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https://www.readbyqxmd.com/read/28538990/measuring-nonlinear-signal-combination-using-eeg
#1
Darren G M Cunningham, Daniel H Baker, Jonathan W Peirce
Relatively little is known about the processes, both linear and nonlinear, by which signals are combined beyond V1. By presenting two stimulus components simultaneously, flickering at different temporal frequencies (frequency tagging) while measuring steady-state visual evoked potentials, we can assess responses to the individual components, including direct measurements of suppression on each other, and various nonlinear responses to their combination found at intermodulation frequencies. The result is a rather rich dataset of frequencies at which responses can be found...
May 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/28532419/a-survey-of-the-complex-transcriptome-from-the-highly-polyploid-sugarcane-genome-using-full-length-isoform-sequencing-and-de-novo-assembly-from-short-read-sequencing
#2
Nam V Hoang, Agnelo Furtado, Patrick J Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P Thirugnanasambandam, Frederik C Botha, Robert J Henry
BACKGROUND: Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS: The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28529717/gene-length-and-detection-bias-in-single-cell-rna-sequencing-protocols
#3
Belinda Phipson, Luke Zappia, Alicia Oshlack
Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, many technical challenges need to be overcome during data generation. Due to minute amounts of starting material, samples undergo extensive amplification, increasing technical variability. A solution for mitigating amplification biases is to include unique molecular identifiers (UMIs), which tag individual molecules...
2017: F1000Research
https://www.readbyqxmd.com/read/28524544/enzymatic-engineering-of-live-bacterial-cell-surface-using-butelase-1
#4
Xiaobao Bi, Juan Yin, Giang K T Nguyen, Chang Rao, Nurashikin Bte Abdul Halim, Xinya Hemu, James P Tam, Chuan-Fa Liu
We show that butelase-mediated ligation (BML) can be used to modify live bacterial cell surfaces with diverse cargo molecules. Surface-displayed butelase recognition motif NHV was first introduced at the C-terminal end of the anchoring protein OmpA on E. coli cells. This then served as a handle of BML for the functionalization of E. coli cell surfaces with fluorescein and biotin tags, a tumor-associated monoglycosylated peptide and mCherry protein. The cell-surface ligation reaction was achieved at low concentrations of butelase and the labeling substrates...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28517015/genetic-incorporation-of-4-fluorohistidine-into-peptides-enables-selective-affinity-purification
#5
Christine M Ring, Emil S Iqbal, David E Hacker, Matthew C T Hartman, T Ashton Cropp
Due to the lowered pKa of 4-fluorohistidine relative to histidine, peptides and proteins containing this amino acid are potentially endowed with novel properties. We report here the optimized synthesis of 4-fluorohistidine and show that it can efficiently replace histidine in in vitro translation reactions. Moreover, peptides containing 6×-fluorohistidine tags are able to be selectively captured and eluted from nickel resin in the presence of his-tagged protein mixtures.
May 18, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28506644/affinity-purification-of-car9-tagged-proteins-on-silica-matrices-optimization-of-a-rapid-and-inexpensive-protein-purification-technology
#6
Jessica Soto-Rodríguez, Brandon L Coyle, Ariana Samuelson, Kannan Aravagiri, François Baneyx
Car9, a dodecapeptide identified by cell surface display for its ability to bind to the edge of carbonaceous materials, also binds to silica with high affinity. The interaction can be disrupted with l-lysine or l-arginine, enabling a broad range of technological applications. Previously, we reported that C-terminal Car9 extensions support efficient protein purification on underivatized silica. Here, we show that the Car9 tag is functional and TEV protease-excisable when fused to the N-termini of target proteins, and that it supports affinity purification under denaturing conditions, albeit with reduced yields...
May 12, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28505584/development-of-a-gold-nanoparticle-based-universal-oligonucleotide-microarray-for-multiplex-and-low-cost-detection-of-foodborne-pathogens
#7
Xiaoqiang Wang, Sisi Ying, Xiaoguang Wei, Jun Yuan
Bacterial foodborne diseases remain major threats to food safety and public health, especially in developing countries. In this study a novel assay, combining gold nanoparticle (GNP)-based multiplex oligonucleotide ligation-PCR and universal oligonucleotide microarray technology, was developed for inexpensive, specific, sensitive, and multiplex detection of eight common foodborne pathogens, including Shigella spp., Campylobacter jejuni, Bacillus cereus, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, and Vibrio parahaemolyticus...
May 9, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28494369/lateral-flow-assay-based-bacterial-detection-using-engineered-cell-wall-binding-domains-of-a-phage-endolysin
#8
Minsuk Kong, Joong Ho Shin, Sunggi Heu, Je-Kyun Park, Sangryeol Ryu
The development of a cost-effective and efficient bacterial detection assay is essential for diagnostic fields, particularly in resource-poor settings. Although antibodies have been widely used for bacterial capture, the production of soluble antibodies is still expensive and time-consuming. Here, we developed a nitrocellulose-based lateral flow assay using cell wall binding domains (CBDs) from phage as a recognition element and colloidal gold nanoparticles as a colorimetric signal for the detection of a model pathogenic bacterium, Bacillus cereus (B...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28490331/quantifying-capture-stress-in-free-ranging-european-roe-deer-capreolus-capreolus
#9
Nikolaus Huber, Sebastian G Vetter, Alina L Evans, Petter Kjellander, Susanne Küker, Ulrika A Bergvall, Jon M Arnemo
BACKGROUND: To understand and reduce the concomitant effects of trapping and handling procedures in wildlife species, it is essential to measure their physiological impact. Here, we examined individual variation in stress levels in non-anesthetized European roe deer (Capreolus capreolus), which were captured in box traps and physically restrained for tagging, biometrics and bio-sampling. In winter 2013, we collected venous blood samples from 28 individuals during 28 capture events and evaluated standard measurements for stress (heart rate, body temperature, neutrophil to lymphocyte ratio, lactate and total cortisol)...
May 10, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28484012/metaplasticity-mechanisms-restore-plasticity-and-associativity-in-an-animal-model-of-alzheimer-s-disease
#10
Qin Li, Sheeja Navakkode, Martin Rothkegel, Tuck Wah Soong, Sreedharan Sajikumar, Martin Korte
Dynamic regulation of plasticity thresholds in a neuronal population is critical for the formation of long-term plasticity and memory and is achieved by mechanisms such as metaplasticity. Metaplasticity tunes the synapses to undergo changes that are necessary prerequisites for memory storage under physiological and pathological conditions. Here we discovered that, in amyloid precursor protein (APP)/presenilin-1 (PS1) mice (age 3-4 mo), a prominent mouse model of Alzheimer's disease (AD), late long-term potentiation (LTP; L-LTP) and its associative plasticity mechanisms such as synaptic tagging and capture (STC) were impaired already in presymptomatic mice...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28483593/the-use-of-smart-technologies-in-enabling-construction-components-reuse-a-viable-method-or-a-problem-creating-solution
#11
Eleni Iacovidou, Phil Purnell, Ming K Lim
The exploitation of Radio Frequency Identification (RFID) for tracking and archiving the properties of structural construction components could be a potentially innovative disruption for the construction sector. This is because RFID can stimulate the reuse of construction components and reduce their wastage, hence addressing sustainability issues in the construction sector. To test the plausibility of that idea, this study explores the potential pre-conditions for RFID to facilitate construction components reuse, and develops a guidance for promoting their redistribution back to the supply chain...
May 5, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28472519/resolving-relationships-among-the-megadiverse-butterflies-and-moths-with-a-novel-pipeline-for-anchored-phylogenomics
#12
Jesse W Breinholt, Chandra Earl, Alan R Lemmon, Emily Moriarty Lemmon, Lei Xiao, Akito Y Kawahara
The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28464688/variability-in-muscle-activation-of-simple-speech-motions-a-biomechanical-modeling-approach
#13
Negar M Harandi, Jonghye Woo, Maureen Stone, Rafeef Abugharbieh, Sidney Fels
Biomechanical models of the oropharynx facilitate the study of speech function by providing information that cannot be directly derived from imaging data, such as internal muscle forces and muscle activation patterns. Such models, when constructed and simulated based on anatomy and motion captured from individual speakers, enable the exploration of inter-subject variability of speech biomechanics. These models also allow one to answer questions, such as whether speakers produce similar sounds using essentially the same motor patterns with subtle differences, or vastly different motor equivalent patterns...
April 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28464345/ion-tagged-oligonucleotides-coupled-with-a-magnetic-liquid-support-for-the-sequence-specific-capture-of-dna
#14
Kevin D Clark, Marcelino Varona, Jared Anderson
The isolation of specific nucleic acid sequences is a major bottleneck in molecular diagnostics. Magnetic beads/particles are typically used as solid supports for the capture of DNA targets to improve sample throughput, but aggregate over time resulting in lower capture efficiency and obstruction of liquid handling devices. Here, we describe a particle-free approach to sequence-specific DNA extraction using a magnetic liquid support and ion-tagged oligonucleotide (ITO) probes. ITO conjugates were synthesized with the highest yields ever achieved for the radical thiol-ene coupling of a substrate and oligonucleotide...
May 2, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28460522/nanobody-based-immunoassay-for-human-soluble-epoxide-hydrolase-detection-using-polymeric-horseradish-peroxidase-polyhrp-for-signal-enhancement-the-rediscovery-of-polyhrp
#15
Dongyang Li, Yongliang Cui, Christophe Morisseau, Shirley J Gee, Candace S Bever, Xiangjiang Liu, Jian Wu, Bruce D Hammock, Yibin Ying
Soluble epoxide hydrolase (sEH) is a potential pharmacological target for treating hypertension, vascular inflammation, cancer, pain, and multiple cardiovascular related diseases. A variable domain of the heavy chain antibody (termed single domain antibody (sdAb), nanobody, or VHH) possesses the advantages of small size, high stability, ease of genetic manipulation, and ability for continuous manufacture, making such nanobody a superior choice as an immunoreagent. In this work, we developed an ultrasensitive nanobody based immunoassay for human sEH detection using polymeric horseradish peroxidase (PolyHRP) for signal enhancement...
May 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28458052/production-of-monoclonal-antibodies-and-development-of-a-quantitative-immuno-polymerase-chain-reaction-assay-to-detect-and-quantify-recombinant-glutathione-s-transferase
#16
Abud Je, Luque Eh, Ramos Jg, Rodriguez Ha
GST-tagged proteins are important tools for the production of recombinant proteins. Removal of GST tag from its fusion protein, frequently by harsh chemical treatments or proteolytic methods, is often required. Thus, the monitoring of the proteins in tag-free form requires a significant effort to determine the remnants of GST during purification process. In the present study, we developed both a conventional enzyme-linked immunosorbent assay (ELISA) and an immuno-polymerase chain reaction (IPCR) assay, both specific for detection of recombinant GST (rGST)...
April 27, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28453563/reproductive-success-is-energetically-linked-to-foraging-efficiency-in-antarctic-fur-seals
#17
Tiphaine Jeanniard-du-Dot, Andrew W Trites, John P Y Arnould, Christophe Guinet
The efficiency with which individuals extract energy from their environment defines their survival and reproductive success, and thus their selective contribution to the population. Individuals that forage more efficiently (i.e., when energy gained exceeds energy expended) are likely to be more successful at raising viable offspring than individuals that forage less efficiently. Our goal was to test this prediction in large long-lived mammals under free-ranging conditions. To do so, we equipped 20 lactating Antarctic fur seals (Arctocephalus gazella) breeding on Kerguelen Island in the Southern Ocean with tags that recorded GPS locations, depth and tri-axial acceleration to determine at-sea behaviours and detailed time-activity budgets during their foraging trips...
2017: PloS One
https://www.readbyqxmd.com/read/28451120/total-chemical-synthesis-of-proteins-without-hplc-purification
#18
S F Loibl, Z Harpaz, R Zitterbart, O Seitz
The total chemical synthesis of proteins is a tedious and time-consuming endeavour. The typical steps involve solid phase synthesis of peptide thioesters and cysteinyl peptides, native chemical ligation (NCL) in solution, desulfurization or removal of ligation auxiliaries in the case of extended NCL as well as many intermediary and final HPLC purification steps. With an aim to facilitate and improve the throughput of protein synthesis we developed the first method for the rapid chemical total on-resin synthesis of proteins that proceeds without a single HPLC-purification step...
November 1, 2016: Chemical Science
https://www.readbyqxmd.com/read/28447987/live-cell-imaging-and-3d-analysis-of-angiotensin-receptor-type-1a-trafficking-in-transfected-human-embryonic-kidney-cells-using-confocal-microscopy
#19
Parnika Kadam, Ryan McAllister, Jeffrey S Urbach, Kathryn Sandberg, Susette C Mueller
Live-cell imaging is used to simultaneously capture time-lapse images of angiotensin type 1a receptors (AT1aR) and intracellular compartments in transfected human embryonic kidney-293 (HEK) cells following stimulation with angiotensin II (Ang II). HEK cells are transiently transfected with plasmid DNA containing AT1aR tagged with enhanced green fluorescent protein (EGFP). Lysosomes are identified with a red fluorescent dye. Live-cell images are captured on a laser scanning confocal microscope after Ang II stimulation and analyzed by software in three dimensions (3D, voxels) over time...
March 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28446032/effect-of-intravesical-liposome-based-nerve-growth-factor-antisense-therapy-on-bladder-overactivity-and-nociception-in-a-rat-model-of-cystitis-induced-by-hydrogen-peroxide
#20
Tsuyoshi Majima, Pradeep Tyagi, Koji Dogishi, Mahendra Kashyap, Yasuhito Funahashi, Momokazu Gotoh, Michael B Chancellor, Naoki Yoshimura
The aim of this study was to evaluate whether liposome-based local suppression of nerve growth factor (NGF) in the bladder has effects on bladder hypersensitivity in a rat cystitis model induced by intravesical instillation of hydrogen peroxide (HP). HP (1.5%) was intravesically administered to adult female Sprague-Dawley rats. Liposomes complexed with NGF antisense oligonucleotide (OND) labeled with TYE563 fluorescent tag were intravesically instilled on day 2. Red fluorescence from the TYE 563 tag was observed with fluorescent microscopy on day 3...
April 18, 2017: Human Gene Therapy
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