- Comparative proteomic analysis of plasma of children with congenital heart disease. [Journal Article]
- EElectrophoresis 2019 May 09
- Congenital heart disease is one of the largest class of birth defects. Eight subjects with ventricular septal defect (VSD, a kind of congenital heart disease) and 11 health children were enrolled in …
Congenital heart disease is one of the largest class of birth defects. Eight subjects with ventricular septal defect (VSD, a kind of congenital heart disease) and 11 health children were enrolled in tandem mass tags label-based quantitative proteomic analysis to compare plasma proteins differentially abundance. A total of 66 proteins were significantly upregulated or downregulated in VSD patients compared with healthy children. These proteins were involved in pathways linked to platelet activation, fructose and mannose metabolism, complement and coagulation cascades, glycolysis/gluconeogenesis, regulation of actin cytoskeleton, and carbon metabolism. The amount of ten proteins changed significantly (p < 0.05) in newly recruited 30 VSD compared with 15 control children, which were validated by ELISA. The areas under the receiver operating characteristic curve values of fructose-bisphosphate aldolase B (ALDOB) and thymosin beta-4 (Tβ4) were higher than those of other candidate proteins. ALDOB and Tβ4 might be potential biomarkers applied for identifying VSD in the further works.
- Flux prediction using artificial neural network (ANN) for the upper part of glycolysis. [Journal Article]
- PlosPLoS One 2019; 14(5):e0216178
- The selection of optimal enzyme concentration in multienzyme cascade reactions for the highest product yield in practice is very expensive and time-consuming process. The modelling of biological path…
The selection of optimal enzyme concentration in multienzyme cascade reactions for the highest product yield in practice is very expensive and time-consuming process. The modelling of biological pathways is a difficult process because of the complexity of the system. The mathematical modelling of the system using an analytical approach depends on the many parameters of enzymes which rely on tedious and expensive experiments. The artificial neural network (ANN) method has been successively applied in different fields of science to perform complex functions. In this study, ANN models were trained to predict the flux for the upper part of glycolysis as inferred by NADH consumption, using four enzyme concentrations i.e., phosphoglucoisomerase, phosphofructokinase, fructose-bisphosphate-aldolase, triose-phosphate-isomerase. Out of three ANN algorithms, the neuralnet package with two activation functions, "logistic" and "tanh" were implemented. The prediction of the flux was very efficient: RMSE and R2 were 0.847, 0.93 and 0.804, 0.94 respectively for logistic and tanh functions using a cross validation procedure. This study showed that a systemic approach such as ANN could be used for accurate prediction of the flux through the metabolic pathway. This could help to save a lot of time and costs, particularly from an industrial perspective. The R-code is available at: https://github.com/DSIMB/ANN-Glycolysis-Flux-Prediction.
- Fructose-Bisphosphate Aldolase A Regulates Hypoxic Adaptation in Hepatocellular Carcinoma and Involved with Tumor Malignancy. [Journal Article]
- DDDig Dis Sci 2019 Apr 30
- CONCLUSIONS: Data indicated that ALDOA is significantly upregulated in HCC tissue and is closely related to HCC malignancy. ALDOA is likely to regulate HCC progression by regulating HCC tumor cell proliferation, apoptosis, and invasion in both normoxic and hypoxic condition.
- Proteomic analysis of the similarities and differences of soil drought and polyethylene glycol stress responses in wheat (Triticum aestivum L.). [Journal Article]
- PMPlant Mol Biol 2019 Apr 05
- Our results reveal both soil drought and PEG can enhance malate, glutathione and ascorbate metabolism, and proline biosynthesis, whereas soil drought induced these metabolic pathways to a greater deg…
Our results reveal both soil drought and PEG can enhance malate, glutathione and ascorbate metabolism, and proline biosynthesis, whereas soil drought induced these metabolic pathways to a greater degree than PEG. Polyethylene glycol (PEG) is widely used to simulate osmotic stress, but little is known about the different responses of wheat to PEG stress and soil drought. In this study, isobaric tags for relative quantification (iTRAQ)-based proteomic techniques were used to determine both the proteomic and physiological responses of wheat seedlings to soil drought and PEG. The results showed that photosynthetic rate, stomatal conductance, intercellular CO2 concentration, transpiration rate, maximum potential efficiency of PS II, leaf water content, relative electrolyte leakage, MDA content, and free proline content exhibited similar responses to soil drought and PEG. Approximately 15.8% of differential proteins were induced both by soil drought and PEG. Moreover, both soil drought and PEG inhibited carbon metabolism and the biosynthesis of some amino acids by altering the accumulation of glyceraldehyde-3-phosphate dehydrogenase, ribulose-bisphosphate carboxylase, and phosphoglycerate kinase, but they both enhanced the metabolism of malate, proline, glutathione, and ascorbate by increasing the accumulation of key enzymes including malate dehydrogenase, monodehydroascorbate reductase, pyrroline-5-carboxylate dehydrogenase, pyrroline-5-carboxylate synthetase, ascorbate peroxidase, glutathione peroxidase, and glutathione S-transferase. Notably, the latter five of these enzymes were found to be more sensitive to soil drought. In addition, polyamine biosynthesis was specifically induced by increased gene expression and protein accumulation of polyamine oxidase and spermidine synthase under PEG stress, whereas fructose-bisphosphate aldolase and arginase were induced by soil drought. Therefore, present results suggest that PEG is an effective method to simulate drought stress, but the key proteins related to the metabolism of malate, glutathione, ascorbate, proline, and polyamine need to be confirmed under soil drought.
- Design of a mimotope-peptide based double epitope vaccine against disseminated candidiasis. [Journal Article]
- VVaccine 2019 Apr 24; 37(18):2430-2438
- Hematogenously disseminated candidiasis in humans is the third leading cause of nosocomial bloodstream infections in the US. There is no FDA approved antifungal vaccine or prophylactic/therapeutic an…
Hematogenously disseminated candidiasis in humans is the third leading cause of nosocomial bloodstream infections in the US. There is no FDA approved antifungal vaccine or prophylactic/therapeutic antibody for use in humans. We first reported novel synthetic peptide and glycopeptide vaccines against Candida albicans cell surface epitopes that protect mice against disseminated candidiasis. We showed that antibodies specific for the peptide Fba (derived from C. albicans cell surface protein fructose bisphosphate aldolase) or for C. albicans cell surface glycan epitope β-1, 2-mannotriose [β-(Man)3]) are both protective. This is an important step forward in vaccine design against disseminated candidiasis in humans. However, given the complexity of oligosaccharide synthesis, in this study we performed a new strategy for use of peptide mimotopes that structurally mimic the protective glycan epitope β-(Man)3 as surrogate immunogens that substitute for the glycan part of glycopeptide [β-(Man)3-Fba] vaccine. All five selected mimotopes are immunogenic in mice and three mimotopes were able to induce protection in mice against disseminated candidiasis. Furthermore, immunization with three mimotope-peptide conjugate vaccines was also able to induce specific antibody responses, and importantly, protection against disseminated candidiasis in mice. Therefore, our new design of a mimotope-peptide based double epitope vaccine against candidiasis is a potential vaccine candidate that is economical to produce, highly efficacious and safe for use in humans.
- Absolute diffusion measurements of active enzyme solutions by NMR. [Journal Article]
- JCJ Chem Phys 2019 Mar 28; 150(12):124201
- The diffusion of enzymes is of fundamental importance for many biochemical processes. Enhanced or directed enzyme diffusion can alter the accessibility of substrates and the organization of enzymes w…
The diffusion of enzymes is of fundamental importance for many biochemical processes. Enhanced or directed enzyme diffusion can alter the accessibility of substrates and the organization of enzymes within cells. Several studies based on fluorescence correlation spectroscopy report enhanced diffusion of enzymes upon interaction with their substrate or inhibitor. In this context, major importance is given to the enzyme fructose-bisphosphate aldolase, for which enhanced diffusion has been reported even though the catalysed reaction is endothermic. Additionally, enhanced diffusion of tracer particles surrounding the active aldolase enzymes has been reported. These studies suggest that active enzymes can act as chemical motors that self-propel and give rise to enhanced diffusion. However, fluorescence studies of enzymes can, despite several advantages, suffer from artefacts. Here, we show that the absolute diffusion coefficients of active enzyme solutions can be determined with Pulsed Field Gradient Nuclear Magnetic Resonance (PFG-NMR). The advantage of PFG-NMR is that the motion of the molecule of interest is directly observed in its native state without the need for any labelling. Furthermore, PFG-NMR is model-free and thus yields absolute diffusion constants. Our PFG-NMR experiments of solutions containing active fructose-bisphosphate aldolase from rabbit muscle do not show any diffusion enhancement for the active enzymes, nor the surrounding molecules. Additionally, we do not observe any diffusion enhancement of aldolase in the presence of its inhibitor pyrophosphate.
- Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism. [Journal Article]
- MGMol Genet Genomics 2019; 294(3):739-755
- The legume endosymbiont Sinorhizobium meliloti can utilize a broad range of carbon compounds to support its growth. The linear, six-carbon polyol galactitol is abundant in vascular plants and is meta…
The legume endosymbiont Sinorhizobium meliloti can utilize a broad range of carbon compounds to support its growth. The linear, six-carbon polyol galactitol is abundant in vascular plants and is metabolized in S. meliloti by the contribution of two loci SMb21372-SMb21377 and SMc01495-SMc01503 which are found on pSymB and the chromosome, respectively. The data suggest that several transport systems, including the chromosomal ATP-binding cassette (ABC) transporter smoEFGK, contribute to the uptake of galactitol, while the adjacent gene smoS encodes a protein for oxidation of galactitol into tagatose. Subsequently, genes SMb21374 and SMb21373, encode proteins that phosphorylate and epimerize tagatose into fructose-6-phosphate, which is further metabolized by the enzymes of the Entner-Doudoroff pathway. Of note, it was found that SMb21373, which was annotated as a 1,6-bis-phospho-aldolase, is homologous to the E. coli gene gatZ, which is annotated as encoding the non-catalytic subunit of a tagatose-1,6-bisphosphate aldolase heterodimer. When either of these genes was introduced into an Agrobacterium tumefaciens strain that carries a tagatose-6-phosphate epimerase mutation, they are capable of complementing the galactitol growth deficiency associated with this mutation, strongly suggesting that these genes are both epimerases. Phylogenetic analysis of the protein family (IPR012062) to which these enzymes belong, suggests that this misannotation is systemic throughout the family. S. meliloti galactitol catabolic mutants do not exhibit symbiotic deficiencies or the inability to compete for nodule occupancy.
- Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis. [Journal Article]
- SRSci Rep 2019 Mar 14; 9(1):4478
- The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinical…
The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.
- Fructose-1,6-bisphosphate aldolase is involved in Mycoplasma bovis colonization as a fibronectin-binding adhesin. [Journal Article]
- RVRes Vet Sci 2019; 124:70-78
- Mycoplasma bovis is a common pathogenic microorganism of cattle and represents an important hazard on the cattle industry. Adherence to host cells is a significant component of mycoplasma-pathogenesi…
Mycoplasma bovis is a common pathogenic microorganism of cattle and represents an important hazard on the cattle industry. Adherence to host cells is a significant component of mycoplasma-pathogenesis research. Fibronectin (Fn), an extracellular matrix protein, is a common host cell factor that can interact with the adhesions of pathogens. The aims of this study were to investigate the Fn-binding properties of M. bovis fructose-1,6-bisphosphate aldolase (FBA) and evaluate its role as a cell adhesion factor during mycoplasma colonization. The fba (MBOV_RS00435) gene of M. bovis was cloned and expressed, with the resulting recombinant protein used to prepare rabbit polyclonal antibodies. The purified recombinant FBA (rFBA) was shown to have fructose bisphosphate aldolase activity. Western blot indicated that FBA was an antigenically conserved protein in several M. bovis strains. Western blot combined with immunofluorescent assay (IFA) revealed that FBA was dual-localized to both cytoplasm and membrane in M. bovis. IFA showed that rFBA was able to adhere to embryonic bovine lung (EBL) cells. Meanwhile, an adhesion inhibition assay demonstrated that anti-rFBA antibodies could significantly block the adhesion of M. bovis to EBL cells. Moreover, a dose-dependent binding of rFBA to Fn was found by dot blotting and enzyme-linked immunosorbent assays. Together these results provided evidence that FBA is a surface-localized and antigenic protein of M. bovis, suggesting that it may function as a virulence determinant through interacting with host Fn.
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- Comparative physiological and leaf proteome analysis between drought-tolerant chickpea Cicer reticulatum and drought-sensitive chickpea C. arietinum. [Journal Article]
- JBJ Biosci 2019; 44(1)
- Comparative physiological and proteomic analysis were performed to understand the stress responses of two chickpea species (C. reticulatum and C. arietinum) against drought. Our study revealed that d…
Comparative physiological and proteomic analysis were performed to understand the stress responses of two chickpea species (C. reticulatum and C. arietinum) against drought. Our study revealed that drought stress reduced root length, leaf water content, and enhanced free proline content in both species. Effect of drought stress appeared to be greater in C. arietinum compared to C. reticulatum. A total of 24 differently expressed proteins were identified by using MALDI-TOF/ TOF-MS/MS in response to drought. The proteins involved in photosynthesis and energy mechanisms were up-regulated in C. reticulatum and down-regulated in C. arietinum under drought. Our results suggest that the photosynthesis capacity of C. reticulatum is greater than that of C. arietinum under drought stress. Abundance of proline and sucrose biosynthesis related proteins, glutamine synthetase and cyctosolic fructose-bisphosphate aldolase, respectively, also increased in C. reticulatum under drought stress. The findings of this proteome analysis will help in understanding the mechanism of drought resistance in chickpea and may be also helpful in developing drought-resistant transgenic plants.