SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database.

BMC Bioinformatics. 2018 Apr 20;19(1):149

Authors: Anekthanakul K, Hongsthong A, Senachak J, Ruengjitchatchawalya M

Abstract
BACKGROUND: Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo. In this study, we developed an efficient computational method, SpirPep, which offers many advantages over the currently available tools.
RESULTS: The SpirPep web application tool is a one-stop analysis and visualization facility to assist bioactive peptide discovery. The tool is equipped with 15 customized enzymes and 1-3 miscleavage options, which allows in silico digestion of protein sequences encoded by protein-coding genes from single, multiple, or genome-wide scaling, and then directly classifies the peptides by bioactivity using an in-house database that contains bioactive peptides collected from 13 public databases. With this tool, the resulting peptides are categorized by each selected enzyme, and shown in a tabular format where the peptide sequences can be tracked back to their original proteins. The developed tool and webpages are coded in PHP and HTML with CSS/JavaScript. Moreover, the tool allows protein-peptide alignment visualization by Generic Genome Browser (GBrowse) to display the region and details of the proteins and peptides within each parameter, while considering digestion design for the desirable bioactivity. SpirPep is efficient; it takes less than 20 min to digest 3000 proteins (751,860 amino acids) with 15 enzymes and three miscleavages for each enzyme, and only a few seconds for single enzyme digestion. Obviously, the tool identified more bioactive peptides than that of the benchmarked tool; an example of validated pentapeptide (FLPIL) from LC-MS/MS was demonstrated. The web and database server are available at http://spirpepapp.sbi.kmutt.ac.th .
CONCLUSION: SpirPep, a web-based bioactive peptide discovery application, is an in silico-based tool with an overview of the results. The platform is a one-stop analysis and visualization facility; and offers advantages over the currently available tools. This tool may be useful for further bioactivity analysis and the quantitative discovery of desirable peptides.

PMID: 29678128 [PubMed - in process]

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"systems biology"

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"systems biology"

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New suggestion title: Bone Marrow - Mesenchymal Stem Cells Impacts on the U937 Cells in the Presence of Staphylococcal Enterotoxin B (SEB).

Clin Exp Pharmacol Physiol. 2018 Apr 14;:

Authors: Ejtehadifar M, Halabian R, Ghazavi A, Khansarinejad B, Mosayebi G, Imani Fooladi AA

Abstract
The growing resistance against conventional chemotherapy in acute myeloid leukemia (AML) is a noticeable clinical concern. Therefore, many researchers are looking for novel substances to overcome drug resistance in cancer.Staphylococcal enterotoxin B (SEB) is a superantigen (SAg) and a promising compound whichhas lethal effects on malignant cells. Inthis unprecedented study, SEB was used against U937 cells in a co-culture system in the presence of human bone marrow-mesenchymal stem cells (hBM-MSCs). The effects of hBM-MSCs on the proliferation and survival of U937 cell line with SEB was assessed using MTT assay and AnnexinV/PI flowcytometry, respectively. Moreover, the expression of IL-6, IL-10, TGF-β, and IKKb was evaluated by real-time PCR technique. Same experiments were also carried out using hBM-MSCs-conditioned medium (hBM-MSCs-CM).The results showed that SEB reduced the proliferation and survival of U937 cell line, but hBM-MSCs or hBM-MSCs-CM suppressed the effects of SEB. Furthermore, real-timePCR demonstrated that SEB could decrease the expression of IL-6, IL-10, and TGF-β in hBM-MSCs (P<0.05), while the production of IKKb was increased in comparison with the control group.These findings help us to have a broader understanding ofthe usage of SEB in the treatment of hematological malignancies, especially if it is targeted against hBM-MSCs to disrupt their supportive effects on malignant cells. This article is protected by copyright. All rights reserved.

PMID: 29655181 [PubMed - as supplied by publisher]

Proteomic approach and expression analysis revealed the differential expression of predicted leptospiral proteases capable of ECM degradation.

Biochim Biophys Acta. 2018 Apr 11;:

Authors: Gunasekaran D, Sikha T, Pinto SM, Kiran Kumar M, Patel K, Kumar M, Kumar V, Tennyson J, Satheeshkumar PK, Gowda H, Keshava Prasad TS, Madanan MG

Abstract
Leptospira, the causative agent of leptospirosis is known to have many proteases with potential to degrade extracellular matrix. However, a multipronged approach to identify, classify, characterize and elucidate their role has not been attempted. Our proteomic approach using high-resolution LC-MS/MS analysis of Triton X-114 fractions of Leptospira interrogans resulted in the identification of 104 proteases out of 130 proteases predicted by MEROPS. In Leptospira approximately 3.5% of the genome complements for proteases, which include catalytic types of metallo-, serine-, cysteine-, aspartic-, threonine- and asparagine- peptidases. Comparison of proteases from different serovars revealed that M04, M09B, M14A, M75, M28A, A01 and U73 protease families are exclusively present in pathogenic form. The M23 and S33 protease families are represented with >14 members in Leptospira. The differential expression under physiological temperature (37 °C) and osmolarity (300 mOsM) showed that proteases belonging to the catalytic type of Metallo-peptidases are upregulated significantly in pathogenic conditions. In silico prediction and characterization of the proteases revealed that several proteases are membrane anchored and secretory, classical as well as non-classical system. The study demonstrates the diversity and complexity of proteases, while maintaining conservation across the serovars in Leptospira and their differential expression under pathogenic conditions.

PMID: 29654978 [PubMed - as supplied by publisher]

FOXO1 inhibition potentiates endothelial angiogenic functions in diabetes via suppression of ROCK1/Drp1-mediated mitochondrial fission.

Biochim Biophys Acta. 2018 Apr 11;:

Authors: Shi Y, Fan S, Wang D, Huyan T, Chen J, Chen J, Su J, Li X, Wang Z, Xie S, Yun C, Li X, Tie L

Abstract
Diabetes-induced endothelial cell (EC) dysfunction and neovascularization impairment constitute vascular complications with limited treatment regimens. Transcription factor FOXO1 is a key angiogenic regulator and plays a pathologic role in progression of diabetes. The present study was designed to determine the involvement of FOXO1 in impaired EC function and post-ischemic neovascularization in diabetes and investigate underlying mechanisms. We found that FOXO1-selective inhibitor AS1842856 improved blood flow recovery and capillary density in ischemic hindlimb, and rescued the delay of wound closure with a concomitant augmentation of mean perfusion rate in diabetic mice. In vitro, treatment with AS1842856 or FOXO1 siRNA abrogated high glucose-induced apoptosis and ameliorated capillary tube formation in human umbilical vein endothelial cells (HUVECs). FOXO1 inhibition relieved alterations in mitochondrial networks and significantly suppressed the overproduction of mitochondrial reactive oxygen species (mtROS) induced by high glucose in ECs. Expression of dynamin-relatedprotein-1 (Drp1) and phosphorylation at Ser616, a protein required for mitochondrial fission, were enhanced by hyperglycemia, which could be neutralized by FOXO1 inhibition. Moreover, the transcription of Rho-associated coiled-coil containing protein kinase 1 (ROCK1), which phosphorylates Drp1 at Ser616, was shown by luciferase assay to be directly regulated by FOXO1. These findings suggested that FOXO1 is critical to preserve mitochondrial quantity and function in ECs, and FOXO1 may serve as a therapeutic target for microvascular complications of diabetes.

PMID: 29654945 [PubMed - as supplied by publisher]

Characterization of therapeutic antibodies in the presence of human serum proteins by AU-FDS analytical ultracentrifugation.

Anal Biochem. 2018 Apr 11;:

Authors: Wright RT, Hayes DB, Stafford WF, Sherwood PJ, Correia JJ

Abstract
The preclinical characterization of biopharmaceuticals seeks to determine the stability, state of aggregation, and interaction of the antibody/drug with other macromolecules in serum. Analytical ultracentrifugation is the best experimental method to understand these factors. Sedimentation velocity experiments using the AU-FDS system were performed in order to quantitatively characterize the nonideality of fluorescently labeled therapeutic antibodies in high concentrations of human serum proteins. The two most ubiquitous serum proteins are human serum albumin, HSA and γ-globulins, predominantly IgG. Tracer experiments were done pairwise as a function of HSA, IgG, and therapeutic antibody concentration. The sedimentation coefficient for each fluorescently labeled component as a function of the concentration of the unlabeled component yields the hydrodynamic nonideality (ks). This generates a 3x3 matrix of ks values that describe the nonideality of each pairwise interaction. The ks matrix is validated by fitting both 2:1 mixtures of HSA (1-40 mg/ml) and IgG (0.5-20 mg/ml) as serum mimics, and human serum dilutions (10-100%). The data are well described by SEDANAL global fitting with the ks nonideality matrix. The ks values for antibodies are smaller than expected and appear to be masked by weak association. Global fitting to ks and K2 models significantly improve the fits.

PMID: 29654743 [PubMed - as supplied by publisher]

Untargeted GC-MS Metabolomics.

Methods Mol Biol. 2018;1738:133-147

Authors: Papadimitropoulos MP, Vasilopoulou CG, Maga-Nteve C, Klapa MI

Abstract
Untargeted metabolomics refers to the high-throughput analysis of the metabolic state of a biological system (e.g., tissue, biological fluid, cell culture) based on the concentration profile of all measurable free low molecular weight metabolites. Gas chromatography-mass spectrometry (GC-MS), being a highly sensitive and high-throughput analytical platform, has been proven a useful tool for untargeted studies of primary metabolism in a variety of applications. As an omic analysis, GC-MS metabolomics is a multistep procedure; thus, standardization of an untargeted GC-MS metabolomics protocol requires the integrated optimization of pre-analytical, analytical, and computational steps. The main difference of GC-MS metabolomics compared to other metabolomics analytical platforms, including liquid chromatography-MS, is the need for the derivatization of the metabolite extracts into volatile and thermally stable derivatives, the latter being quantified in the metabolic profiles. This analytical step requires special care in the optimization of the untargeted GC-MS metabolomics experimental protocol. Moreover, both the derivatization of the original sample and the compound fragmentation that takes place in GC-MS impose specialized GC-MS metabolomic data identification, quantification, normalization and filtering methods. In this chapter, we describe the integrated protocol of untargeted GC-MS metabolomics with both the analytical and computational steps, focusing on the GC-MS specific parts, and provide details on any sample depending differences.

PMID: 29654587 [PubMed - in process]

DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity.

Proc Natl Acad Sci U S A. 2018 Apr 13;:

Authors: Anchang B, Davis KL, Fienberg HG, Williamson BD, Bendall SC, Karacosta LG, Tibshirani R, Nolan GP, Plevritis SK

Abstract
An individual malignant tumor is composed of a heterogeneous collection of single cells with distinct molecular and phenotypic features, a phenomenon termed intratumoral heterogeneity. Intratumoral heterogeneity poses challenges for cancer treatment, motivating the need for combination therapies. Single-cell technologies are now available to guide effective drug combinations by accounting for intratumoral heterogeneity through the analysis of the signaling perturbations of an individual tumor sample screened by a drug panel. In particular, Mass Cytometry Time-of-Flight (CyTOF) is a high-throughput single-cell technology that enables the simultaneous measurements of multiple ([Formula: see text]40) intracellular and surface markers at the level of single cells for hundreds of thousands of cells in a sample. We developed a computational framework, entitled Drug Nested Effects Models (DRUG-NEM), to analyze CyTOF single-drug perturbation data for the purpose of individualizing drug combinations. DRUG-NEM optimizes drug combinations by choosing the minimum number of drugs that produce the maximal desired intracellular effects based on nested effects modeling. We demonstrate the performance of DRUG-NEM using single-cell drug perturbation data from tumor cell lines and primary leukemia samples.

PMID: 29654148 [PubMed - as supplied by publisher]

Deregulation of LIMD1-VHL-HIF-1α-VEGF pathway is associated with different stages of cervical cancer.

Biochem J. 2018 Apr 13;:

Authors: Chakraborty C, Mitra S, Roychowdhury A, Samadder S, Dutta S, Roy A, Das P, Mandal RK, Sharp TV, Roychoudhury S, Panda CK

Abstract
To understand the mechanism of cellular stress in basal-parabasal layers of normal-cervix and during different stages of cervical carcinoma, we analyzed the alterations (expression/methylation/copy-number variation/mutation) of HIF-1α and its associated genes LIMD1, VHL and VEGF in disease free normal-cervix (n=9), adjacent normal-cervix of tumors (n=70), CIN (n=32), CACX (n=174) samples and two CACX cell lines. In basal-parabasal layers of normal-cervix, LIMD1 showed high protein-expression while low protein expression of VHL was concordant with high expression of HIF-1α and VEGF irrespective of HPV16 infection. This was in concordance with the low promoter methylation of LIMD1 and high in VHL in the basal-parabasal layers of normal-cervix. LIMD1 expression was significantly reduced while VHL expression was unchanged during different stages of cervical carcinoma. This was in concordance with their frequent methylation during different stages of this tumor. In different stages of cervical carcinoma, the expression pattern of HIF-1α and VEGF was high as seen in basal-parabasal layers and inversely correlated with the expression of LIMD1 and VHL. This was validated by demethylation experiments using 5-aza-dC in CACX cell lines. Additional deletion of LIMD1 and VHL in CIN/CACX provided an additional growth advantage during cervical carcinogenesis through reduced expression of genes and associated with poor prognosis of patients. Our data showed that overexpression of HIF-1α and its target gene VEGF in the basal-parabasal layers of normal-cervix was due to frequent inactivation of VHL by its promoter methylation. This profile was maintained during different stages of cervical carcinoma with additional methylation/deletion of VHL and LIMD1.

PMID: 29654110 [PubMed - as supplied by publisher]

Suspended polyhydroxyalkanoate microspheres as 3D carriers for mammalian cell growth.

Artif Cells Nanomed Biotechnol. 2018 Apr 13;:1-11

Authors: Wei DX, Dao JW, Liu HW, Chen GQ

Abstract
Different forms of biopolyester PHBVHHx microspheres were prepared so as to compare the mammalian cell behaviors in suspension cultivation system. Based on a microbial terpolyester PHBVHHx consisting of 3-hydroxybutyrate (HB), 3-hydroxyvalerate (HV), and 3-hydroxyhexanoate (HHx), solid microspheres (SMSs), hollow microspheres (HMSs), and porous microspheres (PMS) were successfully prepared by a modified solvent evaporation method involving gas-in-oil-in-water (G1/O/W2) double emulsion, water-in-oil-in-water (W1/O/W2) double emulsion and oil-in-water (O/W) single emulsion, respectively. Generally, PMSs have diameters ranging from 330 to 400 μm with pore sizes of 10 to 60 μm. The pores inside the PMSs were found well interconnected compared with PHBVHHx prepared by the traditional solvent evaporation method, resulting in the highest water uptake ratio. When inoculated with human osteoblast-like cells lasting 6 days, PMS showed much better cell attachment and proliferation compared with other less porous microspheres due to its large inner space as a 3 D carrier. Cell migration towards surface and other interconnected inner pores was clearly observable. Dead or apoptotic cells were found more common among less porous SMSs or HMSs compared with highly porous PMSs. It is therefore concluded that porous PHBVHHx microspheres with larger surface open pores and interconnected inner pores can serve as a carrier or scaffold supporting more and better cell growth for either injectable purposes or simply supporting cell growth.

PMID: 29653500 [PubMed - as supplied by publisher]

25 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/04/14

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

25 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/04/14

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

34 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/04/13

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

32 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/04/13

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.