bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of ultracentrifugation and a commercial kit for isolation of exosomes derived from glioblastoma and breast cancer cells
Authors: Skottvoll Frøydis Sved , Berg Henriette Engen , Bjørseth Kamilla , Lund Kaja , Roos Norbert , Bekhradnia Sara , Thiede Bernd , Sandberg Cecilie , Vik-Mo Einar , Roberg-Larsen Hanne , Nyström Bo , Lundanes Elsa , Wilson Steven Ray
Published: March 2018

Exosomes are small extracellular vesicles around 30-100 nm in diameter that are secreted from cells and can be found in most body fluids. Exosomes can be a vital source of biomarkers as they contain various substances (e.g. lipids, RNAs, metabolites and proteins) that can reflect the cell of origin (e.g. cancer cells). For isolation of exosomes present in biological matrices, ultracentrifugation (UC)-based procedures are most common. Other approaches exist, including commercial kits developed for easy and low sample volume isolation. In this study, differential UC and an isolation kit from a major vendor (Total Exosome Isolation Reagent from Thermo Fisher Scientific) were compared. Exosomes were isolated from cell culture media of two different cell sources (patient derived cells from glioblastoma multiforme and the breast cancer cell line MDA-MB-231). For both isolation methods, transmission electron microscopy, dynamic light scattering and western blotting indicated the presence of exosomes. The kit- and UC isolates contained similar amounts of protein measured by the bicinchoninic acid (BCA) assay with absorbance at 562 nm. Using western blot, positive exosome markers were identified in all isolates, and additional exosome markers were identified using MS-based proteomics. For the glioblastoma exosome isolates, the number of proteins identified with liquid chromatography tandem MS (LC-MS/MS) was higher for the UC isolates than the kit isolates when injecting equal protein amounts, contrary to that for the breast cancer exosome isolates. However, negative exosome markers were also found in glioblastoma isolates using LC-MS/MS. Thus, we would not use the term “exosome isolation” as impurities may be present with both isolation methods. Notably, potential biomarkers for both diseases were identified in the isolates using LS-MS/MS. In our opinion, the two isolation methods had rather similar performance, although with some minor differences based on cell of origin.
Cortical recruitment determines learning dynamics and strategy
Authors: Ceballo Sebastian , Bourg Jacques , Kempf Alexandre , Piwkowska Zuzanna , Daret Aurélie , Deneux Thomas , Rumpel Simon , Bathellier Brice
Published: March 2018

Salience is a broad and widely used concept in neuroscience whose neuronal correlates, however, remain elusive. In behavioral conditioning, salience is used to explain various effects, such as stimulus overshadowing, and refers to how fast and strongly a stimulus can be associated with a conditioned event. Here, we show that sounds of diverse quality, but equal intensity and perceptual detectability, can recruit different levels of population activity in mouse auditory cortex. When using these sounds as cues in a Go/NoGo discrimination task, the degree of cortical recruitment matches the salience parameter of a reinforcement learning model used to analyze learning speed. We test an essential prediction of this model by training mice to discriminate light-sculpted optogenetic activity patterns in auditory cortex, and verify that cortical recruitment causally determines association or overshadowing of the stimulus components. This demonstrates that cortical recruitment underlies major aspects of stimulus salience during reinforcement learning.
MoDentify: a tool for phenotype-driven module identification in multilevel metabolomics networks
Authors: Do Kieu Trinh , Rasp David J.N.-P. , Kastenmüller Gabi , Suhre Karsten , Krumsiek Jan
Published: March 2018

Metabolomics is an established tool to gain insights into (patho)physiological outcomes. Associations of metabolism with such outcomes are expected to span functional modules, which are defined as sets of correlating metabolites that are coordinately regulated. Moreover, these associations occur at different scales, from entire pathways to only a few metabolites, which is an aspect that has not been addressed by previous methods. Here we present MoDentify, a freely available R package to identify regulated modules in metabolomics networks at different layers of resolution. Importantly, MoDentify shows higher statistical power than classical association analysis. Moreover, the package offers direct visualization of results as interactive networks in Cytoscape. We present an application example using a complex, multifluid metabolomics dataset. Owing to its generic character, the method is widely applicable to any dataset with a phenotype variable, a data matrix, and optional pathway annotations.

Availability and Implementation

MoDentify is freely available from GitHub: https://github.com/krumsiek/MoDentify

The package vignette contains a detailed tutorial of the analysis workflow.

Contact

jan.krumsiek@helmholtz-muenchen.de
Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts
Authors: Kelliher Michael T. , Yue Yang , Ng Ashley , Kamiyama Daichi , Huang Bo , Verhey Kristen J. , Wildonger Jill
Published: March 2018

Neuronal polarity relies on the selective localization of cargo to axons or dendrites. The molecular motor kinesin-1 moves cargo into axons but is also active in dendrites. This raises the question of how kinesin-1 activity is regulated to maintain the compartment-specific localization of cargo. Our in vivo structure-function analysis of endogenous Drosophila kinesin-1 reveals a novel role for autoinhibition in enabling the dendrite-specific localization of Golgi outposts. Mutations that disrupt kinesin-1 autoinhibition result in the axonal mislocalization of Golgi outposts. Autoinhibition also regulates kinesin-1 localization. Uninhibited kinesin-1 accumulates in axons and is depleted from dendrites, correlating with the change in outpost distribution and dendrite growth defects. Genetic interaction tests show that a balance of kinesin-1 inhibition and dynein activity is necessary to localize Golgi outposts to dendrites and keep them from entering axons. Our data indicate that kinesin-1 activity is precisely regulated by autoinhibition to achieve the selective localization of dendritic cargo.

Neuronal polarity relies on the axon-or dendrite-specific localization of cargo by molecular motors such as kinesin-1. These studies show autoinhibition regulates both kinesin-1 activity and localization to keep dendritic cargo from entering axons.
Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity
Authors: Zhu Qian , Shah Sheel , Dries Ruben , Cai Long , Yuan Guo-Cheng
Published: March 2018

Both the intrinsic regulatory network and spatial environment are contributors of cellular identity and result in cell state variations. However, their individual contributions remain poorly understood. Here we present a systematic approach to integrate both sequencing-and imaging-based single-cell transcriptomic profiles, thereby combining whole-transcriptomic and spatial information from these assays. We applied this approach to dissect the cell-type and spatial domain associated heterogeneity within the mouse visual cortex region. Our analysis identified distinct spatially associated signatures within glutamatergic and astrocyte cell compartments, indicating strong interactions between cells and their spatial environment. Using these signatures as a guide to analyze single cell RNAseq data, we identified previously unknown, but spatially associated subpopulations. As such, our integrated approach provides a powerful tool for dissecting the roles of intrinsic regulatory networks and spatial environment in the maintenance of cellular states.
Different inhibitory interneuron cell classes make distinct contributions to visual perception
Authors: Cone Jackson J. , Scantlen Megan D. , Histed Mark H. , Maunsell John H.R.
Published: March 2018

While recent work has revealed how different inhibitory interneurons influence cortical responses to sensory stimuli, little is known about how their activity contributes to sensory perception. Here, we optogenetically stimulated different genetically defined interneurons (parvalbumin (PV), somatostatin (SST), vasoactive intestinal peptide (VIP)) in visual cortex (V1) of mice working at threshold in contrast increment or decrement detection tasks. The visual stimulus was paired with optogenetic stimulation to assess how enhancing V1 inhibitory neuron activity synchronously during cortical responses altered task performance. PV or SST activation impaired, while VIP stimulation improved, contrast increment detection. Notably, PV or SST stimulation also impaired contrast decrement detection, when opsin-evoked inhibition would exaggerate stimulus-evoked decrements in firing rate, and thus might improve performance. The impairment produced by PV or SST stimulation persisted throughout many weeks of testing. In contrast mice learned to reliably detect VIP activation in the absence of natural visual stimulation. Thus, different inhibitory signals make distinct contributions to visual contrast perception.
Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation
Authors: Bartman Caroline , Keller Cheryl A. , Giardine Belinda , Hardison Ross C. , Blobel Gerd A. , Raj Arjun
Published: March 2018

Transcriptional regulation occurs via changes to the rates of various biochemical processes. Sequencing-based approaches that average together many cells have suggested that polymerase binding and polymerase release from promoter-proximal pausing are two key regulated steps in the transcriptional process. However, single cell studies have revealed that transcription occurs in short, discontinuous bursts, suggesting that transcriptional burst initiation and termination might also be regulated steps. Here, we develop and apply a quantitative framework to connect changes in both Pol II ChIP-seq and single cell transcriptional measurements to changes in the rates of specific steps of transcription. Using a number of global and targeted transcriptional regulatory perturbations, we show that burst initiation rate is indeed a key regulated step, demonstrating that transcriptional activity can be frequency modulated. Polymerase pause release is a second key regulated step, but the rate of polymerase binding is not changed by any of the biological perturbations we examined. Our results establish an important role for transcriptional burst regulation in the control of gene expression.
Persistent Underrepresentation of Women’s Science in High Profile Journals
Authors: Shen Yiqin Alicia , Webster Jason M. , Shoda Yuichi , Fine Ione
Published: March 2018

Yiqin Alicia Shen, Jason M. Webster, Yuichi Shoda, and Ione Fine Department of Psychology, University of Washington Past research has demonstrated an under-representation of female editors and reviewers in top scientific journals, but less is known about the representation of women authors within original research articles. We collected research article publication records from 15 high-profile multidisciplinary and neuroscience journals for 2005-2017 and analyzed the representation of women over time, as well as its relationship with journal impact factor. We find that women authors have been persistently underrepresented in high-profile journals. This under-representation has persisted over more than a decade, with glacial improvement over time. Even within our limited group of high profile journals, the percent of female first and last authors is negatively associated with journal impact factor. Since publishing in high-profile journals is a gateway to academic success, this underrepresentation of women may contribute to the lack of women at the top of the academic ladder.
Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal
Authors: Kearney Sean M. , Gibbons Sean M. , Erdman SE , Alm EJ
Published: March 2018

Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. While probiotic or prebiotic approaches typically lead to a transient pulse in an organism’s abundance, persistent establishment of an introduced species may require alternative strategies. Here, we introduce the concept of orthogonal niche engineering in the gut, where we include a resource typically absent from the diet, seaweed, to establish a customized niche for an introduced organism. We show that in the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource,B. plebeiusDSM 17135, enables it to colonize at a median abundance of 1%, frequently increasing in abundance to 10 or more percent. We construct a mathematical model of the system to infer thatB. plebeiuscompetitively acquires endogenous resources. We provide evidence that it competes with native commensals to achieve its observed abundance. We observe a diet-dependent loss in seaweed responsiveness ofB. plebeiusin the long term and show the potential for IgA-mediated control of putative invaders by the immune system. These results point to the potential for diet-based intervention as a means to introduce target organisms, but also indicate potential modes for failure of this strategy in the long term.
A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination
Authors: Feulner Philine G.D. , Schwarzer Julia , Haesler Marcel P. , Meier Joana I. , Seehausen Ole
Published: March 2018

Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P. sp. “red head”). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1.01 cM. This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination gene (amh).
Dynamic control of hippocampal spatial coding resolution by local visual cues
Authors: Bourboulou Romain , Marti Geoffrey , Michon FranÇois-Xavier , Nouguier Morgane , Robbe David , Koenig Julie , Epsztein Jérôme
Published: March 2018

The ability to flexibly navigate an environment relies on a hippocampal-dependent internal cognitive map. Explored space can be internally mapped at different spatial resolutions. However, whether hippocampal spatial coding resolution can be dynamically controlled within and between environments is unknown. In this work we recorded the firing of hippocampal principal cells in mice navigating virtual reality environments, which differed by the presence of local visual cues (virtual 3D objects). Objects improved spatial coding resolution globally with a higher proportion of place cells, smaller place fields, increased spatial selectivity and stability. Spatial coding resolution was notably enhanced locally near objects and could be rapidly tuned by their manipulations. In the presence of objects, place cells also displayed improved theta phase precession and theta timescale spike coordination. These results suggest that local visual cues can rapidly tune the resolution of the hippocampal mapping system within and between environments.
Anti-HIV-1 B cell responses are dependent on B cell precursor frequency and antigen binding affinity
Authors: Dosenovic Pia , Kara Ervin E. , Pettersson Anna-Klara , McGuire Andrew , Gray Matthew , Hartweger Harald , Thientosapol Eddy S. , Stamatatos Leonidas , Nussenzweig Michel C.
Published: March 2018

The discovery that humans can produce potent broadly neutralizing antibodies (bNAbs) to several different epitopes on the HIV-1 spike has reinvigorated efforts to develop an antibody based HIV-1 vaccine. Antibody cloning from single cells revealed that nearly all bNAbs show unusual features that could help explain why it has not been possible to elicit them by traditional vaccination, and instead that it would require a sequence of different immunogens. This idea is supported by experiments with genetically modified immunoglobulin knock-in mice. Sequential immunization with a series of specifically designed immunogens was required to shepherd the development of bNAbs. However, knock-in mice contain super-physiologic numbers of bNAb precursor expressing B cells and therefore how these results can be translated to a more physiologic setting remains to be determined. Here we make use of adoptive transfer experiments using knock-in B cells that carry a synthetic intermediate in the pathway to anti-HIV-1 bNAb development to examine how the relationship between B cell receptor affinity and precursor frequency affects germinal center B cell recrutiment and clonal expansion. Immunization with soluble HIV-1 antigens can recruit bNAb precursor B cells to the germinal center when there are as few as 10 such cells per mouse. However, at low precursor frequencies the extent of clonal expansion is directly proportional to the affinity of the antigen for the B cell receptor, and recruitment to germinal centers is variable and dependent on re-circulation.

Significance statement

An essential requirement for an HIV-vaccine is to elicit antibodies to conserved regions of the spike protein (Env) becasue these antibodies can protect against infection. Although broadly neutralizing antibodies develop naturally in rare individuals after prolongued HIV infection, eliciting them by vaccination has only been possible in artificial knock-in mouse models wherein the number of B cells expressing the antibody precursor is super-physiologic. To understand the relationship between precursor frequency, antigen affinity and germinal center recruitment we have performed adoptive transfer experiments in which fixed numbers of precursor cells are engrafted in wild type mice. Our results provide a framework for understanding how precursor frequency and antigen affinity shape humoral immunity to HIV.
Bayesian and likelihood placement of fossils on phylogenies from quantitative morphometries
Authors: Parins-Fukuchi Caroline
Published: March 2018

Abstract

Jointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.
BIC Defacing Algorithm
Authors: Fonov Vladimir S. , Collins Louis D.
Published: March 2018

Public distribution of imaging information from several MRI data processing projects at the BIC has lead to the development of this DEFACING algorithm that is used as part of anonymisation process. Key features of the algorithm include: the defacing should modify voxels associated with face of the subject, making a rendering of the face unrecognisable, it should work on data in the native scanner space and it should not significantly affect subsequent data processing outcome (model based registration, brain extraction, brain tissue classification and brain segmentation). The algorithm is implemented using the MINC library and source code is publicly available. The effect of the defacing algorithm on the data processing was verified using the ICBM database of 152 scans of young adults.
Rapid and Accurate Interpretation of Clinical Exomes Using Phenoxome: a Computational Phenotype-driven Approach
Authors: Wu Chao , Devkota Batsal , Zhao Xiaonan , Baker Samuel W , Niazi Rojeen , Cao Kajia , Gonzalez Michael A , Jayaraman Pushkala , Conlin Laura K , Krock Bryan L , Deardorff Matthew A , Spinner Nancy B , Krantz Ian D , Santani Avni B , Tayoun Ahmad N Abou , Sarmady Mahdi
Published: March 2018

Clinical exome sequencing (CES) has become the preferred diagnostic platform for complex pediatric disorders with suspected monogenic etiologies, solving up to 20%-50% of cases depending on indication. Despite rapid advancements in CES analysis, the major challenge still resides in identifying the casual variants among the thousands of variants detected during CES testing, and thus establishing a molecular diagnosis. To improve the clinical exome diagnostic efficiency, we developed Phenoxome, a robust phenotype-driven model that adopts a network-based approach to facilitate automated variant prioritization and subsequent classification. Phenoxome dissects the phenotypic manifestation of a patient in conjunction with their genomic profile to filter and then prioritize putative pathogenic variants. To validate our method, we have compiled a clinical cohort of 105 positive patient samples (i.e. at least one reported ‘pathogenic’ variant) that represent a wide range of genetic heterogeneity from The Children’s Hospital of Philadelphia. Our approach identifies the causative variants within the top 5, 10, or 25 candidates in more than 50%, 71%, or 88% of these patient samples respectively. Furthermore, we show that our method is optimized for clinical testing by yielding superior ranking of the pathogenic variants compared to current state-of-art methods. The web application of Phenoxome is available to the public at http://phenoxome.chop.edu/.
Towards region-specific propagation of protein functions
Authors: Emily Koo Da Chen , Bonneau Richard
Published: March 2018

Motivation

Due to the nature of experimental annotation, most protein function prediction methods operate at the protein-level, where functions are assigned to full-length proteins based on overall similarities. However, most proteins function by interacting with other proteins or molecules, and many functional associations should be limited to specific regions rather than the entire protein length. Most domain-centric function prediction methods depend on accurate domain family assignments to infer relationships between domains and functions, with regions that are unassigned to a known domain-family left out of functional evaluation. Given the abundance of residue-level annotations currently available, we present a function prediction methodology that automatically infers function labels of specific protein regions using protein-level annotations and multiple types of region-specific features.

Results

We apply this method to local features obtained from InterPro, UniProtKB and amino acid sequences and show that this method improves both the accuracy and region-specificity of protein function transfer and prediction by testing on both human and yeast proteomes. We compare region-level predictive performance of our method against that of a whole-protein baseline method using a held-out dataset of proteins with structurally-verified binding sites and also compare protein-level temporal holdout predictive performances to expand the variety and specificity of GO terms we could evaluate. Our results can also serve as a starting point to categorize GO terms into site-specific and whole-protein terms and select prediction methods for different classes of GO terms.

Availability

The code is freely available at: https://github.com/ek1203/region_spec_func_pred
Immediate early gene activation throughout the brain is associated with dynamic changes in social context
Authors: Williamson Cait M. , Klein Inbal S. , Lee Won , Curley James P.
Published: March 2018

Social competence is dependent on successful processing of social context information. The social opportunity paradigm is a methodology in which dynamic shifts in social context are induced through removal of the alpha male in a dominance hierarchy, leading to rapid ascent in the hierarchy of the beta male and of other subordinate males in the social group. In the current study, we use the social opportunity paradigm to determine what brain regions respond to this dynamic change in social context, allowing an individual to recognize the absence of the alpha male and subsequently perform status-appropriate social behaviors. Replicating our previous work, we show that following removal of the alpha male, beta males rapidly ascend the social hierarchy and attain dominant status by increasing aggression towards more subordinate individuals. Analysis of patterns of Fos immunoreactivity throughout the brain indicates that in individuals undergoing social ascent, there is increased activity in regions of the social behavior network, as well as the infralimbic and prelimbic regions of the prefrontal cortex and areas of the hippocampus. Our findings demonstrate that male mice are able to respond to changes in social context and provide insight into the how the brain processes these complex behavioral changes.
Network-based prediction of protein interactions
Authors: Kovács István A. , Luck Katja , Spirohn Kerstin , Wang Yang , Pollis Carl , Schlabach Sadie , Bian Wenting , Kim Dae-Kyum , Kishore Nishka , Hao Tong , Calderwood Michael A. , Vidal Marc , Barabási Albert-László
Published: March 2018

As biological function emerges through interactions between a cell’s molecular constituents, understanding cellular mechanisms requires us to catalogue all physical interactions between proteins [1–4]. Despite spectacular advances in high-throughput mapping, the number of missing human protein-protein interactions (PPIs) continues to exceed the experimentally documented interactions [5, 6]. Computational tools that exploit structural, sequence or network topology information are increasingly used to fill in the gap, using the patterns of the already known interactome to predict undetected, yet biologically relevant interactions [7–9]. Such network-based link prediction tools rely on the Triadic Closure Principle (TCP) [10–12], stating that two proteins likely interact if they share multiple interaction partners. TCP is rooted in social network analysis, namely the observation that the more common friends two individuals have, the more likely that they know each other [13, 14]. Here, we offer direct empirical evidence across multiple datasets and organisms that, despite its dominant use in biological link prediction, TCP is not valid for most protein pairs. We show that this failure is fundamental - TCP violates both structural constraints and evolutionary processes. This understanding allows us to propose a link prediction principle, consistent with both structural and evo-lutionary arguments, that predicts yet uncovered protein interactions based on paths of length three (L3). A systematic computational cross-validation shows that the L3 principle significantly outperforms existing link prediction methods. To experimentally test the L3 predictions, we perform both large-scale high-throughput and pairwise tests, finding that the predicted links test positively at the same rate as previously known interactions, suggesting that most (if not all) predicted interactions are real. Combining L3 predictions with experimen-tal tests provided new interaction partners of FAM161A, a protein linked to retinitis pigmentosa, offering novel insights into the molecular mechanisms that lead to the disease. Because L3 is rooted in a fundamental biological principle, we expect it to have a broad applicability, enabling us to better understand the emergence of biological function under both healthy and pathological conditions.

We unveil a fundamental organizing principle of biological networks and demonstrate its predictive power for uncovering novel protein interactions.
A three-dimensional culture model of innervated human skeletal muscle enables studies of the adult neuromuscular junction and disease modeling
Authors: Bakooshli Mohsen Afshar , Lippmann Ethan S , Mulcahy Ben , Iyer Nisha R , Nguyen Christine T , Tung Kayee , Stewart Bryan A , van den Dorpel Hubrecht , Fuehrmann Tobias , Shoichet Molly S , Bigot Anne , Pegoraro Elena , Ahn Henry , Ginsberg Howard , Zhen Mei , Ashton Randolph S , Gilbert Penney M
Published: March 2018

Two-dimensional (2D) human skeletal muscle fiber cultures are ill equipped to support the contractile properties of maturing muscle fibers. This limits their application to the study of adult human neuromuscular junction (NMJ) development, a process requiring maturation of muscle fibers in the presence of motor neuron endplates. Here we describe a three-dimensional (3D) co-culture method whereby human muscle progenitors mixed with human pluripotent stem cell-derived motor neurons self-organize to form functional NMJ connections within two weeks. Functional connectivity between motor neuron endplates and muscle fibers is confirmed with calcium transient imaging and electrophysiological recordings. Notably, we only observed epsilon acetylcholine receptor subunit protein upregulation and activity in 3D co-culture. This demonstrates that the 3D co-culture system supports a developmental shift from the embryonic to adult form of the receptor that does not occur in 2D co-culture. Further, 3D co-culture treatments with myasthenia gravis patient sera shows the ease of studying human disease with the system. This work delivers a simple, reproducible, and adaptable method to model and evaluate adult human NMJ de novo development and disease in culture.
OsIQD14 regulates rice grain shape through modulating the microtubule cytoskeleton
Authors: Yang Baojun , Wendrich Jos R. , Rybel Bert De , Weijers Dolf , Xue HongWei
Published: March 2018

Cortical microtubule (MT) arrays play a critical role in plant cell shape determination by defining the direction of cell expansion1-3. The control of plant organ shape and architecture is a major target of cereal crop improvement. Given the pleiotropic effects of MT modification, however, it is challenging to exploiting MT array organization for crop improvement. Moreover, as plants continuously adapt cell growth and expansion to ever-changing environmental conditions, multiple environmental (e.g. light4) and developmental (e.g. hormones5,6) inputs need to be translated into changes of the MT cytoskeleton. Here, we identify and functionally characterize an auxin-inducible and MT-localized protein OsIQ67-DOMAIN14 (OsIQD14), which is highly expressed in rice seed hull cells. While deficiency of OsIQD14 results in short and wide seeds and increases overall yield, overexpression leads to narrow and long seeds, caused by changes in the direction of MT arrangement. We further show that OsIQD14-mediated MT reordering is regulated through interacting with SPIRAL2, a MT-binding protein involved in KATANIN1-mediated MT rearrangement7,8, and with calmodulin proteins. As such, OsIQD14 acts as an integrator of auxin and calcium inputs into MT rearrangements, and allows effective local cell shape manipulation to improve a key rice yield trait.
IQD proteins integrate auxin and calcium signaling to regulate microtubule dynamics duringArabidopsisdevelopment
Authors: Wendrich Jos R. , Yang Bao-Jun , Mijnhout Pieter , Xue Hong-Wei , Rybel Bert De , Weijers Dolf
Published: March 2018

Geometry and growth and division direction of individual cells are major contributors to plant organ shape and these processes are dependent on dynamics of microtubules (MT). Different MT structures, like the cortical microtubules, preprophase band and mitotic spindle, are characterized by diverse architectural dynamics (Hashimoto, 2015). While several MT binding proteins have been identified that have various effects on MT stability and architecture, they do not discriminate between the different MT structures. It is therefore likely that specific MT binding proteins exist that differentiate between MT structures in order to allow for the differences in architectural dynamics. Although evidence for the effect of specific cues, such as light and auxin, on MT dynamics has been shown in recent years (Lindeboomet al., 2013; Chenet al., 2014), it remains unknown how such cues are integrated and lead to specific effects. Here we provide evidence for how auxin and calcium signaling can be integrated to modulate MT dynamics, by means of IQD proteins. We show that theArabidopsisIQD15-18 subclade of this family is regulated by auxin signaling, can bind calmodulins in a calcium-dependent manner and are evolutionarily conserved. Furthermore, AtIQD15-18 directly bind SPIRAL2 proteinin vitroandin vivoand modulate its function, likely in a calmodulin-dependent way, thereby providing a missing link between two important regulatory pathways of MT dynamics.

One sentence summary

IQD proteins integrate auxin and calcium signaling, two major signaling pathways, to control the cytoskeleton dynamics and cell shape ofArabidopsis.
Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination
Authors: Elhanati Yuval , Sethna Zachary , Callan Curtis G. , Mora Thierry , Walczak Aleksandra M.
Published: March 2018

Despite the extreme diversity of T cell repertoires, many identical T cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely-shared sequences, often referred to as ‘public‘, have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here we show that even for large cohorts the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations we propose a public/private sequence classifier, ‘PUBLIC’ (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes.
Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome
Authors: Booker Tom R. , Keightley Peter D.
Published: March 2018

A major goal of population genetics has been to determine the extent to which selection at linked sites influences patterns of neutral nucleotide diversity in the genome. Multiple lines of evidence suggest that diversity is influenced by both positive and negative selection. For example, in many species there are troughs in diversity surrounding functional genomic elements, consistent with the action of either background selection (BGS) or selective sweeps. In this study, we investigated the causes of the diversity troughs that are observed in the wild house mouse genome. Using the unfolded site frequency spectrum (uSFS), we estimated the strength and frequencies of deleterious and advantageous mutations occurring in different functional elements in the genome. We then used these estimates to parameterize forward-in-time simulations of chromosomes, using realistic distributions of functional elements and recombination rate variation in order to determine if selection at linked sites can explain the observed patterns of nucleotide diversity. The simulations suggest that BGS alone cannot explain the dips in diversity around either exons or conserved non-coding elements (CNEs). A combination of BGS and selective sweeps, however, can explain the troughs in diversity around CNEs. This is not the case for protein-coding exons, where observed dips in diversity cannot be explained by parameter estimates obtained from the uSFS. We discuss the extent to which our results provide evidence of sweeps playing a role in shaping patterns of nucleotide diversity and the limitations of using the uSFS for obtaining inferences of the frequency and effects of advantageous mutations.

Author Summary

We present a study examining the causes of variation in nucleotide diversity across the mouse genome. The status of mice as a model organism in the life sciences makes them an excellent model system for studying molecular evolution in mammals. In our study, we analyse how natural selection acting on new mutations can affect levels of nucleotide diversity through the processes of background selection and selective sweeps. To perform our analyses, we first estimated the rate and strengths of selected mutations from a sample of wild mice and then use our estimates in realistic population genetic simulations. Analysing simulations, we find that both harmful and beneficial mutations are required to explain patterns of nucleotide diversity in regions of the genome close to gene regulatory elements. For protein-coding genes, however, our approach is not able to fully explain observed patterns and we think that this is because there are strongly advantageous mutations that occur in protein-coding genes that we were not able to detect.
Case of punctate palmoplantar keratoderma type I treated with combination of low‐dose oral acitretin and topical salicylic acid and steroid
Authors: Jo Jeong Won , Jeong Do Seon , Kim Chi Yeon
Published: March 2018

Palmoplantar keratodermas (PPK) are heterogeneous disorders characterized by abnormal keratinization. Especially, punctate PPK (PPPK), one of the subtypes of hereditary PPK, is a rare punctate keratoderma characterized by tiny “raindrop” keratoses having a tendency to coalesce on the edge of soles, which are exposed to sustained pressure. If typical punctate lesions are confined to the palms and soles and the patient has a family history and late onset, it can be considered as PPPK type I (PPKP1), also called Buschke–Fisher–Brauer disease. The exact etiology of PPPK has not been fully understood. Furthermore, no standardized treatment for PPPK has been established and treatment options are limited. Above all, traditional systemic retinoids have been used in several cases, but dose‐related adverse effects are common. Therefore, combination of low‐dose systemic retinoids and adjuvant topical therapy can be an alternative treatment option for PPPK. Herein, we report a case of PPKP1 treated with combination of low‐dose oral acitretin (10 mg/day) and topical salicylic acid and steroid. Despite low capacity, low‐dose acitretin showed excellent regression of the lesions by combined use of topical ointments. The supplementary topical therapy may be useful in reducing the dose of systemic retinoids and preventing potential toxicity.
Splice site mutation in COL7A1 resulting in aberrant in‐frame transcripts identified in a case of recessive dystrophic epidermolysis bullosa, pretibial
Authors: Masunaga Takuji , Kubo Akiharu , Ishiko Akira
Published: March 2018

Dystrophic epidermolysis bullosa (DEB), pretibial, a rare subtype of epidermolysis bullosa (EB), is characterized by recurrent blisters and erosions predominantly on the pretibial region. We report the case of a 60‐year‐old Japanese woman with persistent blistering eruptions and scar formation on the pretibial region and elbows. Mutational analysis revealed a previously reported c.5797C>T mutation in exon 70 (p.R1933X) and a novel c.6348+1G>A mutation in intron 76 of COL7A1. Reverse transcription polymerase chain reaction revealed that the c.6348+1G>A mutation resulted in the skipping of exon 76 (69 bp) and the retention of intron 76 (75 bp), and both transcripts were in‐frame. From these results, we diagnosed the patient as having recessive DEB, pretibial. A review of previously reported mutations in DEB, pretibial, revealed that one‐third of DEB, pretibial, cases showed a recessive inheritance pattern, and no case had a combination of premature termination codon (PTC)/PTC mutations. The DEB, pretibial, case described herein is the first reported case of a compound heterozygote with PTC/in‐frame mutations. Although no special characteristic features of the mutations were identified, a high diversity of COL7A1 mutations was shown even in DEB, pretibial.
Changes in salivary chromogranin A levels in adults with atopic dermatitis are correlated with changes in their condition
Authors: Cai Liang , Kaneko Sakae , Morita Eishin
Published: March 2018

Stress‐induced scratching is an issue in patients with adult atopic dermatitis (AD). Symptoms of stress‐induced AD are common in clinical practise. Salivary chromogranin A (CgA) level has research value as a possible index related to a patient's psychological stress. Using saliva, which is easily collectable, we compared two assessments of the severities of AD and stress with the levels of stress proteins in the saliva of 30 patients with AD in the Department of Dermatology of Shimane University between April 2015 and May 2017. The severities of AD and stress were assessed using the Scoring Atopic Dermatitis (SCORAD) score and State–Trait Anxiety Inventory score, respectively. Additionally, the assessments included those of personality using the Tokyo University Egogram (TEG)‐II score and quality of life using the Dermatology Life Quality Index score. Simultaneously, we measured their salivary CgA levels. The change in salivary CgA per protein in patients with AD was correlated with their changes in SCORAD score (correlation coefficient, r = 0.596, P = 0.001) and objective SCORAD (r = 0.608, P < 0.001). The changes in CgA per protein correlated with those in TEG‐II A (r = 0.370, P = 0.022), while the changes in SCORAD score correlated with those in DLQI (r = 0.309, P = 0.048). Our results suggest that changes in a patient's condition are reflective of the changes in the patient's stress. The changes in salivary CgA level in patients with AD correlated with the changes in their condition.
Association between serum autotaxin or phosphatidylserine‐specific phospholipase A1 levels and melanoma
Authors: Kurano Makoto , Miyagaki Tomomitsu , Miyagawa Takuya , Igarashi Koji , Shimamoto Satoshi , Ikeda Hitoshi , Aoki Junken , Sato Shinichi , Yatomi Yutaka
Published: March 2018

Autotaxin (ATX), a producing enzyme for lysophosphatidic acids, was first identified from the medium of a melanoma cell line and has been considered to be one of the candidate targets to treat melanoma; however, the association between serum ATX and melanoma in human subjects has not been elucidated. Along with ATX, phosphatidylserine‐specific phospholipase A1 (PS‐PLA1) is a producing enzyme for lysophosphatidylserine, a similar glycero‐lysophospholipid mediator to lysophosphatidic acids. In the present study, we aimed to investigate the association between serum ATX or PS‐PLA1 levels and melanoma. We measured the serum levels of ATX, ATX isoforms and PS‐PLA1 in subjects with melanoma (n = 57) and healthy subjects (n = 58). We further investigated the existence of trends according to the clinical stages of melanoma. We observed that serum total ATX and classical ATX levels were significant higher and serum novel ATX levels tended to be higher in male subjects with melanoma, while no significant difference was observed between the two groups in female subjects. The trend test revealed that the serum total ATX and ATX isoforms were significantly associated with the clinical stages of female subjects with melanoma. Regarding PS‐PLA1, serum PS‐PLA1 levels were significantly higher in the melanoma subjects and associated with the clinical stages. The present study is the first study which revealed the association between ATX or PS‐PLA1 and melanoma, suggesting the possible involvement of ATX/lysophosphatidic acids or PS‐PLA1/lysophosphatidylserine axis in the pathogenesis of melanoma.
Cultural adaptation and psychometric testing of The Scenario Test UK for people with aphasia
Authors: Hilari Katerina , Galante Lara , Huck Anneline , Pritchard Madeleine , Allen Lucy , Dipper Lucy
Published: March 2018

Background

This study explores the psychometric properties of The Scenario Test UK, a culturally adapted version of the Dutch original (The Scenario Test) developed by van der Meulen et al. in 2010, which evaluates functional, daily‐life communication in aphasia. The Scenario Test assesses communication in an interactive context with a supportive communication partner.

Aims

To evaluate the reliability (internal consistency, interrater and test–retest reliability) and construct validity (convergent, discriminant and known‐groups validity) of The Scenario Test UK.

Methods & Procedures

The Scenario Test UK and other language, cognition and praxis assessments were administered to persons with aphasia after stroke (3+ months post‐stroke) and to non‐aphasic controls. Participants were recruited primarily through community stroke groups. Measures were completed in an interview format. Standard psychometric criteria were used to evaluate reliability and construct validity.

Outcomes & Results

A total of 74 participants with aphasia and 20 participants without aphasia took part in The Scenario Test UK. The test showed high levels of reliability. Internal consistency (Cronbach's α = 0.92), interrater reliability (ICC = 0.95) and test–retest reliability (ICC = 0.96) were excellent. Interrater agreement in scores on the individual items ranged from good to excellent (κ = 0.41–1.00) for all but two items (item 4c κ = 0.38, item 6c κ = 0.36). The test demonstrated good levels of convergent (ρ = 0.37–0.75) and discriminant validity (ρ = –0.04 to 0.23). There was strong evidence for known groups validity (U = 132.50, p < .001), with those with aphasia scoring significantly lower [median (interquartile range—IQR) = 47 (39.8–51.0)] than those without aphasia [53 (52–54)].

Conclusions & Implications

The data support the reliability and validity of the Scenario Test UK as an assessment of functional, daily‐life communication for persons with aphasia. Further testing is needed in independent samples on the measure's psychometric properties, including its sensitivity to change. Pending this testing, The test can be used as an assessment tool to evaluate communication skills with people with aphasia, to guide goal setting for therapy and to measure outcomes in response to therapy.