bluuebunny/crossref_metadata_2025 huggingface dataset:
Larval microbiota primes theDrosophilaadult gustatory response
Authors: Montanari Martina , Manière Gérard , Berthelot-Grosjean Martine , Dusabyinema Yves , Gillet Benjamin , Grosjean Yaël , Kurz C. Léopold , Royet Julien
Published: March 2023

The survival of animals depends, among other things, on their ability to identify threats in their surrounding environment. Senses such as olfaction, vision and taste play an essential role in sampling their living environment, including microorganisms, some of which are potentially pathogenic. This study focuses on the mechanisms of detection of bacteria by theDrosophilagustatory system. We demonstrate that the peptidoglycan (PGN) that forms the cell wall of bacteria triggers an immediate feeding aversive response when detected by the gustatory system of adult flies. Although we identify ppk23+ and Gr66a+ gustatory neurons as necessary to transduce fly response to PGN, we demonstrate that they play very different roles in the process. Time-controlled functional inactivation andin vivocalcium imaging demonstrate that while ppk23+ neurons are required in the adult flies to directly transduce PGN signal, Gr66a+ neurons must be functional in larvae to allow future adults to become PGN sensitive. Furthermore, the ability of adult flies to respond to bacterial PGN is lost when they hatch from larvae reared under axenic conditions. Recolonization of axenic larvae, but not adults, with a single bacterial species,Lactobacillus brevis,is sufficient to restore the ability of adults to respond to PGN. Our data demonstrate that the genetic and environmental characteristics of the larvae are essential to make the future adults competent to respond to certain sensory stimuli such as PGN.
LEP-AD: Language Embedding of Proteins and Attention to Drugs predicts drug target interactions
Authors: Daga Anuj , Khan Sumeer Ahmad , Cabrero David Gomez , Hoehndorf Robert , Kiani Narsis , Tegner Jesper
Published: March 2023

Predicting drug-target interactions is a tremendous challenge for drug development and lead optimization. Recent advances include training algorithms to learn drug-target interactions from data and molecular simulations. Here we utilize Evolutionary Scale Modeling (ESM-2) models to establish a Transformer protein language model for drug-target interaction predictions. Our architecture, LEP- AD, combines pre-trained ESM-2 and Transformer-GCN models predicting bind-ing affinity values. We report new best-in-class state-of-the-art results compared to competing methods such as SimBoost, DeepCPI, Attention-DTA, GraphDTA, and more using multiple datasets, including Davis, KIBA, DTC, Metz, ToxCast, and STITCH. Finally, we find that a pre-trained model with embedding of proteins (the LED-AD) outperforms a model using an explicit alpha-fold 3D representation of proteins (e.g., LEP-AD supervised by Alphafold). The LEP-AD model scales favorably in performance with the size of training data. Code available at https://github.com/adaga06/LEP-AD.
In Need of Age-Appropriate Cardiac Models: Impact of Cell Age on Extracellular Matrix Therapy Outcomes
Authors: Ozcebe S. Gulberk , Zorlutuna Pinar
Published: March 2023

Aging is the main risk factor for cardiovascular disease (CVD). As the world’s population ages rapidly and CVD rates rise, there is a growing need for physiologically relevant models of aging hearts to better understand cardiac aging. Translational research relies heavily on young animal models, however, these models correspond to early ages in human life, therefore cannot fully capture the pathophysiology of age-related CVD. Here, we chronologically aged human induced pluripotent stem cell-derived cardiomyocytes (iCMs) and compared in vitro iCM aging to native human cardiac tissue aging. We showed that 14-month-old advanced aged iCMs had an aging profile similar to the aged human heart and recapitulated age-related disease hallmarks. We then used aged iCMs to study the effect of cell age on the young extracellular matrix (ECM) therapy, an emerging approach for myocardial infarction (MI) treatment and prevention. Young ECM decreased oxidative stress, improved survival, and post-MI beating in aged iCMs. In the absence of stress, young ECM improved beating and reversed aging-associated expressions in 3-month-old iCMs while causing the opposite effect on 14-month-old iCMs. The same young ECM treatment surprisingly increased SASP and impaired beating in advanced aged iCMs. Overall, we showed that young ECM therapy had a positive effect on post-MI recovery, however, cell age was determinant in the treatment outcomes without any stress conditions. Therefore, “one-size-fits-all” approaches to ECM treatments fail, and cardiac tissue engineered models with age-matched human iCMs are valuable in translational basic research for determining the appropriate treatment, particularly for the elderly.
Mycobacteriumtrehalose polyphleates are required for infection by therapeutically useful mycobacteriophages BPs and Muddy
Authors: Wetzel Katherine S. , Illouz Morgane , Abad Lawrence , Aull Haley G. , Russell Daniel A. , Garlena Rebecca A. , Cristinziano Madison , Malmsheimer Silke , Chalut Christian , Hatfull Graham F. , Kremer Laurent
Published: March 2023

Mycobacteriophages are good model systems for understanding their bacterial hosts and show promise as therapeutic agents for nontuberculous mycobacterium infections. However, little is known about phage recognition ofMycobacteriumcell surfaces, or mechanisms of phage resistance. We show here that surface-exposed trehalose polyphleates (TPPs) are required for infection ofMycobacterium abscessusandMycobacterium smegmatisby clinically useful phages BPs and Muddy, and that TPP loss leads to defects in adsorption, infection, and confers resistance. Transposon mutagenesis indicates that TPP loss is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss, and someM. abscessusclinical isolates are phage-insensitive due to TPP absence. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, andM. abscessusmutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
Persistence of SARS-CoV-2 and its surrogate, bacteriophage Phi6, on surfaces and in water
Authors: Pitol Ana K. , Venkatesan Samiksha , Hoptroff Michael , Hughes Grant L.
Published: March 2023

The COVID-19 pandemic has motivated research on the persistence of infectious SARS-CoV-2 in environmental reservoirs such as surfaces and water. Viral persistence data has been collected for SARS-CoV-2 and its surrogates, including bacteriophage Phi6. Despite its wide use, no side-by-side comparisons between Phi6 and SARS-CoV-2 exist. Here, we quantified the persistence of SARS-CoV-2 and Phi6 on surfaces (plastic and metal) and in water and evaluated the influence that the deposition solution has on viral persistence by using four commonly used deposition solutions: two culture media (DMEM and Tryptone Soya Broth (TSB)), Phosphate Buffered Saline (PBS), and human saliva. Phi6 remained infectious in water significantly longer than SARS-CoV-2, having a half-life of 27 hours as compared with 15 hours for SARS-CoV-2. The persistence of viruses on surfaces was significantly influenced by the virus used and the deposition solution, but not by the surface material. Phi6 remained infectious significantly longer than SARS-CoV-2 when the inoculation solution was culture media (DMEM, TSB) and saliva. Using culture media and saliva led to half-lives between 9 hours and 2 weeks for Phi6, as compared to 0.5 to 2 hours for SARS-CoV-2. Using PBS as a deposition solution led to half-lives shorter than 4 hours for both viruses on all surfaces. Our results showed that, although it has been frequently used as a surrogate for coronaviruses, bacteriophage Phi6 is not an adequate surrogate for studies quantifying SARS-CoV-2 persistence, as it over-estimates infectiousness. Additionally, our findings reveal the need of using adequate deposition solutions when evaluating viral persistence on surfaces.
Brain fingerprinting using fMRI spectral signatures on high-resolution cortical graphs
Authors: Ferritto Carlo , Preti Maria Giulia , Moia Stefano , Van De Ville Dimitri , Behjat Hamid
Published: March 2023

Resting-state fMRI has proven to entail subject-specific signatures that can serve as a fingerprint to identify individuals. Conventional methods are based on building a connectivity matrix based on correlation between the average time course of pairs of brain regions. This approach, first, disregards the exquisite spatial detail manifested by fMRI due to working on average regional activities, second, cannot disentangle correlations associated to cognitive activity and underlying noise, and third, does not account for cortical morphology that spatially constraints function. Here we propose a method to address these shortcomings via leveraging principles from graph signal processing. We build high spatial resolution cortical graphs that encode each individual’s cortical morphology and treat region-specific, whole-hemisphere fMRI maps as signals that reside on the graphs. fMRI graph signals are then decomposed using systems of graph spectral kernels to extract structure-informed functional signatures, which are in turn used for fingerprinting. Results on 100 subjects showed the overall superior subject differentiation power of the proposed signatures over the conventional method. Moreover, placement of the signatures within canonical functional brain networks revealed the greater contribution of high-level cognitive networks in subject identification.
Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes inTrichoderma
Authors: Scott Kelsey , Konkel Zachary , Gluck-Thaler Emile , David Guillermo E. Valero , Simmt Coralie Farinas , Grootmyers Django , Chaverri Priscila , Slot Jason
Published: March 2023

Trichodermais a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera likeTrichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eightTrichodermagenomes representing the full breadth of environmentalTrichoderma’s diverse lifestyles and nutritional modes. We generated four newTrichoderma endophyticumgenomes to improve the sampling of endophytic isolates from this genus. As predicted, endophyticTrichodermagenomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with theTrichodermaendophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophyticTrichodermagenomes. Most genomic differences betweenTrichodermalifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster toTrichoderma.
Epithelial galectin-3 induces mitochondrial complex inhibition and cell cycle arrest of CD8+T Cells in severe/critical ill COVID-19
Authors: Wang Yudie , Yang Cheng , Wang Zhongyi , Wang Yi , Yan Qing , Feng Ying , Liu Yanping , Zhang Xiaolan , Zhao Jingwei , Huang Juan , Zhou Jingjiao
Published: March 2023

Several studies have identified the presence of functionally depleted CD8+T cells in COVID-19 patients, and particularly abnormally reduced CD8+T cells in severe/critical patients, which may be a major cause of disease progression and poor prognosis. In this study, a proliferating-depleted CD8+T cell phenotype was observed in severe/critical COVID-19 patients through scRNA-seq and scTCR-seq analysis. These CD8+T cells were subsequently found to be characterized by cell cycle arrest and downregulation of mitochondrial biogenesis and respiratory chain complex genes. Cellchat analysis revealed that the Galectin signaling pathways between infected lung epithelial cells and CD8+T cells play the key role in inducing CD8+T cell reduction and dysfunction in severe/critical COVID-19. We used SARS-COV-2 ORF3a to transfect A549 epithelial cells, and co-cultured with CD8+T cells. The ex vivo experiments confirmed that galectin-3 inhibited the transcription of mitochondrial respiratory chain complex III/IV genes in CD8+T cells by suppressing the nuclear translocation of nuclear respiratory factor 1 (NRF1). In addition, the regulatory effect of galectin-3 was correlated with the activation of ERK signaling and/or the inhibition of Akt signaling. Galectin-3 inhibitor, TD-139, promoted nuclear translocation of NRF1, and enhanced mitochondrial respiratory chain complex III/IV gene expression and mitochondrial biogenesis, then restore the expansion ability of CD8+T cells. Our study improved the understanding the immunopathogenesis and provided new target for the prevention and treatment of severe/critical COVID-19.
A bi-kinase module sensitizes and potentiates plant immune signaling
Authors: Köster Philipp , He Gefeng , Dong Qiuyan , Hake Katarina , Schmitz-Thom Ina , Heinkow Paulina , Eirich Jürgen , Wallrad Lukas , Hashimoto Kenji , Schültke Stefanie , Finkemeier Iris , Romeis Tina , Kudla Jörg
Published: March 2023

Systemic signaling is an essential hallmark of multicellular life. Pathogen encounter occurs locally but triggers organ-scale and organismic immune responses. In plants, elicitor perception provokes systemically expanding Ca2+and H2O2signals conferring immunity. Here, we identify a Ca2+sensing bi-kinase module as becoming super-activated through mutual trans-phosphorylation and imposing synergistically enhanced NADPH oxidase activation. A combined two-layer bi-kinase/substrate phospho-code allows for sensitized signaling initiation already by near-resting elevations of Ca2+concentration at the infection site. Subsequently, it facilitates further signal wave proliferation with minimal amplitude requirement, triggering protective defense responses throughout the plant. Our study reveals how plants build and perpetuate trans-cellular immune signal proliferation while avoiding disturbance of ongoing cellular signaling along the path of response dissemination.

One sentence summary

Mutual trans-activation of a Ca2+sensing bi-kinase module potentiates NADPH oxidase activation to facilitate systemic immunity.
Lights, Camera, Mirrors, Action! Toolbox for 3D Reconstruction and Analysis Using a Single Camera and Planar Mirrors
Authors: hussain Muhammad wajahat , Naveed Mahum , Khan Asad , Khan Taimoor Hasan , Anjum Muhammad Latif , Rasool Shahzad , Maqsood Adnan
Published: March 2023

With the commercialization of high speed cameras we have started revealing interesting animal behaviors. Analyzing animal kinematics in 3D requires multiple high speed cameras. These special cameras are extremely expensive. In this work, we leverage a classic approach of capturing simultaneous and multiple views using a single camera and planar mirrors. We present a user-friendly toolbox which enables calibration of this low cost setup, and 3D analysis of high speed maneuvers. Within ~15 minutes, a single high speed camera is calibrated and can be used to acquire 3D data. We accompany the toolbox with detailed user guide and video tutorial (https://tinyurl.com/yckm9y6b) for ease of use. We reconstruct wing-beats of multiple flies (dragonfly, butterfly) with high accuracy.
VIP interneurons regulate cortical size tuning and visual perception
Authors: Ferguson Katie A. , Salameh Jenna , Alba Christopher , Selwyn Hannah , Barnes Clayton , Lohani Sweyta , Cardin Jessica A.
Published: March 2023

Local cortical circuit function is regulated by diverse populations of GABAergic interneurons with distinct properties and extensive interconnectivity. Inhibitory-to-inhibitory interactions between interneuron populations may play key roles in shaping circuit operation according to behavioral context. A specialized population of GABAergic interneurons that co-express vasoactive intestinal peptide (VIP-INs) are activated during arousal and locomotion and innervate other local interneurons and pyramidal neurons. Although modulation of VIP-IN activity by behavioral state has been extensively studied, their role in regulating information processing and selectivity is less well understood. Using a combination of cellular imaging, short and long-term manipulation, and perceptual behavior, we examined the impact of VIP-INs on their synaptic target populations in the primary visual cortex of awake behaving mice. We find that loss of VIP-IN activity alters the behavioral state-dependent modulation of somatostatin-expressing interneurons (SST-INs) but not pyramidal neurons (PNs). In contrast, reduced VIP-IN activity disrupts visual feature selectivity for stimulus size in both populations. Inhibitory-to inhibitory interactions thus directly shape the selectivity of GABAergic interneurons for sensory stimuli. Moreover, the impact of VIP-IN activity on perceptual behavior varies with visual context and is more acute for small than large visual cues. VIP-INs thus contribute to both state-dependent modulation of cortical circuit activity and sensory context-dependent perceptual performance.
Sulfide oxidation promotes hypoxic angiogenesis and neovascularization
Authors: Kumar Roshan , Vitvitsky Victor , Seth Proud , Hiraki Harrison L. , Bell Hannah , Andren Anthony , Singhal Rashi , Baker Brendon M. , Lyssiotis Costas A. , Shah Yatrik M. , Banerjee Ruma
Published: March 2023

Angiogenic programming in the vascular endothelium is a tightly regulated process to maintain tissue homeostasis and is activated in tissue injury and the tumor microenvironment. The metabolic basis of how gas signaling molecules regulate angiogenesis is elusive. Herein, we report that hypoxic upregulation of NO synthesis in endothelial cells reprograms the transsulfuration pathway and increases H2S biogenesis. Furthermore, H2S oxidation by mitochondrial sulfide quinone oxidoreductase (SQOR) rather than downstream persulfides, synergizes with hypoxia to induce a reductive shift, limiting endothelial cell proliferation that is attenuated by dissipation of the mitochondrial NADH pool. Tumor xenografts in whole-body WBCreSQORfl/flknockout mice exhibit lower mass and reduced angiogenesis compared to SQORfl/flcontrols. WBCreSQORfl/flmice also exhibit reduced muscle angiogenesis following femoral artery ligation, compared to controls. Collectively, our data reveal the molecular intersections between H2S, O2and NO metabolism and identify SQOR inhibition as a metabolic vulnerability for endothelial cell proliferation and neovascularization.

Highlights

Hypoxic induction of •NO in endothelial cells inhibits CBS and switches CTH reaction specificity

Hypoxic interruption of the canonical transsulfuration pathway promotes H2S synthesis

Synergizing with hypoxia, SQOR deficiency induces a reductive shift in the ETC and restricts proliferation

SQOR KO mice exhibit lower neovascularization in tumor xenograft and hind limb ischemia models
Early-adult methionine restriction reduces methionine sulfoxide and extends lifespan inDrosophila
Authors: Kosakamoto Hina , Obata Fumiaki , Kuraishi Junpei , Aikawa Hide , Okada Rina , Johnstone Joshua N. , Onuma Taro , Piper Matthew D. W. , Miura Masayuki
Published: March 2023

Methionine restriction (MetR) extends lifespan in various organisms, but its mechanistic understanding remains incomplete. Whether MetR during a specific period of adulthood increases lifespan is not shown. InDrosophila, MetR is reported to extend lifespan only when amino acid levels are low. Here, by using an exome-matched holidic medium, we show that decreasing Met levels to 10% extendsDrosophilalifespan with or without decreasing total amino acid levels. MetR during the first four weeks of adult life robustly extends lifespan. MetR induces the expression ofMethionine sulfoxide reductase A(MsrA) in young flies, which reduces the oxidatively-damaged Met.MsrAinduction isfoxo-dependent and persists for two weeks after cessation of the MetR diet. Loss ofMsrAattenuates lifespan extension by early-adult MetR. Our study highlights the age-dependency of the organismal response to specific nutrient and suggests that nutrient restriction at a particular period of life is sufficient for healthspan extension.
Saccadic omission revisited: What saccade-induced smear looks like
Authors: Schweitzer Richard , Doering Mara , Seel Thomas , Raisch Jörg , Rolfs Martin
Published: March 2023

During active visual exploration, saccadic eye movements rapidly shift the visual image across the human retina. Although these high-speed shifts occur at a high rate and introduce considerable amounts of motion smear during natural vision, our perceptual experience is oblivious to it. This saccadic omission, however, does not entail that saccadeinduced motion smear cannot be perceived in principle. Using tachistoscopic displays of natural scenes, we rendered saccade-induced smear highly conspicuous. By systematically manipulating peri-saccadic display durations we studied the dynamics of smear in a time-resolved manner, assessing identification performance of smeared scenes, as well as perceived smear amount and direction. Both measures showed distinctive, U-shaped time courses throughout the saccade, indicating that generation and reduction of perceived smear occurred during saccades. Moreover, low spatial frequencies and orientations parallel to the direction of the ongoing saccade were identified as the predominant visual features encoded in motion smear. We explain these findings using computational models that assume no more than saccadic velocity and human contrast sensitivity profiles, and present a motion-filter model capable of predicting observers’ perceived amount of smear based on their eyes’ trajectories, suggesting a direct link between perceptual and saccade dynamics. Replays of the visual consequences of saccades during fixation led to virtually identical results as actively making saccades, whereas the additional simulation of perisaccadic contrast suppression heavily reduced this similarity, providing strong evidence that no extra-retinal process was needed to explain our results. Saccadic omission of motion smear may be conceptualized as a parsimonious visual mechanism that emerges naturally from the interplay of retinal consequences of saccades and early visual processing.
A computationally informed comparison between the strategies of rodents and humans in visual object recognition
Authors: Schnell Anna Elisabeth , Leemans Maarten , Vinken Kasper , de Beeck Hans Op
Published: March 2023

Many species are able to recognize objects, but it has been proven difficult to pinpoint and compare how different species solve this task. Recent research suggested to combine computational and animal modelling in order to obtain a more systematic understanding of task complexity and compare strategies between species. In the present study, we created a large multidimensional stimulus set and designed a visual discrimination task partially based upon modelling with a convolutional deep neural network (CNN). Experiments included rats (N = 11; 1115 daily sessions in total for all rats together) and humans (N = 45). Each species was able to master the task and generalize to a variety of new images. Nevertheless, rats and humans showed very little convergence in terms of which object pairs were associated with high and low performance, suggesting the use of different strategies. There was an interaction between species and whether stimulus pairs favoured early or late processing in a CNN. A direct comparison with CNN representations and visual feature analyses revealed that rat performance was best captured by late convolutional layers and partially by visual features such as brightness and pixel-level similarity, while human performance related more to the higher-up fully connected layers. These findings highlight the additional value of using a computational approach for the design of object recognition tasks. Overall, this computationally informed investigation of object recognition behaviour reveals a strong discrepancy in strategies between rodent and human vision.
Contrasting Response of Microeukaryotic and Bacterial Communities to the Interplay of Seasonality and Stochastic Events in Shallow Soda Lakes
Authors: Márton Zsuzsanna , Csitári Bianka , Felföldi Tamás , Jordán Ferenc , Hidas András , Szabó Attila , Székely Anna J.
Published: March 2023

Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. Yet, unexpected departures from general seasonal successional trends are often reported. To understand the role of local stochastic events in modifying seasonal succession, we sampled fortnightly throughout three seasons (spring, summer, and autumn) five nearby shallow soda lakes exposed to the same seasonal meteorological changes. We characterised their microeukaryotic and bacterial communities by 18S and 16S rRNA gene sequencing, respectively. Biological interactions were inferred by the analyses of synchronous and time-shifted interaction networks, and the keystone taxa were topologically identified. The pans showed similar succession patterns during the study period with spring being characterised by high relevance of trophic interactions and certain level of community stability followed by a more dynamic and variable summer-autumn period both in respect of community composition and microbial interactions. Adaptation to general seasonal changes happened through the abundant shared core microbiome of the pans. However, stochastic events such as desiccation and cyanobacterial blooms disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. These were more pronounced for microeukaryotes than for bacteria which was reflected in increased turnover and contribution of non-core microeukaryotes. Our results demonstrated that despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet random stochastic events such as droughts can instigate substantial deviations from prevalent trends for the microeukaryotic but not bacterial communities.
From root to shoot; Quantifying nematode tolerance inArabidopsis thalianaby high-throughput phenotyping of plant development
Authors: Willig Jaap-Jan , Sonneveld Devon , van Steenbrugge Joris J.M. , Deurhof Laurens , van Schaik Casper C. , Teklu Misghina G. , Goverse Aska , Lozano-Torres Jose L. , Smant Geert , Sterken Mark G.
Published: March 2023

Nematode migration, feeding site formation, withdrawal of plant assimilates, and activation of plant defence responses have a significant impact on plant growth and development. Plants display intraspecific variation in tolerance limits for root-feeding nematodes. Although disease tolerance has been recognised as a distinct trait in biotic interactions of mainly crops, we lack mechanistic insights. Progress is hampered by difficulties in quantification and laborious screening methods. We turned to the model plantArabidopsis thaliana, since it offers extensive resources to study the molecular and cellular mechanisms underlying nematode-plant interactions. Through imaging of tolerance-related parameters the green canopy area was identified as an accessible and robust measure for assessing damage due to cyst nematode infection. Subsequently, a high-throughput phenotyping platform simultaneously measuring the green canopy area growth of 960A. thalianaplants was developed. This platform can accurately measure cyst- and root-knot nematode tolerance limits inA. thalianathrough classical modelling of tolerance limits. Furthermore, real-time monitoring provided data for a novel view of tolerance, identifying a compensatory growth response. These findings show that our phenotyping platform will enable further studies into a mechanistic understanding of tolerance to below-ground biotic stress.

Highlight

The mechanisms of tolerance to root-parasitic nematodes remain unknown. We developed a high-throughput phenotyping system that enables unravelling the underlying mechanisms of tolerance to nematodes.
Quality matters: stoichiometry of resources modulates spatial feedbacks in aquatic-terrestrial meta-ecosystems
Authors: Pichon Benôıt , Thébault Elisa , Lacroix Gérard , Gounand Isabelle
Published: March 2023

Species dispersal and resource spatial flows greatly affect the dynamics of connected ecosystems. So far, research on meta-ecosystems has mainly focused on the quantitative effect of subsidy flows. Yet, resource exchanges at heterotrophic-autotrophic (e.g.,aquatic-terrestrial) ecotones display a stoichiometric asymmetry that likely matters for functioning. Here, we joined ecological stoichiometry and the meta-ecosystem framework to understand how subsidy stoichiometry mediates the response of the meta-ecosystem to subsidy flows. Our model results demonstrate that resource flows between ecosystems can induce a positive spatial feedback loop, leading to higher production at the meta-ecosystem scale by relaxing local ecosystem limitations (“spatial complementarity”). Furthermore, we show that spatial flows can also have an unexpected negative impact on production when accentuating the stoichiometric mismatch between local resources and basal species needs. This study paves the way for studies on the interdependancy of ecosystems at the landscape extent.

Data:The code and the data, as well as a small tutorial to run the model are available on Github via Zenodo:https://doi.org/10.5281/zenodo.7733880
Skewed distribution of spines is independent of presynaptic transmitter release and synaptic plasticity and emerges early during adult neurogenesis
Authors: Rößler Nina , Jungenitz Tassilo , Sigler Albrecht , Bird Alexander , Mittag Martin , Rhee Jeong Seop , Deller Thomas , Cuntz Hermann , Brose Nils , Schwarzacher Stephan W. , Jedlicka Peter
Published: March 2023

Dendritic spines are crucial for excitatory synaptic transmission as the size of a spine head correlates with the strength of its synapse. The distribution of spine head sizes follows a lognormal-like distribution with more small spines than large ones. We analysed the impact of synaptic activity and plasticity on the spine size distribution in adult-born hippocampal granule cells from rats with induced homo- and heterosynaptic long-term plasticity in vivo and CA1 pyramidal cells from Munc-13-1-Munc13-2 knockout mice with completely blocked synaptic transmission. Neither induction of extrinsic synaptic plasticity nor the blockage of presynaptic activity degrades the lognormal-like distribution but changes its mean, variance and skewness. The skewed distribution develops early in the life of the neuron. Our findings and their computational modelling support the idea that intrinsic synaptic plasticity is sufficient for the generation, while a combination of intrinsic and extrinsic synaptic plasticity maintains lognormal like distribution of spines.
Polytypism of Ln(SeO3)(HSeO3)·2H2O compounds: synthesis and crystal structure of the first monoclinic modification of Nd(SeO3)(HSeO3)·2H2O, DFT calculations and order/disorder description
Authors: Murtazoev Alisher F. , Berdonosov Peter S. , Aksenov Sergey M. , Kuznetsov Alexey N. , Dolgikh Valery A. , Nelyubina Yulia V. , Merlino Stefano
Published: March 2023

Compounds with the general formula Ln3+(SeO3)(HSeO3)·2H2O, where Ln = Sm3+, Tb3+, Nd3+and Lu3+, are characterized by orthorhombic symmetry with space groupP212121and unit-cell parameters in the rangesa∼ 6.473–6.999,b∼ 6.845–7.101,c∼ 16.242–16.426 Å. Light-purple irregularly shaped crystals of a new monoclinic polytype of neodymium selenite Nd(SeO3)(HSeO3)·2H2O have been obtained during a mild-condition hydrothermal synthesis. The monoclinic unit-cell parameters are:a= 7.0815 (2),b= 6.6996 (2),c= 16.7734 (5) Å, β = 101.256 (1)°,V= 780.48 (6) Å3; space groupP21/c. The crystal structures of Nd(SeO3)(HSeO3)·2H2O polymorphs show order–disorder (OD) character and can be described using the same OD groupoid family, more precisely a family of OD structures built up from two kinds of non-polar layers (category IV). The first monoclinic maximum degree order (MDO) structure (MDO1-polytype) with space groupP21/ccan be obtained when the inversion centre is active in theL2n-type layers, while the second MDO structure (MDO2-polytype) is orthorhombic with space groupP212121and can be obtained when the [21--] operation is active in theL2n-type layers. The structural complexity parameters and DFT calculations of both polytypes show that the polytype structures are extremely close energy-wise and almost equally viable from the point of total energy of the structure.
Crystal structure of tert-butyl 3,6-diiodocarbazole-9-carboxylate
Authors: Sielaff Elizabeth N. , Staples Richard J. , Biros Shannon M.
Published: March 2023

The molecular structure of tert-butyl 3,6-diiodocarbazole-9-carboxylate, C17H15I2NO2, features a nearly planar 13-membered carbazole ring with C—I bond lengths of 2.092 (4) and 2.104 (4) Å. The carbamate group has key bond lengths of 1.404 (6) Å (N—C), 1.330 (5) Å (O—C), and 1.201 (6) Å (C=O). The crystal contains intermolecular π–π interactions, as well as both type I and type II intermolecular I...I interactions.
Mediation of learning orientation on market orientation and business performance: evidence from Brazilian Small and Medium Enterprises (SMEs)
Authors: Guerra Rodrigo Marques de Almeida , Camargo Maria Emilia
Published: March 2023

Purpose

The aim of this study is to investigate the mediating effect of learning orientation on the market orientation and business performance of industrial Small and Medium Enterprises (SMEs) in the metal-mechanic and wine sectors in southern Brazil, an emerging economy country.

Design/methodology/approach

Survey data were collected from 309 Brazilian managers of SMEs in the metal-mechanic and wine sectors. The study analyzed overall model fit and causal relationships by confirmatory factor analysis and structural equation modeling.

Findings

The survey results show that there is a positive and significant relationship between the variables market orientation, learning orientation and business performance in the investigated sectors. Learning orientation mediates the relationship between market orientation and business performance.

Practical implications

This article provides insight to guide industrial managers of Brazilian SMEs in the metal-mechanic and wine sectors in a prosperous region with a thriving economy. The mediating effect of learning orientation can help managers in their commitment to learning, market vision and open-mindedness in teams that work with multiple orientations.

Originality/value

Few studies focus on analyzing the mediating effect of learning orientation in industrial SMEs in the metal-mechanic and wine sectors. This article differs from others due to the relationships between the constructs, LO mediation over MO and BP, relevance of the investigated sectors for the region and multiple guidelines for managers of the investigated SMEs. Previous studies are scarce on the indirect effect of LO on MO and BP in developing countries.
There and back again: staff and service user perspectives on readmission to a secure mental health hospital
Authors: Whittaker Maria , Cook Andy , Marrocco Marisa , Osborne David
Published: March 2023

Purpose

Readmission to hospital can be distressing, costly for the National Health Service (NHS) and legally it should be a last resort as it entails restriction of liberty. This study aims to develop an understanding of factors leading to readmission for a cohort of service users under the care of a community forensic mental health team (CFMHT) in England to consider how support could be improved to reduce incidence of future readmissions.

Design/methodology/approach

Thematic analysis was used to examine case recording relating to 13 service users who were readmitted to hospital within a specified time period. The same service users were invited to complete questionnaires regarding their views of what contributed to the readmission to cross-reference with themes identified.

Findings

The analysis of case notes produced eight sub-themes. These were sorted into three overarching themes, illustrating the challenges that service users face upon discharge from hospital, the sense they make of these challenges and the impact upon relational patterns, in particular with the CFMHT. Researchers highlight that the multiple challenges can increase service users’ sense of being under threat which can lead to distrust of professionals.

Practical implications

Practical suggestions arising from the study were fed back to the subject team and are listed at the end of the paper.

Originality/value

Findings from this study parallel those previously reported. This study contributes an inter-relational aspect of the factors and the central role of meaning-making in the path of recovery and building a life in the community.
Global challenge and opportunities for libraries and big data
Authors: Oladokun Bolaji David , Aboyade Modupe Aduke , Aboyade Wahab Akanmu
Published: March 2023

Purpose

This study aims to find out the role of big data in the field of library and information science by considering the opportunities and challenges.

Design/methodology/approach

This study, which was conducted on a desk, examined the rise and significance of big data in the field of library and information science in Nigeria. Also, systematic literature review is done, exploring blogs and wikis to gather data on the use of big data.

Findings

This study emphasizes that as data is the primary component in the creation of information, professionals in the fields of library and information science must develop the knowledge and abilities necessary to support big data analysis. It was determined that offering and facilitating big data analysis would guarantee our place as a priceless and crucial resource in the digital workplace.

Originality/value

To the best of the authors’ knowledge, this study will be one of its kind to examine the role of big data in the field of library and information science profession. Furthermore, the results of the study will expose librarians and information professionals on the opportunities and challenges inherent in the use of big data technologies.
Elucidation of the effect of heat exposure on hair colored by permanent and semipermanent colorants using surface‐enhanced Raman spectroscopy
Authors: Steczkowski Mackenzi , Kurouski Dmitry
Published: March 2023

Confirmatory identification of hair colorants can be used to establish a connection between a suspect and the crime science or demonstrate the absence of such connections. A growing body of evidence shows that surface‐enhanced Raman spectroscopy (SERS) could be a confirmatory, minimally destructive, and fully noninvasive analysis of hair colorants. In SERS, a signal that provide the information about the chemical structure of both permanent and semipermanent dyes present on hair is enhanced by a million‐fold using noble metal nanostructures. However, it is unclear whether the information of hair colorants can be revealed if hair was contaminated or exposed to harsh environments such as sunlight and heat. In this work, we determine the effect of a short‐ and long‐term heat exposure on SERS‐based analysis of hair colored with blue and red permanent and semipermanent dyes. We found that short and especially long‐term heat exposure at 220°C could alter chemical structure, and consequently SERS spectra, of permanent and semipermanent colorants. This thermal degradation of permanent dyes complicates their direct identification using SERS. We also found that partial least squares discriminant analysis can be used to overcome this issue allowing for highly accurate identification of both permanent and semipermanent dyes on colored hair that was exposed to 220°C for 6–12 min. These results show that heat exposure of colored hair should be strongly considered upon their SERS‐based examination to avoid both false positive or false negative identification of chemical dyes.
Rodent management in Aotearoa New Zealand: approaches and challenges to landscape‐scale control
Authors: INNES John G. , NORBURY Grant , SAMANIEGO Araceli , WALKER Susan , WILSON Deborah J.
Published: March 2023

Aotearoa—New Zealand has only four rodent species, all introduced. In order of arrival, they are Pacific rat Rattus exulans, brown rat R. norvegicus, house mouse Mus musculus, and black rat R. rattus. Rodent management in New Zealand aims mainly to conserve indigenous biodiversity rather than to protect crops or manage diseases, as is usual elsewhere. We describe four major “regimes” and one major vision for rodent control in New Zealand to meet ecological restoration objectives. Current challenges for island eradications are for large islands that are remote or populated by people. Aerial 1080 is the only large‐scale (tens of thousands of hectares) option for black rat control, but its application requires adjustment to counter subsequent rapid black rat repopulation. Unfenced “ecosanctuaries” (mean 720 ha) use ground‐based traps and poisons to target mainly black rats and face constant reinvasion. Ecosanctuaries with mammal‐resistant fences (up to 3500 ha) limit reinvasion and target more pest species and have enabled the return of previously extirpated taxa to the main islands. Predator Free 2050 aims to eradicate the rat species (but not mice) plus some other introduced mammals from New Zealand by 2050. This vision is not attainable with current tools, but research and experimental management is exploring techniques and technologies. The large scale (to 100 000 ha) at which black rats are now targeted for control to extremely low abundance seems to be unique to New Zealand.
Quaternary Intrusions from the Zhongjiannan Basin, South China Sea: Their Relationship with the Hainan Mantle Plume and Influence on Hydrocarbon Reservoirs
Authors: HE Yanxin , LIU Jianping , WANG Lei , TIAN Wei
Published: March 2023

The transportation of magma in sedimentary basins often occurs through extensive dyke‐sill networks. The role of sills on the plumbing system in rifted margins and the impact of sills on hydrocarbon reservoirs of prospective sedimentary basins has long been an area of great industrial interest and scientific debate. Based on 2D seismic reflection, we present data on how the sills emplaced to form a magmatic plumbing system of the volcanic system for the Zhongjiannan Basin (ZJNB). The results show that sixty‐nine sills and fourteen forced folds have been identified. The distribution and geometry of the sills suggest that magma flowed from west to east and then ascended to near the surface. The onlap relationship of the forced folds indicates that the timing of magmatic activities can be constrained at ca. 0.2 Ma. The spatial and temporal occurrences of intrusions imply that the strong post‐rift magmatism in ZJNB was associated with the Hainan mantle plume arising from the core‐mantle boundary. Furthermore, these forced folds could produce several types of hydrocarbon traps, due to accommodation through bending and uplift of the overlying rock and free surface, but it is critical to evaluate the effect of such emplacement when setting exploration targets.
The Paleoproterozoic and Neoproterozoic Carbon Cycle Promoted the Evolution of a Habitable Earth
Authors: LIU Zhicheng , ZHANG Lifei
Published: March 2023

The carbon cycle is an important process that regulates Earth's evolution. We compare two typical periods, in the Paleoproterozoic and Neoproterozoic, in which many geological events occurred. It remains an open question when modern plate tectonics started on Earth and how it has influenced the carbon cycle through time. In the Paleoproterozoic, intense weathering in a highly CO2 and CH4 rich atmosphere caused more nutritional elements to be carried into the ocean. Terrestrial input boosted high biological productivity, deposition of sediments and the formation of an altered oceanic crust, which may have promoted an increase in the oxygen content. Sediment lubrication and a decrease in mantle potential temperature made cold and deep subduction possible, which carried more carbon into the deep mantle. Carbon can be stored in the mantle as diamond and carbonated mantle rocks, being released by arc and mid‐ocean ridge outgassing at widely different times. From the Paleoproterozoic through the Neoproterozoic to the Phanerozoic, the carbon cycle has promoted the evolution of a habitable Earth.
Grassland management intensification affects the soil fauna in a subtropical highland
Authors: dos Peron Rafaela Alves Santos , Tomazelli Daniela , Kraft Elston , Baldissera Tiago Celso , Baretta Dilmar , Pinto Cassiano Eduardo , Goss‐Souza Dennis , de Oliveira Filho Luís Carlos Iuñes , Klauberg‐Filho Osmar
Published: March 2023

The conversion of natural grasslands to cultivated pastures can have a significant impact on the composition and structure of soil macro‐ and mesofauna groups, compromising the resilience of these organisms and the ecosystem services they provide. We studied the responses of these groups to increasing levels of soil disturbance across a gradient of four land management practices: Natural grassland (NG), Improved‐natural grassland (IG), Perennial‐cultivated pasture (PP), and Annual‐cultivated pasture (AP). The NG area had a higher abundance of macrofauna, greater dominance of certain groups, particularly Isoptera, and a lower abundance of mesofauna. On the other hand, the IG area had a higher abundance and diversity of macro‐ and mesofauna, with a lower dominance of specific groups. The PP area had a higher abundance of Coleoptera, Oligochaeta, and Hemiptera, whereas the AP area, despite soil disturbance, showed a higher abundance of mesofauna, particularly mites, Collembola, and Enchytraeidae, but lower diversity. Different grassland management practices have significantly altered the composition and structure of macro‐ and mesofauna groups, resulting in high dissimilarity between communities. We recommend IG as a more productive and sustainable alternative to the total replacement of natural vegetation (NG) with intensified converted pastures (PP and AP), as it maintains soil fauna diversity and ecosystem services.