bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclin E1 protein is stabilized inBRCA1mutated breast cancers leading to synergy between CDK2 and PARP inhibitors
Authors: Aziz Diar , Portman Neil , Fernandez Kristine J. , Lee Christine , Alexandrou Sarah , Llop-Guevara Alba , Yong Aliza , Wilkinson Ashleigh , Sergio C. Marcelo , Ferraro Danielle , Etemadmoghadam Dariush , Bowtell David , Investigators kConFab , Serra Violeta , Waring Paul , Lim Elgene , Caldon C. Elizabeth 
Published: January 2020

ABSTRACTBasal-like breast cancers (BLBC) are aggressive breast cancers that respond poorly to targeted therapies and chemotherapies. In order to define therapeutically targetable subsets of BLBC we examined two markers: cyclin E1 andBRCA1loss. In high grade serous ovarian cancer (HGSOC) these markers are mutually exclusive, and define therapeutic subsets. We tested the same hypothesis for BLBC.Using a BLBC cohort enriched forBRCA1loss, we identified convergence betweenBRCA1loss and high cyclin E1 expression, in contrast to HGSOC in whichCCNE1amplification drives increased cyclin E1 gene expression. Instead,BRCA1loss stabilized cyclin E1 during the cell cycle. Using siRNA we showed thatBRCA1loss leads to stabilization of cyclin E1 by reducing phospho-cyclin E1-T62, and conversely the overexpression ofBRCA1increased phospho-T62. Mutation of cyclin E1-T62 to alanine increased cyclin E1 stability. We showed that tumors with high cyclin E1/BRCA1mutation in the BLBC cohort had decreased phospho-T62, supporting this hypothesis.Since cyclin E1/CDK2 protects cells from DNA damage and cyclin E1 is elevated inBRCA1mutant cancers, we hypothesized that CDK2 inhibition would sensitize these cancers to PARP inhibition. CDK2 inhibition induced DNA damage and synergized with PARP inhibitors to reduce cell viability inBRCA1mutated cell lines. Treatment of BLBC patient-derived xenograft models with combination PARP and CDK2 inhibition led to tumor regression and increased survival. We conclude thatBRCA1status and high cyclin E1 have potential as predictive biomarkers to dictate the therapeutic use of combination CDK inhibitors/PARP inhibitors in BLBC.
Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome
Authors: Tosar Juan Pablo , Segovia Mercedes , Gámbaro Fabiana , Akiyama Yasutoshi , Fagúndez Pablo , Costa Bruno , Possi Tania , Hill Marcelo , Ivanov Pavel , Cayota Alfonso 
Published: January 2020

ABSTRACTA major proportion of extracellular RNAs (exRNAs) do not co-isolate with extracellular vesicles (EVs) and remain in ultracentrifugation supernatants of cell-conditioned medium or mammalian blood serum. However, little is known about exRNAs beyond EVs. We have previously shown that the composition of the nonvesicular exRNA fraction is highly biased toward specific tRNA-derived fragments capable of forming RNase-protecting dimers. To solve the problem of stability in exRNA analysis, we developed RI-SEC-seq: a method based on sequencing the size exclusion chromatography (SEC) fractions of nonvesicular extracellular samples treated with RNase inhibitors (RI). This method revealed dramatic compositional changes in exRNA population when enzymatic RNA degradation was inhibited. We demonstrated the presence of ribosomes and full-length tRNAs in cell-conditioned medium of a variety of mammalian cell lines. Their fragmentation generates some small RNAs that are highly resistant to degradation. The extracellular biogenesis of some of the most abundant exRNAs demonstrates that extracellular abundance is not a reliable input to estimate RNA secretion rates. Finally, we showed that chromatographic fractions containing extracellular ribosomes can be sensed by dendritic cells. Extracellular ribosomes and/or tRNAs could therefore be decoded as damage-associated molecular patterns.
Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program
Authors: Srinivasan Rajalakshmi , Walvekar Adhish S. , Seshasayee Aswin , Laxman Sunil 
Published: January 2020

AbstractGrowth and starvation are considered opposite ends of a spectrum. To sustain growth, cells must manage biomolecule supply to balance constructive metabolism with high translation, through coordinated gene expression programs. Global growth programs couple increased ribosomal biogenesis with sufficient carbon metabolism, amino acid and nucleotide biosynthesis, and how this is collectively managed is a fundamental question. Conventionally, the role of the Gcn4/ATF4 transcription factor has been studied only in the context of amino acid starvation. However, high Gcn4/ATF4 has been observed in contexts of rapid cell proliferation, and the specific role of Gcn4 in growth contexts are unclear. Here, using a methionine-induced growth program in yeast, we show that Gcn4/ATF4 is the fulcrum through which metabolic supply dependent sustenance of translation outputs is maintained. Integrating time-matched transcriptome and ChIP-Seq analysis, we decipher genome-wide direct and indirect roles for Gcn4 in this growth program. Genes that enable metabolic precursor biosynthesis indispensably require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 directly binds promoter-regions and transcribes a subset of metabolic genes, particularly driving lysine and arginine biosynthesis. Gcn4 also globally represses lys/arg enriched transcripts, which include the translation machinery. The sustained Gcn4 dependent lys/arg supply is required to maintain sufficient translation capacity, by allowing the synthesis of the translation machinery itself. Gcn4 thereby enables metabolic-precursor supply to bolster protein synthesis, and drive a growth program. Thus, we illustrate how growth and starvation outcomes are both controled using the same Gcn4 transcriptional outputs, in entirely distinct contexts.
Learning to Integrate an Artificial Sensory Device: Early Bayesian Integration and Conscious Perception
Authors: Mahani Mohammad-Ali Nikouei , Bausenhart Karin Maria , Ulrich Rolf , Ahmadabadi Majid Nili 
Published: January 2020

AbstractThe present study examines how artificial tactile stimulation from a novel non-invasive sensory device is learned and integrated with information from another sensory system. Participants were trained to identify the direction of visual dot motion stimuli with a low, medium, and high signal-to-noise ratio. In bimodal trials, this visual direction information was paired with reliable symbolic tactile information. Over several training blocks, discrimination performance in unimodal tactile test trials and subjects’ confidence in their decision improved, indicating that participants were able to associate the visual and tactile information consciously and thus learned the meaning of the symbolic tactile cues. Formal analysis of the results in bimodal trials showed that both modalities are being integrated already in the early learning phases. Our modeling results revealed that this integration is consistent with a Bayesian model, which is an optimal integration of sensory information. Furthermore, we showed that a confidence-based Bayesian integration explains the observed behavioral data better than the classical variance-based Bayesian integration. Thus, the present study demonstrates that humans can consciously learn and integrate an artificial sensory device that delivers symbolic tactile information. This finding connects the field of multisensory integration research to the development of sensory substitution systems.
Dynamic landscape of protein occupancy across the Escherichia coli chromosome
Authors: Freddolino Peter L. , Amemiya Haley M. , Goss Thomas J. , Tavazoie Saeed 
Published: January 2020

AbstractFree-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein-DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (IPOD-HR), and present a pilot application to E. coli. We observe that the E. coli protein-DNA interactome organizes into two distinct prototypic features: (1) highly dynamic condition-dependent transcription factor occupancy, and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence-specificity models for the majority of active transcription factors. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria which are not amenable to routine genetic manipulation.
Deoxyribozyme-based Method for Site-specific Absolute Quantification of N6-methyladenosine Modification Fraction
Authors: Bujnowska Magda , Zhang Jiacheng , Dai Qing , Heideman Emily M. , Fei Jingyi 
Published: January 2020

ABSTRACTN6-methyladenosine (m6A) is the most prevalent modified base in eukaryotic messenger RNA (mRNA) and long noncoding RNA (lncRNA). Although candidate sites for m6A modification are identified at the transcriptomic level, site-specific quantification methods for m6A modifications are still limited. Herein, we present a facile method implementing deoxyribozyme that preferentially cleaves the unmodified RNA. We leverage reverse transcription and real-time quantitative PCR along with key control experiments to quantify the absolute methylation fraction of specific m6A sites. We validate the accuracy of the method using synthetic RNA with controlled methylation fraction and apply our method on several endogenous sites that were previously identified in sequencing-based studies. This method provides a time and cost-effective approach for absolute quantification of the m6A fraction at specific loci, expanding the current toolkit for studying RNA modifications.
Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures
Authors: Simoneau Joël , Gosselin Ryan , Scott Michelle S. 
Published: January 2020

ABSTRACTRNA-seq is a modular experimental and computational approach that aims in identifying and quantifying RNA molecules. The modularity of the RNA-seq technology enables adaptation of the protocol to develop new ways to explore RNA biology, but this modularity also brings forth the importance of methodological thoroughness. Liberty of approach comes with the responsibility of choices, and such choices must be informed. Here, we present an approach that identifies gene group specific quantification biases in currently used RNA-seq software and references by processing sequenced datasets using a wide variety of RNA-seq computational pipelined, and by decomposing these expression datasets using an independent component analysis matrix factorisation method. By exploring the RNA-seq pipeline using a systemic approach, we highlight the yet inadequately characterized central importance of genome annotations in quantification results. We also show that the different choices in RNA-seq methodology are not independent, through interactions between genome annotations and quantification software. Genes were mainly found to be affected by differences in their sequence, by overlapping genes and genes with similar sequence. Our approach offers an explanation for the observed biases by identifying the common features used differently by the software and references, therefore providing leads for the betterment of RNA-seq methodology.
Grip strength is associated with retinal and choroidal thickness in type 2 diabetes mellitus patients without retinopathy
Authors: Qiu Zihan , Wang Wei , Tan Yan , He Miao , Wang Lanhua , Li Yuting , Gong Xia , Huang Wenyong 
Published: February 2020

AbstractObjectiveTo determine the relationship between grip strength and retinal or choroidal thickness in Chinese patients with type 2 diabetes mellitus.DesignObservational study-cross-sectional design.Setting and ParticipantsThe study was conducted among diabetes patients without retinopathy registered in the community health system in Guangzhou, China.MeasuresGrip strength was measured twice for each hand with a dynamometer in kilograms (kg). The retinal and choroidal thickness in macular Early Treatment Diabetic Retinopathy Study (ETDRS) sectors were measured by commercial swept-source optical coherence tomography (SS-OCT; DRI OCT-2 Triton; Topcon, Tokyo, Japan).ResultsA total of 1,029 patients were included in the study. Both retinal thickness and choroidal thickness increased with the higher quartile of grip strength. Regression analyses indicated that the average retinal and choroidal thickness increased by 0.14 μm (95%CI: 0.03-0.25 μm, P=0.011) and 0.57 μm (95%CI: 0.03-1.11 μm, P=0.037) for each additional kg of grip strength following adjustment for age and gender. Further adjustments were made for axial length, HbA1c, length of time the patient had diabetes, insulin usage, height, weight and systolic and diastolic blood pressure, which resulted in an average retinal and choroidal thickness increase of 0.13 μm (95%CI: 0.02-0.24 μm, P=0.024) and 0.65 μm (95%CI: 0.13-1.16 μm, P=0.013) for each additional kg of grip strength. Consistent results were obtained in the analyses in ETDRS 9 sectors.ConclusionGreater hand grip strength was found to be significantly associated with thicker retinal and choroidal layers in diabetic patients. Grip strength may provide a useful indicator of retinal health in diabetic patients. Further studies are needed to determine directionality and causality, and to examine whether improving muscle strength has a positive effect on retinal and choroidal thickness.Article summaryStrengths and limitations of this studyGrip strength is an indicator of upper limb muscle function and tension, and it is one of the important indicators of aging in the human population. This is one of the few studies to examined the relationship between grip strength and retinal thickness and choroidal thickness in a large sample size of patients with diabetes mellitus.Greater hand grip strength was found to be significantly associated with thicker retinal and choroidal thickness in diabetic patients, and grip strength may provide an easily-administered marker of retinal health in diabetic patients.Causal inferences could not be inferred due to the cross-sectional design of the study.The dynamic changes in grip strength and their impact on retinal and choroidal thickness are warranted to be explored in longitudinal studies.
LAG3 is a Central Regulator of NK Cell Cytokine Production
Authors: Narayanan Sriram , Ahl Patricia J. , Bijin Veonice Au , Kaliaperumal Nivashini , Lim Seng Gee , Wang Cheng-I , Fairhurst Anna-Marie , Connolly John E. 
Published: February 2020

AbstractNatural killer (NK) cells are innate effectors, which play a crucial role in controlling viral infections. Administration of IFN-α has shown promising results as a therapeutic, controlling HIV, and chronic viral hepatitis. However the downstream mechanisms by which IFN-α mediates its anti-viral effects is largely unknown. In this investigation, we evaluated the impact of IFN-α on peripheral blood NK cells from healthy donors. High dimensional flow cytometry analysis of NK cell surface receptors following exposure to IFN-α showed an increased expression of the check point inhibitor LAG3. Further characterization revealed that LAG3 was expressed in a subset of NK cells with high expression of activation and maturation markers. Assessment of metabolic pathways showed that LAG3+ NK cells had enhanced rates of glycolysis and glycolytic capacity, suggesting that it is a primed effector subset with enhanced glucose metabolism. Inhibition of LAG3 on NK cells using antibodyin vitroresulted in a profound increase in secretion of cytokines IFN-γ, TNF-α, MIP-1α and MIP-1β, without affecting the cytotoxic activity. Taken together, these results showed that LAG3 is a negative regulator of cytokine production by mature NK cells.
The stress specific impact of ALKBH1 on tRNA cleavage and tiRNA generation
Authors: Rashad Sherif , Han Xiaobo , Sato Kanako , Mishima Eikan , Abe Takaaki , Tominaga Teiji , Niizuma Kuniyasu 
Published: February 2020

AbstracttiRNAs are small non-coding RNAs produced when tRNA is cleaved under stress. tRNA methylation modifications has emerged in recent years as important regulators for tRNA structural stability and sensitivity to cleavage and tiRNA generation during stress, however, the specificity and higher regulation of such a process is not fully understood. Alkbh1 is a m1A demethylase that leads to destabilization of tRNA and enhanced tRNA cleavage. We examined the impact of Alkbh1 targeting via gene knockdown or overexpression on B35 rat neuroblastoma cell line fate following stresses and on tRNA cleavage. We show that Alkbh1 impact on cell fate and tRNA cleavage is a stress specific process that is impacted by the demethylating capacity of the cellular stress in question. We also show that not all tRNAs are cleaved equally following Alkbh1 manipulation and stress, and that Alkbh1 KD fails to rescue tRNAs from cleavage following demethylating stresses. These findings shed a light on the specificity and higher regulation of tRNA cleavage and should act as a guide for future work exploring the utility of Alkbh1 as a therapeutic target for cancers or ischemic insult.
Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
Authors: Yu Timothy C. , Liu Winnie L. , Brinck Marcia , Davis Jessica E. , Shek Jeremy , Bower Grace , Einav Tal , Insigne Kimberly D. , Phillips Rob , Kosuri Sriram , Urtecho Guillaume 
Published: February 2020

AbstractA crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case ofEscherichia coliinducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8,269 rationally designed IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. Using these data, we fit a statistical mechanics model that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three novel promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.
Effects of host species identity and diet on biodiversity of oral and rectal microbiomes of Puerto Rican bats
Authors: Presley Steven J. , Graf Joerg , Hassan Ahmad F. , Sjodin Anna R. , Willig Michael R. 
Published: February 2020

AbstractMicrobiomes perform vital functions for their mammalian hosts, making them potential drivers of host evolution. Understanding effects of environmental factors and host characteristics on the composition and biodiversity of microbiomes may provide novel insights into the origin and maintenance of these symbiotic relationships. Our goals were to (1) characterize biodiversity of oral and rectal microbiomes of bats in Puerto Rico; and (2) determine the effects of geographic location and host characteristics on that biodiversity. We collected bats and their microbiomes from 3 sites, and used 4 metrics (species richness, Shannon diversity, Camargo evenness, Berger-Parker dominance) to characterize biodiversity. We evaluated the relative importance of site, host sex, host species identity, and host foraging guild on microbiome biodiversity. Microbiome biodiversity was highly variable among conspecifics. Geographical location exhibited consistent effects, whereas host sex did not do so. Within each host guild, host species exhibited consistent differences in oral and rectal microbiome biodiversity. Oral microbiome biodiversity was indistinguishable between guilds, whereas rectal microbiome biodiversity was significantly greater in carnivores than in herbivores. The high intraspecific and spatial variation in microbiome biodiversity necessitate a large number of samples to isolate the effects of environmental or host characteristics on microbiomes. Species-specific biodiversity of oral microbiomes suggests these communities are structured by direct interactions with the host immune system via epithelial receptors. In contrast, the number of microbial taxa that a host gut supports may be contingent on the number and kinds of functions a host requires of its microbiome.
Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease
Authors: Bamberger Casimir , Pankow Sandra , Martínez-Bartolomé Salvador , Ma Michelle , Diedrich Jolene , Rissman Robert A. , Yates John R. 
Published: February 2020

AbstractThe 3D structures of aberrant protein folds have been visualized in exquisite detail, yet no method has been able to quantitatively measure protein misfolding across a proteome. Here, we present Covalent Protein Painting (CPP), a mass spectrometry-based structural proteomics approach to quantify the accessibility of lysine ε-amines for chemical modification at the surface of natively folded proteins. We used CPP to survey 2,645 lysine residues in the proteome of HEK293T cellsin vivoand found that mild heat shock increased rather than decreased lysine accessibility for chemical modification. CPP was able to differentiate patients with Alzheimer disease (AD) or Lewy body disease (LBD) or both from controls based on relative accessibility of lysine residues K147, K137, and K28 in Tubulin-β, Succinate dehydrogenase, and amyloid-β peptide, respectively. The alterations of Tubulin-β and Succinate dehydrogenase hint to broader perturbations of the proteome in AD beyond amyloid-β and hyper-phosphorylated tau.