bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous oxycodone withdrawal disrupts sleep, circadian, and electrophysiological dynamics in rats
Authors: Gulledge M , Carlezon WA , McHugh R Kathryn , Prerau M. , Chartoff EH 
Published: January 2024

AbstractOpioid dependence is defined by an aversive withdrawal syndrome upon drug cessation that can motivate continued drug-taking, development of opioid use disorder, and precipitate relapse. An understudied but common opioid withdrawal symptom is disrupted sleep, reported as both insomnia and daytime sleepiness. Despite the prevalence and severity of sleep disturbances during opioid withdrawal, there is a gap in our understanding of their interactions. The goal of this study was to establish an in-depth, temporal signature of spontaneous oxycodone withdrawal effects on the circadian composition of discrete sleep stages and the dynamic spectral properties of the electroencephalogram (EEG) signal in male rats. We continuously recorded EEG and electromyography (EMG) signals for 8 d of spontaneous withdrawal after a 14-d escalating-dose oxycodone regimen (0.5 - 8.0 mg/kg, 2×d; SC). During withdrawal, there was a profound loss and gradual return of circadian structure in sleep, body temperature, and locomotor activity, as well as increased sleep and wake fragmentation dependent on lights on/off. Withdrawal was associated with significant alterations in the slope of the aperiodic 1/f component of the EEG power spectrum, an established biomarker of arousal level. Early in withdrawal, NREM exhibited an acute flattening and return to baseline of both low (1-4 Hz) and high (15-50 Hz) frequency components of the 1/f spectrum. These findings suggest temporally dependent withdrawal effects on sleep, reflecting the complex way in which the allostatic forces of opioid withdrawal impinge upon sleep and circadian processes. These foundational data based on continuous tracking of nocturnal rhythms, sleep stage composition, and spectral EEG properties provide a detailed construct with which to form and test hypotheses on the mechanisms of opioid-sleep interactions.
Changes in neural progenitor lineage constituent during astrocytic differentiation of human iPSCs
Authors: Li Zongze , Cardo Lucia Fernandez , Rokicki Michal , Monzón-Sandoval Jimena , Volpato Viola , Wessely Frank , Webber Caleb , Li Meng 
Published: January 2024

AbstractThe regional specificity of stem cell-derived astrocytes is believed to be an important prerequisite for their application in disease modelling and cell-based therapies. Due to the lack of subtype-defining markers for astrocytes in different regions of the brain, the regional identity ofin vitro-derived astrocytes is often declared by the dominant positional characteristics of their antecedent neural progenitors, patterned to a fate of interest, with the assumption that the positional trait is preserved by the derived astrocytes via linear descent. Using a human induced pluripotent stem cell line designed for tracing derivatives of LMX1A+cells combined with a ventral midbrain induction paradigm, we show that astrocytes originating from LMX1A+progenitors can only be generated if these progenitors are purified prior to the astrocyte differentiation process, or their progenies are gradually lost to progenies of LMX1A-progenitors. This finding indicates that the lineage composition of iPSC-derived astrocytes may not accurately recapitulate the founder progenitor population. Using deep single-cell RNA sequencing, we identified distinct transcriptomic signatures in astrocytes derived from the LMX1A+progenitor cells. Our study highlights the need for rigorous characterization of pluripotent stem cell-derived regional astrocytes, and provides a resource for assessing LMX1A+ventral midbrain progenitor-derived human astrocytes.
MetaIBS - large-scale amplicon-based meta analysis of irritable bowel syndrome
Authors: Carcy Salomé , Ostner Johannes , Tran Viet , Menden Michael , Müller Christian L. 
Published: January 2024

AbstractBackgroundIrritable Bowel Syndrome (IBS) is a chronic functional bowel disorder causing abdominal discomfort, as well as transit deregulation with constipation and/or diarrhea. The pathophysiology of IBS is poorly understood and believed to be multifactorial. The role of gut microbiota in IBS has been investigated in several case-control studies, in particular via 16S rRNA amplicon sequencing surveys. These studies, however, have not yet led to a consistent picture of significant changes in gut microbial compositions across health and disease. One key bottleneck is the modest cohort sizes of most individual studies and a high diversity of experimental, bioinformatics, and statistical analysis approaches across studies.ResultsWe address these shortcomings by presenting MetaIBS, an open-access data repository and associated meta-analysis workflow of thirteen 16S rRNA amplicon datasets comprising both fecal matter and sigmoid biopsy samples spanning ∽2,500IBS and healthy individuals. MetaIBS includes a tailored computational framework that (i) enables coherentde novoprocessing and taxonomic assignments of the raw 16S rRNA amplicon reads across experimental protocols and sequencing technologies, and (ii) statistical workflows for visualization and analysis at different taxonomic ranks and data granularity. Our statistical meta-analysis shows that popular high-level microbiome summary statistics, including Firmicutes/Bacteroidota ratios or diversity indices, are insufficient for reliable discrimination between IBS patients and healthy controls. Fine-grained multi-method differential abundance and classification analysis, however, can identify sets of differentially abundant taxa that replicateacross multiple datasets, includingCoprococcus eutactusandAlistipes finegoldii.ConclusionsMetaIBS provides a curated and reproducible data and (meta-)analysis resource for amplicon-based IBS research at unprecedented scale. MetaIBS allows assessing the heterogeneity of IBS cohorts across multiple experimental protocols, sample types, and IBS phenotypes. Our framework will likely contribute to more coherent insights into the role of the microbiome in IBS and the discovery of reliable microbial IBS biomarkers for follow-up functional and translational studies.
Intensive environmental sampling and whole genome sequence-based characterization ofListeriain small and medium sized dairy plants reveal opportunities for simplified and size-appropriate environmental monitoring strategies
Authors: Bolten Samantha , Lott Timothy T. , Ralyea Robert D. , Gianforte Anika , Trmcic Aljosa , Orsi Renato H. , Martin Nicole H. , Wiedmann Martin 
Published: January 2024

ABSTRACTSmall and medium sized dairy processing plants (SMDPs) may face unique challenges with respect to controllingListeriain their processing environments, e.g., due to limited resources. The aim of this study was to implement and evaluate environmental monitoring programs (EMPs) forListeriacontrol in eight SMDPs in a ∼1-year longitudinal study; this included a comparison of pre-operation (i.e., after cleaning and sanitation and prior to production) and mid-operation (i.e., at least 4 h into production) sampling strategies. Among 2,072 environmental sponge samples collected across all plants, 272 (13%) were positive forListeria.Listeriaprevalence among pre- and mid-operation samples (15 and 17%, respectively), was not significantly different. Whole genome sequencing (WGS) performed on select isolates to characterizeListeriapersistence patterns revealed repeated isolation of closely relatedListeriaisolates (i.e., ≤20 high quality single nucleotide polymorphism [hqSNP] differences) in 5/8 plants over >6 months, suggestingListeriapersistence and/or re-introduction was relatively common among the SMDPs evaluated here. WGS furthermore showed that for 41 sites where samples collected pre- and mid- operation were positive forListeria,Listeriaisolates obtained were highly related (i.e., ≤10 hqSNP differences), suggesting that pre-operation sampling alone may be sufficient and more effective for detecting sites ofListeriapersistence. Importantly, our data also showed that only 1/8 plants showed a significant decrease inListeriaprevalence over 1 year, indicating continued challenges withListeriacontrol in at least some SMDPs. We conclude that options for simplifiedListeriaEMP programs (e.g., with a focus on pre-operation sampling, which allows for more rapid identification of likely persistence sites) may be valuable for improvedListeriacontrol in SMDPs.
Subthalamic nucleus activity dynamics preceding clinical manifestations in a progressive Parkinson’s disease model
Authors: Bertrand Mathilde , Chabardes Stephan , De Leiris Nicolas , Reboulet Ghislaine , Baudin Bruno , Bastin Julien , Piallat Brigitte 
Published: January 2024

ABSTRACTBackgroundParkinson’s disease (PD) diagnosis relies on motor symptoms such as akinesia, rigidity, and tremor, which manifest late in the disease course, contributing to delayed diagnosis. However, cognitive, and limbic manifestations may precede motor symptoms, offering an earlier diagnostic opportunity, but their early kinetics require further characterization. Although high frequency deep brain stimulation (DBS) of the subthalamic nucleus (STN) significantly improves motor symptoms, it does not specifically address non-motor symptoms. Here, we aimed to correlate STN activity with the onset of motor, cognitive, and limbic symptoms of PD and propose specific STN-DBS paradigm to address both motor and non-motor symptoms.MethodsLocal field potentials of the STN were recorded in two non-human primates (Macaca fascicularis) performing a behavioral task assessing motor, cognitive, and limbic reward-related behaviors. A progressive model of PD, consisting of small injections of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP, 0.2-0.5mg/kg), was used to characterize behavior for several months until the onset of motor symptoms. Finally, when a stable parkinsonian syndrome was established, the behavioral effects of high- (HFS, 130Hz) and low- (LFS, 4Hz) frequency stimulations were investigated.ResultsAfter the first MPTP injections, we observed a progressive parkinsonian syndrome from stage 1, asymptomatic, to stage 3 with limbic, cognitive, and motor symptoms. Each stage was associated with specific changes in STN electrophysiological activity. Stage 1 was characterized by a decrease in the power of reward-related gamma/theta oscillations. Stage 2 featured an early decline in motivation and decreased theta-band activity during decision-making. Later, an increase in error on Switch trials was observed, illustrating the stage 2’, along with a decrease in beta-gamma power following movement. Finally, stage 3 was defined by an increase in motor response time while maintaining all the STN neuronal changes. In stage 3, HFS applied in dorsal STN improved motor reaction time, while LFS applied in ventral STN improved motivation.ConclusionOur results highlight a progressive timeline in the onset of behavioral parkinsonian manifestations, with limbic symptoms followed by cognitive and then motor symptoms. We identified specific electrophysiological biomarkers in the STN correlating with and preceding the onset of each symptom, providing insights into their pathophysiology. Finally, our results suggest that combined stimulation of HFS in the dorsal STN and LFS in the ventral STN may optimize STN-DBS outcomes, reducing both motor and non-motor symptoms.
Phenotypic screening of covalent compound libraries identifies chloromethyl ketone antibiotics and MiaA as a new target
Authors: Jin Yizhen , Jana Sadhan , Abbasov Mikail E. , Lin Hening 
Published: January 2024

AbstractThe emerging antibiotic resistance requires the development of new antibiotics working on novel bacterial targets. Here, we reported an antibiotic discovery workflow by combining the cysteine-reactive compound library phenotypic screening with activity-based protein profiling, which enables the rapid identification of lead compounds as well as new druggable targets in pathogens. Compounds featuring chloromethyl ketone scaffolds exhibited a notably high hit rate against both gram-negative and gram-positive bacterial strains, but not the more commonly used warheads such as acrylamide or chloroacetamide. Target identification of the lead compound, 10-F05, revealed that its primary targets inS. flexneriare FabH Cys112 and MiaA Cys273. We validated the target relevance through biochemical and genetic interactions. Mechanistic studies revealed modification of MiaA by 10-F05 impair substrate tRNA binding, leading to decreased bacterial stress resistance and virulence. Our findings underscore chloromethyl ketone as a novel antibacterial warhead in covalent antibiotic design. The study showcases that combining covalent compound library phenotypic screening with chemoproteomics is an efficient way to identify new drug targets as well as lead compounds, with the potential to open new research directions in drug discovery and chemical biology.Graphic Abstract
Reanalysis of published histological data can help to characterize neuronal death after Spinal Cord Injury
Authors: Amezcua Pablo Ruiz , Barranco Nadia Ibáñez , Reigada David , Novillo Algaba Irene , Soto Altea , Barreda-Manso M. Asunción , Galdeano Teresa Muñoz- , Maza Rodrigo M. , Esteban Francisco J. , Nieto Díaz Manuel 
Published: January 2024

ABSTRACTSpinal cord injury (SCI) is a disabling disorder of the spinal cord resulting from trauma or disease. Neuronal death is a central event in the pathophysiology of spinal cord injury. Despite its importance and the large number of research studies carried out, we only have a fragmentary vision of the process focused on the specific targets of each study. It is our opinion that the research community has accumulated enough information which may be reanalyzed with novel tools to get a much more detailed, integrated vision of neuronal death after SCI. This work embeds this vision by creating NeuroCluedo, an open data repository to store and share images as well as the results from their analysis. We have employed this repository to upload the raw and processed images of spinal cord sections from a mouse model of moderate contusive SCI (Reigada et al., 2015) and used this information to: compare manual-, threshold-, and neuronal network-based neuron identifications; and to explore neuronal death at the injury penumbra 21 days after injury and the neuroprotective effects of the anti-apoptotic drug ucf-101. The results from these analyses i) indicate that the three identification methods yield coherent estimates of the total number of neurons per section; ii) identified the neural network as the optimal method, even in spinal sections with major artifacts and marked autofluorescence associated with spinal damage; iii) characterize neuronal distribution among Rexed laminae in the mice T11; iv) reveal that neuronal death distributes through all the gray matter in the penumbrae sections closer to the injury epicenter but concentrate in the intermediate region in sections located farther away; and that v) antiapoptotic effects of UCF-101 are highest in the intermediate region of the gray substance of the caudal segments closest to the injury epicenter. All methods and results, including raw and processed images, software, macros, and scripts, together with all data matrixes and results have been deposited and documented in the Open Science Framework (OSF) repository Neurocluedo (https://osf.io/n32z9/).
EXO1-mediated ssDNA gap expansion is essential for ATR activation and to maintain viability in BRCA1-deficient cells
Authors: García-Rodríguez Néstor , Domínguez-Pérez María del Carmen , Huertas Pablo 
Published: January 2024

ABSTRACTDNA replication faces challenges from DNA lesions originated from endogenous or exogenous sources of stress, leading to the accumulation of single-stranded DNA (ssDNA) that triggers the activation of the ATR checkpoint response. To complete genome replication in the presence of damaged DNA, cells employ DNA damage tolerance mechanisms that operate not only at stalled replication forks but also at ssDNA gaps originated by repriming of DNA synthesis downstream of lesions. Here, we demonstrate that human cells accumulate post-replicative ssDNA gaps following replicative stress induction. These gaps, initiated by PrimPol repriming and expanded by the long-range resection factors EXO1 and DNA2, constitute the principal origin of the ssDNA signal responsible for ATR activation upon replication stress, in contrast to stalled forks. Furthermore, we show that EXO1-deficient cells exhibit marked sensitivity to translesion synthesis inhibition, a distinctive characteristic of mutations in proteins essential for repairing ssDNA gaps via template switching, such as BRCA1/2. Strikingly, EXO1 loss results in synthetic lethality when combined with BRCA1 deficiency, but not BRCA2. Indeed, BRCA1-deficient cells become addicted to the overexpression ofEXO1 DNA2orBLM. This dependence on long-range resection unveils a new vulnerability of BRCA1-mutant tumors, shedding light on potential therapeutic targets for these cancers.
Interaction of adenylate cyclase CyaC with regulators Smc01817 and Clr ofSinorhizobium meliloti: cAMP as an ON/OFF trigger in sensor-regulator complexes?
Authors: Klein Robin , Wissig Juliane , Küllmer Katharina , Unden Gottfried 
Published: January 2024

AbstractThe symbiotic bacteriumSinorhizobium meliloticontains a large number of adenylate cyclases (AC) for the control of different life styles. ACs produce cyclic AMP (cAMP) as a secondary messenger. Earlier, the redox responsive membrane-intrinsic AC CyaC has been shown to produce a trimeric signalling complex CyaC×CycR×cAMP-Clr. Here, use of the bacterial two-hybrid system BACTH showed that the LysR-type transcriptional regulator Smc01817 interactsin vivowith CyaC and the general cAMP-regulator Clr, suggesting the formation of a sensor-regulator complex CyaC×Smc01817×cAMP-Clr. Therefore, formation of sensor-regulator complexes from ACs and transcriptional regulators seems to be a means inS. melilotito setup specific signalling routes in a background with a large number of signalling routes applying the same signalling molecule (cAMP). Use of caged cAMP allows to address a specific signalling route and set of regulators, which is at variance with the classical role of cAMP as a diffusing secondary messenger.
Development of blood-cerebrospinal fluid barrier model expressing pharmaceutically important transporters
Authors: Majerova Petra , Khiratkar Krutika , James Kevin , Olesova Dominika , Vegh Jozef , Kovac Andrej 
Published: January 2024

AbstractWe have established and optimized a protocol for the high-yield isolation of primary epithelial cells from rat choroid plexus. The addition of cytosine arabinoside suppressed the growth of contaminating cells, and epithelial culture was grown into a confluent impermeable monolayer within 5-6 days after seeding. To form anin vitroblood-CSF barrier, epithelial cells were plated on inverted coated polycarbonate support of Transwell inserts. Morphologically, the polarized cells remained cuboidal in shape and expressed TJ proteins at a high rate. The filter-grown monolayers displayed transendothelial resistance (TEER) values in the range of 160 to 180 Ω × cm2and remained at this level for 3 days, indicating the persistent formation of continuous TJs. The cells were able to secrete cerebrospinal fluid (CSF) actively. Epithelial cells showed expression of selective influx and efflux transporters. To conclude, our BCSFB model exhibits tight, functional barrier characteristics and shows the functional expression of the pharmaceutically important influx/efflux transporters. The recent model is suitable forin vitroinvestigations of BCSFB and routine pre-clinical drug discovery.
Molecular Cloning and Biochemical Characterisation of a Novel Acidic Laminarinase Derived from Jermuk Hot Spring Metagenome
Authors: Paloyan Ani , Karapetyan Mariam , Grigoryan Hasmik , Krüger Anna , Burkhardt Christin , Antranikian Garabed 
Published: January 2024

AbstractLaminarinase, an enzyme with a specific affinity for laminarin—a complex polysaccharide found in the cell walls of brown algae and select marine organisms—was investigated in this study. We cloned and characterised a gene encoding a putative glycoside hydrolase family 16 (GH16) laminarinase from the Jermuk hot spring metagenome by heterologous expression inEscherichia coli. The resulting product, named Jermuk-LamM, represents a novel endo-1,3-β-D-glucanase (EC 3.2.1.39) with only 48.1 % amino acid sequence similarity to previously characterised GH16 family members catalogued in the NCBI database. To date, this stands as the sole described endo-1,3-β-D-glucanase within theMarinimicrobiaphylum.Jermuk-LamM, identified as an acidic laminarinase, exhibits robust enzymatic activity at pH 5.0 and a temperature of 55 °C, maintaining its function for a duration of at least 7 hours. Notably, this enzyme effectively catalyses the hydrolysis of both soluble and insoluble (1,3)-β-D-glucans, as well as (1,3;1,4)-β-D-glucans, displaying a pronounced preference for laminarin. The specificity of Jermuk-LamM lies in its cleavage of 1,3-β-D-glucosidic linkages, yielding monosaccharides, disaccharides, and oligosaccharides. These breakdown products hold the potential for conversion into energy carriers, including alcohols, methane, and hydrogen.The enzyme’s exceptional specific activities, coupled with its resistance to various additives, render Jermuk-LamM a promising candidate for various industrial applications, encompassing the realms of biofuel and pharmaceutical production.
Perturbing nuclear glycosylation in the mouse preimplantation embryo slows down embryonic growth
Authors: Formichetti Sara , Chitnavis Urvashi , Sadowska Agnieszka , Liu Na , Boskovic Ana , Boulard Matthieu 
Published: January 2024

SummaryThe only known form of intracellular protein glycosylation (O-GlcNAc) is reversible and has been mapped on thousands of cytoplasmic and nuclear proteins, including RNA polymerase II, transcription factors and chromatin modifiers. The O-GlcNAc modification is catalyzed by a single enzyme known as O-GlcNAc Transferase (OGT), that is required for mammalian early development. Remarkably, the regulatory function of protein O-GlcNAcylation in the embryo as well as the embryonic O-GlcNAc proteome remain unknown. Here, we devised a new method to enzymatically remove O-GlcNAc from preimplantation embryonic nuclei, where it accumulates coincidently with embryonic genome activation (EGA). Unexpectedly, the depletion of nuclear O-GlcNAc to undetectable levels has no impact on EGA, but dampens the transcriptional activation of the translational machinery, and triggers a spindle checkpoint response. These molecular alterations were phenotypically associated with a developmental delay starting from early cleavage stages and persisting after embryo implantation, establishing a novel link between nuclear glycosylation and embryonic growth.