bluuebunny/crossref_metadata_2025_split huggingface dataset:
tarsal-less is expressed as a gap gene but has no gap gene phenotype in the moth midge Clogmia albipunctata
Authors: Jiménez-Guri Eva , Wotton Karl R. , Jaeger Johannes 
Published: February 2018

AbstractGap genes are involved in segment determination during early development of the vinegar fly Drosophila melanogaster and other dipteran insects (flies, midges, and mosquitoes). They are expressed in overlapping domains along the antero-posterior (A–P) axis of the blastoderm embryo. While gap domains cover the entire length of the A–P axis in Drosophila, there is a region in the blastoderm of the moth midge Clogmia albipunctata, which lacks canonical gap gene expression. Is a non-canonical gap gene functioning in this area? Here, we characterize tarsal-less (tal) in C. albipunctata. The homolog of tal in the flour beetle Tribolium castaneum (called milles-pattes, mlpt) is a bona fide gap gene. We find that Ca-tal is expressed in the region previously reported as lacking gap gene expression. Using RNA interference, we study the interaction of Ca-tal with gap genes. We show that Ca-tal is regulated by gap genes, but only has a very subtle effect on tailless (Catll), while not affecting other gap genes at all. Moreover, cuticle phenotypes of Ca-tal depleted embryos do not show any gap phenotype. We conclude that Ca-tal is expressed and regulated like a gap gene, but does not function as a gap gene in C. albipunctata.
FDAAA TrialsTracker: A live informatics tool to monitor compliance with FDA requirements to report clinical trial results
Authors: DeVito Nicholas J. , Bacon Seb , Goldacre Ben 
Published: February 2018

AbstractIntroductionNon-publication of clinical trials results is an ongoing issue. In 2016 the US government updated the results reporting requirements to ClinicalTrials.gov for trials covered under the FDA Amendments Act 2007. We set out to develop and deliver an online tool which publicly monitors compliance with these reporting requirements, facilitates open public audit, and promotes accountability.MethodsWe conducted a review of the relevant legislation to extract the requirements on reporting results. Specific areas of the statutes were operationalized in code based on the results of our policy review, publicly available data from ClinicalTrials.gov, and communications with ClinicalTrials.gov staff. We developed methods to identify trials required to report results, using publicly available registry data; to incorporate additional relevant information such as key dates and trial sponsors; and to determine when each trial became due. This data was then used to construct a live tracking website.ResultsThere were a number of administrative and technical hurdles to successful operationalization of our tracker. Decisions and assumptions related to overcoming these issues are detailed along with clarifications directly from ClinicalTrials.gov. The FDAAA TrialsTracker was successfully launched in February 2018 and provides users with an overview of results reporting compliance.DiscussionClinical trials continue to go unreported despite numerous guidelines, commitments, and legal frameworks intended to address this issue. In the absence of formal sanctions from the FDA and others, we argue tools such as ours - providing live data on trial reporting - can improve accountability and performance. In addition, our service helps sponsors identify their own individual trials that have not yet reported results: we therefore offer positive practical support for sponsors who wish to ensure that all their completed trials have reported.
A comment on“Species are not most abundant in the centre of their geographic range or climatic niche”
Authors: Soberón Jorge , Peterson A. Townsend , Osorio-Olvera Luis 
Published: February 2018

AbstractA study recently published argued against a relationship between population density and position in geographic and environmental spaces. We found a number of methodological problems underlying the analysis. We discuss the main issues and conclude that these problems hinder a robust conclusion about the original question.
Stress response ofChironomus ripariusto changes in water temperature and oxygen concentration in a lowland stream
Authors: Manfrin Alessandro , Larsen Stefano , Scalici Massimiliano , Wuertz Sven , Monaghan Michael T. 
Published: February 2018

AbstractThe increasing impairment of lotic ecosystems has promoted a growing effort into assessing their ecological status by means of biological indicators. While community-based approaches have proven valuable to assess ecosystem integrity, they mostly reflect long-term changes and might not be suitable for tracking and monitoring short-term events. Responses to rapid changes in environmental conditions have been rarely studied under natural conditions. Biomarkers offer the benefit of integrating biological responses at different time scales. Here we used a field experiment to test how the synthesis of heat shock protein 70 (HSP70) and Haemoglobin (Hb) in laboratory-reared larvae ofChironomus riparius(Diptera, Chironomidae) were influenced by short-term changes to water temperature and oxygen concentration in a lowland stream. Our aim was to determine whether HSP70 mRNA expression and Hb content could be used as anin situ“early warning system” for freshwater habitats undergoing environmental change. HSP70 exhibited a clear response to changes in temperature measured over a one-day period, confirming its suitability as an indicator of environmental stress. Hb concentration was related to oxygen concentration, but not to temperature. Our findings support the hypothesis that depletion in oxygen induces Hb synthesis inC. ripariuslarvae. Because tolerance to low oxygen is not only related to total Hb, but also to a more efficient uptake (binding to Hb, e.g. Bohr effect) and release of oxygen to the cell (Root effect), we cannot discern from our data whether increased efficiency played a role. We suggest thatC. ripariusis a suitable model organism for monitoring sub-lethal stress in the field and that the approach could be applied to other species as more genomic data are available for non-model organisms.
Characterizing protein-DNA binding event subtypes in ChIP-exo data
Authors: Yamada Naomi , Lai William K.M. , Farrell Nina , Pugh B. Franklin , Mahony Shaun 
Published: February 2018

AbstractMotivationRegulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein-protein interactions with other regulators. Each recruitment mechanism may be associated with distinct motifs and may also result in distinct characteristic patterns in high-resolution protein-DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein-DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5’ → 3’ exonuclease digestion. Since different regulatory complexes will result in different protein-DNA crosslinking signatures, analysis of ChIP-exo tag enrichment patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type or rely on motifs to cluster binding events into subtypes.ResultsTo systematically detect multiple protein-DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype memberships of binding events using both ChIP-exo tag distribution patterns and DNA motifs. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix identifies possible recruitment mechanisms of FoxA1 and ERα, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes.AvailabilityChExMix is available from https://github.com/seqcode/chexmixContactmahony@psu.edu
Quantifying configuration-sampling error in Langevin simulations of complex molecular systems
Authors: Fass Josh , Sivak David A. , Crooks Gavin E. , Beauchamp Kyle A. , Leimkuhler Benedict , Chodera John D. 
Published: February 2018

AbstractWhile Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configuration-space probability density departs from the desired target density due to the use of a finite integration timestep. In [1], Sivaket al. introduced a convenient approach to approximating a natural measure of error between the sampled density and the target equilibrium density, the KL divergence, inphase space, but did not specifically address the issue ofconfiguration-space properties, which are much more commonly of interest in molecular simulations. Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, validating it against a complex but exact nested Monte Carlo estimator to show that it reproduces the KL divergence with high fidelity. To illustrate its utility, we employ this new near-equilibrium estimator to assess a claim that a recently proposed Langevin integrator introduces extremely small configuration-space density errors up to the stability limit at no extra computational expense. Finally, we show how this approach to quantifying sampling bias can be applied to a wide variety of stochastic integrators by following a straightforward procedure to compute the appropriate shadow work, and describe how it can be extended to quantify the error in arbitrary marginal or conditional distributions of interest.
The axon initial segment drives the neuron’s extracellular action potential
Authors: Bakkum Douglas J. , Radivojevic Milos , Obien Marie Engelene J. , Jaeckel David , Frey Urs , Takahashi Hirokazu , Hierlemann Andreas 
Published: February 2018

AbstractExtracellular voltage fields produced by a neuron’s action potentials provide a primary means for studying neuron function, yet their biophysical sources remain ambiguous. The neuron’s soma and dendrites are thought to drive the extracellular action potential (EAP), while the axon is usually ignored. However, by recording voltages of single neurons in dissociated rat cortical cultures and Purkinje cells in acute mouse cerebellar slices at hundreds of sites, we find instead that the axon initial segment dominates the EAP, and, surprisingly, the soma shows little or no influence. As expected, this signal has negative polarity (charge entering the cell) and initiates at the distal end. Interestingly, signals with positive polarity (charge exiting the cell) occur near some but not all dendritic branches and occur after a delay. Such basic knowledge about which neuronal compartments contribute to the extracellular voltage field is important for interpreting results from all electrical readout schemes. Moreover, this finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology.Key points summaryThe neuron’s soma and dendrites are thought to give rise to its extracellular voltage signal, while signals from the axon are usually considered negligible.Instead, we found that the largest amplitude of the extracellular signal originates from the axon initial segment, not from the soma.This finding shows that changes in the AIS position and function can be observed in high spatiotemporal detail by means of high-density extracellular electrophysiology.AbbreviationsACSFartificial cerebrospinal fluidAISaxon initial segmentAnkGankyrin-GCMOScomplementary-metal-oxide-semiconductorDMEMDulbecco’s modified eagle mediumEAPextracellular action potentialGAD67-GFPglutamic acid decarboxylase 67-green fluorescent proteinMAP2microtubule-associated protein 2.
Mavacamten stabilizes a folded-back sequestered super-relaxed state of β-cardiac myosin
Authors: Anderson Robert L. , Trivedi Darshan V. , Sarkar Saswata S. , Henze Marcus , Ma Weikang , Gong Henry , Rogers Christopher S. , Wong Fiona L. , Morck Makenna M. , Seidman Jonathan G. , Ruppel Kathleen M. , Irving Thomas C. , Cooke Roger , Green Eric M. , Spudich James A. 
Published: February 2018

Summary:Mutations in β-cardiac myosin, the predominant motor protein for human heart contraction, can alter power output and cause cardiomyopathy. However, measurements of the intrinsic force, velocity and ATPase activityof myosin have not provided a consistent mechanism to link mutations to muscle pathology. An alternative modelpositsthat mutations in myosin affect the stability ofa sequestered, super-relaxed state (SRX) of the proteinwith very slow ATP hydrolysis and thereby change the number of myosin heads accessible to actin. Here, using a combination of biochemical and structural approaches, we show that purified myosin enters aSRX thatcorresponds to a folded-back conformation, which in muscle fibersresults insequestration of heads around the thick filament backbone. Mutations that cause HCM destabilize this state, while the small molecule mavacamtenpromotes it. These findings provide a biochemical and structural link between the genetics and physiology ofcardiomyopathywith implications for therapeutic strategies.
Constriction rate modulation can drive cell size control and homeostasis inC. crescentus
Authors: Lambert Ambroise , Vanhecke Aster , Archetti Anna , Holden Seamus , Schaber Felix , Pincus Zachary , Laub Michael T. , Goley Erin , Manley Suliana 
Published: February 2018

AbstractRod-shaped bacteria typically grow first via sporadic and dispersed elongation along their lateral walls, then via a combination of zonal elongation and constriction at the division site to form the poles of daughter cells. Although constriction comprises up to half of the cell cycle, its impact on cell size control and homeostasis has rarely been considered. To reveal the roles of cell elongation and constriction in bacterial size regulation during cell division, we captured the shape dynamics ofCaulobacter crescentuswith time-lapse structured illumination microscopy and used molecular markers as cell-cycle landmarks. We perturbed constriction rate using a hyperconstriction mutant or fosfomycin inhibition. We report that constriction rate contributes to both size control and homeostasis, by determining elongation during constriction, and by compensating for variation in pre-constriction elongation on a single-cell basis.
Detection and Degradation of Nonsense-mediated mRNA Decay Substrates Involve Two Distinct Upf1-bound Complexes
Authors: Dehecq Marine , Decourty Laurence , Namane Abdelkader , Proux Caroline , Kanaan Joanne , Le Hir Hervé , Jacquier Alain , Saveanu Cosmin 
Published: February 2018

AbstractNonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway involved in many cellular pathways and crucial for telomere maintenance and embryo development. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals, but a universal NMD model is lacking. We used affinity purification coupled with mass spectrometry and an improved data analysis protocol to obtain the first large-scale quantitative characterization of yeast NMD complexes in yeast (112 experiments). Unexpectedly, we identified two distinct complexes associated with Upf1: Detector (Upf1/2/3) and Effector. Effector contained the mRNA decapping enzyme, together with Nmd4 and Ebs1, two proteins that globally affected NMD and were critical for RNA degradation mediated by the Upf1 C-terminal helicase region. The fact that Nmd4 association to RNA was dependent on Detector components and the similarity between Nmd4/Ebs1 and mammalian Smg5-7 proteins suggest that in all eukaryotes NMD operates through successive Upf1-bound Detector and Effector complexes.
SETD3 protein is the actin-specific histidineN-methyltransferase
Authors: Kwiatkowski Sebastian , Seliga Agnieszka K. , Veiga-da-Cunha Maria , Vertommen Didier , Terreri Marianna , Ishikawa Takao , Grabowska Iwona , Jagielski Adam K , Drozak Jakub 
Published: February 2018

AbstractProtein histidine methylation is rarely studied posttranslational modification of unknown biochemical importance. In vertebrates, only a few methylhistidne-containing proteins have been reported so far, including β-actin as an essential example. The evolutionary conserved methylation of β-actin H73 residue is catalyzed by a specific histidineN-methyltransferase that has never been identified molecularly. In the present investigation, we have purified actin-specific histidineN-methyltransferase from rat muscles about 1200-fold. Its activity was studied by the radiochemical assay employing either homogeneous recombinant human β-actin produced inE. colior its mutated form exhibiting substitution of H73 by Ala residue (H73A) as substrates. Three polypeptides of ≈65, 75 and 90 kDa coeluting with the enzyme activity were identified in the preparation. Mass spectrometry analysis of these polypeptides resulted in the identification of SETD3 methyltransferase as the only plausible candidate. Rat SETD3 and its human ortholog were expressed in COS-7 cells, purified to homogeneity and shown to catalyze methylation of β-actin at H73 residue as confirmed by mass spectrometry analysis. The SETD3 enzyme was active towards a synthetic peptide corresponding to residues 69-77 of β-actin, but not to its mutated form exhibiting His-to-Ala substitution. Finally, Setd3-deficient HAP1 cells were devoid of methylated H73 in β-actin and exhibited phenotypic changes, including a decrease in F-actin content and an increased glycolytic activity. We conclude that SETD3 is the actin-specific histidineN-methyltransferase. The data show for the first time the molecular identity of protein histidine N-methyltransferase in vertebrates and throw new light on the substrate specificity of SET-domain-containing enzymes.
Network analysis of ChIP-seq data by VULCAN identifies GRHL2 as a key co-regulator of ERa in luminal breast cancer
Authors: Holding Andrew N. , Giorgi Federico M. , Donnelly Amanda , Cullen Amy E. , Nagarajan Sankari , Selth Luke A , Markowetz Florian 
Published: February 2018

AbstractVULCAN infers regulatory interactions of transcription factors by overlaying networks generated from tumor expression data onto ChIP-seq data. VULCAN analysis of estrogen receptor (ER) activation in breast cancer highlighted key components of the ER complex alongside a novel interaction with GRHL2. We demonstrate that GRHL2 is recruited to a subset of ER binding sites and regulates the transcriptional output of ER, as evidenced by: changes in ER-associated eRNA expression; and stronger ER binding at active enhancers (H3K27ac sites) after GRHL2 knockdown. Our findings provide new insight into ER signaling and demonstrate VULCAN, available from Bioconductor, as a powerful predictive tool.
DeepLoco: Fast 3D Localization Microscopy Using Neural Networks
Authors: Boyd Nicholas , Jonas Eric , Babcock Hazen , Recht Benjamin 
Published: February 2018

AbstractSingle-molecule localization super-resolution microscopy (SMLM) techniques like STORM and PALM have transformed cellular microscopy by substantially increasing spatial resolution. In this paper we introduce a new algorithm for a critical part of the SMLM process: estimating the number and locations of the fluorophores in a single frame. Our algorithm can analyze a 20000-frame experimental 3D SMLM dataset in about one second — substantially faster than real-time and existing algorithms. Our approach is straightforward but very different from existing algorithms: we train a neural network to minimize the Bayes’ risk under a generative model for single SMLM frames. The neural network maps a frame directly to a collection of fluorophore locations, which we compare to the ground truth using a novel loss function. While training the neural network takes several hours, it only has to be done once for a given experimental setup. After training, localizing fluorophores in new images is extremely fast — orders of magnitude faster than existing algorithms. Faster recovery opens the door to real-time calibration and accelerated acquisition, and future work could tackle more complicated optical systems and more realistic simulators.
Generation of tumorigenic porcine pancreatic ductal epithelial cells: toward a large animal model of pancreatic cancer
Authors: Remmers Neeley , Cox Jesse L. , Grunkemeyer James A. , Aravind Shruthi , Arkfeld Christopher K. , Hollingsworth Michael A. , Carlson Mark A. 
Published: February 2018

AbstractBackground. A large animal model of pancreatic cancer would permit development of diagnostic and interventional technologies not possible in murine models, and also would provide a more biologically-relevant platform for penultimate testing of novel therapies, prior to human testing. Here, we describe our initial studies in the development of an autochthonous, genetically-defined, large animal model of pancreatic cancer, using immunocompetent pigs.Methods. Primary pancreatic epithelial cells were isolated from pancreatic duct of domestic pigs; epithelial origin was confirmed with immunohistochemistry. Three transformed cell lines subsequently were generated from these primary cells using expression of oncogenic KRAS and dominant negative p53, with/without knockdown of p16 and SMAD4. We tested these cell lines using in vitro and in vivo assays of transformation and tumorigenesis.Results. The transformed cell lines outperformed the primary cells in terms proliferation, population doubling time, soft agar growth, 2D migration, and Matrigel invasion, with the greatest differences observed when all four genes (KRAS, p53, p16, and SMAD4) were targeted. All three transformed cell lines grew tumors when injected subcutaneously in nude mice, demonstrating undifferentiated morphology, mild desmoplasia, and staining for both epithelial and mesenchymal markers. Injection into the pancreas of nude mice resulted in distant metastases, particularly when all four genes were targeted.Conclusions. Tumorigenic porcine pancreatic cell lines were generated. Inclusion of four genetic “hits” (KRAS, p53, p16, and SMAD4) appeared to produce the best results in our in vitro and in vivo assays. The next step will be to perform autologous or syngeneic implantation of these cell lines into the pancreas of immunocompetent pigs. We believe that the resultant large animal model of pancreatic cancer could supplement existing murine models, thus improving preclinical research on diagnostic, interventional, and therapeutic technologies.
A fully automatic method yielding initial models from high-resolution electron cryo-microscopy maps
Authors: Terwilliger Thomas C. , Adams Paul D. , Afonine Pavel V. , Sobolev Oleg V. 
Published: February 2018

AbstractA fully automated procedure for optimization and interpretation of reconstructions from cryo-EM is developed and applied to 476 datasets with resolution of 4.5 Å or better, including reconstructions of 47 ribosomes and 32 other protein-RNA complexes. The median fraction of residues in the deposited structures reproduced automatically was 71% for reconstructions determined at resolutions of 3 Å or better and 47% for those at lower resolution.