bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adipose Stem Cells from Lipedema and Control Adipose Tissue Respond Differently to Adipogenic Stimulation In Vitro
Authors: Bauer Anna-Theresa , von Lukowicz Dominik , Lossagk Katrin , Hopfner Ursula , Kirsch Manuela , Moog Philipp , Bauer Hannelore , Machens Hans-Guenther , Schmauss Daniel 
Published: June 2019

Background:
Lipedema is characterized by localized accumulation of fat in the extremities, which is typically unresponsive to dietary regimens or physical activity. Although the disease is well described and has a high incidence, little is known regarding the molecular and cellular mechanisms underlying its pathogenesis. The aim of this study was to investigate the pathophysiology of lipedema adipose cells in vitro.

Methods:
Adipose-derived stem cells were isolated from lipoaspirates derived from lipedema and nonlipedema patients undergoing tumescent liposuction. In vitro differentiation studies were performed for up to 14 days using adipogenic or regular culture medium. Supernatants and cell lysates were tested for adiponectin, leptin, insulin-like growth factor-1, aromatase (CYP19A1), and interleukin-8 content at days 7 and 14, using enzyme-linked immunosorbent assays. Adipogenesis was evaluated by visualizing and measuring cytoplasmic lipid accumulation.

Results:
Lipedema adipose-derived stem cells showed impeded adipogenesis already at early stages of in vitro differentiation. Concomitant with a strongly reduced cytoplasmic lipid accumulation, significantly lower amounts of adiponectin and leptin were detectable in supernatants from lipedema adipose-derived stem cells and adipocytes compared with control cells. In addition, lipedema and nonlipedema cells differed in their expression of insulin-like growth factor-1, aromatase (CYP19A1), and interleukin-8 and in their proliferative activity.

Conclusions:
The authors’ findings indicate that in vitro adipogenesis of lipedema adipose-derived stem cells is severely hampered compared with nonlipedema adipose-derived stem cells. Lipedema adipose cells differ not only in their lipid storage capacity but also in their adipokine expression pattern. This might serve as a valuable marker for diagnosis of lipedema, probably from an early stage on.
Air retaining grids—a novel technology to maintain stable air layers under water for drag reduction
Authors: Mail M. , Moosmann M. , Häger P. , Barthlott W. 
Published: June 2019

Extreme water repellent ‘superhydrophobic’ surfaces evolved in plants and animals about 450 Ma: a combination of hydrophobic chemistry and hierarchical structuring causes contact angles of greater than 150°. Technical biomimetic applications and technologies for water repellency, self-cleaning (Lotus Effect) and drag reduction (Salvinia Effect) have become increasingly important in the last two decades. Drag reduction (e.g. for ship hulls) requires the presence of a rather thick and persistent air layer under water. All existing technical solutions are based on fragile elastic hairs, micro-pillars or other solitary structures, preferably with undercuts (Salvinia Effect). We propose and provide experimental data for a novel alternative technology to trap persistent air layers by superhydrophobic grids or meshes superimposed to the solid surface: AirGrids. AirGrids provide a simple and stable solution to generate air trapping surfaces for drag reduction under water as demonstrated by first prototypes. Different architectural solutions, including possible recovery techniques for the air layer under hydrodynamic conditions, are discussed. The most promising target backed by first results is the combination of Air Retaining Grids with the existing microbubble technology.
This article is part of the theme issue ‘Bioinspired materials and surfaces for green science and technology (part 2)’.
A Generalized Similarity Metric for Predicting Peptide Binding Affinity
Authors: Rodriguez Jacob , Rath Siddharth , Francis-Landau Jonathan , Demirci Yekta , Üstündağ Burak Berk , Sarikaya Mehmet 
Published: June 2019

AbstractThe ability to capture the relationship between similarity and functionality would enable the predictive design of peptide sequences for a wide range of implementations from developing new drugs to molecular scaffolds in tissue engineering and biomolecular building blocks in nanobiotechnology. Similarity matrices are widely used for detecting sequence homology but depend on the assumption that amino acid mutational frequencies reflected by each matrix are relevant to the system in which they are applied. Increasingly, neural networks and other statistical learning models solve problems related to functional prediction but avoid using known features to circumvent unconscious bias. We demonstrated an iterative alignment method that enhances predictive power of similarity matrices based on a similarity metric, the Total Similarity Score. A generalized method is provided for application to amino acid sequences from inorganic and organic systems by benchmarking it on the debut quartz-binder set and 3 peptide-protein sets from the Immune Epitope Database. Pearson and Spearman Rank Correlations show that by treating the gapless Total Similarity Score as a predictor of relative binding affinity, prediction of test data has a 0.5-0.7 Pearson and Spearman Rank correlation. with respect to size of the dataset. Since the benchmarks used herein are from a solid-binding peptide and a protein-peptide system, our proposed method could prove to be a highly effective general approach for establishing the predictive sequence-function relationships of among the peptides with different sequences and lengths in a wide range of biotechnology, nanomedicine and bioinformatics applications.Author SummaryThe significance of this work is to expand the applicability of a known metric for describing the function of tiny proteins also called peptides. The Total Similarity Score (TSS) can describe how ‘similar’ a peptide, or a group of peptides are to another group of sequences with a known or suspected function. A peptide/group of peptides will always have a high TSS if it contains the same or ‘similar’ amino acids in the same positions. This metric can therefore be used to select peptides for useful functions based purely on conserved amino acids in unknown positions. The greedy search algorithm used to learn how similar amino acids are to each other has been shown to be marginally effective in this larger dataset. Therefore, we argue that the TSS metric is a highly useful one for predicting peptide affinity but a different machine learning algorithm should be applied to make full use of it.
Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen(Populus tremula)
Authors: Apuli Rami-Petteri , Bernhardsson Carolina , Schiffthaler Bastian , Robinson Kathryn M. , Jansson Stefan , Street Nathaniel R. , Ingvarsson Pär K. 
Published: June 2019

AbstractThe rate of meiotic recombination is one of the central factors determining levels of linkage disequilibrium and the efficiency of natural selection, and many organisms show a positive correlation between local rates of recombination and levels of nucleotide diversity indicating that linked selection is an important factor determining genome-wide levels of nucleotide diversity. Several methods for estimating recombination rates from segregating polymorphisms in natural populations have recently been developed. These methods have been extensively used in part because they are relatively simple to implement even in many non-model organisms, but also because they potentially offer higher resolution than traditional map-based methods. However, thorough comparisons of LD and map-based estimates of recombination are not readily available in plants. Here we present a new, high-resolution linkage map forPopulus tremulaand use this to estimate variation in recombination rates across theP. tremulagenome. We compare these results to recombination rates estimated based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identify a number of genomic regions with very high recombination rates that the map-based method fail to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome.
Decoding commensal-host communication through genetic engineering ofStaphylococcus epidermidis
Authors: Chen Y. Erin , Bouladoux Nicolas , Hurabielle Charlotte , Mattke Aiden M. , Belkaid Yasmine , Fischbach Michael A. 
Published: June 2019

SUMMARYCommensal skin bacteria elicit potent, antigen-specific immune responses in the skin without barrier breach or visible inflammation. While microbial modulation of immune homeostasis has profound consequences for epithelial health and inflammatory skin diseases, the mechanisms of microbe-immune crosstalk in the skin are largely unknown. A key barrier to mechanistic work has been genetic intractability of one of the most prevalent skin colonists,Staphylococcus epidermidis(S. epidermidis). Here, we develop a novel method to create a library of mutants with defined cell envelope alterations in primary humanS. epidermidisisolates. By colonizing mice with these mutants, we uncover bacterial molecules involved in the induction of defined immune signatures. Notably, we show that under conditions of physiologic colonization,S. epidermidiscell envelope glycolipids are sensed by C-type lectin receptors, likely in non-myeloid cells, in conjunction with Toll-like receptors. This combinatorial signaling determines the quality of T cell responses and results in the potential for greater specificity toward commensal microbiota than previously appreciated. Additionally, the microbial molecules required for the colonization-induced immune response are dispensable for T cells responses in a model ofS. epidermidisinfection, but differentially modulate innate inflammatory responses. Thus, the same microbe uses distinct sets of molecules to signal to the immune system commensal versus pathogenic behavior, and differential sensing of these microbial signals depends on host context.
Transcriptomic signatures of brain regional vulnerability to Parkinson’s disease
Authors: Keo Arlin , Mahfouz Ahmed , Ingrassia Angela M.T. , Meneboo Jean-Pascal , Villenet Celine , Mutez Eugénie , Comptdaer Thomas , Lelieveldt Boudewijn P.F. , Figeac Martin , Chartier-Harlin Marie-Christine , van de Berg Wilma D.J. , van Hilten Jacobus J. , Reinders Marcel J.T. 
Published: June 2019

AbstractThe molecular mechanisms underlying the caudal-to-rostral progression of Lewy body pathology in Parkinson’s disease (PD) remain poorly understood. Here, we aimed to unravel transcriptomic signatures across brain regions involved in Braak Lewy body stages in non-neurological controls and PD donors. Using human postmortem brain datasets of non-neurological adults from the Allen Human Brain Atlas, we identified expression patterns related to PD progression, including genes found in PD genome-wide associations studies: SNCA, ZNF184, BAP1, SH3GL2, ELOVL7, and SCARB2. We confirmed these patterns in two datasets of non-neurological subjects (Genotype-Tissue Expression project and UK Brain Expression Consortium) and found altered patterns in two datasets of PD patients. Additionally, co-expression analysis across vulnerable regions identified two modules associated with dopamine synthesis, the motor and immune system, blood-oxygen transport, and contained microglial and endothelial cell markers, respectively. Alterations in genes underlying these region-specific functions may contribute to the selective regional vulnerability in PD brains.
Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya
Authors: Gichuhi Joseph , Subramanian Sevgan , Khamis Fathiya M. , Van den Berg Johnnie , du Plessis Hannalene , Ekesi Sunday , Herren Jeremy K 
Published: June 2019

AbstractThe invasive fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in their success and adaptability. However, these bacterial communities remain poorly studied, especially for S. frugiperda in Africa. We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of bacterial 16S rRNA gene. We identified Proteobacteria and Firmicutes as the most dominant phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. Several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to several known entomopathogenic bacterial clades as well as the non-bacterial entomopathogen, Metarhizium rileyi (Farl.) Kepler, Rehner & Humber (2014), were observed. Mitochondrial DNA haplotyping of the S. frugiperda population in Kenya indicated the presence of both ‘Rice’ and ‘Corn’ strains, with a higher prevalence of the ‘Rice’ strain. Insights into the microbiota may ultimately provide alternative avenues for controlling of this pest.
DOT: Gene-set analysis by combining decorrelated association statistics
Authors: Vsevolozhskaya Olga A. , Shi Min , Hu Fengjiao , Zaykin Dmitri V. 
Published: June 2019

AbstractHistorically, the majority of statistical association methods have been designed assuming availability of SNP-level information. However, modern genetic and sequencing data present new challenges to access and sharing of genotype-phenotype datasets, including cost management, difficulties in consolidation of records across research groups, etc. These issues make methods based on SNP-level summary statistics particularly appealing. The most common form of combining statistics is a sum of SNP-level squared scores, possibly weighted, as in burden tests for rare variants. The overall significance of the resulting statistic is evaluated using its distribution under the null hypothesis. Here, we demonstrate that this basic approach can be substantially improved by decorrelating scores prior to their addition, resulting in remarkable power gains in situations that are most commonly encountered in practice; namely, under heterogeneity of effect sizes and diversity between pairwise LD. In these situations, the power of the traditional test, based on the added squared scores, quickly reaches a ceiling, as the number of variants increases. Thus, the traditional approach does not benefit from information potentially contained in any additional SNPs, while our decorrelation by orthogonal transformation (DOT) method yields steady gain in power. We present theoretical and computational analyses of both approaches, and reveal causes behind sometimes dramatic difference in their respective powers. We showcase DOT by analyzing breast cancer data, in which our method strengthened levels of previously reported associations and implied the possibility of multiple new alleles that jointly confer breast cancer risk.
Time Machine: Can a Dye from 1928 be Re-Purposed for Modern, Fluorescence-Based Detection of Amyloid-Like Fibrils?
Authors: Antimonova O. I. , Grudinina N. A. , Egorov V. V. , Ilyin V. V. , Zabrodskaya Y. A. , Ramsay E. S. , Polukeev V. A. , Shavlovsky M. M. 
Published: June 2019

AbstractThis manuscript describes the chemical synthesis of a compound similar to fluorene and Congo red, including characterization of its spectral properties. It was shown that the dye, during interaction with amyloid-like fibrils of several proteins (lysozyme, insulin, and beta-2-microglobulin), has the ability to change fluorescent spectrum. In contrast, monomeric forms of these proteins did not induce significant spectral changes.
Correlated evolution of sex allocation and mating system in wrasses and parrotfishes
Authors: Hodge Jennifer R. , Santini Francesco , Wainwright Peter C. 
Published: June 2019

AbstractIn accordance with predictions of the size-advantage model, comparative evidence confirms that protogynous sex change is lost when mating behavior is characterized by weak size advantage. However, we lack comparative evidence supporting the adaptive significance of sex change. Specifically, it remains unclear whether increasing male size advantage induces transitions to protogynous sex change across species, as it can within species. We show that in wrasses and parrotfishes (Labridae), the evolution of protogynous sex change is correlated with polygynous mating, and that the degree of male size advantage expressed by polygynous species influences transitions between different types of protogynous sex change. Phylogenetic reconstructions reveal strikingly similar patterns of sex allocation and mating system evolution with comparable lability. Despite the plasticity of sex determination mechanisms in labrids, transitions trend towards monandry (all males derived from sex-changed females), with all observed losses of protogyny accounted for by shifts in the timing of sex change to prematuration. Likewise, transitions in mating system trend from the ancestral condition of lek-like polygyny toward greater male size advantage, characteristic of haremic polygyny. The results of our comparative analyses are among the first to confirm the adaptive significance of sex change as described by the size-advantage model.
A Bacterial Surface Layer Protein Exploits Multi-step Crystallization for Rapid Self-assembly
Authors: Herrmann Jonathan , Li Po-Nan , Jabbarpour Fatemeh , Chan Anson C. K. , Rajkovic Ivan , Matsui Tsutomu , Shapiro Lucy , Smit John , Weiss Thomas , Murphy Michael E. P. , Wakatsuki Soichi 
Published: June 2019

AbstractSurface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the C. crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multi-step assembly pathway. This pathway involves two domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2D crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using time-resolved electron cryo-microscopy (Cryo-EM) reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the two domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.Significance StatementMany microbes assemble a crystalline protein layer on their outer surface as an additional barrier and communication platform between the cell and its environment. Surface layer proteins efficiently crystallize to continuously coat the cell and this trait has been utilized to design functional macromolecular nanomaterials. Here, we report that rapid crystallization of a bacterial surface layer protein occurs through a multi-step pathway involving a crystalline intermediate. Upon calcium-binding, sequential changes occur in the structure and arrangement of the protein, which are captured by time-resolved small angle x-ray scattering and transmission electron cryo-microscopy. We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization in vivo.
Diving beetle offspring oviposited in amphibian spawn prey on the tadpoles upon hatching
Authors: Gould John , Valdez Jose W. , Clulow Simon , Clulow John 
Published: June 2019

AbstractIn highly ephemeral freshwater habitats, predatory vertebrates are typically unable to become established, leaving an open niche often filled by macroinvertebrate predators. However, these predators are faced with the challenge of finding sufficient food sources as the rapid rate of desiccation prevents the establishment of extended food chains and limits the number of prey species present. It could therefore be advantageous for adults to oviposit their offspring in the presence of future prey within sites of extreme ephemerality. We report the first case of adult diving beetles ovipositing their eggs within spawn of the sandpaper frog, Lechriodus fletcheri. This behaviour was found among several pools used by L. fletcheri for reproduction. Beetle eggs oviposited in frog spawn were found to hatch within 24 hours of the surrounding L. fletcheri eggs, with the larvae becoming voracious consumers of the hatched tadpoles. Although it has yet to be established experimentally whether this is an adaptive behaviour, the laying of eggs among potential future tadpole prey in this instance should confer significant fitness benefits for the offspring upon hatching, ensuring that they are provided an immediate source of food at the start of their development and potentially throughout. This oviposition behaviour may be common among diving beetles and could form a significant predatory threat for amphibians with a free-swimming larval stage in ephemeral freshwater habitats.