Numerical Simulations and Long-Column Tests of LNAPL Displacement and Trapping by a Fluctuating Water Table

Long-column laboratory tests were performed to validate improvements to the MOFAT program for simulating LNAPL displacement and entrapment in response to a fluctuating water table. The long-column tests consisted of a fluctuating water table and its subsequent displacement and entrapment of an LNAPL. The modifications of MOFAT include a linear LNAPL trapping estimate and a new scaling technique for the inhibition portion of the fluctuation (water table rise). Improved prediction of the LNAPL trapping was obtained by assuming the amount of LNAPL that is trapped by a rising water table is proportional to the antecedent water content of the porous medium. The pressure-saturation relationship for the air-water drainage system was scaled to estimate the LNAPL-water and air-LNAPL drainage relationships. Scaled inhibition pressure-saturation relationships are improved by incorporating a correction for contact angle hysteresis and surface roughness. The incorporation of these changes into MOFAT led to noticable improvements in the numerical simulation of the experimental data.     

Mesoscale Modeling of Amphiphilic Fluid Dynamics

Abstract

So-called “vector models”, in which surfactant molecules retain only translational and orientational degrees of freedom, have been used to study the equilibrium properties of amphiphilic fluids for nearly a decade now. We demonstrate that hydrodynamic lattice-gas automata provide an effective means of coupling the Hamiltonian of such vector models to hydrodynamic flow with conserved momentum, thereby providing a self-consistent treatment of the hydrodynamics of amphiphilic fluids. In this “talk”, we describe these hydrodynamic lattice-gas models in two and three dimensions, and present their application to problems of amphiphilic-fluid hydrodynamics, including the dynamics of phase separation and the shear-induced sponge-to-lamellar phase transition.     

Mechanobiology of neural development

As the brain develops, proliferating cells organize into structures, differentiate, migrate, extrude long processes, and connect with other cells. These biological processes produce mechanical forces that further shape cellular dynamics and organ patterning. A major unanswered question in developmental biology is how the mechanical forces produced during development are detected and transduced by cells to impact biochemical and genetic programs of development. This gap in knowledge stems from a lack of understanding of the molecular players of cellular mechanics and an absence of techniques for measuring and manipulating mechanical forces in tissue. In this review article, we examine recent advances that are beginning to clear these bottlenecks and highlight results from new approaches that reveal the role of mechanical forces in neurodevelopmental processes.     

Proximal fluid proteomics for the discovery of digestive cancer biomarkers

Most digestive malignancies have asymptomatic course, often progressing to poor outcome stages. Surgical resection usually represents the only potentially curative option but a prior assumption of the malignant nature of the lesion is mandatory to avoid exposing patients to unnecessary risks. Unfortunately, currently available diagnostic tools lack accuracy in many cases, consequently more reliable markers are needed to improve detection of malignant lesions. In this challenging context, fluids surrounding digestive malignancies represent a valuable source for the search of new potential biomarkers and proteomic tools offer the opportunity to achieve this goal. The new field of proximal fluid proteomics is thus emerging in the arena of digestive cancer biomarker discovery.     

Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling

Cellular biomolecular complexes including protein–protein, protein–RNA, and protein–DNA interactions regulate and execute most biological functions. In particular in brain, protein–protein interactions (PPIs) mediate or regulate virtually all nerve cell functions, such as neurotransmission, cell–cell communication, neurogenesis, synaptogenesis, and synaptic plasticity. Perturbations of PPIs in specific subsets of neurons and glia are thought to underly a majority of neurobiological disorders. Therefore, understanding biological functions at a cellular level requires a reasonably complete catalog of all physical interactions between proteins. An enzyme-catalyzed method to biotinylate proximal interacting proteins within 10 to 300 nm of each other is being increasingly used to characterize the spatiotemporal features of complex PPIs in brain. Thus, proximity labeling has emerged recently as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and PPIs in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte–neuron junctions. In this review, we summarize recent advances in proximity labeling methods and their application to neurobiology.     

A Cysteine Endopeptidase (“Dionain”) Is Involved in the Digestive Fluid of Dionaea muscipula (Venus’s Fly-trap)

The carnivorous plant Dionaea muscipula (Venus’s flytrap) secretes proteinases into the digestive fluid to digest prey proteins. In this study, we obtained evidence that the digestive fluid contains a cysteine endopeptidase, presumably belonging to the papain family, through inhibitor studies and partial amino acid sequencing of the major SDS–PAGE band protein. The name “dionain” is proposed for the enzyme.     

Fluid–structure interaction analysis of the left coronary artery with variable angulation

The aim of this study is to elucidate the correlation between coronary artery branch angulation, local mechanical and haemodynamic forces at the vicinity of bifurcation. Using a coupled fluid–structure interaction (FSI) modelling approach, five idealized left coronary artery models with various angles ranging from 70° to 110° were developed to investigate the influence of branch angulations. In addition, one CT image-based model was reconstructed to further demonstrate the medical application potential of the proposed FSI coupling method. The results show that the angulation strongly alters its mechanical stress distribution, and the instantaneous wall shear stress distributions are substantially moderated by the arterial wall compliance. As high tensile stress is hypothesized to cause stenosis, the left circumflex side bifurcation shoulder is indicated to induce atherosclerotic changes with a high tendency for wide-angled models.     

Adaptations for matrotrophy in the female reproductive system in the pseudoscorpion Chelifer cancroides (Chelicerata: Pseudoscorpiones,Cheliferidae)

Pseudoscorpiones (pseudoscorpions, false scorpions) is an order of small terrestrial chelicerates. While most chelicerates are lecithotrophic, that is, embryos develop due to nutrients (mostly yolk) deposited in the oocyte cytoplasm, pseudoscorpions are matrotrophic, that is, embryos are nourished by the female. Pseudoscorpion oocytes contain only a small amount of yolk. The embryos develop within a brood sac carried on the abdominal site of the female and absorb nutrients by a pumping organ. It is believed that in pseudoscorpions nutrients for developing embryos are produced in the ovary during a postovulatory (secretory) phase of the ovarian cycle. The goal of our study was to analyze the structure of the female reproductive system during the secretory phase in the pseudoscorpion Chelifer cancroides, a representative of the family Cheliferidae, considered to be one of the most advanced pseudoscorpion taxa. We use diverse microscopic techniques to document that the nutritive fluid is produced not only in the ovaries but also by the epithelial cells in the oviducts. The secretory active epithelial cells are hypertrophic and polyploid and release their content by fragmentation of apical parts. Our observations also indicate that fertilization occurs in the oviducts. Moreover, in contrast to previous findings, we show that secretion of the nutritive material starts when the fertilized oocytes reach the brood sac and thus precedes formation of the pumping organ. Summing up, we show that C. cancroides exhibits traits of advanced adaptations for matrotrophy due to coordinated secretion of the nutritive fluid by the ovarian and oviductal epithelial cells, which substantially increases the efficiency of nutritive fluid formation. Since the secretion of nutrients starts before formation of the pumping organ, we suggest that the embryos are able to absorb the nutritive fluid also in the early embryonic stages.     

Modulation of gamete and embryonic microenvironments by oviduct glycoproteins

Studies on protein molecules in oviduct luminal fluid are viewed historically, and then in terms of more recent studies on a possible involvement of unique glycoproteins in embryonic development. As a caution, however, it is noted that incorporation of such molecules into the vitellus may be nonspecific. The question is raised as to whether oviduct glycoproteins could be acting primarily in a physical sense to stabilize differing chemical environments along the oviduct. Equally or more importantly, glycoproteins might be acting as carrier molecules to present cations and metabolic substrates at appropriate concentrations to the vitelline membrane. This latter possibility is examined in some detail and could be tested by manipulating the composition of the perivitelline fluid. Glycoproteins may also be critically involved in regulating the physiological competence of spermatozoa in the pre- and peri-ovulatory oviduct, in maintaining a coordinated pattern of cilial beat, and in immunosuppressive functions within the oviduct, not least in those associated with the masking of paternal antigens on both spermatozoa and embryos. © 1994 Wiley-Liss, Inc.