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PubMed2006

Civilization as a biosystem examined by the comparative analysis of biosystems.

Darwinian evolutionary theory has played a central role in the life sciences. However, this principle is rarely applied to exceptional life-like systems such as human societies and the life-like chemical systems associated with the origin of life. For a description of the nature of these exceptional life-like biosystems, the development of alternative approaches is necessary. The existence of analogies among biosystems at different hierarchical levels has frequently been discussed. The present paper, however, focuses on the analogies of the structures and functions of different biosystems, based on the following perspectives. The roles of an individual biosystem and its building blocks in relation to the environment are evaluated from the standpoint of the hierarchies of organisms, whereby the principle of which hierarchy is regarded as an "individual" biosystem is proposed. In addition, the definition and characteristics of civilization are discussed on the basis of this principle. The analogies between cell-type systems, civilizations, ecosystems, and other biosystems are qualitatively evaluated. It is reasonable to regard all biosystems as possessing clear or ambiguous boundaries. Biosystems at higher levels than prokaryotes comprise both living and non-living building blocks, while prokaryotes comprise only non-living building blocks. The similarities concerning the interactions among the building blocks in relation to their environment are also discussed. Furthermore, the analogy between different biosystems concerning metabolism, self-reproduction, mutation, the relationship between genotype and phenotype (information and function), individuality, and stability are evaluated. The proposed analytical approach not only provides an insight into the characteristics of civilizations as biosystems, but also the characteristics of biosystems at different hierarchical levels.

Biological Evolution↗
PubMed1997

Disruption of mouse RAD54 reduces ionizing radiation resistance and homologous recombination.

Double-strand DNA break (DSB) repair by homologous recombination occurs through the RAD52 pathway in Saccharomyces cerevisiae. Its biological importance is underscored by the conservation of many RAD52 pathway genes, including RAD54, from fungi to humans. We have analyzed the phenotype of mouse RAD54-/- (mRAD54-/-) cells. Consistent with a DSB repair defect, these cells are sensitive to ionizing radiation, mitomycin C, and methyl methanesulfonate, but not to ultraviolet light. Gene targeting experiments demonstrate that homologous recombination in mRAD54-/- cells is reduced compared to wild-type cells. These results imply that, besides DNA end-joining mediated by DNA-dependent protein kinase, homologous recombination contributes to the repair of DSBs in mammalian cells. Furthermore, we show that mRAD54-/- mice are viable and exhibit apparently normal V(D)J and immunoglobulin class-switch recombination. Thus, mRAD54 is not required for the recombination processes that generate functional immunoglobulin and T cell receptor genes.

Alkylating Agents↗
PubMed2001

Character coding of secondary chemical variation for use in phylogenetic analyses.

A coding procedure is presented for secondary chemical data whereby putative biogenetic pathways are coded as phylogenetic characters with enzymatic conversions between compounds representing the corresponding character states. A character state tree or stepmatrix allows direct representation of the secondary chemical biogenetic pathway and avoids problems of non-independence associated with coding schemes that score presence/absence of individual compounds. Stepmatrices are the most biosynthetically realistic character definitions because individual and population level polymorphisms can be scored, reticulate enzymatic conversions within pathways may be represented, and down-weighting of pathway loss versus gain is possible. The stepmatrix approach unifies analyses of secondary chemicals, allozymes, and developmental characters because the biological unity of the pathway, locus, or character ontogeny is preserved. Empirical investigation of the stepmatrix and character state tree coding methods using floral fragrance data in Cypripedium (Orchidaceae) resulted in cladistic relationships which were largely congruent with those suggested from recent DNA and allozyme studies. This character coding methodology provides an effective means for including secondary compound data in total evidence studies. Furthermore, ancestral state reconstructions provide a phylogenetic context within which biochemical pathway evolution may be studied.

Journal Article↗
PubMed1997

Regulation of mucin secretion in human gallbladder epithelial cells: predominant role of calcium and protein kinase C.

BACKGROUND & AIMS: The cellular mechanisms that regulate biliary mucin secretion in humans are unknown. To address this question, human gallbladder epithelial cells were used in primary culture. METHODS: [1-(14)C]-glucosamine-labeled glycoproteins secreted in vitro were analyzed and quantified after exposing cells to activators and inhibitors of the main transduction pathways and to potential biologically active secretagogues. RESULTS: Secreted glycoproteins showed characteristics of biliary mucins. Activators of adenosine 3',5'-cyclic monophosphate-dependent pathway as well as secretin and vasoactive intestinal polypeptide did not significantly modify mucin secretion. By contrast, ionomycin and phorbol-12-myristate 13-acetate increased mucin secretion by 292% +/- 48% and 134% +/- 19% over basal level, respectively. The effects of these two agents were additive and were mediated by a calcium-dependent pathway implicating Ca2+/calmodulin-dependent protein kinase II (Ca2+/CaM-kinase II) and by the activation of protein kinase C (PKC), respectively, as ascertained by using inhibitors. Mucin secretion was stimulated by extracellular adenosine 5'-triphosphate via P2U receptors, cytosolic calcium increase, and PKC and by taurochenodeoxycholate via cytosolic calcium increase and Ca2+/CaM-kinase II. CONCLUSIONS: Mucin secretion in human gallbladder is regulated predominantly by calcium-dependent pathways implicating Ca2+/CaM-kinase II and PKC. Extracellular adenosine 5'-triphosphate and taurochenodeoxycholate may play a role in the regulation of biliary mucin secretion by activating these different signaling pathways.

Adenosine Triphosphate↗
PubMed2006

Influences of TP53 expression on cellular radiation response and its relevance to diagnostic biodosimetry for mission environmental monitoring.

TP53 is a transcriptional activator and regulates genomic instability and cellular responses to DNA damage in response to ionising radiation. The molecular mechanism behind p53-mediated responses, such as, apoptosis and genomic instability remains unclear. An in vitro model of biological effects to irradiation was established. In order to elucidate the functional role of TP53 under different stress-reaction pathways and identify possible biological indicators, p53 was stably transfected into HL-60 cells, which provides a p53 minus background. Significantly enhanced radiosensitivity and growth suppression were observed. G(2) accumulation was obtained. Radiation-induced apoptosis of HL-60 cells was significantly inhibited by TP53, indicating that, in the event of DNA damage, TP53 is able to prevent cell death of HL-60 leukaemia cells by sustaining an arrest of the cell cycle at G(2) phase. Further evidence will be presented to identify specific radiation-targeted genes or signals as possible biomarkers for early diagnosis of radiation damage as well as mission environmental monitoring.

Biological Assay↗
PubMed1996

Afferent and efferent connections of the central prosencephalic nucleus in the Pacific hagfish.

Injections of horseradish peroxidase, or the carbocyanine dye Dil, into the central prosencephalic nucleus of hagfishes reveal reciprocal connections with the septum, preoptic area, habenula, thalamus and hypothalamus. Efferent projections also occur to the olfactory bulb, pallium, posterior tubercle and tegmentum and to the contralateral central prosencephalic nucleus. These connections suggest that the central prosencephalic nucleus of hagfishes may be homologous to portions of the medial pallium and ventral thalamus of other craniates.

Afferent Pathways↗
PubMed2004

Modeling and simulation of biological systems with stochasticity.

Mathematical modeling is a powerful approach for understanding the complexity of biological systems. Recently, several successful attempts have been made for simulating complex biological processes like metabolic pathways, gene regulatory networks and cell signaling pathways. The pathway models have not only generated experimentally verifiable hypothesis but have also provided valuable insights into the behavior of complex biological systems. Many recent studies have confirmed the phenotypic variability of organisms to an inherent stochasticity that operates at a basal level of gene expression. Due to this reason, development of novel mathematical representations and simulations algorithms are critical for successful modeling efforts in biological systems. The key is to find a biologically relevant representation for each representation. Although mathematically rigorous and physically consistent, stochastic algorithms are computationally expensive, they have been successfully used to model probabilistic events in the cell. This paper offers an overview of various mathematical and computational approaches for modeling stochastic phenomena in cellular systems.

Algorithms↗
PubMed1990

The game of the pentose phosphate cycle: a mathematical approach to study the optimization in design of metabolic pathways during evolution.

The optimization of the pathway structure of the pentose phosphate cycle is studied by means of abstraction to a model designed as a mathematical game of combinatorial optimization. The objective of the game is to convert pentoses into hexoses, which is the aim of the non-oxidative phase of the metabolic cycle, and it includes two kinds of hypotheses: (a) the hypothesis of the mechanisms based on the enzyme mechanisms available to cells, and (b) the hypothesis of simplicity which establishes that the optimal solution must have the least number of steps and the least number of carbons in every intermediate. A mathematical proof of the optimal solution of this problem is given, and it is demonstrated that such a solution is the same as occurs in cells. The Calvin cycle and the "L-type" of the pentose cycle are also studied by a similar method, and equivalent results are obtained. These results point out the role which the hypothesis of simplicity may have played in the evolution of metabolic pathways.

Biological Evolution↗
PubMed2000

Abnormal neuronal ionic flux activity: learning paradigms of schizophrenic thought disorders.

New developments in biological psychiatry have prompted the development of our pathophysiological theory of the etiology of schizophrenic thought disorders. We suggest that the presence of brain bionic lesions may produce microneuropathies in certain neuronal electrical pathways, leading to abnormal biological communication. These blockages force the rerouting of incoming electric signals through bypass pathways which divert the message from target to non-target neurons for decoding and integration. Using this model, we were able to link specific schizophrenic disturbances to different types of brain bionic lesion effects. This model should be further investigated to facilitate the understanding of the nature and origin of schizophrenic disorders and to stimulate further interest in this fascinating field.

Brain↗
PubMed2006

Combinations of biomarkers predictive of later life mortality.

A wide range of biomarkers, reflecting activity in a number of biological systems (e.g., neuroendocrine, immune, cardiovascular, and metabolic), have been found to prospectively predict disability, morbidity, and mortality outcomes in older adult populations. Levels of these biomarkers, singly or in combination, may serve as an early warning system of risk for future adverse health outcomes. In the current investigation, 13 biomarkers were examined as predictors of mortality occurrence over a 12-year period in a sample of men and women (n = 1,189) 70-79 years of age at enrollment into the study. Biomarkers examined in analyses included markers of neuroendocrine functioning (epinephrine, norepinephrine, cortisol, and dehydroepiandrosterone), immune activity (C-reactive protein, fibrinogen, IL-6, and albumin), cardiovascular functioning (systolic and diastolic blood pressure), and metabolic activity [high-density lipoprotein (HDL) cholesterol, total to HDL cholesterol ratio, and glycosylated hemoglobin]. Recursive partitioning techniques were used to identify a set of pathways, composed of combinations of different biomarkers, that were associated with a high-risk of mortality over the 12-year period. Of the 13 biomarkers examined, almost all entered into one or more high-risk pathways although combinations of neuroendocrine and immune markers appeared frequently in high-risk male pathways, and systolic blood pressure was present in combination with other biomarkers in all high-risk female pathways. These findings illustrate the utility of recursive partitioning techniques in identifying biomarker combinations predictive of mortal outcomes in older adults, as well as the multiplicity of biological pathways to mortality in elderly populations.

Age Factors↗
PubMed2006

ERK and beyond: insights from B-Raf and Raf-1 conditional knockouts.

The Raf/MEK/ERK cascade is a highly conserved signal transduction module whose activation reportedly results in a plethora of physiological outcomes. Depending on the cell type or the stimulus used, the pathway has been implicated in proliferation, differentiation, survival, and migration. Their wide range of activities renders the component of the Raf/MEK/ERK pathway prime candidates for molecule-targeted therapies, in particular, but not exclusively, in the context of cancer. Ras, Raf and MEK inhibitors have been developed, and some of them are in advanced clinical trials. Somewhat surprising in view of all this interest, our understanding of the fundamental biology of the ERK pathway in vivo is still scanty. Its investigation has been hampered by the fact that conventional targeting of many of these genes results in embryonic lethality. Recently, we and others have generated mouse strains that allow the conditional ablation of the genes coding for Raf-1, B-Raf and MEK-1. We are using these tools to identify the essential biological functions of these kinases, and to understand how the ERK pathway is wired in vivo. Here, we discuss some of the surprises yielded by the analysis of the role of B-Raf and Raf-1 and of their downstream effectors.

Animals↗
PubMed2004

RNA silencing in plants.

There are at least three RNA silencing pathways for silencing specific genes in plants. In these pathways, silencing signals can be amplified and transmitted between cells, and may even be self-regulated by feedback mechanisms. Diverse biological roles of these pathways have been established, including defence against viruses, regulation of gene expression and the condensation of chromatin into heterochromatin. We are now in a good position to investigate the full extent of this functional diversity in genetic and epigenetic mechanisms of genome control.

Arabidopsis Proteins↗
PubMed2004

SH2-B promotes insulin receptor substrate 1 (IRS1)- and IRS2-mediated activation of the phosphatidylinositol 3-kinase pathway in response to leptin.

Leptin regulates energy homeostasis primarily by binding and activating its long form receptor (LRb). Deficiency of either leptin or LRb causes morbid obesity. Leptin stimulates LRb-associated JAK2, thus initiating multiple pathways including the Stat3 and phosphatidylinositol (PI) 3-kinase pathways that mediate leptin biological actions. Here we report that SH2-B, a JAK2-interacting protein, promotes activation of the PI 3-kinase pathway by recruiting insulin receptor substrate 1 (IRS1) and IRS2 in response to leptin. SH2-B directly bound, via its PH and SH2 domain, to both IRS1 and IRS2 both in vitro and in intact cells and mediated formation of a JAK2/SH2-B/IRS1 or IRS2 tertiary complex. Consequently, SH2-B dramatically enhanced leptin-stimulated tyrosine phosphorylation of IRS1 and IRS2 in HEK293 cells stably expressing LRb, thus promoting association of IRS1 and IRS2 with the p85 regulatory subunit of PI 3-kinase and phosphorylation and activation of Akt. SH2-B mutants with lower affinity for IRS1 and IRS2 exhibited reduced ability to promote association of JAK2 with IRS1, tyrosine phosphorylation of IRS1, and association of IRS1 with p85 in response to leptin. Moreover, deletion of the SH2-B gene impaired leptin-stimulated tyrosine phosphorylation of endogenous IRS1 in mouse embryonic fibroblasts (MEF), which was reversed by reintroduction of SH2-B. Similarly, SH2-B promoted growth hormone-stimulated tyrosine phosphorylation of IRS1 in both HEK293 and MEF cells. Our data suggest that SH2-B is a novel mediator of the PI 3-kinase pathway in response to leptin or other hormones and cytokines that activate JAK2.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Progesterone receptors--animal models and cell signalling in breast cancer. Diverse activation pathways for the progesterone receptor: possible implications for breast biology and cancer.

Progesterone and estradiol, and their nuclear receptors, play essential roles in the physiology of the reproductive tract, the mammary gland and the nervous system. Estrogens have traditionally been considered associated with an increased risk of breast cancer. There is, however, compelling evidence that progesterone plays an important role in breast cell proliferation and cancer. Herein, we review the possible role of progestins and the progesterone receptor-associated signaling pathways in the development of breast cancer, as well as the therapeutic possibilities arising from our growing knowledge of the activation of the progesterone receptor by other proliferative mechanisms.

Animals↗
PubMed1999

Stress, superoxide, and signal transduction.

A variety of stressful events can trigger the production of free radicals by exposed cells. For years, the effect of such highly reactive radicals was expected to be damaging to cells, altering their biology irreversibly. However, many recent reports have shown that reactive oxygen species can have additional functions, and contribute to important signaling pathways to regulate key biological responses, including cell migration, mitosis, and apoptosis. With this review, we address the role of the small GTP binding protein, Rac, as a regulatory protein that controls superoxide production, and the effect of superoxide and derived oxidants in cell signaling.

Actins↗
PubMed1977

Effects of ethosuximide on transmission of repetitive impulses and apparent rates of transmitter turnover in the spinal monosynaptic pathway.

The effects of ethosuximide on spinal monosynaptic transmission were studied in cats. The drug in doses of 200 or 400 mg/kg deepened the decline of monosynaptic response amplitude evoked by trains of 10 stimuli to a motor nerve at 2, 5 or 10 Hz, without affecting the transmission of single isolated impulses. The patterns of decline were analyzed under the assumption that they reflect a partial depletion of the apparent transmitter stores in the presynaptic terminals, each incoming volley releasing a constant fraction of the store while a constant fraction of the instant size of the depleted part is being replenished per second. Ethosuximide increased the fractional release without a consistent effect on the fractional rate of replenishment. It is suggested that the resulting more rapid and more profound depletion of the apparent transmitter store could account for the observed preferential depression of repetitive transmission in the spinal monosynaptic pathway by this drug.

Animals↗
PubMed1997

Cadmium uptake by a human hepatic cell line (WRL-68 cells).

A hepatic human cell line (WRL-68 cells) was employed to investigate the uptake of the toxic heavy metal cadmium. Cd accumulation in WRL-68 cells is a time-, temperature- and concentration-dependent process. A rapid initial phase of uptake was followed by a second slower phase. The transport does not require energy and 55% of Cd transport occurs by temperature-insensitive processes, possibly by diffusion. The rest of Cd transport (45%) occurs by temperature-sensitive processes, probably ion channels and carriers, that involve interaction with sulfhydryl groups. The calcium channel blockers nifedipine and verapamil inhibit the uptake of cadmium, with an inhibition of 35% after 30 min incubation with 100 microM verapamil and 10 microM Cd. These data suggest that about one third of the Cd enters WRL-68 cells through the calcium channels. The toxic metals appear to use the transport pathways that exist for biologically essential metals. Our results in human hepatic cells are very similar to those reported in cultured rat hepatocytes. It appears that transport pathways available for Cd uptake are similar and independent of the species of hepatocyte origin. Moreover, the WRL-68 cell line seems to be an excellent in vitro model to study the mechanism of cell damage due to Cd.

Biological Transport↗
PubMed2001

The challenge of pathway and environment-mediated drug resistance.

New insights into cancer biology have allowed the definition of pathways critical to the success of the cancer cell. These include enhanced activity of positive regulators of cell proliferation, including oncogenes, and loss of tumor suppressor gene function; inactivation of cell death or enhancement of srvival functions; activation of telomerase, and enhanced ability of tumor cells to invade and reorganize host stroma. It follows then that these pathways may also mediate drug resistance, in a way that is fundamentally different from classically defined mechanisms for drug resistance which focus on altered handling of the drug or the drug's target by the resistant tumor cell. It is expected that resistance will occur that is predicated on altered pathway predominance in a tumor and altered tumor microenvironment. Cases which exemplify this possibility are presented, including up-regulation of angiogenesis-related regulators in relation to inhibition of EGF-related proliferative and angiogenesis-promoting functions. The implications of this thinking in relation to development of combination regimens targeting distinct pathways are considered.

Antineoplastic Agents↗