bluuebunny/crossref_metadata_2025 huggingface dataset:
New Cell Fate Potentials and Switching Kinetics Uncovered in a Classic Bistable Genetic Switch
Authors: Fang Xiaona , Liu Qiong , Bohrer Christopher , Hensel Zach , Han Wei , Wang Jin , Xiao Jie
Published: November 2017

Bistable switches are common gene regulatory motifs directing two mutually exclusive gene expression states, and consequently distinct cell fates. Theoretical studies suggest that the simple circuitry of bistable switches is sufficient to encode more than two cell fates due to the non-equilibrium, heterogeneous cellular environment, allowing a high degree of adaptation and differentiation. However, new cell fates arising from a classic bistable switch without rewiring the circuitry have not been experimentally observed. By developing a new, dual single-molecule gene-expression reporting system in liveE. colicells, we investigated the expression dynamics of two mutually repressing transcription factors, CI and Cro, in the classic genetic switch of bacteriophage λ. We found that in addition to the two expected high-Cro and high-CI production states, there existed two new ones, in which neither CI nor Cro was produced, or both CI and Cro were produced. We constructed the corresponding potential landscape and mapped the transition kinetics between the four production states, providing insight into possible state-switching rates and paths. These findings uncover new cell fate potentials beyond the classical picture of λ switch, and open a new window to explore the genetic and environmental origins of the cell fate decision-making process in gene regulatory networks.
Resting-state functional brain connectivity best predicts the personality dimension of openness to experience
Authors: Dubois Julien , Galdi Paola , Han Yanting , Paul Lynn K. , Adolphs Ralph
Published: November 2017

Personality neuroscience aims to find associations between brain measures and personality traits. Findings to date have been severely limited by a number of factors, including small sample size and omission of out-of-sample prediction. We capitalized on the recent availability of a large database, together with the emergence of specific criteria for best practices in neuroimaging studies of individual differences. We analyzed resting-state functional magnetic resonance imaging data from 884 young healthy adults in the Human Connectome Project (HCP) database. We attempted to predict personality traits from the “Big Five”, as assessed with the NEO-FFI test, using individual functional connectivity matrices. After regressing out potential confounds (such as age, sex, handedness and fluid intelligence), we used a cross-validated framework, together with test-retest replication (across two sessions of resting-state fMRI for each subject), to quantify how well the neuroimaging data could predict each of the five personality factors. We tested three different (published) denoising strategies for the fMRI data, two inter-subject alignment and brain parcellation schemes, and three different linear models for prediction. As measurement noise is known to moderate statistical relationships, we performed final prediction analyses using average connectivity across both imaging sessions (1 h of data), with the analysis pipeline that yielded the highest predictability overall. Across all results (test/retest; 3 denoising strategies; 2 alignment schemes; 3 models), Openness to experience emerged as the only reliably predicted personality factor. Using the full hour of resting-state data and the best pipeline, we could predict Openness to experience (NEOFAC_O: r=0.24, R2=0.024) almost as well as we could predict the score on a 24-item intelligence test (PMAT24_A_CR: r=0.26, R2=0.044). Other factors (Extraversion, Neuroticism, Agreeableness and Conscientiousness) yielded weaker predictions across results that were not statistically significant under permutation testing. We also derived two superordinate personality factors (“α” and “β”) from a principal components analysis of the NEO-FFI factor scores, thereby reducing noise and enhancing the precision of these measures of personality. We could account for 5% of the variance in the β superordinate factor (r=0.27, R2=0.050), which loads highly on Openness to experience. We conclude with a discussion of the potential for predicting personality from neuroimaging data and make specific recommendations for the field.
Frontal eye field inactivation reduces saccade preparation in the superior colliculus, but does not alter how preparatory activity relates to saccade latency
Authors: Dash Suryadeep , Peel Tyler R. , Lomber Stephen G. , Corneil Brian D.
Published: November 2017

A neural correlate for saccadic reaction times (SRTs) in the gap saccade task is the level of preparatory activity in the intermediate layers of the superior colliculus (iSC) just before visual target onset: greater levels of iSC preparatory activity precede shorter SRTs. The frontal eye fields (FEF) are one likely source of such iSC preparatory activity, since FEF preparatory activity is also inversely related to SRT. To better understand the FEF’s role in saccade preparation, and the way in which such preparation relates to SRT, in two male rhesus monkeys we examined iSC preparatory activity during unilateral reversible cryogenic inactivation of the FEF. FEF inactivation increased contralesional SRTs, and lowered ipsilesional iSC preparatory activity. FEF inactivation also reduced fixation-related activity in the rostral iSC. Importantly, the distributions of SRTs generated with or without FEF inactivation overlapped, enabling us to conduct a novel population-level analyses examining iSC preparatory activity just before generation of SRT-matched saccades. These analyses revealed no change during FEF inactivation in the relationship between iSC preparatory activity and SRT-matched saccades across a range of SRTs, even for the occasional express saccade. Thus, while our results emphasize that the FEF has an overall excitatory influence on preparatory activity in the iSC, the communication between the iSC and downstream oculomotor brainstem is unaltered for SRT-matched saccades, suggesting that the integration of preparatory and visual signals in the SC just before saccade initiation is largely independent of the FEF for saccades generated in this task.

Significance statement

How does the brain decide when to move? Here, we investigate the role of two oculomotor structures, the superior colliculus (SC) and frontal eye fields (FEF), in dictating visually-guided saccadic reaction times (SRTs). In both structures, higher levels of preparatory activity precede shorter SRTs. Here, we show that FEF inactivation increases SRTs and decreases SC preparatory activity. Surprisingly, a population-level analysis of SC preparatory activity showed a negligible impact of FEF inactivation, providing one examines SRT-matched saccades. Thus, while the FEF is one source of preparatory input to the SC, it is not a critical source, and it is not involved in the integration of preparatory activity and visual signals that precedes saccade initiation in simple visually-guided saccade tasks.
Multifactorial Dynamics of White Matter Connectivity During Adolescence
Authors: Tunç Birkan , Parker Drew , Shinohara Russell T. , Elliott Mark A. , Ruparel Kosha , Gur Raquel E. , Gur Ruben C. , Verma Ragini
Published: November 2017

Studying developmental changes in white matter connectivity is critical for understanding neurobiological substrates of cognition, learning, and neuropsychiatric disorders. This becomes especially important during adolescence when a rapid expansion of the behavioral repertoire occurs. Several factors such as brain geometry, genetic expression profiles, and higher level architectural specifications such as the presence of segregated modules have been associated with the observed organization of white matter connections. However, we lack understanding of the extent to which such factors jointly describe the brain network organization, nor have insights into how their contribution changes developmentally. We constructed a multifactorial model of white matter connectivity using Bayesian network analysis and tested it with diffusion imaging data from a large community sample. We investigated contributions of multiple factors in explaining observed connectivity, including architectural specifications, which promote a modular yet integrative organization, and brain’s geometric and genetic features. Our results demonstrated that the initially dominant geometric and genetic factors become less influential with age, whereas the effect of architectural specifications increases. The identified structural modules are associated with well-known functional systems, and the level of association increases with age. This integrative analysis provides a computational characterization of the normative evolution of structural connectivity during adolescence.
The Function of the COPII Gene Paralogs SEC23A and SEC23B Are InterchangeableIn Vivo
Authors: Khoriaty Rami , Hesketh Geoffrey , Bernard Amélie , Weyand Angela C. , Mellacheruvu Dattatreya , Zhu Guojing , Hoenerhoff Mark J. , McGee Beth , Everett Lesley , Adams Elizabeth J. , Zhang Bin , Saunders Thomas , Nesvizhskii Alexey , Klionsky Daniel J. , Shavit Jordan A. , Gingras Anne-Claude , Ginsburg David
Published: November 2017

SEC23 is a core component of the coat protein-complex II (COPII)-coated vesicle, which mediates transport of secretory proteins from the endoplasmic reticulum (ER) to the Golgi1-3. Mammals express 2 paralogs for SEC23 (SEC23A and SEC23B). Though theSEC23gene duplication dates back >500 million years, both SEC23’s are ~85% identical at the amino acid sequence level. In humans, deficiency for SEC23A or SEC23B results in cranio-lenticulo-sutural dysplasia4or congenital dyserythropoietic anemia type II (CDAII), respectively5. The disparate human syndromes and reports of secretory cargos with apparent paralog-specific dependence6,7, suggest unique functions for the two SEC23 paralogs. Here we show indistinguishable intracellular interactomes for human SEC23A and SEC23B, complementation of yeast SEC23 by both human and murine SEC23A/B paralogs, and the rescue of lethality resulting fromSec23bdisruption in zebrafish by aSec23a-expressing transgene. Finally, we demonstrate that theSec23acoding sequence inserted into the endogenous murineSec23blocus fully rescues the mortality and severe pancreatic phenotype previously reported with SEC23B-deficiency in the mouse8-10. Taken together, these data indicate that the disparate phenotypes of SEC23A and SEC23B deficiency likely result from evolutionary shifts in gene expression program rather than differences in protein function, a paradigm likely applicable to other sets of paralogous genes. These findings also suggest the potential for increased expression of SEC23A as a novel therapeutic approach to the treatment of CDAII, with potential relevance to other disorders due to mutations in paralogous genes.
Promoter activity buffering reduces the fitness cost of misregulation
Authors: Schikora-Tamarit Miquel Angel , Lopez-Grado i Salinas Guillem , Gonzalez Navasa Carolina , Calderon Irene , Marcos-Fa Xavi , Sas Miquel , Carey Lucas
Published: November 2017

Cells regulate gene expression by changing the concentration and activity of transcription factors (TFs). The response of each gene to changes in TF activity is generally assumed to be encoded in the promoter. Here we show that, even when the promoter itself remains constant, each gene has a unique TF dose response curve. Many genes have an intrinsic ability to either buffer or amplify the effects of high promoter activity. We present a coupled mathematical model and experimental system for quantifying this property. Promoter activity buffering can be encoded by sequences in both the open reading frame and 3UTR and can be implemented by both autoregulatory feedback loops and by titration of limiting trans regulators. We show experimentally that promoter activity buffering insulates cells from fitness defects due to misexpression. The response of genes to changes in [TF] is encoded by sequences outside of the promoter, and this effect can either insulate or amplify the effects of aneuploidy and misregulation on organismal fitness.
Calcimycocavitological Studies on Seashells from Beaches of North Goa, India
Authors: Dabolkar Sujata , Kamat Nandkumar
Published: November 2017

Calcimycocavitology deals with the study of hollowing out of spaces in hard calcareous seashells by the fungi called calcimycocavites. Endolithic fungi in the shells were first reported and named as the trace fossils in 1889 by Bornet and Flahault. Endolithic fungi bore inside the shell by the process of bioturbation by using organic acids (oxalic acid, citrate) and enzymes (proteases, dehydrogenases and oxidoreductases). Previous reports show the presence of tunnels formed by fungal hyphae in the shells. The present work reports preliminary results of calcimycocavitological studies on the seashells from beaches of north Goa, India. The calcareous sand samples were collected from Arambol, Ashvem, Morjim, Vagator, Anjuna, Baga and Miramar beaches by pool sampling method and were separated into different fractions by using standard sieves. Each fraction of sand was subjected to stereomicroscopic studies which revealed that the sand fraction between 150-250 μm included irregular shell fragments showing positive colonization by calcimycocavites. Hydrochloric acid treatment was used to dissolve the shells and release calcimycocavites biomass which was stained with Congo Red and tentatively identified as distinct microfungal forms. SEM studies of the calcareous shell fragments revealed the microtunneling behavior of the fungi. Digital analysis of SEM images using Mountain premium 7.2 software revealed the fine topography of calcimycocavites hyphae along with unidentified presumptive biomineral encrustations. The ecological, biological and biogeochemical implications of the findings are presented with respect to possible role of calcimycocavites in Calcium and Carbon cycling by breakdown of the calcareous shells and release of inorganic and organic components in the ecosystem.
DriverPower: Combined burden and functional impact tests for cancer driver discovery
Authors: Shuai Shimin , Gallinger Steven , Stein Lincoln ,   on behalf of the PCAWG Drivers and Functional Interpretation Group and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Published: November 2017

We describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify cancer driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1,373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across a variety of tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2,583 cancer genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Group, DriverPower has the highest F1-score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
Correlated selection on amino acid deletion and replacement in mammalian protein sequences
Authors: Zheng Yichen , Graur Dan , Azevedo Ricardo B. R.
Published: November 2017

A low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is a sign of functional constraint caused by purifying selection. Intuitively, the functional constraint would also be expected to prevent such a codon from being deleted. Oddly, to the best of our knowledge, the correlation between the rates of deletion and substitution has never actually been estimated. Here, we use 8,595 protein coding-region sequences from 9 mammalian species to examine the relationship between deletion rate and dN/dS. We found significant positive correlations at both the level of sites and genes. We compared our data against controls consisting of simulated coding sequences evolving along identical phylogenetic trees, where the correlation is not included in the model a priori. A much weaker correlation was found in the corresponding simulated sequences, which is probably caused by alignment errors. In the real data, the correlations cannot be explained by alignment errors. Separate investigations on nonsynonymous (dN) and synonymous (dS) substitution rates indicate that the correlation is most likely due to a similarity in patterns of selection rather than mutation rates.
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

Drosophila 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 Noteworthy

Regulation 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

Ramularia 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

Sequencing 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

Cortical 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

Chitin, 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

Statins 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

Cultured 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

Studies 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

Mechanisms 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

The 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

Regulation 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

Deep 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

Long 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.
Mitochondrial Ultrastructure Is Coupled to Synaptic Performance at Axonal Release Sites
Authors: Cserep Csaba , Posfai Balazs , Schwarcz Anett Dora , Denes Adam
Published: November 2017

Mitochondrial function in neurons is tightly linked with metabolic and signalling mechanisms that ultimately determine neuronal performance. The subcellular distribution of these organelles is dynamically regulated as they are directed to axonal release sites on demand, but whether mitochondrial internal ultrastructure and molecular properties would reflect the actual performance requirements in a synapse-specific manner, remains to be established. Here, we examined performance-determining ultrastructural features of presynaptic mitochondria in GABAergic and glutamatergic axons of mice and human. Using electron-tomography and super-resolution microscopy we found, that these features were coupled to synaptic strength: mitochondria in boutons with high synaptic activity exhibited an ultrastructure optimized for high rate metabolism and contained higher levels of the respiratory chain protein cytochrome-c than mitochondria in boutons with lower activity. The strong, cell-type independent correlation between mitochondrial ultrastructure, molecular fingerprints and synaptic performance suggests that changes in synaptic activity could trigger ultrastructural plasticity of presynaptic mitochondria, likely to adjust their performance to the actual metabolic demand.
Local network-level integration mediates effects of transcranial Alternating Current Stimulation
Authors: Fuscà Marco , Ruhnau Philipp , Neuling Toralf , Weisz Nathan
Published: November 2017

Transcranial alternating current stimulation (tACS) has been proposed as a tool to draw causal inferences on the role of oscillatory activity in cognitive functioning and has the potential to induce long-term changes in cerebral networks. However, the mechanisms of action of tACS are not yet clear, though previous modeling works have suggested that variability may be mediated by local and network-level brain states. We used magnetoencephalography (MEG) to record brain activity from 17 healthy participants as they kept their eyes open (EO) or closed (EC) while being stimulated either with sham, weak, or strong alpha-tACS using a montage commonly assumed to target occipital areas. We reconstructed the activity of sources in all stimulation conditions by means of beamforming. The analysis of resting-state data revealed an interaction of the external stimulation with the endogenous alpha power difference between EO and EC in the posterior cingulate. This region is remote from occipital cortex, which showed strongest EC vs. EO alpha modulation, thus suggesting state-dependency long-range effects of tACS. In a follow-up analysis of this online-tACS effect, we find evidence that this dependency effect could be mediated by functional network changes: connection strength from the precuneus, a region adjusting for a measure of network integration in the two states (EC vs. EO during no-tACS), was significantly correlated with the state-dependency effect in the posterior cingulate (during tACS). No analogous correlation could be found for alpha power modulations in occipital cortex. Altogether, this is the first strong evidence to illustrate how functional network architectures can shape tACS effects.
Basal forebrain GABAergic innervation of olfactory bulb periglomerular interneurons
Authors: Sanz Diez Alvaro , Najac Marion , De Saint Jan Didier
Published: November 2017

Olfactory bulb circuits are dominated by multiple inhibitory pathways that finely tune the activity of mitral and tufted cells, the principal neurons, and regulate odor discrimination. Granule cells mediate interglomerular lateral inhibition between mitral and tufted cells lateral dendrites whereas diverse subtypes of periglomerular (PG) cells mediate intraglomerular lateral inhibition between their apical dendrites. Deep short axon cells form broad intrabulbar inhibitory circuits that regulate both populations of interneurons. Little is known about the extrabulbar GABAergic circuits that control the activity of these various interneurons. We examined this question using patch-clamp recordings and optogenetics in olfactory bulb slices from transgenic mice. We show that axonal projections emanating from diverse basal forebrain GABAergic neurons densely project in all layers of the olfactory bulb. These long-range GABAergic projections provide a prominent synaptic input on granule and short axon cells in deep layers as well as on selective subtypes of PG cells. Specifically, three different subclasses of type 2 PG cells receive robust and target-specific basal forebrain inputs but have little local interactions with other PG cells. In contrast, type 1 PG cells are not innervated by basal forebrain fibers but do interact with other PG cells. Thus, attention-regulated basal forebrain inputs regulate inhibition in all layers of the olfactory bulb with a previously overlooked synaptic complexity that further defines interneuron subclasses.

Key points summary

Basal forebrain long-range projections to the olfactory bulb are important for olfactory sensitivity and odor discrimination.

Using optogenetics, we confirm that basal forebrain afferents mediate IPSCs on granule and deep short axon cells. We also show that they selectively innervate specific subtypes of periglomerular (PG) cells.

Three different subtypes of type 2 PG cells receive GABAergic IPSCs from the basal forebrain but not from other PG cells.

Type 1 PG cells, in contrast, do not receive inputs from the basal forebrain but do receive inhibition from other PG cells.

These results bring new light on the complexity and specificity of glomerular inhibitory circuits, as well as on their modulation by the basal forebrain.
Do priority effects outweigh environmental filtering in a guild of dominant freshwater macroinvertebrates?
Authors: Little Chelsea J. , Altermatt Florian
Published: November 2017

Abiotic conditions have long been considered essential in structuring freshwater macroinvertebrate communities. Ecological drift, dispersal, and biotic interactions also structure communities, and although these mechanisms are more difficult to detect, they may be of equal importance in natural communities. Here, we conducted repeated surveys of locally-dominant amphipod species across ten naturally replicated stream catchments. We then used a hierarchical joint species distribution model to assess the influence of different drivers on species co-occurrences. The species had unique environmental requirements, but a distinct spatial structure in their distributions was unrelated to habitat. Species co-occurred much less frequently than predicted by their niches, which was surprising because laboratory and field evidence suggests they are capable of coexisting in equal densities. We suggest that niche preemption may limit their distribution and that a blocking effect determines which species colonizes and dominates a given stream catchment, thus resolving a long-standing conundrum in freshwater ecology.