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PubMed2006

From macro- to nanoscopic templating with nanographenes.

A hexa-peri-hexabenzocoronene carrying six long, branched alkyl chains has been processed in nano- and macroscopic pore templates. An extraordinary self-organization of this material was observed within macroscopically large glass capillaries after cooling from the isotropic phase. Thereby, the columnar structures were long-range aligned along the capillary axis over several centimeters. This behavior was explained by the pronounced directional self-assembly of the molecules, whereby the curvature effect of the capillary was negligible. The processing in nanoscopic pores of an inorganic membrane yielded an improved supramolecular organization. It was possible to remove the inorganic template and to obtain bundles and single nanorods. The templating over different dimensions opens a variety of potential applications.

Journal Article↗
PubMed1995

The victimization of children: a developmental perspective.

A framework is presented for a new field called developmental victomology, and two major branches are described. One would analyze developmental changes that affect children's risk for victimization, particularly in three areas: children's suitability as targets, their ability to protect themselves, and the environments they inhabit. A second branch would focus on developmental processes that affect children's reactions to victimizations and in particular, developmental tasks and critical periods, the process of cognitive appraisal, and the forms of symptom expression.

Adolescent↗
PubMed1993

The synaptic vesicle protein synaptotagmin promotes formation of filopodia in fibroblasts.

Neuronal filopodia are actin-rich cytoplasmic extensions that are involved in motility and recognition in growth cones and maturing axonal endings. A detailed understanding of neuronal growth will depend on clarification of the membrane fusion events occurring during filopodial extension. The synaptic vesicle protein synaptotagmin seems to be intimately involved in exocytotic membrane fusion. Here we show that fibroblast cell lines transfected with synaptotagmin form long, highly branched, actin-rich filopodial processes, with the expressed synaptotagmin being incorporated into the plasma membrane. In contrast, cell lines expressing either of two other synaptic vesicle proteins, SV2 or synaptophysin, generate only rudimentary processes, and, like neurons, sort SV2 and synaptophysin to small intracellular vesicles. As presynaptic calcium entry regulates synaptic vesicle fusion, our results indicate that synaptotagmin might link neuronal activity with synaptic growth.

Animals↗
PubMed2002

Local inhibition modulates odor-evoked synchronization of glomerulus-specific output neurons.

At the first stage of olfactory processing in the brain, synchronous firing across glomeruli may help to temporally bind multiple and spatially distributed input streams activated by a given odor. This hypothesis, however, has never been tested in an organism in which the odor-tuning properties of several spatially identifiable glomeruli are known. Using the sphinx moth, an insect that meets these specific criteria, we recorded odor-evoked responses simultaneously from pairs of projection neurons (PNs) innervating the same or different glomeruli in the macroglomerular complex (MGC), which is involved in processing pheromonal information. PNs that branched in the same glomerulus and were activated by the same pheromone component also showed the strongest coincident responses to each odor pulse. Glomerulus-specific PN pairs were also inhibited by the pheromone component that selectively activated PNs in the neighboring glomerulus, and about 70% of all intraglomerular pairs showed increased synchronization when stimulated with a mixture of the two odorants. Thus, when two adjacent glomeruli receive their inputs simultaneously, the temporal tuning of output from each glomerulus is enhanced by reciprocal and inhibitory interglomerular interactions.

Animals↗
PubMed2002

Glucooligosaccharides from Leuconostoc mesenteroides B-742 (ATCC 13146): a potential prebiotic.

There is an emerging market for functional oligosaccharides for use in foods. Currently, technology for the production of oligosaccharides is limited to extraction from plant sources, acid or enzymatic hydrolysis of polysaccharides or synthesis by transglycosylation reactions. Oligosaccharides can also be produced using a Leuconostoc fermentation and restricting the polymer size by addition of maltose. Maltose limits the dextransucrase reaction, yielding high concentrations of alpha-glucooligosaccharides. Branched oligomers produced by this process were readily catabolized by bifidobacteria and lactobacilli but were not readily utilized by either Salmonella sp. or Escherichia coli, pointing toward their use in intestinal microflora modification.

Bifidobacterium↗
PubMed2002

The RuvABC resolvasome.

The RuvABC resolvasome of Escherichia coli catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. This process involves two key steps: branch migration, catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein, and resolution, which is catalysed by the RuvC endonuclease. We have quantified the interaction of the RuvA protein with synthetic Holliday junctions and have shown that the binding of the protein is highly structure-specific, and leads to the formation of a complex containing two tetramers of RuvA per Holliday junction. Our data are consistent with two tetramers of RuvA binding to the DNA recombination intermediate in a co-operative manner. Once formed this complex prevents the binding of RuvC to the Holliday junction. However, the formation of a RuvAC complex can be observed following sequential addition of the RuvC and RuvA proteins. Moreover, by examining the DNA recognition properties of a mutant RuvA protein (E55R, D56K) we show that the charge on the central pin is critical for directing the structure-specific binding by RuvA.

Bacterial Proteins↗
PubMed2004

[Phlebotomus from Madagascar (Diptera: Psychodidae). III--Description of Phlebotomus (Anaphlebotomus) fontenillei n. sp].

The male of Phlebotomus (Anaphlebotomus) fontenillei n. sp. is described from Namoroka area (Madagascar). Its belongs to the subgenus Anaphlebotomus: style with four spines, coxite without basal process and paramere with two branches. It shares with P. berentiensis an original and exclusive antennal formula: 2/III-XII which distinguishes them from P. fertei. P. fontenillei n. sp. differs mainly from P. berentiensis by about 40 setae in tuft on the ventral face of the coxite, the length of the genital ducts and the position of the spines on the style. Sequence of the second internal transcribed spacer (ITS2) of the ribosomal DNA (rDNA) is very informative: the male of P. fontenillei n. sp. cannot be linked to the female of P. huberti (male unknown) regarding the size of amplified DNA fragment (459 bp versus 600 respectively) and the high degree of variability. There are few differences (10 mutations) between the sequences of P. fontenillei n. sp. and P. berentiensis which are closely related species.

Animals↗
PubMed2001

Ramification amplification: a novel isothermal DNA amplification method.

We have developed a novel isothermal DNA amplification method with an amplification mechanism quite different from conventional PCR. This method uses a specially designed circular probe (C-probe) in which the 3' and 5' ends are brought together in juxtaposition by hybridization to a target. The two ends are then covalently linked by a T4 DNA ligase in a target-dependent manner, producing a closed DNA circle. In the presence of an excess of primers (forward and reverse primers), a DNA polymerase extends the bound forward primer along the C-probe and displaces the downstream strand, generating a multimeric single-stranded DNA (ssDNA), analogous to the "rolling circle" replication of bacteriophages in vivo. This multimeric ssDNA then serves as a template for multiple reverse primers to hybridize, extend, and displace downstream DNA, generating a large ramified (branching) DNA complex. This ramification process continues until all ssDNAs become double-stranded, resulting in an exponential amplification that distinguishes itself from the previously described nonexponential rolling circle amplification. In this report, we prove the principle of ramification amplification. By using a unique bacteriophage DNA polymerase, Ø29 DNA Polymerase, that has an intrinsic high processivity, we are able to achieve significant amplification within 1 hour at 35 degrees C. In addition, we applied this technique for in situ detection of Epstein-Barr viral sequences in Raji cells.

Cell Line↗
PubMed1983

Polyadenylylated nuclear RNA contains branches.

A highly charged component can be isolated from a total RNase T2 digest of nuclear polyadenylylated RNA from HeLa cells that is separable from caps by (dihydroxyboryl)aminoethyl-cellulose chromatography. Chemical and enzymatic analyses show that the component contains a 2'-5' phosphodiester bond that creates a branch at the 2'-hydroxyl group of one nucleotide already linked to an adjoining nucleotide through the usual 3'-5' phosphodiester bond. [Formula: see text] This structure was confirmed by analysis of a similar component isolated from nuclease P1 digests of the same nuclear polyadenylylated RNA. Branches occur in roughly 10% of nuclear polyadenylylated RNAs, including those >10S in size, but are absent from cytoplasmic polyadenylylated RNA. Possible implications for branches as intermediates in mRNA processing are discussed.

Cell Nucleus↗
PubMed2000

Intracellular signalling cascades activated by the EGF receptor and/or by integrins, with potential relevance for branching morphogenesis of the fetal mouse submandibular gland.

The fetal mouse submandibular gland grown in vitro is a valuable model system to study epithelio-mesenchymal interactions vital for branching morphogenesis. This basic developmental process is dependent upon simultaneous engagement of receptors for growth factors and components of the extracellular matrix. Here we review intracellular signalling cascades mediated by activation of the EGFR in the developing mouse submandibular gland.

Animals↗
PubMed2003

Environmental health moves into the 21st century.

Over the past half century, environmental health research has branched from a descriptive, observational process into one of hypothesis driven and mechanistically based science. Nevertheless, the meaning of observed effects of exposures in experimental systems to human public health remains elusive. Recent advances in genetics and "omics" hold great promise to further our abilities to assess potential human health effects and to manage exposures properly. But the comfort of 100% certainty will not be available in the foreseeable future, leaving us with the challenge of designing relevant experiments and test systems upon which to base "logical" policy in risk management.

Animals↗
PubMedDate not supplied

Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation.

Rapid, ancient radiations pose one of the most difficult challenges for phylogenetic estimation. We used DNA sequence data of 9,006 aligned base pairs from five genes (chloroplast atpB, matK, rbcL, and 18S and 26S nrDNA) to elucidate relationships among major lineages of Saxifragales (angiosperms, eudicots). These relationships were poorly supported in previous studies, apparently because the lineages originated in rapid succession. Using an array of methods that explicitly incorporate assumptions about evolutionary process (weighted maximum parsimony, maximum likelihood, LogDet/paralinear transformed distances), we show that the initial diversification of Saxifragales was indeed rapid. We suggest that the poor resolution of our best phylogenetic estimate is not due to violations of assumptions or to combining data partitions having conflicting histories or processes. We show that estimated branch lengths during the initial diversification are exceedingly short, and we estimate that acquiring sufficient sequence data to resolve these relationships would require an extraordinary effort (approximately 10(7) bp), assuming a linear increase in branch support with branch length. However, our simulation of much larger data sets containing a distribution of phylogenetic signal similar to that of the five sampled gene sequences suggests a limit to achievable branch support. Using statistical tests of differences in the likelihoods of topologies, we evaluated whether the initial radiation of Saxifragales involved the simultaneous origin of major lineages. Our results are consistent with predictions that resolving the branching order of rapid, ancient radiations requires sampling characters that evolved rapidly at the time of the radiation but have since experienced a slower evolutionary rate.

Base Composition↗
PubMed2005

Joint Bayesian estimation of alignment and phylogeny.

We describe a novel model and algorithm for simultaneously estimating multiple molecular sequence alignments and the phylogenetic trees that relate the sequences. Unlike current techniques that base phylogeny estimates on a single estimate of the alignment, we take alignment uncertainty into account by considering all possible alignments. Furthermore, because the alignment and phylogeny are constructed simultaneously, a guide tree is not needed. This sidesteps the problem in which alignments created by progressive alignment are biased toward the guide tree used to generate them. Joint estimation also allows us to model rate variation between sites when estimating the alignment and to use the evidence in shared insertion/deletions (indels) to group sister taxa in the phylogeny. Our indel model makes use of affine gap penalties and considers indels of multiple letters. We make the simplifying assumption that the indel process is identical on all branches. As a result, the probability of a gap is independent of branch length. We use a Markov chain Monte Carlo (MCMC) method to sample from the posterior of the joint model, estimating the most probable alignment and tree and their support simultaneously. We describe a new MCMC transition kernel that improves our algorithm's mixing efficiency, allowing the MCMC chains to converge even when started from arbitrary alignments. Our software implementation can estimate alignment uncertainty and we describe a method for summarizing this uncertainty in a single plot.

Algorithms↗
PubMed1955

The fine structure of the renal glomerulus of the mouse.

Sections of mouse renal glomerulus fixed by perfusion with buffered osmium tetroxide solution have been studied with the electron microscope. Four components are recognized in the mouse glomerulus: epithelium, basement membrane, endothelium, and intercapillary cell. The three cellular components all display in their cytoplasm mitochondria, Golgi bodies, endoplasmic reticulum, and uncharacterized vesicles. The concepts of Hall, of Pease, and of Rhodin regarding the glomerular filtration surface are confirmed. The epithelial cells are characterized by intricate, branching, interdigitating ridge-like processes or pedicels, the summits of which press against the urinary surface of the basement membrane, covering the glomerular capillary tuft almost completely except for narrow spaces about 200 to 300 A wide between the processes. These spaces are termed the epithelial filtration slits, and are bridged by a very delicate gossamer-like membrane about 30 A thick,-the filtration slit membrane. The basement membrane is interposed everywhere between epithelial processes and endothelium, and between epithelial and intercapillary cells. The basement membrane of the filtration surface of the glomerular capillary has smooth surfaces and is about 800 A thick. It consists of three layers-a thick central lamina densa, appearing to have a very delicate felt-like structure, flanked on each side by thinner lamina rara externa and lamina rara interna. This membrane continues to the intercapillary space and makes a complicated sponge-work of varying thickness in which the intercapillary cells are enmeshed. The endothelial cells are of moderate thickness in the nuclear region, but send out thin sheet-like extensions over the filtration surface. These extensions are about 300 to 400 A thick and are characterized by numerous round endothelial filtration pores about 500 to 1000 A in diameter. The intercapillary tissue or mesangium is composed of the network of the basement membrane and the intercapillary cells. The intercapillary cells, with characteristic fine fibrillar cytoplasm, make contact with epithelial and endothelial cells and are enmeshed within the network of the basement membrane. Rounded processes of intercapillary cells penetrate into the endothelial cell through the basement membrane, and may even perforate entirely through the endothelium. Such processes are called (after Zimmermann) the intracapillary colliculi. In the endothelial cytoplasm close to the intracapillary colliculi are many dense endothelial juxtacollicular vesicles and caveolae. The cell boundaries of the endothelial cell resemble terminal bars. Some physiological speculations relating to glomerular structure are advanced. The description of Zimmermann (54), based on a light microscope study, is confirmed in many respects.

Animals↗
PubMed2000

Laboratory investigation of the contribution of complex aromatic/aliphatic polycyclic hybrid molecular structures to interstellar ultraviolet extinction and infrared emission.

We have demonstrated by experiment that, in an energetic environment, a simple polycyclic aromatic hydrocarbon (PAH) such as naphthalene will undergo chemical reactions that produce a wide array of more complex species (an aggregate). For a stellar wind of a highly evolved star (post-asymptotic giant branch [post-AGB]), this process would be in addition to what is expected from reactions occurring under thermodynamic equilibrium. A surprising result of that work was that produced in substantial abundance are hydrogenated forms that are hybrids of polycyclic aromatic and polycyclic alkanes. Infrared spectroscopy described here reveals a spectral character for these materials that has much in common with that observed for the constituents of circumstellar clouds of post-AGB stars. It can be demonstrated that a methylene (-CH2-) substructure, as in cycloalkanes, is the likely carrier of the 6.9 microns band emission of dust that has recently been formed around IRAS 22272+5433, NGC 7027, and CPD -56 8032. Ultraviolet spectroscopy previously done with a lower limit of 190 nm had revealed that this molecular aggregate can contribute to the interstellar extinction feature at 2175 angstroms. We have now extended our UV spectroscopy of these materials to 110 nm by a vacuum ultraviolet technique. That work, described here, reveals new spectral characteristics and describes how material newly formed during the late stages of stellar evolution could have produced an extinction feature claimed to exist at 1700 angstroms in the spectrum of HD 145502 and also how the newly formed hydrocarbon material would be transformed/aged in the general interstellar environment. The contribution of this molecular aggregate to the rise in interstellar extinction at wavelengths below 1500 angstroms is also examined. The panspectral measurements of the materials produced in the laboratory, using plasmas of H, He, N, and O to convert the simple PAH naphthalene to an aggregate of complex species, provide insight into possible molecular structure details of newly formed hydrocarbon-rich interstellar dust and its transformation into aged material that becomes resident in the interstellar medium. Specifically the presence of naphthalene-like and butadiene-like conjugated structures as chromophores for the 2175 angstroms ultraviolet extinction feature is indicated.

Cosmic Dust↗
PubMed2004

Axons in cat visual cortex are topologically self-similar.

The axonal arbors of the different types of neocortical and thalamic neurons appear highly dissimilar when viewed in conventional 2D reconstructions. Nevertheless, we have found that their one-dimensional metrics and topologies are surprisingly similar. To discover this, we analysed the axonal branching pattern of 39 neurons (23 spiny, 13 smooth and three thalamic axons) that were filled intracellularly with horseradish peroxidase (HRP) during in vivo experiments in cat area 17. The axons were completely reconstructed and translated into dendrograms. Topological, fractal and Horton-Strahler analyses indicated that axons of smooth and spiny neurons had similar complexity, length ratios (a measure of the relative increase in the length of collateral segments as the axon branches) and bifurcation ratios (a measure of the relative increase in the number of collateral segments as the axon branches). We show that a simple random branching model (Galton-Watson process) predicts with reasonable accuracy the bifurcation ratio, length ratio and collateral length distribution of the axonal arbors.

Animals↗
PubMed1977

Methylazoxymethanol-induced aberrant Purkinje cell dendritic development.

Purkinje cell dendrites develop with a specific orientation and relationship to related neurons and glia. Their dendritic spine postsynaptic membrane specialization may, in turn, require a permanent presynaptic contact by parallel fibers. To determine whether changes in the surrounding cells influence the normal development of the cerebellar Purkinje cell dendrites and spine specializations, destruction on the differentiating cell layer was induced in the postnatal mouse by administration of methylazoxymethanol acetate (MAM) (0.05 micronl/gm body weight) at day zero. The Purkinje cells were examined by light and electron microscopy on the tenth postnatal day. The midsagittal surface area of the cerebellar vermis in treated animals was reduced by an average of 60%. MAM-induced granule cell depletion and Purkinje cell dislocation were observed by light microscopy. When compared to controls, examination following Golgi impregnation revealed random orientation of Purkinje cell apical poles, and multiple primary dendrites of reduced length with few branches, branchlets and spines. Vertical processes of Golgi epithelial (Bergmann) cells were obliquely directed, reduced in length and complexity in MAM-treated mice. Ultrastructural examination revealed naked Purkinje cell dendritic spine specializations in both groups. Although necrotic debris persisted in astrocytes and macrophages, degenerating presynaptic terminals were not found. This study suggests that permanent presynaptic contact by parallel fibers is not essential for spine development. Astrocytic reactions to injury, in association with the reduced folial expansion, may have contributed to the observed abnormalities and disorientation of the Purkinje cells. The data suggests that Purkinje cell dendritic development may be strongly influenced by changes in surrounding cells.

Animals↗
PubMed2003

Absorbing phase transitions of branching-annihilating random walks.

The phase transitions to absorbing states of the branching-annihilating reaction-diffusion processes mA-->(m+k)A, nA-->(n-l)A are studied systematically in one space dimension within a new family of models. Four universality classes of nontrivial critical behavior are found. This provides, in particular, the first evidence of universal scaling laws for pair and triplet processes.

Journal Article↗