bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissection and internal observation of the giant tropical bont tickAmblyomma variegatum
Authors: Pature Naomie , Pagès Nonito , Rodrigues Valérie , Meyer Damien F. 
Published: February 2025

ABSTRACTTicks are ectoparasites that feed on the blood of animals and humans and are among the arthropods responsible for numerous human and animal diseases worldwide. The tropical bont tick,Amblyomma variegatum, is a significant natural vector ofEhrlichia ruminantium, the causative agent of heartwater. This disease is endemic in many countries, including those in sub-Saharan Africa and certain Caribbean islands. Due to the potential of heartwater and its vector to pose an economic and health threats to non-endemic regions, they have been designated as high-consequence foreign animal diseases and pests by the United States Department of Agriculture’s Animal and Plant Health Inspection Service. Understanding the ecology and biology ofA. variegatumis critical for developing effective control methods to limit its spread to other geographic regions. A key step in this process is the isolation of tick organs and further elucidation of their functions (i.e. vector competence). However, the literature contains limited documentation of the complete internal structure ofAmblyommatick species. In this study, we describe the internal structure of unfed nymphs, partially engorged males, and unfed and partially engorged females of the tick speciesA. variegatum. The objective is to facilitate the identification and the localization organs of interest while highlighting the morphological differences between the tropical bont tick and other tick species. This foundational work will support the development of various applications following the isolation of tick organs. These findings not only deepen our understanding ofAmblyomma variegatumanatomy but also provide a critical foundation for tackling the broader challenges of tick-borne diseases and advancing vector control strategies in both endemic and non-endemic regions.
Toxoplasma gondiias a Causal Factor in Schizophrenia: Evidence from Two Large Cohorts
Authors: Israel Ariel , Weizman Avi , Israel Sarah , Stokar Joshua , Ashkenazi Shai , Vinker Shlomo , Magen Eli , Merzon Eugene 
Published: February 2025

BackgroundSchizophrenia (SCZ) is a debilitating psychiatric disorder with a complex and poorly understood etiology. Numerous studies have reported a high prevalence ofToxoplasma gondii-specific immunoglobulins in SCZ patients, indicating past infection, yet the clinical significance of this association remains unclear.MethodsWe investigated the impact of medication purchases and past medical conditions on SCZ risk in two large cohorts. In a national cohort, we compared 3,273 individuals diagnosed with SCZ to 32,730 matched controls, adjusting for gender, age, ethnicity, socioeconomic status, and year of enrollment. Key findings were validated prospectively on the U.S. TriNetX collaborative network, which includes over 117 million individuals.ResultsIn both cohorts, individuals who used atovaquone had a significantly lower risk of developing SCZ over the next decade (adjusted odds ratio = 0.26 in the national cohort; hazard ratio = 0.29 in the TriNetX cohort, bothP< 0.001). A similar reduction in SCZ risk was observed with clindamycin use, consistent with the known efficacy of both atovaquone and clindamycin againstT. gondii.DiscussionBased on new epidemiological associations identified by this study, we propose a novel hypothesis for SCZ pathogenesis, in which persistentT. gondiicolonization in the microbiome, combined with prolonged dissemination into the central nervous system due to an impaired immune response, liver function, and/or alterations in the skin microbiome, may contribute to SCZ development in genetically susceptible individuals.ConclusionIndividuals who received medications known to targetT. gondiihad significantly lower SCZ risk, suggesting a causative role for this pathogen and highlighting potential preventive or therapeutic roles for these medications in SCZ. The observed associations provide new insights into the mechanisms linkingT. gondiito SCZ, opening novel avenues for research and intervention strategies.
Large-scale global molecular epidemiology of antibiotic resistance determinants inStreptococcus pneumoniae
Authors: Shawrob Kazi Shefaul Mulk , Dhariwal Achal , Salvadori Gabriela , Gladstone Rebecca Ashley , Junges Roger 
Published: February 2025

AbstractBackgroundStreptococcus pneumoniaeis a leading pathogen in terms of deaths attributable to or associated with antimicrobial resistance globally. Thus, monitoring antibiotic resistance determinants constitutes a key aspect of surveillance efforts.AimLeveraging on publicly available whole-genome sequencing data, we aimed to investigate the presence and distribution patterns of antibiotic resistance inS. pneumoniaewith a focus on multi-drug resistance and serotype distribution.MethodsMetadata and genomes were obtained from the National Center for Biotechnology Information Pathogen Detection database. Curation and harmonization were performed in R and SPSS. Data on resistance patterns was defined according to AMRFinderPlus and a combination of prediction tools were employed forin silicoserotyping.ResultsAnalyses involved 75,161 genomes totaling 122,673 gene/allele counts from 14 antibiotic classes. Multi-drug resistance was observed in 16.7% of isolates with the highest increasing rates in Asia and South America. Within antibiotic classes, increase in macrolide resistance genes was highlighted, particularly in the proportion of genomes presentingmefA/msrD. Over a third of isolates with serotypes 19F, 23F, 15A, 6B, and 19A showed multi-drug resistance. We further observed the highest significant increases in the presence of resistance in 33F, 22F, 10A, and 23A. Serotype 13, not included in any vaccine formulation, presented high multi-drug resistance rates with a strong increasing trend.ConclusionsThe findings of this study highlight variations in resistance determinants globally and across serotypes over time. Collectively these data underscore the added value of utilizing public whole-genome sequencing data to investigate the effectiveness and repercussions of treatment and vaccination strategies on managing antibiotic resistance.
Gene Editing forATXN3Inactivation in Machado-Joseph disease: CRISPR-Cas9 as a Therapeutic Alternative to TALEN-Induced Toxicity
Authors: Lopes Sara Monteiro , Lopes Miguel Monteiro , Oliveira Daniela , Santana Magda Matos , Fernandes Ana Rita , Vasconcelos-Ferreira Ana , Pereira Dina , Casquinha Maria , Nóbrega Clévio , Matos Carlos A. , Sanjana Neville E. , Hsu Patrick D. , Ran Fei Ann , Swiech Lukasz , Cong Le , Zhang Feng , Nobre Rui Jorge , de Almeida Luís Pereira 
Published: February 2025

ABSTRACTMachado-Joseph disease (MJD) is an autosomal dominantly-inherited neurodegenerative disorder, caused by an over-repetition of the polyglutamine-codifying region in theATXN3gene. Strategies based on the suppression of the deleterious gene products have demonstrated promising results in pre-clinical studies. Nonetheless, these strategies do not target the root cause of the disease. In order to prevent the downstream toxic pathways, our goal was to develop gene editing-based strategies to permanently inactivate the humanATXN3gene. TALENs and CRISPR-Cas9 systems were designed to target exon 2 of this gene and functional characterization was performed in a human cell line. After the demonstration of TALEN’s and CRISPR-Cas9 efficiency on gene disruption, a sequence of each system was selected for furtherin vivoexperiments. Although both TALENs and CRISPR-Cas9 systems led to a drastic reduction of ATXN3 aggregates in the striatum of a lentiviral-based mouse model of MJD/SCA3, only CRISPR-Cas9 system allowed the improvement of key neuropathological markers of the disease. Importantly, the administration of the engineered system in YAC-MJD84.2/84.2 mice mediated a delay in disease progression, when compared with non-treated littermates. These data provide the firstin vivoevidence of the efficacy of a CRISPR-Cas9-based approach to permanently inactivate theATXN3gene in the brain of two mouse models of the disease, supporting its potential as a new therapeutic avenue in the context of MJD/SCA3.
Decoding auditory working memory load from EEG alpha oscillations
Authors: Yuan Yichen , Gayet Surya , Wisman Derk Christiaan , van der Stigchel Stefan , van der Stoep Nathan 
Published: February 2025

AbstractWorking memory (WM) enables temporary retention of task-relevant information for imminent use. Increases in visual WM load are accompanied by elevated contralateral delay activity (CDA), and EEG alpha-band power. While most WM research focuses on the visual domain, it remains unknown whether similar EEG responses also reflect WM load in the auditory domain. Using EEG, we set out to establish such neuro-markers of auditory WM load. Participants memorized the pitches of 1 to 4 pure tones presented to one ear, with 1 to 4 consistent distractor tones presented to the other ear. Behaviorally, auditory WM capacity plateaued between set-sizes two and three. Unlike for visual WM, auditory WM load was not reflected in lateralized EEG responses. This shows that the CDA is a vision-specific rather than domain-general neuro-marker of WM load. Applying multivariate pattern analyses on the delay activity revealed that auditory WM load is reflected in (mostly temporal) patterns of alpha-band oscillations. Surprisingly, a temporal generalization analysis revealed that the alpha patterns reflecting specific load conditions changed throughout the maintenance period (despite load being inherently constant), revealing dynamic coding of auditory WM load.
Sex-related gut microbiota in three geographically separated Norway lobster (Nephrops norvegicus) populations
Authors: Rusanova Polina , Nikouli Eleni , Casini Michele , Bono Gioacchino , Mente Elena , Meziti Alexandra , Kormas Konstantinos 
Published: February 2025

ABSTRACTDespite the ecological and economic interest of the Norway lobster (Nephrops norvegicus), its gut microbiota remains largely understudied. The current study aimed at investigating the gut bacterial microbiota in three geographically separatedN. norvegicuspopulations from the Mediterranean and the North Sea and detect any potential sex-related microbiota differences, by high-throughput sequencing of the V3-V4 16S rRNA gene diversity of the gut tissue. From the Greek population, egg-bearing females were also caught. A total of 2,385 operational taxonomic units (OTUs) were identified and between 417 and 1290 occurred in each population/sex group. The dominant OTUs belonged to the Fusobacteriia and Bacteroidia (Sweden), Bacilli and Gammaproteobacteria (Italy) and Spirochaetia and Bacilli (Greece) classes. In the eggs, the Actinobacteria, Alphaproteobacteria and Gammproteobacteria prevailed. Four OTUs related to theOceanispirochaeta,Kordiimonas, Desulfovibrio, Carboxylicivirgagenera and one unafilliated OTU were positively correlated (p values between 0.001 and 0.04) to body size indicating their potential role in the animal’s nutrition and growth. No statistically significant differences were found between males-females in any of the populations. However, statistically significant differences between populations for each sex, were found for all females (p values between 0.008 and 0.032) and for the males between the most distant populations, i.e. Italy and Sweden (p=0.021) and, Greece and Sweden (p=0.015). The eggs microbiota was statistically different from both the adult females (p=0.027) and males (p=0.046) gut microbiota. Overall, this study showed thatN. norvegicusgut microbiota vary for each sex between geographically distant populations.
Zebra finches produce intralaryngeal laminar flow whistles during panting
Authors: Anttonen Tommi , Loning Hugo , Felbo Freja M. , Christensen-Dalsgaard Jakob , Griffith Simon C. , Naguib Marc , Elemans Coen P.H. 
Published: February 2025

SummaryBirds and mammals converged upon the same physical mechanism of vocal fold vibration to produce their broad range of voiced sounds critical to communication1. The frequency range of vocal fold vibration is limited per species by biophysical constraints to 3-4 octaves2. However, recent work reported vocalizations in zebra finches with apparent fundamental frequencies of 7-11 kHz3that far exceed the range of regular calls and song (0.5-1.5 kHz)4,5. These “heat” or “incubation” calls are suggested to have close-range communicative relevance in the global temperature rise context3,6, but their acoustics are poorly described and by what biophysical mechanism they are produced remains unknown. We recorded heat calls in adult zebra finchesin vivoand show they are extremely soft, frequency-modulated calls with source levels of 13.9 ± 3.3 dB SPL at one meter with dominant frequencies of 6.8 ± 0.6 kHz. Through a series ofin vitroexperiments, we establish that these calls are aerodynamic whistles produced inside the avian larynx, not syrinx, during inspiration. Respiratory air flow during whistle production is an order of magnitude higher than song and consistent with thermal panting for evaporative cooling6,7. Laryngeal geometry and dimensional flow analysis suggest that these whistles are laminar flow whistles that occur when a flow boundary layer is in a transition phase from laminar to turbulent flows8,9. Birds, like some rodents10-12, are thus able to produce both voiced sounds and aerodynamical whistles in their vocal tract.
LCLNCRdb: A Comprehensive Resource for Investigating long non-coding RNAs in Lung Cancer
Authors: Dwivedi Ayushi , Zulfia S Afrin , Thippana Mallikarjuna , Cholleti Sai Nikhith , Vindal Vaibhav 
Published: February 2025

AbstractLung cancer is a primary cause of death worldwide, accounting for a substantial number of mortalities. It involves several molecular mechanisms that are influenced by long non-coding RNAs (lncRNAs), a specific types of RNA molecules that do not code for proteins. Several research have revealed the importance of long non-coding RNAs (lncRNAs) in the initiation, progression, and development of resistance to lung cancer therapy. However, there are no centralized web resources or databases that collect and integrate information regarding lung cancer associated lncRNAs. This led to the development of the LCLNCRdb, a manually curated database that includes data from various sources, such as published research articles, and The Cancer Genome Atlas (TCGA) data portal. This database contains detailed information on 1102 lncRNAs that have differential expression patterns in lung cancer patients, such as lncRNA name, entrez ID, Ensemble ID, HGNC ID, NONCODE ID, lung cancer type, source, lncRNA expression pattern, experimental techniques, network analysis, and survival analysis details. The database offers a user-friendly platform for browsing, retrieving, and downloading data, and it features a dedicated submission page for researchers to share newly identified lncRNAs related to lung cancer. LCLNCRdb aims to enhance our knowledge of lncRNA deregulation in lung cancer and provides a valuable and timely resource for lncRNA research. The database is freely accessible at (https://dbtcmi.in/tools/lclncrdb/main.html).
Release of Flavonoids by the Soybean Cultivars McCall and Peking and Their Perception as Signals by the Nitrogen-Fixing SymbiontSinorhizobium fredii1
Authors: Pueppke Steven G. , Bolaños-Vásquez Maria Cristina , Werner Dietrich , Bec-Ferté Marie-Pierre , Promé Jean-Claude , Krishnan Hari B. 
Published: July 2002

Abstract
Sinorhizobium frediistrain USDA191 forms N-fixing nodules on the soybean (Glycine max L. Merr.) cultivars (cvs) McCall and Peking, but S. fredii strain USDA257 nodulates only cv Peking. We wondered whether specificity in this system is conditioned by the release of unique flavonoid signals from one of the cultivars or by differential perception of signals by the strains. We isolated flavonoids and usednodC and nolX, which arenod-box-dependent and -independent nodgenes, respectively, to determine how signals activate genes in the microsymbionts. Seeds of cv McCall and cv Peking contain the isoflavones daidzein, genistein, and glycitein, as well as their glucosyl and malonylglucosyl glycosides. Roots exude picomolar concentrations of daidzein, genistein, glycitein, and coumestrol. Amounts are generally higher in cv Peking than in cv McCall, and the presence of rhizobia markedly influences the level of specific signals. Nanomolar concentrations of daidzein, genistein, and coumestrol induce expression of nodC and nolX in strain USDA257, but the relative nolX-inducing activities of these signals differ in strain USDA191. Glycitein and the conjugates are inactive. Strain USDA257 deglycosylates daidzin and genistin into daidzein and genistein, respectively, thereby converting inactive precursors into active inducers. Although neither soybean cultivar contains unique nod-gene-inducing flavonoids, strain- and cultivar-specific interactions are characterized by distinct patterns of signal release and response.
Characterization of Spermidine Binding to Solubilized Plasma Membrane Proteins from Zucchini Hypocotyls1
Authors: Tassoni Annalisa , Antognoni Fabiana , Luisa Battistini Maria , Sanvido Olivier , Bagni Nello 
Published: July 2002

AbstractIn this work [14C]spermidine binding to total proteins solubilized from plasma membrane purified from zucchini (Cucurbita pepo L.) hypocotyls was investigated. Proteins were solubilized using octyl glucoside as a detergent. Specific polyamine binding was thermolabile, reversible, pH dependent with an optimum at pH 8.0, and had a Kd value of 5 μm, as determined by glass-fiber-filter assays. Sephadex G-25 M gel-filtration assays confirmed the presence of a spermidine-protein(s) complex with a specific binding activity. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and native polyacrylamide gel electrophoresis of collected fractions having the highest specific spermidine-binding activity, several protein bands (113, 75, 66, and 44 kD) were identified. The specificity of spermidine binding was examined by gel-filtration competition experiments performed using other polyamines and compounds structurally related to spermidine. Partial purification on Sephadex G-200 led to the identification of 66- and 44-kD protein bands, which may represent the putative spermidine-binding protein(s) on the plasmalemma.
Developmental and Light Regulation of Desacetoxyvindoline 4-Hydroxylase in Catharanthus roseus (L.) G. Don.1
Authors: Vazquez-Flota Felipe A. , De Luca Vincenzo 
Published: July 2002

Abstract
The expression of desacetoxyvindoline 4-hydroxylase (D4H), which catalyzes the second to the last reaction in vindoline biosynthesis inCatharanthus roseus, appears to be under complex, multilevel developmental and light regulation. Developmental studies with etiolated and light-treated seedlings suggested that although light had variable effects on the levels of d4htranscripts, those of D4H protein and enzyme activity could be increased, depending on seedling development, up to 9- and 8-fold, respectively, compared with etiolated seedlings. However, light treatment of etiolated seedlings could stop and reverse the decline ofd4h transcripts at later stages of seedling development. Repeated exposure of seedlings to light was also required to maintain the full spectrum of enzyme activity observed during seedling development. Further studies showed that a photoreversible phytochrome appeared to be involved in the activation of D4H, since red-light treatment of etiolated seedlings increased the detectable levels ofd4h transcripts, D4H protein, and D4H enzyme activity, whereas far-red-light treatment completely reversed this process. Additional studies also confirmed that different major isoforms of D4H protein exist in etiolated (isoelectric point, 4.7) and light-grown (isoelectric point, 4.6) seedlings, suggesting that a component of the light-mediated activation of D4H may involve an undetermined posttranslational modification. The biological reasons for this complex control of vindoline biosynthesis may be related to the need to produce structures that could sequester away from cellular activities the cytotoxic vinblastine and vincristine dimers that are derived partially from vindoline.
Distinct Calcium Signaling Pathways Regulate Calmodulin Gene Expression in Tobacco
Authors: van der Luit Arnold H. , Olivari Claudio , Haley Ann , Knight Marc R. , Trewavas Anthony J. 
Published: July 2002

AbstractCold shock and wind stimuli initiate Ca2+ transients in transgenic tobacco (Nicotiana plumbaginifolia) seedlings (named MAQ 2.4) containing cytoplasmic aequorin. To investigate whether these stimuli initiate Ca2+ pathways that are spatially distinct, stress-induced nuclear and cytoplasmic Ca2+ transients and the expression of a stress-induced calmodulin gene were compared. Tobacco seedlings were transformed with a construct that encodes a fusion protein between nucleoplasmin (a major oocyte nuclear protein) and aequorin. Immunocytochemical evidence indicated targeting of the fusion protein to the nucleus in these plants, which were named MAQ 7.11. Comparison between MAQ 7.11 and MAQ 2.4 seedlings confirmed that wind stimuli and cold shock invoke separate Ca2+ signaling pathways. Partial cDNAs encoding two tobacco calmodulin genes, NpCaM-1 andNpCaM-2, were identified and shown to have distinct nucleotide sequences that encode identical polypeptides. Expression ofNpCaM-1, but not NpCaM-2, responded to wind and cold shock stimulation. Comparison of the Ca2+dynamics with NpCaM-1 expression after stimulation suggested that wind-induced NpCaM-1 expression is regulated by a Ca2+ signaling pathway operational predominantly in the nucleus. In contrast, expression ofNpCaM-1 in response to cold shock is regulated by a pathway operational predominantly in the cytoplasm.
Identification by Large-Scale Screening of Phytochrome-Regulated Genes in Etiolated Seedlings of Arabidopsis Using a Fluorescent Differential Display Technique
Authors: Kuno Norihito , Muramatsu Takamichi , Hamazato Fumiaki , Furuya Masaki 
Published: July 2002

Abstract
Phytochrome A (PhyA)-regulated genes in 6-d-old etiolated seedlings of Arabidopsis Landsbergerecta were identified by fluorescent differential display. To screen for PhyA-regulated genes, mRNA fingerprints of the wild type and the phyA-201 mutant were compared from samples prepared 4 h after far-red light irradiation. Approximately 30,000 bands of cDNA were displayed by fluorescent differential display, and 24 differentially expressed bands were observed. Sequence analysis revealed that they represent 20 distinct genes. Among them, 15 genes were confirmed as PhyA regulated by northern-blot (or reverse transcription-polymerase chain reaction) analysis. Thirteen up-regulated genes included 12 known genes that encode nine photosynthetic proteins, two enzymes involved in the biosynthesis of chlorophyll, one DNA damage repair/toleration-related protein, and one unknown gene. Two down-regulated genes were identified as encoding a xyloglucan endotransglycosylase-related protein and a novel member of the ASK protein kinase family. In thephyA-201 mutant and the phyA-201phyB-1double mutant, expression of all of these genes was photoreversibly up- or down-regulated by type II phytochromes. The results indicate that modes of photoperception differ between PhyA and PhyB, but that both types of phytochromes have overlapping effects on the photoregulation of gene expression.