bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associative learning in larval and adult Drosophila is impaired by the dopamine-synthesis inhibitor 3-Iodo-L-tyrosine
Authors: Thoener Juliane , König Christian , Weiglein Aliće , Toshima Naoko , Mancini Nino , Amin Fatima , Schleyer Michael 
Published: October 2020

AbstractAcross the animal kingdom, dopamine plays a crucial role in conferring reinforcement signals that teach animals about the causal structure of the world. In the fruit flyDrosophila melanogaster, the dopamine system has largely been studied using a rich genetic toolbox. Here, we suggest a complementary pharmacological approach applying the dopamine-synthesis inhibitor 3-Iodo-L-tyrosine (3IY), which causes acute systemic inhibition of dopamine signaling. Using Pavlovian conditioning, across developmental stages (3rdinstar larva versus adult), valence domains (reward versus punishment), and types of reinforcement (natural versus optogenetically induced), we find that 3IY feeding specifically impairs associative learning, whereas additional feeding of L-3,4-dihydroxyphenylalanine (L-DOPA), a precursor of dopamine, rescues this impairment. This study establishes a simple, quick, and comparably low-cost approach that can be combined with the available genetic tools to manipulate and clarify the functions of the dopaminergic system – inD. melanogasterand other animals.
Roughness and dynamics of proliferating cell fronts as a probe of cell-cell interactions
Authors: Rapin Guillaume , Caballero Nirvana , Gaponenko Iaroslav , Ziegler Benedikt , Rawleigh Audrey , Moriggi Ermanno , Giamarchi Thierry , Brown Steven A. , Paruch Patrycja 
Published: October 2020

Juxtacellular interactions play an essential but still not fully understood role in both normal tissue development and tumour invasion. Using proliferating cell fronts as a model system, we explore the effects of cell-cell interactions on the geometry and dynamics of these one-dimensional biological interfaces. We observe two distinct scaling regimes of the steady state roughness ofin-vitropropagating Rat1 fibroblast cell fronts, suggesting different hierarchies of interactions at sub-cell lengthscales and at a lengthscale of 2–10 cells. Pharmacological modulation significantly affects the proliferation speed of the cell fronts, and those modulators that promote cell mobility or division also lead to the most rapid evolution of cell front roughness. By comparing our experimental observations to numerical simulations of elastic cell fronts with purely short-range interactions, we demonstrate that the interactions at few-cell lengthscales play a key role. Our methodology provides a simple framework to measure and characterise the biological effects of such interactions, and could be useful in tumour phenotyping.Proliferating cell fronts underpin wound healing, tumour invasion, and morphogenesis, and are governed by a complex and still not fully understood interplay of multiple mechanical and chemical factors. From a physics perspective, these cell fronts can be described as elastic interfaces in disordered media. Thus, analysing their geometric properties and dynamics can reveal the characteristic lengthscales of the dominant interactions, and point towards the underlying biological pathways. Here, we show that the roughness of proliferating fronts of Rat1 fibroblasts is governed by two different hierarchies of interactions, with distinct behaviour at sub-cell and few-cell lengthscales. Using in-vitro scratch assays, we find moreover that pharmacological modulators significantly affect the proliferation speed of the cell fronts as well as the evolution of their roughness, increased when cell-cell communication via gap junctions is perturbed, and decreased when cell division is repressed. We determine that our experimental observations cannot be reproduced by numerical simulations of elastic cell fronts with purely short-range interactions, demonstrating the key role of juxtacellular interactions at few-cell lengthscales. Our approach provides a simple framework to measure and characterise the biological effects of such interactions, and could be useful in tumour phenotyping.
Microtubules and Gαo-signaling independently regulate the preferential secretion of newly synthesized insulin granules in pancreatic islet β cells
Authors: Hu Ruiying , Zhu Xiaodong , Yuan Mingyang , Ho Kung-Hsien , Kaverina Irina , Gu Guoqiang 
Published: October 2020

AbstractFor sustainable function, each pancreatic islet β cell maintains thousands of insulin granules (IGs) at all times. Glucose stimulation induces the secretion of a small portion of these IGs and simultaneously triggers IG biosynthesis to sustain this stock. The failure of these processes, often induced by sustained high-insulin output, results in type 2 diabetes. Intriguingly, newly synthesized IGs are more likely secreted during glucose-stimulated insulin secretion. The older IGs tend to lose releasability and be degraded, which represents a futile metabolic load that can sensitize β cells to workload-induced dysfunction and even death. Here, we examine the factor(s) that allows the preferential secretion of younger IGs. We show that β cells without either microtubules (MTs) or Gαo signaling secrete a bigger portion of older IGs, which is associated with increased IG docking on plasma membrane. Yet Gαo inactivation does not alter the β-cell MT network. These findings suggest that Gαo and MT regulate the preferential release of newer IGs via parallel pathways and provide two potential models to further explore the underlying mechanisms and physiological significance of this regulation in functional β cells.
The effect of basal core promoter and pre-core mutations on HBV replication and persistence in mice
Authors: Chen Yi , Xu Zhiwei , Zeng Yanli , Liu Junping , Tian Yongjun , Kang Yi 
Published: October 2020

AbstractThe appearance of the BCP or Pre-C mutations, which reduce or abolish HBeAg production, could increase HBV replication. The remove of the HBeAg often lead to a vigorous immune response, which has an important role in HBV related fulminant outcome. In this study, BCP mutations and Pre-C mutations were separately introduced by site-directed mutagenesis in the same genetic background of an HBV infectious clone, to determine the effect of these mutations per se on replication. BCP and Pre-C mutations increased HBV replication both invitroandin vivo. HBV could persist in mice injected with wild type HBV infectious clone for about 7 weeks. However, HBV could persist about 5 weeks in mice injected with BCP HBV infectious clone, and 3 weeks only in mice injected with Pre-C HBV infectious clone. HBV related CD8+ CTL response in BCP HBV infectious clone injected mice only slightly increased, but significantly increased in Pre-C HBV infectious clone injected mice compared with that in wild type HBV infectious clone injected mice. The population of Tregs significantly increased in liver but not in spleen of mice injected with Pre-C HBV infectious clone. In summary, we demonstrate that HBeAg plays an important role in suppressing the CTL response, which is related with increasing the frequency of Tregs in mouse. Lack of HBeAg expression leads to the partial loss of immune tolerance.
SDF-1/CXCR4 inhibition prevents paradoxical generation of cisplatin-induced pro-metastatic niches
Authors: Bertolini Giulia , Cancila Valeria , Milione Massimo , Russo Giuseppe Lo , Fortunato Orazio , Zaffaroni Nadia , Tortoreto Monica , Centonze Giovanni , Chiodoni Claudia , Facchinetti Federica , Giovinazzo Francesca , Moro Massimo , Camisaschi Chiara , De Toma Alessandro , D’Alterio Crescenzo , Pastorino Ugo , Tripodo Claudio , Scala Stefania , Sozzi Gabriella , Roz Luca 
Published: October 2020

AbstractPlatinum-based chemotherapy remains widely used in advanced non-small cell lung cancer (NSCLC) despite its ineffectiveness in long-term control of metastasis.Here, we uncover the interconnected pathways subtending cisplatin-induced metastasis promotion.We report that cisplatin treatment of tumor-free mice results in bone-marrow expansion of CCR2+CXCR4+Ly6Chighinflammatory monocytes (IM) concomitantly with increased levels in the lungs of stromal SDF-1, the CXCR4 ligand. In experimental metastasis assays, cisplatin-induced IM favor tumor cells extravasation and expansion of CD133+CXCR4+ metastasis initiating cells (MICs), facilitating lung metastasis formation. At the primary tumor, cisplatin reduces tumor size but induces tumor release of SDF-1 triggering MICs expansion and recruitment of pro-invasive CXCR4+ macrophages. Co-recruitment of MICs and CCR2+CXCR4+ IM at SDF-1-enriched distant sites also promotes spontaneous metastasis. Combination treatment with a CXCR4 inhibitor prevents cisplatin-induced IM/MICs recruitment and interaction thus precluding metastasis overgrowth. Finally, we observe in NSCLC patients’ specimens that SDF-1 levels are higher in platinum-treated samples and correlate with worse outcome.Our findings suggest a possible novel combination therapy based on CXCR4 blockade to control metastatic disease, paradoxically promoted by cisplatin.
Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
Authors: Bhatt Pramod R. , Scaiola Alain , Loughran Gary , Leibundgut Marc , Kratzel Annika , McMillan Angus , O’ Connor Kate M. , Bode Jeffrey W. , Thiel Volker , Atkins John F. , Ban Nenad 
Published: October 2020

AbstractProgrammed ribosomal frameshifting is the key event during translation of the SARS-CoV-2 RNA genome allowing synthesis of the viral RNA-dependent RNA polymerase and downstream viral proteins. Here we present the cryo-EM structure of the mammalian ribosome in the process of translating viral RNA paused in a conformation primed for frameshifting. We observe that the viral RNA adopts a pseudoknot structure lodged at the mRNA entry channel of the ribosome to generate tension in the mRNA that leads to frameshifting. The nascent viral polyprotein that is being synthesized by the ribosome paused at the frameshifting site forms distinct interactions with the ribosomal polypeptide exit tunnel. We use biochemical experiments to validate our structural observations and to reveal mechanistic and regulatory features that influence the frameshifting efficiency. Finally, a compound previously shown to reduce frameshifting is able to inhibit SARS-CoV-2 replication in infected cells, establishing coronavirus frameshifting as target for antiviral intervention.
Bombesin-like peptide recruits disinhibitory cortical circuits and enhances fear memories
Authors: Melzer Sarah , Newmark Elena , Mizuno Grace Or , Hyun Minsuk , Philson Adrienne C. , Quiroli Eleonora , Righetti Beatrice , Gregory Malika R. , Huang Kee Wui , Levasseur James , Tian Lin , Sabatini Bernardo L. 
Published: October 2020

SummaryDisinhibitory neurons throughout the mammalian cortex are powerful enhancers of circuit excitability and plasticity. The differential expression of neuropeptide receptors in disinhibitory, inhibitory and excitatory neurons suggests that each circuit motif is controlled by distinct neuropeptidergic systems. Here, we reveal that a bombesin-like neuropeptide, gastrin-releasing peptide (GRP), recruits disinhibitory cortical microcircuits through selective targeting and activation of vasoactive intestinal peptide (VIP)-expressing cells. Using a newly-developed genetically-encoded GRP sensor and trans-synaptic tracing we reveal that GRP regulates VIP cells via extrasynaptic diffusion from several putative local and long-range sources.In vivophotometry and CRISPR/Cas9-mediated knockout of the GRP receptor (GRPR) in auditory cortex indicate that VIP cells are strongly recruited by novel sounds and aversive shocks, and that GRP-GRPR signaling enhances auditory fear memories. Our data establish peptidergic recruitment of selective disinhibitory cortical microcircuits as a mechanism to regulate fear memories.
Transfer learning from simulations improves the classification of OCT images of glandular epithelia
Authors: Ostvar Sassan , Truong Han , Silver Elisabeth R. , Lightdale Charles J. , Hur Chin , Tatonetti Nicholas P. 
Published: October 2020

AbstractEsophageal adenocarcinoma (EAC) is a rare but lethal cancer with rising incidence in several global hotspots including the United States. The five-year survival rate for patients diagnosed with advanced disease can be as low as 5% in EAC, making early detection and preventive intervention crucial. The current standard of care for EAC targets patients with Barrett’s esophagus (BE), the main precursor to EAC and a relatively common condition in adults with chronic acid reflux disease. Preventive care for EAC requires repeated surveillance endoscopies of BE patients with biopsy sampling, and can be intrusive, error-prone, and costly. The integration of minimally-invasive subsurface tissue imaging in the current standard of care can reduce the need for exhaustive tissue sampling and improve the quality of life in BE patients. Effective adoption of subsurface imaging in EAC care can be facilitated by computer-aided detection (CAD) systems based on deep learning. Despite their recent successes in lung and breast cancer imaging, the development of deep neural networks for rare conditions like EAC remains challenging due to data scarcity, heavy bias in existing datasets toward non-cases, and uncertainty in image labels. Here we explore the use of synthetic datasets–specifically data derived from simulations of optical back-scattering during imaging– in the development of CAD systems based on deep learning. As a proof of concept, we studied the binary classification of esophageal OCT into normal squamous and glandular mucosae, typical of BE. We found that deep convolutional networks trained on synthetic data had improved performance over models trained on clinical datasets with uncertain labels. Model performance also improved with dataset size during training on synthetic data. Our findings demonstrate the utility of transfer from simulations to real data in the context of medical imaging, especially in the severely data-poor regime and when significant uncertainty in labels are present, and motivate further development of transfer learning from simulations to aid the development of CAD for rare malignancies.
Evolutionary dynamics of neutral phenotypes under DNA substitution models
Authors: Zabad Shadi , Moses Alan M 
Published: October 2020

AbstractWe study the evolution of quantitative molecular traits in the absence of selection. Using Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to those predicted by the widely-used OU model for stabilizing selection and the house-of-cards model for phenotype evolution. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for nonadditive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.
The genomic epidemiology of SARS-CoV-2 in Palestine
Authors: Qutob Nouar , Salah Zaidoun , Richard Damien , Darwish Hisham , Sallam Husam , Shtayeh Issa , Najjar Osama , Ruzayqat Mahmoud , Najjar Dana , Balloux François , van Dorp Lucy 
Published: October 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause significant public health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many independent introductions of SARS-CoV-2 during the early stages of the pandemic. However, this situation may change with local lockdown policies and restrictions on travel leading to the emergence of more geographically structured viral populations and lineages transmitting locally. Here, we report the first SARS-CoV-2 genomes from Palestine sampled from early March, when the first cases were observed, through to August of 2020. SARS-CoV-2 genomes from Palestine fall across the diversity of the global phylogeny, consistent with at least nine independent introductions into the region. We identify one locally predominant lineage in circulation represented by 50 Palestinian SARS-CoV-2, grouping with isolated viral samples from patients in Israel and the UK. We estimate the age of introduction of this lineage to 05/02/2020 (16/01/2020 - 19/02/2020), suggesting SARS-CoV-2 was already in circulation in Palestine predating its first detection in Bethlehem in early March. Our work highlights the value of ongoing genomic surveillance and monitoring to reconstruct the epidemiology of COVID-19 at both local and global scales.
Modifying adaptive therapy to enhance competitive suppression
Authors: Hansen Elsa , Read Andrew F. 
Published: October 2020

AbstractAdaptive therapy is a promising new approach to cancer treatment. It is designed to leverage competition between drug-sensitive and drug-resistant cells in order to suppress resistance and maintain tumor control for longer. Prompted by encouraging results from a recent pilot clinical trial, we evaluate the design of this initial test of adaptive therapy and identify three simple modifications that should improve performance. These modifications are designed to increase competition and are easy to implement. Using the mathematical model that supported the recent adaptive therapy trial, we show that the suggested modifications further delay time to tumor progression and also increase the range of patients who can benefit from adaptive therapy.
Synergistic Combination of Cytotoxic Chemotherapy and Cyclin Dependent Kinase 4/6 Inhibitors in Biliary Tract Cancers
Authors: Arora Mansi , Bogenberger James M. , Abdelrahman Amro M. , Yonkus Jennifer , Alva-Ruiz Roberto , Leiting Jennifer L. , Chen Xianfeng , Junior Pedro Luiz Serrano Uson , Dumbauld Chelsae R. , Baker Alexander T. , Gamb Scott I. , Egan Jan B. , Zhou Yumei , Nagalo Bolni Marius , Meurice Nathalie , Eskelinen Eeva-Liisa , Salomao Marcela A. , Kosiorek Heidi E. , Braggio Esteban , Barrett Michael T. , Buetow Kenneth H. , Sonbol Mohamad B. , Mansfield Aaron S. , Roberts Lewis R. , Bekaii-Saab Tanios S. , Ahn Daniel H. , Truty Mark J. , Borad Mitesh J. 
Published: October 2020

AbstractBiliary tract cancers (BTCs) are uncommon but highly lethal gastrointestinal malignancies. Gemcitabine/cisplatin is a standard-of-care (SOC) systemic therapy, but has a modest impact on survival and harbor toxicities including myelosuppression, nephropathy, neuropathy and ototoxicity. While BTCs are characterized by aberrations activating the cyclinD1-CDK4/6-CDKN2A-RB pathway, clinical use of CDK4/6 inhibitors as monotherapy is limited by lack of validated biomarkers, diffident pre-clinical efficacy and development of acquired drug resistance. Emerging studies have explored therapeutic strategies to enhance the anti-tumor efficacy of CDK4/6 inhibitors by combination with chemotherapy-regimens but their mechanism of action remains elusive. Here, we reportin vitroandin vivosynergy in BTC models, showing enhanced efficacy, reduced toxicity and better survival with a combination comprising gemcitabine/cisplatin and CDK4/6 inhibitors. Furthermore, we demonstrated that abemaciclib monotherapy had only modest efficacy due to autophagy induced resistance. Notably, triplettherapy was able to potentiate efficacy through elimination of the autophagic flux. Correspondingly, abemaciclib potentiated RRM1 reduction, resulting in sensitization to gemcitabine. Conclusions: As such, these data provide robust pre-clinical mechanistic evidence of synergy between gemcitabine/cisplatin and CDK4/6 inhibitors, and delineate a path forward for translation of these findings to preliminary clinical studies in advanced BTC patients.
Dinucleotides as simple models of the base stacking-unstacking component of DNA ‘breathing’ mechanisms
Authors: Beyerle Eric R. , Dinpajooh Mohammadhasan , Ji Huiying , von Hippel Peter H. , Marcus Andrew H. , Guenza Marina G. 
Published: October 2020

AbstractRegulatory protein access to the DNA duplex ‘interior’ depends on local DNA ‘breathing’ fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding, present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with experiments. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson-Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.
Timing variability and midfrontal ~4 Hz rhythms correlate with cognition in Parkinson’s disease
Authors: Singh Arun , Cole Rachel C. , Espinoza Arturo I. , Evans Aron , Cao Scarlett , Cavanagh James F. , Narayanan Nandakumar S. 
Published: October 2020

ABSTRACTPatients with Parkinson’s disease (PD) can have significant cognitive dysfunction; however, the mechanisms for these cognitive symptoms are unknown. Here, we used scalp electroencephalography (EEG) to investigate the cortical basis for PD-related cognitive impairments during interval timing, which requires participants to estimate temporal intervals of several seconds. Time estimation is an ideal task demand for investigating cognition in PD because it is simple, requires medial frontal cortical areas, and recruits basic executive processes such as working memory and attention.However, interval timing has never been systematically studied in PD patients with cognitive impairments. We report three main findings. First, 71 PD patients had increased temporal variability compared to 37 demographically-matched controls, and this variability correlated with cognitive dysfunction as measured by the Montreal Cognitive Assessment (MOCA). Second, PD patients had attenuated ~4 Hz EEG oscillatory activity at midfrontal electrodes in response to the interval-onset cue, which was also predictive of MOCA. Finally, trial-by-trial linear mixed-effects modeling demonstrated that cue-triggered ~4 Hz power predicted subsequent temporal estimates as a function of PD and MOCA. Our data suggest that impaired cue-evoked midfrontal ~4 Hz activity predicts increased timing variability that is indicative of cognitive dysfunction in PD. These findings link PD-related cognitive dysfunction with cortical mechanisms of cognitive control, which could advance novel biomarkers and neuromodulation for PD.