bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel RAB11-containing adaptor complex anchoring myosin-5 to secretory vesicles
Authors: Pinar Mario , Alonso Ana , de los Ríos Vivian , Bravo-Plaza Ignacio , Gandara Álvaro , Arias-Palomo Ernesto , Á. Peñalva Miguel 
Published: September 2021

AbstractHyphal fungi grow rapidly by apical extension, providing a notorious example of polarized growth. The continuous supply of secretory vesicles necessary to meet the demands of the extending tip and the long intracellular distances existing between the tip and the basal septum, often localized > 100 µm away from the former, impose the need of efficient networks of intracellular traffic involving exquisite cooperation between microtubule- and actin-mediated transport. In Aspergillus nidulans kinesin-1 conveys secretory vesicles to the hyphal tip, where they are transferred to myosin-5, which focuses them at the growing apex, thereby determining cell shape. This relay mechanism and the central role played by myosin-5 in hyphal morphogenesis suggested that the mechanisms anchoring secretory vesicles to this motor should involve specific adaptor(s) ensuring the robustness of actomyosin-dependent transport.Secretory vesicles are charged with RAB11, a regulatory GTPase that determines the Golgi to post-Golgi identity transition. By using a combination of shotgun proteomics, GST-RAB pull-down assays, in vitro reconstitution experiments, targeted reverse genetics and multidimensional fluorescence microscopy with endogenously tagged proteins we show that RAB11, the master regulator of fungal exocytosis, mediates myosin-5 engagement both by contacting the motor and by recruiting UDS1, a homologue of an as yet uncharacterized Schizosaccharomyces protein ‘upregulated during mitosis’, which we demonstrate to be a novel RAB11 effector. Analytical ultracentrifugation determined that UDS1 is an elongated dimer and negative-stain electron microscopy showed that, in agreement, UDS1 is rod-shaped. UDS1 does not contact myosin-5 directly, but rather recruits the coiled-coil HMSV, which bridges RAB11/UDS1 to myosin-5. An HMSV-scaffolded complex containing UDS1 and myosin-5 is present in cells, and a RAB11-UDS1-HMSV complex can be reconstituted in vitro in a RAB nucleotide state-dependent manner. In the absence of UDS1/HMSV the steady state levels of myosin-5 at the apical vesicle supply center diminish markedly, such that microtubule-dependent transport spreading vesicles across the apical dome predominates over apex-focused actin-mediated transport. As a consequence, RAB11 and chitin-synthase B (a cargo of the RAB11 pathway) are not focused at the apex, being distributed instead across the apical dome. Therefore, the RAB11 effector UDS1/HMSV cooperates with the GTPase to adapt secretory vesicles to myosin-5, which is required for the apical targeting of RAB11 cargoes and thus for the normal morphology of the hyphae.
Germline Missense Variants in CDC20 Result in Aberrant Mitotic Progression and Familial Cancer
Authors: Chen Owen J. , Castellsagué Ester , Moustafa-Kamal Mohamed , Nadaf Javad , Rivera Barbara , Fahiminiya Somayyeh , Wang Yilin , Gamache Isabelle , Pacifico Caterina , Jiang Lai , Carrot-Zhang Jian , Witkowski Leora , Berghuis Albert M. , Schoenberger Stefan , Schneider Dominik , Bens Susanne , Siebert Reiner , Stewart Colin J. R. , Zhang Ziguo , Chao William C. , Greenwood Celia M.T. , Barford David , Tischkowitz Marc , Majewski Jacek , Foulkes William D. , Teodoro Jose G. 
Published: September 2021

SUMMARYCDC20 is a co-activator of the anaphase promoting complex/cyclosome (APC/C) and is essential for mitotic progression. APC/CCDC20 is inhibited by the spindle assembly checkpoint (SAC), which prevents premature separation of sister chromatids and aneuploidy in daughter cells. Although overexpression of CDC20 is common in many cancers, oncogenic mutations have never been identified in humans. Using whole exome sequencing, we identified heterozygous missense CDC20 variants (L151R and N331K) that segregate with cancer in two families. Characterization of these mutants showed they retain APC/C activation activity but show reduced binding to BUBR1, a component of the SAC. Expression of L151R and N331K promoted mitotic slippage in HeLa cells and primary skin fibroblasts derived from carriers. CRISPR/Cas9 was used to generate mice carrying N331K. Homozygous mice carrying N331K were non-viable, however, heterozygotes displayed accelerated oncogenicity in Myc-driven cancers. These findings highlight an unappreciated role for CDC20 variants as tumor promoting genes in humans.
A cell-based platform for oxidative stress monitoring in motor neurons using genetically encoded biosensors of H2O2
Authors: Ustyantseva Elizaveta I. , Zakian Suren M. , Medvedev Sergey P. 
Published: September 2021

ABSTRACTBackgroundOxidative stress plays an important role in the development of neurodegenerative diseases: it either can be the initiator or part of a pathological cascade leading to the neuron’s death. Although a lot of methods are known for oxidative stress study, most of them operate on non-native cellular substrates or interfere with the cell functioning. Genetically encoded (GE) biosensors of oxidative stress demonstrated their general functionality and overall safety in various live systems. However, there is still insufficient data regarding their use for research of disease-related phenotypes in relevant model systems, such as human cells.MethodsWe applied CRISPR/Cas9 genome editing to introduce mutations (c.272A>C and c.382G>C) in the associated with amyotrophic lateral sclerosis SOD1 gene of induced pluripotent stem cells (iPSC) obtained from a healthy individual. Using CRISPR/Cas9, we modified these mutant iPSC lines, as well as the parental iPSC line, and a patient-specific SOD1D91A/D91A iPSC line with ratiometric GE biosensors of cytoplasmic (Cyto-roGFP2-Orp1) and mitochondrial (Mito-roGFP2-Orp1) H2O2. The biosensors sequences along with a specific transactivator for doxycycline-controllable expression were inserted in the “safe harbor” AAVS1 (adeno-associated virus site 1) locus. We differentiated these transgenic iPSCs into motor neurons and investigated the functionality of the biosensors in such a system. We measured relative oxidation in the cultured motor neurons and its dependence on culture conditions, age, and genotype, as well as kinetics of H2O2 elimination in real-time.ResultsWe developed a cell-based platform consisting of isogenic iPSC lines with different genotypes associated with amyotrophic lateral sclerosis. The iPSC lines were modified with GE biosensors of cytoplasmic and mitochondrial H2O2. We provide proof-of-principle data showing that this approach may be suitable for monitoring oxidative stress in cell models of various neurodegenerative diseases as the biosensors reflect the redox state of neurons.ConclusionWe found that the GE biosensors inserted in the AAVS1 locus remain functional in motor neurons and reflect pathological features of mutant motor neurons, although the readout largely depends on the severity of the mutation.
The RNA-binding protein DRBD18 regulates processing and export of the mRNA encoding Trypanosoma brucei RNA-binding protein 10
Authors: Tshitenge Tania Bishola , Liu Bin , Clayton Christine 
Published: September 2021

AbstractThe parasite Trypanosoma brucei grows as bloodstream forms in mammalian hosts, and as procyclic forms in tsetse flies. Trypanosome protein coding genes are arranged in polycistronic transcription units, so gene expression regulation depends heavily on post-transcriptional mechanisms. The essential RNA-binding protein RBP10 is expressed only in mammalian-infective forms, where it targets procyclic-specific mRNAs for destruction. We show that developmental regulation of RBP10 expression is mediated by the exceptionally long 7.3 Kb 3’-UTR of its mRNA. Different regulatory sequences that can independently enhance mRNA stability and translation in bloodstream forms, or destabilize and repress translation in procyclic forms, are scattered throughout the 3’-UTR. The RNA-binding protein DRBD18 is implicated in the export of a subset of mRNAs from the nucleus in procyclic forms. We confirmed that in bloodstream forms, DRBD18 copurifies the outer ring of the nuclear pore, mRNA export proteins and exon junction complex proteins. Loss of DRBD18 in bloodstream forms caused accumulation of several shortened RBP10 mRNA isoforms, with loss of longer species, but RNAi targeting the essential export factor MEX67 did not cause such changes, demonstrating specificity. Long RBP10 mRNAs accumulated in the nucleus, while shorter ones reached the cytoplasm. We suggest that DRBD18 binds to processing signals in the RBP10 3’-UTR, simultaneously preventing their use and recruiting mRNA export factors. DRBD18 depletion caused truncation of the 3’-UTRs of more than 100 other mRNAs, suggesting that it has an important role in regulating use of alternative processing sites.
Constitutive loss of DNMT3A causes morbid obesity through misregulation of adipogenesis
Authors: Tovy Ayala , Reyes Jaime M. , Zhang Linda , Huang Yung-Hsin , Rosas Carina , Daquinag Alexes C. , Guzman Anna G. , Ramabadran Raghav , Chen Chun-Wei , Gu Tianpeng , Gupta Sinjini , Ortinau Laura , Park Dongsu , Cox Aaron R. , Rau Rachel E , Hartig Sean M. , Kolonin Mikhail G , Goodell Margaret A. 
Published: September 2021

AbstractDNA Methyltransferase 3A (DNMT3A) is an important facilitator of differentiation of both embryonic and hematopoietic stem cells. Heterozygous germline mutations in DNMT3A lead to Tatton-Brown-Rahman Syndrome (TBRS), characterized by obesity and excessive height. While DNMT3A is known to impact feeding behavior via the hypothalamus, here we investigated a role in adipocyte progenitors utilizing heterozygous knockout mice that recapitulate cardinal TBRS phenotypes. These mice become morbidly obese due to adipocyte enlargement and tissue expansion. Adipose tissue in these mice exhibited defects in preadipocyte maturation and precocious activation of inflammatory gene networks, including interleukin-6 signaling. Adipocyte progenitor cell lines lacking DNMT3A exhibited aberrant differentiation. Furthermore, mice in which Dnmt3a was specifically ablated in adipocyte progenitors showed enlarged fat depots and increased progenitor numbers, partly recapitulating the TBRS obesity phenotypes. Loss of DNMT3A led to constitutive DNA hypomethylation, such that the DNA methylation landscape of young adipocyte progenitors resemble that of older wild-type mice. Together, our results demonstrate that DNMT3A coordinates both the central and local control of energy storage required to maintain normal weight and prevent inflammatory obesity.
Secretin channel-interactors prevent antibiotic influx during type IV pili assembly in Pseudomonas aeruginosa
Authors: Kwon Oh Hyun , Sher Joel W , Kim Bi-o , Cho You-Hee , Cho Hongbaek 
Published: September 2021

AbstractType IV pili (T4P) are important virulence factors involved in host attachment and other aspects of bacterial pathogenesis. In Gram-negative bacteria, the T4P filament is polymerized from pilin subunits at the platform complex in the inner membrane (IM) and exits the outer membrane (OM) through the OM secretin channel. Although essential for T4P assembly and function, the OM secretin complexes can potentially impair the permeability barrier function of the OM and allow the entry of antibiotics and other toxic molecules. The mechanism by which Gram-negative bacteria prevent secretin-mediated OM leakage is currently not well understood. Here, we report a discovery of SlkA and SlkB (PA5122 and PA5123) that prevent permeation of several classes of antibiotics through the secretin channel of Pseudomonas aeruginosa type IV pili. We found these periplasmic proteins interact with the OM secretin complex and prevent toxic molecules from entering through the channel when there is a problem in the assembly of the T4P IM subcomplexes or when docking between the OM and IM complexes is defective. Thus, our results indicate that the secretin channel-interacting proteins play an important role in maintaining the OM permeability barrier, suggesting they may be attractive targets for potentiators that sensitize Gram-negative pathogens to antibiotics that are normally ineffective at penetrating the OM.
Axial multi-layer perceptron architecture for automatic segmentation of choroid plexus in multiple sclerosis
Authors: Schmidt-Mengin Marius , Ricigliano Vito A.G. , Bodini Benedetta , Morena Emanuele , Colombi Annalisa , Hamzaoui Mariem , Yazdan Panah Arya , Stankoff Bruno , Colliot Olivier 
Published: September 2021

ABSTRACTChoroid plexuses (CP) are structures of the brain ventricles which produce most of the cerebrospinal fluid (CSF). Several postmortem and in vivo studies have pointed towards their role in the inflammatory processes in multiple sclerosis (MS). Automatic segmentation of CP from MRI thus has high value for studying their characteristics in large cohorts of patients. To the best of our knowledge, the only freely available tool for CP segmentation is FreeSurfer but its accuracy for this specific structure is poor. In this paper, we propose to automatically segment CP from non-contrast enhanced T1-weighted MRI. To that end, we introduce a new model called “Axial-MLP” based on an assembly of Axial multi-layer perceptrons (MLPs). This is inspired by recent works which showed that the self-attention layers of Transformers can be replaced with MLPs. This approach is systematically compared with a standard 3D U-Net, nnU-Net, Freesurfer and FastSurfer. For our experiments, we make use of a dataset of 141 subjects (44 controls and 97 patients with MS). We show that all the tested deep learning (DL) methods outperform FreeSurfer (Dice around 0.7 for DL vs 0.33 for FreeSurfer). Axial-MLP is competitive with U-Nets even though it is slightly less accurate. The conclusions of our paper are two-fold: 1) the studied deep learning methods could be useful tools to study CP in large cohorts of MS patients; 2) Axial-MLP is a potentially viable alternative to convolutional neural networks for such tasks, although it could benefit from further improvements.
Selective Modulator of Nuclear Receptor PPARγ with Reduced Adipogenic Potential Ameliorates Experimental Nephrotic Syndrome
Authors: Burton Claire , Rask Galen , Waller Amanda P , Webb Amy , Galdino-Pitta Marina R , Amato Angelica A. , Cianciolo Rachel , Becknell Brian , Kerlin Bryce A , Neves Francisco A. R. , Fornoni Alessia , Agrawal Shipra 
Published: September 2021

AbstractBackgroundGlomerular disease, often manifesting as nephrotic syndrome (NS) with high proteinuria, can be refractory to standard treatment and is typically associated with hypoalbuminemia, hypercholesterolemia and hypercoagulopathy. We hypothesized that the nuclear receptor PPARγ can be selectively modulated using a novel partial agonist, GQ-16, to gain therapeutic advantage over traditional PPARγ agonists (e.g. thiazolidinediones) for the treatment of glomerular disease.MethodsNephropathy was induced with puromycin amino-nucleoside (PAN) in Wistar rats and treated with Pioglitazone (Pio) or GQ-16. Plasma, serum, and urine chemistries were performed, and kidneys, glomeruli, liver, and white adipose tissue (WAT) were harvested. Lipid accumulation and adipogenic gene expression were measured in adipocytes.ResultsPAN-induced proteinuria was significantly reduced with Pio to 64% of PAN-value. It was reduced robustly with GQ-16 to 81% of PAN, which was comparable to controls. While both GQ-16 and Pio restored glomerularNphs1and hepaticPcsk9expression and reduced hypercholesterolemia, GQ-16 also restored glomerularNrf2, and reduced hypoalbuminemia and hypercoagulopathy. Furthermore, RNA-seq analysis identified both common and distinct restored glomerular genes downstream of Pio and GQ-16. Pio but not GQ-16 significantly inducedaP2(fatty acid binding protein) in adipocytes and in WAT. Pio induced more lipid accumulation than GQ-16 in differentiated adipocytes. Both, Pio and GQ-16 induced insulin sensitizing adipokines in WAT with varying degrees.ConclusionsSelective modulation of PPARγ by a partial agonist, GQ-16, is more advantageous than pioglitazone in reducing proteinuria and NS associated co-morbidities, while reducing the adipogenic side-effects conferred by traditional PPARγ full agonists.Translational StatementThe authors have previously reported that type-II diabetes drugs, thiazolidinediones (PPARγ agonists), also provide beneficial effects in reducing podocyte and glomerular injury. However, these drugs are associated with adverse effects such as weight gain, and their effects on glomerular disease-associated features are largely unexplored. Their current findings demonstrate that PPARγ can be selectively modulated by its partial agonist, GQ-16, which reduces proteinuria and improves nephrotic syndrome (NS) with reduced side-effects typically conferred by thiazolidinediones. These findings not only deepen our molecular understanding of the role of PPARγ in glomerular disease and underscore the potential for partial agonists of PPARγ, such as GQ-16 as a treatment modality for NS, but also lend the possibility of its potential benefits in diabetic nephropathy.
Development of a novel, pan-variant aerosol intervention for COVID-19
Authors: Shoemaker Robert H. , Panettieri Reynold A. , Libutti Steven K. , Hochster Howard S. , Watts Norman R. , Wingfield Paul T. , Starkl Philipp , Pimenov Lisabeth , Gawish Riem , Hladik Anastasiya , Knapp Sylvia , Boring Daniel , White Jonathan M. , Lawrence Quentin , Boone Jeremy , Marshall Jason D. , Matthews Rebecca L. , Cholewa Brian D. , Richig Jeffrey W. , Chen Ben T. , McCormick David L. , Gugensberger Romana , Höller Sonja , Penninger Josef M. , Wirnsberger Gerald 
Published: September 2021

AbstractTo develop a universal strategy to block SARS-CoV-2 cellular entry and infection represents a central aim for effective COVID-19 therapy. The growing impact of emerging variants of concern increases the urgency for development of effective interventions. Since ACE2 is the critical SARS-CoV-2 receptor and all tested variants bind to ACE2, some even at much increased affinity (see accompanying paper), we hypothesized that aerosol administration of clinical grade soluble human recombinant ACE2 (APN01) will neutralize SARS-CoV-2 in the airways, limit spread of infection in the lung and mitigate lung damage caused by deregulated signaling in the renin-angiotensin (RAS) and Kinin pathways. Here we show that intranasal administration of APN01 in a mouse model of SARS-CoV-2 infection dramatically reduced weight loss and prevented animal death. As a prerequisite to a clinical trial, we evaluated both virus binding activity and enzymatic activity for cleavage of Ang II following aerosolization. We report successful aerosolization for APN01, retaining viral binding as well as catalytic RAS activity. Dose range-finding and IND-enabling repeat-dose aerosol toxicology testing were conducted in dogs. Twice daily aerosol administration for two weeks at the maximum feasible concentration revealed no notable toxicities. Based on these results, a Phase I clinical trial in healthy volunteers can now be initiated, with subsequent Phase II testing in individuals with SARS-CoV-2 infection. This strategy could be used to develop a viable and rapidly actionable therapy to prevent and treat COVID-19, against all current and future SARS-CoV-2 variants.One Sentence SummaryPreclinical development and evaluation of aerosolized soluble recombinant human ACE2 (APN01) administered as a COVID-19 intervention is reported.
Controls on the isotopic composition of microbial methane
Authors: Gropp Jonathan , Jin Qusheng , Halevy Itay 
Published: September 2021

AbstractMicrobial methane production (methanogenesis) is responsible for more than half of the annual emission of this major greenhouse gas to the atmosphere. Though the stable isotopic composition of methane is often used to characterize its sources and sinks, strictly empirical descriptions of the isotopic signature of methanogenesis currently limit such attempts. We developed a biochemical-isotopic model of methanogenesis by CO2 reduction, which predicts carbon and hydrogen isotopic fractionations, and clumped isotopologue distributions, as functions of the cell’s environment. We mechanistically explain multiple-isotopic patterns in laboratory and natural settings and show that such patterns constrain the in-situ energetics of methanogenesis. Combining our model with environmental data, we infer that in almost all marine environments and gas deposits, energy-limited methanogenesis operates close to chemical and isotopic equilibrium.
Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes
Authors: Bergman Juraj , Schierup Mikkel Heide 
Published: September 2021

AbstractThe pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. As the largest point of contact between the X and Y, PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and associated mutational processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes and two archaic human genome sequences. We find that the PAR1 sequence is closer to nucleotide equilibrium than autosomal telomeric sequences. We detect a difference between long-term substitution patterns and extant diversity in PAR1 that is mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. Additionally, we detect excess C→G mutations in PAR1 of all great ape species, specific to the mutagenic effect of male recombination. Analysis of differences between frequencies of alleles segregating in females and males provided no evidence for sexually antagonistic selection in this region. Furthermore, despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence, as is the case for the X chromosome and the autosomes. Lastly, we study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis. Our study provides an unprecedented quantification of population genetic forces and insight into evolutionary processes governing PAR1 biology.