bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hackflex library preparation enables low-cost metagenomic profiling
Authors: Goldman Samantha L. , Sanders Jon G. , Sprockett Daniel D. , Landers Abigail , Yan Weiwei , Moeller Andrew H. 
Published: April 2024

AbstractShotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.
Phages indirectly maintain plant pathogen defense through regulation of the commensal microbiome
Authors: Debray Reena , Conover Asa , Koskella Britt 
Published: April 2024

ABSTRACTMany infectious diseases are associated with altered communities of bacteriophage viruses (phages). As parasites of bacteria, phages can regulate microbiome diversity and composition and may therefore affect disease susceptibility. Yet observational studies alone do not allow us to determine whether altered phage profiles are a contributor to disease risk, a response to infection, or simply an indicator of dysbiosis. To address this question, we used size-selective filtration to separate plant-associated microbial communities from their respective phages, then transplanted them together or separately onto tomato plants that we subsequently challenged with the bacterial pathogenPseudomonas syringae. Microbial and phage communities together were more disease-protective than either component was alone, an effect that could not be explained by direct effects of phages on eitherP. syringaeor the plant host. Moreover, the protective effect of phages was strongest when microbial and phage communities were isolated from neighboring field locations (allopatric phages), rather than from the same host plant (sympatric phages). This suggests a Goldilocks effect in which moderate rates of phage lysis maintain a microbiome community structure that is most resistant to pathogen invasion. Overall, our results support the idea that phage communities contribute to plant defenses by modulating the microbiome.
The robust, high-throughput, and temporally regulated roxCre and loxCre reporting systems for genetic modificationsin vivo
Authors: Shi Mengyang , Li Jie , Liu Xiuxiu , Liu Kuo , He Lingjuan , Pu Wenjuan , Weng Wendong , Zhang Shaohua , Zhao Huan , Lui Kathy O. , Zhou Bin 
Published: April 2024

AbstractCre-loxP technology, a cornerstone in fate mapping andin vivogene function studies, faces challenges in achieving precise and efficient conditional mutagenesis through inducible systems. This study introduces two innovative genetic tools designed to overcome these limitations. The first, roxCre, enables DreER-mediated Cre release, paving the way for intersectional genetic manipulation that permits increased precision and efficiency. The second, loxCre, facilitates conditional gene targeting by allowing any CreER line to induce Cre expression with significantly enhanced efficiency. These tools incorporate a fluorescent reporter for genetic lineage tracing, simultaneously revealing efficient gene knockout in cells marked by the reporter. These strategies hold great potential for precise and efficient exploration of lineage-specific gene functions, marking a significant advancement in genetic research methodologies.
First application of digital-PCR in oenology for the specific detection of intact cells ofBrettanomyces bruxellensisin the winemaking process
Authors: Gruet Cécile , Mattia Jérémy Di , Hiaumet Magali , Pestel Dylan , Araiz Caroline , Saadi Sarah , Ducousso Marie , Courot Olivier 
Published: April 2024

AbstractWine is a complex matrix resulting from a fermentation process carried out by specific microbial communities. These communities can be in competition and the development of some microorganisms, as the yeastBrettanomyces bruxellensis, can impact the fermentation process and lead to organoleptic alterations of wine. To manage this risk, microbiological diagnostic methods as microscopic observations, qPCR or flow cytometry are already used in oenology, but remain either not specific enough, or tedious. In this context, IAGE (Ingénierie et Analyses en Génétique Environnementale) has developed the first digital-PCR system enabling the detection and quantification ofB. bruxellensisduring the whole winemaking process. Furthermore, wine DNA extraction was optimized to enable a representative and sensitive analysis ofB. bruxellensisintact cells, as well as an easy-to-implement protocol to cope with the increasing number of samples to analyze. The IAGE workflow forB. bruxellensisquantification has been proven to be successful when analyzing naturally-contaminated samples during the different steps of the winemaking process and offers a robust method to oenologists for appropriate treatments and risk management in wine cellars.HighlightsDevelopment of a dPCR method led to a highly-specific analysis ofB. bruxellensisintact cells in different steps of the winemaking process.DNA extraction method has been optimized to be robust across various types of wine with varying concentrations of inhibitors, as well as throughout different stages of the wine making process.The complete process was proven successful in analyzing a large number of naturally-contaminated samples, giving results in less than 48 hours.
Anatomical circuits for flexible spatial mapping by single neurons in posterior parietal cortex
Authors: Ahmed Bashir , Ko Hee Kyoung , Rüsseler Maria , Smith Jackson E. T. , Krug Kristine 
Published: April 2024

AbstractPrimate lateral intraparietal area (LIP) is critical for cognitive processing. Its contribution to categorization and decision-making has been causally linked to neurons’ spatial sensorimotor selectivity. We reveal the intrinsic anatomical circuits and neuronal responses within LIP that provide the substrate for this flexible generation of motor responses to sensory targets. Retrograde tracers delineate a loop between two distinct operational compartments, with a sensory-like, point-to-point projection from ventral to dorsal LIP and an asymmetric, more widespread projection in reverse. Neurophysiological recordings demonstrate that especially more ventral LIP neurons exhibit motor response fields that are spatially distinct from its sensory receptive field. The different associations of response and receptive fields in single neurons tile visual space. These anatomical circuits and neuronal responses provide the basis for the flexible allocation of attention and motor responses to salient or instructive visual input across the visual field.
Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects
Authors: Parajuli Anirudra , Mäkela Iida , Roslund Marja I. , Ringqvist Emma , Manninen Juulia , Sun Yan , Nurminen Noora , Oikarinen Sami , Laitinen Olli H. , Hyöty Heikki , Flodström-Tullberg Malin , Sinkkonen Aki 
Published: April 2024

AbstractReduced contact with the microbiota from the natural environment has been suggested to contribute to the rising incidence of immune-mediated inflammatory disorders (IMIDs) in the western, highly urbanized societies. In line with this, we have previously shown that exposure to environmental microbiota in the form of a blend comprising of soil and plant-based material (biodiversity blend; BDB) enhances the diversity of human commensal microflora and promotes immunoregulation that may be associated with a reduced risk for IMIDs. To provide a framework for future preclinical studies and clinical trials, this study describes how the preparation of BDB was standardized, its microbial content and safety assessments. Multiple batches of BDB were manufactured and microbial composition analyzed using 16S rRNA gene sequencing. We observed a consistently high alpha diversity and relative abundance of bacteria normally found in soil and vegetation. We also found that inactivation of BDB by autoclaving effectively inactivates human and murine bacteria, viruses and parasites. Finally, we demonstrate that experimental mice prone to develop IMIDs (non-obese diabetic, NOD, mouse model) can be exposed to BDB without causing adverse effects on animal health and welfare. Our study lays the foundation for a safe, sustainable, and affordable way to mimic exposure to natural microbiota that has the potential to have enormous health- and socio-economic impacts.
Cell-type aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plantCatharanthus roseus
Authors: Li Chenxin , Colinas Maite , Wood Joshua C. , Vaillancourt Brieanne , Hamilton John P. , Jones Sophia L. , Caputi Lorenzo , O’Connor Sarah E. , Buell C. Robin 
Published: April 2024

AbstractIn plants, the biosynthetic pathways of some specialized metabolites are partitioned into specialized or rare cell types, as exemplified by the monoterpenoid indole alkaloid (MIA) pathway ofCatharanthus roseus(Madagascar Periwinkle), the source of the anti-cancer compounds vinblastine and vincristine. In the leaf, theC. roseusMIA biosynthetic pathway is partitioned into three cell types with the final known steps of the pathway expressed in the rare cell type termed idioblast. How cell-type specificity of MIA biosynthesis is achieved is poorly understood. Here, we generated single-cell multi-omics data fromC. roseusleaves. Integrating gene expression and chromatin accessibility profiles across single cells, as well as transcription factor (TF) binding site profiles, we constructed a cell-type-aware gene regulatory network for MIA biosynthesis. We showcased cell-type-specific transcription factors as well as cell-type-specificcis-regulatory elements. Using motif enrichment analysis, co-expression across cell types, and functional validation approaches, we discovered a novel idioblast specific TF (IdioblastMYB1, CrIDM1) that activates expression of late stage vinca alkaloid biosynthetic genes in the idioblast. These analyses not only led to the discovery of the first documented cell-type-specific TF that regulates the expression of two idioblast specific biosynthetic genes within an idioblast metabolic regulon, but also provides insights into cell-type-specific metabolic regulation.
The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell
Authors: Andreas Michael P. , Giessen Tobias W. 
Published: April 2024

AbstractTerpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacteriumStreptomyces griseus. Here, we revise the function of EshA, now referred to asSgEnc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find thatSgEnc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein.SgEnc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show thatSgEnc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity andSgEnc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.
Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states
Authors: MacTavish Brian , Zhu Di , Shang Jinsai , Shao Qianzhen , Yang Zhongyue J. , Kamenecka Theodore M. , Kojetin Douglas J. 
Published: April 2024

ABSTRACTNuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.
Ribosome Profiling Reveals Translational Reprogramming via mTOR Activation in Omacetaxine Resistant Multiple Myeloma
Authors: Walker Zachary J. , Vaeth Katherine F. , Baldwin Amber , Ohlstrom Denis J. , Reiman Lauren T. , Idler Beau M. , Stevens Brett M. , Mukherjee Neelanjan , Sherbenou Daniel W. 
Published: April 2024

ABSTRACTProtein homeostasis is critical to the survival of multiple myeloma (MM) cells. While this is targeted with proteasome inhibitors, mRNA translation inhibition has not entered trials. Recent work illustrates broad sensitivity MM cells to translation inhibitor omacetaxine. We hypothesized that understanding how MM cells become omacetaxine resistant will lead to the development of drug combinations to prevent or delay relapse. We generated omacetaxine resistance in H929 and MM1S MM cell lines and compared them to their parental lines. Resistant lines displayed decreased sensitivity to omacetaxine, with EC50 > 100 nM, compared to parental line sensitivity of 24-54 nM. To adapt to omacetaxine, H929 and MM1S exhibited an increased percentage of multi-nucleated polyaneuploid cells that led to distinct molecular mechanisms of resistance. Interestingly, both resistant lines showed a defect in oncologic potential via extended survival in a MM xenograft model. Since omacetaxine inhibits protein synthesis, we performed both RNA-sequencing and ribosome profiling (Ribo-seq) to identify shared and unique regulatory strategies of resistance. Transcripts encoding translation factors and containing Terminal OligoPyrimidine (TOP) motifs in their 5’ UTR were translationally upregulated in both resistant cell lines. The mTOR pathway promotes the translation of TOP motif containing mRNAs. Indeed, mTOR inhibition restored partial sensitivity to omacetaxine in both resistant cell lines. Primary MM cells from patient samples were sensitive to combinations of omacetaxine and mTOR inhibitors rapamycin and Torin 1. These results provide a rational approach for omacetaxine-based combination in patients with multiple myeloma, which have historically shown better responses to multi-agent regimens.
eXtended Reality Enhanced Mental Health Consultation Training
Authors: Hiley Katherine , Mohammad Zanib Bi , Taylor Luke , Dawson Rebecca Burgess- , Patterson Dominic , Puttick Devon , Gay Chris , Hiscoe Janette , Munsch Chris , Richardson Sally , Knowles-Lee Mark , Beecham Celia , Ralph Neil , Chatterjee Arunangsu , Mathew Ryan K , Mushtaq Faisal 
Published: April 2024

AbstractObjectivesGiven the growing societal and healthcare service need for trained mental health and care workers, coupled with the heterogeneity of exposure during training and the shortage of placement opportunities, we explored the feasibility and utility of a novel XR tool for mental health consultation training.DesignEvaluation of a novel XR training simulation for mental health consultation.SettingMental health and primary care training environments. Including Universities and NHS hospitals.ParticipantsA total of 123 participants completed the study, including Mental Health Nursing trainees, General Practitioner Doctors in Training, and students in psychology and medicine.InterventionsWe set out to evaluate a training simulation created through a collaboration between software developers, clinicians and learning technologists. Participants engaged with a virtual patient, ‘Stacey’, through a virtual reality or augmented reality head-mounted display. The tool was designed to provide trainee healthcare professionals with an immersive experience of a consultation with a patient presenting with perinatal mental health symptoms. Users verbally interacted with the patient, and a human instructor selected responses from a repository of pre-recorded voice-acted clips.Primary and Secondary Outcome MeasuresThe primary outcomes were cognitive and affective learning outcomes, including understanding, motivation, and anxiety related to mental health consultations. Secondary outcomes were considerations towards careers in perinatal mental health, experiences of presence, system usability.ResultsWe found significant enhancements in learning metrics across all participant groups. Notably, there was a marked increase in understanding (p<.001) and motivation (p<.001), coupled with decreased anxiety related to mental health consultations (p<.001). There were also significant improvements to considerations towards careers in perinatal mental health (p<.001).ConclusionsThese findings show, for the first time, that XR can be used to provide an effective, standardised, and reproducible tool for trainees to develop their mental health consultation skills. We suggest that XR could provide a solution to overcoming the current resource challenges associated with equipping current and future healthcare professionals, which are likely to be exacerbated by workforce expansion plan.
Repetitive transcranial magnetic stimulation to the motor cortex leads to a sequential increase in phase synchronization and power of TMS-evoked electroencephalographic recordings
Authors: Martino Enrico De , Casali Adenauer Girardi , Nascimento Couto Bruno Andry , Graven-Nielsen Thomas , Ciampi de Andrade Daniel 
Published: April 2024

ABSTRACTBackgroundHigh-frequency (10 Hz) repetitive transcranial magnetic stimulation (rTMS) to the primary motor cortex (M1) is used to treat several neuropsychiatric disorders, but its main mechanism of action remains unclear.ObjectiveTo probe four cortical hubs used for rTMS (M1; dorsolateral-prefrontal cortex, DLPFC; anterior cingulate cortex, ACC; posterosuperior insula, PSI) with TMS coupled with high-density electroencephalography (TMS-EEG) and measure cortical excitability and oscillatory dynamics before and after active and sham rTMS to M1.MethodsBefore and immediately after active or sham M1-rTMS (15 min, 3,000 pulses at 10 Hz), single-pulse TMS evoked EEG were recorded at the four targets in 20 healthy individuals. Measures of cortical excitability and oscillatory dynamics were extracted at the main frequency bands (α [8-13 Hz], low-β [14-24 Hz], high-β [25-35 Hz]).ResultsComparing active and sham M1 rTMS, M1 TMS-EEG demonstrated an increase in high-β synchronization in electrodes around M1 stimulation area and remotely in the contralateral hemisphere (p=0.026). The increase in high-β synchronization (48-83 ms after TMS-EEG stimulation) was succeeded by an enhancement in low-β power (86-144 ms after TMS-EEG stimulation) both locally and in the contralateral hemisphere (p=0.006). No significant differences were observed in TMS-EEG responses probing DLPFC, ACC, or PSI.ConclusionM1-rTMS engaged a sequence of enhanced phase synchronization, followed by an increase in power occurring within M1, that spread to remote areas and was measurable after the end of the stimulation session. These results are relevant to understanding the M1 neuroplastic effects of rTMS and associated changes in cortical activity dynamics.
Contrasting genetic predisposition and diagnosis in psychiatric disorders: a multi-omic single-nucleus analysis of the human orbitofrontal cortex
Authors: Gerstner Nathalie , Fröhlich Anna S. , Matosin Natalie , Gagliardi Miriam , Cruceanu Cristiana , Ködel Maik , Rex-Haffner Monika , Tu Xinming , Mostafavi Sara , Ziller Michael J. , Binder Elisabeth B. , Knauer-Arloth Janine 
Published: April 2024

AbstractPsychiatric disorders like schizophrenia, bipolar disorder, and major depressive disorder exhibit significant genetic and clinical overlap. However, their molecular architecture remains elusive due to their polygenic nature and complex brain cell interactions. Here, we integrated clinical data with genetic susceptibility to investigate gene expression and chromatin accessibility in the orbitofrontal cortex of 92 postmortem human brain samples at the single-cell level. Through single-nucleus (sn) RNA-seq and snATAC-seq, we analyzed approximately 800,000 and 400,000 nuclei, respectively. We observed cell type-specific dysregulation related to clinical diagnosis and genetic risk across cortical cell types. Dysregulation in gene expression and chromatin accessibility associated with diagnosis was pronounced in excitatory neurons. Conversely, genetic risk predominantly impacted glial and endothelial cells. Notably,INO80EandHCN2genes exhibited dysregulation in excitatory neurons superficial layers 2/3 influenced by schizophrenia polygenic risk. This study unveils the complex genetic and epigenetic landscape of psychiatric disorders, emphasizing the importance of cell type-specific analyses in understanding their pathogenesis and contrasting genetic predisposition with clinical diagnosis.