bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm
Authors: Schooley Allana , Venev Sergey V. , Aksenova Vasilisa , Navarrete Emily , Dasso Mary , Dekker Job 
Published: September 2024

AbstractIdentity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, this chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. This microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis.
Shared subcortical arousal systems across sensory modalities during transient modulation of attention
Authors: Khalaf Aya , Lopez Erick , Li Jian , Horn Andreas , Edlow Brian L. , Blumenfeld Hal 
Published: September 2024

AbstractSubcortical arousal systems are known to play a key role in controlling sustained changes in attention and conscious awareness. Recent studies indicate that these systems have a major influence on short-term dynamic modulation of visual attention, but their role across sensory modalities is not fully understood. In this study, we investigated shared subcortical arousal systems across sensory modalities during transient changes in attention using block and event-related fMRI paradigms. We analyzed massive publicly available fMRI datasets collected while 1,561 participants performed visual, auditory, tactile, and taste perception tasks. Our analyses revealed a shared circuit of subcortical arousal systems exhibiting early transient increases in activity in midbrain reticular formation and central thalamus across perceptual modalities, as well as less consistent increases in pons, hypothalamus, basal forebrain, and basal ganglia. Identifying these networks is critical for understanding mechanisms of normal attention and consciousness and may help facilitate subcortical targeting for therapeutic neuromodulation.
RalB uncoupled exocyst mediates endothelial Weibel-Palade body exocytosis
Authors: Yang Moua , Boye-Doe Alexandra , Abosabie Salma A.S. , Barr Alexandra M. , Mendez Lourdes M. , Sharda Anish V. 
Published: September 2024

AbstractRas-like (Ral) GTPases play essential regulatory roles in many cellular processes, including exocytosis. Cycling between GDP- and GTP-bound states, Ral GTPases function as molecular switches and regulate effectors, specifically the multi-subunit tethering complex exocyst. Here, we show that Ral isoform RalB controls regulated exocytosis of Weibel-Palade bodies (WPBs), the specialized endothelial secretory granules that store hemostatic protein von Willebrand factor. Remarkably, unlike typical small GTPase-effector interactions, RalB binds exocyst in its GDP-bound state in resting endothelium. Upon endothelial cell stimulation, exocyst is uncoupled from RalB-GTP resulting in WPB tethering and exocytosis. Furthermore, we report that PKC-dependent phosphorylation of the C-terminal hypervariable region (HVR) of RalB modulates its dynamic interaction with exocyst in endothelium. Exocyst preferentially interacts with phosphorylated RalB in resting endothelium. Dephosphorylation of RalB either by endothelial cell stimulation, or PKC inhibition, or expression of nonphosphorylatable mutant at a specific serine residue of RalB HVR, disengages exocyst and augments WPB exocytosis, resembling RalB exocyst-binding site mutant. In summary, it is the uncoupling of exocyst from RalB that mediates endothelial Weibel-Palade body exocytosis. Our data shows that Ral function may be more dynamically regulated by phosphorylation and may confer distinct functionality given high degree of homology and the shared set of effector protein between the two Ral isoforms.
More than fruity scents: floral biology, scent and spectral reflectance of Annonaceae species
Authors: Liu Ming-Fai , Chen Junhao , Pang Chun-Chiu , Scharaschkin Tanya , Saunders Richard M. K. 
Published: September 2024

ABSTRACTPremiseThe family Annonaceae possesses a broad array of floral phenotypes and pollination specialisations, and are important in the plant-pollinator interactions of tropical rainforests. Although there has been considerable effort to assess their interactions with pollinators, attempts to characterise their visual and olfactory communication channels are scarce.MethodsHere, we investigated the pollination biology of 12 Annonaceae species from five genera, viz.Meiogyne,Monoon,Polyalthia,Pseuduvaria, andUvaria. Furthermore, their floral colour was characterised by reflectance spectroscopy and floral odour chemistry was assessed using gas chromatography-mass spectrometry. Floral scent was further compared across the whole family using non-metric dimensional scaling plots to identify specialisation in floral odour.ResultsTheMeiogynespecies are likely pollinated by small beetles; thePolyalthiaandPseuduvariaspecies are likely pollinated by beetles and flies; and theUvariaspecies is likely pollinated by beetles and bees. Flowers of most species are UV non-reflective, and have various spectral reflectance profile across the remaining visible spectra. Multiple species produce floral odour resembling ripe fruits. The flowers ofMeiogynespecies andPolyalthia xanthocarpaemitted mostly branched-chain esters, while flowers ofUvariareleased mainly straight-chain esters. ThePseuduvariaspecies instead emitted scent reminiscent of rotten fruits, largely consisting of 2,3-butanediol. The inner petal corrugation inMeiogynefunctions as a food reward, and the inner petal growth serves as a nectary gland forPseuduvaria.ConclusionsOur study identifies the visual and olfactory cues of multiple Annonaceae species and provides insights into how Annonaceae flowers attract different guilds of pollinators.
HiFi long-read genomes for difficult-to-detect clinically relevant variants
Authors: Höps Wolfram , Weiss Marjan M. , Derks Ronny , Galbany Jordi Corominas , den Ouden Amber , van den Heuvel Simone , Timmermans Raoul , Smits Jos , Mokveld Tom , Dolzhenko Egor , Chen Xiao , van den Wijngaard Arthur , Eberle Michael A. , Yntema Helger G. , Hoischen Alexander , Gilissen Christian , Vissers Lisenka E.L.M. 
Published: September 2024

SummaryClinical short-read exome and genome sequencing approaches have positively impacted diagnostic testing for rare diseases. Yet, technical limitations associated with short reads challenge their use for detection of disease-associated variation in complex regions of the genome. Long-read sequencing (LRS) technologies may overcome these challenges, potentially qualifying as a first-tier test for all rare diseases. To test this hypothesis, we performed LRS (30x HiFi genomes) for 100 samples with 145 known clinically relevant germline variants that are challenging to detect using short-read sequencing and necessitate a broad range of complementary test modalities in diagnostic laboratories.We show that relevant variant callers readily re-identify the majority of variants (120/145, 83%), including ∼90% of structural variants, SNVs/InDels in homologous sequences and expansions of short tandem repeats. Another 10% (n=14) was visually apparent in the data but not automatically detected. Our analyses also identified systematic challenges for the remaining 7% (n=11) of variants such as the detection of AG-rich repeat expansions. Titration analysis showed that 89% of all automatically called variants could also be identified using 15-fold coverage.Thus, long-read genomes identified 93% of pathogenic variants that are most challenging to detect using short-read technologies. Even with reduced coverage, the vast majority of variants remained detectable, possibly enhancing cost-effective diagnostic implementation. Most importantly, we show the potential to use a single technology to accurately identify all types of clinically relevant variants.
Structural basis for immune cell binding ofFusobacterium nucleatumvia the trimeric autotransporter adhesin CbpF
Authors: Marongiu Gian Luca , Fink Uwe , Oder Andreas , von Kries Jens Peter , Roderer Daniel 
Published: September 2024

AbstractFusobacterium nucleatum(Fn), a commensal in the human oral cavity, is overrepresented in the colon microbiota of colorectal cancer (CRC) patients and is linked to tumor chemoresistance, metastasis, and a poor therapeutic prognosis. Fn produces numerous adhesins that mediate tumor colonization and downregulation of the host’s anti-tumor immune response. One of these, the trimeric autotransporter adhesin (TAA) CEACAM binding protein ofFusobacterium(CbpF), targets CEACAM1 on T-cells and has been associated with immune evasion of Fn-colonized tumors. Whereas the role of CEACAM1 in homophilic and heterophilic cell interactions and immune evasion is well described, the mechanistic details of its interaction with fusobacterial CbpF remain unknown due to the lack of a high-resolution structure of the adhesin-receptor complex.Here, we present two structures of CbpF alone and in complex with CEACAM1, obtained by cryogenic electron microscopy and single particle analysis. They reveal that CbpF forms a stable homotrimeric complex whose N-terminal part of the extracellular domain comprises a 64 Å long β roll domain with a unique lateral loop extension. CEACAM1 binds to this loop via its N-terminal IgV-like domain with high affinity with a nanomolar dissociation constant, as obtained by surface plasmon resonance. This study provides the first structural description of a fusobacterial TAA, illustrates a yet undescribed CEACAM1 binding mode, and paves the way for rational drug design targeting Fn in CRC.
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription
Authors: Taghbalout Aziz , Tung Chia-Hao , Clow Patricia A. , Wang Ping , Tjong Harianto , Wong Chee Hong , Mao Diane D. , Maurya Rahul , Huang Meng-Fan , Ngan Chew Yee , Kim Albert H. , Wei Chia-Lin 
Published: September 2024

SummaryExtrachromosomal, circular DNA (ecDNA) is a prevalent oncogenic alteration in cancer genomes, often associated with aggressive tumor behavior and poor patient outcome. While previous studies proposed a chromatin-based mobile enhancer model for ecDNA-driven oncogenesis, its precise mechanism and impact remains unclear across diverse cancer types. Our study, utilizing advanced multi-omics profiling, epigenetic editing, and imaging approaches in three cancer models, reveals that ecDNA hubs are an integrated part of nuclear condensates and exhibit cancer-type specific chromatin connectivity. Epigenetic silencing of the ecDNA-specific regulatory modules or chemically disrupting liquid-liquid phase separation breaks down ecDNA hubs, displaces MED1 co-activator binding, inhibits oncogenic transcription, and promotes cell death. These findings substantiate thetrans-activator function of ecDNA and underscore a structural mechanism driving oncogenesis. This refined understanding expands our views of oncogene regulation and opens potential avenues for novel therapeutic strategies in cancer treatment.
SLC39A8.p.(Ala391Thr) is associated with poorer cognitive ability: a cross-sectional study of schizophrenia and the general UK population
Authors: Smart Sophie E , Legge Sophie E. , Fenner Eilidh , Pardiñas Antonio F. , Woolway Grace , Lynham Amy J. , Escott-Price Valentina , Hall Jeremy , Wilkinson Lawrence , Holmans Peter , O’Donovan Michael C. , Owen Michael J. , Walters James T.R. 
Published: September 2024

AbstractThe missense SNP NC_000004.12:g.102267552C>T (SLC39A8.p.(Ala391Thr), rs13107325) inSLC39A8,which encodes a zinc transporter, has been linked to schizophrenia and is the likely causal variant for one of the genome-wide association loci associated with the disorder.We tested whether the schizophrenia-risk allele at p.(Ala391Thr) was associated with schizophrenia-related phenotypes, including positive, negative, and disorganised symptoms, cognitive ability, educational attainment, and age of psychosis onset, within three schizophrenia cohorts (combined N=1,232) and, with equivalent phenotypes, in a sample of population controls (UK Biobank, N=355,069). We used regression analyses controlling for age, sex, and population stratification.Within the schizophrenia cohorts, after correction for multiple testing, p.(Ala391Thr) was not significantly associated with any schizophrenia-related phenotypes. In the unaffected participants from the UK Biobank, the schizophrenia-risk allele at p.(Ala391Thr) was associated with significantly poorer cognitive ability and fluid intelligence, a lower probability of obtaining GCSEs or a degree-level qualification, and fewer years in education. There was no association between p.(Ala391Thr) and self-reported psychotic experiences in this cohort.The schizophrenia-risk allele was associated with poorer cognitive ability, but not psychotic experiences, in a volunteer sample drawn from of the general population. To determine whether p.(Ala391Thr) is associated with cognitive phenotypes in people with schizophrenia, and to understand the role of p.(Ala391Thr) in the aetiology of cognitive impairment in schizophrenia, larger independent samples are required.
Functional connectivity is dominated by aperiodic, rather than oscillatory, coupling
Authors: Monchy N. , Duprez J. , Houvenaghel J-F. , Legros A. , Voytek B. , Modolo J. 
Published: September 2024

ABSTRACTFunctional connectivity has attracted significant interest in the identification of specific circuits underlying brain (dys-)function. Classical analyses to estimate functional connectivity (i.e., filtering electrophysiological signals in canonical frequency bands and using connectivity metrics) assume that these reflect oscillatory networks. However, this approach conflates non-oscillatory, aperiodic neural activity with oscillations; raising the possibility that these functional networks may reflect aperiodic rather than oscillatory activity. Here, we provide the first study quantifying, in two different human electroencephalography (EEG) databases, the contribution of aperiodic activity on reconstructed oscillatory functional networks in resting state. We found that more than 99% of delta, theta, and gamma functional networks, more than 90% of beta functional networks and between 23 and 55% of alpha functional networks were actually driven by aperiodic activity. While there is no universal consensus on how to identify and quantify neural oscillations, our results demonstrate that oscillatory functional networks are drastically sparser than commonly assumed. These findings suggest that most functional connectivity studies focusing on resting state actually reflect aperiodic networks instead of oscillations-based networks. We highly recommend that oscillatory network analyses first check the presence of aperiodicity-unbiased neural oscillations before estimating their statistical coupling to strengthen the robustness, interpretability, and reproducibility of functional connectivity studies.
In-cell processing enables rapid and in-depth proteome analysis of low-inputCaenorhabditis elegans
Authors: Elsayyid Malek , Tanis Jessica E. , Yu Yanbao 
Published: September 2024

AbstractCaenorhabditis elegansis a widely used genetic model organism, however, the worm cuticle complicates extraction of intracellular proteins, a prerequisite for typical bottom-up proteomics. Conventional physical disruption procedures are not only time-consuming, but can also cause significant sample loss, making it difficult to perform proteomics with low-input samples. Here, for the first time, we present an on-filter in-cell (OFIC) processing approach, which can digestC. elegansproteins directly in the cells of the organism after methanol fixation. With OFIC processing and single-shot LCMS analysis, we identified over 9,400 proteins from a sample of only 200 worms, the largestC. elegansproteome reported to date that did not require fractionation or enrichment. We systematically evaluated the performance of the OFIC approach by comparing it with conventional lysis-based methods. Our data suggest equivalent and unbiased performance of OFIC processing forC. elegansproteome identification and quantitation. We further evaluated the OFIC approach with even lower input samples, then used this method to determine how the proteome is impacted by loss of superoxide dismutasesod-1, the ortholog of humanSOD-1, a gene associated with amyotrophic lateral sclerosis (ALS). Analysis of 8,800 proteins from only 50 worms as the initial input showed that loss ofsod-1affects the abundance of proteins required for stress response, ribosome biogenesis, and metabolism. In conclusion, our streamlined OFIC approach, which can be broadly applied to other systems, minimizes sample loss while offering the simplest workflow reported to date forC. elegansproteomics analysis.
Cleland immunoblotting unmasks unexpected cysteine redox proteoforms
Authors: Cobley James N. , Noble Anna , Guille Matthew 
Published: September 2024

AbstractCysteine redox proteoforms are virtually unstudied because they are extremely difficult to detect. They are difficult to detect by immunoblotting when the polyethylene glycol (PEG)-payloads used to mobility-shift proteoforms into distinct bands block antibody binding. Here, we synthesised a novel compound to reversibly crosslink the PEG-payloads to oxidised cysteines using disulfide bonds. To reductively release the PEG-payloads from mobility-shifted proteoforms, we soaked the gel in Cleland’s reagent: 1,4-dithiothreitol (DTT). Hence, Cleland immunoblotting. Cleland immunoblotting unmasked hitherto undetectable cysteine redox proteoforms. InXenopusoocytes, we detected 2 cdc20-specific coordinates in an otherwise abstract space housing 1,024 theoretical proteoforms. The coordinates mapped to the fully, all 10 cysteine residues, 100%-reduced and 100%-oxidised proteoforms. The unexpected absence of partially oxidised molecules along the 10-reaction path to the 100%-oxidised proteoform implies novel biology. By providing the technological means to detect cysteine redox proteoforms, Cleland immunoblotting opens new avenues of discovery.
Herpes Simplex Virus Assembly and Spread in murine skin after infection from the outside
Authors: Richardo Timmy , Liu Xiaokun , Döhner Katinka , Buch Anna , Binz Anne , Pohlmann Anja , de le Roi Madeleine , Baumgärtner Wolfgang , Brand Korbinian , Bauerfeind Rudolf , Förster Reinhold , Sodeik Beate , Halle Stephan 
Published: September 2024

ABSTRACTHerpes simplex viruses (HSV) cause many skin diseases, particularly in immunocompromised patients. HSV-1 infection of murine skin recapitulates many aspects of human pathology. However, many protocols rely on mechanical or enzymatic skin disruption to induce lesions, although this can alter skin homeostasis and prime antiviral inflammation before inoculation. To investigate the initial events following HSV-1 primary skin infection before the onset of symptoms, we developed a novel murineex vivoexplant model using gentle depilation but no further scarification and infected keratinocytes from the outside with minimal tissue damage. Two-photon microscopy studies showed that HSV-1 spread exclusively in the epidermis. The infection centers increased in number and size over time and contained hundreds of infected keratinocytes. We investigated the HSV-1 spread at the cellular level, using reporter strains with fluorescently-tagged capsid protein VP26, and monitored the formation of nuclear capsid assembly sites, nuclear capsid egress, and the recruitment of the inner tegument protein pUL37GFP, the outer tegument protein VP11/12GFP, and the envelope protein gDGFP to cytoplasmic capsids. By electron microscopy, the skin appeared intact, and keratinocytes contained many nuclear capsids, primary virions in the nuclear envelope, cytosolic membrane-associated capsids, and enveloped virions. Our protocol provides a robust and reproducible approach to investigate the very early events of HSV-1 spread in the skin, to characterize the phenotypes of HSV-1 mutants in terminally differentiated skin tissues, and to evaluate potentially antiviral small molecules in a preclinicalex vivoinfection model.IMPORTANCEThis study describes a novel murineex vivoskin explant model to investigate early events in HSV-1 infection without causing significant tissue damage. To infect from the outside, via the apical keratinocytes, this method relies on gentle depilation, which maintains skin integrity. HSV-1 spread exclusively within the epidermis, with infection centers growing over time and involving hundreds of keratinocytes. Using advanced microscopy techniques, we tracked HSV-1 spread at the cellular level and intracellular assembly of all intermediate virus structures. This model offers a valuable tool for studying the initial stages of HSV-1 infection, assessing viral mutant phenotypes, and testing antiviral compounds in a more physiological context to provide critical insights into HSV-1 pathogenesis and therapeutic strategies.
Acute increase of protein O-GlcNAcylation in mice leads to transcriptome changes in the brain opposite to what is observed in Alzheimer’s Disease
Authors: Bell Margaret , Kane Mariame S , Ouyang Xiaosen , Young Martin E , Jegga Anil G , Chatham John C. , Darley-Usmar Victor , Zhang Jianhua 
Published: September 2024

ABSTRACTEnhancing protein O-GlcNAcylation by pharmacological inhibition of the enzyme O-GlcNAcase (OGA) is explored as a strategy to decrease tau and amyloid-beta phosphorylation, aggregation, and pathology in Alzheimer’s disease (AD). There is still more to be learned about the impact of enhancing global protein O-GlcNAcylation, which is important for understanding the mechanistic path of using OGA inhibition to treat AD. In this study, we investigated the acute effect of pharmacologically increasing O-GlcNAc levels, using OGA inhibitor Thiamet G (TG), on normal mouse brains. We hypothesized that the transcritome signature in respones to TG treatment provides a comprehensive view of the effect of OGA inhibition. We sacrificed the mice and dissected their brains after 3 hours of saline or 50 mg/kg TG treatment, and then performed mRNA sequencing using NovaSeq PE 150 (n=5 each group). We identified 1,234 significant differentially expressed genes with TG versus saline treatment. Functional enrichment analysis of the upregulated genes identified several upregulated pathways, including genes normally down in AD. Among the downregulated pathways were the cell adhesion pathway as well as genes normally up in AD and aging. When comparing acute to chronic TG treatment, protein autophosphorylation and kinase activity pathways were upregulated, whereas cell adhesion and astrocyte markers were downregulated in both datasets. Interestingly, mitochondrial genes and genes normally down in AD were up in acute treatment and down in chronic treatment. Data from this analysis will enable the evaluation of the mechanisms underlying the potential benefits of OGA inhibition in the treatment of AD. In particular, although OGA inhibitors are promising to treat AD, their downstream chronic effects related to bioenergetics may be a limiting factor.Abstract Figure