An approach to studying lung cancer-related proteins in human blood

Early stage lung cancer detection is the first step toward successful clinical therapy and increased patient survival. Clinicians monitor cancer progression by profiling tumor cell proteins in the blood plasma of afflicted patients. Blood plasma, however, is a difficult cancer protein assessment medium because it is rich in albumins and heterogeneous protein species. We report herein a method to detect the proteins released into the circulatory system by tumor cells. Initially we analyzed the protein components in the conditioned medium (CM) of lung cancer primary cell or organ cultures and in the adjacent normal bronchus using one-dimensional PAGE and nano-ESI-MS/MS. We identified 299 proteins involved in key cellular process such as cell growth, organogenesis, and signal transduction. We selected 13 interesting proteins from this list and analyzed them in 628 blood plasma samples using ELISA. We detected 11 of these 13 proteins in the plasma of lung cancer patients and non-patient controls. Our results showed that plasma matrix metalloproteinase 1 levels were elevated significantly in late stage lung cancer patients and that the plasma levels of 14-3-3 sigma, beta, and eta in the lung cancer patients were significantly lower than those in the control subjects. To our knowledge, this is the first time that fascin, ezrin, CD98, annexin A4, 14-3-3 sigma, 14-3-3 beta, and 14-3-3 eta proteins have been detected in human plasma by ELISA. The preliminary results showed that a combination of CD98, fascin, polymeric immunoglobulin receptor/secretory component and 14-3-3 eta had a higher sensitivity and specificity than any single marker. In conclusion, we report a method to detect proteins released into blood by lung cancer. This pilot approach may lead to the identification of novel protein markers in blood and provide a new method of identifying tumor biomarker profiles for guiding both early detection and therapy of human cancer.     

A systems biology approach to studying the role of microbes in human health

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Highlights► Constraint-based modeling has been applied to the metabolism of single organisms. ► We summarize studies using this approach for microbe–microbe models. ► Host–microbe interactions can also be modeled with this approach. ► We also highlight current challenges in multi-organism modeling. ► This approach is very promising for studying the role of microbes in human health.     

Systematic approach to studying proteins from human platelets. Two-dimensional mapping]

Total proteins of human platelets and their membranes were studied by two-dimensional electrophoresis using the lysis in sodium dodecyl sulfate solution. Analysis of platelets from 30 donors revealed the presence of 105 repeating fractions on the electrophoregrams. A two-dimensional map of platelet proteins in the molecular mass versus relative electrophoretic mobility plot was constructed. This map made it possible to localize membrane proteins and albumin as well as a protein immunologically related to phenylalanine hydroxylase. Electrophoretic variants of 13 platelet polypeptides were identified.     

An informational approach to sensory adaptation

Summary Concepts from information theory can enhance our understanding of perceptual processes by providing a unified picture of the process of perception. A single equation is shown to embrace adaptation phenomena, stimulus-response relations, and differential thresholds. Sensory adaptation is regarded as representing a gain in information by the receptor. It is calculated that for constant stimuli in the form of step inputs, insects and arachnids obtain approximately the same amount of information per stimulus from their respective environments as do human beings.     

Ontogenetic approach to studying natural avian populations]

The asymmetry of digit folidosis and the correlation of exterior characteristics have been studied in 20 passerine species. The level of the characteristic asymmetry depends on the phylopatry level and regularly increases in the species disposed to annual change of the nesting site. We assume that the revealed variability reflects interpopulation flow of genes. Age-, sex-, and biotope-related changes associated with urbanization have been revealed in the correlation of characteristics. Older birds have more pronounced correlation of characteristics; it is also more specific for males than females. Correlation of characteristics is less pronounced in the urban avian populations. These differences are interpreted in terms of stabilizing selection within intraspecific groups.     

An approach for studying the mediators of pathogenesis inMycobacterium tuberculosis

Mycobacterium tuberculosis is an example of an intracellular pathogen that mediates the disease state through complex interactions with the host’s immune system. Not only does this organism replicate in the hostile environment prevailing within the infected macrophage, but it has also developed intricate mechanisms to inhibit several defence mechanisms of the host’s immune system. It is postulated here that the mediators of these interactions with the host are products of differentially expressed genes in the pathogen. B and T cell responses of the host are hence to be used as tools to identify such gene products from an expression library of theMycobacterium tuberculosis genome. The various pathways of generating a productive immune response that may be targeted by the pathogen are discussed     

An artificial neural network approach for studying phytoplankton succession

Artificial neural networks are used to model phytoplankton succession and gain insight into the relative strengths of bottom-up and top-down forces shaping seasonal patterns in phytoplankton biomass and community composition. Model comparisons indicate that patterns in chlorophyll aconcentrations response instantaneously to patterns in nutrient concentrations (phosphorous (P), nitrite and nitrate (NO₂/NO₃–N) and ammonium (NH₄–H) concentrations) and zooplankton biomass (daphnid cladocera and copepoda biomass); whereas lagged responses in an index of algal community composition are evident. A randomization approach to neural networks is employed to reveal individual and interacting contributions of nutrient concentrations and zooplankton biomass to predictions of phytoplankton biomass and community composition. The results show that patterns in chlorophyll aconcentrations are directly associated with P, NO₂/NO₃–N and daphnid cladocera biomass, as well as related to interactions between daphnid cladocera biomass, and NO₂/NO₃–N and P. Similarly, patterns in phytoplankton community composition are associated with NO₂/NO₃–N and daphnid cladocera biomass; however show contrasting patterns in nutrient– zooplankton and zooplankton–zooplankton interactions. Together, the results provide correlative evidence for the importance of nutrient limitation, zooplankton grazing and nutrient regeneration in shaping phytoplankton community dynamics. This study shows that artificial neural networks can provide a powerful tool for studying phytoplankton succession by aiding in the quantification and interpretation of the individual and interacting contributions of nutrient limitation and zooplankton herbivory on phytoplankton biomass and community composition under natural conditions.     

An approach to quantifying the exploitability of human ecosystems

Patterns of ecosystem resiliency and differential exploitability by man exist, but they have not yet been worked out in detail This article presents a systematic approach for quantifying the responses of different ecosystems to various levels of human exploitation. It presents a model of the operations of natural ecosystems and suggests a useful analogue between exploitation ecosystems and different stages in ecological succession. This analogue enables us to define a coefficient of exploitability which relates the intensity of ecosystem responses to the intensity of management. The coefficient should prove useful in elucidating a number of types of man-environment interactions. It can be calculated from empirical data. Since it is a function of independent ecosystem variables such as climate, we can also suggest its probable global distribution patterns. Sample values of are calculated from two different types of data. The range of values is greater than one order of magnitude, and their trends are entirely consistent with their predicted distribution.     

Interactions between intrinsic membrane protein and electric field. An approach to studying nerve excitability

We have approached the problem of nerve excitability through three questions: (a) What is the diagram for a channel? That is, what conformational states can the protein assume, and what transitions between these conformations are permitted? (b) What is the channel conductance associated with each conformation the channel can assume? (c) How do the rates for conformational transition depend upon membrane potential? These three questions arise from a standard statistical mechanical treatment of a nerve membrane containing several classes of identical, independent channels. Gating of channels, in this view, is associated with conformational changes of the channel protein, and it is assumed these conformations are distinct. The precise formulation of these questions is presented in terms of the theoretical treatment, and the approaches we have taken to answer the questions are indicated. Our present results indicate: Transition rates should depend exponentially on membrane potential over a limited voltage range, but probably will show a more complex dependence for extremes of the range; channels probably can take on only two conductances, open and shut, but more complicated situations are not entirely excluded; the diagram for a channel cannot be determined from standard voltage clamp data alone, but by studying gating currents and conductance fluctuations, it should be possible to select between alternative plausible physical mechanisms.     

An integrative approach for studying the etiology of alcoholism and other addictions.

Studies of alcoholism etiology often focus on genetic or psychosocial approaches, but not both. Greater understanding of the etiology of alcohol, tobacco and other addictions will come from integration of these research traditions. A research approach is outlined to test three models for the etiology of addictions--behavioral undercontrol, pharmacologic vulnerability, negative affect regulation--addressing key questions including (i) mediators of genetic effects, (ii) genotype-environment correlation effects, (iii) genotype x environment interaction effects, (iv) the developmental unfolding of genetic and environmental effects, (v) subtyping including identification of distinct trajectories of substance involvement, (vi) identification of individual genes that contribute to risk, and (vii) the consequences of excessive use. By using coordinated research designs, including prospective assessment of adolescent twins and their siblings and parents; of adult substance dependent and control twins and their MZ and DZ cotwins, the spouses of these pairs, and their adolescent offspring; and of regular families; by selecting for gene-mapping approaches sibships screened for extreme concordance or discordance on quantitative indices of substance use; and by using experimental (drug challenge) as well as survey approaches, a number of key questions concerning addiction etiology can be addressed. We discuss complementary strengths and weaknesses of different sampling strategies, as well as methods to implement such an integrated approach illustrated for the study of alcoholism etiology. A coordinated program of twin and family studies will allow a comprehensive dissection of the interplay of genetic and environmental risk-factors in the etiology of alcoholism and other addictions.     

A chemical-genetic approach to studying neurotrophin signaling

Trk tyrosine kinases are receptors for members of the neurotrophin family and are crucial for growth and survival of specific populations of neurons. Yet, the functions of neurotrophin-Trk signaling in postnatal development as well as maintenance and plasticity of the adult nervous system are less clear. We report here the generation of mice harboring Trk knockin alleles that allow for pharmacological control of Trk kinase activity. Nanomolar concentrations of either 1NMPP1 or 1NaPP1, derivatives of the general kinase inhibitor PP1, inhibit NGF and BDNF signaling in TrkA(F592A) and TrkB(F616A) neurons, respectively, while no such Trk inhibition is observed in wild-type neurons. Moreover, oral administration of 1NMPP1 leads to specific inhibition of TrkA(F592A), TrkB(F616A), and TrkC(F167A) signaling in vivo. Thus, Trk knockin mice provide valuable tools for selective, rapid, and reversible inhibition of neurotrophin signaling in vitro and in vivo.     

Method for studying the adaptation of Escherichia coli to the acidification of the medium

Apparatus permitting to regulate the growth rate of turbidostat culture of microorganisms has been worked out. The process of adaptation of culture microorganisms to the medium acidity has been investigated by the stabilization of growth rate method. The correlation coefficients between adaptation time and changes of acid concentration in medium have been determined. The effect of aeration and density of microorganisms on the parameters of adaptation process has been considered. The conclusion concerning prospects of the growth rate stabilization method application for studying the regularities of culture microorganisms adaptation to the action of the stress has been made.     

A comparative method for studying adaptation to a randomly evolving environment

Most phylogenetic comparative methods used for testing adaptive hypotheses make evolutionary assumptions that are not compatible with evolution toward an optimal state. As a consequence they do not correct for maladaptation. The "evolutionary regression" that is returned is more shallow than the optimal relationship between the trait and environment. We show how both evolutionary and optimal regressions, as well as phylogenetic inertia, can be estimated jointly by a comparative method built around an Ornstein-Uhlenbeck model of adaptive evolution. The method considers a single trait adapting to an optimum that is influenced by one or more continuous, randomly changing predictor variables.     

An experimental psychophysiological approach to human bradycardiac reflexes

Bradycardic reflexes in man are both of scientific and clinical interest. Using the methods of experimental psychophysiology, control over relevant independent variables permits the study of fine-grained temporal physiologic response topographies, and of psychological factors that may modify the reflex. In addition, information can also be sought through interdisciplinary collaborations with experimental physiologists in order to shed light on the mechanism of the reflexes. These general features of the approach are illustrated by presenting data on two bradycardic reflex preparations: the laboratory dive analog, and the 90-degree negative tilt. The dive-analog studies have shown that a) the dive-reflex proper is a late-occurring bradycardia accompanied by a late-occurring vasoconstriction; and b) for the elicitation of this reflex, both breath-holding and face immersion are necessary. In addition, the physiologic manipulation of temperature affects the reflex in an inverse way over the range of 10 degrees to 40 degrees C, while the sense of control (a psychological variable) attenuates the reflex. The negative-tilt preparation produces a bradycardic response that is ideal as a Pavlovian unconditional response. Some Pavlovian conditioning arrangements, especially an "imaginational" form, do produce significant conditional bradycardic responding, and this has both potential clinical (e.g., biofeedback-related) and theoretical (e.g., S-R vs. S-S accounts of Pavlovian conditioning) applications. The paper ends with a comment on the cognitive paradigm shift in psychology. Although this shift is of importance, it is suggested that it is also important to "remember the response."