Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.     

Lysosomal degradation of membrane lipids

The constitutive degradation of membrane components takes place in the acidic compartments of a cell, the endosomes and lysosomes. Sites of lipid degradation are intralysosomal membranes that are formed in endosomes, where the lipid composition is adjusted for degradation. Cholesterol is sorted out of the inner membranes, their content in bis(monoacylglycero)phosphate increases, and, most likely, sphingomyelin is degraded to ceramide. Together with endosomal and lysosomal lipid-binding proteins, the Niemann-Pick disease, type C2-protein, the GM2-activator, and the saposins sap-A, -B, -C, and -D, a suitable membrane lipid composition is required for degradation of complex lipids by hydrolytic enzymes.     

The EPR spectrum of cytochrome b-563 in the cytocrhome bf complex from spinach: (1993) FEBS Letters 164, 71–74

Blood group H antigen with globo-series structure, reacting with the monoclonal antibody MBrl, was isolated and characterized from human blood group O erythrocytes. The structure was identified by methylation analysis, direct probe mass spectrometry, and ¹H-nuclear magnetic resonance spectroscopy as shown below: Fucαl → 2Galβl → 3GalNAcβl → 3Galαl → 4Galβl → 4Glcβl → 1Cer     

The Practical and Pedagogical Advantages of an Ambigraphic Nucleic Acid Notation

The universally applied IUPAC notation for nucleic acids was adopted primarily to facilitate the mental association of G, A, T, C, and the related ambiguity characters with the bases they represent. However, it is possible to create a notation that offers greater support for the basic manipulations and analyses to which genetic sequences frequently are subjected. By designing a nucleic acid notation around ambigrams, it is possible to simplify the frequently applied process of reverse complementation and aid the visualization of palindromes. The ambigraphic notation presented here also uses common orthographic features such as stems and loops to highlight guanine and cytosine rich regions, support the derivation of ambiguity characters, and aid educators in teaching the fundamentals of molecular genetics.     

Mechanism of binding site conformational switching in the CD44-hyaluronan protein-carbohydrate binding interaction

The transmembrane protein CD44, which has been implicated in cancer biology and inflammation, mediates cell adhesion through multimeric interactions with the linear extracellular glycosaminoglycan hyaluronan (HA; in megadaltons). Affinity switching of CD44 from a low-affinity state to a high-affinity state is required for normal CD44 physiological function; crystal structures of the CD44 hyaluronan binding domain complexed with HA oligomers point to a conformational rearrangement at a binding site loop, leading to the formation of direct contact between the oligomer and an arginine side chain as a molecular basis for affinity switching. Here, all-atom explicit-solvent molecular dynamics simulations were used to characterize the dynamics and thermodynamics of oligomeric hyaluronan (oHA) and its two crystallographic complexes with the CD44 hyaluronan binding domain: the “A-form,” which lacks arginine-HA close contact, and the “B-form,” which has direct arginine side-chain-HA contact. From the simulations, the conformational properties of oHA are essentially unaltered in going from the unbound state to either the A-form or the B-form bound state, with the oligomer retaining its flexibility when bound and with only two of the eight monosaccharides in the oligomer maintaining uninterrupted contact with the protein. Biased simulations revealed that altering the backbone conformation of a tyrosine residue in the arginine loop can induce the A-form → B-form conformational transition and that a large free-energy barrier prevents ready interconversion between the two forms, thereby suggesting that the tyrosine backbone forms a molecular switch.     

Human cancer-associated gangliosides defined by a monoclonal antibody (IB9) directed to sialosyl alpha 2 leads to 6 galactosyl residue: a preliminary note

A new monoclonal antibody (IB9) was prepared by hybridoma technique directed specifically to sialosyl alpha 2 leads to 6 galactosyl residue. With this reagent, accumulation of two major gangliosides in human colonic and liver adenocarcinoma has been detected, and these gangliosides were isolated and characterized as structures A and B (below). Another ganglioside with a ceramide nonasaccharide structure, which reacted to anti-X-hapten antibody after desialylation, was also isolated and partially characterized. (formula; see text) These gangliosides were absent or present in very small quantity in normal tissue and may represent human cancer-associated markers.     

Tissue-specific distribution patterns of retinoids and didehydroretinoids in rainbow trout Oncorhynchus mykiss

Retinoids (vitamin A) are known to be involved in many key biological functions in mammals, such as embryonic development, reproduction or vision. Besides standard vitamin A forms, freshwater fish tissues contain high levels of didehydroretinoids or vitamin A₂ forms. However, the tissue distribution, metabolism and function of both standard and particularly the didehydroretinoids are still poorly known in fish. In this study, we have quantified the levels of retinoids, including retinol, retinaldehyde, retinyl palmitate and their corresponding didehydro forms, as well as the levels of the active polar retinoids all-trans-, 9-cis- and 13-cis-retinoic acid in distinct tissues of juvenile rainbow trout. Our results indicate that the liver is clearly the main retinoid storage tissue in juvenile rainbow trout. Didehydroretinoids were dominant over retinoids in all analyzed tissues with the exception of plasma. Additionally, significant differences among tissues were observed between retinoids and didehydroretinoids, such as differences in the ester profiles and the proportions between free and esterified forms, suggesting that mechanisms that favor the utilization or storage of one of the other groups of compounds might exist in fish. Our data also show the presence of polar retinoids in different tissues of fish at the fmol/g scale. Overall, this study clearly demonstrates the presence of tissue-specific patterns of accumulation of both polar and nonpolar retinoids in fish tissues. The biological relevance of these findings should be the focus of future studies.