bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequential EMT-MET induces neuronal conversion through Sox2
Authors: He Songwei , Chen Jinlong , Zhang Yixin , Zhang Mengdan , Yang Xiao , Li Yuan , Sun Hao , Lin Lilong , Fan Ke , Liang Lining , Feng Chengqian , Wang Fuhui , Zhang Xiao , Guo Yiping , Pei Duanqing , Zheng Hui 
Published: May 2017

AbstractDirect neuronal conversion can be achieved with combinations of small-molecule compounds and growth factors. Here, by studying the first or induction phase of the neuronal conversion induced by defined 5C medium, we show that the Sox2-mediated switch from early epithelial–mesenchymal transition (EMT) to late mesenchymal–epithelial transition (MET) within a high proliferation context is essential and sufficient for the conversion from mouse embryonic fibroblasts (MEFs) to TuJ+ cells. At the early stage, insulin and basic fibroblast growth factor (bFGF)-induced cell proliferation, early EMT, the up-regulation of Stat3 and Sox2, and the subsequent activation of neuron projection. Up-regulated Sox2 then induced MET and directed cells towards a neuronal fate at the late stage. Inhibiting either stage of this sequential EMT-MET impaired the conversion. In addition, Sox2 could replace sequential EMT-MET to induce a similar conversion within a high proliferation context, and its functions were confirmed with other neuronal conversion protocols and MEFs reprogramming. Therefore, the critical roles of the sequential EMT-MET were implicated in direct cell fate conversion in addition to reprogramming, embryonic development and cancer progression.
Non-interferometric photoacoustic remote sensing microscopy
Authors: Hajireza Parsin , Shi Wei , Bell Kevan , Paproski Robert J , Zemp Roger J 
Published: June 2017

AbstractElasto-optical refractive index modulation due to photoacoustic initial pressure transients produced significant reflection of a probe beam when the absorbing interface had an appreciable refractive index difference. This effect was harnessed in a new form of non-contact optical resolution photoacoustic microscopy called photoacoustic remote sensing microscopy. A non-interferometric system architecture with a low-coherence probe beam precludes detection of surface oscillations and other phase-modulation phenomenon. The probe beam was confocal with a scanned excitation beam to ensure detection of initial pressure-induced intensity reflections at the subsurface origin where pressures are largest. Phantom studies confirmed signal dependence on optical absorption, index contrast and excitation fluence. In vivo imaging of superficial microvasculature and melanoma tumors was demonstrated with ~2.7±0.5 μm lateral resolution.
CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome
Authors: Shin Ha Youn , Wang Chaochen , Lee Hye Kyung , Yoo Kyung Hyun , Zeng Xianke , Kuhns Tyler , Yang Chul Min , Mohr Teresa , Liu Chengyu , Hennighausen Lothar 
Published: May 2017

AbstractAlthough CRISPR/Cas9 genome editing has provided numerous opportunities to interrogate the functional significance of any given genomic site, there is a paucity of data on the extent of molecular scars inflicted on the mouse genome. Here we interrogate the molecular consequences of CRISPR/Cas9-mediated deletions at 17 sites in four loci of the mouse genome. We sequence targeted sites in 632 founder mice and analyse 54 established lines. While the median deletion size using single sgRNAs is 9 bp, we also obtain large deletions of up to 600 bp. Furthermore, we show unreported asymmetric deletions and large insertions of middle repetitive sequences. Simultaneous targeting of distant loci results in the removal of the intervening sequences. Reliable deletion of juxtaposed sites is only achieved through two-step targeting. Our findings also demonstrate that an extended analysis of F1 genotypes is required to obtain conclusive information on the exact molecular consequences of targeting events.
Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data
Authors: Sinha Subarna , Thomas Daniel , Chan Steven , Gao Yang , Brunen Diede , Torabi Damoun , Reinisch Andreas , Hernandez David , Chan Andy , Rankin Erinn B. , Bernards Rene , Majeti Ravindra , Dill David L. 
Published: May 2017

AbstractTwo genes are synthetically lethal (SL) when defects in both are lethal to a cell but a single defect is non-lethal. SL partners of cancer mutations are of great interest as pharmacological targets; however, identifying them by cell line-based methods is challenging. Here we develop MiSL (Mining Synthetic Lethals), an algorithm that mines pan-cancer human primary tumour data to identify mutation-specific SL partners for specific cancers. We apply MiSL to 12 different cancers and predict 145,891 SL partners for 3,120 mutations, including known mutation-specific SL partners. Comparisons with functional screens show that MiSL predictions are enriched for SLs in multiple cancers. We extensively validate a SL interaction identified by MiSL between the IDH1 mutation and ACACA in leukaemia using gene targeting and patient-derived xenografts. Furthermore, we apply MiSL to pinpoint genetic biomarkers for drug sensitivity. These results demonstrate that MiSL can accelerate precision oncology by identifying mutation-specific targets and biomarkers.
R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein
Authors: Cloutier Philippe , Poitras Christian , Durand Mathieu , Hekmat Omid , Fiola-Masson Émilie , Bouchard Annie , Faubert Denis , Chabot Benoit , Coulombe Benoit 
Published: May 2017

AbstractThe R2TP/Prefoldin-like (R2TP/PFDL) complex has emerged as a cochaperone complex involved in the assembly of a number of critical protein complexes including snoRNPs, nuclear RNA polymerases and PIKK-containing complexes. Here we report on the use of multiple target affinity purification coupled to mass spectrometry to identify two additional complexes that interact with R2TP/PFDL: the TSC1–TSC2 complex and the U5 small nuclear ribonucleoprotein (snRNP). The interaction between R2TP/PFDL and the U5 snRNP is mostly mediated by the previously uncharacterized factor ZNHIT2. A more general function for the zinc-finger HIT domain in binding RUVBL2 is exposed. Disruption of ZNHIT2 and RUVBL2 expression impacts the protein composition of the U5 snRNP suggesting a function for these proteins in promoting the assembly of the ribonucleoprotein. A possible implication of R2TP/PFDL as a major effector of stress-, energy- and nutrient-sensing pathways that regulate anabolic processes through the regulation of its chaperoning activity is discussed.
Expression of CD226 is associated to but not required for NK cell education
Authors: Wagner Arnika K. , Kadri Nadir , Snäll Johanna , Brodin Petter , Gilfillan Susan , Colonna Marco , Bernhardt Günter , Höglund Petter , Kärre Klas , Chambers Benedict J. 
Published: May 2017

AbstractDNAX accessory molecule-1 (DNAM-1, also known as CD226) is an activating receptor expressed on subsets of natural killer (NK) and T cells, interacts with its ligands CD155 or CD112, and has co-varied expression with inhibitory receptors. Since inhibitory receptors control NK-cell activation and are necessary for MHC-I-dependent education, we investigated whether DNAM-1 expression is also involved in NK-cell education. Here we show an MHC-I-dependent correlation between DNAM-1 expression and NK-cell education, and an association between DNAM-1 and NKG2A that occurs even in MHC class I deficient mice. DNAM-1 is expressed early during NK-cell development, precedes the expression of MHC-I-specific inhibitory receptors, and is modulated in an education-dependent fashion.Cd226−/−mice have missing self-responses and NK cells with a normal receptor repertoire. We propose a model in which NK-cell education prevents or delays downregulation of DNAM-1. This molecule endows educated NK cells with enhanced effector functions but is dispensable for education.
Cancer-cell intrinsic gene expression signatures overcome intratumoural heterogeneity bias in colorectal cancer patient classification
Authors: Dunne Philip D. , Alderdice Matthew , O'Reilly Paul G. , Roddy Aideen C. , McCorry Amy M. B. , Richman Susan , Maughan Tim , McDade Simon S. , Johnston Patrick G. , Longley Daniel B. , Kay Elaine , McArt Darragh G. , Lawler Mark 
Published: May 2017

AbstractStromal-derived intratumoural heterogeneity (ITH) has been shown to undermine molecular stratification of patients into appropriate prognostic/predictive subgroups. Here, using several clinically relevant colorectal cancer (CRC) gene expression signatures, we assessed the susceptibility of these signatures to the confounding effects of ITH using gene expression microarray data obtained from multiple tumour regions of a cohort of 24 patients, including central tumour, the tumour invasive front and lymph node metastasis. Sample clustering alongside correlative assessment revealed variation in the ability of each signature to cluster samples according to patient-of-origin rather than region-of-origin within the multi-region dataset. Signatures focused on cancer-cell intrinsic gene expression were found to produce more clinically useful, patient-centred classifiers, as exemplified by the CRC intrinsic signature (CRIS), which robustly clustered samples by patient-of-origin rather than region-of-origin. These findings highlight the potential of cancer-cell intrinsic signatures to reliably stratify CRC patients by minimising the confounding effects of stromal-derived ITH.
In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes at physiological temperature
Authors: Jaballah Soumeya A. , Bailey Graham D. , Desfosses Ambroise , Hyun Jaekyung , Mitra Alok K. , Kingston Richard L. 
Published: May 2017

AbstractDuring a proteolytically-driven maturation process, the orthoretroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at near-physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.
Optimisation of a murine splenocyte mycobacterial growth inhibition assay using virulent Mycobacterium tuberculosis
Authors: Jensen Christina , Lindebo Holm Line , Svensson Erik , Aagaard Claus , Ruhwald Morten 
Published: May 2017

AbstractIn the absence of a validated correlate of protection or robust animal models for human tuberculosis, Mycobacterial growth inhibition assays (MGIAs) aim to assess vaccines ability to inhibit mycobacterial growth in-vitro. We optimised a reproducible murine splenocyte MGIA based on in-vitro infection with ﻿virulent Mycobacterium tuberculosis (M.tb) Erdman. We identified splenocyte viability as a problem in state-of-art MGIA protocols, which can be improved by simple changes in culture conditions (viability increase from 21% to 46% at last day of culture). The growth inhibitory potential in mice immunised with either BCG, H56:CAF01 or H56:CAF01 administered side-by-side with BCG was significantly better compared to placebo in all groups (0.3 log10 CFU [±0.2, p = 0.049], 0.5 [±0.2, p = 0.016] and 0.6 [±0.1, p = 0.0007], respectively) corresponding to the levels of in-vivo protection. Unexpectedly the CAF01 adjuvant control group also induced significant growth inhibition of 0.3 log10 CFU (±0.2, p = 0.047). Finally, we explored vaccine-associated T cell effector functions. Despite presence of high levels of vaccine-specific T cells, we found no increase in CD4+ T cell number or cytokine expression profile, nor a difference in cytokine levels in the supernatant after four days culture with or without M.tb. Spontaneous IFN-γ release correlated with growth inhibition levels (p = 0.02), however the cellular source was not found.
Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)
Authors: Kwong Qi Bin , Ong Ai Ling , Teh Chee Keng , Chew Fook Tim , Tammi Martti , Mayes Sean , Kulaveerasingam Harikrishna , Yeoh Suat Hui , Harikrishna Jennifer Ann , Appleton David Ross 
Published: May 2017

AbstractGenomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), Cπ (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection.
Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype
Authors: da Silveira W. A. , Palma P. V. B. , Sicchieri R. D. , Villacis R. A. R. , Mandarano L. R. M. , Oliveira T. M. G. , Antonio H. M. R. , Andrade J. M. , Muglia V. F. , Rogatto S. R. , Theillet C. , du Manoir S. , Tiezzi D. G. 
Published: May 2017

AbstractBreast cancer is the most common cancer in women worldwide and metastatic dissemination is the principal factor related to death by this disease. Breast cancer stem cells (bCSC) are thought to be responsible for metastasis and chemoresistance. In this study, based on whole transcriptome analysis from putative bCSC and reverse engineering of transcription control networks, we identified two networks associated with this phenotype. One controlled by SNAI2, TWIST1, BNC2, PRRX1 and TBX5 drives a mesenchymal or CSC-like phenotype. The second network is controlled by the SCML4, ZNF831, SP140 and IKZF3 transcription factors which correspond to immune response modulators. Immune response network expression is correlated with pathological response to chemotherapy, and in the Basal subtype is related to better recurrence-free survival. In patient-derived xenografts, the expression of these networks in patient tumours is predictive of engraftment success. Our findings point out a potential molecular mechanism underlying the balance between immune surveillance and EMT activation in breast cancer. This molecular mechanism may be useful to the development of new target therapies.
Rumen Fluid Metabolomics Analysis Associated with Feed Efficiency on Crossbred Steers
Authors: Artegoitia Virginia M. , Foote Andrew P. , Lewis Ronald M. , Freetly Harvey C. 
Published: May 2017

AbstractThe rumen has a central role in the efficiency of digestion in ruminants. To identify potential differences in rumen function that lead to differences in average daily gain (ADG), rumen fluid metabolomic analysis by LC-MS and multivariate/univariate statistical analysis were used to identify differences in rumen metabolites. Individual feed intake and body-weight was measured on 144 steers during 105 d on a high concentrate ration. Eight steers with the greatest ADG and 8 steers with the least-ADG with dry matter intake near the population average were selected. Blood and rumen fluid was collected from the 16 steers 26 d before slaughter and at slaughter, respectively. As a result of the metabolomics analysis of rumen fluid, 33 metabolites differed between the ADG groups based on t-test, fold changes and partial least square discriminant analysis. These metabolites were primarily involved in linoleic and alpha-linolenic metabolism (impact-value 1.0 and 0.75, respectively; P < 0.05); both pathways were down-regulated in the greatest-ADG compared with least-ADG group. Ruminal biohydrogenation might be associated with the overall animal production. The fatty acids were quantified in rumen and plasma using targeted MS to validate and evaluate the simple combination of metabolites that effectively predict ADG.
Burkholderia pseudomallei in a lowland rice paddy: seasonal changes and influence of soil depth and physico-chemical properties
Authors: Manivanh L. , Pierret A. , Rattanavong S. , Kounnavongsa O. , Buisson Y. , Elliott I. , Maeght J. -L. , Xayyathip K. , Silisouk J. , Vongsouvath M. , Phetsouvanh R. , Newton P. N. , Lacombe G. , Ribolzi O. , Rochelle-Newall E. , Dance D. A. B. 
Published: June 2017

AbstractMelioidosis, a severe infection with the environmental bacterium Burkholderia pseudomallei, is being recognised increasingly frequently. What determines its uneven distribution within endemic areas is poorly understood. We cultured soil from a rice field in Laos for B. pseudomallei at different depths on 4 occasions over a 13-month period. We also measured physical and chemical parameters in order to identify associated characteristics. Overall, 195 of 653 samples (29.7%) yielded B. pseudomallei. A higher prevalence of B. pseudomallei was found at soil depths greater than the 30 cm currently recommended for B. pseudomallei environmental sampling. B. pseudomallei was associated with a high soil water content and low total nitrogen, carbon and organic matter content. Our results suggested that a sampling grid of 25 five metre square quadrats (i.e. 25 × 25 m) should be sufficient to detect B. pseudomallei at a given location if samples are taken at a soil depth of at least 60 cm. However, culture of B. pseudomallei in environmental samples is difficult and liable to variation. Future studies should both rely on molecular approaches and address the micro-heterogeneity of soil when investigating physico-chemical associations with the presence of B. pseudomallei.
A Haptotaxis Assay for Neutrophils using Optical Patterning and a High-content Approach
Authors: Roy Joannie , Mazzaferri Javier , Filep János G. , Costantino Santiago 
Published: May 2017

AbstractNeutrophil recruitment guided by chemotactic cues is a central event in host defense against infection and tissue injury. While the mechanisms underlying neutrophil chemotaxis have been extensively studied, these are just recently being addressed by using high-content approaches or surface-bound chemotactic gradients (haptotaxis)in vitro. Here, we report a haptotaxis assay, based on the classic under-agarose assay, which combines an optical patterning technique to generate surface-bound formyl peptide gradients as well as an automated imaging and analysis of a large number of migration trajectories. We show that human neutrophils migrate on covalently-bound formyl-peptide gradients, which influence the speed and frequency of neutrophil penetration under the agarose. Analysis revealed that neutrophils migrating on surface-bound patterns accumulate in the region of the highest peptide concentration, thereby mimickingin vivoevents. We propose the use of a chemotactic precision index, gyration tensors and neutrophil penetration rate for characterizing haptotaxis. This high-content assay provides a simple approach that can be applied for studying molecular mechanisms underlying haptotaxis on user-defined gradient shape.
Size and specimen-dependent strategy for x-ray micro-ct and tem correlative analysis of nervous system samples
Authors: Parlanti P. , Cappello V. , Brun F. , Tromba G. , Rigolio R. , Tonazzini I. , Cecchini M. , Piazza V. , Gemmi M. 
Published: May 2017

AbstractCorrelative approaches are a powerful tool in the investigation of biological samples, but require specific preparation procedures to maintain the strength of the employed methods. Here we report the optimization of the embedding protocol of nervous system samples for a correlative synchrotron X-ray computed microtomography (micro-CT) and transmission electron microscopy (TEM) approach. We demonstrate that it is possible to locate, with the micrometric resolution of micro-CT, specific volumes of interest for a further ultrastructural characterization to be performed with TEM. This approach can be applied to samples of different size and morphology up to several cm. Our optimized method represents an invaluable tool for investigating those pathologies in which microscopic alterations are localized in few confined regions, rather than diffused in entire tissues, organs or systems. We present a proof of concept of our method in a mouse model of Globoid Cells Leukodistrophy.
Estimation of the thermocapillary force and its applications to precise droplet control on a microfluidic chip
Authors: Won By June , Lee Wooyoung , Song Simon 
Published: June 2017

AbstractDroplet control through the use of light-induced thermocapillary effects has recently garnered attention due to its non-intrusive and multifunctional nature. An important issue in droplet control is the estimation of the thermocapillary force. The purpose of the present study is to estimate the thermocapillary force and propose empirical equations between the force and simply measurable key parameters such as droplet diameter and power of heat source. In addition, we aim to shift the droplet trajectory and develop an on-demand droplet routing system based on the estimation of the thermocapillary force. We illuminated a continuous phase with a 532 nm laser beam to minimize possible damage or property changes to target molecules contained within droplets. A mixture of light-absorbing material and oleic acid was used for the continuous phase fluid, while deionized water (DI water) was used for the dispersed phase fluid. We proposed empirical equations to estimate the thermocapillary force, which was then applied to precise droplet shifting and routing. We found that the shifting distance was linearly proportional to the thermocapillary force, and that an on-demand droplet routing system resulted in a success rate greater than 95%.
Direct measurement of optical trapping force gradient on polystyrene microspheres using a carbon nanotube mechanical resonator
Authors: Yasuda Masaaki , Takei Kuniharu , Arie Takayuki , Akita Seiji 
Published: May 2017

AbstractOptical tweezers based on optical radiation pressure are widely used to manipulate nanoscale to microscale particles. This study demonstrates direct measurement of the optical force gradient distribution acting on a polystyrene (PS) microsphere using a carbon nanotube (CNT) mechanical resonator, where a PS microsphere with 3 μm diameter is welded at the CNT tip using laser heating. With the CNT mechanical resonator with PS microsphere, we measured the distribution of optical force gradient with resolution near the thermal noise limit of 0.02 pN/μm in vacuum, in which condition enables us to high accuracy measurement using the CNT mechanical resonator because of reduced mechanical damping from surrounding fluid. The obtained force gradient and the force gradient distribution agree well with theoretical values calculated using Lorenz–Mie theory.