bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Eag by ca2+/calmodulin controls presynaptic excitability inDrosophila
Authors: Bronk Peter , Kuklin Elena A. , Gorur-Shandilya Srinivas , Liu Chang , Wiggin Timothy D. , Reed Martha L. , Marder Eve , Griffith Leslie C. 
Published: November 2017

AbstractDrosophila ether-à-go-go (eag) is the founding member of a large family of voltage-gated K+channels, the KCNH family, which includes Kv10, 11 and 12, (Ganetzky et al. 1999). Concurrent binding of calcium/calmodulin (Ca2+/CaM) to N-and C-terminal sites inhibits mammalian EAG1 channels at sub-micromolar Ca2+concentrations (Schonherr et al. 2000), likely by causing pore constriction (Whicher and MacKinnon 2016). Although theDrosophilaEAG channel was believed to be Ca2+-insensitive (Schonherr et al. 2000), both the N-and C-terminal sites are conserved. Here we show thatDrosophilaEAG is inhibited by high Ca2+concentrations that are only present at plasma membrane Ca2+channel microdomains. To test the role of this regulationin vivo, we engineered mutations that block CaM-binding to the major C-terminal site of the endogenouseaglocus, disrupting Ca2+-dependent inhibition.eagCaMBD mutants have reduced evoked release from larval motor neuron presynaptic terminals and show decreased Ca2+influx in stimulated adult projection neuron presynaptic terminals, consistent with an increase in K+conductance. These results are predicted by a conductance-based multi-compartment model of the presynaptic terminal in which some fraction of EAG is localized to the Ca2+channel microdomains that control neurotransmitter release. The reduction of release in the larval neuromuscular junction drives a compensatory increase in motor neuron somatic excitability. This misregulation of synaptic and somatic excitability has consequences for systems-level processes and leads to defects in associative memory formation in adults.New and NoteworthyRegulation of excitability is critical to tuning the nervous system for complex behaviors. We demonstrate here that the EAG family of voltage-gated K+channels exhibit conserved gating by Ca2+/CaM. Disruption of this inhibition inDrosophilaresults in decreased evoked neurotransmitter release due to truncated Ca2+influx in presynaptic terminals. In adults, disrupted Ca2+dynamics cripples memory formation. These data demonstrate that the biophysical details of channels have important implications for cell function and behavior.
The evolutionary history of the current globalRamularia collo-cygniepidemic
Authors: Stam Remco , Sghyer Hind , Münsterkötter Martin , Pophaly Saurabh , Tellier Aurélien , Güldener Ulrich , Hückelhoven Ralph , Hess Michael 
Published: November 2017

AbstractRamularia Leaf Spot (RLS) has emerged as a threat for barley production in many regions of the world. Late appearance of unspecific symptoms caused thatRamularia collo-cygnicould only by molecular diagnostics be detected as the causal agent of RLS. Although recent research has shed more light on the biology and genomics of the pathogen, the cause of the recent global spread remains unclear.To address urgent questions, especially on the emergence to a major disease, life-cycle, transmission, and quick adaptation to control measures, we de-novo sequenced the genome ofR. collo-cygni(urug2 isolate). Additionally, we sequenced fungal RNA from 6 different conditions, which allowed for an improved genome annotation. This resulted in a high quality draft assembly of about 32 Mb, with only 78 scaffolds with an N50 of 2.1 Mb. The overall annotation enabled the prediction of 12.346 high confidence genes. Genomic comparison revealed thatR. collo-cygnihas significantly diverged from relatedDothidiomycetes, including gain and loss of putative effectors, however without obtaining species-specific genome features.To evaluate the species-wide genetic diversity, we sequenced the genomes of 19R. collo-cygniisolates from multiple geographic locations and diverse hosts and mapped sequences to our reference genome. Admixture analyses show thatR. collo-cygniis world-wide genetically uniform and that samples do not show a strong clustering on either geographical location or host species. To date, the teleomorph ofR. collo-cygnihas not been observed. Analysis of linkage disequilibrium shows that in the world-wide sample set there are clear signals of recombination and thus sexual reproduction, however these signals largely disappear when excluding three outliers samples, suggesting that the main global expansion ofR. collo-cygnicomes from mixed or clonally propagating populations. We further analysed the historic population size (Ne) ofR. collo-cygniusing Bayesian simulations.We discuss how our genomic data and population genetics analysis can help understand the currentR. collo-cygniepidemic and provide different hypothesis that are supported by our data. We specifically highlight how recombination, clonal spreading and lack of host-specificity could further support global epidemics of this increasingly recognized plant disease and suggest specific approaches to combat this pathogen.
Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture
Authors: Peters Lucy , Spatharis Sofie , Dario Maria Augusta , Roca Inaki J T , Kintner Anna , Kanstad-Hanssen Øyvind , Llewellyn Martin S. , Praebel Kim 
Published: November 2017

AbstractSequencing of environmental DNA (eDNA-seq) is an emergent new monitoring tool that promises to facilitate the accurate and cost effective detection of species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA-seq to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of meta-barcoding markers reflect the true species’ identity and abundances in biological samples, and (b) establish a low-cost sequencing method to enable the bulk processing of environmental samples. In this study, we employed an elaborate experimental design whereby different combinations of five biological agents were crossed at three abundance levels and exposed to pre-filtered and normal seawater, prior to coarse filtering and then eDNA ultrafiltration of the resultant material. We then benchmarked the low-cost, scalable, Ion Torrent sequencing method against the current gold-standard Illumina platform for eDNAseq detection in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we found that Illumina and Ion Torrent were equally good in identifying the two parasite species (Lepeophtheirus salmonis and Paramoeba perurans), whereas the microalgae species Prymnesium parvum, Pseudo-nitzschia seriata and P. delicatissima could be assigned correctly only to the genus level. Illumina and Ion Torrent were also equally able to reflect community composition in our samples, whereas Ion Torrent was more sensitive in detecting species richness when the medium was unfiltered seawater. Both methods were able to reflect the correct abundances of 4 out of 5 species in samples from unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA-seq offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is equally as accurate as Illumina.
Chronic silencing of corticothalamic layer 6 pyramidal cells affects cortical excitability and tactile behavior
Authors: Humanes-Valera Desire , Aguila Jordi , Gondzik Veronika , Moxon Karen A. , Schwarz Martin K. , Krieger Patrik 
Published: November 2017

AbstractCortical projections originating in layer 6 (L6) in mouse primary somatosensory cortex have an important function controlling both cortical and sub-cortical activity. To study cortical plasticity and communication between somatosensory and motor cortex, L6-Ntsr1 cells were chronically silenced using tetanus toxin and the effect this had on cortical activity and behavior was investigated. A 2 Hz stimulation protocol was used to potentiate whisker evoked local field potentials (LFP) in a layer-dependent manner in both cortices. Silencing L6 pyramidal cells, the LFP potentiation in both cortices was affected without a change in the spontaneous multi-unit activity. Animals with L6 chronically silenced used more low-amplitude whisks, which presumably compensates for a reduction in cortical excitability. These results suggest that L6 is not only an important cortical output layer that modulates sub-cortical circuits, but also that it controls cortical dynamics.
Spin coated chitin films for biosensors and its analysis are depended on chitin-surface interactions
Authors: Casteleijn Marco G. , Richardson Dominique , Parkkila Petteri , Granqvist Niko , Urtti Arto , Viitala Tapani 
Published: November 2017

AbstractChitin, abundant in nature, is a renewable resource with many possible applications in bioengineering. Biosensors, capable of label-free and in-line evaluation, play an important role in the investigation of chitin synthesis, degradation and interaction with other materials. This work presents a comparative study of the usefulness of a chitin surface preparation, either on gold (Au) or on polystyrene (PS). In both cases the most common method to dissolve chitin was used, followed by a simple spin-coating procedure. Multi-parametric surface plasmon resonance (MP-SPR), modeling of the optical properties of the chitin layers, scanning electron microscopy, and contact angle goniometry were used to confirm: the thickness of the layers in air and buffer, the refractive indices of the chitin layers in air and buffer, the hydrophobicity, the binding properties of the chitin binding domain (CBD) ofBacillus circulans, and the split-intein capture process. Binding of the CBD differed between chitin on Au versus chitin on PS in terms of binding strength and binding specificity due to a less homogenous structured chitin-surface on Au in comparison to chitin on PS, despite a similar thickness of both chitin layers in air and after running buffer over the surfaces. The use of the simple method to reproduce chitin films on a thin polystyrene layer to study chitin as a biosensor and for chitin binding studies was obvious from the SPR studies and the binding studies of CBD as moiety of chitinases or as protein fusion partner. In conclusion, stable chitin layers for SPR studies can be made from chitin in a solution of dimethylacetamide (DMA) and lithium chloride (LiCl) followed by spin-coating if the gold surface is protected with PS.
Biomarker identification for statin sensitivity of cancer cell lines
Authors: Raghu Vineet K. , Beckwitt Colin H. , Warita Katsuhiko , Wells Alan , Benos Panayiotis V. , Oltvai Zoltán N. 
Published: November 2017

ABSTRACTStatins are potent cholesterol reducing drugs that have been shown to reduce tumor cell proliferationin vitroand tumor growth in animal models. Moreover, retrospective human cohort studies demon-strated decreased cancer-specific mortality in patients taking statins. We previously implicated membrane E-cadherin expression as both a marker and mechanism for resistance to atorvastatin-mediated growth suppression of cancer cells; however, a transcriptome-profile-based biomarker signature for statin sensitivity has not yet been reported. Here, we utilized transcriptome data from fourteen NCI-60 cancer cell lines and their statin dose-response data to produce gene expression signatures that identify statin sensitive and resistant cell lines. We experimentally confirmed the validity of the identified biomarker signature in an independent set of cell lines and extended this signature to generate a proposed statin-sensitive subset of tumors listed in the TCGA database. Finally, we predicted drugs that would synergize with statins and found several predicted combination therapies to be experimentally confirmed. The combined bioinformatics-experimental approach described here can be used to generate an initial biomarker sensitivity for statin therapy.
Dose-dependent spatiotemporal responses of mammalian cells to an alkylating agent
Authors: Rancourt Ann , Sato Sachiko , Satoh Masahiko S. 
Published: November 2017

AbstractCultured cell populations are composed of heterogeneous cells, and previous single-cell lineage tracking analysis of individual HeLa cells provided empirical evidence for significant heterogeneity of cell fates. Nevertheless, such cell lines have been used for investigations of cellular responses to various substances, resulting in incomplete characterizations. This problem caused by heterogeneity within cell lines could be overcome by analyzing the spatiotemporal responses of individual cells to a substance. However, no approach to investigate the responses using spatiotemporal data is currently available. Thus, the current study aimed to analyze the spatiotemporal responses of individual HeLa cells to cytotoxic, sub-cytotoxic, and non-cytotoxic doses of the well-characterized carcinogen, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Although cytotoxic doses of MNNG are known to induce cell death, the single-cell tracking approach revealed that cell death occurred following at least four different cellular events, suggesting that cell death is induced via multiple processes. We also found that HeLa cells exposed to sub-cytotoxic doses of MNNG were in a state of equilibrium between cell proliferation and cell death, with cell death again induced through different processes. However, exposure of cells to non-cytotoxic doses of MNNG promoted growth by reducing the cell doubling time, thus promoting the growth of a sub-population of cells previously recognized as putative cancer stem cells. These results demonstrate that the responses of cells to MNNG can be analyzed precisely using spatiotemporal data, regardless of the presence of heterogeneity among cultured cells, suggesting that single-cell lineage tracking analysis can be used as a novel and accurate analytical method to investigate cellular responses to various substances.
Postural sway during single-legged standing is dependent on the body position assumption strategy and supports the stability and mobility trade-off hypothesis
Authors: Bacik Bogdan , Sobota Grzegorz , Fredyk Artur , Słomka Kajetan J. , Juras Grzegorz 
Published: November 2017

AbstractStudies that would address the problem of balance in the context of either the preceding or subsequent movement are scarce. We would like to propose the inverse relationship between stability and mobility as a general principle and that depending on the preceding action the postural sway characteristics in quiet standing would significantly differ. Thirteen female ballet school students were examined. Their mean age was: 15.1±0.95 years and the total of about 2500 (5th school grade) and 4200 (6th school grade) hours of dance training. The force plate was used to register ground reaction forces and moments. During the 30s trials subjects were to assume the Passé position in gait initiation (G-I) and gait termination (G-T) task condition. The following parameters were analyzed after restabilisation point estimation: the range of COP position, standard deviation of COP position, mean velocity in both planes and mean resultant velocity. The results showed significant differences between the G-I and G-T tasks in postural sway characteristics and confirmed our hypothesis. The practical implication of our study is the way of preparation to test position (PTTP) strategy might be as important as the measurement itself in the posture study protocols.
Continuous high-resolutionin vivoimaging reveals tumor-specific dissemination in an embryonic zebrafish xenograft model
Authors: Asokan N , Daetwyler S , Bernas SN , Schmied C , Vogler S , Lambert K , Wobus M , Wermke M , Kempermann G , Huisken J , Brand M , Bornhäuser M 
Published: November 2017

AbstractMechanisms mediating tumor metastasis are crucial for diagnostic and therapeutic targeting. Here, we take advantage of a transparent embryonic zebrafish xenograft model (eZXM) to visualize and track injected human leukemic and breast cancer cells in real time using selective plane illumination microscopy (SPIM) for up to 30 hours. Injected cells exhibited disease-specific patterns of intravascular distribution with leukemic cells moving faster than breast cancer cells. While breast cancer cells predominantly adhered to nearby regions, about 30% invaded the avascularized tissue, reminiscent of their metastatic phenotype. Survival of the injected tumor cells was partly inhibited by the cellular innate immune system of the recipient embryos and leukemic cell dissemination was effectively inhibited by pharmacological ROCK1 blockade. These observations, and the ability to image several embryos simultaneously, support the use of eZXM and SPIM imaging as a functional screening platform to identify compounds that restricts cancer cell spread and invasion.
Swr1 mediated H2A.ZPht1 incorporation designates centromere DNA for de novo CENP-ACnp1 assembly
Authors: Kulasegaran-Shylini Raghavendran , Subramanian Lakxmi , Kerr Alastair R. W. , Spanos Christos , Rappsilber Juri , Allshire Robin C. 
Published: November 2017

SUMMARYThe underlying hallmark of centromeres is the presence of specialized nucleosomes in which histone H3 is replaced by CENP-A. The events that mediate the installation of CENP-A in place of H3 remain poorly characterized. H2A.Z is linked to transcriptional competence and associates with mammalian centromeres. We find that H2A.ZPht1 and the Swr1 complex are enriched in fission yeast CENP-ACnp1 chromatin. Our analysis shows that Swr1, Msc1 and H2A.ZPht1 are required to maintain CENP-ACnp1 chromatin integrity. Cell cycle analyses demonstrate that H2A.ZPht1 is deposited in S phase, coincident with the deposition of placeholder H3, and prior to CENP-ACnp1 replenishment in G2. Establishment assays reveal that H2A.ZPht1 and Swr1 are required for de novo assembly of CENP-ACnp1 onto naïve centromere DNA. We propose that features akin to promoters within centromere DNA program the incorporation of H2A.ZPht1 via Swr1, and mediate the replacement of resident H3 nucleosomes with CENP-A nucleosomes thereby defining centromeres.
Bulk degradation of dendritic cargos requires Rab7-dependent transport in Rab7-positive/LAMP1-negative endosomes to somatic lysosomes
Authors: Yap C.C. , Digilio L. , McMahon L.P. , Garcia A.D.R. , Winckler B. 
Published: November 2017

AbstractRegulation of protein homeostasis (“proteostasis”) is necessary for maintaining healthy cells. Disturbances in proteostasis lead to aggregates, cellular stress and can result in toxicity. There is thus great interest in when and where proteins are degraded in cells. Neurons are very large as well as very long-lived, creating unusually high needs for effective regulation of protein turnover in time and space. We previously discovered that the dendritic membrane proteins Nsg1 and Nsg2 are short-lived with half-lives of less than two hours. Their short half-lives enabled us to ask whether these proteins are degraded by local degradative pathways in dendrites. We discovered a striking spatial gradient of late endosomes/lysosomes in dendrites, with late endosomes (Rab7-positive/LAMP1-negative/cathepsinB-negative) found in distal portion of dendrites, and degradative lysosomes (LAMP1-positive/cathepsinB-positive) being overwhelmingly found in the soma and in the proximal portion of dendrites. Surprisingly, the majority of dendritic Rab7-positive late endosomes do not contain LAMP1, unlike Rab7-positive late endosomes in fibroblasts. Secondly, Rab7 activity is required to mobilize these distal pre-degradative dendritic late endosomes for transport to the soma and degradation. We conclude that the vast majority of dendritic LAMP1-positive endosomes are not degradative lysosomes and that bulk degradation of dendritic cargos, such as Nsg1, Nsg2, and DNER, requires Rab7-dependent transport in late endosomes to somatic lysosomes.
Revealing structure components of the retina by deep learning networks
Authors: Yan Qi , Yu Zhaofei , Chen Feng , Liu Jian K. 
Published: November 2017

AbstractDeep convolutional neural networks (CNNs) have demonstrated impressive performance on visual object classification tasks. In addition, it is a useful model for predication of neuronal responses recorded in visual system. However, there is still no clear understanding of what CNNs learn in terms of visual neuronal circuits. Visualizing CNN’s features to obtain possible connections to neuronscience under-pinnings is not easy due to highly complex circuits from the retina to higher visual cortex. Here we address this issue by focusing on single retinal ganglion cells with a simple model and electrophysiological recordings from salamanders. By training CNNs with white noise images to predicate neural responses, we found that convolutional filters learned in the end are resembling to biological components of the retinal circuit. Features represented by these filters tile the space of conventional receptive field of retinal ganglion cells. These results suggest that CNN could be used to reveal structure components of neuronal circuits.
Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
Authors: Jung Hyunchul , Choi Jung Kyoon , Lee Eunjung Alice 
Published: November 2017

ABSTRACTLong interspersed nuclear element-1 (L1) retrotransposons are normally suppressed in somatic tissues mainly by DNA methylation and antiviral defense. However, L1s can be desuppressed in cancers to act as insertional mutagens and cause genomic instability by creating DNA double strand breaks and chromosomal rearrangements. Whereas the frequency of somatic L1 insertions varies greatly among individual tumors, much remains to be learned about underlying genetic, cellular, or environmental factors. Here, our pan-gastrointestinal cancer genome analyses for stomach, colorectal, and esophageal tumors identified multiple correlates of L1 activity. Clinical indicators of tumor progression, such as tumor grade and patient age, showed positive association. Potential L1 expression suppressors such as TP53 and DNMT1, a DNA methyltransferase, were inactivated in tumors with frequent L1 insertions. Importantly, tumors with high immune activity, for example, due to viral infection or high tumor-antigen load, tended to carry a low number of L1 insertions in their genomes with high expression levels of L1 suppressors such as APOBEC3s and SAMHD1. Our analysis of the transcriptional effects of intragenic retrotransposon insertions demonstrated an increased risk of gene disruption in retrotransposition-prone cancers. In particular, we found a splicing-disrupting L1 insertion in an exon of MOV10, a key L1 suppressor, which caused exon skipping with evidence of nonsense-mediated decay in a tumor with a high L1 insertion load. Our results indicate that cancer immunity may contribute to genome stability by suppressing L1 retrotransposition particularly in gastrointestinal cancers.