bluuebunny/crossref_metadata_2025 huggingface dataset:
The dorsolateral striatum regulates habits by way of performance vigor when actions are initiated
Authors: Crego Adam C.G. , Štoček Fabián , Marchuk Alec G. , Carmichael James E. , van der Meer Matthijs A.A. , Smith Kyle S.
Published: September 2018

Despite clear evidence linking basal ganglia control to habits, it remains unclear through what mechanisms this control occurs. Here, we demonstrate that a key function of the dorsolateral striatum (DLS) is to regulate the vigor of a learned behavior at the moment of initiation in a habit-promoting manner. Shifts in vigor by phasic DLS perturbations coincide closely with how outcome-insensitive (i.e., habitual) the behaviors are in both response-based and cue-based task situations. Surprisingly, the control over habit strength by way of changes in vigor occurs without consistent changes in accuracy, suggesting that mechanisms controlling habit and vigor are dissociable from performance governed task rules. Finally, we show that increased DLS activity improves vigor preferentially when learned outcome values are stable, while reduced DLS activity dampens vigor preferentially when outcome values change. These data indicate that improving action vigor could be a principle route by which the basal ganglia facilitate habits.
CaSpER: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data
Authors: Harmancı Akdes Serin , Harmanci Arif O. , Zhou Xiaobo
Published: September 2018

RNA sequencing experiments generate large amounts of information about expression levels of genes. Although they are mainly used for quantifying expression levels, they contain much more biologically important information such as copy number variants (CNV). Here, we propose CaSpER, a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data. CaSpER performs smoothing of the genome-wide RNA sequencing signal profiles in different multiscale resolutions, identifying CNV events at different length scales. CaSpER also employs a novel methodology for generation of genome-wide B-allele frequency (BAF) signal profile from the reads and utilizes it in multiscale fashion for correction of CNV calls. The shift in allelic signal is used to quantify the loss-of-heterozygosity (LOH) which is valuable for CNV identification. CaSpER uses Hidden Markov Models (HMM) to assign copy number states to regions. The multiscale nature of CaSpER enables comprehensive analysis of focal and large-scale CNVs and LOH segments. CaSpER performs well in accuracy compared to gold standard SNP genotyping arrays. In particular, analysis of single cell Glioblastoma (GBM) RNA sequencing data with CaSpER reveals novel mutually exclusive and co-occurring CNV sub-clones at different length scales. Moreover, CaSpER discovers gene expression signatures of CNV sub-clones, performs gene ontology (GO) enrichment analysis and identifies potential therapeutic targets for the sub-clones. CaSpER increases the utility of RNA-sequencing datasets and complements other tools for complete characterization and visualization of the genomic and transcriptomic landscape of single cell and bulk RNA sequencing data, especially in cancer research.
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia
Authors: Collado-Torres L , Burke EE , Peterson A , Shin JH , Straub RE , Rajpurohit A , Semick SA , Ulrich WS , BrainSeq Consortium , Valencia C , Tao R , Deep-Soboslay A , Hyde TM , Kleinman JE , Weinberger DR , Jaffe AE
Published: September 2018

Recent large-scale genomics efforts have better characterized the molecular correlates of schizophrenia in postmortem human neocortex, but not hippocampus which is a brain region prominently implicated in its pathogenesis. Here in the second phase of the BrainSeq Consortium (Phase II), we have generated RiboZero RNA-seq data for 900 samples across both the dorsolateral prefrontal cortex (DLPFC) and the hippocampus (HIPPO) for 551 individuals (286 affected by schizophrenia disorder: SCZD). We identify substantial regional differences in gene expression, in both pre- and post-natal life, and find widespread differences in how genes are regulated across development. By extending quality surrogate variable analysis (qSVA) to multiple brain regions, we identified 48 and 245 differentially expressed genes (DEG) by SCZD diagnosis (FDR<5%) in HIPPO and DLPFC, respectively, with surprisingly minimal overlap in DEG between the two brain regions. We further identified 205,618 brain region-dependent eQTLs (FDR<1%) and found that 124 GWAS risk loci contain eQTLs in at least one of the regions. We also identify potential molecular correlates of in vivo evidence of altered prefrontal-hippocampal functional coherence in schizophrenia. These results underscore the complexity and regional heterogeneity of the transcriptional correlates of schizophrenia, and suggest future schizophrenia therapeutics may need to target molecular pathologies localized to specific brain regions.
A bacterial DNA repair pathway specific to a natural antibiotic
Authors: Burby Peter E. , Simmons Lyle A.
Published: September 2018

All organisms possess several DNA repair pathways to maintain the integrity of their genetic material. Although there are several DNA repair pathways that are well understood, we recently identified several genes inBacillus subtilisthat are important for surviving treatment with drugs that damage DNA. Here, we report a drug specific DNA repair pathway inB. subtilis. We identified genes coding for a previously uncharacterized helicase and exonuclease,mrfAandmrfB, respectively. Deletion ofmrfAandmrfBresulted in sensitivity to the DNA damaging agent mitomycin C, but not other types of DNA damage. We found that MrfAB operate independently of canonical nucleotide excision repair, forming a novel excision repair pathway in bacteria. A phylogenetic analysis demonstrates that MrfAB homologs are present in diverse bacterial phyla, and a cross-complementation assay shows that MrfAB function is conserved in closely related species. Mitomycin C is a natural antibiotic that is produced by the soil dwelling bacteriumStreptomyces lavendulae, andB. subtilisis also a soil dwelling organism. The specificity of the ΔmrfABphenotype suggests that MrfAB have been adapted as a countermeasure to mitomycin producing bacteria.

Abbreviated Summary

Bacteria possess DNA repair pathways to maintain the integrity of their genetic material. The helicase MrfA and the exonuclease MrfB are part of a mitomycin C specific DNA repair pathway inBacillus subtilis. Despite being present in many bacterial species, MrfAB activity in repairing MMC damaged DNA appears to be restricted to closely related species, suggesting that these proteins have likely been adapted to the specific needs of each bacterium.
Macroscale estimates of species abundance reveal evolutionary drivers of biodiversity
Authors: Fukaya Keiichi , Kusumoto Buntarou , Shiono Takayuki , Fujinuma Junichi , Kubota Yasuhiro
Published: September 2018

Evolutionary processes underpin the biodiversity on the planet. Theories advocate that the form of the species abundance distribution (SAD), presented by the number of individuals for each species within an ecological community, is intimately linked to speciation modes such as point mutation and random fission. This prediction has rarely been, however, verified empirically; the fact that species abundance data can be obtained only from local communities critically limits our ability to infer the role of macroevolution in shaping ecological patterns. Here, we developed a novel statistical model to estimate macroscale SADs, the hidden macroecological property, by integrating spatially replicated multispecies detection-nondetection observations and the data on species geographic distributions. We determined abundance of 1,248 woody plant species at a 10 km grid square resolution over East Asian islands across subtropical to temperate biomes, which produced a metacommunity (i.e. species pool) SAD in four insular ecoregions along with its absolute size. The metacommunity SADs indicated lognormal-like distributions, which were well explained by the unified neutral theory of biodiversity and biogeography (UNTB) with protracted speciation, a mode of speciation intermediate between point mutation and random fission. Furthermore, the analyses yielded an estimate of speciation rate in each region that highlighted the importance of geographic characteristics in macroevolutionary processes and predicted the average species lifetime that was congruent with previous estimates. The estimation of macroscale SADs plays a remarkable role in revealing evolutionary diversification of regional species pools.
Automated, predictive, and interpretable inference of C. elegans escape dynamics
Authors: Daniels Bryan C. , Ryu William S. , Nemenman Ilya
Published: September 2018

The roundworm C. elegans exhibits robust escape behavior in response to rapidly rising temperature. The behavior lasts for a few seconds, shows history dependence, involves both sensory and motor systems, and is too complicated to model mechanistically using currently available knowledge. Instead we model the process phenomenologically, and we use the Sir Isaac dynamical inference platform to infer the model in a fully automated fashion directly from experimental data. The inferred model requires incorporation of an unobserved dynamical variable, and is biologically interpretable. The model makes accurate predictions about the dynamics of the worm behavior, and it can be used to characterize the functional logic of the dynamical system underlying the escape response. This work illustrates the power of modern artificial intelligence to aid in discovery of accurate and interpretable models of complex natural systems.
A Reptilian Endogenous Foamy Virus Sheds Light on the Early Evolution of Retroviruses
Authors: Wei Xiaoman , Chen Yicong , Duan Guangqian , Holmes Edward C. , Cui Jie
Published: September 2018

Endogenous retroviruses (ERVs) can be thought of as host genomic fossils of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFV) have previously been discovered in mammals, amphibians and fish. Here we report a novel endogenous foamy virus, named SpuEFV, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that SpuEFV has likely co-diverged with its host over a period of many millions of years. The discovery of SpuEFV fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.
Rational design of hidden thermodynamic driving through DNA mismatch repair
Authors: Haley Natalie E. C. , Ouldridge Thomas E. , Geraldini Alessandro , Louis Ard A. , Bath Jonathan , Turberfield Andrew J.
Published: September 2018

Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a new mechanism for enhancing thermodynamic drive of DNA strand displacement reactions whilst barely perturbing forward reaction rates - introducing mismatches in an internal location within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of nonequilibrium systems that rely on catalytic control and must be robust to leak reactions.
Chemosensory structure and function in the filarial nematode, Brugia malayi
Authors: Fraser Lisa M. , Madriz R. Isai , Srinivasan Divyaa , Zamanian Mostafa , Bartholomay Lyric C. , Kimber Michael J.
Published: September 2018

Nematode chemosensory behaviors underlie fundamental processes and activities in development, reproduction, tropisms and taxes. For parasitic species, chemosensation is essential for host seeking and host and tissue invasion behaviors. Such fundamental biology presents an attractive target for developing behavior-blocking anthelminthic drugs, but the anatomy and functional relevance of parasitic nematode chemosensory machinery are poorly understood. The goals of this study were to better understand the chemosensory apparatus and behaviors of infectious stage Brugia malayi (Spirurida: Onchocercidae), a mosquito-borne nematode and etiological agent of Lymphatic Filariasis. Scanning electron microscopy revealed that amphids, the major chemosensory organs, are present on adult B. malayi and arranged in a conserved manner. Internal sensory neuroanatomy display structural differences between life stages, and a simpler chemosensory architecture as compared to free-living nematodes. Positive and negative chemotactic behaviors were identified for a repertoire of chemicals with known chemostimulatory activity for the mosquito host that may facilitate host-selectivity and invasion. This is the first description of chemosensory anatomy and chemotactic behaviors in B. malayi that reveal the involvement of chemosensation in parasite transmission and host invasion.

Key findings

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Amphidial arrangement in B. malayi is less complex than free-living nematodes.

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Chemosensory neuroanatomy is stage-specific and simpler than free-living nematodes.

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B. malayi responses to stimuli can be measured using a plate-based assay.

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Chemostimulants associated with mosquito host-seeking induce negative and positive tropisms for L3 stage B. malayi.
Visualization of the relative contributions of conductances in neuronal models with similar behavior and different conductance densities
Authors: Alonso Leandro M. , Marder Eve
Published: September 2018

Conductance-based models of neural activity produce large amounts of data that can be hard to visualize and interpret. Here we introduce two novel visualization methods to display the dynamics of the ionic currents, and to investigate how the contribution of each current changes in response to perturbation. We explored the solutions of a single compartment, conductance-based model of neural activity with seven voltage-gated ionic currents and a leak channel. We employed landscape optimization to find sets of maximal conductances that produce similar target activity and displayed the dynamics of the currents. We examined in detail six examples of a bursting model neuron that differ as much as 3-fold in the conductance densities of each of the 8 currents in the model. The maximal conductance of each current does not simply predict the importance of the current for neuronal dynamics. We then compared the effects of systematically reducing the conductances of each current for neuronal dynamics, and demonstrate that models that appear similar under starting conditions behave dramatically differently to the decreases in conductance densities. These examples provide heuristic insight into why individuals with similar behavior can nonetheless respond widely differently to perturbations.
Molecular Nearest Neighbors Determine Generalization of Odorant Mixtures
Authors: Brackney Ryan J. , Dai Kael , Der-Ghazarian Taleen , Smith Brian H. , Gerkin Richard C.
Published: September 2018

Most natural odors arise from mixtures of multiple odorants. Some such mixtures are perceived “elementally”, with each odorant component clearly identifiable, while others are perceived “configurally”, with the mixture adopting a perceptual quality distinct from any of the components. While the perceptual similarity of two mixtures is presumably related in some way to the similarity of the corresponding components, given the elemental/configural dichotomy it is unclear if any formal principle can be used to predict mixture similarity. To investigate this problem, we trained mice to respond to a binary reference mixture of structurally similar odorants (S+) and then tested generalization of this response to other structurally related binary test mixtures. Across 5 experiments, we parametrically varied these mixtures in distinct ways to test candidate models for the perceptual similarity of mixtures. The best-performing model predicted behavioral responses by considering, for each component of theS+, only the similarity of the most structurally similar (”nearest neighbor”) component of each test mixture. We conclude that for mixture generalization tasks the olfactory system may deemphasize or discard information about mixture components not perceptually “near” enough to any of those in theS+, consistent with a sparse and elemental rule for perception of structurally-related binary mixtures.
Non-canonicalDrosophilaX chromosome dosage compensation and repressive topologically-associated domains
Authors: Lee Hangnoh , Oliver Brian
Published: September 2018

Background

In animals withXYsex chromosomes,X-linked genes from a singleXchromosome in males are imbalanced relative to autosomal genes. To minimize the impact of genic imbalance in maleDrosophila, there is a dosage compensation complex (MSL), that equilibratesX-linked gene expression with the autosomes. There are other potential contributions to dosage compensation. Hemizygous autosomal genes located in repressive chromatin domains are often de-repressed. If this homolog-dependent repression occurs on theX, which has no pairing partner, then de-repression could contribute to male dosage compensation.

Results

We asked whether different chromatin states or topological associations correlate withXchromosome dosage compensation, especially in regions with little MSL occupancy. Our analyses demonstrated that maleXchromosome genes that are located in repressive chromatin states are depleted of MSL occupancy, however they show dosage compensation. The genes in these repressive regions were also less sensitive to knockdown of MSL components.

Conclusions

Our results suggest that this non-canonical dosage compensation is due to the same trans-acting de-repression that occurs on autosomes. This mechanism would facilitate immediate compensation during the evolution of sex chromosomes from autosomes. This mechanism is similar to that ofC. elegans, where enhanced recruitment ofXchromosomes to the nuclear lamina dampensXchromosome expression as part of the dosage compensation response inXXindividuals.
Mitochondrial DNA Repair in anArabidopsis thalianaUracil N-Glycosylase Mutant
Authors: Wynn Emily , Purfeerst Emma , Christensen Alan
Published: September 2018

Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways, however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determine the repair outcomes when that pathway is missing. Surprisingly, no single nucleotide polymorphisms (SNPs) were fixed in any line in generation 11. The pattern of heteroplasmic SNPs was also unaltered through 11 generations. When the rate of cytosine deamination was increased by mitochondrial expression of the cytosine deaminase APOBEC3G, there was an increase in heteroplasmic SNPs, but only in mature leaves. Clearly DNA maintenance in reproductive meristem mitochondria is very effective in the absence of UNG, while mitochondrial genomes in differentiated tissue are maintained through a different mechanism, or not at all. Several genes involved in DSBR are upregulated in the absence of UNG, indicating that double strand break repair is a general system of repair in plant mitochondria. It is important to note that the developmental stage of tissues is critically important for these types of experiments.
Untangling the dynamics of persistence and colonization in microbial communities
Authors: Ranjeva Sylvia L. , Mihaljevic Joseph R. , Joseph Maxwell B. , Giuliano Anna R. , Dwyer Greg
Published: September 2018

A central goal of community ecology is to infer biotic interactions from observed distributions of co-occurring species. Evidence for biotic interactions, however, can be obscured by shared environmental requirements, posing a challenge for statistical inference. Here we introduce a dynamic statistical model that quantifies the effects of spatial and temporal covariance in longitudinal co-occurrence data. We separate the fixed pairwise effects of species occurrences on persistence and colonization rates, a potential signal of direct interactions, from latent pairwise correlations in occurrence, a potential signal of shared environmental responses. We apply our modeling approach to a pressing epidemiological question by examining how human papillomavirus (HPV) types coexist. Our results suggest that while HPV types respond similarly to common host traits, direct interactions are sparse and weak, so that HPV type diversity depends largely on shared environmental drivers. Our modeling approach is widely applicable to microbial communities and provides valuable insights that should lead to more directed hypothesis testing and mechanistic modeling.
Rapid CD4 cell loss is caused by specific CRF01_AE cluster with V3 signatures favoring CXCR4 usage
Authors: Song Hongshuo , Ou Weidong , Feng Yi , Zhang Junli , Li Fan , Hu Jing , Peng Hong , Xing Hui , Ma Liying , Tan Qiuxiang , Wu Beili , Shao Yiming
Published: September 2018

HIV-1 evolved into various genetic subtypes and circulating recombinant forms (CRFs) in the global epidemic, with the same subtype or CRF usually having similar phenotype. Being one of the world’s major CRFs, CRF01_AE infection was reported to associate with higher prevalence of CXCR4 (X4) viruses and faster CD4 decline. However, the underlying mechanisms remain unclear. We identified eight phylogenetic clusters of CRF01_AE in China and hypothesized that they may have different phenotypes. In the national HIV molecular epidemiology survey, we discovered that people infected by CRF01_AE cluster 4 had significantly lower CD4 count (391 vs. 470,p< 0.0001) and higher prevalence of predicted X4-using viruses (17.1% vs. 4.4%,p< 0.0001) compared to those infected by cluster 5. In a MSM cohort, X4-using viruses were only isolated from sero-convertors infected by cluster 4, which associated with rapid CD4 loss within the first year of infection (141 vs. 440,p= 0.01). Using co-receptor binding model, we identified unique V3 signatures in cluster 4 that favor CXCR4 usage. We demonstrate for the first time that HIV-1 phenotype and pathogenicity can be determined at the phylogenetic cluster level in a single subtype. Since its initial spread to human from chimpanzee in 1930s, HIV-1 remains undergoing rapid evolution in larger and more diverse population. The divergent phenotype evolution of two major CRF01_AE clusters highlights the importance in monitoring the genetic evolution and phenotypic shift of HIV-1 to provide early warning for the appearance of more pathogenic strains such as CRF01_AE cluster 4.

Significance Statement

Past studies on HIV-1 evolution were mainly at the genetic level. This study provides well-matched genotype and phenotype data and demonstrates disparate pathogenicity of two major CRF01_AE clusters. While both CRF01_AE cluster 4 and cluster 5 are mainly spread through the MSM route, cluster 4 but not cluster 5 causes fast CD4 loss, which is associated with the higher prevalence CXCR4 viruses in cluster 4. The higher CXCR4 use tendency in cluster 4 is derived from its unique V3 loop favoring CXCR4 binding. This study for the first time demonstrates disparate HIV-1 phenotype between different phylogenetic clusters. It is important to monitor HIV-1 evolution at both the genotype and phenotype level to identify and control more pathogenic HIV-1 strains.
pavo 2: new tools for the spectral and spatial analysis of colour in R
Authors: Maia Rafael , Gruson Hugo , Endler John A. , White Thomas E.
Published: September 2018

Biological colouration presents a canvas for the study of ecological and evolutionary processes. Enduring interest in colour-based phenotypes has driven, and been driven by, improved techniques for quantifying colour patterns in ever-more relevant ways, yet the need for flexible, open frameworks for data processing and analysis persists.

Here we introduce pavo 2, the latest iteration of the R package pavo. This release represents the extensive refinement and expansion of existing methods, as well as a suite of new tools for the cohesive analysis of the spectral and (now) spatial structure of colour patterns and perception. At its core, the package retains a broad focus on (a) the organisation and processing of spectral and spatial data, and tools for the alternating (b) visualisation, and (c) analysis of data. Significantly, pavo 2 introduces image-analysis capabilities, providing a cohesive workflow for the comprehensive analysis of colour patterns.

We demonstrate the utility of pavo with a brief example centred on mimicry in Heliconius butterflies. Drawing on visual modelling, adjacency, and boundary strength analyses, we show that the combined spectral (colour and luminance) and spatial (pattern element distribution and boundary salience) features of putative models and mimics are closely aligned.

pavo 2 offers a flexible and reproducible environment for the analysis of colour, with renewed potential to assist researchers in answering fundamental questions in sensory ecology and evolution.
Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies
Authors: Untaroiu Ana M. , Carey Maureen A. , Guler Jennifer L. , Papin Jason A.
Published: September 2018

Malaria is a major global health problem, with thePlasmodium falciparumprotozoan parasite causing the most severe form of the disease. Prevalence of drug-resistantP. falciparumhighlights the need to understand the biology of resistance and to identify novel combination therapies that are effective against resistant parasites. Resistance has compromised the therapeutic use of many antimalarial drugs, including chloroquine, and limited our ability to treat malaria across the world. Fortunately, chloroquine resistance comes at a fitness cost to the parasite; this can be leveraged in developing combination therapies or to reinstate use of chloroquine. To understand biological changes induced by chloroquine treatment, we compared transcriptomics data from chloroquine-resistant parasites in the presence or absence of the drug. Using both linear models and a genome-scale metabolic network reconstruction of the parasite to interpret the expression data, we identified targetable pathways in resistant parasites. This study identified an increased importance of lipid synthesis, glutathione production/cycling, isoprenoids biosynthesis, and folate metabolism in response to chloroquine. We identified potential drug targets for chloroquine combination therapies. Significantly, our analysis suggests that the combination of chloroquine and sulfadoxine-pyrimethamine or fosmidomycin may be more effective against chloroquine-resistant parasites than either drug alone; further studies will explore the use of these drugs as chloroquine resistance blockers. Additional metabolic weaknesses were found in glutathione generation and lipid synthesis during chloroquine treatment. These processes could be targeted with novel inhibitors to reduce parasite growth and reduce the burden of malaria infections. Thus, we identified metabolic weaknesses of chloroquine-resistant parasites and propose targeted chloroquine combination therapies.
Oocyte Host-Transfer and Maternal mRNA Depletion Experiments in Xenopus
Authors: Houston Douglas W.
Published: September 2018

This protocol details the oocyte host-transfer method in Xenopus, using transplantation by intraperitoneal injection. This approach is suitable for the overexpression of mRNAs and for the use of antisense oligonucleotides to deplete maternal mRNAs, which are not replaced until zygotic genome activation in the mid-blastula transition. Xenopus oocyte host-transfer can also be used for highly efficient mutagenesis in the F0 generation by prefertilization injection of genome editing reagents.
Lineage Tracing and Fate Mapping in Xenopus Embryos
Authors: Moody Sally A.
Published: September 2018

Fate mapping approaches reveal what types of cells, tissues, and organs are derived from specific embryonic cells. Classical fate maps were made by microscopic techniques using embryos comprising small numbers of transparent cells. More complex and opaque embryos require use of a vital or lipophilic dye that labels small groups of cells. Intracellular injection of a lineage tracer that labels the injected cell and all of its descendants can be used to mark a single cell in Xenopus embryos, whose large cells are easy to microinject and usually cleave in regular patterns. Intracellular lineage tracers must be neutral compounds that do not interact with cellular processes that might change the developmental fate of the injected cell, be small enough to diffuse quickly throughout the cytoplasm before the cell divides so that all descendants are labeled, and be large enough to not diffuse to adjacent cells via gap junctions. They should not be diluted by cell division or intracellular degradation, and should be easily detected by histochemical reactions (enzymes) or direct imaging (fluorescent compounds). Several types of lineage tracers have been used, including small, fluorescently tagged dextrans and mRNAs encoding enzymes or fluorescent proteins, described here. Many lineage tracers can be combined with cell type–specific mRNA and protein expression assays, making lineage tracing a powerful tool for testing the function of genes and cell fate commitment.
Cleavage Blastomere Explant Culture in Xenopus
Authors: Moody Sally A.
Published: September 2018

The individual blastomeres of Xenopus two- to 32-cell embryos have been fate mapped. This work identified the precursors of most of the embryonic cell types, tissues and organs; however, the maps do not reveal the cell interactions or signaling pathways that are required for establishing cell fates. This protocol describes an explant culture approach for culturing blastomeres in isolation to test whether a cell's fate has been determined. Cleavage blastomeres can be cultured in a simple salt medium without added factors because they contain intracellular yolk platelets, which provide an intrinsic energy source. This method allows one to test whether an isolated blastomere can produce specific cell types or express tissue-specific genes independent of interactions with other cells or specific signaling pathways. The role of cell–cell interactions can be revealed by co-culturing different sets of blastomeres. One can identify the molecules that are required for those cell fates by applying knockdown approaches to the isolated cell. One also can determine the developmental time at which cell fates are committed by explanting blastomere lineages at different stages.
Dissecting and Culturing Animal Cap Explants
Authors: Dingwell Kevin S. , Smith James C.
Published: September 2018

The animal cap explant is a simple but adaptable tool available to developmental biologists. The use of animal cap explants in demonstrating the presence of mesoderm-inducting activity in the Xenopus embryo vegetal pole is one of many elegant examples of their worth. Animal caps respond to a range of growth factors (e.g., Wnts, FGF, TGF-β), making them especially useful for studying signal transduction pathways and gene regulatory networks. Explants are also suitable for examining cell behavior and have provided key insights into the molecular mechanisms controlling vertebrate morphogenesis. In this protocol, we outline two methods to isolate animal cap explants from Xenopus laevis, both of which can be applied easily to Xenopus tropicalis. The first method is a standard manual method that can be used in any laboratory equipped with a standard dissecting microscope. For labs planning on dissecting large numbers of explants on a regular basis, a second, high throughput method is described that uses a specialized microcautery surgical instrument.
ChIP-Sequencing in Xenopus Embryos
Authors: Hontelez Saartje , van Kruijsbergen Ila , Veenstra Gert Jan C.
Published: September 2018

Chromatin immunoprecipitation (ChIP) followed by deep sequencing (ChIP-seq) is a powerful technique for mapping in vivo, genome-wide DNA–protein interactions. The interplay between DNA and proteins determines the transcriptional state of the genome. Using specific antibodies for the ChIP, it is possible to generate genome-wide profiles of histone posttranslational modifications, providing insight into the epigenetic memory and developmental potential of cells. The interactions between DNA and proteins involved in epigenetic regulation and transcription are highly dynamic during embryonic development. ChIP-seq allows for a detailed analysis of these dynamic changes in DNA–protein binding during embryogenesis. ChIP-seq is performed on protein epitopes that have been cross-linked to genomic DNA. After shearing the DNA, fragments bound by the (modified) protein of interest are captured with antibodies. The genomic loci of interest are identified by sequencing. Here, we provide a step-by-step ChIP-seq protocol that efficiently captures epitopes from relatively small embryo samples.
Following Endocrine-Disrupting Effects on Gene Expression in Xenopus laevis
Authors: Spirhanzlova Petra , Leemans Michelle , Demeneix Barbara A. , Fini Jean-Baptiste
Published: September 2018

Endocrine-disrupting chemicals (EDCs), found in all categories of chemicals, are suspected to be a cause of declining well-being and human health, both as single molecules and as mixtures. It is therefore necessary to develop high throughput methods to assess the endocrine-disrupting potential of multiple chemicals currently on the market that are as yet untested. An advantage of in vivo chemical screening is that it provides a full spectrum of physiological impacts exerted by a given chemical. Xenopus laevis is an ideal model organism to test thyroid axis disruption in vivo as thyroid hormones (THs) are highly conserved across vertebrates and orchestrate tadpole metamorphosis. In particular, NF stage 45 Xenopus laevis are most apt for in vivo screening as at this stage the tadpoles possess all the main elements of thyroid hormone signaling (thyroid receptors, deiodinases transporters) and are metabolically competent, while fitting into multiple well plates, allowing the use of small amounts of test chemicals. One way to assess the endocrine-disrupting potential of chemicals or mixtures thereof is to analyze gene expression in organisms after a short time exposure to the chemical(s). Here we describe a protocol using Xenopus laevis embryos to detect endocrine disruption of the thyroid axis by analysis of gene expression and an alternative protocol for fluorescence read-out using a transgenic GFP-expressing Xenopus laevis line. Taken together, these methods allow detection of subtle changes in TH signaling by EDCs that either activate or inhibit TH signaling in vivo.
Methods for Investigating the Larval Period and Metamorphosis in Xenopus
Authors: Buchholz Daniel R. , Shi Yun-Bo
Published: September 2018

Anuran metamorphosis resembles postembryonic development in mammals, a period around birth when many organs/tissues mature into their adult form as circulating thyroid and stress hormone levels are high. Unlike uterus-enclosed mammalian embryos, tadpoles develop externally and undergo the dramatic changes of hormone-dependent development totally independent of maternal influence, making them a valuable model in which to study vertebrate postembryonic organ development and maturation. Various protocols have been developed and/or adapted for studying metamorphosis in Xenopus laevis and X. tropicalis, two highly related and well-studied frog species. Here, we introduce some of the methods for contemporary cell and molecular studies of gene function and regulation during metamorphosis.
Melting point, molecular symmetry and aggregation of tetrachlorobenzene isomers: the role of halogen bonding
Authors: Bujak Maciej
Published: September 2018

Tetrachlorobenzenes represent one of the best known, but not yet fully understood, group of isomers of the structure–melting point relationship. The differences in melting temperatures of these structurally related compounds were rationalized in terms of the hierarchy and nature of formed noncovalent interactions, and the molecular aggregation that is influenced by molecular symmetry. The highest melting point is associated with the highly symmetric 1,2,4,5-tetrachlorobenzene isomer. The structures of less symmetrical 1,2,3,4-tetrachlorobenzene and 1,2,3,5-tetrachlorobenzene, determined at 270 and 90 K, show a distinct pattern of halogen bonds, characterized by the different numbers and types of interactions. The evolution of Cl...Cl/H distances with temperature indicates the attractive character of intermolecular interactions and their importance to the structural and thermodynamic parameters of isomeric compounds. The favoured Cl...Cl halogen bonds were found to play a decisive role in differentiating the melting temperatures of tetrachlorobenzene isomers. It was also found that, besides the molecular symmetry and ability to form specific intermolecular interactions, both the type and the distribution of interactions are the important factors responsible for the melting behaviour of the studied isomers. The observed preferences, in tetrachlorobenzenes, for the formation of specific noncovalent interactions correspond to the distribution of calculated partial atomic charges and to the magnitudes of electrostatic potential on the molecular surfaces as well as correlate with the enthalpy of melting parameters.
Crystalline transformers: more within than meets the eye
Authors: Falvello Larry R.
Published: September 2018

Studies of phase transitions in molecular crystals are becoming more commonplace as improvements in instrumentation and technique enable more efficient exploration of the behavior of samples with varying external conditions, usually temperature. This scientific commentary provides contextual background on this type of study, with reference to an article on transformations in a ferrocenyl–acetylide–gold(I) complex [Makal (2018). Acta Cryst. B74, 427–435].
Modelling of a permanent magnet synchronous machine using isogeometric analysis
Authors: Bhat Prithvi , Bontinck Zeger , Corno Jacopo , Schöps Sebastian , DeGersem Herbert
Published: September 2018

Purpose

This paper aims to propose the use of isogeometric analysis (IGA) for the simulation of electrical machines to represent their geometries exactly and obtain numerical solutions of high accuracy and regularity.

Design/methodology/approach

IGA makes use of non-uniform rational b-splines to parametrise the domain and approximate the solution spaces. Dealing with the different stator and rotor topologies, the computational domain is split into two non-overlapping parts on which Maxwell’s equations are solved independently and are interconnected by a classical Schwarz domain decomposition scheme. The results are compared with the conventional polynomial finite element method (FEM).

Findings

The new methodology is reliable and efficient. The obtained solutions of the fields are in good agreement with the ones obtained by the FEM approach. IGA offers a better accuracy than FEM.

Originality/value

The application of IGA combined with domain decomposition to the model of an electric machine is a new and original contribution.
3D harmonic modeling of eddy currents in segmented conducting structures
Authors: Custers C.H.H.M. , Jansen J.W. , van Beurden M.C. , Lomonova E.A.
Published: September 2018

Purpose

The purpose of this paper is to describe a semi-analytical modeling technique to predict eddy currents in three-dimensional (3D) conducting structures with finite dimensions. Using the developed method, power losses and parasitic forces that result from eddy current distributions can be computed.

Design/methodology/approach

In conducting regions, the Fourier-based solutions are developed to include a spatially dependent conductivity in the expressions of electromagnetic quantities. To validate the method, it is applied to an electromagnetic configuration and the results are compared to finite element results.

Findings

The method shows good agreement with the finite element method for a large range of frequencies. The convergence of the presented model is analyzed.

Research limitations/implications

Because of the Fourier series basis of the solution, the results depend on the considered number of harmonics. When conducting structures are small with respect to the spatial period, the number of harmonics has to be relatively large.

Practical implications

Because of the general form of the solutions, the technique can be applied to a wide range of electromagnetic configurations to predict, e.g. eddy current losses in magnets or wireless energy transfer systems. By adaptation of the conductivity function in conducting regions, eddy current distributions in structures containing holes or slit patterns can be obtained.

Originality/value

With the presented technique, eddy currents in conducting structures of finite dimensions can be modeled. The semi-analytical model is for a relatively low number of harmonics computationally faster than 3D finite element methods. The method has been validated and shown to be computationally accurate.
Teaching marketing to non-marketers: some experiences from New Zealand and the UK
Authors: Crick James M.
Published: September 2018

Purpose

The purpose of this paper is to explore how marketing can be taught to students originating from non-marketing or non-business backgrounds (non-marketers), so that academics can engage such students in lectures and tutorials.

Design/methodology/approach

The research design involved a qualitative methodology using data from two undergraduate marketing courses (one in New Zealand and one in the UK) that contained a large proportion of non-marketing students. Data were collected from a combination of empirical and archival sources and were analysed using self-reflection techniques, alongside other checks for methodological credibility.

Findings

When teaching marketing to non-marketing students, it is important to integrate theory with practice to help their learning (e.g. through practical case studies). Marketing educators must also maximise their interactivity with their students and have in-class discussions to engage the cohort. Further, lecturers and tutors should relate marketing theories and concepts with non-business subjects to demonstrate the subject’s relevance to students with limited commercial knowledge. These teaching and learning strategies were important for students intending to become entrepreneurs after graduating from university, as well as those planning to enter paid employment.

Originality/value

Prior studies have focussed on teaching marketing to specialist marketing students; however, they have scarcely considered how educators can teach non-specialist marketing to students with non-marketing and non-business backgrounds. This viewpoint solves this research problem, by discussing the best ways that academics can maximise such students’ engagement. It is proposed that the main way that non-marketers can be engaged is through linking marketing with their subjects-of-origin, to demonstrate how marketing activities apply to all organisations and should not be overlooked. A framework is presented, based on the empirical data, to help academics teach marketing to non-marketers. This paper ends with some directions for future research.
Research on 3D reconstruction of late Victorian riding skirts
Authors: Kuzmichev Victor , Moskvin Aleksei , Moskvina Mariia , Pryor Jane
Published: September 2018

Purpose

Virtual design of contemporary and historical clothes is a very intensive and developing area of science that can be considered as a bridge between costume heritage and modern way of its presentation by means of CAD. The purpose of this paper is to apply 2D and 3D existing CAD for virtual reconstruction of the very specific kind of women’s clothes such as a side-saddle riding habit (RH) used in 1875–1915.

Design/methodology/approach

The construction of RH was adapted to the aesthetic rules of the mentioned time, ergonomic posture of a woman sitting on a horse, surface of the horse’s body which the woman is sitting on. For the new method, the huge databases were obtained after analyzing the historical pattern manuals and features of pattern blocks used, possible postures of riding, construction of RH and converting it into virtual system “avatar – RH.” To reconstruct the side-saddle RH in virtual reality, the images dated 1887 and authentic pattern blocks were used. Special attention has been given to the topology of contacting areas existing between the sitting woman and “shaped” riding skirt and to the method of presenting it by means of special points combination.

Findings

The authors have developed a new method of virtual reconstruction of an RH that is based on automatic consideration of all joining elements such as “shaped” riding skirt, avatar and its ergonomic posture. The new approach allows reconstruction of the clothes in virtual reality in three ways: by using the real skirts, the historical pattern blocks or pictures.

Originality/value

The results obtained allow increased possibilities of virtual reconstruction and include in the list new objects of engineering achievements of the nineteenth century such as the side-saddle RH. This study should help researchers and practical specialists to recreate and save the historical treasure in a digital way.