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1.
Braz. j. biol ; 83: e249424, 2023. graf
Article in English | MEDLINE, LILACS, VETINDEX | ID: biblio-1345538

ABSTRACT

Abstract Hypoxia is a prominent feature of head and neck cancer. However, the oxygen element characteristics of proteins and how they adapt to hypoxia microenvironments of head and neck cancer are still unknown. Human genome sequences and proteins expressed data of head and neck cancer were retrieved from pathology atlas of Human Protein Atlas project. Then compared the oxygen and carbon element contents between proteomes of head and neck cancer and normal oral mucosa-squamous epithelial cells, genome locations, pathways, and functional dissection associated with head and neck cancer were also studied. A total of 902 differentially expressed proteins were observed where the average oxygen content is higher than that of the lowly expressed proteins in head and neck cancer proteins. Further, the average oxygen content of the up regulated proteins was 2.54% higher than other. None of their coding genes were distributed on the Y chromosome. The up regulated proteins were enriched in endocytosis, apoptosis and regulation of actin cytoskeleton. The increased oxygen contents of the highly expressed and the up regulated proteins might be caused by frequent activity of cytoskeleton and adapted to the rapid growth and fast division of the head and neck cancer cells. The oxygen usage bias and key proteins may help us to understand the mechanisms behind head and neck cancer in targeted therapy, which lays a foundation for the application of stoichioproteomics in targeted therapy and provides promise for potential treatments for head and neck cancer.


Resumo A hipóxia é uma característica proeminente do câncer de cabeça e pescoço. No entanto, as características do elemento oxigênio das proteínas e como elas se adaptam aos microambientes de hipóxia do câncer de cabeça e pescoço ainda são desconhecidas. Sequências do genoma humano e dados expressos de proteínas de câncer de cabeça e pescoço foram recuperados do atlas de patologia do projeto Human Protein Atlas. Em seguida, comparou o conteúdo do elemento de oxigênio e carbono entre proteomas de câncer de cabeça e pescoço, e células epiteliais escamosas da mucosa oral normal, localizações do genoma, vias e dissecção funcional associada ao câncer de cabeça e pescoço também foram estudadas. Um total de 902 proteínas expressas diferencialmente foi observado onde o conteúdo médio de oxigênio é maior do que as proteínas expressas de forma humilde em proteínas de câncer de cabeça e pescoço. Além disso, o conteúdo médio de oxigênio das proteínas reguladas positivamente foi 2,54% maior do que das outras. Nenhum de seus genes codificadores foi distribuído no cromossomo Y. As proteínas reguladas positivamente foram enriquecidas em endocitose, apoptose e regulação do citoesqueleto de actina. O conteúdo aumentado de oxigênio das proteínas altamente expressas e reguladas pode ser causado pela atividade frequente do citoesqueleto e adaptado ao rápido crescimento e divisão das células cancerosas de cabeça e pescoço. O viés do uso de oxigênio e as proteínas-chave podem nos ajudar a entender os mecanismos por trás do câncer de cabeça e pescoço na terapia direcionada, o que estabelece uma base para a aplicação da estequioproteômica na terapia direcionada e oferece uma promessa para potenciais tratamentos para o câncer de cabeça e pescoço.


Subject(s)
Humans , Head and Neck Neoplasms/genetics , Oxygen , Carbon , Proteome/genetics , Tumor Microenvironment
2.
J. venom. anim. toxins incl. trop. dis ; 28: 20210034, 2022. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1365076

ABSTRACT

The word venomics was coined to acknowledge the studies that use omics to investigate venom proteins and peptides. Venomics has evolved considerably over the last 20 years. The first works on scorpion or spider venomics were published in the early 2000's. Such studies relied on peptide mass fingerprinting (PMF) to characterize venom complexity. After the introduction of new mass spectrometers with higher resolution, sensitivity and mass accuracy, and the next-generation nucleotide sequencing, the complexity of data reported in research on scorpion and spider venomics increased exponentially, which allowed more comprehensive studies. In the present review article, we covered key publications on scorpion venomics and spider venomics, presenting historical grounds and implemented technologies over the last years. The literature presented in this review was selected after searching the PubMed database using the terms "(scorpion venom) AND (proteome)" for scorpion venomics, and "(spider venom) AND (proteome)" for publications on spider venomics. We presented the key aspects related to proteomics in the covered papers including, but not restricted to, the employed proteomic strategy (i.e., PMF, two-dimensional gel electrophoresis, shotgun/bottom-up and/or top-down/peptidome), and the type of mass spectrometer used. Some conclusions can be drawn from the present study. For example, the scorpion genus Tityus is the most studied concerning venomics, followed by Centruroides; whereas for spiders the studied genera were found more equally distributed. Another interesting conclusion is the lack of high throughput studies on post-translational modifications (PTMs) of scorpion and spider proteins. In our opinion, PTMs should be more studied as they can modulate the activity of scorpion and spider toxins.(AU)


Subject(s)
Animals , Arthropod Venoms , Scorpion Venoms , Spider Venoms , Toxicology , Proteome
3.
J. venom. anim. toxins incl. trop. dis ; 27: e20210051, 2021. tab, graf, ilus
Article in English | LILACS, VETINDEX | ID: biblio-1356458

ABSTRACT

King Cobra (Ophiophagus hannah) has a significant place in many cultures, and is a medically important venomous snake in the world. Envenomation by this snake is highly lethal, manifested mainly by neurotoxicity and local tissue damage. King Cobra may be part of a larger species complex, and is widely distributed across Southeast Asia, southern China, northern and eastern regions as well as the Western Ghats of India, indicating potential geographical variation in venom composition. There is, however, only one species-specific King Cobra antivenom available worldwide that is produced in Thailand, using venom from the snake of Thai origin. Issues relating to the management of King Cobra envenomation (e.g., variation in the composition and toxicity of the venom, limited availability and efficacy of antivenom), and challenges faced in the research of venom (in particular proteomics), are rarely addressed. This article reviews the natural history and sociocultural importance of King Cobra, cases of snakebite envenomation caused by this species, current practice of management (preclinical and clinical), and major toxinological studies of the venom with a focus on venom proteomics, toxicity and neutralization. Unfortunately, epidemiological data of King Cobra bite is scarce, and venom proteomes reported in various studies revealed marked discrepancies in details. Challenges, such as inconsistency in snake venom sampling, varying methodology of proteomic analysis, lack of mechanistic and antivenomic studies, and controversy surrounding antivenom use in treating King Cobra envenomation are herein discussed. Future directions are proposed, including the effort to establish a standard, comprehensive Pan-Asian proteomic database of King Cobra venom, from which the venom variation can be determined. Research should be undertaken to characterize the toxin antigenicity, and to develop an antivenom with improved efficacy and wider geographical utility. The endeavors are aligned with the WHO´s roadmap that aims to reduce the disease burden of snakebite by 50% before 2030.(AU)


Subject(s)
Animals , Poisoning , Snake Bites , Snakes , Antivenins , Proteome , Elapid Venoms , Natural History
4.
J. venom. anim. toxins incl. trop. dis ; 27: e20210023, 2021. tab, graf, ilus, mapas
Article in English | LILACS, VETINDEX | ID: biblio-1346437

ABSTRACT

Diverse and unique bioactive neurotoxins known as conopeptides or conotoxins are produced by venomous marine cone snails. Currently, these small and stable molecules are of great importance as research tools and platforms for discovering new drugs and therapeutics. Therefore, the characterization of Conus venom is of great significance, especially for poorly studied species. Methods: In this study, we used bioanalytical techniques to determine the venom profile and emphasize the functional composition of conopeptides in Conus taeniatus, a neglected worm-hunting cone snail. Results: The proteomic analysis revealed that 84.0% of the venom proteins were between 500 and 4,000 Da, and 16.0% were > 4,000 Da. In C. taeniatus venom, 234 peptide fragments were identified and classified as conotoxin precursors or non-conotoxin proteins. In this process, 153 conotoxin precursors were identified and matched to 23 conotoxin precursors and hormone superfamilies. Notably, the four conotoxin superfamilies T (22.87%), O1 (17.65%), M (13.1%) and O2 (9.8%) were the most abundant peptides in C. taeniatus venom, accounting for 63.40% of the total conotoxin diversity. On the other hand, 48 non-conotoxin proteins were identified in the venom of C. taeniatus. Moreover, several possibly biologically active peptide matches were identified, and putative applications of the peptides were assigned. Conclusion: Our study showed that the composition of the C. taeniatus-derived proteome is comparable to that of other Conus species and contains an effective mix of toxins, ionic channel inhibitors and antimicrobials. Additionally, it provides a guidepost for identifying novel conopeptides from the venom of C. taeniatus and discovering conopeptides of potential pharmaceutical importance.(AU)


Subject(s)
Animals , Proteome , Conotoxins , Conus Snail , Mollusk Venoms , Neurotoxins , Biological Products
5.
J. venom. anim. toxins incl. trop. dis ; 27: e20200196, 2021. tab, graf, ilus
Article in English | LILACS, VETINDEX | ID: biblio-1346436

ABSTRACT

Snake venoms are complex mixtures of toxic proteins or peptides encoded by various gene families that function synergistically to incapacitate prey. In the present study, in order to unravel the proteomic repertoire of Deinagkistrodon acutus venom, some trace abundance components were analyzed. Methods Shotgun proteomic approach combined with shotgun nano-LC-ESI-MS/MS were employed to characterize the medically important D. acutus venom, after collected samples were enriched with the combinatorial peptide ligand library (CPLL). Results This avenue helped us find some trace components, undetected before, in D. acutus venom. The results indicated that D. acutus venom comprised 84 distinct proteins from 10 toxin families and 12 other proteins. These results are more than twice the number of venom components obtained from previous studies, which were only 29 distinct proteins obtained through RP-HPLC for the venom of the same species. The present results indicated that in D. acutus venom, the most abundant components (66.9%) included metalloproteinases, serine proteinases, and C-type lectin proteins; the medium abundant components (13%) comprised phospholipases A2 (PLA2) and 5'-nucleotidases and nucleases; whereas least abundant components (6%) were aminopeptidases, L-amino acid oxidases (LAAO), neurotoxins and disintegrins; and the trace components. The last were undetected before the use of conventional shotgun proteomics combined with shotgun nano-LC-ESI-MS/MS, such as cysteine-rich secretory proteins Da-CRPa, phospholipases B-like 1, phospholipases B (PLB), nerve growth factors (NGF), glutaminyl-peptide cyclortransferases (QC), and vascular non-inflammatory molecules 2 (VNN2). Conclusion These findings demonstrated that the CPLL enrichment method worked well in finding the trace toxin proteins in D. acutus venom, in contrast with the previous venomic characterization of D. acutus by conventional LC-MS/MS. In conclusion, this approach combined with the CPLL enrichment was effective for allowing us to explore the hidden D. acutus venomic profile and extended the list of potential venom toxins.(AU)


Subject(s)
Animals , Oxidoreductases , Peptides , Viper Venoms , Proteome , Neurotoxins
6.
Article in Chinese | WPRIM | ID: wpr-921528

ABSTRACT

Objective To obtain the proteome and acetylome profiles of livers in mice during normal aging.Methods We applied tandem mass tag labeling and liquid chromatography tandem mass spectrometry and achieved proteome and acetylome data in C57BL/6J male mice aged 2 and 18 months under physiological conditions.Results A total of 4712 proteins were quantified by proteome profiling,and 4818 acetylated sites in 1367 proteins by acetylome profiling.The proteome and acetylome revealed moderate differences in the livers of young and old mice.There were 195 differentially expressed proteins in the proteome and 113 differentially expressed acetylated sites corresponding to 76 proteins in the acetylome.Functional enrichment analysis for the proteome showed that aging-associated upregulated proteins were mainly involved in fatty acid metabolism,epoxygenase P450 pathway,drug catabolic process,organic hydroxy compound metabolic process,and arachidonic acid metabolic process,while the downregulated proteins were related to regulation of gene silencing,nucleosome assembly,protein heterotetramerization,response to interferon,protein-DNA complex assembly and other processes.For the acetylome,the proteins with aging-associated upregulated acetylated sites mainly participated in cofactor metabolism,small molecule catabolic process,ribose phosphate metabolic process,ribonucleotide metabolic process,and purine-containing compound metabolic process,while the proteins with downregulated acetylated sites were associated with sulfur compound metabolic process,response to unfolded protein,and amino acid metabolic process.Conclusion We profiled the proteome and acetylome of livers in mice during normal aging and generated datasets for further research on aging.


Subject(s)
Acetylation , Aging , Animals , Liver , Lysine/metabolism , Male , Mice , Mice, Inbred C57BL , Proteome/metabolism
7.
Chinese Journal of Biotechnology ; (12): 4102-4110, 2021.
Article in Chinese | WPRIM | ID: wpr-921491

ABSTRACT

The abundance of proteins in human urine is low and easily to be masked by high-abundance proteins during mass spectrometry analysis. Development of efficient and highly selective enrichment methods is therefore a prerequisite for achieving deep coverage of urine protein markers. Notably, different experimental methods would affect the urine protein enrichment efficacy and the coverage of urine proteome. In this study, ultrafiltration, nitrocellulose membrane enrichment and saturated ammonium sulfate precipitation were used to process 10 mL urine samples from five healthy volunteers and five bladder cancer patients. The urine proteins were enriched and separate by SDS-PAGE to compare the purification efficiency of different methods. Moreover, the peptide identification effects of different purification methods were analyzed by mass spectrometry to determine the best method for enriching urine protein histones. Saturated ammonium sulfate precipitation method outperformed the ultrafiltration and the nitrocellulose membrane enrichment methods in terms of the protein enrichment efficacy and quality. The interference of highly abundant albumin was reduced, whereas the amount of low-abundance protein was increased, and the sensitivity of mass spectrometry identification was increased. The saturated ammonium sulfate precipitation method may be applied for large-scale urine processing for screening clinical diagnostic markers through proteomics.


Subject(s)
Histones , Humans , Mass Spectrometry , Proteome , Proteomics , Urinalysis
8.
Chinese Journal of Biotechnology ; (12): 276-289, 2021.
Article in Chinese | WPRIM | ID: wpr-878561

ABSTRACT

Different microorganisms can cause intraperitoneal infection. This study was to distinguish different microbial infections by urine analysis. Rats were intraperitoneally injected with Escherichia coli, Staphylococcus aureus, and Candida albicans, separately. Urine samples were collected from rats at 0, 12, 36 and 72 h after infection. Urinary proteins were profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with the control (without infection), a total of 69 differential proteins were identified in rats injected with E. coli. A total of 31 differences proteins were identified in rats injected with S. aureus. A total of 38 differential proteins were identified in rats injected with C. albicans. Urine proteome was different when rats were infected by different microorganisms, suggesting that urine may have the potential for differential diagnosis of different intraperitoneal infections.


Subject(s)
Animals , Chromatography, Liquid , Escherichia coli , Proteome , Rats , Staphylococcus aureus , Tandem Mass Spectrometry
9.
Braz. j. med. biol. res ; 53(1): e9001, Jan. 2020. tab, graf
Article in English | LILACS | ID: biblio-1055477

ABSTRACT

Due to its various structures in bio-compounds, snake venom is the indisputable result of evolutionary stages of molecules with an increasingly complex structure, high specificity, and of great importance for medicine because of their potential. The present study proposed an underpinning examination of venom composition from nine species of venomous snakes using a useful and replicable methodology. The objective was the extension of the evaluation of protein fractions in the field up to 230 kDa to permit possible identification of some fractions that are insufficiently studied. The gel capillary electrophoresis method on the chip was performed using an Agilent 2100 bioassay with the 80 and 230-LabChip Protein kits. Interpretation of electrophoresis was performed using the Protein 2100 expert (Agilent) test software as follows: a) Protein 80 (peak size scale): 1.60, 3.5, 6.50, 15.00, 28.00, 46.00, 63.00, 95.00 kDa; b) Protein 230 (peak size scale): 4.50, 7.00, 15.00, 28.00, 46.00, 63.00, 95.00, 150.00, 240.00 kDa. The screening revealed the presence of compounds with a molecular weight greater than 80 kDa, in the case of Vipera aspis and Vipera xantina palestinae. For V. aspis, a 125 kDa molecular weight pro-coagulant protein was identified, known as being involved in the reduction of plasma clotting time without any direct activity in the fibrinogen coagulation process. The samples examined on the Protein 230-LabChip electrophoresis chip can be considered as a novelty with possible uses in medicine, requiring further approaches by advanced proteomics techniques to confirm the intimate structural features and biological properties of snake venoms.


Subject(s)
Animals , Viper Venoms/chemistry , Proteins/chemistry , Viperidae/classification , Viper Venoms/analysis , Proteins/isolation & purification , Proteins/analysis , Electrophoresis, Capillary , Proteome/classification , Proteome/chemistry , Proteomics/methods
10.
J. appl. oral sci ; 28: e20200189, 2020. tab, graf
Article in English | LILACS, BBO | ID: biblio-1134804

ABSTRACT

Abstract Saliva is the major contributor for the protein composition of the acquired enamel pellicle (AEP), a bacteria-free organic layer formed by the selective adsorption of salivary proteins on the surface of the enamel. However, the amount of proteins that can be recovered is even smaller under in vitro condition, due to the absence of continuous salivary flow. Objective This study developed an in vitro AEP protocol for proteomics analysis using a new formation technique with different collection solutions. Methodology 432 bovine enamel specimens were prepared (4x4 mm) and divided into four groups (n=108). Unstimulated saliva was provided by nine subjects. The new AEP formation technique was based on saliva resupply by a new one every 30 min within 120 minutes at 37ºC under agitation. AEP was collected using an electrode filter paper soaked in the collection solutions according with the group: 1) 3% citric acid (CA); 2) 0.5% sodium dodecyl sulfate (SDS); 3) CA followed by SDS (CA+SDS); 4) SDS followed by CA (SDS+CA). The pellicles collected were processed for analysis through LC-ESI-MS/MS technique. Results A total of 55 proteins were identified. The total numbers of proteins identified in each group were 40, 21, 28 and 41 for the groups CA, SDS, CA+SDS and SDS+CA, respectively. Twenty-three typical AEP proteins were identified in all groups, but Mucin was only found in CA and CA+SDS, while three types of PRP were not found in the SDS group. Moreover, a typical enamel protein, Enamelin, was identified in the CA+SDS group only. Conclusion The new technique of the in vitro AEP formation through saliva replacement was essential for a higher number of the proteins identified. In addition, considering practicality, quantity and quality of identified proteins, citric acid seems to be the best solution to be used for collection of AEP proteins.


Subject(s)
Animals , Cattle , Proteome , Proteomics , Dental Pellicle , Saliva , Salivary Proteins and Peptides , Dental Enamel , Tandem Mass Spectrometry
11.
J. venom. anim. toxins incl. trop. dis ; 26: e20200053, 2020. graf
Article in English | LILACS, VETINDEX | ID: biblio-1135159

ABSTRACT

Snakebites remain a major life-threatening event worldwide. It is still difficult to make a positive identification of snake species by clinicians in both Western medicine and Chinese medicine. The main reason for this is a shortage of diagnostic biomarkers and lack of knowledge about pathways of venom-induced toxicity. In traditional Chinese medicine, snakebites are considered to be treated with wind, fire, and wind-fire toxin, but additional studies are required. Methods: Cases of snakebite seen at the Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine were grouped as follows: fire toxin - including four cases of bites by Agkistrodon acutus and three bites by Trimeresurus stejnegeri - and wind-fire toxin - four cases of bites by vipers and three bites by cobras. Serum protein quantification was performed using LC-MS/MS. Differential abundance proteins (DAPs) were identified from comparison of snakebites of each snake species and healthy controls. The protein interaction network was constructed using STITCH database. Results: Principal component analysis and hierarchical clustering of 474 unique proteins exhibited protein expression profiles of wind-fire toxins that are distinct from that of fire toxins. Ninety-three DAPs were identified in each snakebite subgroup as compared with healthy control, of which 38 proteins were found to have significantly different expression levels and 55 proteins displayed no expression in one subgroup, by subgroup comparison. GO analysis revealed that the DAPs participated in bicarbonate/oxygen transport and hydrogen peroxide catabolic process, and affected carbon-oxygen lyase activity and heme binding. Thirty DAPs directly or indirectly acted on hydrogen peroxide in the interaction network of proteins and drug compounds. The network was clustered into four groups: lipid metabolism and transport; IGF-mediated growth; oxygen transport; and innate immunity. Conclusions: Our results show that the pathways of snake venom-induced toxicity may form a protein network of antioxidant defense by regulating oxidative stress through interaction with hydrogen peroxide.(AU)


Subject(s)
Animals , Snake Venoms , Biomarkers , Oxidative Stress , Hydrogen Peroxide , Antioxidants , Trimeresurus , Proteome/analysis
12.
J. venom. anim. toxins incl. trop. dis ; 26: e20190058, 2020. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1135137

ABSTRACT

Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design. Methods: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca. Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment. Results: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin. Conclusion: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.(AU)


Subject(s)
Animals , Bothrops , Bothrops/physiology , Proteome , Crotalid Venoms , Gene Expression Profiling , Metalloproteases , Transcriptome , Molecular Biology , Cluster Analysis , High-Throughput Nucleotide Sequencing
13.
J. venom. anim. toxins incl. trop. dis ; 26: e20190103, 2020. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1101265

ABSTRACT

The Brazil's lancehead, Bothrops brazili, is a poorly studied pit viper distributed in lowlands of the equatorial rainforests of southern Colombia, northeastern Peru, eastern Ecuador, southern and southeastern Venezuela, Guyana, Suriname, French Guiana, Brazil, and northern Bolivia. Few studies have been reported on toxins isolated from venom of Ecuadorian and Brazilian B. brazili. The aim of the present study was to elucidate the qualitative and quantitative protein composition of B. brazili venom from Pará (Brazil), and to carry out a comparative antivenomics assessment of the immunoreactivity of the Brazilian antibothropic pentavalent antivenom [soro antibotrópico (SAB) in Portuguese] against the venoms of B. brazili and reference species, B. jararaca. Methods: We have applied a quantitative snake venomics approach, including reverse-phase and two-dimensional electrophoretic decomplexation of the venom toxin arsenal, LC-ESI-MS mass profiling and peptide-centric MS/MS proteomic analysis, to unveil the overall protein composition of B. brazili venom from Pará (Brazil). Using third-generation antivenomics, the specific and paraspecific immunoreactivity of the Brazilian SAB against homologous (B. jararaca) and heterologous (B. brazili) venoms was investigated. Results: The venom proteome of the Brazil's lancehead (Pará) is predominantly composed of two major and three minor acidic (19%) and two major and five minor basic (14%) phospholipase A2 molecules; 7-11 snake venom metalloproteinases of classes PI (21%) and PIII (6%); 10-12 serine proteinases (14%), and 1-2 L-amino acid oxidases (6%). Other toxins, including two cysteine-rich secretory proteins, one C-type lectin-like molecule, one nerve growth factor, one 5'-nucleotidase, one phosphodiesterase, one phospholipase B, and one glutaminyl cyclase molecule, represent together less than 2.7% of the venom proteome. Third generation antivenomics profile of the Brazilian pentabothropic antivenom showed paraspecific immunoreactivity against all the toxin classes of B. brazili venom, with maximal binding capacity of 132.2 mg venom/g antivenom. This figure indicates that 19% of antivenom's F(ab')2 antibodies bind B. brazili venom toxins. Conclusion: The proteomics outcome contribute to a deeper insight into the spectrum of toxins present in the venom of the Brazil's lancehead, and rationalize the pathophysiology underlying this snake bite envenomings. The comparative qualitative and quantitative immunorecognition profile of the Brazilian pentabothropic antivenom toward the venom toxins of B. brazili and B. jararaca (the reference venom for assessing the bothropic antivenom's potency in Brazil), provides clues about the proper use of the Brazilian antibothropic polyvalent antivenom in the treatment of bites by the Brazil's lancehead.(AU)


Subject(s)
Animals , Oxidoreductases , Snake Bites , Snake Venoms , Bites and Stings , Antivenins , Bothrops , Proteome
14.
Article in English | WPRIM | ID: wpr-811113

ABSTRACT

BACKGROUND: Platelet-rich plasma (PRP) is a plasma component of autologous blood containing a high concentration of platelets. PRP is used to promote healing of damaged tissues. However, there are not many studies on the composition and expression patterns of active proteins in PRP. The purpose of this study was to identify unknown factors that contribute to tissue healing by proteomic analysis of proteins in PRP.METHODS: Three men in their 30s with no basal disease participated in this study. All identified proteins were classified for tissue healing-related functions on the basis of the gene ontology analysis of adhesion molecule with Ig-like domain 2 (AmiGO2). PRP was prepared by using the ACP kit and GPS III kit.RESULTS: We identified a total of 125 proteins related to wound healing, along with three proteins for angiogenesis involved in wound healing, two proteins for fibroblast migration, four proteins for collagen biosynthesis process, two proteins for glycosaminoglycan biosynthesis process, and 13 proteins for glycosaminoglycan binding. So, in addition to the growth factors that have been already known to be involved in tissue healing, 25 new proteins were identified.CONCLUSIONS: We identified the unknown proteins associated with tissue healing in PRP. Our findings may serve as a foundation for the establishment of basic medical evidence for PRP applications.


Subject(s)
Classification , Collagen , Fibroblasts , Gene Ontology , Humans , Intercellular Signaling Peptides and Proteins , Male , Plasma , Platelet-Rich Plasma , Proteome , Wound Healing
15.
Article in Chinese | WPRIM | ID: wpr-828379

ABSTRACT

Magnolia officinalis is a traditional Chinese medicine,with many years of cultivating process, M. officinalis leaves show more differentiation types due to the exchange of seeds from different provenances. "Da Ao"(DA), "Xiao Ao"(XA), "Chuan Hou"(CH),and "Liu Ye"(LY)are the main types of M. officinalis in Sichuan province of China,and there were obvious differences in growth rate,chemical composition,leaf shape and leaf colour. This study selected different types of M. officinalis leaves(DA,XA,LY and CH)from Sichuan to determine their chlorophyll content. Transcriptomic level sequencing of different types of M. officinalis leaf tissues was by high-throughput sequencing analysis and proteomics used an integrated approach involving TMT labelling and LC-MS/MS to quantify the dynamic changes of the whole proteome of M. officinalis. The results showed that CH had the lowest chlorophyll content while DA had the highest chlorophyll content. Furthermore,transcriptome and proteomics results showed that chlorophyll synthesis pathway in DA glutamine-tRNA reductase,urinary porphyrins decarboxylase(UROD),oxygen-dependent protoporphyrin(ODCO),the original-Ⅲ oxidase protoporphyrin oxidase(PPO),magnesium chelating enzyme subunit ChlD,protoporphyrin magnesium Ⅸ monomethyl ester [oxidative] cyclase(MPPMC)were significantly higher than CH,XA and LY,consistent in the results of determination of chlorophyll content(chlorophyll content was highest of 37.56 mg·g~(-1) FW). Some rate-limiting enzymes related to the chlorophyll synthesis,such as ODCO,PPO and MPPMC were tested by Parallel Reaction Monitoring(PRM),and the results showed that the rate-limiting enzyme content in DA was higher than that in other three types. Therefore,based on the differences in leaf color of four types of M. officinalis,the research conducted a preliminary study on the chlorophyll metabolism pathway in leaves of different types of M. officinalis,and explored relevant genes and proteins causing leaf color differences from the molecular level,so as to lay a foundation for studying the differences in growth and development of different types of M. officinalis.


Subject(s)
China , Chlorophyll , Chromatography, Liquid , Magnolia , Plant Leaves , Proteome , Tandem Mass Spectrometry , Transcriptome
16.
Article in English | WPRIM | ID: wpr-816620

ABSTRACT

BACKGROUND: Adrenal cortical carcinoma (ACC) is a rare cancer with a variable prognosis. Several prognostic factors of ACC have been previously reported, but a proteomic analysis has not yet been performed. This study aimed to investigate prognostic biomarkers for ACC using a proteomic approach.METHODS: We used reverse-phase protein array data from The Cancer Proteome Atlas, and identified differentially expressed proteins in metastatic ACCs. Multivariate Cox regression analysis adjusted by age and staging was used for survival analysis, and the C-index and category-free net reclassification improvement (cfNRI) were utilized to evaluate additive prognostic value.RESULTS: In 46 patients with ACC, cyclin B1, transferrin receptor (TfR1), and fibronectin were significantly overexpressed in patients with distant metastasis. In multivariate models, high expression of cyclin B1 and TfR1 was significantly associated with mortality (hazard ratio [HR], 6.13; 95% confidence interval [CI], 1.02 to 36.7; and HR, 6.59; 95% CI, 1.14 to 38.2; respectively), whereas high fibronectin expression was not (HR, 3.92; 95% CI, 0.75 to 20.4). Combinations of high cyclin B1/high TfR1, high cyclin B1/high fibronectin, and high TfR1/high fibronectin were strongly associated with mortality ([HR, 13.72; 95% CI, 1.89 to 99.66], [HR, 9.22; 95% CI, 1.34 to 63.55], and [HR, 18.59; 95% CI, 2.54 to 135.88], respectively). In reclassification analyses, cyclin B1, TfR1, fibronectin, and combinations thereof improved the prognostic performance (C-index, 0.78 to 0.82–0.86; cfNRI, all P values <0.05).CONCLUSION: In ACC patients, the overexpression of cyclin B1, TfR1, and fibronectin and combinations thereof were associated with poor prognosis.


Subject(s)
Adrenocortical Carcinoma , Biomarkers , Cyclin B1 , Cyclins , Fibronectins , Humans , Mortality , Neoplasm Metastasis , Prognosis , Protein Array Analysis , Proteome , Proteomics , Receptors, Transferrin , Transferrin
17.
Article in English | WPRIM | ID: wpr-880485

ABSTRACT

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.


Subject(s)
Acetylation , Lysine/metabolism , Oryza/metabolism , Plant Proteins/metabolism , Protein Interaction Maps , Protein Processing, Post-Translational , Proteome/metabolism , Ubiquitin/metabolism , Ubiquitination
18.
Electron. j. biotechnol ; 39: 82-90, may. 2019. graf, ilus
Article in English | LILACS | ID: biblio-1052045

ABSTRACT

BACKGROUND: The infection of peanut (Arachis hypogaea L.) seed coat by the pathogenic fungus Aspergillus flavus has highly negative economic and health impacts. However, the molecular mechanism underlying such defense response remains poorly understood. This study aims to address this issue by profiling the transcriptomic and proteomic changes that occur during the infection of the resistant peanut cultivar J11 by A. flavus. RESULTS: Transcriptomic study led to the detection of 13,539 genes, among which 663 exhibited differential expression. Further functional analysis found the differentially expressed genes to encode a wide range of pathogenesis- and/or defense-related proteins such as transcription factors, pathogenesis-related proteins, and chitinases. Changes in the expression patterns of these genes might contribute to peanut resistance to A. flavus. On the other hand, the proteomic profiling showed that 314 of the 1382 detected protein candidates were aberrantly expressed as a result of A. flavus invasion. However, the correlation between the transcriptomic and proteomic data was poor. We further demonstrated by in vitro fungistasis tests that hevamine-A, which was enriched at both transcript and protein levels, could directly inhibit the growth of A. flavus. Conclusions: The results demonstrate the power of complementary transcriptomic and proteomic analyses in the study of pathogen defense and resistance in plants and the chitinase could play an important role in the defense response of peanut to A. flavus. The current study also constitutes the first step toward building an integrated omics data platform for the development of Aspergillus-resistant peanut cultivars


Subject(s)
Arachis/genetics , Proteome/analysis , Transcriptome , Arachis/microbiology , Aspergillus flavus/physiology , Seeds/genetics , Gene Expression , Chitinases , Aflatoxins , Disease Resistance/genetics , Real-Time Polymerase Chain Reaction , RNA-Seq
19.
Braz. oral res. (Online) ; 33: e043, 2019. tab, graf
Article in English | LILACS | ID: biblio-1001605

ABSTRACT

Abstract: Proteomic techniques have become popular in medicine and dentistry because of their widespread use in analyzing bodily fluids such as blood, saliva, urine, and gingival crevicular fluids as well as hard tissues such as enamel, dentine, and cementum. This review is a guide to proteomic techniques in general dentistry, summarizing techniques and their clinical application in understanding and diagnosing diseases and their use in identifying biomarkers of various diseases.


Subject(s)
Humans , Saliva/chemistry , Sjogren's Syndrome/diagnosis , Proteome , Proteomics/methods , Salivary Proteins and Peptides/chemistry , Mass Spectrometry/methods , Mouth Neoplasms/diagnosis , Biomarkers/chemistry , Electrophoresis, Polyacrylamide Gel
20.
São Paulo; s.n; s.n; 2019. 123 p. graf, tab.
Thesis in Portuguese | LILACS | ID: biblio-1049822

ABSTRACT

Xanthomonas citri subsp. citri, é uma bactéria pertencente à classe das Gamaproteobactérias, fitopatogênica, que exibe uma especificidade patógeno-hospedeiro extremamente alta. X. citri infecta plantas do gênero Citrus, causando o cancro cítrico, uma doença destrutiva encontrada em cultivos ao redor do mundo. Esta bactéria apresenta em seu genoma 34 genes que codificam proteínas relacionadas com o metabolismo do segundo mensageiro c-di-GMP. Em geral, níveis elevados de c-di-GMP favorecem a sessilidade e a produção de exopolissacarídeos, enquanto níveis mais baixos resultam em maior motilidade e aumento na dispersão do biofilme. Com o intuito inicial de buscar novos alvos de X. citri que dependessem dos níveis intracelulares desse segundo mensageiro, foram analisados os proteomas de linhagens mutantes em diguanilato ciclases específicas. Nas análises proteômicas por eletroforese bidimensional foram identificadas 15 proteínas diferencialmente expressas presentes em mais de um dos proteomas dos mutantes analisados. Entre estas, duas proteínas reguladoras de resposta e preditas de participar de sistemas de dois componentes, XAC0834 e XAC3443, foram encontradas sendo mais expressas em mutantes que apresentavam fenótipo de alto c-di-GMP; enquanto uma proteína hipotética provavelmente presente na membrana, XAC3657, estava mais expressa em linhagens com fenótipos relacionados a baixos níveis de c-di-GMP. Por meio de uma análise por qRT-PCR foi verificado que os níveis de mRNA para XAC0834 e XAC3443 não variam entre as linhagens e, portanto, a diferença nos níveis de expressão destas proteínas deve ocorrer póstranscricionalmente. Como os sistemas de dois componentes e proteínas de membrana são importantes para a adaptação das bactérias a diferentes condições ambientais, o objetivo do presente trabalho foi a caracterização funcional de XAC0834, XAC3433 e XAC3657, com maiorênfase em XAC0834 e na provável proteína sensora cognata, XAC0835, de forma a contribuir para a melhor compreensão dos processos de regulação da virulência de bactérias. Na análise da organização gênica dos genes que codificam estas proteínas, foi verificado que os genes XAC0834 e XAC0835 formam um operon, juntamente com a tioesterase XAC0833 e, portanto, o nível transcricional destes genes ocorre pelos mesmos reguladores, apoiando a hipótese de se tratarem de um sistema de dois componentes; assim como os genes XAC3442 e XAC3443. Utilizando uma linhagem mutante em XAC0834, mostramos que esta proteína impacta positivamente a motilidade sliding e a formação de biofilme, e tem efeito contrário no crescimento de X. citri em meio rico 2xTY e na motilidade twitching. Como estes fenótipos são modulados por c-di-GMP, é possível que a deleção deste gene altere significativamente os níveis de c-di-GMP nas células. Além disto, foi verificado que as proteínas XAC0835, XAC3443 e XAC3657 não afetam a motilidade sliding, mas, individualmente, XAC0835 é importante para a formação de biofilme; XAC3657 afeta negativamente o crescimento de X. citri em meio rico 2xTY; e XAC3443 afeta negativamente a motilidade twitching. Na análise do transcritoma da superexpressão de XAC0834, foi observado que havia aumento na expressão de genes relacionados ao sistema de secreção do tipo IV e na montagem do pilus do tipo IV, em comparação com a linhagem selvagem, o que pode estar relacionado aos fenótipos observados. Este trabalho forneceu subsídios importantes para a compreensão do papel fisiológico do sistema de dois componentes XAC0834/XAC0835, assim como do regulador de resposta XAC3443 e da proteína hipotética, XAC3657, em X. citri, o que pode contribuir para o entendimento da relação de c-di-GMP com os sistemas de dois componentes


Xanthomonas citri subsp. citri, is a phytopathogenic Gammaproteobacteria, with extremely high pathogen-host specificity. X. citri infects plants of the genus Citrus, causing citrus canker, a destructive disease found in crops around the world. The genome of X. citri pv. citri 306 (XAC 306) contains 34 genes encoding proteins related to the second messenger c-di-GMP metabolism. In general, high levels of c-di-GMP favor the sessility and exopolysaccharide production, whereas lower levels result in greater motility and increased biofilm dispersion. In order to initially search for new X. citri targets that depend on the intracellular levels of this second messenger, the proteomes of specific diguanylate cyclase mutant strains were analyzed by two-dimensional electrophoresis. Fifteen differentially expressed proteins present in more than one of the mutant proteomes compared to wild type were identified. Among these, two proteins predicted to participate as response regulators in two-component systems, XAC0834 and XAC3443, were found to be more expressed in mutants with high c-di-GMP phenotypes; whereas a hypothetical membrane protein, XAC3657, was more expressed in strains with low cdi-GMP-related phenotypes. Relative mRNA levels for XAC0834 and XAC3443, as determined by qRT-PCR, do not vary among the analyzed strains, suggesting post-transcriptional regulation. Because two-component systems and membrane proteins are important for the adaptation of bacteria to different environmental conditions, the aim of this work was the functional characterization of XAC0834, XAC3433 and XAC3657, with greater emphasis on XAC0834 and its probable cognate sensor protein, XAC0835, contributing to a better understanding of the processes of bacterial virulence regulation. Genes XAC0834 and XAC0835 form an operon, together with the XAC0833 coding for a thioesterase, suggesting that they are co-regulated, aswell as the XAC3442 and XAC3443 genes. Using a mutant strain in XAC0834, we show that this protein positively impacts sliding motility and biofilm formation and has the opposite effect on X. citri growth in rich medium and twitching motility. Because these phenotypes are modulated by c-di-GMP, deletion of this gene may alter cellular c-di-GMP levels. In addition, we found that XAC0835, XAC3443 and XAC3657 proteins do not affect sliding motility, but XAC0835 is important for biofilm formation; XAC3657 negatively affects X. citri growth in rich medium; and XAC3443 negatively affects twitching motility. The RNA-seq transcriptome of X. citri overexpressing XAC0834 was compared to the control strain, and there was an increase in the expression of genes for the type IV secretion system and the assembly of the type IV pilus, which may be related to the observed phenotypes. This work provided important insights for understanding the physiological role of the XAC0834/XAC0835 two-component system as well as the XAC3443 response regulator and the hypothetical protein XAC3657, in X. citri which may contribute to the understanding of the relationship of c- di-GMP with two-component systems


Subject(s)
Xanthomonas/metabolism , Citrus/classification , Biofilms , Proteome/analysis , Molecular Biology
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