bluuebunny/crossref_metadata_2025 huggingface dataset:
Real-time DNA barcoding in a remote rainforest using nanopore sequencing
Authors: Pomerantz Aaron , Peñafiel Nicolás , Arteaga Alejandro , Bustamante Lucas , Pichardo Frank , Coloma Luis A. , Barrio-Amorós César L. , Salazar-Valenzuela David , Prost Stefan
Published: September 2017

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility forin situmolecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the world’s most imperiled biodiversity hotspots: the Ecuadorian Chocó rainforest. We utilized portable equipment, including the MinION DNA sequencer (Oxford Nanopore Technologies) and miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcode sequencing of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnológica Indoamérica in Quito for the recently re-discovered Jambato toadAtelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snakeTrilepida guayaquilensis, and two undescribed species ofDipsassnakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts.
fingertipsR: an R package for accessing population health information in England
Authors: Fox Sebastian , Flowers Julian , Thelwall Simon , Flint Daniel , Hain Doris
Published: September 2017

Fingertips is a major public repository of population and public health indicators for England, built and maintained by Public Health England (PHE). The indicators are arranged in thematic or topical profiles covering a wide range of health issues including:

broad Health Profiles

specific topics such as liver disease and end of life

risk factors including alcohol, smoking, physical activity

population healthcare health services data for general practices, cancer, mental health

health protection data on general health protection, TB, antimicrobial resistance

lifecourse profiles for younger and older people

mortality and morbidity.

Fingertips makes data available for more than 1,500 indicators spread across more than 70 profiles. The data can be accessed fromhttps://fingertips.phe.org.ukwhere the data are visualised in variety of ways including heatmaps, choropleth maps, line charts for trends, “spine” charts (graphs which compare multiple indicators for a single geographic area), scatter plots and so on. Data can be obtained as downloads or figures which can be exported or cut and paste into reports and slides.

A recent addition to the Fingertips platform was an Automated Programming Interface (API) to enable developers to re-use the data. To facilitate access to Fingertips data we have designed anRpackage -fingertipsR- enabling rapid and easy access to the data by analysts and data scientists. The package is available from the Comprehensive R Archive Network (CRAN).

This paper describes thefingertipsRpackage which provides tools accessing a wide range of public health data for England from the Fingertips website using its API.
In silico mechanobiochemical modeling of morphogenesis in cell monolayers
Authors: Marzban Bahador , Ma Xiao , Qing Xiaoliang , Yuan Hongyan
Published: September 2017

Cell morphogenesis is a fundamental process involved in tissue formation. One of the challenges in the fabrication of living tissues in vitro is to recapitulate the complex morphologies of individual cells. Despite tremendous progress in understanding biophysical principles underlying tissue/organ morphogenesis at the organ level, little work has been done to understand morphogenesis at the cellular and microtissue level. In this work, we developed a 2D computational model for studying cell morphogenesis in monolayer tissues. The model is mainly composed of four modules: mechanics of cytoskeleton, cell motility, cell-substrate interaction, and cell-cell interaction. The model integrates the biochemical and mechanical activities within individual cells spatiotemporally. Finite element method (FEM) is used to model the irregular shapes of cells and to solve the resulting system of reaction-diffusion-stress equations. Automated mesh generation is used to handle the element distortion in FEM due to the large shape changes of the cells. The computer program can simulate tens to hundreds of cells interacting with each other and with the elastic substrate on desktop workstations efficiently. The simulations demonstrated that our computational model can be used to study cell polarization, single cell migration, durotaxis, and morphogenesis in cell monolayers.
Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision
Authors: Xu Yungang , Wang Yongcui , Luo Jiesi , Zhao Weiling , Zhou Xiaobo
Published: September 2017

Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network. With the advantages of epigenetic features, DeepCode significantly improves the performance in predicting the splicing patterns and their changes during hESC differentiation. Meanwhile, DeepCode reveals the superiority of epigenomic features and their dominant roles in decoding AS patterns, highlighting the necessity of including the epigenetic properties when assembling a more comprehensive splicing code. Moreover, DeepCode allows the robust predictions across cell lineages and datasets. Especially, we identified a putative H3K36me3-regulated AS event leading to a nonsense-mediated mRNA decay of BARD1. Reduced BARD1 expression results in the attenuation of ATM/ATR signalling activities and further the hESC differentiation. These results suggest a novel candidate mechanism linking histone modifications to hESC fate decision. In addition, when trained in different contexts, DeepCode can be expanded to a variety of biological and biomedical fields.
A novel mechanism for volitional locomotion in larval zebrafish
Authors: Ehrlich David E. , Schoppik David
Published: September 2017

To locomote stably, animals must coordinate volitional actions that change posture with opposing reflexes that hold posture constant [1–8]. These conflicting actions are thought to necessitate integrated control, in which reflexes are modulated to permit or even produce volitional movements [9–14]. Here we report that larval zebrafish (Danio rerio) utilize a simpler control scheme featuring independent volitional and reflexive movements. We present behavioral evidence that larvae swim in depth by appending destabilizing trunk rotations to steer with independent rotations to balance. When we manipulated buoyancy to deflect fish up or down, they redirected steering without coordinated changes to their balance reflex. As balance developed and increasingly opposed destabilization-mediated steering, larvae acquired compensatory use of their pectoral fins to steer. Removing the pectoral fins from older larvae impaired steering but preserved the strong balance reflex. Consequentially, older larvae without fins were strikingly less maneuverable — unable to revert to destabilization-mediated steering — revealing a rigidity inherent within the framework of independent volitional and reflexive control. Larval zebrafish therefore produce effective but inflexible locomotion by sequencing independent volitional and reflexive movements. These results reveal a simple control scheme, applicable for robotic design, that solves the general problem of coordinating volitional movements with the vital reflexes that oppose them.
Time-conditional properties of branches in coalescent gene trees
Authors: Platt Alexander
Published: September 2017

Coalescent gene trees have proven to be a powerful framework for formulating and solving problems in population genetics both in theory and practice. Using them, geneticists have been able to generate expectations for many attributes of a random sample of genotypes from a population given a model of the history of the population. This paper derives three new properties of coalescent gene trees that will help characterize the present-day impacts of historical events. Considering a single branch sampled at a given timetsin the past, it presents distributions describing 1) the length of time a branch sampledtsgenerations in the past had existed at the time of sampling, 2) the length of time that branch continues from timetstowards the present, and3) the the probability that the branch is ancestral toxindividuals in a modern sample.
Repeated performance in problem-solving tasks attenuates human cortical responses
Authors: Meshulam Meir , Golan Tal , Harel Michal , Groppe David , Keller Corey J. , Mégevand Pierre , Mehta Ashesh , Malach Rafael
Published: September 2017

A ubiquitous characteristic of human cortical networks is their tendency to rapidly change their response properties upon repetition. While this phenomenon has been amply documented using simple sensory-motor tasks, it is still unclear to what extent brain activations change on a short time scale when we are engaged in high level, complex tasks. Here, we examined this question using three types of high-level visual problems. We analyzed data from intracranial recordings performed in eight patients, focusing on the location and type of changes and on their relationship to overt behavior. Our results show significant repetition effects, manifested as signal decrease with repetition, in three different groups of electrodes:Visualsites, which increased their activity during stimuli presentation;Processing Positivesites, which demonstrated increased activity throughout the experimental trial; andProcessing Negativesites, which demonstrated suppression of activity during the trial as compared to baseline. Interestingly, despite these significant repetition effects, response time remained unchanged with repetition. These findings bear directly upon our ability to interpret results aggregated across multiple repetitions of the same complex task.
Telomere repeats induce domains of H3K27 methylation in Neurospora
Authors: Jamieson Kirsty , McNaught Kevin J. , Ormsby Tereza , Leggett Neena A. , Honda Shinji , Selker Eric U.
Published: September 2017

Development in higher organisms requires selective gene silencing, directed in part by di-/tri-methylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungusNeurospora crassato elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (∼225 kb) of H3K27me2/3. This provides an example of acis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.
A globalBrassicapest and a sympatric cryptic ally,Plutella australiana(Lepidoptera: Plutellidae), show strong divergence despite the capacity to hybridize
Authors: Perry Kym D. , Baker Gregory J. , Powis Kevin J. , Kent Joanne K. , Ward Christopher M. , Baxter Simon W.
Published: September 2017

The diamondback moth,Plutella xylostella, has been intensively studied due to its ability to evolve insecticide resistance and status as the world’s most destructive pest of brassicaceous crops. The surprise discovery of a cryptic ally,Plutella australianaLandry & Hebert, with apparent endemism to Australia, immediately raised questions regarding the extent of ecological and genetic diversity between these two species, whether gene flow could occur, and ultimately if specific management was required. Here, we show that despite sympatric distributions and the capacity to hybridize in controlled laboratory experiments, striking differences in genetic and phenotypic traits exist that are consistent with contrasting colonization histories and reproductive isolation after secondary contact. Almost 1500Plutellaindividuals were collected from wild and cultivated brassicaceous plants at 75 locations throughout Australia.Plutella australianawas commonly found on allBrassicahost types sampled except commercial vegetables, which are routinely sprayed with insecticide. Bioassays using four commonly-used insecticides found thatP. australianawas 19-306 fold more susceptible thanP. xylostella. Genome-wide SNPs derived from RADseq revealed substantially higher levels of genetic diversity acrossP. australianacompared withP. xylostellanuclear genomes, yet both species showed limited variation in mtDNA. Infection with a singleWolbachiasubgroup B strain was fixed inP. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5 % ofP. xylostella. AlthoughP. australianais a potential pest of brassica crops, it is of secondary importance toP. xylostella.
Assessing the virulence ofCryptococcus neoformanscausing meningitis in HIV infected and uninfected patients in Vietnam
Authors: Thanh Lam Tuan , Toffaletti Dena L. , Tenor Jennifer L. , Giamberardino Charles , Sempowski Gregory D. , Asfaw Yohannes , Phan Hai Trieu , Van Duong Anh , Nguyen Trinh Mai , Thwaites Guy E. , Ashton Philip M. , Van Vinh Nguyen Chau , Baker Stephen G. , Perfect John R. , Day Jeremy N.
Published: September 2017

We previously observed a substantial burden of cryptococcal meningitis in Vietnam atypically arising in HIV-uninfected individuals. This disease was associated with a single genotype ofCryptococcus neoformans(Sequence Type (ST)5), which was significantly less common in HIV-infected individuals. Aiming to compare the phenotypic characteristics of ST5 and non-ST5 C. neoformans we selected 30 representative Vietnamese isolates, compared theirin vitropathogenic potential andin vivovirulence. ST5 and non-ST5 organisms exhibited comparable characteristics with respect toin vitrovirulence markers including melanin production, replication at 37°C, and growth in cerebrospinal fluid. However, the ST5 isolates had significantly increased variability in cellular and capsular sizing compared with non-ST5 organisms (p<0.001). Counter-intuitively, mice infected with ST5 isolates had significantly longer survival with lower fungal burdens at day 7 than non-ST5 isolates. Notably, ST5 isolates induced significantly greater initial inflammatory responses than non-ST5 strains, measured by TNF-α concentrations (p<0.001). Despite being generally less virulent in the mouse model, we hypothesize that the significant within strain variation seen in ST5 isolates in the tested phenotypes may represent an evolutionary advantage enabling adaptation to novel niches including apparently immunocompetent human hosts.
Attentional fluctuations induce shared variability in macaque primary visual cortex
Authors: Denfield George H. , Ecker Alexander S. , Shinn Tori J. , Bethge Matthias , Tolias Andreas S.
Published: September 2017

Variability in neuronal responses to identical stimuli is frequently correlated across a population. Attention is thought to reduce these correlations by suppressing noisy inputs shared by the population. However, even with precise control of the visual stimulus, the subject’s attentional state varies across trials. While these state fluctuations are bound to induce some degree of correlated variability, it is currently unknown how strong their effect is, as previous studies generally do not dissociate changes in attentional strength from changes in attentional state variability. We designed a novel paradigm that does so and find both a pronounced effect of attentional fluctuations on correlated variability at long timescales and attention-dependent reductions in correlations at short timescales. These effects predominate in layers 2/3, as expected from a feedback signal such as attention. Thus, significant portions of correlated variability can be attributed to fluctuations in internally generated signals, like attention, rather than noise.
Atomic structure of the mitochondrial inner membrane AAA+ protease YME1 reveals the mechanism of substrate processing
Authors: Puchades Cristina , Rampello Anthony J. , Shin Mia , Giuliano Christopher J. , Wiseman R. Luke , Glynn Steven E. , Lander Gabriel C.
Published: September 2017

We present the first atomic model of a substrate-bound inner mitochondrial membrane AAA+ quality control protease, YME1. Our ~3.4 Å cryo-EM structure reveals how the ATPases form a closed spiral staircase encircling an unfolded substrate, directing it toward the flat, symmetric protease ring. Importantly, the structure reveals how three coexisting nucleotide states allosterically induce distinct positioning of tyrosines in the central channel, resulting in substrate engagement and translocation to the negatively charged proteolytic chamber. This tight coordination by a network of conserved residues defines a sequential, around-the-ring ATP hydrolysis cycle that results in step-wise substrate translocation. Furthermore, we identify a hinge-like linker that accommodates the large-scale nucleotide-driven motions of the ATPase spiral independently of the contiguous planar proteolytic base. These results define the first molecular mechanism for a mitochondrial inner membrane AAA+ protease and reveal a translocation mechanism likely conserved for other AAA+ ATPases.
SCGN Administration prevents Insulin Resistance and Diabetic Complications in High-Fat Diet Fed Animals
Authors: Sharma Anand Kumar , Khandelwal Radhika , Chadalawada Swathi , Ram N Sai , Raj T Avinash , Mahesh Kumar M Jerald , Sharma Yogendra
Published: September 2017

Secretagogin (SCGN) is poorly-studied secretory/cytosolic CaBP enriched in pancreaticβ-cells. Recent studies implicated SCGN in diabetes; however, its function and therapeutic prospect remain uncharted. Based on the apparent synchrony of SCGN and insulin secretion (and its disruption in HFD-fed animals) and consideringSCGNdownregulation in Type 2 diabetes, we hypothesized that SCGN is a key regulator of insulin response. To test this, we administered rSCGN to HFD-fed animals. We here report that a novel SCGN-insulin interaction stabilizes insulin and potentiates insulin action. Moreover, a chronic rSCGN administration improves insulin response and alleviates obesity associated risk factors such as weight gain, liver steatosis and cholesterol imbalance in DIO animals. Beside the anti-diabetic effects, prolonged rSCGN treatment also induces β-cell regeneration. These effects seem to originate from SCGN mediated regulation of insulin concentration & function as validated in insulin-deficient STZ animals. Our results demonstrate the prospects of the therapeutic potential of SCGN against diabetes.
Genome-wide Variants of Eurasian Facial Shape Differentiation and a prospective model of DNA based Face Prediction
Authors: Qiao Lu , Yang Yajun , Fu Pengcheng , Hu Sile , Zhou Hang , Peng Shouneng , Tan Jingze , Lu Yan , Lou Haiyi , Lu Dongsheng , Wu Sijie , Guo Jing , Jin Li , Guan Yaqun , Wang Sijia , Xu Shuhua , Tang Kun
Published: September 2017

It is a long standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics. Genome-wide association analyses were conducted on a discovery panel of Uyghurs. Six significant loci were identified four of which, rs1868752, rs118078182, rs60159418 at or near UBASH3B, COL23A1, PCDH7 and rs17868256 were replicated in independent cohorts of Uyghurs or Southern Han Chinese. A prospective model was also developed to predict 3D faces based on top GWAS signals, and tested in hypothetic forensic scenarios.
The Early Diagnosis in Lung Cancer by the Detection of Circulating Tumor DNA
Authors: Tian Geng , Li Xiaohua , Xie Yuancai , Xu Feiyue , Yu Dan , Cao Fengjun , Wang Xuanbin , Yu Fenglei , Zhong Weiquan , Lu Shixin , Tu Xiaonian , Yao Xumei , He Jiankui , Liu Chaoyu
Published: September 2017

Background

Remarkable advances for clinical diagnosis and treatment in cancers including lung cancer involve cell-free circulating tumor DNA (ctDNA) detection through next generation sequencing. However, before the sensitivity and specificity of ctDNA detection can be widely recognized, the consistency of mutations in tumor tissue and ctDNA should be evaluated. The urgency of this consistency is extremely obvious in lung cancer to which great attention has been paid to in liquid biopsy field.

Methods

We have developed an approach named systematic error correction sequencing (Sec-Seq) to improve the evaluation of sequence alterations in circulating cell-free DNA. Averagely 10 ml preoperative blood samples were collected from 30 patients containing pulmonary space occupying pathological changes by traditional clinic diagnosis. cfDNA from plasma, genomic DNA from white blood cells, and genomic DNA from solid tumor of above patients were extracted and constructed as libraries for each sample before subjected to sequencing by a panel contains 50 cancer-associated genes encompassing 29 kb by custom probe hybridization capture with average depth >40000, 7000, or 6300 folds respectively.

Results

Detection limit for mutant allele frequency in our study was 0.1%. The sequencing results were analyzed by bioinformatic expertise based on our previous studies on the baseline mutation profiling of circulating cell-free DNA and the clinicopathological data of these patients. Among all the lung cancer patients, 78% patients were predicted as positive by ctDNA sequencing when the shreshold was defined as at least one of the hotspot mutations detected in the blood (ctDNA) was also detected in tumor tissue. Pneumonia and pulmonary tuberculosis were detected as negative according to the above standard. When evaluating all hotspots in driver genes in the panel, 24% mutations detected in tumor tissue (tDNA) were also detected in patients blood (ctDNA). When evaluating all genetic variations in the panel, including all the driver genes and passenger genes, 28% detected in tumor tissue (tDNA) were also detected in patients blood (ctDNA). Positive detection rates of plasma ctDNA in stage I lung cancer patients is 85%, compared with 17% of tumor biomarkers.

Conclusion

We demonstrated the importance of sequencing both circulating cell-free DNA and genomic DNA in tumor tissue for ctDNA detection in lung cancer currently. We also determined and confirmed the consistency of ctDNA and tumor tissue through NGS according to the criteria explored in our studies. Our strategy can initially distinguish the lung cancer from benign lesions of lung. Our work shows that the consistency will be benefited from the optimization in sensitivity and specificity in ctDNA detection.
PartsGenie: an integrated tool for optimising and sharing synthetic biology parts
Authors: Swainston Neil , Dunstan Mark , Jervis Adrian J. , Robinson Christopher J. , Carbonell Pablo , Williams Alan R. , Faulon Jean-Loup , Scrutton Nigel S. , Kell Douglas B.
Published: September 2017

Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. While repositories of such parts exist to promote their reuse, there is still a need to design novel parts from scratch.

PartsGenie, freely available athttp://parts.synbiochem.co.uk, is introduced to facilitate the computational design of such synthetic biology parts. PartsGenie has been designed to bridge the gap between optimisation tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language (SBOL), and their sharing in journal-recommended data repositories.

Consisting of a drag-and-drop web interface, a number of DNA optimisation algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimisation and dissemination of reusable synthetic biology parts through a single, integrated application. PartsGenie can therefore be used as a single, stand-alone tool, or integrated into larger synthetic biology pipelines that are being developed in the SYNBIOCHEM centre and elsewhere.
Spatial cytoskeleton organization supports targeted intracellular transport
Authors: Hafner Anne E. , Rieger Heiko
Published: September 2017

The efficiency of intracellular cargo transport from specific source to target locations is strongly dependent upon molecular motor-assisted motion along the cytoskeleton. Radial transport along microtubules and lateral transport along the filaments of the actin cortex underneath the cell membrane are characteristic for cells with a centrosome. The interplay between the specific cytoskeleton organization and the motor performance realizes a spatially inhomogeneous intermittent search strategy. In order to analyze the efficiency of such intracellular search strategies we formulate a random velocity model with intermittent arrest states. We evaluate efficiency in terms of mean first passage times for three different, frequently encountered intracellular transport tasks: i) the narrow escape problem, which emerges during cargo transport to a synapse or other specific region of the cell membrane, ii) the reaction problem, which considers the binding time of two particles within the cell, and iii) the reaction-escape problem, which arises when cargo must be released at a synapse only after pairing with another particle. Our results indicate that cells are able to realize efficient search strategies for various intracellular transport tasks economically through a spatial cytoskeleton organization that involves only a narrow actin cortex rather than a cell body filled with randomly oriented actin filaments.
Sensory noise increases metacognitive efficiency
Authors: Bang Ji Won , Shekhar Medha , Rahnev Dobromir
Published: September 2017

Visual metacognition is the ability to employ confidence ratings in order to predict the accuracy of ones decisions about visual stimuli. Despite years of research, it is still unclear how visual metacognitive efficiency can be manipulated. Here we show that a hierarchical model of confidence generation makes a counterintuitive prediction: Higher sensory noise should increase metacognitive efficiency. The reason is that sensory noise has a large negative influence on the decision (where it is the only corrupting influence) but a smaller negative influence on confidence (where it is one of two corrupting influences; the other one being metacognitive noise). To test this prediction, we used a perceptual learning paradigm to decrease the amount of sensory noise. In Experiment 1, seven days of training led to significant decrease in noise as well as a corresponding decrease in metacognitive efficiency. Experiment 2 showed the same effect in a brief 97-trial learning for each of two different tasks. Finally, in Experiment 3, we experimentally manipulated stimulus contrast to increase sensory noise and observed a corresponding increase in metacognitive efficiency. Our findings demonstrate the existence of a robust positive relationship between sensory noise and metacognitive efficiency. These results could not be captured by a standard model in which decision and confidence judgments are made based on the same underlying information. Thus, our study provides a novel way to directly manipulate metacognitive efficiency and suggests the existence of metacognitive noise that corrupts confidence but not the perceptual decision.
Pre-post synaptic alignment through neuroligin tunes synaptic transmission efficiency
Authors: Haas Kalina T. , Compans Benjamin , Letellier Mathieu , Bartol Thomas M , Grillo-Bosch Dolors , Sejnowski Terrence J , Sainlos Matthieu , Choquet Daniel , Thoumine Olivier , Hosy Eric
Published: September 2017

The nanoscale organization of neurotransmitter receptors relative to pre-synaptic release sites is a fundamental determinant of both the amplitude and reliability of synaptic transmission. How modifications in the alignment between pre- and post-synaptic machineries affect synaptic current properties has only been addressed with computer modeling, and therefore remains hypothetical. Using dual-color single molecule based super-resolution microscopy, we found a strong spatial correlation between AMPA receptor (AMPAR) nanodomains and the post-synaptic adhesion protein neuroligin-1 (NLG1). Expression of a C-terminal truncated form of NLG1 disrupted this correlation without affecting the intrinsic organization of AMPAR nanodomains. Moreover, this NLG1 dominant-negative mutant significantly shifted the pre-synaptic release machinery from AMPAR synaptic clusters. Electrophysiology and computer modeling show that this physical shift is sufficient to induce a significant decrease in synaptic transmission. Thus, our results suggest the necessity for synapses to release glutamate in front of AMPAR nanodomains, to maintain a high efficiency of synaptic responses.
redkmer: an assembly-free pipeline for the identification of abundant and specific X-chromosome target sequences for X-shredding by CRISPR endonucleases
Authors: Papathanos Philippos Aris , Windbichler Nikolai
Published: September 2017

CRISPR-based synthetic sex ratio distorters, that operate by shredding the X-chromosome during male meiosis, are promising tools for the area-wide control of harmful insect pest or disease vector species. However, the selection of gRNA targets, in the form of high-copy sequence repeats on the X chromosome of a given species, is difficult since such repeats are not accurately resolved in genome assemblies and can’t be assigned to chromosomes with confidence. We have therefore developed the redkmer computational pipeline, designed to identify short and highly-abundant sequence elements occurring uniquely on the X-chromosome. Redkmer was designed to use as input exclusively raw WGS data from males and females. We tested redkmer with suitable short and long read WGS data ofAn. gambiae, the major vector of human malaria, in which the X-shredding paradigm was originally developed. Redkmer establishes long reads as chromosomal proxies with excellent correlation to the genome assembly and uses them to rank X-candidate kmers for their level of X-specificity and abundance. Redkmer identified a high-confidence set of 25-mers, many of which belong to previously known X-chromosome specific repeats ofAn. gambiae, including the ribosomal gene array and the selfish genetics elements harbored within it. WGS data from a control strain in which these repeats are also present on the Y chromosome confirmed the elimination of these kmers in the filtering steps. Finally, we show that redkmer output can be linked directly to gRNA selection and can also inform gRNA off-target prediction. The redkmer pipeline is designed to enable the generation of synthetic sex ratio distorters for the control of harmful insect species of medical or agricultural importance. It proceeds from WGS input data to deliver candidate X-specific CRISPR gRNA candidate target sequences. In addition the output of redkmer, including the prediction of chromosomal origin of single-molecule long reads and chromosome specific kmers, could also be used for the characterization of other biologically relevant sex chromosome sequences, a task that is frequently hampered by the repetitiveness of sex chromosome sequence content.
plot2DO: a tool to assess the quality and distribution of genomic data
Authors: Chereji Răzvan V.
Published: September 2017

Micrococcal nuclease digestion followed by deep sequencing (MNase-seq) is the most used method to investigate nucleosome organization on a genome-wide scale. We presentplot2DO, a software package for creating 2D occupancy plots, which allows biologists to evaluate the quality of MNase-seq data and to visualize the distribution of nucleosomes near the functional regions of the genome (e.g. gene promoters, origins of replication, etc.).

Availability And Implementation

Theplot2DOopen source package is freely available on GitHub athttps://github.com/rchereji/plot2DOunder the MIT license.

Contact

razvan.chereji@nih.gov

Supplementary Information

Supplementary data are available atBioinformaticsonline.
CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
Authors: Aughey Gabriel N. , Estacio Gomez Alicia , Thomson Jamie , Yin Hang , Southall Tony D.
Published: September 2017

Regulation of eukaryotic gene expression is coordinated by dynamic changes to chromatin states throughout development. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst the chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic stem cell lineages are not well defined. Here we show that tissue specific chromatin accessibility data can be produced via ectopic expression ofE. coliDam methylasein vivo, without the requirement for cell-sorting. We have profiled chromatin accessibility in individual cell types of theDrosophilaneural and midgut stem cell lineages. Functional cell-type specific enhancers were identified, as well as novel motifs enriched at diferent stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their diferentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell diferentiation and provide a novel approach to understanding the gene regulatory mechanisms underlying development.
The brain compass: a perspective on how self-motion updates the head direction cell attractor
Authors: Laurens Jean , Angelaki Dora E.
Published: September 2017

Head Direction cells form an internal compass that signals head azimuth orientation even in the absence of visual landmarks. It is well accepted that head direction properties are generated through a ring attractor that is updated using rotation self-motion cues. The properties and origin of this self-motion velocity drive remain, however, unknown. We propose a unified, quantitative framework whereby the attractor velocity input represents a multisensory self-motion estimate computed through an internal model that uses sensory prediction error based on vestibular, visual, and somatosensory cues to improve on-line motor drive. We show how context-dependent strength of recurrent connections within the attractor itself, rather than the self-motion input, explain differences in head direction cell firing between free foraging and restrained movements. We also summarize recent findings on how head tilt relative to gravity influences the azimuth coding of head direction cells, and explain why and how these effects reflect an updating self-motion velocity drive that is not purely egocentric. Finally, we highlight recent findings that the internal compass may be three-dimensional and hypothesize that the additional vertical degrees of freedom are defined based on global allocentric gravity cues.
The separation of auditory experience and the temporal structure of MEG recorded brain activity
Authors: Allen Chris
Published: September 2017

Do brain oscillations limit the temporal dynamics of experience? This pre-registered study used the separation of auditory stimuli to track perceptual experience and related this to oscillatory activity using magnetoencephalography. The rates at which auditory stimuli could be individuated matched the rates of oscillatory brain activity. Stimuli also entrained brain activity at the frequencies at which they were presented and a progression of high frequency gamma band events appeared to predict successful separation. These findings support a generalised function for brain oscillations, across frequency bands, in the alignment of activity to delineate representations.
Adaptive coding for dynamic sensory inference
Authors: Młynarski Wiktor , Hermundstad Ann M.
Published: September 2017

Behavior relies on the ability of sensory systems to infer properties of the environment from incoming stimuli. The accuracy of inference depends on the fidelity with which behaviorally-relevant properties of stimuli are encoded in neural responses. High-fidelity encodings can be metabolically costly, but low-fidelity encodings can cause errors in inference. Here, we discuss general principles that underlie the tradeoff between encoding cost and inference error. We then derive adaptive encoding schemes that dynamically navigate this tradeoff. These optimal encodings tend to increase the fidelity of the neural representation following a change in the stimulus distribution, and reduce fidelity for stimuli that originate from a known distribution. We predict dynamical signatures of such encoding schemes and demonstrate how known phenomena, such as burst coding and firing rate adaptation, can be understood as hallmarks of optimal coding for accurate inference.
Failure to reactivate salient episodic information during indirect and direct tests of memory retrieval
Authors: Price Mason H. , Johnson Jeffrey D.
Published: September 2017

Several fMRI and EEG studies have demonstrated that successful episodic retrieval is accompanied by the reactivation of cortical regions that were active during encoding. These findings are consistent with influential models of episodic memory that posit that conscious retrieval (recollection) relies on hippocampally-mediated cortical reinstatement. Evidence of reactivation corresponding to episodic information that is beyond conscious awareness at the time of memory retrieval, however, is limited. A recent exception is from an EEG study by Wimber, Maaβ, Staudigl, Richardson-Klavehn, and Hanslmayr (2012) in which words were encoded in the context of highly salient visual flicker entrainment and then presented at retrieval in the absence of any flicker. In that study, coherent (phase-locked) neural activity was observed at the corresponding entrained frequencies during retrieval, consistent with the notion that encoding representations were reactivated. Given the important implications of unconscious reactivation to past findings and the modeling literature, the current study set out to provide a direct replication of the previous study. Additionally, an attempt was made to extend such findings to intentional retrieval by acquiring EEG while subjects were explicitly asked to make memory judgments about the flicker frequency from encoding. Throughout a comprehensive set of analyses, the current study consistently failed to demonstrate evidence for unconscious reactivation, and instead provided support that test items were indistinguishable according to their prior encoding context. The findings thus establish an important boundary condition for the involvement of cortical reinstatement in episodic memory.
Transcription factor co-binding patterns drive conserved regulatory outcomes
Authors: Diehl Adam G. , Boyle Alan P.
Published: September 2017

The mouse has been widely used as a model system in which to study human genetic mechanisms. However, part of the difficulty in translating findings from mouse is that, despite high levels of gene conservation, regulatory control networks between human and mouse have been extensively rewired. To understand common themes of regulatory control we look beyond physical sharing of regulatory sequence, where extensive turnover of individual transcription factor binding sites complicates cross-species prediction of specific functions, and instead look at conserved properties of the regulatory code itself. We define regulatory conservation in terms of a grammar with shared, species-specific, and tissue-specific segments, and show that this grammar is more predictive of shared chromatin states and gene expression profiles than shared occupancy alone. Furthermore, we demonstrate a marked enrichment of disease associated variation in conserved grammatical patterns. These findings offer new understanding of transcriptional regulatory mechanisms shared between human and mouse.
Biomarker evaluation of plasma microRNA-122, high-mobility group box-1 and keratin-18 in acute gallstone disease
Authors: Th’ng Francesca , Vliegenthart Bastiaan , Lea Jonathan D , Antoine Daniel J. , Dear James W , Mole Damian J.
Published: September 2017

Background

A biomarker that stratifies patients with complications of gallstone disease from the denominator pool of people with acute biliary-type symptoms is needed. Circulating microRNA-122 (miRNA-122), high-mobility group box1 (HMGB1), full-length keratin-18 (flk-18) and caspase-cleaved keratin-18 (cck-18) are established hepatocyte injury biomarkers. The aim of this study was to evaluate the discriminatory power of these biomarkers in plasma to identify potential biliary complications that may require acute intervention.

Method

An observational biomarker cohort study was carried out in a University teaching hospital for 12 months beginning 3rdSeptember 2014. Blood samples were collected from adults referred with acute biliary-type symptoms. miRNA-122 was measured by quantitative real-time polymerase chain reaction, and HMGB1, cck-18 and flk-18 by ELISA.

Results

300 patients were screened and 289 patients were included. Plasma miRNA-122, cck-18 and flk-18 concentrations were increased in patients with gallstones compared to those without (miRNA-122: median: 2.89 × 104copies/ml vs. 0.95 × 104copies/ml [P<0.001];cck-18:121.9 U/L vs. 104.6 U/L [P = 0.041];flk-18: 252.4 U/L vs. 151.8 U/L [P<0.001]). Uncomplicated gallstone disease was associated with higher miRNA-122 and cck-18 concentrations than complicated disease (miRNA-122: 5.72 × 104copies/ml vs. 2.26x104copies/ml [P=0.022];cck-18: 139.7 U/L vs. 111.4 U/L [P=0.049]). There was no significant difference in HMGB1 concentration between patients with and without gallstones [P=0.480]. Separation between groups for all biomarkers was modest.

Conclusion

microRNA-122 and keratin-18 plasma concentrations are elevated in patients with gallstones. However, these biomarkers were not sufficiently discriminatory to be progressed as clinically useful biomarkers in this context.
Invariant errors reveal limitations in motor correction rather than constraints on error sensitivity
Authors: Kim Hyosub E. , Morehead J. Ryan , Parvin Darius E. , Moazzezi Reza , Ivry Richard B.
Published: September 2017

Implicit sensorimotor adaptation is traditionally described as a process of error reduction, whereby a fraction of the error is corrected for with each movement. Here, in our study of healthy human participants, we characterize two constraints on this learning process: the size of adaptive corrections is only related to error size when errors are smaller than 6°, and learning functions converge to a similar level of asymptotic learning over a wide range of error sizes. These findings are problematic for current models of sensorimotor adaptation, and point to a new theoretical perspective in which learning is constrained by the size of the error correction, rather than sensitivity to error.
Dynamic changes in oligomeric complexes of UPR sensors induced by misfolded proteins in the ER
Authors: Sundaram Arunkumar , Appathurai Suhila , Mariappan Malaiyalam
Published: September 2017

The endoplasmic reticulum (ER) localized unfolded protein response (UPR) sensors, IRE1α, PERK, and ATF6α, are activated upon accumulation of misfolded proteins caused by ER stress. It is debated whether these UPR sensors are activated either by the release of their negative regulator BiP chaperone or directly binding to misfolded proteins during ER stress. Here we simultaneously examined oligomerization and activation of all three endogenous UPR sensors. We found that UPR sensors existed as preformed oligomers even in unstressed cells, which shifted to large oligomers for PERK and small oligomers for ATF6α, but little changed for IRE1α upon ER stress. Neither depletion nor overexpression of BiP had significant effects on oligomeric complexes of UPR sensors both in unstressed and stressed cells. Thus, our results find less evidence for the BiP-mediated activation of UPR sensors in mammalian cells and support that misfolded proteins bind and activate the preformed oligomers of UPR sensors.
ELMOD1 stimulates ARF6-GTP hydrolysis to stabilize apical structures in developing vestibular hair cells
Authors: Krey Jocelyn F. , Dumont Rachel A. , Wilmarth Philip A. , David Larry L. , Johnson Kenneth R. , Barr-Gillespie Peter G.
Published: September 2017

Sensory hair cells require control of physical properties of their apical plasma membranes for normal development and function. Members of the ARF small GTPase family regulate membrane trafficking and cytoskeletal assembly in many cells. We identified ELMOD1, a guanine nucleoside triphosphatase activating protein (GAP) for ARF6, as the most highly enriched ARF regulator in hair cells. To characterize ELMOD1 control of trafficking, we used a mouse strain lacking functional ELMOD1 (roundabout; rda). In rda/rda mice, cuticular plates of utricle hair cells initially formed normally, then degenerated after postnatal day 5 (P5); large numbers of vesicles invaded the compromised cuticular plate. Hair bundles initially developed normally, but the cell’s apical membrane lifted away from the cuticular plate, and stereocilia elongated and fused. Membrane trafficking in type I hair cells, measured by FM1-43 dye labeling, was altered in rda/rda mice. Consistent with the proposed GAP role for ELMOD1, the ARF6 GTP/GDP ratio was significantly elevated in rda/rda utricles as compared to controls, and the level of ARF6-GTP was correlated with the severity of the rda/rda phenotype. These results suggest that conversion of ARF6 to its GDP-bound form is necessary for final stabilization of the hair bundle.

Significance Statement

Assembly of the mechanically sensitive hair bundle of sensory hair cells requires growth and reorganization of apical actin and membrane structures. Hair bundles and apical membranes in mice with mutations in theElmod1gene degenerate after formation, suggesting that the ELMOD1 protein stabilizes these structures. We show that ELMOD1 is a GTPase-activating protein in hair cells for the small GTP-binding protein ARF6, known to participate in actin assembly and membrane trafficking. We propose that conversion of ARF6 into the GDP-bound form in the apical domain of hair cells is essential for stabilizing apical actin structures like the hair bundle and ensuring that the apical membrane forms appropriately around the stereocilia.