The multidimensional space of integral characteristics: Invariance of its structure to various biocenotic assemblages

In the virtual multidimensional space of integral biocenotic characteristics, such as abundance, the sizes of individuals, and the components of species diversity, which are scaled on corresponding coordinate axes, the points that represent samples from various biocenotic assemblages, form similar multi-layered hill-shaped figures. The examples we considered are the pelagic macrofauna of the Bering Sea, the Sea of Okhotsk, the Sea of Japan and the adjacent waters of the Northwestern Pacific Ocean; the phytoplankton, zooplankton, and zoobenthos of Lake Ladoga, the Neva Bay, and the Gulf of Finland in the Baltic Sea; the beetle guild in the rainforest of Borneo Island on the Malay Archipelago; and the bird taxocenes and biotope groups of soil mites in North America, among others. The obvious similarity of the composed diagrams results from the close interrelationships of all the integral characteristics and also from the universality of the structure of links between them, which is tolerant to movements in the real space-time continuum and invariant towards the subject of the studies. The multidimensional domain of the analyzed variables is a set of points that are aggregated along a segment, whose length and orientation relative to the coordinate axes determine the general rules of the biocenotic organization of the living matter.     

Consideration of digitization precision when building local coordinate axes for a foot model

This study investigated whether points digitized for the purpose of embedding coordinate systems into the foot accurately represented the orientation of the bone described. Eight complete data sets were collected from 9 adult cadaver specimens. Palpable landmarks defined 5 segments to include the calcaneus, navicular, medial cuneiform, first metatarsal, and hallux. With use of the Flock of Birds electromagnetic motion tracking device, a single examiner digitized a minimum of 3 points for each segment. Coordinate definitions followed the right-hand rule, with left-sided data converted to right-sided equivalency. Local axes were created where X projected approximately forward, Y upward, and Z laterally. Matrix transformation computations calculated the angular precision in degrees between coordinates built from points digitized pre- and post-dissection of surface tissues covering bone. The condition of post-dissection was considered the criterion standard for comparison. Change about the X-axis represented the angular precision of the coordinate in the frontal anatomical plane; Y-axis in the transverse plane; Z-axis in the sagittal plane. The calcaneus and navicular coordinate axes changed by an average of <3° across conditions. Mean coordinate angulation of the cuneiform X, Y, Z axes changed by 6.0°, 4.6°, 11.9°, respectively. Change in coordinate angulation was largest for the X-axis at the first metatarsal (48.6°) and hallux (36.5°). A two-way repeated measures ANOVA found a significant interaction between the axis and segment (F=8.87, P=0.00). Tukey post-hoc comparisons indicated the change in coordinate angulation at the X-axis for the cuneiform, metatarsal, and hallux to be significantly different (P <0.05) from the calcaneus and navicular. The X-axis of the first metatarsal and hallux was different from all other axis-segment combinations except for the Z-axis of the cuneiform. Differences in locating landmarks reduced angular precision of the coordinate axes most in the smallest foot segments where points digitized were located close together. We can recommend the proposed landmarks for the calcaneus and navicular segments, but kinematics determined about the coordinate axes for the small sized medial cuneiform, and the long (X) axis for the first metatarsal and hallux have excessive error.     

Culturable Bacterial Flora Associated with the Dinoflagellate Green Noctiluca miliaris During Active and Declining Bloom Phases in the Northern Arabian Sea

A massive algal bloom of the dinoflagellate Noctiluca miliaris (green) was located in the Northern Arabian Sea by IRS-P4-2 (OCM-II) for microbiological studies, during two consecutive cruises of February-March 2009. Culturable bacterial load during bloom were ～2–3-fold higher in comparison to non-bloom waters and ranged from 3.20?×?10⁵ to 6.84?×?10⁵?cfu?ml^?1. An analysis of the dominant heterotrophs associated with Noctiluca bloom resulted in phylogenetic and a detailed metabolic characterization of 70 bacterial isolates from an overlapping active and declining bloom phase location near north-central Arabian Sea. The active phase flora was dominated by Gram-positive forms (70.59 %), a majority of which belonged to Bacillus (35.29 %) of Firmicutes. As the bloom declined, Gram-negative forms (61.11 %) emerged dominant, and these belonged to a diverse γ-proteobacterial population consisting of Shewanella (16.67 %) and equal fractions of a Cobetia–Pseudomonas-Psychrobacter–Halomonas population (36.11 %). A Unifrac-based principal coordinate analysis of partial 16S rDNA sequences showed significant differences among the active and declining phase flora and also with reported endocytic flora of Noctiluca (red). A nonparametric multidimensional scaling (NMDS) of antibiogram helped differentiation among closely related strains. The organic matter synthesized by N. miliaris appears to be quickly utilized and remineralized as seen from the high efficiency of isolates to metabolize various complex and simple C/N substrates such as carbohydrates, proteins/amino acids, lipids, sulfide production from organic matter, and solubilize phosphates. The ability of a large fraction of these strains (50–41.67 %) to further aerobically denitrify indicates their potential for nitrogen removal from these high-organic microniches of the Noctiluca bloom in the Arabian Sea, also known for high denitrification activity. The results indicate that culturable euphotic bacterial associates of Noctiluca are likely to play a critical role in the biogeochemical ramifications of these unique seasonally emerging tropical open-water blooms of the Northern Arabian Sea.     

Interpreting plots of a multidimensional dose-response surface in a parallel coordinate system

The dose-response surface for a combination of drugs is a multidimensional figure. Consequently, it is not possible to view such a surface using orthogonal axes when the number of dimensions exceeds 3. Parallel axes have been used to represent hyperdimensional figures. This paper reports on the use of parallel coordinate axes to plot the dose-response surface and its contours of constant response (isobols) for a combination of drugs. It is shown that patterns formed by intersecting line segments in the parallel system can aid in the interpretation of the fitted dose-response surface. More generally, analytic results are developed that permit the ready visualization and characterization of interaction effects of a polynomial model.     

Application of Empirical Wave Run-Up Formulas to the Polish Baltic Sea Coast

Advanced, multidimensional models are typically applied when researching processes occurring in the nearshore. Relatively simple, empirical equations are commonly used in coastal engineering practice in order to estimate extreme wave run-up on beaches and coastal structures. However, they were mostly calibrated to the characteristics of oceanic coasts, which have different wave regime than a semi-enclosed basin like the Baltic Sea. In this paper we apply the formulas to the Polish Baltic Sea coast. The equations were adjusted to match local conditions in two test sites in Międzyzdroje and Dziwnówek, where beaches are under continuous video surveillance. Data from WAM wave model and coastal gauge stations were used, as well as precise measurements of the beaches'' cross-sections. More than 600 run-up events spanning from June to December 2013 were analysed, including surges causing dune erosion. Extreme wave run-up R_2% was calculated and presented as a percentage value indicating what part of the beach was inundated. The method had a root-mean-square error of 6.1 and 6.5 percentage points depending on the test site. We consider it is a fast and computationally undemanding alternative to morphodynamic models. It will constitute a part of the SatBałtyk Operating System-Shores, delivering forecasts of wave run-up on the beaches for the entire Polish coastline.     

The kinetics of intrinsic factor-vitamin B12 binding

The kinetic behaviour of intrinsic factor-vitamin B₁₂ binding has been examined under varying conditions using an albuminised charcoal separation technique. The overall reaction obeys second order rate laws. The intrinsic factor considered alone obeys first order laws; the velocity of reaction of vitamin B₁₂ is too fast for measurement by the technique described but by deduction obeys first order laws. Rate constants as three temperatures, (k₂ at 25°C=1.56·10⁸·mole^?1·s^?1) the activation energy (E=12.7 kJ·mole^?1) and Arrhenius constant (A=2.7·10¹⁰ 1·mole^?1·s^?1 have been calculated. There is the possibility of diffusion control of the reaction in which case the E and A values are invalid. The effect of pH on the reaction has been studied and the results discussed in relation to the pH studies of other workers whose results show disagreement. Albumin coated charcoal was shown to discriminate between intrinsic factor-vitamin B₁₂ and free vitamn B₁₂ over a wide pH range. The apparent under-estimation of intrinsic factor in dilute solution was shown to be due to adsorption of the intrinsic factor to plastic tubes.     

The mobilization of defence mechanisms in the early stages of pea seed germination against Ascochyta pisi

Ascochyta pisi is a necrotrophic pathogenic fungus, which mainly survives between seasons through infected seeds. Defence responses of pea embryo axes to A. pisi were investigated in the heterotrophic phase of seed germination and during the transition from the heterotrophic to the autotrophic phase. Germinated pea seeds, both non-inoculated and inoculated with A. pisi, were cultured in perlite for 96 h. Polarographic studies performed on intact embryo axes of germinating pea seeds infected with A. pisi showed a high respiratory intensity in time from 48 to 96 h after inoculation. Forty-eight-hour embryo axes of germinating pea seeds exhibited the highest respiration rate, which in infected axes was maintained at the following time points after inoculation. Moreover, at 72 and 96 h after inoculation, respiratory intensity was by 64% and 73% higher than in the control. Electron paramagnetic resonance analysis revealed a higher concentration of semiquinone free radicals with g values of g _||?=?2.0031?±?0.0004 and g _⊥?=?2.0048?±?0.0004 in infected axes than in the control. Generation of superoxide anion radical was also higher in infected axes than in the control but stronger at 72 and 96 h after inoculation. Starting from 72 h after infection, the level of Mn²⁺ ions in infected axes decreased in relation to the control. At the same time, the highest activity of superoxide dismutase (EC 1.15.1.1) and catalase (EC 1.11.1.6) was observed in 72-h infected axes. In turn, the activity of peroxidase (EC 1.11.1.7) up to 72 h after infection was lower than in the control. In 48-h infected embryo axes, a very high level of pterocarpan pisatin was observed. Infection of germinating pea seeds with A. pisi restricted mainly the growth of the epicotyl, but did not inhibit the increase in length and fresh weight of root embryo axes versus cultivation time. These results indicate that in pea during the stages of seed germination and early seedling growth, protective mechanisms are induced in embryo axes against A. pisi.     

The renaissance of Ca2+-binding proteins in the nervous system: secretagogin takes center stage

Effective control of the Ca²⁺ homeostasis in any living cell is paramount to coordinate some of the most essential physiological processes, including cell division, morphological differentiation, and intercellular communication. Therefore, effective homeostatic mechanisms have evolved to maintain the intracellular Ca²⁺ concentration at physiologically adequate levels, as well as to regulate the spatial and temporal dynamics of Ca²⁺signaling at subcellular resolution. Members of the superfamily of EF-hand Ca²⁺-binding proteins are effective to either attenuate intracellular Ca²⁺ transients as stochiometric buffers or function as Ca²⁺ sensors whose conformational change upon Ca²⁺ binding triggers protein-protein interactions, leading to cell state-specific intracellular signaling events. In the central nervous system, some EF-hand Ca²⁺-binding proteins are restricted to specific subtypes of neurons or glia, with their expression under developmental and/or metabolic control. Therefore, Ca²⁺-binding proteins are widely used as molecular markers of cell identity whilst also predicting excitability and neurotransmitter release profiles in response to electrical stimuli. Secretagogin is a novel member of the group of EF-hand Ca²⁺-binding proteins whose expression precedes that of many other Ca²⁺-binding proteins in postmitotic, migratory neurons in the embryonic nervous system. Secretagogin expression persists during neurogenesis in the adult brain, yet becomes confined to regionalized subsets of differentiated neurons in the adult central and peripheral nervous and neuroendocrine systems. Secretagogin may be implicated in the control of neuronal turnover and differentiation, particularly since it is re-expressed in neoplastic brain and endocrine tumors and modulates cell proliferation in vitro. Alternatively, and since secretagogin can bind to SNARE proteins, it might function as a Ca²⁺ sensor/coincidence detector modulating vesicular exocytosis of neurotransmitters, neuropeptides or hormones. Thus, secretagogin emerges as a functionally multifaceted Ca²⁺-binding protein whose molecular characterization can unravel a new and fundamental dimension of Ca²⁺signaling under physiological and disease conditions in the nervous system and beyond.     

The scope of phage display for membrane proteins

Numerous examples of phage display applied to soluble proteins demonstrate the power of the technique for protein engineering, affinity reagent discovery and structure-function studies. Recent reports have expanded phage display to include membrane proteins (MPs). The scope and limitations of MP display remain undefined. Therefore, we report data from the phage display of representative types of membrane-associated proteins including plasma, nuclear, peripheral, single and multipass. The peripheral MP neuromodulin displays robustly with packaging by conventional M13-KO7 helper phage. The monotopic MP Nogo-66 can also display on the phage surface, if packaged by the modified M13-KO7⁺ helper phage. The modified phage coat of KO7⁺ can better mimic the zwitterionic character of the plasma membrane. Four examples of putatively α-helical, integral MPs failed to express as fusions to an anchoring phage coat protein and therefore did not display on the phage surface. However, the β-barrel MPs ShuA (Shigella heme uptake A) and MOMP (major outer membrane protein), which pass through the membrane 22 and 16 times, respectively, can display surprisingly well on the surfaces of both conventional and KO7⁺ phages. The results provide a guide for protein engineering and large-scale mutagenesis enabled by the phage display of MPs.     

The species composition and quantitative distribution of the diatom genus Pseudo-nitzschia H. Peragallo, 1990 in Russian waters of the Sea of Japan and the Sea of Okhotsk

This paper studies the species composition and quantitative distribution of diatoms that belong to the genus Pseudo-nitzschia in the Russian waters of the Sea of Japan and the Sea of Okhotsk. In total, 11 species of this genus were found in the area, including 7 that are known as being potentially toxic. The highest concentrations of Pseudo-nitzschia microalgae (1.4 × 10⁶–2.7 × 10⁶ cells/L) were found in the summer and autumn in the Peter the Great Bay of the Sea of Japan and the lowest concentrations (2.5 × 10²–1 × 10⁴ cells/L) were found in the Sakhalinsky and Akademiya bays of the Sea of Okhotsk. The species diversity of potentially toxic diatoms was greatest (seven species) and the cell concentrations highest (over 6 × 10⁵ cells/L) in the Peter the Great Bay, Sea of Japan, and in the Aniva Bay, Sea of Okhotsk. The density of potentially toxic species was highest near the northeastern coast of Sakhalin Island, in the Amur River estuary, and in adjacent waters. This paper also presents geographical distribution maps of Pseudo-nitzschia species and maps of the density distribution of potentially toxic microalgae over the studied area and identifies potential amnesic shellfish poisoning areas.     

On the Role of Stored mRNA in Protein Synthesis in Embryonic Axes of Germinating Vigna unguiculata Seeds

Polyadenylated (poly A⁺) RNAs were prepared from both dry and incubated embryonic axes of Vigna unguiculata seeds and were translated by a wheat germ translation system. Analysis with gel electrophoresis and fluorography showed that translation products of poly A⁺ RNA from dry embryonic axes were nearly the same as those from 2-hour incubated axes but somewhat different from those of 4- to 24-hour incubated axes, and that translation products remained almost unchanged between the 4- and 24-hour stages of postimbibition. The results indicate the possibility that the stored mRNA (poly A⁺ RNA from dry embryonic axes) directs the protein synthesis required for early stages of germination. This is supported by comparison of the in vitro translation products of poly A⁺ RNAs with those of polysomal RNAs. Experiments with α-amanitin, a specific inhibitor of RNA polymerase II (J. Jendrisak 1980 J Biol Chem 255: 8529-8533), suggested that the synthesis of some of the stored mRNA species is resumed as early as 4 hours after the onset of imbibition.     

Testing the hypothesis of tolerance strategies in Hiatella arctica L. (Mollusca: Bivalvia)

The physiological and biocenotic optima of Hiatella arctica L. inhabiting shallow water fouling communities of the White Sea were compared. The biomass and proportion of H. arctica in communities were used for the estimation of biocenotic optima or community success. The physiological state of populations was assessed by means of the fluctuating asymmetry. The fluctuating asymmetry of H. arctica was calculated using the valve weights. It was determined that the shell of H. arctica possesses a slight directional asymmetry, the right valve usually being larger (and heavier) than the left one. The relationship between fluctuating and directional asymmetries is discussed. High biomass and proportion of H. arctica in the community generally correspond with high levels of fluctuating asymmetry. Thus, a discrepancy between physiological and ecological optima is observed, which is recognised as being characteristic of a tolerance strategy. However, in the absence of pressure from major filter-feeding competitors such as the mussel Mytilus edulis L. and the solitary ascidian Styela rustica L., populations of H. arctica possess a high biomass and low levels of fluctuating asymmetry. It appears that H. arctica prefers to inhabit shelters or depressions, or to be covered by other organisms. Populations of H. arctica existing in the absence of shelter had extremely high levels of fluctuating asymmetry despite the absence of filter-feeding competitors. Thus, the strategy adopted by H arctica L. in the investigated upper 5 m layer of water in the White Sea can be described as a stress- and competitor-tolerant strategy.     

The role of the catalytic domain of E. coli GluRS in tRNA discrimination

Discrimination of tRNA^Gln is an integral function of several bacterial glutamyl-tRNA synthetases (GluRS). The origin of the discrimination is thought to arise from unfavorable interactions between tRNA^Gln and the anticodon-binding domain of GluRS. From experiments on an anticodon-binding domain truncated Escherichia coli (E. coli) GluRS (catalytic domain) and a chimeric protein, constructed from the catalytic domain of E. coli GluRS and the anticodon-binding domain of E. coli glutaminyl-tRNA synthetase (GlnRS), we show that both proteins discriminate against E. coli tRNA^Gln. Our results demonstrate that in addition to the anticodon-binding domain, tRNA^Gln discriminatory elements may be present in the catalytic domain in E. coli GluRS as well.     

A low-resolution study of testicular lactate dehydrogenase using the molecular replacement technique

The orientation of the molecular 2-fold axes of mouse testicular lactate dehydrogenase (LDHase³-C₄) was determined by a rotation function search. These were subsequently identified with the P, Q, and R axes of dogfish LDHase-M₄. Since LDHase-C₄ crystallized with one molecule in a triclinic cell, the origin of the co-ordinate system was arbitrarily fixed at the molecular center. Structure factor phases were derived from an appropriately oriented dogfish apo LDHase-M₄ phasing model and combined with the observed structure amplitudes to produce a hybrid electron density map. Density points related by the molecular 222 point symmetry were averaged so as to remove the bias of the phasing model. At 7.5 Å resolution, the structure of the crystallized mouse LDHase-C₄ was found to be without coenzyme, with a conformation indistinguishable from that of dogfish apo LDHase-M₄.     

Epsilonproteobacteria Represent the Major Portion of Chemoautotrophic Bacteria in Sulfidic Waters of Pelagic Redoxclines of the Baltic and Black Seas

Recent studies have indicated that chemoautotrophic Epsilonproteobacteria might play an important role, especially as anaerobic or microaerophilic dark CO₂-fixing organisms, in marine pelagic redoxclines. However, knowledge of their distribution and abundance as actively CO₂-fixing microorganisms in pelagic redoxclines is still deficient. We determined the contribution of Epsilonproteobacteria to dark CO₂ fixation in the sulfidic areas of central Baltic Sea and Black Sea redoxclines by combining catalyzed reporter deposition-fluorescence in situ hybridization with microautoradiography using [¹⁴C]bicarbonate and compared it to the total prokaryotic chemoautotrophic activity. In absolute numbers, up to 3 × 10^{5 14}CO₂-fixing prokaryotic cells ml⁻¹ were enumerated in the redoxcline of the central Baltic Sea and up to 9 × 10^{4 14}CO₂-fixing cells ml⁻¹ were enumerated in the Black Sea redoxcline, corresponding to 29% and 12%, respectively, of total cell abundance. ¹⁴CO₂-incorporating cells belonged exclusively to the domain Bacteria. Among these, members of the Epsilonproteobacteria were approximately 70% of the cells in the central Baltic Sea and up to 100% in the Black Sea. For the Baltic Sea, the Sulfurimonas subgroup GD17, previously assumed to be involved in autotrophic denitrification, was the most dominant CO₂-fixing group. In conclusion, Epsilonproteobacteria were found to be mainly responsible for chemoautotrophic activity in the dark CO₂ fixation maxima of the Black Sea and central Baltic Sea redoxclines. These Epsilonproteobacteria might be relevant in similar habitats of the world's oceans, where high dark CO₂ fixation rates have been measured.     

Purine nucleotide metabolism of germinating soybean embryonic axes

Isolated soybean (Glycine max L. cv. Kent) embyronic axes metabolized [¹⁴C]glycine to ATP within the 1 hour of imbibition. Radioactivity was not detected in GTP until the 3rd hour. Throughout most of the first 24 hours of germination about 10 to 26 times as much label from [¹⁴C]glycine appears in ATP as GTP. About five times as much [¹⁴C]hypoxanthine and [¹⁴C]inosine was converted into GTP as into ATP in embryonic axes. Two independent pools of IMP appear to be used in purine nucleotide synthesis of soybean axes.     

Hydrodynamics in the renal tubule

Explicit solutions of the Navier-Stokes equations are presented for axially symmetric slow flow in an infinite cylinder whose walls reabsorb fluid at a rate which varies exponentially with the longitudinal coordinate. Results similar to those of a previous paper which assumed a constant rate of reabsorption are obtained. When the radius of the tube is small the solutions resemble Poiseuille flow; the longitudinal velocity profile is parabolic, and the drop in mean pressure is proportional to the mean axial flow, the length of tube between reference points, and inversely proportional to the fourth power of the radius. By expressing the tubular reabsorption as a Fourier integral, solutions are obtained for the general case where the rate of reabsorption is an arbitrary function of the longitudinal coordinate.     

Dispersal and development ofMarenzelleria spp. (Polychaeta, Spionidae) populations in NW Europe and The Netherlands

The North American spionid polychaeteMarenzelleria cf.wireni was first recorded in the North Sea by Scotland in 1982.Marenzelleria cf.viridis was first found in the Baltic Sea in 1985. Tentative routes of dispersal since then are presented in this paper. In the Netherlands, a biological monitoring programme has revealed populations ofM. cf.wireni in the Ems estuary, Wadden Sea, and in the SW Netherlands. In the Dollard (Ems estuary) a large population has developed (2000–3000 individuals m^?2; 8–16 g ash-free dry weight m^?2). Since the introduction, the macrozoobenthic community has changed from being dominated (by biomass) by bivalves, to domination by polychaetes. Recently, a similar population started to develop at Balgzand (western Dutch Wadden Sea).     

Effect of integral membrane proteins on the lateral mobility of plastoquinone in phosphatidylcholine proteoliposomes

Pyrene fluorescence quenching by plastoquinone was used to estimate the rate of plastoquinone lateral diffusion in soybean phosphatidylcholine proteoliposomes containing the following integral membrane proteins: gramicidin D, spinach cytochrome bf complex, spinach cytochrome f, reaction centers from Rhodobacter sphaeroides, beef heart mitochondrial cytochrome bc₁, and beef heart mitochondrial cytochrome oxidase. The measured plastoquinone lateral diffusion coefficient varied between 1 and 3 · 10^-7 cm² s^-1 in control liposomes that lacked protein. When proteins were added, these values decreased: a 10-fold decrease was observed when 16-26% of the membrane surface area was occupied by protein for all the proteins but gramicidin. The larger protein complexes (cytochrome bf, Rhodobacter sphaeroides reaction centers, cytochrome bc₁, and cytochrome oxidase), whose hydrophobic volumes were 15-20 times as large as that of cytochrome f and the gramicidin transmembrane dimer, were 15-20 times as effective in decreasing the lateral-diffusion coefficient over the range of concentrations studied. These proteins had a much stronger effect than that observed for bacteriorhodopsin in fluorescence photobleaching recovery measurements. The effect of high-protein concentrations in gramicidin proteoliposomes was in close agreement with fluorescence photobleaching measurements. The results are compared with the predictions of several theoretical models of lateral mobility as a function of integral membrane concentration.