2,743 research outputs found

    Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification

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    Proteins can move from blood circulation into salivary glands through active transportation, passive diffusion or ultrafiltration, some of which are then released into saliva and hence can potentially serve as biomarkers for diseases if accurately identified. We present a novel computational method for predicting salivary proteins that come from circulation. The basis for the prediction is a set of physiochemical and sequence features we found to be discerning between human proteins known to be movable from circulation to saliva and proteins deemed to be not in saliva. A classifier was trained based on these features using a support-vector machine to predict protein secretion into saliva. The classifier achieved 88.56% average recall and 90.76% average precision in 10-fold cross-validation on the training data, indicating that the selected features are informative. Considering the possibility that our negative training data may not be highly reliable (i.e., proteins predicted to be not in saliva), we have also trained a ranking method, aiming to rank the known salivary proteins from circulation as the highest among the proteins in the general background, based on the same features. This prediction capability can be used to predict potential biomarker proteins for specific human diseases when coupled with the information of differentially expressed proteins in diseased versus healthy control tissues and a prediction capability for blood-secretory proteins. Using such integrated information, we predicted 31 candidate biomarker proteins in saliva for breast cancer

    Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network

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    Determining the body fluids where secreted proteins can be secreted into is important for protein function annotation and disease biomarker discovery. In this study, we developed a network-based method to predict which kind of body fluids human proteins can be secreted into. For a newly constructed benchmark dataset that consists of 529 human-secreted proteins, the prediction accuracy for the most possible body fluid location predicted by our method via the jackknife test was 79.02%, significantly higher than the success rate by a random guess (29.36%). The likelihood that the predicted body fluids of the first four orders contain all the true body fluids where the proteins can be secreted into is 62.94%. Our method was further demonstrated with two independent datasets: one contains 57 proteins that can be secreted into blood; while the other contains 61 proteins that can be secreted into plasma/serum and were possible biomarkers associated with various cancers. For the 57 proteins in first dataset, 55 were correctly predicted as blood-secrete proteins. For the 61 proteins in the second dataset, 58 were predicted to be most possible in plasma/serum. These encouraging results indicate that the network-based prediction method is quite promising. It is anticipated that the method will benefit the relevant areas for both basic research and drug development

    PUEPro : A Computational Pipeline for Prediction of Urine Excretory Proteins

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    This work is supported by the National Natural Science Foundation of China (Grant Nos. 81320108025, 61402194, 61572227), Development Project of Jilin Province of China (20140101180JC) and China Postdoctoral Science Foundation (2014T70291).Postprin

    MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions

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    During blood feeding haematophagous arthropods inject into their hosts a cocktail of salivary proteins whose main role is to counteract host haemostasis, inflammation and immunity. However, animal body fluids are known to also carry miRNAs. To get insights into saliva and salivary gland miRNA repertoires of the African malaria vector Anopheles coluzzii we used small RNA-Seq and identified 214 miRNAs, including tissue-enriched, sex-biased and putative novel anopheline miRNAs. Noteworthy, miRNAs were asymmetrically distributed between saliva and salivary glands, suggesting that selected miRNAs may be preferentially directed toward mosquito saliva. The evolutionary conservation of a subset of saliva miRNAs in Anopheles and Aedes mosquitoes, and in the tick Ixodes ricinus, supports the idea of a non-random occurrence pointing to their possible physiological role in blood feeding by arthropods. Strikingly, eleven of the most abundant An. coluzzi saliva miRNAs mimicked human miRNAs. Prediction analysis and search for experimentally validated targets indicated that miRNAs from An. coluzzii saliva may act on host mRNAs involved in immune and inflammatory responses. Overall, this study raises the intriguing hypothesis that miRNAs injected into vertebrates with vector saliva may contribute to host manipulation with possible implication for vector-host interaction and pathogen transmission

    Als3 is a Candida albicans invasin that binds to cadherins and induces endocytosis by host cells.

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    Candida albicans is the most common cause of hematogenously disseminated and oropharyngeal candidiasis. Both of these diseases are characterized by fungal invasion of host cells. Previously, we have found that C. albicans hyphae invade endothelial cells and oral epithelial cells in vitro by inducing their own endocytosis. Therefore, we set out to identify the fungal surface protein and host cell receptors that mediate this process. We found that the C. albicans Als3 is required for the organism to be endocytosed by human umbilical vein endothelial cells and two different human oral epithelial lines. Affinity purification experiments with wild-type and an als3delta/als3delta mutant strain of C. albicans demonstrated that Als3 was required for C. albicans to bind to multiple host cell surface proteins, including N-cadherin on endothelial cells and E-cadherin on oral epithelial cells. Furthermore, latex beads coated with the recombinant N-terminal portion of Als3 were endocytosed by Chinese hamster ovary cells expressing human N-cadherin or E-cadherin, whereas control beads coated with bovine serum albumin were not. Molecular modeling of the interactions of the N-terminal region of Als3 with the ectodomains of N-cadherin and E-cadherin indicated that the binding parameters of Als3 to either cadherin are similar to those of cadherin-cadherin binding. Therefore, Als3 is a fungal invasin that mimics host cell cadherins and induces endocytosis by binding to N-cadherin on endothelial cells and E-cadherin on oral epithelial cells. These results uncover the first known fungal invasin and provide evidence that C. albicans Als3 is a molecular mimic of human cadherins

    The Salivary Secretome

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    Recently, proteomics has emerged as an important tool for understanding biological systems, protein–protein interactions, and networks that ultimately lead to a deeper understanding of the underlying mechanisms of certain diseases. More recently, the study of secretomes, a type of proteomics, has also been highlighted as a potential next step in the field of diagnosis/prognosis. The secretome is the set of proteins expressed by an organism and secreted into the extracellular space, comprising 13–20% of all proteins. Since almost all, if not all, organs produce secretomes, this means that it is possible to study secretomes and trace these proteins back to their origin, supporting the idea that this could indeed be very important in diagnosing certain diseases. This is often combined with techniques such as mass spectrometry to measure the secretome of, for example, a particular tissue, and bioinformatics tools and databases to give us an idea of what to expect (prediction). In this paper, we will give a general overview of this world, but with a focus on the new bioinformatics tools and databases, their advantages and disadvantages, as well as a deeper look at isolation systems for proteomes, specifically salivary secretomes. Indeed, the salivary secretome represents a valuable new tool capable of providing insights into immunopathology and potentially aiding in diagnostics. Furthermore, we will explore applications of these methods and give an idea of what the future holds for such promising techniques: Salivary secretome in conjunction with bioinformatics tools/databases in the diagnosis of diseases (such as diabetes, Sjogren’s syndrome, and cardiovascular disease)

    A deeper insight into the sialome of male and female Culex quinquefasciatus mosquitoes

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    Introduction: During evolution, blood-feeding arthropods developed a complex salivary mixture that can interfere with host haemostatic and immune response, favoring blood acquisition and pathogen transmission. Therefore, a survey of the salivary gland contents can lead to the identification of molecules with potent pharmacological activity in addition to increase our understanding of the molecular mechanisms underlying the hematophagic behaviour of arthropods. The southern house mosquito, Culex quinquefasciatus, is a vector of several pathogenic agents, including viruses and filarial parasites that can affect humans and wild animals. Results: Previously, a Sanger-based transcriptome of the salivary glands (sialome) of adult C. quinquefasciatus females was published based on the sequencing of 503 clones organized into 281 clusters. Here, we revisited the southern mosquito sialome using an Illumina-based RNA-sequencing approach of both male and female salivary glands. Our analysis resulted in the identification of 7,539 coding DNA sequences (CDS) that were functionally annotated into 25 classes, in addition to 159 long non-coding RNA (LncRNA). Additionally, comparison of male and female libraries allowed the identification of female-enriched transcripts that are potentially related to blood acquisition and/or pathogen transmission. Conclusion: Together, these findings represent an extended reference for the identification and characterization of the proteins containing relevant pharmacological activity in the salivary glands of C. quinquefasciatus mosquitoes.This work was supported by the Intramural Research Program of the Division of Intramural Research (AI001246 and AI000810), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH). This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov). Open Access funding provided by the National Institutes of Health (NIH).S

    Biomarker profiles in serum and saliva of experimental Sjögren's syndrome: associations with specific autoimmune manifestations

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    Introduction Sjögren's syndrome (SS) is a systemic autoimmune disease that mainly targets the exocrine glands. The aim of this study was to investigate the involvement of 87 proteins measured in serum and 75 proteins analyzed in saliva in spontaneous experimental SS. In addition, we intended to compute a model of the immunological situation representing the overt disease stage of SS. Methods Nondiabetic, nonobese diabetic (NOD) mice aged 21 weeks were evaluated for salivary gland function, salivary gland inflammation and extraglandular disease manifestations. The analytes, comprising chemokines, cytokines, growth factors, autoantibodies and other biomarkers, were quantified using multi-analyte profile technology and fluorescence-activated cell sorting. Age-matched and sex-matched Balb/c mice served as a reference. Results We found NOD mice to exhibit impaired salivary flow, glandular inflammation and increased secretory SSB (anti-La) levels. Thirty-eight biomarkers in serum and 34 in saliva obtained from NOD mice were significantly different from those in Balb/c mice. Eighteen biomarkers in serum and three chemokines measured in saliva could predict strain membership with 80% to 100% accuracy. Factor analyses identified principal components mostly correlating with one clinical aspect of SS and having distinct associations with components extracted from other families of proteins. Conclusion Autoimmune manifestations of SS are greatly independent and associated with various immunological processes. However, CD40, CD40 ligand, IL-18, granulocyte chemotactic protein-2 and anti-muscarinic M3 receptor IgG3 may connect the different aspects of SS. Processes related to the adaptive immune system appear to promote SS with a strong involvement of T-helper-2 related proteins in hyposalivation. This approach further established saliva as an attractive biofluid for biomarker analyses in SS and provides a basis for the comparison and selection of potential drug targets and diagnostic markers

    New Targets for Zika

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    Protein target highlights in CASP15: Analysis of models by structure providers

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    We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology
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