bluuebunny/crossref_metadata_2025 huggingface dataset:
TuBA: Tunable Biclustering Algorithm Reveals Clinically Relevant Tumor Transcriptional Profiles in Breast Cancer
Authors: Singh Amartya , Bhanot Gyan , Khiabanian Hossein
Published: January 2018

Background

Traditional clustering approaches for gene expression data are not well adapted to address the complexity and heterogeneity of tumors, where small sets of genes may be aberrantly co-expressed in specific subsets of tumors. Biclustering algorithms that perform local clustering on subsets of genes and conditions help address this problem. We propose a graph-based Tunable Biclustering Algorithm (TuBA) based on a novel pairwise proximity measure, examining the relationship of samples at the extremes of genes’ expression profiles to identify similarly altered signatures.

Results

TuBA’s predictions are consistent in 3,940 Breast Invasive Carcinoma (BRCA) samples from three independent sources, employing different technologies for measuring gene expression (RNASeq and Microarray). Over 60% of biclusters identified independently in each dataset had significant agreement in their gene sets, as well as similar clinical implications. About 50% of biclusters were enriched in the ER-/HER2- (or basal-like) subtype, while more than 50% were associated with transcriptionally active copy number changes. Biclusters representing gene co-expression patterns in stromal tissue were also identified in tumor specimens.

Conclusion

TuBA offers a simple biclustering method that can identify biologically relevant gene co-expression signatures not captured by traditional unsupervised clustering approaches. It complements biclustering approaches that are designed to identify constant or coherent submatrices in gene expression datasets, and outperforms them in identifying a multitude of altered transcriptional profiles that are associated with observed genomic heterogeneity of diseased states in breast cancer, both within and across tumor subtypes, a promising step in understanding disease heterogeneity, and a necessary first step in individualized therapy.
Toxoplasma gondiiinfection triggers chronic cachexia and sustained commensal dysbiosis in mice
Authors: Hatter Jessica A. , Kouche Yue Moi , Melchor Stephanie J. , Ng Katherine , Bouley Donna M. , Boothroyd John C. , Ewald Sarah E.
Published: January 2018

Toxoplasma gondiiis a protozoan parasite with a predation-mediated transmission cycle between rodents and felines. Intermediate hosts acquireToxoplasmaby eating parasite cysts which invade the small intestine, disseminate systemically and finally establish host life-long chronic infection in brain and muscles. Here we show thatToxoplasmainfection can trigger a severe form of sustained cachexia: a disease of progressive weight loss that is a causal predictor of mortality in cancer, chronic disease and many infections.Toxoplasmacachexia is characterized by acute anorexia, systemic inflammation and loss of 20% body mass. Although mice recover from symptoms of peak sickness they fail to regain muscle mass or visceral adipose depots. We asked whether the damage to the intestinal microenvironment observed at acute time points was sustained in chronic infection and could thereby play a role the sustaining cachexia. We found that parasites replicate in the same region of the distal jejunum/proximal ileum throughout acute infection, inducing the development of secondary lymphoid structures and severe, regional inflammation. Small intestine pathology was resolved by 5 weeks post-infection. However, changes in the commensal populations, notably an outgrowth ofClostridia spp., were sustained in chronic infection. Importantly, uninfected animals co-housed with infected mice display similar changes in commensal microflora but never display symptoms of cachexia, indicating that altered commensals are not sufficient to explain the cachexia phenotype alone. These studies indicate thatToxoplasmainfection is a novel and robust model to study the immune-metabolic interactions that contribute chronic cachexia development, pathology and potential reversal.
Markov Katana: a Novel Method for Bayesian Resampling of Parameter Space Applied to Phylogenetic Trees
Authors: Pollard Stephen T. , Fukushima Kenji , Wang Zhengyuan O. , Castoe Todd A. , Pollock David D.
Published: January 2018

Phylogenetic inference requires a means to search phylogenetic tree space. This is usually achieved using progressive algorithms that propose and test small alterations in the current tree topology and branch lengths. Current programs search tree topology space using branch-swapping algorithms, but proposals do not discriminate well between swaps likely to succeed or fail. When applied to datasets with many taxa, the huge number of possible topologies slows these programs dramatically. To overcome this, we developed a statistical approach for proposal generation in Bayesian analysis, and evaluated its applicability for the problem of searching phylogenetic tree space. The general idea of the approach, which we call ‘Markov katana’, is to make proposals based on a heuristic algorithm using bootstrapped subsets of the data. Such proposals induce an unintended sampling distribution that must be determined and removed to generate posterior estimates, but the cost of this extra step can in principle be small compared to the added value of more efficient parameter exploration in Markov chain Monte Carlo analyses. Our prototype application uses the simple neighbor-joining distance heuristic on data subsets to propose new reasonably likely phylogenetic trees (including topologies and branch lengths). The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset. This prototype implementation indicates that the Markov katana approach could be easily incorporated into existing phylogenetic search programs and may prove a useful alternative in conjunction with existing methods. The general features of this statistical approach may also prove useful in disciplines other than phylogenetics. We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.
Multiplex Chromatin Interaction Analysis with Single-Molecule Precision
Authors: Zheng Meizhen , Tian Simon Zhongyuan , Maurya Rahul , Lee Byoungkoo , Kim Minji , Capurso Daniel , Piecuch Emaly , Gong Liang , Zhu Jacqueline Jufen , Wong Chee Hong , Ngan Chew Yee , Wang Ping , Ruan Xiaoan , Wei Chia-Lin , Ruan Yijun
Published: January 2018

We describe a microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision. In multiplex chromatin interaction analysis (multi-ChIA), individual chromatin complexes are partitioned into droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts. Thus, multi-ChIA has the unprecedented ability to uncover multiplex chromatin interactions at single-molecule level, which has been impossible using previous methods that rely on analyzing pairwise contacts via proximity ligation. We demonstrate that multiplex chromatin interactions predominantly contribute to topologically associated domains, and clusters of gene promoters and enhancers provide a fundamental topological framework for co-transcriptional regulation.
Structure, Asymmetry and Segmentation of the Human Parietal Aslant and Vertical Occipital Fasciculi
Authors: Panesar Sandip S , A Belo Joao Tiago , Yeh Fang-Cheng , Fernandez-Miranda Juan C
Published: January 2018

We previously proposed a bipartite ‘dorsal-ventral’ model of human arcuate fasciculus (AF) morphology. This model does not, however, account for the ‘vertical,’ temporoparietal subdivision of the AF described in earlier dissection and tractographic studies. In an effort to address the absence of the vertical AF (VAF) within the ‘dorsal-ventral’ model, we conducted a dedicated tractographic and white-matter dissection study of this tract and another short, vertical, posterior-hemispheric fascicle: the vertical occipital fasciculus (VOF). We conducted atlas-based, non-tensor, deterministic tractography in 30 single subjects from the Human Connectome Project database and verified our results using an average diffusion atlas comprising 842 separate normal subjects. We also performed white-matter dissection in 4 cadaveric hemispheres. Our tractographic results demonstrate that the VAF is in fact a bipartite system connecting the ventral-parietal and ventral-temporal regions, with variable connective and no volumetric lateralization. The VOF is a nonlateralized, non-segmented system connecting lateral occipital areas with basal-temporal regions. Importantly, the VOF was distinctly dissociated from the VAF. As the VAF demonstrates no overall connective or volumetric lateralization, we postulate its distinction from the AF system and propose its renaming to the ‘parietal aslant tract,’ (PAT) with unique dorsal and ventral subdivisions. Our tractography results were supported by diffusion atlas and white matter dissection findings.
Mind your gaps: Overlooking assembly gaps confounds statistical testing in genome analysis
Authors: Domanska Diana , Kanduri Chakravarthi , Simovski Boris , Sandve Geir Kjetil
Published: January 2018

Background

The difficulties associated with sequencing and assembling some regions of the DNA sequence result in gaps in the reference genomes that are typically represented as stretches of Ns. Although the presence of assembly gaps causes a slight reduction in the mapping rate in many experimental settings, that does not invalidate the typical statistical testing comparing read count distributions across experimental conditions. However, we hypothesize that not handling assembly gaps in the null model may confound statistical testing of co-localization of genomic features.

Results

First, we performed a series of explorative analyses to understand whether and how the public genomic tracks intersect the assembly gaps track (hg19). The findings rightly confirm that the genomic regions in public genomic tracks intersect very little with assembly gaps and the intersection was observed only at the beginning and end regions of the assembly gaps rather than covering the whole gap sizes. Further, we simulated a set of query and reference genomic tracks in a way that nullified any dependence between them to test our hypothesis that not avoiding assembly gaps in the null model would result in spurious inflation of statistical significance. We then contrasted the distributions of test statistics and p-values of Monte Carlo simulation-based permutation tests that either avoided or not avoided assembly gaps in the null model when testing for significant co-localization between a pair of query and reference tracks. We observed that the statistical tests that did not account for the assembly gaps in the null model resulted in a distribution of the test statistic that is shifted to the right and a distribu tion of p-values that is shifted to the left (leading to inflated significance).

Conclusion

Our results shows that not accounting for assembly gaps in statistical testing of co-localization analysis may lead to false positives and over-optimistic findings.
Developmental genetics of corolla tube formation: role of the tasiRNA-ARF pathway and a conceptual model
Authors: Ding Baoqing , Xia Rui , Lin Qiaoshan , Gurung Vandana , Sagawa Janelle M. , Stanley Lauren E. , Strobel Matthew , Diggle Pamela K. , Meyers Blake C. , Yuan Yao-Wu
Published: January 2018

More than 80,000 angiosperm species produce flowers with petals fused into a corolla tube. As an important element of the tremendous diversity of flower morphology, the corolla tube plays a critical role in many specialized interactions between plants and animal pollinators (e.g., beeflies, hawkmoths, hummingbirds, nectar bats), which in turn drives rapid plant speciation. Despite its clear significance in plant reproduction and evolution, the corolla tube remains one of the least understood plant structures from a developmental genetics perspective. Through mutant analyses and transgenic experiments, here we show that the tasiRNA-ARF pathway is required for corolla tube formation in the monkeyflower speciesMimulus lewisii. Loss-of-function mutations in theM. lewisiiorthologs ofARGONAUTE7andSUPPRESSOR OF GENE SILENCING 3cause a dramatic decrease in abundance ofTAS3-derived small RNAs and a moderate up-regulation ofAUXIN RESPONSE FACTOR 3(ARF3) andARF4, which lead to inhibition of lateral expansion of the bases of petal primordia and complete arrest of the upward growth of the inter-primordial regions, resulting in unfused corollas. By using an auxin reporter construct, we discovered that auxin distribution is continuous along the petal primordium base and the inter-primordial region during the critical stage of corolla tube formation in the wild-type, and that this auxin distribution is much weaker and more restricted in the mutant. Together, these results suggest a new conceptual model highlighting the central role of auxin directed synchronized growth of the petal primordium base and the inter-primordial region in corolla tube formation.
INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance
Authors: Borges Vítor , Pinheiro Miguel , Pechirra Pedro , Guiomar Raquel , Gomes João Paulo
Published: January 2018

A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. Here, we launch INSaFLU (“INSide the FLU”), which, to the best of our knowledge, is the first influenza-specific bioinformatics free web-based suite that deals with primary data (reads) towards the automatic generation of the output data that are actually the core first-line “genetic requests” for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants’ annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform advanced, multi-step software intensive analyses in a user-friendly manner without previous training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects’ management, being a transparent and highly flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus completely cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tune data analysis. This platform additionally flags samples as “putative mixed infections” if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional “consensus-based” influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants, but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. In summary, INSaFLU supplies public health laboratories and influenza researchers with an open “one size fits all” framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus.

INSaFLU can be accessed through https://insaflu.insa.pt (see homepage view in Figure 1).
Quantitative variation within a species for traits underpinning C4 photosynthesis
Authors: Reeves Gregory , Singh Pallavi , Rossberg Timo A. , Deedi Sogbohossou E. O. , Eric Schranz M. , Hibberd Julian M.
Published: January 2018

Engineering C4 photosynthesis into C3 crops such as rice or wheat could substantially increase their yield by alleviating photorespiratory losses1,2. This objective is challenging because the C4 pathway involves complex modifications to the biochemistry, cell biology and anatomy of leaves3. Forward genetics has provided limited insight into the mechanistic basis of these characteristics and there have been no reports of significant quantitative intra-specific variation of C4 attributes that would allow trait-mapping4,5. Here we show that accessions of C4Gynandropsis gynandra collected from locations across Africa and Asia exhibit natural variation in key characteristics of C4 photosynthesis. Variable traits include bundle sheath size and vein density, gas exchange parameters and carbon-isotope discrimination associated with the C4 state, but also abundance of transcripts encoding core enzymes of the C4 cycle. Traits relating to water use showed more quantitative variation than those associated with carbon assimilation. We propose variation in these traits likely adapted the hydraulic system for increased water use efficiency rather than improving carbon fixation, indicating that selection pressure may drive C4 diversity in G. gynandra by acting to modify water use rather than photosynthesis. As these accessions can be easily crossed and produce fertile offspring, our findings indicate that natural variation within a C4 species is sufficiently large to allow genetic-mapping of key anatomical C4 traits and regulators.
Three-dimensional human axon tracts derived from cerebral organoids
Authors: Cullen D. Kacy , Struzyna Laura A. , Jgamadze Dennis , Gordián-Vélez Wisberty J. , Lim James , Wofford Kathryn L. , Browne Kevin D. , Chen H. Isaac
Published: January 2018

Reestablishing cerebral connectivity is a critical part of restoring neuronal network integrity and brain function after trauma, stroke, and neurodegenerative diseases. Creating transplantable axon tracts in the laboratory is a novel strategy for overcoming the common barriers limiting axon regeneration in vivo, including growth-inhibiting factors and the limited outgrowth capacity of mature neurons in the brain. We describe the generation and phenotype of three-dimensional human axon tracts derived from cerebral organoid tissue. These centimeter-long constructs are encased in an agarose shell that permits physical manipulation and are composed of discrete cellular regions spanned by axon tracts and dendrites, mirroring the separation of grey and white matter in the brain. Features of cerebral cortex also are emulated, as evidenced by the presence of neurons with different cortical layer phenotypes. This engineered neural tissue has the translational potential to reconstruct brain circuits by physically replacing discrete cortical neuron populations as well as long-range axon tracts in the brain.

eTOC Blurb

Restoring axonal connectivity after brain damage is crucial for improving neurological and cognitive function. Cullen, et al. have generated anatomically inspired, three-dimensional human axon tracts projecting from cerebral organoids in a transplantable format that may facilitate the reconstruction of large-scale brain circuits.

Highlights

A neural tissue engineering approach is applied to human cerebral organoids.

Three-dimensional axon tracts are generated in a transplantable format.

The growth characteristics of the engineered axons are examined.

The cellular phenotypes of the organoid tissue and axons are characterized.
Influenza Virus Infection Model With Density Dependence Supports Biphasic Viral Decay
Authors: Smith Amanda P. , Moquin David J. , Bernhauerova Veronika , Smith Amber M.
Published: January 2018

Mathematical models that describe infection kinetics help elucidate the time scales, effectiveness, and mechanisms underlying viral growth and infection resolution. For influenza A virus (IAV) infections, the standard viral kinetic model has been used to investigate the effect of different IAV proteins, immune mechanisms, antiviral actions, and bacterial coinfection, among others. We sought to further define the kinetics of IAV infections by infecting mice with influenza A/PR8 and measuring viral loads with high frequency and precision over the course of infection. The data highlighted dynamics that were not previously noted, including viral titers that remain elevated for several days during mid-infection and a sharp 4-5 log10decline in virus within one day as the infection resolves. The standard viral kinetic model, which has been widely used within the field, could not capture these dynamics. Thus, we developed a new model that could simultaneously quantify the different phases of viral growth and decay with high accuracy. The model suggests that the slow and fast phases of virus decay are due to the infected cell clearance rate changing as the density of infected cells changes. To characterize this model, we fit the model to the viral load data, examined the parameter behavior, and connected the results and parameters to linear regression estimates. The resulting parameters and model dynamics revealed that the rate of viral clearance during resolution occurs 25 times faster than the clearance during mid-infection and that small decreases to this rate can significantly prolong the infection. This likely reflects the high efficiency of the adaptive immune response. The new model provides a well-characterized representation of IAV infection dynamics, is useful for analyzing and interpreting viral load dynamics in the absence of immunological data, and gives further insight into the regulation of viral control.
A structural equation model for imaging genetics using spatial transcriptomics
Authors: Huisman Sjoerd M.H. , Mahfouz Ahmed , Batmanghelich Nematollah K. , Lelieveldt Boudewijn P.F. , Reinders Marcel J.T.
Published: January 2018

Alzheimer’s disease is a neurodegenerative disorder that causes changes in the structure of the brain, observable with MRI scans, and that has a strong heritable component, reflected in the DNA. Imaging genetics deals with such relationships between genetic variation and imaging variables, often in a disease context. The complex relationships between brain volumes and genetic variants have been explored both with dimension reduction methods and model based approaches. However, these models usually do not make use of the extensive knowledge of the spatio-anatomical patterns of gene activity. We present a method for integrating genetic markers (single nucleotide polymorphisms) and imaging features, which is based on a causal model and, at the same time, uses the power of dimension reduction. We use structural equation models to find latent variables that explain brain volume changes in a disease context, and which are in turn affected by genetic variants. We make use of publicly available spatial transcriptome data from the Allen Human Brain Atlas to specify the model structure, which reduces noise and improves interpretability. The model is tested in a simulation setting, and applied on a case study of the Alzheimer’s Disease Neuroimaging Initiative.
Loss of mCHH islands in maize chromomethylase and DDM1-type nucleosome remodeler mutants
Authors: Fu Fang-Fang , Dawe R. Kelly , Gent Jonathan I.
Published: January 2018

Plants make use of three types of DNA methylation, each characterized by distinct DNA methyltransferases. One type, RNA-directed DNA methylation (RdDM), is guided by siRNAs to the edges of transposons that are close to genes, areas called mCHH islands in maize. Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DDM1-type nucleosome remodelers, which facilitate chromomethylation. Both sets of double mutants were nonviable but produced embryos and endosperm. RdDM was severely compromised in the double mutant embryos, both in terms of DNA methylation and siRNAs. Loss of 24nt siRNA from mCHH islands was coupled with a gain of 21, 22, and 24nt siRNAs in heterochromatin. These results reveal a requirement for both chromomethylation and DDM1-type nucleosome remodeling for RdDM in mCHH islands, which we hypothesize is due to dilution of RdDM components across the genome when heterochromatin is compromised.
PIN7 auxin carrier is a terminator of radial root expansion inArabidopsis thaliana
Authors: Ruiz Rosquete Michel , Kleine-Vehn Jürgen
Published: January 2018

Directional growth of lateral roots is critical for radial expansion and soil coverage. Despite its importance, almost nothing is known about its molecular determinants. Initially, young lateral roots (LRs) grow away from the parental root maintaining the angle acquired shortly after emergence. A second downwards bending response to gravity terminates the so-called plateau phase and thereby limits the radial root expansion. Here we show that the exit from the plateau phase correlates with an increase in auxin signalling at the tip of LRs. Moreover, the increase in auxin levels induces the termination of the plateau phase, which requires PIN auxin efflux carriers. Our data suggests that the developmental increase of auxin triggers the preferential de-repression of PIN7 in gravity-sensing columella cells. The subsequent polarization of PIN7 heralds the bending towards gravity and, hence, the exit from the plateau phase. This developmental framework reveals the distinct roles of PIN auxin efflux carriers in controlling the radial growth of root systems.
Conditional Upregulation of KCC2 selectively enhances neuronal inhibition during seizures
Authors: Goulton CS , Watanabe M , Cheung DL , Wang KW , Oba T , Khoshaba A , Lai D , Inada H , Eto K , Nakamura K , Power JM , Lewis TM , Housley GD , Wake H , Nabekura J , Moorhouse AJ
Published: January 2018

Abstract/Summary

Efficacious neuronal inhibition is sustained by the neuronal K+Cl- co-transporter KCC2, and loss of KCC2 function through injury or mutation is associated with altered GABAergic signalling and neuronal seizures. Here we report a transgenic mouse with conditional KCC2 overexpression that results in increased membrane transport function. Increased KCC2 has little impact on behavioural and in vitro assays of neuronal excitability and GABAA receptor responses under resting conditions. In contrast, increased KCC2 imparts resistance to seizure-like neuronal activity in hippocampal slices and prevents the progression of mice into behavioural status epilepticus following multiple kainic acid doses. Our results demonstrate a transgenic mouse to facilitate investigations into the role of KCC2 in brain function, and provide a proof of principle that targeting KCC2 may be an effective way to selectively enhance neuronal inhibition to mitigate against diseases that involve an imbalance between excitation and inhibition.
Patterns of microsatellite distribution reflect the evolution of biological complexity
Authors: Srivastava Surabhi , Avvaru Akshay Kumar , Sowpati Divya Tej , Mishra Rakesh K
Published: January 2018

Microsatellites, also known as Simple Sequence Repeats (SSRs), are evolutionarily conserved repeat elements distributed non-randomly in all genomes. Many studies have investigated their pattern of occurrence in order to understand their role, but their identification has largely been non-exhaustive and limited to a few related species or model organisms. Here, we identify ~685 million microsatellites from 719 eukaryotes and analyze their evolutionary trends from protists to mammals. We document novel patterns uniquely demarcating closely related species, including in pathogens like Leishmania as well as in higher organisms such as Drosophila, birds, primates, and cereal crops. The distribution of SSRs in coding and non-coding regions reveals taxon-specific variations in their exonic, intronic and intergenic densities. We also show that specific SSRs accumulate at longer lengths in higher organisms indicating an evolutionary selection pressure. In general, we observe greater constraints in the SSR composition of multicellular organisms with complex cell types, while simpler organisms show more diversity. The conserved microsatellite trends and species-specific signatures identified in this study closely mirror phylogenetic relationships and we hypothesize that SSRs are integral components in speciation and the evolution of organismal complexity. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and unparalleled scope for understanding their roles across the evolutionary landscape.
Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome
Authors: Bush Stephen J. , Muriuki Charity , McCulloch Mary E. B. , Farquhar Iseabail L. , Clark Emily L. , Hume David A.
Published: January 2018

mRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. In many cases, therefore, lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNA, we comparedde novoassembled lncRNA derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNA assembled in cattle and human. Few lncRNA could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNA assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNA to identify a consensus set of ruminant lncRNA and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. The majority of lncRNA were encoded by single exons, and expressed at < 1 TPM. In sheep, 20-30% of lncRNA had expression profiles significantly correlated with neighbouring protein-coding genes, suggesting association with enhancers. Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNA in other species.
Core Proteome and Architecture of COPI Vesicles
Authors: Rhiel Manuel , Hessling Bernd , Gao Qi , Hellwig Andrea , Adolf Frank , Wieland Felix T.
Published: January 2018

Retrieval of escaped ER-residents and intra-Golgi transport is facilitated by coat protein complex I (COPI)-coated vesicles. Their formation requires the activated small GTPase ADP-ribosylation factor (Arf) and the coat complex coatomer. Here we assess the protein composition of COPI vesicles by combining stable isotope labeling with amino acids in cell culture (SILAC) within vitroreconstitution of COPI vesicles from semi-intact cells (SIC) using the minimal set of recombinant coat proteins. This approach yields an unbiased picture of the proteome of these carriers. We define a set of ~40 proteins common to COPI vesicles produced from different human as well as murine cell lines. Almost allbona fideCOPI vesicle proteins are either ER-Golgi cycling proteins or Golgi-residents, while only a minor portion of secreted proteins was found. Moreover, we have investigated a putative role of γ- and ζ-COP as well as Arf isoforms in sorting and recruitment of specific proteins into COPI vesicles. As opposed to the related COPII system, all isoforms of coatomer and all COPI-forming isoforms of the small GTPase Arf produce COPI-coated vesicles with strikingly similar protein compositions. We present a model for the core architecture of COPI vesicles.
Woolly Ash Aphid Prociphilus Fraxinifolii (Riley, 1879) (Hemiptera: Eriosomatidae), A New Invasive Alien Pest of Ash Trees (Fraxinus) in Russia
Authors: Bieńkowski Andrzej , Orlova-Bienkowskaja Marina
Published: January 2018

Woolly ash aphid or ash leaf curl aphid Prociphilus fraxinifolii (Riley, 1879) is an alien invasive pest of ash trees native to North America. After its first record in Europe in 2003 in Hungary it has spread to the Ukraine, Serbia, Bulgaria, Great Britain, Spain, Poland and Germany. In 2016 P. fraxinifolii was firstly recorded at the southwestern border of Russia. Now Prociphilus fraxinifolii is firstly recorded in the center of European Russia, namely in Moscow Region, which is more than 700 km far from all other known localities of the species. In September 2017 five groups of ash trees (Fraxinus pennsylvanica) with colonies of Prociphilus fraxinifolii were found in Moscow Region. The example of Prociphilus fraxinifolii shows that alien pest insects can spread in Europe very quickly. Now Moscow region is the only regions of Europe, where the expanding range of Prociphilus fraxinifolii has overlapped with expanding ranges of other invasive alien species established in Europe in the last 20 years and severely damaging ash trees: ash dieback fungus Hymenoscyphus fraxineus Baral et al., 2014 (Ascomycota) and emerald ash borer Agrilus planipennis Fairmaire, 1888 (Coleoptera: Buprestidae).
Ecological feedback on diffusion dynamics
Authors: Park Hye Jin , Gokhale Chaitanya S.
Published: January 2018

Spatial patterns are ubiquitous across different scales of organization. Animal coat pattern, spatial organization of insect colonies, and vegetation in arid areas are prominent examples from such diverse ecologies. Typically, pattern formation has been described by reaction-diffusion equations, which considers individuals dispersing between sub-populations of a global pool. This framework applied to public goods game nicely showed the endurance of populations via diffusion and generation of spatial patterns. However, how the spatial characteristics, such as diffusion, are related to the eco-evolutionary process as well as the nature of the feedback from evolution to ecology and vice versa, has been so far neglected. We present a thorough analysis of the ecologically driven evolutionary dynamics in a spatially extended version of ecological public goods games. We show how these evolutionary dynamics feedback into shaping the ecology thus together determining the fate of the system.
Reduced-nutrient leachates in cash cover crop-soybean systems
Authors: Thom Matthew D. , Forcella Frank , Eberle Carrie A. , Matthees Heather L. , Weyers Sharon L. , Gesch Russ W. , Ott Matthew A. , Feyereisen Gary W. , Strock Jeffrey S. , Wyse Don
Published: January 2018

Over-wintering crops are known to reduce nutrients in soil leachate in spring, but little economic incentive is available to grow these crops in the Upper Midwest. New oilseed-bearing cash cover crops, such as winter camelina and pennycress, may provide the needed incentives. However, the abilities of these crops to sequester labile soil nutrients are unknown. We used lysimeters buried at 30, 60, and 100 cm to examine nitrate and soil reactive phosphorus (SRP) in six soybean cropping system treatments: clean till, no-till, and autumn-seeded radish, winter rye, pennycress, and winter camelina. Radish winter-killed naturally, winter rye was killed with a glyphosate, and pennycress and winter camelina were allowed to mature naturally after relay sowing of soybean. Leachate chemistry was studied for the autumn, spring, and summer periods over two growing season. In autumn, leachates under radish and winter rye tended to have the lowest nitrate levels. In spring, differences among nitrate levels across treatments were greater than at any other time period, with values much lower under pennycress and winter camelina treatments than other treatments. In summer, nitrate levels were more uniform, with the lowest values occurring where soybean grew best. In general, cash cover crops like pennycress and winter camelina provide both environmental and economic resources to growers in that they represent cash-generating grain crops that sequester labile soil nutrients, especially in spring, and protect and promote soil health from autumn through early summer.
Texture of nanocrystalline solids: atomic scale characterization and applications
Authors: E J. C. , Cai Y. , Zhong Z. Y. , Tang M. X. , Zhu X. R. , Wang L. , Luo S. N.
Published: January 2018

A methodology is presented to characterize the crystallographic texture of atomic configurations on the basis of Euler angles. Texture information characterized by orientation map, orientation distribution function, texture index, pole figure and inverse pole figure is obtained. The paper reports the construction and characterization of the texture of nanocrystalline configurations with different grain numbers, grain sizes and percentages of preferred orientation. The minimum grain number for texture-free configurations is ∼2500. The effect of texture on deducing grain size from simulated X-ray diffraction curves is also explored as an application case of texture analysis. In addition, molecular dynamics simulations are performed on initially texture-free nanocrystalline Ta under shock-wave loading, which shows a 〈001〉 + 〈111〉 double fiber texture after shock-wave compression.
Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals
Authors: Awel Salah , Kirian Richard A. , Wiedorn Max O. , Beyerlein Kenneth R. , Roth Nils , Horke Daniel A. , Oberthür Dominik , Knoska Juraj , Mariani Valerio , Morgan Andrew , Adriano Luigi , Tolstikova Alexandra , Xavier P. Lourdu , Yefanov Oleksandr , Aquila Andrew , Barty Anton , Roy-Chowdhury Shatabdi , Hunter Mark S. , James Daniel , Robinson Joseph S. , Weierstall Uwe , Rode Andrei V. , Bajt Saša , Küpper Jochen , Chapman Henry N.
Published: January 2018

High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.
Interpretation of solution scattering data from lipid nanodiscs
Authors: Graziano Vito , Miller Lisa , Yang Lin
Published: January 2018

The structural information contained in solution scattering data from empty lipid nanodiscs is examined in the context of a multi-component geometric model. X-ray scattering data were collected on nanodiscs of different compositions at scattering vector magnitudes up to 2.0 Å−1. Through the calculation of the partial form factor for each of the nanodisc components before the isotropic average, structural parameters in the model were correlated to the features observed in the X-ray scattering data and to the corresponding distance distribution function. It is shown that, in general, the features at ∼0.3–0.6 Å−1 in the scattering data correlate to the bilayer structure. The data also support the argument that the elliptical shape of nanodiscs found in model fitting is physical, rather than an artefact due to the nanodisc size distribution. The lipid chain packing peak at ∼1.5 Å−1 is visible in the data and reflects the lipid bilayer phase transition. The shape change in the distance distribution function across the phase transition suggests that the nanodiscs are more circular in the fluid phase. The implication of these findings for model fitting of empty and protein-loaded nanodiscs is discussed.
In situ ferromagnetic resonance capability on a polarized neutron reflectometry beamline
Authors: Kostylev Mikhail , Causer Grace L. , Lambert Charles-Henri , Schefer Thomas , Weiss Charles , Callori Sara J. , Salahuddin Sayeef , Wang Xiaolin L. , Klose Frank
Published: January 2018

This article describes a novel approach which allows for the mutual determination of a ferromagnetic thin film's static and dynamic magnetic behaviours in the presence of an external thermodynamic stimulus. Using a combination of polarized neutron reflectometry (PNR) and ferromagnetic resonance (FMR) techniques, it is shown that information such as magnetic depth profiles and magnetization dynamics can be obtained for a ferromagnetic film in both transient and static states in the presence of a hydrogen gas atmosphere. Presented here are the proposed scheme, the instrumentation concept and the first experimental results obtained from implementing a custom-made PNR with an in situ FMR sample chamber on the PLATYPUS time-of-flight reflectometer beamline at the Australian Centre for Neutron Scattering (ANSTO).
X-ray crystallographic and high-speed AFM studies of peroxiredoxin 1 fromChlamydomonas reinhardtii
Authors: Charoenwattanasatien Ratana , Tanaka Hideaki , Zinzius Karen , Hochmal Ana K. , Mutoh Risa , Yamamoto Daisuke , Hippler Michael , Kurisu Genji
Published: January 2018

Peroxiredoxins (PRXs) are a group of antioxidant enzymes that are found in all organisms, including plants and green algae. The 2-Cys PRX fromChlamydomonas reinhardtii(CrPRX1) is a chloroplast-localized protein that is critical for clearing reactive oxygen species in chloroplasts.CrPRX1 is reduced by thioredoxins or calredoxin (CrCRX), a recently identified calcium-dependent redox protein. The molecular interaction between PRXs and thioredoxin/CrCRX is functionally important, but discussion has been limited owing to a lack of structural information onCrPRX1, especially regarding its oligomeric state. In this study, high-speed atomic force microscopy (HS-AFM) images ofCrPRX1 and an X-ray crystallographic analysis have enabled examination of the oligomeric state ofCrPRX1. Diffraction data from a crystal of the Cys174Ser mutant ofCrPRX1 indicate the existence of noncrystallographic fivefold symmetry. HS-AFM images ofCrPRX1 further show thatCrPRX1 particles form rings with pentagonal rotational symmetry. On the basis of these findings, the oligomeric state ofCrPRX1 is discussed and it is concluded that this PRX exists in a ring-shaped decameric form comprising a pentamer of dimers.
Structure of bovine cytochromecoxidase in the ligand-free reduced state at neutral pH
Authors: Luo Fangjia , Shinzawa-Itoh Kyoko , Hagimoto Kaede , Shimada Atsuhiro , Shimada Satoru , Yamashita Eiki , Yoshikawa Shinya , Tsukihara Tomitake
Published: January 2018

Cytochromecoxidase (CcO), the terminal oxidase in cellular respiration, couples proton pumping to O2reduction. Mammalian CcO resides in the inner mitochondrial membrane. Previously, a model of H-pathway proton pumping was proposed based on various CcO crystal structures. However, all previously determined structures were solved using crystals obtained at pH 5.7, which differs from the environmental pH of CcO in the inner membrane. The structures of fully oxidized and ligand-free reduced CcO at pH 7.3 have now been determined. Structural comparison between the oxidized and reduced states revealed that the structural alterations that occurred upon redox change at pH 5.7 in Asp51, the magnesium-containing cluster, haem groups and helix X, which provide important structural evidence for the H-pathway proton-pumping proposal, also occur at pH 7.3. These structural alterations were restricted to a local region of CcO; no domain movement was detected, nor were significant structural alterations detected in peripheral regions at either pH value. These observations indicate that the small and precise structural alterations that occur over the course of the reaction cycle are not affected by pH change, and that isolated CcO precisely performs proton pumpingviathe H-pathway over a wide pH range. Because the pH is not uniform across the molecular surface of CcO, the fact that the overall structure of CcO is not affected by pH changes ensures the high enzymatic efficiency of this protein in the mitochondria.
Structural characterization ofPorphyromonas gingivalisenoyl-ACP reductase II (FabK)
Authors: Hevener Kirk E. , Santarsiero Bernard D. , Lee Hyun , Jones Jesse A. , Boci Teuta , Johnson Michael E. , Mehboob Shahila
Published: January 2018

Enoyl-acyl carrier protein (ACP) reductase II (FabK) is a critical rate-limiting enzyme in the bacterial type II fatty-acid synthesis (FAS II) pathway. FAS II pathway enzymes are markedly disparate from their mammalian analogs in the FAS I pathway in both structure and mechanism. Enzymes involved in bacterial fatty-acid synthesis represent viable drug targets for Gram-negative pathogens, and historical precedent exists for targeting them in the treatment of diseases of the oral cavity. The Gram-negative organismPorphyromonas gingivalisrepresents a key causative agent of the costly and highly prevalent disease known as chronic periodontitis, and exclusively expresses FabK as its enoyl reductase enzyme in the FAS-II pathway. Together, these characteristics distinguishP. gingivalisFabK (PgFabK) as an attractive and novel narrow-spectrum antibacterial target candidate.PgFabK is a flavoenzyme that is dependent on FMN and NADPH as cofactors for the enzymatic reaction, which reduces the enoyl substrateviaa ping-pong mechanism. Here, the structure of thePgFabK enzyme as determined using X-ray crystallography is reported to 1.9 Å resolution with endogenous FMN fully resolved and the NADPH cofactor partially resolved.PgFabK possesses a TIM-barrel motif, and all flexible loops are visible. The determined structure has allowed insight into the structural basis for the NADPH dependence observed inPgFabK and the role of a monovalent cation that has been observed in previous studies to be stringently required for FabK activity. ThePgFabK structure and the insights gleaned from its analysis will facilitate structure-based drug-discovery efforts towards the prevention and treatment ofP. gingivalisinfection.
Xylanase B fromClostridium cellulovorans743B: overexpression, purification, crystallization and X-ray diffraction analysis
Authors: Nakajima Daichi , Nagano Akihiko , Shibata Toshiyuki , Tanaka Reiji , Kuroda Kouichi , Ueda Mitsuyoshi , Miyake Hideo
Published: January 2018

Clostridium cellulovoransproduces multi-enzyme complexes called cellulosomes capable of efficiently degrading cellulosic biomass. There are three xylanase genes containing a sequence corresponding to a dockerin domain that are necessary for constructing cellulosomes in the genome. Among the xylanases encoded by these genes, xylanase B (XynB) contains a catalytic domain belonging to glycoside hydrolase family 10 and a carbohydrate-binding module (CBM) at the N-terminus, making it a member of CBM family 22. In this study, XynB was cloned, overexpressed, purified and crystallized. XynB was crystallized using the hanging-drop vapour-diffusion method in the presence of 0.2 Msodium acetate trihydrate, 0.1 MTris–HCl pH 8.5, 32%(w/v) PEG 4000 at 293 K. X-ray diffraction analysis revealed that the crystal diffracted to 1.95 Å resolution and belonged to space groupP212121, with unit-cell parametersa = 74.28,b= 77.55,c= 88.20 Å, α = β = γ = 90°. The data-evaluation statistics revealed high quality of the collected data, thereby establishing a solid basis for determination of the structure of cellulosomal xylanase fromC. cellulovorans.