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Proteomes, Volume 8, Issue 2 (June 2020) – 8 articles

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25 pages, 2046 KiB  
Article
The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines
by Delphine Vincent, Keith Savin, Simone Rochfort and German Spangenberg
Proteomes 2020, 8(2), 13; https://doi.org/10.3390/proteomes8020013 - 15 Jun 2020
Cited by 3 | Viewed by 3825
Abstract
Cannabis research has taken off since the relaxation of legislation, yet proteomics is still lagging. In 2019, we published three proteomics methods aimed at optimizing protein extraction, protein digestion for bottom-up and middle-down proteomics, as well as the analysis of intact proteins for [...] Read more.
Cannabis research has taken off since the relaxation of legislation, yet proteomics is still lagging. In 2019, we published three proteomics methods aimed at optimizing protein extraction, protein digestion for bottom-up and middle-down proteomics, as well as the analysis of intact proteins for top-down proteomics. The database of Cannabis sativa proteins used in these studies was retrieved from UniProt, the reference repositories for proteins, which is incomplete and therefore underrepresents the genetic diversity of this non-model species. In this fourth study, we remedy this shortcoming by searching larger databases from various sources. We also compare two search engines, the oldest, SEQUEST, and the most popular, Mascot. This shotgun proteomics experiment also utilizes the power of parallel digestions with orthogonal proteases of increasing selectivity, namely chymotrypsin, trypsin/Lys-C and Asp-N. Our results show that the larger the database the greater the list of accessions identified but the longer the duration of the search. Using orthogonal proteases and different search algorithms increases the total number of proteins identified, most of them common despite differing proteases and algorithms, but many of them unique as well. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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15 pages, 1610 KiB  
Article
Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins
by Ekaterina Poverennaya, Olga Kiseleva, Ekaterina Ilgisonis, Svetlana Novikova, Arthur Kopylov, Yuri Ivanov, Alexei Kononikhin, Mikhail Gorshkov, Nikolay Kushlinskii, Alexander Archakov and Elena Ponomarenko
Proteomes 2020, 8(2), 12; https://doi.org/10.3390/proteomes8020012 - 23 May 2020
Cited by 3 | Viewed by 3786
Abstract
Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a [...] Read more.
Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300). Full article
(This article belongs to the Special Issue Human Proteomics)
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26 pages, 2558 KiB  
Review
Milk-Derived Extracellular Vesicles in Inter-Organism, Cross-Species Communication and Drug Delivery
by Rahul Sanwlani, Pamali Fonseka, Sai V. Chitti and Suresh Mathivanan
Proteomes 2020, 8(2), 11; https://doi.org/10.3390/proteomes8020011 - 13 May 2020
Cited by 88 | Viewed by 8529
Abstract
Milk is considered as more than a source of nutrition for infants and is a vector involved in the transfer of bioactive compounds and cells. Milk contains abundant quantities of extracellular vesicles (EVs) that may originate from multiple cellular sources. These nanosized vesicles [...] Read more.
Milk is considered as more than a source of nutrition for infants and is a vector involved in the transfer of bioactive compounds and cells. Milk contains abundant quantities of extracellular vesicles (EVs) that may originate from multiple cellular sources. These nanosized vesicles have been well characterized and are known to carry a diverse cargo of proteins, nucleic acids, lipids and other biomolecules. Milk-derived EVs have been demonstrated to survive harsh and degrading conditions in gut, taken up by various cell types, cross biological barriers and reach peripheral tissues. The cargo carried by these dietary EVs has been suggested to have a role in cell growth, development, immune modulation and regulation. Hence, there is considerable interest in understanding the role of milk-derived EVs in mediating inter-organismal and cross-species communication. Furthermore, various attributes such as it being a natural source, as well as its abundance, scalability, economic viability and lack of unwarranted immunologic reactions, has generated significant interest in deploying milk-derived EVs for clinical applications such as drug delivery and disease therapy. In this review, the role of milk-derived EVs in inter-organismal, cross-species communication and in drug delivery is discussed. Full article
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15 pages, 1360 KiB  
Article
Fractional Synthesis Rates of Individual Proteins in Rat Soleus and Plantaris Muscles
by Connor A. Stead, Stuart J. Hesketh, Samuel Bennett, Hazel Sutherland, Jonathan C. Jarvis, Paulo J. Lisboa and Jatin G. Burniston
Proteomes 2020, 8(2), 10; https://doi.org/10.3390/proteomes8020010 - 11 May 2020
Cited by 10 | Viewed by 4734
Abstract
Differences in the protein composition of fast- and slow-twitch muscle may be maintained by different rates of protein turnover. We investigated protein turnover rates in slow-twitch soleus and fast-twitch plantaris of male Wistar rats (body weight 412 ± 69 g). Animals were assigned [...] Read more.
Differences in the protein composition of fast- and slow-twitch muscle may be maintained by different rates of protein turnover. We investigated protein turnover rates in slow-twitch soleus and fast-twitch plantaris of male Wistar rats (body weight 412 ± 69 g). Animals were assigned to four groups (n = 3, in each), including a control group (0 d) and three groups that received deuterium oxide (D2O) for either 10 days, 20 days or 30 days. D2O administration was initiated by an intraperitoneal injection of 20 μL of 99% D2O-saline per g body weight, and maintained by provision of 4% (v/v) D2O in the drinking water available ad libitum. Soluble proteins from harvested muscles were analysed by liquid chromatography–tandem mass spectrometry and identified against the SwissProt database. The enrichment of D2O and rate constant (k) of protein synthesis was calculated from the abundance of peptide mass isotopomers. The fractional synthesis rate (FSR) of 44 proteins in soleus and 34 proteins in plantaris spanned from 0.58%/day (CO1A1: Collagen alpha-1 chain) to 5.40%/day NDRG2 (N-myc downstream-regulated gene 2 protein). Eight out of 18 proteins identified in both muscles had a different FSR in soleus than in plantaris (p < 0.05). Full article
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18 pages, 2056 KiB  
Article
Urinary Extracellular Vesicles and Salt-Losing Tubulopathies: A Proteomic Approach
by Francesca Raimondo, Clizia Chinello, Luigi Porcaro, Fulvio Magni and Marina Pitto
Proteomes 2020, 8(2), 9; https://doi.org/10.3390/proteomes8020009 - 9 May 2020
Cited by 6 | Viewed by 3496
Abstract
Renal tubular cells release urinary extracellular vesicles (uEV) that are considered a promising source of molecular markers for renal dysfunction and injury. We investigated uEV proteomes of patients with hereditary salt-losing tubulopathies (SLTs), focusing on those caused by Gitelman and Bartter (BS) syndromes, [...] Read more.
Renal tubular cells release urinary extracellular vesicles (uEV) that are considered a promising source of molecular markers for renal dysfunction and injury. We investigated uEV proteomes of patients with hereditary salt-losing tubulopathies (SLTs), focusing on those caused by Gitelman and Bartter (BS) syndromes, to provide potential markers for differential diagnosis. Second morning urine was collected from patients with genetically proven SLTs and uEV were isolated by the ultracentrifugation-based protocol. The uEV proteome was run through a diagonal bidimensional electrophoresis (16BAC/SDS-PAGE), to improve hydrophobic protein resolution. Sixteen differential spots from the proteome of two variants (BS2 and BS3) were analysed by nLC-ESI-MS/MS after in-gel tryptic digestion. A total of 167 protein species were identified from 7 BS2 spots and 9 BS3 spot. Most of these proteins were membrane-associated proteins, in particular transmembrane proteins, and were related to typical renal functions. The differential content of some uEV was then validated by immunoblotting. Our work suggests that uEV proteomics represents a promising strategy for the identification of differential SLT proteins. This could play a role in understanding the pathophysiological disease mechanisms and may support the recognition of different syndromes. Full article
(This article belongs to the Special Issue Human Proteomics)
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17 pages, 713 KiB  
Review
Proteomics of Brucella
by Ansgar Poetsch and María Inés Marchesini
Proteomes 2020, 8(2), 8; https://doi.org/10.3390/proteomes8020008 - 22 Apr 2020
Cited by 6 | Viewed by 5661
Abstract
Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the [...] Read more.
Brucella spp. are Gram negative intracellular bacteria responsible for brucellosis, a worldwide distributed zoonosis. A prominent aspect of the Brucella life cycle is its ability to invade, survive and multiply within host cells. Comprehensive approaches, such as proteomics, have aided in unravelling the molecular mechanisms underlying Brucella pathogenesis. Technological and methodological advancements such as increased instrument performance and multiplexed quantification have broadened the range of proteome studies, enabling new and improved analyses, providing deeper and more accurate proteome coverage. Indeed, proteomics has demonstrated its contribution to key research questions in Brucella biology, i.e., immunodominant proteins, host-cell interaction, stress response, antibiotic targets and resistance, protein secretion. Here, we review the proteomics of Brucella with a focus on more recent works and novel findings, ranging from reconfiguration of the intracellular bacterial proteome and studies on proteomic profiles of Brucella infected tissues, to the identification of Brucella extracellular proteins with putative roles in cell signaling and pathogenesis. In conclusion, proteomics has yielded copious new candidates and hypotheses that require future verification. It is expected that proteomics will continue to be an invaluable tool for Brucella and applications will further extend to the currently ill-explored aspects including, among others, protein processing and post-translational modification. Full article
(This article belongs to the Special Issue Microbial Proteomics II)
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10 pages, 858 KiB  
Article
Analysis of Reference Ranges of Total Serum Protein in Namibia: Clinical Implications
by Josephine N. Henok, Benjamin I. Okeleye, Elizabeth I. Omodanisi, Seteno K. O. Ntwampe and Yapo G. Aboua
Proteomes 2020, 8(2), 7; https://doi.org/10.3390/proteomes8020007 - 15 Apr 2020
Cited by 5 | Viewed by 3927
Abstract
A reference range is an essential part of clinical laboratory test interpretation and patient care. The levels of total serum protein (TSP) are measured in sera to assess nutritional, liver, and kidney disorders. This study determined the TSP reference range with respect to [...] Read more.
A reference range is an essential part of clinical laboratory test interpretation and patient care. The levels of total serum protein (TSP) are measured in sera to assess nutritional, liver, and kidney disorders. This study determined the TSP reference range with respect to gender, age, and region in Namibia. A retrospective cross-sectional study was conducted to determine the TSP reference range among 78,477 healthy participants within the ages of less than one year to more than 65 yrs in 14 regions of Namibia. The reference range of TSP was 51–91 g/L for females and 51–92 g/L for males. A reduced TSP range of 48.00–85.55 g/L (2.5–97.5 percentiles) was established at <1–5 years and increased towards adolescence. An uttermost range of 54–93 g/L was observed from 36–65 years of age. At the age >65 years; a steady decline in the reference range (51.00–89 g/L) was recorded. An upper TSP range of 53–92 g/L (2.5–97.5 percentiles) was detected in Erongo, Zambezi, Hardap, Kavango East, and a comparable trend was also seen in Omusati with a 54–91 g/L range. Meanwhile; a reduced TSP range of 50–89 g/L was identified in Ohangwena. This study showed that gender, age, and geographical location can impact TSP levels with a significant clinical difference (p < 0.05) between each category. Full article
(This article belongs to the Special Issue Human Proteomics)
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16 pages, 2089 KiB  
Article
Vesiculation of Red Blood Cells in the Blood Bank: A Multi-Omics Approach towards Identification of Causes and Consequences
by Joames K. Freitas Leal, Edwin Lasonder, Vikram Sharma, Jürgen Schiller, Giuseppina Fanelli, Sara Rinalducci, Roland Brock and Giel Bosman
Proteomes 2020, 8(2), 6; https://doi.org/10.3390/proteomes8020006 - 31 Mar 2020
Cited by 14 | Viewed by 5789
Abstract
Microvesicle generation is an integral part of the aging process of red blood cells in vivo and in vitro. Extensive vesiculation impairs function and survival of red blood cells after transfusion, and microvesicles contribute to transfusion reactions. The triggers and mechanisms of microvesicle [...] Read more.
Microvesicle generation is an integral part of the aging process of red blood cells in vivo and in vitro. Extensive vesiculation impairs function and survival of red blood cells after transfusion, and microvesicles contribute to transfusion reactions. The triggers and mechanisms of microvesicle generation are largely unknown. In this study, we combined morphological, immunochemical, proteomic, lipidomic, and metabolomic analyses to obtain an integrated understanding of the mechanisms underlying microvesicle generation during the storage of red blood cell concentrates. Our data indicate that changes in membrane organization, triggered by altered protein conformation, constitute the main mechanism of vesiculation, and precede changes in lipid organization. The resulting selective accumulation of membrane components in microvesicles is accompanied by the recruitment of plasma proteins involved in inflammation and coagulation. Our data may serve as a basis for further dissection of the fundamental mechanisms of red blood cell aging and vesiculation, for identifying the cause-effect relationship between blood bank storage and transfusion complications, and for assessing the role of microvesicles in pathologies affecting red blood cells. Full article
(This article belongs to the Special Issue Red Blood Cell Multi-Omics)
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