bluuebunny/crossref_metadata_2025_split huggingface dataset:
Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples
Authors: Zeka Fjoralba , Vanderheyden Katrien , De Smet Els , Cuvelier Claude A. , Mestdagh Pieter , Vandesompele Jo 
Published: February 2016

AbstractFragmented RNA from formalin-fixed paraffin-embedded (FFPE) tissue is a known obstacle to gene expression analysis. In this study, the impact of RNA integrity, gene-specific reverse transcription and targeted cDNA preamplification was quantified in terms of reverse transcription polymerase chain reaction (RT-qPCR) sensitivity by measuring 48 protein coding genes on eight duplicate cultured cancer cell pellet FFPE samples and twenty cancer tissue FFPE samples. More intact RNA modestly increased gene detection sensitivity by 1.6 fold (earlier detection by 0.7 PCR cycles, 95% CI = 0.593–0.850). Application of gene-specific priming instead of whole transcriptome priming during reverse transcription further improved RT-qPCR sensitivity by a considerable 4.0 fold increase (earlier detection by 2.0 PCR cycles, 95% CI = 1.73–2.32). Targeted cDNA preamplification resulted in the strongest increase of RT-qPCR sensitivity and enabled earlier detection by an average of 172.4 fold (7.43 PCR cycles, 95% CI = 6.83–7.05). We conclude that gene-specific reverse transcription and targeted cDNA preamplification are adequate methods for accurate and sensitive RT-qPCR based gene expression analysis of FFPE material. The presented methods do not involve expensive or complex procedures and can be easily implemented in any routine RT-qPCR practice.
Droplet Breakup in Expansion-contraction Microchannels
Authors: Zhu Pingan , Kong Tiantian , Lei Leyan , Tian Xiaowei , Kang Zhanxiao , Wang Liqiu 
Published: February 2016

AbstractWe investigate the influences of expansion-contraction microchannels on droplet breakup in capillary microfluidic devices. With variations in channel dimension, local shear stresses at the injection nozzle and focusing orifice vary, significantly impacting flow behavior including droplet breakup locations and breakup modes. We observe transition of droplet breakup location from focusing orifice to injection nozzle and three distinct types of recently-reported tip-multi-breaking modes. By balancing local shear stresses and interfacial tension effects, we determine the critical condition for breakup location transition and characterize the tip-multi-breaking mode quantitatively. In addition, we identify the mechanism responsible for the periodic oscillation of inner fluid tip in tip-multi-breaking mode. Our results offer fundamental understanding of two-phase flow behaviors in expansion-contraction microstructures and would benefit droplet generation, manipulation and design of microfluidic devices.
Progestins alter photo-transduction cascade and circadian rhythm network in eyes of zebrafish (Danio rerio)
Authors: Zhao Yanbin , Fent Karl 
Published: February 2016

AbstractEnvironmental progestins are implicated in endocrine disruption in vertebrates. Additional targets that may be affected in organisms are poorly known. Here we report that progesterone (P4) and drospirenone (DRS) interfere with the photo-transduction cascade and circadian rhythm network in the eyes of zebrafish. Breeding pairs of adult zebrafish were exposed to P4 and DRS for 21 days with different measured concentrations of 7–742 ng/L and 99-13´650 ng/L, respectively. Of totally 10 key photo-transduction cascade genes analyzed, transcriptional levels of most were significantly up-regulated, or normal down-regulation was attenuated. Similarly, for some circadian rhythm genes, dose-dependent transcriptional alterations were also observed in the totally 33 genes analyzed. Significant alterations occurred even at environmental relevant levels of 7 ng/L P4. Different patterns were observed for these transcriptional alterations, of which, the nfil3 family displayed most significant changes. Furthermore, we demonstrate the importance of sampling time for the determination and interpretation of gene expression data and put forward recommendations for sampling strategies to avoid false interpretations. Our results suggest that photo-transduction signals and circadian rhythm are potential targets for progestins. Further studies are required to assess alterations on the protein level, on physiology and behavior, as well as on implications in mammals.
A microRNA-mediated decrease in eukaryotic initiation factor 2α promotes cell survival during PS-341 treatment
Authors: Jiang Lili , Zang Dan , Yi Songgang , Li Xiaofen , Yang Changshan , Dong Xiaoxian , Zhao Chong , Lan Xiaoying , Chen Xin , Liu Shouting , Liu Ningning , Huang Hongbiao , Shi Xianping , Wang Xuejun , Liu Jinbao 
Published: February 2016

AbstractMicroRNAs (miRs) play pivotal roles in carcinogenesis and endoplasmic reticulum (ER) that performs the folding, modification and trafficking of proteins targeted to the secretory pathway. Cancer cells often endure ER stress during tumor progression but use the adaptive ER stress response to gain survival advantage. Here we report: (i) A group of miRs, including miR-30b-5p and miR-30c-5p, are upregulated by proteasome inhibitor PS-341 treatment, in HepG2 and MDA-MB-453 cells. (ii) Two representative PS-341-induced miRs: miR-30b-5p and miR-30c-5p are found to promote cell proliferation and anti-apoptosis in both tumor cells. (iii) eIF2α is confirmed as the congenerous target of miR-30b-5p and miR-30c-5p, essential to the anti-apoptotic function of these miRs. (iv) Upregulation of miR-30b-5p or miR-30c-5p, which occurs latter than the increase of phosphorylated eIF2α (p-eIF2α) in the cell under ER stress, suppresses the p-eIF2α/ATF4/CHOP pro-apoptotic pathway. (v) Inhibition of the miR-30b-5p or miR-30c-5p sensitizes the cancer cells to the cytotoxicity of proteasome inhibition. In conclusion, we unravels a new miRs-based mechanism that helps maintain intracellular proteostasis and promote cell survival during ER stress through upregulation of miR-30b-5p and miR-30c-5p which target eIF2α and thereby inhibit the p-eIF2α/ATF4/CHOP pro-apoptotic pathway, identifying miR-30b-5p and miR-30c-5p as potentially new targets for anti-cancer therapies.
Oscillating primary transcripts harbor miRNAs with circadian functions
Authors: Wang Haifang , Fan Zenghua , Zhao Meng , Li Juan , Lu Minghua , Liu Wei , Ying Hao , Liu Mofang , Yan Jun 
Published: February 2016

AbstractThe roles of miRNAs as important post-transcriptional regulators in the circadian clock have been suggested in several studies. But the search for circadian miRNAs has led to disparate results. Here we demonstrated that at least 57 miRNA primary transcripts are rhythmically transcribed in mouse liver. Most of these transcripts are under the regulation of circadian transcription factors such as BMAL1/CLOCK and REV-ERBα/β. However, the mature miRNAs derived from these transcripts are either not oscillating or oscillating at low amplitudes, which could explain the inconsistency of different circadian miRNA studies. In order to show that these circadian primary transcripts can give rise to miRNAs with circadian functions, we over-expressed one of them, miR-378, in mouse by adenovirus injection. We found a significant over-representation of circadian oscillating genes under-expressed by miR-378 over-expression in liver. In particular, we observed that miR-378 modulates the oscillation amplitudes of Cdkn1a in the control of cell cycle and Por in the regulation of oxidation reduction by forming partnership with different circadian transcription factors. Our study suggests that circadian transcription of miRNA at primary transcript level can be a good indicator for circadian miRNA functions.
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling
Authors: Zur Hadas , Aviner Ranen , Tuller Tamir 
Published: February 2016

AbstractTwo novel approaches were recently suggested for genome-wide identification of protein aspects synthesized at a given time. Ribo-Seq is based on sequencing all the ribosome protected mRNA fragments in a cell, while PUNCH-P is based on mass-spectrometric analysis of only newly synthesized proteins. Here we describe the first Ribo-Seq/PUNCH-P comparison via the analysis of mammalian cells during the cell-cycle for detecting relevant differentially expressed genes between G1 and M phase. Our analyses suggest that the two approaches significantly overlap with each other. However, we demonstrate that there are biologically meaningful proteins/genes that can be detected to be post-transcriptionally regulated during the mammalian cell cycle only by each of the approaches, or their consolidation. Such gene sets are enriched with proteins known to be related to intra-cellular signalling pathways such as central cell cycle processes, central gene expression regulation processes, processes related to chromosome segregation, DNA damage and replication, that are post-transcriptionally regulated during the mammalian cell cycle. Moreover, we show that combining the approaches better predicts steady state changes in protein abundance. The results reported here support the conjecture that for gaining a full post-transcriptional regulation picture one should integrate the two approaches.
Use of lead-210 as a novel tracer for lead (Pb) sources in plants
Authors: Yang Handong , Appleby Peter G. 
Published: February 2016

AbstractLead (Pb) released from anthropogenic sources and stored in environmental repositories can be a potential source for secondary pollution. Here we develop a novel approach for tracking Pb from atmospheric deposition and other sources in the environment using fallout 210Pb as a tracer, and apply the method to samples collected from Richmond Park, London, the UK. The mean ratio of 210Pb to total Pb in atmospheric depositions collected from a site adjacent to the park during August–October 2012 was 96 Bq mg−1, while the ratio in surface soils from the park was typically an order of magnitude lower. The difference between these values made it possible to trace the source of Pb in the plants. The 210Pb/Pb ratios in plants varied from 0 to 34 Bq mg−1 indicating different levels of Pb absorption from the atmosphere. The ratio in mosses had an average value of 22 Bq mg−1. This suggests that only around 20% of the Pb they contain was from direct atmospheric deposition, revealing possible limitations in the use of terrestrial mosses for monitoring atmospheric pollution. As well as tracking sources, variations in the 210Pb/Pb ratio can also reveal ways in which Pb is transferred within plants.
Interplay of histidine residues of the Alzheimer’s disease Aβ peptide governs its Zn-induced oligomerization
Authors: Istrate Andrey N. , Kozin Sergey A. , Zhokhov Sergey S. , Mantsyzov Alexey B. , Kechko Olga I. , Pastore Annalisa , Makarov Alexander A. , Polshakov Vladimir I. 
Published: February 2016

AbstractConformational changes of Aβ peptide result in its transformation from native monomeric state to the toxic soluble dimers, oligomers and insoluble aggregates that are hallmarks of Alzheimer’s disease (AD). Interactions of zinc ions with Aβ are mediated by the N-terminal Aβ1–16 domain and appear to play a key role in AD progression. There is a range of results indicating that these interactions trigger the Aβ plaque formation. We have determined structure and functional characteristics of the metal binding domains derived from several Aβ variants and found that their zinc-induced oligomerization is governed by conformational changes in the minimal zinc binding site 6HDSGYEVHH14. The residue H6 and segment 11EVHH14, which are part of this site are crucial for formation of the two zinc-mediated interaction interfaces in Aβ. These structural determinants can be considered as promising targets for rational design of the AD-modifying drugs aimed at blocking pathological Aβ aggregation.
Insight into Coenzyme A cofactor binding and the mechanism of acyl-transfer in an acylating aldehyde dehydrogenase from Clostridium phytofermentans
Authors: Tuck Laura R. , Altenbach Kirsten , Ang Thiau Fu , Crawshaw Adam D. , Campopiano Dominic J. , Clarke David J. , Marles-Wright Jon 
Published: February 2016

AbstractThe breakdown of fucose and rhamnose released from plant cell walls by the cellulolytic soil bacterium Clostridium phytofermentans produces toxic aldehyde intermediates. To enable growth on these carbon sources, the pathway for the breakdown of fucose and rhamnose is encapsulated within a bacterial microcompartment (BMC). These proteinaceous organelles sequester the toxic aldehyde intermediates and allow the efficient action of acylating aldehyde dehydrogenase enzymes to produce an acyl-CoA that is ultimately used in substrate-level phosphorylation to produce ATP. Here we analyse the kinetics of the aldehyde dehydrogenase enzyme from the fucose/rhamnose utilisation BMC with different short-chain fatty aldehydes and show that it has activity against substrates with up to six carbon atoms, with optimal activity against propionaldehyde. We have also determined the X-ray crystal structure of this enzyme in complex with CoA and show that the adenine nucleotide of this cofactor is bound in a distinct pocket to the same group in NAD+. This work is the first report of the structure of CoA bound to an aldehyde dehydrogenase enzyme and our crystallographic model provides important insight into the differences within the active site that distinguish the acylating from non-acylating aldehyde dehydrogenase enzymes.
Cogeneration topology for wind energy conversion system using doubly‐fed induction generator
Authors: Parida Adikanda , Chatterjee Debashis 
Published: February 2016

A novel wind energy conversion system (WECS) with cogeneration topology is presented in this study. In the proposed scheme, doubly‐fed induction generator (DFIG) is used as the major source for power generation in grid‐isolated mode. The wind turbine operated DFIG is integrated with a permanent magnet ac generator and a solar photovoltaic (PV) module to supplement the both rotor power requirement of DFIG and part of the average load power demand. The performance of a grid‐isolated WECS, over wide speed range can be significantly improved through the sequential extraction of wind power along with an augmented solar PV source. The proposed scheme is economically viable with feasible unit cost of generated power. The control scheme has been simulated and experimentally validated with a practical 2.5 kW DFIG using dSPACE DS1104 module, which produced satisfactory results.
PON-Sol: prediction of effects of amino acid substitutions on protein solubility
Authors: Yang Yang , Niroula Abhishek , Shen Bairong , Vihinen Mauno 
Published: February 2016

Abstract
Motivation: Solubility is one of the fundamental protein properties. It is of great interest because of its relevance to protein expression. Reduced solubility and protein aggregation are also associated with many diseases.
Results: We collected from literature the largest experimentally verified solubility affecting amino acid substitution (AAS) dataset and used it to train a predictor called PON-Sol. The predictor can distinguish both solubility decreasing and increasing variants from those not affecting solubility. PON-Sol has normalized correct prediction ratio of 0.491 on cross-validation and 0.432 for independent test set. The performance of the method was compared both to solubility and aggregation predictors and found to be superior. PON-Sol can be used for the prediction of effects of disease-related substitutions, effects on heterologous recombinant protein expression and enhanced crystallizability. One application is to investigate effects of all possible AASs in a protein to aid protein engineering.
Availability and implementation: PON-Sol is freely available at http://structure.bmc.lu.se/PON-Sol. The training and test data are available at http://structure.bmc.lu.se/VariBench/ponsol.php
Contact: mauno.vihinen@med.lu.se
Supplementary information: Supplementary data are available at Bioinformatics online.
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling
Authors: Bhattacharya Debswapna , Adhikari Badri , Li Jilong , Cheng Jianlin 
Published: February 2016

Abstract
Motivation: Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment.
Results: Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input–Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality.
Availability and implementation: Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/. It is bundled with a manual and example data.
Contact: chengji@missouri.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification
Authors: Van Riper Susan K. , Higgins LeeAnn , Carlis John V. , Griffin Timothy J. 
Published: February 2016

Abstract
Summary: RIPPER is a framework for mass-spectrometry-based label-free relative quantification for proteomics and metabolomics studies. RIPPER combines a series of previously described algorithms for pre-processing, analyte quantification, retention time alignment, and analyte grouping across runs. It is also the first software framework to implement proximity-based intensity normalization. RIPPER produces lists of analyte signals with their unnormalized and normalized intensities that can serve as input to statistical and directed mass spectrometry (MS) methods for detecting quantitative differences between biological samples using MS.
Availability and implementation: http://www.z.umn.edu/ripper.
Contact: vanr0014@umn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mammary-tumor-educated B cells acquire LAP/TGF-β and PD-L1 expression and suppress anti-tumor immune responses
Authors: Zhang Yu , Morgan Richard , Chen Chuan , Cai Yancheng , Clark Emily , Khan Wasif Noor , Shin Seung-Uon , Cho Hyun-Mi , Al Bayati Ahmed , Pimentel Augustin , Rosenblatt Joseph D. 
Published: February 2016

Abstract
B lymphocytes play a role in inhibiting the immune response against certain tumors, but the underlying mechanisms are poorly understood. EMT-6 mammary tumors grow well in wild-type (WT) mice but show reduced growth in B-cell-deficient μ−/− BALB/c mice (BCDM). WT mice demonstrate extensive B-cell infiltration into the tumor bed, reduced CD8+ T cell and CD49+ NK cell infiltration, and markedly reduced cytolytic T-cell response relative to BCDM. Expression of LAP/TGF-β1, CD80, CD86 and PD-L1 is significantly increased in tumor-infiltrating B cells (TIL-B) relative to splenic B cells. LAP/TGF-β1 expression on TIL-B progressively increased from 5.4±1.7% on day 8 to 43.1±6.1% by day 21 post tumor implantation. Co-culture of EMT-6 tumor cells with Naive-B cells ex vivo generated B cells (EMT6-B) with a similar immunophenotype to TIL-B. Purified TIL-B, or in-vitro-generated EMT6-B suppressed CD4+, CD8+ and CD4+CD25− T-cell proliferation, and Th1 cytokine secretion, and also suppressed purified NK-cell proliferation in response to IL-15, compared to naive splenic B cells. Acquired B regulatory function required direct tumor cell: B-cell contact, and was partially reversed by antibody to TGF-β or PD-L1, leading to tumor rejection in vivo. B-cell acquisition of a suppressive phenotype following tumor infiltration may result in profound inhibition of T-cell anti-tumor responses.
Radio-loud Narrow Line Seyfert 1 under a different perspective: a revised black hole mass estimate from optical spectropolarimetry
Authors: Baldi Ranieri D. , Capetti Alessandro , Robinson Andrew , Laor Ari , Behar Ehud 
Published: February 2016

Abstract
Several studies indicate that radio-loud (RL) active galactic nuclei (AGNs) are produced only by the most massive black holes (BH), MBH ∼ 108–1010 M⊙. This idea has been challenged by the discovery of RL Narrow Line Seyfert 1 (RL NLSy1), having estimated masses of MBH ∼ 106–107 M⊙. However, these low MBH estimates might be due to projection effects. Spectropolarimetry allows us to test this possibility by looking at RL NLSy1s under a different perspective, i.e. from the viewing angle of the scattering material. We here report the results of a pilot study of Very Large Telescope spectropolarimetric observations of the RL NLSy1 PKS 2004−447. Its polarization properties are remarkably well reproduced by models in which the scattering occurs in an equatorial structure surrounding its broad-line region, seen close to face-on. In particular, we detect a polarized Hα line with a width of ∼9000 km s−1, ∼6 times broader than the width seen in direct light. This corresponds to a revised estimate of MBH ∼ 6 × 108 M⊙, well within the typical range of RL AGN. The double-peaked polarized broad Hα profile of the target suggests that the rare combination of the orientation effects and a broad line region dominated by the rotation might account for this class of objects, casting doubts on the virial estimates of BH mass for type-I AGN.
Probing O-enrichment in C-rich dust planetary nebulae
Authors: García-Hernández D. A. , Ventura P. , Delgado-Inglada G. , Dell'Agli F. , Di Criscienzo M. , Yagüe A. 
Published: February 2016

Abstract
The abundance of O in planetary nebulae (PNe) has been historically used as a metallicity indicator of the interstellar medium (ISM), where they originated; e.g. it has been widely used to study metallicity gradients in our Galaxy and beyond. However, clear observational evidence for O self-enrichment in low-metallicity Galactic PNe with C-rich dust has been recently reported. Here, we report asymptotic giant branch (AGB) nucleosynthesis predictions for the abundances of the CNO elements and helium in the metallicity range Z⊙/4 &lt; Z &lt; 2 Z⊙. Our AGB models, with diffusive overshooting from all the convective borders, predict that O is overproduced in low-Z low-mass (∼1–3 M⊙) AGB stars and nicely reproduce the recent O overabundances observed in C-rich dust PNe. This confirms that O is not always a good proxy of the original ISM metallicity and other chemical elements such as Cl or Ar should be used instead. The production of oxygen by low-mass stars should be thus considered in galactic-evolution models.