bluuebunny/crossref_metadata_2025 huggingface dataset:
Restoration of Eastern oyster populations with positive density dependence
Authors: Moore Jacob L , Puckett Brandon , Schreiber Sebastian J
Published: July 2017

ABSTRACT

Positive density dependence can create a threshold of population states below which extinction of the population occurs. The existence of this threshold, which can often be a complex, multi-dimensional surface, rather than a single point, is of particular importance in degraded populations for which there is a desire for successful restoration. Here, we incorporated positive density dependence into a closed, size- and age-structured integral projection model parameterized with empirical data from an Eastern oyster,Crassostrea virginica, population in Pamlico Sound, North Carolina. To understand the properties of the threshold surface, and implications for restoration, we introduced a general method based on a linearization of the threshold surface at its unique, unstable equilibrium. We estimated the number of oysters of a particular age (i.e. stock enhancement), or the surface area of hard substrate required (i.e. habitat enhancement), to move a population from an extinction trajectory to a persistent trajectory. The location of the threshold surface was strongly affected by changes in the amount of local larval retention. Traditional stock enhancement with oysters less than a year old (i.e. spat) required three times as many oysters relative to stock enhancement with oysters between ages three and seven, while the success of habitat enhancement depended upon the initial size distribution of the population. The methodology described here demonstrates the importance of considering positive density dependence in oyster populations, and also provides insights into effective management and restoration strategies when dealing with a high dimensional threshold separating extinction and persistence.
Accurate detection of complex structural variations using single molecule sequencing
Authors: Sedlazeck Fritz J. , Rescheneder Philipp , Smolka Moritz , Fang Han , Nattestad Maria , Haeseler Arndt von , Schatz Michael C.
Published: July 2017

Structural variations (SVs) are the largest source of genetic variation, but remain poorly understood because of limited genomics technology. Single molecule long read sequencing from Pacific Biosciences and Oxford Nanopore has the potential to dramatically advance the field, although their high error rates challenge existing methods. Addressing this need, we introduce open-source methods for long read alignment (NGMLR,https://github.com/philres/ngmlr) and SV identification (Sniffles,https://github.com/fritzsedlazeck/Sniffles) that enable unprecedented SV sensitivity and precision, including within repeat-rich regions and of complex nested events that can have significant impact on human disorders. Examining several datasets, including healthy and cancerous human genomes, we discover thousands of novel variants using long reads and categorize systematic errors in short-read approaches. NGMLR and Sniffles are further able to automatically filter false events and operate on low amounts of coverage to address the cost factor that has hindered the application of long reads in clinical and research settings.
An MM and QM Study of Biomimetic Catalysis of Diels-Adler Reactions Using Cyclodextrins
Authors: Chen Wei , Sun Lipeng , Tang Zhiye , Chang Chia-en A.
Published: July 2017

We performed computational research to investigate the mechanism by which cyclodextrins (CDs) catalyze Diels-Alder reactions between 9-anthracenemethanol and N-cyclohexylmaleimide. Hydrogen bonds (Hbonds) between N-cyclohexylmaleimide and the hydroxyl groups of cyclodextrins were suggested to play an important role in the catalysis.However, our free energy calculations and molecular dynamics simulations showed that these Hbonds are not stable, and quantum mechanics calculations suggested that the reaction is not promoted by these Hbonds. The binding of 9-anthracenemethanol and N-cyclohexylmaleimide to cyclodextrins was the key to the catalysis. Cyclodextrins act as a container to hold the two reactants in the cavity, pre-organizes them for the reactions, and thus reduces the entropy penalty to the activation free energy. Dimethyl-β-CD was a better catalyst for this specific reaction than β-CD because of its stronger van der Waals interaction with the pre-organized reactants and better performance in reducing the activation energy. This computational work sheds light on the mechanism of the catalytic reaction by cyclodextrins and introduces new perspectives of supramolecular catalysis.
Revealing mechanisms of infectious disease transmission through empirical contact networks
Authors: Sah Pratha , Otterstatter Michael , Leu Stephan T. , Leviyang Sivan , Bansal Shweta
Published: July 2017

The spread of pathogens fundamentally depends on the underlying contacts between individuals. Modeling infectious disease dynamics through contact networks is sometimes challenging, however, due to a limited understanding of pathogen transmission routes and infectivity. We developed a novel tool, INoDS (Identifying Network models of infectious Disease Spread) that estimates the predictive power of empirical contact networks to explain observed patterns of infectious disease spread. We show that our method is robust to partially sampled contact networks, incomplete disease information, and enables hypothesis testing on transmission mechanisms. We demonstrate the applicability of our method in two host-pathogen systems:Crithidia bombiin bumble bee colonies and Salmonella in wild Australian sleepy lizard populations. The performance of INoDS in synthetic and complex empirical systems highlights its role in identifying transmission pathways of novel or neglected pathogens, as an alternative approach to laboratory transmission experiments, and overcoming common data-collection constraints.
A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery
Authors: Chen Wei , Tang Zhiye , Cholko Tim , Chang Chia-en A.
Published: July 2017

The activities of CDK8 with partner Cyclin C (CycC) are a common feature of many diseases, especially cancers. Here we report the study of dynamic behaviors and energy profiles of 13 CDK8/CycC systems, including the DMG-in and DMG-out conformations as well as 5 type I ligands and 5 type II ligands, with all-atom unbiased molecular dynamics (MD) simulations. We observed numerous regional motions within CDK8, which move in concert to form five major protein motions. The motion of the activation loop doesn’t appear to influence the binding of both types of ligands. Type I ligands remarkably reduce the motion of the C-terminal tail through the strong cation-π interaction between the ligands and ARG356, and type II ligands stabilize the αC helix by forming stable hydrogen bonds with GLU66. The MD calculations also confirmed the importance of CycC to the stability of the CDK8 system as well as the ligand binding. The MMPB/SA results show that van der Waals interaction is the main driving force for the binding of both types of ligands, but electrostatic energy and entropy penalty plays important roles in the binding of type II ligands. The volume analysis results indicate that the induced fitting theory applies in the binding of type I ligands. These results would help to improve the affinities of the existing ligands. Our MD work is complementary to crystal structures and may have implications in the development of new CDK8 inhibitors as well as in the field of drug discovery.
Transient states and barriers from molecular simulations and milestoning theory: kinetics in ligand-protein recognition and compound design
Authors: Tang Zhiye , Chen Si-Han , Chang Chia-en A.
Published: July 2017

This study applies a novel computational strategy to investigate molecular recognition and binding kinetics using five pyrazolourea ligands dissociating from cyclin-dependent kinase 8 with cyclin C (CDK8/CycC) as an example. The computed free energy barriers guide designing compounds using the transient conformations unavailable in experiments. The intermediates and their free energy profile during ligand association and discussion processes control ligand-protein binding kinetics and bring a more complete picture of ligand-protein binding. We used metadynamics and a pathway search method to sample pathways and applied combined reduced dimensionality, molecular dynamics (MD) simulations and milestoning theory to construct the free energy profile and estimate the residence time. The binding free energy and the trend of binding kinetics agreed with experiments. We explain the why of the barriers and the kinetics and use the information to assist ligand design. Guided by a barrier of a ligand passing an αC helix and activation loop, we introduced one hydroxyl group to parent compounds to design our ligands with increased residence time and validated our prediction by experiments. This work provides a novel and robust approach to investigate dissociation kinetics of large and flexible systems for understanding unbinding mechanisms and designing new small molecule drugs with desired binding kinetics.

Significance Statement

The transient conformations during ligand binding/unbinding control non-covalent binding kinetics. However, the transient structures and their free energy landscape of flexible ligand-protein systems are unavailable in experiments and challenging to model. Due to lack of understanding in binding kinetics, even scientists know that kinetic properties can be important in drug development, calculations using the intermediate states to design ligands with preferred binding kinetics are absent. We overcome these challenges and compute ligand-protein unbinding free energy profile using a novel method with molecular dynamics simulations, reduced dimensionality, and milestoning theory to deepen our understanding in molecular recognition. We also designed compounds based on the computed free energy barriers and experimentally validated that our designed compound can increase residence time.
Genetics of vaccination-related narcolepsy
Authors: Ollila Hanna M. , Wennerstrom Annika , Partinen Markku , Mignot Emmanuel , Saarela Janna , Kirjavainen Turkka , Hublin Christer , Schneider Logan D. , Himanen Sari-Leena , Saarenpää-heikkilä Outi , Saavalainen Paivi , Tienari Pentti J. , Vaarala Outi , Perola Markus
Published: July 2017

Narcolepsy type 1 is a severe hypersomnia affecting 1/3000 individuals. It is caused by a loss of neurons producing hypocretin/orexin in the hypothalamus. In 2009/2010, an immunization campaign directed towards the new pandemic H1N1 Influenza-A strain was launched and increased risk of narcolepsy reported in Northern European countries following vaccination with Pandemrix®, an adjuvanted H1N1 vaccine resulting in ~250 vaccination-related cases in Finland alone. Using whole genome sequencing data of 2000 controls, exome sequencing data of 5000 controls and HumanCoreExome chip genotypes of 81 cases with vaccination-related narcolepsy and 2796 controls, we, built a multilocus genetic risk score with established narcolepsy risk variants. We also analyzed, whether novel risk variants would explain vaccine-related narcolepsy. We found that previously discovered risk variants had strong predictive power (accuracy of 73% and P<2.2*10−16; and ROC curve AUC 0.88) in vaccine-related narcolepsy cases with only 4.9% of cases being assigned to the low risk category. Our findings indicate genetic predisposition to vaccine-triggered narcolepsy, with the possibility of identifying 95% of people at risk.
Identification of disease resistance genes from a Chinese wild 1 grapevine (Vitis davidii) by analysing grape transcriptomes and transgenic Arabidopsis plants
Authors: Zhang Ying , Yao Jia-Long , Feng Hu , Jiang Jianfu , Fan Xiucai , Sun Haisheng , Jia Yun-Fei , Zhu Yanyan , Wang Ran , Liu Chonghuai
Published: July 2017

Highlight

Transcription profiles showed that 20 candidate genes were obviously co-expressed at 12 hpi in 30Vitis davidii.

VdWRKY53 trancription factor enhanced the resisitance in grapevine and Arabidopsis.

The molecular mechanisms underlying disease tolerance in grapevines remain uncharacterized, even though there are substantial differences in the resistance of grapevine species to fungal and bacterial diseases. In this study, we identified genes and genetic networks involved in disease resistance in grapevines by comparing the transcriptomes of a strongly resistant clone of Chinese wild grapevine (Vitis davidiicv. Ciputao 941,DAC) and a susceptible clone of European grapevine (Vitis viniferacv. Manicure Finger,VIM) before and after infection with white rot disease (Coniella diplodiella). Disease resistance-related genes were triggered inDACapproximately 12 hours post infection (hpi) withC. diplodiella. Twenty candidate resistant genes were co-expressed inDAC. One of these candidate genes,VdWRKY53(GenBank accessionKY124243), was over-expressed in transgenicArabidopsis thalianaplants and was found to provide these plants with enhanced resistance toC. diplodiella,Pseudomonas syringaepvtomatoPDC3000, andGolovinomyces cichoracearum. This result indicates thatVdWRKY53may be involved in nonspecific resistance via interaction with fungal and oomycete elicitor signals and the activation of defence gene expression. These results provide potential gene targets for molecular breeding to develop resistant grape cultivars.
Insulin Does Not AugmentIn VitroTumor Growth Under A Hyperglycemia-Mimicking Milieu And In A Calorie Restriction-Resembling Manner
Authors: Liao Tao , Li Xiao-Hui , Chen Yan-Ping , Tan Li-Li , Zhang Ji-Da , Huang Xin-An , Xu Qin , Huang Sui-Qing , Li Chang-Qing , Zeng Qing-Ping
Published: July 2017

Background

Whether insulin enhances or represses tumor cell proliferation remains debating and inconclusive although epidemiological data indicated insulin use raises a risk of cancer incidence in patients with diabetes mellitus (DM).

Methodology/Principle Findings

We cultured rat pituitary adenoma cells in a high-glucose medium to simulate hyperglycemia occurring in DM patients. Upon incubation with or without insulin, repressed tumor cell proliferation and downregulated tumor marker expression occur accompanying with mitigated oxidative stress and compromised apoptosis. Mechanistically, insulin resistance-abrogated glucose uptake was suggested to create an intracellular low-glucose milieu, leading to cellular starvation resembling calorie restriction (CR). While downregulation of insulin-like growth factor 1 (IGF-1) occurring in CR was validated, oncogene downregulation and tumor suppressor gene upregulation seen in CR was also replicated byNOS2knockdown.

Conclusions/Significance

Cellular starvation can exert CR-like anti-tumor effects regardless of insulin presence or absence.
PhaMers identifies novel bacteriophage sequences from thermophilic hot springs
Authors: Deaton Jonathan , Yu Feiqiao Brian , Quake Stephen R.
Published: July 2017

Metagenomic sequencing approaches have become popular for the purpose of dissecting environmental microbial diversity, leading to the characterization of novel microbial lineages. In addition of bacterial and fungal genomes, metagenomic analysis can also reveal genomes of viruses that infect microbial cells. Because of their small genome size and limited knowledge of phage diversity, discovering novel phage sequences from metagenomic data is often challenging. Here we describe PhaMers (Phagek-Mers). a phage identification tool that uses supervised learning to classify metagenomic contigs as phage or non-phage on the basis of tetranucleotide frequencies. a technique that does not depend on existing gene annotations. PhaMers compares the tetranucleotide frequencies of metagenomic contigs to phage and bacteria references from online databases. resulting in assignments of lower level phage taxonomy based on sequence similarity. Using PhaMers. we identified 103 novel phage sequences from hot spring samples of Yellowstone National Park based on data generated from a microfluidic-based minimetagenomic approach. We analyzed assembled contigs over 5 kbp in length using PhaMers and compared the results with those generated by VirSorter, a publicly available phage identification and annotation package. We analyzed the performance of phage genome prediction and taxonomic classification using PhaMers. and presented putative hosts and taxa for some of the novel phage sequences. Finally. mini-metagenomic occurrence profiles of phage and prokaryotic genomes were used to verify putative hosts.
Glioma CpG Island Methylator Phenotype (G-CIMP): Biological and Clinical Implications
Authors: Malta Tathiane M. , Souza Camila F. , Sabedot Thais S. , Silva Tiago C. , Mosella Maritza Q. S. , Kalkanis Steven N. , Snyder James , Castro Ana Valeria B. , Noushmehr Houtan
Published: July 2017

Gliomas are a heterogeneous group of brain tumors with distinct biological and clinical properties. Despite advances in surgical techniques and clinical regimens, treatment of high-grade glioma remains challenging and carries dismal rates of therapeutic success and overall survival. Challenges include the molecular complexity of gliomas, as well as inconsistencies in histopathological grading, resulting in an inaccurate prediction of disease progression and failure in the use of standard therapy. The updated 2016 World Health Organization (WHO) classification of tumors of the central nervous system reflects a refinement of tumor diagnostics by integrating the genotypic and phenotypic features, thereby narrowing the defined subgroups. The new classification recommends the molecular diagnosis of the IDH mutational status in gliomas. IDH-mutant gliomas manifest the CpG Island Methylator Phenotype (G-CIMP). Notably, the recent identification of clinically relevant subsets of G-CIMP tumors (G-CIMP-high and G-CIMP-low) provide a further refinement in glioma classification that is independent of grade and histology. This scheme may be useful for predicting patient outcome and may be translated into effective therapeutic strategies tailored to each patient. In this review, we highlight the evolution of our understanding of the G-CIMP subsets and how recent advances in characterizing the genome and epigenome of gliomas may influence future basic and translational research.
Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legumeParasponia
Authors: van Velzen Robin , Holmer Rens , Bu Fengjiao , Rutten Luuk , van Zeijl Arjan , Liu Wei , Santuari Luca , Cao Qingqin , Sharma Trupti , Shen Defeng , Roswanjaya Yuda P. , Wardhani Titis A.K. , Kalhor Maryam Seifi , Jansen Joëlle , van den Hoogen D. Johan , Güngör Berivan , Hartog Marijke , Hontelez Jan , Verver Jan , Yang Wei-Cai , Schijlen Elio , Repin Rimi , Schilthuizen Menno , Schranz M. Eric , Heidstra Renze , Miyata Kana , Fedorova Elena , Kohlen Wouter , Bisseling Ton , Smit Sandra , Geurts Rene
Published: July 2017

Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomyceteFrankiaas microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses. However, insight in the evolutionary trajectory of nodulation is lacking. We conducted comparative studies usingParasponia(Cannabaceae), the only non-legume able to establish nitrogen fixing nodules with rhizobium. This revealed thatParasponiaand legumes utilize a large set of orthologous symbiosis genes. Comparing genomes ofParasponiaand its non-nodulating relativeTremadid not reveal specific gene duplications that could explain a recent gain of nodulation inParasponia. Rather,Tremaand other non-nodulating species in the Order Rosales show evidence of pseudogenization or loss of key symbiosis genes. This demonstrates that these species have lost the potential to nodulate. This finding challenges a long-standing hypothesis on evolution of nitrogen-fixing symbioses, and has profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
Antisense transcriptional interference mediates condition-specific gene repression in budding yeast
Authors: Nevers Alicia , Doyen Antonia , Malabat Christophe , Néron Bertrand , Kergrohen Thomas , Jacquier Alain , Badis Gwenael
Published: July 2017

Pervasive transcription generates many unstable non-coding transcripts in budding yeast. The transcription of such noncoding RNAs, in particular antisense RNAs (asRNAs), has been shown in a few examples to repress the expression of the associated mRNAs. Yet, such mechanism is not known to commonly contribute to the regulation of a given class of genes. Using a mutant context that stabilised pervasive transcripts, we observed that the least expressed mRNAs during the exponential phase were associated with high levels of asRNAs. These asRNAs also overlapped their corresponding gene promoters with a much higher frequency than average. Interrupting antisense transcription of a subset of genes corresponding to quiescence-enriched mRNAs restored their expression. The underlying mechanism acts incisand involves several chromatin modifiers. Our results convey that transcription interference represses up to 30% of the 590 least expressed genes, which includes 163 genes with quiescence-enriched mRNAs. We also found that pervasive transcripts constitute a higher fraction of the transcriptome in quiescence relative to the exponential phase, consistent with gene expression itself playing an important role to suppress pervasive transcription. Accordingly, theHIS1asRNA, normally only present in quiescence, is expressed in exponential phase uponHIS1mRNA transcription interruption.
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Authors: Martín-Gálvez David , de Segonzac Denis Dunoyer , John Ma Man Chun , Kwitek Anne E , Thybert David , Flicek Paul
Published: July 2017

The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key strains. Comparison of genomic variation between two closely related rat strains with different phenotypes has been proposed as an effective strategy for the discovery of candidate strain-specific regions involved in phenotypic differences.

We developed a method to prioritise strain-specific haplotypes by integrating genomic variation and genomic regulatory data predicted to be involved in specific phenotypes. To identify genomic regions associated with metabolic syndrome, a disorder of energy utilization and storage affecting several organ systems, we compared two Lyon rat strains, LH/Mav which is susceptible to MetS, and LL/Mav, which is susceptible to obesity as an intermediate MetS phenotype, with a third strain (LN/Mav) that is resistant to both MetS and obesity. Applying a novel metric, we ranked the identified strain-specific haplotypes using evolutionary conservation of the occupancy three liver-specific transcription factors (HNF4A, CEBPA, and FOXA1) in five rodents including rat.

Consideration of regulatory information effectively identified regions with liver-associated genes and rat orthologues of human GWAS variants related to obesity and metabolic traits. We attempted to find possible causative variants and compared them with the candidate genes proposed by previous studies. In strain-specific regions with conserved regulation, we found a significant enrichment for published evidence to obesity—one of the metabolic symptoms shown by the Lyon strains—amongst the genes assigned to promoters with strain-specific variation.

Our results show that the use of functional regulatory conservation is a potentially effective approach to select strain-specific genomic regions associated with phenotypic differences among Lyon rats and could be extended to other systems.
HPCDb: an integrated database of pancreatic cancer
Authors: Tan Yonggang , Tan Yongqiang , Lu Lin , Zhang Heying , Sun Cheng , Liang Yusi , Zeng Juan , Yang Xianghong , Li Dan , Zou Huawei
Published: July 2017

We have established a database of Human Pancreatic Cancer (HPCDb) through effectively mining, extracting, analyzing, and integrating PC-related genes, single-nucleotide polymorphisms (SNPs), and microRNAs (miRNAs), now available online athttp://www.pancancer.org/. Data were extracted from established databases, ≥5 published literature (PubMed), and microarray chips (screening of differentially expressed genes using limma package in R, |log2fold change (FC)| > 1). Further, protein–protein interactions (PPIs) were investigated through the Human Protein Reference Database. miRNA–target relationships were also identified using the online software TargetScan. Currently, HPCDb contains 3284 genes, 120 miRNAs, 589 SNPs, 10,139 PPIs, and 3904 miRNA–target pairs. The detailed information on PC-related genes (e.g., gene identifier (ID), symbol, synonyms, full name, chip sets, expression alteration, PubMed ID, and PPIs), miRNAs (e.g., accession number, chromosome location, related disease, PubMed ID, and miRNA–target interactions), and SNPs (e.g., SNP ID, allele, gene, PubMed ID, chromosome location, and disease) is presented through user-friendly query interfaces or convenient links to NCBI GEO, NCBI PubMed, NCBI Gene, NCBI dbSNP, and miRBase. Overall, HPCDb provides biologists with relevant information on human PC-related molecules at multiple levels, helping to generate new hypotheses or identify candidate markers.
Very low depth whole genome sequencing in complex trait association studies
Authors: Gilly Arthur , Southam Lorraine , Suveges Daniel , Kuchenbaecker Karoline , Moore Rachel , Melloni Giorgio E.M. , Hatzikotoulas Konstantinos , Farmaki Aliki-Eleni , Ritchie Graham , Schwartzentruber Jeremy , Danecek Petr , Kilian Britt , Pollard Martin O. , Ge Xiangyu , Tsafantakis Emmanouil , Dedoussis George , Zeggini Eleftheria
Published: July 2017

Motivation

Very low depth sequencing has been proposed as a cost-effective approach to capture low-frequency and rare variation in complex trait association studies. However, a full characterisation of the genotype quality and association power for very low depth sequencing designs is still lacking.

Results

We perform cohort-wide whole genome sequencing (WGS) at low depth in 1,239 individuals (990 at 1x depth and 249 at 4x depth) from an isolated population, and establish a robust pipeline for calling and imputing very low depth WGS genotypes from standard bioinformatics tools. Using genotyping chip, whole-exome sequencing (WES, 75x depth) and high-depth (22x) WGS data in the same samples, we examine in detail the sensitivity of this approach, and show that imputed 1x WGS recapitulates 95.2% of variants found by imputed GWAS with an average minor allele concordance of 97% for common and low-frequency variants. In our study, 1x further allowed the discovery of 140,844 true low-frequency variants with 73% genotype concordance when compared to high-depth WGS data. Finally, using association results for 57 quantitative traits, we show that very low depth WGS is an efficient alternative to imputed GWAS chip designs, allowing the discovery of up to twice as many true association signals than the classical imputed GWAS design.

Supplementary Data

Supplementary Data are appended to this manuscript.
A Framework to Simulate Cortical microtubule Dynamics in Arbitrary Shaped Plant Cells
Authors: Chakrabortty Bandan , Scheres Ben , Mulder Bela
Published: July 2017

Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells. It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes. This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules. To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed. To date, however, these models have been restricted to 2D planes or geometrically simple surfaces in 3D, which strongly limits their applicability as plant cells display a wide variety of shapes. This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array. Here we describe a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces. This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images. We validate the framework against expected or known results for the spherical and cubical geometry. We then use it to systematically study the individual contributions of global geometry, edge-induced catastrophes and cell face-induced stability to array organization in a cuboidal geometry. Finally, we apply our framework to analyze the highly non-trivial geometry of leaf pavement cells ofNicotiana benthamianaandHedera helix.We show that our simulations can predict multiple features of the array structure in these cells, revealing, among others, strong constraints on the orientation of division planes.
Redesigning chromosomes for optimized Hi-C assay provides insights on loop formation and homologs pairing during meiosis
Authors: Héloïse Muller , Vittore Scolari F. , Guillaume Mercy , Nicolas Agier , Piazza Aurèle , Luciana Lazar-Stefanita , Stephane Descorps-Declere , Olivier Espeli , Bertrand Llorente , Gilles Fischer , Julien Mozziconacci , Romain Koszul
Published: July 2017

In all chromosome conformation capture based experiments the accuracy with which contacts are detected varies considerably because of the uneven distribution of restriction sites along genomes. In addition, repeated sequences as well as homologous, large identical regions remain invisible to the assay because of the ambiguities they introduce during the alignment of the sequencing reads along the genome. As a result, the investigation of homologs during meiosis prophase through 3C studies has been limited. Here, we redesigned and reassembled in yeast a 145kb region with regularly spaced restriction sites for various enzymes. Thanks to this Syn-3C design, we enhanced the signal to noise ratio and improved the visibility of the entire region. We also improved our understanding of Hi-C data and definition of resolution. The redesigned sequence is now distinguishable from its native homologous counterpart in an isogenic diploid strain. As a proof of principle, we track the establishment of homolog pairing during meiotic prophase in a synchronized population. This provides new insights on the individualization and pairing of homologs, as well as on their internal restructuration into arrays of loops during meiosis prophase. Overall, we show the interest of redesigned genomic regions to explore complex biological questions otherwise difficult to address.
Efficient hydrogen-dependent carbon dioxide reduction byEscherichia coli
Authors: Roger Magali , Brown Fraser , Gabrielli William , Sargent Frank
Published: July 2017

The formate hydrogenlyase (FHL) complex ofEscherichia coliis normally produced under anaerobic fermentative conditions when its physiological role is to oxidise formate to carbon dioxide and couple that reaction directly to the reduction of protons to molecular hydrogen. This forward reaction is the major route of hydrogen production byE. coliand the physiology, genetics and biochemistry of this process are reasonably well understood. However, studies of the reverse reaction - hydrogen-dependent carbon dioxide reduction – have been rather less extensive. Harnessing the alternative reverse reaction has the potential to unlock FHL as a carbon dioxide cycling enzyme, or could potentially lead to the development of bio-based carbon capture technologies. In this work, it is established that FHL can operate as a highly efficient CO2reductase. A controllable pressure system was designed with the intention of maximising substrate availability to the FHL enzyme. By placing gaseous CO2and H2are under pressure (up to 10 bar), and by using a compartmentalised intact whole cell approach where the produced formate is excreted, the optimised experimental system was observed to convert 100 % of gaseous CO2to formic acid and generate >500 mM formate in solution at an initial rate of 1.2 g formateperlitreperhour.
riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data
Authors: Lauria Fabio , Tebaldi Toma , Bernabò Paola , Groen Ewout J.N. , Gillingwater Thomas H. , Viero Gabriella
Published: July 2017

Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies.

Availability and Implementation

riboWaltz was implemented in R and is available athttps://github.com/LabTranslationalArchitectomics/RiboWaltz

Contact

gabriella.viero@cnr.itorfabio.lauria@unitn.it
Mechanistic view and genetic control of DNA recombination during meiosis
Authors: Marsolier-Kergoat Marie-Claude , Khan Md Muntaz , Schott Jonathan , Zhu Xuan , Llorente Bertrand
Published: July 2017

Meiotic recombination is essential for fertility and allelic shuffling. Canonical recombination models fail to capture the observed complexity of meiotic recombinants. Here we revisit these models by analyzing meiotic heteroduplex DNA tracts genome-wide in combination with meiotic DNA double-strand break (DSB) locations. We provide unprecedented support to the synthesis-dependent strand annealing model and establish estimates of its associated template switching frequency and polymerase processivity. We show that resolution of double Holliday junctions (dHJs) is biased toward cleavage of the pair of strands containing newly synthesized DNA near the junctions. The suspected dHJ resolvase Mlh1-3 as well as Mlh1-2, Exo1 and Sgs1 promote asymmetric positioning of crossover intermediates relative to the initiating DSB and bidirectional conversions. Finally, we show that crossover-biased dHJ resolution depends on Mlh1-3, Exo1, Msh5 and to a lesser extent on Sgs1. These properties are likely conserved in eukaryotes containing the ZMM proteins, which includes mammals.
How evolution draws trade-offs
Authors: Bourg Salomé , Jacob Laurent , Menu Frédéric , Rajon Etienne
Published: July 2017

Recent empirical evidence suggest that trade-off shapes can evolve, challenging the classical image of their high entrenchment. Here we model the evolution of the physiological mechanism that controls the allocation of a resource to two traits, by mutating the expression and the conformation of its constitutive hormones and receptors. We show that trade-off shapes do indeed evolve in this model through the combined action of genetic drift and selection, such that their evolutionarily expected curvature and length depend on context. In particular, a trade-off’s shape should depend on the cost associated with the resource storage, itself depending on the traded resource and on the ecological context. Despite this convergence at the phenotypic level, we show that a variety of physiological mechanisms may evolve in similar simulations, suggesting redundancy at the genetic level. This model should provide a useful frame-work to interpret and link the overly complex observations of evolutionary endocrinology and evo-lutionary ecology.
The nucleoid as a scaffold for the assembly of bacterial signaling complexes
Authors: Moine Audrey , Espinosa Leon , Martineau Eugenie , Yaikhomba Mutum , Jazleena P J , Byrne Deborah , Biondi Emanuele G. , Notomista Eugenio , Brilli Matteo , Molle Virginie , Gayathri Pananghat , Mignot Tâm , Mauriello Emilia M.F.
Published: July 2017

The FrzCD chemoreceptor from the gliding bacteriumMyxococcus xanthusforms cytoplasmic clusters that occupy a large central region of the cell body also occupied by the nucleoid. In this work, we show that FrzCD directly binds to the nucleoid with its N-terminal positively charged tail and recruits active signaling complexes at this location. The FrzCD binding to the nucleoid occur in a DNA-sequence independent manner and leads to the formation of multiple distributed clusters that explore constrained areas. This organization might be required for cooperative interactions between clustered receptors as observed in membrane-bound chemosensory arrays.

AUTHOR SUMMARY

In this work, we show that the cytoplasmic chemoreceptor of the Frz chemosensory system, FrzCD, does not bind the cytoplasmic membrane like most MCPs but bind the bacterial nucleoid directly, thus forming distributed protein clusters also containing the Frz kinase.In vitroandin vivoexperiments show that DNA-binding is not sequence-specific and is mediated by a basic aminoacid sequence of the FrzCD N-terminal domain. The deletion of this motif abolishes FrzCD DNA-binding and cooperativity in the response to signals. This work shows the importance of the nucleoid in the organization and functioning of cytoplasmic signaling systems in bacteria.
Intrinsically photosensitive retinal ganglion cell mediated pupil function is impaired in Parkinson’s disease
Authors: Joyce Daniel S. , Feigl Beatrix , Kerr Graham , Roeder Luisa , Zele Andrew J.
Published: July 2017

Parkinson’s disease is characterised by non-motor symptoms including sleep and circadian disruption, but the underlying aetiology is not well understood. Melanopsin-expressing intrinsically photosensitive Retinal Ganglion Cells (ipRGC) transmit light signals from the eye to brain areas controlling circadian rhythms and the pupil light reflex. Here we evaluate the hypothesis that these non-motor symptoms in people with Parkinson’s disease may be linked to ipRGC dysfunction. Using chromatic pupillometry, we measured intrinsic (melanopsin-mediated) ipRGC and extrinsic (rod/cone photoreceptor-mediated) inputs to the pupil control pathway in a group of optimally medicated participants with a diagnosis of Parkinson’s disease (PD,n= 17) compared to controls (n= 12). Autonomic tone was evaluated by measuring pupillary unrest in darkness. The PD participants underwent additional clinical assessments using the Unified Parkinson’s disease Rating Scale (UPDRS) and the Hoehn and Yahr scale (H&Y).

Compared to controls, the PD group demonstrated an attenuated pupil constriction amplitude in response to long wavelength pulsed stimulation, and reduced post-illumination pupil response (PIPR) amplitude in response to both short wavelength pulsed and sinusoidal stimulation. In the PD group, PIPR amplitude did not correlate with measures of sleep quality, retinal nerve fibre layer thickness, UPDRS or H&Y score, or medication dosage. Both groups exhibited similar pupillary unrest in darkness.

We show that melanopsin and the rod/cone-photoreceptor contributions to the pupil control pathway are impaired in people with early-stage Parkinson’s disease. Given that the deficits are independent of clinical assessment severity and are observed despite optimal medication, the melanopsin-mediated PIPR may be a biomarker for the detection of Parkinson’s disease and its continued monitoring in both medicated and unmedicated individuals.
RNA structure inference through chemical mapping after accidental or intentional mutations
Authors: Cheng Clarence Y. , Kladwang Wipapat , Yesselman Joseph , Das Rhiju
Published: July 2017

Despite the critical roles RNA structures play in regulating gene expression, sequencing-based methods for experimentally determining RNA base pairs have remained inaccurate. Here, we describe a multidimensional chemical mapping method called M2-seq (mutate-and-map read out through next-generation sequencing) that takes advantage of sparsely mutated nucleotides to induce structural perturbations at partner nucleotides and then detects these events through dimethyl sulfate (DMS) probing and mutational profiling. In special cases, fortuitous errors introduced during DNA template preparation and RNA transcription are sufficient to give M2-seq helix signatures; these signals were previously overlooked or mistaken for correlated double DMS events. When mutations are enhanced through error-prone PCR,in vitroM2-seq experimentally resolves 33 of 68 helices in diverse structured RNAs including ribozyme domains, riboswitch aptamers, and viral RNA domains with a single false positive. These inferences do not require energy minimization algorithms and can be made by either direct visual inspection or by a new neural-net-inspired algorithm called M2-net. Measurements on the P4-P6 domain of theTetrahymenagroup I ribozyme embedded inXenopusegg extract demonstrate the ability of M2-seq to detect RNA helices in a complex biological environment.

SIGNIFICANCE STATEMENT

The intricate structures of RNA molecules are crucial to their biological functions but have been difficult to accurately characterize. Multidimensional chemical mapping methods improve accuracy but have so far involved painstaking experiments and reliance on secondary structure prediction software. A methodology called M2-seq now lifts these limitations. Mechanistic studies clarify the origin of serendipitous M2-seq-like signals that were recently discovered but not correctly explained and also provide mutational strategies that enable robust M2-seq for new RNA transcripts. The method detects dozens of Watson-Crick helices across diverse RNA foldsin vitroand within frog egg extract, with low false positive rate (< 5%). M2-seq opens a route to unbiased discovery of RNA structuresin vitroand beyond.
Image velocimetry and spectral analysis enable quantitative characterization of larval zebrafish gut motility
Authors: Ganz Julia , Baker Ryan P. , Hamilton M. Kristina , Melancon Ellie , Diba Parham , Eisen Judith S. , Parthasarathy Raghuveer
Published: July 2017

Summary Statement

We present a new image analysis technique using image velocimetry and spectral analysis that returns quantitative measures of gut contraction strength, frequency, and wave speed that can be used to study gut motility and other cellular movements.

Normal gut function requires rhythmic and coordinated movements that are affected by developmental processes, physical and chemical stimuli, and many debilitating diseases. The imaging and characterization of gut motility, especially regarding periodic, propagative contractions driving material transport, are therefore critical goals. Whereas previous image analysis approaches have successfully extracted properties related to temporal frequency of motility modes, robust measures of contraction magnitude remain elusive. We developed a new image analysis method based on image velocimetry and spectral analysis that reveals temporal characteristics such as frequency and wave propagation speed, while also providing quantitative measures of the amplitude of gut motions. We validate this approach using several challenges to larval zebrafish, imaged with differential interference contrast microscopy. Both acetylcholine exposure and feeding increase frequency and amplitude of motility. Larvae lacking enteric nervous system gut innervation show the same average motility frequency, but reduced and less variable amplitude compared to wild-types. Our image analysis approach enables insights into gut dynamics in a wide variety of developmental and physiological contexts and can also be extended to analyze other types of cell movements.
Assaying uptake of endocrine disruptor compounds in zebrafish embryos and larvae
Authors: Souder J. Paige , Gorelick Daniel A.
Published: July 2017

To study the effects of environmental endocrine disruptors (EEDs) on aquatic animals, embryos and larvae are typically incubated in water containing defined concentrations of EEDs. However, the amount of EED uptake into the animal is often difficult to determine. Using radiolabeled estradiol ([3H]E2), we previously developed a rapid, straightforward assay to measure estradiol uptake from water into zebrafish embryos and larvae. Here, we extend this approach to measure the uptake of two additional EEDs, bisphenol A (BPA) and ethinyl estradiol (EE2). As with E2, the uptake of each compound by individual larvae was low (< 6%), and increased with increasing concentration, duration, and developmental stage. We found that E2 and EE2 had similar uptake under equivalent exposure conditions, while BPA had comparatively lower uptake. One application of this assay is to test factors that influence EED uptake or efflux. It has been suggested that persistent organic pollutants (POPs) inhibit ABC transporters that may normally efflux EEDs and their metabolites, inducing toxicity in aquatic organisms. We measured [3H]E2 levels in zebrafish in the presence or absence of the POP PDBE-100, and cyclosporine A, a known inhibitor of ABC transporters. Neither chemical significantly affected [3H]E2 levels in zebrafish, suggesting that zebrafish maintain estradiol efflux in the presence of PDBE-100, independently of cyclosporine A-responsive transporters. These uptake results will be a valuable reference for EED exposure studies in developing zebrafish, and provide a rapid assay to screen for chemicals that influence estrogen-like EED levelsin vivo.
Spectrum evaluation‐assisted eicosanoid metabolomics for global eicosanoid profiling in human vascular endothelial cells
Authors: Bao Qiankun , Liu Yajin , Song Hao , Yang Nan , Ai Ding , Zhu Yi , Zhang Xu
Published: July 2017

Eicosanoids are hundreds of metabolites derived from poly‐unsaturated fatty acids (PUFAs), which regulate biological processes from multiple angles via a complex metabolic network. Targeted eicosanoid metabolomics is used to study the eicosanoid profile in biological samples but only for eicosanoids with available standards. To expand the coverage of eicosanoids detected, we identified the eicosanoids without available standards by estimation of the retention time and comparison of the MS/MS spectra with the reference ones which was collected in a database from literature. Scheduled multiple reaction monitoring‐ information dependent acquisition‐ enhanced product ion (sMRM‐IDA‐EPI) scan mode was applied in this method, which was called Spectrum Evaluation‐assisted Eicosanoid Metabolomics (SEEM). By using this method, 243 eicosanoids (167 without standards) could be relatively quantified with precision over 90 percent. We applied the method to analyze the global profile of eicosanoids secreted by human umbilical vascular endothelial cells at the basal level and with n‐3 PUFA treatment. 26 putative eicosanoids showed altered levels, despite no available standards. In general, n‐3 PUFA treatment increased most of their own metabolites and decreased the epoxy‐, hydroxyl‐ and keto‐ linoleic acid metabolites. The application of the SEEM method proved its potency of identification and quantification of eicosanoids without standards.