bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell cycle oscillators underlying orderly proteolysis of E2F8
Authors: Wasserman Danit , Nachum Sapir , Cohen Meital , Enrico Taylor P , Noach-Hirsh Meirav , Parasol Jasmin , Zomer-Polak Sarit , Auerbach Naomi , Sheinberger-Chorni Evelin , Nevenzal Hadas , Levi-Dadon Nofar , Wang Xianxi , Lahmi Roxane , Michaely Efrat , Gerber Doron , Emanuele Michael J. , Tzur Amit 
Published: June 2019

AbstractE2F8 is a transcriptional repressor that antagonizes the canonical cell cycle transcription factor E2F1. Despite the importance of this atypical E2F family member in cell cycle, apoptosis and cancer, we lack a complete description of the mechanisms that control its dynamics. To address this question, we developed a complementary set of static and dynamic cell-free systems of human origin, which recapitulate inter-mitotic and G1 phases, and a full transition from pro-metaphase to G1. This revealed an interlocking molecular switch controlling E2F8 degradation at mitotic exit, involving dephosphorylation of Cdk1 sites in E2F8 and the activation of APC/CCdh1, but not APC/CCdc20. Further, we revealed a differential stability of E2F8, accounting for its accumulation in late G1 while APC/CCdh1 is still active and suggesting a key role for APC/C in controlling G1-S transcription. Finally, we identified SCF-Cyclin F as the ubiquitin ligase controlling E2F8 in G2-phase. Altogether, our data provide new insights into the regulation of E2F8 throughout the cell cycle, illuminating an extensive coordination between phosphorylation, ubiquitination and transcription in promoting orderly cell cycle progression.
Rapid single-step affinity purification of HA-tagged mitochondria from Arabidopsis thaliana
Authors: Kuhnert Franziska , Stefanski Anja , Overbeck Nina , Stühler Kai , Weber Andreas P.M. 
Published: June 2019

ABSTRACTPhotosynthesis in plant cells would not be possible without the supportive role of mitochondria. However, isolation of mitochondria from plant cells, for physiological and biochemical analyses, is a lengthy and tedious process. Established isolation protocols require multiple centrifugation steps and substantial amounts of starting material. To overcome these limitations, we tagged mitochondria in Arabidopsis thaliana with a triple haemagglutinin-tag for rapid purification via a single affinity purification step. This protocol yields a substantial quantity of highly pure mitochondria from 1 g of Arabidopsis seedlings. The purified mitochondria were suitable for enzyme activity analyses and yielded sufficient amounts of proteins for deep proteomic profiling. We applied this method for the proteomic analysis of the Arabidopsis bou-2 mutant deficient in the mitochondrial glutamate transporter À bout de souffle (BOU) and identified 27 differentially expressed mitochondrial proteins compared with transgenic Col-0 controls. Our work also sets the stage for the development of advanced mitochondria isolation protocols for distinct cell types.One-sentence summaryAffinity-tagging of mitochondria in plant cells with a triple hemagglutinin-tag enables single-step affinity purification of mitochondria in less than 20 min.
Robust Normalization of Luciferase Reporter Data
Authors: Repele Andrea , Manu  
Published: June 2019

AbstractTransient Luciferase reporter assays are widely used in the study of gene regulation and intracellular cell signaling. In order to control for sample-to-sample variation in luminescence arising from variability in transfection efficiency and other sources, an internal control reporter is co-transfected with the experimental reporter. The luminescence of the experimental reporter is normalized against the control by taking the ratio of the two. Here we show that this method of normalization, “ratiometric”, performs poorly when the transfection efficiency is low and leads to biased estimates of relative activity. We propose an alternative methodology based on linear regression that is much better suited for the normalization of reporter data, especially when transfection efficiency is low. We compare the ratiometric method against three regression methods on both simulated and empirical data. Our results suggest that robust errors-in-variables (REIV) regression performs the best in normalizing Luciferase reporter data. We have made the R code for Luciferase data normalization using REIV available on GitHub.
Bone marrow adipose tissue is a unique adipose subtype with distinct roles in systemic glucose homeostasis
Authors: Suchacki Karla J. , Tavares Adriana A.S. , Mattiucci Domenico , Scheller Erica L. , Papanastasiou Giorgos , Gray Calum , Sinton Matthew C. , Ramage Lynne E. , McDougald Wendy A. , Lovdel Andrea , Sulston Richard J. , Thomas Benjamin J. , Nicholson Bonnie M. , Drake Amanda J. , Alcaide-Corral Carlos J. , Said Diana , Poloni Antonella , Cinti Saverio , MacPherson Gavin J. , Dweck Marc R. , Andrews Jack P.M. , Williams Michelle C. , Wallace Robert J. , van Beek Edwin J.R. , MacDougald Ormond A. , Morton Nicholas M. , Stimson Roland H. , Cawthorn William P. 
Published: June 2019

SUMMARYBone marrow adipose tissue (BMAT) represents >10% of total adipose mass, yet unlike white or brown adipose tissues (WAT or BAT), its role in systemic metabolism remains unclear. Using transcriptomics, we reveal that BMAT is molecularly distinct to WAT but is not enriched for brown or beige adipocyte markers. Instead, pathway analysis indicated altered glucose metabolism and decreased insulin responsiveness in BMAT. We therefore tested these functions in mice and humans using positron emission tomography–computed tomography (PET/CT) with18F-fluorodeoxyglucose, including establishing a new method for BMAT identification from clinical CT scans. This revealed that BMAT resists insulin- and cold-stimulated glucose uptake and is thus functionally distinct to WAT and BAT. However, BMAT displayed greater basal glucose uptake than axial bones or subcutaneous WAT, underscoring its potential to influence systemic glucose homeostasis. These PET/CT studies are the first to characterise BMAT functionin vivoand identify BMAT as a distinct, major subtype of adipose tissue.HIGHLIGHTSBone marrow adipose tissue (BMAT) is molecularly distinct to other adipose subtypes.BMAT is less insulin responsive than WAT and, unlike BAT, is not cold-responsive.Human BMAT has greater basal glucose uptake than axial bone or subcutaneous WAT.We establish a PET/CT method for BMAT localisation and functional analysisin vivo.
Functions of ventral visual cortex after bilateral hippocampal loss
Authors: Kim Jiye G. , Gregory Emma , Landau Barbara , McCloskey Michael , Turk-Browne Nicholas B. , Kastner Sabine 
Published: June 2019

AbstractRepeated stimuli elicit attenuated responses in visual cortex relative to novel stimuli. This adaptation phenomenon can be considered a form of rapid learning and a signature of perceptual memory. Adaptation occurs not only when a stimulus is repeated immediately, but also when there is a lag in terms of time and other intervening stimuli before the repetition. But how does the visual system keep track of which stimuli are repeated, especially after long delays and many intervening stimuli? We hypothesized that the hippocampus supports long-lag adaptation, given that it learns from single experiences, maintains information over delays, and sends feedback to visual cortex. We tested this hypothesis with fMRI in an amnesic patient, LSJ, who has encephalitic damage to the medial temporal lobe resulting in complete bilateral hippocampal loss. We measured adaptation at varying time lags between repetitions in functionally localized visual areas that were intact in LSJ. We observed that these areas track information over a few minutes even when the hippocampus is unavailable. Indeed, LSJ and controls were identical when attention was directed away from the repeating stimuli: adaptation occurred for lags up to three minutes, but not six minutes. However, when attention was directed toward stimuli, controls now showed an adaptation effect at six minutes but LSJ did not. These findings suggest that visual cortex can support one-shot perceptual memories lasting for several minutes but that the hippocampus is necessary for adaptation in visual cortex after longer delays when stimuli are task-relevant.
Mitochondrial DNA Copy Number (mtDNA-CN) Can Influence Mortality and Cardiovascular Disease via Methylation of Nuclear DNA CpGs
Authors: Castellani Christina A. , Longchamps Ryan J. , Sumpter Jason A. , Newcomb Charles E. , Lane John A. , Grove Megan L. , Bressler Jan , Brody Jennifer A. , Floyd James S. , Bartz Traci M. , Taylor Kent D. , Wang Penglong , Tin Adrienne , Coresh Josef , Pankow James S. , Fornage Myriam , Guallar Eliseo , O’Rourke Brian , Pankratz Nathan , Liu Chunyu , Levy Daniel , Sotoodehnia Nona , Boerwinkle Eric , Arking Dan E. 
Published: June 2019

ABSTRACTBackgroundMitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation.MethodsTo investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European American (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study. To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1,995). We further assessed the effect of experimental modification of mtDNA-CN through knockout of TFAM, a regulator of mtDNA replication, via CRISPR-Cas9.ResultsThirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5×10-8). Meta-analysis across all cohorts identified six mtDNA-CN associated CpGs at genome-wide significance (P<5×10-8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including coronary heart disease, cardiovascular disease, and mortality. Experimental modification of mtDNA-CN demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the ‘neuroactive ligand receptor interaction’ KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24×10-12), as well as the TFAM knockout methylation (P=4.41×10-4) and expression (P=4.30×10-4) studies.ConclusionsThese results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential expression of specific genes that may impact human health and disease via altered cell signaling.
Do African savanna elephants (Loxodonta africana) eat crops because they crave micronutrients?
Authors: Vogel Susanne Marieke , de Boer Willem Frederik , Masake Moses , Songhurst Anna Catherine , McCulloch Graham , Stronza Amanda , Henley Michelle Deborah , Coulson Tim 
Published: June 2019

AbstractElephants can cause negative consequences for both themselves and for humans by consuming agricultural crops. It is unclear whether savanna elephant crop consumption is merely opportunistic behaviour or related to insufficient quality of natural forage. We analysed the role of vegetation quality on elephant crop consumption. We focused on the role of micronutrients, as natural elephant diets are thought to be insufficient in elements such as sodium and phosporus, which can influence their foraging decisions.For 12 months across four seasons we collected elephant feeding trail data along with tree, grass and crop samples. We investigated how the quality and availability of these items influenced elephant dietary choices across months and seasons. Subsequently, we compared levels of fibre, digestible energy, dry matter intake, and micronutrients, together with secondary compounds (tannins) across the three vegetation groups. As elephants do not make dietary choices based on one component, we also analysed the nutrient balance of food items with right-angle mixture models.The levels of phosphorus, magnesium and dry matter intake corresponded to foraging preference. Compared to trees and grasses, crops contained significantly higher amounts of digestible energy content, dry matter intake, nitrogen, phosphorus, calcium and magnesium. PCA results showed that crops differed in phosphorus and magnesium levels. The right-angle mixture models indicated that except for one tree species, all food items elephants consumed were relatively deficient in phosphorus.The combined results of these analyses suggest a phosphorus deficiency in elephant diet in northern Botswana. Crops, with their high absolute phosphorus levels and dry matter intake, provide an alternative source of phosphorus to reduce the deficiency. This may explain the high intensity of crop consumption in the wet season in our study area. A potential mitigation measure against elephant crop consumption might be to provide supplementary phosphorus sources.
Estrogen induces mammary ductal dysplasia
Authors: Itou Junji , Takahashi Rei , Sasanuma Hiroyuki , Tsuda Masataka , Morimoto Suguru , Matsumoto Yoshiaki , Ishii Tomoko , Sato Fumiaki , Takeda Shunichi , Toi Masakazu 
Published: June 2019

AbstractMammary ductal dysplasia is a phenotype observed in precancerous lesions and early-stage breast cancer. However, the mechanism of dysplasia formation remains elusive. Here we show, by establishing a novel dysplasia model system, that estrogen, a female hormone, has the potential to cause mammary ductal dysplasia. We injected estradiol (E2), the most active form of estrogen, daily into scid mice with a defect in nonhomologous end joining repair and observed dysplasia formation with cell proliferation at day 30. Moreover, we found that isoflavones inhibited E2-induced dysplasia formation. Our dysplasia model system provides insight into the mechanistic understanding of breast tumorigenesis, and the development of breast cancer prevention.
Calretinin positive neurons form an excitatory amplifier network in the spinal cord dorsal horn
Authors: Smith KM , Browne TJ , Davis O , Coyle A , Boyle KA , Watanabe M , Dickinson SA , Iredale JA , Gradwell MA , Jobling P , Callister RJ , Dayas CV , Hughes DI , Graham BA 
Published: June 2019

AbstractThe passage of nociceptive information is relayed through the spinal cord dorsal horn, a critical area in sensory processing. The neuronal circuits in this region that underpin sensory perception must be clarified to better understand how dysfunction can lead to pathological pain. This study used an optogenetic approach to selectively activate neurons that contain the calcium-binding protein calretinin (CR). We show that CR+ interneurons form an interconnected network that can initiate and sustain enhanced excitatory signaling, and directly relays signals to lamina I projection neurons. In vivo photoactivation of CR+ interneurons resulted in a significant nocifensive behavior that was morphine sensitive and cause a conditioned place aversion. Furthermore, halorhodopsin-mediated inhibition of CR+ interneurons elevated sensory thresholds. These results suggest that neuronal circuits in the superficial dorsal horn that involve excitatory CR+ neurons are important for the generation and amplification of pain, and identify these interneurons as a future analgesic target.
KCND3 is a novel susceptibility locus for early repolarization
Authors: Teumer Alexander , Trenkwalder Teresa , Kessler Thorsten , Jamshidi Yalda , van den Berg Marten E. , Kaess Bernhard , Nelson Christopher P. , Bastiaenen Rachel , De Bortoli Marzia , Rossini Alessandra , Deisenhofer Isabel , Stark Klaus , Assa Solmaz , Braund Peter S. , Cabrera Claudia , Dominiczak Anna F. , Gögele Martin , Hall Leanne M. , Ikram M. Arfan , Kavousi Maryam , Lackner Karl J. ,   Lifelines Cohort Study, Müller Christian , Münzel Thomas , Nauck Matthias , Padmanabhan Sandosh , Pfeiffer Norbert , Spector Tim D. , Uitterlinden Andre G. , Verweij Niek , Völker Uwe , Warren Helen R. , Zafar Mobeen , Felix Stephan B. , Kors Jan A. , Snieder Harold , Munroe Patricia B. , Pattaro Cristian , Fuchsberger Christian , Schmidt Georg , Nolte Ilja M. , Schunkert Heribert , Pramstaller Peter , Wild Philipp S. , van der Harst Pim , Stricker Bruno H. , Schnabel Renate B. , Samani Nilesh J. , Hengstenberg Christian , Dörr Marcus , Behr Elijah R. , Reinhard Wibke 
Published: June 2019

AbstractThe presence of an early repolarization pattern (ERP) on the surface electrocardiogram (ECG) is associated with risk of ventricular fibrillation and sudden cardiac death. Family studies have shown that ERP is a highly heritable trait but molecular genetic determinants are unknown. We assessed the ERP in 12-lead ECGs of 39,456 individuals and conducted a two-stage meta-analysis of genome-wide association studies (GWAS). In the discovery phase, we included 2,181 cases and 23,641 controls from eight European ancestry studies and identified 19 genome-wide significant (p<5E-8) variants in the KCND3 (potassium voltage gated channel subfamily D member 3) gene with a p-value of 4.6E-10. Replication of two loci in four additional studies including 1,124 cases and 12,510 controls confirmed the association at the KCND3 gene locus with a pooled odds ratio of 0.82, p=7.7E-12 (rs1545300 minor allele T). A subsequent GWAS meta-analysis combining all samples did not reveal additional loci. The lead SNP of the discovery stage (rs12090194) was in strong linkage disequilibrium with rs1545300 (r2=0.96, D’=1). Summary statistics based conditional analysis did not reveal any secondary signals. Co-localization analyses indicate causal effects of KCND3 gene expression levels on ERP in both the left ventricle of the heart and in tibial artery.In this study we identified for the first time a genome-wide significant association of a genetic variant with ERP. Our findings of a locus in the KCND3 gene not only provide insights into the genetic determinants but also into the pathophysiological mechanism of ERP, revealing a promising candidate for functional studies.
Vimentin intermediate filaments undergo irreversible conformational changes during cyclic loading
Authors: Forsting Johanna , Kraxner Julia , Witt Hannes , Janshoff Andreas , Köster Sarah 
Published: June 2019

AbstractIntermediate filaments (IFs) are part of the cytoskeleton of eukaryotic cells and are thus largely responsible for the cell’s mechanical properties. IFs are characterized by a pronounced extensibility and remarkable resilience that enable them to support cells in extreme situations. Previous experiments showed that under strain, α-helices in vimentin IFs might unfold to β-sheets. Upon repeated stretching, the filaments soften, however, the remaining plastic strain is negligible. Here we observe that vimentin IFs do not recover their original stiffness on reasonable time scales, and we explain these seemingly contradicting results by introducing a third, less well-defined conformational state. Reversibility on the nanoscale can be fully rescued by introducing crosslinkers that prevent transition to the β-sheet. Our results classify IFs as a nano-material with intriguing mechanical properties, which is likely to play a major role for the cell’s local adaption to external stimuli.
Comparative molecular life history of spontaneous canine and human gliomas
Authors: Amin Samirkumar B. , Anderson Kevin J. , Boudreau C. Elizabeth , Martinez-Ledesma Emmanuel , Kocakavuk Emre , Johnson Kevin C. , Barthel Floris P. , Varn Frederick S. , Kassab Cynthia , Ling Xiaoyang , Kim Hoon , Barter Mary , Ngan Chew Yee , Chapman Margaret , Koehler Jennifer W. , Miller Andrew D. , Miller C. Ryan , Porter Brian F. , Rissi Daniel R. , Mazcko Christina , LeBlanc Amy K. , Dickinson Peter J. , Packer Rebecca , Taylor Amanda R. , Rossmeisl John H. , Heimberger Amy , Levine Jonathan M. , Verhaak Roel G. W. 
Published: June 2019

SummarySporadic gliomas in companion dogs provide a window on the interaction between tumorigenic mechanisms and host environment. We compared the molecular profiles of canine gliomas with those of human pediatric and adult gliomas to characterize evolutionarily conserved mammalian mutational processes in gliomagenesis. Employing whole genome-, exome-, transcriptome-and methylation-sequencing of 81 canine gliomas, we found alterations shared between canine and human gliomas such as the receptor tyrosine kinases, p53 and cell cycle pathways, andIDH1R132. Canine gliomas showed high similarity with human pediatric gliomas per robust aneuploidy, mutational rates, relative timing of mutations, and DNA methylation patterns. Our cross-species comparative genomic analysis provides unique insights into glioma etiology and the chronology of glioma-causing somatic alterations.SignificanceDiffuse gliomas are the most common malignant brain tumors, with high-grade tumors carrying a dismal prognosis. Preclinical models have proven themselves as poor predictors of clinical efficacy. Spontaneous glioma in dogs provides an attractive alternative model, because of their comparable tumor microenvironment and tumor life history. We determined the similarities and differences between human and canine gliomas through genomic profiling, and leveraged our datasets to identify conserved somatic drivers, mutational processes and temporal ordering of somatic glioma events across species. We show that canine gliomas resemble human gliomas at (epi-)genetic levels and are more reminiscent of pediatric than adult disease, thus rationalizing sporadic canine glioma as a preclinical model tailored to measuring treatment efficacies in patients with canine or human glioma.
Ste5 Membrane Localization Allows MAPK Pathway Signalingin transBetween Kinases on Separate Scaffold Molecules
Authors: Lamson Rachel E. , Winters Matthew J. , Pryciak Peter M. 
Published: June 2019

SUMMARYThe MAP kinase cascade is a ubiquitous eukaryotic signaling module that can be controlled by a diverse group of scaffold proteins. In budding yeast, activation of the mating MAP kinase cascade involves regulated membrane recruitment of the archetypal scaffold protein Ste5. This event promotes activation of the first kinase, but it also enhances subsequent signal propagation through the remainder of the cascade. By studying this latter effect, we find that membrane recruitment promotes signalingin transbetween kinases on separate Ste5 molecules. First,transsignaling requires all Ste5 domains that mediate membrane recruitment, including both protein-binding and membrane-binding domains. Second, artificial membrane tethering of Ste5 can drivetranssignaling, bypassing the need for native localization domains. Third,transsignaling can occur even if the first kinase does not bind the scaffold but instead is localized independently to the plasma membrane. Moreover, thetranssignaling reaction allowed us to separate Ste5 into distinct functional domains, and then achieve normal regulation of signal output by tethering one domain to the membrane and stimulating membrane recruitment of the other. Overall, the results support a heterogeneous “ensemble” model of signaling in which scaffolds need not organize multiprotein complexes but instead can serve as binding sinks that co-concentrate enzymes and substrates at specific subcellular locales. These properties relax assembly constraints for scaffold proteins, increase regulatory flexibility, and can facilitate both natural evolution and artificial design of new signaling proteins and pathways.