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https://www.readbyqxmd.com/read/28633360/expression-properties-exhibit-correlated-patterns-with-the-fate-of-duplicated-genes-their-divergence-and-transcriptional-plasticity-in-saccharomycotina
#1
Florian Mattenberger, Beatriz Sabater-Muñoz, Christina Toft, Gaurav Sablok, Mario A Fares
Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed...
June 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28629618/conditioning-and-robustness-of-rna-boltzmann-sampling-under-thermodynamic-parameter-perturbations
#2
Emily Rogers, David Murrugarra, Christine Heitsch
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28622587/statistical-characterization-of-noise-for-spatial-standardization-of-ct-scans-enabling-comparison-with-multiple-kernels-and-doses
#3
Gonzalo Vegas-Sánchez-Ferrero, Maria J Ledesma-Carbayo, George R Washko, Raúl San José Estépar
Computerized tomography (CT) is a widely adopted modality for analyzing directly or indirectly functional, biological and morphological processes by means of the image characteristics. However, the potential utilization of the information obtained from CT images is often limited when considering the analysis of quantitative information involving different devices, acquisition protocols or reconstruction algorithms. Although CT scanners are calibrated as a part of the imaging workflow, the calibration is circumscribed to global reference values and does not circumvent problems that are inherent to the imaging modality...
June 7, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28619587/chemicalome-and-metabolome-profiling-of-polymethoxylated-flavonoids-in-citri-reticulatae-pericarpium-based-on-an-integrated-strategy-combining-background-subtraction-and-modified-mass-defect-filter-in-a-microsoft-excel-platform
#4
Su-Ling Zeng, Li Duan, Bai-Zhong Chen, Ping Li, E-Hu Liu
Detection of metabolites in complex biological matrixes is a great challenge because of the background noise and endogenous components. Herein, we proposed an integrated strategy that combined background subtraction program and modified mass defect filter (MMDF) data mining in a Microsoft Excel platform for chemicalome and metabolome profiling of the polymethoxylated flavonoids (PMFs) in Citri Reticulatae Pericarpium (CRP). The exogenously-sourced ions were firstly filtered out by the developed Visual Basic for Applications (VBA) program incorporated in the Microsoft Office...
June 9, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28618495/robustness-of-synthetic-oscillators-in-growing-and-dividing-cells
#5
Joris Paijmans, David K Lubensky, Pieter Rein Ten Wolde
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. Elowitz and Leibler [Nature (London) 403, 335 (2000)NATUAS0028-083610.1038/35002125] showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator. More recently, Stricker et al. [Nature (London) 456, 516 (2008)NATUAS0028-083610.1038/nature07389] presented another synthetic oscillator, called the dual-feedback oscillator, which is more stable...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28616711/integrating-noe-and-rdc-using-sum-of-squares-relaxation-for-protein-structure-determination
#6
Y Khoo, A Singer, D Cowburn
We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame...
June 14, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28609671/salting-out-assisted-liquid-liquid-extraction-combined-with-gas-chromatography-mass-spectrometry-for-the-determination-of-pyrethroid-insecticides-in-high-salinity-and-biological-samples
#7
Zongliang Niu, Chunwei Yu, Xiaowen He, Jun Zhang, Yingying Wen
A salting-out assisted liquid-liquid extraction (SALLE) combined with gas chromatography-mass spectrometry (GC-MS) method was developed for the determination of four pyrethroid insecticides (PYRs) in high salinity and biological samples. Several parameters including sample pH, salting-out solution volume and salting-out solution pH influencing the extraction efficiency were systematically investigated with the aid of orthogonal design. The optimal extraction conditions of SALLE were: 4mL of salting-out solution with pH=4 and the sample pH=3...
June 3, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28607529/ev-associated-mmp9-in-high-grade-serous-ovarian-cancer-is-preferentially-localized-to-annexin-v-binding-evs
#8
Agnes T Reiner, Sisareuth Tan, Christiane Agreiter, Katharina Auer, Anna Bachmayr-Heyda, Stefanie Aust, Nina Pecha, Mattias Mandorfer, Dietmar Pils, Alain R Brisson, Robert Zeillinger, Sai Kiang Lim
High-grade serous ovarian cancer (HGSOC) is the most aggressive type of ovarian cancer and is responsible for most deaths caused by gynecological cancers. Numerous candidate biomarkers were identified for this disease in the last decades, but most were not sensitive or specific enough for clinical applications. Hence, new biomarkers for HGSOC are urgently required. This study aimed to identify new markers by isolating different extracellular vesicle (EV) types from the ascites of ovarian cancer patients according to their affinities for lipid-binding proteins and analyzing their protein cargo...
2017: Disease Markers
https://www.readbyqxmd.com/read/28607218/improved-signal-recovery-for-flow-cytometry-based-on-spatially-modulated-emission
#9
Stephan Quint, Jörn Wittek, Peter Spang, Nadav Levanon, T Walther, Michael Baßler
Recently, the technique of `spatially modulated emission' has been introduced which improves the signal-to-noise ratio (SNR) for detecting biological cells in the field of flow cytometry. Based on this concept, we developed two advanced signal processing methods which further enhance the SNR and selectivity for cell detection. The improvements are achieved by adapting digital filtering methods from RADAR technology and mainly address inherent offset elimination, increased signal dynamics and moreover reduction of erroneous detections due to processing artifacts...
June 13, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28595723/stable-isotope-n-phosphoryl-amino-acids-labeling-for-quantitative-profiling-of-amine-containing-metabolites-using-liquid-chromatography-mass-spectrometry
#10
Shanshan Zhang, Jinwen Shi, Changkai Shan, Chengting Huang, Yile Wu, Rong Ding, Yuhua Xue, Wen Liu, Qiang Zhou, Yufen Zhao, Pengxiang Xu, Xiang Gao
Stable isotope chemical labeling liquid chromatography-mass spectrometry (LC-MS) is a powerful strategy for comprehensive metabolomics profiling, which can improve metabolites coverage and quantitative information for exploration of metabolic regulation in complex biological systems. In the current work, a novel stable isotope N-phosphoryl amino acids labeling strategy (SIPAL) has been successful developed for quantitative profiling of amine-containing metabolites in urine based on organic phosphorus chemistry...
July 25, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28595284/infertility-diagnosis-has-a-significant-impact-on-the-transcriptome-of-developing-blastocysts
#11
Blair R McCallie, Jason C Parks, Darren K Griffin, William B Schoolcraft, Mandy G Katz-Jaffe
STUDY QUESTION: Is the human blastocyst transcriptome associated with infertility diagnosis, specifically: polycystic ovaries (PCO), male factor (MF), and unexplained (UE)? SUMMARY ANSWER: The global blastocyst transcriptome was significantly altered in association with a PCO, MF, and UE infertility diagnosis. WHAT IS KNOWN ALREADY: Infertility diagnosis has an impact on the probability for a successful outcome following an IVF cycle. Limited information is known regarding the relationship between a specific infertility diagnosis and blastocyst transcription during pre-implantation development...
June 8, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28594468/application-of-an-advanced-maximum-likelihood-estimation-restoration-method-for-enhanced-resolution-and-contrast-in-second-harmonic-generation-microscopy
#12
Mayandi Sivaguru, Mohammad M Kabir, Manas Rangan Gartia, David S C Biggs, Barghav S Sivaguru, Vignesh A Sivaguru, Glenn A Fried, Gang Logan Liu, Sakthivel Sadayappan, Kimani C Toussaint
Second-harmonic generation (SHG) microscopy has gained popularity because of its ability to perform submicron, label-free imaging of noncentrosymmetric biological structures, such as fibrillar collagen in the extracellular matrix environment of various organs with high contrast and specificity. Because SHG is a two-photon coherent scattering process, it is difficult to define a point spread function (PSF) for this modality. Hence, compared to incoherent two-photon processes like two-photon fluorescence, it is challenging to apply the various PSF-engineering methods to improve the spatial resolution to be close to the diffraction limit...
June 8, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28593248/human-efficiency-in-detecting-and-discriminating-biological-motion
#13
Hongjing Lu, Bosco S Tjan, Zili Liu
Using an "information meter" provided by ideal observer analysis, we measured the efficiency with which human observers processed different walking stimuli against luminance noise and spatial uncertainty to either detect the presence of a walker or to discriminate the walking direction. Human efficiency was examined across four renderings of a human walker: contour, point lights, silhouette, and skeleton. We replicated the previous finding of low discrimination efficiency in biological motion (Gold, Tadin, Cook, & Blake, 2008) and also found low detection efficiency for biological motion...
June 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/28590035/interindividual-epigenetic-variability-sound-or-noise
#14
REVIEW
J Ramón Tejedor, Mario F Fraga
Interindividual variability is an inherent characteristic of biological systems. Whereas the underlying molecular sources of interindividual variability remain poorly understood, recent work by Ecker et al. (Ecker S, Chen L, Pancaldi V, Bagger FO, et al. 2017. Genome Biol 18: 18.) sheds light on the characterization of this phenomenon in a complex biological scenario. By combining data from the BLUEPRINT Epigenome Project with a novel analytical approach, these authors were able to measure the degree of transcriptional and epigenetic variability across a wide panel of samples and types of immune cell...
June 7, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28589853/n-of-1-pathways-mixenrich-advancing-precision-medicine-via-single-subject-analysis-in-discovering-dynamic-changes-of-transcriptomes
#15
Qike Li, A Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li, Hao Helen Zhang, Yves A Lussier
BACKGROUND: Transcriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions, these methods are not designed to address single-patient transcriptome analyses. We previously developed and validated the N-of-1-pathways framework using two methods, Wilcoxon and Mahalanobis Distance (MD), for personal transcriptome analysis derived from a pair of samples of a single patient...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589684/chimeric-rnas-in-cancer-and-normal-physiology
#16
REVIEW
Katarzyna Chwalenia, Loryn Facemire, Hui Li
Traditionally, chimeric RNAs were considered to be exclusive to cancer cells. When occasionally observed in normal samples, they were usually considered to be transcriptional 'noises,' or artifacts due to template switching during the reverse transcription and/or Polymerase chain reaction (PCR) steps of experimentation. However, with the advances being made in next generation sequencing technologies and software tools, as well as the accumulation of new experimental evidences, increasing numbers of chimeric transcripts are being identified in noncancerous tissues and cells...
June 7, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28584126/temperature-variability-is-integrated-by-a-spatially-embedded-decision-making-center-to-break-dormancy-in-arabidopsis-seeds
#17
Alexander T Topham, Rachel E Taylor, Dawei Yan, Eiji Nambara, Iain G Johnston, George W Bassel
Plants perceive and integrate information from the environment to time critical transitions in their life cycle. Some mechanisms underlying this quantitative signal processing have been described, whereas others await discovery. Seeds have evolved a mechanism to integrate environmental information by regulating the abundance of the antagonistically acting hormones abscisic acid (ABA) and gibberellin (GA). Here, we show that hormone metabolic interactions and their feedbacks are sufficient to create a bistable developmental fate switch in Arabidopsis seeds...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28581003/mathematical-modeling-reveals-differential-regulation-of-mapk-activity-by-phosphatase-proteins-in-the-yeast-pheromone-response-pathway
#18
Nathan Dyjack, Cassandra Azeredo-Tseng, Necmettin Yildirim
To prevent indefinite cellular responses to external signals, cells utilize various adaptation mechanisms. The yeast mating-response pathway is a model cellular system that exhibits adaptation to persistent external signals. This pathway employs a mitogen-activated protein kinase (MAPK) cascade which is composed of two well-known negative feedback inhibitions that involve the yeast phosphatase proteins Ptp3 and Msg5. The phosphorylated form of the yeast MAPK protein Fus3 (pFus3) triggers the phosphorylation of both phosphatases, but transcriptionally upregulates only Msg5...
June 5, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28579632/a-multi-functional-microelectrode-array-featuring-59760-electrodes-2048-electrophysiology-channels-stimulation-impedance-measurement-and-neurotransmitter-detection-channels
#19
Jelena Dragas, Vijay Viswam, Amir Shadmani, Yihui Chen, Raziyeh Bounik, Alexander Stettler, Milos Radivojevic, Sydney Geissler, Marie Obien, Jan Müller, Andreas Hierlemann
Biological cells are characterized by highly complex phenomena and processes that are, to a great extent, interdependent. To gain detailed insights, devices designed to study cellular phenomena need to enable tracking and manipulation of multiple cell parameters in parallel; they have to provide high signal quality and high spatiotemporal resolution. To this end, we have developed a CMOS-based microelectrode array system that integrates six measurement and stimulation functions, the largest number to date. Moreover, the system features the largest active electrode array area to date (4...
June 2017: IEEE Journal of Solid-state Circuits
https://www.readbyqxmd.com/read/28576556/correlative-super-resolution-fluorescence-and-electron-microscopy-using-conventional-fluorescent-proteins-in-vacuo
#20
Christopher J Peddie, Marie-Charlotte Domart, Xenia Snetkov, Peter O'Toole, Banafshe Larijani, Michael Way, Susan Cox, Lucy M Collinson
Super-resolution light microscopy, correlative light and electron microscopy, and volume electron microscopy are revolutionising the way in which biological samples are examined and understood. Here, we combine these approaches to deliver super-accurate correlation of fluorescent proteins to cellular structures. We show that YFP and GFP have enhanced blinking properties when embedded in acrylic resin and imaged under partial vacuum, enabling in vacuo single molecule localisation microscopy. In conventional section-based correlative microscopy experiments, the specimen must be moved between imaging systems and/or further manipulated for optimal viewing...
May 30, 2017: Journal of Structural Biology
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