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Tagging and capture

Ruobing Jia, Peiwei Chai, He Zhang, Xianqun Fan
Exploring gene function is critical for understanding the complexity of life. DNA sequences and the three-dimensional organization of chromatin (chromosomal interactions) are considered enigmatic factors underlying gene function, and interactions between two distant fragments can regulate transactivation activity via mediator proteins. Thus, a series of chromosome conformation capture techniques have been developed, including chromosome conformation capture (3C), circular chromosome conformation capture (4C), chromosome conformation capture carbon copy (5C), and high-resolution chromosome conformation capture (Hi-C)...
November 17, 2017: Molecular Cancer
João Vidigal, Bárbara Fernandes, Mafalda M Dias, Marco Patrone, António Roldão, Manuel J T Carrondo, Paula M Alves, Ana P Teixeira
Conformationally complex membrane proteins (MPs) are therapeutic targets in many diseases, but drug discovery has been slowed down by the lack of efficient production tools. Co-expression of MPs with matrix proteins from enveloped viruses is a promising approach to obtain correctly folded proteins at the surface of virus-like particles (VLPs), preserving their native lipidic environment. Here, we implemented a site-specific recombinase-mediated cassette exchange (RMCE) strategy to establish a reusable HIV-1 Gag-expressing insect cell line for fast production of target MPs on the surface of Gag-VLPs...
November 16, 2017: Applied Microbiology and Biotechnology
Birgitte I McDonald, Mark Johnson, Peter T Madsen
The dive response, a decrease in heart rate (ƒH) and peripheral vasoconstriction, is the key mechanism allowing breath-hold divers to perform long duration dives. This pronounced cardiovascular response to diving has been investigated intensely in pinnipeds, but comparatively little is known for cetaceans, in particular in ecologically relevant settings. Here we studied the dive ƒH response in one the smallest cetaceans, the harbour porpoise (Phocoena phocoena). We used a novel multi-sensor data logger to record dive behaviour, ƒH, ventilations and feeding events in three trained porpoises, providing the first evaluation of cetacean ƒH regulation while performing a variety of natural behaviours, including prey capture...
November 9, 2017: Journal of Experimental Biology
Eiki Sekine, Nora Schmidt, David Gaboriau, Peter O'Hare
We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes (HSVEdC). In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports that allowed coupling to external capture agents and demonstrated that the vast majority of individual virions contained bioorthogonally-tagged genomes. Using HSVEdC in vivo we reveal novel aspects of the kinetics, localisation, mechanistic entry requirements and morphological transitions of infecting genomes...
November 9, 2017: PLoS Pathogens
Vinícius Silva Belo, Claudio José Struchiner, Guilherme Loureiro Werneck, Rafael Gonçalves Teixeira Neto, Gabriel Barbosa Tonelli, Clóvis Gomes de Carvalho Júnior, Renata Aparecida Nascimento Ribeiro, Eduardo Sérgio da Silva
The existence of free-roaming dogs raises important issues in animal welfare and in public health. A proper understanding of these animals' ecology is useful as a necessary input to plan strategies to control these populations. The present study addresses the population dynamics and the effectiveness of the sterilization of unrestricted dogs using capture and recapture procedures suitable for open animal populations. Every two months, over a period of 14 months, we captured, tagged, released and recaptured dogs in two regions in a city in the southeast region of Brazil...
2017: PloS One
Nicholas J DeLuca, Richard B Miles, Naibo Jiang, Waruna D Kulatilaka, Anil K Patnaik, James R Gord
We report the use of femtosecond laser electronic excitation tagging (FLEET) for velocimetry at a 100-kHz imaging rate. Sequential, single-shot, quantitative velocity profiles of an underexpanded supersonic nitrogen jet were captured at a 100-kHz rate. The signal and lifetime characteristics of the FLEET emission were investigated in a methane flame above a Hencken burner at varying equivalence ratios, and room temperature gas mixtures involving air, methane, and nitrogen. In the post-flame region of the Hencken burner, the emission lifetime was measured as two orders of magnitude lower than lab air conditions...
November 1, 2017: Applied Optics
Fangxu Xing, Jerry L Prince, Maureen Stone, Van J Wedeen, Georges El Fakhri, Jonghye Woo
Representation of human tongue motion using three-dimensional vector fields over time can be used to better understand tongue function during speech, swallowing, and other lingual behaviors. To characterize the inter-subject variability of the tongue's shape and motion of a population carrying out one of these functions it is desirable to build a statistical model of the four-dimensional (4D) tongue. In this paper, we propose a method to construct a spatio-temporal atlas of tongue motion using magnetic resonance (MR) images acquired from fourteen healthy human subjects...
2017: Proceedings of SPIE
Joseph L Costello, Christopher J Kershaw, Lydia M Castelli, David Talavera, William Rowe, Paul F G Sims, Mark P Ashe, Christopher M Grant, Simon J Hubbard, Graham D Pavitt
BACKGROUND: Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5' cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with individual mRNAs likely contribute to differences in translation initiation frequencies between mRNAs. As translation initiation is globally reprogrammed by environmental stresses, we were interested in determining whether eIF4F interactions with individual mRNAs are reprogrammed and how this may contribute to global environmental stress responses...
October 27, 2017: Genome Biology
Li Li, Chang Liu, Xiaowei Cao, Lianqiao Tan, Wenbo Lu
AIM: Here, a multiplex surface-enhanced Raman scattering (SERS) based assay for simultaneous quantitation of carcinoembryonic antigen (CEA) and α-fetoprotein (AFP) was developed. METHODS: SERS tags of nanostars and SERS substrates of nanobowl arrays were functionalized with labeling and capturing antibodies, respectively. In presence of antigens, SERS tags, antigens and SERS substrates formed sandwich structure. RESULTS: The SERS-based technique showed a wide linear range from 0...
October 26, 2017: Bioanalysis
Timothy D Cummins, Gopal P Sapkota
Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient nature (Huang and Kim, PloS One 8:e61430, 2013; Gao et al., J Vis Exp doi: 10.3791/51387, 2014). Here we describe a detailed methodology for a cell culture-based proteomic approach. We describe the generation of cells stably expressing green fluorescent protein (GFP)-tagged proteins under the tetracycline-inducible promoter and subsequent proteomic analysis of GFP-interacting proteins...
October 25, 2017: Methods in Molecular Biology
Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier
Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale...
2018: Methods in Molecular Biology
Katharina Lechner, Nicole Erickson, Benjamin Lechner, Florian Horn
Cardiovascular disease is the number one cause of death globally. Poor diet constitutes a key factor in the initiation and progression of cardiovascular disease and has become the leading risk factor for disability and death worldwide. Therefore, addressing suboptimal nutrition is of key prognostic relevance in primary and secondary prevention of metabolic vascular syndrome.Metabolic vascular syndrome is a multidimensional network of acquired cardiometabolic risk factors closely related to insulin resistance (IR) and concomitant hyperinsulinemia...
October 2017: Deutsche Medizinische Wochenschrift
Wenlong Xia, Huipeng Lu, Yangyang Li, Jun Cao, Xiaohui Zhou, Xinyu Zhang, Xiaoli Xia, Huaichang Sun
Chicken egg yolk immunoglobulin (IgY) is a superior alternative to mammalian immunoglobulin, but its practical application is limited due to the complex purification procedure. In this study, the C2 domain of streptococcal protein G (SPG) with the binding affinity for chicken IgY was expressed in E. coli as an elastin-like polypeptide (ELP) fusion protein, and purified to a high purity by inverse transition cycling (ITC). Binding experiments showed that chicken IgY could bind to and eluted off the ELP-C2 fusion protein in pH-, temperature- and/or time-dependent manners...
October 2017: Veterinary Immunology and Immunopathology
Hui Zhang, Feifei Li, Yan Jia, Bingxiang Xu, Yiqun Zhang, Xiaoli Li, Zhihua Zhang
High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD_loop) that predicts chromatin-chromatin interactions (CCIs) from low-resolution Hi-C data...
October 3, 2017: Nucleic Acids Research
Shuzhen Lv, Yi Li, Kangyao Zhang, Zhenzhen Lin, Dianping Tang
A class of 0-dimensional/2-dimensional (0D/2D) nanoheterostructures based on carbon quantum dots (CQDs) and graphitic carbon nitride (g-C3N4) was designed as the signal-generation tags for the sensitive photoelectrochemical (PEC) immunoassay of prostate-specific antigen (PSA) coupling with the copper nanoclusters (CuNCs). Combination of CQDs with g-C3N4 promoted the photoexcited electron/hole separation and largely increased the photocurrents of the nanoheterostructures. Initially, a sandwich-type immunoreaction was carried out on monoclonal anti-PSA antibody-coated microplate by using PSA aptamer linked with CuNCs as the tracer...
November 8, 2017: ACS Applied Materials & Interfaces
G D Raby, T B Johnson, S T Kessel, T J Stewart, A T Fisk
In the present study, pop-off data storage tags (pDST) without any transmitting capabilities were attached to 118 adult salmonids in a 19 000 km(2) freshwater system (Lake Ontario). The 9·3 cm long cylindrical tags were externally attached to fishes using a backpack-style harness, set to record pressure (dBar ≈ depth in m) and temperature every 70 s (and at some key times, every 5 s) and programmed to release from the harness and float to the surface after c. 1 year. Recapture of the bright-orange tags for data retrieval relied on members of the public finding tags on shore, or on anglers capturing fishes with tags attached and using the contact information displayed on each tag to mail tags to the research team in exchange for a monetary reward...
October 12, 2017: Journal of Fish Biology
Rebecca J McFarland, Sharlene P Brown, Eudorah Vital, Jonathan M Werner, Rachel M Brewster
Microtubules (MTs) are dynamic and fragile structures that are challenging to image in vivo, particularly in vertebrate embryos. Immunolabeling methods are described here to analyze distinct populations of MTs in the developing neural tube of the zebrafish embryo. While the focus is on neural tissue, this methodology is broadly applicable to other tissues. The procedures are optimized for early to mid-somitogenesis-stage embryos (1 somite to 12 somites), however they can be adapted to a range of other stages with relatively minor adjustments...
September 20, 2017: Journal of Visualized Experiments: JoVE
Dang-Dang Xu, Cui Liu, Cheng-Yu Li, Chong-Yang Song, Ya-Feng Kang, Chu-Bo Qi, Yi Lin, Dai-Wen Pang, Hong-Wu Tang
As an emerging fascinating fluorescent nanomaterial, carbon nanodots (CDs) have attracted much attention owing of their unique properties such as small size, antiphotobleaching, and biocompatibility. However, its use in biomedical analysis is limited because of its low quantum yield. Herein, we constructed a dual amplification fluorescence sensor by incorporating immunohybridization chain reaction (immuno-HCR) and metal-enhanced fluorescence (MEF) of CDs for the detection of alpha fetal protein (AFP). The immunoplasmonic slide and detection antibodies-conjugated oligonucleotide initiator are served to capture and probe AFP molecules, respectively...
October 19, 2017: ACS Applied Materials & Interfaces
A Lagesson, T Brodin, J Fahlman, J Fick, M Jonsson, J Persson, P Byström, J Klaminder
An increasing number of short-term laboratory studies on fish reports behavioral effects from exposure to aquatic contaminants or raised carbon dioxide levels affecting the GABAA receptor. However, how such GABAergic behavioral modifications (GBMs) impact populations in more complex natural systems is not known. In this study, we induced GBMs in European perch (Perca fluviatilis) via exposure to a GABA agonist (oxazepam) and followed the effects on growth and survival over one summer (70days) in replicated pond ecosystems...
February 15, 2018: Science of the Total Environment
Wei Li, Xuede Zhang, Wei Wang, Ruiying Sun, Boxuan Liu, Yuefeng Ma, Wei Zhang, Li Ma, Yaofeng Jin, Shuanying Yang
Lung adenocarcinoma is the most common type of lung cancer. Unfortunately, lung adenocarcinoma has a poor prognosis and the pathogenesis remains unclear. Mitochondria are important mediators of tumorigenesis. However, the proteomics profile of lung adenocarcinoma mitochondrial proteins has not been elucidated. In this study, we investigated differences in the mitochondrial protein profiles between lung adenocarcinomas and normal tissue. Laser capture microdissection (LCM) was used to isolate the target cells from lung adenocarcinomas and normal tissue...
2017: American Journal of Translational Research
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