bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences
Authors: Boehm Volker , Gerbracht Jennifer V. , Marx Marie-Charlotte , Gehring Niels H. 
Published: December 2016

AbstractThe turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5′–3′ mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3′ UTRs of cytokine mRNAs reveals the contribution of 5′–3′ decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.
Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction
Authors: Hanebuth Marie A. , Kityk Roman , Fries Sandra J. , Jain Alok , Kriel Allison , Albanese Veronique , Frickey Tancred , Peter Christine , Mayer Matthias P. , Frydman Judith , Deuerling Elke 
Published: December 2016

AbstractHsp70 chaperones assist de novo folding of newly synthesized proteins in all cells. In yeast, the specialized Hsp70 Ssb directly binds to ribosomes. The structural basis and functional mode of recruitment of Ssb to ribosomes is not understood. Here, we present the molecular details underlying ribosome binding of Ssb in Saccharomyces cerevisiae. This interaction is multifaceted, involving the co-chaperone RAC and two specific regions within Ssb characterized by positive charges. The C-terminus of Ssb mediates the key contact and a second attachment point is provided by a KRR-motif in the substrate binding domain. Strikingly, ribosome binding of Ssb is not essential. Autonomous ribosome attachment becomes necessary if RAC is absent, suggesting a dual mode of Ssb recruitment to nascent chains. We propose, that the multilayered ribosomal interaction allows positioning of Ssb in an optimal orientation to the tunnel exit guaranteeing an efficient nascent polypeptide interaction.
Revealing region-specific biofilm viscoelastic properties by means of a micro-rheological approach
Authors: Cao Huayu , Habimana Olivier , Safari Ashkan , Heffernan Rory , Dai Yihong , Casey Eoin 
Published: December 2016

AbstractParticle-tracking microrheology is an in situ technique that allows quantification of biofilm material properties. It overcomes the limitations of alternative techniques such as bulk rheology or force spectroscopy by providing data on region specific material properties at any required biofilm location and can be combined with confocal microscopy and associated structural analysis. This article describes single particle tracking microrheology combined with confocal laser scanning microscopy to resolve the biofilm structure in 3 dimensions and calculate the creep compliances locally. Samples were analysed from Pseudomonas fluorescens biofilms that were cultivated over two timescales (24 h and 48 h) and alternate ionic conditions (with and without calcium chloride supplementation). The region-based creep compliance analysis showed that the creep compliance of biofilm void zones is the primary contributor to biofilm mechanical properties, contributing to the overall viscoelastic character.
Spatial and temporal analysis of extreme sea level and storm surge events around the coastline of the UK
Authors: Haigh Ivan D. , Wadey Matthew P. , Wahl Thomas , Ozsoy Ozgun , Nicholls Robert J. , Brown Jennifer M. , Horsburgh Kevin , Gouldby Ben 
Published: December 2016

AbstractIn this paper we analyse the spatial footprint and temporal clustering of extreme sea level and skew surge events around the UK coast over the last 100 years (1915–2014). The vast majority of the extreme sea level events are generated by moderate, rather than extreme skew surges, combined with spring astronomical high tides. We distinguish four broad categories of spatial footprints of events and the distinct storm tracks that generated them. There have been rare events when extreme levels have occurred along two unconnected coastal regions during the same storm. The events that occur in closest succession (<4 days) typically impact different stretches of coastline. The spring/neap tidal cycle prevents successive extreme sea level events from happening within 4–8 days. Finally, the 2013/14 season was highly unusual in the context of the last 100 years from an extreme sea level perspective.
Dataset of eye disease-related proteins analyzed using the unfolding mutation screen
Authors: McCafferty Caitlyn L. , Sergeev Yuri V. 
Published: December 2016

AbstractA number of genetic diseases are a result of missense mutations in protein structure. These mutations can lead to severe protein destabilization and misfolding. The unfolding mutation screen (UMS) is a computational method that calculates unfolding propensities for every possible missense mutation in a protein structure. The UMS validation demonstrated a good agreement with experimental and phenotypical data. 15 protein structures (a combination of homology models and crystal structures) were analyzed using UMS. The standard and clustered heat maps, and patterned protein structure from the analysis were stored in a UMS library. The library is currently composed of 15 protein structures from 14 inherited eye diseases including retina degenerations, glaucoma, and cataracts, and contains data for 181,110 mutations. The UMS protein library introduces 13 new human models of eye disease related proteins and is the first collection of the consistently calculated unfolding propensities, which could be used as a tool for the express analysis of novel mutations in clinical practice, next generation sequencing, and genotype-to-phenotype relationships in inherited eye disease.
Colonic luminal microbiota and bacterial metabolite composition in pregnant Huanjiang mini-pigs: effects of food composition at different times of pregnancy
Authors: Kong Xiang-feng , Ji Yu-jiao , Li Hua-wei , Zhu Qian , Blachier F. , Geng Mei-mei , Chen Wen , Yin Yu-long 
Published: December 2016

AbstractThe gut harbours diverse and complex microbiota, which influence body health including nutrient metabolism, immune development, and protection from pathogens. Pregnancy is associated with immune and metabolic changes that might be related to microbiota compositional dynamics. We therefore investigated the colonic luminal bacteria community in Huanjiang mini-pigs fed diets with different nutrient levels from the first to third trimester of pregnancy. The concentrations of intestinal metabolites including short-chain fat acids, NH3-N, indole, skatole, and bioamines were also determined. We found that the colonic bacteria species richness estimators (Chao1 and ACE) decreased with increased gestational age. The dominant phyla identified were Firmicutes and Bacteroidetes; the dominant genera were Lactobacillus, Treponema, Ruminococcus, Clostridium, and Prevotella. In addition, microbiota displayed spatial and temporal heterogeneity in composition, diversity, and species abundance in different colonic segments from the first to third trimester of pregnancy. Furthermore, the bacterial metabolites also changed according to the diet used and the pregnancy stage. These findings suggest that colonic bacteria richness decreased as gestational age increased, and that the higher nutrient level diet increased the production of metabolites related to nitrogen metabolism. However, although the higher nutrient diet was associated with pregnancy syndrome, causal links remain to be determined.
Submillimetre Network Formation by Light-induced Hybridization of Zeptomole-level DNA
Authors: Iida Takuya , Nishimura Yushi , Tamura Mamoru , Nishida Keisuke , Ito Syoji , Tokonami Shiho 
Published: December 2016

AbstractMacroscopic unique self-assembled structures are produced via double-stranded DNA formation (hybridization) as a specific binding essential in biological systems. However, a large amount of complementary DNA molecules are usually required to form an optically observable structure via natural hybridization, and the detection of small amounts of DNA less than femtomole requires complex and time-consuming procedures. Here, we demonstrate the laser-induced acceleration of hybridization between zeptomole-level DNA and DNA-modified nanoparticles (NPs), resulting in the assembly of a submillimetre network-like structure at the desired position with a dramatic spectral modulation within several minutes. The gradual enhancement of light-induced force and convection facilitated the two-dimensional network growth near the air-liquid interface with optical and fluidic symmetry breakdown. The simultaneous microscope observation and local spectroscopy revealed that the assembling process and spectral change are sensitive to the DNA sequence. Our findings establish innovative guiding principles for facile bottom-up production via various biomolecular recognition events.
Purslane (Portulaca oleracea) Seed Consumption And Aerobic Training Improves Biomarkers Associated with Atherosclerosis in Women with Type 2 Diabetes (T2D)
Authors: Dehghan Firouzeh , Soori Rahman , Gholami Khadijeh , Abolmaesoomi Mitra , Yusof Ashril , Muniandy Sekaran , Heidarzadeh Sara , Farzanegi Parvin , Ali azarbayjani Mohammad 
Published: December 2016

AbstractThe aim of this study was to investigate the responses of atherosclerosis plaque biomarkers to purslane seed consumption and aerobic training in women with T2D. 196 women with T2D were assigned into; (1) placebo (PL), (2) aerobic training+placebo (AT + PL), 3) purslane seeds (PS), aerobic training+purslane seeds (AT + PS). The training program and purslane seeds consumption (2.5 g lunch and 5 g dinner) were carried out for 16 weeks. The components of purslane seed were identified and quantified by GC–MS. Blood samples were withdrawn via venipuncture to examine blood glucose, low-density lipoprotein (LDL), high-density lipoprotein (HDL), cholesterol, triglycerides (TG), creatinine, urea, uric acid, NF-κB, GLP1, GLP1R, TIMP-1, MMP2, MMP9, CRP, CST3, and CTSS expressions. Blood glucose, LDL, cholesterol, TG, creatinine, urea, and uric acid levels in the (P), (AT), and (AT + PS) groups were significantly decreased compared to the pre-experimental levels or the placebo group, while HDL, significantly increased. Furthermore, the protein and mRNA levels of NF-κB, TIMP-1, MMP2 &9, CRP, CST3, and CTSS in the (P), (AT), (AT + PS) significantly decreased compared to pre-experimental or the placebo group, while level of GLP1 and GLP1-R increased drastically. Findings suggest that purslane seed consumption alongside exercising could improve atherosclerosis plaque biomarkers through synergistically mechanisms in T2D.
Dynamical tuning between nearly perfect reflection, absorption, and transmission of light via graphene/dielectric structures
Authors: Linder Jacob , Halterman Klaus 
Published: December 2016

AbstractExerting well-defined control over the reflection (R), absorption (A), and transmission (T) of electromagnetic waves is a key objective in quantum optics. To this end, one often utilizes hybrid structures comprised of elements with different optical properties in order to achieve features such as high R or high A for incident light. A desirable goal would be the possibility to tune between all three regimes of nearly perfect reflection, absorption, and transmission within the same device, thus swapping between the cases R → 1, A → 1, and T → 1 dynamically. We here show that a dielectric interfaced with a graphene layer on each side allows for precisely this: by tuning only the Fermi level of graphene, all three regimes can be reached in the THz regime and below. Moreover, we show that the inclusion of cylindrical defects in the system offers a different type of control of the scattering of electromagnetic waves by means of the graphene layers.
Soluble Amyloid-beta Aggregates from Human Alzheimer’s Disease Brains
Authors: Esparza Thomas J. , Wildburger Norelle C. , Jiang Hao , Gangolli Mihika , Cairns Nigel J. , Bateman Randall J. , Brody David L. 
Published: December 2016

AbstractSoluble amyloid-beta (Aβ) aggregates likely contribute substantially to the dementia that characterizes Alzheimer’s disease. However, despite intensive study of in vitro preparations and animal models, little is known about the characteristics of soluble Aβ aggregates in the human Alzheimer’s disease brain. Here we present a new method for extracting soluble Aβ aggregates from human brains, separating them from insoluble aggregates and Aβ monomers using differential ultracentrifugation, and purifying them >6000 fold by dual antibody immunoprecipitation. The method resulted in <40% loss of starting material, no detectible ex vivo aggregation of monomeric Aβ, and no apparent ex vivo alterations in soluble aggregate sizes. By immunoelectron microscopy, soluble Aβ aggregates typically appear as clusters of 10–20 nanometer diameter ovoid structures with 2-3 amino-terminal Aβ antibody binding sites, distinct from previously characterized structures. This approach may facilitate investigation into the characteristics of native soluble Aβ aggregates, and deepen our understanding of Alzheimer’s dementia.
Self-cleaning of Surfaces: the Role of Surface Wettability and Dust Types
Authors: Quan Yun-Yun , Zhang Li-Zhi , Qi Rong-Hui , Cai Rong-Rong 
Published: December 2016

AbstractThe self-cleaning property is usually connected to superhydrophobic surfaces (SHSs) where the dust particles can be easily removed by the rolling motion of droplets. It seems that superhydrophobicity (its durability is questionable nowadays) is a necessity. However here, it is disclosed that self-cleaning can also be realized on an ordinary surface by droplet impinging. The effects of surface wettability and the types of dust particles are considered. The self-cleaning is realized by two steps: (1) the pickup of particles by the water-air interface of an impinging droplet, (2) the release of the impinging droplets from the surface. It can be observed that only the trailing edges of the droplets can pick up particles when the droplets recoil from the inclined surfaces. The hydrophilic surface can also achieve self-cleaning under some conditions. This interesting finding may be helpful for the successful implementation of self-cleaning with common surfaces.
Apparent Negative Reflection with the Gradient Acoustic Metasurface by Integrating Supercell Periodicity into the Generalized Law of Reflection
Authors: Liu Bingyi , Zhao Wenyu , Jiang Yongyuan 
Published: December 2016

AbstractAs the two dimensional version of the functional wavefront manipulation metamaterial, metasurface has become a research hot spot for engineering the wavefront at will with a subwavelength thickness. The wave scattered by the gradient metasurface, which is composed by the periodic supercells, is governed by the generalized Snell’s law. However, the critical angle that derived from the generalized Snell’s law circles the domain of the incident angles that allow the occurrence of the anomalous reflection and refraction, and no free space scattering waves could exist when the incident angle is beyond the critical angle. Here we theoretically demonstrate that apparent negative reflection can be realized by a gradient acoustic metasurface when the incident angle is beyond the critical angle. The underlying mechanism of the apparent negative reflection is understood as the higher order diffraction arising from the interaction between the local phase modulation and the non-local effects introduced by the supercell periodicity. The apparent negative reflection phenomena has been perfectly verified by the calculated scattered acoustic waves of the reflected gradient acoustic metasurface. This work may provide new freedom in designing functional acoustic signal modulation devices, such as acoustic isolator and acoustic illusion device.
Catalytic Conversion of Lipophilic Substrates by Phase constrained Enzymes in the Aqueous or in the Membrane Phase
Authors: Cebula Marcus , Turan Ilke Simsek , Sjödin Birgitta , Thulasingam Madhuranayaki , Brock Joseph , Chmyrov Volodymyr , Widengren Jerker , Abe Hiroshi , Mannervik Bengt , Haeggström Jesper Z. , Rinaldo-Matthis Agnes , Akkaya Engin U. , Morgenstern Ralf 
Published: December 2016

AbstractBoth soluble and membrane-bound enzymes can catalyze the conversion of lipophilic substrates. The precise substrate access path, with regard to phase, has however, until now relied on conjecture from enzyme structural data only (certainly giving credible and valuable hypotheses). Alternative methods have been missing. To obtain the first experimental evidence directly determining the access paths (of lipophilic substrates) to phase constrained enzymes we here describe the application of a BODIPY-derived substrate (PS1). Using this tool, which is not accessible to cytosolic enzymes in the presence of detergent and, by contrast, not accessible to membrane embedded enzymes in the absence of detergent, we demonstrate that cytosolic and microsomal glutathione transferases (GSTs), both catalyzing the activation of PS1, do so only within their respective phases. This approach can serve as a guideline to experimentally validate substrate access paths, a fundamental property of phase restricted enzymes. Examples of other enzyme classes with members in both phases are xenobiotic-metabolizing sulphotransferases/UDP-glucuronosyl transferases or epoxide hydrolases. Since specific GSTs have been suggested to contribute to tumor drug resistance, PS1 can also be utilized as a tool to discriminate between phase constrained members of these enzymes by analyzing samples in the absence and presence of Triton X-100.
Physically Transient Memory on a Rapidly Dissoluble Paper for Security Application
Authors: Bae Hagyoul , Lee Byung-Hyun , Lee Dongil , Seol Myeong-Lok , Kim Daewon , Han Jin-Woo , Kim Choong-Ki , Jeon Seung-Bae , Ahn Daechul , Park Sang-Jae , Park Jun-Young , Choi Yang-Kyu 
Published: December 2016

AbstractWe report the transient memory device by means of a water soluble SSG (solid sodium with glycerine) paper. This material has a hydroscopic property hence it can be soluble in water. In terms of physical security of memory devices, prompt abrogation of a memory device which stored a large number of data is crucial when it is stolen because all of things have identified information in the memory device. By utilizing the SSG paper as a substrate, we fabricated a disposable resistive random access memory (RRAM) which has good data retention of longer than 106 seconds and cycling endurance of 300 cycles. This memory device is dissolved within 10 seconds thus it can never be recovered or replicated. By employing direct printing but not lithography technology to aim low cost and disposable applications, the memory capacity tends to be limited less than kilo-bits. However, unlike high memory capacity demand for consumer electronics, the proposed device is targeting for security applications. With this regards, the sub-kilobit memory capacity should find the applications such as one-time usable personal identification, authentication code storage, cryptography key, and smart delivery tag. This aspect is attractive for security and protection system against unauthorized accessibility.
A closer look into the α-helix basin
Authors: Haimov Boris , Srebnik Simcha 
Published: December 2016

Abstractα-Helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. Representation of α-helical structures with the common (φ, ψ) dihedrals, as in Ramachandran maps, does not provide informative details regarding the helical structure apart for the abstract geometric meaning of the dihedrals. We present an alternative coordinate system that describes helical conformations in terms of residues per turn (ρ) and angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ, ψ and ρ, ϑ). In this way, valuable information on the helical structure becomes directly available. Analysis of α-helical conformations acquired from the Protein Data Bank (PDB) demonstrates that a conformational energy function of the α-helix backbone can be harmonically approximated on the (ρ, ϑ) space, which is not applicable to the (φ, ψ) space due to the diagonal distribution of the conformations. The observed trends of helical conformations obtained from the PDB are captured by four conceptual simulations that theoretically examine the effects of residue bulkiness, external electric field, and externally applied mechanical forces. Flory’s isolated pair hypothesis is shown to be partially correct for α-helical conformations.
NIPTRIC: an online tool for clinical interpretation of non-invasive prenatal testing (NIPT) results
Authors: Sikkema-Raddatz Birgit , Johansson Lennart F. , de Boer Eddy N. , Boon Elles M. J. , Suijkerbuijk Ron F. , Bouman Katelijne , Bilardo Catia M. , Swertz Morris A. , Dijkstra Martijn , van Langen Irene M. , Sinke Richard J. , te Meerman Gerard J. 
Published: December 2016

AbstractTo properly interpret the result of a pregnant woman’s non-invasive prenatal test (NIPT), her a priori risk must be taken into account in order to obtain her personalised a posteriori risk (PPR), which more accurately expresses her true likelihood of carrying a foetus with trisomy. Our aim was to develop a tool for laboratories and clinicians to calculate easily the PPR for genome-wide NIPT results, using diploid samples as a control group. The tool takes the a priori risk and Z-score into account. Foetal DNA percentage and coefficient of variation can be given default settings, but actual values should be used if known. We tested the tool on 209 samples from pregnant women undergoing NIPT. For Z-scores < 5, the PPR is considerably higher at a high a priori risk than at a low a priori risk, for NIPT results with the same Z-score, foetal DNA percentage and coefficient of variation. However, the PPR is effectively independent under all conditions for Z-scores above 6. A high PPR for low a priori risks can only be reached at Z-scores > 5. Our online tool can assist clinicians in understanding NIPT results and conveying their true clinical implication to pregnant women, because the PPR is crucial for individual counselling and decision-making.