bluuebunny/crossref_metadata_2025_split huggingface dataset:
Red blood cell dynamics in extravascular biological tissues modelled as canonical disordered porous media
Authors: Zhou Qi , Schirrmann Kerstin , Doman Eleanor , Chen Qi , Singh Naval , Selvaganapathy P. Ravi , Bernabeu Miguel O. , Jensen Oliver E. , Juel Anne , Chernyavsky Igor L. , Krüger Timm 
Published: June 2022

AbstractThe dynamics of blood flow in the smallest vessels and passages of the human body, where the cellular character of blood becomes prominent, plays a dominant role in the transport and exchange of solutes. Recent studies have revealed that the micro-haemodynamics of a vascular network is underpinned by its interconnected structure, and certain structural alterations such as capillary dilation and blockage can substantially change blood flow patterns. However, for extravascular media with disordered microstructure (e.g., the porous intervillous space in the placenta), it remains unclear how the medium’s structure affects the haemodynamics. Here, we simulate cellular blood flow in simple models of canonical porous media representative of extravascular biological tissue, with corroborative microfluidic experiments performed for validation purposes. For the media considered here, we observe three main effects: first, the relative apparent viscosity of blood increases with the structural disorder of the medium; second, the presence of red blood cells (RBCs) dynamically alters the flow distribution in the medium; third, increased structural disorder of the medium can promote a more homogeneous distribution of RBCs. Our findings contribute to a better understanding of the cellscale haemodynamics that mediates the relationship linking the function of certain biological tissues to their microstructure.
Anamnestic Humoral Correlates of Immunity Across SARS-CoV-2 Variants of Concern
Authors: McNamara Ryan P. , Maron Jenny S. , Bertera Harry L. , Boucau Julie , Roy Vicky , Barczak Amy K. ,   The Positives Study Staff, Franko Nicholas , Li Jonathan Z. , McLellan Jason S. , Siedner Mark J. , Lemieux Jacob E. , Chu Helen Y. , Alter Galit 
Published: June 2022

AbstractWhile immune correlates against SARS-CoV-2 are typically defined at peak immunogenicity following vaccination, immunologic responses that expand selectively during the anamnestic response following infection can provide mechanistic and detailed insights into the immune mechanisms of protection. Moreover, whether anamnestic correlates are conserved across VoCs, including the Delta and more distant Omicron variant of concern (VoC), remains unclear. To define the anamnestic correlates of immunity, across VOCs, we deeply profiled the humoral immune response in individuals recently infected with either the Delta or Omicron VoC. While limited acute N-terminal domain and RBD-specific immune expansion was observed following breakthrough, a significant immunodominant expansion of opsinophagocytic Spike-specific antibody responses focused largely on the conserved S2-domain of SARS-CoV-2 was observed 1 week after breakthrough infection. This S2-specific functional humoral response continued to evolve over 2-3 weeks following both Delta and Omicron breakthrough infection, targeting multiple VoCs and common coronaviruses. These responses were focused largely on the fusion peptide 2 and heptad repeat 1, both associated with enhanced rates of viral clearance. Taken together, our results point to a critical role of highly conserved, functional S2-specific responses in the control of SARS-CoV-2 infection, across VOCs, and thus humoral response linked to virus attenuation can guide next-generation generation vaccine boosting approaches to confer broad protection against future SARS-CoV-2 VoCs.
α-Synuclein Aggregation is Triggered by Amyloid-β Oligomers via Heterogeneous Primary Nucleation
Authors: Vadukul Devkee M. , Papp Marcell , Thrush Rebecca J. , Wang Jielei , Jin Yiyun , Arosio Paolo , Aprile Francesco A. 
Published: June 2022

ABSTRACTAn increasing number of cases where amyloids of different proteins are found in the same patient are being reported. This observation complicates diagnosis and clinical intervention. Amyloids of the amyloid-β peptide or the protein α-synuclein are traditionally considered hallmarks of Alzheimer’s and Parkinson’s diseases, respectively. However, the co-occurrence of amyloids of these proteins has also been reported in patients diagnosed with either disease. Here, we show that soluble species containing amyloid-β can induce the aggregation of α-synuclein. Fibrils formed under these conditions are solely composed of α-synuclein to which amyloid-β can be found associated, but not as part of the core of the fibrils. Importantly, by global kinetic analysis, we found that the aggregation of α-synuclein under these conditions occurs via heterogeneous primary nucleation, triggered by soluble aggregates containing amyloid-β.
Pregabalin silences oxaliplatin-activated sensory neurons to relieve cold allodynia
Authors: Iseppon Federico , Luiz Ana P. , Linley John E. , Wood John N. 
Published: June 2022

AbstractOxaliplatin is a platinum-based chemotherapeutic agent that causes cold and mechanical allodynia in up to 90% of patients. Silent NaV1.8-positive nociceptive cold sensors have been shown to be unmasked by oxaliplatin and other neuropathic insults. This event has been causally linked to the development of cold and mechanical allodynia. Pregabalin is an anti-epileptic and analgesic drug that acts through a calcium channel α2δ-1 subunit to lower neurotransmitter release. Recent data also suggest pregabalin can act on NMDA receptors and other proteins, but the site of analgesic action has been considered to be the central nervous system. We examined the effects of pregabalin on oxaliplatin-evoked unmasking of cold sensitive neurons using mice expressing GCaMP-3 driven by a Pirt promoter in all sensory neurons. We found that in mice treated with oxaliplatin, intravenous injection of pregabalin significantly decreased cold allodynia. Interestingly, pregabalin also decreased the number of sensory neurons responding to cold nociceptive stimuli by altering their excitability and their temperature thresholds. These silenced neurons are medium/large cells responding to both painful mechanical and cold stimuli, corresponding to the “silent” cold sensors that become active in numerous neuropathic pain models. Deletion of α2δ-1 subunits abolished the effects of pregabalin on both cold allodynia and the silencing of sensory neuron unmasked by oxaliplatin. Taken together, these results define a novel, peripheral inhibitory effect of pregabalin on the excitability of silent cold-sensing neurons in a model of oxaliplatin-dependent cold allodynia.Abbreviated SummaryIseppon et al. report a novel, peripheral effect of pregabalin on oxaliplatin-dependent cold allodynia. The drug exerts its effect by silencing a specific sub-population of neurons responding to cold and mechanical stimuli in the dorsal root ganglion, and this effect is dependent on the α2δ-1 subunit of voltage-gated calcium channels.
Endogenous Rab38 regulates LRRK2’s membrane recruitment and substrate Rab phosphorylation in melanocytes
Authors: Unapanta Alexandra , Shavarebi Farbod , Porath Jacob , Balen Carson , Nguyen Albert , Tseng Josh , Shen Yiyi , Liu Michelle , Lis Pawel , Di Pietro Santiago M. , Hiniker Annie 
Published: June 2022

AbstractPoint mutations in LRRK2 cause Parkinson’s Disease and augment LRRK2’s kinase activity. However, cellular pathways that enhance LRRK2 kinase function have not been identified. While overexpressed Rab29 draws LRRK2 to Golgi membranes to increase LRRK2 kinase activity, there is little evidence that endogenous Rab29 performs this function under physiological conditions. Here we identify Rab38 as a novel physiological regulator of LRRK2. In mouse melanocytes, which express high levels of Rab38, Rab32, and Rab29, knockdown of Rab38 but not Rab32 or Rab29 decreases phosphorylation of multiple LRRK2 substrates, including Rab10 and Rab12, by both exogenous and endogenous LRRK2. In B16-F10 mouse melanoma cells, Rab38 drives LRRK2 membrane association, and overexpressed kinase-active but not kinase-inactive LRRK2 shows striking pericentriolar recruitment, which is dependent on the presence of endogenous Rab38 but not Rab32 or Rab29. Deletion or mutation of LRRK2 at the Rab38 binding site in the N-terminal armadillo domain decreases LRRK2 membrane association, pericentriolar recruitment, and ability to phosphorylate Rab10. Consistently, overexpression of LRRK2350-550, a fragment that encompasses the Rab38 binding site, blocks endogenous LRRK2’s phosphorylation of Thr73-Rab10. Finally, disruption of BLOC-3, the guanine nucleotide exchange factor for Rab38 and 32, inhibits Rab38’s regulation of LRRK2. In sum, our data identify Rab38 as a physiologic regulator of LRRK2 function and lend support to a model in which LRRK2 plays a central role in Rab GTPase coordination of vesicular trafficking.
Type III CRISPR–Cas provides resistance against nucleus-forming jumbo phages via abortive infection
Authors: Mayo-Muñoz David , Smith Leah M. , Garcia-Doval Carmela , Malone Lucia M. , Harding Kate R. , Jackson Simon A. , Hampton Hannah G. , Fagerlund Robert D. , Gumy Laura F. , Fineran Peter C. 
Published: June 2022

SUMMARYBacteria have diverse defences against phages. In response, jumbo phages evade multiple DNA-targeting defences by protecting their DNA inside a nucleus-like structure. We previously demonstrated that RNA-targeting type III CRISPR–Cas systems provide jumbo phage immunity by recognising viral mRNA exported from the nucleus for translation. Here, we demonstrate that recognition of phage mRNA by the type III system activates a cyclic triadenylate-dependent accessory nuclease, NucC. Although unable to access phage DNA in the nucleus, NucC degrades the bacterial chromosome, triggers cell death, and disrupts phage replication and maturation. Hence, type III-mediated jumbo phage immunity occurs via abortive infection, with suppression of the viral epidemic protecting the population. We further show that type III systems targeting jumbo phages have diverse accessory nucleases, including RNases that provide immunity. Our study demonstrates how type III CRISPR–Cas systems overcome the inaccessibility of jumbo phage DNA to provide robust immunity.
Paralog dispensability shapes homozygous deletion patterns in tumor genomes
Authors: De Kegel Barbara , Ryan Colm J. 
Published: June 2022

AbstractGenomic instability is a hallmark of cancer, resulting in tumor genomes having large numbers of genetic aberrations, including homozygous deletions of protein coding genes. That tumor cells remain viable in the presence of such gene loss suggests high robustness to genetic perturbation. In model organisms and cancer cell lines, paralogs have been shown to contribute substantially to genetic robustness – they are generally more dispensable for growth than singletons. Here, by analyzing copy number profiles of >10,000 tumors, we test the hypothesis that the increased dispensability of paralogs shapes tumor genome evolution. We find that genes with paralogs are more likely to be homozygously deleted and that this cannot be explained by other factors known to influence copy number variation. Furthermore, features that influence paralog dispensability in cancer cell lines correlate with paralog deletion frequency in tumors. Finally, paralogs that are broadly essential in cancer cell lines are less frequently deleted in tumors than non-essential paralogs. Overall our results suggest that homozygous deletions of paralogs are more frequently observed in tumor genomes because paralogs are more dispensable.
Clean-PIE: a novel strategy for efficiently constructing precise circRNA with thoroughly minimized immunogenicity to direct potent and durable protein expression
Authors: Qiu Zonghao , Hou Qiangbo , Zhao Yang , Zhu Jiafeng , Zhai Mengting , Li Daolei , Li Yi , Liu Chunxi , Li Na , Cao Yifei , Yang Jiali , Sun Zhenhua , Zuo Chijian 
Published: June 2022

AbstractTranslatable circular RNAs (circRNAs) are emerging as a crucial molecular format for transient protein expression, with high potential to be an alternative for linear mRNA to reshape the landscape of mRNA pharmaceutical industry. Canonical Anabaena permuted intron-exon (Ana PIE) format that developed by ORNA is an efficient method for RNA circularization, and the engineered circRNAs direct supreme protein expression in eukaryotic cells. However, recent studies revealed that this method may unavoidably result in a remain of immunogenicity in the circRNA products, albeit after thorough RNA purification. In the current study, we develop a novel strategy for efficient generation of circRNA, via the permuted T4Td introns mediated autocatalytically ribozymatic reaction mediated ligation of the flanking segment sequences that concealing in ORF or translation initiation sequence (normally equal to IRES). This strategy universally realizes around 90% circularization effectivity, and the circRNA products can be purified to around 90% purity by our new purification method, and presented thoroughly minimized immunogenicity, thus is termed “Clean-PIE”. The purified circRNAs are found to direct potent and durable expression of various proteins in vitro and in vivo. The partly purified Fluc circRNA by HPLC-SEC was found to direct Fluc expression in muscle for no less than 20 days. The highly purified circRNA exhibits much stronger protein expression in vitro and in vivo, and presumed a longer duration. Additionally, the scale-up of RNA circularization with the RNA precursors from 1 L transcription revealed high circularization effectivity (around 90%) and a high productivity of the final circRNA products. Collectively, Clean-PIE is a novel circRNA platform that possesses high circularization effectivity, enabled high RNA purity and thoroughly minimized immunogenicity, as well as scaling-up accessibility and directing extreme durability of protein expression, thus has the potential to develop advanced RNA vaccines and therapeutics in pharmaceutical industrial scale.
Surface productivity gradients govern changes in abundance and physiological status of deep ocean prokaryotes across the tropical and subtropical Atlantic
Authors: Gómez-Letona Markel , Arístegui Javier , Hernández-Hernández Nauzet , Pérez-Lorenzo María , Álvarez-Salgado Xosé Antón , Teira Eva , Sebastián Marta 
Published: June 2022

AbstractProkaryotes represent a major fraction of marine biomass and play a key role in the global carbon cycle. We studied the vertical profiles (from surface down to the bathypelagic realm) of abundance, cytometric signatures, and activity of prokaryotic communities along a productivity gradient in the subtropical and tropical Atlantic to assess whether there is a vertical linkage between surface productivity regimes and deep ocean prokaryotic communities. We found that latitudinal changes in the vertical patterns of cytometric variables were coupled with surface productivity: higher prokaryotic abundances and viabilities, and smaller cell sizes were observed below highly productive surface waters, an effect reaching down to the bathypelagic layer. On the contrary, leucine uptake rates in deep waters showed no clear relationship with surface productivity. Changes in resource and energy allocation to growth vs. maintenance in hostile environments, cell-size-dependent metabolic requirements and variability in leucine to carbon conversion may all be part of the array of factors involved in controlling prokaryotic activity patterns that were measured. Our work adds to the recent findings that highlight the importance of vertical connectivity for prokaryotic communities in the dark ocean.
Dynamic Compartmentalisation of Intracellular Sodium in collecting duct cells
Authors: Assmus A. , Mullins L. , Sherborne C. , Peter A. , Early J. , Claeyssens F. , Haycock J. W. , Hunter R. , Mullins J. J. 
Published: June 2022

AbstractIn Principal cells (PC) of the cortical collecting duct (CCD), the highly regulated and coordinated reabsorption of sodium occurs through the epithelial sodium channel (ENaC) at the apical membrane and Na/K ATPase at the basolateral membrane. However, it is not known how sodium ions (Na+) are transported across the cell. We investigated intracellular transport in mCCDcl1 cells using a fluorescent sodium dye, CoroNa Green AM. Dye uptake was stimulated by aldosterone, blocked by amiloride (an ENaC inhibiter), and basolateral transport was prevented by ouabain (an Na/K ATPase blocker) thus validating the dye’s apparently faithful replication of sodium transport. Cells exhibited a consistent pattern of sodium-containing vesicles, of various sizes, surrounded by cytoskeleton and lipid membrane. While the smallest vesicles (∼0.5μm) co-stained with lysotracker, larger vesicles (up to 6.4μm) did not co-stain with either lysosomal- or mitochondrial-specific dyes and appeared to have internal structure, suggesting that they were multivesicular bodies. Time-lapse imaging showed a subset of these multivesicular bodies release or take up sodium dye in a controlled manner. Our novel data suggest that intracellular sodium compartmentalisation is highly regulated and offer new insights into intracellular sodium dynamics in the collecting duct, revealing potential new targets for control of sodium homeostasis.New and NoteworthyThe article shows for the first time, to our knowledge, intracellular sodium transport mechanism in mCCDcl1 cells in the form of dynamic vesicular bodies. These structures offer new targets for the regulation of sodium homeostasis and transport in the kidney collecting duct, with wider implications for blood pressure regulation.
Analysis of pre-symptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration
Authors: Garcia-Vaquero Marina , Heim Marjorie , Flix Barbara , Pereira Marcelo , Palin Lucile , Marques Tânia M. , Pinto Francisco R. , de Las Rivas Javier , Voigt Aaron , Besse Florence , Gama-Carvalho Margarida 
Published: June 2022

AbstractSpinal Muscular Atrophy (SMA) and Amyotrophic Lateral Sclerosis (ALS) share phenotypic and molecular commonalities, including the fact that they can be caused by mutations in ubiquitous proteins involved in RNA metabolism, namely SMN, TDP-43 and FUS. Although this suggests the existence of common disease mechanisms, there is currently no model to explain the resulting motor neuron dysfunction. In this work we generated a parallel set of Drosophila models for adult-onset RNAi and tagged neuronal expression of the fly orthologues of the three human proteins, named Smn, TBPH and Caz, respectively. We profiled nuclear and cytoplasmic bound mRNAs using a RIP-seq approach and characterized the transcriptome of the RNAi models by RNA-seq. To unravel the mechanisms underlying the common functional impact of these proteins on neuronal cells, we devised a computational approach based on the construction of a tissue-specific library of protein functional modules, selected by an overall impact score measuring the estimated extent of perturbation caused by each gene knockdown. Transcriptome analysis revealed that the three proteins do not bind to the same RNA molecules and that only a limited set of functionally unrelated transcripts is commonly affected by their knock-down. However, our integrative approach revealed they exert a concerted effect on protein functional modules, acting through distinct targets. Most strikingly, functional annotation revealed that these modules are involved in critical cellular pathways for motor neurons, including neuromuscular junction function. Furthermore, selected modules were found to be significantly enriched in orthologues of human neuronal disease genes. The results presented here show that SMA and ALS disease-associated genes linked to RNA metabolism functionally converge on neuronal protein complexes, providing a new hypothesis to explain the common motor neuron phenotype. The functional modules identified represent promising biomarkers and therapeutic targets, namely given their alteration in asymptomatic settings.
Theileria annulata histone deacetylase 1 (TaHDAC1) initiates schizont to merozoite stage conversion
Authors: Tajeri Shahin , Momeux Laurence , Saintpierre Benjamin , Mfarrej Sara , Chapple Alexander , Mourier Tobias , Shiels Brian , Ariey Frédéric , Pain Arnab , Langsley Gordon 
Published: June 2022

AbstractA fungal metabolite, FR235222, specifically inhibits a histone deacetylase of the apicomplexan parasite Toxoplasma gondii and TgHDAC3 has emerged as a key factor regulating developmental stage transition in this species. Here, we exploited FR235222 to ask if changes in histone acetylation regulate developmental stage transition of Theileria annulata, another apicomplexan species. We found that FR235222 treatment of T. annulata-infected transformed leukocytes induced a proliferation arrest. The blockade in proliferation was due to drug-induced conversion of intracellular schizonts to merozoites that lack the ability to maintain host leukocyte cell division. Induction of merogony by FR235222 leads to an increase in expression of merozoite-marker (rhoptry) proteins. RNA-seq of FR235222-treated T. annulata-infected B cells identified deregulated expression of 468 parasite genes including a number encoding parasite ApiAP2 transcription factors. Thus, similar to T. gondii, FR235222 inhibits T. annulata HDAC (TaHDAC1) activity and places parasite histone acetylation as a major regulatory event of the transition from schizonts to merozoites.
Cancer cells survival is dependent on the lincRNA JUNI
Authors: Kumar Vikash , Sabaté-Cadenas Xavier , Soni Isha , Stern Esther , Carine Vias , Ginsberg Doron , Dodel Martin , Mardakheh Faraz K. , Shkumatava Alena , Shaulian Eitan 
Published: June 2022

SummaryIdentification of key factors for cellular survival is a basis for therapy. We identified JUNI (linc01135) as a stress-regulated lncRNA, essential for cell survival and implicated in cancer. Besides regulating c-Jun expression we demonstrate c-Jun-independent, robust requirement for cell survival. Analysis of median survival of cancer patients suffering from various types of cancer reveals correlations of JUNI expression levels with alterations in patients’ survival. JUNI’s antagonistic interaction with DUSP14, a negative regulator of the JNK pathway, underlies the regulation of c-Jun and partial effects on cellular survival. Consistently, DUSP14 expression is coherently inversely-correlated with the survival of patients suffering from the same types of cancer. Our data suggests that JUNI is a novel master regulator of cell fate.SummaryJUNI is a novel regulator of cell survival, JNK activation and c-Jun expression, implicated in survival of cancer patients
Identification of a guanine-specific pocket in the protein N of SARS-CoV-2
Authors: Ciges-Tomas J. Rafael , Franco María Luisa , Vilar Marçal 
Published: June 2022

ABSTRACTThe SARS-CoV-2 nucleocapsid protein (N) is responsible for RNA binding. Here we report the crystal structure of the C-terminal domain (NCTD) in open and closed conformations and in complex with guanine triphosphate, GTP. The crystal structure and biochemical studies reveals a specific interaction between the guanine, a nucleotide enriched in the packaging signals regions of coronaviruses, and a highly conserved tryptophan residue (W330). In addition, EMSA assays with SARS-CoV-2 derived RNA hairpin loops from a putative viral packaging sequence showed the preference interaction of the N-CTD to RNA oligonucleotides containing G and the loss of the specificity in the mutant W330A. Here we propose that this interaction may facilitate the viral assembly process. In summary we have identified a specific guanine-binding pocket in the N protein that may be used to design viral assembly inhibitors.