Principles and pitfalls in designing site-directed peptide ligands

An immunoglobulin light chain dimer with a large generic binding cavity was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports were systematically tested for binding activity by enzyme linked immunosorbent assays (ELISA). Key members of the binding series were synthesized in milligram quantities and diffused into crystals of the host molecule for X-ray analyses. These peptides were incrementally increased in size and affinity until they nearly filled the cavity. Progressive changes in binding patterns were mapped by comparisons of crystallo-graphically refined structures of 14 peptide–protein complexes at 2.7 Å resolution. These comparisons led to guidelines for ligand design and also suggested ways to modify previously established binding patterns. By manipulating equilibria involving histidine, for example, it was possible to abolish one important intramolecular interaction of the bound ligand and substitute another. These events triggered a change inconformation of the ligand from a compact to an extended form and a comprehensive change in the mode of binding to the protein. In dipeptides of histidine and proline, protonation of both imidazolium nitrogen atoms was used to program anend-to-end reversal of the direction in which the ligand was inserted into the binding cavity. Peptides cocrystallized with proteins produced complexes somewhat different in structure from those in which ligandswere diffused into preexisting crystals. In sucha large and malleable cavity, space utilization was thus different when a ligand was introduced before the imposition of crystal packing restraints. © 1993 Wiley-Liss, Inc.     

A structured decision making analysis to increase a Red-cockaded Woodpecker population and balance stakeholder objectives for a National Forest

Longleaf pine (Pinus palustris) savanna is a biodiverse ecosystem native to the southeastern United States. Due to fire suppression and timber harvest, longleaf pine has declined to 3% of its original range. The extant forest provides habitat for many threatened and endangered species, including the endangered Red-cockaded Woodpecker (Picoides borealis; RCW), a cavity-nesting bird that co-evolved with fire-maintained forest, resulting in savanna-like old-growth forest as the bird’s preferred habitat. Our study site, the Oakmulgee Ranger District of the Talladega National Forest, harbors the largest RCW population in Alabama and is managed with an emphasis on RCW conservation. The United States Forest Service (USFS) also manages the Oakmulgee for uses such as wildlife conservation, recreation, and timber harvest. Despite efforts to restore RCW habitat and install artificial cavities in the Oakmulgee, the number of RCW groups has not exceeded 123, although the Recovery Plan objective is 394 groups. Our project was motivated by the USFS expressing interest in determining why the RCW population has not exceeded 123 groups. We proposed using structured decision making (SDM) with the USFS and other stakeholders to address this problem. Our goals were to explicitly define management objectives, build a Bayesian belief network with a model of how decision alternatives are believed to affect management objectives, and use a sensitivity analysis to determine the part of the model to which RCW population growth was most sensitive. Therefore, results from the analysis were expected to give insights into 1) ecological factors limiting RCW population growth, 2) how management can overcome these limits, plus 3) the relative expected ability of different decision alternatives to satisfy multiple objectives in addition to increasing RCW group number. We held four SDM workshops with representatives from the USFS, the Animal and Plant Health Inspection Service, the Longleaf Alliance, the Birmingham Audubon Society, and local residents. Stakeholder objectives consisted of maximizing the following: RCW group number, forest health, recreational enjoyment, community economic health, and aesthetics. Cavity insert installation had the greatest probability of increasing the number of RCW groups. The number of RCW groups was most affected by cavity availability, adult survival, reproductive output, food availability, and herbaceous understory. Prescribed burning was most likely to meet the combination of stakeholder objectives, followed by midstory removal. Our findings suggest that cavity installation efforts may need to be increased in the Oakmulgee to increase RCW group number. Also it could be beneficial to investigate how RCWs select cavity tree locations with the goal of increasing the chance that RCWs use artificial cavities to form new groups. The Bayesian belief network provided insights into factors limiting RCW population growth and how management can overcome these limits. The Bayesian belief network also can be used to prioritize management methods in the Oakmulgee given stakeholder objectives and time constraints.     

Carbonic Anhydrases in Chick Extra-embryonic Structures: A Role for CA in Bicarbonate Reabsorption Through the Chorioallantoic Membrane

The villus cavity cells, a specific cell type of the chick chorioallantoic membrane, express both cytosolic carbonic anhydrase in their cytoplasm and [Formula: See Text] anion exchangers at their basolateral membranes. By immunohistochemical analysis, we show here that villus cavity cells specifically react with antibodies directed against the membrane-associated form of carbonic anhydrase, CAIV. Staining is restricted to the apical cell membranes, characteristically invaginated toward the shell membrane, as well as to endothelia of blood vessels present in the mesodermal layer. The occurrence of a membrane-associated CA form at the apical pole of villus cavity cells, when definitively confirmed, would be fairly consistent with the role proposed for these cells in bicarbonate reabsorption from the eggshell so to prevent metabolic acidosis in the embryo during development.     

Ultrastructure of Microvillar Coelomocytes from the Trunk Coelom of Thysanocardia nigra Ikeda, 1904 (Sipuncula) from the Sea of Japan

This research is part of a study on the ultrastructure of coelomocytes and cellular complexes from the body cavity of sipunculans. New free-swimming elements called microvillar cells in the trunk coelom of Thysanocardia nigra Ikeda, 1904 are examined using transmission electron microscopy. The cell harbors a giant vesicle filled with a fibrous matrix and rosettes of minute osmiophilous granules. The nucleus is peripheral, and a few cell organelles are situated between the cell membrane and the vesicular membrane. The cell membrane bears numerous microvilli with enlarged apical points. Numerous small microvillar vesicles swimming in the coelomic fluid separate from the microvillar cells. The functional morphology of coelomocytes and cellular complexes is discussed.Original Russian Text Copyright © 2005 by Biologiya Morya, Maiorova, Adrianov.     

Distribution of Streptococcus troglodytae and Streptococcus dentirousetti in chimpanzee oral cavities

The aim of this study was to analyze the distribution and phenotypic properties of the indigenous streptococci in chimpanzee (Pan troglodytes) oral cavities. Eleven chimpanzees (aged from 9 to 44 years, mean ± SD, 26.9 ± 12.6 years) in the Primate Research Institute of Kyoto University were enrolled in this research and brushing bacterial samples collected from them. Streptococci were isolated from the oral cavities of all chimpanzees. The isolates (n = 46) were identified as thirteen species by 16S rRNA genes analysis. The predominant species was Streptococcus sanguinis of mitis streptococci from five chimpanzees (45%). Mutans streptococci were isolated from six chimpanzees (55%). The predominant species in the mutans streptococci were Streptococcus troglodytae from four chimpanzees (36%), this species having been proposed as a novel species by us, and Streptococcus dentirousetti from three chimpanzees (27%). Streptococcus mutans was isolated from one chimpanzee (9%). However, Streptococcus sobrinus, Streptococcus macacae and Streptococcus downei, which are indigenous to human and monkey (Macaca fasciclaris) oral habitats, were not isolated. Of the mutans streptococci, S. troglodytae, S. dentirousetti, and S. mutans possessed strong adherence activity to glass surface.     

Molecular recognition of a model globular protein apomyoglobin by synthetic receptor cyclodextrin: effect of fluorescence modification of the protein and cavity size of the receptor in the interaction

Labelling of proteins with some extrinsic probe is unavoidable in molecular biology research. Particularly, spectroscopic studies in the optical region require fluorescence modification of native proteins by attaching polycyclic aromatic fluoroprobe with the proteins under investigation. Our present study aims to address the consequence of the attachment of a fluoroprobe at the protein surface in the molecular recognition of the protein by selectively small model receptor. A spectroscopic study involving apomyoglobin (Apo‐Mb) and cyclodextrin (CyD) of various cavity sizes as model globular protein and synthetic receptors, respectively, using steady‐state and picosecond‐resolved techniques, is detailed here. A study involving Förster resonance energy transfer, between intrinsic amino acid tryptophan (donor) and N, N‐dimethyl naphthalene moiety of the extrinsic dansyl probes at the surface of Apo‐Mb, precisely monitor changes in donor acceptor distance as a consequence of interaction of the protein with CyD having different cavity sizes (β and γ variety). Molecular modelling studies on the interaction of tryptophan and dansyl probe with β‐CyD is reported here and found to be consistent with the experimental observations. In order to investigate structural aspects of the interacting protein, we have used circular dichroism spectroscopy. Temperature‐dependent circular dichroism studies explore the change in the secondary structure of Apo‐Mb in association with CyD, before and after fluorescence modification of the protein. Overall, the study well exemplifies approaches to protein recognition by CyD as a synthetic receptor and offers a cautionary note on the use of hydrophobic fluorescent labels for proteins in biochemical studies involving recognition of molecules. Copyright © 2013 John Wiley & Sons, Ltd.     

Background levels of hydrogen cyanide in human breath measured by infrared cavity ring down spectroscopy

Hydrogen cyanide (HCN) in breath has been suggested as a diagnostic tool for cyanide poisoning and for cyanide-producing bacterial infections. To distinguish elevated levels of breath HCN, baseline data are needed. Background levels of HCN were measured in mixed exhaled air from 40 healthy subjects (26 men, 14 women, age 21–61 years; detection limit: 1.5?ppb; median: 4.4?ppb; range <1.5–14?ppb) by near-infrared cavity ring down spectroscopy (CRDS). No correlation was observed with smoking habits, recent meals or age. However, female subjects had slightly higher breath levels of HCN than male subjects. CRDS has not previously been used for this purpose.     

Natural cavity restoration as an alternative to nest box supplementation

Nest box supplementation is widely used to increase nest‐site availability for cavity nesting animals but the analysis of its effects on individuals breeding in natural cavities is often neglected. This study offers a novel restoration technique to revert abandonment of natural breeding sites by a secondary cavity avian bird, the European roller (Coracias garrulus), and other ecologically similar species. We found that, after a program of nest box supplementation with ensuing monitoring, rollers gradually abandon nesting in natural and seminatural cavities in favor of nest boxes because the latter are of higher quality. We examine whether reducing the entrance size of natural and seminatural cavities improves their suitability for rollers. A 6‐year program reduced the diameter of the entrance of sandstone cavities and cavities in bridges. This led to a high occupancy (59%) of manipulated nest‐sites. Manipulated sites were most frequently occupied by rollers and little owls (Athene noctua) (31 and 18% of sites, respectively). Manipulation did not affect clutch size or fledgling success. We suggest that nest‐site diversity and nesting in natural cavities should be preserved to reduce nest box dependence. Our study illustrates the value of nest boxes when used alongside restoration of natural breeding sites and provides insights for the management of natural cavities.     

Inverse Optical Cavity Design for Ultrabroadband Light Absorption Beyond the Conventional Limit in Low‐Bandgap Nonfullerene Acceptor–Based Solar Cells

In the subwavelength regime, several nanophotonic configurations have been proposed to overcome the conventional light trapping or light absorption enhancement limit in solar cells also known as the Yablonovitch limit. It has been recently suggested that establishing such limit should rely on computational inverse electromagnetic design instead of the traditional approach combining intuition and a priori known physical effect. In the present work, by applying an inverse full wave vector electromagnetic computational approach, a 1D nanostructured optical cavity with a new resonance configuration is designed that provides an ultrabroadband (≈450 nm) light absorption enhancement when applied to a 107 nm thick active layer organic solar cell based on a low‐bandgap (1.32 eV) nonfullerene acceptor. It is demonstrated computationally and experimentally that the absorption enhancement provided by such a cavity surpasses the conventional limit resulting from an ergodic optical geometry by a 7% average over a 450 nm band and by more than 20% in the NIR. In such a cavity configuration the solar cells exhibit a maximum power conversion efficiency above 14%, corresponding to the highest ever measured for devices based on the specific nonfullerene acceptor used.     

Bats relocate maternity colony after the natural loss of roost trees

Understanding the ephemerality of trees used as roosts by wildlife, and the number of roost trees needed to sustain their populations, is important for forest management and wildlife conservation. Several studies indicate that roosts are limiting to bats, but few studies have monitored longevity of roost trees used by bats over several years. From 2004–2007 in Cypress Hills Interprovincial Park, Saskatchewan, Canada, several big brown bats (Eptesicus fuscus) from a maternity group roosted in cavities in trembling aspen (Populus tremuloides) trees approximately 7 km southeast away from their original known roosting area (RA1). Using a long-term data set of the roost trees used by bats in this area from 2000–2007, we evaluated whether the movement of bats to the new roosting area (RA4) corresponded with annual and cumulative losses of roost trees. We also determined whether longevity of the roosts from the time we discovered bats first using them differed between the 2 roosting areas based on Kaplan-Meier estimates. Bats began using RA4 in addition to RA1 in 2004, when the cumulative loss of roost trees in RA1 over 3 consecutive years reached 18%. Most bats exclusively roosted in RA4 in 2007, when the cumulative loss of roost trees over 6 consecutive years had reached 46% in RA1. Annual survival for roost trees, from when we first discovered bats using them, was generally lower in RA1 than in RA4. Our results suggest that the movement of bats to the new roosting area corresponded with high losses of roost trees in RA1. This provides additional evidence that to maintain high densities of suitable roost trees for bats in northern temperature forests over several decades, management plans need to recruit live and dead trees in multiple age classes and stages of decay that will be suitable for the formation of new cavities. © 2019 The Wildlife Society.