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Article
Open AccessA resource database for protein kinase substrate sequence-preference motifs based on large-scale mass spectrometry data
Protein phosphorylation is one of the most prevalent posttranslational modifications involved in molecular control of cellular processes, and is mediated by over 520 protein kinases in humans and other mammals...
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Article
Open AccessSignaling mechanisms in renal compensatory hypertrophy revealed by multi-omics
Loss of a kidney results in compensatory growth of the remaining kidney, a phenomenon of considerable clinical importance. However, the mechanisms involved are largely unknown. Here, we use a multi-omic approa...
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Article
Open AccessIdentification of Daboia siamensis venome using integrated multi-omics data
Snakebite, classified by World Health Organization as a neglected tropical disease, causes more than 100,000 deaths and 2 million injuries per year. Currently, available antivenoms do not bind with strong spec...
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Article
Open AccessBayesian analysis of dynamic phosphoproteomic data identifies protein kinases mediating GPCR responses
A major goal in the discovery of cellular signaling networks is to identify regulated phosphorylation sites (“phosphosites”) and map them to the responsible protein kinases. The V2 vasopressin receptor is a G-...
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Article
Open AccessNGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors
Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughpu...
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Article
Open AccessPhosphorylation Changes in Response to Kinase Inhibitor H89 in PKA-Null Cells
Protein phosphorylation, mediated by protein kinases, plays a crucial role in cellular regulation. One of the most important protein kinases is protein kinase A (PKA). N-[2-p-bromocinnamylamino-ethyl]-5-isoqui...
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Article
Open AccessSystems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin
Vasopressin-mediated regulation of renal water excretion is defective in a variety of water balance disorders in humans. It occurs in part through long-term mechanisms that regulate the abundance of the aquapo...
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Protocol
Peptide Labeling Using Isobaric Tagging Reagents for Quantitative Phosphoproteomics
Isobaric tagging reagents have become an invaluable tool for multiplexed quantitative proteomic analysis. These reagents can label multiple, distinct peptide samples from virtually any source material (e.g., t...
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Article
Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures
Modern mass spectrometers can produce large numbers of peptide spectra from complex biological samples in a short time. A substantial amount of redundancy is observed in these data sets from peptides that may ...
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Article
Vasopressin and the regulation of aquaporin-2
Water excretion is regulated in large part through the regulation of osmotic water permeability of the renal collecting duct epithelium. Water permeability is controlled by vasopressin through regulation of th...
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Article
Open AccessPhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data
Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues help...
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Protocol
Isolation and Purification of Exosomes in Urine
Exosomes represent an important and readily isolated subset of the urinary proteome that has the potential to shed much insight on the health status of the kidney. Each segment of the nephron sheds exosomes in...
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Article
Molecular coin slots for urea
Membrane-bound protein channels that allow only urea to pass through are vital to the kidney's ability to conserve water. Crystal structures show that the channels select urea molecules by passing them through...
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Article
Courier service for ammonia
Physiological studies in mice demonstrate a surprising role for a kidney protein related to the rhesus factor of red blood cells. Similar research would aid further annotation of mammalian genomes.
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Article
Vasopressin: friend or foe?
Vasopressin plays a vital part in homeostasis by regulating water excretion in the kidney. But it seems that vasopressin also dampens the inflammatory response to uropathogenic Escherichia coli—a finding that add...
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Chapter
Regulation of Renal Aquaporins and Sodium Transporters During Vasopressin-Escape in the Rat
Several clinical conditions, e.g., congestive heart failure and cirrhosis are associated with inappropriately elevated vasopressin levels relative to serum osmolality (Bichet et al., 1992). In addition, ectopic p...
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Chapter
Oxytocin: One of the Factors for Regulating AQP2 Localization and Urinary AQP2 Excretion
Aquaporin-2 (AQP2), an essential water channel for urinary concentration, is mainly located in the apical plasma membrane of collecting duct epithelial cells, and vasopressin is the major factor for regulation...
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Chapter
Studies of Renal Aquaporin-2 Expression during Renal Escape from Vasopressin-Induced Antidiuresis
In animal models of the syndrome of inappropriate antidiuresis (SIADH), sustained administration of vasopressin and water results in free-water retention and progressive hyponatremia for several days, which is...
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Chapter
Ultramicro-Analysis of Tubular Fluid by Continuous-Flow Methodology
The measurement of net transepithelial fluxes in isolated perfused tubule experiments requires highly sensitive analytical methods, capable of precise determination of solute concentrations in 1–30 nanoliter s...
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Chapter
Urinary Concentrating and Diluting Processes
Body fluid osmolality is normally maintained within narrow bounds through the control of body water balance. Water intake is regulated to some degree by the thirst mechanism.(1) However, the chief means by whi...
