bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of Mitochondrial Genomic Variation with Corticobasal Degeneration, Progressive Supranuclear Palsy, and Neuropathological Tau Measures
Authors: Valentino Rebecca R. , Tamvaka Nikoleta , Heckman Michael G. , Johnson Patrick W. , Soto-Beasley Alexandra I. , Walton Ronald L. , Koga Shunsuke , Uitti Ryan J. , Wszolek Zbigniew K. , Dickson Dennis W. , Ross Owen A. 
Published: July 2020

AbstractMitochondrial health is important in ageing and dysfunctional oxidative phosphorylation (OXPHOS) accelerates ageing and influences neurodegeneration. Mitochondrial DNA (mtDNA) codes for vital OXPHOS subunits and mtDNA background has been associated with neurodegeneration; however, no study has characterised mtDNA variation in Progressive supranuclear palsy (PSP) or Corticobasal degeneration (CBD) risk or pathogenesis. In this case-control study, 916 (42.5% male) neurologically-healthy controls, 1051 (54.1% male) pathologically-confirmed PSP cases, and 173 (51.4% male) pathologically-confirmed CBD cases were assessed to determine how stable mtDNA polymorphisms, in the form of mtDNA haplogroups, were associated with risk of PSP, risk of CBD, age of PSP onset, PSP disease duration, and neuropathological tau pathology measures for neurofibrillary tangles (NFT), neuropil threads (NT), tufted astrocytes (TA), and oligodendroglial coiled bodies (CB). 767 PSP cases and 152 CBD cases had quantitative tau pathology scores. mtDNA was genotyped for 39 unique SNPs using Agena Bioscience iPlex technologies and mitochondrial haplogroups were defined to mitochondrial phylogeny. After adjustment for multiple testing, we observed a significant association with risk of CBD for mtDNA sub-haplogroup H4 (OR=4.49, P=0.001) and the HV/HV0a haplogroup was associated with a decreased severity of NT tau pathology in PSP cases (P=0.0023). Our study reports that mitochondrial genomic background may be associated with risk of CBD and may be influencing tau pathology measures in PSP. Replication of these findings will be important.
Modelling co-translational dimerisation for programmable nonlinearity in synthetic biology
Authors: Stoof Ruud , Goñi-Moreno Ángel 
Published: July 2020

AbstractNonlinearity plays a fundamental role in the performance of both natural and synthetic biological networks. Key functional motifs in living microbial systems, such as the emergence of bistability or oscillations, rely on nonlinear molecular dynamics. Despite its core importance, the rational design of nonlinearity remains an unmet challenge. This is largely due to a lack of mathematical modelling that accounts for the mechanistic basics of nonlinearity. We introduce a model for gene regulatory circuits that explicitly simulates protein dimerization—a well-known source of nonlinear dynamics. Specifically, our approach focusses on modelling co-translational dimerization: the formation of protein dimers during—and not after—translation. This is in contrast to the prevailing assumption that dimer generation is only viable between freely diffusing monomers (i.e., post-translational dimerization). We provide a method for fine-tuning nonlinearity on demand by balancing the impact of co- versus post-translational dimerization. Furthermore, we suggest design rules, such as protein length or physical separation between genes, that may be used to adjust dimerization dynamics in-vivo. The design, build and test of genetic circuits with on-demand nonlinear dynamics will greatly improve the programmability of synthetic biological systems.
The variation among sites of protein structure divergence is shaped by mutation and scaled by selection
Authors: Marcos María Laura , Echave Julian 
Published: July 2020

AbstractProtein structures do not evolve uniformly, but the degree of structure divergence varies among sites. The resulting site-dependent structure divergence patterns emerge from a process that involves mutation and selection, which may both, in principle, influence the emergent pattern. In contrast with sequence divergence patterns, which are known to be mainly determined by selection, the relative contributions of mutation and selection to structure divergence patterns is unclear. Here, studying 6 protein families with a mechanistic biophysical model of protein evolution, we untangle the effects of mutation and selection. We found that even in the absence of selection, structure divergence varies from site to site because the mutational sensitivity is not uniform. Selection scales the profile, increasing its amplitude, without changing its shape. This scaling effect follows from the similarity between mutational sensitivity and sequence variability profiles.
Nogo-A Beyond the RhoA/ROCK Pathway – Novel Components of Intracellular Nogo-A Signaling Cascades
Authors: Maibach Martina A. , Piovesana Ester , Kaiser Julia , Holm Mea M. , Risic Zorica , Maurer Michael , Schwab Martin E. 
Published: July 2020

AbstractNogo-A is a well-characterized myelin-associated membrane protein that restricts fibre growth and the regenerative capacity of the adult central nervous system after injury. To date Nogo-A post-receptor signalling pathway research focused on the RhoA/ROCK cascade, which can lead to growth cone collapse and neurite retraction. Much less is known about continued intracellular Nogo-A signalling mediating long-term neurite outgrowth inhibition resulting from transcriptional and translational changes. Here, we propose a simple but highly reproduciblein vitroassay to study Nogo-A related signaling and neurite outgrowth inhibition in general. Furthermore, we identified ERK1/2 as downstream effector of Nogo-A, partially mediating its neurite outgrowth inhibition. We describe ERK1/2 dependent changes of translational events such as elevation of RhoA levels within the growth cone, which may potentiate the cells’ responses to Nogo-A. We also observed Nogo-A dependent upregulation of the JAK/STAT pathway inhibitors SOCS3 and KLF4 and downregulation of insulin mediated phosphorylation of AKT, indicating direct negative crosstalk between Nogo-A signalling and the growth promoting JAK/STAT and AKT/mTORC1 pathways.
YAP/TAZ and EZH2 synergize to impair tumor suppressor activity of TGFBR2 in non-small cell lung cancer
Authors: Sardo Federica Lo , Pulito Claudio , Sacconi Andrea , Korita Etleva , Sudol Marius , Strano Sabrina , Blandino Giovanni 
Published: July 2020

AbstractLung cancer is the leading cause of cancer-related deaths, worldwide. Non–small cell lung cancer (NSCLC) is the most prevalent lung cancer subtype. YAP and TAZ have been implicated in lung cancer by acting as transcriptional co-activators of oncogenes or as transcriptional co-repressors of tumor suppressor genes. Previously we reported that YAP and TAZ regulate microRNAs expression in NSCLC. Among the set of regulated miRNAs, the oncogenic miR-25, 93, and 106b, clustering within the MCM7 gene were selected for further studies. We firstly identified Transforming Growth Factor-β (TGF-β) Receptor 2 (TGFBR2), a member of the TGF-β signaling, as a target of the miRNA cluster, which exhibited prognostic value because of its tumor suppressor activity. We found that YAP/TAZ-mediated repression of TGFBR2 occurs both: post-transcriptionally through the miR-106b-25 cluster and transcriptionally by engaging the EZH2 epigenetic repressor that we reported here as a novel target gene of YAP/TAZ. Furthermore, we document that YAP/TAZ and EZH2 cooperate in lung tumorigenesis by transcriptionally repressing a specific subset of tumor suppressor genes, including TGFBR2. Our findings point to YAP/TAZ and EZH2 as potential therapeutic targets for NSCLC treatment.
Induction of a SALL4-dependency for targeted cancer therapy
Authors: Yang Junyu , Gao Chong , Liu Miao , Chen Zhiyuan , Liu Yao-Chung , Kwon Junsu , Qi Jun , Tian Xi , Stein Alicia , Liu Yanjing , Kong Nikki R. , Wu Yue , Yin Shenyi , Xi Jianzhong Jeff , Luo Hongbo , Silberstein Leslie E. , Thoms Julie A. I. , Unnikrishnan Ashwin , Pimanda John E. , Tenen Daniel G. , Chai Li 
Published: July 2020

AbstractOncofetal protein SALL4 is critical for tumor cell survival, making it a promising target in cancer therapy. However, it is detectable only in a subset of cancer patients, which limits the therapeutic impact of a SALL4 targeted therapy. Here we report that SALL4 can be activated and/or upregulated pharmacologically by hypomethylating agents, such as 5-Aza-2’-deoxycytidine (DAC), which are used clinically, and that SALL4 negative cancer cells become SALL4 dependent following exogenous expression of SALL4. In addition, the histone deacetylase inhibitor Entinostat (ENT) negatively regulates SALL4 expression by upregulating miR-205. Both ENT and miR-205 treatment induced cell apoptosis, rescuable by SALL4 expression or miR-205 inhibition. Finally, DAC pre-treatment sensitizes SALL4 negative cancer cell lines to ENT both in culture andin vivoby upregulating SALL4. Overall, we propose a framework whereby the scope of targeted therapy can be expanded by sensitizing cancer cells to treatment by target induction and engineered dependency.SignificanceThis proof of concept study demonstrates that targeted cancer therapy can be achieved by inducing a targetable gene establishing a survival-dependency for cancer cells. For SALL4, sequential treatment of DAC and ENT could expand the scope of SALL4 targeted cancer therapy.
The DNA methyltransferase 1 (DNMT1) acts on neurodegeneration by modulating proteostasis-relevant intracellular processes
Authors: Bayer Cathrin , Pitschelatow Georg , Hannemann Nina , Linde Jenice , Reichard Julia , Pensold Daniel , Zimmer-Bensch Geraldine 
Published: July 2020

AbstractThe limited regenerative capacity of neuronal cells requires tight orchestration of cell death and survival regulation in the context of longevity, as well as age-associated and neurodegenerative diseases. Subordinate to genetic networks, epigenetic mechanisms, like DNA methylation and histone modifications, are involved in the regulation of neuronal functionality, and emerge as key contributors to the pathophysiology of neurodegenerative diseases. DNA methylation, a dynamic and reversible process, is executed by DNA methyltransferases (DNMTs). DNMT1 was previously shown to regulate neuronal survival in the aged brain, whereby a DNMT1-dependent modulation of processes relevant for protein degradation was proposed as underlying mechanism. Functional proteostasis networks are a mandatory prerequisite for the functionality and long-term survival of neurons. Malfunctioning proteostasis is found, inter alia, in neurodegenerative contexts. Here, we investigated whether DNMT1 affects critical aspects of the proteostasis network by a combination of expression studies, life cell imaging and biochemical analyses. We found that DNMT1 negatively impacts retrograde trafficking and autophagy, both being involved in the clearance of aggregation-prone proteins by the aggresome-autophagy pathway. In line with this, we found that the transport of GFP-labeled mutant HTT to perinuclear regions, proposed to by cytoprotective, also depends on DNMT1. Depletion ofDnmt1accelerated HTT perinuclear HTT aggregation and improved the survival of cells transfected with mutant HTT. This suggests that mutant HTT-induced cytotoxicity is at least in part mediated by DNMT1-dependent modulation of degradative pathways.
DNA damage alters nuclear mechanics through chromatin reorganisation
Authors: dos Santos Ália , Cook Alexander W. , Gough Rosemarie E , Schilling Martin , Olszok Nora Aleida , Brown Ian , Wang Lin , Aaron Jesse , Martin-Fernandez Marisa L. , Rehfeldt Florian , Toseland Christopher P. 
Published: July 2020

ABSTRACTDNA double-strand breaks (DSBs) drive genomic instability. For efficient and accurate repair of these DNA lesions, the cell activates DNA damage repair pathways. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency.Here, we used Atomic Force Microscopy (AFM) to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance.
The genotype-phenotype landscape of an allosteric protein
Authors: Tack Drew S. , Tonner Peter D. , Pressman Abe , Olson Nathanael D. , Levy Sasha F. , Romantseva Eugenia F. , Alperovich Nina , Vasilyeva Olga , Ross David 
Published: July 2020

AbstractAllostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Quantitative methods to characterize the genotype-phenotype relationships for allosteric proteins would provide data needed to improve engineering of biological systems, to uncover the role of allosteric mis-regulation in disease, and to develop allosterically targeted drugs1. Here we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: thelacrepressor fromEscherichia coli, LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively determine the dose-response curves for nearly 105variants of the LacI sensor. With the resulting data, we train a deep neural network (DNN) capable of predicting the dose-response curves for additional LacI genotypesin silico.We then map the impact of amino acid substitutions on the allosteric function of LacI. Additionally, we demonstrate engineering of allosteric function with unprecedented accuracy by identifying LacI variants from the measured landscape with quantitatively specified dose-response curves. Finally, we discover sensors with previously unreported band-stop dose-response curves. Overall, our results provide the first high-coverage, quantitative view of genotype-phenotype relationships for an allosteric protein, revealing a surprising diversity of phenotypes and showing that each phenotype is accessible via multiple distinct genotypes.
Development of conformational BRET biosensors that monitor Ezrin, Radixin and Moesin activation in real-time
Authors: Leguay Kévin , Decelle Barbara , He Yu Yan , Hogue Mireille , Kobayashi Hiroyuki , Gouill Christian Le , Bouvier Michel , Carréno Sébastien 
Published: July 2020

SUMMARYEzrin, Radixin and Moesin compose the family of ERM proteins. They link actin and microtubule filaments to the plasma membrane to control signaling and cell morphogenesis. Importantly, their activity promotes invasive properties of metastatic cells from different cancer origins. Therefore, a precise understanding of how these proteins are regulated is important for the understanding of the mechanism controlling cell shape as well as providing new opportunities for the development of innovative cancer therapies. ERMs are believed to exist in two main conformational states: a close-inactive conformation in the cytoplasm that is recruited at the plasma membrane to convert into an open-active conformation. Here, we developed and characterized novel BRET-based conformational biosensors, compatible with high throughput screening, that monitor Ezrin, Radixin or Moesin individual activation in living cells. We showed that these biosensors faithfully monitor ERM activation and can be used to quantify the impact of small molecules, mutation of regulatory amino acids or depletion of upstream regulators on their activity. The use of these biosensors allowed us to uncover a novel aspect of ERM activation process involving a pool of closed-inactive ERMs stably associated with the plasma membrane. Upon stimulation, this pool serves as a cortical reserve that is rapidly activated before the recruitment of cytoplasmic ERMs.
Polymeric Pathogen-like Particles-Based Combination Adjuvants Elicit Potent Mucosal T Cell Immunity to Influenza A Virus
Authors: Kingstad-Bakke Brock , Toy Randall , Lee Woojong , Pradhan Pallab , Vogel Gabriela , Marinaik Chandranaik , Larsen Autumn , Kawaoka Yoshihoro , Roy Krishnendu , Suresh M 
Published: July 2020

ABSTRACTEliciting durable and protective T cell-mediated immunity in the respiratory mucosa remains a significant challenge. Polylactic-co-glycolic acid (PLGA)-based cationic pathogen-like particles (PLPs) loaded with TLR agonists mimic biophysical properties of microbes and hence, simulate pathogen-pattern recognition receptor interactions to safely and effectively stimulate innate immune responses. We generated micro particle PLPs loaded with TLR4 (glucopyranosyl lipid adjuvant, GLA) or TLR9 (CpG) agonists, and formulated them with and without a mucosal delivery enhancing carbomer-based nanoemulsion adjuvant (ADJ). These adjuvants delivered intranasally to mice elicited high numbers of influenza nucleoprotein (NP)-specific CD8+/ CD4+ effector and tissue-resident memory T cells (TRMs) in lungs and airways. PLPs delivering TLR4 versus TLR9 agonists drove phenotypically and functionally distinct populations of effector and memory T cells. While PLPs loaded with CpG or GLA provided immunity, combining the adjuvanticity of PLP-GLA and ADJ synergistically enhanced the development of airway and lung TRMs and protective immunity to pathogenic influenza A virus. Further, balanced CD8 (Tc1/Tc17) and CD4 (Th1/Th17) recall responses were linked to effective influenza virus control in the lungs. These studies provide mechanistic insights into vaccine-induced T cell immunity in the respiratory tract and pave the way for the development of a universal influenza vaccine.
Effect of sunlight on the efficacy of commercial antibiotics used in agriculture
Authors: Khan Sebastian , Osborn Amanda , Eswara Prahathees J. 
Published: July 2020

ABSTRACTAntibiotic stewardship is of paramount importance to limit the emergence of antibiotic-resistant bacteria in not only hospital settings, but also in animal husbandry, aquaculture, and agricultural sectors. Currently, large quantities of antibiotics are applied to treat agricultural diseases like citrus greening disease (CGD). The two commonly used antibiotics approved for this purpose are streptomycin and oxytetracycline. Although investigations are ongoing to understand how efficient this process is to control the spread of CGD, to our knowledge, there have been no studies that evaluate the effect of environmental factors such as sunlight on the efficacy of the above-mentioned antibiotics. We conducted a simple disc-diffusion assay to study the efficacy of streptomycin and oxytetracycline after exposure to sunlight for 7- or 14-day periods usingEscherichia coliandBacillus subtilisas the representative strains of Gram-negative and Gram-positive organisms respectively. Freshly prepared discs and discs stored in the dark for 7 or 14 days served as our controls. We show that the antibiotic potential of oxytetracycline exposed to sunlight dramatically decreases over the course of 14 days against bothE. coliandB. subtilis. However, the effectiveness of streptomycin was only moderately impacted by sunlight. It is important to note that antibiotics that last longer in the environment may play a deleterious role in the rise and spread of antibiotic-resistant bacteria. Further studies are needed to substantively analyze the safety and efficacy of antibiotics used for broader environmental applications.IMPORTANCEAlthough antibiotics have been used for agricultural purposes for decades, due to the rapid rise in antibiotic resistance this usage needs to be revisited. Questions remain on the appropriate mode of application of antibiotics and the actual benefits of using antibiotics for treating the infections caused by plant pathogens, especially for the ones that are intracellular in nature. Here we show that the two commonly used commercial antibiotics, oxytetracycline and streptomycin, lose their efficacy at different rates in the presence of sunlight. While the former loses its potency within days the latter remains active for many days. Thus, oxytetracycline may not be active long enough to produce desired effect and streptomycin may persist in the environment and as a side effect due to its selective pressure, may force the rise of streptomycin-resistant pathogens.
EP3 signaling is decoupled from regulation of glucose-stimulated insulin secretion in β-cells compensating for obesity and insulin resistance
Authors: Schaid Michael D. , Harrington Jeffrey M. , Kelly Grant M. , Sdao Sophia M. , Merrins Matthew J. , Kimple Michelle E. 
Published: July 2020

ABSTRACTOf the β-cell signaling pathways altered by non-diabetic obesity and insulin resistance, some are adaptive while others actively contribute to β-cell failure and demise. Cytoplasmic calcium (Ca2+) and cyclic AMP (cAMP), which control the timing and amplitude of insulin secretion, are two important signaling intermediates that can be controlled by stimulatory and inhibitory G protein-coupled receptors. Previous work has shown the importance of the cAMP-inhibitory EP3 receptor in the beta-cell dysfunction of type 2 diabetes. To examine alterations in β-cell cAMP during diabetes progression we utilized a β-cell specific cAMP biosensor in tandem with islet Ca2+recordings and insulin secretion assays. Three groups of C57BL/6J mice were used as a model of the progression from metabolic health to type 2 diabetes: wildtype, normoglycemicLeptinOb, and hyperglycemicLeptinOb. Here, we report robust increases in β-cell cAMP and insulin secretion responses in normoglycemicLeptinobmice as compared to wild-type: an effect that was lost in islets from hyperglycemicLeptinobmice, despite elevated Ca2+duty cycle. Yet, the correlation of EP3 expression and activity to reduce cAMP levels and Ca2+duty cycle with reduced insulin secretion only held true in hyperglycemicLeptinObmice. Our results suggest alterations in beta-cell EP3 signaling may be both adaptive and maladaptive and define β-cell EP3 signaling as much more nuanced than previously understood.