bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-assembly of mutant huntingtin exon-1 fragments into large complex fibrillar structures involves nucleated branching
Authors: Wagner Anne S. , Politi Antonio Z. , Ast Anne , Bravo-Rodriguez Kenny , Baum Katharina , Buntru Alexander , Strempel Nadine U. , Brusendorf Lydia , Hänig Christian , Boeddrich Annett , Plassmann Stephanie , Klockmeier Konrad , Ramirez-Anguita Juan M. , Sanchez-Garcia Elsa , Wolf Jana , Wanker Erich E. 
Published: October 2017

AbstractHuntingtin (HTT) fragments with extended polyglutamine (polyQ) tracts self-assemble into amyloid-like fibrillar aggregates. Elucidating the fibril formation mechanism is critical for understanding Huntington’s disease pathology and for developing novel therapeutic strategies. Here, we performed systematic experimental and theoretical studies to examine the self-assembly of an aggregation-prone N-terminal HTT exon-1 fragment with 49 glutamines (Ex1Q49). Using high resolution imaging techniques such as electron microscopy and atomic force microscopy, we show that Ex1Q49 fragments in cell-free assays spontaneously convert into large, highly complex bundles of amyloid fibrils with multiple ends and fibril branching points. Furthermore, we present experimental evidence that two nucleation mechanisms control spontaneous Ex1Q49 fibrillogenesis: (1) a relatively slow primary fibril-independent nucleation process, which involves the spontaneous formation of aggregation-competent fibrillary structures, and (2) a fast secondary fibril-dependent nucleation process, which involves nucleated branching and promotes the rapid assembly of highly complex fibril bundles with multiple ends. The proposed aggregation mechanism is supported by studies with the small molecule O4, which perturbs early events in the aggregation cascade and delays Ex1Q49 fibril assembly, comprehensive mathematical and computational modelling studies, and seeding experiments with small, preformed fibrillar Ex1Q49 aggregates that promote the assembly of amyloid fibrils. Together, our results suggest that nucleated branchingin vitroplays a critical role in the formation of complex fibrillar HTT exon-1 aggregates with multiple ends.
Myosin IIA interacts with the spectrin-actin membrane skeleton to control red blood cell membrane curvature and deformability
Authors: Smith Alyson S. , Nowak Roberta B. , Zhou Sitong , Giannetto Michael , Gokhin David S. , Papoin Julien , Ghiran Ionita C. , Blanc Lionel , Wan Jiandi , Fowler Velia M. 
Published: October 2017

AbstractThe biconcave disc shape and deformability of mammalian red blood cells (RBCs) relies upon the membrane skeleton, a viscoelastic network of short, membrane-associated actin filaments (F-actin) cross-linked by long, flexible spectrin tetramers. Nonmuscle myosin II (NMII) motors exert force on diverse F-actin networks to control cell shapes, but a function for NMII contractility in the 2D spectrin-F-actin network in RBCs has not been tested. Here, we show that RBCs contain membrane skeleton-associated NMIIA puncta, identified as bipolar filaments by super-resolution fluorescence microscopy. NMIIA association with the membrane skeleton is ATP-dependent, consistent with NMIIA motor domains binding to membrane skeleton F-actin and contributing to membrane mechanical stability. In addition, the NMIIA heavy and light chains are phosphorylatedin vivoin RBCs, indicating active regulation of NMIIA motor activity and filament assembly, while reduced heavy chain phosphorylation of membrane skeleton-associated NMIIA indicates assembly of stable filaments at the membrane. Treatment of RBCs with blebbistatin, an inhibitor of NMII motor activity, decreases the number of NMIIA filaments associated with the membrane and enhances local, nanoscale membrane oscillations, suggesting decreased membrane tension. Blebbistatin-treated RBCs also exhibit elongated shapes, loss of membrane curvature, and enhanced deformability, indicating a role for NMIIA contractility in promoting membrane stiffness and maintaining RBC biconcave disc cell shape. As structures similar to the RBC membrane skeleton are conserved in many metazoan cell types, these data demonstrate a general function for NMII in controlling specialized membrane morphology and mechanical properties through contractile interactions with short F-actin in spectrin-F-actin networks.Significance statementThe biconcave disc shape and deformability of the mammalian RBC is vital to its circulatory function, relying upon a 2D viscoelastic spectrin-F-actin network attached to the membrane. A role for myosin II (NMII) contractility in generating tension in this network and controlling RBC shape has never been tested. We show that NMIIA forms phosphorylated bipolar filaments in RBCs, which associate with F-actin at the membrane. NMIIA motor activity is required for interactions with the spectrin-F-actin network, and regulates RBC biconcave shape and deformability. These results provide a novel mechanism for actomyosin force generation at the plasma membrane, and may be applicable to other cell types such as neurons and polarized epithelial cells with a spectrin-F-actin-based membrane skeleton.
Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum
Authors: Pattabiraman Chitra , Dias Mary , Siddappa Shilpa , Gowda Malali , Shet Anita , Smith Derek , Muehlemann Barbara , Tamma Krishnapriya , Solomon Tom , Jones Terry , Krishna Sudhir 
Published: October 2017

ABSTRACTBackgroundMosquito-borne flaviviruses causing diseases such as dengue and Japanese encephalitis are devastating, particularly in the tropics. Although, multiple flaviviruses are known to co-circulate in India, when a patient presents with febrile illness, testing is usually limited to specific pathogens. Unbiased metagenomic sequencing of febrile cases can reveal the presence of multiple pathogens and provide complete genome information. Sequence information, a cornerstone for tracing virus evolution, is relevant for the design of vaccines and therapeutics. In order to assess the usefulness of unbiased metagenomic sequencing for the identification of viruses associated with febrile illness, we sequenced serum from four individuals and plasma from one individual, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illnesses, together with one healthy control in 2014.ResultsWe identified and assembled a complete dengue virus type 3 (DENV3) sequence from the serum of a case classified as severe dengue. We also found a small number of Japanese encephalitis virus (JEV) sequences in the serum of two adults with febrile illness, including the one who had dengue. Phylogenetic analysis of the dengue sequence indicates that it belongs to a predominantly Asian, DENV3, genotype III clade. It had an estimated divergence time of 13.86 years (95% Highest Posterior Densities 12.94 - 14.83 years) with the closest Indian strain. Amino acid substitutions were present throughout the sequenced genome, including 11 substitutions in the antigenic envelope protein compared to the strain used for the development of the first commercial dengue vaccine. Of these one substitution (E361D) was unique and six were in critical antigenic sites.ConclusionsWe demonstrate that both genome assembly and detection of a low number of viral sequences are possible by unbiased sequencing of clinical material. Complete dengue virus sequence analysis places the sequenced genome in a recent, predominantly Asian clade within genotype III of DENV3. The detection of JEV, an agent not routinely tested in febrile illness in India, warrants further analysis and highlights the need to study co-circulating flaviviruses in parallel.
Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative
Authors: Fritsche Lars G. , Gruber Stephen B. , Wu Zhenke , Schmidt Ellen M. , Zawistowski Matthew , Moser Stephanie E. , Blanc Victoria M. , Brummett Chad M. , Kheterpal Sachin , Abecasis Gonçalo R. , Mukherjee Bhramar 
Published: October 2017

AbstractHealth systems are stewards of patient electronic health record (EHR) data with extraordinarily rich depth and breadth, reflecting thousands of diagnoses and exposures. Measures of genomic variation integrated with EHRs offer a potential strategy to accurately stratify patients for risk profiling and discover new relationships between diagnoses and genomes. The objective of this study was to evaluate whether Polygenic Risk Scores (PRS) for common cancers are associated with multiple phenotypes in a Phenome-wide Association Study (PheWAS) conducted in 28,260 unrelated, genotyped patients of recent European ancestry who consented to participate in the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine. PRS for 12 cancer traits were calculated using summary statistics from the NHGRI-EBI catalog. A total of 1,711 synthetic case-control studies was used for PheWAS analyses. There were 13,490 (47.7%) patients with at least one cancer diagnosis in this study sample. PRSs exhibited strong association for several cancer traits they were designed for including female breast cancer, prostate cancer, melanoma, basal cell carcinoma, squamous cell carcinoma and thyroid cancer. Phenome-wide significant associations were observed between PRS and many non-cancer diagnoses. To differentiate PRS associations driven by the primary trait from associations arising through shared genetic risk profiles, the idea of “exclusion PRS PheWAS” was introduced. This approach led to phenome-wide significant associations between a lower risk for hypothyroidism in patients with high thyroid cancer PRS and a higher risk for actinic keratosis in patients with high squamous cell carcinoma PRS after removing all cases of the primary cancer trait. Further analysis of temporal order of the diagnoses improved our understanding of these secondary associations. This is the first comprehensive PheWAS study using PRS instead of a single variant.
Ongoing brain rhythms shape I-wave properties in a computational model
Authors: Schaworonkow Natalie , Triesch Jochen 
Published: October 2017

AbstractBackgroundResponses to transcranial magnetic stimulation (TMS) are notoriously variable. Previous studies have observed a dependence of TMS-induced responses on ongoing brain activity, for instance sensorimotor rhythms. This suggests an opportunity for the development of more effective stimulation protocols through closed-loop TMS-EEG. However, it is not yet clear how features of ongoing activity affect the responses of cortical circuits to TMS.Objective/HypothesisHere we investigate the dependence of TMS-responses on power and phase of ongoing oscillatory activity in a computational model of TMS-induced I-waves.MethodsThe model comprises populations of cortical layer 2/3 (L2/3) neurons and a population of cortical layer 5 (L5) neurons and generates I-waves in response to TMS. Oscillatory input to the L2/3 neurons induces rhythmic fluctuations in activity of L5 neurons. TMS pulses are simulated at different phases and amplitudes of the ongoing rhythm.ResultsThe model shows a robust dependence of I-wave properties on phase and power of ongoing rhythms, with the strongest response occurring for TMS at maximal L5 depolarization. The amount of phase-modulation depends on stimulation intensity, with stronger modulation for lower intensity.ConclusionThe model predicts that responses to TMS are highly variable for low stimulation intensities if ongoing brain rhythms are not taken into account. Closed-loop TMS-EEG holds promise for obtaining more reliable TMS effects.
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT
Authors: Raj Bushra , Wagner Daniel E. , McKenna Aaron , Pandey Shristi , Klein Allon M. , Shendure Jay , Gagnon James A. , Schier Alexander F. 
Published: October 2017

ABSTRACTHundreds of cell types are generated during development, but their lineage relationships are largely elusive. Here we report a technology, scGESTALT, which combines cell type identification by single-cell RNA sequencing with lineage recording by cumulative barcode editing. We sequenced ~60,000 transcriptomes from the juvenile zebrafish brain and identified more than 100 cell types and marker genes. We engineered an inducible system that combines early and late barcode editing and isolated thousands of single-cell transcriptomes and their associated barcodes. The large diversity of edited barcodes and cell types enabled the generation of lineage trees with hundreds of branches. Inspection of lineage trajectories identified restrictions at the level of cell types and brain regions and helped uncover gene expression cascades during differentiation. These results establish scGESTALT as a new and widely applicable tool to simultaneously characterize the molecular identities and lineage histories of thousands of cells during development and disease.
DNA unwinding is the primary determinant of CRISPR-Cas9 activity
Authors: Gong Shanzhong , Yu Helen Hong , Johnson Kenneth A. , Taylor David W. 
Published: October 2017

SummaryBacterial adaptive immunity utilizes RNA-guided surveillance complexes composed of CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single guide RNA that base-pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and RuvC nuclease domains can cleave opposing strands. Cas9 has been repurposed for a variety of important genome engineering applications. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge. Our detailed kinetic characterization of the enzyme reveals that DNA binding is reversible, R-loop formation is rate-limiting, occurring in two steps, one for each of the nuclease domains. Although the HNH nuclease activity is stimulated by Mg2+ with a single measureable Kd, the RuvC activity requires two distinct Mg2+ binding events. The specificity constant for cleavage is determined through an induced-fit mechanism as the product of the equilibrium binding affinity for DNA and the rate of R-loop formation.
Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity inRhizophagus irregularis
Authors: Maeda Taro , Kobayashi Yuuki , Kameoka Hiromu , Okuma Nao , Takeda Naoya , Yamaguchi Katsushi , Bino Takahiro , Shigenobu Shuji , Kawaguchi Masayoshi 
Published: October 2017

AbstractArbuscular mycorrhizal fungus (AMF) species are one of the most widespread symbionts of land plants. Our substantially improved reference genome assembly of a model AMF,Rhizophagus irregularisDAOM-181602 (total contigs = 210), facilitated discovery of repetitive elements with unusual characteristics.R. irregularishas only ten or eleven copies of complete 45S rDNAs, whereas the general eukaryotic genome has tens to thousands of rDNA copies.R. irregularisrDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis that rDNA heterogeneity depends on the lack of tandem repeat structures. RNA-Seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphisms may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA/rRNA may facilitate adaptation to a various environmental condition including the broad host range.
Topographical and spectral signatures of infant and adult movement artifacts in naturalistic EEG
Authors: Georgieva Stanimira , Lester Suzannah , Yilmaz Meryem Nazli , Wass Sam , Leongi Victoria 
Published: October 2017

ABSTRACTElectroencephalography (EEG) is perhaps the most widely used brain-imaging technique for paediatric populations. However, EEG signals are prone to distortion by motion. Compared to adults, infants’ motion is both more frequent and less stereotypical yet motion effects on the infant EEG signal are largely undocumented. Here, we present a systematic assessment of naturalistic motion effects on the infant and adult EEG signal. In Study 1, we documented the prevalence of 27 naturally occurring facial and body motions by video-coding five mother-infant pairs during naturalistic play. In Study 2, we elicited a subset of the most common facial, limb and postural motions from one adult and one infant actor while their EEG was recorded. In Study 3, we recorded EEG signals from a larger group of 12 infants whilst they produced the same motions spontaneously. Our findings from Study 2 suggested that adult movements mainly generated increases in spectral power relative to resting state, primarily at peripheral sites and in delta and high-beta frequency bands. In infants, both elicited motions (N=1, Study 2) and spontaneously-occurring motions (N=12, Study 3) produced decreases in theta, alpha and beta power over central regions and increased beta/delta power at peripheral sites. We also observed that infants’ jaw and upper limb movements generated more pronounced EEG artifacts than lower limb movements. It is intended that this work will inform future development of methods for addressing EEG motion-related artifacts and support wider use of naturalistic paradigms in social and developmental neuroscience.
Mathematical modelling of cortical neurogenesis reveals that the founder population does not necessarily scale with neuronal output
Authors: Picco Noemi , García-Moreno Fernando , Woolley Thomas E. , Maini Philip K. , Molnár Zoltán 
Published: October 2017

AbstractThe mammalian cerebral neocortex has a unique structure, composed of layers of different neuron types, interconnected in a stereotyped fashion. While the overall developmental program seems to be conserved, there are divergent developmental factors generating cortical diversity amongst mammalian species. In terms of cortical neuronal numbers some of the determining factors are the size of the founder population, the duration of cortical neurogenesis, the proportion of different progenitor types, and the fine-tuned balance between self-renewing and differentiative divisions. We develop a mathematical model of neurogenesis that, accounting for these factors, aims at explaining the high diversity in neuronal numbers found across mammalian species. By framing our hypotheses in rigorous mathematical terms, we are able to identify paths of neurogenesis that match experimentally observed patterns in mouse, macaque and human. Additionally, we use our model to identify key parameters that would particularly benefit from accurate experimental investigation. We find that the timing of a switch in favor of symmetric neurogenic divisions produces the highest variation in cortical neuronal numbers. Surprisingly, in our model the increase in cortical neuronal numbers does not necessarily reflect a larger size of founder population, a prediction that identified a specific need for experimental quantifications.
RNA velocity in single cells
Authors: La Manno Gioele , Soldatov Ruslan , Hochgerner Hannah , Zeisel Amit , Petukhov Viktor , Kastriti Maria E. , Lönnerberg Peter , Furlan Alessandro , Fan Jean , Liu Zehua , van Bruggen David , Guo Jimin , Sundström Erik , Castelo-Branco Gonçalo , Adameyko Igor , Linnarsson Sten , Kharchenko Peter V. 
Published: October 2017

AbstractRNA abundance is a powerful indicator of the state of individual cells, but does not directly reveal dynamic processes such as cellular differentiation. Here we show that RNA velocity—the time derivative of RNA abundance—can be estimated by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. We show that RNA velocity is a vector that predicts the future state of individual cells on a timescale of hours. We validate the accuracy of RNA velocity in the neural crest lineage, demonstrate its use on multiple technical platforms, reconstruct the branching lineage tree of the mouse hippocampus, and measure RNA kinetics in human embryonic brain. We expect RNA velocity to greatly aid the analysis of developmental lineages and cellular dynamics, particularly in humans.
Cryo-EM Reveals the Structural Basis of Microtubule Depolymerization by Kinesin-13s
Authors: Benoit Matthieu P. M. H. , Asenjo Ana B. , Sosa Hernando 
Published: October 2017

SummaryKinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promotes microtubule depolymerization and lacks motile activity. The molecular mechanism by which the kinesins depolymerize microtubules and are adapted to perform a seemingly very different activity from other kinesins is still unclear. To address this issue we obtained near atomic resolution cryo-electron microscopy (cryo-EM) structures of Drosophila melanogaster kinesin-13 KLP10A constructs bound to curved or straight tubulin in different nucleotide states. The structures show how nucleotide induced conformational changes near the catalytic site are coupled with kinesin-13-specific structural elements to induce tubulin curvature leading to microtubule depolymerization. The data highlight a modular structure that allows similar kinesin core motor-domains to be used for different functions, such as motility or microtubule depolymerization.
The scent of the fly
Authors: Becher Paul G. , Lebreton Sebastien , Wallin Erika A. , Hedenström Erik , Borrero Felipe , Bengtsson Marie , Jörger Volker , Witzgall Peter 
Published: October 2017

Abstract(Z)-4-undecenal (Z4-11Al) is the volatile pheromone produced by females of the vinegar fly Drosophila melanogaster. Female flies emit Z4-11Al for species-specific communication and mate-finding. A sensory panel finds that synthetic Z4-11Al has a characteristic flavour, which we perceive even at the small amounts produced by one female fly. Since only females produce Z4-11Al, and not males, we can reliably distinguish between single D. melanogaster males and females, according to their scent. Females release Z4-11Al at 2.4 ng/h and we readily sense 1 ng synthetic Z4-11Al in a glass of wine (0.03 nmol/L), while a tenfold concentration is perceived as a loud off-flavour. This corroborates the observation that a glass of wine is spoilt by a single D. melanogaster fly falling into it, which we here show is caused by Z4-11Al. The biological role of Z4-11Al or structurally related aldehydes in humans and the basis for this semiochemical convergence remains yet unclear.