otherwise pollinator-friendly gardens. Whether pesticide use practices were driven by expert opinion and the respondents’ gender were the best predictors of pesticide use. Although most respondents supported pollinators, pesticides are also widely used among home garden owners, which can pose a non-evident ecological trap for pollinator populations in the gardens.

CONCLUSION

Special attention should be paid to implementing measures to reduce pesticide, use not only in farmlands but also in home gardens. Environmental education and financial support through agroecological schemes could efficiently promote the transition. However, whereas farmers can be encouraged to reduce pesticide use mostly by expert advice, garden owners are likely to rely on more conventional information channels. The attitude of Hungarian plant growers can provide an insight into pesticide use practices of Central and Eastern European countries, but similar surveys are needed across Europe for a complete understanding of broad-scale processes. This work lays the foundations for similar studies which can inform and facilitate the transformation processes to pesticide-free farming and gardening.
Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics
Authors: Yang Hsin-Chou , Wang Jen-Hung , Yang Chih-Ting , Lin Yin-Chun , Hsieh Han-Ni , Chen Po-Wen , Liao Hsiao-Chi , Chen Chun-houh , Liao James C.
Published: April 2022

SARS-CoV-2 continues to evolve, causing waves of the pandemic. Up to March 2022, eight million genome sequences have accumulated, which are classified into five major variants of concern. With the growing number of sequenced genomes, analysis of the big dataset has become increasingly challenging. Here we developed systematic approaches for comprehensive subtyping and pattern recognition for transmission dynamics. By analyzing the first two million viral genomes as of July 2021, we found that different subtypes of the same variant exhibited distinct temporal trajectories. For example, some Delta subtypes did not spread rapidly, while others did. We identified sets of characteristic single nucleotide variations (SNVs) that appeared to enhance transmission or decrease efficacy of antibodies for some subtypes of the Delta and Alpha variants. We also identified a set of SNVs that appeared to suppress transmission or increase viral sensitivity to antibodies. These findings are later confirmed in an analysis of six million genomes as of December 2021. For the Omicron variant, the dominant type in the world, we identified the subtypes with enhanced and suppressed transmission in an analysis of seven million genomes as of January 2022 and further confirmed the findings in a later analysis of eight million genomes as of March 2022. While the “enhancer” SNVs exhibited an enriched presence on the spike protein, the “suppressor” SNVs are mainly elsewhere. Disruption of the SNV correlation largely destroyed the enhancer-suppressor phenomena. These results suggest the importance of fine subtyping of variants, and point to potential complex interactions among SNVs.
Super-Resolution NMR Spectroscopy using the Intersection of Non-Redundant Information on Resonance Groups
Authors: Lorieau Justin L , Malooley Alexander , Banerjee Indrani
Published: April 2022

The resolution of spectra is a major limitation in the application of Nuclear Magnetic Resonance (NMR) spectroscopy to large and complex molecular systems. In this report, we introduce a technique to enhance the resolution of NMR spectra beyond the intrinsic limitations of a spectrometer for a single spectrum by using the Intersection of Non-Redundant Information on Resonance Groups (INIR). With INIR, we reconstruct 900-MHz (21.1T) spectra from a 500-MHz (11.7T) NMR spectrometer, which compare favorably to experimental 900-MHz spectra. INIR holds promise in significantly enhancing the resolution of NMR spectra and in extending the size and complexity of molecules studied by NMR.
Multimodal single cell data integration challenge: results and lessons learned
Authors: Lance Christopher , Luecken Malte D. , Burkhardt Daniel B. , Cannoodt Robrecht , Rautenstrauch Pia , Laddach Anna , Ubingazhibov Aidyn , Cao Zhi-Jie , Deng Kaiwen , Khan Sumeer , Liu Qiao , Russkikh Nikolay , Ryazantsev Gleb , Ohler Uwe ,   NeurIPS 2021 Multimodal data integration competition participants, Pisco Angela Oliveira , Bloom Jonathan , Krishnaswamy Smita , Theis Fabian J.
Published: April 2022

Biology has become a data-intensive science. Recent technological advances in single-cell genomics have enabled the measurement of multiple facets of cellular state, producing datasets with millions of single-cell observations. While these data hold great promise for understanding molecular mechanisms in health and disease, analysis challenges arising from sparsity, technical and biological variability, and high dimensionality of the data hinder the derivation of such mechanistic insights. To promote the innovation of algorithms for analysis of multimodal single-cell data, we organized a competition at NeurIPS 2021 applying the Common Task Framework to multimodal single-cell data integration. For this competition we generated the first multimodal benchmarking dataset for single-cell biology and defined three tasks in this domain: prediction of missing modalities, aligning modalities, and learning a joint representation across modalities. We further specified evaluation metrics and developed a cloud-based algorithm evaluation pipeline. Using this setup, 280 competitors submitted over 2600 proposed solutions within a 3 month period, showcasing substantial innovation especially in the modality alignment task. Here, we present the results, describe trends of well performing approaches, and discuss challenges associated with running the competition.
Two-photon microscopy in vivo reveals brain vessel type-specific loss of glycocalyx caused by apoM/S1P signaling impairment
Authors: Kucharz Krzysztof , Mathiesen Janiurek Mette , Christoffersen Christina , Lauritzen Martin
Published: April 2022

Increases in adsorptive mediated transcytosis (AMT) at the blood-brain barrier (BBB) are linked to many brain disorders. In a healthy brain, AMT is suppressed by sphingosine-1-phosphate (S1P) receptor 1 (S1PR1) signaling. Low levels of S1P lead to a rise in AMT, but the mechanisms are incompletely understood. Here, we explored whether the rises in AMT are caused by the loss of the endothelial glycocalyx (gcx). We used two-photon microscopy in mice with low S1P plasma levels (Apom-/-) and developed a novel photobleaching approach to measure gcx in vivo at distinct classes of cerebral microvessels, i.e., arterioles, capillaries and venules. We show that S1P signaling impairment reduced gcx in arterioles but not in other vessel segments. The location of gcx loss corresponded to the vascular topology of AMT increases. The S1PR1 agonist SEW2871 restores low levels of AMT in Apom-/- mice but did not restore the gcx within the same time window. We propose that while the gcx loss may contribute to AMT increase, restoring gcx is not necessary for AMT to return to normal. These data establish a new imaging method to study gcx in the living mouse brain, demonstrate zonation of gcx in cerebral microvessels, and suggest differences in vascular susceptibility to gcx loss in disease states.
Identification of a novel AP2 transcription factor in zygotes with an essential role in Plasmodium ookinete development
Authors: Nishi Tsubasa , Kaneko Izumi , Iwanaga Shiroh , Yuda Masao
Published: April 2022

The sexual phase of Plasmodium represents a crucial step in malaria transmission, during which these parasites fertilize and form ookinetes to infect mosquitoes. Plasmodium development after fertilization is thought to proceed with female-stored mRNAs until the formation of a retort-form ookinete; thus, transcriptional activity in zygotes has previously been considered quiescent. In this study, we reveal the essential role of transcriptional activity in zygotes by investigating the function of a newly identified AP2 transcription factor, AP2-Z. ap2-z was previously reported as a female transcriptional regulator gene whose disruption resulted in developmental arrest at the retort stage of ookinetes. In this study, although ap2-z was transcribed in females, we show that it was translationally repressed by the DOZI complex and translated after fertilization with peak expression at the zygote stage. ChIP-seq analysis of AP2-Z shows that it binds on specific DNA motifs, targeting the majority of genes known as an essential component of ookinetes, which largely overlap with the AP2-O targets, as well as genes that are unique among the targets of other sexual transcription factors. The results of this study also indicate the existence of a cascade of transcription factors, beginning with AP2-G, that proceeds from gametocytogenesis to ookinete formation.

Author summary

Sexual development in Plasmodium parasites, a causative agent of malaria, is essential for their transmission from vertebrate hosts to mosquitoes. This important developmental process proceeds as follows: formation of a gametocyte/gamete, fertilization and conversion of the zygote into the mosquito midgut invasive stage, called the ookinete. As a target of transmission blocking strategies, it is important to understand the mechanisms regulating Plasmodium sexual development. In this study, we assessed transcriptional regulation after fertilization by investigating the function of a novel transcription factor, AP2-Z. The results revealed the essential role of de novo transcription activated by AP2-Z in zygotes for promoting ookinete development. As transcriptional activity during the zygote stage has previously been considered silent in Plasmodium, novel genes important for ookinete formation can now be explored in the target genes of AP2-Z. Investigating the functions of these genes can help us understand the mechanisms of Plasmodium zygote/ookinete development and identify new targets for transmission blocking vaccines.
A phenotypic screen of Marfan syndrome iPSC-derived vascular smooth muscle cells uncovers GSK3β as a new target
Authors: Davaapil Hongorzul , McNamara Madeline , Granata Alessandra , Macrae Robyn G.C. , Hirano Mei , Fitzek Martina , Aragon-Martin Jose Antonio , Child Anne , Smith David M. , Sinha Sanjay
Published: April 2022

Marfan syndrome (MFS) is a rare connective tissue disorder caused by mutations in FBN1. Patients with MFS notably suffer from aortic aneurysm and dissection. Despite considerable effort, animal models have proven to be poorly predictive for therapeutic intervention in human aortic disease. Using a “humanised” model system may be more appropriate in identifying new therapeutic targets. Patient-derived induced pluripotent stem cells can be differentiated into vascular smooth muscle cells (VSMCs) and recapitulate major features of MFS. We have screened 1,022 small molecules in our in vitro model, exploiting the highly-proteolytic nature of MFS-VSMCs, and identified 36 effective compounds. Further analysis identified GSK3β as a recurring target in the compound screen. GSK3β inhibition/knockdown did not ameliorate the proliferation defect in MFS-VSMCs but improved MFS-VSMC apoptosis and proteolysis. To conclude, we have identified GSK3β as a novel target for MFS, forming the foundation for future work in MFS and other aortic diseases.
The conservation of human functional variants and their effects across mammals
Authors: Zhao R. , Talenti A. , Fang L. , Liu S. , Liu G. , Hong N.P. Chue , Tenesa A. , Hassan M. A. , Prendergast J.G.D.
Published: April 2022

Despite the clear potential of livestock models of human functional variants to provide important insights into the biological mechanisms driving human diseases and traits, their use to date has been limited. Generating such models via genome editing is costly and time consuming, and it is unclear which variants will have conserved effects across species. In this study we address these issues by studying naturally occurring livestock models of human functional variants. We show that orthologues of over 1.6 million human variants are already segregating in domesticated mammalian species, including several hundred previously directly linked to human traits and diseases. Models of variants linked to particular phenotypes, including metabolomic disorders and height, have been preferentially maintained across species, meaning studying the genetic basis of these phenotypes is particularly tractable in livestock. Using machine learning we demonstrate it is possible to identify human variants that are more likely to have an existing livestock orthologue, and, importantly, we show that the effects of functional variants are often conserved in livestock, acting on orthologous genes with the same direction of effect. Consequently, this work demonstrates the substantial potential of naturally occurring livestock carriers of orthologues of human functional variants to disentangle their functional impacts.
Shared neurophysiological resources between exogenous and endogenous visuospatial attentional processes
Authors: Landry Mathieu , Da Silva Castanheira Jason , Baillet Sylvain , Sackur Jérôme , Raz Amir
Published: April 2022

Prevailing accounts of visuospatial attention differentiate exogenous (involuntary shifts) from endogenous (voluntary control) orienting of attention. While these two forms of attentional processes are functionally separable, their interactions have been at the center of ongoing debates for more than two decades. One hypothesis is that exogenous and endogenous attention interfere because they share processing resources. Here, we confirm that endogenous attention alters exogenous attention processing, and examine the role of alpha-band neurophysiological activity in such interference events. We contrast the effects of exogenous attention across two experimental conditions: a single-cueing condition where exogenous attention is engaged alone, and a double-cueing condition where exogenous attention is concurrently engaged with endogenous attention. Our results show that the engagement of endogenous attention alters the emergence of exogenous attention across cue-related and target-related brain processes. Importantly, we also report that classifiers trained to decode exogenous attention from the power and phase of alpha-band brain activity in the single-cueing condition fail to do so in the doublecueing condition, where endogenous attention is also engaged. Taken together, our observations challenge the idea that exogenous attention operates independently from top-down processes and demonstrate that both forms of attention orienting engage shared brain processes, which constrain their interactions.

Significance Statement

Visuospatial attention is often dichotomized into top-down and bottom-up components: Top-down attention reflects slow voluntary shifts of attention orienting, while bottom-up attention is recruited by emerging demands from the environment. A large body of previous findings support the view that these two forms of attention orienting are functionally separable, with some interactions. The current study examines such interactions between top-down and bottom-up attention. Using electroencephalography (EEG) and multivariate pattern classification techniques, the researchers show that top-down attention interferes with the brain activity patterns of bottom-up attention. Moreover, machine learning classifiers trained to detect bottom-up attention based on brain activity in the alpha band (8-12 Hz), a marker of visuospatial attention, fail systematically when top-down attention is also engaged. The authors therefore conclude that both forms of visuospatial orienting are supported by overlapping processes that share brain resources.
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
Authors: Benito-Vaquerizo Sara , Olm Ivette Parera , de Vroet Thijs , Schaap Peter J. , Sousa Diana Z , Martins dos Santos Vitor A.P. , Suarez-Diez Maria
Published: April 2022

Background

Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate.

Results

Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium.

Conclusions

The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
A population of gray matter oligodendrocytes directly associates with the vasculature
Authors: Palhol Justine S. C. , Balia Maddalena , Terán Fernando Sánchez-Román , Labarchède Mélody , Gontier Etienne , Battefeld Arne
Published: April 2022

Oligodendrocyte lineage cells interact with the vasculature in the gray matter. Physical and functional interactions between blood vessels and oligodendrocyte precursor cells play an essential role in both the developing and adult brain. Oligodendrocyte precursor cells have been shown to migrate along the vasculature and subsequently detach from it during their differentiation to oligodendrocytes. However, the association of mature oligodendrocytes with blood vessels has been noted since the discovery of this glial cell type almost a century ago and this interaction remains poorly explored. Here, we systematically investigated the extent of mature oligodendrocyte interaction with the vasculature in mouse. We found that ~17% of oligodendrocytes were in contact with blood vessels in cortex, hippocampus and cerebellum. Contacts were made mainly with capillaries and sparsely with larger arterioles or venules. By combining light and serial electron microscopy, we demonstrated that oligodendrocytes are in direct contact with the vascular basement membrane, raising the possibility of direct signaling pathways and metabolite exchange with endothelial cells. During experimental remyelination in the adult, oligodendrocytes were regenerated and associated with blood vessels in the same proportion compared to control cortex, suggesting a homeostatic regulation of the vasculature-associated oligodendrocyte population. Based on the frequent and close association with blood vessels, we propose that vasculature-associated oligodendrocytes should be considered as an integral part of the vasculature microenvironment. This particular location could underlie specific functions of vasculature-associated oligodendrocytes, while contributing to the vulnerability of mature oligodendrocytes in neurological diseases.
Receptor binding domain of SARS-CoV-2 is a functional αv-integrin agonist
Authors: Norris Emma G. , Pan Xuan Sabrina , Hocking Denise C.
Published: April 2022

Among the novel mutations distinguishing SARS-CoV-2 from similar respiratory coronaviruses is a K403R substitution in the receptor-binding domain (RBD) of the viral spike (S) protein within its S1 region. This amino acid substitution occurs near the angiotensin-converting enzyme 2 (ACE2)-binding interface and gives rise to a canonical RGD adhesion motif that is often found in native extracellular matrix proteins, including fibronectin. In the present study, the ability of recombinant S1-RBD to bind to cell surface integrins and trigger downstream signaling pathways was assessed and compared to RGD-containing, integrin-binding fragments of fibronectin. S1-RBD supported adhesion of both fibronectin-null mouse embryonic fibroblasts as well as primary human small airway epithelial cells. Cell adhesion to S1-RBD was cation- and RGD-dependent, and was inhibited by blocking antibodies against αvand β3, but not α5or β1, integrins. Similarly, direct binding of S1-RBD to recombinant human αvβ3and αvβ6integrins, but not α5β1integrins, was observed by surface plasmon resonance. Adhesion to S1-RBD initiated cell spreading, focal adhesion formation, and actin stress fiber organization to a similar extent as fibronectin. Moreover, S1-RBD stimulated tyrosine phosphorylation of the adhesion mediators FAK, Src, and paxillin, Akt activation, and supported cell proliferation. Together, these data demonstrate that the RGD sequence within S1-RBD can function as an αv-selective integrin agonist. This study provides evidence that cell surface αv-containing integrins can respond functionally to spike protein and raise the possibility that S1-mediated dysregulation of ECM dynamics may contribute to the pathogenesis and/or post-acute sequelae of SARS-CoV-2 infection.
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
Authors: Veglia Alex J. , Bistolas Kalia S.I. , Voolstra Christian R. , Hume Benjamin C. C. , Planes Serge , Allemand Denis , Boissin Emilie , Wincker Patrick , Poulain Julie , Moulin Clémentine , Bourdin Guillaume , Iwankow Guillaume , Romac Sarah , Agostini Sylvain , Banaigs Bernard , Boss Emmanuel , Bowler Chris , de Vargas Colomban , Douville Eric , Flores Michel , Forcioli Didier , Furla Paola , Galand Pierre , Gilson Eric , Lombard Fabien , Pesant Stéphane , Reynaud Stéphanie , Sunagawa Shinichi , Thomas Olivier , Troublé Romain , Zoccola Didier , Correa Adrienne M.S. , Vega Thurber Rebecca L.
Published: April 2022

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
Analysis of community connectivity in spatial transcriptomics data
Authors: Allen Carter , Jung Kyeong Joo , Chang Yuzhou , Ma Qin , Chung Dongjun
Published: April 2022

The advent of high throughput spatial transcriptomics (HST) has allowed for unprecedented characterization of spatially distinct cell communities within a tissue sample. While a wide range of computational tools exist for detecting cell communities in HST data, none allow for characterization of community connectivity, i.e., the relative similarity of cells within and between found communities – an analysis task that can elucidate cellular dynamics in important settings such as the tumor microenvironment. To address this gap, we introduce the concept of analysis of community connectivity (ACC), which entails not only labeling distinct cell communities within a tissue sample, but understanding the relative similarity of cells within and between communities. We develop a Bayesian multi-layer network model called BANYAN for integration of spatial and gene expression information to achieve ACC. We use BANYAN to implement ACC in invasive ductal carcinoma, and uncover distinct community structure relevant to the interaction of cell types within the tumor microenvironment. Next, we show how ACC can help clarify ambiguous annotations in a human white adipose tissue sample. Finally, we demonstrate BANYAN’s ability to recover community connectivity structure via a simulation study based on real sagittal mouse brain HST data.

Availability

An R package banyan is available at https://github.com/carter-allen/banyan.

Contact

chung.911@osu.edu

Supplementary information

Supplementary data are available online.

Author Summary

The proliferation of spatial transcriptomics technologies have prompted the development of numerous statistical models for characterizing the makeup of a tissue sample in terms of distinct cell sub-populations. However, existing methods regard inferred sub-populations as static entities and do not offer any ability to discover the relative similarity of cells within and between communities, thereby obfuscating the true interactive nature of cells in a tissue sample. We develop BANYAN: a statistical model for implementing analysis of community connectivity (ACC), i.e., the process of inferring the similarity of cells within and between cell sub-populations. We demonstrate the utility of ACC through the analysis of a publicly available breast cancer data set, which revealed distinct community structure between tumor suppressive and invasive cancer cell sub-populations. We then showed how ACC may help elucidate ambiguous sub-population annotations in a publicly available human white adipose tissue data set. Finally, we implement a simulation study to validate BANYAN’s ability to recover true community connectivity structure in HST data.
Extracellular vesicles secreted byBrugia malayimicrofilariae modulate the melanization pathway in the mosquito host
Authors: Loghry Hannah J. , Kwon Hyeogsun , Smith Ryan C , Sondjaja Noelle A , Minkler Sarah J , Young Sophie , Wheeler Nicolas J , Zamanian Mostafa , Bartholomay Lyric C , Kimber Michael J
Published: April 2022

Vector-borne, filarial nematode diseases represent a significant and affecting disease burden in humans, domestic animals, and livestock worldwide. Parasitic filarial nematodes require both an intermediate (vector) host and a definitive (mammalian) host during the course of their life cycle. In either host, the nematode must evade the host elicited immune response in order to develop and establish infection. There is direct evidence of parasite-derived immunomodulation in mammals, however, there is less evidence of parasite immunomodulation of the vector host. We have previously reported that all life stages ofBrugia malayi, a causative agent of lymphatic filariasis, secrete extracellular vesicles (EVs). Here we investigate the immunomodulatory effects of microfilariae derived EVs on the vector hostAedes aegypti.RNA-seq analysis of anA. aegypticell line treated withB. malayimicrofilariae EVs showed differential expression of both mRNAs and miRNAs, some with roles in immune regulation. One downregulated gene, AAEL002590, identified as a serine protease, was shown to have direct involvement in the phenoloxidase (PO) cascade through analysis of PO activity. Similarly, injection of adult female mosquitoes withB. malayimicrofilariae EVs validated these resultsin vivo, eliciting a downregulation of the AAEL002590 transcript and a significant reduction in PO activity. Our data indicates that parasite-derived EVs are capable of interfering with critical immune responses in the vector host, particularly immune responses such as melanization that target extracellular parasites. In addition, this data provides novel targets for transmission control strategies for LF and other parasitic diseases.

Author Summary

Vector-borne, filarial nematode diseases represent a significant and affecting disease burden in humans, domestic animals and livestock worldwide. Parasitic nematodes must evade the elicited immune response of their hosts in order to develop and establish infection. While there is evidence for immunomodulation of the mammalian host, the mechanism of this immunomodulation is not fully clear and there is limited evidence for immunomodulation of the vector host. Here we have shown that parasite-derived extracellular vesicles are effector structures for immunomodulation of the vector host. In particular, we have identified that parasite-derived extracellular vesicles can interfere with critical mosquito immune responses against parasites. This data provides insight into parasite biology and novel targets for transmission control strategies for parasitic diseases.
Beyond bold versus shy: Zebrafish exploratory behavior falls into several behavioral clusters and is influenced by strain and sex
Authors: Rajput Neha , Parikh Kush , Kenney Justin W.
Published: April 2022

Consistent individual differences in exploratory behavior have been found across a range of taxa, including zebrafish, and are thought to contribute to evolutionary fitness. Animals that explore more of a novel environment, and visit areas of high predation risk, are considered bold, whereas animals with the opposite pattern of behavior are considered shy. Here, we examined whether this bimodal characterization of bold versus shy adequately captures the breadth of exploratory behavior exhibited by zebrafish or if, instead, behavior falls into multiple distinct behavioral subtypes. To identify the presence of behavioral subtypes, we applied unsupervised machine learning to behaviors extracted from three-dimensional swim traces from over 400 adult zebrafish across four strains (AB, TL, TU, and WIK) and both sexes. We found that behavior stratified into four distinct clusters. These included previously described bold and shy behavior as well as two new behavioral types: wall-huggers and active explorers. Consistent with prior work that found individual differences to be stable across time and influenced by biological factors like genetics and sex, the behavioral subtypes we identified were stable for up to 10 weeks and were influenced by the strain and sex of the animals. Taken together, our work suggests that individual differences in zebrafish exploratory behavior goes beyond bold versus shy and exhibits greater complexity than is typically assumed.
On the interaction between Janzen-Connell effects and habitat partitioning in spatially structured environments
Authors: Smith Daniel J. B.
Published: April 2022

Janzen-Connell Effects and Habitat Partitioning have both been proposed as potential stabilizing mechanisms in species-rich forest communities. Janzen-Connell Effects describe the process in which specialized predators are attracted to adult trees, which reduce the survivorship of nearby conspecific juveniles. This is thought to generate stabilizing negative frequency dependence. Habitation Partitioning describes when species exhibit different fitness responses to spatially heterogeneous environmental factors, typically causing species to aggregate into favorable habitat types. Despite substantial empirical evidence that both processes occur simultaneously in empirical systems, the theoretical implications of how their interactions shape species diversity remain underdeveloped. In this study, I examine a spatially explicit model that incorporates both processes. I show that Janzen-Connell Effects and Habitat Partitioning can act synergistically to promote coexistence such that their contribution to species coexistence is greater than the sum of their parts when environmental spatial heterogeneity is positively autocorrelated. The results of this study highlight the need to explicitly model the interaction between co-occurring spatially dependent coexistence mechanisms to understand the role they play in the maintenance of species diversity.

Significance Statement

A primary goal of ecology is to explain the maintenance of species diversity. However, the mechanisms that underlie the coexistence of highly diverse tropical rainforests remain contentious. Two leading hypotheses are Janzen-Connell Effects and Habitat Partitioning. Both hypotheses are based on space. Janzen-Connell Effects are based on the observation that natural enemies attracted to adult trees reduce the survival of their nearby seeds and seedlings. In contrast, Habitation Partitioning states that diversity can be maintained when species exhibit different responses to spatially varying environmental conditions such that species congregate into their preferred habitat types. In this paper, I demonstrate that these mechanisms can interact synergistiacally to promote high species diversity.
Multi-trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea (Pisum sativum L.)
Authors: Atanda Sikiru Adeniyi , Steffes Jenna , Lan Yang , Al Bari Md Abdullah , Kim Jeonghwa , Morales Mario , Johnson Josephine , Saludares Rica Amor , Worral Hannah , Piche Lisa , Ross Andrew , Grusak Michael A , Coyne Clarice J. , McGee Rebecca J. , Rao Jiajia , Bandillo Nonoy
Published: April 2022

The superiority of multi-trait genomic selection (MT-GS) over univariate genomic selection (UNI-GS) can be improved by redesigning the phenotyping strategy. In this study, we used about 300 advanced breeding lines from North Dakota State University (NDSU) pulse breeding program and about 200 USDA accessions evaluated for ten nutritional traits to assess the efficiency of sparse testing in MT-GS. Our results showed that sparse phenotyping using MT-GS consistently outperformed UNI-GS when compared to partially balanced phenotyping using MT-GS. This strategy can be further extended to multi-environment multi-trait GS to improve prediction performance and reduce the cost of phenotyping and time-consuming data collection process. Given that MT-GS relies on borrowing information from genetically correlated traits and relatives, consideration should be given to trait combinations in the training and prediction sets to improve model parameters estimate and ultimately prediction performance. Our results point to heritability and genetic correlation between traits as possible parameters to achieve this objective.
Reducing peptide sequence bias in quantitative mass spectrometry data with machine learning
Authors: Dincer Ayse , Lu Yang , Schweppe Devin , Oh Sewoong , Noble William Stafford
Published: April 2022

Quantitative mass spectrometry measurements of peptides necessarily incorporate sequence-specific biases that reflect the behavior of the peptide during enzymatic digestion, liquid chromatography, and in the mass spectrometer. These sequence-specific effects impair quantification accuracy, yielding peptide quantities that are systematically under- or over-estimated. We provide empirical evidence for the existence of such biases, and we use a deep neural network, called Pepper, to automatically identify and reduce these biases. The model generalizes to new proteins and new runs within a related set of MS/MS experiments, and the learned coefficients themselves reflect expected physicochemical properties of the corresponding peptide sequences. The resulting adjusted abundance measurements are more correlated with mRNA-based gene expression measurements than the unadjusted measurements. Pepper is suitable for data generated on a variety of mass spectrometry instruments, and can be used with labeled or label-free approaches, and with data-independent or data-dependent acquisition.
Differences in the genetic structure between and within two landlocked Ayu groups with different migration patterns in Lake Biwa revealed by environmental DNA analysis
Authors: Tsuji Satsuki , Shibata Naoki , Sawada Hayato , Watanabe Katsutoshi
Published: April 2022

Ayu,Plecoglossus altivelis, is largely an annual amphidromous fish, although a landlocked population lives in Lake Biwa, the largest lake in Japan. The landlocked population comprises two migrant groups, spring migrants and autumn migrants, which run to inlet rivers from the lake at different seasons. We used environmental DNA (eDNA) analysis, which is reported to be more sensitive and cost-effective than capture surveys, to clarify the genetic structure of this landlocked Ayu population with different migration patterns in Lake Biwa. We took water samples in 11 inlet rivers in the spring and autumn for two years in a row and quantitatively detected a total of 265 haplotypes of the mitochondrial D-loop region. The pairwise fixation index (FST) value and haplotype diversity indicated that there were genetic differences between the two migrant groups in their respective rivers, and theFSTvalues were negatively related to latitude and the presence of artificial fish release. Additionally, the isolation by distance within each migrant group was observed when the lake was divided into the east and west sides. These findings show that the landlocked Ayu population in Lake Biwa has the genetic structure associated with migration patterns and geographical distance. This study demonstrates that the eDNA approach will be effective for conducting a large-scale investigation of genetic structure beyond simple presence/absence tests.
Causal contributions of the domain-general (Multiple Demand) and the language-selective brain networks to perceptual and semantic challenges in speech comprehension
Authors: MacGregor Lucy J. , Gilbert Rebecca A. , Balewski Zuzanna , Mitchell Daniel J. , Erzinclioglu Sharon W. , Rodd Jennifer M. , Duncan John , Fedorenko Evelina , Davis Matthew H.
Published: April 2022

1.

Listening to spoken language engages domain-general Multiple Demand (MD, fronto-parietal) regions of the human brain, in addition to domain-selective (fronto-temporal) language regions, particularly when comprehension is challenging. However, there is limited evidence that the MD network makes a functional contribution to core aspects of comprehension. In a behavioural study of volunteers (n=19) with chronic brain lesions, but without aphasia, we assessed the causal role of these networks in perceiving, comprehending and adapting to challenging spoken sentences. A first task measured word report for acoustically degraded (noise-vocoded) sentences before and after training. Participants with greater damage to MD but not language regions required more vocoder channels to achieve 50% word report indicating impaired perception. Perception improved following training, reflecting adaptation to acoustic degradation, but perceptual learning was unrelated to lesion location or extent. A second task used sentence coherence judgements to measure the speed and accuracy of comprehension of spoken sentences using lower-frequency meanings of semantically ambiguous words. Comprehension accuracy was high and unaffected by lesion location or extent. The availability of the lower-frequency meaning, as measured in a subsequent word association task, increased following comprehension (word-meaning priming). Word-meaning priming was reduced for participants with greater damage to language but not MD regions. We conclude that language and MD networks make dissociable contributions to challenging speech comprehension: using recent experience to update word meaning preferences depends on language specialised regions, whereas the domain-general MD network plays a causal role in reporting words from degraded speech.
Crystal structure of μ3-tetrathioantimonato-tris[(cyclam)zinc(II)] tetrathioantimonate acetonitrile disolvate dihydrate showing Zn disorder over the cyclam ring planes (cyclam = 1,4,8,11-tetraazacyclotetradecane)
Authors: Näther Christian , Danker Felix , Bensch Wolfgang
Published: April 2022

Reaction of Zn(ClO4)2·6H2O with cyclam (cyclam = 1,4,8,11-tetraazacyclotetradecane, C10H24N4) and Na3SbS4 in an acetonitrile/water mixture led to the formation of crystals of the title compound, [Zn3(SbS4)(C10H24N4)3](SbS4)·2CH3CN·2H2O or [(Zn-cyclam)3(SbS4)2](H2O)2(acetonitrile)2. The set-up of the crystal structure is similar to that of [(Zn-cyclam)3(SbS4)2].8H2O reported recently [Danker et al. (2021). Dalton Trans. 50, 18107–18117]. The crystal structure of the title compound consists of three crystallographically independent ZnII cations (each disordered around centers of inversion), three centrosymmetric cyclam ligands, one SbS4
3– anion, one water and one acetonitrile molecule occupying general positions. The acetonitrile molecule is equally disordered over two sets of sites. Each Zn2+ cation is bound to four nitrogen atoms of a cyclam ligand and one sulfur atom of the SbS4
3– anion within a distorted square-pyramidal coordination. The cation disorder of the [Zn(cyclam)]2+ complexes is discussed in detail and is also observed in other compounds, where identical ligands are located above and below the [Zn(cyclam)]2+ plane. In the title compound, the building units are arranged in layers parallel to the bc plane forming pores in which the acetonitrile solvate molecules are located. Intermolecular C—H...S hydrogen bonding links these units to the SbS4
3– anions. Between the layers, additional water solvate molecules are present that act as acceptor and donor groups for intermolecular N—H...O and O—H...S hydrogen bonding.
4-[(Benzylamino)carbonyl]-1-methylpyridinium bromide hemihydrate: X-ray diffraction study and Hirshfeld surface analysis
Authors: Rudiuk Vitalii V. , Shaposhnik Anna M. , Baumer Vyacheslav M. , Levandovskiy Igor A. , Shishkina Svitlana V.
Published: April 2022

The hemihydrate of 4-[(benzylamino)carbonyl]-1-methylpyridinium bromide, C14H15N2O+·Br−·0.5H2O, was studied by single-crystal and powder X-ray diffraction methods. In the asymmetric unit, two organic cations of similar conformation, two bromide anions and one water molecule are present. In the crystal, N—H...Br hydrogen bonds link the cations and anions. The formation of a set of intermolecular C—H...Br and C—H...π interactions result in double chains extending parallel to [011]. A Hirshfeld surface analysis showed high contributions of H...H and C...H/H...C short contacts to the total Hirshfeld surfaces of the cations.
Sticky market webs of connection – human and nonhuman market co-codification dynamics across social media
Authors: Schöps Jonathan David , Reinhardt Christian , Hemetsberger Andrea
Published: April 2022

Purpose

Digital markets are increasingly constructed by an interplay between (non)human market actors, i.e. through algorithms, but, simultaneously, fragmented through platformization. This study aims to explore how interactional dynamics between (non)human market actors co-codify markets through expressive and networked content across social media platforms.

Design/methodology/approach

This study applies digital methods as cross-platform analysis to analyze two data sets retrieved from YouTube and Instagram using the keywords “sustainable fashion” and #sustainablefashion, respectively.

Findings

The study shows how interactional dynamics between (non)human market actors, co-codify markets across two social media platforms, i.e. YouTube and Instagram. The authors introduce the notion of sticky market webs of connection, illustrating how these dynamics foster cross-platform market codification through relations of exteriority.

Research limitations/implications

Research implications highlight the necessity to account for all involved entities, including digital infrastructure in digital markets and the methodological potential of cross-platform analyses.

Practical implications

Practical implications highlight considerations managers should take into account when designing market communication for digital markets composed of (non)human market actors.

Social implications

Social implications highlight the possible effects of (non)human market co-codification on markets and consumer culture, and corresponding countermeasures.

Originality/value

This study contributes to an increased understanding of digital market dynamics by illuminating interdependent market co-codification dynamics between (non)human market actors, and how these dynamics (de)territorialize digital market assemblages through relations of exteriority across platforms.
Mindfulness practice improves managers’ job demands-resources, psychological detachment, work-nonwork boundary control, and work-life balance – a randomized controlled trial
Authors: Mellner Christin , Osika Walter , Niemi Maria
Published: April 2022

Purpose

Contemporary workplaces undergo frequent reorganizations in order to stay competitive in a working life characterized by globalization, digitalization, economic uncertainty, and ever-increased complexity. Managers are in the frontline of these challenges, leading themselves, organizations and their employees in high stress environments. This raises questions on how to support managers’ work-life sustainability, which is crucial for organizational sustainability. Mindfulness has been related to enhanced capacities to cope with challenges that are associated with organizational change. The authors evaluated short- and long-term effects of an eight-week mindfulness-based intervention in a company setting, which was going through reorganization.

Design/methodology/approach

Forty managers (42.5% males), mean age 54.53 (SD 5.13), were randomized to the mindfulness intervention or a non-active wait-list control. Self-report data were provided on individual sustainability factors in a work context: job demands and resources, psychological detachment, i.e. possibilities for letting go of work-related thoughts during leisure, control over work-nonwork boundaries, work-life balance, and mindfulness at baseline, postintervention, and at 6-month follow-up.

Findings

Linear mixed models (LMMs) analysis (all ps < 0.005 to 0.05) showed that the intervention group had a larger decrease in job demands and a smaller decrease in job resources, a larger increase in psychological detachment, work-nonwork boundary control, work-life balance, and mindfulness from baseline to postintervention when compared with the reference group. These initial effects were sustained at 6-month follow-up.

Originality/value

The study provides evidence that mindfulness practice can enhance managers’ long-term capacity to cope with challenging working conditions, and increase their work-life sustainability in times of organizational change and disruption.