bluuebunny/crossref_metadata_2025_split huggingface dataset:
The m6A reader HNRNPC promotes glioma progression by enhancing the stability of IRAK1 mRNA through the MAPK pathway
Authors: Chen Jun-Jun , Lu Tian-Zhu , Wang Tao , Yan Wen-Hui , Zhong Fang-Yan , Qu Xin-Hui , Gong Xiao-Chang , Li Jin-Gao , Tou Fang-Fang , Jiang Li-Ping , Han Xiao-Jian 
Published: June 2024

AbstractGlioma is the most common and aggressive type of primary malignant brain tumor. The N6-methyladenosine (m6A) modification widely exists in eukaryotic cells and plays an important role in the occurrence and development of human tumors. However, the function and mechanism of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an RNA-binding protein and m6A reader in gliomas remains to be comprehensively and extensively explored. Herein, we found that HNRNPC mRNA and protein overexpression were associated with a poor prognosis for patients with gliomas, based on the data from TCGA, the CGGA, and the TMAs. Biologically, HNRNPC knockdown markedly repressed malignant phenotypes of glioma in vitro and in vivo, whereas ectopic HNRNPC expression had the opposite effect. Integrative RNA sequencing and MeRIP sequencing analyses identified interleukin-1 receptor-associated kinase 1 (IRAK1) as a downstream target of HNRNPC. The glioma public datasets and tissue microarrays (TMAs) data indicated that IRAK1 overexpression was associated with poor prognosis, and IRAK1 knockdown significantly repressed malignant biological behavior in vitro. Mechanistically, HNRNPC maintains the mRNA stability of IRAK1 in an m6A-dependent manner, resulting in activation of the mitogen-activated protein kinase (MAPK) signaling pathway, which was necessary for the malignant behavior of glioma. Our findings demonstrate the HNRNPC–IRAK1–MAPK axis as a crucial carcinogenic factor for glioma and the novel underlying mechanism of IRAK1 upregulation, which provides a rationale for therapeutically targeting epitranscriptomic modulators in glioma.
Ru(II)-based complexes containing 2-thiouracil derivatives suppress liver cancer stem cells by targeting NF-κB and Akt/mTOR signaling
Authors: Bomfim Larissa M. , Neves Sara P. , Coelho Amanda M. R. M. , Nogueira Mateus L. , Dias Rosane B. , Valverde Ludmila de F. , Rocha Clarissa A. G. , Soares Milena B. P. , Batista Alzir A. , Correa Rodrigo S. , Bezerra Daniel P. 
Published: June 2024

AbstractCancer stem cells (CSCs) are defined as a rare population of cancer cells related to tumor initiation and maintenance. These cells are primarily responsible for tumor growth, invasion, metastasis, recurrence, and resistance to chemotherapy. In this paper, we demonstrated the ability of Ru(II)-based complexes containing 2-thiouracil derivatives with the chemical formulas trans-[Ru(2TU)(PPh3)2(bipy)]PF6 (1) and trans-[Ru(6m2TU)(PPh3)2(bipy)]PF6 (2) (where 2TU = 2-thiouracil and 6m2TU = 6-methyl-2-thiouracil) to suppress liver CSCs by targeting NF-κB and Akt/mTOR signaling. Complexes 1 and 2 displayed potent cytotoxic effects on cancer cell lines and suppressed liver CSCs from HepG2 cells. Increased phosphatidylserine exposure, loss of mitochondrial transmembrane potential, increased PARP (Asp214) cleavage, DNA fragmentation, chromatin condensation and cytoplasmic shrinkage were detected in HepG2 cells treated with these complexes. Mechanistically, complexes 1 and 2 target NF-κB and Akt/mTOR signaling in HepG2 cells. Cell motility inhibition was also detected in HepG2 cells treated with these complexes. Complexes 1 and 2 also inhibited tumor progression in mice with HepG2 cell xenografts and exhibited tolerable systemic toxicity. Taken together, these results indicate that these complexes are new anti-HCC drug candidates that can suppress liver CSCs.
Bicarbonate-binding catalysis for the enantioselective desymmetrization of keto sulfonium salts
Authors: Alemán José , Humbrías-Martín Jorge , del Río-Rodríguez Roberto , Aguilar-Galindo Fernando , Díaz-Tendero Sergio , Fernández-Salas Jose A. 
Published: June 2024

AbstractHerein, an enantioselective desymmetrization of cyclic keto sulfonium salts through enantioselective deprotonation/ring opening process by anion-binding catalysis is presented. We report a squaramide/HCO3- complex as catalytic active species which is able to stereo-differentiate two enantiomeric protons, triggering the ring opening event taking advantage of the great tendency of sulfonium salts to act as leaving groups. Thus, this desymmetrization methodology give rise to β-methylsulfenylated sulfa-Michael addition type products with excellent yields and very good enantioselectivities. The bifunctional organocatalyst has been demonstrated to be capable of activating simultaneously the base and the keto sulfonium salt by DFT calculations and experimental proofs.
Microbiome and epigenetic variation in wild fish with low genetic diversity
Authors: Anka Ishrat Z. , Uren Webster Tamsyn M. , Berbel-Filho Waldir M. , Hitchings Matthew , Overland Benjamin , Weller Sarah , Garcia de Leaniz Carlos , Consuegra Sofia 
Published: June 2024

AbstractNon-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
Sororin is an evolutionary conserved antagonist of WAPL
Authors: Prusén Mota Ignacio , Galova Marta , Schleiffer Alexander , Nguyen Tan-Trung , Kovacikova Ines , Farias Saad Carolina , Litos Gabriele , Nishiyama Tomoko , Gregan Juraj , Peters Jan-Michael , Schlögelhofer Peter 
Published: June 2024

AbstractCohesin mediates sister chromatid cohesion to enable chromosome segregation and DNA damage repair. To perform these functions, cohesin needs to be protected from WAPL, which otherwise releases cohesin from DNA. It has been proposed that cohesin is protected from WAPL by SORORIN. However, in vivo evidence for this antagonism is missing and SORORIN is only known to exist in vertebrates and insects. It is therefore unknown how important and widespread SORORIN’s functions are. Here we report the identification of SORORIN orthologs in Schizosaccharomyces pombe (Sor1) and Arabidopsis thaliana (AtSORORIN). sor1Δ mutants display cohesion defects, which are partially alleviated by wpl1Δ. Atsororin mutant plants display dwarfism, tissue specific cohesion defects and chromosome mis-segregation. Furthermore, Atsororin mutant plants are sterile and separate sister chromatids prematurely at anaphase I. The somatic, but not the meiotic deficiencies can be alleviated by loss of WAPL. These results provide in vivo evidence for SORORIN antagonizing WAPL, reveal that SORORIN is present in organisms beyond the animal kingdom and indicate that it has acquired tissue specific functions in plants.
Evidence for dynastic succession among early Celtic elites in Central Europe
Authors: Gretzinger Joscha , Schmitt Felicitas , Mötsch Angela , Carlhoff Selina , Lamnidis Thiseas Christos , Huang Yilei , Ringbauer Harald , Knipper Corina , Francken Michael , Mandt Franziska , Hansen Leif , Freund Cäcilia , Posth Cosimo , Rathmann Hannes , Harvati Katerina , Wieland Günther , Granehäll Lena , Maixner Frank , Zink Albert , Schier Wolfram , Krausse Dirk , Krause Johannes , Schiffels Stephan 
Published: June 2024

AbstractThe early Iron Age (800 to 450 BCE) in France, Germany and Switzerland, known as the ‘West-Hallstattkreis’, stands out as featuring the earliest evidence for supra-regional organization north of the Alps. Often referred to as ‘early Celtic’, suggesting tentative connections to later cultural phenomena, its societal and population structure remain enigmatic. Here we present genomic and isotope data from 31 individuals from this context in southern Germany, dating between 616 and 200 BCE. We identify multiple biologically related groups spanning three elite burials as far as 100 km apart, supported by trans-regional individual mobility inferred from isotope data. These include a close biological relationship between two of the richest burial mounds of the Hallstatt culture. Bayesian modelling points to an avuncular relationship between the two individuals, which may suggest a practice of matrilineal dynastic succession in early Celtic elites. We show that their ancestry is shared on a broad geographic scale from Iberia throughout Central-Eastern Europe, undergoing a decline after the late Iron Age (450 BCE to ~50 CE).
High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection
Authors: Wang Benjamin X. , Leshchiner Dmitry , Luo Lijuan , Tuncel Miles , Hokamp Karsten , Hinton Jay C. D. , Monack Denise M. 
Published: June 2024

AbstractSalmonella entericais comprised of genetically distinct ‘serovars’ that together provide an intriguing model for exploring the genetic basis of pathogen evolution. Although the genomes of numerousSalmonellaisolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi and Paratyphi A)Salmonellaat unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adaptedSalmonella. Overall, this work highlights specific vulnerabilities encoded within human-restrictedSalmonellathat are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.
Detailed mapping of the complex fiber structure and white matter pathways of the chimpanzee brain
Authors: Eichner Cornelius , Paquette Michael , Müller-Axt Christa , Bock Christian , Budinger Eike , Gräßle Tobias , Jäger Carsten , Kirilina Evgeniya , Lipp Ilona ,   EBC Consortium,   Data Analysis and Writing,   Brain Extraction, Møller Torsten , Olofsson-Sannö Karin , Morawski Markus , Rusch Henriette , Wenk Patricia , Weiskopf Nikolaus , Wittig Roman M. , Crockford Catherine , Friederici Angela D. , Anwander Alfred 
Published: June 2024

AbstractLong-standing questions about human brain evolution may only be resolved through comparisons with close living evolutionary relatives, such as chimpanzees. This applies in particular to structural white matter (WM) connectivity, which continuously expanded throughout evolution. However, due to legal restrictions on chimpanzee research, neuroscience research currently relies largely on data with limited detail or on comparisons with evolutionarily distant monkeys. Here, we present a detailed magnetic resonance imaging resource to study structural WM connectivity in the chimpanzee. This open-access resource contains (1) WM reconstructions of a postmortem chimpanzee brain, using the highest-quality diffusion magnetic resonance imaging data yet acquired from great apes; (2) an optimized and validated method for high-quality fiber orientation reconstructions; and (3) major fiber tract segmentations for cross-species morphological comparisons. This dataset enabled us to identify phylogenetically relevant details of the chimpanzee connectome, and we anticipate that it will substantially contribute to understanding human brain evolution.
A decade-long study demonstrates that a population of invasive sea lamprey (Petromyzon marinus) can be controlled by introducing sterilized males
Authors: Johnson Nicholas S. , Lewandoski Sean A. , Jubar Aaron K. , Symbal Matthew J. , Solomon Benson M. , Bravener Gale A. , Barber Jessica M. , Siefkes Michael J. 
Published: June 2024

AbstractThe release of sterilized insects to control pest populations has been used successfully during the past 6 decades, but application of the method in vertebrates has largely been overlooked or met with failure. Here, we demonstrate for the first time in fish, that a small population of sea lamprey (Petromyzon marinus; Class Agnatha), arguably one of the most impactful invasive fish in the world, can be controlled by the release of sterilized males. Specifically, the release of high numbers of sterile males (~ 1000's) into a geographically isolated population of adult sea lamprey resulted in the first multiyear delay in pesticide treatment since treatments began during 1966. Estimates of percent reduction in recruitment of age-1 sea lamprey due to sterile male release ranged from 7 to 99.9% with the precision of the estimate being low because of substantial year-to-year variability in larval density and distribution. Additional monitoring that accounts for recruitment variability in time and space would reduce uncertainty in the degree to which sterile male release reduces recruitment rates. The results are relevant to vertebrate pest control programs worldwide, especially as technical opportunities to sterilize vertebrates and manipulate sex ratios expand.
3D-bioprinted GelMA/gelatin/amniotic membrane extract (AME) scaffold loaded with keratinocytes, fibroblasts, and endothelial cells for skin tissue engineering
Authors: Pazhouhnia Zahra , Noori Alireza , Farzin Ali , Khoshmaram Keyvan , Hoseinpour Mahdieh , Ai Jafar , Ebrahimi Marzieh , Lotfibakhshaiesh Nasrin 
Published: June 2024

AbstractGelatin-methacryloyl (GelMA) is a highly adaptable biomaterial extensively utilized in skin regeneration applications. However, it is frequently imperative to enhance its physical and biological qualities by including supplementary substances in its composition. The purpose of this study was to fabricate and characterize a bi-layered GelMA-gelatin scaffold using 3D bioprinting. The upper section of the scaffold was encompassed with keratinocytes to simulate the epidermis, while the lower section included fibroblasts and HUVEC cells to mimic the dermis. A further step involved the addition of amniotic membrane extract (AME) to the scaffold in order to promote angiogenesis. The incorporation of gelatin into GelMA was found to enhance its stability and mechanical qualities. While the Alamar blue test demonstrated that a high concentration of GelMA (20%) resulted in a decrease in cell viability, the live/dead cell staining revealed that incorporation of AME increased the quantity of viable HUVECs. Further, gelatin upregulated the expression of KRT10 in keratinocytes and VIM in fibroblasts. Additionally, the histological staining results demonstrated the formation of well-defined skin layers and the creation of extracellular matrix (ECM) in GelMA/gelatin hydrogels during a 14-day culture period. Our study showed that a 3D-bioprinted composite scaffold comprising GelMA, gelatin, and AME can be used to regenerate skin tissues.
Bioinformatics analysis of signature genes related to cell death in keratoconus
Authors: Liu Jinghua , Gao Juan , Xing Shulei , Yan Yarong , Yan Xinlin , Jing Yapeng , Li Xuan 
Published: June 2024

AbstractKeratoconus is corneal disease in which the progression of conical dilation of cornea leads to reduced visual acuity and even corneal perforation. However, the etiology mechanism of keratoconus is still unclear. This study aims to identify the signature genes related to cell death in keratoconus and examine the function of these genes. A dataset of keratoconus from the GEO database was analysed to identify the differentially expressed genes (DEGs). A total of 3558 DEGs were screened from GSE151631. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that they mainly involved in response to hypoxia, cell–cell adhesion, and IL-17 signaling pathway. Then, the cell death-related genes datasets were intersected with the above 3558 DEGs to obtain 70 ferroptosis-related DEGs (FDEGs), 32 autophagy-related DEGs (ADEGs), six pyroptosis-related DEGs (PDEGs), four disulfidptosis-related DEGs (DDEGs), and one cuproptosis-related DEGs (CDEGs). After using Least absolute shrinkage and selection operator (LASSO), Random Forest analysis, and receiver operating characteristic (ROC) curve analysis, one ferroptosis-related gene (TNFAIP3) and five autophagy-related genes (CDKN1A, HSPA5, MAPK8IP1, PPP1R15A, and VEGFA) were screened out. The expressions of the above six genes were significantly decreased in keratoconus and the area under the curve (AUC) values of these genes was 0.944, 0.893, 0.797, 0.726, 0.882 and 0.779 respectively. GSEA analysis showed that the above six genes mainly play an important role in allograft rejection, asthma, and circadian rhythm etc. In conclusion, the results of this study suggested that focusing on these genes and autoimmune diseases will be a beneficial perspective for the keratoconus etiology research.
Annealing temperature-dependent induced supramolecular chiroptical response of copolymer thin films studied by pump-modulated transient circular dichroism spectroscopy
Authors: Gust Domenic , Scholz Mirko , Schumacher Vivien , Mulatier Jean-Christophe , Pitrat Delphine , Guy Laure , Oum Kawon , Lenzer Thomas 
Published: June 2024

AbstractCopolymer thin films showing induced supramolecular chirality are of considerable interest for optoelectronic applications such as organic light-emitting diodes. Here, we introduce a new helicene-like chiral additive with two octyloxy substituents which displays excellent chiral induction properties in an achiral polyfluorene copolymer, leading to a circular dichroism (CD) response of up to 10,000 mdeg. This chiral inducer also displays very good thermal stability, which enables us to perform an extended study on the induced chiroptical properties of the cholesteric copolymer thin films annealed at different temperatures in the range 140–260 °C. Starting from about 180 °C, a distinct change in the morphology of the CD-active film is observed by CD microscopy, from micrometre-size granular to extended CD-active regions, where the latter ones display skewed distributions of the dissymmetry parameter gabs. Broadband Müller matrix spectroscopy finds a pronounced CD and circular birefringence (CB) response and only weak linear dichroism (LD, LD’) and linear birefringence (LB, LB’). Ultrafast transient CD spectroscopy with randomly polarised excitation reveals a clean mirror-image-type transient response, which shows a second-order decay of the S1 population due to singlet–singlet annihilation processes.
Effect of cellular senescence on the response of human peritoneal mesothelial cells to TGF-β
Authors: Kawka Edyta , Herzog Rebecca , Ruciński Marcin , Malińska Agnieszka , Unterwurzacher Markus , Sacnun Juan Manuel , Wagner Anja , Kowalska Katarzyna , Jopek Karol , Kucz-Chrostowska Agata , Kratochwill Klaus , Witowski Janusz 
Published: June 2024

AbstractTransforming growth factor β (TGF-β) is implicated in both mesothelial-to-mesenchymal transition (MMT) and cellular senescence of human peritoneal mesothelial cells (HPMCs). We previously showed that senescent HPMCs could spontaneously acquire some phenotypic features of MMT, which in young HPMCs were induced by TGF-β. Here, we used electron microscopy, as well as global gene and protein profiling to assess in detail how exposure to TGF-β impacts on young and senescent HPMCs in vitro. We found that TGF-β induced structural changes consistent with MMT in young, but not in senescent HPMCs. Of all genes and proteins identified reliably in HPMCs across all treatments and states, 4,656 targets represented overlapping genes and proteins. Following exposure to TGF-β, 137 proteins and 46 transcripts were significantly changed in young cells, compared to 225 proteins and only 2 transcripts in senescent cells. Identified differences between young and senescent HPMCs were related predominantly to wound healing, integrin-mediated signalling, production of proteases and extracellular matrix components, and cytoskeleton structure. Thus, the response of senescent HPMCs to TGF-β differs or is less pronounced compared to young cells. As a result, the character and magnitude of the postulated contribution of HPMCs to TGF-β-induced peritoneal remodelling may change with cell senescence.
Quantifying the effects of landscape and habitat characteristics on structuring bird assemblages in urban habitat patches
Authors: Zhu Yun , Liu Yu , Sheng Shang , Zheng Jinfeng , Wu Su , Cao Zhaoyang , Zhang Kai , Xu Yu 
Published: June 2024

AbstractUnderstanding the determinants of biodiversity in fragmented habitats is fundamental for informing sustainable landscape development, especially in urban landscapes that substantially fragment natural habitat. However, the relative roles of landscape and habitat characteristics, as emphasized by two competing frameworks (the island biogeography theory and the habitat diversity hypothesis), in structuring species assemblages in fragmented habitats have not been fully explored. This study investigated bird assemblages at 26 habitat patches (ranging in size from 0.3 to 290.4 ha) in an urban landscape, southwest China, among which habitat type composition and woody plant species composition varied significantly. Through 14 bird surveys conducted over six breeding seasons from 2017 to 2022, we recorded 70 breeding bird species (excluding birds recorded only once and fly-overs, such as raptors, swallows and swifts), with an average of 26 ± 10 (SD) species per patch. We found that patch area had significant direct and indirect effects on bird richness, with the indirect effects mediated by habitat richness (i.e., the number of habitat types). Isolation (measured as the distance to the nearest patch), perimeter to area ratio (PAR), and woody plant richness did not significantly predict variation in bird richness. Furthermore, none of these factors significantly sorted bird species based on their functional traits. However, the overall makeup of bird assemblages was significantly associated with the specific habitat types and woody plant species present in the patches. The results suggest that neither the island biogeography theory nor the habitat diversity hypothesis can fully explain the impacts of habitat fragmentation on bird richness in our study system, with their roles primarily being linked to patch area. The findings that habitat and plant compositions were the major drivers of variation in bird assemblage composition offer valuable insights into urban planning and green initiatives. Conservation efforts should focus not only on preserving large areas, but also on preventing urban monocultures by promoting diverse habitats within those areas, contributing to the persistence of meta-communities.