bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing CRISPR interference to resensitize laboratory strains and clinical isolates to last resort antibiotics
Authors: Frusteri Chiacchiera Angelica , Casanova Michela , Bellato Massimo , Piazza Aurora , Migliavacca Roberta , Batt Gregory , Magni Paolo , Pasotti Lorenzo 
Published: January 2025

AbstractThe global race against antimicrobial resistance requires novel antimicrobials that are not only effective in killing specific bacteria, but also minimize the emergence of new resistances. Recently, CRISPR/Cas-based antimicrobials were proposed to address killing specificity with encouraging results. However, the emergence of target sequence mutations triggered by Cas-cleavage was identified as an escape strategy, posing the risk of generating new antibiotic-resistance gene (ARG) variants. Here, we evaluated an antibiotic re-sensitization strategy based on CRISPR interference (CRISPRi), which inhibits gene expression without damaging target DNA. The resistance to four antibiotics, including last resort drugs, was significantly reduced by individual and multi-gene targeting of ARGs in low- to high-copy numbers in recombinant E. coli. Escaper analysis confirmed the absence of mutations in target sequence, corroborating the harmless role of CRISPRi in the selection of new resistances. E. coli clinical isolates carrying ARGs of severe clinical concern were then used to assess the robustness of CRISPRi under different growth conditions. Meropenem, colistin and cefotaxime susceptibility was successfully increased in terms of MIC (up to > 4-fold) and growth delay (up to 11 h) in a medium-dependent fashion. ARG repression also worked in a pathogenic strain grown in human urine, as a demonstration of CRISPRi-mediated re-sensitization in host-mimicking media. This study laid the foundations for further leveraging CRISPRi as antimicrobial agent or research tool to selectively repress ARGs and investigate resistance mechanisms.
Hypoxia traits imprinted in otolith δ13C from individual to global scales
Authors: Howard Evan M. , Deutsch Curtis A. 
Published: January 2025

Abstract
Hypoxia tolerance and its variation with temperature, activity, and body mass, are critical ecophysiological traits through which climate impacts marine ectotherms. To date, experimental determination of these traits is limited to a small subset of modern species. We leverage the close coupling of carbon and oxygen in animal metabolism to mechanistically relate these traits to the carbon isotopes in fish otoliths (δ13Coto). The model reproduces the major empirical patterns in δ13Coto at individual to global scales. The weak dependence on body size and strong, non-linear, dependence on temperature reflect the same balance between metabolism and ventilatory gas exchange that underlies organisms’ hypoxia tolerance. The global relationship between temperature and δ13Coto records both the fractionation by aragonite precipitation and the variation in hypoxia traits across ocean biomes. Because hypoxia tolerance is imprinted on both otolith geochemistry and species biogeography, the model allows the aerobic limits of species geographic ranges to be predicted from fish δ13Coto. This physiologically grounded model provides a foundation for the use of otolith chemistry to reconstruct modern spatial patterns and paleoceanographic changes in key traits that shape aerobic habitat of aquatic species.
Solution combustion synthesis of ZnO doped CuO nanocomposite for photocatalytic and sensor applications
Authors: Kumar A. Naveen , Balakrishna M. , Desai Usha , Rakshith R. , Ambika K. M. , Soumya P. , Ravikumar C. R. , Vadivu S. Senthil , Naik Nithesh 
Published: January 2025

AbstractZnO-doped CuO nanocomposites (CuO-ZnO NPs) of 1, 3, and 5 mol% were prepared by the solution combustion method using ODH as a fuel (Oxlyl-hydrazide) at 500 °C and calcining at 1000 °C for two hours and the Structural, photocatalytic, and electrochemical properties were investigated by experimental and theoretical methods. X-ray diffraction (XRD) patterns revealed a crystallite size (D) range of 25 to 31 nm for pure CuO and 1, 3, and 5 mol% CuO-ZnO NPs. According to calculations, the optical energy band gap (Eg) of the NPs is between 2.1 and 2.5 eV. Under UV light irradiation, the photocatalytic degradation of CuO + 3%ZnO NPs on Congo Red (CR) and Methylene Blue (MB) dye was assessed under the influence of UV light. The degradation efficiency increased with the catalyst dosage (10 − 60 mg L− 1). At a concentration of the catalyst of 60 mg, the degradation efficiency can even reached 70% after 120 min. The electrochemical properties of the prepared NPs were studied using cyclic voltammetry and electrochemical impedance spectroscopy (EIS). Solutions of glucose and ascorbic acid were effectively sensed using modified carbon paste electrodes. These innovative results can be considered for the expansion of novel resources to scale for dual applications in the areas of photocatalysis and sensors.
Enhancing betalains production and antioxidant activity in Celosia argentea cell suspension cultures using biotic and abiotic elicitors
Authors: Mueangnak Kanchanok , Kitwetcharoen Haruthairat , Thanonkeo Sudarat , Klanrit Preekamol , Apiraksakorn Jirawan , Klanrit Poramaporn , Klanrit Poramate , Thanonkeo Pornthap 
Published: January 2025

AbstractCelosia argentea is a plant known for producing bioactive compounds, including betalains, which possess various biological and pharmaceutical properties. This study aimed to investigate the effect of biotic and abiotic elicitors on betalains production and their antioxidant activity in cell suspension cultures of C. argentea. Various concentrations of chitosan, yeast extract, salicylic acid, methyl jasmonate, copper sulfate (CuSO4), and cobalt chloride (CoCl2) were evaluated. The results revealed that chitosan, salicylic acid, methyl jasmonate, and CuSO4 significantly improved betalains production in the cell suspension cultures. Among these elicitors, chitosan at 5.0 mg/L and CuSO4 at 6.4 µM were the most effective in enhancing betalains production, yielding the highest concentrations of 4.65 and 4.99 mg/g dry weight, respectively. Notably, the betalains derived from the elicitor-treated cultures exhibited greater antioxidant activity compared to the control. These findings suggest that chitosan and CuSO4 are promising elicitors for sustainable in vitro production of betalains from C. argentea cell suspension cultures on a commercial scale, owing to their ability to enhance betalains production and antioxidant activity.
Exploring the catalytic hydrothermal liquefaction of Namibian encroacher bush
Authors: Cutz Luis , Bias Nikos , Al-Naji Majd , de Jong Wiebren 
Published: January 2025

AbstractAn urgent ecological issue is the threat posed by invasive species, which are becoming more widespread especially in Africa. These encroachments damage ecosystems, pose a threat to biodiversity, and outcompete local plants and animals. This article focuses on converting Acacia Mellifera from Namibia, commonly known as encroacher bush (EB) into high-quality drop-in intermediates for the chemical and transport industry via hydrothermal liquefaction (HTL). HTL tackles the growing need for sustainable energy carriers while simultaneously halting the spread of the invasive species. A surface response methodology was used to optimize the HTL process for the following operational conditions: temperature (250–340 °C), residence time (5–60 min) and catalyst loading (0–10 wt%). The catalyst of choice was determined after evaluating the energy recovery (ER) of four different catalysts (Zeolite, La2O3, Hydrotalcite, Ni/SiO2–Al2O3) under the same HTL operational conditions. The results indicate that the addition of hydrotalcite results in high yields of bio-crude oil (13–28 wt%), without compromising the high heating value (HHV, 26–31 MJ/kg), water content (0.47 wt%) or increasing the content of oxygenated compounds compared to the non-catalytic experiment. For the experimental conditions tested, we observed a global maximum in conversion in the 330 °C and 30 min range. Our findings indicate that the most significant factor on the conversion of EB into bio-crude oil was temperature, followed by the catalyst loading. Furthermore, biochars produced at 330 °C and 30 min show potential as solid biofuels with HHVs up to 28.30 MJ/kg.
Parasites specific to centipedes form a new major lineage of terrestrial gregarines
Authors: Miroliubova Tatiana S. , Mikhailov Kirill V. , Simdyanov Timur G. , Aleoshin Vladimir V. , Dũng Đinh Thế , Kudriavkina Aleksandra I. 
Published: January 2025

AbstractGregarines from the families Dactylophoridae and Trichorhynchidae parasitize exclusively centipedes and have a distinct morphology among other terrestrial eugregarines, but their evolutionary relationships have not yet been studied with molecular methods. Here we obtain rDNA operon sequences for the dactylophorids and trichorhynchids. We describe a new species Trichorhynchus efeykini sp. n. from a scutigeromorph Thereuopoda longicornis from Vietnam. Phylogenetic analyses with combined SSU, 5.8S and LSU rDNA dataset support the previously proposed separation of Trichorhynchus to the Trichorhynchidae based on morphology and recover the dactylophorids and trichorhynchids as sister groups in a monophyletic clade. This clade appears sister to the clade of the Actinocephaloidea and Stylocephaloidea, and represents a new major lineage of terrestrial gregarines that we designate as a new superfamily Dactylophoroidea.
Sex differences in aggression and its neural substrate in a cichlid fish
Authors: Jackson Lillian R. , Dumitrascu Mariam , Alward Beau A. 
Published: January 2025

AbstractAggression is ubiquitous among social species and can function to maintain social dominance hierarchies. The African cichlid fish Astatotilapia burtoni is an ideal study species for studying aggression due to their dominance hierarchy and robust behavioral repertoire. To further understand the potential sex differences in aggression in this species, we characterized aggression in male and female A. burtoni in a mirror assay. We then quantified neural activation patterns in brain regions of the social behavior network (SBN) to investigate if differences in behavior are reflected in the brain with immunohistochemistry by detecting the phosphorylated ribosome marker phospho-S6 ribosomal protein (pS6), a marker for neural activation. We found that A. burtoni perform both identical and sex-specific aggressive behaviors in response to a mirror assay. Females had greater pS6 immunoreactivity than males in the Vv (ventral part of the ventral telencephalon), a homolog of the lateral septum in mammals. Males but not females had higher pS6 immunoreactivity in the ATn after the aggression assay. The ATn (anterior tuberal nucleus) is a homolog of the ventromedial hypothalamus in mammals, which is strongly implicated in the regulation of aggression in males. Several regions also have higher pS6 immunoreactivity in negative controls than fish exposed to a mirror, implicating a role for inhibitory neural processes in suppressing aggression until a relevant stimulus is present. Male and female A. burtoni display both similar and different behavioral patterns in aggression in response to a mirror assay. There are also sex differences in the corresponding neural activation patterns in the SBN. In mirror males but not females, the ATn clusters with the POA, revealing a functional connectivity of these regions that is triggered in an aggressive context in males. These findings suggest that distinct neural circuitry underlie aggressive behavior in male and female A. burtoni, serving as a foundation for future work investigating the molecular and neural underpinnings of sex differences in behavior in this species to reveal fundamental insights into understanding aggression.
Genome-wide association studies in lettuce reveal the interplay of seed age, color, and germination under high temperatures
Authors: Oh Sookyung , Ahn Ezekiel , Shi Ainong , Mou Beiquan , Park Sunchung 
Published: January 2025

AbstractThermoinhibition, the suppression of seed germination by high temperatures, is an adaptive trait that ensures successful seedling establishment in natural environments. While beneficial for wild plants, thermoinhibition can adversely affect crop yields due to uneven and reduced germination rates, particularly in the face of climate change. To understand the genetic basis of thermoinhibition, we conducted a comprehensive genetic analysis of a diverse panel of Lactuca spp. accessions. Our findings revealed that L. serriola, a wild ancestor of cultivated lettuce, showed relaxed thermoinhibition response compared to cultivated lettuce, suggesting that this trait may have been positively selected during early domestication in the Mediterranean region with hot, dry summers. Additionally, we found that thermoinhibition intensified with seed age but was less pronounced in dark-colored seeds, which showed increased germination under high temperatures. Genome-wide association studies identified genomic regions associated with thermoinhibition, including genes involved in ethylene and ABA signaling. Interestingly, some of these regions were also linked to seed color, suggesting a potential genetic coupling between black seed color and reduced thermoinhibition. These results highlighted the complex interplay between thermoinhibition, seed color, and domestication in lettuce, indicating a complicated nature of thermoinhibition regulation. By elucidating the genetic architecture of thermoinhibition, our study provides a valuable foundation for breeding strategies to enhance lettuce resilience to climate change.
Determining optimum assembly zone for modular reconfigurable robots using multi-objective genetic algorithm
Authors: Pasumarthi Ravikiran , Samarakoon S. M. Bhagya P. , Elara Mohan Rajesh , Sheu Bing J. 
Published: January 2025

AbstractReconfigurable modular robots can be used in application domains such as exploration, logistics, and outer space. The robots should be able to assemble and work as a single entity to perform a task that requires high throughput. Selecting an optimum assembly position with minimum distance traveled by robots in an obstacle surrounding the environment is challenging. Therefore, this paper proposes a novel approach for optimizing the assembly zone of modular robots in heterogeneous obstacle environments. The method uses a multi-objective Genetic Algorithm (GA) to minimize total travel distance and individual distance disparities. Utilizing the A* algorithm for path planning ensures efficient navigation. A generic kinematic model enabling holonomic locomotion with any reconfiguration and a new modular robot design are also introduced. Hardware experiments have been conducted to validate the kinematic model’s applicability for holonomic navigation across different robot configurations. Simulations and physical experiments demonstrated the effectiveness of the proposed method in determining assembly zones, with GA outperforming multi-objective pattern search and random selection in terms of total distance and individual distances traveled by the robots.
Bio particle swarm optimization and reinforcement learning algorithm for path planning of automated guided vehicles in dynamic industrial environments
Authors: Lin Shiwei , Wang Jianguo , Huang Bomin , Kong Xiaoying , Yang Hongwu 
Published: January 2025

AbstractAutomated guided vehicles play a crucial role in transportation and industrial environments. This paper presents a proposed Bio Particle Swarm Optimization (BPSO) algorithm for global path planning. The BPSO algorithm modifies the equation to update the particles’ velocity using the randomly generated angles, which enhances the algorithm’s searchability and avoids premature convergence. It is compared with Particle Swarm Optimization (PSO), Genetic Algorithm (GA), and Transit Search (TS) algorithms by benchmark functions. It has great performance in unimodal optimization problems, and it gains the best fitness value with fewer iterations and average runtime than other algorithms. The Q-learning method is implemented for local path planning to avoid moving obstacles and combines with the proposed BPSO for the safe operations of automated guided vehicles. The presented BPSO-RL algorithm combines the advantages of the swarm intelligence algorithm and the Q-learning method, which can generate the globally optimal path with fast computational speed and support in dealing with dynamic scenarios. It is validated through computational experiments with moving obstacles and compared with the PSO algorithm for AGV path planning.
Kaolinite induces rapid authigenic mineralisation in unburied shrimps
Authors: Corthésy Nora , Saleh Farid , Antcliffe Jonathan B. , Daley Allison C. 
Published: January 2025

AbstractFossils preserving soft tissues and lightly biomineralized structures are essential for the reconstruction of past ecosystems and their evolution. Understanding fossilization processes, including decay and mineralisation, is crucial for accurately interpreting ancient morphologies. Here we investigate the decay of marine and freshwater shrimps deposited on the surface of three different clay beds. In experimental set ups containing kaolinite, cryogenic scanning electron microscopy shows a black film comprised of newly formed anhedral and cryptocrystalline aluminosilicates on marine shrimp cuticles, which stabilise the overall morphology. This is the first experimental evidence for the replication of arthropod lightly biomineralized structures in aluminosilicates shortly after death, while carcasses are not buried by sediments. The preservation of morphology through aluminosilicates could result in carcasses persisting on the seafloor for weeks without losing much external anatomical information. In this context, instantaneous burial capturing animals alive may not be a prerequisite for exceptional preservation as usually thought.
An umbrella review of health outcomes following traumatic brain injury
Authors: Ogonah Maya G. T. , Botchway Stella , Yu Rongqin , Schofield Peter W. , Fazel Seena 
Published: January 2025

AbstractWhile numerous reviews have assessed the association between traumatic brain injury (TBI) and various mental and physical health outcomes, a comprehensive evaluation of the scope, validity, and quality of evidence is lacking. Here we present an umbrella review of a wide range of health outcomes following TBI and outline outcome risks across subpopulations. On 17 May 2023, we searched Embase, Medline, Global Health, PsycINFO, and Cochrane Database of Systematic Reviews for systematic reviews and meta-analyses. We compared risk ratios across different outcomes for risks compared with people without TBI and examined study quality, including heterogeneity, publication bias, and prediction intervals. The study was registered with PROSPERO (CRD42023432255). We identified 24 systematic reviews and meta-analyses covering 24 health outcomes in 31,397,958 participants. The current evidence base indicates an increased risk of multiple mental and physical health outcomes, including psychotic disorders, attention-deficit/hyperactivity disorder, suicide, and depression. Three outcomes—dementia, violence perpetration, and amyotrophic lateral sclerosis—had meta-analytical evidence of at least moderate quality, which suggest targets for more personalized assessment. Health-care services should review how to prevent adverse long-term outcomes in TBI.
The Asgard archaeal ESCRT-III system forms helical filaments and remodels eukaryotic-like membranes
Authors: Melnikov Nataly , Junglas Benedikt , Halbi Gal , Nachmias Dikla , Zerbib Erez , Gueta Noam , Upcher Alexander , Zalk Ran , Sachse Carsten , Bernheim-Groswasser Anne , Elia Natalie 
Published: January 2025

Abstract
The ESCRT machinery mediates membrane remodeling in numerous processes in cells including cell division and nuclear membrane reformation. The identification of ESCRT homologs in Asgard archaea, currently considered the closest prokaryotic relative of eukaryotes, implies a role for ESCRTs in the membrane remodeling processes that occurred during eukaryogenesis. Yet, the function of these distant ESCRT homologs is mostly unresolved. Here we show that Asgard ESCRT-III proteins of the Lokiarcheota self-assemble into helical filaments, a hallmark of the ESCRT system. We determined the cryo-EM structure of the filaments at 3.6 Å resolution and found that they share features of bacterial and eukaryotic ESCRT-III assemblies. Markedly, Asgard ESCRT-III filaments bound and deformed eukaryotic-like membrane vesicles. Oligonucleotides facilitated the assembly of ESCRT-III filaments and tuned the extent of membrane remodeling. The ability of Asgard archaeal ESCRTs to remodel eukaryotic-like membranes, which are fundamentally different from archaeal membranes, and the structural properties of these proteins places them at the junction between prokaryotes and eukaryotes.
MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays
Authors: Meurs Romane , De Matos Mara , Bothe Adrian , Guex Nicolas , Weber Tobias , Teleman Aurelio A , Ban Nenad , Gatfield David 
Published: January 2025

Abstract
Ribosomes scanning from the mRNA 5′ cap to the start codon may initiate at upstream open reading frames (uORFs), decreasing protein biosynthesis. Termination at a uORF can lead to re-initiation, where 40S subunits resume scanning and initiate another translation event downstream. The noncanonical translation factors MCTS1-DENR participate in re-initiation at specific uORFs, but knowledge of other trans-acting factors or uORF features influencing re-initiation is limited. Here, we establish a cell-free re-initiation assay using HeLa lysates to address this question. Comparing in vivo and in vitro re-initiation on uORF-containing reporters, we validate MCTS1-DENR-dependent re-initiation in vitro. Using this system and ribosome profiling in cells, we found that knockdown of the MCTS1-DENR homolog eIF2D causes widespread gene deregulation unrelated to uORF translation, and thus distinct to MCTS1-DENR-dependent re-initiation regulation. Additionally, we identified MCTS2, encoded by an Mcts1 retrogene, as a DENR partner promoting re-initiation in vitro, providing a plausible explanation for clinical differences associated with DENR vs. MCTS1 mutations in humans.
The proximity-based protein interactome and regulatory logics of the transcription factor p65 NF-κB/RELA
Authors: Leib Lisa , Juli Jana , Jurida Liane , Mayr-Buro Christin , Priester Jasmin , Weiser Hendrik , Wirth Stefanie , Hanel Simon , Heylmann Daniel , Weber Axel , Schmitz M Lienhard , Papantonis Argyris , Bartkuhn Marek , Wilhelm Jochen , Linne Uwe , Meier-Soelch Johanna , Kracht Michael 
Published: January 2025

Abstract
The protein interactome of p65/RELA, the most active subunit of the transcription factor (TF) NF-κB, has not been previously determined in living cells. Using p65-miniTurbo fusion proteins and biotin tagging, we identify >350 RELA interactors from untreated and IL-1α-stimulated cells, including many TFs (47% of all interactors) and >50 epigenetic regulators belonging to different classes of chromatin remodeling complexes. A comparison with the interactomes of two point mutants of p65 reveals that the interactions primarily require intact dimerization rather than DNA-binding properties. A targeted RNAi screen for 38 interactors and subsequent functional transcriptome and bioinformatics studies identify gene regulatory (sub)networks, each controlled by RELA in combination with one of the TFs ZBTB5, GLIS2, TFE3/TFEB, or S100A8/A9. The large, dynamic and versatile high-resolution interactome of RELA and its gene regulatory logics provides a rich resource and a new framework for explaining how RELA cooperativity determines gene expression patterns.