Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.

An outer-table suspension technique for endoscopic browlift

For the past 2 years, we have sought to develop a stable and reliable technique for soft-tissue suspension in the endoscopic browlift, while eliminating the need for permanent or temporary anchoring screws. To this end, we have developed an outer calvarial table fixation technique. This technique allows direct fixation of the periosteum or galea to the outer table of the frontal bone through the use of an outer table calvarial tunnel. The technique has been used in 34 patients, 21 of which were followed for more than a year. The results have been consistent and reliable. We feel this technique affords precise control of soft tissue suspension during endoscopic browlift, providing long-lasting elevation and lateral advancement of the brow complex.

Production of poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) in a recombinant Escherichia coli strain

An Escherichia coli strain has been constructed that produces the copolymer poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) P(HB-co-HV). This has been accomplished by placing the PHB biosynthetic genes from Alcaligenes eutrophus into an E. coli fadR atoC(Con) mutant and culturing the strain in M9 minimal medium containing glucose and propionate. 3-Hydroxyvalerate incorporation is absolutely dependent on the presence of both glucose and propionate, and 3-hydroxybutyrate-3-hydroxyvalerate ratios in the copolymer can be manipulated by altering the propionate concentration and/or the glucose concentration in the culture. P(HB-co-HV) production can be accomplished by using a wide variety of feeding regimens, but the most efficient is to allow the culture to grow to late log phase in minimal medium containing acetate and then add glucose and propionate to initiate copolymer production. A broad range of propionate concentrations can be used in the culture to stimulate 3-hydroxyvalerate incorporation; however, the most efficient utilization of propionate occurs at concentrations below 10 mM. 3-Hydroxyvalerate molar percentages in the copolymer are relatively constant over the course of growth. The copolymer has been purified and confirmed to be P(HB-co-HV) by gas chromatography/mass spectrometry and differential scanning calorimetry.

Molecular biology of serotonin (5-HT) receptors

The recent cloning of three types of 5-hydroxytryptamine (5-HT, serotonin) receptors substantiates radioligand-based definitions of 5-HT receptors, and provides a framework in which to understand the function and evolution of the receptors. The primary sequences determined by molecular cloning of the 5-HT1c, 5-HT1a and 5-HT2 receptors place each of these 5-HT receptor subtypes into the class of G protein-coupled receptors. These receptors all share similar functional and structural features. Each receptor is positioned in the lipid bilayer with seven membrane-spanning domains and corresponding intracellular and extracellular domains. By analogy to the known functional structures of the beta-adrenergic receptor, the binding site of 5-HT is proposed to be in the membrane domains and the intracellular domain is important for G protein interaction. The primary sequences and the second messenger systems of the receptors indicate the 5-HT2 and 5-HT1c receptors are closely related, whereas the 5-HT1a receptor is more distantly related to the 5-HT2 and 5-HT1c receptors.

Noncompetitive inhibitors reach their binding site in the acetylcholine receptor by two different paths

Electron spin resonance was used to contrast the accessibility of tertiary and quaternary local anesthetics to their high affinity binding site in the desensitized acetylcholine receptor (AChR). The time dependence of agonist addition on the association of spin-labeled local anesthetics with the nicotinic AChR-enriched membranes from Torpedo californica was studied. Preincubation of AChR-enriched membranes with agonist for more than a few minutes before the addition of C6SLMel, a quaternary amine local anesthetic, resulted in substantial reduction in the initial association of the label with the receptor. The time-dependent reduction in the initial association of the label with the receptor is modeled by an exponential function having a rate constant of approximately 0.2 min-1. In contrast, agonist preincubation did not produce a comparable decrease in the association of C6SL, a tertiary amine analog, with the AChR. These findings show that whereas the affinity of either anesthetic for the AChR is dependent on the presence of agonist, for C6SLMel the timing of agonist addition is an important factor in determining the rate of anesthetic association with the receptor. Our results are concerned with the desensitized receptor at an early phase, when the average open-channel time limits the anesthetic binding to the receptor. We interpret our results by a model in which the cationic local anesthetic reaches its high affinity binding site in the receptor by an aqueous path that is accessible only when the channel is open. On the other hand, anesthetic in its uncharged form is not restricted only to the aqueous path of access. An additional path, probably through the lipid bilayer, allows uncharged forms of anesthetics to reach the high affinity binding site in the AChR even when the aqueous path is closed. During the "open state" of the receptor both cationic and uncharged anesthetics have access to the high affinity site through the aqueous path. However, after this open state, the channel opens only intermittently. The rapidly decreasing open time results in the time-dependent reduction in the binding of cationic anesthetics. This model is consistent with the open channel hypothesis of anesthetic binding to the AChR immediately after agonist stimulation; however, our model also includes an additional hydrophobic path of access for uncharged and reversibly charged anesthetics.