bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of bronchiolitis and vaccine-induced enhanced respiratory disease in Syrian hamsters caused by respiratory syncytial virus infection
Authors: Zhao Binbin , Zhang Gengxin , Wu Jing , Ding Xiaoyue , Wei Xiaohui , Peng Wanjun , Rong Na , Yang Hekai , Liu Jiangning
Published: July 2024

Respiratory syncytial virus (RSV) presents a significant health risk to pediatric and old populations. The quest for developing effective RSV vaccines and immunoprophylactic measures remains highly active, while the catastrophic enhanced respiratory disease (ERD) reaction triggered by RSV vaccines poses lingering concerns. Meanwhile, as the basis of vaccine research, the development of animal models of RSV infection has shown less substantial progress, with considerable disparities in immunological and pathological responses compared to humans. The Syrian hamster, which is reported to be susceptible to RSV infection, seems promising, but the lack of in-depth studies has hampered its application. Consequently, we have refined the RSV-infected hamster model by establishing infection models at different ages, reanalyzing virological and pathological data, and applying vaccination with heat-inactivated RSV virus for ERD reaction. In general, neonatal hamsters exhibited the highest level of viral amplification, while old hamsters displayed the most severe pathological manifestations, with adult hamsters in between. Although Syrian hamsters were moderately susceptible to RSV infection, they showed typical pathological changes of bronchitis in all age groups, with adult and old animals even showing clinical signs of coughing. In addition, hamsters demonstrated the typical ERD response to heat-inactivated virus, characterized by the exacerbation of lung injury with extensive neutrophil and eosinophil infiltration, as well as TH2 polarization. Collectively, these characteristics suggest that the Syrian hamster model has significant potential for investigating the pathogenesis of RSV infection, elucidating the mechanism of ERD, and evaluating vaccine efficacy and safety.

Importance

The Syrian hamster has been shown in our study to be a potential model for respiratory syncytial virus (RSV) infection, according to the following characteristics:

Hamsters of three different age groups all developed typical pulmonary bronchiolitis following RSV infection, whereas adult and old hamsters showed typical cough symptoms, comparable to those observed in clinical patients.

Hamsters of different ages showed considerable variability. Neonatal hamsters tolerated more viral replication, while old hamsters suffered the most severe pulmonary pathology.

Hamsters exhibited typical ERD responses after inoculation with heat-inactivated RSV virus, including enhanced lung pathology, pulmonary eosinophilic and neutrophil infiltration, and Th2 polarization, which was remarkable and more similar to the typical characteristics of the ERD response in humans.
Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity
Authors: Chikhi Rayan , Raffestin Brice , Korobeynikov Anton , Edgar Robert , Babaian Artem
Published: July 2024

The NCBI Sequence Read Archive (SRA) is the largest public repository of DNA sequencing data, containing the most comprehensive snapshot of Earth’s genetic diversity to date. As its size exceeds 50.0 petabases across >27 million sequencing datasets, the entirety of these data cannot be searched for genetic sequences of interest in a reasonable time. To drastically increase the accessibility of this data we perform genome assembly over each SRA dataset using massively parallel cloud computing. The resulting Logan assemblage is the largest dataset of assembled sequencing data to date, and we believe will enable a new-era of accessible petabase-scale computational biology inquiry. We provide free and unrestricted access to the Logan assemblage and disseminate these datasets to foster early adoption. To illustrate the usefulness of Logan we align a diverse set of sequence queries across all of the SRA, completing queries in as little as 11 hours.
Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions
Authors: Ellison Erika L. , Zhou Peng , Chu Yi-Hsuan , Hermanson Peter , Gomez-Cano Lina , Myers Zachary A. , Abnave Ankita , Gray John , Hirsch Candice N. , Grotewold Erich , Springer Nathan M.
Published: July 2024

Transcription factors (TFs) play important roles in regulation of gene expression and phenotype. A variety of approaches have been utilized to develop gene-regulatory networks (GRNs) to predict the regulatory targets for each TF, such as yeast-one-hybrid (Y1H) screens and gene co-expression network (GCN) analysis. Here we identified potential TF targets and used a reverse genetics approach to test the predictions of several GRNs in maize. Loss-of-function mutant alleles were isolated for 22 maize TFs. These mutants did not exhibit obvious morphological phenotypes. However, transcriptomic profiling identified differentially expressed genes in each of the mutant genotypes, and targeted metabolic profiling indicated variable phenolic accumulation in some mutants. An analysis of expression levels for predicted target genes based on Y1H screens identified a small subset of predicted targets that exhibit altered expression levels. The analysis of predicted targets from GCN-based methods found significant enrichments for prediction sets of some TFs, but most predicted targets did not exhibit altered expression. This could result from false-positive GCN predictions, a TF with a secondary regulatory role resulting in minor effects on gene regulation, or redundant gene regulation by other TFs. Collectively, these findings suggest that loss-of-function for single uncharacterized TFs might have limited phenotypic impacts but can reveal subsets of GRN predicted targets with altered expression.
Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control
Authors: Treffon Patrick , Vierling Elizabeth
Published: July 2024

Plant fertility is fundamental to plant survival and requires the coordinated interaction of developmental pathways and signaling molecules. Nitric oxide (NO) is a small gaseous signaling molecule that plays crucial roles in plant fertility as well as other developmental processes and stress responses. NO influences biological processes through S-nitrosation, the posttranslational modification of protein cysteines to S-nitrosocysteine (R-SNO). NO homeostasis is controlled by S-nitrosoglutathione reductase (GSNOR), which reduces S-nitrosoglutathione (GSNO), the major form of NO in cells. GSNOR mutants (hot5-2/gsnor1) have defects in female gametophyte development along with elevated levels of reactive nitrogen species and R-SNOs. To better understand the fertility defects inhot5-2we investigated thein vivonitrosoproteome of floral tissues coupled with quantitative proteomics of pistils. To identify protein-SNOs we employed, for the first time in plants, an organomercury-based method that involves direct reaction with S-nitrosocysteine, enabling specific identification of S-nitrosocysteine–containing peptides and S-nitrosated proteins. We identified 1102 endogenously S-nitrosated proteins in floral tissues, of which 1049 were unique tohot5-2.Among the identified proteins, 728 were novel S-nitrosation targets. Notably, specific UGT-glycosyltransferases and argonaute proteins are S-nitrosated in floral tissues and differentially regulated in pistils. We also discovered S-nitrosation of proteins of the 26S proteasome together with increased abundance of proteasomal components and enhanced trypsin-like proteasomal activity inhot5-2pistils. Our data establish a new method for nitrosoprotein detection in plants, expand knowledge of the plant S-nitrosoproteome, and suggest that nitro-oxidative modification and NO homeostasis are critical to protein quality control in reproductive tissues.
Identification of Glyoxalase A in Group BStreptococcusand its contribution to methylglyoxal tolerance and virulence
Authors: Akbari Madeline S. , Joyce Luke R. , Spencer Brady L. , Brady Amanda , McIver Kevin S. , Doran Kelly S.
Published: July 2024

Group BStreptococcus(GBS) is a Gram-positive pathobiont that commonly colonizes the gastrointestinal and lower female genital tracts but can cause sepsis and pneumonia in newborns and is a leading cause of neonatal meningitis. Despite the resulting disease severity, the pathogenesis of GBS is not completely understood, especially during the early phases of infection. To investigate GBS factors necessary for blood stream survival, we performed a transposon (Tn) mutant screen in our bacteremia infection model using a GBSmarinertransposon mutant library previously developed by our group. We identified significantly underrepresented mutations in 623 genes that contribute to survival in the blood, including those encoding known virulence factors such as capsule, the β-hemolysin, and inorganic metal ion transport systems. Most of the underrepresented genes have not been previously characterized or studied in GBS, includinggloAandgloB,which are homologs for genes involved in methylglyoxal (MG) detoxification. MG is a byproduct of glycolysis and a highly reactive toxic aldehyde that is elevated in immune cells during infection. Here, we observed MG sensitivity across multiple GBS isolates and confirm thatgloAcontributes to MG tolerance and invasive GBS infection. We show specifically thatgloAcontributes to GBS survival in the presence of neutrophils and depleting neutrophils in mice abrogates the decreased survival and infection of thegloAmutant. The requirement of the glyoxalase pathway during GBS infection suggests that MG detoxification is important for bacterial survival during host-pathogen interactions.
MLCK/MLCP regulates mammalian axon regeneration and redistributes the growth cone F-actin
Authors: Saijilafu  , Wang Wei-Hua , Ma Jin-Jin , Yin Yin , Ma Yan-Xia
Published: July 2024

Axon regrowth is a key determinant of the restoration of the biological function of the nervous system after trauma. However, mature mammalian neurons have limited capacity for axon regeneration. We have previously demonstrated that neuronal axon growth both in the central and the peripheral nervous systems is markedly enhanced when non-muscle myosin II (NMII) is inhibited with blebbistatin. The activity of NMII is primarily regulated by MLCK and MLCPviathe phosphorylation and dephosphorylation of its light chain, respectively; however, the functional roles of MLCK and MLCP in mammalian axonal regeneration remain unknown. In the present study, we provide strong evidence that the inhibition of MLCK activity significantly blocks axon regeneration in mice. Conversely, the inhibition of MLCP promotes axon regrowth of both the peripheral and central nervous system. Our findings further indicate that the MLCK/MLCP regulates axon regeneration and redistributes the growth cone F-actin, and this result suggests that direct regulation of the growth cone machinery is a potential strategy to promote axon regeneration.
Receptor Binding Specificity of a Bovine A(H5N1) Influenza Virus
Authors: Chopra Pradeep , Page Caroline K. , Shepard Justin D. , Ray Sean D. , Kandeil Ahmed , Jeevan Trushar , Bowman Andrew S. , Ellebedy Ali H. , Webby Richard J. , de Vries Robert P. , Tompkins S. Mark , Boons Geert-Jan
Published: July 2024

Outbreaks in the US of highly pathogenic avian influenza virus (H5N1) in dairy cows have been occurring for months creating new possibilities for direct contact between the virus and humans. Eisfeldet al. examined the pathogenicity and transmissibility of a bovine HPAI H5N1 virus isolated from New Mexico in a series ofin vitroandin vivoassays. They found the virus has a dual human- and avian virus-like receptor-binding specificity as measured in a solid phase glycan binding assay. Here, we examined the receptor specificity of a bovine HPAI H5N1 virus (A/bovine/OH/B24OSU-432/2024, H5N1, clade 2.3.4.4b) employing four different assays including glycan array technology, bio-layer interferometry (BLI), a solid phase capture assay and hemagglutination of glycan remodeled erythrocytes. As controls, well characterized avian (A/Vietnam/1203/2004, H5N1, clade 1) and human (A/CA/04/2009, H1N1) IAVs were included that bind α2,3- and α2,6-sialosides, respectively. We found that A/bovine/OH/B24OSU-432/2024 preferentially binds to “avian type” receptors (α2,3-sialosides). Furthermore, sequence alignments showed that A/bovine has maintained amino acids in its HA associated with α2,3-sialoside (avian) receptor specificity. We conclude that while we find no evidence that A/bovine has acquired human virus receptor binding specificity, ongoing efforts must be placed on monitoring for this trait.
Closing the genome ofTeredinibacter turneraeT7902 by long-read nanopore sequencing
Authors: Gasser Mark T. , Liu Annie , Flatau Ron , Altamia Marvin , Filone Claire Marie , Distel Dan
Published: July 2024

We present the complete closed circular genome sequence derived from Oxford Nanopore sequencing of the shipworm endosymbiontTeredinibacter turneraeT7902 (DSM 15152, ATCC 39867), originally isolated from the shipwormLyrodus pedicellatus(1). This sequence will aid in the comparative genomics of shipworm endosymbionts and the understanding of host-symbiont evolution.
Effect of assortative mating and sexual selection on polygenic barriers to gene flow
Authors: Surendranadh Parvathy , Sachdeva Himani
Published: July 2024

Assortative mating and sexual selection are widespread in nature and can play an important role in speciation, through the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified. Here, we consider a polygenic ‘magic’ trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at individual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early generation hybrids. Our analysis clarifies how ‘tipping points’ (characterised by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI.
Quorum sensing employs a dual regulatory mechanism to repress T3SS gene expression
Authors: Paul Payel , Podicheti Ram , Geyman Logan J. , Papenfort Kai , van Kessel Julia C.
Published: July 2024

The type III secretion system (T3SS) is a needle-like complex used by numerous bacterial pathogens in host infection by directly injecting exotoxins into the host cell cytoplasm, leading to cell death. The T3SS is a known virulence factor in the shrimp pathogenVibrio campbellii. The ∼40 genes comprising theV. campbelliiT3SS are regulated by a network of transcription factors in response to changes in the cell’s environment: cell density (quorum sensing; QS), temperature, calcium, and host cell contact. Under positive environmental stimuli, the master T3SS transcription factor ExsA activates expression of the four structural T3SS operons required for needle formation. Previous studies identified a key role of the master QS transcription factor LuxR: repression ofexsAtranscription via DNA binding at theexsBApromoter. Here we uncovered a new regulatory role of LuxR: indirect post-translational repression of ExsA activity via direct transcriptional repression of the gene encoding the anti-anti-activator ExsC. InV. campbellii, ExsC is a positive regulator of T3SS transcription: high ExsC expression leads to full ExsA transcription activation of the T3SS structural promoters. LuxR binding at theexsCpromoter represses transcription ofexsCthrough disruption of ExsA binding. Our findings collectively show thatV. campbelliiresponds to high cell density signals to shut down the expression of the T3SS. We postulate that this dual regulatory mechanism by LuxR enables both the rapid inactivation of existing ExsA protein and blocks its further synthesis, leading to a rapid shutdown of T3SS activity at high cell density.

Importance

Vibrio campbelliiutilizes the type III secretion system (T3SS) as a mechanism of pathogenesis, which is a highly studied ‘injectisome’ complex that delivers exotoxins into host cells during infection. The T3SS pathogenicity island inV. campbelliicomprises ∼40 genes that are organized into four structural operons. In this study, we determined that quorum sensing – a method of bacterial communication – regulates T3SS genes both at the transcriptional and post-translational levels to shut down T3SS gene expression at high population densities.
Phosphorylation of Zearalenone retains its toxicity
Authors: Asaduzzaman Muhammad , Pavlov Ivan , St-Jean Guillaume , Zhu Yan , Castex Mathieu , Chorfi Younes , del Castillo Jerome R E , Zhou Ting , Alassane-Kpembi Imourana
Published: July 2024

Microbial biotransformation of Zearalenone (ZEN) is a promising deactivation approach. The residual toxicity and stability of Zearalenone-14-phosphate (ZEN-14-P) and Zearalenone-16-phosphate (ZEN-16-P), two novel microbial phosphorylation products of ZEN, remain unknown.

We investigated the cytotoxicity, oxidative stress, pro-inflammatory, and estrogenic activity of phosphorylated ZENs using porcine intestinal cells and uterine explants, and human endometrial cells, and traced their metabolic fate by LC-MS/MS analysis.

The phosphorylated ZENs significantly decreased the viability of IPEC-J2 and Ishikawa cells. Similar to ZEN, phosphorylation products induced significant oxidative stress, activated the expression of pro-inflammatory cytokines, and demonstrated estrogenic activity through upregulation of estrogen-responsive genes, activation of alkaline phosphatase and proliferation of endometrial glands. LC-MS/MS analysis pointed that although phosphorylated ZENs are partially hydrolyzed to ZEN, their respective metabolic pathways differ. We conclude that phosphorylation might not be sufficient to detoxify ZEN, leaving its cytotoxic, pro-inflammatory and estrogenic properties intact.

Graphical abstract
Cryo-EM Structure ofSalmonella typhimuriumArnC; the Key Enzyme in Lipid-A Modification Conferring Polymyxin Resistance
Authors: Patel Dhruvin H. , Karimullina Elina , Guo Yirui , Semper Cameron , Patel Deepak T. , Emde Tabitha , Borek Dominika , Savchenko Alexei
Published: July 2024

1

Polymyxins are last-resort antimicrobial peptides administered clinically against multi-drug resistant bacteria, including Gram-negative ESKAPE pathogens. However, an increasing number of pathogens employ a defense strategy involving a relay of enzymes encoded by thepmrE(ugd)loci and thearnBCDTEFoperon. As a result, an Ara-4N headgroup is added to the lipid-A component of outer membrane (OM) lipopolysaccharides (LPS) rendering polymyxins ineffective. Here, we report the cryo-EM structures of glycosyltransferase ArnC fromSalmonella typhimuriumresolved in both apo and UDP-bound forms at resolutions 2.75 Å and 3.8 Å, respectively. The structure of the ArnC protomer comprises of three distinct regions: an N-terminal glycosyltransferase domain, transmembrane region, and the interface helices (IHs). ArnC forms a stable tetramer with C2 symmetry through interactions in the C-terminal region, which is expected to protrude into the cytosol, where the β8 strand inserts into the adjacent protomer. ArnC protomers have two distinct types of interfaces involving multiple hydrogen bonds and salt bridges. The binding of UDP induces conformational changes that stabilizes structurally labile A-loop, spanning residues 201 to 213, and part of the putative catalytic pocket formed by IH1 and IH2. The comparative analysis of ArnC structures with homologs GtrB and DPMS suggests the key residues involved in ArnC catalytic activity.
Personality assessment of synanthropic rhesus macaques: implications and challenges
Authors: Gill Taniya , Gautam Anshul , Massen Jorg J.M. , Bhattacharjee Debottam
Published: July 2024

“What makes animals thrive in human-dominated environments?” is a question that has been extensively researched transcending disciplines, but findings remain inconclusive. Consistent inter-individual differences or personalities can potentially explain the functional significance of habitat-specific traits and their variations that help animals successfully coexist with humans. Rhesus macaques (Macaca mulatta) are the most successful non-human primate in the Anthropocene, living in diverse climatic and environmental conditions. Studying the personalities of synanthropic rhesus macaques can provide insights into the biological traits that facilitate their success in human-dominated environments. We employed a multi-method ‘bottom-up’ approach of behavioral observations and novelty experiments, standardized for assessing captive non-human primates, to evaluate the personalities of synanthropic adult rhesus macaques (N=52). To our surprise, novelty experiments encountered significant challenges, limiting their effectiveness. However, behavioral observations in the form of focal sampling revealed two repeatable traits:sociabilityandcautiousness. We found an effect of sex on sociability, where males were more sociable than females. In an additional analysis, we found that individuals who obtained food through contact provisioning had higher cautiousness scores than individuals who obtained food through non-contact provisioning. We discuss how the observed personality traits and their variations potentially offer adaptive advantages in human-dominated environments, where rhesus macaques face both benefits, such as anthropogenic subsidies and reduced predation, and costs, like exposure to anthropogenic stressors. We also emphasize that protocols designed for captive conditions may not be directly applicable to free-living animals. Thus, the study underscores the need to reconsider experimental designs to obtain comparable empirical evidence between captive and non-captive populations to enhance the ecological validity of personality assessments. Nevertheless, empirically identifying traits using observations in synanthropic species like rhesus macaques can still provide valuable insights into the mechanisms that enable certain animals to thrive amidst a rapid expansion of anthropogenic activities.

Research highlights

Studying personalities of synanthropic animals can shed light on the biological traits that help them thrive in human-dominated environments.

A ‘bottom-up’ multi-method approach, standardized for assessing captive NHP personalities, was employed to study a population of synanthropic rhesus macaques.

Behavioral observations captured two repeatable traits, namelysociabilityandcautiousness, where comparatively more cautious individuals obtained food through contact provisioning. Novelty experiments faced significant challenges.
Visual Congruency Modulates Music Reward through Sensorimotor Integration
Authors: Zhang Lei , Du Yi , Zatorre Robert J.
Published: July 2024

There is emerging evidence that a performer’s body movements may enhance the music-induced pleasure of audiences. However, the neural mechanism underlying such modulation remains largely unexplored. This study utilized psychophysiological and electroencephalographic data collected from listeners as they watched and listened to manipulated vocal (Mandarin lyrics) and violin performances of Japanese and Chinese pop music. All participants were unfamiliar with the violin or Mandarin. The auditory and visual elements of the stimuli were either congruent (original recording) or incongruent (drawn from unrelated music videos). We found that congruent visual movements, as opposed to incongruent ones, increased both subjective pleasure ratings and skin conductance responses but only during vocal performances. Then, we examined the coherence between the music signal and sensorimotor Mu-band oscillatory neural activity and found that congruent visual movements enhanced Mu entrainment exclusively to vocal music signal. Further, mediation analysis demonstrated that neural entrainment to vocal music significantly mediated the visual modulation of music-induced pleasure. In conclusion, our study provides novel evidence on how congruent visual movements can heighten music-induced pleasure through enhanced sensorimotor integration.
Evolution of divergent daily temporal niches shaped by male-male competition can generate sympatric speciation
Authors: Bouinier Titouan , Brunaud Arthur , Smadi Charline , Llaurens Violaine
Published: July 2024

Specialisation into different ecological niches can participate to species divergence and co-existence in sympatry. Here, we focus on the partitioning into different timings of reproductive activities during the day, as observed in many insect species living in sympatry. We thus investigate the evolution of the reproductive activity timing of individuals within populations, using a comprehensive stochastic model, employing a Doob-Gillespie-like simulation process. We model the evolution of (1) the timing of reproductive activity as a quantitative trait and (2) neutral loci that may generate genetic incompatibilities among divergent individuals. We specifically explore how male-male competition for female access can generate negative frequency-dependence on the timing of reproductive activities and fuel population divergence. Our simulations in finite populations highlight the strong effect of male-male competition and operational sex-ratio on the evolution of divergent temporal niches. It also shows how genetic incompatibilities fuel the differentiation among populations with divergent temporal niches, but may impair their co-existence. We then compare our results on the evolution of daily temporal niches to a previous model investigating the evolution of seasonal phenology and show the significant effect of overlapping vs. non-overlapping generations on the evolution of daily vs. seasonal niches. Our model therefore highlights male-male competition as an important factor shaping the evolution of diel niches, that may fuel sympatric speciation.
The ontogeny of chimpanzee technological efficiency
Authors: Berdugo Sophie , Cohen Emma , Davis Arran J. , Matsuzawa Tetsuro , Carvalho Susana
Published: July 2024

Primate extractive foraging requires years of dedicated learning. Throughout this period, learners peer at conspecifics engaging in the behaviour (“models”), interacting with the model and their tools, and sometimes stealing the freshly extracted resource. This also corresponds to an extended period of tolerance from the models. Yet the long-term effect of variation in experiences during this period on the technological efficiency of individuals is unknown for primate tool use, and no research has assessed the role of both the learner and the model(s) in generating individual differences. Using >680 hours of video spanning 25 years, we assessed whether experiences during the stone tool use social learning period (“early learning period”; ages 0–5) predicted the post-early learning period (ages 6+) technological efficiency in wild chimpanzees in Bossou, Guinea. We found that learners varied in how frequently they peered at the models’ whole nut-cracking bouts, how many learning opportunities their mothers presented, and the amount of tolerance and intolerance they experienced from all selected models. Learners who experienced more intolerance became less efficient tool users, whereas learners who were exposed to more social learning opportunities and tolerance became more efficient. Peering at the whole nut-cracking bout decreased subsequent efficiency, hinting at learners acquiring less efficient cultural components of the behaviour. Our findings highlight the role of social learning in the acquisition of stone tool use and support the view that social learning opportunities within a tolerant environment are key in explaining the emergence and maintenance of complex forms of primate technology.

Significance Statement

The capacity and inclination to learn from others, along with social learning opportunities provided by tolerant groupmates, are thought to have enabled the evolution of technology in primates, including hominins. The influence of the learning period on long-term individual variation in technological efficiency remains unknown for non-human primates but has significant implications for cultural transmission and evolution. We provide longitudinal support for the hypothesis that exposure to social learning opportunities during development predicts subsequent technological efficiency. Moreover, we show that low amounts ofintolerance, not just general tolerance, is key in the ontogeny of technological efficiency. Finally, we find aspects of behavioural acquisition relating to accurate transmission of cultural traits rather than to learning to use tools efficiently.
Expanding the space of self-reproducing ribozymes using probabilistic generative models
Authors: Lambert Camille N. , Opuu Vaitea , Calvanese Francesco , Zamponi Francesco , Hayden Eric , Weigt Martin , Smerlak Matteo , Nghe Philippe
Published: July 2024

Estimating the plausibility of RNA self-reproduction is central to origin-of-life scenarios but self-reproduction has been shown in only a handful of systems. Here, we populated a vast sequence space of ribozymes using statistical covariation models and secondary structure prediction. Experimentally assayed sequences were found active as far as 65 mutations from a reference natural sequence. The number of potentially generated sequences together with the experimental success rate indicate that at least ∼1039such ribozymes may exist. Randomly sampled artificial ribozymes exhibited autocatalytic self-reproduction akin to the reference sequence. The combination of high-throughput screening and probabilistic modeling considerably improves our estimation of the number of self-reproducing systems, paving the way for a statistical approach to the origin of life.
Isolation and characterization of cell wall and extracellular polysaccharides from cultures of the mycoparasitic strainTirochoderma koningiopsis
Authors: Nowak Artur , Wlizło Kamila , Komaniecka Iwona , Szymańska-Chargot Monika , Zdunek Artur , Kapral-Piotrowska Justyna , Tyśkiewicz Katarzyna , Jaroszuk-Ściseł Jolanta
Published: July 2024

TheTrichoderma koningiopsisstrain showed an extracellular polymers (EPS) synthesis capacity of 1.17 g/L in an optimised Czapek-Dox medium containing sucrose (30 g/L) and yeast extract (7.5 g/L). Three fractions of wall polymers were extracted from the biomass obtained after culture: cold water soluble (WPSZ), hot water soluble (WPSC) and alkali soluble (WPSNaOH), which accounted for 13.3%, 1.8% and 20.2% of the mycelial dry weight, respectively. Structural analyses indicated that the EPS obtained was mannan, and the WPS fractions were glucans containing predominantly →4)-Glc-(1→ linked residues, with branching at →3,6)- as well as →4,6)-positions. FT-IR and FT-Raman analyses showed that α-bonds dominate in the WPSZ and WPSC fractions, whereas β-bonds dominate in the EPS and WPSNaOH fractions. The obtained polymer fractions (PS) showed antioxidant properties in the ABTS, DPPH and FRAP methods and the ability to bind bisphenol A from an aqueous environment. The most important property of the obtained PSs is their ability to reduce germination and inhibit the growth of mycelia of the phytopathogenicFusarium culmorumstrain. The obtained polymers exhibit a number of bioactive properties and can be used in various areas of human life.

Highlights

Trichoderma koningiopsishas the ability to synthesise EPS

EPS are mainly composed of mannose and WPS of glucose

PS have the ability to chelate BPA and have antioxidant properties

The PS obtained has inhibitory properties againstF. culmorum.

Graphical Abstract
Genomic and transcriptomic analyses ofHeteropoda venatoriareveal the expansion of P450 family for starvation resistance in spider
Authors: Zhang Guoqing , Wang Yiru , Jiang Hongcen , Wang Yi
Published: July 2024

Background

Spiders generally exhibit robust starvation resistance, with hunting spiders, represented byHeteropoda venatoria, being particularly outstanding in this regard. Given the challenges posed by climate change and habitat fragmentation, understanding how spiders adjust their physiology and behavior to adapt to the uncertainty of food resources is crucial for predicting ecosystem responses and adaptability.

Results

We sequenced the genome ofH. venatoriaand, through comparative genomic analysis, discovered significant expansions in gene families related to lipid metabolism, such as cytochrome P450 and steroid hormone biosynthesis genes. We also systematically analyzed the gene expression characteristics ofH. venatoriaat different starvation resistance stages and found that the fat body plays a crucial role during starvation in spiders. This study indicates that during the early stages of starvation,H. venatoriarelies on glucose metabolism to meet its energy demands. In the middle stage, gene expression stabilizes, whereas in the late stage of starvation, pathways for fatty acid metabolism and protein degradation are significantly activated, and autophagy is increased, serving as a survival strategy under extreme starvation. Additionally, analysis of expanded P450 gene families revealed thatH. venatoriahas many duplicated CYP3 clan genes that are highly expressed in the fat body, which may help maintain a low-energy metabolic state, allowingH. venatoriato endure longer periods of starvation. We also observed that the motifs of P450 families inH. venatoriaare less conserved than those in insects, which may be related to the greater polymorphism of spider genomes.

Conclusions

This research not only provides important genetic and transcriptomic evidence for understanding the starvation mechanisms of spiders but also offers new insights into the adaptive evolution of arthropods.
Sleep homeostasis in lizards and the role of cortex
Authors: Hatori Sena , Yamaguchi Sho T. , Kobayashi Riho , Matsui Futaba , Zhou Zhiwen , Norimoto Hiroaki
Published: July 2024

Although their phenotypes are diverse, slow-wave sleep (SWS) and rapid eye movement sleep (REMS) are the two primary components of electrophysiological sleep (e-sleep) in mammals and birds. Slow waves in the cortex not only characterize SWS but are also used as biological markers for sleep homeostasis, given their rebound after sleep deprivation (SD). Recently, it has been reported that the Australian dragonPogona vitticepsexhibits two-stage sleep pattern in the dorsal ventricular ridge (DVR), which includes a homologue of the mammalian claustrum (CLA). It remains unclear whether reptilian e-sleep, which has been characterized by activity outside the cortex, compensates for sleep loss, as observed in mammals. We here report a significant rebound in the local field potential (LFP) after 7 hours of SD, during both SWS and REMS. Meanwhile, the cycle and mean bout length of SWS/REMS remained unaffected. We further investigated a possible role of the cortex in e-sleep regulation and homeostasis inPogonaand found that, although a corticotomy had no obvious effect on the LFP features investigated, it abolished LFP power rebound in the CLA/DVR after SD. These findings suggest that e-sleep homeostasis is a common feature in amniotes, and that cortex is involved in regulating activity rebounds in reptiles and mammals.
Addressing Underestimation of Waterborne Disease Risks Due to Fecal Indicator Bacteria Bound in Aggregates
Authors: Angelescu Dan E. , Abi-Saab David , Ganaye Raphael , Wanless David , Wong Joyce
Published: July 2024

Microbiological water quality monitoring is critical for managing waterborne disease risk; currently, regulations rely on quantifying culturable fecal indicator bacteria using traditional culture-based methods. These approaches cannot distinguish between planktonic forms and aggregates harboring higher loads of bacteria and associated pathogens, potentially underestimating exposure risks. By using size fractionation and ALERT, an automated rapid method for comprehensive quantification of culturable bacteria, we reveal widespread and substantial presence of aggregate-bound indicator bacteria across a variety of water matrices and geographies. We observe comprehensive bacteria counts exceeding traditional method counts by significant multiples (e.g., 3.4× on average at the Seine River 2024 Olympic venue, occasionally 100× in irrigation canals and wastewater plant effluent). The results, corroborated by microscopic and molecular analyses, highlight a major systematic bias in global water safety regulatory frameworks. Automated comprehensive culture-based rapid quantification methods could provide higher-accuracy risk assessments, enabling effective monitoring, including in remote and resource-limited settings.
Machine Learning Reveals Key Glycoprotein Mutations and Rapidly Assigns Lassa Virus Lineages
Authors: Daodu Richard Olumide , Uwe-Ulrich Jens , Kühnert Denise
Published: July 2024

Lassa fever, caused by the Lassa virus (LASV), remains a major public health concern in West Africa, causing numerous fatalities annually and several intercontinental cases since its discovery in 1969. Despite ongoing research, no approved vaccines are available, with current efforts focusing on immunotherapy. LASV is divided into distinct lineages that circulate in specific geographic regions, elicit varying immune responses, and exhibit different pathophysiological effects. Understanding the genetic differences between these lineages is crucial for developing, improving, and distributing diagnostics, treatments, and vaccines. In this study, we analyzed the LASV glycoprotein complex (GPC), the only surface protein, using statistics, machine learning, and phylogenetics. At a population scale, we identified key amino acid differences between Nigerian lineages and those in other West African regions, particularly near the stable signal peptide cleavage site and other immune-related regions (e.g., AA positions 59–76). Additionally, we found that GPC sequences from Lineages II and III are shorter than those from Lineage IV, due to the high prevalence of a codon insertion at positions 178–180 (amino acid position 60). This insertion may contribute to inaccuracies observed in molecular diagnostics for LASV and may also play a role in the increased fatality associated with Lineage IV. The insertion has reemerged and persisted in Lineage II which may indicate a fitness advantage. Furthermore, we developed a fast and highly accurate lineage classification tool called CLASV that allows rapid identification of LASV lineages, improving the ability to monitor emerging outbreaks and exported cases.
Human PrP E219K as a new and promising substrate for RT-QuIC amplification of human prion strains: a first step towards strain discrimination
Authors: Marin-Moreno A. , Reine F. , Jaffrézic F. , Herzog L. , Rezaei H. , Quadrio I. , Haïk S. , Béringue V. , Martin D.
Published: July 2024

Prion diseases are fatal neurodegenerative diseases that affect mammals through the transconformation of a host protein, the prion protein (PrP), into a toxic and pathogenic conformer termed PrPSc. Until now, the diagnosis is only confirmed with a post-mortem histology study of the central nervous system. Among the methods to detect the etiological agent,in vitroamplification techniques have emerged as very sensitive, highly specific and rapid tools, even though some prion strains remain refractory or difficult to amplify. Here we report the use of a new recombinant substrate for Real-Time Quaking Induced Conversion (RT-QuIC), a natural polymorphism of human prion protein with a lysine at position 219 instead of a glutamic acid, PrP E219K. This substrate amplifies the six sporadic human strains responsible for Creutzfeldt-Jakob Disease (CJD) and the strain responsible for its variant form in a few hours and over a large dilution range of the seeds. Moreover, based on the lag time of the amplification reactions, the PrP E219K substrate allows to discriminate between sporadic and variant CJD strains, a first step towards an ante-mortem typing of the prion strain affecting a patient.
An outline on the chemical phenotype flexibility of forest species: an eco-metabolomics study of Pinus uncinata along an altitudinal gradient
Authors: Rivas-Ubach Albert , Aranda Ismael , Sardans Jordi , Liu Yina , Díaz de Quijano María , Paša-Tolić Ljiljana , Oravec Michal , Urban Otmar , Peñuelas Josep
Published: July 2024

The altitudinal distribution of plant populations is mainly determined by a set of environmental variables, including temperature, water availability, UV radiation, among others, which gradually shift with elevation. Therefore, altitudinal gradients in ecology could serve as “natural laboratories” providing insights into the phenotypic plasticity of natural plant populations. Plants can adjust their phenotypes to cope with specific environments. However, the adjustment capacity directly depends on the plasticity and flexibility of plant phenotypes. Plants growing at the edges of their distribution gradients may present limited flexibility due to the sub-optimal environmental conditions they experience.

We analyzed the foliar metabolomes of a mountain pine population in the Pyrenees to assess their chemical phenotypic flexibility along an altitudinal gradient. We found significant changes in foliar metabolomes across different altitudes, with the most contrasting foliar metabolomes observed at the lowest and highest altitudes. Trees growing at the boundaries of the altitudinal distribution considerably shifted their foliar metabolome compared to those at more central locations with an overall upregulation of sugars, amino acids, and antioxidants. Metabolomics analyses suggested higher oxidative activity at lower altitude, presumably due to the drier and warmer conditions. However, oxidative stress indicators were also detected at the tree line, potentially associated with chilling, UV, and tropospheric O3exposure.

In addition to the inability of many species to keep pace with the rapid speed of climate change by migrating upward in altitude or latitude to find more optimum environments, their migration to higher elevations may be hindered by the presence of other environmental factors at high altitudes. Eco-metabolomics studies along environmental gradients can provide crucial insights into the chemical phenotypic flexibility of natural plant populations while providing pivotal clues regarding which plant metabolic pathway are prioritized to cope with specific environments.
Optimal organelle inheritance strategies under different changing environments and mutational pressures
Authors: García-Pascual Belén , Nordbotten Jan M. , Johnston Iain G.
Published: July 2024

Mitochondrial and chloroplast DNA (mtDNA and cpDNA) encode essential cellular apparatus. This organelle DNA (oDNA) exists at high copy number (ploidy) in eukaryotic cells, which must both mitigate mutational damage and allow adaptation to changing demands. Across eukaryotes, a range of inheritance strategies are used for oDNA, including uniparental and doubly uniparental inheritance (DUI), paternal leakage, recombination-mediated repair and gene conversion, and an effective “genetic bottleneck” imposed between generations. Here, we use modelling and simulation to investigate how these different strategies support the robustness and evolvability of oDNA populations under different challenges of mutation and changes in selection imposed by the environment. We find a general tradeoff between maintaining heterozygosity for flexible adaptation and supporting purifying selection against dysfunctional mutants. Different combinations of leakage and bottleneck size provide optimal resolutions to this tradeoff under different sets of challenges. The model explains many observed behaviours, including the appearance of non-minimal bottleneck sizes, a tradeoff between high ploidy for heterozygosity and repair and tight bottlenecks for segregation, and environmental dependence of the benefits of leakage and DUI. We connect different strategies observed across eukaryotes with the ecology of the organisms involved to explore support for the predictions of this theory.
Connecting self-report and instrumental behavior during incubation of food craving in humans
Authors: Ruiz Nicholas A. , Eckardt Devlin , Briand Lisa A. , Wimmer Mathieu , Murty Vishnu P.
Published: July 2024

Incubation of craving is a phenomenon describing the intensification of craving for a reward over extended periods of abstinence from reinforcement. Animal models use instrumental markers of craving to reward cues to examine incubation, while human paradigms rely on subjective self-reports. Here, we characterize an animal-inspired, novel human paradigm that showed strong positive relationships between self-reports and instrumental markers of craving for favored palatable foods. Further, we found consistent nonlinear relationships with time since last consumption and self-reports, and preliminary patterns between time and instrumental responses. These findings provide a novel approach to establishing an animal-inspired human model of incubation.
Relative-belief inference in quantum information theory
Authors: Teo Y. S. , Shringarpure S. U. , Jeong H. , Prasannan N. , Brecht B. , Silberhorn C. , Evans M. , Mogilevtsev D. , Sánchez-Soto L. L.
Published: July 2024

We introduce the framework of Bayesian relative belief that directly evaluates whether or not the experimental data at hand support a given hypothesis regarding a quantum system by directly comparing the prior and posterior probabilities for the hypothesis. In model-dimension certification tasks, we show that the relative-belief procedure typically chooses Hilbert spaces that are never smaller in dimension than those selected from optimizing a broad class of information criteria, including Akaike's criterion. As a concrete and focused exposition of this powerful evidence-based technique, we apply the relative-belief procedure to an important application: . In particular, just by comparing prior and posterior probabilities based on data, we demonstrate its capability of tracking multiphoton emissions using (realistically lossy) single-photon detectors in order to assess the actual quality of photon sources without making assumptions, thereby reliably safeguarding source integrity for general quantum-information and communication tasks with Bayesian reasoning. Finally, we discuss how relative belief can be exploited to carry out parametric model certification and estimate the total dimension of the quantum state for the combined (measured) physical and interacting external systems described by the Tavis-Cummings model.

Published by the American Physical Society
2024