Database on natural and transgenic luminous microorganisms: "BiolumBase"

The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with lux genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.     

Mutational analysis of the "regulatory module" of hormone-sensitive lipase

Hormone-sensitive lipase (HSL) is a rate-limiting enzyme in lipolysis that displays broad substrate specificity. HSL function is regulated by reversible phosphorylation that occurs within a 150 aa "regulatory module" of the protein. The current studies used mutational analysis to dissect the contribution of the "regulatory module" in HSL activity and substrate specificity. Deletion of the entire "regulatory module" or replacement of the "regulatory module" with the "lid" of lipoprotein lipase resulted in enzymatically inactive proteins. Deletion of sequentially longer stretches of the "regulatory module" resulted in a stepwise reduction in hydrolytic activity. Analysis of 7-19 amino acid deletional mutants that spanned the "regulatory module" showed that the N-terminal partial deletion mutants retained normal hydrolytic activity and activation by PKA. In contrast, the C-terminal partial deletion mutants displayed reduced hydrolytic activities, with preferential loss of activity against lipid-, as opposed to water-soluble, substrates. Single amino acid mutations of F650C, P651A, and F654D reduced activity against lipid-, but not water-soluble, substrates. The current results suggest that the length of the "regulatory module" and specific sequences within the C-terminal portion of the "regulatory module" of HSL (amino acids 644-683) are crucial for activity and appear to be responsible for determining lipase activity.     

Medical concepts related to individual risk are better explained with "plausibility" rather than "probability"

Background

The concept of risk has pervaded medical literature in the last decades and has become a familiar topic, and the concept of probability, linked to binary logic approach, is commonly applied in epidemiology and clinical medicine. The application of probability theory to groups of individuals is quite straightforward but can pose communication challenges at individual level. Few articles by the way have tried to focus the concept of "risk" at the individual subject level rather than at population level.

Discussion

The author has reviewed the conceptual framework which has led to the use of probability theory in the medical field in a time when the principal causes of death were represented by acute disease often of infective origin. In the present scenario, in which chronic degenerative disease dominate and there are smooth transitions between health and disease the use of fuzzy logic rather than binary logic would be more appropriate. The use of fuzzy logic in which more than two possible truth-value assignments are allowed overcomes the trap of probability theory when dealing with uncertain outcomes, thereby making the meaning of a certain prognostic statement easier to understand by the patient.

Summary

At individual subject level the recourse to the term plausibility, related to fuzzy logic, would help the physician to communicate to the patient more efficiently in comparison with the term probability, related to binary logic. This would represent an evident advantage for the transfer of medical evidences to individual subjects.     

Amino acid sequence around a "hinge" region and its "autophosphorylation" site in bovine Lung cGMP-dependent protein kinase

An exposed "hinge" region of cGMP-dependent protein kinase is known to be susceptible to both limited proteolysis and autophosphorylation. A 91-residue fragment has been isolated from this region and its amino acid sequence has been compared with the analogous regions of the cAMP-dependent protein kinases. Although a resemblance among these sequences is not striking, the phosphorylation sites are in corresponding regions toward the NH2 termini, and there are indications of homology in the vicinity of their autophosphorylation sites. As in the cAMP-dependent protein kinase, the site of autophosphorylation and the site of susceptibility to limited proteolysis are very near each other in the primary structure. The actual site of autophosphorylation (the underlined threonine residue in Pro-Arg-Thr-Thr-Arg) is quite different from those in the regulatory subunit of Type II cAMP-dependent kinase or the site in Type I regulatory subunit that can be phosphorylated by the cGMP-dependent protein kinase.     

(Un)Necessary Toughness?: Those "Loud Black Girls" and Those "Quiet Asian Boys"

This article examines the process of identity construction and its relationship to discursive and representational acts in producing students as academic and social beings. Drawing on Judith Butler's work on gender performativity, I focus on two student populations—black females and Southeast Asian American males—and analyze the symbolic and material effects of the production of them as racialized, gendered Other through the repeated stylization of their bodies and behavior. The materialization of the students as "loud black girls" and "quiet Asian boys," however, opens up the potential for disrupting the hegemonicfbrces of regulatory norms.     

High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology

Background

The hypothalamic-pituitary-adrenal (HPA) axis is a central regulator of stress response and its dysfunction has been associated with a broad range of complex illnesses including Gulf War Illness (GWI) and Chronic Fatigue Syndrome (CFS). Though classical mathematical approaches have been used to model HPA function in isolation, its broad regulatory interactions with immune and central nervous function are such that the biological fidelity of simulations is undermined by the limited availability of reliable parameter estimates.

Method

Here we introduce and apply a generalized discrete formalism to recover multiple stable regulatory programs of the HPA axis using little more than connectivity between physiological components. This simple discrete model captures cyclic attractors such as the circadian rhythm by applying generic constraints to a minimal parameter set; this is distinct from Ordinary Differential Equation (ODE) models, which require broad and precise parameter sets. Parameter tuning is accomplished by decomposition of the overall regulatory network into isolated sub-networks that support cyclic attractors. Network behavior is simulated using a novel asynchronous updating scheme that enforces priority with memory within and between physiological compartments.

Results

Consistent with much more complex conventional models of the HPA axis, this parsimonious framework supports two cyclic attractors, governed by higher and lower levels of cortisol respectively. Importantly, results suggest that stress may remodel the stability landscape of this system, favoring migration from one stable circadian cycle to the other. Access to each regime is dependent on HPA axis tone, captured here by the tunable parameters of the multi-valued logic. Likewise, an idealized glucocorticoid receptor blocker alters the regulatory topology such that maintenance of persistently low cortisol levels is rendered unstable, favoring a return to normal circadian oscillation in both cortisol and glucocorticoid receptor expression.

Conclusion

These results emphasize the significance of regulatory connectivity alone and how regulatory plasticity may be explored using simple discrete logic and minimal data compared to conventional methods.

     

Catabolic action of insulin in rat arcuate nucleus is not enhanced by exogenous "tub" expression

The central nervous system (CNS) protein "tub" has been identified from the genetically obese "tubby" mouse. Although the native function of tub in situ is not understood, cell-based studies suggest that one of its roles may be as an intracellular signaling target for insulin. In normal animals, insulin acts at the hypothalamic arcuate nucleus (ARC) to regulate energy balance. Here we used a Herpes Simplex viral expression system to evaluate whether tub overexpression in the ARC of normal rats enhances this action of insulin. In chow-fed rats, tub overexpression had no effect on insulin action. In rats fed a high-fat diet snack in addition to chow, simulating the diet of Westernized societies, the body weight regulatory action of insulin was impaired, and tub overexpression further impaired insulin action. Thus an excess of tub at the ARC does not enhance the in vivo effectiveness of insulin and is not able to compensate for the "downstream" consequences of a high-fat diet to impair CNS body weight regulatory mechanisms.     

The Ambiguity of the Word "Complexity" a Proposal for Clarification

There are two different ways of defining complexity.1) Traditionally, the word "complexity" is considered synonymous to "organization". The transformation of species is an expression of victory against random indifferencism.2) The means of measuring complexity that was conceived by Kolmogorov has the advantage of having an external reference. Therefore, its logical reliability is considerable. But Kolmogorov's complexity will be at its best in cases of pure randomness.These mutually incompatible definitions explicitly demand a classification system.The first definition of complexity is contrary to the second one. This must be explained more precisely in order not to disturb the logic of Kolmogorov's conception and to enable to add to this conception, as closely as possible, along the logical rules derived from Gödel's incompleteness.The author proposes a beginning of complexity typology, founded on the necessity of laws that rule a random substract aiming at organization. The generality of laws to be selected will have a direct effect on the logical strength of the "biologists' definition" of complexity.Two fundamental laws are expressed, one derived from mathematics and the other from physics, two fields alien to biology. This fact improves the logical accordance to the argument.     

Spontaneous renal allograft acceptance associated with "regulatory" dendritic cells and IDO

MHC-mismatched DBA/2 renal allografts are spontaneously accepted by C57BL/6 mice by poorly understood mechanisms, but both immune regulation and graft acceptance develop without exogenous immune modulation. Previous studies have shown that this model of spontaneous renal allograft acceptance is associated with TGF-beta-dependent immune regulation, suggesting a role for T regulatory cells. The current study shows that TGF-beta immune regulation develops 30 days posttransplant, but is lost by 150 days posttransplant. Despite loss of detectable TGF-beta immune regulation, renal allografts continue to function normally for >200 days posttransplantation. Because of its recently described immunoregulatory capabilities, we studied IDO expression in this model, and found that intragraft IDO gene expression progressively increases over time, and that IDO in "regulatory" dendritic cells (RDC) may contribute to regulation associated with long-term maintenance of renal allografts. Immunohistochemistry evaluation confirms the presence of both Foxp3+ T cells and IDO+ DCs in accepted renal allografts, and localization of both cell types within accepted allografts suggests the possibility of synergistic involvement in allograft acceptance. Interestingly, at the time when RDCs become detectable in spleens of allograft acceptors, approximately 30% of these mice challenged with donor-matched skin allografts accept these skin grafts, demonstrating progression to "true" tolerance. Together, these data suggest that spontaneous renal allograft acceptance evolves through a series of transient mechanisms, beginning with TGF-beta and T regulatory cells, which together may stimulate development of more robust regulation associated with RDC and IDO.     

Humicola insolens cellobiose dehydrogenase: cloning, redox chemistry, and "logic gate"-like dual functionality

1Cellobiose dehydrogenase is a hemoflavoenzyme that catalyzes the sequential electron-transfer from an electron-donating substrate (e.g. cellobiose) to a flavin center, then to an electron-accepting substrate (e.g. quinone) either directly or via a heme center after an internal electron-transfer from the flavin to heme. We cloned the dehydrogenase from Humicola insolens, which encodes a protein of 761 amino acid residues containing an N-terminal heme domain and a C-terminal flavin domain, and studied how the catalyzed electron transfers are regulated. Based on the correlation between the rate and redox potential, we demonstrated that with a reduced flavin center, the enzyme, as a reductase, could export electron from its heme center by a "outer-sphere" mechanism. With the "resting" flavin center, however, the enzyme could have a peroxidase-like function and import electron to its heme center after a peroxidative activation. The dual functionality of its heme center makes the enzyme a molecular "logic gate", in which the electron flow through the heme center can be switched in direction by the redox state of the coupled flavin center.     

Interaction of preparation "ATP-LONG" with distearoylphosphatidylcholine monolayer

Interaction of ATP and its derivative "ATP-LONG", the preparations raising general resistanse of an organism to physical stress, with the model phospholipid monolayer membrane of distearoylphosphatidylcholine has been investigated. It is shown, that these substances interact with a monolayer under partial embedding of a purine base between the phospholipid molecules. However their regulatory influence cannot be explained only by the effect of plasmatic membrane lipid components on physical parameters.     

"Actually, I don't feel that bad": managing diabetes and the clinical encounter

A major issue for persons treating and managing adult-onset diabetes (NIDDM) is the "problem of compliance." I consider the clinical encounter in the overall context of diabetes management as a punctuated experience focused on the cultivation of an ideal self whose "technologies" and "ethics of self-care" mimic a capitalist logic that links self-discipline, productivity, and health. Both clinicians and their patients share and identify with many of the cultural referents and social values that circulate through medical advice and practice. However, using individual examples, I show how this shared logic can produce idiosyncratic regimes of self-care and clinical practice that result in hybrid medical practices incorporating differing objectives and emphases concerned with a tolerable present or an ideal future. Rather than organizing principles for research and medical practice, I suggest that medical compliance and noncompliance should be considered part of the rhetoric to be explained within the regimes of a pursuit of health.     

Caspase cleavage of phospholipase D1 in vitro alters its regulation and reveals a novel property of the "loop" region

Phospholipase D (PLD) has been implicated in mediating vesicular transport, mitosis, differentiation and apoptosis. The product of PLD activity, phosphatidic acid (PA) has mitogenic potential and elevated PLD expression has been detected in many tumor cell lines. Several reports have demonstrated that distinct PLD domains regulate its activity and that truncated forms of PLD retain enzymatic activity. We hypothesized that during apoptosis caspase cleavage of PLDs could result in modification of their activities. To test this idea, we have used in vitro translation of PLD1 and PLD2 which generated active enzymes exhibiting properties mimicking those of the endogenous proteins. Here we demonstrate that PLD1 was rapidly cleaved in vitro by caspases-8, -3 and -7. In contrast, PLD2 cleavage was delayed and its activity was unaffected by incubation with caspase-3. Significantly, following caspase cleavage the response of PLD1 to regulatory stimuli was altered; it was no longer activated by PKC and instead exhibited an increased activity in response to small GTPases. Notably, this enhanced activity was due to cleavage of PLD1 in the "loop" domain, a region previously associated with negative regulatory function. Thus our data have identified a novel regulatory domain in PLD1.     

Biological Signal Processing with a Genetic Toggle Switch

Complex gene regulation requires responses that depend not only on the current levels of input signals but also on signals received in the past. In digital electronics, logic circuits with this property are referred to as sequential logic, in contrast to the simpler combinatorial logic without such internal memory. In molecular biology, memory is implemented in various forms such as biochemical modification of proteins or multistable gene circuits, but the design of the regulatory interface, which processes the input signals and the memory content, is often not well understood. Here, we explore design constraints for such regulatory interfaces using coarse-grained nonlinear models and stochastic simulations of detailed biochemical reaction networks. We test different designs for biological analogs of the most versatile memory element in digital electronics, the JK-latch. Our analysis shows that simple protein-protein interactions and protein-DNA binding are sufficient, in principle, to implement genetic circuits with the capabilities of a JK-latch. However, it also exposes fundamental limitations to its reliability, due to the fact that biological signal processing is asynchronous, in contrast to most digital electronics systems that feature a central clock to orchestrate the timing of all operations. We describe a seemingly natural way to improve the reliability by invoking the master-slave concept from digital electronics design. This concept could be useful to interpret the design of natural regulatory circuits, and for the design of synthetic biological systems.     

Ascorbic acid as a factor controlling "in vivo" its biosynthetic pathway

The capacity of ascorbic acid biosynthesis in potato tuber tissue is closely correlated with the ascorbic acid content of the cells: the lower the endogenous content of ascorbic acid, the greater its biosynthesis. At the highest level of ascorbic acid found in the cells, the biosynthetic capacity is virtually zero. In these conditions, adding glucose (the first precursor of ascorbic acid) has no effect whatsoever, whereas adding galactono-gamma-lactone (the last precursor) induces a high rate of ascorbic acid synthesis. It is suggested that AA biosynthesis is subject to a regulatory mechanism "in vivo" which controls an initial step in the biosynthetic pathway. The last step in this pathway, catalyzed by galactone oxidase, is never blocked and, moreover, its activity is greater than that of the preceding steps.