Unique Peptides of Cathelicidin-1 in the Early Detection of Mastitis-In Silico Analysis.

Based on the results of previously performed clinical studies, cathelicidin-1 has been proposed as a potential biomarker for the early diagnosis of mastitis in ewes. It has been hypothesized that the detection of unique peptides (defined as a peptide, irrespective of its length, that exists in only one protein of a proteome of interest) and core unique peptides (CUPs) (representing the shortest peptide that is unique) of cathelicidin-1 may potentially improve its identification and consequently the diagnosis of sheep mastitis. Peptides of sizes larger than those of the size of CUPs, which include consecutive or over-lapping CUPs, have been defined as 'composite core unique peptides' (CCUPs). The primary objective of the present study was the investigation of the sequence of cathelicidin-1 detected in ewes' milk in order to identify its unique peptides and core unique peptides, which would reveal potential targets for accurate detection of the protein. An additional objective was the detection of unique sequences among the tryptic digest peptides of cathelicidin-1, which would improve accuracy of identification of the protein when performing targeted MS-based proteomics. The potential uniqueness of each peptide of cathelicidin-1 was investigated using a bioinformatics tool built on a big data algorithm. A set of CUPs was created and CCUPs were also searched. Further, the unique sequences in the tryptic digest peptides of cathelicidin-1 were also detected. Finally, the 3D structure of the protein was analyzed from predicted models of proteins. In total, 59 CUPs and four CCUPs were detected in cathelicidin-1 of sheep origin. Among tryptic digest peptides, there were six peptides that were unique in that protein. After 3D structure analysis of the protein, 35 CUPs were found on the core of cathelicidin-1 of sheep origin and among them, 29 were located on amino acids in regions of the protein with 'very high' or 'confident' estimates of confidence of the structure. Ultimately, the following six CUPs: QLNEQ, NEQS, EQSSE, QSSEP, EDPD, DPDS, are proposed as potential antigenic targets for cathelicidin-1 of sheep. Moreover, another six unique peptides were detected in tryptic digests and offer novel mass tags to facilitate the detection of cathelicidin-1 during MS-based diagnostics.

Unique peptide signatures of SARS-CοV-2 virus against human proteome reveal variants' immune escape and infectiveness.

SARS-CoV-2 pandemic has necessitated the identification of sequence areas in the viral proteome that are capable to serve as antigenic sites and treatment targets. In the present study, we have applied a novel approach for mechanistically illuminating the virus-host organism interactions, by analyzing the Unique Peptides (UPs) of the virus featured by a minimum amino acid sequence length being defined as Core Unique Peptides (CrUPs), not of the virus per se, but against the entire proteome of the host organism. This approach resulted in the identification of CrUPs of the virus itself, which could not be recognized in the host organism proteome. Thereby, we analyzed the SARS-CoV-2 proteome for identification of CrUPs against the human proteome, which have been defined as C/H-CrUPs. We herein reveal that SARS-CoV-2 include 7.503 C/H-CrUPs, with the SPIKE_SARS2 being detected as the protein with the highest density of C/H-CrUPs. Extensive analysis has indicated that the critical P681R mutation produces new C/H-CrUPs around the R685 cleavage site, while the L452R mutation causes loss of antigenicity of the NF9 peptide and strong(er) binding of the virus to its ACE2 receptor protein. Simultaneous formation of these mutations in detrimental variants like Delta leads to the immune escape of the virus, its massive entrance into the host cell, a notable increase in virus formation, and its massive release and thus elevated infectivity of human target cells.

Prediction of SARS-CoV-2 Omicron Variant Immunogenicity, Immune Escape and Pathogenicity, through the Analysis of Spike Protein-Specific Core Unique Peptides.

The recently discovered Omicron variant of the SARS-CoV-2 coronavirus has raised a new, global, awareness. In this study, we identified the Core Unique Peptides (CrUPs) that reside exclusively in the Omicron variant of Spike protein and are absent from the human proteome, creating a new dataset of peptides named as SARS-CoV-2 CrUPs against the human proteome (C/H-CrUPs), and we analyzed their locations in comparison to the Alpha and Delta variants. In Omicron, 115 C/H-CrUPs were generated and 119 C/H-CrUPs were lost, almost four times as many compared to the other two variants. At the Receptor Binding Motif (RBM), 8 mutations were detected, resulting in the construction of 28 novel C/H-CrUPs. Most importantly, in the Omicron variant, new C/H-CrUPs carrying two or three mutant amino acids were produced, as a consequence of the accumulation of multiple mutations in the RBM. These C/H-CrUPs could not be recognized in any other viral Spike variant. Our findings indicated that the virus binding to the ACE2 receptor is facilitated by the herein identified C/H-CrUPs in contact point mutations and Spike cleavage sites, while the immunoregulatory NF9 peptide is not detectably affected. Thus, the Omicron variant could escape immune-system attack, while the strong viral binding to the ACE2 receptor leads to the highly efficient fusion of the virus to the target cell. However, the intact NF9 peptide suggests that Omicron exhibits reduced pathogenicity compared to the Delta variant.

Dataset of milk whey proteins of two indigenous greek goat breeds.

Due to its rarity and unique biological traits, as well as its growing financial value, milk of dairy Greek small ruminants is continuously attracting interest from both the scientific community and industry. For the construction of the present dataset, cutting-edge proteomics methodologies were employed, in order to investigate and characterize, for the first time, the milk whey proteome from the two indigenous Greek goat breeds, Capra prisca and Skopelos. In total 822 protein groups were identified in milk whey of the two breeds, The present data are further discussed in the research article "Milk of Greek sheep and goat breeds; characterization by means of proteomics" [1].

Dataset of milk whey proteins of three indigenous Greek sheep breeds.

The importance and unique biological traits, as well as the growing financial value, of milk from small Greek ruminants is continuously attracting interest from both the scientific community and industry. In this regard the construction of a reference dataset of the milk of the Greek sheep breeds is of great interest. In order to obtain such a dataset we employed cutting-edge proteomics methodologies to investigate and characterize, the proteome of milk from the three indigenous Greek sheep breeds Mpoutsko, Karagouniko and Chios. In total, more than 1300 protein groups were identified in milk whey from these breeds, reporting for the first time the most detailed proteome dataset of this precious biological material. The present results are further discussed in the research paper "Milk of Greek sheep and goat breeds; characterization by means of proteomics" (Anagnostopoulos et al. 2016) [1].

Milk of Greek sheep and goat breeds; characterization by means of proteomics.

UNLABELLED: Over the past 30years there has been a growing interest to unravel the dynamic framework of the milk proteome, and now that available technology is mature enough to enable techniques of protein fractionation and identification, this process is on-going. Due to its rarity and unique biological traits, as well as its growing financial value, milk of dairy Greek animals is continuously attracting interest from both the scientific community and industry. In the present study we employed cutting-edge proteomics methodologies to investigate and characterize, in depth, the proteome of whey from all pure-breed Greek sheep and goats. A mean of >500 protein groups were identified in whey from each breed of each animal species, reporting for the first time the proteome dataset of this precious biological material. Given its high nutritional value, the protein properties exposed herein will govern future steps in optimizing characteristics and features of sheep and goat milk products. SIGNIFICANCE: In the present study we employed cutting-edge proteomics methodologies to investigate and characterize, in depth, the proteome of milk from all pure-breed Greek sheep and goats. A mean of >500 protein groups were identified in milk whey from each breed of each animal species, reporting for the first time the proteome dataset of this precious biological material. Given its high nutritional value, the protein properties exposed herein will govern future steps in optimizing characteristics and features of sheep and goat milk products.