scholarly journals Protein quantification across hundreds of experimental conditions

2009 ◽  
Vol 106 (37) ◽  
pp. 15544-15548 ◽  
Author(s):  
Zia Khan ◽  
Joshua S. Bloom ◽  
Benjamin A. Garcia ◽  
Mona Singh ◽  
Leonid Kruglyak
Keyword(s):  
Data Structures ◽  
Quantitative Data ◽  
Transcript Abundance ◽  
Protein Quantification ◽  
Protein Abundance ◽  
Proteomics Data ◽  
Space Partitioning ◽  
Experimental Conditions ◽  
Graph Theoretic ◽  
Quantitative Studies

Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.

Branchial expression of an aquaporin 3 (AQP-3) homologue is downregulated in the European eelAnguilla anguillafollowing seawater acclimation

2002 ◽  
Vol 205 (17) ◽  
pp. 2643-2651 ◽  
Author(s):  
Christopher P. Cutler ◽  
Gordon Cramb
Keyword(s):  
Northern Blot Analysis ◽  
Transcript Abundance ◽  
European Eel ◽  
Aquaporin 3 ◽  
Quantitative Studies ◽  
Silver Eels ◽  
Polymerase Chain ◽  
Seawater Acclimation ◽  
Yellow Eels ◽  
Specific Mrna

SUMMARYA cDNA encoding the homologue of mammalian aquaporin 3 (AQP-3) was isolated by reverse transcription—polymerase chain reaction from the gill of the European eel. The derived amino acid sequence shares 67-70% homology with other vertebrate AQP-3 homologues. Northern blot analysis revealed two AQP-3-specific mRNA species of 2.4 kb and 7 kb. AQP-3 mRNA is expressed predominantly in the eye, oesophagus, intestine (as found in mammals) and the gill; no expression could be demonstrated in the stomach and only low and sporadic levels in the kidney. Quantitative studies demonstrated that,following the 3-week acclimation of freshwater (FW)-adapted yellow and silver eels to seawater (SW), transcript abundance in the gill was reduced by 76% and 97%, respectively. The half time of branchial AQP-3 mRNA downregulation in yellow eels was approximately 10 h, with a maximal 94% decrease in expression after 2 days in SW (compared to time-matched FW controls). However, in fish acclimated to SW for more than 4 days, the fall in AQP-3 mRNA abundance recovered slightly, such that after 3 weeks, expression was 16% of that in time-matched FW controls. The potential roles for this aquaporin isoform in water or solute transport in the eel gill are discussed.

scholarly journals Integrative Transcriptomics and Proteomics Analyses to Reveal the Developmental Regulation of Metorchis orientalis: A Neglected Trematode With Potential Carcinogenic Implications

2021 ◽  
Vol 11 ◽  
Author(s):  
Jun-Feng Gao ◽  
Qing-Bo Lv ◽  
Rui-Feng Mao ◽  
Yun-Yi Sun ◽  
Ying-Yu Chen ◽  
...  
Keyword(s):  
Nucleocytoplasmic Transport ◽  
Protein Quantification ◽  
Differentially Expressed ◽  
Receptor Protein ◽  
Proteomics Data ◽  
Potential Threat ◽  
Serine Threonine Kinase ◽  
Specific Expression ◽  
Threonine Kinase ◽  
Gene And Protein Expression

Metorchis orientalis is a neglected zoonotic parasite of the gallbladder and bile duct of poultry, mammals, and humans. It has been widely reported in Asian, including China, Japanese, and Korea, where it is a potential threat to public health. Despite its significance as an animal and human pathogen, there are few published transcriptomic and proteomics data available. Transcriptome Illumina RNA sequencing and label-free protein quantification were performed to compare the gene and protein expression of adult and metacercariae-stage M. orientalis, resulting in 100,234 unigenes and 3,530 proteins. Of these, 13,823 differentially expressed genes and 1,445 differentially expressed proteins were identified in adult versus metacercariae. In total, 570 genes were differentially expressed consistent with the mRNA and protein level in the adult versus metacercariae stage. Differential gene transcription analyses revealed 34,228 genes to be expressed in both stages, whereas 66,006 genes showed stage-specific expression. Compared with adults, the metacercariae stage was highly transcriptional. GO and KEGG analyses based on transcriptome and proteome revealed numerous up-regulated genes in adult M. orientalis related to microtubule-based processes, microtubule motor activity, and nucleocytoplasmic transport. The up-regulated genes in metacercariae M. orientalis were mainly related to transmembrane receptor protein serine/threonine kinase activity, transmembrane receptor protein serine/threonine kinase signaling pathway. Transcriptome and proteome comparative analyses showed numerous up-regulated genes in adult stage were mainly enriched in actin filament capping, spectrin, and glucose metabolic process, while up-regulated genes in metacercariae stage were mainly related to cilium assembly, cilium movement, and motile cilium. These results highlight changes in protein and gene functions during the development of metacercariae into adults, and provided evidence for the mechanisms involved in morphological and metabolic changes at both the protein and gene levels. Interestingly, many genes had been proved associated with liver fibrosis and carcinogenic factors were identified highly expressed in adult M. orientalis, which suggests that M. orientalis is a neglected trematode with potential carcinogenic implications. These data provide attractive targets for the development of therapeutic or diagnostic interventions for controlling M. orientalis.

scholarly journals Thyroid hormone stimulates the renal Na/H exchanger NHE3 by transcriptional activation

1999 ◽  
Vol 276 (1) ◽  
pp. C102-C108 ◽  
Author(s):  
Adriana Cano ◽  
Michel Baum ◽  
Orson W. Moe
Keyword(s):  
Thyroid Hormone ◽  
Transcriptional Activation ◽  
Transcript Abundance ◽  
Epithelial Cell Line ◽  
Protein Abundance ◽  
Renal Epithelial Cell ◽  
Opossum Kidney ◽  
Ok Cells ◽  
Transcript Stability ◽  
Renal Epithelial Cell Line

Thyroid hormone stimulates renal proximal tubule NaCl and NaHCO3 absorption in part by activating the apical membrane Na/H exchanger NHE3. We used a renal epithelial cell line, the opossum kidney (OK) cell, to define the mechanism by which 3,5,3′-triiodothyronine (T3) increases NHE3 activity. T3 stimulated NHE3 activity, an effect that was blocked by inhibition of cellular transcription or translation. The increase in activity was associated with increases in steady-state cell surface and total cellular NHE3 protein and NHE3 transcript abundance. T3stimulated transcription of the NHE3 gene and had no effect on NHE3 transcript stability. The transcriptional activity of the 5′-flanking region of the rat NHE3 gene was stimulated by T3 when expressed in OK cells. When heterologously expressed rat NHE3 transcript levels were clamped constant with a constitutive promoter in OK cells, T3 has no effect on rat NHE3 protein abundance, suggesting the absence of regulation of NHE3 protein stability or translation. These studies demonstrate that T3 stimulates NHE3 activity by activating NHE3 gene transcription and increasing NHE3 transcript and protein abundance.

scholarly journals Initiation of Conceptus Elongation Coincides with an Endometrium Basic Fibroblast Growth Factor (FGF2) Protein Increase in Heifers

2020 ◽  
Vol 21 (5) ◽  
pp. 1584 ◽  
Author(s):  
Daniel Chiumia ◽  
Katy Schulke ◽  
Anna E. Groebner ◽  
Nadine Waldschmitt ◽  
Horst-Dieter Reichenbach ◽  
...  
Keyword(s):  
Growth Factors ◽  
Fibroblast Growth Factors ◽  
Transcript Abundance ◽  
Potential Contribution ◽  
Protein Abundance ◽  
Fibroblast Growth ◽  
Mrna Transcript ◽  
Pregnancy Status ◽  
A Minor

Fibroblast growth factors (FGF) play an important role during embryo development. To date, the role of FGF and the respective receptors (FGFR) during the preimplantation phase in cattle are not fully characterized. We examined FGF1, FGF2, FGFR1, FGFR2, and FGFR3 in cyclic and early pregnant heifers at Days 12, 15, and 18 after insemination (Day 0). Endometrial FGF1 mRNA transcript abundance in heifers varied significantly with respect to the day after insemination, the pregnancy status, and their interaction. The expression was higher in nonpregnant than in pregnant heifers at Day 18. The conceptus transcripts abundance of FGFR2 and FGFR3 were significantly lower at Day 15 than 18. In the endometrium, FGF1 protein abundance significantly decreased from Day 12 onwards and FGF2 protein abundance showed a minor, but a significant increase at Day 15 in comparison to Days 12 and 18. We concluded that the decrease in FGF1 mRNA expression in pregnant heifers at Day 18 points towards a potential contribution of FGF1 in the preimplantation process. Additionally, successful embryo elongation might require a spatiotemporal FGF2 protein increase in the endometrium.

scholarly journals Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development

2015 ◽  
Vol 26 (11) ◽  
pp. 1827-1836 ◽  
Author(s):  
Michael Riffle ◽  
Gennifer E. Merrihew ◽  
Daniel Jaschob ◽  
Vagisha Sharma ◽  
Trisha N. Davis ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Protein Abundance ◽  
Proteomics Data

scholarly journals Integrating identification and quantification uncertainty for differential protein abundance analysis with Triqler

2020 ◽  
Author(s):  
Matthew The ◽  
Lukas Käll
Keyword(s):  
Missing Values ◽  
Shotgun Proteomics ◽  
Protein Quantification ◽  
Protein Abundance ◽  
Posterior Distributions ◽  
Label Free ◽  
Differential Abundance ◽  
Complicated Process ◽  
Python Package ◽  
Different Parts

AbstractProtein quantification for shotgun proteomics is a complicated process where errors can be introduced in each of the steps. Triqler is a Python package that estimates and integrates errors of the different parts of the label-free protein quantification pipeline into a single Bayesian model. Specifically, it weighs the quantitative values by the confidence we have in the correctness of the corresponding PSM. Furthermore, it treats missing values in a way that reflects their uncertainty relative to observed values. Finally, it combines these error estimates in a single differential abundance FDR that not only reflects the errors and uncertainties in quantification but also in identification. In this tutorial, we show how to (1) generate input data for Triqler from quantification packages such as MaxQuant and Quandenser, (2) run Triqler and what the different options are, (3) interpret the results, (4) investigate the posterior distributions of a protein of interest in detail and (5) verify that the hyperparameter estimations are sensible.

scholarly journals Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

2021 ◽  
Author(s):  
Shengbo Wang ◽  
David García-Seisdedos ◽  
Ananth Prakash ◽  
Deepti Jaiswal Kundu ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Protein Expression ◽  
Rat Tissues ◽  
Protein Abundance ◽  
Proteomics Data ◽  
Pathway Enrichment ◽  
Expression Atlas ◽  
Organ Specific ◽  
High Level ◽  
Widespread Dissemination

The increasingly large amount of public proteomics data enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contains 23 individual datasets, which have a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We compared protein expression between the different organs, including the distribution of proteins across them. We also performed gene ontology and pathway enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples. Finally, it should be noted that protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

scholarly journals MaxQuant software for ion mobility enhanced shotgun proteomics

2019 ◽  
Author(s):  
Nikita Prianichnikov ◽  
Heiner Koch ◽  
Scarlet Koch ◽  
Markus Lubeck ◽  
Raphael Heilig ◽  
...  
Keyword(s):  
Ion Mobility ◽  
Retention Time ◽  
Signal Intensity ◽  
Feature Detection ◽  
Dynamic Range ◽  
Shotgun Proteomics ◽  
Detection Algorithm ◽  
Protein Quantification ◽  
Label Free ◽  
Proteomics Data

SummaryIon mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides, proteins and posttranslational modification sites in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.

scholarly journals Después de usted: Variation and Change in a Spanish Tripartite Politeness System

Languages ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 152
Author(s):  
María Irene Moyna
Keyword(s):  
Latin American ◽  
Quantitative Data ◽  
American Variety ◽  
Quantitative Studies

This study focuses on the address paradigm in the Spanish spoken in Montevideo, the capital of Uruguay, a Latin American variety which presents speakers with three options—one polite (usted), and two familiar (pan-Hispanic tú and regional vos). Recent quantitative studies have shown that the range of polite usted is shrinking in the dialect, as younger respondents reserve it for hierarchical contexts or for much older addressees. Indeed, speakers are uncertain about appropriate address choice to convey deference without distance. The present analysis supplements the previous quantitative data with responses of Montevideo speakers to an attitudinal interview (n = 12) analyzed qualitatively for themes with Atlas.ti. It finds that while speakers reject usted, they have adopted a range of strategies to maintain distinctions in politeness, including address avoidance, mirroring, and the repurposing of tú as an intermediate polite form.

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