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Collagen high throughput

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https://www.readbyqxmd.com/read/29726962/integrated-use-of-bioinformatic-resources-reveals-that-co-targeting-of-histone-deacetylases-ikbk-and-src-inhibits-epithelial-mesenchymal-transition-in-cancer
#1
Farnaz Barneh, Mehdi Mirzaie, Payman Nickchi, Tuan Zea Tan, Jean Paul Thiery, Mehran Piran, Mona Salimi, Fatemeh Goshadrou, Amir R Aref, Mohieddin Jafari
With the advent of high-throughput technologies leading to big data generation, increasing number of gene signatures are being published to predict various features of diseases such as prognosis and patient survival. However, to use these signatures for identifying therapeutic targets, use of additional bioinformatic tools is indispensible part of research. Here, we have generated a pipeline comprised of nearly 15 bioinformatic tools and enrichment statistical methods to propose and validate a drug combination strategy from already approved drugs and present our approach using published pan-cancer epithelial-mesenchymal transition (EMT) signatures as a case study...
May 2, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29715593/microdevice-arrays-with-strain-sensors-for-3d-mechanical-stimulation-and-monitoring-of-engineered-tissues
#2
Haijiao Liu, Luke A MacQueen, Jenna F Usprech, Hoda Maleki, Krista L Sider, Matthew G Doyle, Yu Sun, Craig A Simmons
Native and engineered tissue development are regulated by the integrative effects of multiple microenvironmental stimuli. Microfabricated bioreactor array platforms can efficiently dissect cue-response networks, and have recently integrated critical 2D and 3D mechanical stimulation for greater physiological relevance. However, a limitation of these approaches is that assessment of tissue functional properties is typically limited to end-point analyses. Here we report a new deformable membrane platform with integrated strain sensors that enables mechanical stretching or compression of 3D cell-hydrogel arrays and simultaneous measurement of hydrogel construct stiffness in situ...
April 23, 2018: Biomaterials
https://www.readbyqxmd.com/read/29677166/in-vitro-identification-of-new-transcriptomic-and-mirnomic-profiles-associated-with-pulmonary-fibrosis-induced-by-high-doses-everolimus-looking-for-new-pathogenetic-markers-and-therapeutic-targets
#3
Simona Granata, Gloria Santoro, Valentina Masola, Paola Tomei, Fabio Sallustio, Paola Pontrelli, Matteo Accetturo, Nadia Antonucci, Pierluigi Carratù, Antonio Lupo, Gianluigi Zaza
The administration of Everolimus (EVE), a mTOR inhibitor used in transplantation and cancer, is often associated with adverse effects including pulmonary fibrosis. Although the underlying mechanism is not fully clarified, this condition could be in part caused by epithelial to mesenchymal transition (EMT) of airway cells. To improve our knowledge, primary bronchial epithelial cells (BE63/3) were treated with EVE (5 and 100 nM) for 24 h. EMT markers (α-SMA, vimentin, fibronectin) were measured by RT-PCR. Transepithelial resistance was measured by Millicell-ERS ohmmeter...
April 20, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29676157/high-throughput-assay-for-collagen-secretion-suggests-an-unanticipated-role-for-hsp90-in-collagen-production
#4
Madeline Y Wong, Ngoc Duc Doan, Andrew S DiChiara, Louis J Papa, Jaime H Cheah, Christian K Soule, Nicki Watson, John D Hulleman, Matthew D Shoulders
Collagen overproduction is a feature of fibrosis and cancer, while insufficient deposition of functional collagen molecules and/or the secretion of malformed collagen are common in genetic disorders like osteogenesis imperfecta. Collagen secretion is an appealing therapeutic target in these and other diseases, as secretion directly connects intracellular biosynthesis to collagen deposition and biological function in the extracellular matrix. However, small molecule and biological methods to tune collagen secretion are severely lacking...
April 20, 2018: Biochemistry
https://www.readbyqxmd.com/read/29626520/efficient-protease-based-purification-of-recombinant-matrix-metalloprotease-1-in-e-coli
#5
Lokender Kumar, Warren Colomb, John Czerski, Christopher R Cox, Susanta K Sarkar
MMP1 is an essential enzyme for tissue remodeling both in normal and pathological states. We report a method of purifying activated human MMP1 in E. coli without using urea or 4-Aminophenylmercuric acetate (APMA). Instead, a non-ionic detergent, Triton X-100, was used in the lysis buffer to solubilize MMP1 followed by the protease activities of both trypsin and MMP1 to digest E. coli proteins and activate pro-MMP1. Identity of activated MMP1 was confirmed by Western blot using anti-human MMP1 antibodies, whereas the mass was determined to be 43 kD using matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS)...
April 4, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29624053/large-scale-differentiation-and-site-specific-discrimination-of-hydroxyproline-isomers-by-electron-transfer-higher-energy-collision-dissociation-ethcd-mass-spectrometry
#6
Fengfei Ma, Rui-Xiang Sun, Daniel Tremmel, Sara Sackett, Jon Odorico, Lingjun Li
3- and 4- hydroxyprolines (HyP) are regioisomers that play different roles in various species and organs. Despite their distinct functions inside cells, they are generally considered indistinguishable using mass spectrometry due to their identical masses. Here, we demonstrate, for the first time, that characteristic w ions can be produced by electron-transfer/higher energy collision dissociation (EThcD) dual fragmentation technique to confidently discriminate 3-HyP/ 4-HyP isomers. An integrated and high throughput strategy was developed which combined online LC separation with EThcD for large-scale differentiation of 3-HyP/4-HyP in complex samples...
April 6, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29575101/adherent-agarose-mold-cultures-an-in-vitro-platform-for-multi-factorial-assessment-of-passaged-chondrocyte-redifferentiation
#7
Justin Parreno, Vanessa J Bianchi, Corey Sermer, Suresh C Regmi, David Backstein, Tannin A Schmidt, Rita A, Kandel
Generating the best possible bioengineered cartilage from passaged chondrocytes requires culture condition optimization. In this study the use of adherent agarose mold (adAM) cultures to support redifferentiation of passaged twice (P2) chondrocytes and serve as a scalable platform to assess the effect of growth factor combinations on proteoglycan accumulation by cells was examined. By 2 days in adAM culture, bovine P2 cells were partially redifferentiated as demonstrated by regression of actin-based dedifferentiation signalling and fibroblast matrix and contractile gene expression...
March 25, 2018: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/29526710/a-split-luciferase-based-trimer-formation-assay-as-a-high-throughput-screening-platform-for-therapeutics-in-alport-syndrome
#8
Kohei Omachi, Misato Kamura, Keisuke Teramoto, Haruka Kojima, Tsubasa Yokota, Shota Kaseda, Jun Kuwazuru, Ryosuke Fukuda, Kosuke Koyama, Shingo Matsuyama, Keishi Motomura, Tsuyoshi Shuto, Mary Ann Suico, Hirofumi Kai
Alport syndrome is a hereditary glomerular disease caused by mutation in type IV collagen α3-α5 chains (α3-α5(IV)), which disrupts trimerization, leading to glomerular basement membrane degeneration. Correcting the trimerization of α3/α4/α5 chain is a feasible therapeutic approach, but is hindered by lack of information on the regulation of intracellular α(IV) chain and the absence of high-throughput screening (HTS) platforms to assess α345(IV) trimer formation. Here, we developed sets of split NanoLuc-fusion α345(IV) proteins to monitor α345(IV) trimerization of wild-type and clinically associated mutant α5(IV)...
May 17, 2018: Cell Chemical Biology
https://www.readbyqxmd.com/read/29511829/a-novel-approach-to-producing-uniform-3-d-tumor-spheroid-constructs-using-ultrasound-treatment
#9
Solmaz Karamikamkar, Ehsan Behzadfar, Karen C Cheung
Producing three-dimensional (3-D) multicellular tumor spheroids (TSs) is valuable for characterizing anticancer drugs since they provide a more representative model of the 3-D in vivo tumor than conventional two-dimensional (2-D) monolayer culture. The interaction of tumor cells with the extracellular matrix (ECM) in a 3-D culture environment is more similar to a tumor in vivo than in a 2-D environment; cell-cell and cell-ECM interaction can influence cell behaviour, such as in response to drug treatment. In vitro tumor spheroid models have been developed using microfluidic systems to generate 3-D hydrogel beads containing components of alginate and ECM protein, such as collagen, with high uniformity and throughput...
March 6, 2018: Biomedical Microdevices
https://www.readbyqxmd.com/read/29491489/genome-wide-analysis-revealed-that-dznep-reduces-tubulointerstitial-fibrosis-via-down-regulation-of-pro-fibrotic-genes
#10
Imari Mimura, Yosuke Hirakawa, Yasuharu Kanki, Ryo Nakaki, Yutaka Suzuki, Tetsuhiro Tanaka, Hiroyuki Aburatani, Masaomi Nangaku
Tubulointerstitial fibrosis has been recently reported to be caused by the collapse of the epigenetic regulation of kidney diseases. We examined whether pharmacological inhibition of histone modification is effective against renal fibrosis. DZNep (3-deazaneplanocin A) was originally developed as an anti-cancer drug to inhibit the repressive histone mark, H3K27me3. We used a model of chronic tubulointerstitial fibrosis induced by unilateral ischaemia/reperfusion and administered DZNep intravenously to the mice for 8 weeks...
February 28, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29481479/a-3-dimensional-biomimetic-platform-to-interrogate-the-safety-of-autologous-fat-transfer-in-the-setting-of-breast-cancer
#11
Yoshiko Toyoda, Karel-Bart Celie, Jonathan T Xu, Justin S Buro, Julia Jin, Alexandra J Lin, Kristy A Brown, Jason A Spector
INTRODUCTION: Obesity is a known risk factor for the development and prognosis of breast cancer. Adipocytes have been identified as a source of exogenous lipids in other cancer types and may similarly provide energy to fuel malignant survival and growth in breast cancer. This relationship is of particular relevance to plastic surgery, because many reconstructions after oncologic mastectomy achieve optimal aesthetics and durability using adjunctive autologous fat transfer (AFT). Despite the increasing ubiquity and promise of AFT, many unanswered questions remain, including safety in the setting of breast cancer...
April 2018: Annals of Plastic Surgery
https://www.readbyqxmd.com/read/29438711/detection-of-substrate-binding-of-a-collagen-specific-molecular-chaperone-hsp47-in-solution-using-fluorescence-correlation-spectroscopy
#12
Akira Kitamura, Yoshihito Ishida, Hiroshi Kubota, Chan-Gi Pack, Takayuki Homma, Shinya Ito, Kazutaka Araki, Masataka Kinjo, Kazuhiro Nagata
Heat shock protein 47 kDa (HSP47), an ER-resident and collagen-specific molecular chaperone, recognizes collagenous hydrophobic amino acid sequences (Gly-Pro-Hyp) and assists in secretion of correctly folded collagen. Elevated collagen production is correlated with HSP47 expression in various diseases, including fibrosis and keloid. HSP47 knockdown ameliorates liver fibrosis by inhibiting collagen secretion, and inhibition of the interaction of HSP47 with procollagen also prevents collagen secretion. Therefore, a high-throughput system for screening of drugs capable of inhibiting the interaction between HSP47 and collagen would aid the development of novel therapies for fibrotic diseases...
February 26, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29414702/single-molecule-assay-for-proteolytic-susceptibility-force-induced-collagen-destabilization
#13
Michael W H Kirkness, Nancy R Forde
Force plays a key role in regulating dynamics of biomolecular structure and interactions, yet techniques are lacking to manipulate and continuously read out this response with high throughput. We present an enzymatic assay for force-dependent accessibility of structure that makes use of a wireless mini-radio centrifuge force microscope to provide a real-time readout of kinetics. The microscope is designed for ease of use, fits in a standard centrifuge bucket, and offers high-throughput, video-rate readout of individual proteolytic cleavage events...
February 6, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29328472/combined-analysis-of-gene-expression-and-genome-binding-profiles-identified-potential-therapeutic-targets-of-ciclopirox-in-ewing-sarcoma
#14
Baisheng Yuan, Wei Ji, Haipeng Xia, Jianmin Li
Ciclopirox (CPX) is a synthetic antifungal drug that is mainly used to treat dermatomycoses. The aim of the present study was to determine whether CPX could influence Ewing sarcoma progression. The present study suggested that CPX treatment may inhibit Ewing sarcoma (ES) progression through Ewing sarcoma breakpoint region 1‑Friend leukemia integration 1 (EWS‑FLI1), a common fusion transcript structure in patients with ES. To determine the underlying mechanisms of ES progression, cross analysis was conducted on three high‑throughput genome or transcript me datasets from the Gene Expression Omnibus...
March 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29247254/dynamic-hydrostatic-pressure-regulates-nucleus-pulposus-phenotypic-expression-and-metabolism-in-a-cell-density-dependent-manner
#15
Bhranti S Shah, Nadeen O Chahine
Dynamic hydrostatic pressure (HP) loading can modulate nucleus pulposus (NP) cell metabolism, extracellular matrix (ECM) composition, and induce transformation of notochordal NP cells into mature phenotype. However, the effects of varying cell density and dynamic HP magnitude on NP phenotype and metabolism are unknown. This study examined the effects of physiological magnitudes of HP loading applied to bovine NP cells encapsulated within three-dimensional (3D) alginate beads. Study 1: seeding density (1 M/mL versus 4 M/mL) was evaluated in unloaded and loaded (0...
February 1, 2018: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/29172004/early-onset-myopathies-clinical-findings-prevalence-of-subgroups-and-diagnostic-approach-in-a-single-neuromuscular-referral-center-in-germany
#16
K Vill, A Blaschek, D Gläser, M Kuhn, T Haack, B Alhaddad, M Wagner, R Kovacs-Nagy, M Tacke, L Gerstl, A S Schroeder, I Borggraefe, C Mueller, B Schlotter-Weigel, B Schoser, M C Walter, W Müller-Felber
BACKGROUND: Early-onset myopathies are a heterogeneous group of neuromuscular diseases with broad clinical, genetic and histopathological overlap. The diagnostic approach has considerably changed since high throughput genetic methods (next generation sequencing, NGS) became available. OBJECTIVE: We present diagnostic subgroups in a single neuromuscular referral center and describe an algorithm for the diagnostic work-up. METHODS: The diagnostic approach of 98 index patients was retrospectively analysed...
2017: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/29161047/mapping-extracellular-matrix-proteins-in-formalin-fixed-paraffin-embedded-tissues-by-maldi-imaging-mass-spectrometry
#17
Peggi M Angel, Susana Comte-Walters, Lauren E Ball, Kacey Talbot, Anand Mehta, Kelvin G M Brockbank, Richard R Drake
Collagens and elastin form the fundamental framework of all tissues and organs, and their expression and post-translational processing are tightly regulated in disease and health. Because of their unique structural composition and properties, it is a recognized challenge to access these protein structures within the complex tissue microenvironment to understand how localized changes modulate tissue health. We describe a new workflow using a combination of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) with matrix metalloproteinase (MMP) enzymes to access and report on spatial localization of collagen and elastin sequences in formalin-fixed, paraffin-embedded (FFPE) tissues...
January 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29156109/a-microfabricated-96-well-wound-healing-assay
#18
Shaoliang Luan, Rui Hao, Yuanchen Wei, Deyong Chen, Beiyuan Fan, Fengliang Dong, Wei Guo, Junbo Wang, Jian Chen
This article presents a microfabricated 96-well wound-healing assay enabling high-throughput measurement of cellular migration capabilities. Within each well, the middle area is the wound region, made of microfabricated gold surface with self-assembled PEG repellent for cell seeding. After the formation of a cellular confluent monolayer around the wound region, collagen solution was applied to form three-dimensional matrix to cover the PEG surface, initiating the wound-healing process. By interpreting the numbers of migrated cells into the wound regions as a function of specific stimuli with different concentrations, EC50 (half-maximal effective concentration) was obtained...
December 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/29096610/therapy-response-testing-of-breast-cancer-in-a-3d-high-throughput-perfused-microfluidic-platform
#19
Henriette L Lanz, Anthony Saleh, Bart Kramer, Junmei Cairns, Chee Ping Ng, Jia Yu, Sebastiaan J Trietsch, Thomas Hankemeier, Jos Joore, Paul Vulto, Richard Weinshilboum, Liewei Wang
BACKGROUND: Breast cancer is the most common invasive cancer among women. Currently, there are only a few models used for therapy selection, and they are often poor predictors of therapeutic response or take months to set up and assay. In this report, we introduce a microfluidic OrganoPlate® platform for extracellular matrix (ECM) embedded tumor culture under perfusion as an initial study designed to investigate the feasibility of adapting this technology for therapy selection. METHODS: The triple negative breast cancer cell lines MDA-MB-453, MDA-MB-231 and HCC1937 were selected based on their different BRCA1 and P53 status, and were seeded in the platform...
November 2, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29077384/modeling-glyco-collagen-conjugates-using-a-host-guest-strategy-to-alter-phenotypic-cell-migration-and-in-vivo-wound-healing
#20
Sivakoti Sangabathuni, Raghavendra Vasudeva Murthy, Madhuri Gade, Harikrishna Bavireddi, Suraj Toraskar, Mahesh V Sonar, Krishna N Ganesh, Raghavendra Kikkeri
The constructs and study of combinatorial libraries of structurally defined homologous extracellular matrix (ECM) glycopeptides can significantly accelerate the identification of cell surface markers involved in a variety of physiological and pathological processes. Herein, we present a simple and reliable host-guest approach to design a high-throughput glyco-collagen library to modulate the primary and secondary cell line migration process. 4-Amidoadamantyl-substituted collagen peptides and β-cyclodextrin appended with mono- or disaccharides were used to construct self-assembled glyco-collagen conjugates (GCCs), which were found to be thermally stable, with triple-helix structures and nanoneedles-like morphologies that altered cell migration processes...
December 26, 2017: ACS Nano
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