bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis and refined design of CRISPR knockout screens
Authors: Chen Chen-Hao , Li Wei , Xiao Tengfei , Xu Han , Jiang Peng , Meyer Clifford A. , Brown Myles , Liu X. Shirley 
Published: February 2017

AbstractGenome-wide CRISPR-Cas9 screen has been widely used to interrogate gene functions. However, the analysis remains challenging and rules to design better libraries beg further refinement. Here we present MAGeCK-NEST, which integrates protein-protein interaction (PPI), improves the inference accuracy when fewer guide-RNAs (sgRNAs) are available, and assesses screen qualities using information on PPI. MAGeCK-NEST also adopts a maximum-likelihood approach to remove sgRNA outliers, which are characterized with higher G-nucleotide counts, especially in regions distal from the PAM motif. Using MAGeCK-NEST, we found that choosing non-targeting sgRNAs as negative controls lead to strong bias, which can be mitigated by sgRNAs targeting the “safe harbor” regions. Custom-designed screens confirmed our findings, and further revealed that 19nt sgRNAs consistently gave the best signal-to-noise separation. Collectively, our method enabled robust calling of CRISPR screen hits and motivated the design of an improved genome-wide CRISPR screen library.
Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1
Authors: Elnatan Daniel , Betegon Miguel , Liu Yanxin , Ramelot Theresa , Kennedy Michael A. , Agard David A. 
Published: February 2017

AbstractHsp90 is a homodimeric ATP-dependent molecular chaperone that remodels its substrate “client” proteins, facilitating their folding and activating them for biological function. Despite decades of research, the mechanism connecting ATP hydrolysis and chaperone function remains elusive. Particularly puzzling has been the apparent lack of cooperativity in hydrolysis of the ATP in each protomer. A crystal structure of the mitochondrial Hsp90, TRAP1, revealed that the catalytically active state is closed in a highly-strained asymmetric conformation. This asymmetry, unobserved in other Hsp90 homologs, is due to buckling of one of the protomers and is most pronounced at the broadly conserved client-binding region. Here, we show that rather than being cooperative or independent, ATP hydrolysis on the two protomers is sequential and deterministic. Moreover, dimer asymmetry sets up differential hydrolysis rates for each protomer, such that the buckled conformation favors ATP hydrolysis. Remarkably, after the first hydrolysis, the dimer undergoes a flip in the asymmetry while remaining in a closed state for the second hydrolysis. From these results, we propose a model where direct coupling of ATP hydrolysis and conformational flipping rearranges client-binding sites, providing a paradigm of how energy from ATP hydrolysis can be used for client remodeling.
Evidence for time division multiplexing: Single neurons may encode simultaneous stimuli by switching between activity patterns
Authors: Caruso Valeria C. , Mohl Jeff T. , Glynn Christopher , Lee Jungah , Willett Shawn M. , Zaman Azeem , Ebihara Akinori F. , Estrada Rolando , Freiwald Winrich A. , Tokdar Surya T. , Groh Jennifer M. 
Published: February 2017

ABSTRACTHow the brain preserves information about multiple simultaneous items is poorly understood. We report that single neurons can represent multiple different stimuli by interleaving different signals across time. We record single units in an auditory region, the inferior colliculus, while monkeys localize 1 or 2 simultaneous sounds. During dual-sound trials, we find that some neurons fluctuate between firing rates observed for each single sound, either on a whole-trial or on a sub-trial timescale. These fluctuations are correlated in pairs of neurons, can be predicted by the state of local field potentials prior to sound onset, and, in one monkey, can predict which sound will be reported first. We find corroborating evidence of fluctuating activity patterns in a separate data set involving responses of inferotemporal cortex neurons to multiple visual stimuli. Alternation between activity patterns corresponding to each of multiple items may therefore be a general strategy to enhance the brain processing capacity, potentially linking such disparate phenomena as variable neural firing, neural oscillations, and limits in attentional/memory capacity.
Evolutionary and functional data power search for obsessive-compulsive disorder genes
Authors: Noh Hyun Ji , Tang Ruqi , Flannick Jason , O’Dushlaine Colm , Swofford Ross , Howrigan Daniel , Genereux Diane P. , Johnson Jeremy , van Grootheest Gerard , Grünblatt Edna , Andersson Erik , Djurfeldt Diana R. , Patel Paresh D. , Koltookian Michele , Hultman Christina , Pato Michele T. , Pato Carlos N. , Rasmussen Steven A. , Jenike Michael A. , Hanna Gregory L. , Stewart S. Evelyn , Knowles James A. , Ruhrmann Stephan , Grabe Hans-Jörgen , Wagner Michael , Rück Christian , Mathews Carol A. , Walitza Susanne , Cath Daniëlle C. , Feng Guoping , Karlsson Elinor K. , Lindblad-Toh Kerstin 
Published: February 2017

SUMMARYObsessive-compulsive disorder (OCD) is a severe psychiatric disorder linked to abnormalities in the cortico-striatal circuit and in glutamate signaling. We sequenced coding and regulatory elements for 608 genes implicated in OCD from humans and two animal models (mouse and dog). Using a new method, PolyStrat, which prioritizes variants disrupting evolutionarily conserved, functional regions, we found four strongly associated genes when comparing 592 cases to 560 controls. These results were validated in a second, larger cohort.NRXN1andHTR2Aare enriched for coding variants altering postsynaptic protein-binding domains, whileCTTNBP2(synapse maintenance) andREEP3(vesicle trafficking) are enriched for regulatory variants. The rare coding variant burden inNRXN1achieves genomewide significance (p=6.37×10−11) when we include public data for 33,370 controls. Of 17 regulatory variants identified inCTTNBP2andREEP3, we show that at least six alter transcription factor-DNA binding in human neuroblastoma cells. Our findings suggest synaptic adhesion as a key function in compulsive behaviors across three species, and demonstrate how combining targeted sequencing with functional annotations can identify potentially causative variants in both coding and noncoding regions, even when genomic data is limited.
MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia
Authors: Brown Fiona C. , Still Eric , Cifani Paolo , Takao Sumiko , Reed Casie , Ficarro Scott B. , Koche Richard P. , Romanienko Peter , Mark Willie , O’Donnell Conor , Spitzer Barbara , Stutzke Crystal , Krivtsov Andrei V. , Pouliot Gayle , Gray Nathanael , Marto Jarrod A. , Armstrong Scott , Kentsis Alex 
Published: February 2017

HIGHLIGHTSMEF2C S222 phosphorylation is a specific marker of chemotherapy resistance in diagnostic AML patient specimens.MEF2C S222 phosphorylation is dispensable for normal hematopoiesis in mice, as established using genome editing in vivo, but is required for MLL-AF9 induced leukemogenesis.MARK kinases specifically phosphorylate MEF2C S222, potentiating its transcriptional activity.Chemical inhibition of MARK-induced MEF2C phosphorylation overcomes chemotherapy resistance of and exhibits selectivity toxicity against MEF2C-activated human AML cells.SUMMARYIn acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that Mef2cS222A/S222A knock-in mutant mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9. MEF2C phosphorylation was required for leukemia stem cell maintenance, and induced by MARK kinases in cells. Treatment with the selective MARK inhibitor MRT199665 caused apoptosis of MEF2C-activated human AML cell lines and primary patient specimens, but not those lacking MEF2C phosphorylation. These findings identify kinase-dependent dysregulation of transcription factor control as a determinant of therapy response in AML, with immediate potential for improved diagnosis and therapy for this disease.
Dynamic Functional Connectivity between Order and Randomness and its Evolution across the Human Adult Lifespan
Authors: Battaglia Demian , Boudou Thomas , Hansen Enrique C. A. , Lombardo Diego , Chettouf Sabrina , Daffertshofer Andreas , McIntosh Anthony R. , Zimmermann Joelle , Ritter Petra , Jirsa Viktor 
Published: February 2017

AbstractFunctional Connectivity (FC) during resting-state or task conditions is not fixed but inherently dynamic. Yet, there is no consensus on whether fluctuations in FC may resemble isolated transitions between discrete FC states rather than continuous changes. This quarrel hampers advancing the study of dynamic FC. This is unfortunate as the structure of fluctuations in FC can certainly provide more information about developmental changes, aging, and progression of pathologies. We merge the two perspectives and consider dynamic FC as an ongoing network reconfiguration, including a stochastic exploration of the space of possible steady FC states. The statistical properties of this random walk deviate both from a purely “order-driven” dynamics, in which the mean FC is preserved, and from a purely “randomness-driven” scenario, in which fluctuations of FC remain uncorrelated over time. Instead, dynamic FC has a complex structure endowed with long-range sequential correlations that give rise to transient slowing and acceleration epochs in the continuous flow of reconfiguration. Our analysis for fMRI data in healthy elderly revealed that dynamic FC tends to slow down and becomes less complex as well as more random with increasing age. These effects appear to be strongly associated with age-related changes in behavioural and cognitive performance.HighlightsDynamic Functional Connectivity (dFC) at rest and during cognitive task performs a “complex” (anomalous) random walk.Speed of dFC slows down with aging.Resting dFC replaces complexity by randomness with aging.Task performance correlates with the speed and complexity of dFC.
Between semelparity and iteroparity: empirical evidence for a continuum of modes of parity
Authors: Hughes P. William 
Published: February 2017

ABSTRACTThe number of times an organism reproduces (i.e. its mode of parity) is a fundamental life-history character, and evolutionary and ecological models that compare the relative fitness of strategies are common in life history theory and theoretical biology. Despite the success of mathematical models designed to compare intrinsic rates of increase between annual-semelparous and perennial-iteroparous reproductive schedules, there is widespread evidence that variation in reproductive allocation among semelparous and iteroparous organisms alike is continuous. This paper reviews the ecological and molecular evidence for the continuity and plasticity of modes of parity––that is, the idea that annual-semelparous and perennial-iteroparous life histories are better understood as endpoints along a continuum of possible strategies. I conclude that parity should be understood as a continuum of different modes of parity, which differ by the degree to which they disperse or concentrate reproductive effort in time. I further argue that there are three main implications of this conclusion: (1) That seasonality should not be conflated with parity; (2) that mathematical models purporting to explain the evolution of semelparous life histories from iteroparous ones (or vice versa) should not assume that organisms can only display either an annual-semelparous life history or a perennial-iteroparous one; and (3) that evolutionary ecologists should examine the physiological or molecular basis of traits underlying different modes of parity, in order to obtain a general understanding of how different life history strategies can evolve from one another.
On the relationship between indenation hardness and modulus, and the damage resistance of biological materials
Authors: Labonte David , Lenz Anne-Kristin , Oyen Michelle L. 
Published: February 2017

AbstractThe remarkable mechanical performance of biological materials is based on intricate structure-function relationships. Nanoindentation has become the primary tool for characterising biological materials, as it allows to relate structural changes to variations in mechanical properties on small scales. However, the respective theoretical background and associated interpretation of the parameters measured via indentation derives largely from research on ‘traditional’ engineering materials such as metals or ceramics. Here, we discuss the functional relevance of indentation hardness in biological materials by presenting a meta-analysis of its relationship with indentation modulus. Across seven orders of magnitude, indentation hardness was directly proportional to indentation modulus, illustrating that hardness is not an independent material property. Using a lumped parameter model to deconvolute indentation hardness into components arising from reversible and irreversible deformation, we establish criteria which allow to interpret differences in indentation hardness across or within biological materials. The ratio between hardness and modulus arises as a key parameter, which is a proxy for the ratio between irreversible and reversible deformation during indentation, and the material’s yield strength. Indentation hardness generally increases upon material dehydration, however to a larger extend than expected from accompanying changes in indentation modulus, indicating that water acts as a ‘plasticiser’. A detailed discussion of the role of indentation hardness, modulus and toughness in damage control during sharp or blunt indentation yields comprehensive guidelines for a performance-based ranking of biological materials, and suggests that quasi-plastic deformation is a frequent yet poorly understood damage mode, highlighting an important area of future research.
Functional Bias and Demographic History Obscure Patterns of Selection among Single-Copy Genes in a Fungal Species Complex
Authors: Sánchez-Ramírez Santiago , Moncalvo Jean-Marc 
Published: February 2017

AbstractMany different evolutionary processes may be responsible for explaining natural variation within genomes, some of which include natural selection at the molecular level and changes in population size. Fungi are highly adaptable organisms, and their relatively small genomes and short generation times make them pliable for evolutionary genomic studies. However, adaptation in wild populations has been relatively less documented compared to experimental or clinical studies. Here, we analyzed DNA sequences from 502 putative single-copy orthologous genes in 63 samples that represent seven recently diverged North AmericanAmanita(jacksonii-complex) lineages. For each gene and each species, we measured the genealogical sorting index (gsi) and infinite-site-based summary statistics, such as,andDTajin coding and intron regions. MKT-based approaches and likelihood-ratio-testKn/Ksmodels were used to measure natural selection in all coding sequences. Multi-locus (Extended) Bayesian Skyline Plots (eBSP) were used to model intraspecific demographic changes through time based on unlinked, putative neutral regions (introns). Most genes show evidence of long-term purifying selection, likely reflecting a functional bias implicit in single-copy genes. We find that two species have strongly negatively skewed Tajima’sD, while three other have a positive skew, corresponding well with patterns of demographic expansion and contraction. Standard MKT analyses resulted in a high incidence of near-zero α with a tendency towards negative values. In contrast, α estimates based on the distribution of fitness effects (DFE), which accounts for demographic effects and slightly deleterious mutations, suggest a higher proportion of sites fixed by positive selection. The difference was more notorious in species with expansion signatures or with historically low population sizes, evidencing the concealing effects of specific demographic histories. Finally, we attempt to mitigate Gene Ontology term overrepresentation, highlighting the potential adaptive or ecological roles of some genes under positive selection.
Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells
Authors: Kumar Sandeep , Peng Xiangdong , Daley James M. , Yang Lin , Shen Jianfeng , Nguyen Nghi , Bae Goeun , Niu Hengyao , Peng Yang , Hsieh Hui-Ju , Wang Lulu , Rao Chinthalapally , Stephan Clifford C. , Sung Patrick , Ira Grzegorz , Peng Guang 
Published: February 2017

AbstractReplication stress is a characteristic feature of cancer cells, which is resulted from sustained proliferative signaling induced by activation of oncogenes or loss of tumor suppressors. In cancer cells, oncogene-induced replication stress manifests as replication-associated lesions, predominantly double-strand DNA breaks (DSBs). An essential mechanism utilized by cells to repair replication-associated DSBs is homologous recombination (HR). In order to overcome replication stress and survive, cancer cells often require enhanced HR repair capacity. Therefore, the key link between HR repair and cellular tolerance to replication-associated DSBs provides us with a mechanistic rationale for exploiting synthetic lethality between HR repair inhibition and replication stress. Our studies showed that DNA2 nuclease is an evolutionarily conserved essential component of HR repair machinery. Here we demonstrate that DNA2 is indeed overexpressed in pancreatic cancers, one of the deadliest and more aggressive forms of human cancers, where mutations in the KRAS are present in 90%-95% of cases. In addition, depletion of DNA2 significantly reduces pancreatic cancer cell survival and xenograft tumor growth, suggesting the therapeutic potential of DNA2 inhibition. Finally, we develop a robust high-throughput biochemistry assay to screen for inhibitors of the DNA2 nuclease activity. The top inhibitors were shown to be efficacious against both yeast Dna2 and human DNA2. Treatment of cancer cells with DNA2 inhibitors recapitulates phenotypes observed upon DNA2 depletion, including decreased DNA end resection and attenuation of HR repair. Similar to genetic ablation of DNA2, chemical inhibition of DNA2 selectively attenuates the growth of various cancer cells with oncogene-induced replication stress. Taken together, our findings open a new avenue to develop a new class of anti-cancer drugs by targeting druggable nuclease DNA2. We 4, 16. In propose DNA2 inhibition as new strategy in cancer therapy by targeting replication stress, a molecular property of cancer cells that is acquired as a result of oncogene activation instead of targeting undruggable oncoprotein itself such as KRAS.
Computational Analysis of Lifespan Experiment Reproducibility
Authors: Petrascheck Michael , Miller Dana L. 
Published: February 2017

SummaryIndependent reproducibility is essential to the generation of scientific knowledge. Optimizing experimental protocols to ensure reproducibility is an important aspect of scientific work. Genetic or pharmacological lifespan extensions are generally small compared to the inherent variability in mean lifespan even in isogenic populations housed under identical conditions. This variability makes reproducible detection of small but real effects experimentally challenging. In this study, we aimed to determine the reproducibility ofC. eleganslifespan measurements under ideal conditions, in the absence of methodological errors or environmental or genetic background influences. To accomplish this, we generated a parametric model ofC. eleganslifespan based on data collected from 5,026 wild-type N2 animals. We use this model to predict how different experimental practices, effect sizes, number of animals, and how different ‘shapes’ of survival curves affect the ability to reproduce real longevity effects. We find that the chances of reproducing real but small effects are exceedingly low and would require substantially more animals than are commonly used. Our results indicate that many lifespan studies are underpowered to detect reported changes and that, as a consequence, stochastic variation alone can account for many failures to reproduce longevity results. As a remedy, we provide power of detection tables that can be used as guidelines to plan experiments with statistical power to reliably detect real changes in lifespan and limit spurious false positive results. These considerations will improve best-practices in designing lifespan experiment to increase reproducibility.
Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism
Authors: Du Bin , Zielinski Daniel C. , Palsson Bernhard O. 
Published: February 2017

AbstractLinear analysis of kinetic models of metabolism can help in understanding the dynamic response of metabolic networks. Central to linear analysis of these models are two key matrices: the Jacobian matrix (J) and its modal matrix (M-1). The modal matrix contains dynamically independent motions of the kinetic model, and it is sparse in practice. Understanding the sparsity structure of the modal matrix provides insight into metabolic network dynamics. In this study, we analyze the relationship betweenJandM-1. First, we show that diagonal dominance occurs in a substantial fraction of the rows ofJ, resulting in simple modal structures withinM-1. Dominant diagonal elements inJapproximate the eigenvalues corresponding to these simple modes, in which a single metabolite is driven back to its reference state on a characteristic timescale. Second, we analyze more complicated mode structures inM-1, in which two or more variables move in a certain ratio relative to one another on defined time scales. We show that complicated modes originate from sub-matrices of topologically connected elements of similar magnitude inJ. Third, we describe the origin of these mode structure features based on the network stoichiometric matrixSand the reaction kinetic gradient matrixG.We demonstrate that the topologically-connected reaction sensitivities of similar magnitude inGplay a central role in determining the mode structure. Ratios of these reaction sensitivities represent equilibrium balances of half reactions that are defined by linearization of the bilinear mass action rate laws followed by enzymatic reactions. These half-reaction equilibrium ratios are key determinants of modal structure for both simple and complicated modes. The work presented here helps to establish a foundation for understanding the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions.
Ind_X: program for indexing single-crystal diffraction patterns
Authors: Morawiec A. 
Published: February 2017

Indexing is an essential step in analysis of diffraction patterns. Diffraction of monochromatic radiation by a single crystal provides approximate positions of some nodes of the reciprocal lattice of the crystal, and the indexing problem lies in determining a lattice matching these positions.Ind_X is a program for indexing diffraction data given in the form of several approximate reciprocal lattice nodes. The applied method relies on testing potential volumes of the primitive cell of the reciprocal lattice. A subset of reciprocal lattice vectors supporting a given test volume is used to obtain tentative lattice bases. These are bases of low-index superlattices of lattices based on triplets of supporting vectors. TheInd_X solution of the indexing problem consists of a list of best bases. The method turns out to be quite robust to data inaccuracies and spurious reflections. The program is relatively versatile, easily operated and freely accessible.