bluuebunny/crossref_metadata_2025 huggingface dataset:
Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection
Authors: Sanderson Nicholas D , Street Teresa L , Foster Dona , Swann Jeremy , Atkins Bridget L. , Brent Andrew J. , McNally Martin A. , Oakley Sarah , Taylor Adrian , Peto Tim E A , Crook Derrick , Eyre David W
Published: November 2017

Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq. Here, we compare direct-from-clinical-sample metagenomic Illumina sequencing with Nanopore sequencing, and report a real-time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections.

DNA was extracted from the sonication fluids of seven explanted orthopaedic devices, and additionally from two culture negative controls, and was sequenced on the Oxford Nanopore Technologies MinION platform. A specific analysis pipeline was assembled to overcome the challenges of identifying the true infecting pathogen, given high levels of host contamination and unavoidable background lab and kit contamination.

The majority of DNA classified (>90%) was host contamination and discarded. Using negative control filtering thresholds, the species identified corresponded with both routine microbiological diagnosis and MiSeq results. By analysing sequences in real time, causes of infection were robustly detected within minutes from initiation of sequencing.

We demonstrate initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data. The high proportion of human DNA in extracts prevents full genome analysis from complete coverage, and methods to reduce this could increase genome depth and allow antimicrobial resistance profiling.
Neurotransmitter imbalance in the brain and Alzheimer’s pathology
Authors: Snowden Stuart G. , Ebshiana Amera A. , Hye Abdul , Pletnikova Olga , O’Brien Richard , Yang An , Troncoso John , Legido-Quigley Cristina , Thambisetty Madhav
Published: November 2017

INTRODUCTION

Three of the four treatments for Alzheimer’s disease are cholinesterase inhibitors targeting the pathological reduction of acetylcholine levels. Here we aimed to determine the role of other neurotransmitter pathways in AD pathology.

METHODS

Tissue samples were obtained from three groups, controls, AD and ‘asymptomatic AD’ i.e. cognitively normal individuals that had significant AD neuropathology. Three brain areas were studied, the middle frontal gyrus (MFG) the inferior temporal gyrus (ITG) and the cerebellum.

RESULTS

11 of 15 measured metabolites were shown to be associated with disease. Decreases in dopamine were seen in the ASYMAD group in the MFG when compared to control and AD patients (FC=0.78, p=4.1×10-3). In AD patients changes were mainly seen in the ITG’s inhibitory GABAergic system.

DISCUSSION

These results indicate that dopamine could be depleted in brains with Alzheimer’s pathology but intact cognition, while and imbalance of several neurotransmitters is evident in the brain of AD patients.
Atypical domain communication and domain functions of a Hsp110 chaperone
Authors: Kumar Vignesh , Peter Joshua Jebakumar , Sagar Amin , Ray Arjun , Ashish  , mapa koyeli
Published: November 2017

Hsp110s are well recognized nucleotide exchange factors (NEFs) of Hsp70s, in addition they are implicated in various aspects of cellular proteostasis as discrete chaperones with yet enigmatic molecular mechanism. Stark similarity in domain organization and structure between Hsp110s and Hsp70s, is easily discernible although the nature of domain communication and domain functions of Hsp110s are still puzzling. Here, we report atypical domain communication of yeast Hsp110, Sse1 using single molecule FRET, small angle X-ray scattering measurements (SAXS) and Molecular Dynamic simulations. Our data show that Sse1 lacks typical domain movements as exhibited by Hsp70s, albeit it undergoes unique structural alteration upon nucleotide and substrate binding. Hsp70-like domain-movements can be artificially salvaged in chimeric constructs of Hsp110-Hsp70 although such salvaging proves detrimental for the NEF activity of the protein. Furthermore, we show that substrate binding domain (SBD) of Hsp110, chaperones self, as well as foreign nucleotide binding domains (NBD). Interestingly, the substrate binding specificity of Hsp110 is largely determined by its NBD rather than SBD, the latter being the foremost substrate binding region for Hsp70s.
Newly identified relatives of botulinum neurotoxins shed light on their molecular evolution
Authors: Mansfield MJ , Wentz TG , Zhang S , Lee EJ , Dong M , Sharma SK , Doxey AC
Published: November 2017

The evolution of bacterial toxins is a central question to understanding the origins of human pathogens and infectious disease. Through genomic data mining, we traced the evolution of the deadliest known toxin family, clostridial neurotoxins, comprised of tetanus and botulinum neurotoxins (BoNT). We identified numerous uncharacterized lineages of BoNT-related genes in environmental species outside ofClostridium, revealing insights into their molecular ancestry. Phylogenetic analysis pinpointed a sister lineage of BoNT-like toxins in the gram-negative organism,Chryseobacterium piperi, that exhibit distant homology at the sequence level but preserve overall domain architecture. Resequencing and assembly of theC. piperigenome confirmed the presence of BoNT-like proteins encoded within two toxin-rich gene clusters. AC. piperiBoNT-like protein was validated as a novel toxin that induced necrotic cell death in human kidney cells. Mutagenesis of the putative active site abolished toxicity and indicated a zinc metalloprotease-dependent mechanism. TheC. piperitoxin did not cleave common SNARE substrates of BoNTs, indicating that BoNTs have diverged from related families in substrate specificity. The new lineages of BoNT-like toxins identified by computational methods represent evolutionary missing links, and suggest an origin of clostridial neurotoxins from ancestral toxins present in environmental bacteria.

Significance statement

The origins of bacterial toxins that cause human disease is a key question in our understanding of pathogen evolution. To explore this question, we searched genomes for evolutionary relatives of the deadliest biological toxins known to science, botulinum neurotoxins. Genomic and phylogenetic analysis revealed a group of toxins in theChryseobacterium piperigenome that are a sister lineage to botulinum toxins. Genome sequencing of this organism confirmed the presence of toxin-rich gene clusters, and a predictedC. piperitoxin was shown to induce necrotic cell death in human cells. These newly predicted toxins are missing links in our understanding of botulinum neurotoxin evolution, revealing its origins from an ancestral family of toxins that may be widespread in the environment.
Ethology as a physical science
Authors: Brown André EX , de Bivort Benjamin
Published: November 2017

Behaviour is the ultimate output of an animal’s nervous system and choosing the right action at the right time can be critical for survival. The study of the organisation of behaviour in its natural context, ethology, has historically been a primarily qualitative science. A quantitative theory of behaviour would advance research in neuroscience as well as ecology and evolution. However, animal posture typically has many degrees of freedom and behavioural dynamics vary on timescales ranging from milliseconds to years, presenting both technical and conceptual challenges. Here we review 1) advances in imaging and computer vision that are making it possible to capture increasingly complete records of animal motion and 2) new approaches to understanding the resulting behavioural data sets. With the right analytical approaches, these data are allowing researchers to revisit longstanding questions about the structure and organisation of animal behaviour and to put unifying principles on a quantitative footing. Contributions from both experimentalists and theorists are leading to the emergence of a physics of behaviour and the prospect of discovering laws and developing theories with broad applicability. We believe that there now exists an opportunity to develop theories of behaviour which can be tested using these data sets leading to a deeper understanding of how and why animals behave.
Efficient online-group-screening designs for agent identification
Authors: Gao Tianxiang , Finkel Omri , Dangl Jeff , Jojic Vladimir
Published: November 2017

Identifying significant causal agents among a large number of candidates is challenging. When experimental resources are limited, exhaustively screening a large number of agents for the desired effect could incur a large cost and take a substantial amount of time. However, in many large scale experiments, such as high-throughput screening (HTS), the ratio of causal to non-causal agents is usually very low.

In this paper, we introduce a group-screening strategy to efficiently screen causal agents by grouping them into treatments. Our analysis shows that when a large number of candidates factors are screened and true agent percentage is very low (less than 1%), even in the worst case we could save up to 80% of the experiment runs. In the case where experiments span many rounds, we provide an online version of the group-screening that can determine the best strategy automatically based on the existing results. We applied this method to a real HTS experiment with 50,000 candidates that would require 9 rounds to finish in an exhaustive case. Our analysis showed that by applying the online-group-screening method, in the worst case, we can use 3 rounds and 19.7% (9828/50000) total tests to identify all the agents.

Finally, we show that with minor modifications, this framework extends to more complex agent discovery problems.
Fast ordered sampling of DNA sequence variants
Authors: Greenberg Anthony J.
Published: November 2017

Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme. I illustrate its utility by developing a method to quickly estimate genome-wide patterns of linkage disequilibrium (LD) decay with distance. I provide open-source software that samples loci from several variant format files, a separate program that performs LD decay estimates, and a C++ library that lets developers incorporate these methods into their own projects.
Gene buddies: Linked balanced polymorphisms reinforce each other even in the absence of epistasis
Authors: Tennessen Jacob A
Published: November 2017

The fates of genetic polymorphisms maintained by balancing selection depend on evolutionary dynamics at linked sites. While coevolution across linked, epigenetically-interacting loci has been extensively explored, such supergenes may be relatively rare. However, genes harboring adaptive variation can occur in close physical proximity while generating independent effects on fitness. Here, I present a model in which two linked loci without epistasis are both under balancing selection for unrelated reasons. Using forward-time simulations, I show that recombination rate strongly influences the retention of adaptive polymorphism, especially for intermediate selection coefficients. A locus is more likely to retain adaptive variation if it is closely linked to another locus under balancing selection, even if the two loci have no interaction. Thus, two linked polymorphisms can both be retained indefinitely even when they would both be lost to drift if unlinked. Such clusters of mutually reinforcing genes may underlie phenotypic variation in natural populations. Future studies that measure selection coefficients and recombination rates among closely linked genes will be fruitful for characterizing the extent of this phenomenon.
A Multilevel Computational Characterization of Endophenotypes in Addiction
Authors: Fiore Vincenzo G. , Ognibene Dimitri , Adinoff Bryon , Gu Xiaosi
Published: November 2017

Substance use disorders are characterized by a profound intersubject (phenotypic) variability in the expression of addictive symptomatology and propensity to relapse following treatment. However, laboratory investigations have primarily focused on common neural substrates in addiction, and have not yet been able to identify mechanisms that can account for the multifaceted phenotypic behaviors reported in literature. To investigate this knowledge gap theoretically, here we simulated phenotypic variations in addiction symptomology and responses to putative treatments, using both a neural model based on cortico-striatal circuit dynamics, and an algorithmic model of reinforcement learning. These simulations rely on the widely accepted assumption that both the ventral, model-based, goal-directed system and the dorsal, model-free, habitual system are vulnerable to extra-physiologic dopamine reinforcements triggered by drug consumption. We found that endophenotypic differences in the balance between the two circuit or control systems resulted in an inverted U-shape in optimal choice behavior. Specifically, greater unbalance led to a higher likelihood of developing addiction and more severe drug-taking behaviors. Furthermore, endophenotypes with opposite asymmetrical biases among cortico-striatal circuits expressed similar addiction behaviors, but responded differently to simulated treatments, suggesting personalized treatment development could rely on endophenotypic rather than phenotypic differentiations. We propose our simulated results, confirmed across neural and algorithmic levels of analysis, inform on a fundamental and, to date, neglected quantitative method to characterize clinical heterogeneity in addiction.
The global distribution and spread of the mobilized colistin resistance gene mcr-1
Authors: Wang Ruobing , van Dorp Lucy , Shaw Liam , Bradley Phelim , Wang Qi , Wang Xiaojuan , Jin Longyang , Zhang Qing , Liu Yuqing , Rieux Adrien , Dorai-Schneiders Thamarai , Weinert Lucy Anne , Iqbal Zamin , Didelot Xavier , Wang Hui , Balloux Francois
Published: November 2017

Colistin represents one of the very few available drugs for treating infections caused by carbapenem resistant Enterobacteriaceae (CRE). As such, the recent plasmid-mediated spread of the mobilized colistin resistance gene mcr-1 poses a significant public health threat requiring global monitoring and surveillance. In this work, we characterize the global distribution of mcr-1 using a dataset of 457 mcr-1 positive sequenced isolates consisting of currently publicly available mcr-1 carrying sequences combined with an additional 110 newly sequenced mcr-1 positive isolates from China. We find mcr-1 in a diversity of plasmid backgrounds but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002-2008; 95% higher posterior density), followed by a dramatic demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of mobile elements carrying antibiotic resistance genes across multiple levels of genomic organization.
Ecological Insights from the Evolutionary History of Microbial Innovations
Authors: Muscarella Mario E. , O’Dwyer James P.
Published: November 2017

Bacteria and Archaea represent the base of the evolutionary tree of life and contain the vast majority of phylogenetic and functional diversity. Because these organisms and their traits directly impact ecosystems and human health, a focus on functional traits has become increasingly common in microbial ecology. These trait-based approaches have the potential to link microbial communities and their ecological function. But an open question is how, why, and in what order microorganisms acquired the traits we observe in the present day. To address this, we reconstructed the evolutionary history of microbial traits using genomic data to understand the evolution, selective advantage, and similarity of traits in extant organisms and provide insights into the composition of genomes and communities. We used the geological timeline and physiological expectations to provide independent evidence in support of this evolutionary history. Using this reconstructed evolutionary history, we explored hypotheses related to the composition of genomes. We showed that gene transition rates can be used to make predictions about the size and type of genes in a genome: generalist genomes comprise many evolutionarily labile genes while specialist genomes comprise more highly conserved functional genes. These findings suggest that generalist organisms do not build up and hoard an array of functions, but rather tend to experiment with functions related to environmental sensing, transport, and complex resource degradation. Our results provide a framework for understanding the evolutionary history of extant microorganisms, the origin and maintenanceof traits, and linking evolutionary relatedness and ecological function.
Wide-field dynamic monitoring of immune cell trafficking in murine models of glioblastoma
Authors: SoRelle Elliott D. , Yecies Derek , Liba Orly , Bennett F. Chris , Graef Claus Moritz , Dutta Rebecca , Mitra Siddhartha S. , Joubert Lydia-Marie , Cheshier Samuel H. , Grant Gerald A. , de la Zerda Adam
Published: November 2017

Leukocyte populations, especially tumor-associated macrophages (TAMs), are capable of mediating both anti- and pro-tumor processes and play significant roles in the tumor microenvironment. Moreover, TAMs have been shown to exert substantial influence on the efficacy of various cancer immunotherapy treatment strategies. Laboratory investigation into the behavior of TAMs has been limited by a lack of methods capable of resolving thein vivodistribution and dynamics of this cell population across wide fields of view. Recent studies have employed magnetic resonance imaging and intravital microscopy in conjunction with nanoparticle labeling methods to detect TAMs and observe their responses to therapeutic agents. Here we describe a novel method to enable high-resolution, wide-field, longitudinal imaging of leukocytes based on contrast-enhanced Speckle-Modulating Optical Coherence Tomography (SM-OCT), which substantially reduces imaging noise. We were able to specifically label TAMs and activated microgliain vivowith large gold nanorod contrast agents (LGNRs) in an orthotopic murine glioblastoma model. After labeling, we demonstrated near real-time tracking of leukocyte migration and distribution within the tumors. The intrinsic resolution, imaging depth, and sensitivity of this method may facilitate detailed studies of the fundamental behaviors of TAMsin vivo, including their intratumoral distribution heterogeneity and the roles they play in modulating cancer proliferation. In future studies, the method described herein may also provide the necessary means to characterize TAM responses to immunotherapeutic regimens in a range of solid tumors.
Closed-loop feedback control for microfluidic systems through automated capacitive fluid height sensing
Authors: Soenksen L. R. , Kassis T. , Noh M. , Griffith L.G. , Trumper D.L.
Published: November 2017

Precise fluid height sensing in open-channel microfluidics has long been a desirable feature for a wide range of applications. However, performing accurate measurements of the fluid level in small-scale reservoirs (<1mL) has proven to be an elusive goal, especially if direct fluid-sensor contact needs to be avoided. In particular, gravity-driven systems used in several microfluidic applications to establish pressure gradients and impose flow remain open-loop and largely unmonitored due to these sensing limitations. Here we present an optimized self-shielded coplanar capacitive sensor design and automated control system to provide submillimeter fluid-height resolution (~250 μm) and control of small-scale open reservoirs without the need for direct fluid contact. Results from testing and validation of our optimized sensor and system also suggest that accurate fluid height information can be used to robustly characterize, calibrate and dynamically control a range of microfluidic systems with complex pumping mechanisms, even in cell culture conditions. Capacitive sensing technology provides a scalable and cost-effective way to enable continuous monitoring and closed-loop feedback control of fluid volumes in small-scale gravity-dominated wells in a variety of microfluidic applications.
HIV-1-induced cytokines deplete homeostatic ILCs and expand TCF7-dependent memory NK cells: Supplemental Figures and Tables
Authors: Wang Yetao , Gellatly Kyle , McCauley Sean , Vangala Pranitha , Kim Kyusik , Derr Alan , Jaiswal Smita , Kucukural Alper , McDonel Patrick , Lifshitz Lawrence , Greenough Thomas , Houghton JeanMarie , Garber Manuel , Luban Jeremy
Published: November 2017

HIV-1-infected people who take medications that suppress viremia, preserve CD4+ T cells, and prevent AIDS, have chronic inflammation with increased cardiovascular mortality. To investigate the etiology of this inflammation, the effect of HIV-1 on innate lymphoid cells (ILCs) and NK cells was examined. Homeostatic ILCs in blood and intestine were depleted permanently. NK cells were skewed towards a memory subset. Cytokines that are elevated during HIV-1 infection reproduced both abnormalities ex vivo. Pseudotime analysis of single NK cell transcriptomes revealed a developmental trajectory towards a subset with expression profile, chromatin state, and biological function like memory T lymphocytes. Expression of TCF7, a WNT transcription factor, increased over the course of the trajectory. TCF7 disruption, or WNT inhibition, prevented memory NK cell induction by inflammatory cytokines. These results demonstrate that inflammatory cytokines associated with HIV-1 infection irreversibly disrupt homeostatic ILCs and cause developmental shift towards TCF7+ memory NK cells.
Self-organised attractor dynamics in the developing head direction circuit
Authors: Bassett Joshua , Wills Tom , Cacucci Francesca
Published: November 2017

Head direction (HD) cells signal the orientation of an animal’s head relative to its environment. During post-natal development, HD cells are the earliest spatially modulated neurons in the hippocampal circuit to emerge. However, before eye-opening, HD cell responses in rat pups carry low directional information content and are directionally unstable. Using Bayesian decoding, we characterise this instability and identify its source: despite the directional signal being internally coherent, it consistently under-signals angular head velocity (AHV), incompletely shifting in proportion to head turns. We find evidence that geometric cues (corners) can be used to mitigate this under-signalling, and stabilise the directional signal even before eye-opening. Crucially, even when directional firing cannot be stabilised, ensembles of unstable HD cells show short-timescale (1-10 sec) temporal and spatial couplings consistent with an adult-like HD network, through which activity drifts unanchored to landmark cues. The existence of fixed spatial and temporal offsets across co-recorded cells and of an AHV-responsive signal, even before HD responses become spatially stable, suggests that the HD circuit is assembled through internal, self-organising processes, without reference to external landmarks. The HD network is widely modelled as a continuous attractor whose output is one coherent activity peak, updated during movement by angular head velocity (AHV) signals, and anchored by landmark cues. Our findings present strong evidence for this model, and demonstrate that the required network circuitry is in place and functional during development, independent of reference to landmark information.
Discovery of a new song mode in Drosophila reveals hidden structure in the sensory and neural drivers of behavior
Authors: Clemens Jan , Coen Philip , Roemschied Frederic A. , Pereira Talmo , Mazumder David , Pacheco Diego , Murthy Mala
Published: November 2017

Deciphering how brains generate behavior depends critically on an accurate description of behavior. If distinct behaviors are lumped together, separate modes of brain activity can be wrongly attributed to the same behavior. Alternatively, if a single behavior is split into two, the same neural activity can appear to produce different behaviors [1]. Here, we address this issue in the context of acoustic communication in Drosophila. During courtship, males utilize wing vibration to generate time-varying songs, and females evaluate songs to inform mating decisions [2-4]. Drosophila melanogaster song was thought for 50 years to consist of only two modes, sine and pulse, but using new unsupervised classification methods on large datasets of song recordings, we now establish the existence of at least three song modes: two distinct, evolutionary conserved pulse types, along with a single sine mode. We show how this seemingly subtle distinction profoundly affects our interpretation of the mechanisms underlying song production, perception and evolution. Specifically, we show that sensory feedback from the female influences the probability of producing each song mode and that male song mode choice affects female responses and contributes to modulating his song amplitude with distance [5]. At the neural level, we demonstrate how the activity of three separate neuron types within the fly’s song pathway differentially affect the probability of producing each song mode. Our results highlight the importance of carefully segmenting behavior to accurately map the underlying sensory, neural, and genetic mechanisms.
Reconstruction of resting-state networks from macaque electrocorticographic data
Authors: Hindriks R. , Micheli C. , Bosman C.A. , Oostenveld R. , Lewis C. , Mantini D. , Fries P. , Deco G.
Published: November 2017

The discovery of haemodynamic (BOLD-fMRI) resting-state networks (RSNs) has brought about a fundamental shift in our thinking about the role of intrinsic brain activity. The electrophysiological underpinnings of RSNs remain largely elusive and it has been shown only recently that electrophysiological cortical rhythms are organized into RSNs. Most electrophysiological studies into RSNs use magnetoencephalography (MEG) or electroencephalography (EEG), which limits the spatial scale on which RSNs can be investigated. Due to their close proximity to the cortical surface, electroencephalographic (ECoG) recordings can potentially provide a more detailed picture of the functional organization of resting-state cortical rhythms. In this study we propose using source-space independent component analysis for identifying generators of resting-state cortical rhythms as recorded with ECoG and reconstructing their network structure. Their network structure is characterized by two kinds of connectivity: instantaneous correlations between band-limited amplitude envelopes and oscillatory phase-locking. Using simulated data, we find that the reconstruction of oscillatory phase-locking is more challenging than that of amplitude correlations, particularly for low signal-to-noise levels. Specifically, phase-lags can both be over- and underestimated as a consequence of first-order and higher-order volume-conduction effects, which troubles the interpretation of interaction measures based on imaginary phase-locking or coherence. The methodology is applied to resting-state beta (15-30 Hz) rhythms within the motor system of a macaque monkey and leads to the identification of a functional network of seven cortical generators that are distributed across the sensorimotor system. The spatial extent of the identified generators, together with consistent phase-lags, suggests that these rhythms can be viewed as being spatially continuous with complex dynamics including traveling waves. Our findings illustrate the level of spatial detail attainable with source-projected ECoG and motivates wider use of the methodology for studying resting-state as well as event-related cortical dynamics in macaque and human.
Mechanical variations in proteins with large-scale motions highlight the formation of structural locks
Authors: Sacquin-Mora Sophie
Published: November 2017

Protein function depends just as much on flexibility as on structure, and in numerous cases, a protein’s biological activity involves transitions that will impact both its conformation and its mechanical properties. Here, we use a coarse-grain approach to investigate the impact of structural changes on protein flexibility. More particularly, we focus our study on proteins presenting large-scale motions. We show how calculating directional force constants within residue pairs, and investigating their variation upon protein closure, can lead to the detection of a limited set of residues that form astructural lockin the protein’s closed conformation. This lock, which is composed of residues whose side-chains are tightly interacting, highlights a new class of residues that are important for protein function by stabilizing the closed structure, and that cannot be detected using earlier tools like local rigidity profiles or distance variations maps, or alternative bioinformatics approaches, such as coevolution scores.
Significant abundance ofcisconfigurations of mutations in diploid human genomes
Authors: Hoehe Margret R. , Herwig Ralf , Mao Qing , Peters Brock A. , Drmanac Radoje , Church George M. , Huebsch Thomas
Published: November 2017

To fully understand human genetic variation, one must assess the specific distribution of variants between the two chromosomal homologues of genes, and any functional units of interest, as the phase of variants can significantly impact gene function and phenotype. To this end, we have systematically analyzed 18,121 autosomal protein-coding genes in 1,092 statistically phased genomes from the 1000 Genomes Project, and an unprecedented number of 184 experimentally phased genomes from the Personal Genome Project. Here we show that mutations predicted to functionally alter the protein, and coding variants as a whole, are not randomly distributed between the two homologues of a gene, but do occur significantly more frequently incis-thantrans-configurations, withcis/transratios of ∼60:40. Significantcis-abundance was observed in virtually all individual genomes in all populations. Nearly all variable genes exhibited eithercis, ortransconfigurations of protein-altering mutations in significant excess, allowing distinction ofcis- andtrans-abundant genes. These common patterns of phase were largely constituted by a shared, global set of phase-sensitive genes. We show significant enrichment of this global set with gene sets indicating its involvement in adaptation and evolution. Moreover,cis- andtrans-abundant genes were found functionally distinguishable, and exhibited strikingly different distributional patterns of protein-altering mutations. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their potential functional significance. Thus, it highlights the importance of phase for the interpretation of protein-coding genetic variation, challenging the current conceptual and functional interpretation of autosomal genes.
USP7 as part of non-canonical PRC1.1 is a druggable target in leukemia
Authors: Maat Henny , Jaques Jennifer , Rodríguez López Aida , Hogeling Shanna M. , Vries Marcel P. de , Gravesteijn Chantal , Brouwers-Vos Annet Z. , van der Meer Nisha , Huls Gerwin , Vellenga Edo , van den Boom Vincent , Schuringa Jan Jacob
Published: November 2017

Acute myeloid leukemia (AML) is a highly heterogeneous disease in which genetic and epigenetic changes disturb regulatory mechanisms controlling stem cell fate and maintenance. AML still remains difficult to treat, in particular in poor risk AML patients carrying TP53 mutations. Here, we identify the deubiquitinase USP7 as an integral member of non-canonical PRC1.1 and show that targeting of USP7 provides an alternative therapeutic approach for AML. USP7 inhibitors effectively induced apoptosis in (primary) AML cells, also independent of the USP7-MDM2-TP53 axis, whereby survival of both the cycling as well as quiescent populations was affected. MLL-AF9-induced leukemia was significantly delayed in vivo in human leukemia xenografts. We previously showed that non-canonical PRC1.1 is critically important for leukemic stem cell self-renewal, and that genetic knockdown of the PRC1.1 chromatin binding component KDM2B abrogated leukemia development in vitro and in vivo [1]. Here, by performing KDM2B interactome studies in TP53mut cells we identify that USP7 is an essential component of PRC1.1 and is required for its stability and function. USP7 inhibition results in disassembly of the PRC1.1 complex and consequently loss of binding to its target loci. Loss of PRC1.1 binding coincided with reduced H2AK119ub and H3K27ac levels and diminished gene transcription, whereas H3K4me3 levels remained unaffected. Our studies highlight the diverse functions of USP7 and link it to Polycomb-mediated epigenetic control. USP7 inhibition provides an efficient therapeutic approach for AML, also in the most aggressive subtypes with mutations in TP53.

Key points

USP7 is a therapeutic target in leukemia, including poor risk TP53mut AML.

USP7 is an essential component of non-canonical PRC1.1 and is required for its stability and function.
glactools: a command-line toolset for the management of genotype likelihoods and allele counts
Authors: Renaud Gabriel
Published: November 2017

Motivation

Research projects involving population genomics routinely need to store genotyping information, population allele frequencies, combine files from different samples, query the data and export it to various formats. This is often done using bespoke in-house scripts which cannot be easily adapted to new projects and seldom constitute reproducible workflows.

Results

We introduce glactools, a set of command-line utilities which can import data from genotypes or population-wide allele frequencies into an intermediate representation, compute various operations on it and export the data to several file formats used by population genetics software. This intermediate format can take 2 forms, one to store per-individual genotype likelihoods and a second for allele counts from one or more individuals. glactools allows users to perform operations such as intersecting datasets, merging individuals into populations, creating subsets, perform queries (e.g. return sites where a given population does not share an allele with a second one) and compute summary statistics to answer biologically relevant questions.

Availability

glactools is freely available for use under the GPL. It requires a C++ compiler and the htslib library. (https://grenaud.github.io/glactools/).

Contact

gabriel.reno@gmail.com

Supplementary information

Supplementary methods and results are available at Bioinformatics online.
Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD
Authors: Bernhardt Nathan A. , Hansmann Ulrich H.E.
Published: November 2017

Proteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.

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Selective attention modulates surface filling-in
Authors: Harrison William J. , Ayeni Alvin J. , Bex Peter J.
Published: November 2017

The visual system is required to compute objects from partial image structure so that figures can be segmented from their backgrounds. Although early clinical, behavioral, and modeling data suggested that such computations are performed pre-attentively, recent neurophysiological evidence suggests that surface filling-in is influenced by attention. In the present study we developed a variant of the classical Kanizsa illusory triangle to investigate whether voluntary attention modulates perceptual filling-in. Our figure consists of “pacmen” positioned at the tips of an illusory 6-point star and alternating in polarity such that two illusory triangles are implied to compete with one another within the figure. On each trial, observers were cued to attend to only one triangle, and then compared its lightness with a matching texture-defined triangle. We found that perceived lightness of the illusory shape depended on the polarity of pacmen framing the attended triangle, although the magnitude of this effect was weaker than when all inducers were of the same polarity. Our findings thus reveal that voluntary attention can influence lightness filling-in, and provide important data linking neurophysiological effects to phenomenology.
Deficiency of nucleotide excision repair explains mutational signature observed in cancer
Authors: Jager Myrthe , Blokzijl Francis , Kuijk Ewart , Bertl Johanna , Vougioukalaki Maria , Janssen Roel , Besselink Nicolle , Boymans Sander , Ligt Joep de , Pedersen Jakob Skou , Hoeijmakers Jan , Pothof Joris , Boxtel Ruben van , Cuppen Edwin
Published: November 2017

Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Tumors deficient in NER are more sensitive to cisplatin treatment. Characterization of the mutational consequences of NER-deficiency may therefore provide important diagnostic opportunities. Here, we analyzed the somatic mutational profiles of adult stem cells (ASCs) from NER-deficientErcc1-/Δmice, using whole-genome sequencing analysis of clonally derived organoid cultures. Our results indicate that NER-deficiency increases the base substitution load in liver, but not in small intestinal ASCs, which coincides with a tissue-specific aging-pathology observed in these mice. The mutational landscape changes as a result of NER-deficiency in ASCs of both tissues and shows an increased contribution of Signature 8 mutations, which is a pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the acquired base substitutions indicates that deficiency of global-genome NER (GG-NER) is responsible for the altered mutational landscape. In line with this, we observed increased Signature 8 mutations in a GG-NER-deficient human organoid culture in whichXPCwas deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations may therefore serve as a biomarker for NER-deficiency and could improve personalized cancer treatment strategies.
Stopping Transformed Growth with Cytoskeletal Proteins: Turning a Devil into an Angel
Authors: Yang Bo , Wolfenson Haguy , Nakazawa Naotaka , Liu Shuaimin , Hu Junqiang , Sheetz Michael P.
Published: November 2017

The major hallmark of cancer cells is uncontrollable growth on soft matrices (transformed growth), which indicates that they have lost the ability to properly sense the rigidity of their surroundings. Recent studies of fibroblasts show that local contractions by cytoskeletal rigidity sensor units block growth on soft surfaces and their depletion causes transformed growth. The contractile system involves many cytoskeletal proteins that must be correctly assembled for proper rigidity sensing. We tested the hypothesis that cancer cells lack rigidity sensing due to their inability to assemble contractile units because of altered cytoskeletal protein levels. In four widely different cancers, there were over ten-fold fewer rigidity-sensing contractions compared with normal fibroblasts. Restoring normal levels of cytoskeletal proteins restored rigidity sensing and rigidity-dependent growth in transformed cells. Most commonly, this involved restoring balanced levels of the tropomyosins 2.1 (often depleted by miR-21) and 3 (often overexpressed). Restored cells could be transformed again by depleting other cytoskeletal proteins including myosin IIA. Thus, the depletion of rigidity sensing modules enables growth on soft surfaces and many different perturbations of cytoskeletal proteins can disrupt rigidity sensing thereby causing transformed growth of cancer cells.
The evolution of social life in family groups
Authors: Kramer Jos , Meunier Joël
Published: November 2017

Family life forms an integral part of the life-history of species across the animal kingdom, and plays a crucial role in the evolution of animal sociality. Our current understanding of family life, however, is almost exclusively based on studies that (i) focus on parental care and associated family interactions (such as those arising from sibling rivalry and parent-offspring conflict), and (ii) investigate these phenomena in the advanced family systems of mammals, birds, and eusocial insects. Here, we argue that these historical biases have fostered the neglect of key processes shaping social life in ancestral family systems, and thus profoundly hamper our understanding of the (early) evolution of family life. Based on a comprehensive survey of the literature, we first illustrate that the strong focus on parental care in advanced social systems has deflected scrutiny of other important social processes such as sibling cooperation, parent-offspring competition and offspring assistance. We then show that accounting for these neglected processes – and their changing role in the course of evolution – could profoundly change our understanding of the evolutionary origin and subsequent consolidation of family life. Finally, we outline how this diachronic perspective on the evolution of family living could provide novel insights into general processes driving social evolution. Overall, we infer that the explicit consideration of thus far neglected facets of family life, together with their study across the whole diversity of family systems, are crucial to advance our understanding of the processes that shape the evolution of social life.
LRRTM1 underlies synaptic convergence in visual thalamus
Authors: Monavarfeshani Aboozar , Stanton Gail , Name Jonathan Van , Su Kaiwen , Mills William A. , Swilling Kenya , Kerr Alicia , Su Jianmin , Fox Michael A.
Published: November 2017

It has long been thought that the mammalian visual system is organized into parallel pathways, with incoming visual signals being parsed in the retina based on feature (e.g. color, contrast and motion) and then transmitted to the brain in unmixed, feature-specific channels. To faithfully convey feature-specific information from retina to cortex, thalamic relay cells must receive inputs from only a small number of functionally similar retinal ganglion cells. However, recent studies challenged this by revealing substantial levels of retinal convergence onto relay cells. Here, we sought to identify mechanisms responsible for the assembly of such convergence. Using an unbiased transcriptomics approach and targeted mutant mice, we discovered a critical role for the synaptic adhesion molecule Leucine Rich Repeat Transmembrane Neuronal 1 (LRRTM1) in the emergence of retinothalamic convergence. Importantly, LRRTM1 mutant mice display impairment in visual behaviors, suggesting a functional role of retinothalamic convergence in vision.
Motor selection dynamics in FEF explain the reaction time variance of saccades to single targets
Authors: Hauser Christopher K. , Zhu Dantong , Stanford Terrence R. , Salinas Emilio
Published: November 2017

In studies of voluntary movement, a most elemental quantity is the reaction time (RT) between the onset of a visual stimulus and a saccade toward it. However, this RT demonstrates extremely high variability, which in spite of extensive research remains unexplained. It is well established that, when a visual target appears, oculomotor activity gradually builds up until a critical level is reached, at which point a saccade is triggered. Here, we further characterize the dynamics of this rise-to-threshold process based on computational work and single-neuron recordings from the frontal eye field (FEF) of behaving monkeys. We find that the baseline activity, build-up rate, and threshold level show strong, nonlinear co-dependencies that explain the distinct RT distributions observed experimentally. The results indicate that intrinsic randomness contributes little to saccade variance, which results mainly from an intricate, fundamentally deterministic mechanism of motor conflict resolution that has subtle yet highly characteristic manifestations.
Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis
Authors: Fiddes Ian T , Lodewijk Gerrald A , Mooring Meghan , Bosworth Colleen M , Ewing Adam D , Mantalas Gary L , Novak Adam M , van den Bout Anouk , Bishara Alex , Rosenkrantz Jimi L , Lorig-Roach Ryan , Field Andrew R , Haeussler Maximillian , Russo Lotte , Bhaduri Aparna , Nowakowski Tomasz J. , Pollen Alex A. , Dougherty Max L. , Nuttle Xander , Addor Marie-Claude , Zwolinski Simon , Katzman Sol , Kreigstein Arnold , Eichler Evan E. , Salama Sofie R , Jacobs Frank MJ , Haussler David
Published: November 2017

Genetic changes causing dramatic brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and a determinant of neuronal number in the mammalian cortex. We find three paralogs of human-specific NOTCH2NL are highly expressed in radial glia cells. Functional analysis reveals different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation. NOTCH2NL genes provide the breakpoints in typical cases of 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism, and deletions with microcephaly and schizophrenia. Thus, the emergence of hominin-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger hominin neocortex accompanied by loss of genomic stability at the 1q21. 1 locus and a resulting recurrent neurodevelopmental disorder.