Network organization in health and disease: on being a reductionist and a systems biologist too

Whereas the challenge for traditional mechanistic science was to identify parts and operations, the current challenge in many fields of biology is to understand how the many parts of mechanisms are organized in networks and their operations coordinated across these networks. This paper explores how tools from graph theory are enabling analysis of organization at both macro- and micro-levels. In applying these approaches to brain regions, systems neuroscientists are identifying both small-world organization with hubs at the macro-scale and frequently occurring subgraphs that link specific brain regions at a more micro-scale. This has lead to the discovery of networks in which activity in multiple brain regions exhibits coherent oscillations and demonstrations that these networks are disrupted in various mental disorders.

The class III phosphatidylinositol 3-kinase PIK3C3/VPS34 regulates endocytosis and autophagosome-autolysosome formation in podocytes

Phosphatidylinositol phosphates are key regulators of vesicle identity, formation and trafficking. In mammalian cells, the evolutionarily conserved class III PtdIns 3-kinase PIK3C3/VPS34 is part of a large multiprotein complex that catalyzes the localized phosphorylation of phosphatidylinositol to phosphatidylinositol-3-phosphate (PtdIns3P). We demonstrate that PIK3C3 has a key function in vesicular trafficking, endocytosis and autophagosome-autolysosome formation in the highly specialized glomerular podocytes.

Vps34 deficiency reveals the importance of endocytosis for podocyte homeostasis

The molecular mechanisms that maintain podocytes and consequently, the integrity of the glomerular filtration barrier are incompletely understood. Here, we show that the class III phosphoinositide 3-kinase vacuolar protein sorting 34 (Vps34) plays a central role in modulating endocytic pathways, maintaining podocyte homeostasis. In mice, podocyte-specific conditional knockout of Vps34 led to early proteinuria, glomerular scarring, and death within 3-9 weeks of age. Vps34-deficient podocytes exhibited substantial vacuolization and foot process effacement. Although the formation of autophagosomes and autophagic flux were impaired, comparisons between podocyte-specific Vps34-deficient mice, autophagy-deficient mice, and doubly deficient mice suggested that defective autophagy was not primarily responsible for the severe phenotype caused by the loss of Vps34. In fact, Rab5-positive endosomal compartments, endocytosis, and fluid-phase uptake were severely disrupted in Vps34-deficient podocytes. Vps34 deficiency in nephrocytes, the podocyte-like cells of Drosophila melanogaster, resulted in a block between Rab5- and Rab7-positive endosomal compartments. In summary, these data identify Vps34 as a major regulator of endolysosomal pathways in podocytes and underline the fundamental roles of endocytosis and fluid-phase uptake for the maintenance of the glomerular filtration barrier.

Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks

A thorough characterization of the transcriptome and proteome of endogenous podocytes has been hampered by low cell yields during isolation. Here we describe a double fluorescent reporter mouse model combined with an optimized bead perfusion protocol and efficient single cell dissociation to yield more than 500,000 podocytes per mouse allowing for global, unbiased downstream applications. Combining mRNA and miRNA transcriptional profiling with quantitative proteomic analyses revealed programs of highly specific gene regulation tightly controlling cytoskeleton, cell differentiation, endosomal transport, and peroxisome function in podocytes. Strikingly, the analyses further predict that these podocyte-specific gene regulatory networks are accompanied by alternative splicing of respective genes. Thus, our 'omics' approach will facilitate the discovery and integration of novel gene, protein, and organelle regulatory networks that deepen our systematic understanding of podocyte biology.

Modulation of intercellular ROS signaling of human tumor cells

Tumor cells are resistant against apoptosis-inducing intercellular reactive oxygen species (ROS) signaling but can be resensitized by the inhibition of catalase. Hydrogen peroxide exhibits a dual role in the modulation of intercellular ROS signaling. When suboptimal concentrations of the catalase inhibitior 3-aminotriazole (3-AT) are applied, additional exogenous hydrogen peroxide shifts apoptosis induction to its optimum. When hydrogen peroxide is added at optimal concentrations of 3-AT, or when higher concentrations of 3-AT are applied, the subsequent consumption between HOCl and hydrogen peroxide blunts overall apoptosis induction. These supraoptimal conditions can be brought back to the optimum through excess myeloperoxidase (MPO), partial removal of hydrogen peroxide through the catalase mimetic EUK-134 or partial inhibition of NADPH oxidase. Exogenous nitric oxide (NO) interferes with HOCl signaling through consumption of hydrogen peroxide. Site-specific generation of hydroxyl radicals at the cell membrane of tumor cells induces apoptosis, whereas random HOCl-superoxide anion interaction, and ferrous iron-induced Fenton chemistry of HOCl inhibit intercellular ROS signaling.

Catalase protects tumor cells from apoptosis induction by intercellular ROS signaling

Transformed cells are subject to intercellular induction of apoptosis by neighbouring nontransformed cells and to autocrine apoptotic self-destruction. Both processes depend on extracellular superoxide anion generation by the transformed cells and on the release of peroxidase from both nontransformed and transformed cells. This concerted action results in HOCl synthesis, HOCl-superoxide anion interaction and generation of apoptosis-inducing hydroxyl radicals. In contrast to transformed cells, ex vivo tumor cells are resistant against intercellular induction of apoptosis and autocrine apoptotic self-destruction. Resistance of tumor cells against intercellular ROS signaling depends on interference through catalase expression on the membrane. Intercellular ROS signaling of tumor cells can be restored when i) exogenous HOCl is added; ii) exogenous hydrogen peroxide is supplied, or iii) catalase is inhibited. These findings define the biochemical basis for specific apoptosis induction in tumor cells through re-establishment of intercellular ROS signaling, a potential novel approach in tumor prevention and therapy.

Nitric oxide mediates apoptosis induction selectively in transformed fibroblasts compared to nontransformed fibroblasts

Nitric oxide (NO) mediates apoptosis induction in fibroblasts with constitutive src or induced ras oncogene expression, whereas nontransformed parental cells and revertants are not affected. This direct link between the transformed phenotype and sensitivity to NO-mediated apoptosis induction seems to be based on the recently described extracellular superoxide anion generation by transformed cells, as NO-mediated apoptosis induction in transformed cells is inhibited by extracellular superoxide dismutase (SOD), by SOD mimetics and by apocynin, an inhibitor of NADPH oxidase. Furthermore, nonresponsive nontransformed cells can be rendered sensitive for NO-mediated apoptosis induction when they are supplemented with xanthine oxidase/xanthine as an extracellular source for superoxide anions. As superoxide anions and NO readily interact in a diffusion-controlled reaction to generate peroxynitrite, peroxynitrite seems to be the responsible apoptosis inducer in NO-mediated apoptosis induction. In line with this conclusion, NO-mediated apoptosis induction in superoxide anion-generating transformed cells is inhibited by the peroxynitrite scavengers ebselen and FeTPPS. Moreover, direct application of peroxynitrite induces apoptosis both in transformed and nontransformed cells, indicating that peroxynitrite is no selective apoptosis inducer per se, but that selective apoptosis induction in transformed cells by NO is achieved through selective peroxynitrite generation. The interaction of NO with target cell derived superoxide anions represents a novel concept for selective apoptosis induction in transformed cells. This mechanism may be the basis for selective apoptosis induction by natural antitumor systems (like macrophages, natural killer cells, granulocytes) that utilize NO for antitumor action. Apoptosis induction mediated by NO involves mitochondrial depolarization and is blocked by Bcl-2 overexpression.

Consciousness: perspectives from symbolic and connectionist AI

While consciousness has not been a major concern of most AI researchers, some theorists have tried to explore how computational models might explain consciousness. I explore how far computational models might go in explaining consciousness, focusing on three aspects of conscious mental states: their intrinsic intentionality, the awareness a subject has of the contents of these intentional states, and the distinctive qualitative character of these states. I describe and evaluate strategies for developing connectionist systems that satisfy these aspects of consciousness.

Hydronephrosis of pregnancy

During pregnancy, up to 90 percent of women have some degree of asymptomatic dilatation of the renal calyces, the renal pelves and the upper two-thirds of the ureters. Such changes occur in the face of increased renal blood flow and are well tolerated. However, the dilatation may be responsible for the increased propensity of asymptomatic bacteriuria to progress to symptomatic infection during pregnancy. Pathologic hydronephrosis manifested by acute pain, refractory urosepsis or even renal failure has been reported. A case of spontaneous extravasation of urine in a 19-year-old primigravida during the 28th week of gestation is reported. The ureteral obstruction in this patient required percutaneous nephrostomy drainage until delivery of the fetus.

An experimental evaluation of microcapsules for arterial chemoembolization

Microcapsules, 106 micron (range, 50-350 micron), of different capsular materials (monoglyceride, monodiglyceride, natural wax, cellulose polymer, or lactic acid polymer) with and without floxuridine (2'-deoxy-5-fluorouridine, FUDR) were intraarterially injected into dog kidneys. The drug-release characteristics of the microcapsules, as determined by analysis of renal and systemic venous blood samples over a 6-hour period, were uniphasic or multiphasic depending on the capsular material. Histologic changes of varying degrees were noted in all kidneys embolized except for those subjected to capsules of the cellulose polymer. The most striking changes were produced by the lactide polymer capsules. The potential applications of microencapsuled chemotherapeutic agents in intraarterial transcatheter treatment of cancer are discussed.

Gluteal artery occlusion: intra-arterial chemotherapy of pelvic neoplasms

Intra-arterial chemotherapy of pelvic tumors may be complicated by coincident flow to the buttocks. Transcatheter occlusion of both the superior and inferior gluteal arteries may have a role in directing the flow of chemotherapeutic agents away from the buttocks and toward the true pelvis. The results of flow studies using technetium-99m-labeled macroaggregated human serum albumin were compared in 12 consecutive patients examined before and after transcatheter arterial occlusion, and the best results were obtained by selective occlusion of those arteries that demonstrated increased flow to the buttock on the initial study. Without the preselection of patients in whom the initial flow went mainly to the buttock, the results were inconsistent. Because of the increase in the procedure time and the occurrence of minor complications, such as local pain during or after the occlusion procedure, in all patients, proper patient selection is important.

Transcatheter thrombolysis in cancer patients

Arterial thrombolysis was successfully accomplished in 15 of 18 (83%) cancer patients by the continuous intraarterial transcatheter administration of streptokinase (70 units/kg/h or 5000 u/h and/or urokinase (400-500 u/kg/h) over 24-96 h. In 16 of these patients, the arterial thrombosis was a complication of transcatheter infusion of chemotherapeutic agents or embolization therapy. A combination of streptokinase, urokinase and heparin (10,000-25,000 U/day) was utilized without significant side effect and was effective in all 8 patients receiving treatment. Creating a tunnel through the clot, daily monitoring of the catheter with repositioning when necessary, and adjusting the type and dose of thrombolytic agent aided the therapeutic management.

Infusion-embolization

Transcatheter intra-arterial therapy for the cancer patient encompasses infusion of chemotherapy and embolization. Intra-arterial infusion of chemotherapeutic agents has been resurrected because of the availability of new drugs, combinations of drugs, and the capability of percutaneous selective catheter placement. Intra-arterial infusion has been effective in patients with carcinomas of the liver, bladder, prostate, uterus, ovary, and lung and in bone and soft tissue sarcomas, melanomas, and tumors of the brain. Embolization of the arterial supply, creating ischemia of the neoplasm, has been employed in the therapeutic management of patients with primary and secondary neoplasms of the liver, kidney, and bone. The median survival of 100 patients with neoplasms of the liver from the time of hepatic artery embolization was 11.5 months. In 100 patients with pulmonary metastases from carcinoma of the kidney, 28 experienced a response to renal artery embolization, a therapeutic delay of 4 to 7 days, nephrectomy, and Depo-Provera (medroxyprogesterone). Seven of 12 patients with giant cell tumor of the pelvis and lumbar spine responded to arterial embolization after all other therapy failed. Chemoembolization, the combination of arterial infusion of chemotherapy and embolization, can be accomplished by the use of microencapsulated agents, liposomes, and particulate emboli with drugs. This approach integrates the advantages of infusion and occlusion, and has considerable potential. Intra-arterial immunotherapy has been initiated with bacillus Calmette-Guerin (BCG) administration into renal neoplasms in patients with metastatic disease.

Experimental evaluation of intraarterial occlusion-infusion chemotherapy

Intraarterial occlusion-infusion of vincristine and Adriamycin was performed in six dogs using balloon infusion catheters. Tissue toxicity was compared with that obtained when the same drugs were administered by simple arterial infusion. Balloon occlusion of the external iliac artery produced reversed blood flow in the deep femoral, caudal femoral, and superficial circumflex iliac arteries, potentially altering the distribution of the drugs. Thrombosis of arterial branches occurred in three dogs, sooner but no more often in the groups receiving occlusion-infusion chemotherapy. Skin ulceration and dilatation of peripheral small vessels were significantly more frequent and extensive in the groups receiving occlusion-infusion. One infusion dog developed a single small ulcer on the hind paw; five of the six occlusion-infusion dogs developed multiple skin ulcers on the thigh and/or distal extremity. These findings suggest that even though intraarterial occlusion-infusion chemotherapy is not applicable in all instances, the technique does produce significantly greater drug-related effects than simple intraarterial infusion.

Case report of translumbar renal angiography and embolization

The translumbar approach was used for renal angiography and transcatheter embolization in a patient whose usual sites of vascular entry were not available because of arteriosclerotic occlusive vascular disease. A description is given of the reasons for embolization and the method used.

Ethanol for hepatic artery embolization

Reflecting on the studies by O'Riordan et al. and Doppman and Girton that are reported in this issue, the authors discuss the safety of using ethanol for hepatic artery embolization (HAE) and stress that the optimal indications for this procedure are still to be established. They indicate that the caution necessary with any technique can direct rather than inhibit action.

Middle sacral arteriography: diagnostic and therapeutic implications

The authors review the anatomy of the middle sacral artery and its relationship to the lower lumbar and internal iliac arteries. Middle sacral arteriography was performed in 8 patients, transcatheter tumor embolization in 6, and infusion chemotherapy in 1. There were no complications. The authors consider selective middle sacral arteriography beneficial in the diagnosis and treatment of sacral tumors.

Alteration in starch microsphere degradation following contrast angiography in the dog kidney

Six adult mongrel dogs received bilateral sequential renal arterial injections of degradable starch microspheres following preadministration arteriograms. Renal arterial flow was measured using electromagnetic flow probes, and microspheres were administered until flow was blocked completely. One kidney in each dog was subjected to immediate postembolization arteriography, while the contralateral kidney served as a control. In the control kidneys, arterial flow returned to 90-95% of baseline within 30 minutes of embolization, and angiography at this time revealed a normal nephrogram. Blood flow in the kidneys that received postembolization arteriography returned to only 60-65% of baseline, even when followed up to 1 hour. Angiography at this time revealed persistent defects in the nephrogram. The effect of heparin, Renografin-60, and distilled deionized water on amylase activity was evaluated in vitro. No change in enzyme activity was noted.