bluuebunny/crossref_metadata_2025_split huggingface dataset:
The BRD4-SRPK2-SRSF2 signal modulates the splicing efficiency of ACSL3 pre-mRNA and influences erastin-induced ferroptosis in osteosarcoma cells
Authors: Luo Shun-Hong , Tian Jia-Ming , Chu Yi , Zhu Hong-Yi , Ni Jiang-Dong , Huang Jun 
Published: November 2023

AbstractLipid metabolism is the key to ferroptosis susceptibility. However, little is known about the underlying mechanisms in osteosarcoma cells. Functional restriction of bromodomain-containing protein 4 (BRD4) reduced the susceptibility to erastin-induced ferroptosis of osteosarcoma cells both in vitro and in vivo. Mechanically, BRD4 controls the splicing efficiency of the RNA precursor (pre-mACSL3) of ACSL3 (ACSL3) by recruiting serinerich/threonine protein kinase 2 (SRPK2) to assemble the splicing catalytic platform. Moreover, the AMP-binding domain of ACSL3 significantly influences arachidonic acid synthesis and thus determines the susceptibility to erastin-induced ferroptosis. Overall, we found a BRD4-mediated pre-mACSL3 splicing influences erastin-induced ferroptosis by affecting arachidonic acid synthesis in osteosarcoma cells. Data in this study fills some of the gap in understanding the post-transcriptional regulatory mechanisms of ACSL3 and provides new insights into the mechanisms of lipid metabolism regulation and its effect on susceptibility to ferroptosis in osteosarcoma cells.
Reversal of MYB-dependent suppression of MAFB expression overrides leukaemia phenotype in MLL-rearranged AML
Authors: Negri A. , Ward C. , Bucci A. , D’Angelo G. , Cauchy P. , Radesco A. , Ventura A. B. , Walton D. S. , Clarke M. , Mandriani B. , Pappagallo S. A. , Mondelli P. , Liao K. , Gargano G. , Zaccaria G. M. , Viggiano L. , Lasorsa F. M. , Ahmed A. , Di Molfetta D. , Fiermonte G. , Cives M. , Guarini A. , Vegliante M. C. , Ciavarella S. , Frampton J. , Volpe G. 
Published: November 2023

AbstractThe transcription factor MYB plays a pivotal role in haematopoietic homoeostasis and its aberrant expression is involved in the genesis and maintenance of acute myeloid leukaemia (AML). We have previously demonstrated that not all AML subtypes display the same dependency on MYB expression and that such variability is dictated by the nature of the driver mutation. However, whether this difference in MYB dependency is a general trend in AML remains to be further elucidated. Here, we investigate the role of MYB in human leukaemia by performing siRNA-mediated knock-down in cell line models of AML with different driver lesions. We show that the characteristic reduction in proliferation and the concomitant induction of myeloid differentiation that is observed in MLL-rearranged and t(8;21) leukaemias upon MYB suppression is not seen in AML cells with a complex karyotype. Transcriptome analyses revealed that MYB ablation produces consensual increase of MAFB expression in MYB-dependent cells and, interestingly, the ectopic expression of MAFB could phenocopy the effect of MYB suppression. Accordingly, in silico stratification analyses of molecular data from AML patients revealed a reciprocal relationship between MYB and MAFB expression, highlighting a novel biological interconnection between these two factors in AML and supporting new rationales of MAFB targeting in MLL-rearranged leukaemias.
Deciphering the interaction between Twist1 and PPARγ during adipocyte differentiation
Authors: Sun Leilei , Ji Shaoping , Xie Xuan , Si Lei , Liu Shaohao , Lin Yao , Wang Yahui , Song Zhenhua , Fang Na , An Yang , Yang Jian 
Published: November 2023

AbstractObesity, a worldwide epidemic in recent years, is mainly due to the uncontrolled development of adipose tissues, which includes adipocyte hypertrophy and hyperplasia. Adipocyte differentiation is a process involving multiple transcription factor cascades, and the exact mechanism has not yet been defined. As a bHLH transcription factor, Twist1 exerts its activity by forming homo- or heterodimers with other factors. In this study, we showed Twist1 restricts adipogenesis through PPARγ. Expression of various differentiation markers (including PPARγ and adiponectin) and triglyceride-containing lipid droplets were decreased with overexpression of Twist1. Pathway enrichment analysis of RNA-seq data showed that differentially expressed genes (DEGs) caused by Twist1 overexpression were significantly related to lipolysis and PPARγ signaling. This implicates that Twist1 plays important regulatory roles in these processes. ChIP and dual luciferase assays showed that Twist1 could bind either PPARγ or adiponectin promoter to repress their respective transcription or directly to PPARγ protein to regulate its transcriptional activity. Furthermore, Twist1 directly interacted RXRα, which usually forms heterodimer with PPARγ to regulate adipogenesis. Taken together, our results suggest that Twist1 is an inhibitory modulator of adipogenesis and its function is likely through direct interaction with PPARγ protein or its gene promoter.
Targeting protein methylation in pancreatic cancer cells results in KRAS signaling imbalance and inhibition of autophagy
Authors: Montenegro María F. , Martí-Díaz Román , Navarro Ana , Tolivia Jorge , Sánchez-del-Campo Luis , Cabezas-Herrera Juan , Rodríguez-López José Neptuno 
Published: November 2023

AbstractPancreatic cancer cells with mutant KRAS require strong basal autophagy for viability and growth. Here, we observed that some processes that allow the maintenance of basal autophagy in pancreatic cancer cells are controlled by protein methylation. Thus, by maintaining the methylation status of proteins such as PP2A and MRAS, these cells can sustain their autophagic activity. Protein methylation disruption by a hypomethylating treatment (HMT), which depletes cellular S-adenosylmethionine levels while inducing S-adenosylhomocysteine accumulation, resulted in autophagy inhibition and endoplasmic reticulum stress-induced apoptosis in pancreatic cancer cells. We observed that by reducing the membrane localization of MRAS, hypomethylation conditions produced an imbalance in KRAS signaling, resulting in the partial inactivation of ERK and hyperactivation of the PI3K/AKT–mTORC1 pathway. Interestingly, HMT impeded CRAF activation by disrupting the ternary SHOC2 complex (SHOC2/MRAS/PP1), which functions as a CRAF-S259 holophosphatase. The demethylation events that resulted in PP2A inactivation also favored autophagy inhibition by preventing ULK1 activation while restoring the cytoplasmic retention of the MiT/TFE transcription factors. Since autophagy provides pancreatic cancer cells with metabolic plasticity to cope with various metabolic stress conditions, while at the same time promoting their pathogenesis and resistance to KRAS pathway inhibitors, this hypomethylating treatment could represent a therapeutic opportunity for pancreatic adenocarcinomas.
Hi-C metagenome sequencing reveals soil phage–host interactions
Authors: Wu Ruonan , Davison Michelle R. , Nelson William C. , Smith Montana L. , Lipton Mary S. , Jansson Janet K. , McClure Ryan S. , McDermott Jason E. , Hofmockel Kirsten S. 
Published: November 2023

AbstractBacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi–C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.
BioE3 identifies specific substrates of ubiquitin E3 ligases
Authors: Barroso-Gomila Orhi , Merino-Cacho Laura , Muratore Veronica , Perez Coralia , Taibi Vincenzo , Maspero Elena , Azkargorta Mikel , Iloro Ibon , Trulsson Fredrik , Vertegaal Alfred C. O. , Mayor Ugo , Elortza Felix , Polo Simona , Barrio Rosa , Sutherland James D. 
Published: November 2023

AbstractHundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.
Nod1-dependent NF-kB activation initiates hematopoietic stem cell specification in response to small Rho GTPases
Authors: Cheng Xiaoyi , Barakat Radwa , Pavani Giulia , Usha Masuma Khatun , Calderon Rodolfo , Snella Elizabeth , Gorden Abigail , Zhang Yudi , Gadue Paul , French Deborah L. , Dorman Karin S. , Fidanza Antonella , Campbell Clyde A. , Espin-Palazon Raquel 
Published: November 2023

AbstractUncovering the mechanisms regulating hematopoietic specification not only would overcome current limitations related to hematopoietic stem and progenitor cell (HSPC) transplantation, but also advance cellular immunotherapies. However, generating functional human induced pluripotent stem cell (hiPSC)-derived HSPCs and their derivatives has been elusive, necessitating a better understanding of the developmental mechanisms that trigger HSPC specification. Here, we reveal that early activation of the Nod1-Ripk2-NF-kB inflammatory pathway in endothelial cells (ECs) primes them to switch fate towards definitive hemogenic endothelium, a pre-requisite to specify HSPCs. Our genetic and chemical embryonic models show that HSPCs fail to specify in the absence of Nod1 and its downstream kinase Ripk2 due to a failure on hemogenic endothelial (HE) programming, and that small Rho GTPases coordinate the activation of this pathway. Manipulation of NOD1 in a human system of definitive hematopoietic differentiation indicates functional conservation. This work establishes the RAC1-NOD1-RIPK2-NF-kB axis as a critical intrinsic inductor that primes ECs prior to HE fate switch and HSPC specification. Manipulation of this pathway could help derive a competent HE amenable to specify functional patient specific HSPCs and their derivatives for the treatment of blood disorders.
A robust and tunable Luttinger liquid in correlated edge of transition-metal second-order topological insulator Ta2Pd3Te5
Authors: Wang Anqi , Li Yupeng , Yang Guang , Yan Dayu , Huang Yuan , Guo Zhaopeng , Gao Jiacheng , Huang Jierui , Zeng Qiaochu , Qian Degui , Wang Hao , Guo Xingchen , Meng Fanqi , Zhang Qinghua , Gu Lin , Zhou Xingjiang , Liu Guangtong , Qu Fanming , Qian Tian , Shi Youguo , Wang Zhijun , Lu Li , Shen Jie 
Published: November 2023

AbstractThe interplay between topology and interaction always plays an important role in condensed matter physics and induces many exotic quantum phases, while rare transition metal layered material (TMLM) has been proved to possess both. Here we report a TMLM Ta2Pd3Te5 has the two-dimensional second-order topology (also a quadrupole topological insulator) with correlated edge states - Luttinger liquid. It is ascribed to the unconventional nature of the mismatch between charge- and atomic- centers induced by a remarkable double-band inversion. This one-dimensional protected edge state preserves the Luttinger liquid behavior with robustness and universality in scale from micro- to macro- size, leading to a significant anisotropic electrical transport through two-dimensional sides of bulk materials. Moreover, the bulk gap can be modulated by the thickness, resulting in an extensive-range phase diagram for Luttinger liquid. These provide an attractive model to study the interaction and quantum phases in correlated topological systems.
Ultrasmall and tunable TeraHertz surface plasmon cavities at the ultimate plasmonic limit
Authors: Aupiais Ian , Grasset Romain , Guo Tingwen , Daineka Dmitri , Briatico Javier , Houver Sarah , Perfetti Luca , Hugonin Jean-Paul , Greffet Jean-Jacques , Laplace Yannis 
Published: November 2023

AbstractThe ability to confine THz photons inside deep-subwavelength cavities promises a transformative impact for THz light engineering with metamaterials and for realizing ultrastrong light-matter coupling at the single emitter level. To that end, the most successful approach taken so far has relied on cavity architectures based on metals, for their ability to constrain the spread of electromagnetic fields and tailor geometrically their resonant behavior. Here, we experimentally demonstrate a comparatively high level of confinement by exploiting a plasmonic mechanism based on localized THz surface plasmon modes in bulk semiconductors. We achieve plasmonic confinement at around 1 THz into record breaking small footprint THz cavities exhibiting mode volumes as low as $${V}_{cav}/{\lambda }_{0}^{3} \sim 1{0}^{-7}-1{0}^{-8}$$

V

c
a
v

/

λ

0

3

~
1

0

−
7

−
1

0

−
8

, excellent coupling efficiencies and a large frequency tunability with temperature. Notably, we find that plasmonic-based THz cavities can operate until the emergence of electromagnetic nonlocality and Landau damping, which together constitute a fundamental limit to plasmonic confinement. This work discloses nonlocal plasmonic phenomena at unprecedentedly low frequencies and large spatial scales and opens the door to novel types of ultrastrong light-matter interaction experiments thanks to the plasmonic tunability.
Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms
Authors: Reuter Christian , Hauf Laura , Imdahl Fabian , Sen Rituparno , Vafadarnejad Ehsan , Fey Philipp , Finger Tamara , Jones Nicola G. , Walles Heike , Barquist Lars , Saliba Antoine-Emmanuel , Groeber-Becker Florian , Engstler Markus 
Published: November 2023

AbstractTransmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the fly’s bite. We introduce an advanced human skin equivalent and use tsetse flies to naturally infect the skin with trypanosomes. We detail the chronological order of the parasites’ development in the skin by single-cell RNA sequencing and find a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Here we show that after the establishment of a proliferative population, the parasites enter a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We term these quiescent trypanosomes skin tissue forms, a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.
Competing charge-density wave instabilities in the kagome metal ScV6Sn6
Authors: Cao Saizheng , Xu Chenchao , Fukui Hiroshi , Manjo Taishun , Dong Ying , Shi Ming , Liu Yang , Cao Chao , Song Yu 
Published: November 2023

AbstractOwing to its unique geometry, the kagome lattice hosts various many-body quantum states including frustrated magnetism, superconductivity, and charge-density waves (CDWs). In this work, using inelastic X-ray scattering, we discover a dynamic short-range $$\sqrt{3}\times \sqrt{3}\times 2$$

3

×

3

×
2
CDW that is dominant in the kagome metal ScV6Sn6 above TCDW ≈ 91 K, competing with the $$\sqrt{3}\times \sqrt{3}\times 3$$

3

×

3

×
3
CDW that orders below TCDW. The competing CDW instabilities lead to an unusual CDW formation process, with the most pronounced phonon softening and the static CDW occurring at different wavevectors. First-principles calculations indicate that the $$\sqrt{3}\times \sqrt{3}\times 2$$

3

×

3

×
2
CDW is energetically favored, while a wavevector-dependent electron-phonon coupling (EPC) promotes the $$\sqrt{3}\times \sqrt{3}\times 3$$

3

×

3

×
3
CDW as the ground state, and leads to enhanced electron scattering above TCDW. These findings underscore EPC-driven correlated many-body physics in ScV6Sn6 and motivate studies of emergent quantum phases in the strong EPC regime.
Ultrathin covalent organic overlayers on metal nanocrystals for highly selective plasmonic photocatalysis
Authors: Acharya Anubhab , Mete Trimbak Baliram , Kumari Nitee , Yoon Youngkwan , Jeong Hayoung , Jang Taehyung , Song Byeongju , Choi Hee Cheul , Han Jeong Woo , Pang Yoonsoo , Yun Yongju , Kumar Amit , Lee In Su 
Published: November 2023

AbstractMetal nanoparticle-organic interfaces are common but remain elusive for controlling reactions due to the complex interactions of randomly formed ligand-layers. This paper presents an approach for enhancing the selectivity of catalytic reactions by constructing a skin-like few-nanometre ultrathin crystalline porous covalent organic overlayer on a plasmonic nanoparticle surface. This organic overlayer features a highly ordered layout of pore openings that facilitates molecule entry without any surface poisoning effects and simultaneously endows favourable electronic effects to control molecular adsorption–desorption. Conformal organic overlayers are synthesised through the plasmonic oxidative activation and intermolecular covalent crosslinking of molecular units. We develop a light-operated multicomponent interfaced plasmonic catalytic platform comprising Pd-modified gold nanoparticles inside hollow silica to achieve the highly efficient and selective semihydrogenation of alkynes. This approach demonstrates a way to control molecular adsorption behaviours on metal surfaces, breaking the linear scaling relationship and simultaneously enhancing activity and selectivity.
Crown-hydroxylamines are pH-dependent chelating N,O-ligands with a potential for aerobic oxidation catalysis
Authors: Lesnikov Vladislav K. , Golovanov Ivan S. , Nelyubina Yulia V. , Aksenova Svetlana A. , Sukhorukov Alexey Yu. 
Published: November 2023

AbstractDespite the rich coordination chemistry, hydroxylamines are rarely used as ligands for transition metal coordination compounds. This is partially because of the instability of these complexes that undergo decomposition, disproportionation and oxidation processes involving the hydroxylamine motif. Here, we design macrocyclic poly-N-hydroxylamines (crown-hydroxylamines) that form complexes containing a d-metal ion (Cu(II), Ni(II), Mn(II), and Zn(II)) coordinated by multiple (up to six) hydroxylamine fragments. The stability of these complexes is likely to be due to a macrocycle effect and strong intramolecular H-bonding interactions between the N−OH groups. Crown-hydroxylamine complexes exhibit interesting pH-dependent behavior where the efficiency of metal binding increases upon deprotonation of the hydroxylamine groups. Copper complexes exhibit catalytic activity in aerobic oxidation reactions under ambient conditions, whereas the corresponding complexes with macrocyclic polyamines show poor or no activity. Our results show that crown-hydroxylamines display anomalous structural features and chemical behavior with respect to both organic hydroxylamines and polyaza-crowns.
Electron pairing and nematicity in LaAlO3/SrTiO3 nanostructures
Authors: Nethwewala Aditi , Lee Hyungwoo , Li Jianan , Briggeman Megan , Pai Yun-Yi , Eom Kitae , Eom Chang-Beom , Irvin Patrick , Levy Jeremy 
Published: November 2023

AbstractStrongly correlated electronic systems exhibit a wealth of unconventional behavior stemming from strong electron-electron interactions. The LaAlO3/SrTiO3 (LAO/STO) heterostructure supports rich and varied low-temperature transport characteristics including low-density superconductivity, and electron pairing without superconductivity for which the microscopic origins is still not understood. LAO/STO also exhibits inexplicable signatures of electronic nematicity via nonlinear and anomalous Hall effects. Nanoscale control over the conductivity of the LAO/STO interface enables mesoscopic experiments that can probe these effects and address their microscopic origins. Here we report a direct correlation between electron pairing without superconductivity, anomalous Hall effect and electronic nematicity in quasi-1D ballistic nanoscale LAO/STO Hall crosses. The characteristic magnetic field at which the Hall coefficient changes directly coincides with the depairing of non-superconducting pairs showing a strong correlation between the two distinct phenomena. Angle-dependent Hall measurements further reveal an onset of electronic nematicity that again coincides with the electron pairing transition, unveiling a rotational symmetry breaking due to the transition from paired to unpaired phases at the interface. The results presented here highlights the influence of preformed electron pairs on the transport properties of LAO/STO and provide evidence of the elusive pairing “glue” that gives rise to electron pairing in SrTiO3-based systems.
Steam recovery from flue gas by organosilica membranes for simultaneous harvesting of water and energy
Authors: Moriyama Norihiro , Takeyama Akihiro , Yamatoko Taichi , Sawamura Ken-ichi , Gonoi Koji , Nagasawa Hiroki , Kanezashi Masakoto , Tsuru Toshinori 
Published: November 2023

AbstractSteam recovery from the spent gases from flues could be a key step in addressing the water shortage issue while additionally benefiting energy saving. Herein, we propose a system that uses organosilica membranes consisting of a developed layered structure to recover steam and latent heat from waste. Proof-of-concept testing is conducted in a running incinerator plant. The proposed system eliminates the need for a water supply while simultaneously recovering latent heat from the waste stream. First, the long-term stability of an organosilica membrane is confirmed over the course of six months on a laboratory-scale under a simulated waste stream. Second, steam recovery is demonstrated in a running waste incinerator plant (bench-scale), which confirms the steady operation of this steam recovery system with a steam recovery rate comparable to that recorded in the laboratory-scale test. Third, process simulation reveals that this system enables water-self-reliance with energy recovery that approximates 70% of waste combustion energy.