bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bifurcation Model for Characterization of Pulmonary Architecture
Authors: Lee Dongyoub , Park Seong S. , Ban‐Weiss George A. , Fanucchi Michelle V. , Plopper Charles G. , Wexler Anthony S. 
Published: January 2008

AbstractA flexible mathematical model of an asymmetric bronchial airway bifurcation is presented. The bifurcation structure is automatically determined after the user specifies geometric parameters: radius of parent airway, radii of daughter airways, radii of curvature of the daughter branch toroids, bifurcation angles, and radius of curvature of carina ridge. Detailed shape in the region where the three airways merge is defined by several explicit functions and can be changed with ease in accordance with observed lung structure. These functions take into account the blunt shape of the carina, the smooth transition from the outer transition zone to the inner one, and the shift in carinal ridge starting position as a function of bifurcation asymmetry. We validated the bifurcation model by comparing it to a computed tomography image of a rat lung cast. Three‐dimensional representations of the bifurcation geometry can be viewed at http://mae.ucdavis.edu/wexler/lungs/bifurc.htm. Anat Rec, 291:379–389, 2008. © 2008 Wiley‐Liss, Inc.
Anatomic Geometry of Sound Transmission and Reception in Cuvier's Beaked Whale (Ziphius cavirostris)
Authors: Cranford Ted W. , Mckenna Megan F. , Soldevilla Melissa S. , Wiggins Sean M. , Goldbogen Jeremy A. , Shadwick Robert E. , Krysl Petr , St. Leger Judy A. , Hildebrand John A. 
Published: January 2008

AbstractThis study uses remote imaging technology to quantify, compare, and contrast the cephalic anatomy between a neonate female and a young adult male Cuvier's beaked whale. Primary results reveal details of anatomic geometry with implications for acoustic function and diving. Specifically, we describe the juxtaposition of the large pterygoid sinuses, a fibrous venous plexus, and a lipid‐rich pathway that connects the acoustic environment to the bony ear complex. We surmise that the large pterygoid air sinuses are essential adaptations for maintaining acoustic isolation and auditory acuity of the ears at depth. In the adult male, an acoustic waveguide lined with pachyosteosclerotic bones is apparently part of a novel transmission pathway for outgoing biosonar signals. Substitution of dense tissue boundaries where we normally find air sacs in delphinoids appears to be a recurring theme in deep‐diving beaked whales and sperm whales. The anatomic configuration of the adult male Ziphius forehead resembles an upside‐down sperm whale nose and may be its functional equivalent, but the homologous relationships between forehead structures are equivocal. Anat Rec, 291:353–378, 2008. © 2008 Wiley‐Liss, Inc.
Visualization and experimental analysis of blood vessel formation using transgenic zebrafish
Authors: Cha Young Ryun , Weinstein Brant M. 
Published: January 2008

AbstractThe mechanisms of blood vessel formation have become a subject of enormous scientific and clinical interest. However, it is difficult to visualize the developing vasculature in most living animals due to the ubiquitous and deep localization of vessels within other tissues. The establishment of vascular‐specific transgenic zebrafish with fluorescently “tagged” blood vessels has facilitated high‐resolution imaging studies of developing blood and lymphatic vessels in vivo. Use of these transgenic lines for genetic and chemical screening, experimental manipulations, and time‐lapse imaging has extended our knowledge of how complex networks of vessels assemble in vivo. Birth Defects Research (Part C) 81:286–296, 2007. Published 2008 Wiley‐Liss, Inc.
Agent‐based modeling of multicell morphogenic processes during development
Authors: Thorne Bryan C. , Bailey Alexander M. , DeSimone Douglas W. , Peirce Shayn M. 
Published: January 2008

AbstractA central challenge in the field of developmental biology is to understand how mechanisms at one level of biological scale (i.e., cell‐level) interact to produce higher‐level (i.e., tissue‐level) phenomena. This challenge is particularly relevant to the study of tissue morphogenesis, the process that generates newly formed, remodeled, or regenerated tissue structures. Morphogenesis arises from the spatially‐ and temporally‐dynamic interactions of individual cells with each other and their local environment. Computational models have been combined with experimental efforts to accelerate the discovery processes. Agent‐based modeling (ABM) is a computational technique that can be used to model collections of individual biological cells and compute their interactions, which generate emergent tissue‐level results. Recently, ABM has been applied to the study of various developmental morphogenic processes, and the purpose of this review is to summarize these studies in order to demonstrate the types of advances that can be expected from pursuing a multicell ABM approach. We also highlight some challenges associated with ABM and suggest strategies for overcoming them. While ABM's application to the study of ecology, epidemiology, and social sciences has a much longer history, we suggest that the application of ABM to the study of morphogenesis has great utility, and when paired with benchtop experimentation, ABM can provide new insights and direct future experimentation. Birth Defects Research (Part C) 81:344–353, 2007. © 2008 Wiley‐Liss, Inc.
Mechanisms controlling human endothelial lumen formation and tube assembly in three‐dimensional extracellular matrices
Authors: Davis George E. , Koh Wonshill , Stratman Amber N. 
Published: January 2008

AbstractRecent data have revealed new mechanisms that underlie endothelial cell (EC) lumen formation during vascular morphogenic events in development, wound repair, and other disease states. It is apparent that EC interactions with extracellular matrices (ECMs) establish signaling cascades downstream of integrin ligation leading to activation of the Rho GTPases, Cdc42 and Rac1, which are required for lumen formation. In large part, this process is driven by intracellular vacuole formation and coalescence, which rapidly leads to the creation of fluid‐filled matrix‐free spaces that are then interconnected via EC–EC interactions to create multicellular tube structures. EC vacuoles markedly accumulate in a polarized fashion directly adjacent to the centrosome in a region that strongly accumulates Cdc42 protein as indicated by green fluorescent protein (GFP)‐Cdc42 during the lumen formation process. Downstream of Cdc42‐mediated signaling, key molecules that have been identified to be required for EC lumen formation include Pak2, Pak4, Par3, Par6, and the protein kinase C (PKC) isoforms ζ and ε. Together, these molecules coordinately regulate the critical EC lumen formation process in three‐dimensional (3D) collagen matrices. These events also require cell surface proteolysis mediated through membrane type 1 matrix metalloproteinase (MT1‐MMP), which is necessary to create vascular guidance tunnels within the 3D matrix environment. These tunnels represent physical spaces within the ECM that are necessary to regulate vascular morphogenic events, including the establishment of interconnected vascular tube networks as well as the recruitment of pericytes to initiate vascular tube maturation (via basement membrane matrix assembly) and stabilization. Current research continues to analyze how specific molecules integrate signaling information in concert to catalyze EC lumen formation, pericyte recruitment, and stabilization processes to control vascular morphogenesis in 3D extracellular matrices. Birth Defects Research (Part C) 81:270–285, 2007. © 2008 Wiley‐Liss, Inc.
Variation and robustness of the mechanics of gastrulation: The role of tissue mechanical properties during morphogenesis
Authors: von Dassow Michelangelo , Davidson Lance A. 
Published: January 2008

AbstractDiverse mechanisms of morphogenesis generate a wide variety of animal forms. In this work, we discuss two ways that the mechanical properties of embryonic tissues could guide one of the earliest morphogenetic movements in animals, gastrulation. First, morphogenetic movements are a function of both the forces generated by cells and the mechanical properties of the tissues. Second, cells could change their behavior in response to their mechanical environment. Theoretical studies of gastrulation indicate that different morphogenetic mechanisms differ in their inherent sensitivity to tissue mechanical properties. Those few empirical studies that have investigated the mechanical properties of amphibian and echinoderm gastrula‐stage embryos indicate that there could be high embryo‐to‐embryo variability in tissue stiffness. Such high embryo‐to‐embryo variability would imply that gastrulation is fairly robust to variation in tissue stiffness. Cell culture studies demonstrate a wide variety of cellular responses to the mechanical properties of their microenvironment. These responses are likely to be developmentally regulated, and could either increase or decrease the robustness of gastrulation movements depending on which cells express which responses. Hence both passive physical and mechanoregulatory processes will determine how sensitive gastrulation is to tissue mechanics. Addressing these questions is important for understanding the significance of diverse programs of early development, and how genetic or environmental perturbations influence development. We discuss methods for measuring embryo‐to‐embryo variability in tissue mechanics, and for experimentally perturbing those mechanical properties to determine the sensitivity of gastrulation to tissue mechanics. Birth Defects Research (Part C) 81:253–269, 2007. © 2008 Wiley‐Liss, Inc.
Cellular mechanobiology and cancer metastasis
Authors: Makale Milan 
Published: January 2008

AbstractThe primary cause of cancer treatment failure is invasion and metastasis, and invading tumor cells utilize many of the motility patterns that have been documented for normal morphogenesis. Recently, the role of mechanical forces in guiding various tissue and cell movements in embryonic development has been systematically analyzed with new experimental and computational methods. The tissue and cellular mechanobiology approach also holds promise for increasing the understanding of tumor invasion. In fact, the mechanical stiffness of tumors has correlated with invasiveness, and manipulation of extracellular matrix (ECM) stiffness in vitro has suppressed the cancer phenotype. Several important signaling molecules reside on the cytoskeleton, which is affected by external stress imparted by the ECM, and deformation of the nucleus can trigger the activation of certain genes. All these observations suggest that a synthesis of the biology of cancer cell invasion and cellular mechanobiology may offer new targets for the treatment of malignant disease. Accordingly, sensitive and relevant in vivo models and methods to study cancer mechanobiology are needed. Birth Defects Research (Part C) 81:329–343, 2007. © 2008 Wiley‐Liss, Inc.
New insights into elastic fiber assembly
Authors: Wagenseil Jessica E. , Mecham Robert P. 
Published: January 2008

AbstractElastic fibers provide recoil to tissues that undergo repeated stretch, such as the large arteries and lung. These large extracellular matrix (ECM) structures contain numerous components, and our understanding of elastic fiber assembly is changing as we learn more about the various molecules associated with the assembly process. The main components of elastic fibers are elastin and microfibrils. Elastin makes up the bulk of the mature fiber and is encoded by a single gene. Microfibrils consist mainly of fibrillin, but also contain or associate with proteins such as microfibril associated glycoproteins (MAGPs), fibulins, and EMILIN‐1. Microfibrils were thought to facilitate alignment of elastin monomers prior to cross‐linking by lysyl oxidase (LOX). We now know that their role, as well as the overall assembly process, is more complex. Elastic fiber formation involves elaborate spatial and temporal regulation of all of the involved proteins and is difficult to recapitulate in adult tissues. This report summarizes the known interactions between elastin and the microfibrillar proteins and their role in elastic fiber assembly based on in vitro studies and evidence from knockout mice. We also propose a model of elastic fiber assembly based on the current data that incorporates interactions between elastin, LOXs, fibulins and the microfibril, as well as the pivotal role played by cells in structuring the final functional fiber. Birth Defects Research (Part C) 81:229–240, 2007. © 2008 Wiley‐Liss, Inc.
Activator‐inhibitor dynamics of vertebrate limb pattern formation
Authors: Newman Stuart A. , Bhat Ramray 
Published: January 2008

AbstractThe development of the vertebrate limb depends on an interplay of cellular differentiation, pattern formation, and tissue morphogenesis on multiple spatial and temporal scales. While numerous gene products have been described that participate in, and influence, the generation of the limb skeletal pattern, an understanding of the most salient feature of the developing limb—its quasiperiodic arrangement of bones, requires additional organizational principles. We review several such principles, drawing on concepts of physics and chemical dynamics along with molecular genetics and cell biology. First, a “core mechanism” for precartilage mesenchymal condensation is described, based on positive autoregulation of the morphogen transforming growth factor (TGF)‐β, induction of the extracellular matrix (ECM) protein fibronectin, and focal accumulation of cells via haptotaxis. This core mechanism is shown to be part of a local autoactivation‐lateral inhibition (LALI) system that ensures that the condensations will be regularly spaced. Next, a “bare‐bones” model for limb development is described in which the LALI‐core mechanism is placed in a growing geometric framework with predifferentiated “apical,” differentiating “active,” and irreversibly differentiated “frozen” zones defined by distance from an apical source of a fibroblast growth factor (FGF)‐type morphogen. This model is shown to account for classic features of the developing limb, including the proximodistal (PD) emergence over time of increasing numbers of bones. We review earlier and recent work suggesting that the inhibitory component of the LALI system for condensation may not be a diffusible morphogen, and propose an alternative mechanism for lateral inhibition, based on synchronization of oscillations of a Hes mediator of the Notch signaling pathway. Finally, we discuss how viewing development as an interplay between molecular‐genetic and dynamic physical processes can provide new insight into the origin of congenital anomalies. Birth Defects Research (Part C) 81:305–319, 2007. © 2008 Wiley‐Liss, Inc.
Ingression of primary mesenchyme cells of the sea urchin embryo: A precisely timed epithelial mesenchymal transition
Authors: Wu Shu‐Yu , Ferkowicz Michael , McClay David R. 
Published: January 2008

AbstractEpithelial‐mesenchyme transitions (EMTs) are familiar to all scholars of development. Each animal system utilizes an EMT to produce mesenchyme cells. In vertebrates, for example, there are a number of EMTs that shape the embryo. Early, entry of epiblast cells into the primitive streak is followed by the emergence of mesoderm via an EMT process. The departure of neural crest cells from the margin of the neural folds is an EMT process, and the delamination of cells from the endomesoderm to form the supporting mesenchyme of the lung, liver, and pancreas are EMTs. EMTs are observed in Drosophila following invagination of the ventral furrow, and even in Cnidarians, which have only two germ layers, yet mesoglial and stem cells delaminate from the epithelia and occupy the matrix between the ectoderm and endoderm. This review will focus on a classic example of an EMT, which occurs in the sea urchin embryo. The primary mesenchyme cells (PMCs) ingress from the vegetal plate of this embryo precociously and in advance of archenteron invagination. Because ingression is precisely timed, the PMC lineage precisely known, and the embryo easily observed and manipulated, much has been learned about how the ingression of PMCs works in the sea urchin. Though the focus of this review is the sea urchin PMCs, there is evidence that all EMTs share many common features at both cellular and molecular levels, and many of these mechanisms are also shown to be involved in tumor progression, especially metastasizing carcinomas. Birth Defects Research (Part C) 81:241–252, 2007. © 2008 Wiley‐Liss, Inc.
Yeast as a model for studying human neurodegenerative disorders
Authors: Miller‐Fleming Leonor , Giorgini Flaviano , Outeiro Tiago F. 
Published: January 2008

AbstractProtein misfolding and aggregation are central events in many disorders including several neurodegenerative diseases. This suggests that alterations in normal protein homeostasis may contribute to pathogenesis, but the exact molecular mechanisms involved are still poorly understood. The budding yeast Saccharomyces cerevisiae is one of the model systems of choice for studies in molecular medicine. Modeling human neurodegenerative diseases in this simple organism has already shown the incredible power of yeast to unravel the complex mechanisms and pathways underlying these pathologies. Indeed, this work has led to the identification of several potential therapeutic targets and drugs for many diseases, including the neurodegenerative diseases. Several features associated with these diseases, such as formation of protein aggregates, cellular toxicity mediated by misfolded proteins, oxidative stress and hallmarks of apoptosis have been faithfully recapitulated in yeast, enabling researchers to take advantage of this powerful model to rapidly perform genetic and compound screens with the aim of identifying novel candidate therapeutic targets and drugs. Here we review the work undertaken to model human brain disorders in yeast, and how these models provide insight into novel therapeutic approaches for these diseases.
Using a commercial DNA extraction kit to obtain RNA for RT‐PCR from starchy rice endosperm
Authors: Belefant‐Miller Helen , Ledbetter Cindy , Bennett Selester 
Published: January 2008

AbstractThe extraction of RNA from a starchy plant material, such as many common food grains, is difficult, and especially so from the mature endosperm of rice. Most commercial RNA kits are not suitable for starchy materials. Traditional RNA extraction procedures, in addition to being laborious and time consuming, leave hazardous organic wastes that result in expensive disposal costs. Interestingly, the numerous commercial DNA isolation kits now available often include directions for eliminating co‐isolated RNA. This indicated an approach to obtain the generally unwanted RNA by‐product by treating the total extraction product to intentionally retain RNA. A method was developed by which a two‐step DNase procedure was applied to the product of the Cartagen Food DNA extraction kit that eliminated the DNA but left the co‐extracted RNA. This modified procedure was compared with several other commercial and standard methods that are promoted as being able to work under high polysaccharide conditions. Successful extraction was determined by the production and amplification of cDNA by RT‐PCR of actin. Extraction was successful from milled rice, as well as from cornmeal and wheat flour. The modification provides an RNA extraction method that is quick, easy, and inexpensive, and also eliminates the production of hazardous wastes.
A General Concept for the Preparation of Hierarchically Structured π‐Conjugated Polymers
Authors: Frauenrath Holger , Jahnke Eike 
Published: January 2008

AbstractTypical biopolymers exhibit structures and order on different length scales. By contrast, the number of synthetic polymers with a similar degree of hierarchical structure formation is still limited. Starting from recent investigations on the structures of amyloid proteins as well as research activities toward nanoscopic scaffolds from synthetic oligopeptides and their polymer conjugates, a general strategy toward hierarchically structured π‐conjugated polymers can be developed. The approach relies on the supramolecular self‐assembly of diacetylene macromonomers based on β‐sheet forming oligopeptides equipped with hydrophobic polymer segments. Polymerization of these macromonomers proceeds under retention of the previously assembled hierarchical structure and yields π‐conjugated polymers with multi‐stranded, multiple‐helical quaternary structures.
Selective Gas Adsorption and Unique Structural Topology of a Highly Stable Guest‐Free Zeolite‐Type MOF Material with N‐rich Chiral Open Channels
Authors: Li Jian‐Rong , Tao Ying , Yu Qun , Bu Xian‐He , Sakamoto Hirotoshi , Kitagawa Susumu 
Published: January 2008

AbstractA new multifunctional di‐topic tetrazolate‐based ligand, 2,3‐di‐1H‐tetrazol‐5‐ylpyrazine (H2dtp) has been designed and synthesized. The solvothermal reaction of this ligand with ZnCl2 gave a robust guest‐free three‐dimensional zeolite‐like chiral metal‐organic framework (MOF) complex, [Zn(dtp)], which crystallized in chiral space group P61 and possessed chiral open channels with nitrogen‐rich walls and the diameter of approximately 4.1 Å. This framework presents a unique uniform etd (8,3) topology, is the first example of its type in MOFs, and exhibits high thermal stability with the decomposition temperature above 380 °C and permanent porosity. It is interesting that this material is able to selectively adsorb O2 and CO2 over N2 gas, being a rare example in MOFs. In addition, C2H2 and MeOH adsorption results show that although the framework channel holds nitrogen‐rich walls that may provide H‐bonding sites, no N⋅⋅⋅H H‐bond effect between the guest molecules and microporous surface was observed.
Reactive Sieving with Foldamers: Inspiration from Nature and Directions for the Future
Authors: Smaldone Ronald A. , Moore Jeffrey S. 
Published: January 2008

AbstractOver the past several decades, chemists have designed a myriad of supramolecular scaffolds for the purpose of mimicking enzyme behavior and creating more advanced catalysts. Foldamers, one class of supramolecular structures that feature rapid, modular synthesis and dynamic structural properties and have been widely investigated for their molecular recognition properties. Specifically, our group has designed a reactive m‐phenyleneethynylene foldamer, which mimics the selective properties (“reactive sieving”) of the isoleucine tRNA synthetase enzyme. In this concept we discuss examples that have inspired our research as well as potential directions for future advancement of this field.
Synthesis, Evaluation, and Computational Studies of Naphthalimide‐Based Long‐Wavelength Fluorescent Boronic Acid Reporters
Authors: Jin Shan , Wang Junfeng , Li Minyong , Wang Binghe 
Published: January 2008

AbstractBoronic acids that change fluorescence properties upon sugar binding are very useful for the synthesis of carbohydrate sensors. Along this line, boronic acids that fluoresce beyond 500 nm are especially useful. A series of boronic acid fluorescent reporter compounds based on the 4‐amino‐1,8‐naphthalimide structure have been synthesized (1 a–d) and evaluated under near physiological conditions. These compounds showed good water solubility and significant changes in fluorescence properties after binding with sugars, with the emission wavelength being at around 570 nm. Analogues in this series with different substitutions showed similar properties. We have also examined the mechanism of the observed fluorescence changes for these compounds.