bluuebunny/crossref_metadata_2025 huggingface dataset:
A climosequence of chronosequences in southwestern Australia
Authors: Turner Benjamin L. , Hayes Patrick E. , Laliberté Etienne
Published: March 2017

To examine how climate affects soil development and nutrient availability over long timescales, we studied a series of four long-term chronosequences along a climate gradient in southwestern Australia. Annual rainfall ranged from 533 mm to 1185 mm (water balance from –900 mm to +52 mm) and each chronosequence included Holocene (≤6.5 ka), Middle Pleistocene (120–500 ka), and Early Pleistocene (∼2000 ka) dunes. Vegetation changed markedly along the climosequence, from shrubland at the driest site toEucalyptusforest at the wettest. The carbonate and P content of the parent sand declined along the climosequence, presumably linked to variation in offshore productivity. However, soil development and associated nutrient status followed remarkably consistent patterns along the four chronosequences. Pedogenesis involved decalcification and secondary carbonate precipitation in Holocene soils and leaching of iron oxides from Middle Pleistocene soils, ultimately yielding bleached quartz sands on the oldest soils. Along all chronosequences soil pH and total P declined, while C:P and N:P ratios increased, consistent with the predicted shift from N to P limitation of vegetation during ecosystem development. The expected unimodal pattern of leaf area index was most pronounced along wetter chronosequences, suggesting an influence of climate on the expression of retrogression. The four chronosequences do not appear to span a pedogenic climate threshold, because exchangeable phosphate and base cations declined consistently during long-term pedogenesis. However, the proportion of the total P in organic form was greater along wetter chronosequences. We conclude that soils and nutrient availability on the coastal sand plains of southwestern Australia change consistently during long-term pedogenesis, despite marked variation in modern vegetation and climate. The four chronosequences provide a rare soil-age × climate framework within which to study long-term ecosystem development.
Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer
Authors: Volders Pieter-Jan , Vandesompele Jo , Lefever Steve , Baute Shalina , Nuytens Justine , Vanderheyden Katrien , Menten Björn , Mestdagh Pieter
Published: March 2017

The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancer remains largely unexplored. While the majority of lncRNAs remains to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that is currently reported, it is conceivable that several lncRNAs might function as oncogenes or tumor suppressor genes.

We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 20 418 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs involved in cancer pathogenesis.
Negative frequency-dependent selection is frequently confounding
Authors: Brisson Dustin
Published: March 2017

This preprint has been reviewed and recommended by Peer Community in Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100024).The existence of persistent genetic variation within natural populations presents an evolutionary problem as natural selection and genetic drift tend to erode genetic diversity. Models of balancing selection were developed to account for the high and sometimes extreme levels of polymorphism found in many natural populations. Negative frequency-dependent selection may be the most powerful selective force maintaining balanced natural polymorphisms but it is also commonly misinterpreted. The aim of this review is to clarify the processes underlying negative frequency-dependent selection, describe classes of natural polymorphisms that can and cannot result from these processes, and discuss observational and experimental data that can aid in accurately identifying the processes that generated or are maintain diversity in nature. Finally, I consider the importance of accurately describing the processes affecting genetic diversity within populations as it relates to research progress.
An indicator cell assay for blood-based diagnostics
Authors: Danziger Samuel A. , Miller Leslie R. , Singh Karanbir , Whitney G. Adam , Peskind Elaine R. , Li Ge , Lipshutz Robert J. , Aitchison John D. , Smith Jennifer J.
Published: March 2017

We have established proof of principle for the Indicator Cell Assay Platform™ (iCAP™), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patients’ blood. To develop an assay, indicator cells are exposedin vitroto serum from case or control subjects and their global differential response patterns are used to train reliable, cost-effective disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified samples from a murine Huntington’s disease model as non-carriers of ALS. In a preliminary human disease assay, the iCAP detected early stage Alzheimer’s disease with 72% cross-validated accuracy (p-Value=3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assay’s relevance for disease research.
The exported chaperone PfHsp70x is dispensable for thePlasmodium falciparumintraerythrocytic lifecycle
Authors: Cobb David W. , Florentin Anat , Fierro Manuel A. , Krakowiak Michelle , Moore Julie M. , Muralidharan Vasant
Published: March 2017

Export of parasite proteins into the host erythrocyte is essential for survival ofPlasmodium falciparumduring its asexual lifecycle. While several studies described key factors within the parasite that are involved in protein export, the mechanisms employed to traffic exported proteins within the host cell are currently unknown. Members of the Hsp70 family of chaperones, together with their Hsp40 co-chaperones, facilitate protein trafficking in other organisms, and are thus likely used byP. falciparumin the trafficking of its exported proteins. A large group of Hsp40 proteins is encoded by the parasite and exported to the host cell, but only one Hsp70, PfHsp70x, is exported with them.

PfHsp70x is absent from mostPlasmodiumspecies and is found only inP. falciparumand closely-related species that infect Apes. Herein, we have utilized CRISPR/Cas9 genome editing inP. falciparumto investigate the essentiality of PfHsp70x. We show that parasitic growth was unaffected by knockdown of PfHsp70x using both the DHFR-based Destabilization Domain and theglmSribozyme system. Similarly, a complete gene knockout of PfHsp70x did not affect the ability ofP. falciparumto proceed through its intraerythrocytic lifecycle. The effect of PfHsp70x knockdown/knockout on the export of proteins to the host RBC, including the critical virulence factor PfEMP1, was tested and we found that this process was unaffected. These data show that although PfHsp70x is the sole exported Hsp70, it is not essential for the asexual development ofP. falciparum.

Importance

Half of the world’s population lives at risk for malaria. The intraerythrocytic lifecycle ofPlasmodiumspp. is responsible for clinical manifestations of malaria; therefore, knowledge of the parasite’s ability to survive within the erythrocyte is needed to combat the deadliest agent of malaria,P. falciparum. An outstanding question in the field is howP. falciparumundertakes the essential process of trafficking its proteins within the host cell. In most organisms, chaperones such as Hsp70 are employed in protein trafficking. Of the human-disease causing Plasmodium species, the chaperone PfHsp70x is unique toP. falciparum,and it is the only parasite protein of its kind exported to the host (1). This has placed PfHsp70x as an ideal target to inhibit protein trafficking and kill the parasite. However, we show that PfHsp70x is not required for export of parasite effectors nor is it essential for parasite survival inside of the RBC.
Individual differences in frequency and topography of slow and fast sleep spindles
Authors: Cox Roy , Schapiro Anna C. , Manoach Dara S. , Stickgold Robert
Published: March 2017

Sleep spindles are transient oscillatory waveforms occurring during non-rapid eye movement (NREM) sleep and are implicated in plasticity and memory processes. In humans, spindles can be classified as either slow or fast, but large individual differences in spindle frequency as well as methodological difficulties have hindered progress towards understanding their function. Using two nights of high-density electroencephalography recordings from healthy individuals, we first characterize the individual variability of NREM spectra and demonstrate the difficulty of determining subject-specific spindle frequencies. We then introduce a novel spatial filtering approach that can reliably separate subject-specific spindle activity into slow and fast components that are stable across nights and across N2 and N3 sleep. We then proceed to provide detailed analyses of the topographical expression of individualized slow and fast spindle activity. Group-level analyses conform to known spatial properties of spindles, but also uncover novel differences between sleep stages and spindle classes. Moreover, subject-specific examinations reveal that individual topographies show considerable variability that is stable across nights. Finally, we demonstrate that topographical maps depend nontrivially on the spindle metric employed. In sum, our findings indicate that group-level approaches mask substantial individual variability of spindle dynamics, in both the spectral and spatial domains. We suggest that leveraging, rather than ignoring, such differences may prove useful to further our understanding of the physiology and functional role of sleep spindles.
Image processing techniques for high-resolution structure determination from badly ordered 2D crystals
Authors: Biyani Nikhil , Scherer Sebastian , Righetto Ricardo D. , Kowal Julia , Chami Mohamed , Stahlberg Henning
Published: March 2017

2D electron crystallography can be used to study small membrane proteins in their native environment. Obtaining highly ordered 2D crystals is difficult and time-consuming. However, 2D crystals diffracting to only 10-12 Å can be prepared relatively conveniently in most cases. We have developed image-processing algorithms allowing to generate a high resolution 3D structure from cryo-electron crystallography images of badly ordered crystals. These includemovie-mode unbending, refinement over sub-tiles of the images in order to locally refine the sample tilt geometry; implementation of different CTF correction schemes; and an iterative method to apply known constraints in the real and reciprocal space to approximate amplitudes and phases in the so-called missing cone regions. These algorithms applied to a dataset of the potassium channel MloK1 show significant resolution improvements to approximately 5Å.

Abbreviations

2D

two dimensions / dimensional

3D

three dimensions / dimensional

Amp

amplitude

cAMP

cyclic adenosine monophosphate

CCD

charge coupled devices

CMOS

complementary metal-oxide-semiconductor

CNBD

cyclic nucleotide-binding domain

cryo-EM

cryo-electron microscopy

CTF

contrast transfer function

DED

direct electron detector

DQE

detector quantum efficiency

EM

electron microscope

FOM

figure-of-merit

Pha

phase

SNR

signal-to-noise ratio
Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection
Authors: Greninger Alexander L. , Pepper Gregory , Shean Ryan C. , Cent Anne , Palileo Isabel , Kuypers Jane M. , Schiffer Joshua T. , Jerome Keith R.
Published: March 2017

We describe metagenomic next-generation sequencing (mNGS) of a human coronavirus 229E from a patient with AML and persistent upper respiratory symptoms, who underwent hematopoietic cell transplantation (HCT). mNGS revealed a 548-nucleotide deletion, which comprised the near entirety of the ORF4 gene, and no minor allele variants were detected to suggest a mixed infection. As part of her pre-HCT conditioning regimen, the patient received myeloablative treatment with cyclophosphamide and 12 Gy total body irradiation. Iterative sequencing and RT-PCR confirmation of 4 respiratory samples over the 4-week peritransplant period revealed that the pre-conditioning strain contained an intact ORF4 gene, while the deletion strain appeared just after conditioning and persisted over a 2.5-week period. This sequence represents one of the largest genomic deletions detected in a human RNA virus and describes large-scale viral mutation associated with myeloablation for HCT.
Cartilage microRNA dysregulation in mouse osteoarthritis overlaps with patient disease candidates
Authors: Kung Louise H. W. , Ravi Varshini , Rowley Lynn , Angelucci Constanza , Fosang Amanda J , Bell Katrina M , Little Christopher B , Bateman John F
Published: March 2017

To explore the role of microRNAs in osteoarthritis (OA), we conducted microRNA expression profiling on micro-dissected tibial cartilage and subchondral bone in a mouse model of OA produced by medial meniscus destabilization (DMM). DMM mice had characteristic cartilage degeneration, subchondral bone sclerosis and osteophyte formation. While subchondral bone showed no microRNA dysregulation, 139 microRNAs were differentially expressed in DMM cartilage at 1 and/or 6 weeks after OA initiation. To prioritize OA-candidates, dysregulated microRNAs with human orthologues were filtered using paired microRNA:mRNA expression analysis to identify those with corresponding changes in mRNA target transcripts in the DMM cartilage. An important cohort overlapped with microRNAs identified in human end-stage OA. Comparisons with microRNAs dysregulation in DMM mouse cartilage where aggrecan cleavage was genetically-ablated demonstrated that all were independent of aggrecan breakdown, earmarking these as important to the critical stages of OA initiation. Our comprehensive analyses identified high-priority microRNA candidates that have potential as human OA-biomarkers and therapeutic targets.

Kung et al. conducted global analysis of microRNA dysregulation in joint tissues of a well-established mouse osteoarthritis model. Stringent filtering against human microRNA orthologues, integrated mRNA target analysis and comparison with published studies on human end-stage osteoarthritis identified microRNA candidates of potential clinical relevance.
Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing
Authors: Ushio Masayuki , Murakami Hiroaki , Masuda Reiji , Sado Tetsuya , Miya Masaki , Sakurai Sho , Yamanaka Hiroki , Minamoto Toshifumi , Kondoh Michio
Published: March 2017

Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analyzing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, we added internal standard DNAs (i.e., known amounts of short DNA fragments from fish species that have never been observed in a sampling area) to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Kyoto, Japan (from April 2015 to March 2016), and performed metabarcoding analysis using Illumina MiSeq to simultaneously identify fish species and quantify fish eDNA copy numbers. A correction equation was obtained for each sample using the relationship between the number of sequence reads and the added amount of the standard DNAs, and this equation was used to estimate the copy numbers from the sequence reads of non-standard fish eDNA. The calculated copy numbers showed significant positive correlation with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled useful quantification of eDNA. Furthermore, for samples that show a high level of PCR inhibition, our method might allow more accurate quantification than qPCR because the correction equations generated using internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced > 70 quantitative fish eDNA time series in our study, showing that our method could contribute to more efficient and quantitative monitoring of biodiversity.
Intratumor Heterogeneity and Circulating Tumor Cell Clusters
Authors: Ahmed Zafarali , Gravel Simon
Published: March 2017

Genetic diversity plays a central role in tumor progression, metastasis, and resistance to treatment. Experiments are shedding light on this diversity at ever finer scales, but interpretation is challenging. Using recent progress in numerical models, we simulate macroscopic tumors to investigate the interplay between growth dynamics, microscopic composition, and circulating tumor cell cluster diversity. We find that modest differences in growth parameters can profoundly change microscopic diversity. Simple outwards expansion leads to spatially segregated clones and low diversity, as expected. However, a modest cell turnover can result in an increased number of divisions and mixing among clones resulting in increased microscopic diversity in the tumor core. Using simulations to estimate power to detect such spatial trends, we find that multiregion sequencing data from contemporary studies is marginally powered to detect the predicted effects. Slightly larger samples, improved detection of rare variants, or sequencing of smaller biopsies or circulating tumor cell clusters would allow one to distinguish between leading models of tumor evolution. The genetic composition of circulating tumor cell clusters, which can be obtained from non-invasive blood draws, is therefore informative about tumor evolution and its metastatic potential.

Highlights

Numerical and theoretical models show interaction of front expansion, mutation, and clonal mixing in shaping tumor heterogeneity.

Cell turnover increases intratumor heterogeneity.

Simulated circulating tumor cell clusters and microbiopsies exhibit substantial diversity with strong spatial trends.

Simulations suggest attainable sampling schemes able to distinguish between prevalent tumor growth models.
Signatures of natural selection in the drug metabolizing enzyme genes: Opportunity for developing personalized and precision medicine
Authors: Nizamuddin Sheikh , Thangaraj K.
Published: March 2017

Modern human experienced various selective pressures; including range of xenobiotics which contributed to heterogeneity of drug response. Many genes involve in pharmacokinetics and dynamics of drug, have been reported under natural selection. However, none of the studies have utilized comprehensive information of drug-centered PharmGKB pathways. We have extended this work and aimed to investigate sweep signals, using 1,798 subjects, from 53 Indian and 15 other world populations. We observed that modifiers which alters the biochemical function of other genes, have excess of natural selection (median std-z score=0.033±0.95; p-value=1.7×10−9-3.7×10−3). Taxane and statin primarily used for chemotherapy and lowering cholesterol level, respectively; and well known for heterogeneous drug response. We observed that pharmacokinetic pathway of taxane and statins are under natural selection (p-value=2.53×10−9and 2.73×10−9-1.09×10−4; q-value=1.28×10−7and 6.91×10−6-1.1×10−3). We also observed signal of selection in Ibuprofen pharmacokinetics (p-value=1.76×10−5; q-value =2.22×10−4), beta-agonist/beta-blocker pharmacodynamics (p-value=4.79×10−4; q-value =4.04×10−4) and Zidovudin pharmacokinetics/dynamic pathway (p-value=7.0×10−4; q-value =5.06×10−4). Hard sweeps signals were observed in a total of 322 loci. Of which, 53 affect mRNA expression (p-value<0.001) and 16 were already reported with therapeutic response. Interestingly, we observed that Africans have experience 2 phases of natural selection, one at ~30,000 another at ~10,000 years before present.
Reduced representation optical methylation mapping (R2OM2)
Authors: Grunwald Assaf , Sharim Hila , Gabrieli Tslil , Michaeli Yael , Torchinsky Dmitry , Arieli Rani , Juhasz Matyas , Wagner Kathryn R , Pevsner Jonathan , Reifenberger Jeff , Hastie Alex R , Cao Han , Weinhold Elmar , Ebenstein Yuval
Published: March 2017

Reduced representation methylation analysis utilizes a subset of CpGs in order to report the overall methylation status of the probed genomic regions. Here, we use this concept in order to create fluorescent optical methylation profiles along chromosomal DNA molecules for epigenetic profiling. Reduced representation optical methylation mapping (R2OM2) in combination with Bionano Genomics next generation genome mapping (NGM) technology provides a hybrid genetic/epigenetic genome map of individual chromosome segments spanning hundreds of kilobase pairs (kbp). These long reads, along with the single-molecule resolution, allow for epigenetic variation calling and methylation analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell next generation sequencing (NGS). We show that in addition to the inherent long-read benefits of R2OM2, it provides genomic methylation patterns comparable to whole genome bisulfite sequencing (WGBS) while retaining single-molecule information. The method is applied here to detect methylation along genes, around regulatory histone marks and to study facioscapulohumeral muscular dystrophy (FSHD), simultaneously recording the haplotype, copy number and methylation status of the disease-associated, highly repetitive locus onchromosome 4q.
REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial genomes
Authors: Ndah Elvis , Jonckheere Veronique , Giess Adam , Valen Eivind , Menschaert Gerben , Van Damme Petra
Published: March 2017

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), ade novoalgorithm that takes advantage of experimental protein translation evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs. Our predictions were supported by matching mass spectrometry (MS) proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to performde novoORF delineation in bacterial genomes irrespective of the sequence context of the reading frame.
Representing Genetic Determinants in Bacterial GWAS with Compacted De Bruijn Graphs
Authors: Jaillard Magali , Tournoud Maud , Lima Leandro , Lacroix Vincent , Veyrieras Jean-Baptiste , Jacob Laurent
Published: March 2017

Motivation

Antimicrobial resistance has become a major worldwide public health concern, calling for a better characterization of existing and novel resistance mechanisms. GWAS methods applied to bacterial genomes have shown encouraging results for new genetic marker discovery. Most existing approaches either look at SNPs obtained by sequence alignment or consider sets of kmers, whose presence in the genome is associated with the phenotype of interest. While the former approach can only be performed when genomes are similar enough for an alignment to make sense, the latter can lead to redundant descriptions and to results which are hard to interpret.

Results

We propose an alignment-free GWAS method detecting haplotypes of variable length associated to resistance, using compacted De Bruijn graphs. Our representation is flexible enough to deal with very plastic genomes subject to gene transfers while drastically reducing the number of features to explore compared to kmers, without loss of information. It accomodates polymorphisms in core genes, accessory genes and noncoding regions. Using our representation in a GWAS leads to the selection of a small number of entities which are easier to visualize and interpret than fixed-length kmers. We illustrate the benefit of our approach by describing known as well as potential novel determinants of antimicrobial resistance inP. aeruginosa,a pathogenic bacteria with a highly plastic genome.

Availability and implementation

The code and data used in the experiments will be made available upon acceptance of this manuscript.

Contact

magali.dancette@biomerieux.com
Development of a Novel CD4+TCR Transgenic Line that Reveals a Dominant Role for CD8+DC and CD40-Signaling in the Generation of Helper and CTL Responses to Blood Stage Malaria
Authors: Fernandez-Ruiz Daniel , Lau Lei Shong , Ghazanfari Nazanin , Jones Claerwen M , Ng Wei Yi , Davey Gayle M , Berthold Dorothee , Holz Lauren , Kato Yu , Bayarsaikhan Ganchimeg , Hendriks Sanne H. , James Kylie R , Cozijnsen Anton , Mollard Vanessa , de Koning-Ward Tania F , Gilson Paul R , Kaisho Tsuneyasu , Haque Ashraful , Crabb Brendan S , Carbone Francis R , McFadden Geoffrey I. , Heath William R
Published: March 2017

We describe an MHC II (IAb)-restricted T cell receptor (TCR) transgenic mouse line that produces CD4+T cells specific forPlasmodiumspecies. This line, termed PbT-II, was derived from a CD4+T cell hybridoma generated to blood-stagePlasmodium bergheiANKA (PbA). PbT-II cells responded to allPlasmodiumspecies and stages tested so far, including rodent (PbA,P. bergheiNK65,P. chabaudiAS andP. yoelii17XNL) and human (P.falciparum)blood-stage parasites as well as irradiated PbA sporozoites. PbT-II cells can provide help for generation of antibody toP. chabaudiinfection and can control this otherwise lethal infection in CD40L-deficient mice. PbT-II cells can also provide help for development of CD8+T cell-mediated experimental cerebral malaria (ECM) during PbA infection. Using PbT-II CD4+ T cells and the previously described PbT-I CD8+T cells, we determined the dendritic cell (DC) subsets responsible for immunity to PbA blood-stage infection. CD8+DC (a subset of XCR1+DC) were the major antigen presenting cell (APC) responsible for activation of both T cell subsets, though other DC also contributed to CD4+T cell responses. Depletion of CD8+DC at the beginning of infection prevented ECM development and impaired both Th1 and Tfh responses; in contrast, late depletion did not affect ECM. This study describes a novel and versatile tool for examining CD4+T cell immunity during malaria and provides evidence that CD4+T cell help, acting via CD40L signalling, can promote immunity or pathology to blood stage malaria largely through antigen presentation by CD8+DC.
Rational design of proteins that exchange on functional timescales
Authors: Davey James A. , Damry Adam M. , Goto Natalie K. , Chica Roberto A.
Published: March 2017

Proteins are intrinsically dynamic molecules that can exchange between multiple conformational states, enabling them to carry out complex molecular processes with extreme precision and efficiency. Attempts to design novel proteins with tailored functions have mostly failed to yield efficiencies matching those found in nature because standard methods do not allow for the design of exchange between necessary conformational states on a functionally-relevant timescale. Here, we develop a broadly-applicable computational method to engineer protein dynamics that we term meta-multistate design. We used this methodology to design spontaneous exchange between two novel conformations introduced into the global fold of Streptococcal protein G domain β1. The designed proteins, named DANCERs, forDynamic And Native Conformational ExchangeRs, are stably folded and exchange between predicted conformational states on the millisecond timescale. The successful introduction of defined dynamics on functional timescales opens the door to new applications requiring a protein to spontaneously access multiple conformational states.
Determinants of participating in training: a Canadian-based analysis
Authors: Weaver Robert , Habibov Nazim
Published: March 2017

Purpose

The purpose of this paper is to estimate and compare the across-time individual and contextual factors influencing the participation of Canadian residents in adult education and training during the 1990s and the early twenty-first century. This era is characterized by the social investment state (SIS), a policy paradigm adopted by various developed nations throughout the world, including Canada, during the latter part of the twentieth century.

Design/methodology/approach

The authors analyzed data obtained from the 1994, 1998, and 2003 versions of the Adult Education and Training Survey, which is administered by Statistics Canada. They employed binomial logit regression so as to predict the likelihood of the respondents participating in training.

Findings

Participants whose level of education was below the post-secondary level were less likely to participate in training, as were adult residents of households in which pre-school children also lived. These findings occurred across all three periods of data collection. Furthermore, urban residents exhibited an increasingly greater likelihood to participate in training across-time.

Research limitations/implications

Future studies should consider the funding source for training, be it from the public or private sector, and how this may affect participation. The impact that various types of training have on employment and earning patterns in developed nations should also be further assessed.

Originality/value

This study, with its use of the most recent available data to analyze across-time changes in the determinants of participating in training in Canada, has contributed to the knowledge base regarding the SIS in Canada and how it compares to its European counterparts.
Dual recombinant Lactococcus lactis for enhanced delivery of DNA vaccine reporter plasmid pPERDBY
Authors: Yagnik Bhrugu , Sharma Drashya , Padh Harish , Desai Priti
Published: March 2017

Food grade Lactococcus lactis has been widely used as an antigen and DNA delivery vehicle. We have previously reported the use of non‐invasive L. lactis to deliver the newly constructed immunostimulatory DNA vaccine reporter plasmid, pPERDBY. In the present report, construction of dual recombinant L. lactis expressing internalin A of Listeria monocytogenes and harboring pPERDBY (LL InlA + pPERDBY) to enhance the efficiency of delivery of DNA by L. lactis is outlined. After confirmation and validation of LL InlA + pPERDBY, its DNA delivery potential was compared with previously developed non‐invasive r‐ L. lactis::pPERDBY. The use of invasive L. lactis resulted in around threefold increases in the number of enhanced green fluorescent protein‐expressing Caco‐2 cells. These findings reinforce the prospective application of invasive strain of L. lactis for delivery of DNA/RNA and antigens.
Caregiver perceptions of inclusive playgrounds targeting toddlers and preschoolers with disabilities: has recent international and national policy improved overall satisfaction?
Authors: Stanton‐Chapman Tina L. , Schmidt Eric L.
Published: March 2017

The purpose of the current study was to survey and interview caregivers of children with disabilities (ages 2–5 years) to obtain their input as to whether current playground equipment meets their child's needs. A total of 149 participants agreed to participate. Caregivers (i) indicated that their child with a disability could not fully participate in the playground's offerings, (ii) felt that the playground was not appropriate for their child with a disability and (iii) dreamed of a fully inclusive playground that met their child's needs. The results also demonstrate that social participation barriers continue to remain for families who have children with disabilities despite the passing of international human rights standards targeting individuals with disabilities and a global focus in improving the overall well‐being of children with disabilities.
Examining the physical and human dichotomy in geography: existing divisions and possible mergers in pedagogic outlooks
Authors: Dasgupta Rajarshi , Patel Priyank Pravin
Published: March 2017

The physical‐human dichotomy in geography is long standing, revolving around the topics studied and outlooks adopted by the two groups of geographers. Three reasons are identified for its continuation—the present structure of academic geography, constrained interactions between physical and human geographers, and their publication strategies. Critics suggest that physical and human geography have become divergent strains because the physical environment has been accorded little relevance in human geographic studies, also putting forward the failure of physical geographers to integrate the human influence on physical processes and neglecting space in their studies. Citing examples, this paper argues that physical and human geography influence each other. It also demonstrates that physical geographers have sufficiently considered both space and time, and even space‐time, through the concepts of scale and ergodicity. Some measures have been proposed to resuscitate the links between these two branches. These are reconnecting university and school geography, merging departments, teaching courses on geographical philosophies and theory building, engaging in integrative discourses, innovative classroom strategies, joint fieldwork, using geoinformatics, and conducting collaborative research. The paper concludes that physical and human geographers must communicate with each other more and engage in cross‐disciplinary studies. Otherwise, they might undermine their responsibilities as geographers and spatial thinkers/analysts.
Genome‐wide survey of nuclear protein‐coding markers for beetle phylogenetics and their application in resolving both deep and shallow‐level divergences
Authors: Che Li‐Heng , Zhang Shao‐Qian , Li Yun , Liang Dan , Pang Hong , Ślipiński Adam , Zhang Peng
Published: March 2017

Beetles (Coleoptera) are the most diverse and species‐rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of ‘traditional markers’ (e.g. mitochondrial genes and nuclearrDNAs) for beetle phylogenetics is small, and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome‐wide survey to search nuclear protein‐coding (NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community forNPCmarker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95NPCmarkers which can bePCRamplified from standard genomicDNAextracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support >95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the ‘traditional markers’, and show great potential to expedite resolution of many parts in the Beetle Tree of Life.
Integrative review of older adult loneliness and social isolation in Aotearoa/New Zealand
Authors: Wright‐St Clair Valerie A , Neville Stephen , Forsyth Vanessa , White Lindsey , Napier Sara
Published: March 2017

Objective

To conduct an integrative review of empirical studies of loneliness for older people in Aotearoa/New Zealand. Loneliness is a risk factor for older people's poor physical and cognitive health, serious illness and mortality. A national survey showed loneliness rates vary by gender and ethnicity.

Methods

A systematic search of health and social science databases was conducted. Of 21 scrutinised articles, nine were eligible for inclusion and subjected to independent quality appraisal. One qualitative and eight quantitative research articles were selected.

Results

Reported levels and rates of loneliness vary across age cohorts. Loneliness was significantly related to social isolation, living alone, depression, suicidal ideation, being female, being Māori and having a visual impairment. Qualitatively, older Korean immigrants experienced loneliness and social isolation, along with language and cultural differences.

Conclusion

Amongst older New Zealanders loneliness is commonly experienced by particular ethnic groups, highlighting a priority for targetted health and social services.
Interferon‐γ‐induced insufficient autophagy contributes to p62‐dependent apoptosis of epithelial cells in chronic rhinosinusitis with nasal polyps
Authors: Wang B‐F. , Cao P‐P. , Wang Z‐C. , Li Z‐Y. , Wang Z‐Z. , Ma J. , Liao B. , Deng Y‐K. , Long X‐B. , Xu K. , Wang H. , Wang H. , Zeng M. , Lu X. , Liu Z.
Published: March 2017

Background

Autophagy is a lysosomal degradation pathway that is essential for cell survival, differentiation, and homeostasis. This study aimed to investigate the contribution of autophagy to the pathogenesis of CRS with nasal polyps (CRSwNP).

Methods

The expression of autophagic proteins [microtubule‐associated protein 1 light chain 3B (LC3B)‐II, autophagy‐related proteins (Atg), and Beclin 1], substrate proteins (p62 and ubiquitinated proteins), and apoptotic signaling molecules [cysteine‐aspartic protease‐3 and cysteine‐aspartic protease‐8, and poly‐ADP‐ribose polymerase] in the sinonasal mucosa and nasal epithelial cells (NECs) was detected by immunohistochemistry and Western blotting. Autophagic vacuoles were observed with transmission electron microscopy. BEAS‐2B cells and NECs were treated with rapamycin, bafilomycin A1, or various cytokines. In some experiments, cultured NECs were transfected with small interfering RNA targeting p62 (sip62) or Atg5 (siAtg5). Cultured cells were analyzed with Western blotting and flow cytometry.

Results

Although autophagic protein expression and autophagic vacuole formation were increased in both eosinophilic and noneosinophilic CRSwNP, particularly in NECs, there was also an up‐regulation of substrate proteins and apoptotic signaling molecules. IFN‐γ, but not IL‐4, IL‐13, or IL‐17A, simultaneously enhanced LC3B‐II and p62 levels as well as cell apoptosis in BEAS‐2B cells and/or normal NECs. Bafilomycin A1 up‐regulated the levels of LC3B‐II and p62 in polyp NECs and IFN‐γ‐treated normal NECs. IFN‐γ‐induced apoptosis of normal NECs was exaggerated by bafilomycin A1 and siAtg5. Sip62 suppressed apoptosis of polyp NECs and IFN‐γ‐treated NECs. IFN‐γ protein levels were increased in both eosinophilic and noneosinophilic CRSwNP.

Conclusions

IFN‐γ induces activated but insufficient autophagy and thus contributes to a degree to p62‐dependent apoptosis of NECs in CRSwNP.
Changes in lipidomic profile of aqueous humour in Fuchs endothelial dystrophy
Authors: Cabrerizo Javier , Urcola Javier Aritz , Vecino Elena , Melles Gerrit
Published: March 2017

Purpose

To identify and determine differences in lipid profile of aqueous humour (AH) in patients with Fuchs endothelial corneal dystrophy (FECD).

Methods

Lipidomic profile of eight AH samples of FECD patients and 10 control samples was analysed. Patients with previous history of anterior segment surgery, anterior segment pathology or intraocular injections were excluded. Topical ocular medications within the last 6 months were reported. Aqueous humour (AH) was obtained during the first step of Descemet membrane endothelial keratoplasty in FECD patients and during refractive lensectomy in the control group. Lipidomic ultra‐performance liquid chromatography mass spectrometry was used to perform an optimal profiling of glycerolipids, sterol lipids, sphingolipids and glycerophospholipids. Metabolite extraction was accomplished by fractionating the samples into pools of species with similar physicochemical properties.

Results

The levels of 27 of 110 lipids change significantly in the AH of FECD eyes when compared to control samples. The concentration of most diacylglycerophosphocholines and 1‐ether, 2‐acylglycerophosphocholines increases in the AH of FECD eyes when compared to healthy controls. In addition, eight sphingomyelins and up to two long‐chain highly unsaturated cholesteryl esters present higher levels in FECD samples when compared to controls.

Conclusion

The lipid composition of AH in FECD patients differs from that of healthy subjects. Those changes may reflect oxidative stress‐related changes in the lipid metabolism of the corneal endothelial cells in FECD.
The multidisciplinary fetal center: clinical expertise is only part of the experience
Authors: Kett Jennifer C. , Wolfe Elana , Vernon Margaret M. , Woodrum David , Diekema Douglas
Published: March 2017

Aim

Multidisciplinary foetal centres have recently emerged in partnership with children's hospitals throughout the United States. The aim of this investigation was to describe the patient experience of pregnant women who were referred to our foetal centres for the evaluation of foetal congenital anomalies.

Methods

A qualitative interview study of women referred to our foetal centres was conducted using semi‐structured telephone interviews. The data were coded and analysed using thematic networks analysis.

Results

Six themes were identified (i) foetal centre evaluations had a far‐reaching impact on participants’ lives, (ii) participants appreciated both expertise and support from providers, (iii) participants recognised the need to cope with uncertainty, (iv) participants sought additional support from multiple arenas, (v) participants specifically looked to the Internet for both information and support and (vi) participants had pre‐established views about pregnancy termination.

Conclusion

Multidisciplinary foetal centres can provide a unified source of clinical expertise to women who are carrying a foetus with a suspected or identified congenital anomaly. Despite this diagnostic acumen, uncertainty is pervasive and patients seek support and additional information from a variety of other sources. This investigation is an important initial step in the evaluation of this emerging model of care.
Neonatal somatosensory evoked potentials persist during hypothermia
Authors: Nevalainen Päivi , Lauronen Leena , Metsäranta Marjo , Lönnqvist Tuula , Ahtola Eero , Vanhatalo Sampsa
Published: March 2017

Aim

Treatment with therapeutic hypothermia has challenged the use of amplitude‐integrated electroencephalography in predicting outcomes after perinatal asphyxia. In this study, we assessed the feasibility and gain of somatosensory evoked potentials (SEP) during hypothermia.

Methods

This retrospective study comprised neonates from 35 + 6 to 42 + 2 gestational weeks and treated for asphyxia or hypoxic‐ischaemic encephalopathy at Helsinki University Hospital between 14 February 2007 and 23 December 2009. This period was partly before the introduction of routine therapeutic hypothermia, which enabled us to include normothermic neonates who would these days receive hypothermia treatment. We analysed SEPs from 47 asphyxiated neonates and compared the results between 23 normothermic and 24 hypothermic neonates.

Results

Our data showed that hypothermia led to SEP latencies lengthening by a few milliseconds, but the essential gain for predicting outcomes by SEPs was preserved during hypothermia. Of the 24 hypothermic neonates, bilaterally absent SEPs were associated with poor outcome in 2/2 neonates, normal SEPs were associated with good outcomes in 13/15 neonates and 5/7 neonates with unilaterally absent or grossly delayed SEPs had a poor outcome.

Conclusion

Our findings indicated that SEPs were a reliable tool for evaluating the somatosensory system in asphyxiated neonates in both normothermic and hypothermic conditions.
Resting state functional connectivity in women with bipolar disorder during clinical remission
Authors: Syan Sabrina K , Minuzzi Luciano , Smith Mara , Allega Olivia R , Hall Geoffrey BC , Frey Benicio N
Published: March 2017

Objectives

Periods of euthymia in bipolar disorder (BD) serve as a valuable time to study trait‐based pathophysiology. The use of resting state functional connectivity (Rs‐FC) can aid in the understanding of BD pathophysiology free of task or mood state biases. The present study investigated two unexplored areas of Rs‐FC research in bipolar remission: (i) Rs‐FC in women, controlling for the potential influence of premenstrual symptoms, and (ii) the use of both independent component analysis (ICA) and seed‐based analysis (SBA) to investigate Rs‐FC.

Methods

We investigated Rs‐FC of the default mode network, meso‐paralimbic network and fronto‐parietal network in a sample of 32 euthymic women with BD and 36 age‐matched controls during the mid‐follicular phase of their menstrual cycle. Rs‐FC was assessed with ICA and SBA using the posterior cingulate cortex (PCC), amygdala and dorsolateral prefrontal cortex (dlPFC) as seed points for their respective resting state networks.

Results

In BD, compared to controls, SBAs revealed increased coupling between the PCC and the angular gyrus (P=.002, false discovery rate [FDR]‐corrected) and between the right dlPFC and the brainstem (P=.03, FDR‐corrected). In BD only, PCC−angular gyrus coupling was correlated with anxiety symptoms. Group differences in Rs‐FC using ICA did not survive multiple comparisons.

Conclusions

Negative findings from whole‐brain ICA Rs‐FC may reflect a state of clinical remission in BD. Heightened activation between the PCC and the angular gyrus and between the dlPFC and the brainstem may reflect (i) an abnormal trait integration of affective information during clinical remission and/or (ii) an adaptive compensatory mechanism required for clinical stabilization.