Rings, circles, and null-models for point pattern analysis in ecology

A large number of methods for the analysis of point pattern data have been developed in a wide range of scientific fields. First-order statistics describe large-scale variation in the intensity of points in a study region, whereas second-order characteristics are summary statistics of all point-to-point distances in a mapped area and offer the potential for detecting both different types and scales of patterns. Second-order analysis based on Ripley's K-function is increasingly used in ecology to characterize spatial patterns and to develop hypothesis on underlying processes; however, the full range of available methods has seldomly been applied by ecologists. The aim of this paper is to provide guidance to ecologists with limited experience in second-order analysis to help in the choice of appropriate methods and to point to practical difficulties and pitfalls. We review (1) methods for analytical and numerical implementation of two complementary second-order statistics, Ripley's K and the O-ring statistic, (2) methods for edge correction, (3) methods to account for first-order effects (i.e. heterogeneity) of univariate patterns, and (4) a variety of useful standard and non-standard null models for univariate and bivariate patterns. For illustrative purpose, we analyze examples that deal with non-homogeneous univariate point patterns. We demonstrate that large-scale heterogeneity of a point-pattern biases Ripley's K-function at smaller scales. This bias is difficult to detect without explicitly testing for homogeneity, but we show that it can be removed when applying methods that account for first-order effects. We synthesize our review in a number of step-by-step recommendations that guide the reader through the selection of appropriate methods and we provide a software program that implements most of the methods reviewed and developed here.     

Complete subunit sequences, structure and evolution of the 6 x 6-mer hemocyanin from the common house centipede, Scutigera coleoptrata.

Hemocyanins are large oligomeric copper-containing proteins that serve for the transport of oxygen in many arthropod species. While studied in detail in the Chelicerata and Crustacea, hemocyanins had long been considered unnecessary in the Myriapoda. Here we report the complete molecular structure of the hemocyanin from the common house centipede Scutigera coleoptrata (Myriapoda: Chilopoda), as deduced from 2D-gel electrophoresis, MALDI-TOF mass spectrometry, protein and cDNA sequencing, and homology modeling. This is the first myriapod hemocyanin to be fully sequenced, and allows the investigation of hemocyanin structure-function relationship and evolution. S. coleoptrata hemocyanin is a 6 x 6-mer composed of four distinct subunit types that occur in an approximate 2 : 2 : 1 : 1 ratio and are 49.5-55.5% identical. The cDNA of a fifth, highly diverged, putative hemocyanin was identified that is not included in the native 6 x 6-mer hemocyanin. Phylogenetic analyses show that myriapod hemocyanins are monophyletic, but at least three distinct subunit types evolved before the separation of the Chilopoda and Diplopoda more than 420 million years ago. In contrast to the situation in the Crustacea and Chelicerata, the substitution rates among the myriapod hemocyanin subunits are highly variable. Phylogenetic analyses do not support a common clade of Myriapoda and Hexapoda, whereas there is evidence in favor of monophyletic Mandibulata.     

The effect of light levels on daily patterns of chlorophyll fluorescence and organic acid accumulation in the tropical CAM treeClusia hilariana

Sandy plains are characteristic of the coastal region of Brazil. We investigated the diel patterns of changes in organic acid levels, leaf conductance and chlorophylla fluorescence for sun-exposed and shaded plants ofClusia hilariana, one of the dominant woody species in the sandy coastal plains of northern Rio de Janeiro state. Both exposed and shaded plants showed a typical CAM pattern with considerable diel oscillations in organic acid levels. The degradation of both malic and citric acids during the midday stomatal closure period could lead to potential CO₂ fixation rates of 28 mol m^-2 s^-1 in exposed leaves. Moreover, exposed leaves exhibited large increases in total non-photochemical quenching (q_N) accompanied by a substantial decrease in effective quantum yield during the course of the day. However, these potential high rates of CO₂ fixation and the increases inqn of exposed plants were not enough to maintain the primary electron acceptor of photosystem II (q_A) in a low reduction state, similar to that of shaded plants. As a result, there was a moderate increase in the reduction state of q_A throughout the day. Most of the decline in photochemical efficiency of exposed leaves ofC. hilariana was reversible, as evidenced by the high levels of pre-dawn potential quantum yields (F_v/F_m) and their rapid recovery after sunset. However, the depletion of the organic acid pool in the afternoon resulted in an accentuated subsequent drop in F_v/F_m, suggesting that prolonged periods of water stress accompanied by high irradiance levels may expose plants ofC. hilariana in unprotected habitats to the danger of photoinhibition.     

Localization of collagens and alkaline phosphatase activity during mineralization and ossification of human first rib cartilage

The localization of type X collagen and alkaline phosphatase activity was examined in order to gain a better understanding of tissue remodelling during development of human first rib cartilage. First rib cartilages from children and adolescents showed no staining for type X collagen and alkaline phosphatase activity. After onset of mineralization in the late second decade, a peripheral ossification process preceded by mineralized fibrocartilage could be distinguished from a more central one preceded by mineralized hyaline cartilage. No immunostaining for type X collagen was found in either type of cartilage. However, strong staining for alkaline phosphatase activity was detected around chondrocyte-like cells within fibrocartilage adjacent to the peripheral mineralization front, while a weaker staining pattern was observed around chondrocytes of hyaline cartilage near the central mineralization front. In addition, the territorial matrix of some chondrocytes within the hyaline cartilage revealed staining for type I collagen, suggesting that these cells undergo a dedifferentiation process, which leads to a switch from type II to type I collagen synthesis. The study provides evidence that mineralization of the hyaline cartilage areas in human first rib cartilage occurs in the absence of type X collagen synthesis but in the presence of alkaline phosphatase. Thus, mineralization of first rib cartilage seems to follow a different pattern from endochondral ossification in epiphyseal discs.     

Clathrin-associated adaptor proteins - putting it all together

Adaptors are multifunctional linker proteins that, as a coated vesicle assembles, tether the clathrin lattice to the underlying membrane bud site. Each adaptor is composed of four distinct protein submits, but how these assemble into the functional complex is not clear. Here, some features of the protein sequences are discussed in an attempt to develop a speculative, low-resolution structural model of possible subunit interactions.     

Anamylopsoraceae — a new family of lichenized ascomycetes with stipitate apothecia (Lecanorales: Agyriineae)

The anatomy, chemistry and developmental morphology ofAnamylopsora pulcherrima is investigated. Some characters, including the ascus structure, suggest a close affinity with theAgyriaceae. However, the chemistry and the pycnidial structure differ as well as the ascoma ontogeny.Anamylopsora has a gymnocarpous ascoma development and the ascogonia are produced in stipes.Trapelia coarctata, as a typical member of theAgyriaceae, shows a hemiangiocarpous ascoma ontogeny. The anatomical, chemical and ontogenetical characters of several families are compared withAnamylopsora and it is shown that the genus is best placed in a monotypic familyAnamylopsoraceae Lumbsch & Lunke, fam. nova, which is placed in theAgyriineae (Lecanorales).This paper is dedicated to Prof. DrAino Henssen (Marburg) on the occasion of the 70th birthday.     

Model of synchronized population bursts in electrically coupled interneurons containing active dendritic conductances

We constructed a computer model of 128 interneurons, each with multiple dendritic branches and an axonal segment. The model neurons were interconnected by gap junctions between dendritic compartments, as are known to occur in rat and guinea-pig hilar interneurons. The model contained no excitatory synapses. In the presence of low-frequency spontaneous action potentials, the model generated synchronized population bursts, when gap junction resistance was 50 M and there were at least two gap junctions per neuron on average. Population bursts occurred only when the dendrites of model neurons were electrically excitable. Consistent with experiment, somatic hyperpolarization during the population burst uncovered partial spikes. In the model, partial spikes originated in electrically active dendrites driven by coupled dendrites. This model may account for population bursts in hilar interneurons that occur in 4-aminopyridine (4AP) together with blockers of GABA_A and excitatory amino acid (EAA) receptors.     

Pyramidal cell-to-inhibitory cell spike transduction explicable by active dendritic conductances in inhibitory cell

In the guinea-pig hippocampal CA3 region, the synaptic connection from pyramidal neurons tostratum pyramidale inhibitory neurons is remarkable. Anatomically, the connection usually consists of a single release site on an interneuronal dendrite, sometimes 200 m or more from the soma. Nevertheless, the connection is physiologically powerful, in that a single presynaptic action potential can evoke, with probability 0.1 to 0.6, a postsynaptic action potential with latency 2 to 6 ms. We construct a model interneuron and show that the anatomical and physiological observations can be reconciled if the interneuron dendrites are electrically excitable. Excitable dendrites could also account for depolarization-induced amplification of the pyramidal cell-interneuron EPSP in the voltage range subthreshold for spike generation.     

Gap junctions in several tissues share antigenic determinants with liver gap junctions.

Using affinity-purified antibodies against mouse liver gap junction protein (26 K), discrete fluorescent spots were seen by indirect immunofluorescence labelling on apposed membranes of contiguous cells in several mouse and rat tissues: pancreas (exocrine part), kidney, small intestine (epithelium and circular smooth muscle), Fallopian tube, endometrium, and myometrium of delivering rats. No reaction was seen on sections of myocardium, ovaries and lens. Specific labelling of gap junction plaques was demonstrated by immunoelectron microscopy on ultrathin frozen sections through liver and the exocrine part of pancreas after treatment with gold protein A. Weak immunoreactivity was found on the endocrine part of the pancreas (i.e., Langerhans islets) after glibenclamide treatment of mice and rats, which causes an increase of insulin secretion and of the size as well as the number of gap junction plaques in cells of Langerhans islets. Furthermore, the affinity purified anti-liver 26 K antibodies were shown by immunoblot to react with proteins of similar mol. wt. in pancreas and kidney membranes. Taken together these results suggest that gap junctions from several, morphogenetically different tissues have specific antigenic sites in common. The different extent of specific immunoreactivity of anti-liver 26 K antibodies with different tissues is likely due to differences in size and number of gap junctions although structural differences cannot be excluded.     

Inhibition of protein synthesis in a polyribosome-dependent cell-free system by a specific ribonuclease prepared from the follicles of two different stages of development of the silkmothAntherea pernyi

Summary Crude, cell-free protein-synthesizing systems were prepared from follicles of two different stages of development in the ovariole of the silkmothAntherea pernyi. The efficiency of the translation of natural and synthetic mRNAs in these systems was compared with that in a cell-free wheat germ system. A postmitochondrial extract (S-30) from the follicles almost completely inhibited protein synthesis in a polyribosome-dependent, cell-free systems. A specific ribonuclease, obtained from the post mitochondrial extract by ammonium sulphate precipitation, heat denaturation and DEAE-cellulose chromatography, inhibited polyribosome-dependent protein synthesis. The effect of this specific ribonuclease on the structural integrity of radioactive RNAs and ribosomal subunits, which were isolated from Ehrlich ascites tumor cells, was also studied.