Structural and Functional Comparison of Polysaccharide-Degrading Enzymes

Sugar molecules as well as enzymes degrading them are ubiquitously present in physiological systems, especially for vertebrates. Polysaccharides have at least two aspects to their function, one due to their mechanical properties and the second one involves multiple regulatory processes or interactions between molecules, cells, or extracellular space. Various bacteria exert exogenous pressures on their host organism to diversity glycans and their structures in order for the host organism to evade the destructive function of such microbes. Many bacterial organism produce glycan-degrading enzymes in order to facilitate their invasion of host tissues. Such polysaccharide degrading enzymes utilize mainly two modes of polysaccharide-degradation, a hydrolysis and a β-elimination process. The three-dimensional structures of several of these enzymes have been elucidated recently using X-ray crystallography. There are many common structural motifs among these enzymes, mainly the presence of an elongated cleft transversing these molecules which functions as a polysaccharide substrate binding site as well as the catalytic site for these enzymes. The detailed structural information obtained about these enzymes allowed formulation of proposed mechanisms of their action. The polysaccharide lyases utilize a proton acceptance and donation mechanism (PAD), whereas polysaccharide hydrolases use a direct double displacement (DD) mechanism to degrade their substrates.     

Beyond Eyeballing: Fitting Models to Experimental Data

Abstract

As we learn more about the biology of the Toll-like receptors (TLRs), a wide range of molecules that can activate this fascinating family of pattern recognition receptors emerges. In addition to conserved pathogenic components, endogenous danger signals created upon tissue damage are also sensed by TLRs. Detection of these types of stimuli results in TLR mediated inflammation that is vital to fight pathogenic invasion and drive tissue repair. Aberrant activation of TLRs by pathogenic and endogenous ligands has also been linked with the pathogenesis of an increasing number of infectious and autoimmune diseases, respectively. Most recently, allergen activation of TLRs has also been described, creating a third broad class of TLR stimulus that has helped to shed light on the pathogenesis of allergic disease. To date, microbial activation of TLRs remains best characterized. Each member of the TLR family senses a specific subset of pathogenic ligands, pathogen associated molecular patterns (PAMPS), and a wealth of structural and biochemical data continues to reveal the molecular mechanisms of TLR activation by PAMPs, and to demonstrate how receptor specificity is achieved. In contrast, the mechanisms by which endogenous molecules and allergens activate TLRs remain much more mysterious. Here, we provide an overview of our current knowledge of how very diverse stimuli activate the same TLRs and the structural basis of these modes of immunity.     

Molecular Chaperones HscA/Ssq1 and HscB/Jac1 and Their Roles in Iron-Sulfur Protein Maturation

ABSTRACT

Genetic and biochemical studies have led to the identification of several cellular pathways for the biosynthesis of iron-sulfur proteins in different organisms. The most broadly distributed and highly conserved system involves an Hsp70 chaperone and J-protein co-chaperone system that interacts with a scaffold-like protein involved in [FeS]-cluster preassembly. Specialized forms of Hsp70 and their co-chaperones have evolved in bacteria (HscA, HscB) and in certain fungi (Ssq1, Jac1), whereas most eukaryotes employ a multifunctional mitochondrial Hsp70 (mtHsp70) together with a specialized co-chaperone homologous to HscB/Jac1. HscA and Ssq1 have been shown to specifically bind to a conserved sequence present in the [FeS]-scaffold protein designated IscU in bacteria and Isu in fungi, and the crystal structure of a complex of a peptide containing the IscU recognition region bound to the HscA substrate binding domain has been determined. The interaction of IscU/Isu with HscA/Ssq1 is regulated by HscB/Jac1 which bind the scaffold protein to assist delivery to the chaperone and stabilize the chaperone-scaffold complex by enhancing chaperone ATPase activity. The crystal structure of HscB reveals that the N-terminal J-domain involved in regulation of HscA ATPase activity is similar to other J-proteins, whereas the C-terminal domain is unique and appears to mediate specific interactions with IscU. At the present time the exact function(s) of chaperone-[FeS]-scaffold interactions in iron-sulfur protein biosynthesis remain(s) to be established. In vivo and in vitro studies of yeast Ssq1 and Jac1 indicate that the chaperones are not required for [FeS]-cluster assembly on Isu. Recent in vitro studies using bacterial HscA, HscB and IscU have shown that the chaperones destabilize the IscU[FeS] complex and facilitate cluster delivery to an acceptor apo-protein consistent with a role in regulating cluster release and transfer. Additional genetic and biochemical studies are needed to extend these findings to mtHsp70 activities in higher eukaryotes.     

Review of Dinosaur Tail Traces

Since 1858, when Hitchcock first recorded dinosaur tail traces from the Jurassic of Massachusetts, USA, a number of dinosaur tail traces have been reported. Although considered rare, at least 38 records of dinosaur tail traces have previously been reported in the literature. These occurrences are herein reviewed in order to understand their geographic and stratigraphic distribution, types of tail trace makers, and characteristics of dinosaur tail traces. Several terms for dinosaur tail traces have been employed and they are divided into tail impressions (TIs) for resting traces, and tail drag impressions (TDIs) for locomotion traces. Possible criteria for distinguishing, measuring and comparing TIs and TDIs are suggested. In addition, herringbone structures, one of the characteristic features of tail traces associated with ornithopod and theropod tracks, are discussed. Estimated speeds of tail trace makers are shown to be rather low. Finally, the abundance of tail traces associated with bipedal, rather than quadrupedal, dinosaurs is considered a reflection of behavior.     

Amyloid from a histochemical perspective. A review of the structure,properties and types of amyloid,and a proposed staining mechanism for Congo red staining

Amyloid is a diverse group of unrelated peptides or proteins that have positive functionality or are associated with various pathologies. Despite vast differences, all amyloids share several features that together uniquely define the group. 1) All amyloids possess a characteristic cross-ß pattern with X-ray diffraction typical of ß-sheet secondary protein structures. 2) All amyloids are birefringent and dichroic under polarizing microscopy after staining with Congo red, which indicates a crystalline-like (ordered) structure. 3) All amyloids cause a spectral shift in the peak wavelength of Congo red with conventional light microscopy due to perturbation of π electrons of the dye. 4) All amyloids show heightened intensity of fluorescence with Congo red, which suggests an unusual degree of packing of the dye onto the substrate. The ß portion of amyloid molecules, the only logical substrate for specific Congo red staining under histochemical conditions, consists of a stack of ß-sheets laminated by hydrophilic and hydrophobic interactions between adjacent pairs. Only the first and last ß-sheets are accessible to dyes. Each sheet is composed of numerous identical peptides running across the width of the sheet and arranged in parallel with side chains in register over the length of the fibril. Two sets of grooves are bordered by side chains. X grooves run perpendicular to the long axis of the fibril; these grooves are short (the width of the sheet) and number in the hundreds or thousands. Y grooves are parallel with the long axis. Each groove runs the entire length of the fibril, but there are very few of them. While Congo red is capable of ionic bonding with proteins via two sulfonic acid groups, physical constraints on the staining solution preclude ionic interactions. Hydrogen bonding between dye amine groups and peptide carbonyls is the most likely primary bonding mechanism, because all ß-sheets possess backbone carbonyls. Various amino acid residues may form secondary bonds to the dye via any of three van der Waals forces. It is possible that Congo red binds within the Y grooves, but that would not produce the characteristic staining features that are the diagnostic hallmarks of amyloid. Binding in the X grooves would produce a tightly packed series of dye molecules over the entire length of the fibril. This would account for the signature staining of amyloid by Congo red: dichroic birefringence, enhanced intensity of fluorescence and a shift in visible absorption wavelength.     

Hematoxylin and related compounds – an annotated bibliography concerning their origin,properties, chemistry,and certain applications

Abstract

This bibliography covers the historical aspects of hematoxylin and its close relative brazilin from their origin in dyewoods to their recently understood chemical reactions and properties. Until the end of the 19th century, dyewoods such as logwood were among the most commercially important natural dyes and investigations over a long period of time led to an extensive literature. The ready oxidation of hematoxylin to hematein, which subsequently can be complexed with metal ions or undergo reactions with acid to give isohematein, has provided a wealth of work for the organic chemist. The elucidation of the structure and subsequent synthesis of hematoxylin has proved to be a major incentive to chemists to discover novel chemical reagents for many years.     

Peroxiredoxin 2, glutathione peroxidase,and catalase in the cytosol and membrane of erythrocytes under H2O2-induced oxidative stress

Abstract

Erythrocytes are continuously exposed to risk of oxidative injury due to oxidant oxygen species. To prevent damage, they have antioxidant agents namely, catalase (Cat), glutathione peroxidase (GPx), and peroxiredoxin 2 (Prx2). Our aim was to contribute to a better understanding of the interplay between Prx2, Cat, and GPx under H₂O₂-induced oxidative stress, by studying their changes in the red blood cell cytosol and membrane, in different conditions. These three enzymes were quantified by immunoblotting. Malondialdehyde, that is, lipoperoxidation (LPO) in the erythrocyte membrane, and membrane-bound hemoglobin (MBH) were evaluated, as markers of oxidative stress. We also studied the erythrocyte membrane protein profile, to estimate how oxidative stress affects the membrane protein structure. We showed that under increasing H₂O₂ concentrations, inhibition of the three enzymes with or without metHb formation lead to the binding of Prx2 and GPx (but not Cat) to the erythrocyte membrane. Prx2 was detected mainly in its oxidized form and the linkage of metHb to the membrane seems to compete with the binding of Prx2. Catalase played a major role in protecting erythrocytes from high exogenous flux of H₂O₂, since whenever Cat was active there were no significant changes in any of the studied parameters. When only Cat was inhibited, Prx2 and GPx were unable to prevent H₂O₂-induced oxidative stress resulting in increasing MBH and membrane LPO. Additionally, the inhibition of one or more of these enzymes induced changes in the anchor/linker proteins of the junctional complexes of the membrane cytoskeleton–lipid bilayer, which might lead to membrane destabilization.     

How to Deal with Resource Productivity

Resource productivity enhancement stands at the center of tackling issues on environmental pollution and resource scarcity. Identifying influential socioeconomic factors should be the first step in establishing and improving resource management policy. This study compares and analyzes data from multiple countries to construct a resource productivity simulation model. The socioeconomic factors and their characteristic patterns are discussed in detail. The results demonstrate that the major factors influencing resource productivity include income level, population density, economic structure, energy structure, and raw material trade. Among these factors, the three most important are income level, population density, and economic structure. The influencing patterns can be summarized as follows: (1) Resource productivity increases with increasing income levels. (2) Countries with high population density are inclined to demonstrate high resource productivity. (3) The economic structure shows a biphase influence on resource productivity, that is, during industrialization, decreased agricultural activity and increased industrial activity lead to higher resource productivity. On the other hand, after industrialization, decreasing industrial activity and an expanding service sector become the major impetus of resource productivity enhancement. (4) Raw material export demonstrates a negative effect on resource productivity. Countries that depend heavily on raw material export show a unique resource productivity evolution pattern. For these countries, relatively high resource productivity in low income phases and relatively low resource productivity in high income phases show only small increases in resource efficiency and economic growth. Finally, insights from the study are transformed into suggestions for sustainable resource management and resource productivity enhancement.     

Gel-forming algal polysaccharides: structural characterisation and technological applications

Abstract

Some aspects of both the chemical and physico-chemical properties of gelling algal polysaccharides are reviewed in connection with their technological and biotechnological uses. In fact, besides the traditional applications, which are mainly in the field of food industry, recent sophisticated biotechnological manipulations opened the way for the exploitation of these molecules for very advanced applications like the formulation of micro spheres for cell incubation. Some aspects of the structure of alginate gel beads used for cell immobilisation are illustrated.     

Relations between apical structure and growth patterns in Pinus halepensis Mill,seedlings

Abstract

The process of primary growth in 2-year-old seedlings of 11 populations of Pinus halepensis Mill. is described. At the end of the first growing season one type of apical structure was observed: type-1, a tuft of primary needles placed close together, surrounding and protecting a meristematic apex.

At the end of the 2nd growing season, three types of apical structure were observed: type-1; type-2, a terminal winter bud; and type-3; a «bud» with characteristics of both type-1 and type-2.

Morphological observation along with an anatomical examination of the winter bud led to the conclusion that the definitive growth pattern in juvenile P. halepensis is monocyclic with a variable number of summer shoots. This growth pattern is reached by some P. halepensis populations in 3–4 years, by contrast, in other pine species two years are usually needed.

The populations studied differed both in growth potential (differences in number of cycles, ratio of first cycle to total growth, growth rates) and in the developmental stages of the apical meristem.

Four groups could be identified: (i) Morocco and Spain, (a limited growth, few cycles, a high ratio of 1st cycle to total growth, and growth in 2nd season almost entirely due to free growth); (ii) Algeria and Greece, (moderate to low growth, a large number of cycles, a low ratio of 1st cycle to total growth, and very early formation of apical structure with preformed primordia); (iii) Israel and Central Italy (a high growth, a large number of cycles, a medium ratio of 1st cycle to total growth, and early formation of apical structure with preformed primordia); (iiii) Greece, France and Italy, which was intermediate between group (i) and the other 2 groups.