Periodic band pattern as a dissipative structure in ion transport systems with cylindrical shape

A theory is presented for appearance of periodic band patterns of ion concentration and electric potential associated with electric current surrounding a unicellular or multicellular system of a cylindrical shape. A flux continuity at the membrane (or the surface) is reduced to a nonlinear equation expressing passive and active fluxes across the membrane and intracellular diffusion flux. It is shown that, when an external parameter is varied from the sub-critical region, i.e. the homogeneous flux state, a symmetry breaking along a longitudinal axis usually appears prior to the one along a circumferential direction. The spectrum analysis shows that the correlation length is longer in the longitudinal direction. Growth of the band pattern from a patch-shaped pattern is demonstrated by the use of numerical calculations of proton concentration on the two-dimensional space of cylindrical surface. An experimental example of formative process of H⁺ banding is given for the internodal cell ofChara. It is shown that small patches on the surface decline or are sometimes gathered to the band surrounding the circle. The resulting pattern is suggested as a kind of dissipative structure appearing far from equilibrium.     

RNA secondary structure as a reusable interface to biological information resources

The dissemination of biological information has become critically dependent on the Internet and World Wide Web (WWW), which enable distributed access to information in a platform independent manner. The mode of interaction between biologists and on-line information resources, however, has been mostly limited to simple interface technologies such has hypertext links, tables and forms. The introduction of platform-independent runtime environments facilitates the development of more sophisticated WWW-based user interfaces. Until recently, most such interfaces have been tightly coupled to the underlying computation engines, and not separated as reusable components. We believe that many subdisciplines of biology have intuitive and familiar graphical representations of knowledge that can serve as multipurpose user interface elements. We call such graphical idioms “domain graphics”. In order to illustrate the power of such graphics, we have built a reusable interface based on the standard two dimensional (2D) layout of RNA secondary structure. The interface can be used to represent any pre-computed layout of RNA, and takes as a parameters the sets of actions to be performed as a user interacts with the interface. It can provide to any associated application program information about the base, helix, or subsequence selected by the user. We show the versatility of this interface by using it as a special purpose interface to BLAST, Medline and the RNA MFOLD search/compute engines. These demonstrations are available at: ir|url|http://www-smi.stanford.edu/projects/helix/pubs/ gene-combis-96/     

Nuclear structure as a source of cancer specific biomarkers

There are few biomarkers that have been developed which have proven clinical utility for the detection and prognosis of cancer. Cancer is diagnosed today, in large part, by examining cells under the microscope and determining the shape and texture of the nucleus. The molecular underpinnings of this hallmark of cancer are the components of the nuclear matrix. Utilizing proteomics focused on this subset of proteins, biomarkers have been identified that are specific for cancer types including prostate, colon and bladder cancer. These cancer biomarkers now serve as the basis of assays which can specifically identify individuals with cancer by sampling their blood and/or urine. In addition, these may serve as potential therapeutic targeting or imaging approaches.     

Immunotherapy as a therapeutic treatment for neurodegenerative disorders

Human neurodegenerative illnesses such as Alzheimer's disease and Creutzfeldt-Jakob disease exact an enormous cost on individuals, families and society. For these and related disorders, current treatment is largely symptomatic without influencing the underlying disease process. Until recently, the development of immunotherapeutic approaches to neurodegenerative disorders had been almost completely ignored despite growing successes against other non-infectious diseases such as cancer. However, since Schenk and colleagues described the antibody-mediated clearance of amyloid plaques in a transgenic mouse model of Alzheimer's disease, a number of studies have confirmed the feasibility of this strategy for several neurodegenerative disorders including Huntington's disease and prion diseases. These reports offer the exciting prospect that either the immune system or its derivative components can be harnessed to fight the misfolded and/or aggregated proteins that accumulate in many neurodegenerative illnesses. If the remarkable power of clonal expansion, specificity and efficiency of the immune system can successfully inactivate these abnormal proteins, real hope exists that effective immunotherapeutic treatments for neurodegenerative illnesses may be available in the near future.     

Salinity as a determinant of the structure of biological communities in salt lakes

The paper considers the extent to which salinity determines the structure of biological communities (composition and species richness and diversity) in saline lakes, i.e. inland bodies of water with salinities in excess of 3 g l-1. It also considers the extent to which oxygen, ionic composition, pH, hydrological patterns (degree of permanence and impermanence of water), geographical position, palaeoclimatic events, chance, human intervention, and biological interactions especially predation determine biological communities in salt lakes. It suggests that salinity is less significant as a determinant of community structure in salt lakes than has been assumed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Immunotherapy for superficial bladder cancer

The treatment of superficial bladder cancer requires adjuvant therapies besides transurethral resection because of a high recurrence rate after this standard treatment alone. Current adjuvant therapies involve intravesical chemotherapy for patients at low and intermediate risk for recurrence and progression, and intravesical bacillus Calmette-Guérin for patients at intermediate and high risk. However, these adjuvant therapies fail in a significant number of patients, dictating the need for new and improved adjuvant treatment modalities for superficial bladder cancer. Immunotherapy aiming at the modulation of the immune system of the patient is a promising alternative adjuvant. This review discusses the current status of the clinical development of various immunotherapy approaches for superficial bladder cancer, including passive immunotherapy, immune stimulants, immunogene therapy and cancer vaccination.     

Immunotherapy for advanced prostate cancer

The absence of curative therapies for advanced or recurrent forms of prostate cancer mandates continued development of novel, more effective treatment regimens. Due to recent advances in basic and translational research, therapeutic vaccines and monoclonal antibody-based therapies are steadily gaining ground as promising treatment modalities against prostate cancer. Several immunotherapeutic products have recently been investigated in later-phase trials and have reported evidence for clinical benefit while maintaining an excellent quality of life for participants. The cumulative clinical results available to date indicate that immune-based therapies will likely play a role in the treatment of patients with prostate and other malignancies. The objective of this article is to increase awareness of contemporary immunologic therapies and clinical trials of new biologic reagents against prostate cancer. We also seek to encourage urologists to actively participate in clinical trials and evaluate the potential of immunotherapeutic drugs for impacting standards of care.     

Formation of a regular dissipative structure: a bifurcation and non-linear analysis.

A non-linear reaction diffusion model of a negative feedback epigenetic control system is presented. The model involves synthesis of the mitotic inducing and inhibiting proteins, simultaneously with intercellular self-diffusion and cross-diffusion of the latter only. The importance of negative cross-diffusion for creating a regular dissipative structure is shown. A bifurcation analysis of the non-linear diffusive system has been performed and it is concluded that bifurcation is supercritical. Lastly, using Liapunov's direct method, it is shown that the pattern evolved by the system is globally asymptotically stable.     

Immunotherapy of cancer with dendritic-cell-based vaccines

 Animal studies have shown that vaccination with genetically modified tumor cells or with dendritic cells (DC) pulsed with tumor antigens are potent strategies to elicit protective immunity in tumor-bearing animals, more potent than “conventional” strategies that have been tested in clinical settings with limited success. While both vaccination strategies are forms of cell therapy requiring complex and costly ex vivo manipulations of the patient’s cells, current protocols using dendritic cells are considerably simpler and would be more widely available. Vaccination with defined tumor antigens presented by DC has obvious appeal. However, in view of the expected emergence of antigen-loss variants as well as natural immunovariation, effective vaccine formulations must contain mixtures of commonly, if not universally, expressed tumor antigens. When, or even if, such common tumor antigens will be identified cannot be, predicted, however. Thus, for the foreseeable future, vaccination with total-tumor-derived material as source of tumor antigens may be preferable to using defined tumor antigens. Vaccination with undefined tumor-derived antigens will be limited, however, by the availability of sufficient tumor tissue for antigen preparation. Because the mRNA content of single cells can be amplified, tumor mRNA, or corresponding cDNA libraries, offer an unlimited source of tumor antigens. DC transfected with tumor RNA were shown to engender potent antitumor immunity in animal studies. Thus, immunotherapy using autologous DC loaded with unfractionated tumor-derived antigens in the form of RNA emerges as a potentially powerful and broadly useful vaccination strategy for cancer patients. Received: 10 October 1997 / Accepted: 12 January 1998     

Immunotherapy of tumors with xenogeneic endothelial cells as a vaccine

The breaking of immune tolerance against autologous angiogenic endothelial cells should be a useful approach for cancer therapy. Here we show that immunotherapy of tumors using fixed xenogeneic whole endothelial cells as a vaccine was effective in affording protection from tumor growth, inducing regression of established tumors and prolonging survival of tumor-bearing mice. Furthermore, autoreactive immunity targeting to microvessels in solid tumors was induced and was probably responsible for the anti-tumor activity. These observations may provide a new vaccine strategy for cancer therapy through the induction of an autoimmune response against the tumor endothelium in a cross-reaction.