Effects of hydration on scale factors for ab initio force constants. IV. trans and cis N-methylacetamide

Scaled quantum mechanical force fields have been calculated using the 4-31G basis for trans and cis conformers of both isolated and water-solvated N-methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between the trans and cis conformers. This is also true of a single set of scale factors for trans and cis NMA in water. The total standard deviation between measured and calculated frequencies for trans NMA in both isolated and solvated states is 6 cm^?1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA · nH₂O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water-solvated or otherwise hydrogen-bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen-bonded to water, using frequencies measured from water-solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen-bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be generally transferable.     

Studies on the distribution of alkalophilic and alkali-tolerant soil fungi II: Fungal flora in two limestone caves in Japan

In a series of studies on the distribution of alkalophilic and alkali-tolerant fungi, soil fungi were isolated from five alkaline calcareous soil samples in two closely located limestone caves (stalactite caves) in Japan using slightly acidic and alkaline media. Some common soil fungi that can grow in alkaline conditions were obtained in high frequencies. The growth response to pH of the isolates revealed that approximately one third (30.8%) of the isolates had the optimum pH in the alkaline range. All isolates of fourAcremonium species and twoChrysosporium species grew well in alkaline conditions, of whichAcremonium sp. andChrysosporium sp. were pronounced alkalophiles. These fungi were thought to be indigenous species in this alkaline environment. The fungal flora in the Japanese alkaline soils was considerably different from the flora reported in alkaline environments in other countries.     

The role of irregular unit,GAAS, on the secondary structure of Bombyx mori silk fibroin studied with 13C CP/MAS NMR and wide-angle X-ray scattering

Bombyx mori silk fibroin is a fibrous protein whose fiber is extremely strong and tough, although it is produced by the silkworm at room temperature and from an aqueous solution. The primary structure is mainly Ala-Gly alternative copolypeptide, but Gly-Ala-Ala-Ser units appear frequently and periodically. Thus, this study aims at elucidating the role of such Gly-Ala-Ala-Ser units on the secondary structure. The sequential model peptides containing Gly-Ala-Ala-Ser units selected from the primary structure of B. mori silk fibroin were synthesized, and their secondary structure was studied with (13)C CP/MAS NMR and wide-angle X-ray scattering. The (13)C isotope labeling of the peptides and the (13)C conformation-dependent chemical shifts were used for the purpose. The Ala-Ala units take antiparallel beta-sheet structure locally, and the introduction of one Ala-Ala unit in (Ala-Gly)(15) chain promotes dramatical structural changes from silk I (repeated beta-turn type II structure) to silk II (antiparallel beta-sheet structure). Thus, the presence of Ala-Ala units in B. mori silk fibroin chain will be one of the inducing factors of the structural transition for silk fiber formation. The role of Tyr residue in the peptide chain was also studied and clarified to induce "locally nonordered structure."     

pH tolerance of the biofouling invasive hydrozoan <Emphasis Type="Italic">Cordylophora caspia</Emphasis>

The hydrozoan Cordylophora caspia, with its origin in the Caspian and Black Seas, is considered an invasive biofouling species to power stations and water treatment plants in Brazil, causing economic and ecological impacts. Tolerance of the species to variation in pH was tested to evaluate its resistance to acidic and basic pH levels. Values of pH were tested over a range from 4.0 to 10.0. The colonies were exposed for 6 h to each treatment, using phosphoric acid and NaOH to set water pH to the desired acidic or basic levels, respectively. Colonies of C. caspia displayed 100% mortality only at pH 4 and 10, and showed high survival rates (>50%) within the pH range of 5.0–8.5. The species demonstrated tolerance to a wide range of pH levels, and the results will help in the development of techniques to reduce biofouling by this species. Treatments that keep the pH below 5 or above 8.5 for at least 6 h are suggested to control and eradicate C. caspia where fouling causes significant economic impacts.     

Conformational changes induced by ionic strength and pH in two bovine myelin basic proteins.

The structures of two biologically different myelin proteins, A1 from the central nervous system and P2 from the peripheral nervous system, were investigated. Both proteins were isolated from nerve tissues. Conformational changes in the homogeneous proteins were examined in aqueous solutions by means of circular dichroism measurements. The secondary structures of both proteins proved to be very stable between pH 2.5 and pH 11.7. Unlike the P2 protein, the A1 protein is stable up to pH 13 without detectable conformational changes. The stereochemistry of the polypeptide chains of both proteins is markedly different in the presence of urea. While the value of theta222 for the A1 protein changes linearly with increasing urea concentration, a sigmoidal curve was obtained for the P2 protein. The observed differences in the dichroic properties of the basic myelin proteins A1 and P2 indicate the possibility of further structure - function correlations.     

Floristic diversity of an eastern Mediterranean dwarf shrubland: the importance of soil pH

Questions: Does plant species richness and composition of eastern Mediterranean dwarf shrubland (phrygana) correlate with soil pH? How important is the effect of pH on species diversity in relation to other environmental factors in this ecosystem? What is the evolutionary background of the diversity–pH relationship? Location: Western Crete, Greece. Methods: Species composition of vascular plants, soil and other environmental variables were sampled in 100‐m² plots on acidic and basic bedrock in phrygana vegetation. The relationships between species composition and environmental variables (including climate) were tested using canonical correspondence analysis, and relationships between species richness and environment using correlation and regression analyses. Data were analysed separately for different plant functional types based on life form and life span. Results: Although soil pH varied across a narrow range (5.9‐8.1), species composition changed significantly along the pH gradient within all plant functional types. For most functional types, the effect of soil pH on species composition was stronger than that of other environmental variables. Species richness of annuals, geophytes and suffruticose chamaephytes increased with soil pH, while richness of hemicryptophytes and shrubs was not correlated with pH. Conclusions: The results are consistent with the evolutionary species pool hypothesis. High numbers of calcicole annuals, geophytes and suffruticose chamaephytes may be a result of the evolution of these groups on base‐rich dry soils in the Mediterranean climate. In contrast, hemicryptophytes, a life form typical of the temperate zone, evolved on both acidic and basic soils and therefore their species numbers do not respond to soil pH across the narrow range studied. The lack of a relationship between shrub species richness and pH is difficult to explain: it may reflect the more diverse or older origin of Mediterranean woody species and their conservative niches.     

Diversity of mesophilic clostridia in Costa Rican soils

Costa Rica is located in the Tropic, one of the most biologically diverse regions of the world; its soil is an important epicenter of biodiversity and Clostridium spp. are among the most frequent bacteria. The diversity of clostridia in Costa Rican soils and its possible association with geographic zone, pH or type of soil was studied in 117 soil samples: 18 from the Atlantic Zone, 30 from the Central Plateau, 30 from the Dry Pacific, 13 from the North Zone, and 26 from the South Pacific. The pH and the mesophilic clostridia species were determined for each sample. For bacterial isolation, a selective methodology for spores and pre-reduced anaerobically sterilized media were used. A total of 1945 strains of clostridia were isolated, 98% were identified and corresponded to 54 species; the most frequent species were C. subterminale (56%), C. oceanicum (51%), C. bifermentans and C. glycolicum (50%, each), C. sporogenes (49%), and C. sordellii (42%). An average of 7.1 species per sample was obtained; the Atlantic Zone showed the greatest diversity: 8.6 species per sample and a total of 45 species. Except for C. chauvoei, all described toxigenic clostridia species were isolated; C. sordellii (42%) and C. perfringens (38%) were the most frequent. No statistical relation could be established between geographic zone or type of soil and any species, showing that clostridia had a high adaptation capability to grow in different soil conditions; only some clostridia were isolated from very acidic samples while others from soils with a wide range of pH. In general, a uniform distribution of most species and a high variety of clostridia in Costa Rican soils were observed, in agreement with the high biodiversity described for other living beings in this country.     

Origin and significance of the production of carbon dioxide during the ozonization of 13C-labeled D-glucose at different pH values.

[1-(13)C], [2-(13)C] and [6-(13)C] D-glucose were, respectively, ozonized in a semi-batch reactor in acidic and basic conditions. The composition of the gas phase was evaluated by on-line mass spectrometry measurements. The quantitative and isotopic analyses of the carbon dioxide formed during ozonization are presented and discussed. The data, correlated with previous literature results, clearly show that at pH 2.5 the production of carbon dioxide from C-6 and C-1 carbon atoms is nearly equivalent. Conversely, at higher pH values, CO(2) is released with a greater selectivity from the reducing end. The importance of the decarboxylation reaction in the formation of by-products with fewer than six carbon atoms is also demonstrated.     

Herb abundance and life-history traits in two contrasting alpine habitats in southern Norway

Colonisation is often a critical stage in the life history of plants, and recruitment success is expected to have a strong impact on plant frequencies especially among herbs. Several plant traits (seed size, plant height, leaf dry weight and specific leaf area) are suggested to be functionally important in early life stages, and the impact of such traits is expected to increase with habitat harshness. In this comparative study we examine the relative role of different plant traits for herb community patterns on both a local and regional scale in two contrasting alpine ecosystems in southern Norway: (1) a sub-continental region with more dry and productive, base-rich soils (Ho1, Hallingdal) and (2) an oceanic region, with humid acidic soils (Setesdal). Differences in species richness between regions were mainly due to higher herb richness in the base-rich region (n=55) than in the acidic region (n=13). Among traits, herb species seed weight was higher at the acidic site. The relative importance of traits for explaining herb local abundance and regional distribution tended to be stronger at the acidic site. No trait had a significant effect at the base-rich site, although seed weight and seed number were marginally non-significant. Plant clonality was positively related to local abundance and marginally to regional distribution at the acidic site. Plant frequency-trait correlations were generally higher in the acidic region then in the base-rich region. There was further a (marginal) increase of herbs with large seeds and with a dependence on sexual reproduction with increasing pH levels in Ho1. Soil pH was also the most important environmental variable for herb richness in Ho1, while no environmental variable was significantly related to herb richness in Setesdal. The study suggests that recruitment through seed is critical for the alpine herb community patterns especially in harsh habitats. Possible explanations for recruitment constraints include both soil acidity (low pH and Ca levels in addition to possible aluminium toxicity) and disturbance through grazing.     

Characterization of two partially purified xyloglucan endotransglycosylases from parsley (<Emphasis Type="Italic">Petroselinum crispum</Emphasis>) roots

Two forms of xyloglucan endotransglycosylase differing in isoelectric points were isolated from the protein mixture obtained from parsley roots and partially characterized. Both forms were glycoproteins differing in their specific activities but other features were almost the same. Activity and stability of both enzymes in broad pH region were observed with two pH optima, one at acidic pH (5.8) and the second one at basic pH (8.8). The enzymes behaved as typical transglycosylases since no activity was observed in the absence of xyloglucan oligosaccharides in the viscometric assay. Small hetero-transglycosylating activities were observed when hydroxyethyl-or carboxymethyl-celluloses instead of xyloglucan as donor substrate were used as well as when cello-oligosaccharides instead of xyloglucan oligosaccharides were used as the acceptor substrate.     

Leaf breakdown, detrital resources, and food webs in streams affected by mine drainage

Breakdown of leaf litter is essential for providing detrital resources for food webs but can be impaired by anthropogenic activities, which may disrupt energy flow to consumers. We investigated the relationship between leaf breakdown and food web structure in 12 streams with or without mining impacts on South Island, New Zealand. Six streams received inputs of acid mine drainage (pH 2.5–4.9), three were naturally acidic (pH ~5.0), and three were circumneutral (pH ~6.8). Streams affected by mining either had highly acidic water (pH <3) or iron precipitates present on substrata. Breakdown rates of leaves were significantly lower in mining-affected streams than circumneutral (by almost 50%) but not naturally acidic streams and were driven primarily by microbial activity, as shredding invertebrates were often absent. Mining-affected stream webs were simplified structures with fewer species and links than those in other streams. With few species to process leaf litter and transfer detrital resources, inputs of AMD disrupted both the mechanisms responsible for breakdown and links for energy flow. While faster breakdown rates were associated with larger food webs, limited function maintained in mining-affected streams was sufficient to support primary consumers and small food webs.     

Ecophysiology of Fe-cycling bacteria in acidic sediments

Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocella-related strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacter-related clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 × 10(5) gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.     

Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria

Two continuous‐flow bench‐scale bioreactor systems populated by mixed communities of acidophilic sulfate‐reducing bacteria were constructed and tested for their abilities to promote the selective precipitation of transition metals (as sulfides) present in synthetic mine waters, using glycerol as electron donor. The objective with the first system (selective precipitation of copper from acidic mine water containing a variety of soluble metals) was achieved by maintaining a bioreactor pH of ～2.2–2.5. The second system was fed with acidic (pH 2.5) synthetic mine water containing 3 mM of both zinc and ferrous iron, and varying concentrations (0.5–30 mM) of aluminium. Selective precipitation of zinc sulfide was possible by operating the bioreactor at pH 4.0 and supplementing the synthetic mine water with 4 mM glycerol. Analysis of the microbial populations in the bioreactors showed that they changed with varying operational parameters, and novel acidophilic bacteria (including one sulfidogen) were isolated from the bioreactors. The acidophilic sulfidogenic bioreactors provided ‘proof of principle’ that segregation of metals present in mine waters is possible using simple online systems within which controlled pH conditions are maintained. The modular units are versatile and robust, and involve minimum engineering complexity.     

Comparison of starch hydrolysis activity and thermal stability of two Bacillus licheniformis alpha-amylases and insights into engineering alpha-amylase variants active under acidic conditions

Bacillus licheniformis alpha-amylase (BLA) is widely used in various procedures of starch degradation in the food industry, and a BLA species with improved activity at higher temperature and under acidic conditions is desirable. Two BLA species, designated as PA and MA, have been isolated from the wild-type B. licheniformis strain and a mutant strain, respectively. In this study, their starch-hydrolysis activity and thermal stability were examined. MA showed higher activity than PA, especially at acidic pH (pH 5.0-5.5), and even after 1 h of treatment at 90 degrees C. MA was active in the range of pH 4.0-8.0, which is much wider than that (pH 4.5-7.5) of PA. It was shown that the proton dissociation constants on the acidic and alkaline sides (pKa1 and pKa2) were shifted to more acidic and basic values, respectively, by the mutation of PA to MA. The activation energy and thermodynamic parameters for their thermal inactivation indicate that MA is more thermally stable and catalytically active than PA, suggesting that MA could be useful for glucose-production process coupled with reactions catalyzed by beta-amylase.     

Purification and characterization of mojave (Crotalus scutulatus scutulatus) toxin and its subunits

An acidic lethal protein, Mojave toxin, has been isolated from the venom of Crotalus scutulatus scutulatus. The purified toxin had an i.v. LD₅₀ of 0.056 μg/g in white mice. Disc polycrylamide gel electrophoresis at pH values of 9.6 and 3.8 and isoelectric focusing in polyacrylamide gels with a pH 3.5–10 Ampholyte gradient were used to establish the presence of one major protein band. The pI of the most abundant form of the toxin was determined to be 5.5 by polyacrylamide gel isoelectric focusing experiments. The molecular weight was established to be 24,310 daltons from amino acid composition data. Mojave toxin was shown to consist of two subunits, one acidic and one basic with isoelectric point (pI) values of 3.6 and 9.6, respectively. Amino acid analyses established molecular weights of 9593 for the acidic component and 14,673 for the basic component. The acidic subunit consisted of three peptide chains intermolecularly linked by cystine residues. The basic subunit was a single polypeptide chain with six intramolecular disulfide bonds. The basic subunit was lethal to test animals with an intravenous LD₅₀ of 0.58 μg/g. Following recombination of the subunits a recombinant toxin was isolated which was identical to the native toxin by comparisons of electrophoretic mobility and toxicities. Comparisons of circular dichroism spectra also indicated reassociation to the native toxin structure. Phospholytic activity was associated with Mojave toxin and the basic subunit was responsible for this enzymic activity. Phospholipase activity of the basic subunit was inhibited by addition of the acidic subunit.     

Plant communities of extreme acidic waters: The Rio Tinto case

As one of the largest extreme acidic environments in the world the Río Tinto (Spain) constitutes a useful case to study the vegetation resistant to waters, sediments and soils with pH < 3 and high concentrations of S, Fe, Cu and other metals. In this territory two types of water courses coexist: the extreme acidic waters, with a low pH and high amounts of S and Fe, usually of a red color, and those that are not extremely acid, which include colorless acid, neutral and basic waters with much less S and Fe. An exhaustive study of the riparian vegetation present along the two first sections of the Río Tinto and in less extreme, neighboring water courses was carried out (61 inventories). Some water quality variables (pH, redox, Fe, Cu and O₂) were measured in sampled points. Correspondence between plant community composition and water quality was analyzed through hierarchical classification, detrended correspondence analysis and canonical correspondence analysis.Results indicate clear differences in vegetation between extremely acidic and less extreme water courses. A total of 50 emergent plant species have been found in extremely acidic waters. Among them the most frequent were Erica andevalensis Cabezudo and J. Rivera, Scirpoides holoschoenus (L.) Soják and Nerium oleander L. Additionally, pH, redox, Fe and O₂ concentrations were significantly related to the floristic data.     

Bryophyte and vascular plant responses to base-richness and water level gradients in Western Carpathian<Emphasis Type="Italic">Sphagnum</Emphasis>-rich mires

We investigated the importance of water chemistry and water regime for vascular plant and bryophyte species distribution in Western Carpathian mires dominated bySphagnum. Seventy-seven small circle plots distributed across a wide geographical area, a wide range of mineral richness and all possible microtopographical features were sampled in terms of species composition, physical-chemical water properties and water regime during one growing season. Both water chemistry and water regime were found to be important factors for vegetation composition. Bryophytes reflected only one clear gradient, connected to base-richness (pH, conductivity) and maximal water-level, whereas three different environmental gradients determined the occurrence of vascular plants: water-level amplitude, base-richness and an indistinct gradient presumably connected to peat layer thickness. When the entire data set was subjected to DCA ordination, the first resulting axis was governed by the bryophyte subset, whereas the second one was governed by the vascular plant subset. The species density of vascular plants was positively correlated with pH and conductivity. On the contrary, bryophyte species density showed no relationship to environmental factors. We further compared the pH values measured in groundwater and in water squeezed from bryophytes from the same plot; these plots were distributed along the base-richness gradient. Only in the acidic mires did the use of squeezed-water chemistry in the analyses give results similar to the use of groundwater pH. Further, we found thatSphagnum species with a similar response to the base-richness gradient had differentiated niches with respect to the water level gradient and vice versa.Sphagnum contortum andS. warnstorfii exhibiting the same demands for groundwater pH were segregated along the gradient of maximum water level. An analogous pattern was detected for acidophilous speciesSphagnum magellanicum andS. papillosum.     

Reconstruction of pH by chrysophycean scales in some lakes of the Southern Alps

Chrysophycean scales were examined in surface sediments collected from 22 high mountain lakes on the southern slope of the Central Alps, some in Italy and some in Switzerland. The study area receives slightly acidic precipitation and summer lake pH ranges between 5.2 and 8.0. In each lake chrysophycean scale assemblage was dominated by one or two species and its composition was related to lakewater pH. Five short cores were examined in low-alkalinity lakes and evidence of recent lake acidification was found.     

DIET-TISSUE FRACTIONATION OF STABLE CARBON AND NITROGEN ISOTOPES IN PHOCID SEALS

Diet-tissue isotopic fractionation of carbon (C) and nitrogen (N) isotopes in short- and longer-term diet integrators of diet ( i. e. , blood serum and red cells), that involve non-invasive sampling techniques was examined using three species of phocid seals (harbor seals, gray seals, and harp seals) fed a known diet. Variability in diet-tissue fractionation values within and between species was also scrutinized to determine the legitimacy of using values obtained from one species to explore trophic positions and diets of other related species. All captive seals raised on a constant diet had tissues enriched in ¹³C and ¹⁵N relative to their diet. Diet-tissue isotopic fractionation values were generally consistent among conspecifics and among phocid species for a given tissue. Trophic isotopic enrichment in ¹³C was significantly higher in red blood cells (+1.5%±) than in blood serum (+0.8%±), whereas the reverse was observed for nitrogen isotopes (+1.7%± in red cells vs . +3.1%± in serum). However, ¹³C-depleted lipids were not extracted from blood tissues in this study. This results in a downward bias in the diet-tissue fractionation factors for carbon for both red cells and blood serum, particularly the latter because of their significantly higher lipid contents ( ± SD = 14.6 ± 2.3%; n = 20; red blood cells 3.8 ± 0.9%±; n = 50, muscle 7.7 ± 2.0; n = 21) in marine mammals.     

Isolation and characterization of cDNAs encoding beta A2- and beta A4-crystallins: heterologous interactions in the predicted beta A4-beta B2 heterodimer

Except for the two acidic chains, beta A2 and beta A4, the primary structures of all bovine beta-crystallins have previously been elucidated, either by direct protein sequencing or prediction from cDNA sequencing. Both beta A2 and beta A4 were found to be synthesized in half-year-old calf lenses and are therefore likely to be present in a cDNA bovine library constructed from mRNA isolated from lenses of that age. A large number of cDNA clones was screened with all available crystallin, actin, vimentin and lens membrane protein MP26 probes and finally with a randomly primed mRNA probe. Clones positive for the latter, but negative for known lens proteins, were isolated and sequenced. beta A2, comprising 197 aa, and beta A4, comprising 209 aa, were identified. Both proteins have a conserved two-domain structure and an N-terminal extension which is variable. A three-dimensional model of the structure of beta A4 was made based on the coordinates of one subunit from the beta B2 dimer which has recently been solved using x-ray diffraction techniques. The resulting heterodimer structure, together with the compiled bovine beta-crystallin sequences, was used to indicate those regions of the sequences which distinguish acidic from basic beta-crystallins with a view to defining structural features necessary for subunit recognition in beta-crystallin aggregates. With the aid of the present data, the complete evolutionary tree of the bovine beta-crystallin family has been constructed, which confirms the early separation of the genes encoding the three acidic and the three basic beta-crystallins.