Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing.
This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions. ...
Source: Journal of Proteomics - September 14, 2020 Category: Biochemistry Authors: Presslee S, Penkman K, Fischer R, Richards-Slidel E, Southon J, Hospitaleche CA, Collins M, MacPhee R Tags: J Proteomics Source Type: research

Proteomic analysis of liver in diet-induced Hyperlipidemic mice under Fructus Rosa roxburghii action.
Abstract Fructus Rosae Roxburghii (FRR) has been considered as edible and medicinal fruit possessing antiatherosclerotic effect, but the mechanism is still unclear. HLP is material basis for AS formation. Under FRR action, TC, TG, LDL, HDL and ASI in serum were regulated to control level. Differentially expressed proteins in liver were analyzed by using TMT labeling and LC-MS/MS for better understanding the effect and molecular mechanism of FRR on diet-induced hyperlipidemic mice. In total, 4460 proteins were quantified, of which 469 proteins showed dramatic changes between each group. According to molecular funct...
Source: Journal of Proteomics - September 11, 2020 Category: Biochemistry Authors: Song P, Shen X Tags: J Proteomics Source Type: research

N-glycosylation profiling of serum immunoglobulin in opisthorchiasis patients.
In conclusion, O. viverrini infection alters the serum immunoglobulin glycosylation profile and these changes could distinguish between O. viverrini-infected individuals and healthy controls. SIGNIFICANCE: We demonstrate that both quantities and glycoforms of serum immunoglobulin subclasses were altered in Opisthorchis viverrini-infected individuals as investigated by the QqQ-MS-MRM method. Patterns of immunoglobulin with a specific glycoform might contribute to immune responses to O. viverrini infection. PMID: 32927111 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - September 11, 2020 Category: Biochemistry Authors: Onsurathum S, Kailemia MJ, Intuyod K, Haonon O, Pairojkul C, Thanan R, Pinlaor P, Lebrilla CB, Pinlaor S Tags: J Proteomics Source Type: research

Proteasuria in nephrotic syndrome-quantification and proteomic profiling.
c F Abstract Nephrotic syndrome is characterized by urinary excretion of plasma proteases or proteasuria. There is a lack of data on the quantity, activity status and identity of these aberrantly filtered proteases. We established a fluorescence-based substrate assay to quantify protease activity in urine samples from healthy and nephrotic humans and mice. Protease class activity was determined after addition of specific inhibitors. Individual proteases were identified by tandem mass spectrometry (MS/MS). In spot urine samples from 10 patients with acute nephrotic syndrome of various etiology, urinary protease act...
Source: Journal of Proteomics - September 11, 2020 Category: Biochemistry Authors: Wörn M, Bohnert BN, Alenazi F, Boldt K, Klose F, Junger K, Ueffing M, Birkenfeld AL, Kalbacher H, Artunc F Tags: J Proteomics Source Type: research

Mitochondrial proteomic analysis reveals that proteins relate to oxidoreductase activity play a central role in pollen fertility in cotton.
PMID: 32921598 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - September 10, 2020 Category: Biochemistry Authors: Nie H, Cheng C, Hua J Tags: J Proteomics Source Type: research

Differential proteomic analysis of soybean anthers by iTRAQ under high-temperature stress.
In conclusion, the heat-tolerant cultivar performed better under stress than heat-sensitive cultivar through modulation of HSP family proteins, pectinesterase, profilin, S-adenosylmethionine synthase, peroxidase, GST, peptidylprolyl isomerase, and disulfide-isomerase. The results provide novel insight into the mechanism of high-temperature stress response of soybean. SIGNIFICANCE: In recent years, with the high temperature (HT) stress brought by climate change frequently occurs at anthesis and negatively affects soybean productivity. The molecular mechanism underlying the response of soybean anthers to HT is a relatively c...
Source: Journal of Proteomics - September 7, 2020 Category: Biochemistry Authors: Li J, Nadeem M, Chen L, Wang M, Wan M, Qiu L, Wang X Tags: J Proteomics Source Type: research

N-Glycome changes reflecting resistance to platinum-based chemotherapy in ovarian cancer.
Abstract A number of studies have reported aberrant glycosylation in connection with malignancy. Our investigation further expands on this topic through the examination of N-glycans, which could be associated with the resistance of advanced stage, high-grade non-mucinous ovarian cancer to platinum/taxane based chemotherapy. We used tissue samples of 83 ovarian cancer patients, randomly divided into two independent cohorts (basic and validation). Both groups involved either cases with/without postoperative tumor residue or the cases determined either resistant or sensitive to this chemotherapy. In the validation co...
Source: Journal of Proteomics - September 5, 2020 Category: Biochemistry Authors: Zahradnikova M, Ihnatova I, Lattova E, Uhrik L, Stuchlikova E, Nenutil R, Valik D, Nalezinska M, Chovanec J, Zdrahal Z, Vojtesek B, Hernychova L, Novotny MV Tags: J Proteomics Source Type: research

Technical report: Targeted proteomic analysis reveals enrichment of atypical ubiquitin chains in contractile murine tissues.
In this study, we optimised sample preparation and chromatographic separation of Ubiquitin peptides for Absolute Quantification by Parallel Reaction Monitoring (Ub-AQUA-PRM). Using this refined Ub-AQUA-PRM assay, we were able to quantify all ubiquitin chain types in 10-min LC-MS/MS runs. We used this method to determine the ubiquitin chain-linkage composition in murine bone marrow-derived macrophages and different mouse tissues. We could show tissue-specific differences in ubiquitin levels in murine tissues, with polyubiquitin chain types contributing a small proportion to the total pool of ubiquitin. Interestingly, we obs...
Source: Journal of Proteomics - September 5, 2020 Category: Biochemistry Authors: Heunis T, Lamoliatte F, Marín-Rubio JL, Dannora A, Trost M Tags: J Proteomics Source Type: research

Profiling of IgG N-glycome during mouse aging: Fucosylated diantennary glycans containing one Neu5Gc-linked LacNAc are highly associated with age.
In this study, we systemically investigated the changes in serum IgG N-glycome in C57BL/6 mice during aging at 12 time points (6-80 weeks) via ultraperformance liquid chromatography with fluorescence detection. The study demonstrated several important findings. First, four chromatographic IgG N-glycan peaks were identified for the first time, including a high-mannose glycan, a monoantennary glycan, and two afucosylated glycans. Second, most of the IgG glycan levels changed significantly and presented pronounced gender-related differences from 6 to 12 weeks. Interestingly, all the IgG glycan levels tended to be similar ...
Source: Journal of Proteomics - September 3, 2020 Category: Biochemistry Authors: Han J, Pan Y, Gu Y, Xu X, Zhao R, Sha J, Zhang R, Gu J, Ren S Tags: J Proteomics Source Type: research

Integrated transcriptome and phosphoproteome analyses reveal that fads2 is critical for maintaining body LC-PUFA homeostasis.
Abstract Fatty acid desaturate 2 (Fads2) is associated with many chronic diseases. Nevertheless, comprehensive researches on its role have not been performed. We here conducted an integrated analysis of long-chain polyunsaturated fatty acid (LC-PUFA) metabolism of fads2-deletion zebrafish (fads2-/-) by transcriptomics, proteomics and phosphoproteomics. Compared with wild type zebrafish (WT), fads2-/- showed significantly higher contents of hepatic linoleic acid (all-cis-9,12-C18:2), α-linolenic acid (all-cis-9,12,15-C18:3) and docosapetaenoic acid (all-cis-7,10,13,16,19-C22:5), and lower contents of γ-...
Source: Journal of Proteomics - September 3, 2020 Category: Biochemistry Authors: Zhao Y, Yang G, Wu N, Cao X, Gao J Tags: J Proteomics Source Type: research

Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell.
Abstract The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed prom...
Source: Journal of Proteomics - September 3, 2020 Category: Biochemistry Authors: Wang B, Hao J, Pan N, Wang Z, Chen Y, Wan C Tags: J Proteomics Source Type: research

Inhibition of proteasome reveals basal mitochondrial ubiquitination.
Abstract Strict quality control for mitochondrial proteins is necessary to ensure cell homeostasis. Two cellular pathways-Ubiquitin Proteasome System (UPS) and autophagy-contribute to mitochondrial homeostasis under stressful conditions. Here, we investigate changes to the mitochondria proteome and to the ubiquitin landscape at mitochondria in response to proteasome inhibition. Treatment of HeLa cells devoid of Parkin, the primary E3 ligase responsible for mitophagy, with proteasome inhibitor MG132 for a few hours caused mitochondrial oxidative stress and fragmentation, reduced energy output, and increased mitocho...
Source: Journal of Proteomics - August 31, 2020 Category: Biochemistry Authors: Sulkshane P, Duek I, Ram J, Thakur A, Reis N, Ziv T, Glickman MH Tags: J Proteomics Source Type: research

Integrated proteomic and transcriptomic analysis reveals that polymorphic shell colors vary with melanin synthesis in Bellamya purificata snail.
This study provides valuable genomic resources of B. purificata and improves our understanding of molecular mechanisms of biomineralization and shell color polymorphism in snail. PMID: 32871245 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - August 29, 2020 Category: Biochemistry Authors: Huang S, Jiang H, Zhang L, Gu Q, Wang W, Wen Y, Luo F, Jin W, Cao X Tags: J Proteomics Source Type: research

Comparative bioinformatics analysis of prognostic and differentially expressed genes in non-muscle and muscle invasive bladder cancer.
This study has systematically compared prognostic and differentially expressed genes between non-muscle (NMIBC) and muscle invasive (MIBC) bladder cancer, using an integrative bioinformatics approach. Many genes and biological functions were exclusively associated with either NMIBC or MIBC, suggesting that these disease subtypes could be driven by distinct molecular mechanisms. Particularly, prognostic and differentially expressed genes in MIBC were involved in cell migration and invasion, which can help to molecularly differentiate the NMIBC and MIBC subtypes. Moreover, the analysis of co-expression protein interaction ne...
Source: Journal of Proteomics - August 26, 2020 Category: Biochemistry Authors: Silva TA, Azevedo H Tags: J Proteomics Source Type: research

iTRAQ-based protein analysis provides insight into heterologous superinfection exclusion with TMV-43A against CMV in tobacco (Nicotiana benthamiana) plants.
This study provided insights into host responses involving multiple host pathways: photosynthesis, plant defence, carbon metabolism, translation and protein processing, fatty acid metabolism and amino acid biosynthesis. The findings provide a reference database for other viruses and increase our knowledge in host proteins that are correlated to superinfection. PMID: 32858166 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - August 25, 2020 Category: Biochemistry Authors: Yang X, Das PP, Oppenheimer P, Zhou G, Wong SM Tags: J Proteomics Source Type: research

Tissue- and isoform-specific protein complex analysis with natively processed bait proteins.
Abstract Protein-protein interaction analysis is an important tool to elucidate the function of proteins and protein complexes as well as their dynamic behavior. To date, the analysis of tissue- or even cell- or compartment-specific protein interactions is still relying on the availability of specific antibodies suited for immunoprecipitation. Here, we aimed at establishing a method that allows identification of protein interactions and complexes from intact tissues independent of specific, high affinity antibodies used for protein pull-down and isolation. Tagged bait proteins were expressed in human HEK293T cells...
Source: Journal of Proteomics - August 24, 2020 Category: Biochemistry Authors: Beyer T, Klose F, Kuret A, Hoffmann F, Lukowski R, Ueffing M, Boldt K Tags: J Proteomics Source Type: research

Venom variation in Bothrops asper lineages from north-western South America.
Abstract Bothrops asper is a venomous pitviper that is widely distributed and of clinical importance in Mesoamerica and northern South America, where it is responsible for 50-80% of all envenomations by Viperidae species. Previous work suggests that B. asper has a complex phylogeographic structure, with the existence of multiple evolutionarily distinct lineages, particularly in the inter-Andean valleys of north South America. To explore the impact of the evolutionary history of B. asper on venom composition, we have investigated geographic variation in the venom proteome of this species from the populations from t...
Source: Journal of Proteomics - August 20, 2020 Category: Biochemistry Authors: Mora-Obando D, Salazar-Valenzuela D, Pla D, Lomonte B, Guerrero-Vargas JA, Ayerbe S, Gibbs HL, Calvete JJ Tags: J Proteomics Source Type: research

Mitochondrial proteomic analysis reveals that proteins relate to oxidoreductase activity play a central role in pollen fertility in cotton.
PMID: 32830049 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - August 20, 2020 Category: Biochemistry Authors: Nie H, Cheng C, Hua J Tags: J Proteomics Source Type: research

Proteomic analysis of bacterial communities associated with atopic dermatitis.
Abstract Atopic dermatitis (AD) is a relapsing, chronic, and inflammatory skin disorder. Its causes remain unclear. Here, we reported the first proteome study of the bacterial community in AD patients. Bacterial community in 7 patients and 1 healthy control using bottom-up proteomics were examined starting with in-solution digestion followed by purification steps with subsequent analysis using LC-MS/MS and ended with data processing and bioinformatic analysis. Overall, great bacterial changes between patient samples and healthy one were noticed with the presence of Staphylococcus aureus, Aeromonas hydrophila, and ...
Source: Journal of Proteomics - August 18, 2020 Category: Biochemistry Authors: Kandil A, Hanora A, Azab M, Enany S Tags: J Proteomics Source Type: research

Neurobiology of environmental enrichment in pigs: Changes in monoaminergic neurotransmitters in several brain areas and in the hippocampal proteome.
This study expands the knowledge about the biological basis of animal welfare-promoting actions. PMID: 32814107 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - August 16, 2020 Category: Biochemistry Authors: Arroyo L, Valent D, Carreras R, Pato R, Sabrià J, Velarde A, Bassols A Tags: J Proteomics Source Type: research

Plasma fibrin clot proteomics in patients with acute pulmonary embolism: Association with clot properties.
Abstract It has been reported that 476 proteins can be detected in plasma fibrin clots from patients with venous thromboembolism. Plasma fibrin clots proteomic composition in relation to their properties has not been studied in acute pulmonary embolism (PE). Clots generated from plasma of 20 PE patients and 20 healthy controls were assessed using mass spectrometry, clot permeability (Ks), and clot lysis time (CLT). The proteomic composition of plasma fibrin clots from acute PE patients differed from that of control subjects in regard to 198 clot-bound proteins. In the acute PE group, we observed increased clot-bou...
Source: Journal of Proteomics - August 15, 2020 Category: Biochemistry Authors: Bryk A, Natorska J, Ząbczyk M, Zettl K, Wiśniewski JR, Undas A Tags: J Proteomics Source Type: research

Quantitative proteomics and reverse engineer analysis identified plasma exosome derived protein markers related to osteoporosis.
Abstract Alongside an aging population, osteoporosis has become increasingly common, representing a major public health problem. Human blood provides the predominant matrix for pathological targets underlining disease mechanisms. In the present study, the protein profiles of blood plasma exosomes from patients with osteoporosis, osteopenia, and those with normal bone mass were compared. The aim of the study was to search for potential novel diagnostic/therapeutic targets for further investigation in osteoporosis. A total of 60 participants were included from the PLAGH Hip Fracture Database. Quantitative proteomics...
Source: Journal of Proteomics - August 14, 2020 Category: Biochemistry Authors: Chen M, Li Y, Lv H, Yin P, Zhang L, Tang P Tags: J Proteomics Source Type: research

Transcriptomics and proteomics-based analysis of heterosis on main economic traits of silkworm, Bombyx mori.
In this study, the heterosis of silkworm in the aspects of body weight, silk gland and cocoon weight was investigated by means of silkworm hybridization and multi-omics approaches, including transcriptome and proteome. The results showed that heterosis of silkworm body weight, silk gland and cocoon weight was overdominant, but only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Combined analysis obtained six up-regulated genes and four down-regulated genes that were consistent both in transcriptome and proteome. Gene functional enrichment analysis indicated that most up-regu...
Source: Journal of Proteomics - August 14, 2020 Category: Biochemistry Authors: Xiao R, Yuan Y, Zhu F, He S, Ge Q, Wang X, Taha R, Chen K Tags: J Proteomics Source Type: research

Label-free comparative proteomic and physiological analysis provides insight into leaf color variation of the golden-yellow leaf mutant of Lagerstroemia indica.
Abstract GL1 is a golden-yellow leaf mutant that cultivated from natural bud-mutation of Lagerstroemia indica and has a very low level of photosynthetic pigment under sunlight. GL1 can gradually increase its pigment content and turn into pale-green leaf when shading under sunshade net (referred as Re-GL1). The mechanisms that cause leaf color variation are complicated and are not still unclear. Here, we have used a label-free comparative proteomics to investigate differences in proteins abundance and analyze the specific biological process associated with mechanisms of leaf color variation in GL1. A total of 245 a...
Source: Journal of Proteomics - August 14, 2020 Category: Biochemistry Authors: Li S, Wang S, Wang P, Gao L, Yang R, Li Y Tags: J Proteomics Source Type: research

Dynamics of protein synthesis in the initial steps of strobilation in the model cestode parasite Mesocestoides corti (syn. vogae).
Abstract Mesocestoides corti (syn. vogae) is a useful model for developmental studies of platyhelminth parasites of the Cestoda class, such as Taenia spp. or Echinococcus spp. It has been used in studies to characterize cestode strobilation, i.e. the development of larvae into adult worms. So far, little is known about the initial molecular events involved in cestode strobilation and, therefore, we carried out a study to characterize newly synthesized (NS) proteins upon strobilation induction. An approach based on bioorthogonal noncanonical amino acid tagging and mass spectrometry was used to label, isolate, ident...
Source: Journal of Proteomics - August 13, 2020 Category: Biochemistry Authors: de Lima JC, Floriani MA, Debarba JA, Paludo GP, Monteiro KM, Moura H, Barr JR, Zaha A, Ferreira HB Tags: J Proteomics Source Type: research

Proteomic profile of human dental follicle stem cells and apical papilla stem cells.
This study expands our understanding on the molecular mechanisms of tooth development and regeneration, and provide basic support for dental stem cells in clinical applications such as neurological and immune diseases. PMID: 32800794 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - August 12, 2020 Category: Biochemistry Authors: Lei T, Zhang X, Chen P, Li Q, Du H Tags: J Proteomics Source Type: research

Comparison between the proteome of Escherichia coli single colony and during liquid culture.
In this study, we compare the observed proteome of E. coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. By using label-free quantitative analysis we demonstrate that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture with an overlap of 68% of proteins between the two culture conditions. Our analysis further reveal the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated ex...
Source: Journal of Proteomics - August 12, 2020 Category: Biochemistry Authors: Fortuin S, Nel AJM, Blackburn JM, Soares NC Tags: J Proteomics Source Type: research

Comparative label-free proteomic analysis of equine osteochondrotic chondrocytes.
This study provides a comprehensive characterization of proteomic alterations occurring in equine osteochondrotic chondrocytes, the only resident cell type that modulates differentiation and maturation of articular cartilage. The results evidenced alterations in abundance of proteins involved in functional and metabolic pathways and in extracellular matrix remodelling. These findings could help clarify some molecular aspects of osteochondrosis and open new fields of research for elucidating the pathogenesis of this disease. PMID: 32768606 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - August 5, 2020 Category: Biochemistry Authors: Chiaradia E, Pepe M, Sassi P, Mohren R, Orvietani PL, Paolantoni M, Tognoloni A, Sforna M, Eveque M, Tombolesi N, Cillero-Pastor B Tags: J Proteomics Source Type: research

An input-controlled model system for identification of MHC bound peptides enabling laboratory comparisons of immunopeptidome experiments.
Abstract Characterization of MHC-bound peptides by mass spectrometry (MS) is an essential technique for immunologic studies. Many efforts have been made to quantify the number of MHC-presented ligands by MS and to define the limits of detection of a specific MHC ligand. However, these experiments are often complex and comparisons across different laboratories are challenging. Therefore, we compared and orthogonally validated quantitation of peptide:MHC complexes by radioimmunoassay and flow cytometry using TCR mimic antibodies in three model systems to establish a method to control the experimental input of peptid...
Source: Journal of Proteomics - August 3, 2020 Category: Biochemistry Authors: Klatt MG, Aretz ZEH, Curcio M, Gejman RS, Jones HF, Scheinberg DA Tags: J Proteomics Source Type: research

iTRAQ-based quantitative phosphoproteomics provides insights into the metabolic and physiological responses of a carnivorous marine fish (Nibea albiflora) fed a linseed oil-rich diet.
Abstract The limited production of fish oil (FO) cannot meet the increasing demand of the aqua-feed industry. Accordingly, the replacement of FO with sustainable alternatives such as vegetable oils has become imperative. Linseed oil (LO), which has an abundance of α-linolenic acid (ALA), is a promising FO alternative. Nevertheless, high dietary LO inclusion generally causes abnormal hepatic lipid accumulation and growth retardation across carnivorous marine fish species. Previous studies have attempted to elucidate the mechanisms with regard to gene and protein levels; however, little is known about posttran...
Source: Journal of Proteomics - July 29, 2020 Category: Biochemistry Authors: Qin G, Xu D, Lou B, Chen R, Wang L, Tan P Tags: J Proteomics Source Type: research

Analysis of the proteins secreted by Trichoderma harzianum P49P11 under carbon-limited conditions.
Abstract The wild type strain Trichoderma harzianum was able to synthesize enzymes that can catalyse the hydrolysis of p-nitrophenyl-β-D-glucopyranoside (PNPGase) in glucose-limited chemostat cultures. Fructose/glucose and sucrose conditions provided low levels of PNPGase activity. To investigate whether under these conditions other enzymes were produced, a shotgun proteomics analysis of their supernatants was performed. The analysis has indicated that the different carbon sources used influenced the amounts of proteins secreted including 1,3-beta-glucanosyltransferase, alpha-1,2-mannosidase, alpha-galactosid...
Source: Journal of Proteomics - July 28, 2020 Category: Biochemistry Authors: Gelain L, da Cruz Pradella JG, da Costa AC, van der Wielen L, van Gulik WM Tags: J Proteomics Source Type: research

Plasmodium berghei LAPs form an extended protein complex that facilitates crystalloid targeting and biogenesis.
This study sheds important new light on the molecular composition of the crystalloid, an enigmatic parasite organelle that is essential for sporozoite formation and transmission from the insect to the vertebrate host. Our findings provide new mechanistic insight into how proteins are delivered to the crystalloid, and indicate that the molecular mechanisms that underlie crystalloid function are complex, involving multiple protein families unique to Plasmodium and closely related organisms. The many new crystalloid proteins identified will form a useful starting point for future studies aimed at unravelling how the crystallo...
Source: Journal of Proteomics - July 28, 2020 Category: Biochemistry Authors: Tremp AZ, Saeed S, Sharma V, Lasonder E, Dessens JT Tags: J Proteomics Source Type: research

Proteome and phosphoproteome profiling reveals the regulation mechanism of hibernation in a freshwater leech (Whitmania pigra).
In this study, we detected the effects of hibernation on the proteome and phosphoproteome of the leech Whitmania pigra. A total of 2184 proteins and 2598 sites were quantified. Deep-hibernation resulted in 85 up-regulated and 107 down-regulated proteins and 318 up-regulated and 204 down-regulated phosphosites using a 1.5-fold threshold (P
Source: Journal of Proteomics - July 28, 2020 Category: Biochemistry Authors: Shi H, Wang J, Liu F, Hu X, Lu Y, Yan S, Dai D, Yang X, Zhu Z, Guo Q Tags: J Proteomics Source Type: research

Characterization of differentially expressed plasma proteins in patients with acute myocardial infarction.
Abstract Acute myocardial infarction (AMI) remains a leading cause of morbidity and mortality worldwide. Novel biomarkers are needed to identify NSTEMI in AMI patients. The study objective was to use proteomics to identify novel plasma biomarkers for STEMI and NSTEMI patients. iTRAQ analysis was performed on pooled samples from 8 healthy controls and 12 STEMI and 12 NSTEMI patients. Bioinformatics analysis identified 95 differentially expressed proteins that were differentially expressed in the plasma of AMI patients and healthy controls; 28 of these proteins were found in STEMI/Con (22 upregulated and 6 downregul...
Source: Journal of Proteomics - July 28, 2020 Category: Biochemistry Authors: Pan Y, Wang L, Xie Y, Tan Y, Chang C, Qiu X, Li X Tags: J Proteomics Source Type: research

Identification of p115 as a novel ACSL4 interacting protein and its role in regulating ACSL4 degradation.
This study is the first report of a possible coordination of the protein secretion pathway and the UPP in regulating a key metabolic enzyme. Our study lays the foundation to this unique crosstalk between the two major cellular pathways- secretion and protein degradation and opens up a new avenue to explore this partnership in controlling hepatic lipid metabolism. Overall, the complete elucidation of the AA-mediated ACSL4 regulation will help identify key targets in participating pathways that can be further studied for the development of therapeutics against diseases such as NAFLD, NASH and hepatocarcinoma, which are assoc...
Source: Journal of Proteomics - July 28, 2020 Category: Biochemistry Authors: Sen P, Kan CFK, Singh AB, Rius M, Kraemer FB, Sztul E, Liu J Tags: J Proteomics Source Type: research

Integration of quantitative proteomics and metabolomics reveals tissue hypoxia mechanisms in an ischemic-hypoxic rat model.
Abstract Tissues hypoxia caused by hemorrhage is a common complication in many clinical diseases. However, its pathological mechanism remains largely unknown. To partly address this issue, an ischemic-hypoxic rat model was established and the plasma proteomic and metabolic profiles were quantified and analyzed using TMT-based quantitative proteomics and metabolomics. The analysis revealed a total of 177 differentially expressed proteins and 32 metabolites that were uniquely altered in the hypoxic rat plasma, compared to the control. Bioinformatics analysis showed that these altered proteins and metabolites were in...
Source: Journal of Proteomics - July 28, 2020 Category: Biochemistry Authors: He R, Kong Y, Fang P, Li L, Shi H, Liu Z Tags: J Proteomics Source Type: research

Diversity and genome mapping assessment of disordered and functional domains in trypanosomatids.
This study depicts the potential impact of the proximity between protein structural disorder and functional domains in the post-transcriptional regulation of pathogenic versus human non-pathogenic trypanosomatids. Our results revealed a significant statistical relationship between the genome structural locations of these two variables and disordered regions appearing more frequently at upstream or downstream positions of the CDD locus domain. This flexibility feature would maintain structural accessibility of functional sites for post-translational modifications, shedding light into this important aspect of parasite biolog...
Source: Journal of Proteomics - July 25, 2020 Category: Biochemistry Authors: Avelar GST, Gonçalves LO, Guimarães FG, Guimarães PAS, do Nascimento Rocha LG, Carvalho MGR, de Melo Resende D, Ruiz JC Tags: J Proteomics Source Type: research

Shell palaeoproteomics: First application of peptide mass fingerprinting for the rapid identification of mollusc shells in archaeology.
This study aims to obtain molecular barcodes based on peptide mass fingerprints, (PMFs) of intracrystalline proteins, in order to obtain shell identification. Palaeoproteomic applications on shells are challenging, due to low concentration of molluscan proteins and an incomplete understanding of their sequences. We explore different approaches for protein extraction from small-size samples (
Source: Journal of Proteomics - July 23, 2020 Category: Biochemistry Authors: Sakalauskaite J, Marin F, Pergolizzi B, Demarchi B Tags: J Proteomics Source Type: research

Identification of Lysinibacillus sphaericus Binary toxin binding proteins in a malarial mosquito cell line by proteomics: A novel approach towards improving mosquito control.
This study was aimed at identification of mosquito cell proteins binding Bin toxin. Results showed that purified toxin was toxic to Anopheles gambiae larvae and Ag55 cultured cells. Clathrin heavy chain (an endocytosis protein) and glycolytic enzymes such as pyruvate kinase, enolase and dihydrolipoamide dehydrogenase were identified as binders of Bin toxin. The viability of Ag55 cells in the presence of endocytosis inhibitor, pitstop2, was significantly decreased upon Bin treatment, while the inhibitor chlorpromazine did not affect Bin toxicity. Bin toxin treatment decreased ATP production and mitochondrial respiration in ...
Source: Journal of Proteomics - July 23, 2020 Category: Biochemistry Authors: Riaz MA, Adang MJ, Hua G, Rezende TMT, Rezende AM, Shen GM Tags: J Proteomics Source Type: research

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context.
da AM Abstract The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and p...
Source: Journal of Proteomics - July 23, 2020 Category: Biochemistry Authors: Ribeiro DM, Salama A, Vitor ACM, Arguello A, Moncau CT, Santos EM, Caja G, de Oliveira JS, Balieiro JCC, Hernández-Castellano LE, Zachut M, Poleti MD, Castro N, Alves SP, Almeida AM Tags: J Proteomics Source Type: research

Functional milk proteome analysis of genetically diverse goats from different agro climatic regions.
Abstract Goat milk, a choice of substitution to mother's milk for its composition, fulfils nutritional requirement of infants, pregnant mothers and older people. The present study was carried out to unravel the milk proteome profiles from geographically and genetically diverse goat breeds by gel based 2DE and nLC-MS/MS. A total of 1307 functional proteins comprising casein and other low abundance proteins were identified. Gene annotations revealed that the majority of the proteins were involved in binding function, catalytic activity and structural molecules and localised in nucleus and membrane. The distinguished...
Source: Journal of Proteomics - July 22, 2020 Category: Biochemistry Authors: Verma M, Dige MS, Gautam D, De S, Rout PK Tags: J Proteomics Source Type: research

Influence of tetraconazole on the proteome profile of Saccharomyces cerevisiae Lalvin T73 ™ strain.
Influence of tetraconazole on the proteome profile of Saccharomyces cerevisiae Lalvin T73™ strain. J Proteomics. 2020 Jul 22;:103915 Authors: Briz-Cid N, Pose-Juan E, Nicoletti M, Simal-Gándara J, Fasoli E, Rial-Otero R Abstract This work aimed to evaluate the modifications on the proteome profile of Saccharomyces cerevisiae T73™ strain as a consequence of its adaptive response to the presence of tetraconazole molecules in the fermentation medium. Pasteurised grape juices were separately supplemented with tetraconazole or a commercial formulation containing 12.5% w/v of tetraconazol...
Source: Journal of Proteomics - July 22, 2020 Category: Biochemistry Authors: Briz-Cid N, Pose-Juan E, Nicoletti M, Simal-Gándara J, Fasoli E, Rial-Otero R Tags: J Proteomics Source Type: research

Revelation of AbfR in regulation of mismatch repair and energy metabolism in S. epidermidis by integrated proteomic and metabolomic analysis.
This study revealed the regulatory networks of the transcription factor AbfR from a multi-omics view and demonstrated that AbfR played a broad role in not only mismatch repair but also energy metabolism, enabling S. epidermidis to constantly sense and adapt to environmental stress. SIGNIFICANCE: Staphylococcus epidermidis has emerged as a major nosocomial infection causing pathogen. AbfR, a transcription factor of S. epidermidis, plays an important role in oxidative stress, cell aggregation, and biofilm formation; however, the regulatory mechanism of AbfR is unknown. Using proteomic and metabolomic approaches, this study u...
Source: Journal of Proteomics - July 22, 2020 Category: Biochemistry Authors: Gu L, Liu X, Wang YQ, Zhou YT, Zhu HW, Huang J, Lan LF, Zheng J, Yang CG, Zhou H Tags: J Proteomics Source Type: research

Nisin influence on the expression of Listeria monocytogenes surface proteins.
Abstract In this work, a comparative analysis of the peripheral cell component (PCC) proteins of Listeria monocytogenes was carried out. The study was conducted on two set of samples consisting of bacteria treated with sub-lethal concentration of nisin and untreated bacteria as control. PCC proteins were extracted by Tris-Urea-EDTA treatment and then subjected to trypsin digestion and mass spectrometry analysis. The whole cell proteome was analyzed through label-free quantitative proteomics approach. Proteomic analysis was carried out using OrbiTrap Mass Spectrometer coupled to nanoflow liquid chromatography. The ...
Source: Journal of Proteomics - July 21, 2020 Category: Biochemistry Authors: Stincone P, Miyamoto KN, Timbe PPR, Lieske I, Brandelli A Tags: J Proteomics Source Type: research

Proteomic characterization of a trauma-based rat model of heterotopic ossification identifies interactive signaling networks as potential therapeutic targets.
This study has used global unbiased mass spectrometry proteomic approaches, validated by western immunoblots, to interrogate skeletal muscle tissues obtained from a highly reproducible rat model of trauma induced HO. During early the phase of HO development, statistically significant modulation of proteins within the following pathways was identified: coagulation, cyclic AMP, extracellular matrix, immunity/inflammation, NADH metabolism, TGFβ. These metabolic proteins and pathways have the potential to serve as diagnostic, prognostic, and therapeutic targets for this devastating orthopedic condition that has considerab...
Source: Journal of Proteomics - July 21, 2020 Category: Biochemistry Authors: Hoover ME, Martin EC, Llamas CB, Qureshi A, Davis TA, Gimble JM, Freitas MA Tags: J Proteomics Source Type: research

Targeted mass spectrometry for Serum Amyloid A (SAA) isoform profiling in sequential blood samples from experimentally Staphylococcus aureus infected pigs.
PMH Abstract Serum amyloid A (SAA) is a well-described acute phase protein induced during the acute phase response (APR) to infection. Four isoform specific genes are found in most mammals. Depending on species, SAA3 and SAA4 are ge0nerally preferentially expressed extrahepatically whereas SAA1 and SAA2 are hepatic isoforms dominating the SAA serum pool. Little is known about how specific infections affect the serum SAA isoform profile, as SAA isoform discriminating antibodies are not generally available. An antibody independent, quantitative targeted MS method (Selected Reaction Monitoring, SRM) based on availabl...
Source: Journal of Proteomics - July 20, 2020 Category: Biochemistry Authors: Leuchsenring AB, Karlsson C, Bundgaard L, Malmström J, Heegaard PMH Tags: J Proteomics Source Type: research

Global transcriptomic and proteomics analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress.
This study represents an integrated proteomic and transcriptomic analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. Differentially expressed proteins and genes were identified between the proteome and transcriptome of L. plantarum Y44 under different AAPH stress. AAPH-induced response of L. plantarum Y44 appears to be primarily based on ROS scavenging, DNA repair, highly remodeled cell surface and specific metabolic processes. The knowledge about these proteomes and transcriptomes provides significant insights into the oxidative stress response of Lactobaci...
Source: Journal of Proteomics - July 15, 2020 Category: Biochemistry Authors: Gao Y, Liu Y, Ma F, Sun M, Mu G, Tuo Y Tags: J Proteomics Source Type: research

Comprehensive analysis of protein expression levels and phosphorylation levels in host skin in response to tick (Haemaphysalis longicornis) bite.
In this study, we found that tick bites cause the host hair loss and regeneration disorders. For resisting tick bite, the host activates the immune response and initiates vascular repair and wound-healing systems. In addition, some phosphorylated proteins promote host immunity and vascular repair. These results can help us further understand the defence mechanism of the host against tick bites, provide a basis for the development of an anti-tick vaccine, the development of anti-tick drugs, and the diagnosis of tick-borne diseases. PMID: 32682108 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - July 15, 2020 Category: Biochemistry Authors: Zhang X, Zhang B, Masoudi A, Wang X, Xue X, Li M, Xiao Q, Wang M, Liu J, Wang H Tags: J Proteomics Source Type: research

Integrated analysis of sialotranscriptome and sialoproteome of the brown dog tick Rhipicephalus sanguineus (s.l.): Insights into gene expression during blood feeding.
Abstract Tick salivary glands secrete a complex saliva into their hosts which modulates vertebrate hemostasis, immunity and tissue repair mechanisms. Transcriptomic studies revealed a large number of transcripts coding for structural and secreted protein products in a single tick species. These transcripts are organized in several large families according to their products. Not all transcripts are expressed at the same time, transcription profile switches at intervals, characterizing the phenomenon of "sialome switching". In this work, using transcriptomic and proteomic analysis we explored the sialome o...
Source: Journal of Proteomics - July 13, 2020 Category: Biochemistry Authors: Tirloni L, Lu S, Calvo E, Sabadin G, Di Maggio LS, Suzuki M, Nardone G, da Silva Vaz I, Ribeiro JMC Tags: J Proteomics Source Type: research

Proteomic analysis of exosomes derived from procyclic and metacyclic-like cultured Leishmania infantum chagasi.
YM Abstract Leishmania infantum chagasi is the primary etiological agent of visceral leishmaniasis in Latin America, a lethal disease that afflicts hundreds of thousands of people worldwide every year. Previous studies have shown that the parasite releases microvesicles known as exosomes, which prolong and exacerbate infection in the vertebrate vector. However, little is known of their role in the insect vector, the sand fly Lutzomyia longipalpis. Exosomes were isolated from cultured L. i. chagasi in logarithmic (procyclic) (LOG) and stationary phase (metacyclic-like) (STAT) growth stages, which are the parasite ...
Source: Journal of Proteomics - July 13, 2020 Category: Biochemistry Authors: Forrest DM, Batista M, Marchini FK, Tempone AJ, Traub-Csekö YM Tags: J Proteomics Source Type: research