The role of aquatic moss on community composition and drift of fish-food organisms

Macroinvertebrate density, biomass and drift were studied from moss-covered and moss-free channels in the South Fork Salmon River, Idaho. Insect densities were compared for 10 different substrate types and locations involving moss (Fontinalis neo-mexicana), sand, pebbles and cobbles. An ANOVA test demonstrated that insect densities varied significantly with substrate type (P < 0.05), and that total insect density in moss clumps differed significantly from densities in mineral substrates. Insect densities were 4–18 times greater in moss clumps than in mineral substrates under and adjacent to moss; sands under moss supported the lowest densities. During most tests, densities in pebble and cobble substrates adjacent to moss clumps were not significantly different from those found in similar substrates in the moss-free channel. The 20% moss-covered channel had 1.6 to 7.2 greater insect density and 1.4 to 6.1 greater biomass than did the moss-free channel for the tests conducted. Generally, midges (Chironomidae) made up over 50% of the insect community; annelids were the principal non-insect invertebrates.In spite of greater insect density and biomass in a moss-covered than in the moss-free channel, we did not demonstrate universally increased drift of the immature stages from the moss-covered channel, at least during daylight hours. As a consequence, we infer that salmonid fishes, feeding primarily on drifting insects during the daytime, may not derive increased caloric benefit from moss habitats until the insects emerge as adults.     

Purification and Characterization op a 31-Kilodalton Iron-Regulated Periplasmic Protein from Pasteurella Haenolytica A1

ABSTRACT

A prominent iron-regulated periplasmic protein was purified from Pasteurella haemolytica grown in an iron-deficient chemically defined medium. The protein was purified by anion exchange chromatography and appeared as a single band by SDS-PAGE with a molecular weight of 32,000. A yield of five mg was obtained from 91 mg of protein extract. The iron-regulated protein existed as a monomer in the native state with an average molecular weight of 29,877 as determined by analytical ultracentrifugation. The protein had a molecular weight of 30,880 as determined by matrix-assisted laser desorption mass spectrometry, hence the protein is referred to as the 31 kDa protein. Isoelectric focusing showed four bands with pIs of 7.15, 6.8, 6.6, and 5.9, The secondary structure of the protein was determined by circular dichroism and contained 16% α-helical structure. The N-terminal sequence, EPFKVVTTFTVIQDIAQNVAGDKAT, showed a 95% identity with the 31 kDa iron-binding protein from Haemophilus influenzae. Isolation and characterization of iron-regulated proteins are of particular interest because of their potential roles in iron assimilation and microbial virulence.     

High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism

Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.     

Relation to habitat in rotifers

Rotifera should be especially suited for an analysis of habitat relations because this group contains such a high number of species, inhabiting diverse environments. Furthermore, rotifers are to a large extent cosmopolitan, implying that ecological barriers, rather than geographical, are decisive of their distribution. In this review a short characterization of the rotifer fauna in different habitats is given, whereby macroenvironments and microenvironments are reported separately. The macroenvironments are classified as follows: harmonious lakes and ponds, arctic and antarctic waters, hot springs, hypertrophic-saprobic environments, mires, strongly acidic waters, saline waters, temporary water bodies, subterranean waters, running waters, oceans, terrestrial environments. The following microenvironments are distinguished: macrophytes (housing periphytic rotifers), open water (with planktic forms), minerogenous sediments (with psammon and hyporheos), organogenous sediments, other organisms (i.e. parasites and epizoans).Many rotifers are more or less euryecious, while relatively few are strongly restricted in their choice of habitat. In extreme environments a low number of species is found, but often a high number of individuals within these species. These rotifers are usually primary consumers, and for natural reasons extreme environments are characterized by a low number of trophic levels.In environments with a high species number the separate species differ very much in their morphology, making it difficult to find common traits which may be interpreted as adaptations to the respective habitats. The most apparent adaptations ought to be found among the planktic rotifers, and these adaptations seem to constitute largely a protection against predators. Rotifers in extreme environments are usually not very apart in a morphological or taxonomical respect, with their most close relatives living in normal habitats and sometimes euryecious (an apparent exception from this rule is formed by the class Seisonidea). Adaptations to deviating chemical and physical environments may develop relatively rapidly (seen from a geological perspective), while the more fundamental changes (occurring during a longer period of time) seem to be a response to biotic factors (e.g., the development of different types of trophi for facilitating food collection).     

Catalytic residues and substrate specificity of scytalidoglutamic peptidase, the first member of the eqolisin in family (G1) of peptidases

Scytalidoglutamic peptidase (SGP) is the first-discovered member of the eqolisin family of peptidases with a unique structure and a presumed novel catalytic dyad (E136 and Q53) [Fujinaga et al., PNAS 101 (2004) 3364-3369]. Mutants of SGP, E136A, Q53A, and Q53E lost both the autoprocessing and enzymatic activities of the wild-type enzyme. Coupled with the results from the structural analysis of SGP, Glu136 and Gln53 were identified as the catalytic residues. The substrate specificity of SGP is unique, particularly, in the preference at the P3 (basic amino acid), P1' (small a.a.), and P3' (basic a.a.) positions. Superior substrates and inhibitors have been synthesized for kinetic studies based on the results reported here. kcat, Km, and kcat/Km of SGP for D-Dap(MeNHBz)-GFKFF*ALRK(Dnp)-D-R-D-R were 34.8 s-1, 0.065 microM, and 535 microM-1 s-1, respectively. Ki of Ac-FKF-(3S,4S)-phenylstatinyl-LR-NH2 for SGP was 1.2x10(-10) M. Taken together, we can conclude that SGP has not only structural and catalytic novelties but also a unique subsite structure.     

Targeted discovery and identification of novel nucleoside biomarkers in Apostichopus japonicus viscera using metabonomics

In this study, we investigated the metabonomic profiles of Apostichopus japonicus using an LC-MS-based method in conjunction with multivariate data analysis. Based on the PLS-DA model, 85 differential metabolites (VIP value >1.0) were obtained from viscera and body wall samples. The MS/MS and NMR experiments were used for the qualitative identification of the characteristic peaks. Sphingoid-based nucleoside analogues were the main components in Chinese A. japonicus viscera. Our findings demonstrate that A. japonicus viscera contain a large number of compounds that may have applications as nutraceuticals or pharmaceuticals.     

Synthesis and biological evaluation of new active For‐Met‐Leu‐Phe‐OMe analogues containing para‐substituted Phe residues

In the present study, we report synthesis and biological evaluation of the N‐Boc‐protected tripeptides 4a–l and N‐For protected tripeptides 5a–l as new For‐Met‐Leu‐Phe‐OMe (fMLF‐OMe) analogues. All the new ligands are characterized by the C‐terminal Phe residue variously substituted at position 4 of the aromatic ring. The agonism of 5a–l and the antagonism of 4a–l (chemotaxis, superoxide anion production, lysozyme release as well as receptor binding affinity) have been examined on human neutrophils. No synthesized compounds has higher activity than the standard fMLF‐OMe tripeptide to stimulate chemotaxis, although compounds 5a and 5c with ‐CH₃ and ‐C(CH₃)₃, respectively, in position 4 on the aromatic ring, are better than the standard tripeptide to stimulate the production of superoxide anion, in higher concentration. Compounds 4f and 4i , containing ‐F and ‐I in position 4, respectively, on the aromatic ring of phenylalanine, exhibit significant chemotactic antagonism. The influence of the different substitution at the position 4 on the aromatic ring of phenylalanine is discussed. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

A Colorimetric Assay that Specifically Measures Granzyme B Proteolytic Activity: Hydrolysis of Boc-Ala-Ala-Asp-S-Bzl

The serine protease Granzyme B (GzmB) mediates target cell apoptosis when released by cytotoxic T lymphocytes (CTL) or natural killer (NK) cells. GzmB is the most studied granzyme in humans and mice and therefore, researchers need specific and reliable tools to study its function and role in pathophysiology. This especially necessitates assays that do not recognize proteases such as caspases or other granzymes that are structurally or functionally related. Here, we apply GzmB’s preference for cleavage after aspartic acid residues in a colorimetric assay using the peptide thioester Boc-Ala-Ala-Asp-S-Bzl. GzmB is the only mammalian serine protease capable of cleaving this substrate. The substrate is cleaved with similar efficiency by human, mouse and rat GzmB, a property not shared by other commercially available peptide substrates, even some that are advertised as being suitable for this purpose. This protocol is demonstrated using unfractionated lysates from activated NK cells or CTL and is also suitable for recombinant proteases generated in a variety of prokaryotic and eukaryotic systems, provided the correct controls are used. This assay is a highly specific method to ascertain the potential pro-apoptotic activity of cytotoxic molecules in mammalian lymphocytes, and of their recombinant counterparts expressed by a variety of methodologies.     

Peptide substrates for G protein-coupled receptor kinase 2

G protein-coupled receptor kinases (GRKs) control the signaling and activation of G protein-coupled receptors through phosphorylation. In this study, consensus substrate motifs for GRK2 were identified from the sequences of GRK2 protein substrates, and 17 candidate peptides were synthesized to identify peptide substrates with high affinity for GRK2. GRK2 appears to require an acidic amino acid at the −2, −3, or −4 positions and its consensus phosphorylation site motifs were identified as (D/E)X_1–3(S/T), (D/E)X_1–3(S/T)(D/E), or (D/E)X_0–2(D/E)(S/T). Among the 17 peptide substrates examined, a 13-amino-acid peptide fragment of β-tubulin (DEMEFTEAESNMN) showed the highest affinity for GRK2 (K_m, 33.9 μM; V_max, 0.35 pmol min⁻¹ mg⁻¹), but very low affinity for GRK5. This peptide may be a useful tool for investigating cellular signaling pathways regulated by GRK2.     

Optimization of redox reactions employing whole cell biocatalysis

The ability of Saccharomyces cerevisiae to catalyse the reduction reaction of carboxylic acids into alcohols is described. Earlier reports have led to the characterization of the reduction of carbonyl groups into alcohols mediated by the enzyme alcohol dehydrogenase. We investigated the ability of this organism to catalyse the said conversion using the carboxylic acids, acetic acid and butyric acid. In the absence of any previous characterization, whole cell catalysis proved effective. The uptake of these acids from the medium was estimated using a plate assay method involving litmus-agar. The plate assay was found to be a convenient and extremely adaptable method for quantitation of acids in organic as well as aqueous medium. The comparison of existing paradigms in pure protein catalysis with whole cells catalysis proved anomalous. We report that it is solvent toxicity rather than hydrophobic index that correlates with the activity observed in non-aqueous conditions for whole cell biocatalysis. Reduction of acetic acid as well as butyric acid occurred, with efficiency of reaction with butyric acid being marginally higher. The reduction therefore occurs for both the short chain carboxylic acids used in this study. We therefore illustrate the reduction route of acids into alcohols and propose a model two-step pathway for the reaction. Process optimization may be further attempted to enhance the presently moderate reaction efficiencies. Steps made in the direction by studying the pH dependency and use of sacrificial substrate have yielded encouraging results.