Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita

Journal of Proteomics

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Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita

Publication date: 15 May 2023

Source: Journal of Proteomics, Volume 279

Author(s): Mehar Un Nissa, Nevil Pinto, Biplab Ghosh, Urvi Singh, Mukunda Goswami, Sanjeeva Srivastava

March 22, 2023
https://www.sciencedirect.com/science/article/pii/S1874391923000593?dgcid=rss_sd_all

GCā€MS of some Amaryllidaceae alkaloids of homolycorine type

Rapid Communications in Mass Spectrometry

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GCā€MS of some Amaryllidaceae alkaloids of homolycorine type

Rationale

Gas chromatography-mass spectrometry (GC-MS) is the most frequently applied technique for analysis of Amaryllidaceae alkaloids in plant extracts. These compounds, known for their potent bioactivities, are a distinctive chemotaxonomic feature of the Amaryllidoideae subfamily (Amaryllidaceae). The Amaryllidaceae alkaloids of homolycorine type with a C3-C4 double bond generally show molecular and diagnostic ions at the high mass region with low intensity in EIMS mode leading to problematic identification in complex plant extracts.

Methods

Eleven standard homolycorine-type alkaloids (isolated and identified by 1D and 2D nuclear magnetic resonance) were subjected to separation with gas chromatography and studied with electron impact mass spectrometry including single quadropole (GC-EIMS), tandem (GC-EIMS/MS), and high resolution (GC-HR-EIMS) detectors, as well as with chemical ionisation mass spectrometry (GC-CIMS). Alkaloid fractions from two Hippeastrum species and Clivia miniata were subjected to GC-EIMS and GC-CIMS for alkaloid identification.

Results

GC-EIMS in combination with GC-CIMS provided significant structural information for homolycorine-type alkaloids with C3-C4 double bond facilitating their unambiguous identification. Based on the obtained typical fragmentation, other eleven homolycorine-type compounds were identified in extracts from two Hippeastrum species by parallel GC-EIMS, GC-CIMS and LC-ESI/ToF/MS and in extracts from Clivia miniata by GC-EIMS.

Conclusion

GC-MS can be successfully applied for identification of new and known homolycorine-type alkaloids, as well as for chemotaxonomical and chemoecological studies, among others within the Amaryllidoideae subfamily.

Strahil Berkov,
Rumen Denev,
Borjana Sidjimova,
Yancho Zarev,
Alexandar Shkondrov,
Laura Torrasā€Claveria,
Francesc Viladomat,
Jaume Bastida
March 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9506?af=R

How total mRNA influences cell growth

BioRxiv

bioRxiv Subject Collection: Systems Biology
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How total mRNA influences cell growth

While the conventional wisdom is that growth rate is prominently set by ribosome amounts, in many biologically relevant situations the levels of mRNA and RNA polymerase can become a bottleneck for growth. Here, we construct a quantitative model of biosynthesis providing testable predictions for these situations. Assuming that RNA polymerases compete for genes and ribosomes for transcripts, the model gives general expressions relating growth rate, mRNA concentrations, ribosome and RNAP levels. On general grounds, the model predicts how the fraction of ribosomes in the proteome depends on total mRNA concentration, and inspects an underexplored regime in which the trade-off between transcript levels and ribosome abundances sets the cellular growth rate. In particular, we show that the model predicts and clarifies three important experimental observations, in budding yeast and E. coli bacteria: (i) that the growth-rate cost of unneeded protein expression can be affected by mRNA levels, (ii) that resource optimization leads to decreasing trends in mRNA levels at slow growth, and (iii) that ribosome allocation may increase, stay constant, or decrease, in response to transcription-inhibiting antibiotics.
Calabrese, L., Ciandrini, L., Cosentino Lagomarsino, M.
March 22, 2023
http://biorxiv.org/cgi/content/short/2023.03.17.533181v1?rss=1

The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal

BioRxiv

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The intensities of canonical senescence biomarkers integrate the duration of cell-cycle withdrawal

Senescence, a state of permanent cell-cycle withdrawal, is difficult to distinguish from quiescence, a transient state of cell-cycle withdrawal. This difficulty arises because quiescent and senescent cells are defined by overlapping biomarkers, raising the question of whether quiescence and senescence are truly distinct states. To address this, we used single-cell time-lapse imaging to distinguish slow-cycling quiescent cells from bona fide senescent cells after chemotherapy treatment, followed immediately by staining for various senescence biomarkers. We found that the staining intensity of multiple senescence biomarkers is graded rather than binary and primarily reflects the duration of cell-cycle withdrawal, rather than senescence per se. Together, our data suggest that quiescence and senescence are not distinct cellular states but rather fall on a continuum of cell-cycle withdrawal, where the intensities of canonical senescence biomarkers reflect the likelihood of cell-cycle re-entry.
Ashraf, H. M., Fernandez, B., Spencer, S. L.
March 22, 2023
http://biorxiv.org/cgi/content/short/2023.03.18.533242v1?rss=1

Emergence of power-law distributions in protein-protein interaction networks through study bias

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bioRxiv Subject Collection: Systems Biology
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Emergence of power-law distributions in protein-protein interaction networks through study bias

Protein-protein interaction (PPI) networks have been found to be power-law-distributed, ie, in observed PPI networks, the fraction of nodes with degree k often follows a power-law (PL) distribution k-. The emergence of this property is typically explained by evolutionary or functional considerations. However, the experimental procedures used to detect PPIs are known to be heavily affected by technical and study bias. For instance, proteins known to be involved in cancer are often heavily overstudied and proteins used as baits in large-scale experiments tend to have many false-positive interaction partners. This raises the question whether PL distributions in observed PPI networks could be explained by these biases alone. Here, we address this question using statistical analyses of the degree distributions of 1000s of observed PPI networks of controlled provenance as well as simulation studies. Our results indicate that study bias and technical bias can indeed largely explain the fact that observed PPI networks tend to be PL-distributed. This implies that it is problematic to derive hypotheses about the degree distribution and emergence of the true biological interactome from the PL distributions in observed PPI networks.
Lucchetta, M., List, M., Blumenthal, D. B., Schaefer, M. H.
March 22, 2023
http://biorxiv.org/cgi/content/short/2023.03.17.533165v1?rss=1

Identifying a urinary peptidomics profile for hypertension in young adults:The Africanā€PREDICT study

Proteomics (Wiley)

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Identifying a urinary peptidomics profile for hypertension in young adults:The Africanā€PREDICT study

Abstract

Hypertension is one of the most important and complex risk factors for cardiovascular diseases. By using urinary peptidomics analyses, we aimed to identify peptides associated with hypertension, building a framework for future research towards improved prediction and prevention of premature development of cardiovascular disease. We included 78 hypertensive and 79 normotensive participants from the African-PREDICT study (aged 20-30-years), matched for sex (51% male) and ethnicity (49% black and 51% white). Urinary peptidomics data were acquired using capillary-electrophoresis-time-of-flight-mass-spectrometry. Hypertension-associated peptides were identified and combined into a support vector machine-based multidimensional classifier. When comparing the peptide data between the normotensive and hypertensive groups, 129 peptides were nominally differentially abundant (Wilcoxon pĀ <Ā 0.05). Nonetheless, only three peptides, all derived from collagen alpha-1(III), remained significantly different after rigorous adjustments for multiple comparisons. The 37 most significant peptides (all pā‰¤0.001) served as basis for the development of a classifier, with 20 peptides being combined into a unifying score, resulting in an AUC of 0.85 in the ROC analysis (pĀ <Ā 0.001), with 83% sensitivity at 80% specificity. Our study suggests potential value of urinary peptides in the classification of hypertension, which could enable earlier diagnosis and better understanding of the pathophysiology of hypertension and premature cardiovascular disease development.

This article is protected by copyright. All rights reserved

De Beer Dalene,
Mels Catharina MC,
Schutte Aletta E,
Delles Christian,
Mary Sheon,
Mullen William,
Latosinska Agnieszka,
Mischak Harald,
Kruger Ruan
March 22, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200444?af=R

[ASAP] Differentiating Toxic and Nontoxic Tricresyl Phosphate Isomers Using Ionā€“Molecule Reactions with Oxygen

Journal of The American Society for Mass Spectrometry

Journal of the American Society for Mass Spectrometry: Latest Articles (ACS Publications)

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[ASAP] Differentiating Toxic and Nontoxic Tricresyl Phosphate Isomers Using Ionā€“Molecule Reactions with Oxygen

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Journal of the American Society for Mass Spectrometry
DOI: 10.1021/jasms.2c00334

Roshanak Amiri, Meera J. Bissram, Mahin Hashemihedeshi, Frank L. Dorman, David Megson, and Karl J. Jobst
March 21, 2023
http://dx.doi.org/10.1021/jasms.2c00334

Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation

T-cells are critical components of the adaptive immune system. Upon activation, they acquire effector functions through a complex interplay between mRNA transcripts and proteins, the landscape of which remains to be fully elucidated. In this resource article, we present an integrative temporal proteomic and transcriptomic analysis of primary human CD4+ and CD8+ T-cells following ex vivo activation with anti-CD3/CD28 Dynabeads. Our data reveal a time-dependent dissociation between the T-cell transcriptome and proteome during activation. A transient downregulation of GLUT1, the central glucose transporter in T-cells, marked the onset of reprogramming in both CD4+ and CD8+ T-cells. At late activation, CD4+ T-cells upregulated enzymes associated with degradation of fatty acids while CD8+ T-cells preferentially upregulated enzymes in the metabolism of cofactors and vitamins. Surprisingly, we found that activated CD4+ and CD8+ T-cells became transcriptionally more divergent at the same time their proteome became more similar. In addition to the metabolic reprogramming highlighted in our analysis, this dataset provides a public resource for understanding temporal molecular changes governing the acquisition of effector functions by T-cells.
Weerakoon, H., Mohamed, A., Wong, Y., Senadheera, B., Haigh, O., S. Watkins, T., Kazakoff, S., Mukhopadhyay, P., Mulvenna, J., J Miles, J., M. Hill, M., Lepletier, A.
March 21, 2023
http://biorxiv.org/cgi/content/short/2023.03.17.532022v1?rss=1

Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

BioRxiv

bioRxiv Subject Collection: Systems Biology
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Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

While many heterologous molecules can be produced at trace concentrations via microbial bioconversion processes, maximizing their titers, rates, and yields from lignin-derived carbon streams remains challenging. Growth coupling can not only increase titers and yields but also shift the production period from stationary phase to growth phase. These methods for designing growth-coupling strains however require multi-gene edits for implementation which may be perceived as impractical. Here, we computationally evaluated 4,114 potential solutions for growth coupling para-coumarate to indigoidine production and prototype two cut sets in Pseudomonas putida KT2440. We used adaptive laboratory evolution (ALE) on the initial triple deletion strain to restore growth on p-CA. Using X-ray tomography on this post-ALE strain we revealed increased cell density and decreased cell volume. Proteomics identified upregulated peroxidases that mitigate reactive oxygen species formation. Nine iterative stepwise modifications further informed by model-guided and rational approaches realized a growth coupled strain that produced 7.3 g/L indigoidine at 77% MTY in para-coumarate minimal media. These ensemble strategies provide a blueprint for producing target molecules at high product titers, rates, and yields.
Eng, T. T., Banerjee, D., Menasalvas, J., Chen, Y., Gin, J., Choudhary, H., Baidoo, E., Chen, J. H., Ekman, A., Kakumanu, R., Diercks, Y. L., Codik, A., Larabell, C., Gladden, J., Simmons, B. A., Keasling, J. D., Petzold, C. J., Mukhopadhyay, A.
March 21, 2023
http://biorxiv.org/cgi/content/short/2023.03.16.532821v1?rss=1

MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes

BioRxiv

bioRxiv Subject Collection: Systems Biology
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MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes

Background: The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or omes, measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen repositories. However, these biospecimens have been underutilized for multi-omic analysis due to the low throughput of current analytical technologies that impede large-scale studies. Methods: Tissue sampling, preparation, and downstream analysis were integrated into a 96-well format multi-omics workflow, MultiomicsTracks96. Frozen mouse organs were sampled using the CryoGrid system, and matched FFPE samples were processed using a microtome. The 96-well format sonicator, PIXUL, was adapted to extract DNA, RNA, chromatin, and protein from tissues. The 96-well format analytical platform, Matrix, was used for chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), methylated RNA immunoprecipitation (MeRIP), and RNA reverse transcription (RT) assays followed by qPCR and sequencing. LC-MS/MS was used for protein analysis. The Segway genome segmentation algorithm was used to identify functional genomic regions, and linear regressors based on the multi-omics data were trained to predict protein expression. Results: MultiomicsTracks96 was used to generate 8-dimensional datasets including RNA-seq measurements of mRNA expression; MeRIP-seq measurements of m6A and m5C; ChIP-seq measurements of H3K27Ac, H3K4m3, and Pol II; MeDIP-seq measurements of 5mC; and LC-MS/MS measurements of proteins. We observed high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles (ChIP-seq: H3K27Ac, H3K4m3, Pol II; MeDIP-seq: 5mC) was able to recapitulate and predict organ-specific super-enhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic expression profiles can be more accurately predicted by the full suite of multi-omics data, compared to using epigenomic, transcriptomic, or epitranscriptomic measurements individually. Conclusions: The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies, for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.
Mar, D., Babenko, I., Zhang, R., Noble, W. S., Denisenko, O., Vaisar, T., Bomsztyk, K.
March 21, 2023
http://biorxiv.org/cgi/content/short/2023.03.16.533031v1?rss=1

Modelling the dynamics of senescence spread

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Modelling the dynamics of senescence spread

Cellular senescence is a cell surveillance mechanism that arrests the cell cycle in damaged cells. The senescent phenotype can spread from cell to cell through paracrine and juxtacrine signalling, but the dynamics of this process are not well understood. Although senescent cells are important in ageing, wound healing, and cancer, it is unclear how the spread of senescence is contained in senescent lesions. In the absence of the immune system, senescence could theoretically spread infinitely from one cell to another, but this contradicts experimental evidence. To investigate this issue, we developed both a minimal mathematical model and a stochastic simulation of senescence spread. Our results suggest that differences in the number of signalling molecules secreted between subtypes of senescent cells can limit the spread of senescence. We found that dynamic, time-dependent paracrine signalling prevents the uncontrolled spread of senescence and we demonstrate how model parameters can be determined using Bayesian inference in a proposed experiment.
Martin, L. K., Schumacher, L., Chandra, T.
March 21, 2023
http://biorxiv.org/cgi/content/short/2023.03.16.532939v1?rss=1

[ASAP] Global Discovery and Temporal Changes of Human Albumin Modifications by Pan-Protein Adductomics: Initial Application to Air Pollution Exposure

Journal of The American Society for Mass Spectrometry

Journal of the American Society for Mass Spectrometry: Latest Articles (ACS Publications)

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[ASAP] Global Discovery and Temporal Changes of Human Albumin Modifications by Pan-Protein Adductomics: Initial Application to Air Pollution Exposure

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Journal of the American Society for Mass Spectrometry
DOI: 10.1021/jasms.2c00314

Joshua W. Smith, Robert N. Oā€™Meally, Sean M. Burke, Derek K. Ng, Jian-Guo Chen, Thomas W. Kensler, John D. Groopman, and Robert N. Cole
March 20, 2023
http://dx.doi.org/10.1021/jasms.2c00314

[ASAP] prolfqua: A Comprehensive Rā€‘Package for Proteomics Differential Expression Analysis

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] prolfqua: A Comprehensive Rā€‘Package for Proteomics Differential Expression Analysis

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Journal of Proteome Research
DOI: 10.1021/acs.jproteome.2c00441

Witold E. Wolski, Paolo Nanni, Jonas Grossmann, Maria dā€™Errico, Ralph Schlapbach, and Christian Panse
March 20, 2023
http://dx.doi.org/10.1021/acs.jproteome.2c00441

Reaction acceleration in microdroplet mass spectrometry: Inlet capillary and solvent composition effects

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Reaction acceleration in microdroplet mass spectrometry: Inlet capillary and solvent composition effects

Rationale

Microdroplet chemistry has attracted tremendous interest in recent years. We have previously reported that microdroplet mass spectrometry (MS) achieves reaction acceleration. Here we systematically investigated the effect of capillary heating of MS inlet and solvent polarity of microdroplets on the conversion ratios of dehydration and phosphorylation reactions.

Methods

The micron-sized droplets generated by high-speed gas encapsulated the compounds. The conversion ratios of dehydration and phosphorylation reactions were investigated at different capillary temperatures of MS inlet between 30Ā°C and 300Ā°C. Subsequently, the effects of solvent polarity of different microdroplets (acetonitrile, acetonitrile/water [v/v: 9:1], and water) on microdroplet reactions were investigated.

Results

The microdroplets could be used as reaction vessels for rapid dehydration and phosphorylation reactions. Microdroplet MS is characterized by the completion of the reaction in microseconds. The increase in capillary temperature increased the conversion ratio of dehydration reactions but had little effect on phosphorylation reactions. The stability of compounds supports this phenomenon. In addition, the increase in solvent polarity in microdroplets promoted the dehydration reaction but inhibited the nucleophilic substitution reaction (phosphorylation reaction).

Conclusions

Microdroplet MS achieved an acceleration of the reaction, which was attributed to capillary temperature, microdroplet solvents, and the stability of reaction products. This finding suggested that the inlet capillary and solvent system should be considered in the study and interpretation of microdroplet MS.

Yun Ju,
Yuwei He,
Guangfeng Kan,
Kai Yu,
Jie Jiang,
Xiaofei Wang,
Hong Zhang
March 19, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9498?af=R

[ASAP] Evolution of Mass Spectrometry Instruments and Techniques for Blood Proteomics

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

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[ASAP] Evolution of Mass Spectrometry Instruments and Techniques for Blood Proteomics

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Journal of Proteome Research
DOI: 10.1021/acs.jproteome.3c00102

Yang Zhao, Qian Xue, Man Wang, Bo Meng, You Jiang, Rui Zhai, Yong Zhang, Xinhua Dai, and Xiang Fang
March 18, 2023
http://dx.doi.org/10.1021/acs.jproteome.3c00102

A novel dynamic proteomics approach for the measurement of broiler chicken protein fractional synthesis rate

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

A novel dynamic proteomics approach for the measurement of broiler chicken protein fractional synthesis rate

Rationale

The study of protein synthesis in farm animals is uncommon despite its potential to increase knowledge about metabolism and discover new biomarkers of health and growth status. The present study describes a novel dynamic proteomics approach for the measurement of protein fractional synthesis rate (FSR) in broiler chickens.

Methods

Chickens received a 10Ā g/kg oral dose of 2H2O at day 21 of their life. Body water 2H abundance was measured in plasma samples using a portable Fourier transform infrared spectrometer. Free and protein-bound amino acids (AAs) were isolated and had their 2H enrichment measured by gas chromatography with mass spectrometry (GC/MS). Peptide 2H enrichment was measured by proteomics analysis of plasma and muscle samples. Albumin, fibrinogen and muscle protein FSR were calculated from GC/MS and proteomics data.

Results

Ala appeared to be more enriched at the site of protein synthesis than in the AA free pools. Glu was found to be the AA closest to isotopic equilibrium between the different AA pools. Glu was used as an anchor to calculate n(AA) values necessary for chicken protein FSR calculation in dynamic proteomics studies. FSR values calculated using proteomics data and GC/MS data showed good agreement as evidenced by a Blandā€“Altman residual plot.

Conclusions

A new dynamic proteomics approach for the measurement of broiler chicken individual protein FSR based on the administration of a single 2H2O oral bolus has been developed and validated. The proposed approach could facilitate new immunological and nutritional studies on free-living animals.

Jorge Peinadoā€Izaguerri,
Eduardo Zarzuela,
Mark McLaughlin,
Alexandra C. Small,
Francesca Riva,
Dorothy E. F. McKeegan,
Maureen Bain,
Javier MuƱoz,
Mangesh Bhide,
Tom Preston
March 18, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9497?af=R

Editorial from Dominic M. Desiderio

Mass Spectrometry Reviews

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Editorial from Dominic M. Desiderio

Abstract

I retired as an Editor of Mass Spectrometry Reviews. I signed my contract on November 1, 1993, and published my first editorial (Volume 13, Issue 1, 1994) when I joined Nico M. M. Nibbering as Co-Editor. These two editorials frame my 30-year tenure at the journal.

This article is protected by copyright. All rights reserved.

Dom Desiderio
March 18, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21840?af=R

Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

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Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.

Abstract

I am pleased and honored that Dan Fabris has organized this special issue of reviews that reflect many of my research interests. I have been a member of the Editorial Advisory Board of Mass Spectrometry Reviews since 1994 and I regard reviews as an important component of the scientific method. Well done, they collect and integrate knowledge in a particular field and construct a factual foundation that directs and supports the next research frontier.

This article is protected by copyright. All rights reserved.

Catherine Fenselau Cotter
March 18, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21839?af=R