bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-synaptic competition between calcineurin and PKA regulates mammalian sleep-wake cycles
Authors: Wang Yimeng , Cao Siyu , Tone Daisuke , Fujishima Hiroshi , Yamada Rikuhiro G. , Ohno Rei-ichiro , Shi Shoi , Matsuzawa Kyoko , Kaneko Mari , Ukai-Tadenuma Maki , Ukai Hideki , Hanashima Carina , Kiyonari Hiroshi , Sumiyama Kenta , Ode Koji L. , Ueda Hiroki R. 
Published: December 2023

AbstractPhosphorylation of synaptic proteins is a pivotal biochemical reaction that controls the sleep-wake cycle in mammals. Protein phosphorylation in vivo is reversibly regulated by kinases and phosphatases. In this study, we investigated a pair of kinases and phosphatases that reciprocally regulate sleep duration. Through comprehensive screening of Protein kinase A (PKA) and phosphoprotein phosphatase (PPP) family genes via the generation of 40 gene knockout mouse lines including post-natal CRISPR targeting, we identified a regulatory subunit of PKA (Prkar2b), a regulatory subunit of protein phosphatase (PP) 1 (Pppr1r9b), and catalytic and regulatory subunits of PP2B (calcineurin) (Ppp3caandPpp3r1) as sleep control genes. AAV-mediated stimulation of PKA and PP1/calcineurin activities confirmed PKA as a wake-promoting kinase, while PP1 and calcineurin function as sleep-promoting phosphatases. The importance of these phosphatases in sleep regulation is supported by the dramatic changes in sleep duration associated with their increased and decreased activity, ranging from approximately 17.3 hours/day (PP1 expression) to 6.7 hours/day (post-natal CRISPR targeting of calcineurin). For these phosphatases to exert their sleep-promoting effects, localization signals to the excitatory post-synapse were necessary. Furthermore, the wake-promoting effect of PKA localized to the excitatory post-synapse negated the sleep-promoting effect of calcineurin, suggesting that PKA and calcineurin construct a hierarchical phosphorylation control network for sleep regulation at excitatory post-synapses.
A direct estrogenic involvement in the expression of human hypocretin
Authors: Li Haimei , Chen Xinlu , Dong Jingyi , Liu Ripeng , Duan Jinfeng , Huang Manli , Hu Shaohua , Lu Jing 
Published: December 2023

AbstractBackgroundHypocretin-1 may play an important role in depression, which was increased in female depression in LHA in our previous study. Estrogen acts through its nuclear transcriptional receptors.MethodsWe studied the possibility of a direct action of estrogen receptors on the expression of human hypocretin. To explore the activation of ERs by hypocretin, we first investigated the potential presence of co-localization of the estrogen receptors (ERs) in hypocretin-immunoreactive neurons in the lateral hypothalamic area (LHA) in human and nuclear ERs in hypocretin immunoreactive neuroblastoma SK-N-SH cells. We investigated the relationship between E2 and hypocretin in female rats. After we explored the regulating role of exogenous estrogen on hypocretin gene expression via ERs through Chromatin immunoprecipitation, Electrophoretic mobility shift assay and Luciferase assay.ResultsWe found that hypocretin-1 plasma level was significantly higher in female depression. Estrogen receptors (ERα and ERβ) and hypocretin are co-localized in female depression LHA, PC12 and SK-N-SH cell lines. The estrogen receptor response elements (EREs) existing in the hypocretin promoter region may directly regulate the expression of hypocretin, the synchronicity of change of hypocretin and estradiol both in hypothalamus and plasma was verified in female rats. With the presence of estradiol, there is specific binding between human ER and the Hypocretin-ERE. Expression of ER combined with estradiol repressed hypocretin promoter activity through the ERE.Conclusionswe defined that estradiol may affect hypocretin neurons in the human hypothalamus via ER binding to the Hypocretin-ERE directly, which may thus lead to the sex-specific pathogenesis of depression.
On the mechanism for winter stem pressure build-up in walnut trees
Authors: Bozonnet Cyril , Saudreau Marc , Badel Eric , Charrier Guillaume , Améglio Thierry 
Published: December 2023

AbstractXylem embolism is a significant factor in tree mortality. Restoration of hydraulic conductivity after massive embolisation of the vascular system requires the application of positive pressure to the vessels and/or the creation of new conductive elements. Some species generate positive pressure from the root system to propagate pressure in distal, aboveground, organs in spring, whereas other species generate positive pressure locally at the stem level during winter. We provide a mechanistic explanation for winter stem pressure build-up in the walnut tree. We have developed a physical model that accounts for temperature fluctuations and phase transitions. This model is based on the exchange of water and sugars between living cells and vessels. Our computations demonstrate that vessel pressurization can be attributed to the transfer of water between vessels across the parenchyma rays, which is facilitated by a radial imbalance in sugar concentration. The ability to dispose of soluble sugars in living cells, and to transport them between living cells and up to the vessels, are identified as the main drivers of stem pressure build-up in the walnut tree.
Cryo-EM structure of monomeric CXCL12-bound CXCR4 in active state
Authors: Liu Yezhou , Liu Aijun , Li Xinyu , Liao Qiwen , Zhang Weijia , Zhu Lizhe , Ye Richard D. 
Published: December 2023

ABSTRACTCXC chemokine receptor 4 (CXCR4) and its chemokine ligand CXCL12 are crucial to embryonic development, bone marrow retention of hematopoietic progenitor cells, cancer metastasis, angiogenesis and HIV-1 infection. Yet the structural basis for CXCR4 recognition of full-length CXCL12 remains unknown despite available structures of CXCR4 in complex with small molecule antagonists and a viral chemokine. Here we present a cryo-EM structure of monomeric CXCL12-CXCR4 in complex with heterotrimeric Gi proteins at a resolution of 2.65 Å. The CXCL12-CXCR4 interaction at their N termini is stabilized by a polar interaction between the PC motif (C28NTin CXCR4) and CXC motif (the unique P10 in CXCL12). The N terminal 8 amino acids in CXCL12 insert into the transmembrane binding pocket (chemokine recognition site 2, CRS2) of CXCR4 with S4 defining an upward turn of V3, P2 and K1. Polar interactions involving C186ECL2and D187ECL2, along with hydrogen bonding with E2887,39and D2626,58stabilize the N terminus of CXCL12 in CRS2. Hydrophobic interactions between side chains aligning CRS2 and P2, L5 and S6 of CXCL12 further strengthen its binding to the receptor. CXCL12 inserts deep into the binding pocket, and the 3.2Å distance measured between V3 and the ‘toggle switch’ W6.48for G protein activation is among the shortest of all chemokine-receptor pairs. Our findings provide structural insights into the recognition mechanism of CXCR4 for its chemokine ligand CXCL12.
Kappa Opioid Receptors in Mesolimbic Terminals Mediate Escalation of Cocaine Consumption
Authors: Gordon-Fennell L. , Farero R.D. , Burgeno L.M. , Murray N.L. , Abraham A.D. , Soden M.E. , Stuber G.D. , Chavkin C. , Zweifel L.S. , Phillips P.E.M. 
Published: December 2023

ABSTRACTIncreases in drug consumption over time, also known as escalation, is a key behavioral component of substance use disorder (SUD) that is related to potential harm to users, such as overdose. Studying escalation also allows researchers to investigate the transition from casual drug use to more SUD-like drug use. Understanding the neurobiological systems that drive this transition will inform therapeutic treatments in the aim to prevent increases in drug use and the development of SUD. The kappa opioid receptor (KOR) system is typically known for its role in negative affect, which is commonly found in SUD as well. Furthermore, the KOR system has also been implicated in drug use and importantly, modulating the negative effects of drug use. However, the specific neuronal subpopulation expressing KOR involved has not been identified. Here, we first demonstrated that pharmacologically inhibiting KOR in the nucleus accumbens core (NAcC), as a whole, blocks cocaine escalation under long-access self-administration conditions. We then demonstrated that KOR expressed on ventral tegmental area (VTA) neurons but not NAcC neurons is sufficient for blocking cocaine escalation by utilizing a novel virally-mediated CRISPR-SaCas9 knock-out of theoprk1gene. Together, this suggests that activation of KOR on VTA terminals in the NAcC drives the transition to the SUD-like phenotype of escalation of cocaine consumption.
Characterization of peroxidasin expression in histologically normal human adult and fetal kidney tissue
Authors: Brandão Isabel , Silva Roberto , Conde Eduardo , Gomes Bárbara , Sampaio Paula , Braga Ana Costa , Almeida Jorge Reis , Soares Alencastre Inês , Paulo Oliveira João 
Published: December 2023

AbstractPeroxidasin (PXDN) is an enzyme of the peroxidase family that plays a critical role in extracellular matrix (ECM) formation and tissue development. In the kidney, very few studies using animal cells suggested that PXDN may have a role in the maintenance of the structural and functional integrity of the renal ECM. Still, the normal expression and (patho)physiological roles of PDXN in the mature and developing human kidney remain unknown.In this work we used fluorescent immunohistochemistry and advanced microscopy and image processing methodologies to perform a quantitative characterization of PXDN expression in the different anatomic compartments of histologically normal kidney tissue, obtained from adult nephrectomy specimens, and from postmortem fetal and neonatal kidney specimens (excluding death by kidney disease and genitourinary developmental anomalies).Results show that PXDN is expressed in all mature kidney compartments, but at significantly higher levels in tubular epithelial cells, particularly in the distal tubules. A similar PXDN expression pattern was observed in the developing kidney, as early as the in the comma-shaped-body stage. In the fetal kidney, PXDN was diffusely expressed in the branches of the ureteric bud but not in the cells of the metanephric blastema.This is the first demonstration that PXDN is differentially expressed in histologically normal human renal parenchyma, exhibiting a remarkably consistent pattern of predominant tubular expression since the early stages of metanephrogenesis This data suggests a relevant, compartment-specific, role of PXDN in nephrogenesis and in the kidney physiology, highlighting a main role in tubular functions, that is worth further investigation.
Phosphorylation regulates tau’s phase separation behavior and interactions with chromatin
Authors: Abasi Lannah S. , Elathram Nesreen , Movva Manasi , Deep Amar , Corbett Kevin D. , Debelouchina Galia T. 
Published: December 2023

AbstractTau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer’s disease (AD). Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. Models of tau depletion or pathology show loss of genetically silent heterochromatin, aberrant expression of heterochromatic genes, and transposable element activation. The molecular mechanisms behind these observations are currently unclear. Usingin vitrobiophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau’s strong interactions with linker and nucleosomal DNA, while magic angle spinning (MAS) solid-state NMR experiments show that tau binding does not drastically alter nucleosome structure and dynamics. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro
Authors: Chang Zhanhe , Xu Yunfan , Dong Xin , Gao Yawei , Wang Chenfei 
Published: December 2023

AbstractThe accurate reconstruction of gene regulation networks (GRNs) from sparse and noisy single-cell or spatial multi-omics data remains a challenge. Here, we present SCRIPro, a comprehensive computational framework that robustly infers GRNs for both single-cell and spatial multi-omics data. SCRIPro first addresses sample sparseness by a density clustering approach. SCRIPro assesses transcriptional regulator (TR) importance through chromatin reconstruction andin silicodeletion, referencing 1,292 human and 994 mouse TRs. It combines TR-target importance scores with expression levels for precise GRN reconstruction. Finally, we benchmarked SCRIPro on diverse datasets, it outperforms existing motif-based methods and accurately reconstructs cell type-specific, stage-specific, and region-specific GRNs.
Nanoscale profiling of evolving intermolecular interactions in ageing FUS condensates
Authors: Miller Alyssa , Toprakcioglu Zenon , Qamar Seema , St. George-Hyslop Peter , Ruggeri F. Simone , Knowles Tuomas P. J. , Vendruscolo Michele 
Published: December 2023

AbstractIn addition to the native state, proteins can form liquid-like condensates, viscoelastic condensates, such as gels, as well as solid-like condensates, such as amyloid fibrils, crystals and amorphous materials. The material properties of these condensates play important roles in their cellular functions, with aberrant liquid-to-solid phase transitions having been implicated in neurodegenerative diseases. However, the molecular changes and resultant material properties across the whole phase space of condensates are complex and yet to be fully understood. The extreme sensitivity to their environment, which enables their biological function, is also what makes protein condensates particularly challenging experimental targets. Here, we provide a characterisation of the ageing behaviour of the full-length fused in sarcoma (FUS) protein. We achieve this goal by using a microfluidic sample deposition technology to enable the application of surface-based techniques to the study of biological condensates. We first demonstrate that we maintain relevant structural features of condensates in physiologically-relevant conditions on surfaces. Then, using a combination of atomic force microscopy and vibrational spectroscopy, we characterise the spatio-temporal changes in the structure and mechanical properties of the condensates to reveal local phase transitions in individual condensates. We observe that initially dynamic, fluid-like condensates undergo a global increase in elastic response conferred by an increase in the density of cation-π intermolecular interactions. Solid-like structures form first at condensate-solvent interfaces, before heterogeneously propagating throughout the aged fluid core. These solid structures are composed of heterogenous, non-amyloid β-sheets, which are stabilised by hydrogen-bonding interactions not observed in the fluid state. Overall, this study identifies the molecular conformations associated with different physical states of FUS condensates, establishing a technology platform to understand the role of phase behaviour in condensate function and dysfunction.
In vitrodifferentiation of mouse pluripotent stem cells into glucocorticoid-producing adrenocortical cells
Authors: Oikonomakos Ioannis , Tedesco Melina , Motamedi Fariba Jian , Peitzsch Mirko , Nef Serge , Bornstein Stefan , Schedl Andreas , Steenblock Charlotte , Neirijnck Yasmine 
Published: December 2023

SummaryDirected differentiation of pluripotent stem cells into specialized cell types represents an invaluable tool for a wide range of applications. Here, we have exploited single-cell transcriptomic data to develop a step-wisein vitrodifferentiation system from mouse embryonic stem cells into adrenocortical cells. We show that during development the adrenal primordium is embedded in an extracellular matrix containing tenascin and fibronectin. Culturing cells on fibronectin during differentiation increased the expression of the steroidogenic marker NR5A1. Furthermore, 3D cultures in the presence of PKA-pathway activators led to the formation of aggregates composed of different cell types expressing adrenal progenitor or steroidogenic markers, including the adrenocortical specific enzymeCyp21a1. Importantly,in vitrodifferentiated cells secreted thezona Fasciculataspecific corticosterone in response to cAMP activators, but not gonadal hormones, thus confirming the specificity of differentiation towards the adrenal lineage.HighlightsMouse adrenal progenitors differentiate in a tenascin/fibronectin-rich extracellular matrixStepwise differentiation of ES cells yields NR5A1+ adrenocortical cells3D aggregates produce glucocorticoids in response to cAMP signalling
Plant genetic bases explaining microbiota diversity shed light into a novel holobiont generalist gene theory
Authors: Maillet Loeiz , Norest Manon , Kautsky Adam , Geraci Anna , Oddo Elisabetta , Troia Angelo , Guillerm-Erckelboudt Anne-Yvonne , Falentin Cyril , Rousseau-Gueutin Mathieu , Chèvre Anne-Marie , Istace Benjamin , Cruaud Corinne , Belser Caroline , Aury Jean-Marc , Schicchi Rosario , Frachon Léa , Bartoli Claudia 
Published: December 2023

AbstractPlants as animals are strictly associated with a cortege of microbial communities influencing their health, fitness and evolution. Therefore, scientists refer to all living organisms as holobionts; complex genetic units that coevolve simultaneously. This is what has been recently proposed as the hologenome theory of evolution. This exciting and attractive theory has important implications on animal and plant health; however, it still needs consistent proof to be validated. Indeed, holobionts are still poorly studied in their natural habitats where coevolution and natural selective processes occur. Compared to animals and crops, wild plant populations are an excellent and unique model to explore the hologenome theory. These sessile holobionts have strictly coevolved with their microbiota for decades and natural selection and adaptive processes acting on wild plants are likely to regulate the plant-microbe interactions. Here we conducted for the first time a microbiota survey, plant genome sequencing and Genome-Environmental Analysis (GEA) of 26 natural populations of the non-model plant speciesBrassica rapa. We collected plants over two seasons in Italy and France, and analyzed the microbiota on two plant compartments (root and rhizosphere). We identified that plant compartment and season modulateB. rapamicrobiota. More importantly, when conducting GEA we evidenced neat peaks of association correlating with both fungal and bacterial microbiota. Surprisingly, we found 13 common genes between fungal and bacterial diversity descriptors that we referred under the name of Holobiont Generalist Genes (HGG). These genes might strongly regulate the diversity and composition of plant microbiota at the inter-kingdom level.Significance StatementThe novel hologenome concept claims that hosts and their associated microbes (considered as holobionts) are a unique evolutionary unit on which natural selection acts. Thus, the hologenome theory assumes that hosts and microbiomes simultaneously coevolve. This novel vision of universal evolutionary entities is promising for both animal and plant health purposes. However, it is still quietly controversial as it suffers from a lack of tangible evidence. How can we enrich the debate on holobionts? How can we translate this concept in discoveries that can change farming practices? Our study is filling the gaps of the hologenome theory by showing that certain genes under natural selection and regulating plant microbiota are generalist in response to fungal and bacterial communities.
Structural analysis of the dynamic ribosome-translocon complex
Authors: Lewis Aaron J. O. , Zhong Frank , Keenan Robert J. , Hegde Ramanujan S. 
Published: December 2023

AbstractThe protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-EM and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61’s lateral gate, widening Sec61’s central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
Three-step mechanism of promoter escape by RNA polymerase II
Authors: Zhan Yumeng , Grabbe Frauke , Oberbeckmann Elisa , Dienemann Christian , Cramer Patrick 
Published: December 2023

SUMMARYThe transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase (Pol) II and initiation factors are broken to enable promoter escape. Here we reconstitute Pol II promoter escapein vitro, determine high-resolution structures of five transition intermediates, and show that promoter escape occurs in three major steps. First, the growing RNA transcript displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, rewinding of the upstream edge of the growing DNA bubble evicts TFIIA, TFIIB and TBP and repositions parts of TFIIE and TFIIF. Third, binding of DSIF and NELF evicts TFIIE and TFIIH, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of Pol II transcription.