bluuebunny/crossref_metadata_2025 huggingface dataset:
Falls and Physical Activity in Persons With Mild to Moderate Dementia Participating in an Intensive Motor Training
Authors: Zieschang Tania , Schwenk Michael , Becker Clemens , Uhlmann Lorenz , Oster Peter , Hauer Klaus
Published: June 2017

Background:

Physical activity is beneficial in people with dementia. As physical activity increases risk exposure for falls, safety concerns arise. Prior exercise trials in people with dementia have not measured physical activity. Falls in relation to exposure time rather than person-years as outcome measure has been promoted but not investigated in people with dementia.

Methods:

Patients with mild to moderate dementia (n=110) were randomized to an intensive, progressive strength and functional training intervention or to a low-intensity group training for 12 weeks each. Physical activity was measured with a standardized questionnaire. Falls were documented prospectively by calendars for 12 months.

Results:

During the intervention, physical activity was significantly higher in the intervention group (P<0.001) without an increased fall rate (intervention group vs. control group: 2.89 vs. 1.94; incidence rate ratio, 1.49; 95% confidence interval, 0.66-3.36; P=0.333). In the subgroup of multiple fallers, the number of falls per 1000 hours of activity was significantly lower in the intervention group (8.85 vs. 18.67; P=0.017).

Conclusions:

Increased physical activity during exercise intervention was safe in people with mild to moderate dementia. Fall rate adjusted for physical activity is a useful and sensitive outcome measure in addition to fall rate per person-years.
Quantifying uncertainty in the inference of generalized coalescents
Authors: Wallstrom Timothy C. , Bhattacharya Tanmoy , Wilkins Jon F.
Published: June 2017

We develop inference methods for generalized coalescent models, such as theΛ- andΞ-coalescents, which have recently been proposed for populations with broad offspring distributions, repeated selective sweeps, or strong selection. These are all populations that may not be adequately described by the usual Kingman coalescent. A roadblock to the application of such models has been the lack of effective tools for inferring an appropriate model, which stems from difficulties in evaluating the associated likelihoods. We overcome these difficulties by introducing estimators that are both computationally tractable and statistically efficient. We use these estimators to obtain point estimates and confidence intervals for the parameters of the coalescent models, and p-values for the hypothesis that the population is described by the Kingman coalescent. Our approach is based on the theory of unbiased estimating equations, which is more general than composite likelihood and may be applicable in other areas of statistical genetics. Our main focus is on inference from linked site-frequency spectra using parameterized families ofΛ-coalescents. We show that useful inferences may be made from non-singleton data alone if singletons are suspect due to sequencing or data-cleaning errors, although the data requirements are greatly increased. We apply our method to mitochondrial sequence data from Gadus morhua, the Atlantic cod.
Hands-free control of heterologous gene expression in batch cultures
Authors: Borkowski Olivier , Endy Drew , Subsoontorn Pakpoom
Published: June 2017

Background

Autonomous cell-based control of heterologous gene expression can simplify batch-culture bioprocessing by eliminating external monitoring and extrinsic control of culture conditions. Existing approaches use auto-induction media, synthetic cell-cell communication systems, or application-specific biosensors. A simpler, resource-efficient, and general-purpose expression control system responsive to common changes during batch culture would be useful.

Results

We used nativeE.colipromoters and recombinase-based switches to repurpose endogenous transcription signals for control of heterologous gene expression. Specifically, natural changes in transcription from endogenous promoters result in recombinase expression at different phases of batch culture. So-expressed recombinases invert a constitutive promoter regulating expression of arbitrary heterologous genes. We realized reversible and single-use switching, reduced static and dynamic cell-to-cell variation, and overall expression amplification. We used “off-the-shelf” genetic parts and abstraction-based composition frameworks to realize reliable forward engineering of our synthetic genetic systems.

Conclusion

We engineered autonomous control systems for regulating heterologous gene expression. Our system uses generic endogenous promoters to sense and control heterologous expression during growth-phase transitions. Our system does not require specialized auto-induction media, production or activation of quorum sensing, or the development of application-specific biosensors. Cells programmed to control themselves could simplify existing bioprocess operations and enable the development of more powerful synthetic genetic systems.
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
Authors: Mey Antonia S J S , Jiménez Jordi Juárez , Michel Julien
Published: June 2017

The drug design data resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of FXR inhibitors with a semi-automated alchemical free energy calculations workflow featuring the FESetup and SOMD tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature SARs only, and comparable or slightly inferior, to the best submissions from other groups.
Addressing the looming identity crisis in single cell RNA-seq
Authors: Crow Megan , Paul Anirban , Ballouz Sara , Huang Z. Josh , Gillis Jesse
Published: June 2017

Single cell RNA-sequencing technology (scRNA-seq) provides a new avenue to discover and characterize cell types, but the experiment-specific technical biases and analytic variability inherent to current pipelines may undermine the replicability of these studies. Meta-analysis of rapidly accumulating data is further hampered by the use of ad hoc naming conventions. Here we demonstrate our replication framework, MetaNeighbor, that allows researchers to quantify the degree to which cell types replicate across datasets, and to rapidly identify clusters with high similarity for further testing. We first measure the replicability of neuronal identity by comparing more than 13 thousand individual scRNA-seq transcriptomes, sampling with high specificity from within the data to define a range of robust practices. We then assess cross-dataset evidence for novel cortical interneuron subtypes identified by scRNA-seq and find that 24/45 cortical interneuron subtypes have evidence of replication in at least one other study. Identifying these putative replicates allows us to re-analyze the data for differential expression and provide lists of robust candidate marker genes. Across tasks we find that large sets of variably expressed genes can identify replicable cell types and subtypes with high accuracy, suggesting a general route forward for large-scale evaluation of scRNA-seq data.
Environmental factors dominate over host genetics in shaping human gut microbiota composition
Authors: Rothschild Daphna , Weissbrod Omer , Barkan Elad , Korem Tal , Zeevi David , Costea Paul I , Godneva Anastasia , Kalka Iris , Bar Noam , Zmora Niv , Pevsner-Fischer Meirav , Israeli David , Kosower Noa , Malka Gal , Wolf Bat Chen , Avnit-Sagi Tali , Lotan-Pompan Maya , Weinberger Adina , Halpern Zamir , Carmi Shai , Elinav Eran , Segal Eran
Published: June 2017

Human gut microbiome composition is shaped by multiple host intrinsic and extrinsic factors, but the relative contribution of host genetic compared to environmental factors remains elusive. Here, we genotyped a cohort of 696 healthy individuals from several distinct ancestral origins and a relatively common environment, and demonstrate that there is no statistically significant association between microbiome composition and ethnicity, single nucleotide polymorphisms (SNPs), or overall genetic similarity, and that only 5 of 211 (2.4%) previously reported microbiome-SNP associations replicate in our cohort. In contrast, we find similarities in the microbiome composition of genetically unrelated individuals who share a household. We define the termbiome-explainabilityas the variance of a host phenotype explained by the microbiome after accounting for the contribution of human genetics. Consistent with our finding that microbiome and host genetics are largely independent, we find significant biome-explainability levels of 16-33% for body mass index (BMI), fasting glucose, high-density lipoprotein (HDL) cholesterol, waist circumference, waist-hip ratio (WHR), and lactose consumption. We further show that several human phenotypes can be predicted substantially more accurately when adding microbiome data to host genetics data, and that the contribution of both data sources to prediction accuracy is largely additive. Overall, our results suggest that human microbiome composition is dominated by environmental factors rather than by host genetics.
Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly
Authors: Stanek Kimberly A. , Mura Cameron
Published: June 2017

Hfq is a bacterial RNA-binding protein that plays key roles in the post–transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affinities and degrees of sequence specificity. By simultaneously binding to a regulatory small RNA (sRNA) and an mRNA target, Hfq hexamers facilitate productive RNA⋯RNA interactions; the generic nature of this chaperone-like functionality makes Hfq a hub in many sRNA-based regulatory networks. That Hfq is crucial in diverse cellular pathways—including stress response, quorum sensing and biofilm formation— has motivated genetic and ‘RNAomic’ studies of its function and physiology (in vivo), as well as biochemical and structural analyses of Hfq⋯RNA interactions (in vitro). Indeed, crystallographic and bio-physical studies first established Hfq as a member of the phylogenetically-conserved Sm superfamily. Crystallography and other biophysical methodologies enable the RNA-binding properties of Hfq to be elucidated in atomic detail, but such approaches have stringent sample requirements,viz.: reconstituting and characterizing an Hfq•RNA complex requires ample quantities of well-behaved (sufficient purity, homogeneity) specimens of Hfq and RNA (sRNA, mRNA fragments, short oligoribonucleotides, or even single nucleotides). The production of such materials is covered in this Chapter, with a particular focus on recombinant Hfq proteins for crystallization experiments.

Abbreviations

3D

three-dimensional

AU

asymmetric unit

CV

column volume

DEPC

diethyl pyrocarbonate

HDV

hepatitis δ virus

HDVD

hanging-drop vapor diffusion

IMAC

immobilized metal affinity chromatography

MW

molecular weight

MWCO

molecular weight cut-off

nt

nucleotide

PDB

Protein Data Bank

RNP

ribonucleoprotein

RT

room temperature

SDVD

sitting-drop vapor diffusion

Journal format

Methods in Molecular Biology(Springer Protocolsseries); this volume is entitled “Bacterial Regulatory RNA: Methods and Protocols”; an author guide is linked athttp://www.springer.com/series/7651
Selecting among three basic fitness landscape models: additive, multiplicative and stickbreaking
Authors: Miller Craig R. , Van Leuven James T. , Wichman Holly A. , Joyce Paul
Published: June 2017

Fitness landscapes map genotypes to organismal fitness. Their topography depends on how mutational effects interact–epistasis–and is important for understanding evolutionary processes such as speciation, the rate of adaptation, the advantage of recombination, and predictability versus stochasticity of evolution. The growing amount of empirical data has made it possible to better test landscape models empirically. We argue that this endeavor will benefit from the development and use of meaningful null models against which to compare more complex models. Here we develop statistical and computational methods for fitting fitness data from mutation combinatorial networks to three simple models: additive, multiplicative and stickbreaking. We employ a Bayesian framework for doing model selection. Using simulations, we demonstrate that our methods work and we explore their statistical performance: bias, error, and the power to discriminate among models. We then illustrate our approach and its flexibility by analyzing several previously published datasets. An R-package that implements our methods is available in the CRAN repository under the nameStickbreaker.
The SCWISh network is essential for survival under mechanical pressure
Authors: Delarue Morgan , Poterewicz Gregory , Hoxha Ori , Choi Jessica , Yoo Wonjung , Kayser Jona , Holt Liam , Hallatschek Oskar
Published: June 2017

Cells that proliferate within a confined environment build up mechanical compressive stress. For example, mechanical pressure emerges in the naturally space-limited tumor environment. However, little is known about how cells sense and respond to mechanical compression. We developed microfluidic bioreactors to enable the investigation of the effects of compressive stress on the growth of the genetically tractable model organism Saccharomyces cerevisiae. We used this system to determine that compressive stress is partly partly sensed through a module consisting of the mucin Msb2, and the cell wall protein Sho1, which act together as a sensor module in one of the two major osmosensing pathways in budding yeast. This signal is transmitted via the MAPKKK kinase Ste11. Thus, we term this mechanosensitive pathway theSMuShpathway, forSte11 throughMucin /Sho1 pathway. The SMuSh pathway delays cells in the G1 phase of the cell cycle and improves cell survival in response to growth-induced pressure. We also found that the Cell Wall Integrity (CWI) pathway contributes to the response to mechanical compressive stress. These latter results are confirmed in complimentary experiments in the accompanying manuscript from Mishra et al. When both the SMuSh and the CWI pathways are deleted, cells fail to adapt to compressive stress and all cells lyse at relatively low pressure when grown in confinement. Thus, we define a network that is essential for cell survival during growth under pressure. We term this new mechanosensory system the SCWISh (Survival through the CWI and SMuSh) network.

Significance Statement

Growth in confined environments leads to the build up of compressive mechanical stresses, which are relevant to diverse fields, from cancer to microbiology. In contrast to tensile stress, little is known about the molecular integration of compressive stresses. In this study, we elucidate the SMuSh pathway, which, together with the Cell Wall Integrity pathway, is essential for viability of the budding yeastS. cerevisiaewhen growing under mechanical pressure. Pressure-sensing requires the transmembrane mucin, Msb2, which is linked to the actin cortex. Our result raises the intriguing question of whether mucins, widely conserved in eukaryotes and frequently misregulated in cancers, might sense compressive stresses in other organisms, including humans.
The U1 snRNP subunit LUC7 controls plant development and stress response through alternative splicing regulation
Authors: Amorim Marcella de Francisco , Willing Eva-Maria , Francisco-Mangilet Anchilie G. , Droste-Borel Irina , Maček Boris , Schneeberger Korbinian , Laubinger Sascha
Published: June 2017

Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNP). The U1 snRNP, which binds to 5’ splice sites, plays an essential role in early steps of the splicing reaction. Here, we show that Arabidopsis LUC7 proteins, which are encoded by a three-member gene family in Arabidopsis, are important for plant development and stress resistance. We show that LUC7 are U1 snRNP accessory proteins by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affects hundreds of alternative splicing events. Interestingly, LUC7 proteins specifically promote splicing of a subset of terminal introns. Splicing of LUC7-dependent introns is a prerequisite for nuclear export and some splicing events are modulated by stress in a LUC7-dependent manner. Taken together our results highlight the importance of the U1 snRNP component LUC7 in splicing regulation and suggest a previously unrecognized role of a U1 snRNP accessory factor in terminal intron splicing.
Crosslinkers both drive and brake cytoskeletal remodeling and furrowing in cytokinesis
Authors: Descovich Carlos Patino , Cortes Daniel B. , Ryan Sean , Nash Jazmine , Zhang Li , Maddox Paul S. , Nedelec Francois , Maddox Amy Shaub
Published: June 2017

Cytokinesis and other cell shape changes are driven by the actomyosin contractile cytoskeleton. The molecular rearrangements that bring about contractility in non-muscle cells are currently debated. Specifically, both filament sliding by myosin motors, as well as cytoskeletal crosslinking by myosins and non-motor crosslinkers, are thought to promote contractility. Here, we examined how the abundance of motor and non-motor crosslinkers controls the speed of cytokinetic furrowing. We built a minimal model to simulate the contractile dynamics of theC. eleganszygote cytokinetic ring. This model predicted that intermediate levels of non-motor crosslinkers would allow maximal contraction speed, which we found to be the case for the scaffold protein anillin,in vivo. Our model also demonstrated a non-linear relationship between the abundance of motor ensembles and contraction speed.In vivo, thorough depletion of non-muscle myosin II delayed furrow initiation, slowed F-actin alignment, and reduced maximum contraction speed, but partial depletion allowed faster-than-expected kinetics. Thus, both motor and non-motor crosslinkers promote cytokinetic ring closure when present at low levels, but act as a brake when present at higher levels. Together, our findings extend the growing appreciation for the roles of crosslinkers, but reveal that they not only drive but also brake cytoskeletal remodeling.
Mechanisms of transmission ratio distortion at hybrid sterility loci within and betweenMimulusspecies
Authors: Kerwin Rachel E. , Sweigart Andrea L.
Published: June 2017

Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility betweenhybrid male sterility 1(hms1) andhybrid male sterility 2(hms2) in the closely related yellow monkeyflower speciesMimulus guttatusandM. nasutus. By performing reciprocal backcrosses with introgression lines, we find evidence for gametic expression of thehms1-hms2incompatibility. Surprisingly, however, hybrid transmission ratios athms1do not reflect this incompatibility, suggesting additional mechanisms counteract the effects of gametic sterility. Indeed, our backcross experiment shows hybrid transmission bias towardM. guttatusthrough both pollen and ovules, an effect that is particularly strong whenhms2is homozygous forM. nasutusalleles. In contrast, we find little evidence forhms1transmission bias in crosses withinM. guttatus, providing no indication of selfish evolution at this locus. Although we do not yet have sufficient genetic resolution to determine if hybrid sterility and transmission ratio distortion map to the same loci, our preliminary fine-mapping uncovers a genetically independent hybrid lethality system involving at least two loci linked tohms1. This fine-scale dissection of transmission ratio distortion athms1andhms2provides insight into genomic differentiation between closely relatedMimulusspecies and reveals multiple mechanisms of hybrid dysfunction.
Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus
Authors: Djordjevic Djordje , Tang Joshua Y. S. , Chen Yun Xin , Shannon Kwan Shu Lun , Ling Raymond W. K. , Qian Gordon , Woo Chelsea Y. Y. , Ellis Samuel J. , Ho Joshua W. K.
Published: June 2017

There exists over 2.5 million publicly available gene expression samples across 101,000 data series in NCBI’s Gene Expression Omnibus (GEO) database. Due to the lack of the use of standardised ontology terms in GEO’s free text metadata to annotate the experimental type and sample type, this database remains diﬃcult to harness computationally without significant manual intervention.

In this work, we present an interactive R/Shiny tool called GEOracle that utilises text mining and machine learning techniques to automatically identify perturbation experiments, group treatment and control samples and perform differential expression. We present applications of GEOracle to discover conserved signalling pathway target genes and identify an organ specific gene regulatory network.

GEOracle is effective in discovering perturbation gene targets in GEO by harnessing its free text metadata. Its effectiveness and applicability has been demonstrated by cross validation and two real-life case studies. It opens up new avenues to unlock the gene regulatory information embedded inside large biological databases such as GEO. GEOracle is available athttps://github.com/VCCRI/GEOracle.
Final amendment: Ambiguous specification of EGFR mutations compounded by nil or negligible fragmented gene counts and erroneous application of the Kappa statistic reiterates doubts on the veracity of the TEP-study
Authors: Chakraborty Sandeep
Published: June 2017

Final amendment note

This paper had raised two issues - the error-prone classification and mistaken application of the Kappa statistic. The classification critique still holds, and is being taken up with other criticisms athttp://www.biorxiv.org/content/early/2017/07/02/146134. The Kappa statistic was an error on my part since I had failed to see another page in Table S1. Please consider this pre-print closed.

Original abstract

The use of RNA-seq from tumor-educated platelets (TEP) as a ‘liquid biopsy’ source [1] has been refuted recently (http://biorxiv.org/content/early/2017/06/05/146134, not peer-reviewed). The TEP-study also mentioned that mutant epidermal growth factor receptor (EGFR) was ‘accurately distinguished using surrogate TEP mRNA profiles’, which is contested here. It is shown that only 10 out of 24 (a smaller sample set, original study has 60) non-small cell lung carcinoma (NSCLC) samples here has any expression at all. Even there the number of reads (101 bp) are [1, 4, 1, 14, 9, 1, 2, 19, 21, 6], and do not even add up to one complete EGFR gene (about 6000 bp). EGFR mutations have been painstakingly collated inwww.mycancergenome.org/content/disease/lung-cancer/egfr. In stark contrast, the TEP study has no specification of the EGFR mutant used. The TEP study found EGFR mutations in 17/21 (81%), and EGFR wild-type in 4/39 (10%) for NSCLC samples (Table S7, reflected in Fig 3, Panel E in percentages). A major flaw is the assumption that a non “EGFR wild-type” is a “EGFR mutant” since cases zero with EGFR reads (which are almost half of the samples) could be either. The application of the Kappa statistic to this data is erroneous for two reasons. First, the Kappa statistic does not handle “unknowns”, as is the case for samples with zero expression. Secondly, ‘interobserver variation can be measured in any situation in which two or more independent observers are evaluating the same thing’ [2]. The 90% (Fig 3, Panel E) is just the percentage of samples (35/39) that are not “EGFT WT” in one observation. It is not qualified to be in the Kappa matrix, where it translates to 35, leading to a Kappa=0.707, which implies “substantial agreement” [2]. The other observation (looking for EGFR mutation) is in a different set. To summarize, this work reiterates negligible expression of EGFR reads in NSCLC samples, and finds serious shortcomings in the statistical analysis of subsequent mutational analysis from these reads in the TEP-study.
Less is More: Oligomer extraction and hydrothermal annealing increase PDMS bonding forces for new microfluidics assembly and for biological studies
Authors: Millet L. J. , Jain A. , Gillette M. U.
Published: June 2017

Key determinants in the emergence of complex cellular morphologies and functions are cues in the micro-environment. Primary among these is the presence of neighboring cells as networks form. Therefore, for high-resolution analysis, it is crucial to develop micro-environments that permit exquisite control of network formation. This is especially true in cell science, tissue engineering, and clinical biology. We introduce a new approach for assembling polydimethylsiloxane (PDMS)-based microfluidic environments that enhances cell network formation and analyses. We report that the combined processes of PDMS solvent-extraction (E-PDMS) and hydrothermal annealing create unique conditions that produce high-strength bonds between E-PDMS and glass – properties not associated with conventional PDMS. Extraction followed by hydrothermal annealing removes unbound oligomers, promotes polymer cross-linking, facilitates covalent bond formation with glass, and retains the highest biocompatibility. Our extraction protocol accelerates oligomer removal from 5 to 2 days. Resulting microfluidic platforms are uniquely suited for cell-network studies owing to high bond strengths, effectively corralling cellular extensions and eliminating harmful oligomers. We demonstrate simple, simultaneous actuation of multiple microfluidic domains for invoking ATP- and glutamate-induced Ca2+signaling in glial-cell networks. These low-cost, simple E-PMDS modifications and flow manipulations further enable microfluidic technologies for cell-signaling and network studies as well as novel applications.
Scalable composition frameworks for multicellular logic
Authors: Guiziou Sarah , Mayonove Pauline , Ulliana Federico , Moreau Violaine , Leclère Michel , Bonnet Jéróme
Published: June 2017

A major goal of synthetic biology is to reprogram living organisms to solve pressing challenges in manufacturing, environmental remediation, or healthcare. While many types of genetic logic gates have been engineered, their scalability remains limited. Previous work demonstrated that Distributed Multicellular Computation (DMC) enables the implementation of complex logic within cellular consortia. However, current DMC systems require spatial separation of cellular subpopulation to be scalable to N-inputs, and need cell-cell communication channels to operate. Here we present scalable composition frameworks for the systematic design of multicellular consortia performing recombinase-based Boolean or history-dependent logic, and integrating an arbitrary number of inputs. The theoretical designs for both Boolean and history-dependent logic are based on reduced sets of computational modules implemented into specific cellular subpopulations which can then be combined in various manners to implement all logic functions. Our systems mark a departure from previous DMC architectures as they do not require either cell-cell communication nor spatial separation, greatly facilitating their implementation and making them fully autonomous. Due to their scalability and composability, we anticipate that the design strategies presented here will help researchers and engineers to reprogram cellular behavior for various applications in a streamlined manner. We provide an online tool for automated design of DNA architectures allowing the implementation of multicellular N-inputs logic functions at:http://synbio.cbs.cnrs.fr/calin.
Dynamic interactions between top-down expectations and conscious awareness
Authors: Meijs Erik L. , Slagter Heleen A. , de Lange Floris P. , van Gaal Simon
Published: June 2017

It is well known that top-down expectations affect perceptual processes. Yet, remarkably little is known about the relationship between expectations and conscious awareness We address three crucial questions that are outstanding: 1) How do predictions affect the likelihood of conscious stimulus perception?; 2) Does the brain register violations of predictions nonconsciously?; and 3) Do predictions need to be conscious to influence perceptual decisions? We performed three experiments in which we manipulated stimulus predictability within the attentional blink paradigm, while combining visual psychophysics with electrophysiological recordings. We found that valid stimulus expectations increase the likelihood of conscious access of stimuli. Furthermore, our findings suggest a clear dissociation in the interaction between expectations and consciousness: conscious awareness seems crucial for the implementation of top-down predictions, but not for the bottom-up generation of stimulus-evoked prediction errors. These results constrain and update influential theories about the role of consciousness in the predictive brain.
Platform for rapid nanobody discoveryin vitro
Authors: McMahon Conor , Baier Alexander S. , Zheng Sanduo , Pascolutti Roberta , Ong Janice X. , Erlandson Sarah C. , Hilger Daniel , Ring Aaron M. , Manglik Aashish , Kruse Andrew C.
Published: June 2017

Camelid single-domain antibody fragments (“nanobodies”) provide the remarkable specificity of antibodies within a single immunoglobulin VHHdomain. This unique feature enables applications ranging from their use as biochemical tools to therapeutic agents. Virtually all nanobodies reported to date have been obtained by animal immunization, a bottleneck restricting many applications of this technology. To solve this problem, we developed a fullyin vitroplatform for nanobody discovery based on yeast surface display of a synthetic nanobody scaffold. This platform provides a facile and cost-effective method for rapidly isolating nanobodies targeting a diverse range of antigens. We provide a blueprint for identifying nanobodies starting from both purified and non-purified antigens, and in addition, we demonstrate application of the platform to discover rare conformationally-selective nanobodies to a lipid flippase and a G protein-coupled receptor. To facilitate broad deployment of this platform, we have made the library and all associated protocols publicly available.
Out-of-equilibrium statistical dynamics of spatial pattern generating cellular automata
Authors: Olimpio Eduardo P. , Youk Hyun
Published: June 2017

How living systems generate order from disorder is a fundamental question1-5. Metrics and ideas from physical systems have elucidated order-generating collective dynamics of mechanical, motile, and electrical living systems such as bird flocks and neuronal networks6-8. But suitable metrics and principles remain elusive for many networks of cells such as tissues that collectively generate spatial patterns via chemical signals, genetic circuits, and dynamics representable by cellular automata1,9-11. Here we reveal such principles through a statistical mechanics-type framework for cellular automata dynamics in which cells with ubiquitous genetic circuits generate spatial patterns by switching on and off each other’s genes with diffusing signalling molecules. Lattices of cells behave as particles stochastically rolling down a pseudo-energy landscape – defined by a spin glass-like Hamiltonian – that is shaped by “macrostate” functions and genetic circuits. Decreasing the pseudo-energy increases the spatial patterns’ orderliness. A new kinetic trapping mechanism – “pathway trapping” – yields metastable spatial patterns by preventing minimization of the particle’s pseudo-energy. Noise in cellular automata reduces the trapping, thus further increases the spatial order. We generalize our framework to lattices with multiple types of cells and signals. Our work shows that establishing statistical mechanics of computational algorithms can reveal collective dynamics of signal-processing in biological and physical networks.
Dynamic interhemispheric coordination in face processing
Authors: Lu Zhengang , Guo Bingbing , Meng Ming
Published: June 2017

Our conscious experience of the world is normally unified. The brain coordinates different processes from the left and right hemispheres into one experience. However, the neural mechanisms underlying interhemispheric coordination remain poorly understood. A mechanistic approach to understanding interhemispheric coordination is “communication through coherence” (Fries, 2005; 2015). Using a recently developed time-resolved psychophysics (Fiebelkorn, Saalmann, & Kastner, 2013; Landau & Fries, 2012; Song, Meng, Chen, Zhou, & Luo, 2014), combined with fMRI decoding method, we investigated the interhemispheric coordination through coherence, by focusing on a quintessential case of hemispheric lateralized brain function: face processing in the left and right fusiform face area (FFA). We observed coherent oscillatory fMRI multi-voxel patterns in the left and right FFA when two stimuli presented successively cross visual fields, either initiating coordination from the left hemisphere or right hemisphere. When interhemispheric coordination started from the dominant right hemisphere, a coherent 44° phase difference between the left and right FFA in 3-4 Hz was observed; whereas when interhemispheric coordination started from the non-dominant left hemisphere, a coherent −17° phase difference between the left and right FFA in 5.5-6.5 Hz was observed. These results suggest that different phase coherence might mediate the interhemispheric coordination of face perception, depending on whether the initiating hemisphere is dominant or non-dominant. Our findings provide compelling fMRI evidence for interhemispheric coordination through coherence. The time-resolved fMRI decoding approach would be a useful starting point for a more promising approach for future investigation in interhemispheric dynamic coordination with fine-grained spatial and temporal resolution.
Post-exercise cold-water immersion increases Na+,K+-ATPase α2-isoform mRNA content in parallel with elevated Sp1 expression in human skeletal muscle
Authors: Christiansen Danny , Murphy Robyn M. , Broatch James R. , Bangsbo Jens , McKenna Michael J. , Kuang Jujiao , Bishop David J.
Published: June 2017

We investigated the effect of a session of sprint-interval exercise on the mRNA content of NKA isoforms (α1-3, β1-3) and FXYD1 in human skeletal muscle. To explore some of the cellular stressors involved in this regulation, we evaluated the association between these mRNA responses and those of the transcription factors Sp1, Sp3 and HIF-1α. Given cold exposure perturbs muscle redox homeostasis, which may be one mechanism important for increases in NKA-isoform mRNA, we also explored the effect of post-exercise cold-water immersion (CWI) on the mRNA responses. Muscle was sampled from nineteen men before (Pre) and after (+0h, +3h) exercise plus passive rest (CON, n=10) or CWI (10°C; COLD, n=9). In COLD, exercise increased NKAα2and Sp1 mRNA (+0h, p<0.05). These genes remained unchanged in CON (p>0.05). In both conditions, exercise increased NKAα1, NKAβ3and HIF-1α mRNA (+3h; p <0.05), decreased NKAβ2mRNA (+3h; p<0.05), whereas NKAα3, NKAβ1, FXYD1 and Sp3 mRNA remained unchanged (p>0.05). These human findings highlight 1) sprint-interval exercise increases the mRNA content of NKA α1and β3, and decreases that of NKA β2, which may relate, in part, to exercise-induced muscle hypoxia, and 2) post-exercise CWI augments NKAα2mRNA, which may be associated with promoted Sp1 activation.
DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation
Authors: Nacheva Elizabeth , Mokretar Katya , Soenmez Aynur , Pittman Alan M , Grace Colin , Valli Roberto , Ejaz Ayesha , Vattathil Selina , Maserati Emanuela , Houlden Henry , Taanman Jan-Willem , Schapira Anthony H , Proukakis Christos
Published: June 2017

Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array “waves”, and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.
simExTargId: An R package for real-time LC-MS metabolomic data analysis, instrument failure/drift notification and MS2 target identification
Authors: Edmands William M. B. , Rappaport Stephen M.
Published: June 2017

The simExTargId R package provides real-time, autonomous, within-laboratory data analysis during a metabolomic LC-MS1-profiling experiment. Of concern to metabolomic investigators are instrumentation failure (especially for precious samples), outlier identification, instrument signal attenuation and pre-emptive feature identification for MS2 fragmentation.

SimExTargId allows observation of an experiment in progress with PCA plot and peak table outputs and also two shiny applications targetId for MS2 target identification and peakMonitor for signal attenuation monitoring. SimExTargId is ideally utilised on a (temporarily) dedicated workstation or server which is networked to a LC-MS data directory. Features include: email notification for instrument stoppage/drift, file format conversion, peak-picking, pre-processing, PCA-based outlier identification and statistical analysis. Additional MS1/MS2 experiments can be concatenated to a worklist or cleaning/recalibration undertaken if instrument drift is observed.

All source code and a vignette with example data are available on GitHubhttps://github.com/WMBEdmands/simExTargId/.

Contact:edmandsw@berkeley.edu
High-qualityde novogenome assembly of theDekkera bruxellensisUMY321 yeast isolate using Nanopore MinION sequencing
Authors: Fournier Téo , Gounot Jean-Sébastien , Freel Kelle , Cruaud Corinne , Lemainque Arnaud , Aury Jean-Marc , Wincker Patrick , Schacherer Joseph , Friedrich Anne
Published: June 2017

Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is evidently to obtain the complete sequence and high quality assembly of a reference genome. Here, we completely sequenced and assembled a reference genome of the non-conventionalDekkera bruxellensisyeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting thatD. bruxellensisgenome is very dynamic. The whole genome of theD. bruxellensisUMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguousde novoassembly ofD. bruxellensisto date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.
The Neuron Specific Formin Delphilin Nucleates Actin Filaments but Does Not Enhance Elongation
Authors: Silkworth William T. , Kunes Kristina L. , Nickel Grace C. , Phillips Martin L. , Quinlan Margot E. , Vizcarra Christina L.
Published: June 2017

The formin Delphilin binds the glutamate receptor, GluRδ2, in dendritic spines of Purkinje cells. Both proteins play a role in learning. To understand how Delphilin functions in neurons, we studied the actin assembly properties of this formin. Formins have a conserved formin homology 2 domain, which nucleates and remains associated with the fast growing end of actin filaments, influencing filament growth with input from the adjacent formin homology 1 domain. The strength of nucleation and elongation varies widely across formins. Additionally, most formins have conserved domains that regulate actin assembly through an intramolecular interaction. Delphilin is distinct from other formins in several ways: its expression is limited to Purkinje cells; it lacks autoinhibitory domains; its formin homology 1 domains has minimal proline-rich sequence. We found that Delphilin is an actin nucleator that does not accelerate elongation, although it binds tightly to the barbed end of filaments. In addition, Delphilin exhibits a preference for actin isoforms, which has not been described or systematically studied in other formins. Finally, Delphilin is the first formin studied that is not regulated by intramolecular interactions. We speculate how the activity we observe is consistent with its localization in the small dendritic spines.
Evolution of human, chicken, alligator, frog and zebrafish mineralocorticoid receptors: Allosteric influence on steroid specificity
Authors: Katsu Yoshinao , Oka Kaori , Baker Michael E.
Published: June 2017

We studied the response to aldosterone, 11-deoxycorticosterone, 11-deoxycortisol, cortisol, corticosterone, progesterone, 19-norprogesterone and spironolactone of human, chicken, alligator, frog and zebrafish full-length mineralocorticoid receptors (MRs) and truncated MRs, lacking the N-terminal domain (NTD) and DNA-binding domain (DBD), in which the hinge domain and ligand binding domain (LBD) were fused to a GAL4-DBD. Compared to full-length MRs, some vertebrate MRs required higher steroid concentrations to activate GAL4-DBD-MR-hinge/LBD constructs. For example, 11-deoxycortisol activated all full-length vertebrate MRs, but did not activate truncated terrestrial vertebrate MRs and was an agonist for truncated zebrafish MR. Progesterone, 19-norProgesterone and spironolactone did not activate full-length and truncated human, alligator and frog MRs. However, at 10 nM, these steroids activated full-length chicken and zebrafish MRs; at 100 nM, these steroids had little activity for truncated chicken MRs, while retaining activity for truncated zebrafish MRs, evidence that regulation of progestin activation of chicken MR resides in NTD/DBD and of zebrafish MR in hinge-LBD. Zebrafish and chicken MRs contain a serine corresponding to Ser810 in human MR, required for its antagonism by progesterone, suggesting novel regulation of progestin activation of chicken and zebrafish MRs. Progesterone may be a physiological activator of chicken and zebrafish MRs.
Antimicrobial susceptibility and phylogenetic analysis ofPropionibacterium acnesisolated from acne patients in Japan between 2013 and 2015
Authors: Nakase Keisuke , Hayashi Nobukazu , Akiyama Yui , Aoki Sae , Noguchi Norihisa
Published: June 2017

The prevalence of antimicrobial‐resistantPropionibacterium acnesstrains isolated from acne patients has been increasing in Japan. Here, to estimate the current resistance rate, we tested antimicrobial susceptibility amongP. acnesfrom acne patients having visited a specialized dermatology clinic between 2013 and 2015. Rates of resistance to macrolides and clindamycin were 44.3 (31/70) and 38.6% (27/70), respectively.erm(X), which confers high‐level clindamycin resistance (minimum inhibitory concentration ≥256 μg/mL), was detected in six isolates, whereas no resistance determinants were identified in eight strains showing high‐level resistance to clindamycin. Using single‐locus sequence typing, theP. acnesisolates were classified into five clades (A, E, F, H and K), with all high‐level clindamycin‐resistant strains lacking known clindamycin resistance determinants being grouped together (in clade F).P. acnesisolates from patients previously treated with macrolides and clindamycin showed a macrolide resistance rate (55.3%) significantly higher than that of those from patients not having received these treatments (21.7%,P< 0.05). Furthermore, strains of clade F, which were very rarely isolated from healthy individuals, were more frequently recovered from patients with severe acne (40.0%) than those with mild acne (23.3%). Our data showed an increase in macrolide‐resistantP. acnesprevalence in Japan due to the use of antimicrobial agents for acne treatment. Furthermore, we identified strains of specific phylogenetic groups frequently associated with severe acne patients.
Linear immunoglobulin A/G bullous dermatosis associated with ulcerative colitis
Authors: Onoe Asuka , Matsuura Daisuke , Terui Tadashi , Ishii Norito , Hashimoto Takashi , Ochiai Toyoko
Published: June 2017

Linear immunoglobulin (Ig)A/G bullous dermatosis (LAGBD) is an autoimmune bullous disease characterized by formation of subepidermal blisters and linear deposition of IgA and IgG antibodies along the basement membrane zone (BMZ). The association between linear IgA bullous dermatosis and ulcerative colitis (UC) is well recognized, but reports of UC‐associated LAGBD are lacking. We have reported a 24‐year‐old man suffering from LAGBD associated with UC, which occurred before exacerbations of skin rash. A skin biopsy indicated a subepidermal blister with an infiltration of primarily neutrophils and eosinophils in the dermis. Direct immunofluorescence (IF) studies showed a linear deposition of IgA, IgG and C3c. Indirect IF of human skin revealed IgA and IgG anti‐BMZ autoantibodies. Indirect IF of 1 M NaCl‐split human skin demonstrated reactivity of IgA and IgG antibodies at the epidermal side. Immunoblotting showed that IgG antibodies reacted to the BP180 NC16a domain and 120‐kDa linear IgA dermatosis‐1, and enzyme‐linked immunoassay detected IgG anti‐BP230 antibodies. Administration of prednisolone and diaminodiphenyl sulfone (DDS) via the p.o. route improved skin lesions and bowel conditions. These results suggest that the bowel inflammation observed in UC may have a causative effect of initiation of the immune response to the skin and development of the bullous skin lesions in LAGBD. A combination of DDS and corticosteroid could be a recommended therapeutic option for patients with LAGBD with UC.