bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-Scale Genome-Wide Optimization and Prediction of the Cre Recombinase System for Precise Genome Manipulation in Mice
Authors: Erhardt Valerie , Hartig Elli , Lorenzo Kristian , Megathlin Hannah R. , Tarchini Basile , Hosur Vishnu 
Published: June 2024

AbstractThe Cre-Lox recombination system is a powerful tool in mouse genetics, offering spatial-temporal control over gene expression and facilitating the large-scale generation of conditional knockout mice. Its versatility also extends to other research models, such as rats, pigs, and zebrafish. However, the Cre-Lox technology presents a set of challenges that includes high costs, a time-intensive process, and the occurrence of unpredictable recombination events, which can lead to unexpected phenotypic outcomes. To better understand factors affecting recombination, we embarked on a systematic and genome-wide analysis of Cre-mediated recombination in mice. To ensure uniformity and reproducibility, we generated 11 novel strains with conditional alleles at theROSA26locus, utilizing a single inbred mouse strain background, C57BL/6J. We examined several factors influencing Cre-recombination, including the inter-loxPdistance, mutantloxPsites, the zygosity of the conditional alleles, chromosomal location, and the age of the breeders. We discovered that the selection of the Cre-driver strain profoundly impacts recombination efficiency. We also found that successful and complete recombination is best achieved whenloxPsites are spaced between 1 to 4 kb apart, with mutantloxPsites facilitating recombination at distances of 1 to 3 kb. Furthermore, we demonstrate that complete recombination does not occur at an inter-loxPdistance of ≥ 15 kb with wildtypeloxPsites, nor at a distance of ≥ 7 kb with mutantlox71/66sites. Interestingly, the age of the Cre-driver mouse at the time of breeding emerged as a critical factor in recombination efficiency, with best results observed between 8 and 20 weeks old. Moreover, crossing heterozygous floxed alleles with the Cre-driver strain resulted in more efficient recombination than using homozygous floxed alleles. Lastly, maintaining an inter-loxPdistance of 4 kb or less ensures efficient recombination of the conditional allele, regardless of the chromosomal location. While CRISPR/Cas has revolutionized genome editing in mice, Cre-Lox technology remains a cornerstone for the generation of sophisticated alleles and for precise control of gene expression in mice. The knowledge gained here will enable investigators to select a Cre-Lox approach that is most efficient for their desired outcome in the generation of both germline and non-germline mouse models of human disease, thereby reducing time and cost of Cre-Lox technology-mediated genome modification.
Heterogenous organization in condensates of multiple transcription factors in embryonic stem cells
Authors: Mizutani Azuki , Tan Cheng , Sugita Yuji , Takada Shoji 
Published: June 2024

AbstractBiomolecular condensates formed via liquid-liquid phase separation are ubiquitous in cells, especially in the nucleus. While condensates containing one or two kinds of biomolecules have been relatively well characterized, those with more heterogenous biomolecular components and interactions between biomolecules inside are largely unknown. This study used residue-resolution molecular dynamics simulations to investigate heterogeneous protein assemblies that include four master transcription factors in mammalian embryonic stem cells: Oct4, Sox2, Klf4, and Nanog. Simulations of the mixture systems showed highly heterogeneous and dynamic behaviors; the condensates mainly contained Sox2, Klf4, and Nanog, while Oct4 was dissolved into the dilute phase. Condensates consisted of loosely interacting clusters in which Klf4 was the most abundant in the cores. We suggest that Klf4 serves as a scaffold of the condensate where Sox2 and Nanog are bound to stabilize the condensate, whereas Oct4 is moderately recruited to the condensate, serving as a client mainly via its interaction with Sox2.Biological significanceIn eukaryotes, transcription is known to be regulated by many regulatory factors such as transcription factors, co-activators, and RNA polymerases, but precise molecular mechanisms of regulation remain obscured. A recently proposed model suggests that transcription-related proteins condense via liquid-liquid phase separation (LLPS) using their intrinsically disordered regions, which serves to control transcription. Master transcription factors in mammalian embryonic stem cells have been a model system. It was revealed that several master transcription factors exhibit LLPS by themselves, but dynamics and molecular structure of these proteins in their mixture have not been well addressed. In this study, we study molecular structures of condensates in a mixture of four master transcription factors, Oct4, Sox2, Klf4, and Nanog, via molecular dynamics simulation. We found that the three transcription factors Sox2, Klf4, and Nanog form mixed condensates, while Oct4 was largely dissolved. Klf4 mainly served as a scaffold of the condensate. The three proteins formed micelle-like structures as was recently found in the Nanog condensate. The condensates weakly recruited Oct4. Formation of heterogeneous condensates may provide fertile local environments in cells.
Network Analysis Reveals Protein Modules Associated with Childhood Respiratory Diseases
Authors: Prince Nicole , Begum Sofina , Mendez Kevin M , Ramirez Lourdes G , Chen Yulu , Chen Qingwen , Chu Su H , Kachroo Priyadarshini , Levy Ofer , Diray-Arce Joann , Palma Paolo , Litonjua Augusto A , Weiss Scott T , Kelly Rachel S , Lasky-Su Jessica A 
Published: June 2024

AbstractBackgroundThe first year of life is a period of rapid immune development that can impact health trajectories and the risk of developing respiratory-related diseases, such as asthma, recurrent infections, and eczema. However, the biology underlying subsequent disease development remains unknown.MethodsUsing weighted gene correlation network analysis (WGCNA), we derived modules of highly correlated immune-related proteins in plasma samples from children at age 1 year (N=294) from the Vitamin D Antenatal Asthma Reduction Trial (VDAART). We applied regression analyses to assess relationships between protein modules and development of childhood respiratory diseases up to age 6 years. We then characterized genomic, environmental, and metabolomic factors associated with modules.ResultsWGCNA identified four protein modules at age 1 year associated with incidence of childhood asthma and/or recurrent wheeze (Padjrange: 0.02-0.03), respiratory infections (Padjrange: 6.3×10-9-2.9×10-6), and eczema (Padj=0.01) by age 6 years; three modules were associated with at least one environmental exposure (Padjrange: 2.8×10-10-0.03) and disrupted metabolomic pathway(s) (Padjrange: 2.8×10-6-0.04). No genome-wide SNPs were identified as significant genetic risk factors for any protein module. Relationships between protein modules with clinical, environmental, and ‘omic factors were temporally sensitive and could not be recapitulated in protein profiles at age 6 years.ConclusionThese findings suggested protein profiles as early as age 1 year predicted development of respiratory-related diseases through age 6 and were associated with changes in pathways related to amino acid and energy metabolism. These may inform new strategies to identify vulnerable individuals based on immune protein profiling.
Music-related Bodily Sensation Map in Individuals with Depressive Tendencies
Authors: Tanaka Masaki , Daikoku Tatsuya 
Published: June 2024

AbstractMusic has the power to influence people’s emotions. Therefore, music is also used as an intervention to reduce the stress in mental disorders such as depression and anxiety. Recent research has suggested that the body plays a key role in the connection between music and emotion with a correlation between the head sensations and negative emotions while listening to music. Additionally, strong sensations in the head have been suggested as a bodily perception associated with depression. In this study, we investigated the bodily sensations experienced by people with depressive tendencies when listening to music and their association with specific emotional states, using body mapping and musical chord progression. Our results revealed that individuals with depressive tendencies experience strong head sensations, with unpleasantness and low aesthetics, particularly for chord progression with a high level of surprise and uncertainty. This study sheds light on the intricate relationship between music, bodily sensations, and emotional states, providing valuable insights for research on the body and for developing musical therapeutic interventions targeting depression and related conditions.
Dogs density drives the reproductive effort of American Oystercatchers (Haematopus palliatus) in disturbed habitats of the Maule Region, central Chile
Authors: Díaz Jesús , Medrano Fernando , Imbernón Daniel , Villalobos Franco , Silva Juan , Sandvig Erik M. , Montecino Sharon 
Published: June 2024

AbstractThe American Oystercatcher (Haematopus palliatus) is a shorebird specialized in coastal environments across the Americas. Thus, anthropic extensive use of the shoreline including the introduction of dogs and vehicles to beaches could directly impact fitness, and ultimately the persistence of the species’ populations. In this study, we aimed to assess the impact of pedestrians, vehicles and dogs on the nest density, productivity and hatching success of the American Oystercatcher in the Maule Region, central Chile. To this end, we sampled sandy beaches, quantifying the number of nests, eggs, chicks, but also pedestrians, vehicles and dogs during the breeding seasons of 2023 and 2024. We assessed for the influence of these threats on parameters of reproductive output by using Generalized Linear Mixed Models. We found that the number of dogs is the only variable that negatively impacts the number of nests, eggs and chicks of the American Oystercatcher in the sampled areas. Reducing the impact of dogs is a ubiquitous challenge in coastal environments of central Chile, however current regulations do not allow management relying on removal of dogs from important areas for biodiversity.
Sulfur oxidation through rDsr in a novel Sox-free marine Roseobacter lineage
Authors: Lin Xingqin , Feng Xiaoyuan , Wang Xiaojun , Long Hongan , Crowe Sean A. , Luo Haiwei 
Published: June 2024

AbstractSulfur oxidation is an essential biogeochemical process in coastal sediments. Of the two typical sulfur-oxidizing metabolic pathways, the reverse dissimilatory sulfite reductase pathway (rDsr) is recognized for its superior energy conservation efficiency compared to the Sox multi-enzyme system and thus might be important in intertidal habitats where electron acceptors are periodically limited. Here, we isolated 10 intertidal sediment strains that compose a novelRuegerialineage in the globally abundant marine Roseobacter group. They possess a complete rDsr pathway but lack the entire Sox system, whereas all known sulfur-oxidizing Roseobacters rely on Sox. In fact, rDsr-carrying but Sox-free bacteria are rare among all sequenced bacterial genomes (only 20 out of 35798), and how sulfur oxidation is driven exclusively by rDsr has not been investigated. Physiological assays, sulfur intermediate measurements, and transcriptomic analyses reveal that rDsr activation in thisRuegerialineage occurs exclusively under microaerobic conditions and is coupled with thiosulfate oxidation in tandem with denitrification. Metagenomic analysis shows that rDsr sequences are enriched in marine habitats characterized by oxygen depletion, consistent with our physiological data. Further, theRhodobacteralesorder whereRuegeriabelongs accounts for approximately 5% of the rDsr-bearing bacterial community in intertidal sediments globally, underscoring its significant role in sulfur oxidation in this important marine environment.
Weighted variance component test for the integrative multi-omics analysis of microbiome data
Authors: Zhang Angela , Ling Wodan , Little Amarise , Williams-Nguyen Jessica S. , Moon Jee-Young , Burk Robert D. , Knight Rob , Wang Dong D. , Qi Qibin , Kaplan Robert C. , Zhao Ni , Wu Michael C. 
Published: June 2024

AbstractMetabolic dysregulation and alterations have been linked to various diseases and conditions. Innovations in high-throughput technology now allow rapid profiling of the metabolome and metagenome — often the gene content of bacterial populations -– for characterizing metabolism. Due to the small sample sizes and high dimensionality of the data, pathway analysis (wherein the effect of multiple genes or metabolites on an outcome is cumulatively assessed) of metabolomic data is commonly conducted and also represents a standard for metagenomic analysis. However, how to integrate both data types remains unclear. Recognizing that a metabolic pathway can be complementarily characterized by both metagenomics and metabolomics, we propose a weighted variance components framework to test if the joint effect of genes and metabolites in a biological pathway is associated with outcomes. The approach allows analytic p-value calculation, correlation between data types, and optimal weighting. Power simulations show that our approach often outperforms other strategies while maintaining type I error. The approach is illustrated on real data.
Integrative Network Analysis Reveals Novel Moderators of Aβ-Tau Interaction in Alzheimer’s Disease
Authors: Kitani Akihiro , Matsui Yusuke 
Published: June 2024

AbstractBackgroundAlthough interactions between amyloid-beta and tau proteins have been implicated in Alzheimer’s disease (AD), the precise mechanisms by which these interactions contribute to disease progression are not yet fully understood. Moreover, despite the growing application of deep learning in various biomedical fields, its application in integrating networks to analyze disease mechanisms in AD research remains limited. In this study, we employed BIONIC, a deep learning-based network integration method, to integrate proteomics and protein–protein interaction data, with an aim to uncover factors that moderate the effects of the Aβ-tau interaction on mild cognitive impairment (MCI) and early-stage AD.MethodsProteomic data from the ROSMAP cohort were integrated with protein–protein interaction (PPI) data using a Deep Learning-based model. Linear regression analysis was applied to histopathological and gene expression data, and mutual information was used to detect moderating factors. Statistical significance was determined using the Benjamini-Hochberg correction (p < 0.05).ResultsOur results suggested that astrocytes and GPNMB+ microglia moderate the Aβ-tau interaction. Based on linear regression with histopathological and gene expression data, GFAP and IBA1 levels andGPNMBgene expression positively contributed to the interaction of tau with Aβ in non-dementia cases, replicating the results of the network analysis.ConclusionsThese findings indicate that GPNMB+ microglia moderate the Aβ-tau interaction in early AD and therefore are a novel therapeutic target. To facilitate further research, we have made the integrated network available as a visualization tool for the scientific community (URL:https://igcore.cloud/GerOmics/AlzPPMap).
A phage nucleus-associated protein from the jumbophage Churi inhibits bacterial growth through protein translation interference
Authors: Wannasrichan Wichanan , Krobthong Sucheewin , Morgan Chase J , Armbruster Emily G , Gerovac Milan , Yingchutrakul Yodying , Wongtrakoongate Patompon , Vogel Jörg , Aonbangkhen Chanat , Nonejuie Poochit , Pogliano Joe , Chaikeeratisak Vorrapon 
Published: June 2024

AbstractAntibacterial proteins inhibitingPseudomonas aeruginosahave been identified in various phages and explored as antibiotic alternatives. Here, we isolated a phiKZ-like phage, Churi, which encodes 364 open reading frames. We examined 15 early-expressed phage proteins for their ability to inhibit bacterial growth, and found that gp335, closely related to phiKZ-gp14, exhibits antibacterial activity. Similar to phiKZ-gp14, recently shown to form a complex with theP. aeruginosaribosome, we predict experimentally that gp335 interacts with ribosomal proteins, suggesting its involvement in protein translation. GFP-tagged gp335 clusters around the phage nucleus as early as 15 minutes post-infection and remains associated with it throughout the infection, suggesting its role in protein expression in the cell cytoplasm. CRISPR-Cas13-mediated deletion of gp355 reveals that the mutant phage has a prolonged latent period. Altogether, we demonstrate that gp335 is an antibacterial protein of nucleus-forming phages that associates with the ribosomes at the phage nucleus.
Cyclophilin A Facilitates HIV-1 DNA Integration
Authors: Padron Adrian , Dwivedi Richa , Chakraborty Rajasree , Prakash Prem , Kim Kyusik , Shi Jiong , Ahn Jinwoo , Pandhare Jui , Luban Jeremy , Aiken Christopher , Balasubramaniam Muthukumar , Dash Chandravanu 
Published: June 2024

AbstractCyclophilin A (CypA) promotes HIV-1 infection by facilitating reverse transcription, nuclear entry and by countering the antiviral activity of TRIM5α. These multifunctional roles of CypA are driven by its binding to the viral capsid. Interestingly, recent studies suggest that the HIV-1 capsid lattice enters the nucleus of an infected cell and uncoats just before integration. Therefore, we tested whether CypA-capsid interaction regulates post-nuclear entry steps of infection, particularly integration. First, we challenged CypA-expressing (CypA+/+) and CypA-depleted (CypA-/-) cells with HIV-1 particles and quantified the resulting levels of provirus. Surprisingly, CypA-depletion significantly reduced integration, an effect that was independent of CypA’s effect on reverse transcription, nuclear entry, and the presence or absence of TRIM5α. Additionally, cyclosporin A, an inhibitor that disrupts CypA-capsid binding, inhibited HIV-1 integration in CypA+/+cells but not in CypA-/-cells. Accordingly, HIV-1 capsid mutants (G89V and P90A) deficient in CypA binding were also blocked at integration in CypA+/+cells but not in CypA-/-cells. Then, to understand the mechanism, we assessed the integration activity of HIV-1 preintegration complexes (PICs) extracted from infected cells. The PICs from CypA-/-cells had lower activityin vitrocompared to those from CypA+/+cells. PICs from cells depleted for CypA and TRIM5α also had lower activity, suggesting that CypA’s effect on PIC activity is independent of TRIM5α. Finally, addition of CypA protein significantly stimulated the integration activity of PICs extracted from both CypA+/+and CypA-/-cells. Collectively, these results suggest that CypA promotes HIV-1 integration, a previously unknown role of this host factor.ImportanceHIV-1 capsid interaction with host cellular factors is essential for establishing a productive infection. However, the molecular details of such virus-host interactions are not fully understood. Cyclophilin A (CypA) is the first host protein identified to specifically bind to the HIV-1 capsid. Now it is established that CypA promotes reverse transcription and nuclear entry steps of HIV-1 infection. In this report, we show that CypA promotes HIV-1 integration by binding to the viral capsid. Specifically, our results demonstrate that CypA promotes HIV-1 integration by stimulating the activity of the viral preintegration complex and identifies a novel role of CypA during HIV-1 infection. This new knowledge is important because recent reports suggest that an operationally intact HIV-1 capsid enters the nucleus of an infected cell.
Transferrin receptor-based circulating tumor cell enrichment provides a snapshot of the molecular landscape of solid tumors and correlates with clinical outcomes
Authors: Galletti Giuseppe , Halima Ahmed , Gjyrezi Ada , Zhang Jiaren , Zimmerman Bob , Worroll Daniel , Kallergi Galatea , Barreja Rohan , Ocean Allyson , Saxena Ashish , McGraw Timothy E. , Nanus David M. , Elemento Olivier , Altorki Nasser K. , Tagawa Scott T. , Giannakakou Paraskevi 
Published: June 2024

AbstractCirculating tumor cells (CTCs) captured from the bloodstream of patients with solid tumors have the potential to accelerate precision oncology by providing insight into tumor biology, disease progression and response to treatment. However, their potential is hampered by the lack of standardized CTC enrichment platforms across tumor types. EpCAM-based CTC enrichment, the most commonly used platform, is limited by EpCAM downregulation during metastasis and the low EpCAM expression in certain tumor types, including the highly prevalent and lethal NSCLC. In this study we demonstrate that Transferrin Receptor (TfR) is a selective, efficient biomarker for CTC identification and capture in patients with prostate, pancreatic and NSCLC. TfR identifies significantly higher CTC counts than EpCAM, and TfR+-CTC enumeration correlates with disease progression in metastatic prostate and pancreatic cancers, and overall survival and osimetrinib-resistance in non-small cell lung cancer (NSCLC). Profiling of TfR+-CTCs provides a snapshot of the molecular landscape of each respective tumor type and identifies potential mechanisms underlying treatment response to EGFR TKi and immune checkpoint inhibitors in NSCLC.One sentence summaryTransferrin Receptor identifies circulating tumor cells in solid tumors
Efficacy of Mechanical Thrombectomy in Medium Vessel Occlusions of the MCA in the Extended Time Window
Authors: Berger Marcel Cedric , Simgen Andreas , Dietrich Philipp , Naziri Weis 
Published: June 2024

BackgroundMechanical thrombectomy (MT) has significantly improved outcomes in acute ischemic stroke (AIS) due to large vessel occlusions (LVOs) up to 24 hours post-onset. The effectiveness of MT for medium vessel occlusions (MeVOs) in the M2 or M3 segments of the middle cerebral artery beyond 6 hours is less investigated.MethodsThis retrospective study analyzed 80 patients who underwent MT for primary, isolated M2 or M3 segment occlusions between January 2020 and August 2023. Patients were categorized by time from stroke onset to groin puncture into two groups: ≤6 hours (n=61) and >6 hours (n=19). Outcomes assessed included clinical severity (NIH Stroke Scale [NIHSS]), functional outcomes (modified Rankin Scale [mRS]), symptomatic intracranial hemorrhages (sICH), and reperfusion success (modified Thrombolysis in Cerebral Infarction [mTICI] scale).ResultsMean onset-to-puncture time was 192±57 minutes for the ≤6 hours group and 611±327 minutes for the >6 hours group. Baseline NIHSS scores were 9.5 (IQR 9) and 7 (IQR 8), respectively (p=0.418). While the NIHSS improvement was greater in the ≤6 hours group (median: −5 vs. −2; p=0.028), both groups showed significant improvement from baseline NIHSS scores (p<0.001 and p=0.014). Rates of sICH were low in both groups (1.5% vs. 0.5%; p=0.421). Recanalization rates were lower in the >6 hours group (84.2% vs. 96.7%; p=0.084), with more attempts (2.37 vs. 1.66; p=0.024).ConclusionMT for M2 and M3 segment occlusions in the MCA shows benefits beyond 6 hours from stroke onset, with earlier treatment yielding greater improvement. Extending MT’s treatment window could be valuable for MeVOs in the MCA.