Solution conformations of proline rings in proteins studied by NMR spectroscopy

Summary Three different conformations of proline rings in a protein in solution, Up, Down and Twist, have been distinguished, and stereospecific assignments of the pyrrolidine -, - and -hydrogens have been made on the basis of ¹H-¹H vicinal coupling constant patterns and intraresidue NOEs. For all three conformations, interhydrogen distances in the pairs -³, ³-³, ²-², ²-², and ³-³ (2.3 Å) are shorter than those in the pairs -², ²-³, ³-², ²-³, and ³-² (2.7–3.0 Å), resulting in stronger NOESY cross peaks. For the Up conformation, the ³-² and ²-³ spin-spin coupling constants are small (<3 Hz), and weak cross peaks are obtained in a short-mixing-time (10 ms) TOCSY spectrum; all other vicinal coupling constants are in the range 5–12 Hz, and result in medium to strong TOCSY cross peaks. For the Down form, the -², ²-³, and ³-² vicinal coupling constants are small, leading to weak TOCSY cross peaks; all other couplings again are in the range 5–12 Hz, and result in medium to strong TOCSY cross peaks. In the case of a Twist conformation, dynamically averaged coupling constants are anticipated. The procedure has been applied to bovine pancreatic trypsin inhibitor and Cucurbita maxima trypsin inhibitor-V, and ring conformations of all prolines in the two proteins have been determined.     

Effects of α-galactosidase digestion on lectin staining in human pancreas

Summary Effects of -galactosidase (from green coffee beans) digestion on lectin staining were examined in formalin-fixed, paraffin-embedded human pancreatic tissues from individuals of blood-group B and AB. Digestion with the enzyme resulted in almost complete loss of Griffonia simplicifolia agglutinin I-B₄(GSAI-B₄) staining in the acinar cells with concomitant appearance of Ulex europaeus agglutinin-I(UEA-I) staining in the corresponding cells. In addition, reactivity with soybean agglutinin(SBA) was also imparted by the enzyme digestion in GSAI-B₄ positive acinar cells. -Galactosidase digestion following -galactosidase digestion neither reduced the reactivity with SBA nor induced the reactivity with Griffonia simplicifolia agglutinin-II(GSA-II) in GSAI-B₄ positive cells, while in UEA-I positive cells, both reduction of SBA reactivity and appearance of GSA-II reactivity occurred after simple -galactosidase digestion as well as sequential digestion with - and -galactosidase. However, when -l-fucosidase digestion procedure was inserted between - and -galactosidase digestion, UEA-I staining imparted by -galactosidase digestion was markedly decreased in intensity and GSA-II reactivity was appeared in GSAI-B₄ positive acinar cells. Furthermore, after sequential digestion with -galactosidase and fucosidase, reactivity with peanut agglutinin(PNA) was revealed in GSAI-B₄ positive acinar cells as well as UEA-I positive cells in secretors. In non-secretors, strong PNA staining was usually observed in the acinar cells throughout the glands without enzyme digestion. These results confirmed that the -galactosidase induced GSA-II reactivity and the fucosidase induced PNA reactivity are due to precursors of different kinds of blood-group determinants and suggest that at least two kinds of B antigen determinants, i.e. Gal(1-3)[Fuc(1-2)]Gal(1-3,4)GlcNac and Gal(1-3)-[Fuc(1-2)]Gal(1-3)GalNAc are produced in GSAI-B₄ positive acinar cells. The synthesis of the latter type of B antigen is assumed to be controlled under the secretory gene in human pancreas.Abbreviation GalNAc N-acetyl-d-galactosamine - Gal d-galactose - GlcNAc N-acetyl-d-glucosamine - Fuc l-fucose - NeuNAc N-acetylneuraminic acid (sialic acid)     

Ultrastructure and behaviour of the spindle pole body of the aphid-pathogenic fungusErynia neoaphidis

Summary A detailed account of the ultrastructure and behaviour of the spindle pole body (SPB) of the entomophthoraceous fungusErynia neoaphidis is presented for the first time.The SPB consists of extranuclear (ENC) and intranuclear (INC) components. The ENC is a saucepan-shaped structure which lies in a pocket of the nuclear envelope. It is composed of a forked, fibrillar handle and a shallow, cylindrical pan. The pan has a wall of two layers, both of which are thickened with a regular periodicity so that they appear to be beaded. It is postulated that the pan is formed from rough endoplasmic reticulum and that it synthesizes the amorphous, electron-dense material coating the ENC.The INC is a saucer-shaped, electron-dense plaque in which the ends of the spindle microtubules terminate. During metaphase, a clear zone separates the INC from the nuclear envelope and persists until telophase. The roles of the amorphous, electron-dense material and the clear zone as well as the method of SPB replication are discussed.     

Effect of time delay in specific growth rate on the periodic operation of bioreactors with input multiplicities

The effect of time delay in specific growth rate () on the periodic operation of bioreactors with input multiplicities is theoretically analyzed for productivity improvement. A periodic rectangular pulse is applied either in feed substrate concentration (S_f) or in dilution rate (D). Periodic operation under feed substrate concentration cycling gives improvement in productivity at lower value of ¯S_f of the two steady-state multiplicities of S_f only when the time delay in is larger. Whereas the larger value of ¯S_f gives improvement in average productivity for all values of time delay. Dilution rate (D) cycling gives an improvement in average productivity particularly for larger time delay in . This improvement in average productivity is obtained only at smaller value of dilution rate out of the two steady-state input multiplicities of D.List of Symbols D 1/h dilution rate - F memory function - g dummy variable - K_i g/l substrate inhibition constant - K_m g/l substrate saturation constant - P g/l product concentration - P_m g/l product saturation constant - Q g/(hl) product cell produced per unit time - S g/l substrate concentration - S_f g/l feed substrate concentration - S_f,p g/l feed substrate concentration during fraction of a period - X g/l biomass concentration - Y_X/S g/g cell mass yield - w variable either S or Z - Z g/l weighted average of substrate concentration Greek Letters 1/h time delay parameter - ₁ , ₂ product yield parameters, g/g and 1/h - pulse width expressed as a fraction of a period - 1/h specific growth rate - _m 1/h maximum specific growth rate - h period of oscillation - – average value     

The filtration apparatus of Cladocera: Filter mesh-sizes and their implications on food selectivity

Summary The filtering apparatus of eleven Cladoceran species was studied. The distances between the setulae, which act as filters, were measured. Among adult individuals, they vary from 0.2 m in Diaphanosoma brachyurum to 4.7 m in Sida crystallina. Species can be grouped according to the mesh-sizes, as fine mesh filter-feeders: Diaphanosoma brachyurum, Ceriodaphnia quadrangula, Chydorus sphaericus, Daphnia cucullata and Daphnia magna; medium mesh filter-feeders: Daphnia galeata, D. hyalina. D. pulicaria, Bosmina coregoni, and coarse mesh filter-feeders: Holopedium gibberum and Sida crystallina. In Daphnia hyalina, the distances between setulae increase from 0.3–0.4 m in small juveniles, to 0.8–2.0 m in adults. In Daphnia magna, the mesh-size of the filter does not increase significantly with growth. There is good evidence that the relative abundance of the filter-feeding types varies with the trophic state of the lake. In oligotrophic lakes the coarse mesh filter-feeders usually dominate throughout the year. The seasonal succession of zooplankton species in eutrophic lakes can be interpreted as a succession of feeding types; during winter coarse mesh filter-feeders dominate, while fine mesh filter-feeders are most abundant during summer phytoplankton blooms. Our results support the hypothesis that the species composition of filter-feeding zooplankton is strongly influenced by the amount of suspended bacteria which are available as food only for filter-feeding species with fine meshes.     

Intrinsic fluorescence studies on saccharide binding toArtocarpus integrifolia lectin

The combining region ofArtocarpus integrifolia lectin has been studied by using the ligand-induced changes in the fluorescence of the lectin. The saccharide binding properties of the lectin show that C-l, C-2, C-4, and C-6 hydroxyl groups of D-galactose are important loci for sugar binding. The -anorner of galactose binds more strongly than its -counterpart. Inversion in the configuration at C-4 as in glucose results in a loss of binding to the lectin. The C-6 hydroxyl group is also presumably involved in binding as D-fucose does not bind to the lectin.The lectin binds to the Thomsen-Friedenreich antigen (Gal(13)GalNAc) more strongly than the other disaccharides studied, viz. Gal/ (14) Gal and Gal (13) GlcNAc, which are topographically similar to T-antigen. This observation suggests that the combining region ofArtocarpus lectin is complementary to that of T-antigen.Solvent accessibility of the protein fluorophores have been probed by the quenching of protein fluorescence by Iodide ion in the absence and presence of sugar. In the presence of sugar a slight inaccessibility of the fluorophores to the solvent has been observed.Abbreviations MeGal 1-O-methyl--glucopyranoside - MeGal 1-O-methyl--glucopyranoside - GalNAc 2-acetamido-2-deoxy-galactose - Gal Galactose     

Convergent synthesis of neoglycopeptides by coupling of 2-bromoethyl glycosides to cysteine and homocysteine residues in T cell stimulating peptides

The 2-bromoethyl -glycosides of the disaccharide galabiose [Gal(1-4)Gal] and the trisaccharides globotriose [Gal(1-4)Gal(1-4)Glc] and 3-sialyllactose [Neu5Ac(2-3)Gal(1-4)Glc] have been prepared by improved routes. The 2-bromoethyl glycosides were then used in cesium carbonate promoted alkylations of the sulfhydryl groups of cysteine and homocysteine residues in T cell stimulating peptides. This convergent and general approach was used to prepare 16 neoglycopeptides which were obtained in 52–95% yields after purification by HPLC. 1H NMR spectroscopy revealed that -elimination and epimerization of neoglycopeptide stereocentres did not occur during the synthesis.     

Expression of a chimeric stilbene synthase gene in transgenic wheat lines

A chimeric stilbene synthase (sts)gene was transferred into wheat. Stilbene synthases play a role in the defence against fungal diseases in some plant species (e.g. groundnut or grapevine) by producing stilbenetype phytoalexins like resveratrol. Resveratrol is also claimed to have positive effects to human health. Embryogenic scutellar calli derived from immature embryos of the two commercial German spring wheat cultivars Combi and Hanno were used as target tissue for cotransformation by microprojectile delivery. The selectable marker/reporter gene constructs contained the bargene either driven by the ubiquitinpromoter from maize (pAHC 25, also containing the uidAgene driven by the ubiquitinpromoter), or by the actinpromoter (pDM 302) from rice. The cotransferred plasmid pStil 2 consisted of a grapevine stscoding region driven by the ubiquitin promoter. Eight transgenic Combi and one Hanno T_Oplant were obtained and, except one Combi T_Oplant, found to be cotransformants due to the integration of both the stsgene and the selectable marker or reporter genes. Expression of the stsgene was proven by RTPCR, and, for the first time, by detection of the stilbene synthase product resveratrol by HPLC and mass spectrometry. The stsgene was expressed in four of the seven transgenic Combi T_{_o}plants. Two of the respective T₁progenies segregated in a Mendelian manner were still expressing the gene. Investigations into methylation of the stsgene showed that in three nonexpressing progenies inactivation was paralleled by methylation.     

Defective remethylation of homocysteine is related to decreased synthesis of coenzymes B2 in thyroidectomized rats

Summary. We investigated the influence of hypothyroidism on homocysteine metabolism in rats, focusing on a hypothetical deficient synthesis of FAD by riboflavin kinases. Animals were allocated in control group (n=7), thyroidectomized rats (n=6), rats with diet deficient in vitamin B2, B9, B12, choline and methionine (n=7), thyroidectomized rats with deficient diet (n=9). Homocysteine was decreased in operated rats (2.6±1.01 vs. 4.05±1.0mol/L, P=0.02) and increased in deficient diet rats (29.56±4.52 vs. 4.05±1.0mol/L, P=0.001), when compared to control group. Erythrocyte-Glutathione-Reductase-Activation-Coefficient (index of FAD deficiency) was increased in thyroidectomized or deficient diet rats (P=0.004 for both). Methylenetetrahydrofolate-reductase and methionine-synthase activities were decreased in thyroidectomized rats but not in those subjected to deficient diet. Cystathionine--synthase was increased only in operated rats. Taken together, these results showed a defective re-methylation in surgical hypothyroidism, which was due in part to a defective synthesis of vitamin B2 coenzymes. This defective pathway was overcompensated by the increased Cystathionine--synthase activity.     

Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank

Short peptides connecting-helices and-strands have been analyzed in 240 proteins refined at resolutions of 0.25 nm or better. Connecting peptides of lengths between one and five residues have been classified as part of supersecondary motifs of four types:, , , and. Careful consideration has been given to the definition of secondary structures on the basis of hydrogen bonds and main-chain conformational angles. Using five classes of residue conformation—a, b, e, l, t—in the nonregular structure regions of, space, 34 classes of supersecondary motifs occurring at least five times have been identified. Among these 34 classes, 11 classes that occur more than 25 times are commonly occurring supersecondary structure motifs. The patterns and conformations of the 11 commonly occurring supersecondary structure motifs have been characterized, demonstrating that patterns and conformations adopted by supersecondary structure motifs are limited. The results have relevance to structure prediction, comparative modeling, and protein folding.     

Extent and high frequency of a short conversion between the human Aγ and Gγ fetal globin genes

Summary Southern blotting and DNA sequencing after polymerase chain reaction (PCR) amplification provide evidence for the frequent occurrence (in 7 out of 24 chromosomes) of a short conversion GA in the 3 end of the human fetal A globin gene. This short conversion is characterized by the presence, 3 nucleotides downstream from the termination codon of the A gene, of the TCAC sequence that is normally present at the equivalent position at the 3 end of the G gene; it is therefore identical to a conversion already described. Interestingly, we have found that this conversion is associated with the presence of theHindIII polymorphic restriction site in the A IVS2, occuppying an equivalent position in both the G and A genes. Our observations strengthen the hypothesis that the presence of the HindIII polymorphic restriction site in A IVS2 and the presence of the sequence TCAC at the 3 end of the A gene might be the result of a single conversion event.     

Genetic characterization of a new splice variant of the β2 subunit of the voltage-dependent calcium channel

This study reports a novel splice variant form of the voltage-dependent calcium channel ₂ subunit (_2g). This variant is composed of the conserved amino-terminal sequences of the _2a subunit, but lacks the -subunit interaction domain (BID), which is thought essential for interactions with the ₁ subunit. Gene structure analysis revealed that this gene was composed of 13 translated exons spread over 107 kb of the genome. The gene structure of the ₂ subunit was similar in exon-intron organization to the murine ₃ and human ₄ subunits. Electrophysiological evaluation revealed that _2a and _2g affected channel properties in different ways. The _2a subunit increased the peak amplitude, but failed to increase channel inactivation, while _2g had no significant effects on either the peak current amplitude or channel inactivation. Other subunits, such as ₃ and ₄, significantly increased the peak current and accelerated current inactivation.     

Meiotic studies ofElymus nutans andE. jacquemontii (Poaceae,Triticeae) and their hybrids withPseudoroegneria spicata and seventeenElymus species

Hybridizations ofElymus nutans andE. jacquemontii were carried out with one species ofPseudoroegneria (S genome), and 20Elymus species, each containing either of the SH, SY, SYH, or SYW genomes. Chromosome configurations were analysed at metaphase I of the two target taxa and their interspecific hybrids. It is concluded that (i)E. nutans is an allohexaploid containing the SYH genomes, andE. jacquemontii is an allotetraploid having the SY genomes; (ii) the genomic affinity is associated with the geographic distance between the species studied; (iii) minor genomic structural rearrangements have occurred within the hexaploid taxon ofE. nutans.     

Zum Ortstreue-Verhalten des Trauerschn?ppers(Ficedula hypoleuca) im westlichen Randbereich seines mitteleurop?ischen Verbreitungsgebietes

Zusammenfassung 1974–1981 wurden in einem Lärchen-Versuchsforst (320 ha; 600 künstliche Nisthöhlen) in Niedersachsen (52.27 N/7.15 E) 529 Brutvögel des Trauerschnäppers beringt. Geburtsortstreue — auf das Versuchsgebiet bezogen — konnte bei 78 Individuen (=5,2 % der ausgeflogenen Nestlinge) festgestellt werden. Die geburtsortstreuen wurden in der Regel schon im ersten Jahr als Brutvogel nachgewiesen, während die Hälfte der geburtsortstreuen bei der ersten Erfassung ein Alter von mindestens 2 Jahren besaß. In der mittleren Entfernung zwischen Geburts- und erstbekannter Bruthöhle ergab sich zwischen den Geschlechtern kein gesicherter Unterschied ( : 883 m, : 798 m). Geschwister verhielten sich bezüglich Ansiedlungsalter und Ansiedlungs-entfernung nicht einheitlich. Von den als Brutvögel beringten Trauerschnäppern konnten 38,2 % der und 24,0 % der in einem späteren Jahr wiedergefangen werden. Bei den lagen die in aufeinanderfolgenden Jahren besetzten Nisthöhlen näher beieinander als bei den (Mittelwerte: 371 m bzw. 534 m). In der untersuchten Population war in allen Jahren bei den der Prozentsatz brutortstreuer Individuen höher und der Anteil an Zuwanderern geringer als bei den (Mittelwerte: 48 % gegenüber 30 % bzw. 45 % gegenüber 64 %). Diese Befunde wurden unter anderem im Hinblick auf die Lage des Untersuchungsgebietes am Rande des Trauerschnäpper-Areals diskutiert. Die Ortstreue war geringer ausgebildet als in mehreren anderen Populationen.

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On place-fidelity behaviour in the Pied Flycatcher(Ficedula hypoleuca) in the western border area of its Central European range

Summary The evaluation is based on findings from 1974 to 1981, in a 320 ha. experimental larch forest (52.27N, 7.15E), with 600 nestboxes, in western Lower Saxony, from a total of 529 breeding Pied Flycatchers. Fidelity to birthplace — recovery in the study area — was recorded for 78 individuals (=5.2 % of the fledged nestlings). faithful to birthplace were traced, as a rule, in the first year, while half of the who showed this fidelity were at least 2 years old when first recorded. There was no significant difference between sexes in the mean distance between the hole in which they were hatched and the first known breeding hole ( : 883 m, : 798 m). There was no uniformity among siblings in relation to age of settlement and distance of settlement. 38.2 % of and 24.0 % of Pied Flycatchers ringed as breeding birds were recaptured in a later year. Nest boxes occupied in successive years were closer together in the case of than (mean: 371 m and 534 m respectively). The percentage of individuals showing fidelity to birthplace was higher, in all years, and the number of immigrants smaller, in the than in (mean: 48 % against 30 % and 45 % against 64 % respectively). These findings are discussed in relation to the border situation of the study area. The rate of recoveries was lower than in some other populations.

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Gefördert mit Hilfe von Forschungsmitteln des Landes Niedersachsen.     

The taxonomic significance of the trunk limbs of the chydoridae (Cladocera)

Summary The differences in the structure of the trunk limbs allow to outline three sections of Chydoridae (see table I and fig. 1), coinciding with the sections distinguished according to the structure of the head pores.

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Chydoridae (Cladocera)

Chydoridae (. ), , .

     

Synthesis of Gal-β-(1→4)-GlcNAc-β-(1→6)-[Gal-β- (1→3)]-GalNAc-α-OBn oligosaccharides bearing O-methyl or O-sulfo groups at C-3 of the Gal residue: specific acceptors for Gal: 3-O-sulfotransferases

Our recent studies have revealed the existence of two distinct Gal: 3-O-sulfotransferases capable of acting on the C-3 position of galactose in a Core 2 branched structure, e.g., Gal14GlcNAc16(Gal13)GalNac1OBenzyl as acceptor to give 3-O-sulfoGal14GlcNAc13(Gal13)GalNAc1OB 20 and Gal14GlcNAc16(3-O-sulfoGal13)GalNAc1OB 23. We herein report the synthesis of these two compounds and also that of other modified analogs that are highly specific acceptors for the two sulfotransferases. Appropriately protected 1-thio-glycosides 7, 8, and 10 were employed as glycosyl donors for the synthesis of our target compounds.     

The new problem of genetics: A response to Gifford

Recently, Fred Gifford attempted to explicate the meaning of the term genetic as applied to phenotypic traits. He takes as his primary goal the explication of how the term is used and tries to avoid conclusions about how it should be used. He proposes two independent criteria (DF and PI) which together capture much of what biologists mean when they describe traits as genetic. Although Gifford's approach is extremely insightful in many ways, I argue that his analysis is not sufficiently critical concerning the adequacy of common usage.In particular, while DF is a perfectly legitimate and useful measure of heritability in populations, it is not necessarily a genetic one and should not be labeled as such. PI on the other hand, although very intuitive, depends on an extremely problematic distinction between causes and mere conditions (e.g., genes and epigenetic factors). Both criteria will be highly relative and both, via what I term the new problem of genetics, will inspire contradictory analyses based on the same data.Fortunately, as Gifford recognizes, it is not necessary to make sense of genetic at all in order to do biology. Quantitative genetics can do the kind of (heritability) analysis that DF embodies without making questionable claims about genes. Causal-mechanical or bottom-up biology can proceed perfectly well without postulating the priveleged role for genetic causes that PI entails. In short, talk of genetic traits, under either criteria, is unnecessary and misleading.     

Vanadium and molybdenum requirement for the fixation of molecular nitrogen by two Methanosarcina strains

Nitrogen fixation of the Methanosarcina barkeri strains Fusaro (DSM 804) and 227 (DSM 1538) was found to be dependent on the presence of vanadium or molybdenum whereby molybdenum (added as Na₂-molybdate) was preferred to vanadium (added as VCl₃). Strain 227 showed less pronounced effects on diazotrophic growth with respect to vanadium and molybdenum. Rhenium (ReCl₃) or tungsten (Na₂-tungstate) could not replace vanadium or molybdenum. The optimum concentrations were found to be 2M for vanadium and 5M for molybdenum (strain Fusaro). This Mo optimum of methanogenesis was 10-fold higher with N₂ than with NH₄Cl as nitrogen source. A vanadium requirement with NH₄Cl could not be detected. No interferences were observed if molybdenum and vanadium were added simultaneously under diazotrophic conditions. Growth yields were smallest for strain 227 grown diazotrophically ( =0.6g dw/mol in the presence of vanadium and =0.9g dw/mol in the presence of molybdenum), obviously higher for strain Fusaro grown diazotrophically ( =1.15g dw/mol in the presence of V and =1.4g dw/mol with Mo) and highest if M. barkeri was grown on NH₄Cl as N-source ( =3.4g dw/mol with Mo, strain Fusaro).     

DNA sequence patterns in human,mouse, and rabbit immunoglobulin kappa-genes

Summary DNA sequences of the human, mouse, and rabbit immunoglobulin kappa-gene (J-C regions) are compared with respect to various DNA patterns, including dyad symmetry pairings, runs of nucleotides, repeat clusters, and repeats that occur with unusually high frequency. The significant dyad symmetry pairings within each of the sequences emphasize the two control-enhancer elements of the J₅-C intron. Dyad symmetry pairs between the J-C region and a number of kappa variable (V)-gene domains suggest differences in the affinities between the V and J segments. It is the consensus heptamer rather than the consensus nonamer that embodies the longest V-J dyad symmetry combinations. In the rabbit there are long runs and repeat clusters of the sequences that identify regions of high duplication; these regions are absent in the human and mouse sequences. High-frequency oligonucleotides feature the consensus nonamer 5 to the J segments, especially in the mouse sequence.