protein identification
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Dairy ◽  
2022 ◽  
Vol 3 (1) ◽  
pp. 47-58
Author(s):  
Lina Zhang ◽  
Sjef Boeren ◽  
Jeroen Heck ◽  
Jacques Vervoort ◽  
Peng Zhou ◽  
...  

Milk contains all nutrients needed for development of calves. One important group of components responsible for this are the milk proteins. Variation due to feed or animal health, has been studied for the most abundant milk proteins. The aim of this study was to determine the variation between and within cows for their milk serum proteome. Sample Set 1 was collected from Holstein Friesian (HF) cows between November 2011 and March 2012 and prepared using filter aided sample preparation (FASP) followed by LC-MS/MS for protein identification and quantification. The results showed that the milk serum proteome was very constant in mid lactation (four cows at five time points, p > 0.05) between 3 and 6 months in lactation. Sample Set 2 was collected from HF cows in Dec 2012 and analyzed using FASP and dimethyl labeling followed by LC-MS/MS. Significant variation in the milk serum proteome (p < 0.05) between 17 individual cows was found in Sample Set 2. The most variable proteins were immune-related proteins, which may reflect the health status of the individual cow. On the other hand, proteins related to nutrient synthesis and transport were relatively constant, indicating the importance of milk in providing a stable supply of nutrients to the neonate. In conclusion, the milk serum proteome was stable over mid lactation, but differed significantly between individuals, especially in immune-related proteins.


2022 ◽  
Vol 12 ◽  
Author(s):  
Theo Tasoulis ◽  
Tara L. Pukala ◽  
Geoffrey K. Isbister

Understanding snake venom proteomes is becoming increasingly important to understand snake venom biology, evolution and especially clinical effects of venoms and approaches to antivenom development. To explore the current state of snake venom proteomics and transcriptomics we investigated venom proteomic methods, associations between methodological and biological variability and the diversity and abundance of protein families. We reviewed available studies on snake venom proteomes from September 2017 to April 2021. This included 81 studies characterising venom proteomes of 79 snake species, providing data on relative toxin abundance for 70 species and toxin diversity (number of different toxins) for 37 species. Methodologies utilised in these studies were summarised and compared. Several comparative studies showed that preliminary decomplexation of crude venom by chromatography leads to increased protein identification, as does the use of transcriptomics. Combining different methodological strategies in venomic approaches appears to maximize proteome coverage. 48% of studies used the RP-HPLC →1D SDS-PAGE →in-gel trypsin digestion → ESI -LC-MS/MS pathway. Protein quantification by MS1-based spectral intensity was used twice as commonly as MS2-based spectral counting (33–15 studies). Total toxin diversity was 25–225 toxins/species, with a median of 48. The relative mean abundance of the four dominant protein families was for elapids; 3FTx–52%, PLA2–27%, SVMP–2.8%, and SVSP–0.1%, and for vipers: 3FTx–0.5%, PLA2–24%, SVMP–27%, and SVSP–12%. Viper venoms were compositionally more complex than elapid venoms in terms of number of protein families making up most of the venom, in contrast, elapid venoms were made up of fewer, but more toxin diverse, protein families. No relationship was observed between relative toxin diversity and abundance. For equivalent comparisons to be made between studies, there is a need to clarify the differences between methodological approaches and for acceptance of a standardised protein classification, nomenclature and reporting procedure. Correctly measuring and comparing toxin diversity and abundance is essential for understanding biological, clinical and evolutionary implications of snake venom composition.


2022 ◽  
Vol 8 ◽  
Author(s):  
Guoquan Chen ◽  
Ziyang Tan ◽  
Yansheng Liu ◽  
Tingting Weng ◽  
Liqun Xia ◽  
...  

Fish nocardiosis is a chronic, systemic, granulomatous disease in aquaculture. Nocardia seriolae has been reported to be one of the main pathogenic bacteria of fish nocardiosis. There are few studies on the associated virulence factors and pathogenesis of N. seriolae. Alanine dehydrogenase (ALD), which may be a secreted protein, was discovered by analysis using bioinformatics methods throughout the whole genomic sequence of N. seriolae. Nevertheless, the roles of ALD and its homologs in the pathogenesis of N. seriolae are not demonstrated. In this study, the function of N. seriolae ALD (NsALD) was preliminarily investigated by gene cloning, host cell subcellular localization, secreted protein identification, and cell apoptosis detection. Identification of the extracellular products of N. seriolae via mass spectrometry (MS) analysis revealed that NsALD is a secreted protein. In addition, subcellular localization of NsALD-GFP recombinant protein in fathead minnow (FHM) cells showed that the strong green fluorescence co-localized with the mitochondria. Moreover, apoptosis assays demonstrated that the overexpression of NsALD induces apoptosis in FHM cells. This study may lay the foundation for further exploration of the function of NsALD and facilitate further understanding of the pathogenic mechanism and the associated virulence factors of N. seriolae.


2022 ◽  
Vol 60 (2) ◽  
Author(s):  
Valerija Šimunec ◽  
Rea Bertoša ◽  
Anita Šporec ◽  
Igor Lukić ◽  
Diana Nejašmić ◽  
...  

Research background. Baranjski kulen is one of the most popular fermented meat sausages originating from Croatia. It has protected geographical indication, and is traditionally produced in the Baranja region of Croatia. Kulenova seka is a fermented sausage very similar to Baranjski kulen, but it has a different caliber and consequently, a shorter time of production. In recent decades, due to the high demand and popularity of these products, industrially produced Baranjski kulen and Kulenova seka have become available on the market. This work aims to identify specific characteristics of traditional and industrial sausages, Baranjski kulen and Kulenova seka on proteome, peptidome and metabolome level which could potentially lead to better optimization of the industrial production process in order to obtain an equivalent to the traditional product. Experimental approach. Protein profiles of Baranjski kulen and Kulenova seka (traditional and industrial) were analysed using two-dimensional gel electrophoresis followed by differential display analysis and protein identification using mass spectrometry. Peptidomics profiling analysis was performed via liquid chromatography-tandem mass spectrometry. Furthermore, aroma profiles were investigated via headspace solid phase microextraction and gas chromatography-mass spectrometry. Results and conclusions. The major identified characteristics of each product were: industrial Baranjski kulen - specific degradation of MYH1 and TITIN, overabundance of stress-related proteins and increased phenylalanine degradation; traditional Baranjski kulen - decreased concentration of phenylalanine and overabundance of ALDOA and CAH3; industrial Kulenova seka - specific MYH4 and HBA degradation process; traditional Kulenova seka - overabundance of DPYD and MYL1, degradation of ALBU and MYG, decreased concentrations of almost all free amino acids and increased amounts of smoke derived volatile compounds. Novelty and scientific contribution. In this preliminary communication, the first insights into protein degradation processes and generation of peptides, free amino acids and aroma compounds of industrial and traditional Baranjski kulen and Kulenova seka are presented. Although further research is needed to draw general conclusions, the specific profile of proteins, peptides, amino acids, and volatile compounds represents the first step in the industrial production of sausages that meet the characteristics of traditional flavour.


SPERMOVA ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 83-95
Author(s):  
María Alejandra Cardozo ◽  
◽  
Jaime Antonio Cardozo ◽  
Fabian Rueda

Bovine livestock is one of the most important economic and social sectors for many countries. In this sense, the development of strategies to improve reproductive bull fertility and reproduction rates is relevant. It's highlighted the role of seminal plasma proteins (SPP) in reproductive fertility, so it has found close relationships among studies on the structure and biological activity of SPP, with seminal quality, including viability, sperm motility, and morphology. In addition, they have been found to regulate sperm functions such as capacitation, acrosome reaction, and they are even related to protecting sperm against thermal and oxidative stress. Moreover, the methods of separation and protein identification and their contribution to characterizing the bovine SP proteome should be also highlighted. In this sense, the most recent studies have been directed towards developing supplements with SPP that improve quality sperm subjected to cryopreservation processes. Research has begun and should forward to establish how the networks or sets of proteins are related to the functioning and fertility of sperm, the search for biomarkers of fertility, and the use of proteins in biotechnological processes, to increase efficiency reproductive.


2021 ◽  
Vol 1 ◽  
pp. 22-24
Author(s):  
Monika Mani ◽  
Sivasubramaniyan Gnanaskandan ◽  
Shanthi Vijayaraghavan ◽  
Padma Srikanth

Hepatitis B virus (HBV) is a global health concern with 350 million chronic carriers. With respect to HBV India is classified as an intermediate endemic country. The disease progression may be due to many viral factors including HBV viral load, HBe antigen, genotype, mutations in polymerase gene, and X gene. In this case, the individual was a treatment naïve chronic HBV carrier. The reverse transcriptase gene and X gene were sequenced and mutations were analyzed. The individual had D3 subgenotype. rt80I was identified in reverse transcriptase and A102V in HBx protein. Identification of genotype and mutations in reverse transcriptase/X gene may help in predicting and improving the clinical outcomes.


Author(s):  
Nor Aisyah Mohd Zain ◽  
◽  
Sity Aishah Mansur ◽  
‘Aisyah Mohamed Rehan ◽  
◽  
...  

Coronavirus infectious disease 2019 (COVID-19) is a global pandemic declared by the World Health Organization (WHO) in March 2020. This emerging infectious disease is rapidly transmitted and does not only pose a global threat to public health but also badly affects the economy. At present, there is no effective drug to treat COVID-19, leading to a significant challenge upon current global attempts at restraining the outbreak. There are several currently available drugs, also considered as the repurposed drugs are in use for treatment against COVID-19. However, these drugs are not as efficient as it is hoped. Therefore, this study is conducted to further explore into other established antivirus that could function better for COVID-19 treatment. In addition, the pathways that associated with the drugs are identified and potential targeted proteins for the repurposed drugs are also pointed out. The articles for review were selected from several search engine databases, which are ScienceDirect, SpringerLink, PubMed, and Scopus including the keywords COVID-19, SARS, MERS, potential pathways for antiviral drugs as well as repurposed drugs, with more than 50 primary research articles identified. Findings and analysis have discovered potential repurposed drugs that could be used for COVID-19, namely bisoxatin, nitazoxanide and teicoplanin which could be involved in corona-related pathways. Meanwhile, the associated pathways are JAK-STAT, Neprilysin (NEP) and cGAS-STING that counteract excessive immune response and act as a medium for the drugs to access antiviral activities. The repurposed drugs target protein identification is also a critical significance, and it was found that S-protein, TMPRSS2, RdRp and RDB which are the signalling protein can be interrupted by the repurposed drugs, presenting a promising antivirus against SARS-CoV-2. It is concluded that this study will provide information to assist logical design of the repurposed drug for its effectiveness as antivirus against COVID-19


Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6224
Author(s):  
Natália Almeida ◽  
Jimmy Rodriguez ◽  
Indira Pla Parada ◽  
Yasset Perez-Riverol ◽  
Nicole Woldmar ◽  
...  

Plasma analysis by mass spectrometry-based proteomics remains a challenge due to its large dynamic range of 10 orders in magnitude. We created a methodology for protein identification known as Wise MS Transfer (WiMT). Melanoma plasma samples from biobank archives were directly analyzed using simple sample preparation. WiMT is based on MS1 features between several MS runs together with custom protein databases for ID generation. This entails a multi-level dynamic protein database with different immunodepletion strategies by applying single-shot proteomics. The highest number of melanoma plasma proteins from undepleted and unfractionated plasma was reported, mapping >1200 proteins from >10,000 protein sequences with confirmed significance scoring. Of these, more than 660 proteins were annotated by WiMT from the resulting ~5800 protein sequences. We could verify 4000 proteins by MS1t analysis from HeLA extracts. The WiMT platform provided an output in which 12 previously well-known candidate markers were identified. We also identified low-abundant proteins with functions related to (i) cell signaling, (ii) immune system regulators, and (iii) proteins regulating folding, sorting, and degradation, as well as (iv) vesicular transport proteins. WiMT holds the potential for use in large-scale screening studies with simple sample preparation, and can lead to the discovery of novel proteins with key melanoma disease functions.


2021 ◽  
Author(s):  
◽  
Garima Dobhal

<p>Nano-sized extracellular vesicles, released by most types of cells, contain information about the cell they originate from and have been shown to be involved in a variety of cellular processes. However, their detection and characterisation has been challenging and non-standardised, which makes comparisons across literature very challenging. While exosomes are known to exist in complex biological fluids such as saliva, breast milk, blood, and urine, their separation and identification from these media are time-consuming. Many researchers use techniques such as transmission electron microscopy for physical characterisation and western blot for protein identification, which are often not available in medical settings. Additionally, while these fluids can be easily obtained, acquiring similar samples from lung environments is a highly invasive procedure. While breath is known to transmit droplets from the lungs, the presence of exosomes in these condensates is unknown. In this project, functionalised InP/ZnS quantum dots (QDs) were used to target exosomes from a number of biological sources and provide a gateway to more fully characterise their ensemble properties. The InP/ZnS QDs were synthesised, and their size dependency on the band gap was investigated in accordance with the theoretical effective mass approximation model for quantum dots. The QDs were produced with hydrophobic oleylamine ligands, and therefore had to be ligand exchanged to be used in biological applications. A range of ligand exchange methods was surveyed to probe the best balance between retention of original quantum yields and best colloidal stability in aqueous systems.The QDs were further conjugated to an antibody specific for CD63, the protein found on exosomes. The conjugation was confirmed using dynamic light scattering and surface plasmon resonance. Finally, the binding of the QD-Antibody probe to the exosome was confirmed using surface plasmon resonance and confocal microscopy. Further modifications of the assay system could lead to multiplex-detection of the different proteins on the exosomes, their characterisation, and a method for the rapid detection of diseases.</p>


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