Solving dynamical inverse problems by means of Metabolic P systems.

MP (Metabolic P) systems are a class of P systems introduced for modelling metabolic processes. We refer to the dynamical inverse problem as the problem of identifying (discrete) mathematical models exhibiting an observed dynamics. In this paper, we complete the definition of the algorithm LGSS (Log-gain Stoichiometric Stepwise regression) introduced in Manca and Marchetti (2011) for solving a general class of dynamical inverse problems. To this aim, we develop a reformulation of the classical stepwise regression in the context of MP systems. We conclude with a short review of two applications of LGSS for discovering the internal regulation logic of two phenomena relevant in systems biology.

Predator-prey dynamics in P systems ruled by metabolic algorithm.

P systems are used to compute predator-prey dynamics expressed in the traditional formulation by Lotka and Volterra. By governing the action of the transition rules in such systems using the regulatory features of the metabolic algorithm we come up with simulations of the Lotka-Volterra equations, whose robustness is comparable to that obtained using Runge-Kutta schemes and Gillespie's Stochastic Simulation Algorithm. Besides their reliability, the results obtained using the metabolic algorithm on top of P systems have a clear biochemical interpretation concerning the role, of reactants or promoters, of the species involved.

New computing paradigms suggested by DNA computing: computing by carving.

Inspired by the experiments in the emerging area of DNA computing, a somewhat unusual type of computation strategy was recently proposed by one of us: to generate a (large) set of candidate solutions of a problem, then remove the non-solutions such that what remains is the set of solutions. This has been called a computation by carving. This idea leads both to a speculation with possible important consequences--computing non-recursively enumerable languages--and to interesting theoretical computer science (formal language) questions.

Linear IgA bullous dermatosis with autoantibodies to a 290 kd antigen of anchoring fibrils.

We describe a patient with a papulovesicular eruption associated with scarring and severe mucosal lesions that led to blindness. Direct immunofluorescence showed linear IgA deposits at the dermoepidermal junction. Indirect immunofluorescence microscopy showed that the patient's serum reacted with the dermal side of salt-split skin. Direct immunoelectron microscopy showed the IgA deposits to be associated with anchoring fibrils, whereas with Western blot analysis the patient's serum reacted with a 290 kd dermal antigen. On the basis of these findings, we suggest that our case may represent a form of IgA-mediated epidermolysis bullosa acquisita.

Beta-1 integrins in the normal human glomerular capillary wall: an immunoelectron microscopy study.

The localization of the alpha 2, alpha 3 and alpha 6 subunits of the beta 1 integrin family on different cells of the glomerular capillary wall and on juxta-capillary mesangium was investigated using an immunoelectron microscopic technique on freshly harvested normal human glomeruli. Alpha 2 beta 1, alpha 3 beta 1 and alpha 6 beta 1 were weakly expressed on both luminal and abluminal surfaces of glomerular endothelial cells; alpha 2 beta 1 and alpha 3 beta 1 were also found on the mesangium of the juxta-capillary areas. Alpha 3 beta 1 was regularly present in great density on the basal and lateral surface of podocyte foot processes, confirming alpha 3 beta 1 as the unique beta 1 integrin on glomerular epithelial cells. None of these integrins was strictly polarized along the glomerular basement membrane, thus suggesting, in agreement with recent literature, that these molecules perform other biological functions in addition to adhesivity.

Distinctive integrin expression in the newly forming epidermis during wound healing in humans.

The integrin receptor family plays a fundamental role in mediating cell attachment to a variety of extracellular matrix molecules. In normal human epidermis, the alpha 2 beta 1, alpha 3 beta 1, alpha 6 beta 4, and alpha v beta 5 integrin heterodimers are expressed and appear largely confined to the basal cell layer. In the present study, beta 1, beta 4, and alpha v integrin expression in the epidermis during wound healing in humans was examined. Punch biopsies were performed on healthy volunteers. At daily intervals up to day 8, and at days 11, 14, 21, and 28, the wound site was surgically removed. Using immunofluorescence microscopy, several modifications of the integrin expression pattern were observed on migrating keratinocytes during the re-epithelialization phase of the wound-healing process: i) alpha v expression was strongly enhanced and polarized at the basal pole of basal keratinocytes; ii) among the beta 1 integrins, alpha 3 beta 1 was overexpressed and distributed over the entire basal keratinocyte membrane and a weak alpha 5 beta 1 reactivity became evident; and iii) alpha 6 beta 4 was detected as a linear staining along the newly forming dermal-epidermal junction. Moreover, both during the re-epithelialization phase and during the first 2 weeks after wound closure, alpha 3, alpha 6, alpha v, beta 1, and beta 4 were no longer confined to the basal layer, as in normal epidermis, but were also found on several suprabasal cell layers. These results suggest that alpha v beta 5, alpha 3 beta 1, and alpha 5 beta 1 may be the main integrin receptors mediating keratinocyte spreading and migration over the provisional matrix of the wound bed.

Spleen dendritic cells exhibit altered morphology and increased allostimulatory capacity after short-term culture.

Ia-bearing dendritic cells (DC) are a class of bone marrow-derived antigen-presenting cells that appear to possess an increased capacity to stimulate resting T lymphocytes. DC from different tissues share several morphologic, phenotypic and functional attributes. For example, freshly isolated DC from spleen resemble phenotypically and functionally freshly isolated Langerhans cells (LC) from epidermis; in addition, during short-term culture both DC and LC undergo several parallel changes including modifications affecting phenotype, capacity to present protein antigens, and ability to route surface Ia molecules into intracellular acidic compartments (J Immunol 1990: 145: 2820-2826). In the present study we show, using immunoelectron microscopy with anti-Ia and anti-33D1 monoclonal antibodies, freshly isolated DC in suspension to have a smooth cell surface with few and short cytoplasmic projections. By contrast, cultured DC display conspicuous bulbous cytoplasmic protrusions. In addition, spleen DC following culture for 24-48 hours exhibit an increased ability to stimulated allogeneic T lymphocytes in the primary mixed leukocyte reaction. These changes, similar to those described for freshly isolated and cultured LC respectively, further substantiate the close relationship between DC and LC.

Epidermal Langerhans cells after allogeneic bone marrow transplantation: depletion by chemotherapy conditioning regimen alone.

Depletion of Langerhans cells (LC) is known to follow bone marrow transplantation (BMT) and is thought to be mainly related to pretransplant radiation and chemotherapy conditioning regimens. We studied sequential biopsies of clinically normal skin of 22 thalassemic and leukemic patients undergoing allogeneic BMT who had received only chemotherapy (busulfan and cyclophosphamide) as conditioning regimen. LC were identified immunohistochemically using antibodies against CD1a and HLA-DR antigens, and their number expressed per square mm of epidermal vertical section, the latter measured by computerized image analysis. After the preparatory regimen, the number of LC decreased progressively in both leukemic and thalassemic patients. CD1a+ and HLA-DR+ epidermal cells were reduced, respectively, to 68.5% and 64.5% of their original number around Day 2, and to 23.1% and to 18.2% around Day 17. By this time, electron microscopic examination of selected biopsies confirmed the depletion of LC. Variable repopulation was observed between Days 40 and 60. Our results indicate that a conditioning regimen based exclusively on high dose chemotherapy depletes epidermal LC early after BMT, and that such depletion is not related to the development of acute graft-versus-host disease.

VLA protein expression on epidermal cells (keratinocytes, Langerhans cells, melanocytes): a light and electron microscopic immunohistochemical study.

The very late antigens, or VLA proteins, are a family of cell surface heterodimers (alpha 1-b beta 1) that mediate cell adhesion to specific components of the extracellular matrix (collagens, fibronectin, laminin). In normal human epidermis, the common VLA beta 1 subunit is expressed on basal keratinocytes (BK). Langerhans cells (LC) and melanocytes. By means of light and electron microscopic immunostaining procedures, we have investigated the distribution of VLA alpha 1,2,3,4,6 subunits on normal human adult and foetal epidermal cells. alpha 1 antigen expression was not observed on any epidermal cell type. Both during foetal development and in adult epidermis, alpha 2 and alpha 3 were strongly expressed on the cell membrane BK, while alpha 6 was mainly expressed at their dermal pole. These different patterns of distribution suggest that the alpha 6 subunit may mediate BK anchorage to the basement membrane zone, while the alpha 2 and alpha 3 subunits may also be involved in intracellular adhesion. Moreover, with immunoelectron microscopy, LC were seen to be weakly alpha 5 and alpha 6 positive and melanocytes were alpha 3 and alpha 6 positive. Thus, VLA proteins are expressed by epidermal cells in a cell-type-specific pattern that could be related to particular functional roles of these proteins.

[Adhesion molecules in the skin: distribution, biological role and physiopathological implications of integrins]. / Le molecole di adesione nella cute. Distribuzione, ruolo biologico ed implicazioni fisiopatologiche delle integrine.

Cell-cell and cell-substratum interactions are mediated by surface glycoproteins, members of the vast family of "adhesion molecules". These cellular receptors influence many biological processes, including cell-substratum adhesion phenomena, cellular migration during embryogenesis, haemostasis and immune reactions. Among these molecules, in the last few years the integrin family has been extensively studied. Integrins are widely distributed on several cell types, and are also present in the skin with distinct extracellular binding specificities. In the skin, the various members of this family play multiple functions, intervening in keratinocyte adhesion to the basement membrane, in the maintenance of cell polarity, in inflammatory processes and during wound healing.

Oral hairy leukoplakia in AIDS patients: an ultrastructural study.

Hairy leukoplakia is a specific oral lesion associated with the opportunistic development of Epstein-Barr virus in the oral epithelium. It is now considered to be an early sign of HIV-induced immunosuppression. Four cases of oral hairy leukoplakia (OHL) from the lateral borders of the tongue of male AIDS patients were investigated by transmission electron microscopy. At the ultrastructural level, herpes-like viral particles were detected in the oral lesions of all cases. Indirect immunofluorescence performed on two cases showed the presence of EBV antigens in the nuclei and the cytoplasm of the infected epithelial cells. None of the specimens contained ultrastructural evidence of human papillomaviruses.

Ultrastructural study of the skin in a case of juvenile ceroid-lipofuscinosis.

Ceroid-lipofuscinosis (CL) is a neurometabolic disorder due to an as yet unknown enzymatic deficiency. The electron-microscopic study of various organs shows a storage of a lipofuscin-like material. The ultrastructural study of clinically uninvolved skin in a typical case of juvenile CL is reported. Granular osmiophilic deposits were found in several cell types in the dermis, including fibroblasts, endothelial cells, macrophages, Schwann cells, pericytes, and muscle cells. Neither fingerprint nor curvilinear profiles could be observed. These findings demonstrate the involvement of clinically normal skin in CL and confirm the usefulness of the EM study of the skin in the diagnosis of this rare disorder.

[Prolonged preservation of venous allografts for vascular access in hemodialysis]. / Conservation prolongée d'allogreffes veineuses pour les abords vasculaires en hémodialyse.

The technique of deep-freezing in liquid nitrogen of stripped saphenous veins permitted their long-term preservation, and the subsequent creation of a "bank" of venous allografts, used for arteriovenous internal shunts for hemodialysis. Histological, histochemical and immunological tests, and first clinical results have been favorable.

Epidermal growth factor and transferrin receptor expression in human embryonic and fetal epidermal cells.

Epidermal growth factor receptors (EGFR) and transferrin receptors (TFR) are known to be involved in cell proliferation and to be expressed in normal human epidermis. To date little is known about EGFR and TRF expression in human skin during embryonic and fetal development. In the present work, we studied skin specimens from 30 aborted embryos and fetuses ranging from 7 to 31 weeks estimated gestational age. Monoclonal antibodies to EGFR and TFR were applied on frozen skin sections using an amplification biotin-streptavidin-fluorescein technique. TFR was faintly expressed on epidermal basal cells throughout embryonic and fetal development, as it is in adult epidermis. Up to week 12, EGFR was uniformly expressed on cells of the basal, intermediate and periderm cell layers. From the midfetal period onwards, the suprabasal cell layers showed a decreased staining compared with the basal layer. During the third trimester the cornified cell layer was completely negative. The hair germ and heir peg cells were positive. Later, the outer root sheath and hair bulb remained labelled, with less staining of the hair cone. The sebaceous and eccrine sweat glands were also labelled. These results suggest that in embryonic and fetal epidermis, TFR expression is not correlated with cellular proliferation, whereas EGFR appear to be associated with proliferating and undifferentiated cells.

Absence of rejection in cryopreserved saphenous vein allografts for hemodialysis.

Since November 1987, a total of 16 dialysis patients in the authors' Center, received a cryopreserved saphenous vein allograft (CSVA) as "third choice" vascular access. ABO and HLA-A-B compatibilities were determined but not considered. Saphenous veins were cryopreserved in liquid nitrogen for variable periods (1-6 mo), so that there was the opportunity to choose the most suitable in dimension. In February, 1989, a total of 13 patients retained a well-functioning access site, whereas three had died from causes unrelated to CSVA. Because rejection of venous allografts still is debated among angiologists, recipient T lymphocyte subsets (CD3-CD4-CD8 and CD4/8) were examined, as were lymphocytotoxic antibodies, before and on days 15 and 30 after implantation. No evidence of immunologic activation was found. Moreover, in 10 of 16 patients the surgeons subcutaneously implanted a fragment of CSVA, and an immunohistochemical study was carried out using an alkaline phosphatase-antialkaline phosphatase (APAAP) technique and a panel of monoclonal antibodies. Minimal infiltration of the outer layer of adventitia was found, mainly caused by monocyte macrophages (Leu M3+) with few T lymphocytes (CD3+). The authors conclude that rejection is not a major cause of failure in CSVA in dialysis patients.

Single-dose relative biological effectiveness and toxicity studies under conditions of hypothermia and hyperbaric oxygen.

An approach to using hyperbaric oxygen with radiation in a clinical situation has been described in the preceding paper in this issue. To ascertain whether there might be a change in the relative biological effectiveness of radiation on normal mammalian tissue treated under conditions of hypothermia and hyperbaric oxygen, the acute reaction to radiation of pig skin was studied. A single dose enhancement ratio at the erythema reaction level of 1.4 +/- 0.08 was obtained when compared with irradiation at normal body temperature in air. We studied also a series of antioxidant enzymes in rat liver and lung after exposure to hypothermia and hyperbaric oxygen. Enzyme changes were such as to combat oxygen toxicity which might develop as a result of the pre-treatment.

Influence of two haloalkanes on the redox behavior of hepatic microsomal cytochrome b-5 and its possible relationship to stearate desaturase.

The possible interaction of two haloalkanes - bromotrichloromethane and 1,2-dibromo-1,2-dichlorethane - with stearate desaturase was assessed in hepatic microsomes from rats fed a high carbohydrate diet which elevates the levels of stearate desaturase. Both compounds shifted the redox steady state of NADPH reduced hepatic microsomal cytochrome b-5 towards ferricytochrome b-5 and enhanced the re-oxidation of NADH reduced hepatic microsomal cytochrome b-5. The equilibrium constants for the enhancement of microsomal electron transfer by the haloalkanes in these preparations were 2.2 +/- 0.3 mM and 0.46 +/- 0.1 mM for bromotrichloromethane and 1,2-dibromo-1,2-dichlorethane, respectively. The haloalkane mediated enhancement of the oxidation of cytochrome b-5 in hepatic microsomes from rats fed a high carbohydrate diet was diminished by KCN and the inhibitors of cytochrome P-450, CO and/or metyrapone, as well as by fasting of the experimental animals. The I50 values for KCN inhibition of the effects of the haloalkanes on the re-oxidation of cytochrome b-5 (01 mM) were identical to the I50 for KCN inhibition of stearate desaturase (Oshino et al., 1966). The haloalkanes did not affect the activity of hepatic microsomal NADH- or NADPH-cytochrome c reductase, the autoxidation of purified trypsin-cleaved ferrocytochrome b-5 or the conversion of stearoyl CoA to oleate. It is concluded that bromotrichloromethane and 1,2-dibromo-1,2-dichloroethane stimulate hepatic microsomal electron transfer from NADH via cytochrome b-5 by interacting with cytochrome P-450 and with stearate desaturase.