bluuebunny/crossref_metadata_2025 huggingface dataset:
Graphic insights into the network basis for heat-gated TRPV1
Authors: Wang Guangyu
Published: January 2022

Non-covalent interactions in bio-macromolecules are individually weak but collectively important. How they take a concerted action in a complex biochemical reaction network to realize their thermal stability and activity is still challenging to study. Here graph theory was used to investigate how the temperature-dependent non-covalent interactions as identified in the structures of the thermo-gated capsaicin receptor TRPV1 could form a systemic fluidic grid-like mesh network with topological grids to maintain the 3D structure of TRPV1 and to govern heat-sensing. The results showed that the heat-evoked melting of the biggest grid may initiate a specific temperature threshold for both channel activation and inactivation. Meanwhile, a thermostable balance between an open state and a putatively inactivated state from the same pre-open closed state may account for heat efficacy and the use-dependent desensitization, which were further stabilized by smaller grids. Altogether, both the biggest and smaller grids may be necessary for the temperature sensitivity. Therefore, this grid thermodynamic model may be broadly significant for the structural thermostability and the functional thermoactivity of biological macromolecules.

Highlights

Thermo-driven cyclization or decyclization of a DNA hairpin and a network grid in protein was thermodynamically comparable

The temperature thresholds of TRPV1 for channel activation and inactivation were comparable theoretically and experimentally

The thermo-sensitivities of TRPV1 for channel activation and inactivation were comparable theoretically and experimentally

The grid-based systemic thermal instability of TRPV1 was useful to identify different gating states

The release of the phosphatidylinositol lipid from the vanilloid site was required for the heat-evoked activation of TRPV1
An investigation into the spatiotemporal patterns of the Nymphalid butterfly Vagrans egista sinha (Kollar, [1844])
Authors: Pop Paul , Barwal Kuldeep Singh , Singh Randeep , Pandey Puneet , Singh Harminder Pal , Sondhi Sanjay
Published: January 2022

Vagrans egista sinha (Kollar, [1844]), the Himalayan Vagrant is a subspecies of Nymphalid (Brush-footed) butterflies spread across Asia, whose western limit is in the north-west India. Observations of this subspecies have considerably increased over the past half-a-decade, with a spike in new sightings to the west of their previously known range. This has been considered as a range extension. The current study reports new records of this species from Bilaspur District, Himachal Pradesh, India (which are the first records for the district), through systematic and opportunistic sampling. This raises the question of whether the purported range extension towards the west could instead be a range shift or vagrancy, and whether there is any shift in elevational ranges in the populations across their known range. Questions pertaining to spatial differences in elevational ranges and seasonal variation, across their range, also piqued our curiosity. Using data from academic sources (such as published literature and museum collections), supplemented by data from public participation in scientific research and personal observations, these research questions are addressed. The accuracy of results when using citizen science data is also explored using the same dataset, focused on the impact of method of extraction of coordinates, and elevation derived from it under different scenarios. It was discovered that there has not been a range shift (either longitudinal or latitudinal) and observations don’t suggest vagrancy but a case of range extension. Other results indicated that there was no climb of population to higher elevations, no spatial differences in elevational ranges in the populations, or seasonal variation in activities across their range. It was also discovered that the method of data collection by, and extraction from, citizen science databases, can influence the accuracy of the results. Some problems involved in collecting data are discussed, and remedial solutions are suggested.
Antibody response to SARS-CoV-2 mRNA vaccine in lung cancer patients: Reactivity to vaccine antigen and variants of concern
Authors: Valanparambil Rajesh M , Carlisle Jennifer , Linderman Susanne L. , Akthar Akil , Millett Ralph Linwood , Lai Lilin , Chang Andres , McCook Ashley A. , Switchenko Jeffrey , Nasti Tahseen H. , Saini Manpreet , Wieland Andreas , Manning Kelly E. , Ellis Madison , Moore Kathryn M. , Foster Stephanie L. , Floyd Katharine , Davis-Gardner Meredith E. , Edara Venkata-Viswanadh , Patel Mit , Steur Conor , Nooka Ajay K. , Green Felicia , Johns Margaret A. , O’Brein Fiona , Shanmugasundaram Uma , Zarnitsyna Veronika I , Ahmed Hasan , Nyhoff Lindsay E. , Mantus Grace , Garett Michael , Edupuganti Srilatha , Behra Madhusmita , Antia Rustom , Wrammert Jens , Suthar Mehul S. , Dhodapkar Madhav V. , Ramalingam Suresh , Ahmed Rafi
Published: January 2022

Purpose

We investigated SARS-CoV-2 mRNA vaccine-induced binding and live-virus neutralizing antibody response in NSCLC patients to the SARS-CoV-2 wild type strain and the emerging Delta and Omicron variants.

Methods

82 NSCLC patients and 53 healthy adult volunteers who received SARS-CoV-2 mRNA vaccines were included in the study. Blood was collected longitudinally, and SARS-CoV-2-specific binding and live-virus neutralization response to 614D (WT), B.1.617.2 (Delta), B.1.351 (Beta) and B.1.1.529 (Omicron) variants were evaluated by Meso Scale Discovery (MSD) assay and Focus Reduction Neutralization Assay (FRNT) respectively. We determined the longevity and persistence of vaccine-induced antibody response in NSCLC patients. The effect of vaccine-type, age, gender, race and cancer therapy on the antibody response was evaluated.

Results

Binding antibody titer to the mRNA vaccines were lower in the NSCLC patients compared to the healthy volunteers (P=<0.0001). More importantly, NSCLC patients had reduced live-virus neutralizing activity compared to the healthy vaccinees (P=<0.0001). Spike and RBD-specific binding IgG titers peaked after a week following the second vaccine dose and declined after six months (P=<0.001). While patients >70 years had lower IgG titers (P=<0.01), patients receiving either PD-1 monotherapy, chemotherapy or a combination of both did not have a significant impact on the antibody response. Binding antibody titers to the Delta and Beta variants were lower compared to the WT strain (P=<0.0001). Importantly, we observed significantly lower FRNT50 titers to Delta (6-fold), and Omicron (79-fold) variants (P=<0.0001) in NSCLC patients.

Conclusions

Binding and live-virus neutralizing antibody titers to SARS-CoV-2 mRNA vaccines in NSCLC patients were lower than the healthy vaccinees, with significantly lower live-virus neutralization of B.1.617.2 (Delta), and more importantly, the B.1.1.529 (Omicron) variant compared to the wild-type strain. These data highlight the concern for cancer patients given the rapid spread of SARS-CoV-2 Omicron variant.
Distinct roles of core autophagy-related genes (ATGs) in zebrafish definitive hematopoiesis
Authors: Chen Xiang-Ke , Yi Zhen-Ni , Lau Jack Jark-Yin , Ma Alvin Chun-Hang
Published: January 2022

Despite the well-described discrepancy between some of the macroautophagy/autophagy-related genes (ATGs) in the regulation of hematopoiesis, the varying essentiality of core ATGs in vertebrate definitive hematopoiesis remains largely unclear. Here, we employed zebrafish (Danio rerio) to compare the function of six core atgs from the core autophagy machineries, which included atg13, beclin1 (becn1), atg9a, atg2a, atg5, and atg3, in vertebrate definitive hematopoiesis via CRISPR-Cas9 ribonucleoprotein targeting. Zebrafish embryos with various atg mutations showed autophagic deficiency throughout the body, including hematopoietic cells. The atgs mutations unsurprisingly caused distinctive hematopoietic abnormalities in zebrafish. Notably, becn1 or atg9a mutation resulted in hematopoietic stem cells (HSCs) expansion during the development of the embryo into a larva, which can be attributed to the proteomic changes in metabolism, HSCs regulators, and apoptosis. Besides, atg3 mutation lowered the leukocytes in developing zebrafish embryos. Intriguingly, a synergistic effect on HSCs expansion was identified in atg13+becn1 and atg9a+atg2a or atg3 double mutations, in which atg13 mutation and atg2a or atg3 mutation exacerbated and mitigated the HSCs expansion in becn1 and atg9a mutations, respectively. In addition, the myeloid cell type-specific effects of various atgs were also determined between neutrophils and macrophages. Of these, a skewed ratio of neutrophils versus macrophages was found in atg13 mutation, while both of them were reduced in atg3 mutation. These findings demonstrated the distinct roles of atgs and their interplays in zebrafish definitive hematopoiesis, thereby suggested that the vertebrate definitive hematopoiesis is regulated in an atgs-dependent manner.
Missense variants causing Wiedemann-Steiner syndrome preferentially occur in the KMT2A-CXXC domain and are accurately classified using AlphaFold2
Authors: Reynisdottir Tinna , Anderson Kimberley , Boukas Leandros , Bjornsson Hans Tomas
Published: January 2022

Wiedemann-Steiner syndrome (WSS) is a neurodevelopmental disorder caused by de novo variants in KMT2A, which encodes a multi-domain histone methyltransferase. To gain insight into the currently unknown pathogenesis of WSS, we examined the spatial distribution of likely WSS-causing variants across the 15 different domains of KMT2A. Compared to variants in healthy controls, WSS variants exhibit a 64.1-fold overrepresentation within the CXXC domain – which mediates binding to unmethylated CpGs – suggesting a major role for this domain in mediating the phenotype. In contrast, we find no significant overrepresentation within the catalytic SET domain. Corroborating these results, we find that hippocampal neurons from Kmt2a-deficient mice demonstrate disrupted H3K4me1 preferentially at CpG-rich regions, but this has no systematic impact on gene expression. Motivated by these results, we combine accurate prediction of the CXXC domain structure by AlphaFold2 with prior biological knowledge to develop a classification scheme for missense variants in the CXXC domain. Our classifier achieved 96.0% positive and 92.3% negative predictive value on a hold-out test set. This classification performance enabled us to subsequently perform an in silico saturation mutagenesis and classify a total of 445 variants according to their functional effects. Our results yield a novel insight into the mechanistic basis of WSS and provide an example of how AlphaFold2 can contribute to the in silico characterization of variant effects with very high accuracy, establishing a paradigm potentially applicable to many other Mendelian disorders.
Vps68 cooperates with ESCRT-III in intraluminal vesicle formation
Authors: Alsleben Sören , Kölling Ralf
Published: January 2022

The endosomal sorting complex required for transport (ESCRT)-III mediates budding and abscission of intraluminal vesicles (ILVs) into multivesicular endosomes. To further define the role of the ESCRT-III associated protein Mos10/Vps60 in ILV formation, we screened for new interaction partners by SILAC/MS. Here, we focused on the newly identified interaction partner Vps68. Our data suggest that Vps68 cooperates with ESCRT-III in ILV formation. The deletion of VPS68 caused a sorting defect similar to the SNF7 deletion, when the cargo load was high. The composition of ESCRT-III was altered, the level of core components was higher and the level of associated proteins was lower in the deletion strain. This suggests that a shift occurs from an active complex to a disassembly competent complex and that this shift is blocked in the Δvps68 strain. We present evidence that during this shift Snf7 is replaced by Mos10. Vps68 has an unusual membrane topology. Two of its potential membrane helices are amphipathic helices localized to the luminal side of the endosomal membrane. Based on this membrane topology we propose that Vps68 and ESCRT-III cooperate in the abscission step by weakening the luminal and cytosolic leaflets of the bilayer at the abscission site.
Cellular and gene expression patterns associated with root bifurcation in Selaginella
Authors: Fang Tao , Motte Hans , Parizot Boris , Smet Wouter , Yang Xilan , Walker Liam , Njo Maria , Bassel George W. , Beeckman Tom
Published: January 2022

The roots of lycophytes branch through dichotomy or bifurcation, which means that the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, where LRs develop along the root axis at different distances from the apex. The process of root bifurcation is poorly understood, while such knowledge can be important, as it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyteSelaginella moellendorffii. We characterized anin vitrodevelopmental time-frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching inS. moellendorffiiat the microscopical and transcriptional level. Our results show that, in contrast to previous assumptions, initial cells in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages during root branching argues for the occurrence of a symmetric division of the single initial cell resulting in two apical stem cells allowing for root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome, which resulted in the delineation of a subset of core meristem genes. The occurrence of multiple meristem-related orthologues in this dataset, including inversely correlated expression profiles of aSCARECROW (SCR)versus aRETINOBLASTOMA-RELATED1 (RBR1)homologue suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance.

One-sentence summary

The root of the spike mossSelaginella moellendorffiibifurcates following a symmetric cell division of the single stem cell and involves conserved genetic modules known from angiosperm roots.
Controlled exchange of protein and nucleic acid signals from and between synthetic minimal cells
Authors: Heili Joseph M. , Stokes Kaitlin , Gaut Nathaniel J. , Deich Christopher , Gomez-Garcia Jose , Cash Brock , Pawlak Matthew R. , Engelhart Aaron E , Adamala Katarzyna P.
Published: January 2022

Synthetic minimal cells are a class of small liposome bioreactors that have some, but not all functions of live cells. Here, we report a critical step towards the development of a bottom-up minimal cell: cellular export of functional protein and RNA products. We used cell penetrating peptide tags to translocate payloads across a synthetic cell vesicle membrane. We demonstrated efficient transport of active enzymes, and transport of nucleic acid payloads by RNA binding proteins. We investigated influence of a concentration gradient alongside other factors on the efficiency of the translocation, and we show a method to increase product accumulation in one location. We demonstrate the use of this technology to engineer molecular communication between different populations of synthetic cells, to exchange protein and nucleic acid signals. The synthetic minimal cell production and export of proteins or nucleic acids allows experimental designs that approach the complexity and relevancy of natural biological systems.
Long-term dynamic changes of NMDA receptors following an excitotoxic challenge
Authors: Granzotto Alberto , d’Aurora Marco , Bomba Manuela , Gatta Valentina , Onofrj Marco , Sensi Stefano L.
Published: January 2022

Excitotoxicity is a form of neuronal death characterized by the sustained activation of N-methyl-D-aspartate receptors (NMDARs) triggered by the excitatory neurotransmitter glutamate. NADPH-diaphorase neurons [also known as nNOS (+) neurons] are a subpopulation of aspiny interneurons, largely spared following excitotoxic challenges. Unlike nNOS (-) cells, nNOS (+) neurons fail to generate reactive oxygen species in response to NMDAR activation, a key divergent step in the excitotoxic cascade. However, additional mechanisms underlying the reduced vulnerability of nNOS (+) neurons to NMDAR-driven neuronal death have not been explored. Using functional, genetic, and molecular analysis in striatal cultures, we demonstrate that nNOS (+) neurons possess distinct NMDAR properties. These specific features are primarily driven by the peculiar redox milieu of this subpopulation. In addition, we found that nNOS (+) neurons exposed to a pharmacological maneuver set to mimic chronic excitotoxicity alter their responses to NMDAR-mediated challenges. These findings suggest the presence of mechanisms providing long-term dynamic regulation of NMDARs that can have critical implications in neurotoxic settings.
Akkermansia Muciniphilainduces chronic extramedullary hematopoiesis through cooperative IL-1R and TLR signals
Authors: Wang Yuxin , Morishima Tatsuya , Sezaki Maiko , Nakato Gaku , Fukuda Shinji , Li Yuhua , Takizawa Hitoshi
Published: January 2022

Bacterial infections can activate and mobilize hematopoietic stem and progenitor cells (HSPCs) from the bone marrow (BM) to spleen, which is termed as extramedullary hematopoiesis (EMH). Recent studies suggest that commensal bacteria, particularly the microbiota, regulates not only the host immune system but also hematopoietic homeostasis. However, the impact of gut microbial species on hematopoietic pathology remains largely unknown. Here we found that systemic injection ofAkkermansia muciniphila(A. m.), a mucin-degrading bacterium abundantly existing in the human gut rapidly activates BM myelopoiesis, and induces a slow but long-lasting hepato-splenomegaly, characterized by the expansion and differentiation of functional HSPCs, which we termed chronic EMH. Genetic deletion of Toll-like receptor-2 and -4 (TLR2/4) partially diminishedA. m.-induced chronic EMH, while additional pharmacological inhibition of the interleukin-1 receptor (IL-1R) completely alleviated splenomegaly and EMH. Our results demonstrate that cooperative IL-1R- and TLR-mediated innate immune signals regulate commensal bacteria-driven EMH, which might be relevant for certain autoimmune disorders.

Article Summary

The aim of our study is to understand howAkkermansia muciniphila (A.m.), one of the major mucin-degrading microbial species in the human gut activate the immune and hematopoietic systems in a mouse model. We found that a single injection of theA.m. membrane fraction can induce long-lasting hepatosplenomegaly with splenic EMH through cooperative IL-1R- and TLR-mediated innate immune signals.
Plasma and ovarian metabolomic responses to chronic stress in female mice
Authors: Zeleznik Oana A. , Huang Tianyi , Patel Chirag J. , Poole Elizabeth M. , Clish Clary B. , Armaiz-Pena Guillermo N. , Nagaraja Archana S. , Eliassen A. Heather , Shutta Katherine H. , Balasubramanian Raji , Kubzansky Laura D. , Hankinson Susan E. , Sood Anil K. , Tworoger Shelley S.
Published: January 2022

Background

Chronic stress may affect metabolism of amino acids, lipids, and other small molecule metabolites, but these alterations may differ depending on tissue evaluated. We examined metabolomic changes in plasma and ovarian tissue samples from female mice due to chronic stress exposure.

Methods

At 12 weeks old, healthy, female, C57 black mice were randomly assigned to three weeks of chronic stress using daily restraint (2 hours/day; n=9) or normal care (n=10). Metabolomic profiling was conducted on plasma and ovarian tissues. Using the Wilcoxon Rank Test, Metabolite Set Enrichment Analysis, and Differential Network Analysis we identified metabolomic alterations occurring in response to restraint stress. All p-values were corrected for multiple testing using the false discovery rate approach.

Results

In plasma, individual lysophosphatidylcholines (positively) and the metabolite classes carnitines (positively), diacylglycerols and triacylglycerols (inversely) were associated with restraint stress (adjusted-p’s<0.2). In contrast, diacylglycerols and triacylglycerols were increased while carnitines were decreased in ovarian tissue from stressed mice (adjusted-p’s<0.2). However, several metabolites (cholesteryl esters, phosphatidylcholines/ phosphatidylethanolamines plasmalogens and multiple amino acids) were consistently inversely associated with restraint stress in plasma and ovarian tissue (adjusted-p’s<0.2).

Conclusion

We identified differences in multiple lipid and amino acid metabolites in plasma and ovarian tissue of female mice after exposure to chronic stress. Some affected metabolites (primarily triacylglycerols and diacylglycerols) exhibited opposite associations with chronic stress in plasma (a marker of systemic influences) versus in ovarian tissue (representing local changes), suggesting research to understand the biological impact of chronic stress needs to consider both systemic and tissue-specific alterations.
Modelling the distribution of rare invertebrates by correcting class imbalance and spatial bias
Authors: Gaul Willson , Sadykova Dinara , White Hannah J. , León-Sánchez Lupe , Caplat Paul , Emmerson Mark C. , Yearsley Jon M.
Published: January 2022

Aim

Soil arthropods are important decomposers and nutrient cyclers, but are poorly represented on national and international conservation Red Lists. Opportunistic biological records for soil invertebrates are often sparse, and contain few observations of rare species but a relatively large number of non-detection observations (a problem known as class imbalance). Robinson et al. (2018) proposed a method for sub-sampling non-detection data using a spatial grid to improve class balance and spatial bias in bird data. For taxa that are less intensively sampled, datasets are smaller, which poses a challenge because under-sampling data removes information. We tested whether spatial under-sampling improved prediction performance of species distribution models for millipedes, for which large datasets are not available. We also tested whether using environmental predictor variables provided additional information beyond what is captured by spatial position for predicting species distributions.

Location

Island of Ireland.

Methods

We tested the spatial under-sampling method of Robinson et al. (2018) by using biological records to train species distribution models of rare millipedes.

Results

Using spatially under-sampled training data improved species distribution model sensitivity (true positive rate) but decreased model specificity (true negative rate). The decrease in specificity was minimal for rarer species and was accompanied by substantial increases in sensitivity. For common species, specificity decreased more, and sensitivity increased less, making spatial under-sampling most useful for rare species. Geographic coordinates were as good as or better than environmental variables for predicting distributions of two out of six species.

Main Conclusions

Spatial under-sampling improved prediction performance of species distribution models for rare soil arthropod species. Spatial under-sampling was most effective for rarer species. The good prediction performance of models using geographic coordinates is promising for modeling distributions of poorly studied species for which little is known about ecological or physiological determinants of occurrence.
Encoding of speech in convolutional layers and the brain stem based on language experience
Authors: Beguš Gašper , Zhou Alan , Zhao T. Christina
Published: January 2022

Comparing artificial neural networks with outputs of neuroimaging techniques has recently seen substantial advances in (computer) vision and text-based language models. Here, we propose a framework to compare biological and artificial neural computations of spoken language representations and propose several new challenges to this paradigm. The proposed technique is based on a similar principle that underlies electroencephalography (EEG): averaging of neural (artificial or biological) activity across neurons in the time domain, and allows to compare encoding of any acoustic property in the brain and in intermediate convolutional layers of an artificial neural network. Our approach allows a direct comparison of responses to a phonetic property in the brain and in deep neural networks that requires no linear transformations between the signals. We argue that the brain stem response (cABR) and the response in intermediate convolutional layers to the exact same stimulus are highly similar and quantify this observation. The proposed technique not only reveals similarties, but also allows for analysis of the encoding of actual acoustic properties in the two signals: we compare peak latency (i) in cABR relative to the stimulus in the brain stem and in (ii) intermediate convolutional layers relative to the input/output in deep convolutional networks. We also examine and compare the effect of prior language exposure on the peak latency in cABR and in intermediate convolutional layers. Substantial similarities in peak latency encoding between the human brain and intermediate convolutional networks emerge based on results from eight trained networks (including a replication experiment). The proposed technique can be used to compare encoding between the human brain and intermediate convolutional layers for any acoustic property and for other neuroimaging techniques.
A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota
Authors: Amat Samat , Timsit Edouard , Workentine Matthew , Schwinghamer Timothy , van der Meer Frank , Guo Yongmei , Alexander Trevor
Published: January 2022

To address the emergence of antimicrobial-resistant pathogens in livestock, microbiome-based strategies are increasingly being sought to reduce antimicrobial use. Here, we describe the intranasal application of bacterial therapeutics (BTs) for mitigating bovine respiratory disease (BRD) and used structural equation modeling to investigate the causal networks after BT application. Beef cattle received i) an intranasal cocktail of previously characterized BT strains, ii) an injection of metaphylactic antimicrobial (tulathromycin), or iii) intranasal saline. Despite being transient colonizers, inoculated BT strains induced longitudinal modulation of the nasopharyngeal bacterial microbiota while showing no adverse effect on animal health. The BT-mediated changes in bacteria included reduced diversity and richness and strengthened cooperative and competitive interactions. In contrast, tulathromycin increased bacterial diversity and antibiotic resistance, and disrupted bacterial interactions. Overall, a single intranasal dose of BTs can modulate the bovine respiratory microbiota, highlighting that microbiome-based strategies have the potential in being utilized to mitigate BRD in feedlot cattle.
Regulation of PDF receptor signaling controlling daily locomotor rhythms in Drosophila
Authors: Li Weihua , Trigg Jennifer S. , Taghert Paul H.
Published: January 2022

Each day and in conjunction with ambient daylight conditions, neuropeptide PDF regulates the phase and amplitude of locomotor activity rhythms in Drosophila through its receptor, PDFR, a Family B G protein-coupled receptor (GPCR). We studied the in vivo process by which PDFR signaling turns off, by converting as many as half of the 28 potential sites of phosphorylation in its C terminal tail to a non-phosphorylatable residue (alanine). We report that many such sites are conserved evolutionarily, and their conversion creates a specific behavioral syndrome opposite to loss-of-function phenotypes previously described for pdfr. That syndrome includes increases in the amplitudes of both Morning and Evening behavioral peaks, as well as multi-hour delays of the Evening phase. The precise behavioral effects were dependent on day-length, and most effects mapped to conversion of only a few, specific serine residues near the very end of the protein and specific to its A isoform. Behavioral phase delays under entraining conditions were often, but not always correlated with increases in circadian period. The behavioral phenotypes produced by the most severe PDFR variant were ligand-dependent in vivo, and not a consequence of changes to their pharmacological properties, nor of changes in their surface expression, as measured in vitro. The mechanisms underlying termination of PDFR signaling are complex, subject to regulation that is modified by season, and central to a better understanding of the peptidergic modulation of behavior.

AUTHOR SUMMARY

In multi-cellular organisms, circadian pacemakers create output as a series of phase markers across the 24 hour day to allow other cells to pattern diverse aspects of daily rhythmic physiology and behavior. Within circadian pacemaker circuits, neuropeptide signaling is essential to help promote coherent circadian outputs. In the fruit fly Drosophila 150 neurons are dedicated circadian clocks and they all tell the same time. In spite of such strong synchronization, they provide diverse phasic outputs in the form of their discrete, asynchronous neuronal activity patterns. Neuropeptide signaling breaks the clock-generated symmetry and drives many pacemakers away from their preferred activity period in the morning. Each day, neuropeptide PDF is released by Morning pacemakers and delays the phase of activity of specific other pacemakers to later parts of the day or night. When and how the PDF that is released in the morning stops acting is unknown. Furthermore, timing of signal termination is not fixed because day length changes each day, hence the modulatory delay exerted by PDF must itself be regulated. Here we test a canonical model of G protein-coupled receptor physiology to ask how PDF receptor signaling is normally de-activated. We use behavioral measures to define sequence elements of the receptor whose post-translational modifications (e.g., phosphorylation) may define the duration of receptor signaling.
Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line
Authors: Han Shunhua , Dias Guilherme B. , Basting Preston J. , Viswanatha Raghuvir , Perrimon Norbert , Bergman Casey M.
Published: January 2022

Animal cell lines cultured for extended periods often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In Drosophila, many established cell lines also exhibit massive proliferation of transposable elements (TEs) relative to wild-type flies. To better understand the role of transposition during long-term animal somatic cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. Relative to comparable data from inbred whole flies, WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called “TELR” that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a ∼130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by somatic transposition in cell culture after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TE copies within the S2R+ genome, which revealed that proliferation of different TE families during cell line evolution in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are not amenable to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.
mTORC2 loss in oligodendrocyte progenitor cells results in regional hypomyelination in the central nervous system
Authors: Dahl Kristin D. , Hathaway Hannah A. , Almeida Adam R. , Bourne Jennifer , Brown Tanya L. , Finseth Lisbet T. , Wood Teresa L. , Macklin Wendy B.
Published: January 2022

In the central nervous system (CNS), oligodendrocyte progenitor cells (OPCs) differentiate into mature oligodendrocytes to generate myelin, which is essential for normal nervous system function. OPC differentiation is driven by signaling pathways such as mTOR (Mechanistic Target of Rapamycin), which functions in two distinct complexes: mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), containing Raptor or Rictor respectively. In the current studies, mTORC2 signaling was selectively deleted from OPCs in PDGFRα-Cre X Rictorfl/fl mice. This study examined developmental myelination in male and female mice, comparing the impact of mTORC2 deletion in the corpus callosum and spinal cord. In both corpus callosum and spinal cord, Rictor loss in OPCs resulted in early reduction in myelin RNAs and some myelin proteins. However, these deficits rapidly recovered in spinal cord, where normal myelin abundance and thickness was noted at post-natal day 21 and 1.5 months. By contrast, the losses in corpus callosum resulted in severe hypomyelination, and increased unmyelinated axons. The current studies focus on uniquely altered signaling pathways following mTORC2 loss in developing oligodendrocytes. A major mTORC2 substrate is phospho-Akt-S473, which was significantly reduced throughout development in both corpus callosum and spinal cord at all ages measured, yet this had little impact in spinal cord. Loss of mTORC2 signaling resulted in decreased expression of actin regulators such as gelsolin in corpus callosum, but only minimal loss in spinal cord. The current study establishes a regionally-specific role for mTORC2 signaling in OPCs, particularly in the corpus callosum.

Significance Statement

mTORC1 and mTORC2 signaling have differential impact on myelination in the central nervous system. Numerous studies identify a role for mTORC1, but deletion of Rictor (mTORC2 signaling) in late-stage oligodendrocytes had little impact on myelination in the CNS. However, the current studies establish that deletion of mTORC2 signaling from oligodendrocyte progenitor cells results in reduced myelination of brain axons. These studies also establish a regional impact of mTORC2, with little change in spinal cord in these conditional Rictor deletion mice. Importantly, in both, brain and spinal cord, mTORC2 downstream signaling targets were impacted by Rictor deletion. Yet, these signaling changes had little impact on myelination in spinal cord, while they resulted in long term alterations in myelination in brain.
Hemato-vascular specification requiresarnt1andarnt2genes in zebrafish embryos
Authors: Edwards Hailey E. , Edgington Mary Jane , Souder Jaclyn P. , Gorelick Daniel A.
Published: January 2022

During embryonic development, a subset of cells in the mesoderm germ layer are specified as hemato- vascular progenitor cells, which then differentiate into endothelial cells and hematopoietic stem and progenitor cells. In zebrafish, the transcription factornpas4l, also known ascloche, is required for the specification of hemato-vascular progenitor cells. However, it is unclear ifnpas4lis the sole factor at the top of the hemato-vascular specification cascade. Here we show thatarnt1andarnt2genes are required for hemato-vascular specification. We found thatarnt1;arnt2double homozygous mutant zebrafish embryos (herein calledarnt1/2mutants), but notarnt1orarnt2single mutants, lack blood cells and most vascular endothelial cells.arnt1/2mutants have reduced or absent expression ofetsrpandtal1, the earliest known endothelial and hematopoietic transcription factor genes.npas4land thearntgenes are PAS domain-containing bHLH transcription factors that function as dimers. We found that Npas4l binds both Arnt1 and Arnt2 proteinsin vitro, consistent with the idea that PAS domain- containing bHLH transcription factors act in a multimeric complex to regulate gene expression. Our results demonstrate thatnpas4l,arnt1andarnt2act together to regulate endothelial and hematopoietic cell fate, where each gene is necessary, but by itself not sufficient, to drive hemato-vascular specification. Our results also demonstrate thatarnt1andarnt2act redundantly in a transcriptional complex containingnpas4l, but do not act redundantly when interacting with another PAS domain- containing bHLH transcription factor, the aryl hydrocarbon receptor. Altogether, our data enhance our understanding of hemato-vascular specification and the function of PAS domain-containing bHLH transcription factors.
Hybridoma Screening by Antigen Capture: Immunoprecipitation
Authors: Greenfield Edward A.
Published: January 2022

Immunoprecipitation is rarely used for screening hybridoma fusions because the assays are tedious and time-consuming. However, it can be useful when working with complex antigens because the precipitated antigen is normally detected after sodium dodecyl sulfate (SDS)–polyacrylamide electrophoresis and thus it is simple to discriminate between true and false positives. Furthermore, the assay provides information regarding the molecular weight of the antigen.
In Vivo Time-Lapse Imaging and Analysis of Dendritic Structural Plasticity in Xenopus laevis Tadpoles
Authors: He Hai-yan , Lin Chih-Yang , Cline Hollis T.
Published: January 2022

In vivo time-lapse imaging of complete dendritic arbor structures in tectal neurons of Xenopus laevis tadpoles has served as a powerful in vivo model to study activity-dependent structural plasticity in the central nervous system during early development. In addition to quantitative analysis of gross arbor structure, dynamic analysis of the four-dimensional data offers particularly valuable insights into the structural changes occurring in subcellular domains over experience/development-driven structural plasticity events. Such analysis allows not only quantifiable characterization of branch additions and retractions with high temporal resolution but also identification of the loci of action. This allows for a better understanding of the spatiotemporal association of structural changes to functional relevance. Here we describe a protocol for in vivo time-lapse imaging of complete dendritic arbors from individual neurons in the brains of anesthetized tadpoles with two-photon microscopy and data analysis of the time series of 3D dendritic arbors. For data analysis, we focus on dynamic analysis of reconstructed neuronal filaments using a customized open source computer program we developed (4D SPA), which allows aligning and matching of 3D neuronal structures across different time points with greatly improved speed and reliability. File converters are provided to convert reconstructed filament files from commercial reconstruction software to be used in 4D SPA. The program and user manual are publicly accessible and operate through a graphical user interface on both Windows and Mac OSX.
Bulk Dye Loading for In Vivo Calcium Imaging of Visual Responses in Populations of Xenopus Tectal Neurons
Authors: Hogg Peter W. , Haas Kurt
Published: January 2022

Bulk loading of neurons with fluorescent calcium indicators in transparent albino Xenopus tadpoles offers a rapid and easy method for tracking sensory-evoked activity in large numbers of neurons within an awake developing brain circuit. In vivo two-photon time-lapse imaging of an image plane through the optic tectum allows defining receptive field properties from visual-evoked responses for studies of single-neuron and network-level encoding and plasticity. Here, we describe loading the Xenopus tadpole optic tectum with the membrane-permeable AM ester of Oregon Green 488 BAPTA-1 (OGB-1 AM) for in vivo imaging experiments.
Multi-sensor optimal deployment based efficient and synchronous data acquisition in large three-dimensional physical similarity simulation
Authors: Hao Yuyu , Li Shugang , Zhang Tianjun
Published: January 2022

Purpose

This paper aims to propose a deployment optimization and efficient synchronous acquisition method for compressive stress sensors used by stress distribution law research based on the genetic algorithm and numerical simulations. The authors established a new method of collecting the mining compressive stress-strain distribution data to address the problem of the number of sensors and to optimize the sensor locations in physical similarity simulations to improve the efficiency and accuracy of data collection.

Design/methodology/approach

First, numerical simulations were used to obtain the compressive stress distribution curve under specific mining conditions. Second, by comparing the mean square error between a fitted curve and simulation data for different numbers of sensors, a genetic algorithm was used to optimize the three-dimensional (3D) spatial deployment of sensors. Third, the authors designed an efficient synchronous acquisition module to allow distributed sensors to achieve synchronous and efficient acquisition of hundreds of data points through a built-in on-board database and a synchronous sampling communication structure.

Findings

The sensor deployment scheme was established through the genetic algorithm, A synchronous and selective data acquisition method was established for reduced the amount of sensor data required under synchronous acquisition and improved the system acquisition efficiency. The authors obtained a 3D compressive stress distribution when the advancement was 200 m on a large-scale 3D physical similarity simulation platform.

Originality/value

The proposed method provides a new optimization method for sensor deployment in physical similarity simulations, which improves the efficiency and accuracy of system data acquisition, providing accurate acquisition data for experimental data analysis.
The impact of COVID-19 on destination visit intention and local food consumption
Authors: Dedeoğlu Bekir Bora , Mariani Marcello , Shi Fangfang , Okumus Bendegul
Published: January 2022

Purpose

This paper aims to investigate the relationships between motivation and intention to consume local food and between intention to consume local food and intention to visit the destination of that food's origin while examining the moderating effect of risk perception associated with coronavirus disease 2019 (COVID-19).

Design/methodology/approach

Data were collected from two samples of potential Chinese tourists in the contexts of Italian and Thai food. Data obtained from 264 Chinese respondents for Italian food and 277 Chinese respondents for Thai food were analyzed. Partial least squares structural equation modeling was utilized to test the research model.

Findings

The results indicate that, while motivational factors such as cultural experience, novelty and sensory appeal influence potential Chinese tourists' intention to consume Italian food, motivational factors such as cultural experience, health concern, novelty and sensory appeal influence tourists' intention to consume Thai food. The authors found that intention to consume local food positively influences tourists' intention to visit both destinations (Italy and Thailand). Moreover, tourists' risk perceptions of COVID-19 negatively moderate the effect of cultural experience and novelty on the intention to consume Italian food. Regarding the intention to consume Thai food, the authors found that tourists' risk perceptions have a diminishing effect on all motivational factors.

Originality/value

This pioneering study examines the role of COVID-19-related risk perception on the relationships among motivation of local food consumption, intention of local food consumption and destination visit intention in the context of two destination countries. It reveals cross-country differences of the negative effect pertaining to the risk perceptions of COVID-19, which has important implications for international destination marketing.
Workplace incivility and its socio-demographic determinants in India
Authors: Chaudhary Richa , Lata Madhu , Firoz Mantasha
Published: January 2022

Purpose

The purpose of this study is to present an empirical account of the prevalence and socio-demographic determinants of workplace incivility (experienced and instigated) in the Indian workplace.

Design/methodology/approach

The study sample consisted of 1,133 employees working in service organizations mainly banks, hotels, academic institutions and information technology firms. The authors tested the proposed model on the same set of respondents in two different studies. The phenomenon of instigated incivility and its determinants were examined in Study 1, while Study 2 looked at experienced incivility and its antecedents. The data were analyzed using univariate, bivariate, and multivariate statistical operations in SPSS 24.

Findings

The results of both studies revealed that employees’ age, gender, educational qualification, position, nature of the organization, type of the organization and duration of working hours significantly predict the onset of workplace incivility. Nevertheless, marital status and tenure failed to predict the manifestation of uncivil behaviors in the organization.

Research limitations/implications

The scope of this study was restricted to the Indian service sector with a focus on only two types of workplace incivility (instigated and experienced).

Practical implications

The managers are advised to be mindful of employees’ socio-demographic differences while devising interventions to tackle the issues of uncivil acts at work.

Originality/value

This study is one of the pioneer attempts to explore the impact of socio-demographic factors on employees’ tendency to instigate and experience incivility at work in India. In doing so, the study enriches the scant literature on workplace incivility by establishing the role of individual differences in determining the occurrence of incivility in the workplace.
Lean and resilience in the healthcare supply chain – a scoping review
Authors: Alemsan Najla , Tortorella Guilherme , Taboada Rodriguez Carlos Manuel , Balouei Jamkhaneh Hadi , Lima Rui M.
Published: January 2022

Purpose

The importance of a lean health-care supply chain is increasingly discussed. However, it is still not very clear how lean practices relate to resilience capabilities, as there are synergies and divergences between them. This study aims at identifying the relationship between lean practices and resilience capabilities in the health-care supply chain.

Design/methodology/approach

This study conducted a scoping review based on five databases, which allowed the content analysis of 44 articles. Such analysis allowed the verification of trends and volume of studies on this topic. Further, the descriptive numerical and thematic analyses enabled the proposition of a conceptual framework, relating the adoption of lean practices to the development of resilience capabilities according to the tiers of the health-care supply chain in different value streams.

Findings

Three research directions were derived from this scoping review: empirical validation of the contribution of lean practices to resilience capabilities in the health-care supply chain; systemic implementation of lean practices across tier levels of the health-care supply chain; and complementary approaches to lean implementation toward a more resilient health-care supply chain.

Practical implications

The understanding of these relationships provides health-care managers arguments to prioritize the application of lean practices to improve desired resilience capabilities in the entire health-care supply chain.

Originality/value

To the best of the authors’ knowledge, there is no similar study in the literature.