From sphere to torus: A topological view of the metazoan body plan

From the viewpoint of mathematical topology, membrane systems in intact living cells can be described as closed and orientable surfaces, i.e., as surfaces with two sides and no boundary lines so that an ‘inside’ and an ‘outside’ can be distinguished. Usually, biomembranes represent topological spheres, often one embedded in another one. Toroidal membranes are occasionally observed, e.g., in specialized structures of plant cells like the prolamellar body. Here, we propose that rules analogous to those that govern the topology of biomembranes hold for the epithelial cell sheets that cover anatomically external as well as internal surfaces of multicellular animals. We suggest to study the emergence of morphological complexity during metazoan development using concepts from mathematical topology, and propose experimental analyses of those topological transitions that appear to be relevant in development and evolution. Based on a lecture held by H J at the Max Planck-Institute for Physics of Complex Systems, Dresden, 26 April 2001.     

Biodeterioration problems of North Sea oil and gas production—A review

The North Sea is both a highly corrosive and highly biologically productive environment. Oil and gas production structures in this environment not only suffer from the physical effects, corrosion, wave and storm action, of being immersed in this environment, but also the effects of biological activity. Such biodeterioration problems occur both on the external and internal surfaces of the structure and the internal surfaces of any plant or pipework which contains, or has contained, water. The platform jacket may experience biological problems due to external macro- and microfouling or to internal microfouling. Pipelines, risers and topside systems have usually all been hydrostatically tested leaving residual water and possible sites for bacterial activity. Waterflooding with seawater and the separation of produced water from oil also provide sites suitable for biological activity and associated corrosion, slime and blockade problems. This paper reviews these areas in the light of recent advances in investigation and uderstanding of the problems.     

Exploring the Structure of the Voltage-gated Na+ Channel by an Engineered Drug Access Pathway to the Receptor Site for Local Anesthetics

Despite the availability of several crystal structures of bacterial voltage-gated Na⁺ channels, the structure of eukaryotic Na⁺ channels is still undefined. We used predictions from available homology models and crystal structures to modulate an external access pathway for the membrane-impermeant local anesthetic derivative QX-222 into the internal vestibule of the mammalian rNa_V1.4 channel. Potassium channel-based homology models predict amino acid Ile-1575 in domain IV segment 6 to be in close proximity to Lys-1237 of the domain III pore-loop selectivity filter. The mutation K1237E has been shown previously to increase the diameter of the selectivity filter. We found that an access pathway for external QX-222 created by mutations of Ile-1575 was abolished by the additional mutation K1237E, supporting the notion of a close spatial relationship between sites 1237 and 1575. Crystal structures of bacterial voltage-gated Na⁺ channels predict that the side chain of rNa_V1.4 Trp-1531 of the domain IV pore-loop projects into the space between domain IV segment 6 and domain III pore-loop and, therefore, should obstruct the putative external access pathway. Indeed, mutations W1531A and W1531G allowed for exceptionally rapid access of QX-222. In addition, W1531G created a second non-selective ion-conducting pore, bypassing the outer vestibule but probably merging into the internal vestibule, allowing for control by the activation gate. These data suggest a strong structural similarity between bacterial and eukaryotic voltage-gated Na⁺ channels.     

The Yeast Mitochondrial Citrate Transport Protein: MOLECULAR DETERMINANTS OF ITS SUBSTRATE SPECIFICITY*

The objective of this study was to identify the role of individual amino acid residues in determining the substrate specificity of the yeast mitochondrial citrate transport protein (CTP). Previously, we showed that the CTP contains at least two substrate-binding sites. In this study, utilizing the overexpressed, single-Cys CTP-binding site variants that were functionally reconstituted in liposomes, we examined CTP specificity from both its external and internal surfaces. Upon mutation of residues comprising the more external site, the CTP becomes less selective for citrate with numerous external anions able to effectively inhibit [¹⁴C]citrate/citrate exchange. Thus, the site 1 variants assume the binding characteristics of a nonspecific anion carrier. Comparison of [¹⁴C]citrate uptake in the presence of various internal anions versus water revealed that, with the exception of the R189C mutant, the other site 1 variants showed substantial uniport activity relative to exchange. Upon mutation of residues comprising site 2, we observed two types of effects. The K37C mutant displayed a markedly enhanced selectivity for external citrate. In contrast, the other site 2 mutants displayed varying degrees of relaxed selectivity for external citrate. Examination of internal substrates revealed that, in contrast to the control transporter, the R181C variant exclusively functioned as a uniporter. This study provides the first functional information on the role of specific binding site residues in determining mitochondrial transporter substrate selectivity. We interpret our findings in the context of our homology-modeled CTP as it cycles between the outward-facing, occluded, and inward-facing states.     

The relevance of the mesosomal internal structures to the phylogeny of Augochlorini bees (Hymenoptera: Halictinae)

The use of internal skeletal structures is valuable to phylogenetic reconstruction within Hymenoptera; however, these structures were not further investigated for Augochlorini. Previous phylogenetic studies of Augochlorini based only on external morphology were poorly resolved. The objectives of this work are to explore the comparative morphology of internal structures of the mesosoma and to evaluate their potential as information sources for the phylogenetic relationships within the tribe. The internal structures of the Pseudaugochlora graminea (Fabricius, 1804) mesosoma are described in detail and compared with 16 other genera. We propose 24 new character statements for the Augochlorini phylogeny based on internal structures of mesosoma. Prosternum, propleuron and meso/metafurca provided a great number of informative characters. On the other hand, the mesophragma, metanotum and propodeum were less variable. The monophyly of Augochlorini and of all genus groups was corroborated in a parsimony analysis of internal and external morphological characters. Characters derived from internal structures provided the first‐known morphological synapomorphies for the clades: Megaloptidia group + others, Neocorynura group + others and Augochlora group + Megalopta group. These characters helped to elucidate the evolution of the group when analysed together with external morphological characters.     

Accessing Developmental Information of Fossil Hominin Teeth Using New Synchrotron Microtomography-Based Visualization Techniques of Dental Surfaces and Interfaces

Quantification of dental long-period growth lines (Retzius lines in enamel and Andresen lines in dentine) and matching of stress patterns (internal accentuated lines and hypoplasias) are used in determining crown formation time and age at death in juvenile fossil hominins. They yield the chronology employed for inferences of life history. Synchrotron virtual histology has been demonstrated as a non-destructive alternative to conventional invasive approaches. Nevertheless, fossil teeth are sometimes poorly preserved or physically inaccessible, preventing observation of the external expression of incremental lines (perikymata and periradicular bands). Here we present a new approach combining synchrotron virtual histology and high quality three-dimensional rendering of dental surfaces and internal interfaces. We illustrate this approach with seventeen permanent fossil hominin teeth. The outer enamel surface and enamel-dentine junction (EDJ) were segmented by capturing the phase contrast fringes at the structural interfaces. Three-dimensional models were rendered with Phong’s algorithm, and a combination of directional colored lights to enhance surface topography and the pattern of subtle variations in tissue density. The process reveals perikymata and linear enamel hypoplasias on the entire crown surface, including unerupted teeth. Using this method, highly detailed stress patterns at the EDJ allow precise matching of teeth within an individual’s dentition when virtual histology is not sufficient. We highlight that taphonomical altered enamel can in particular cases yield artificial subdivisions of perikymata when imaged using X-ray microtomography with insufficient resolution. This may complicate assessments of developmental time, although this can be circumvented by a careful analysis of external and internal structures in parallel. We further present new crown formation times for two unerupted canines from South African Australopiths, which were found to form over a rather surprisingly long time (> 4.5 years). This approach provides tools for maximizing the recovery of developmental information in teeth, especially in the most difficult cases.     

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.     

Implications of Aberrant Temperature-Sensitive Glucose Transport Via the Glucose Transporter Deficiency Mutant (GLUT1DS) T295M for the Alternate-Access and Fixed-Site Transport Models

In silico glucose docking to the transporter GLUT1 templated to the crystal structure of Escherichia coli XylE, a bacterial homolog of GLUT1–4 (4GBZ.pdb), reveals multiple docking sites. One site in the external vestibule in the exofacial linker between TM7 and -8 is adjacent to a missense T295M and a 4-mer insertion mutation. Glucose docking to the adjacent site is occluded in these mutants. These mutants cause an atypical form of glucose transport deficiency syndrome (GLUT1DS), where transport into the brain is deficient, although unusually transport into erythrocytes at 4 °C appears normal. A model in which glucose traverses the transporter via a network of saturable fixed sites simulates the temperature sensitivity of normal and mutant glucose influx and the mutation-dependent alterations of influx and efflux asymmetry when expressed in Xenopus oocytes at 37 °C. The explanation for the temperature sensitivity is that at 4 °C glucose influx between the external and internal vestibules is slow and causes glucose to accumulate in the external vestibule. This retards net glucose uptake from the external solution via two parallel sites into the external vestibule, consequently masking any transport defect at either one of these sites. At 37 °C glucose transit between the external and internal vestibules is rapid, with no significant glucose buildup in the external vestibule, and thereby unmasks any transport defect at one of the parallel input sites. Monitoring glucose transport in patients’ erythrocytes at higher temperatures may improve the diagnostic accuracy of the functional test of GLUT1DS.     

Plant myosins

Summary Plant myosins are motor proteins that bind to the external surfaces of organelles and interact with the cytoskeletal protein actin (as actin microfilaments), which organizes and directs intracellular movement. Recent progress in physiological, biochemical, immunological, and genetical studies of plant myosin has revealed considerable information about the structures and functions of these important molecules. This article briefly reviews the history of plant myosin research, summarizes recent progress, and highlights directions for future research. Dedicated to the memory of the late Professor Noburo Kamiya (1913–1999)     

Intercalation-mediated synthesis and replication: a new approach to the origin of life

We propose that a molecular midwife, a flat molecule approximately 10 Ax10 A with two hydrophobic faces, was essential to the origin of life. This molecule was positively charged, water soluble and did not strongly associate with itself in solution. It may have been a derivative of phthalocyanine that no longer exists on the Earth today, and might have been formed solely from hydrogen cyanide and formaldehyde. The midwife tended to intercalate between side groups (bases, similar to those in RNA) of polymers to form stacks, which incorporated bare bases. The midwife alternated in these stacks with hydrogen-bonded tetrads of bases. Under conditions of low water activity, as in a desert during the day, bare bases in the stacks were joined together by neutral and chemically heterogeneous backbones of no fixed chirality. The components of the backbones were the products of the formose reaction of formaldehyde, and were involved in the reversible formation of N -glycosides and acetals catalysed by divalent metal ions. The final product of this assemblage was a fully intercalated quadruplex of four information-containing polymer strands (four proto -RNA molecules). This process constituted replication of the original polymer that had seeded the formation of the stack. The stack structure ensured that the polymer's base sequence was replicated faithfully despite the lack of both homochirality and chemical homogeneity in the backbone. At night, water from condensing dew would suddenly come in contact with these products, quenching all chemical reactions and releasing midwife molecules and single- or double-stranded proto-RNA. Evaporation of water during the day then gave new stacks containing one or two proto-RNA strands, bare bases, and midwife molecules, which could begin a new replication cycle. Our model also allows for the generation of new stacks and the extension of existing ones, without restricting the base sequence of either, thereby providing a source of genetic information. The proto-RNA replication cycle is driven purely by concentration changes caused by the Sun and the rotation of the Earth. We propose that this system as a whole could have gradually evolved into the RNA World.     

Bone acidic glycoprotein-75 delineates the extracellular sites of future bone sialoprotein accumulation and apatite nucleation in osteoblastic cultures

Addition of an organophosphate source to UMR osteoblastic cultures activates a mineralization program in which BSP localizes to extracellular matrix sites where hydroxyapatite crystals are subsequently nucleated. This study identifies for the first time novel extracellular spherical structures, termed biomineralization foci (BMF), containing bone acidic glycoprotein-75 (BAG-75), bone sialoprotein (BSP), and alkaline phosphatase that are the exclusive sites of initial nucleation of hydroxyapatite crystals in the UMR model. Importantly, in the absence of added phosphate, UMR cultures after reaching confluency contain two size populations of morphologically identifiable BMF precursors enriched in BAG-75 (15-25 and 150-250 microm in diameter). The shape and size of the smaller population are similar to structures assembled in vitro through self-association of purified BAG-75 protein. After organophosphate addition, BSP accumulates within these BAG-75-containing BMF precursors, with hydroxyapatite crystal nucleation occurring subsequently. In summary, BAG-75 is the earliest detectable biomarker that accurately predicts the extracellular sites of de novo biomineralization in UMR cultures. We hypothesize that BAG-75 may perform a key structural role in the assembly of BMF precursors and the recruitment of other proteins such as alkaline phosphatase and BSP. Furthermore, we propose a hypothetical mechanism in which BAG-75 and BSP function actively in nucleation of apatite within BMF.     

Synaptic information transfer in computer models of neocortical columns

Understanding the direction and quantity of information flowing in neuronal networks is a fundamental problem in neuroscience. Brains and neuronal networks must at the same time store information about the world and react to information in the world. We sought to measure how the activity of the network alters information flow from inputs to output patterns. Using neocortical column neuronal network simulations, we demonstrated that networks with greater internal connectivity reduced input/output correlations from excitatory synapses and decreased negative correlations from inhibitory synapses, measured by Kendall’s τ correlation. Both of these changes were associated with reduction in information flow, measured by normalized transfer entropy (nTE). Information handling by the network reflected the degree of internal connectivity. With no internal connectivity, the feedforward network transformed inputs through nonlinear summation and thresholding. With greater connectivity strength, the recurrent network translated activity and information due to contribution of activity from intrinsic network dynamics. This dynamic contribution amounts to added information drawn from that stored in the network. At still higher internal synaptic strength, the network corrupted the external information, producing a state where little external information came through. The association of increased information retrieved from the network with increased gamma power supports the notion of gamma oscillations playing a role in information processing.     

'boxA'-like sequence between the 16 S/23 S spacer in rRNA operon of mycoplasmas.

We have found that a boxA-like sequence is conserved in the 16 S and 23 S rRNA intergenic spacer regions of mycoplasmas, and that it always locates on loop regions of the hypothetical secondary stem-loop structures. A nucleotide sequence similar to the '-10' box of prokaryotic promoters was identified at upstream sites of the boxA-like sequence in the 16 S/23 S spacer regions. These structures may represent an internal promoter between the 16 S and 23 S rRNA genes in mycoplasmas.     

Interaction between quaternary ammonium ions in the pore of potassium channels. Evidence against an electrostatic repulsion mechanism

We have examined the interaction between internal and external ions in the pore of potassium channels. We found that external tetraethylammonium was able to antagonize block of Shaker channels by internal TEA when the external and internal solutions contained K(+) ions. This antagonism was absent in solutions with Rb(+) as the only permeant ion. An externally applied trivalent TEA analogue, gallamine, was less effective than the monovalent TEA in inhibiting block by internal TEA. In addition, block by external TEA was little affected by changes in the concentration of internal K(+) ions, but was increased by the presence of internal Na(+) ions in the pore. These results demonstrate that external and internal TEA ions, likely located at opposite ends of the pore selectivity filter, do not experience a mutual electrostatic repulsion. We found that these results can be simulated by a simple 4-barrier-3-site permeation model in which ions compete for available binding sites without long-range electrostatic interactions.     

Calcium oxalate and sulphate-containing structures on the thallial surface of the lichen Ramalina lacera: response to polluted air and simulated acid rain

The formation of calcium‐containing structures on the thallial surface of the lichen Ramalina lacera (With.) J.R. Laund. in response to air pollution and to simulated acid rain, was studied in in situ and transplanted thalli. In situ thalli were collected from an unpolluted site and transplanted to heavily polluted and less polluted sites for a 10 month period. Additional thalli were treated either with double distilled water or with simulated acid rain. Scanning electron microscopy and infrared spectrometry revealed that thallial surfaces of in situ R. lacera samples collected in unpolluted sites were covered with two kinds of calcium oxalate crystals: whewellite and weddellite. These aggregates of calcium oxalate crystals appear to disintegrate and provide a crystal layer on the thallial surface. Infrared spectroscopy of powder scraped from thallial surfaces of transplants, retrieved from non‐polluted sites, showed the presence of whewellite and weddellite, whereas powders obtained from thalli retrieved from polluted sites contained whewellite, weddellite and gypsum. It is suggested that a certain fraction of the gypsum detected in crater‐like structures in transplants from polluted sites and in thalli treated with simulated acid rain is endogenous and should be considered a biomineral.     

The Metabolism of 3-Indolylacetic Acid in Plant Tissues3

The nature of metabolic products of 3–indolylacetic acid(IAA) extracted from potato tuber disks treated with aeratedIAA solution has been investigated. Two major products, knownat first as ‘V’ and ‘P’ in these studieshave been isolated and ‘V’ has been identified as3-indolylacetylaspartic acid (IacAsp). The rapid uptake of IAA is inhibitited by metabolic poisonssuch as 10^–3 M. cyanide. The maximum mean internal concentrationexceeds the external concentration well–aerated cultures.The mean internal concentration, however only remains for aperiod and then falls off rapidly as a result of extrusion ofabsorbed IAA into the external solution. This extrusion is notinhibited by 10^-3 cyanide; when the mean internal IAA concentrationis 150 µ mol/ml. and the localized IAA concentration musttherefore exceed this value. We conclude therefore that theIAA concentration in the sites where it has accumulated exceedsthe concentration of IAA outside. Uptake of IAA and also its further conversion are inhibitedby indolylacetonitrile and promoted by aspartate, but this promotionis not associated with any gain in amount of indolylacetylaspartate(IacAsp). The data suggest that IacAsp may be formed in tissue from ‘boundIAA’ rather then free IAA. The ‘accelerator ’ found in potato and beans whichhas similar R_F to IAcAsp has been shown definity to be someother substance or substances and not IAcAsp as was at firstthought possible.     

Distribution of biofilm on internal and external surfaces of upper complete dentures: the effect of hygiene instruction

Objectives: The purpose of this study was to evaluate biofilm distribution over internal and external surfaces of upper complete dentures. It was also aimed at assessing the effect of oral hygiene instructions before and after home use of a disclosing solution. Materials and methods: The sample consisted of 29 complete denture wearers whose upper prostheses were evaluated. Surface biofilm was disclosed by means of a 1% neutral red solution and quantified with regard to internal and external surfaces. Oral hygiene information was provided on an individual basis. During the second stage, an amount of disclosing solution was given for domestic use. Results: Internal and external surfaces presented a similar amount of biofilm, which was concentrated over the area of the posterior teeth area, palatal rugae and the internal vestibular incline of the distobuccal flange. This pattern was maintained during the study. However, overall amounts were reduced following denture hygiene information. The use of disclosing solution by subjects at home resulted in a further reduction. Conclusions: It was concluded that biofilm deposits were similar over assessed surfaces, regardless of the type of procedure but irregular areas presented greater amounts. Oral health instruction was effective in reducing the biofilm, in particular when associated with home use of a disclosing agent.     

Ion channels in icosahedral virus: a comparative analysis of the structures and binding sites at their fivefold axes.

An analysis of the crystallographically determined structures of the icosahedral protein coats of Tomato Bushy Stunt Virus, Southern Bean Mosaic Virus, Satellite Tobacco Necrosis Virus, Human Rhinovirus 14 and Mengovirus around their fivefold axes is presented. Accessibilities surfaces, electrostatic energy profile calculations, ion-protein interaction energy calculations, free energy perturbation methods and comparisons with structures of chelating agents are used in this study. It is concluded that the structures built around the viral fivefold axes would be adequate for ion binding and transport. Relative ion preferences are derived for the binding sites, using free energy perturbation methods, which are consistent with the experimental data when available. In the cases where crystallographic studies determined the existence of ions on the fivefold axes, our results indicate that they would correspond to ions in crystallization or purification buffers. The environment of the fivefold axes are rich in polar residues in all icosahedral viral structures whose atomic coordinates are available, including some that are not being analyzed in detail in this work. The fivefold channel-like structures have most of the basic properties expected for real ion channels including a funnel at the entrance, a polar internal environment with frequent alternation of acidic and basic residues, ion binding sites, the capability to induce ion dehydration and ion transit from the external viral surface to the binding sites.     

Malformed, a mutation of Drosophila melanogaster producing mirror-image duplication of a portion of the orbit.

Clonal analysis using mitotic recombination in Drosophila melanogaster shows that the region of the orbit duplicated within the compound eye of the mutant Malformed often originates from a cell population different from that giving rise to the normal orbital region, although, occasionally, both regions may arise from the same progenitor cell. We prefer an interpretation of the action of this mutation based on the misreading of the positional information at the time late in development when imaginal cells are specified to differentiate into particular cuticular structures, rather than an interpretation based on early localized cell death followed by mirror-image duplication.