bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gains through selection for grain yield in a winter wheat breeding program
Authors: Lozada Dennis N. , Carter Arron H. 
Published: August 2019

AbstractIncreased genetic gains for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selectionRvalues across several selection approaches including phenotypic (PS), marker-based (MS), genomic (GS), and a combination of PS and GS. Five populations of Washington State University (WSU) winter wheat breeding lines evaluated from 2015 to 2018 in Lind and Pullman, WA, USA were used in the study. Selection was conducted by selecting the top 20% of lines based on observed yield (PS strategy), genomic estimated breeding values (GS), presence of yield “enhancing” alleles of the most significant single nucleotide polymorphism (SNP) markers identified from genome-wide association mapping (MS), and high observed yield and estimated breeding values (PS+GS). Overall, PS compared to other individual strategies showed the highest response. However, when combined with GS, a 23% improvement inRfor yield was observed, indicating that gains could be improved by complementing traditional PS with GS. Using GS alone as a selection strategy for grain yield should be taken with caution. MS was not that successful in terms ofRrelative to the other selection approaches. Altogether, we demonstrated that gains through increased response to selection for yield could be achieved in the WSU winter wheat breeding program by implementing different selection strategies either exclusively or in combination.
Pollen morphology of Polish species from the genusRubusL. (Rosaceae) and its systematic importance
Authors: Lechowicz Kacper , Wrońska-Pilarek Dorota , Bocianowski Jan , Maliński Tomasz 
Published: August 2019

AbstractThe genusRubusL. (Rosaceae) has as yet not been investigated satisfactorily in terms of palynology. This genus is taxonomically very difficult due to the large number of species and problems with their delimitation, as well as very different distribution areas of particular species. The aim of this study was to investigate pollen morphology and for the first time the ranges of intrageneric and interspecific variability ofRubusspecies, as well as verify the taxonomic usefulness of these traits in distinguishing studied taxa from this genus. They were analysed for 11 quantitative pollen characteristics and the following qualitative ones: exine ornamentation, pollen outline and shape, as well as bridge structure. Analyses were conducted on a total of 1740 pollen grains, which represent 58 blackberry species belonging to a majority of subgenera and all the sections and series found in Poland. The diagnostic characters included exine ornamentation (exine ornamentation type, width and direction of grooves and striae, number and diameter of perforations) and length of the polar axis (P). The arrangement of the examined species on the dendrogram does not corroborate division of the genusRubusinto subgenera, sections and series currently adopted in taxonomy. The lack of dependence may result from apomixis observed inRubus, which could reduce natural variability. Pollen features should be treated in taxonomy as auxiliary, because they fail to differentiate several (10) individual species, while the other ones create groups with similar pollen traits.
Engineered Living Materials based on Adhesin-mediated Trapping of Programmable Cells
Authors: Guo Shuaiqi , Dubuc Emilien , Rave Yahav , Verhagen Mick P.A. , Twisk Simone A.E. , van der Hek Tim , Oerlemans Guido J.M. , van den Oetelaar Maxime C.M. , van Hazendonk Laura S. , Brüls Mariska , Eijkens Bruno V. , Joostens Pim L. , Keij Sander R. , Xing Weizhou , Nijs Martijn , Stalpers Jetske , Sharma Manoj , Gerth Marieke , Boonen Roy J.E.A. , Verduin Kees , Merkx Maarten , Voets Ilja K. , de Greef Tom F.A. 
Published: August 2019

AbstractEngineered living materials have the potential for wide-ranging applications such as biosensing and treatment of diseases. Programmable cells provide the functional basis for living materials, however, their release into the environment raises numerous biosafety concerns. Current designs that limit the release of genetically engineered cells typically involve the fabrication of multi-layer hybrid materials with sub-micron porous matrices. Nevertheless the stringent physical barriers limit the diffusion of macromolecules and therefore the repertoire of molecules available for actuation in response to communication signals between cells and their environment. Here, we engineer a first-of-its-kind living material entitled ‘Platform for Adhesin-mediated Trapping of Cells in Hydrogels’ (PATCH). This technology is based on engineered E. coli that displays an adhesion protein derived from an Antarctic bacterium with high affinity for glucose. The adhesin stably anchors E. coli in dextran-based hydrogels with large pore diameters (10-100 μm) and reduces the leakage of bacteria into the environment by up to 100-fold. As an application of PATCH, we engineered E. coli to secrete lysostaphin via the Type 1 Secretion System and demonstrated that living materials containing this E. coli inhibit the growth of S. aureus, including the strain resistant to methicillin (MRSA). Our tunable platform allows stable integration of programmable cells in dextran-based hydrogels without compromising free diffusion of macromolecules and could have potential applications in biotechnology and biomedicine.
Proof-of-concept for the detection of early osteoarthritis pathology by endomicroscopy
Authors: Tschaikowsky Mathäus , Brander Sofia , Balzer Bizan N. , Rolauffs Bernd , Hugel Thorsten 
Published: August 2019

AbstractOsteoarthritis (OA) is a degenerative joint disease and the leading cause of global disability. Clinical trials to date have been unable to pinpoint early and potentially reversible disease states with current clinical technology and hence disease-modifying OA drug candidates cannot be tested early in the disease. To overcome this obstacle, we correlate articular cartilage stiffness changes and cellular spatial organization. The former is a well-understood and functionally relevant OA pathology, while the latter allows discriminating between healthy vs early OA, based on distinct cellular spatial patterns. We demonstrated that an extensive loss of atomic force microscopy-detected stiffness can be seen in cartilage tissues with spatial patterns exhibiting the earliest identifiable OA. In addition, the translation of commercially available clinically usable probe-based confocal laser-endomicroscopy allows us to detect these early OA spatial patterns. This study resolves a major clinical trial obstacle by presenting the proof-of-concept that early OA pathology can be detected by already available clinical technology.One Sentence SummaryWe report a correlation between articular cartilage surface nanoscale stiffness and chondrocyte spatial organization; using this correlation enables early pathology detection by currently available clinical optical methods.
Dysfunction of Torr causes a Harlequin-type ichthyosis-like phenotype in Drosophila melanogaster
Authors: Wang Y , Norum M , Oehl K , Yang Y , Zuber R , Yang J , Farine JP , Gehring N , Flötenmeyer M , Ferveur J.-F , Moussian B 
Published: August 2019

AbstractPrevention of desiccation is a constant challenge for terrestrial organisms. Land insects have an extracellular coat, the cuticle, that plays a major role in protection against exaggerated water loss. Here, we report that the ABC transporter Torr - a human ABCA12 paralog - contributes to the waterproof barrier function of the cuticle in the fruit fly Drosophila melanogaster. We show that the reduction or elimination of Torr function provokes rapid desiccation. Torr is also involved in defining the inward barrier against xenobiotics penetration. Consistently, the amounts of cuticular hydrocarbons that are involved in cuticle impermeability decrease markedly when Torr activity is reduced. GFP-tagged Torr localises to membrane nano-protrusions within the cuticle, likely pore canals. This suggests that Torr is mediating the transport of cuticular hydrocarbons (CHC) through the pore canals to the cuticle surface. The envelope, which is the outermost cuticle layer constituting the main barrier, is unaffected in torr mutant larvae. This contrasts with the function of Snu, another ABC transporter needed for the construction of the cuticular inward and outward barriers, that nevertheless is implicated in CHC deposition. Hence, Torr and Snu have overlapping and independent roles to establish cuticular resistance against transpiration and xenobiotic penetration. The torr deficient phenotype parallels the phenotype of Harlequin ichthyosis caused by mutations in the human abca12 gene. Thus, it seems that the cellular and molecular mechanisms of lipid barrier assembly in the skin are conserved in vertebrates in invertebrates.Author SummaryAs in humans, lipids on the surface of the skin of insects protect the organism against excessive water loss and penetration of potentially harmful substances. During evolution, a greasy surface was indeed an essential trait for adaptation to life outside a watery environment. Here, we show that the membrane-gate transporter Torr is needed for the deposition of barrier lipids on the skin surface in the fruit fly Drosophila melanogaster through extracellular nano-tubes, called pore canals. In principle, the involvement of Torr parallels the scenario in humans, where the membrane-gate transporter ABCA12 is implicated in the construction of the lipid-based stratum corneum of the skin. In both cases, mutations in the genes coding for the respective transporter cause rapid water-loss and are lethal soon after birth. We conclude that the interaction between the organism and the environment obviously implies an analogous mechanism of barrier formation and function in vertebrates and invertebrates.
Fascin regulates protrusions and delamination to mediate invasive, collective cell migrationin vivo
Authors: Lamb Maureen C. , Anliker Kelsey K. , Tootle Tina L. 
Published: August 2019

AbstractFascin is an actin bundling protein that is essential for developmental cell migrations and promotes cancer metastasis. In addition to bundling actin, Fascin has several actin-independent roles. Border cell migration duringDrosophilaoogenesis provides an excellent model to study Fascin’s various roles during invasive, collective cell migration. Border cell migration requires Fascin. Fascin functions not only within the migrating border cells, but also within the nurse cells, the substrate for this migration. Loss of Fascin results in increased, shorter and mislocalized protrusions during migration. Data supports the model that Fascin promotes the activity of Enabled, an actin elongating factor, to regulate migration. Additionally, loss of Fascin inhibits border cell delamination. These defects are partially due to altered E-cadherin localization in the border cells; this is predicted to be an actin-independent role of Fascin. Overall, Fascin is essential for multiple aspects of this invasive, collective cell migration, and functions in both actin-dependent and -independent manners. These findings have implications beyondDrosophila, as border cell migration has emerged as a model to study mechanisms mediating cancer metastasis.
DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double stranded RNA foci in human cell models of FSHD
Authors: Shadle Sean C. , Bennett Sean R. , Wong Chao-Jen , Karreman Nancy A. , Campbell Amy E. , van der Maarel Silvère M. , Bass Brenda L. , Tapscott Stephen J. 
Published: August 2019

AbstractThe DUX4 transcription factor is normally expressed in the cleavage stage embryo and regulates genes involved in embryonic genome activation. Mis-expression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the activation of the double-stranded RNA (dsRNA) response pathway and the accumulation of intranuclear dsRNA foci. Here, we determined the composition of DUX4-induced dsRNAs. We found that a subset of DUX4-induced dsRNAs originate from inverted Alu repeats embedded within the introns of DUX4-induced transcripts and from DUX4-induced dsRNA-forming intergenic transcripts enriched for endogenous retroviruses, Alu and LINE-1 elements. However, these repeat classes were also represented in dsRNAs from cells not expressing DUX4. In contrast, pericentric human satellite II (HSATII) repeats formed a class of dsRNA specific to the DUX4 expressing cells. Further investigation revealed that DUX4 can initiate the bidirectional transcription of normally heterochromatin-silenced HSATII repeats. DUX4 induced HSATII RNAs co-localized with DUX4-induced nuclear dsRNA foci and with intranuclear aggregation of EIF4A3 and ADAR1. Finally, gapmer-mediated knockdown of HSATII transcripts depleted DUX4-induced intranuclear ribonucleoprotein aggregates and decreased DUX4-induced cell death, suggesting that HSATII formed dsRNAs contribute to DUX4 toxicity.
Local human movement patterns and land use impact exposure to zoonotic malaria in Malaysian Borneo
Authors: Fornace Kimberly M , Alexander Neal , Abidin Tommy R , Brock Paddy M , Chua Tock H , Vythilingam Indra , Ferguson Heather M. , Manin Benny O. , Wong Meng L. , Ng Sui Hann , Cox Jon , Drakeley Chris J 
Published: August 2019

AbstractHuman movement into insect vector and wildlife reservoir habitats determines zoonotic disease risks; however, few data are available to quantify the impact of land use on pathogen transmission. Here, we utilise GPS tracking devices and novel applications of ecological methods to develop fine-scale models of human space use relative to land cover to assess exposure to the zoonotic malaria Plasmodium knowlesi in Malaysian Borneo. Combining data with spatially explicit models of mosquito biting rates, we demonstrate the role of individual heterogeneities in local space use in disease exposure. At a community level, our data indicate that areas close to both secondary forest and houses have the highest probability of human P. knowlesi exposure, providing quantitative evidence for the importance of ecotones. Despite higher biting rates in forests, incorporating human movement space use into exposure estimates illustrates the importance of intensified interactions between pathogens, insect vectors and people around habitat edges.
The orphan nuclear receptor estrogen-related receptor beta (ERRβ) in triple-negative breast cancer
Authors: Fernandez Aileen I. , Geng Xue , Chaldekas Krysta , Harris Brent , Duttargi Anju , Berry V. Layne , Berry Deborah L. , Mahajan Akanksha , Cavalli Luciane R. , Gyorffy Balázs , Tan Ming , Riggins Rebecca B. 
Published: August 2019

ABSTRACTPurposeTriple negative breast cancer (TNBC)/ basal-like breast cancer (BLBC) is a highly aggressive form of breast cancer prevalent in African-American (AA) women. We previously reported that a small molecule agonist ligand for the orphan nuclear receptor estrogen-related receptor beta (ERRβ orESRRB) has growth inhibitory and anti-mitotic activity in TNBC cell lines. In this study, we evaluate the association ofESRRBmRNA, copy number levels, and protein expression with demographic, clinicopathological, and gene expression features in breast tumor clinical specimens.MethodsESRRBmRNA level expression and clinical associations were analyzed using RNAseq data. Array-based comparative genomic hybridization determinedESRRBcopy number in AA and Caucasian women. Transcription factor activity was measured using promoter-reporter luciferase assays in TNBC cell lines. Semi-automatic quantification of immunohistochemistry measured ERRβ protein expression on a 150-patient tissue microarray series.ResultsESRRBmRNA expression is significantly lower in TNBC/BLBC vs. other breast cancer subtypes. There is no evidence ofESRRBcopy number loss.ESRRBmRNA expression is correlated with the expression of genes associated with neuroactive ligand-receptor interaction, metabolic pathways, and deafness. These genes contain G/C-rich transcription factor binding motifs. TheESRRBmessage is alternatively spliced into three isoforms, which we show have different transcription factor activity in basal-like vs. other TNBC cell lines. We further show that the ERRβ2 and ERRβsf isoforms are broadly expressed in breast tumors at the protein level.ConclusionsDecreasedESRRBmRNA expression, and distinct patterns of ERRβ isoform subcellular localization and transcription factor activity are key features in TNBC/BLBC.
Chromosome 17: neXt-MP50 C-HPP Challenge Completed
Authors: Zhang Hongjiu , Siddiqui Omer , Guan Yuanfang , Omenn Gilbert S. 
Published: August 2019

ABSTRACTThe C-HPP Team for Chromosome 17 has documented meeting the neXt-MP50 Missing Protein Challenge. Protein-level PE1 evidence including MS and protein-protein interaction data from the global proteomics community has reduced the number of PE2,3,4 proteins coded on Chromosome 17 by 50 since the 2016 baseline in neXtProt. As a follow-up to our analysis and prioritization of Chr 17 missing proteins last year, we describe what predictions and guidance were successful in this update and we explain the dynamics of a net reduction of PE2,3,4 Missing Proteins. This analysis can serve as a guide for other C-HPP chromosome teams seeking high-quality evidence for the 2129 remaining missing proteins.
Auxin-induced nanoclustering of membrane signaling complexes underlies cell polarity establishment in Arabidopsis
Authors: Pan Xue , Fang Linjing , Liu Jianfeng , Senay-Aras Betul , Lin Wenwei , Zheng Shuan , Zhang Tong , Manor Uri , Chen Weitao , Yang Zhenbiao 
Published: August 2019

AbstractCell polarity is fundamental to the development of both eukaryotic and prokaryotic organisms, yet the mechanism of its establishment remains poorly understood. Here we show that signal-activated nanoclustering of membrane proteins and a cytoskeleton-based feedback loop provide an important mechanism for the establishment of cell polarity. The phytohormone auxin promoted sterol-dependent nanoclustering of cell surface transmembrane receptor-like kinase 1 (TMK1) to initiate cell polarity during the morphogenesis of Arabidopsis puzzle piece-shaped leaf pavement cells (PC). Auxin-triggered nanoclustering of TMK1 stabilized flotillin-associated ordered nanodomains, which were essential for auxin-mediated formation of ROP6 GTPase nanoclusters that act downstream TMK1 to promote cortical microtubule ordering. Mathematical modeling further demonstrated the essential role of this auxin-mediated stabilization of TMK1 and ROP6 nanoclusters, and predicted the additional requirement of ROP6-dependent cortical microtubules for further stabilization of TMK1-sterol nanodomains and the polarization of PC. This prediction was experimentally validated by genetic and biochemical data. Our studies reveal a new paradigm for polarity establishment: A diffusive signal triggers cell polarization by activating cell surface receptor-mediated lateral segregation of signaling components and a cytoskeleton-mediated positive feedback loop of nanodomain stabilization.HighlightsSterols are required for cell polarity in Arabidopsis leaf epidermal cellsAuxin promotes lipid ordering and polar distribution of ordered lipid nanodomains at the plasma membrane (PM)Auxin stabilizes sterol-dependent nanoclustering of transmembrane kinase (TMK1), a PM auxin signal transducerAuxin-induced TMK1 nanoclustering is required but insufficient for cell polarizationMicrotubule-based feedback stabilization of the auxin-induced TMK1 nanodomains can generate cell polarity
Integrating untargeted metabolomics, genetically informed causal inference, and pathway enrichment to define the obesity metabolome
Authors: Hsu Yu-Han H. , Astley Christina M. , Cole Joanne B. , Vedantam Sailaja , Mercader Josep M. , Metspalu Andres , Fischer Krista , Fortney Kristen , Morgen Eric K. , Gonzalez Clicerio , Gonzalez Maria E. , Esko Tonu , Hirschhorn Joel N. 
Published: August 2019

ABSTRACTBackgroundObesity and its associated diseases are major health problems characterized by extensive metabolic disturbances. Understanding the causal connections between these phenotypes and variation in metabolite levels can uncover relevant biology and inform novel intervention strategies. Recent studies have combined metabolite profiling with genetic instrumental variable (IV) analyses to infer the direction of causality between metabolites and obesity, but often omitted a large portion of untargeted profiling data consisting of unknown, unidentified metabolite signals.MethodsWe expanded upon previous research by identifying body mass index (BMI)-associated metabolites in multiple untargeted metabolomics datasets, and then performing bidirectional IV analysis to classify these metabolites based on their inferred causal relationships with BMI. Meta-analysis and pathway analysis of both known and unknown metabolites across datasets were enabled by our recently developed bioinformatics suite, PAIRUP-MS.ResultsWe identified 10 known metabolites that are more likely to be the causes (e.g. alpha-hydroxybutyrate) or effects (e.g. valine) of BMI, or may have more complex bidirectional cause-effect relationships with BMI (e.g. glycine). Importantly, we also identified about 5 times more unknown than known metabolites in each of these three categories. Pathway analysis incorporating both known and unknown metabolites prioritized 40 enriched (p < 0.05) metabolite sets for the cause versus effect groups, providing further support that these two metabolite groups are linked to obesity via distinct biological mechanisms.ConclusionsThese findings demonstrate the potential utility of our approach to uncover causal connections with obesity from untargeted metabolomics datasets. Combining genetically informed causal inference with the ability to map unknown metabolites across datasets provides a path to jointly analyze many untargeted datasets with obesity or other phenotypes. This approach, applied to larger datasets with genotype and untargeted metabolite data, should generate sufficient power for robust discovery and replication of causal biological connections between metabolites and various human diseases.
Description of a new member of the family Erysipelotrichaceae: Clostridium fusiformis sp. nov., isolated from healthy human feces
Authors: Ghimire Sudeep , Wongkuna Supapit , Scaria Joy 
Published: August 2019

ABSTRACTA Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from the healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the Clostridium cluster XVI, where, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991T and Eubacterium tortuosum DSM 3987T were its closest taxa with 95.15%, 94.49%, 93.28%, and 93.20% sequence identities respectively. The optimal growth temperature and pH for the strain SG502T were 37°C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain SG502T when grown in BHI-M medium. The major cellular fatty acids produced by the strain SG502T were C18:1 ω9c, C18:0 and C16:0. The DNA G+C content of the strain was 34.34 mol%. The average nucleotide identity of the genome of the strain SG502T and its closest neighbor C. innocuum ATCC 14501T was 63.48%. Based on the polyphasic analysis, the type strain SG502T (=DSM 107282T), represents a novel species of the genus Clostridium for which the name Clostridium fusiformis sp. nov. is proposed.