Regression and model-building in conservation biology, biogeography and ecology: The distinction between – and reconciliation of – ‘predictive’ and ‘explanatory’ models

In many large-scale conservation or ecological problems where experiments are intractable or unethical, regression methods are used to attempt to gauge the impact of a set of nominally independent variables (X) upon a dependent variable (Y). Workers often want to assert that a given X has a major influence on Y, and so, by using this indirection to infer a probable causal relationship. There are two difficulties apart from the demonstrability issue itself: (1) multiple regression is plagued by collinear relationships in X; and (2) any regression is designed to produce a function that in some way minimizes the overall difference between the observed and predicted Ys, which does not necessarily equate to determining probable influence in a multivariate setting. Problem (1) may be explored by comparing two avenues, one in which a single best regression model is sought and the other where all possible regression models are considered contemporaneously. It is suggested that if the two approaches do not agree upon which of the independent variables are likely to be significant, then the deductions must be subject to doubt.     

XXXY sex chromosomes in males of the jumping spider genus Pellenes (Araneae: Salticidae)

Observations of male meiosis and female chromosome number indicate that eight species of Pellenes have the X₁X₂O male, X₁X₁X₂X₂ female sex chromosome system typical of salticids, four species have an X₁X₂X₃Y male, X₁X₁X₂X₃X₃X₃ female system, and one species has both X₁X₂O and X₁X₂X₃Y males. This is the first report of a Y chromosome in spiders. It is hypothesized that the X₁X₂X₂Y system was derived from an X₁X₂O system by a tandem X-autosome fusion which yielded the X₂ and a centric autosome-autosome fusion which yielded the Y. Data on heteropycnosis, chiasmata, segregation, chromosome number and arm length support this hypothesis. The distribution of the X₁X₂X₃Y system within the genus is phylogenetically confusing and suggests that the two sex chromosome systems have been maintained together as a polymorphism in some lineages for long periods of time or that there have been repeated derivations of the X₁X₂X₃Y or X₁X₂O systems.     

Novel 2D and 3D multiple-quantum bi-directional HCNCH experiments for the correlation of ribose and base protons/carbons in 13C/15N labeled RNA

Multiple-quantum 2D and 3D bi-directional HCNCH experiments are presented for the correlation of base and ribose protons/carbons in ¹³C/¹⁵N labeled HIV-1 TAR RNA. In both 2D and 3D experiments, the magnetization of H1 is transferred to H6/H8 and H1 through H1-C1-N1/9-C6/8-H6/8 and H1-C1-N1/9-C1-H1 pathways, and the magnetization of H6/8 is transferred to H1 and H6/8 through H6/8-C6/8-N1/9-C1-H1 and H6/8-C6/8-N1/9-C6/8-H6/8 pathways. Chemical shifts of four different nuclei (H1, C1, C6/8 and H6/8) are sampled in the 2D experiment. The correlation of base and ribose protons/carbons is established by the rectangular arrangement of crossover and out-and-back peaks in the proton/carbon correlated spectrum. The rectangular connections can be further resolved using the nitrogen dimension in a ¹H/¹³C/¹⁵N 3D experiment. Furthermore, by taking advantage of the well separated chemical shifts of N1 (pyrimidine) and N9 (purine), the 2D spectrum can be simplified into two sub-spectra based on their base type. Both experiments were tested on a ¹³C/¹⁵N labeled 27-mer HIV-1 TAR RNA containing a UUCG hairpin loop.     

Production of glucosamine containing disaccharides of the Lewis-A and -X types employing glycosidases

Disaccharide derivatives of interest for inhibition studies and for synthesis of the blood group determinants Lewis-a and Lewis-x were obtained with glycosidases as catalysts. Thus, Fuc(1–4)(6-OBn)GlcNH₂SEt and Gal1–3(6-OBn)GlcNH₂-SEt were produced employing (6-OBn)GlcNH₂SEt as acceptor and -L-fucosidase and -D-galactosidase, respectively, as catalysts. The phthalimido derivative of lactosamine, Gal1-4GlcNPhthSEt, was prepared from lactose employing GlcNPhthSEt as the acceptor and a yeast -galactosidase as catalyst. The reactions were both regio- and stereospecific, which allowed straightforward production of pure products on a g scale and higher.     

Optimized set of two-dimensional experiments for fast sequential assignment,secondary structure determination,and backbone fold validation of 13C/15N-labelled proteins

NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional ¹H-¹⁵N HSQC-like spectra. The ¹H-¹⁵N correlation peaks are frequency shifted by an amount ± _X along the ¹⁵N dimension, where _X is the C, C, or H frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces.     

Ecology of Proteus flagellar phages

Summary Phages identical to X ₇ in host range and serological properties are liberated by several Proteus strains. Another Proteus flagellar phage, X ₈, differs from X ₇ antigenically and in host range.     

Origin and trophic importance of detritus-evidence from stable isotopes in the benthos of a small,temperate estuary

Ratios of ¹³C/¹²C and ¹⁵N/¹⁴N were measured in dissolved inorganic carbon (DIC), marginal vegetation, benthic macrodetritus (diameter > 1 mm) and selected invertebrate consumers in the Gamtoos estuary, South Africa to: (1) trace the provenance of benthic detrital deposits, and (2) determine the extent to which three abundant species of macroinvertebrates utilise this resource. DIC was strongly depleted in ¹³C with average ¹³C values (–9.5±0.5) being typical of limnetic waters. Benthic detrital particles (¹³C–24.1±0.3) originated mainly from marginal vegetation (¹³C–25.7±0.3), but their slightly elevated carbon ratio suggests additional input from ¹³C-rich sources-possibly C₄ plants cultivated on the floodplain. Populations of the fossorial ghost shrimp Callianassa kraussi, the bentho-pelagic amphipod Grandidierella lignorum and the epifaunal crab Hymenosoma robiculare together account for 96% of total benthic biomass in the upper regions of this estuary. Marked differences in trophic niches were evident among these three consumer species. Ghost shrimp (¹³C –32.5±0.3) foraged by filter-feeding on fine suspended particulate organic matter (¹³C–31.2±0.5). Amphipods (¹³C–28.0±0.6) utilised some benthic detritus but fed mainly on suspended material. Only the relatively rare crabs (¹³C–23.8±1.5) appeared to utilise benthic detrital particles to any significant extent. In the benthic consumer community of the upper Gamtoos estuary, suspension feeders make up 98% of biomass and thus clearly dominate over deposit feeders. This can be traced to the low contribution of higher plants (c. 13%) to overall carbon production, and detritus originating from macrophytes is consequently relatively unimportant in supporting invertebrate secondary production in this particular system.     

Microradiographic determination of lead in mineralized tissues

Summary A dichromatic contact microradiographic method is presented for quantitative microanalysis of lead in mineralized tissues utilizing the L absorption edges of lead. Sections of mineralized tissue with a thickness of about 100 are exposed to filtered molybdenum K and copper K radiation. Quantitative localization of lead is possible within small areas of the order of 50 ² with an accuracy of 25 · 10^–12g lead. The method has been applied to studies of long term accumulation of lead in bone tissue.     

The appearance of competence for phytochrome-mediated anthocyanin synthesis in the cotyledons of Sinapis alba L.

Summary It is demonstrated that phytochrome-mediated anthocyanin synthesis in the epidermal cells of mustard seedling cotyledons takes place only 27 h after sowing onwards (at 25°C). This starting point cannot be shifted by light treatments or by nutrients. The late appearance of competence for P _fr (P _r and P _fr, red- and far-red absorbing forms of phytochrome, respectively) with regard to anthocyanin synthesis is not related to the phytochrome system per se (P _rP _fr) as this is fully functional immediately after sowing of the seed; nor is it related to the primary reaction of phytochrome: P _fr+XP _fr XP _fr X (X, X, two forms of a receptor for P _fr) or to the initial action of P _fr X:P _fr X+KY (K, coupling element, leading to the product Y, which is no longer photoreversible). Rather, the starting point is determined by internal factors only and is thus not accessible to any specific control by external factors. On the other hand, however, the beginning of the initial action of P _fr X (coupling point) can be shifted by light via phytochrome under high irradiance conditions. Moreover, it is shown that there is no phytochrome-independent effect of blue light on photomorphogenesis in the young mustard seedling and that there is no rapid dark reversion of P _fr which can be detected by physiological means, at least duringAbbreviations P _r red-absorbing forms of phytochrome - P _fr far-red-absorbing forms of phytochrome - P ₁ total spectrophotometrically detectable phytochrome - HS Hoagland's nutrient solution - HIR high irradiance response     

Utilization of malate or aspartate by a yeast lacking malate enzyme

Summary Hansenula anomala, a yeast lacking malate enzyme, was able to grow in media containing malate or aspartate as sole carbon and energy sources. Both aspartate--ketoglutarate transaminase and pyruvate kinase activities changed their levels when the yeast was grown on different carbon sources. Pyruvate kinase activity was increased by fructose 1,6-diphosphate.These results indicate that in this yeast malate enzyme is not indispensable for the formation of pyruvate from malate or aspartate and that C₄ dicarboxylic acids may provide pyruvate through the combined action of phosphoenolpyruvate carboxykinase and pyruvate kinase. It is also concluded that aspartate--ketoglutarate transaminase and pyruvate kinase are under regulatory control in Hansenula anomala.     

Plant regeneration through culture of isolated microspores of Triticum aestivum L.

Wheat microspores mechanically isolated from the anthers before culture and isolated from the anthers during the hole culture period in a chemically defined medium resulted in proembryos, embryos and finally plants. Of the four genotypes included, all responded with proembryos, and the two spring wheats Ciano and Walter gave rise to macroscopic embryos and plants. The frequency of embryo regeneration and the frequency of albino plants in both Ciano and Walter was in accordance with previously obtained results with anther culture derived material.Abbreviations 2,4-d 2,4-dichlorophenoxy acetic acid - NAA 1-naphthaleneacetic acid     

Monosomic analysis of heading date and spikelet number in the common wheat (Triticum aestivum L.) multispikelet line ‘Noa’

Summary Genetic analysis of heading date and spikelet number was carried out in the common wheat (Triticum aestivum L.) multispikelet line Noa, by using the monosomic series of the regular line Mara. Noa's high number of spikelets was found to be controlled by a recessive major gene on chromosome 2D; a slight reduction in spikelet number was induced by another recessive gene on Noa's 7A chromosome. Noa's late heading date was found to be controlled by two recessive genes, located on chromosome 2D (a major effect) and 6B (a minor effect). The nature of the genes located on Noa's 2D chromosome and the relationship between spikelet number and heading date are discussed.     

Copy number and distribution of P and I mobile elements in Drosophila melanogaster populations

The distribution of the number of copies of P and I transposable elements per genome was investigated by in situ hybridization for a large set of Drosophila melanogaster strains. These included the P, Q and M types of the P-M system of hybrid dysgenesis. P element copy number varied widely (range 5–59). P and Q strains had around 40 copies whereas M strains generally had lower numbers (between 5 and 35) with one extreme value (52). The copy number of I elements appeared to be precisely regulated, as no strains were found outside the 15±5 range. The number of copies of the two families were independent. An excess of P copies on the X chromosome compared with the autosomes was found for the P and Q strains, but not for M strains. Among X-inserted P sites, a very high frequency of occupation was found at the tip of the X chromosome (cytological site 1A), especially for P and Q strains. The possible regulatory role in the P-M system of X-inserted P sites is discussed.     

The relationship between permeant size and permeability in lipid bilayer membranes

Permeability coefficients (P _m ) across planar egg lecithin/decane bilayers and bulk hydrocarbon/water partition coefficients (K _whc) have been measured for 24 solutes with molecular volumes, V, varying by a factor of 22 and P _m values varying by a factor of 10⁷ to explore the chemical nature of the bilayer barrier and the effects of permeant size on permeability. A proper bulk solvent which correctly mimics the microenvironment of the barrier domain was sought. Changes in P _m /K_whc were then ascribed to size-dependent partitioning and/or size-dependent diffusivity. The diffusion coefficient-size dependency was described by D _barrier = D ₀ /V ⁿ . When n-decane was used as a reference solvent, the correlation between log P _m /K _whc and log V was poor (r = 0.56) with most of the lipophilic (hydrophilic) permeants lying below (above) the regression line. Correlations improved significantly (r = 0.87 and 0.90, respectively) with more polarizable solvents, 1-hexadecene and 1,9-decadiene. Values of the size selectivity parameter n were sensitive to the reference solvent (n = 0.8 ± 0.3, 1.2 ± 0.1 and 1.4 ± 0.2, respectively, for decane, hexadecene, and decadiene). Decadiene was selected as the most suitable reference solvent. The value for n in bilayer transport is higher than that for bulk diffusion in decane (n = 0.74±0.10), confirming the steep dependence of bilayer permeability on molecular size. Statistical mechanical theory recently developed by the authors suggests that a component of this steep size dependence may reside in size-dependent solute partitioning into the ordered chain region of bilayers. This theory, combined with the above diffusion model, yielded the relationship, P _m /K _Whc=D ₀ exp(V)V ⁿ . A fit of the experimental data to this model gave the best fit (r=0.93) with = 0.0053±0.0021 and n=0.8 ± 0.3, suggesting that both diffusion and partitioning mechanisms may play a role in determining the size dependence of lipid bilayer permeabilities.This work was supported by a research grant from Glaxo, Inc. Instrumentation support was provided by a Biomedical Research Support Grant from the College of Pharmacy, University of Utah, and by a Faculty Research Grant from the University of Utah. The technical assistance of Barbara L. Hoesterey, who determined some of the partition coefficients, is gratefully acknowledged.     

Schmelzverhalten und kalorische Eigenschaften einer Mischung von Rinderserumalbumin,Kochsalz und Wasser

Zusammenfassung Es wurde die mittlere EnthalpiedifferenzH _m von Rinderserumalbumin (RSA)-Salz-Wassergemischen im Temperaturbereich von –47 °C bis 0°C bestimmt.H _m enthält neben der Energie zur Erwärmung auch noch die Schmelzwärme der Mischung. Aus dem Verlauf vonH _m als Funktion des Lösungsmittels (0,5 molale NaCl-Lösung) ergibt sich für den Anteil des kalorisch gebundenen Lösungsmittels ein Wert von 0,54 g Lösungsmittel pro g RSA. Dieser Anteil ist unabhängig von der mittleren Ladung des RSA-Moleküls.Aus einer Analyse der Meßergebnisse nach der Theorie der Mischungen folgt, daß die Partialenthalpie des RSA in verdünnten Mischungen negativ ist. Die Partialenthalpie des Lösungsmittels ist dagegen in diesen verdünnten Gemischen unverändert gleich der Enthalpiedifferenz des Lösungsmittels selbst. Die Messungen wurden mit Hilfe eines Differential-Scanning-Kalorimeters der Fa. Perkin-Elmer durchgeführt.

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Melting behaviour and caloric properties of a mixture of bovine serum albumin, sodium chloride and water

Summary In the temperature range from –47 °C to 0 °C the enthalpy differencesH _m of bovine serum albumin (BSA)-salt-water mixtures were measured.H _m includes the energy to increase the temperatures as well as the melting heat of the mixture. The plot ofH _m as a function of the solvent content (0,5 molal NaCl solution) gives 0,54 g solvent per g dry BSA for the caloric bound solvent. This value is independent of the average charge of the BSA molecule.The theory of mixtures applied to this measurements shows that the partial enthalpy difference of BSA in dilute mixtures is negative while that of the solvent in this mixtures is equal to the enthalpy difference of the pure solvent.The enthalpy differences were measured with a Differential-Scanning-Calorimeter (Perkin-Elmer).

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Herrn Prof. Dr. Dr. h. c. mult. Boris Rajewsky zum 80. Geburtstag gewidmet.     

Negative-ion fast atom bombardment and electrospray ionization tandem mass spectrometry for characterization of sulfated and sialyl Lewis-type glycosphingolipids

Structural characterization of sulfated and sialyl Lewis (Le)-type glycosphingolipids performed by fast atom bombardment (FAB) and electrospray ionization (ESI) mass spectrometry is described. Both FAB and ESI collision-induced dissociation tandem mass spectrometry (CID-MS/MS) of acidic glycosphingolipids allowed identification of the sulfated or sialyl sugar, and provided information on the saccharide chain sequence. The negative-ion tandem FABMS of sulfated Le-type glycosphingolipids having the non-reducing end trisaccharide ion as the precursor can be used to differentiate the Le^a- and Le^X-type oligosaccharides. The ESI CID-MS/MS of multiple-charged ions provided even more detailed structural information, and some of the useful daughter ions appeared with higherm/z values than the precusor because of a lower charge-state. These methodologies can be applied to the structural analyses of glycoconjugates with much larger molecular masses and higher polarity, such as the poly-sulfated and sialyl analogues.Abbreviations CID collision-induced dissociation - ESI electrospray ionization - FABMS fast atom bombardment mass spectrometry - Fuc fucose - Gal galactose - GlcNAc N-acetylglucosamine - Le Lewis - Le^a Lewis^a - Le^X Lewis^X - MS/MS mass spectrometry/mass spectrometry - NeuAc N-acetylneuraminic acid - 3-SO₄-Le^a 3-sulfated Le^a pentaosyl ceramide - 3-SO₄-Le^X 3-sulfated Le^X pentaosyl ceramide - 2,3-SO₄-Le^X 2,3-disulfated Le^X pentaosyl ceramide - 3-S-Le^a 3-sialyl Le^a pentaosyl ceramide - 3-S-Le^x 3-sialyl Le^X heptaosyl ceramide - 3-S-Le^X-Le^X 3-sialyl-Le^x-Le^x octaosyl ceramide.     

Reduced spectral density mapping for proteins: Validity for studies of 13C relaxation

Spectral density mapping provides direct access to protein dynamics with no assumptions as to the nature of the molecule or its dynamic behaviour. Reduced spectral density mapping characterises a protein's motions at a lower experimental burden, assuming that the spectral density function J() is flat around H. This introduces little error for 15N relaxation data but is less valid for 13C studies, perturbing J(C) considerably to an extent that depends on the nature of the molecules motions. We propose the fitting of spectral density at high frequencies to a single Lorentzian and show that the true values of the spectral density lie between those determined by the two approximations.     

Identification of two RAPD markers tightly linked with the Nicotiana debneyi gene for resistance to black root rot of tobacco

Linkage of randomly amplified polymorphic DNA (RAPD) markers with a single dominant gene for resistance to black root rot (Chalara elegans Nag Raj and Kendrick; Syn. Thielaviopsis basicola [Berk. and Broome] Ferraris) of tobacco (Nicotiana tabacum L.), which was transferred from N. debneyi Domin, was investigated in this study. There were 2594 repeatable RAPD fragments generated by 441 primers on DNAs of Delgold tobacco, a BC₅F₈ near isogenic line (NIL) carrying the resistance gene in a Delgold background, and PB19, the donor parent of the resistance gene. Only 7 of these primers produced eight RAPD markers polymorphic between Delgold and PB19, indicating there are few RAPD polymorphisms between them despite relatively dissimilar pedigrees. Five of the eight RAPD markers were not polymorphic between Delgold and the NIL. All of these markers proved to be unlinked with the resistance gene in F₂ linkage tests. Of the remaining three RAPD markers polymorphic between Delgold and the NIL, two were shown to be strongly linked with the resistance gene; one in coupling and the other in repulsion. Application of the two RAPDs in the elimination of linkage drag associated with the N. debneyi resistance gene and marker-assisted selection for the breeding of new tobacco cultivars with the resistance gene is discussed.     

The effect of monensin on intracellular transport and secretion of α-amylase isoenzymes in barley aleurone

The effect of monensin on the secretion of -amylase and other enzymes from the aleurone layer of barley (Hordeum vulgare L. cv. Himalaya) was studied by electrophoresis followed by fluorography and by pulse-chase and organelle-isolation experiments. Monensin markedly inhibits the secretion, but not the synthesis, of -amylase, acid phosphatase, and at least four other proteins from the aleurone layer. Monensin treatment causes -amylase to accumulate within the protoplast, but its effect on the different -amylase isoenzymes is not equal. The accumulation of isoenzyme 2 is not influenced by monensin while isoenzymes 1, 3 and 4 are not secreted but rather accumulate in the cell when monensin is included in the incubation medium. The -amylase and acid-phosphatase activities which accumulate within the aleurone cells following treatment with monensin are localized in an organelle having a buoyant density greater than that of endoplasmic reticulum and less than that of mitochondria. In pulse-chase experiments with [³⁵S]methionine, labelled proteins accumulate in this organelle in the presence of monensin and do not appear in the incubation medium. We conclude that monensin inhibits the secretion of proteins from the barley aleurone layer by influencing their intracellular transport.Abbreviations ER endoplasmic reticulum - GA₃ gibberellic acid - SDS-PAGE sodium dodecyl-sulfate polyacrylamide-gel electrophoresis     

Interactions between anion exchange and other membrane proteins in rabbit kidney medullary collecting duct cells

Summary In separated outer medullary collecting duct (MCD) cells, the time course of binding of the fluorescent stilbene anion exchange inhibitor, DBDS (4,4-dibenzamido-2,2-stilbene disulfonate), to the MCD cell analog of band 3, the red blood cell (rbc) anion exchange protein, can be measured by the stopped-flow method and the reaction time constant, _DBDS, can be used to report on the conformational state of the band 3 analog. In order to validate the method we have now shown that the ID_50,DBDS,MCD (0.5±0.1 m) for the H₂-DIDS (4,4-diisothiocyano-2,2-dihydrostilbene disulfonate) inhibition of _DBDS is in agreement with the ID_50,Cl ^–,_MCD (0.94±0.07 m) for H₂-DIDS inhibition of MCD cell Cl^– flux, thus relating _DBDS directly to anion exchange. The specific cardiac glycoside cation transport inhibitor, ouabain, not only modulates DBDS binding kinetics, but also increases the time constant for Cl^– exchange by a factor of two, from _Cl=0.30±0.02 sec to 0.56±0.06 sec (30mm NaHCO₃). The ID_50,DBDS,MCD for the ouabain effect on DBDS binding kinetics is 0.003±0.001 m, so that binding is about an order of magnitude tighter than that for inhibition of rbc K⁺ flux (K _I,K ⁺,_rbc=0.017 m). These experiments indicate that the Na⁺,K^–-ATPase, required to maintain cation gradients across the MCD cell membrane, is close enough to the band 3 analog that conformational information can be exchanged. Cytochalasin E (CE), which binds to the spectrin/actin complex in rbc and other cells, modulates DBDS binding kinetics with a physiological ID_50,DBDS,MCD (0.076±0.005 m); 2 m CE also more than doubles the Cl^– exchange time constant from 0.20±0.04 sec to 0.50±0.08 sec (30mm NaHCO₃). These experiments indicate that conformational information can also be exchanged between the MCD cell band 3 analog and the MCD cell cytoskeleton.