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ISF Rat Characterization - Extraction and biomolecular analysis of dermal interstitial fluid collected with hollow microneedles

ABSTRACT: Rat ISF Characterization- Quantitative assessment of Rat ISF to matching serum and plasma.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Blood Plasma, Blood Serum

SUBMITTER: Trevor Glaros

LAB HEAD: Trevor Glaros

PROVIDER: PXD010879 | Pride | 2018-09-18

REPOSITORIES: Pride

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			Action	DRS
	Rat_ISF-Serum_Plasma_End.raw	Raw
	Rat_ISF_Serum_Plasma_Fraction1.msf	Msf
	Rat_ISF_Serum_Plasma_Fraction1.raw	Raw
	Rat_ISF_Serum_Plasma_Fraction10.raw	Raw
	Rat_ISF_Serum_Plasma_Fraction11.raw	Raw

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Publications

Extraction and biomolecular analysis of dermal interstitial fluid collected with hollow microneedles.

Miller Philip R PR Taylor Robert M RM Tran Bao Quoc BQ Boyd Gabrielle G Glaros Trevor T Chavez Victor H VH Krishnakumar Raga R Sinha Anupama A Poorey Kunal K Williams Kelly P KP Branda Steven S SS Baca Justin T JT Polsky Ronen R

Communications biology 20181022

Dermal interstitial fluid (ISF) is an underutilized information-rich biofluid potentially useful in health status monitoring applications whose contents remain challenging to characterize. Here, we present a facile microneedle approach for dermal ISF extraction with minimal pain and no blistering for human subjects and rats. Extracted ISF volumes were sufficient for determining transcriptome, and proteome signatures. We noted similar profiles in ISF, serum, and plasma samples, suggesting that IS ...[more]

PMID: 30374463

Similar Datasets

Extraction and biomolecular analysis of dermal interstitial fluid collected with hollow microneedles.

Project description:Dermal interstitial fluid (ISF) is an underutilized information-rich biofluid potentially useful in health status monitoring applications whose contents remain challenging to characterize. Here, we present a facile microneedle approach for dermal ISF extraction with minimal pain and no blistering for human subjects and rats. Extracted ISF volumes were sufficient for determining transcriptome, and proteome signatures. We noted similar profiles in ISF, serum, and plasma samples, suggesting that ISF can be a proxy for direct blood sampling. Dynamic changes in RNA-seq were recorded in ISF from induced hypoxia conditions. Finally, we report the first isolation and characterization, to our knowledge, of exosomes from dermal ISF. The ISF exosome concentration is 12-13 times more enriched when compared to plasma and serum and represents a previously unexplored biofluid for exosome isolation. This minimally invasive extraction approach can enable mechanistic studies of ISF and demonstrates the potential of ISF for real-time health monitoring applications.

| S-EPMC6197253 | biostudies-literature

Proteomic Characterization of Human Dermal Interstitial Fluid

Project description:Proteomic characterization of human dermal interstitial fluid compared to matching serum and plasma.

2019-05-21 | PXD012658 | Pride

Automatic extraction of biomolecular interactions: an empirical approach.

Project description:We describe a method for extracting data about how biomolecule pairs interact from texts. This method relies on empirically determined characteristics of sentences. The characteristics are efficient to compute, making this approach to extraction of biomolecular interactions scalable. The results of such interaction mining can support interaction network annotation, question answering, database construction, and other applications.We constructed a software system to search MEDLINE for sentences likely to describe interactions between given biomolecules. The system extracts a list of the interaction-indicating terms appearing in those sentences, then ranks those terms based on their likelihood of correctly characterizing how the biomolecules interact. The ranking process uses a tf-idf (term frequency-inverse document frequency) based technique using empirically derived knowledge about sentences, and was applied to the MEDLINE literature collection. Software was developed as part of the MetNet toolkit (http://www.metnetdb.org).Specific, efficiently computable characteristics of sentences about biomolecular interactions were analyzed to better understand how to use these characteristics to extract how biomolecules interact.The text empirics method that was investigated, though arising from a classical tradition, has yet to be fully explored for the task of extracting biomolecular interactions from the literature. The conclusions we reach about the sentence characteristics investigated in this work, as well as the technique itself, could be used by other systems to provide evidence about putative interactions, thus supporting efforts to maximize the ability of hybrid systems to support such tasks as annotating and constructing interaction networks.

| S-EPMC3729816 | biostudies-other

Isolated of dermal papilla cells from follicular unit extraction

Project description:Hair follicles were originally obtained in the form of intact hair follicles from human scalp during microscopic hair transplant procedures of Follicular Unit Extraction (FUE). Dermal papilla cells were freshly isolated or traditionally isolated and cultured in basic medium supplied with 10% FBS. Freshly-isolated DPCs and cultured DPCs were sequenced using third generations of sequencing.

2022-12-01 | GSE142095 | GEO

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.

Project description:Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.

| S-EPMC7597623 | biostudies-literature

Gelatin Methacryloyl Microneedle Patches for Minimally Invasive Extraction of Skin Interstitial Fluid.

Project description:The extraction of interstitial fluid (ISF) from skin using microneedles (MNs) has attracted growing interest in recent years due to its potential for minimally invasive diagnostics and biosensors. ISF collection by absorption into a hydrogel MN patch is a promising way that requires the materials to have outstanding swelling ability. Here, a gelatin methacryloyl (GelMA) patch is developed with an 11 × 11 array of MNs for minimally invasive sampling of ISF. The properties of the patch can be tuned by altering the concentration of the GelMA prepolymer and the crosslinking time; patches are created with swelling ratios between 293% and 423% and compressive moduli between 3.34 MPa and 7.23 MPa. The optimized GelMA MN patch demonstrates efficient extraction of ISF. Furthermore, it efficiently and quantitatively detects glucose and vancomycin in ISF in an in vivo study. This minimally invasive approach of extracting ISF with a GelMA MN patch has the potential to complement blood sampling for the monitoring of target molecules from patients.

| S-EPMC7182487 | biostudies-literature

Expression analysis of human aortic valve interstitial cells (hAVICs), mitral valve interstitial cells(hMVICs) and dermal firbroblasts (hDFs)

Project description:Investigation of whole genome gene expression level changes in hAVICs and hMVICs, compared to human dermal fibroblasts.

2013-06-30 | GSE40801 | GEO

Expression analysis of human aortic valve interstitial cells (hAVICs), mitral valve interstitial cells(hMVICs) and dermal firbroblasts (hDFs)

Project description:Investigation of whole genome gene expression level changes in hAVICs and hMVICs, compared to human dermal fibroblasts. A three chip assay using total RNA obtained from primary cultured normal valve interstital cells and human dermal fibroblasts was performed. Each chip measures the expression level of 45,033 genes from normal AVICs,MVICs and DFs.

2013-06-30 | E-GEOD-40801 | biostudies-arrayexpress

Expression data from rat lens epithelial cells after extracapsular lens extraction (ECLE)

Project description:The epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs) has been proposed as a major cause of posterior capsule opacification (PCO) after cataract surgery. Molecular mechanism of PCO progression is still unclear. Using a microarray-based approach, herein we studied the changes in gene expression pattern during rat PCO formation in vivo as a model.

2020-09-30 | GSE152593 | GEO

Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production

Project description:Biomolecular condensates play important roles in diverse biological processes. Many viruses form biomolecular condensates which have been implicated in various functions critical for productive infection of host cells. The adenovirus L1-52/55 kilodalton protein (52K) was recently shown to form viral biomolecular condensates that coordinate viral genome packaging and capsid assembly. Although critical for packaging, we do not know how viral condensates are regulated during adenovirus infection. Here we show that phosphorylation of serine residues 28 and 75 within the N-terminal intrinsically disordered region of 52K modulates viral condensates in vitro and in cells, promoting liquid-like properties over condensate hardening. Furthermore, we demonstrate that phosphorylation of 52K promotes viral genome packaging and production of infectious progeny particles. Collectively, our findings provide insights into how viral condensate properties are regulated and maintained in a state conducive to their function in viral progeny production. In addition, our findings have implications for antiviral strategies aimed at targeting the regulation of viral biomolecular condensates to limit viral multiplication.

2023-12-06 | PXD046971 | Pride

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