Substrate specificity of the erythrocyte Ca2+-ATPase

In the absence of Mg²⁺, the observed activity of the erythrocyte plasma membrane Ca²⁺-ATPase is due to the hydrolysis of CaATP at a low rate. In the presence of Mg²⁺, the activity of the enzyme is much higher, but it is inhibited by high levels of free Mg²⁺. This inhibition appears to be due to competition of Mg²⁺ and Ca²⁺ for a site on the enzyme, rather than for ATP.     

Tissue-specific differences in DNA methylation in various mammals

The only naturally occurring modified base in vertebrate DNA is 5-methylcytosine. Using a precise high-performance liquid chromatographic analysis of DNA enzymatically digested to deoxynucleosides, we have shown that rats, mice and four types of monkey display tissue-specific as well as species-specific differences in the extent of methylation of their cytosine residues. Several similarities in the patterns of tissue-specific DNA methylation in these mammals and in the previously studied human samples were observed. Compared to most other types of DNA examined, brain and thymus DNAs were hypermethylated, which suggests that this hypermethylation is a determinant or a necessary byproduct of mammalian differentiation. In all of the studied rodents and primates, the highly repeated DNA sequence fraction was more methylated than the moderately repetitive or single copy fractions. The tissue-specific differences in overall DNA methylation showed no correlation with what is known about average cell turnover rates nor with the percentage of the genome that is transcribed. Liver regeneration in the rat following partial hepatectomy did not detectably alter 5-methylcytosine levels in liver DNA. A considerable increase in the extent of methylation of total liver DNA was observed during normal development of the rat. The latter phenomenon may be due to a major change in the cellular composition of the liver.     

锌指蛋白的核酸识别特异性研究进展

锌指蛋白是最大的DNA结合蛋白,它能和DNA进行特异性识别,是研究蛋白—DNA相互作用的理想对象。改变锌指元件上的几个保守的氨基酸位点可设计筛选出序列特异的全新锌指蛋白,计算机在锌指蛋白设计方面的应用,使得全新的锌指蛋白识别特异性明显增强。这在基因治疗等方面,具有广阔的应用前景。     

Studies on the specificity of acetylaminoacyl-peptide hydrolase.

In a continuing attempt to explore the types of specificity determinants that may affect protein-protein (peptide) interactions, a number of short (2-5 residues) acetylated peptides have been compared as substrates for the enzyme acetylaminoacyl-peptide hydrolase (EC 3.4.19.1). The reference substrate was Ac-AAAA, and most of the other substrates were derived from this basic structure by single amino acid substitutions. The Km and kcat for the different substrates were determined by standard steady-state kinetics, and the corresponding delta delta GT++ value derived from kcat/Km was used for the comparison, setting delta detal GT++ for Ac-AAAA equal to 0. The best substrates were found to be those containing negative charges (Asp > Glu) or aromatic residues in positions 1', 2', or 3' (delta delta GT++ values of 2-5 kJ); the negative charge provided by the C-terminus of the substrate also appears to be important, since the amide and O-Me ester derivatives caused a change in delta delta GT++ values of -7 to -8 kJ from the reference peptide. The stimulating effect of the negative charges is consistent with the inhibitory effect of positive charges in similar peptides (Krishna RG, Wold F, 1992, Protein Sci 1:582-589), and the proposed active site model incorporates subsites for both charge-charge and hydrophobic interactions. In assessing all the data, it is clear that the properties of the individual substrates reflect the total make-up of each peptide and not only the effect of a single residue in a given position.(ABSTRACT TRUNCATED AT 250 WORDS)     

Factors controlling in vitro hatching of Vairimorpha plodiae (Microspora) spores and their infectivity to Plodia interpunctella,Heliothis virescens, and Pieris brassicae

Factors which influence the hatching of spores and proliferation of stages of the microsporidium Vairimorpha plodiae in two susceptible insects, Plodia interpunctella and Heliothis virescens, and one nonsusceptible insect, Pieris brassicae, were investigated. Spores hatched in 0.1 and 1 m KCl solutions when subjected to a change in pH, from pH 11 to pH 8. K⁺ was essential for hatching; NaCl solutions were not effective. Ca²⁺ and Mg²⁺ inhibited hatching, and calcium and magnesium chelating agents enhanced it. All three insect species had alkaline midgut contents and smooth, fragile peritrophic membranes. Spores hatched inside the midguts of all three insect species (P. interpunctella: maximum rate, 92.5%; H. virescens, 91.5%; P. brassicae, 82%). Sporoplasms were observed in the midgut epithelial and associated tracheole cells of P. brassicae. Both H. virescens and P. brassicae became infected when injected intrahemocoelically with spores.     

Covariate adjustment in continuous biomarker assessment

Continuous biomarkers are common for disease screening and diagnosis. To reach a dichotomous clinical decision, a threshold would be imposed to distinguish subjects with disease from nondiseased individuals. Among various performance metrics, specificity at a controlled sensitivity level (or vice versa) is often desirable because it directly targets the clinical utility of the intended clinical test. Meanwhile, covariates, such as age, race, as well as sample collection conditions, could impact the biomarker distribution and may also confound the association between biomarker and disease status. Therefore, covariate adjustment is important in such biomarker evaluation. Most existing covariate adjustment methods do not specifically target the desired sensitivity/specificity level, but rather do so for the entire biomarker distribution. As such, they might be more prone to model misspecification. In this paper, we suggest a parsimonious quantile regression model for the diseased population, only locally at the controlled sensitivity level, and assess specificity with covariate-specific control of the sensitivity. Variance estimates are obtained from a sample-based approach and bootstrap. Furthermore, our proposed local model extends readily to a global one for covariate adjustment for the receiver operating characteristic (ROC) curve over the sensitivity continuum. We demonstrate computational efficiency of this proposed method and restore the inherent monotonicity in the estimated covariate-adjusted ROC curve. The asymptotic properties of the proposed estimators are established. Simulation studies show favorable performance of the proposal. Finally, we illustrate our method in biomarker evaluation for aggressive prostate cancer.     

Host specialization in habitat specialists and generalists

Generalists and specialists use different cues to find their habitat and essential resources. While generalists have the advantage of exploiting a wider range of resources, they are predicted to be less efficient in using one particular resource compared to specialists. The level of specialization of parasitoids can be either at the habitat or at the host level; strategies used by either type are expected to differ. We examined interactions between three aphid parasitoid species that are a habitat specialist Aphidius rhopalosiphi, a habitat generalist Aphidius ervi, and a host generalist Praon volucre on three cereal aphids, Sitobion avenae, Metopolophium dirhodum and Rhopalosiphum padi. We compared total parasitism rate across behavioral and physiological variation in a non-choice test. Next, we addressed total parasitism in two phases to examine: (1) the response of parasitoids to different hosts through the behavioral sequence from antennation through oviposition, and (2) the physiological suitability of different hosts for oviposition and larval development. Parasitization typically involved the following behavioral steps: (1) antennal contact, (2) abdominal bending, and (3) ovipositor insertion (acceptance). A. rhopalosiphi had the same number of antennal contacts with the three aphids but showed fewer instances of abdominal bending towards R. padi. Pre-contact host preference was found for A. ervi but it did not correspond to the level of acceptance. The number of antennal contacts by P. volucre corresponded to the parasitization level of the aphid species but more mummies were produced on M. dirhodum than on R. padi. These results suggest that parasitoid species that are habitat specialists react similarly to the different host species present in the same habitat, whereas generalist species exhibit clear preferences during host selection. Preferences were, however, not always related to host suitability.     

Relationship between intraspecific variations and host insects of Ophiocordyceps nutans collected in Japan

To investigate the host specificity of Ophiocordyceps nutans against hemipteran insects in the wild, we determined the relationship between host species and rDNA-internal transcribed spacer (ITS) variation in O. nutans. The analyzed fungal specimens infected 16 host species belonging to four families of Hemiptera. The molecular phylogenetic analysis revealed that O. nutans can be classified into two types corresponding to their host families. The genetic distance values between the two types were very remote (>0.084), and the strains of O. nutans that parasitized Halyomorpha halys and Plautia crossota stali, well-known insect pests, formed a subclade. The results suggest that O. nutans should have host specificity which can be valuable for developing biological control agents against specific hemipteran insects.     

Difference in binding-site architecture of the serum-type and liver-type mannose-binding proteins

The carbohydrate-recognition domains (CRDs) of the serum-type and the liver-type mannose-binding proteins (MBPs) from rat display different binding characteristics toward mannose-rich oligosaccharides derived from N-glycosides, despite the overall similarity in their binding site architecture, oligomeric status and actual binding specificity at the monosaccharide level. We found that the liver-type MBP CRD of rat (MBP-C) bound methyl glycosides of certain mannobioses and -trioses, which are part of the mannose-rich N-glycoside, more tightly than methyl α-mannopyranoside. In contrast, the serum-type MBP CRD of rat (MBP-A) bound all the methyl glycosides of manno-oligosaccharide and methyl α-mannopyranoside with similar affinities. The mannobiose and -triose most strongly bound to MBP-C CRD were Manα(1-2)Manα-OMe and Manα (1-2)Manα(1-6)Manα-OMe, respectively. From these and other data, we postulate that the binding site of MBP-C has an extended area of interaction, probably the size of a mannotriose, while MBP-A interacts essentially with one mannose residue. Abbreviations: MBP, mannose-binding protein; CRD, carbohydrate-recognition domain; BSA, bovine serum albumin; TFA-ah, 6-(trifluoroacetyl)aminohexyl; PNP, p-nitrophenyl This revised version was published online in November 2006 with corrections to the Cover Date.     

A site-specific endonuclease from Caulobacter crescentus CB-13: restriction endonuclease CcrI

A site-specific restriction endonuclease (CcrI) has been identified from Caulobacter crescentus CB-13. This enzyme has been purified to homogeneity and the cleavage patterns with various DNAs and sequence data show that CcrI recognizes the same sequence as the XhoI restriction endonuclease (5′-C^↓-T-C-G-A-G-3′). Ccr has an absolute requirement for magnesium ions with an optimum concentration of 4 mM. The enzyme is optimally active at pH 8.0 and is stable up to 70°C. CcrI has a molecular weight of 65300 and exists as a monomer in its native state. Most of the physical characteristics observed for CcrI were similar to those observed for XhoI. Kinetic studies on CcrI and XhoI suggest that the enzymes interact with λ DNA in the same manner; however, with ?X-174 R.F. DNA, CcrI has a greater affinity for the supercoiled molecule than XhoI.     

The relevance of various tests for the study of specificity in immunocytochemical staining: a review

Factors determining the specificity of immunocytochemical (ICC) tissue stainings as well as the various tests to study these factors are discussed. Since every specificity test only deals with particular aspects of the ICC procedure, a practical sequence of known test methods is proposed, which enables the determination of the specificity of the ICC tissue staining and, after possibly needed antiserum purification steps, may result in a monospecific staining. It is made clear that such a sequence has always to include a tissue-spectrum affinity test, in which the spectrum of tissue antigens is controlled for antibody binding. A variety of such tests, consisting of separation of tissue compounds, fixation, and ICC detection, are discussed as well as their pros and cons with respect to their predictability for the actual serum specificity in the tissue section.     

Life history and laboratory host range of Stenopelmus rufinasus, a natural enemy for Azolla filiculoides in South Africa

The frond-feeding weevil, Stenopelmus rufinasus Gyllenhal, was imported into quarantine for testing as a potential natural enemy for the invasive fern Azolla filiculoides Lamarck in South Africa. Adult S. rufinasus lived for approximately 55 days during which the females produced on average 325 offspring. The developmental period for the immature stages (egg, three larval instars and pupation) was about 20 days indicating the potential for several overlapping generations per year. Both the adults and the larvae caused severe damage to A. filiculoides in the laboratory. Host specificity of this insect was determined by adult no-choice oviposition and larval starvation tests on 31 plant species in 19 families. Adult feeding, oviposition and larval development was only recorded on the Azolla species tested (A. filiculoides, A. pinnata subsp. poss. asiatica R.K.M. Saunders and K. Fowler, A. pinnata subsp. africana (Desv.) R.K.M. Saunders and K. Fowler and A. nilotica De Caisne Ex Mett.). A. filiculoides proved to be significantly the most suitable host for the weevil. The low adult emergence from A. nilotica and A. pinnata subsp. africana would most probably prevent the weevil from establishing on them in the field. A. pinnata subsp. poss. asiatica which supported greater development, is thought to be introduced and has a weedy phenology in South Africa and is thus of low conservation value. Therefore, any damage inflicted on this plant in the field may be an acceptable trade-off for the predicted impact of S. rufinasus on the aggressive exotic weed, A. filiculoides.     

The Non-Random Pattern of Insertion of IS2 into the hemB Gene of Escherichia coli

The hemB gene of Escherichia coli has been identified as a hot spot for the insertion of the transposable element IS2. The insertional specificity of IS2 is still unclear. This study reports on the attempt to sequence a statistically significant number of insertions in hemB, in order to determine whether there might be a basis for future studies to determine a molecular basis of IS2 insertional specificity. The results indicate that IS2 inserts in a non-random manner into a 240 bp segment at the 5′ end of the gene (region I). Twenty-one of 24 insertions occurred in region I. Three insertions have been identified in the two middle 250 bp segments of the 975 bp gene, and none in the 3′ terminal segment. A seventeen bp sequence showing 88.2% identity with a segment of IS2, 221 bp from the 3′ terminus has been identified in region I. Four instances of repeated insertion between the same pair of nucleotides have been observed at four different sites.     

Current trends of lectins from microfungi

Lectins are widespread in nature and have been isolated from plants, animals, microorganisms, and viruses. Although several lectins have been reported from microfungi, many more genera still remain unexplored and their physiological role is also uncertain. Microfungal lectins show wide disparity regarding their specificity to erythrocytes. Only a few lectins display specificity to particular human blood types. In addition, they also show agglutination to various animal erythrocytes. Many lectins from microfungi exhibit stringent specificity to animal glycoproteins, while a few have much more simplified sugar binding properties. The role of few microfungal lectins in host-parasite interactions, as storage proteins, and in growth and morphogenesis has been proposed. The current review focuses on an overview of lectins from microfungi, their specificity towards erythrocytes and carbohydrates, physicochemical characteristics, and their possible role and applications.     

Characterization of Bovine Atrial Angiotensin-Converting Enzyme

Bovine atrial angiotensin-converting enzyme (ACE) was purified to electrophoretic homogeneity. The purification procedure included ion-exchange chromatography on DEAE-Toyopearl 650M, affinity chromatography on lisinopril-agarose and gel filtration on Sephadex G-100. The bovine atrial ACE exhibited similar sensitivities to inhibition by lisinopril and captopril as lung ACE (the K _i values for the atrial and lung enzymes differed insignificantly). However, the kinetic parameters of hydrolysis of some synthetic tripeptide substrates (FA-Phe-Gly-Gly, FA-Phe-Phe-Arg, Cbz-Phe-His-Leu, Hip-His-Leu) catalyzed by bovine atrial and lung ACE varied to a greater extent. The enzymes were also characterized by some differences in activation by chloride, nitrate, and sulfate anions. These data support the hypothesis of tissue specificity of ACEs.     

Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases

Isocitrate and isopropylmalalte dehydrogenases are homologous enzymes important for the cell metabolism. They oxidize their substrates using NAD or NADP as cofactors. Thus, they have two specificities, towards the substrate and the cofactor, appearing in three combinations. Although many three-dimensional (3D) structures are resolved, identification of amino acids determining these specificities remains a challenge. We present computational identification and analysis of specificity-determining positions (SDPs). Besides many experimentally proven SDPs, we predict new SDPs, for example, four substrate-specific positions (103Leu, 105Thr, 337Ala, and 341Thr in IDH from E. coli) that contact the cofactor and may play a role in the recognition process.     

The crystal structure of d-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase

d-Mandelate dehydrogenases (d-ManDHs), belonging to a new d-2-hydroxyacid dehydrogenase family, catalyze the conversion between benzoylformate and d-mandelate using NAD as a coenzyme. We determined the first d-ManDH structure, that of ManDH2 from Enterococcus faecalis IAM10071. The overall structure showed ManDH2 has a similar fold to 2-ketopantoate reductase (KPR), which catalyzes the conversion of 2-ketopantoate to d-pantoate using NADP as a coenzyme. They share conserved catalytic residues, indicating ManDH2 has the same reaction mechanism as KPR. However, ManDH2 exhibits significant structural variations in the coenzyme and substrate binding sites compared to KPR. These structural observations could explain their different coenzyme and substrate specificities.     

Substrate specificity of plant UDP-dependent glycosyltransferases predicted from crystal structures and homology modeling

Plant family 1 UDP-dependent glycosyltransferases (UGTs) catalyze the glycosylation of a plethora of bioactive natural products. In Arabidopsis thaliana, 120 UGT encoding genes have been identified. The crystal-based 3D structures of four plant UGTs have recently been published. Despite low sequence conservation, the UGTs show a highly conserved secondary and tertiary structure. The sugar acceptor and sugar donor substrates of UGTs are accommodated in the cleft formed between the N- and C-terminal domains. Several regions of the primary sequence contribute to the formation of the substrate binding pocket including structurally conserved domains as well as loop regions differing both with respect to their amino acid sequence and sequence length. In this review we provide a detailed analysis of the available plant UGT crystal structures to reveal structural features determining substrate specificity. The high 3D structural conservation of the plant UGTs render homology modeling an attractive tool for structure elucidation. The accuracy and utility of UGT structures obtained by homology modeling are discussed and quantitative assessments of model quality are performed by modeling of a plant UGT for which the 3D crystal structure is known. We conclude that homology modeling offers a high degree of accuracy. Shortcomings in homology modeling are also apparent with modeling of loop regions remaining as a particularly difficult task.     

13C-NMR Spectra and Streochemistry of Isoechinulins A,B and C

¹³C-NMR spectra of isoechinulins A, B and C, metabolites from Aspergillus ruber, were fully assigned on the basis of chemical shifts and multiplicities and comparison with their analogues. Taking advantage of the symmetrical structure of the diketopiperazine ring, the stereochemistry of the trisubstituted carbon-carbon double bond in a dehydrotryptophyl moiety was determined as Z (cis) by measuring the coupling constants, , in the proton nondecoupled spectrum of isoechinulin B.     

Mesostigmatid Mites (Acari: Mesostigmata) on Rainforest Tree Trunks: Arboreal Specialists, but Substrate Generalists?

Predatory mites (Acari: Mesostigmata) on tree trunks without significant epiphytic growth in a subtropical rainforest in Eastern Australia were assessed for habitat specificity (i.e. whether they are tree trunk specialists or occupying other habitats) and the influence of host tree and bark structure on their abundance, species richness and species composition. The trunks of nine tree species from eight plant families representing smooth, intermediate and rough bark textures were sampled using a knockdown insecticide spray. In total, 12 species or morphospecies of Mesostigmata (excluding Uropodina sensu stricto) were collected, most of which are undescribed. Comparison with collections from other habitats indicates that epicorticolous Mesostigmata are mainly represented by suspended soil dwellers (six species), secondarily by generalists (four species) and a bark specialist (one species). A typical ground-dwelling species was also found but was represented only by a single individual. In terms of abundance, 50.5% of individuals were suspended soil dwellers, 40.7% bark specialists, and 8.3% generalists. Host species and bark roughness had no significant effect on abundance or species richness. Furthermore, there was no clear effect on species composition. The distribution of the most frequently encountered species suggests that most mesostigmatid mites living on bark use many or most rainforest tree species, independent of bark roughness. These findings support the hypothesis that some epicorticolous Mesostigmata use tree trunks as ‘highways’ for dispersing between habitat patches, while others use it as a permanent habitat.