bluuebunny/crossref_metadata_2025 huggingface dataset:
Traumatic brain injury and Alzheimer’s Disease biomarkers: A systematic review of findings from amyloid and tau positron emission tomography (PET)
Authors: Dybing Kaitlyn M. , Vetter Cecelia J. , Dempsey Desarae A. , Chaudhuri Soumilee , Saykin Andrew J. , Risacher Shannon L.
Published: December 2023

Traumatic brain injury (TBI) has been discussed as a risk factor for Alzheimer’s disease (AD) due to its association with dementia risk and earlier cognitive symptom onset. However, the mechanisms behind this relationship are unclear. Some studies have suggested TBI may increase pathological protein deposition in an AD-like pattern; others have failed to find such associations. This review covers literature that uses positron emission tomography (PET) of amyloid-β and/or tau to examine subjects with history of TBI who are at risk for AD due to advanced age. A comprehensive literature search was conducted on January 9, 2023, and 24 resulting citations met inclusion criteria. Common methodological concerns included small samples, limited clinical detail about subjects’ TBI, recall bias due to reliance on self-reported TBI, and an inability to establish causation. For both amyloid and tau, results were widespread but inconsistent. The regions which showed the most compelling evidence for increased amyloid deposition were the cingulate gyrus, cuneus/precuneus, and parietal lobe. Evidence for increased tau was strongest in the medial temporal lobe, entorhinal cortex, precuneus, and frontal, temporal, parietal, and occipital lobes. However, conflicting findings across most regions of interest in both amyloid- and tau-PET studies indicate the critical need for future work in expanded samples and with greater clinical detail to offer a clearer picture of the relationship between TBI and protein deposition in older subjects at risk for AD.
Population age as a key factor in the COVID-19 pandemic dynamics
Authors: Nesteruk Igor , Keeling Matt
Published: December 2023

The population and governments of many countries are losing interest in the SARS-CoV-2 infection, the number of tests and the number of new cases detected is sharply decreasing. To compare the accumulated numbersCCof cases and deathsDCper million and to answer the question why the less vaccinated Africa has accumulated 36 times lowerCCvalues and 15 times lowerDCvalues than Europe, simple statistical analysis have been performed.CCandDCvalues demonstrated rather strong correlation with the median age of populations. One-year increment in the median year yields 12-18 thousand increase inCCvalues and 52-83 increase inDCvalues. Zero-COVID countries succeed to have much lower numbers of deaths per capita and case fatality ratiosDC/CC.
Inhibitory fear memory engram in the mouse central lateral amygdala
Authors: Hou Wen-Hsien , Jariwala Meet , Wang Kai-Yi , Seewald Anna , Lin Yu-Ling , Ricci Alessia , Ferraguti Francesco , Lien Cheng-Chang , Capogna Marco
Published: December 2023

Engrams are cellular substrates of memory traces that have been identified in various brain areas, including the amygdala. Most engrams identified so far are formed by excitatory, glutamatergic neurons. However, little attention has been paid to defining GABAergic inhibitory engrams. Here, we report an inhibitory engram in the central lateral amygdala (CeL), a crucial area for Pavlovian fear conditioning. This engram is primarily composed of GABAergic somatostatin-expressing (SST+) and to a lesser extent of protein kinase C-δ-expressing [PKC-δ(+)] neurons. Fear memory is accompanied by a preferential enhancement of mIPSC frequency onto PKC-δ(+) neurons as well as a general increment of amplitude. Moreover, non-engram cells exhibit higher mIPSC frequency than engram cells. The inhibition of the CeL GABAergic engram disinhibits the activity of engram-targeted areas and increases selectively the encoded fear expression. Our data defines the behavioral function of an engram formed exclusively by GABAergic inhibitory neurons in the mammalian CNS.
Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data
Authors: Kupperman Michael D. , Ke Ruian , Leitner Thomas
Published: December 2023

Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. Contact tracing generates phylogenies that are less balanced than the underlying transmission process, less representative of the larger epidemiological process, and affects the internal/external branch length ratios that characterize specific epidemiological scenarios. We also examined real data from a 2007-2008 Swedish HIV-1 outbreak and the broader 1998-2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. SEEPS is available atgithub.com/MolEvolEpid/SEEPS.
Hepatic Vagal Afferents Convey Clock-Dependent Signals to Regulate Circadian Food Intake
Authors: Woodie Lauren N. , Melink Lily C. , Midha Mohit , de Araújo Alan M. , Geisler Caroline E. , Alberto Ahren J. , Krusen Brianna M. , Zundell Delaine M. , de Lartigue Guillaume , Hayes Matthew R. , Lazar Mitchell A.
Published: December 2023

Circadian desynchrony induced by shiftwork or jetlag is detrimental to metabolic health, but how synchronous/desynchronous signals are transmitted among tissues is unknown. Here we report that liver molecular clock dysfunction is signaled to the brain via the hepatic vagal afferent nerve (HVAN), leading to altered food intake patterns that are corrected by ablation of the HVAN. Hepatic branch vagotomy also prevents food intake disruptions induced by high-fat diet feeding and reduces body weight gain. Our findings reveal a previously unrecognized homeostatic feedback signal that relies on synchrony between the liver and the brain to control circadian food intake patterns. This identifies the hepatic vagus nerve as a therapeutic target for obesity in the setting of chrono-disruption.

One Sentence Summary

The hepatic vagal afferent nerve signals internal circadian desynchrony between the brain and liver to induce maladaptive food intake patterns.
Sensitivity analysis of a mechanistic model of rumen fermentation and methane production by rumen microbiota in the presence ofAsparagopsis taxiformis
Authors: Merk Katarina , Link Kathryn G. , Guy Robert D. , Hess Matthias
Published: December 2023

Ruminant animals rely on microbes for the conversion of complex plant material into host accessible metabolites. During this anaerobic conversion of plant biomass, termed enteric fermentation, methanogenic archaea convert hydrogen into the potent greenhouse gas methane (CH4). The search for methane mitigation strategies to combat climate change has identified the red seaweedAsparagopsis taxiformisas a promising feed additive that, when added to a regular cattle diet, reduced enteric CH4by over 80%. A more complete understanding of microbial interactions during enteric fermentation is needed for ongoing improvement to mitigation methods. Mathematical models that permitin silicosimulation of enteric fermentation allow for the identification of key parameters that drive rumen methane production. Here we built upon an existing rumen fermentation model and calibrated it using a preliminary classification of functional microbial groups and gas emission data from a previously publishedin vitrorumen fermentation experiment, but many microbes remained functionally unclassified. The model was then used to conduct anin silicoexperiment to explore how the partition of functionally unclassified microbes into functional groups affects methane output. Thesein silicoexperiments identified that model methane production is more sensitive to microbial variation in the presence ofA. taxiformisversus without. The use of local and global sensitivity analysis approaches revealed other rumen parameters to also be drivers of enteric methane production. In the presence ofA. taxiformis, parameters modulating methane production include bromoform concentration, methanogen abundance, total microbial concentration, a parameter effecting the inhibition of methanogen growth rate by the action of bromoform, and the maximum specific utilization rate of hydrogen. WithoutA. taxiformis, feed composition parameters, the hydrolysis rate constant of cell wall carbohydrates, and a parameter affecting the yield factors during sugar utilization were found to be most significant. For possible methane reduction withoutA. taxiformis, we propose an adjustment in feed composition parameters that reduces predicted methane by 25.6%.
Acclimation kinetics of the holoparasitic weedPhelipanche ramosa(Orobanchaceae) during excessive light and heat conditions
Authors: Dayou Olivier , Brun Guillaume , Gennat Charline , Wicke Susann
Published: December 2023

Holoparasitic plants, such as broomrape, have abandoned a photosynthesis, relying entirely on the resources of host plants. This departure from an autotrophic lifestyle necessitates significant genetic and metabolic adaptations, offering a unique model system to elucidate responses independent of canonical plastid functions in green plants. In this study, we examined the acclimation kinetics of the holoparasitic weedPhelipanche ramosa(broomrape) under unfavorable temperature and excessive light conditions through a comprehensive time-course analysis of RNA sequence data and physiological monitoring. Our work unveils that suboptimal abiotic conditions induce transcriptional changes in the parasitic plant, involving coordinated expression of nuclear and plastid-encoded genes. Notably, magnesium transporters, critical for heat-induced chlorophyll conversion, were enriched among heat-repressed genes. Additionally, multiple copies of chloroplast-targeted DnaJ proteins, responsible for maintaining CO2assimilation capacity in non-parasitic plants, were identified. Comparative expression analysis with the parasite’s host plants, tomato andArabidopsis, revealed distinct patterns for certain plastid genes inPhelipanche. Furthermore, an elevation in reactive oxygen species (ROS) in the parasite coincided with the upregulation of numerous heat shock protein (HSP) genes, including HSP21, which associates with thylakoid membranes in photosynthetic plants; noteworthily, thylakoids are absent fromPhelipanche’s plastids. Collectively, our findings suggest that plastids of the nonphotosynthetic model plant retains their ancestral role as environmental sensors. This research opens new avenues for functional-genetic research into the nuanced roles of plastids in the lifecycles of parasitic plants.
The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes
Authors: Riley Amanda K. , Grant Michael , Snell Aidan , Vichas Athea , Moorthi Sitapriya , Urisman Anatoly , Castel Pau , Wan Lixin , Berger Alice H.
Published: December 2023

RIT1is a rare and understudied oncogene in lung cancer. Despite structural similarity to other RAS GTPase proteins such as KRAS, oncogenic RIT1 activity does not appear to be tightly regulated by nucleotide exchange or hydrolysis. Instead, there is a growing understanding that the protein abundance of RIT1 is important for its regulation and function. We previously identified the deubiquitinaseUSP9Xas a RIT1 dependency inRIT1-mutant cells. Here, we demonstrate that both wild-type and mutant forms of RIT1 are substrates of USP9X. Depletion of USP9X leads to decreased RIT1 protein stability and abundance and resensitizes cells to EGFR tyrosine kinase inhibitors. Our work expands upon the current understanding of RIT1 protein regulation and presents USP9X as a key regulator of RIT1-driven oncogenic phenotypes.
Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants
Authors: Florez-Rueda Ana Marcela , Miguel Célia M. , Figueiredo Duarte D.
Published: December 2023

The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world’s population. Here, using Orthofinder to infer orthologue genes among novel and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from representative species of all main angiosperm clades, including those of early diverging basal angiosperms, and a gymnosperm representative. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in new functional studies.

Significance Statement

Within seeds a specialized structure is responsible for nourishing the embryo during its development. These nourishing tissues are also important sources of staple foods and feed. Here, we provide novel gene expression datasets of nourishing tissues of early diverging angiosperms, and use this information for a meta-analysis to identify pathways conserved, or divergent, throughout evolution. Thus, we aim to provide a resource for gene discovery for seed biology studies.
A multi-strategy antimicrobial discovery approach reveals new ways to combatChlamydia
Authors: Ölander Magnus , Vázquez Daniel Rea , Meier Karsten , Mooij Lieke , Fredlund Johanna , Puértolas-Balint Fabiola , Calpe Eduard , Díaz María Rayón , van der Wal Karin , Schroeder Bjoern O. , Sixt Barbara Susanne
Published: December 2023

While the excessive use of broad-spectrum antibiotics is a major driver of the global antibiotic resistance crisis, more selective therapies remain unavailable for the majority of bacterial pathogens. This includesChlamydiaspp., which cause millions of urogenital, ocular, and respiratory infections each year. We here report major conceptual additions to the available toolkit for antichlamydial discovery, including both experimental and computational approaches. Moreover, we report the to date most comprehensive search of the chemical space for novel antichlamydial activities, which identified over sixty compounds that are chemically diverse, structurally different from known antibiotics, non-toxic to human cells, and highly potent in blockingChlamydiagrowth. While some compounds caused a reversible block inChlamydiadevelopment, others could eradicate both established and persistent infections in a bactericidal manner. The most potent antichlamydials displayed compelling selectivity, some also synergies with clinically used antibiotics, as well as interactions profiles enabling predictions of molecular modes of action. Moreover, one compound displayed reduced antichlamydial efficacy in autophagy-deficient cells, suggesting a host- targeted activity. Altogether, we suggest that these novel antichlamydials could serve as tools for advancing our understanding ofChlamydiabiology and as chemical starting points for developing more sustainable therapeutics for one of the most successful groups of intracellular pathogens.
MiRNAs differentially expressed in vegetative and reproductive organs ofMarchantia polymorpha– insights into their expression pattern, gene structures and function
Authors: Aggarwal B , Karlowski MW , Nuc P , Jarmolowski A , Szweykowska-Kulinska Z , Pietrykowska H
Published: December 2023

MicroRNAs (miRNAs) regulate gene expression affecting a variety of plant developmental processes. The evolutionary position ofMarchantia polymorphamakes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that differential expression of conserved miRNAs and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.
High defense system expression broadens protection range at the cost of increased autoimmunity
Authors: Aframian Nitzan , Omer Bendori Shira , Hen Tal , Guler Polina , Eldar Avigdor
Published: December 2023

The evolutionary arms race between bacteria and their phage viruses has given rise to elaborate anti-phage defense mechanisms. Major advances have been made in revealing the molecular details underlying diverse defense systems, but general principles and constraints are largely unkown. Defense systems are often tested against a diverse set of phages, revealing widely varying protection ranges. While these disparities are usually attributed to differences in mechanism, here we show that increasing expression of defense systems can greatly enhance their protection range. This holds true for disparate mechanisms, and is achieved by circumventing phage strategies for overcoming bacterial defense. However, increased defense system expression comes with a heavy cost of autoimmunity. Therefore, the expression level of defense systems controls a tradeoff between protection range on the one hand and autoimmunity on the other. We discuss how this tradeoff may drive the regulation of defense systems expression and the acquisition of multiple systems within the same genome.
Pre-mRNA fate decision safeguards the fidelity of the inflammatory response
Authors: Bestehorn Annika , Fesselet Jeanne , Didusch Sebastian , Zeiler Christina , Doppelmayer Kevin , Borroni Martina , LeHeron Anita , Pfanzagl Vera , Chen WeiQiang , Scinicariello Sara , Baccarini Manuela , Versteeg Gijs A , Hartl Markus , Kovarik Pavel
Published: December 2023

The fidelity of immune responses is dependent on a timely controlled and selective mRNA degradation that is largely driven by RNA-binding proteins (RBPs). It remains unclear whether the selection of an individual mRNA molecule for degradation is governed by stochastic or directed processes. Here, we show that tristetraprolin (TTP, also known as ZFP36), an essential anti-inflammatory RBP, destabilized the target mRNA via a hierarchical molecular assembly. The assembly formation is strictly reliant on TTP interaction with RNA. The TTP homolog ZFP36L1 exhibits similar requirements indicating a broader relevance of this regulatory program. Unexpectedly, the assembly of the cytoplasmic mRNA-destabilization complex is licensed in the nucleus by TTP binding to pre-mRNA while mature cytoplasmic mRNA does not constitute a de novo TTP target. Hence, the fate of an inflammation-induced mRNA is decided concomitantly with its synthesis. This fate decision mechanism prevents the translation of superfluous and potentially harmful inflammation mediators, and ensures an efficient cessation of the immune response irrespective of transcriptional activity.
Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase
Authors: Roy Priti , Walter Zachary , Berish Lauren , Ramage Holly , McCullagh Martin
Published: December 2023

The flavivirus NS3 helicase (NS3h), a highly conserved protein, plays a pivotal role in virus replication and thus represents a potential drug target for flavivirus pathogenesis. NS3h utilizes nucleotide triphosphate, such as ATP, for hydrolysis energy (ATPase) to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. The intermediate states along the ATP binding and hydrolysis cycle, as well as the conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. We use extensive molecular dynamics simulations of apo, ATP, ADP+Pi, and ADP bound to WNV NS3h+ssRNA to model the conformational ensembles along this cycle. Energetic and structural clustering analyses on these trajectories depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). These findings were experimentally corroborated using viral replicons encoding three mutations at the D471 position. Replication assays using these mutants demonstrated a substantial reduction in viral replication compared to the wild-type. Molecular simulations of the D471 mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open ‘valve’ conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a ‘valve’ for the ATP-pocket, presenting a promising target for antiviral development.
The demographic drivers of cultural evolution in bird song: a multilevel study
Authors: Recalde Nilo Merino , Estandía Andrea , Keen Sara C. , Cole Ella F. , Sheldon Ben C.
Published: December 2023

Social learning within communities sometimes leads to behavioural patterns that persist over time, which we know as culture. Examples of culture include learned bird and whale songs, cetacean feeding techniques, and avian and mammalian migratory routes. Shaped by neutral and selective forces, animal cultures evolve dynamically and lead to cultural traditions that differ greatly in their diversity and stability. These cultural traits can influence individual and group survival, population structure, and even inform conservation efforts, underscoring the importance of understanding how other population processes interact with social learning to shape culture. Although the impact of social learning mechanisms and biases has been extensively explored, the role of demographic factors—such as population turnover, immigration, and age structure—on cultural evolution has received theoretical attention but rarely been subject to empirical investigation in natural populations. Doing so requires very complete trait sampling and detailed individual life history data, which are hard to acquire in combination. To this end, we built a multi-generational dataset containing over 109,000 songs from >400 individuals from a population of Great Tits (Parus major), which we study using a deep metric learning model to re-identify individuals and quantify song similarity. We show that demographic variation at the small spatial scales at which learning takes place has the potential to strongly impact the pace and outcome of animal cultural evolution. For example, age distributions skewed towards older individuals are associated with slower cultural change and increased diversity, while higher local population turnover leads to elevated rates of cultural change. Our analyses support theoretical expectations for a key role of demographic processes resulting from individual behaviour in determining cultural evolution, and emphasize that these processes interact with species-specific factors such as the timing of song acquisition. Implications extend to large-scale cultural dynamics and the formation of dialects or traditions.
Simulated digestion, uptake and colonic fermentation of Gorse (Ulex europeaus) suggests safe use as a source of protein concentrates and bioactives
Authors: Iyer Ajay , Duncan Gary J. , Hayward Nicholas J. , Bestwick Charles S. , Duncan Sylvia H. , Russell Wendy R.
Published: December 2023

Background

Invasive plants such as Gorse (Ulex europeaus) may serve as a potentially sustainable source of edible proteins and bioactives through the production of leaf protein concentrates (GLPC). The digestion, uptake and safety of phytochemicals from GLPC and the protein depleted but bioactive rich fraction (PDF) from Gorse was studied using an in vitro simulated digestion model.

Results

Both the Gorse fractions and their digesta maintained the viability of cultured (Caco-2) intestinal cells above the 80% threshold, suggesting a lack of overt toxicity.

In the digestion model, most of the plant metabolites in the digesta were largely confined to the apical fraction of the Caco-2 monolayer (representing the lumen) and were subsequently expected to be delivered to the colon. Food matrix had a significant but marginal effect on the permeability of metabolites across the Caco-2 monolayer. Lastly,in vitrointestinal microbial action appeared to produce beneficial compounds such as enterolactones, and equol.

Conclusion

The Gorse fractions lack general overt toxicity to Caco-2 cells. GLPC and PDF provide metabolic substrates for the colonic microbes to produce secondary compounds that are associated with positive health outcomes.
CRISPR/Cas9-mediated genome editing ofFrankliniella occidentalis,the western flower thrips, via embryonic microinjection
Authors: Han Jinlong , Klobasa William , de Oliveira Lucas , Rotenberg Dorith , Whitfield Anna E. , Lorenzen Marcé D.
Published: December 2023

The western flower thrips,Frankliniella occidentalis, poses a significant challenge in global agriculture as a notorious pest and a vector of economically significant orthotospoviruses. However, the limited availability of genetic tools forF. occidentalishampers the advancement of functional genomics and the development of innovative pest control strategies. In this study, we present a robust methodology for generating heritable mutations inF. occidentalisusing the CRISPR/Cas9 genome editing system. Two eye-color genes,white(Fo-w) andcinnabar(Fo-cn), frequently used to assess Cas9 function in insects were identified in theF. occidentalisgenome and targeted for knockout through embryonic microinjection of Cas9 complexed withFo-worFo-cnspecific guide RNAs. HomozygousFo-wandFo-cnknockout lines were established by crossing mutant females and males. TheFo-wknockout line revealed an age-dependent modification of eye-color phenotype. Specifically, while young larvae exhibit ivory-colored eyes, the color transitions to bright red as they age. Unexpectedly, loss ofFo-wfunction also altered body color, withFo-wmutants having a lighter colored body than wild type, suggesting a dual role forFo-win thrips. In contrast, individuals from theFo-cnknockout line consistently displayed bright red eyes throughout all life stages. Molecular analyses validated precise editing of both target genes. This study offers a powerful tool to investigate thrips gene functions and paves the way for the development of genetic technologies for population suppression and/or population replacement as a means of mitigating virus transmission by this vector.
Shoot phenotyping of cytokinin receptors mutants revealed fluorescence parameters as early markers of drought stress
Authors: Šmeringai Ján , Rudolf Jiří , Trtílek Martin , Procházková Schrumpfová Petra , Pernisová Markéta
Published: December 2023

Plant phenotyping represents an increasing promise in plant research by providing a complex picture of plant development and fitness. In research focused on various environmental stresses, phenotyping can uncover markers that can sensitively assess the stress impact in very early stages before morphological changes. PlantScreenTMSystem represents a tool dedicated for shoot and root phenotyping in soil enabling high-precision, high-throughput phenotyping of small, mid-size and large plants. The system offers wide range of sensors providing the number of non-invasive analyses of morphological and physiological parameters as well as of pigments, water, or metabolite content.

In our work, we combined phenotyping approaches to determine morphological changes and the status of the photosynthetic apparatus in Arabidopsis plants exposed to drought stress. Focused on morphology, the rosette area became smaller after seven days of drought stress when compared to control conditions. Interestingly, cytokinin signalling mutantahk2 ahk3revealed drought resistance compared to other genotypes. The fluorescent parameters showed higher sensitivity even in wild type. Non-photochemical quenching displayed values connected to reduced activity of photosynthetic apparatus after five days of drought stress. Taken together, acquired fluorescence parameters can serve as a marker of drought stress detection before morphological alterations occur.

Highlight

Fluorescence parameters can serve as early markers of drought stress before morphological alterations appear. Shoot phenotyping of cytokinin receptor mutants showed drought resistance in theahk2 ahk3double mutant.
The nucleotide binding domain of NRC-dependent disease resistance proteins is sufficient to activate downstream helper NLR oligomerization and immune signaling
Authors: Contreras Mauricio P. , Pai Hsuan , Thompson Rebecca , Claeys Jules , Adachi Hiroaki , Kamoun Sophien
Published: December 2023

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins with pathogen sensor activities have evolved to initiate immune signaling by activating helper NLRs. However, the mechanisms underpinning helper NLR activation by sensor NLRs remain poorly understood. Although coiled-coil (CC) type sensor NLRs such as thePotato virus Xdisease resistance protein Rx have been shown to activate the oligomerization of their downstream helpers NRC2 and NRC4, the domains involved in sensor-helper signaling are not known. Here, we show that the nucleotide binding (NB) domain within the NB-ARC of thePotato virus Xdisease resistance protein Rx is necessary and sufficient for oligomerization and immune signaling of downstream helper NLRs. In addition, the NB domains of the disease resistance proteins Gpa2 (cyst nematode resistance), Rpi-amr1, Rpi-amr3 (oomycete resistance) and Sw-5b (virus resistance) are also sufficient to activate their respective downstream NRC helpers. Moreover, the NB domain of Rx and its helper NRC2 form a minimal functional unit that can be transferred from solanaceous plants (lamiids) to the Campanulid species lettuce (Lactuca sativa). Our results challenge the prevailing paradigm that NLR proteins exclusively signal via their N-terminal domains and reveal a signaling activity for the NB domain of NRC-dependent sensor NLRs. We propose a model in which helper NLRs monitor the status of the NB domain of their upstream sensors.
Detection of rare plasmid hosts using a targeted Hi-C approach
Authors: Castaneda-Barba Salvador , Ridenhour Benjamin J. , Top Eva M. , Stalder Thibault
Published: December 2023

Despite the significant role plasmids play in microbial evolution, there is limited knowledge of their ecology, evolution, and transfer in microbial communities. Therefore, we developed and implemented a novel approach to identify rare plasmid hosts by combining Hi-C, a proximity ligation method, with enrichment for plasmid-specific DNA. We hereafter refer to this Hi-C enrichment approach as Hi-C+. Our experimental design mimicked scenarios in which the transfer of an antimicrobial resistance plasmid from a donor to a recipient in soil was increasingly rare. We established that Hi-C can link a plasmid to its host in soil when the relative abundance of that plasmid-host pair is as low as 0.001%. The Hi-C+ method further improved the detection limit of Hi-C 100-fold and allowed identification of plasmid hosts at the genus level. Therefore, Hi-C+ will facilitate the exploration of the ecological and evolutionary pathways that affect the spread of plasmids in natural environments.

Teaser

In this study we demonstrate that a target-enriched Hi-C approach can identify rare hosts of a given plasmid in soil.
Up-regulation of Retrograde Response in yeast increases glycerol and reduces ethanol during wine fermentation
Authors: Garrigós Víctor , Vallejo Beatriz , Mollà-Martí Esperanza , Picazo Cecilia , Peltier Emilien , Marullo Philippe , Matallana Emilia , Aranda Agustín
Published: December 2023

Nutrient signaling pathways play a pivotal role in regulating the balance between metabolism, growth and stress response depending on the available food supply. They are key factor for the biotechnological success of the yeastSaccharomyces cerevisiaeduring food-producing fermentations. One such pathway is the Retrograde Response, which controls the use of carbon backbones for the synthesis of amino acids derived from alpha-ketoglutarate, such as glutamate and lysine. The repressorMKS1is linked to the TORC1 complex and negatively regulates this pathway. Deletion ofMKS1on a variety of industrial strains causes an increase in glycerol in winemaking, brewing and baking conditions. This increase is accompanied by a reduction in ethanol production in grape juice fermentations in four commercial wine strains. Interestingly, this does not lead to an increase in volatile acidity, as the levels of acetic acid actually decrease. Aeration during winemaking usually increases acetic acid levels, but this effect is reduced in theMKS1mutant. Although there is an improvement in the metabolites of oenological interest, it comes at a cost, as the mutant showed slower fermentation kinetics when grown in grape juice, malt, and laboratory media using glucose, sucrose, and maltose as carbon sources. The deletion ofRTG2, an activator of the Retrograde Response that acts as an antagonist ofMKS1, also results in a defect in wine fermentation speed. These findings suggest that the deregulation of this pathway causes a fitness defect. Therefore, manipulating the repressorMKS1is a promising approach to modulate yeast metabolism and produce low-ethanol drinks.
Protein tyrosine phosphatase receptor kappa regulates glycolysis andde novolipogenesis to promote hepatocyte metabolic reprogramming in obesity
Authors: Gilglioni Eduardo H. , Li Ao , St-Pierre-Wijckmans Wadsen , Shen Tzu-Keng , Pérez-Chávez Israel , Hovhannisyan Garnik , Lisjak Michela , Negueruela Javier , Vandenbempt Valerie , Bauzá-Martinez Julia , Herranz Jose M. , Ezerina Daria , Demine Stephane , Feng Zheng , Vignane Thibaut , Otero-Sánchez Lukas , Lambertucci Flavia , Prašnická Alena , Devière Jacques , Hay David C. , Encinar Jose A. , Singh Sumeet Pal , Messens Joris , Filipovic Milos R. , Sharpe Hayley J. , Trépo Eric , Wu Wei , Gurzov Esteban N.
Published: December 2023

Fat accumulation,de novolipogenesis, and glycolysis are key drivers of hepatocyte reprogramming and the consequent metabolic dysfunction-associated steatotic liver disease (MASLD). Here we report that obesity leads to dysregulated expression of hepatic protein-tyrosine phosphatases (PTPs). PTPRK was found to be increased in steatotic hepatocytes in both humans and mice, and positively correlated with PPARγ-induced lipogenic signalling. High-fat-fed PTPRK knockout mice displayed reduced weight gain and hepatic fat accumulation. Phosphoproteomic analysis in primary hepatocytes and hepatic metabolomics identified fructose-1,6-bisphosphatase 1 and glycolysis as PTPRK targets in metabolic reprogramming. Silencing PTPRK in hepatoma cell lines resulted in reduced colony-forming ability and PTPRK knockout mice developed smaller tumours after diethylnitrosamine-induced hepatocarcinogenesis. Our study defines a novel role for PTPRK in regulating hepatic glycolysis, lipid metabolism, and tumour development. PTPRK inhibition may provide therapeutic possibilities in obesity-associated liver diseases.

Highlights

Hepatic receptor-type PTPs are increased in MASLD

PTPRK is expressed in hepatocytes and upregulated in obesity

PTPRK deficiency reduces body fat mass and liver steatosis in diet-induced obesity

PTPRK regulates hepatic glycolysis and lipogenesis, promoting tumorigenesis
The S-O-R paradigm in explaining enterprise social network (ESN) discontinuous usage intention
Authors: Olfat Mohammad
Published: December 2023

Purpose

This study aims to show that employees' excessive work-related use of enterprise social networks (ESN) can be accompanied by some work-related strains, hindering them from continuing utilization of ESN at work. To this end, the impact of employees' excessive work-related utilization of ESN on their discontinuous usage intentions by mediating roles of employees' impression management concerns, privacy concerns and ESN fatigue will be evaluated.

Design/methodology/approach

Stimulus-organisms-response (S-O-R) framework has been drawn to support the design of this research. Using an entirely random data collection, 173 ESN users from 10 Iranian organizations were surveyed. The model was assessed using partial least squares structural equations modeling (PLS-SEM).

Findings

The results of the study confirm that employees' excessive work-related use of ESN positively affects impression management and privacy concerns, resulting in ESN fatigue. Furthermore, ESN fatigue plays a predicting role in ESN discontinuous usage intention.

Originality/value

According to the obtained results, if work-related use of ESN exceeds a normal threshold (i.e. excessive usage), employees will stop using ESN in their work due to the work-related strains delivered to them, revealing the dark side of ESN usage in organizations.
The effect of the COVID-19 pandemic on Malaysian residential customers’ energy-saving appliance purchasing behaviour
Authors: Jaaffar Amar Hisham , Kasavan Saraswathy , Mustapa Siti Indati , Al-Amin Abul Quasem
Published: December 2023

Purpose

The COVID-19 pandemic has caused a dramatic impact on energy supply and demand. It is vital to understand households’ behaviour with regard to energy, particularly during the pandemic, to deploy future sustainable energy systems. This study aims to investigate the nexus of Malaysian households’ energy consumption behaviour in relation to various electrical appliances, their energy-saving appliance purchasing behaviour and their current possession of energy-saving appliances during the pandemic, especially during the lockdown period, from the perspective of the energy cultures framework.

Design/methodology/approach

The partial least squares structural equation modelling technique was used to test hypothesised relationships based on the 1,485 pieces of household data collected using an online and physical survey during the lockdown period in Malaysia.

Findings

The energy-saving behaviour cultivated due to the impact of the COVID-19 pandemic led to residential customers’ intentions to purchase energy-saving appliances which subsequently led to their current possession of energy-saving appliances. Indeed, energy-saving behaviours in the kitchen, entertainment, office, home lighting and cooling appliances have more than 77.4% influence on their purchasing behaviour. The consumer’s purchase behaviour for energy-saving appliances has a significant, partially mediating influence on the energy-saving behaviour of various electrical appliances and the consumers’ current possession of energy-saving appliances.

Research limitations/implications

This study could be enhanced by improving the sample using a higher-income group and involving other parts of Malaysia such as the southern region. The findings do extend the energy cultures framework by demonstrating the mediating role of households’ energy-saving appliance purchasing behaviour on the relationship between their energy consumption behaviour in relation to various electrical appliances and their current possession of energy-saving appliances.

Practical implications

The results of this study will help develop future action plans for transitioning to energy-saving appliance practices.

Originality/value

This paper examines the effects of the COVID-19 pandemic on future energy efficiency practices in developing countries from the perspective of the energy cultures framework.
State of the art and future scenarios for bio-packaging market transition: evidence from Poland
Authors: Ocicka Barbara , Kędzia Grażyna , Brzeziński Jakub
Published: December 2023

Purpose

The purpose of this article is twofold. First, this study characterises the current state of the bio-packaging market's development. Second, it identifies key factors influencing and possible scenarios of the bio-packaging market transition to increase the market share of compostable packaging.

Design/methodology/approach

The results of 29 in-depth interviews (IDIs) with representatives of the key groups of bio-packaging supply chains' (SCs') stakeholders were the input for the consideration of the research problem.

Findings

The main economic, legal, social and technological enablers and barriers to the bio-packaging regime transition are recognised, and their impact at the market level is explained. The authors recognised the hybrid transition scenario towards an increase in the market share of compostable packaging related to the three traditional pathways of transformation, reconfiguration and technological substitution.

Originality/value

This study contributes to a better understanding of the socio-technical system theory by examining interdependencies between landscape (external environment), market regime (bio-packaging market) and niche innovations (compostable packaging) as well as system transition pathways. The findings and conclusions on bio-packaging market developments can be important lessons learnt to be applied in different countries due to the same current development stage of the compostable packaging lifecycle worldwide.
Does supply chain concentration improve sustainability performance: the role of operational slack and information transparency
Authors: Jia Fu , Xu Ying , Chen Lujie , Fernandes Kiran
Published: December 2023

Purpose

Despite the increasing interest in the role of supply chain concentration (SCC) in improving performance, its influence on firms' sustainability performance remains unexplored, as do the underlying mechanisms of this relationship. Drawing on resource dependence theory, the authors investigate the relationship between SCC and manufacturing firms' sustainability performance and the moderating roles of operational slack and information transparency.

Design/methodology/approach

The authors use secondary data from 3,581 manufacturing firms listed on the Shanghai and Shenzhen A-share stock markets from 2006 to 2020 to conduct an empirical analysis using panel data regression models.

Findings

Manufacturing firms' SCC is negatively related to sustainability performance until it reaches a certain point, where SCC positively affects sustainability performance, presenting a U-shaped relationship. In addition, operational slack represented by a quick ratio moderates the relationship between SCC and sustainability performance by flattening the curve. Operational slack represented by receivable turnover ratio moderates the relationship between SCC and sustainability performance by steepening the curve and shifting the turning point left. Information transparency strengthens the effect of SCC on the sustainability performance by steepening the curve.

Originality/value

This investigation provides a comprehensive view of the SCC– sustainability performance relationship.
Understanding the effects of specific techno-stressors on strain and job performance: a meta-analysis of the empirical evidence
Authors: Yuan Qin , Kong Jun , Liu Chun , Jiang Yushi
Published: December 2023

Purpose

While the phenomenon of technostress has received significant attention from researchers in recent years, empirical findings concerning the consequences of specific forms of techno-stressors have remained scattered and contradictory. The authors aim to integrate the conclusions of previous studies to understand the effects of specific techno-stressors on strain and job performance.

Design/methodology/approach

This study employs meta-analytic techniques to calibrate the findings of 67 studies investigating more than 63,100 employees.

Findings

In general, not all techno-stressors have adverse effects. In particular, techno-uncertainty does not impact job performance. In addition, relative weight analyses reveal the relative importance of techno-complexity and techno-insecurity as predictors of both strain and job performance. Finally, this study finds that the effects of specific techno-stressors on job performance vary depending on research participants' gender, educational attainment and employment status.

Originality/value

First, this study provides a more nuanced view of the effects of specific techno-stressors. Second, this research clarifies the relative importance of specific techno-stressors as predictors of strain and job performance. Finally, this study reveals the moderating effects of demographic variables on the relationships between specific techno-stressors and job performance.