Diagnosis of Helicobacter pylori in gastric brush and biopsy specimens stained by Rowmanowsky and immunocytochemical methods: comparison with the CLOtest

Helicobacter pylori has been implicated in the pathogenesis of chronic gastritis, gastric and duodenal ulcer, and possibly gastric carcinoma. The organism may be detected by invasive or non‐invasive methods with variable sensitivity. Paired gastric biopsy and gastric brush specimens were collected from 83 patients presenting with non‐ulcer dyspepsia. One biopsy was tested for urease using the CLOtest, the other was processed to paraffin and consecutive sections were stained with haematoxylin and eosin, modified Giemsa and anti‐ H. pylori antisera. The brush specimens were stained with a rapid Romanowsky stain (Hema‐Gurr) and anti‐ H. pylori . The CLOtest was positive in 31 cases, the Giemsa biopsy in 25, the anti‐ H. pylori biopsy in 27, the Hema‐Gurr smear in 27 and the anti‐ H. pylori smear in 19. The sensitivities of the methods after omitting one inadequate biopsy were 96%, 93%, 100%, 96% and 78%, respectively. The specificities were 93% for the CLOtest and 100% for the other methods. While immunocytochemical staining of gastric biopsies may be the most sensitive method for H. pylori identification, the cost and turn around time of the technique may preclude its routine use. Gastric brush cytology is a highly sensitive and specific method for H. pylori detection that is quick and simple to perform. Its application is recommended for the routine diagnosis of H. pylori infection.     

Maternal effect of a hybrid inviability gene in Tribolium castaneum

The Tribolium castaneum hybrid inviability gene, H, was selectively introgressed into a genetic background lacking H through serial paternal backcrosses. This revealed a poor viability phenotype (partial paralysis and poor control of the limbs, referred to as tremor) not present in the parent strains. Tremor cosegregated with H, but was expressed only when transmitted paternally and only when H was not also present maternally. The inferred maternal, self‐suppressive effect of H may explain nonreciprocal incompatibilty previously observed between H and H‐incompatible strains. This revised version was published online in July 2006 with corrections to the Cover Date.     

Hypericum cumulicola demography in unoccupied and occupied Florida scrub patches with different time‐since‐fire

1 Metapopulation models predict that unoccupied, but suitable, patches will exist for species subject to extinction and colonization dynamics. We compared the demographic responses of Hypericum cumulicola , a rare herbaceous species almost entirely restricted to Florida rosemary scrub, when transplanted to occupied or unoccupied patches.
2 Seedlings were transplanted and seeds buried into Florida rosemary scrub patches differing in time since last fire, and in the presence or absence of H. cumulicola. We used a replicated, factorial design to place the transplants and seeds in the field, and monitored their performance for 18 months.
3 Neither time‐since‐fire nor prior H. cumulicola site occupancy affected survival of transplants. Only time‐since‐fire affected growth. Time‐since‐fire, H. cumulicola occupancy, and their interaction affected reproductive effort, but these effects were not consistent between years.
4 Flowering and seed production led to subsequent seedling recruitment near transplants, mainly in recently burned sites. Genetic screening of transplants and seedlings showed that transplants in occupied sites could have crossed with nearby resident plants, but that offspring in sites previously unoccupied were likely to have been parented only by nearby transplants.
5 Seeds buried, and later exhumed, germinated after 1 or 2 years of burial, demonstrating a persistent soil seed bank from which populations could recover after fire. Neither time‐since‐fire nor H. cumulicola occupancy affected seed dormancy or germination.
6 Similar demography in unoccupied and occupied patches suggests that the patchy pattern of site occupancy by H. cumulicola is probably due to limited dispersal and periodic extinction, especially associated with long fire‐free intervals. Conservation measures need to protect unoccupied patches to allow metapopulation dynamics and persistence.     

Peptaibol Derived Helix‐Kink Motif Facilitates Channel Forming of the Artificial α-Aminoisobutyric Acid Rich Helices

Characteristic motifs have been identified in natural channel forming peptides though critical roles of such motifs are not well understood. In this paper, the helix‐kink motif found in peptaibols was embedded into the α-aminoisobutyric acid (Aib) rich template to explore its roles in peptide structure and ion channel functions. According to circular dichroism studies and single channel measurements, the motif reduced helical contents of peptide whereas ion channel forming was facilitated and conductance value was increased.     

Comparative mtDNA sequence (control region, ATPase 6 and NADH‐1) divergence in Hucho taimen(Pallas) across four Siberian river basins

Hucho taimen from eight populations spanning four drainage basins (Amur, Lena, Enisei and Khatanga) were analysed for nucleotide sequence variation across three mitochondrial genes (ATP6, NADH‐1 and control region). Samples of H. hucho , Brachymystax lenok (sharp‐snouted and blunt‐snouted forms) and Parahucho perryi were also included for comparison. Nucleotide variation across a total of 1826 base pairs in H. taimen revealed shared haplotypes between the Amur and Lena basins, further supporting a previous hypothesis of late to post‐Pleistocene hydrological exchange between these now disjunct basins. In contrast to an earlier study using the control region alone, clear phylogeographic structure was seen at a large geographic scale, reflected by two phylogroups, one corresponding to the Amur and Lena basins, and the other to the Enisei and Khatanga basins. Comparative rates of divergence revealed considerably faster and less heterogeneous substitution rates for the two coding genes, especially at interspecific levels compared to the mtDNA control region.     

Dnop56, a Drosophila gene homologous to the yeast nucleolar NOP56 gene

Small nucleolar RNAs (snoRNAs) are trans‐acting factors involved in maturation of rRNA and have been classified into Box C/D and Box H/ACA families. Most of the snoRNAs occur as ribonucleoprotein complexes with snoRNA‐associated proteins (snoRNPs). All Box C/D snoRNAs in yeast form complexes with Nop1p, Nop56p and Nop58p. Similarly, it has been reported that Box H/ACA‐containing snoRNAs form complexes with yeast Gar1p. Nop56p and Nop58p homologs have been described in several species. Here we report the isolation and molecular characterization of the Dnop56 genes from D. melanogaster and D. subobscura which show a very similar structure. Drosophila Nop56p proteins contain lysine‐rich regions at their carboxy‐terminus, and show a high degree of similarity to other Nop56p proteins from different organisms. Phylogenetic relationships among these proteins and other snoRNPs have been established. This revised version was published online in July 2006 with corrections to the Cover Date.     

Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule

We have introduced a G-quadruplex-binding ligand, 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC), to verify the major structure of d(T₂AG₃)₄ (H24) in potassium solution and examine the structural conversion of H24 in sodium solution upon potassium titration. The studies of circular dichroism, induced circular dichroism, spectral titration and gel competition have allowed us to determine the binding mode and binding ratio of BMVC to the H24 in solution and eliminate the parallel form as the major G-quadruplex structure. Although the mixed-type form could not be eliminated as a main component, the basket and chair forms are more likely the main components of H24 in potassium solution. In addition, the circular dichroism spectra and the job plots reveal that a longer telomeric sequence d(T₂AG₃)₁₃ (H78) could form two units of G4 structure both in sodium or potassium solutions. Of particular interest is that no appreciable change on the induced circular dichroism spectra of BMVC is found during the change of the circular dichroism patterns of H24 upon potassium titration. Considering similar spectral conversion detected for H24 and a long sequence H78 together with the G4 structure stabilized by BMVC, it is therefore unlikely that the rapid spectral conversion of H24 and H78 is due to structural change between different types of the G4 structures. With reference to the circular dichroism spectra of d(GAA)₇ and d(GAAA)₅, we suggest that the spectral conversion of H24 upon potassium titration is attributed to fast ion exchange resulting in different loop base interaction and various hydrogen bonding effects.     

Characterization of mitochondrial glutamate dehydrogenase from dark‐grown soybean seedlings

Purified preparations of NAD(H)‐glutamate dehydrogenase (GDH, EC 1.4.1.2.) were assayed to determine the effects of mono‐ and divalent cations, nucleotides and select carbon compounds on NAD(H)‐dependent GDH activity. The amination reaction was stimulated 2‐ to 17‐fold by divalent cations (Ca²⁺ > Cd²⁺ > Co²⁺ > Mg²⁺ > Mn²⁺ > Zn²⁺ between 1 and 1000 µ M ), but the reaction was unaffected by monovalent cations (Na ⁺ and K ⁺). The amination reaction was most responsive to changes in Ca²⁺ in a NADH‐dependent manner. The addition of EDTA or EGTA nullified the stimulatory effects of Ca²⁺. Calmodulin alone or in combination with calmodulin antagonists did not affect the amination reaction. Divalent cations (at 1 m M ) inhibited the rate of the deamination reaction by 15 to 25%, while monovalent cations had no effect. ATP inhibited the amination reaction by 10 to 60%, while ADP had little or no effect. ATP or ADP decreased the rate of the deamination reaction 23 to 60 or 20 to 38%, respectively. Many tricarboxylic acid cycle intermediates inhibited the amination reaction, 20 to 50% of the inhibition could be attributed to the chelating capacity of intermediates. Conversely, most of the carbon sources tested did not affect the deamination reaction, the only appreciable differences were increases in activity with sucrose (21%) and glucose (41%) and a decrease in activity with pyruvate (34%). Inhibitors of sulfhydryl groups were used to examine the importance of reduced thiol groups in the amination or deamination reactions. The amination was not dependent on reduced thiol groups, whereas the deamination reaction was dependent on reduced thiol groups.     

Condensation of DNA by the C-terminal domain of histone H1. A circular dichroism study

The condensation of DNA by the C-terminal domain of histone H1 has been studied by circular dichroism in physiological salt concentration (0.14 M NaF). As the intact H1 molecule, its C-terminal domain induces the so-called psi state of DNA that is characterized by a nonconservative circular dichroism spectrum which is currently attributed to ordered aggregation of the DNA molecules. On a molar basis, intact H1 and its C-terminal domain give spectra of similar intensity. Neither the globular domain of H1 nor an N-terminal fragment, that includes both the globular and N-terminal domains, has any effect on the conservative circular dichroism of DNA. From these results it is concluded that the condensation of DNA mediated by histone H1 is mainly due to its C-terminal domain. The effect of the salt concentration and the size of DNA molecules on the circular dichroism of the complexes are also examined.     

Orientation and linear dichroism characteristics of porphyrin-DNA complexes

The linear dichroism spectra of complexes of tetrakis(N-methyl-4-pyridinio)prophine (H2TMpyP) and its zinc(II) derivative (ZnTMpyP) with DNA oriented in a flow gradient have been investigated. The dichroism of H2TMpyP determined within the Soret band and the Qy band system is consistent with an intercalative conformation in which the plane of the porphyrin ring system is nearly parallel to the planes of the DNA bases. In the case of ZnTMpyP on the other hand, the porphyrin ring system is inclined at angles of 62-67 degrees with respect to the axis of the DNA helix. The pyridyl groups in both cases are characterized by a low degree of orientation with respect to the axis of the helix. In contrast to H2TMpyP which does not significantly affect the degree of alignment of the DNA in the flow gradient, the binding of ZnTMpyP causes a significant decrease (about 50% for a base pair/ZnTMpyP ratio of 20) in the intrinsic dichroism at 260 nm due to the oriented DNA bases; the binding of ZnTMpyP to DNA either gives rise to regions of higher flexibility or causes bends or kinks at the binding sites. Increasing the ionic strength has little influence on the linear dichroism of the ZnTMpyP-DNA complexes, but the number of molecules bound at intercalation sites diminishes in the case of the H2TMpyP-DNA complexes; the accompanying changes in the linear dichroism characteristics suggest that external H2TMpyP complexes are formed at the expense of intercalation complexes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Spectroscopic studies on histone-DNA interactions. II. Three transitions in nucleosomes resolved by salt-titration

The multiple-step transitions in DNA-histone interactions in chicken erythrocyte nucleosomes with increasing ionic strength are resolved by salt-titration spectroscopy. Both the circular dichroism of the DNA and the fluorescence of the histones in nucleosomes change during the titration process with concentrations of NaCl from 0.1 M to 2.5 M. By differentiating the titration curves, three distinct peaks corresponding to three structural transitions are observed. The two peaks near 0.95 M and 1.45 M-NaCl are common to the circular dichroism and fluorescence curves. The circular dichroism curve has another peak near 0.55 M-NaCl. Because the derivative of the fluorescence titration curve for the DNA-(H3, H4) complex has only one peak near 1.45 M-NaCl, that peak is attributed to the dissociation of the histone dimer (H3, H4). The peak near 0.95 M-NaCl corresponds to the dissociation of the dimer (H2A, H2B) from the DNA-(H3, H4) complex, as shown by binding experiments of (H2A, H2B) to the DNA-(H3, H4) complex at the salt concentration near this peak. The peak near 0.55 M-NaCl reflects some inner-core structural change. As the change of the circular dichroism signal is reversible, salt-titration spectroscopy is applicable to equilibrium studies of the physical chemical properties of DNA-histone interactions. By the assumption of a non-co-operative model, the binding constant for the chicken erythrocyte (H2A, H2B) dimer to the DNA-(H3, H4) complex is calculated as 2.8 X 10(6) M-1 at 1.0 M-NaCl (20 degrees C, pH 7.6). The DNA sequence dependence of the stability of the DNA-(H3, H4) interaction is observed in the salt-titration profiles of reconstituted material. Decreasing stability of the interaction of (H3, H4) is observed following the order: poly[(dG)-(dC)] much greater than chicken erythrocyte DNA greater than poly[(dA)-(dT)]. It is concluded that histones (H3, H4) have a different DNA sequence dependence from histones (H2A, H2B).     

Differential zinc and DNA binding by partial peptides of human protamine HP2

The Zn(II) binding by partial peptides of human protamine HP2: HP2_1–15; HP2_1–25, HP2_26–40, HP2_37–47, and HP2_43–57 was studied by circular dichroism (CD). Precipitation of a 20mer DNA by these partial peptides and the effects of Zn(II) thereon were investigated using polyacrylamide gel electrophoresis (GE). The results of this study suggest that reduced HP2 (thiol groups intact) can bind Zn(II) at various parts of the molecule. In the absence of DNA, the primary Zn(II) binding site in reduced HP2 is located in the 37–47 sequence (involving Cys37, His39, His43, and Cys47), while in the presence of DNA, the strongest Zn(II) binding is provided by sequences 12–22 (by His12, Cys13, His19, and His22) and 43–57 (His43, Cys47, Cys53, and His57). In its oxidized form, HP2 can bind zinc through His residues of the 7–22 sequence. Zn(II) markedly enhances DNA binding by all partial peptides. These findings suggest that Zn(II) ions may be a regulatory factor for sperm chromatin condensation processes.     

Modification of the lysine residues of histones H1 and H5: Effects on structure and on the binding to chromatin

The extensive modification of histone H1 from calf thymus with the amino-group reagent dimethylmaleic anhydride (over 35 lysine residues modified per molecule) produces no effect on its secondary structure detectable by circular dichroism (far UV). Fluorescence and circular dichroism (near-UV) of the modified histone show variations in the local environment of its sole tyrosine residue. These changes are reversed on regeneration of the modified amino groups. While histone H1 is easily dissociated with this reagent from calf thymus or chicken erythrocyte chromatin, a much stronger treatment is needed to liberate histone H5 from erythrocyte chromatin. This difference appears to be related to the higher arginine content of histone H5.     

Interaction specificities of a platinum metallointercalation reagent to DNA.

The interaction specificity of salmon sperm DNA with 2-hydroxyethanethionlato(2,2',2'-terpyridine)platinum(II),PtTS has been studied. The results of 1H and 13C nuclear magnetic resonance, flow dichroism and circular dichroism studies are found to be consistent with an intercalation mode of binding as has been proposed earlier by lippard and coworkers.     

Effect of solar radiation (UV and visible) at high altitude on CAM‐cycling and phenolic compound biosynthesis in Sedum album

The field experiment was carried out in order to compare the response of a CAM plant, Sedum album L., to solar radiation at a high altitude (2 100 m) with that at a low altitude location with respect to CAM and phenolic content. Treatment sites included (1) sun‐exposed, low altitude, (2) sun‐exposed, high altitude with different light treatments, including UV‐B and UV‐B + A screening, and (3) shade at high altitude. After a 70‐day treatment period, CAM‐cycling and phenolic compound content were analysed, and high altitude treatments were compared to the low altitude control. The sun‐exposed low altitude control was characterized by CAM‐cycling and a low phenolic compound content during the experiment. In plants transplanted to the high altitude, only the shaded group maintained a CAM‐cycling and a phenolic compound content similar to those of the sun‐exposed low altitude control. Samples under UV‐B and UV‐B + A filters showed similar responses, suggesting the absence of a specific UV‐A radiation effect. The screening of UV‐B or UV‐B + A radiation allowed plants to partially maintain a CAM‐cycling and induced a decrease in phenolic compound content. These responses under UV filters were, however, intermediate between those observed in sun‐exposed and shaded groups. These results demonstrate a specific effect of radiation from both visible (400–800 nm) and UV‐B (280–320 nm) bands on both CAM‐cycling and phenolic biosynthesis in S. album L. plants. These light‐dependent effects are discussed on a physiological basis and a possible interaction between CAM‐cycling and phenolic metabolism is suggested.     

Glycoconjugate distribution in gastric fundic mucosa of Umbrina cirrosa L. revealed by lectin histochemistry

The stomach of adult shi drum Umbrina cirrosa was investigated using a battery of nine horseradish peroxidase‐conjugated lectins combined with enzymatic treatment, in order to distinguish glycoconjugate sugar residues. Epithelial cells showed the presence of galactosyl(β1→4)N‐acetylglucosamine, mannose, N‐acetylgalactosamine, N‐acetylglucosamine, fucose and sialic acid‐galactosyl(β1→3)N‐acetylgalactosamine residues. Gastric pits had similar sugar residues with the exception of N‐acetylgalactosamine which was less diffused. Gastric glands were characterized by the presence of glycoconjugates containing galactosyl(β1→3)N‐acetylgalactosamine, N‐acetylglucosamine, galactosyl(β1→4) N‐acetylglucosamine, N‐acetylgalactosamine and a small amount of sialic acid linked to N‐acetylgalactosamine.     

Postharvest changes in endogenous cytokinins and cytokinin efficacy in potato tubers in relation to bud endodormancy

Using an indirect enzyme‐linked immunosorbent assay (ELISA), the effects of postharvest storage duration and temperature on endogenous cytokinins in potato ( Solanum tuberosum L. cv. Russet Burbank) tuber apical bud tissues in relation to endodormancy status were determined. Following fractionation by HPLC, a total of eight cytokinins were detected and these were: zeatin riboside‐5'‐monophosphate (ZRMP), zeatin‐ O ‐glucoside (ZOG), zeatin (Z), zeatin riboside (ZR), isopentenyl adenosine‐5'‐monophosphate (IPMP), isopentenyl adenine‐9‐glucoside (IP‐9‐G), isopentenyl adenine (IP) and isopentenyl adenosine (IPA). Regardless of postharvest storage temperature or endodormancy status, IP‐9‐G was the most abundant cytokinin detected while ZRMP and ZOG were the least abundant ones. In tubers preincubated at a growth‐permissive temperature (20°C) prior to extraction, the loss of endodormancy was preceded by significant increases in the endogenous levels of Z, ZR, IPMP and IP‐9‐G. When stored continuously at a growth‐inhibiting temperature (3°C), significant increases in ZR, IP‐9‐G and IP + IPA were observed. The total content of cytokinins increased by over 7‐fold during postharvest storage and this increase was a result of de novo biosynthesis. Dose‐response studies using IPA and ZR demonstrated a time‐dependent increase in apparent cytokinin sensitivity during postharvest storage. With the exception of IP‐9‐G, injection of any of these endogenous cytokinins resulted in the rapid and complete termination of tuber endodormancy. The significance of these results with respect to endodormancy regulation and the possible mechanisms controlling cytokinin levels in potato tubers are discussed.     

Immunohistochemical study of the gastrointestinal endocrine cells in the Korean aucha perch

The regional distribution and relative frequency of neurohormonal peptides‐producing cells were demonstrated in the gastrointestinal (GI) tract of the Korean aucha perch Coreoperca herzi , using 10 types of specific antisera raised against mammalian regulatory peptides. The GI tract was divided into four portions: stomach, gastro‐intestinal junction, and small and large intestine. Most of the immunoreactive (IR) cells were in the mucosal epithelium and they were generally spindle shaped with a long cytoplasmic process. In addition, ovoid cells were found in the gastric regions. Serotonin‐, somatostatin‐, glucagon‐, cholecystokinin‐8 (CCK‐8)‐ and pancreatic polypeptide (PP)‐IR cells were observed with various relative frequencies. No chromogranin A‐, secretin‐, vasoactive intestinal peptide‐, substance P‐ or bombesin‐IR cells, however, were found. Serotonin‐IR cells occurred throughout the GI tract and were the most numerous. Somatostatin‐IR cells were restricted to the stomach and gastro‐intestinal junction in numerous and moderate frequencies, respectively, but small numbers of glucagon‐IR cells were restricted to the small intestine. Numerous CCK‐8‐IR cells were found in the small intestine but variable numbers of PP‐IR cells occurred throughout the GI tract except for the large intestine. In general the distribution and relative frequency of these IR cells correspond well to previous reports in teleosts but there are some difference in this species.