Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers

Feathers of today's birds are constructed of beta (β)-keratins, structural proteins of the epidermis that are found solely in reptiles and birds. Discoveries of "feathered dinosaurs" continue to stimulate interest in the evolutionary origin of feathers, but few studies have attempted to link the molecular evolution of their major structural proteins (β-keratins) to the appearance of feathers in the fossil record. Using molecular dating methods, we show that before the appearance of Anchiornis (～155 Million years ago (Ma)) the basal β-keratins of birds began diverging from their archosaurian ancestor ～216?Ma. However, the subfamily of feather β-keratins, as found in living birds, did not begin diverging until ～143?Ma. Thus, the pennaceous feathers on Anchiornis, while being constructed of avian β-keratins, most likely did not contain the feather β-keratins found in the feathers of modern birds. Our results demonstrate that the evolutionary origin of feathers does not coincide with the molecular evolution of the feather β-keratins found in modern birds. More likely, during the Late Jurassic, the epidermal structures that appeared on organisms in the lineage leading to birds, including early forms of feathers, were constructed of avian β-keratins other than those found in the feathers of modern birds. Recent biophysical studies of the β-keratins in feathers support the view that the appearance of the subfamily of feather β-keratins altered the biophysical nature of the feather establishing its role in powered flight.     

Application of living immobilized cells to the acceleration of the continuous conversions of ethanol (wort) to acetic acid (vinegar)—Hydrous titanium(IV) oxide-immobilized Acetobacter species

Various strains of Acetobacter species have been immobilized on hydrous titanium(IV) oxide or hydrous titanium(IV) chelated cellulose and used in the continuous conversion of a dilute aqueous alcoholic solution (in the form of‘charging wort’) into acetic acid (in the form of vinegar) in tower fermenter-type reactors. A strain of Acetobacter species producing extracellular polysaccharide aggregated in the presence of hydrous titanium(IV) oxide thereby enabling higher medium flow rates and an increased acetic acid output to be achieved. A strain of Acetobacter species not producing polysaccharide showed no effect with hydrous titanium(IV) oxide but did produce more acetic acid when a titanium(IV)-cellulose chelate was added to the fermentation, although aggregation was not observed. Mechanisms, which appear to conform to established results, are proposed for the aggregation of both strains of bacteria. Apparently, these water-insoluble titanium compounds can interact with the bacterial cells, increasing their density and thus making them more resistant to ‘wash out’ by increasing the rate at which they sediment in the fermenter. This enables a greater cell mass per unit volume to be achieved which in turn leads to an increase in conversion rate in the reactor.     

pH-dependence of the specific binding of Cu(II) and Zn(II) ions to the amyloid-β peptide

Metal ions like Cu(II) and Zn(II) are accumulated in Alzheimer's disease amyloid plaques. The amyloid-β (Aβ) peptide involved in the disease interacts with these metal ions at neutral pH via ligands provided by the N-terminal histidines and the N-terminus. The present study uses high-resolution NMR spectroscopy to monitor the residue-specific interactions of Cu(II) and Zn(II) with (15)N- and (13)C,(15)N-labeled Aβ(1-40) peptides at varying pH levels. At pH 7.4 both ions bind to the specific ligands, competing with one another. At pH 5.5 Cu(II) retains its specific histidine ligands, while Zn(II) seems to lack residue-specific interactions. The low pH mimics acidosis which is linked to inflammatory processes in vivo. The results suggest that the cell toxic effects of redox active Cu(II) binding to Aβ may be reversed by the protective activity of non-redox active Zn(II) binding to the same major binding site under non-acidic conditions. Under acidic conditions, the protective effect of Zn(II) may be decreased or changed, since Zn(II) is less able to compete with Cu(II) for the specific binding site on the Aβ peptide under these conditions.     

Structure of Poly(dA)·Poly(dT) is not Identical to the AT Rich Regions of the Single Crystal Structure of CGCGAATTBrCGCG. The Consequence of this to Netropsin Binding to Poly(dA)·Poly(dT)

Abstract

The basic assumption of Dickerson and Kopka (J. Biomole. Str. Dyns. 2, 423, 1985) that the conformation of poly(dA)·poly(dT) in solution is identical to the AT rich region of the single crystal structure of the Dickerson dodecamer is not supported by any experimental data. In poly(dA)·poly(dT), NOE and Raman studies indicate that the dA and dT units are conformationally equivalent and display the (anti-S-type sugar)-conformation; incorporation of this nucleotide geometry into a double helix leads to a conventional regular B-helix in which the width of the minor groove is 8A. The derived structure is consistent with all available experimental data on poly(dA)·poly(dT) obtained under solution conditions. In the crystal structure of the dodecamer, the dA and dT units have distinctly different conformations—dA residues adopt (anti, S-type sugar pucker), while dT residues belong to (low anti, N-type sugar pucker). These different conformations of the dA and dT units along with the large propeller twist can be accommodated in a double helix in which the minor groove is shrunk from 8A to less than 4A. In the conventional right handed B-form of poly(dA)·poly(dT) with the 8A wide minor groove, netropsin has to bind asymmetrically along the dA strand to account for the NOE and chemical shift data and to generate a stereochemically sound structure (Sarma et al, J. Biomole. Str. Dyns. 2, 1085, 1985).     

A Supplement to the 《Flora of Xizang》 (2)

The present paper is the Supplement 2 to the Flora of Xizang, based upon a collection in 1980 by Mr. W. L. Chen et al. from Mêdog, the south-eastern part of Xizang. In the paper 11 new species are desribed and 10 new-record species are reported. All the type specimens are kept in the Herbarium of the Institure of Botany, Academia Sinica (PE).     

Nemertea inhabiting the Haploops (Amphipoda) community of the northern Øresund with special reference to the biology of Nipponnemertes pulcher (Hoplonemertea)

The densities of nemerteans and associated fauna on a soft-bottom sampling station (27–30 m deep) in the Øresund were determined from 47 cores (each 135 cm² in cross-section; 20 + cm deep) collected from September to December 1989; these data were compared with 14 cores taken from the same location in December 1982. Nine species of nemerteans were identified from cores and dredge samples: Palaeonemertea — Callinera-like sp.; Heteronemertea — Cerebratulus fuscus, C. marginatus, Lineus bilineatus, Micrura fasciolata, M. purpurea; Hoplonemertea — Amphiporus bioculatus, A. dissimulans, Nipponnemertes pulcher. Mean numbers of heteronemerteans were 32 and 10 m^?2 in 1982 and 1989, respectively, and hoplonemerteans were 90 and 71 m^?2 , respectively. Only one palaeonemertean was collected during both years. Mean densities of the dominant species, N. pulcher, were similar for the two years, 74 and 68 m^?2. The dominant groups of macrofauna (n m^?2) in 1989 were ostracods (1028), amphipods (618), polychaetes (514), and ophiuroids (449). Amphipods (>90% Haploops spp.) and polychaetes (at least 30 spp.) are the major potential prey for hoplonemerteans and heteronemerteans, respectively. Laboratory feeding experiments with N. pulcher revealed that it consumed amphipods (Haploops tenuis and H. tubicola) at a rate of 2.6 worm^?1 d^?1 during the first 12 hours, but after 36 hours and beyond the rate was maintained at approximately 0.2 worm^?1 d^?1. Beyond 12 hours this nemertean showed a tendancy to only partially evacuate its prey. It was demonstrated experimentally that N. pulcher has a supply of toxin capable of killing six amphipods in approximately one hour. Limited tests showed that N. pulcher fed on the cumacean Diastylis tumida, but not on the amphipod Maera loveni or the ostracod Philomedes globosus, and that Amphiporus dissimulans readily attacked Haploops spp., but not Maera or Philomedes. Although the results of laboratory experiments are tentative, they do suggest that suctorial hoplonemerteans can exert a potentially significant effect on benthic communities. Employing seven species of polychaetes as prey for Cerebratulus fuscus and Micrura fasciolata, only the latter responded positively to one of them, Glycera alba. The hermit crab Pagurus bernhardus violently rejected N. pulcher in all feeding trials.     

Contribution of fossil Lagomorpha (Mammalia) to the refinement of the late Miocene–Quaternary palaeobiogeographical setting of Italy

Fossil lagomorphs are very useful palaeogeographical indicators. In the last 15 years, several papers centered on fossil lagomorphs contributed to improve the Italian late Miocene–Quaternary palaeogeographical setting, solving palaeobiogeographical enigmas debated for decades, and providing new, challenging palaeogeographic data. The high number of endemic fossil lagomorphs of Italy is due in part to its complex tectonic history (insular endemisms), and in part to the semi-isolation and the physiography of the Peninsula (continental endemisms). In Italian lagomorphs, a direct causal relationship between dispersal and turnovers is not observed, except for the Toringian. Actually, species replacements are customarily due to archipelago effect (late Miocene), phyletic speciation (Pliocene of Sardinia and Italian mainland) or occur after the extinction of older congeneric species (early Pleistocene).     

Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process

Prions are believed to spontaneously convert from a native, monomeric highly helical form (called PrP(c)) to a largely β-sheet-rich, multimeric and insoluble aggregate (called PrP(sc)). Because of its large size and insolubility, biophysical characterization of PrP(sc) has been difficult, and there are several contradictory or incomplete models of the PrP(sc) structure. A β-sheet-rich, soluble intermediate, called PrP(β), exhibits many of the same features as PrP(sc) and can be generated using a combination of low pH and/or mild denaturing conditions. Studies of the PrP(c) to PrP(β) conversion process and of PrP(β) folding intermediates may provide insights into the structure of PrP(sc). Using a truncated, recombinant version of Syrian hamster PrP(β) (shPrP(90-232)), we used NMR spectroscopy, in combination with other biophysical techniques (circular dichroism, dynamic light scattering, electron microscopy, fluorescence spectroscopy, mass spectrometry, and proteinase K digestion), to characterize the pH-driven PrP(c) to PrP(β) conversion process in detail. Our results show that below pH 2.8 the protein oligomerizes and conversion to the β-rich structure is initiated. At pH 1.7 and above, the oligomeric protein can recover its native monomeric state through dialysis to pH 5.2. However, when conversion is completed at pH 1.0, the large oligomer "locks down" irreversibly into a stable, β-rich form. At pH values above 3.0, the protein is amenable to NMR investigation. Chemical shift perturbations, NOE, amide line width, and T(2) measurements implicate the putative "amylome motif" region, "NNQNNF" as the region most involved in the initial helix-to-β conversion phase. We also found that acid-induced PrP(β) oligomers could be converted to fibrils without the use of chaotropic denaturants. The latter finding represents one of the first examples wherein physiologically accessible conditions (i.e., only low pH) were used to achieve PrP conversion and fibril formation.     

Kinetics and mechanism of the oxidative addition of iodomethane to β-diketonatobis(triphenylphosphite)rhodium(I) complexes

The kinetics and mechanism of the oxidative addition of CH₃I to [Rh(β-diketone)(P(OPh)₃)₂] complexes was studied in acetone medium at various temperatures. The experimental rate law is R = k[Rh(β-diketone)(P(OPh₃)₂][CH₃I]. The order of the effect of the β-diketone on the reactivity of the complexes is acac >; BA >; DBM >; TFAA >; TFBA >; HFAA indicating that electronegative substituents of the β-diketone decrease the reactivity of the complexes towards oxidative addition reactions. The volume of activation for some of the reactions was determined in various solvents. The large negative values of the volume and entropy of the activation indicated a mechanism which occurs via a polar transition state.     

Analysis of Proteins Binding to the ITAM Motif of the β-Subunit of the High-Affinity Receptor for IgE (FcεRI)

Aggregation of the multichain (α β γ₂) high-affinity IgE receptor (Fcε RI) initiates a signaling cascade that results in the release of allergic mediators. The cytoplasmic tails of the Fcε RI-β and -γ subunits contain immunoreceptor tyrosine-based activation motifs (ITAMs). Phosphorylation of the γ ITAM mediates activation of Syk kinase and is sufficient for triggering the responses induced by Fcε RI crosslinking. Phosphorylation of the β ITAM is insufficient to mediate cell activation. The rat β ITAM contains three tyrosines (Tyr²¹⁸, Tyr²²⁴, and Tyr²²⁸) with an intermediate noncanonical tyrosine. Synthetic peptides based on the ITAM of the Fcε RI-β subunit were used to investigate the role of each phosphotyrosine in the binding of signaling proteins to this motif. Among the proteins that bind to phosphorylated β ITAM are Syk, Grb2, Shc, SHIP, and SHP-1, and binding does not depend on previous cell activation. Nonphosphorylated peptides do not bind these proteins. Syk binding to β -peptides is dependent on the number and position of phosphotyrosines in the ITAM. Phosphorylation of Tyr²¹⁸ seems to be most important for Syk binding. Recruitment of Syk and other signaling proteins to the β -subunit might be important for its amplifier role.     

Binding modes of μ-conotoxin to the bacterial sodium channel (NaVAb)

Polypeptide toxins isolated from the venom of cone snails, known as μ-conotoxins, block voltage-gated sodium channels by physically occluding the ion-conducting pathway. Using molecular dynamics, we show that one subtype of μ-conotoxins, PIIIA, effectively blocks the bacterial voltage-gated sodium channel Na_VAb, whose crystal structure has recently been elucidated. The spherically shaped toxin, carrying a net charge of +6 e with six basic residues protruding from its surface, is attracted by the negatively charged residues on the vestibular wall and the selectivity filter of the channel. The side chain of each of these six arginine and lysine residues can wedge into the selectivity filter, whereas the side chains of other basic residues form electrostatic complexes with two acidic residues on the channel. We construct the profile of potential of mean force for the unbinding of PIIIA from the channel, and predict that PIIIA blocks the bacterial sodium channel with subnanomolar affinity.     

Application of the Criterion of Biological Time (τ n /τ0) to the Studies of Embryogenesis in Birds

It was shown on the example of chick embryo that the number ₀ ( _n /₀) can be recommended as a measure of biological time and, for this purpose, the duration of the minimal mitotic cycle during synchronous cleavage divisions should be determined (in minutes) in various avian species. Based on the preliminary data, one can propose the comparability and similarity of the temporal programs of gastrulation and somitogenesis in the chick embryo and embryos of some fish and amphibians.     

The nervous system of Bothriomolus balticus (Proseriata) —a contribution to the knowledge of the orthogon in the Plathelminthes

Summary The nervous system (NS) of Bothriomolus balticus (Proseriata) was studied by the immunocytochemical (ICC) method with antisera to RFamide, SALMFamide and serotonin and with the histochemical GAIF method. The use of the ICC technique provided a much more precise morphological account of the nervous system than had previously been possible. The obtained data are discussed in connection with the comparative morphology of the nerve cords of the Plathelminthes. A similar position does not grant direct correspondence between nerve cords in the taxon Seriata. Marginal cords had probably an independent origin in the Monocelididae and Otoplanidae. The ventral (main) cords of B. balticus seem to correspond to the lateral (main) cords of the Monocelididae. It can be hypothesized that both: (1) a shift of the main cords accompanied by formation of new cords from the plexus and fusion of other cords and (2) a redistribution of nerve processes and perikarya between the cords, take part in the evolution of cords in the Plathelminthes. The first hypothesis seems to explain the difference in the position of main cords in proseriates, though, the second hypothesis might dominate, for example, in the Neorhabdocoela and the Neodermata. The correctness of the evolutionary analysis of the nerve cords in plathelminths can only be provided by neurons or neuron groups marking these structures.     

Is the invasion of Prorocentrum minimum (Dinophyceae) related to the nitrogen enrichment of the Baltic Sea?

The abundance of the invasive, bloom-forming dinoflagellate Prorocentrum minimum (Pavillard) Schiller and triangular, oval, and oval-round cell shapes were examined relative to salinity, temperature, and nutrient concentrations at the selected sites in the Baltic Sea. Based on the multiple regression and multivariate statistical analysis, all cell shapes of P. minimum had highly similar distribution relative to these environmental parameters as well as chlorophyll-a, nitrite + nitrate, ammonium, total nitrogen, phosphate, total phosphorus, and silicate. The species was related positively to total nitrogen, and negatively to salinity, temperature, nitrite + nitrate, and silicate:total nitrogen ratio. The results suggest that P. minimum could well adapt to low salinity and temperature and occurred particularly in coastal waters, rich in total nitrogen relative to silicate or other inorganic nutrients. These results indicate that the recent invasion of P. minimum into the Baltic Sea could have been enhanced by the DON enrichment. The results also support the suggestion that P. minimum is one morphospecies with no distinct subtaxa.     

Fragrance chemotypes of Platanthera (Orchidaceae) - the result of adaptation to pollinating moths?

Floral scent of Platanthera species (Orchidaceae) in S Sweden was collected by head-space adsorption methods in the field and analysed by gas chromatography-mass spectrometry (GC-MS). Variation in scent chemistry of both Platanthera bifolia and P. chlorantha was considerable: different scent chemotypes were found among individuals as well as populations. Mainly linalool, lilac aldehydes and alcohols, geraniol, and methyl benzoate distinguished the chemotypes. Because of a high individual variation, floral scent in Platanthera is not suitable as a taxonomic tool. Scent variation can be the result of differential selection from various pollinators or pollinator groups. However, in a long-spurred race of P. bifolia the scent profile was not clearly different from that of short-spurred races in spite of their different pollinators. The two species form natural hybrids and part of the variation at the individual level may he explained by interspecific introgression. Differences found among populations in different regions may be the result of random genetic drift.