Molecular Paradigm Research Articles

A new biology for a new century.

Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher.

Molar and molecular views of choice

The molar and molecular views of behavior are not different theories or levels of analysis; they are different paradigms. The molecular paradigm views behavior as composed of discrete units (responses) occurring at moments in time and strung together in chains to make up complex performances. The discrete pieces are held together as a result of association by contiguity. The molecular view has a long history both in early thought about reflexes and in associationism, and, although it was helpful to getting a science of behavior started, it has outlived its usefulness. The molar view stems from a conviction that behavior is continuous, as argued by John Dewey, Gestalt psychologists, Karl Lashley, and others. The molar paradigm views behavior as inherently extended in time and composed of activities that have integrated parts. In the molar paradigm, activities vary in their scale of organization—i.e., as to whether they are local or extended—and behavior may be controlled sometimes by short-term relations and sometimes by long-term relations. Applied to choice, the molar paradigm rests on two simple principles: (a) all behavior constitutes choice; and (b) all activities take time. Equivalence between choice and behavior occurs because every situation contains more than one alternative activity. The principle that behavior takes time refers not simply to any notion of response duration, but to the necessity that identifying one action or another requires a sample extended in time. The molecular paradigm’s momentary responses are inferred from extended samples in retrospect. In this sense, momentary responses constitute abstractions, whereas extended activities constitute concrete particulars. Explanations conceived within the molecular paradigm invariably involve hypothetical constructs, because they require causes to be contiguous with responses. Explanations conceived within the molar paradigm retain direct contact with observable variables.

Molar and molecular views of choice.

The molar and molecular views of behavior are not different theories or levels of analysis; they are different paradigms. The molecular paradigm views behavior as composed of discrete units (responses) occurring at moments in time and strung together in chains to make up complex performances. The discrete pieces are held together as a result of association by contiguity. The molecular view has a long history both in early thought about reflexes and in associationism, and, although it was helpful to getting a science of behavior started, it has outlived its usefulness. The molar view stems from a conviction that behavior is continuous, as argued by John Dewey, Gestalt psychologists, Karl Lashley, and others. The molar paradigm views behavior as inherently extended in time and composed of activities that have integrated parts. In the molar paradigm, activities vary in their scale of organization--i.e., as to whether they are local or extended--and behavior may be controlled sometimes by short-term relations and sometimes by long-term relations. Applied to choice, the molar paradigm rests on two simple principles: (a) all behavior constitutes choice; and (b) all activities take time. Equivalence between choice and behavior occurs because every situation contains more than one alternative activity. The principle that behavior takes time refers not simply to any notion of response duration, but to the necessity that identifying one action or another requires a sample extended in time. The molecular paradigm's momentary responses are inferred from extended samples in retrospect. In this sense, momentary responses constitute abstractions, whereas extended activities constitute concrete particulars. Explanations conceived within the molecular paradigm invariably involve hypothetical constructs, because they require causes to be contiguous with responses. Explanations conceived within the molar paradigm retain direct contact with observable variables.

Lateral neuron–glia interactions steer the response of axons to the Robo code

Glia are required for axon pathfinding along longitudinal trajectories, but it is unknown how this relates to the molecular paradigm of axon guidance across the midline. Most interneuron axons in bilateral organisms cross the midline only once. Preventing them from recrossing the midline requires the expression of Robo receptors on the axons. These sense the repulsive signal Slit, which is produced by the midline. The lateral positioning of longitudinal axons depends on the response to Slit by the combination of Robo receptors expressed by the axons, on selective fasciculation, and on longitudinal (lateral) glia. Here, we analyse how longitudinal glia influence reading of the 'Robo code' by axons. We show that whereas loss of robo1 alone only affects the most medial axons, loss of both glial cells missing (gcm) and robo1 causes a severe midline collapse of longitudinal axons, similar to that caused by the loss of multiple Robo receptors. Furthermore, whereas ectopic expression of robo2 is sufficient to displace the medial MP2 axons along a more lateral trajectory, this does not occur in gcm-robo1 double-mutant embryos, where axons either do not extend at all or they misroute exiting the CNS. Hence, lateral neuron-glia interactions steer the response of axons to the Robo code.

A “mitochondrial cascade hypothesis” for sporadic Alzheimer's disease

Alzheimer's disease (AD) includes etiologically heterogenous disorders characterized by senile or presenile dementia, extracellular amyloid protein aggregations containing an insoluble amyloid precursor protein derivative, and intracytoplasmic tau protein aggregations. Recent studies also show excess neuronal aneuploidy, programmed cell death (PCD), and mitochondrial dysfunction. The leading AD molecular paradigm, the “amyloid cascade hypothesis”, is based on studies of rare autosomal dominant variants and does not specify what initiates the common late-onset, sporadic form. We propose for late-onset, sporadic AD a “mitochondrial cascade hypothesis” that comprehensively reconciles seemingly disparate histopathologic and pathophysiologic features. In our model, the inherited, gene-determined make-up of an individual's electron transport chain sets basal rates of reactive oxygen species (ROS) production, which determines the pace at which acquired mitochondrial damage accumulates. Oxidative mitochondrial DNA, RNA, lipid, and protein damage amplifies ROS production and triggers three events: (1) a reset response in which cells respond to elevated ROS by generating the β-sheet protein, beta amyloid, which further perturbs mitochondrial function, (2) a removal response in which compromised cells are purged via PCD mechanisms, and (3) a replace response in which neuronal progenitors unsuccessfully attempt to re-enter the cell cycle, with resultant aneuploidy, tau phosphorylation, and neurofibrillary tangle formation. In addition to defining a role for aging in AD pathogenesis, the mitochondrial cascade hypothesis also allows and accounts for histopathologic overlap between the sporadic, late-onset and autosomal dominant, early onset forms of the disease.

MOLECULAR NONLINEAR OPTICS: FROM PARA-NITROANILINE TO ELECTROCHEMICAL SWITCHING OF THE HYPERPOLARIZABILITY

Molecular nonlinear optics describes the nonlinear optical properties of materials at the molecular level. At this most fundamental level, the nonlinear response can be described in terms of molecular parameters, such as number of polarizable electrons, non-centrosymmetric substitution by electron-donor or electron-accepting groups, molecular conformation, position of charge, or degree of charge transfer. We recount the shifts in molecular paradigms for second-order nonlinear optics, largely based on the instrumental possibilities offered to experimentally determine the nonlinear response. We start at the shift from the dipolar paradigm to the octopolar one, initiated by the possibilities of hyper-Rayleigh scattering, and end with the perspectives recently offered by electrochemical switching of the second-order nonlinear optical response at the molecular level.

Digestive proteases of blood-feeding nematodes.

Blood-feeding parasites employ a battery of proteolytic enzymes to digest the contents of their bloodmeal. Host haemoglobin is a major substrate for these proteases and, therefore, a driving force in the evolution of parasite-derived proteolytic enzymes. This review will focus on the digestive proteases of the major blood-feeding nematodes - hookworms (Ancylostoma spp. and Necator americanus) and the ruminant parasite, Haemonchus contortus - but also compares and contrasts these proteases with recent findings from schistosomes and malaria parasites. Haematophagous nematodes express proteases of different mechanistic classes in their intestines, many of which have proven or putative roles in degradation of haemoglobin and other proteins involved in nutrition. Moreover, the fine specificity of the relationships between digestive proteases and their substrate proteins provides a new molecular paradigm for understanding host-parasite co-evolution. Numerous laboratories are actively investigating these molecules as antiparasite vaccine targets.

Leukemia: beneficial actions of retinoids and rexinoids

Acute promyelocytic leukemia (APL), a subtype of acute myeloid leukemia, is the prototype of a cancer that can be cured by differentiation therapy using combined retinoic acid (RA) and chemotherapy. Acute promyelocytic leukemia is caused by chromosomal translocations, which in the large majority of cases generate the prototypic promyelocytic leukemia–retinoic-acid receptor α (PML–RARα) an oncogenic fusion protein formed from the retinoic-acid receptor α and the so-called PML protein. The fusion protein leads to the deregulation of wild type PML and RARα function, thus inducing the differentiation block and an altered survival capacity of promyelocytes of affected patients. A plethora of studies have revealed molecular details that account for the oncogenic properties of acute promyelocytic leukemia fusion proteins and the events that contribute to the therapy-induced differentiation and apoptosis of patients’ blasts. Illustrating the beneficial mechanisms of action of retinoids for acute promyelocytic leukemia patients this review goes on to discuss a plethora of recently recognized molecular paradigms by which retinoids and rexinoids, alone or in combination with other compounds, regulate growth, differentiation and apoptosis also in non-acute promyelocytic leukemia cells, highlighting their potential as drugs for cancer therapy and prevention.

Interactions of VIP, secretin and PACAP(1-38) with phospholipids: a biological paradox revisited.

Vasoactive intestinal peptide (VIP), secretin and pituitary adenylate cyclase-activating peptide(1-38)(PACAP(1-38)) are widely distributed amphipathic mammalian neuropeptides that exert diverse biological effects in target tissues located distant from their site of release. However, the half-life of exogenously-administered VIP, secretin and PACAP(1-38) in the bloodstream is relatively short (minutes) due to rapid degradation and inactivation. This seemingly paradoxical behavior suggests the presence of an innate system(s) that protects the peptides from degradation in vivo. To this end, VIP, secretin and PACAP(1-38) express distinct biophysical properties that once released may protect them from degradation in biological fluids. They self-aggregate at low (nanomolar) concentrations and interact avidly with biomimetic phospholipid monolayers and bilayers at physiological concentrations. The latter evokes conformational transition of the VIP, secretin and PACAP(1-38) molecules from predominantly random coil in aqueous solution to alpha-helix, the preferred peptide conformation for receptor interaction, in phospholipids. These features increase peptide stability and amplify bioactivity in vivo. Collectively, these data suggest the presence of an endogenous targeted delivery platform for VIP, secretin and PACAP(1-38). This innate system may constitute a novel molecular recognition paradigm that could also apply to other amphipathic neuropeptides. Importantly, the distinct behavior of VIP, secretin and PACAP(1-38) in the presence of phospholipids could be exploited to develop novel, long-acting therapeutic formulations of these peptides.

Genomics and Bacterial Metabolism

The field of bacterial metabolism and physiology is arguably the oldest in microbiology. Much of our understanding of biological processes and molecular paradigms has its roots In early studies of prokaryotic physiology. After a period of declining interest in metabolic studies (prompted by the insurgence of molecular techniques), genomic technologies are revitalizing the study of bacterial metabolism and physiology. These new technologies bring a means to approach metabolic questions with a global perspective. When used in combination with classical and molecular techniques, emerging global technologies will make it feasible to understand the complex integration of metabolic processes that result in an efficient physiology. At the same time, without increased computational capabilities, the massive amounts of data generated by these technologies threaten to overwhelm, rather than facilitate, this work. For genomic technologies to reach their potential for increasing our understanding of bacterial metabolism, microbiologists must become more collaborative and multidisciplinary than at any time in our history.

Decryption of the retinoid death code in leukemia.

The recent elucidation of several molecular paradigms by which retinoids regulate growth, differentiation, and apoptosis highlights their promise as drugs for cancer therapy and prevention. Several novel signaling pathways by which retinoids induce cell death have been identified recently. They comprise (a) the induction by RARalpha-selective retinoids of the tumor-selective death ligand TRAIL that kills acute promyelocytic leukemia (APL) cells in a paracrine mode of action, which is the cause of retinoic acid-induced apoptosis after maturation: (b) a novel RARalpha-independent rexinoid-PKA cross-talk that induces maturation of both ATRA-sensitive and ATRA-resistant APL cells and does not invoke ligand-induced alteration of PML-RARalpha signaling, stability, or compartmentalization; and (c) a novel rexinoid signaling pathway that triggers apoptosis of immature APL cells and may correspond to a default death pathway that is operative in the absence of "survival" factors. This rexinoid apoptosis is inhibited by RXR but not RAR antagonists and is distinct from that triggered by RAR agonists, which control cell maturation and postmaturation apoptosis. Here we discuss the promise of retinoids for cancer treatment and prevention with an emphasis on the recently identified mechanisms by which they control (cancer) cell proliferation.

Molecular effects of novel mutations inHesx1/HESX1associated with human pituitary disorders

The homeobox gene Hesx1/HESX1 has been implicated in the establishment of anterior pattern in the central nervous system (CNS) in a number of vertebrate species. Its role in pituitary development has been documented through loss-of-function studies in the mouse. A homozygous missense point mutation resulting in a single amino acid substitution, Arg160Cys (R160C), is associated with a heritable form of the human condition of septo-optic dysplasia (SOD). We have examined the phenotype of affected members in this pedigree in more detail and demonstrate for the first time a genetic basis for midline defects associated with an undescended or ectopic posterior pituitary. A similar structural pituitary abnormality was observed in a second patient heterozygous for another mutation in HESX1, Ser170Leu (S170L). Association of S170L with a pituitary phenotype may be a direct consequence of the HESX1 mutation since S170L is also associated with a dominant familial form of pituitary disease. However, a third mutation in HESX1, Asn125Ser (N125S), occurs at a high frequency in the Afro-Caribbean population and may therefore reflect a population-specific polymorphism. To investigate the molecular basis for these clinical phenotypes, we have examined the impact of these mutations on the regulatory functions of HESX1. We show that Hesx1 is a promoter-specific transcriptional repressor with a minimal 36 amino acid repression domain which can mediate promoter-specific repression by suppressing the activity of homeodomain-containing activator proteins. Mutations in HESX1 associated with pituitary disease appear to modulate the DNA-binding affinity of HESX1 rather than its transcriptional activity. Wild-type HESX1 binds a dimeric homeodomain site with high affinity (K(d) 31 nM) whilst HESX1(S170L) binds with a 5-fold lower activity (K(d) 150 nM) and HESX1(R160C) does not bind at all. Although HESX1(R160C) has only been shown to be associated with the SOD phenotype in children homozygous for the mutation, HESX1(R160C) can inhibit DNA binding by wild-type HESX1 both in vitro and in vivo in cell culture. This dominant negative activity of HESX1(R160C) is mediated by the Hesx1 repression domain, supporting the idea that the repression domain is implicated in interactions between homeodomain proteins. Our data suggest a possible molecular paradigm for the dominant inheritance observed in some pituitary disorders.

Issues in representation of molecular structure: The development of molecular connectivity

Significant issues in the representation of molecular structure and the development of the molecular connectivity paradigm are presented. In the molecular connectivity paradigm, molecular structure is represented directly. Kier and Hall developed the method by creating ways to encode electronic information based on the paradigm developed from the Randić branching index. The simple and valence δ values were created to encode atomic and valence-state electronic information through counts of sigma, pi, and lone pair electrons. A family of indices was created to provide a wide range of structure information. The key aspects of the development are presented and discussed in such a way as to reveal, at least in part, the imaginative thinking involved in the process. Possible future roles for molecular connectivity chi indices are discussed.

Overall connectivity — a next generation molecular connectivity

The development of molecular connectivity concept and some of its key elements — Randić’s inverse-square-root function and the detailed subgraph characterization — are analyzed. The concept of overall connectivity recently advanced is presented as a next step in unfolding the ideas of molecular connectivity by combining them with those of molecular complexity. Definitions of overall connectivity index, eth-order overall connectivities, and overall connectivity vector are presented along with formulae for calculating these sets of topological indices for several classes of graphs of chemical relevance. Based on sums of adjacencies over all subgraphs (or up to a limiting subgraph size in large molecules), the overall connectivities increase both with molecule size and complexity, as expressed in branching and cyclicity of molecular skeleton. When applied to molecules containing heteroatoms, valence overall connectivities are constructed employing the Kier and Hall scheme. The usefulness of the novel indices is demonstrated by modeling physicochemical properties of alkane compounds. A detailed comparison is made with other models derived for the same set of compounds, proceeding from molecular connectivity, as well as with two other probe connectivity functions — the overall connectivity versions of the second Zagreb index, and a derivative inverse function of this index. The favorable comparisons indicate the need of molecular connectivity paradigm revisiting, and show the potential of the overall connectivity indices for QSPR/QSAR applications.

Crystal Structure of the IL-10/IL-10R1 Complex Reveals a Shared Receptor Binding Site

Interleukin 10 (IL-10) is a dimeric cytokine that plays a central role in suppressing inflammatory responses. These activities are dependent on the interaction of IL-10 with its high-affinity receptor (IL-10R1). This intermediate complex must subsequently recruit the low-affinity IL-10R2 chain before cell signaling can occur. Here we report the 2.9 Å crystal structure of IL-10 bound to a soluble form of IL-10R1 (sIL-10R1). The complex consists of two IL-10s and four sIL-10R1 molecules. Several residues in the IL-10/sIL-10R1 interface are conserved in all IL-10 homologs and their receptors. The data suggests that formation of the active IL-10 signaling complex occurs by a novel molecular recognition paradigm where IL-10R1 and IL-10R2 both recognize the same binding site on IL-10.

Molecular imaging paradigms and cancer therapy

Molecular imaging paradigms and cancer therapy

Applying biomarker research.

Public health and environmental professionals have generally focused on monitoring the ambient environment to assess exposures to the public. To understand exposures and effects and predict onset or course of disease, it is also important to look inside the (human) organism. Biomarkers-measurable internal indicators of changes in organisms at the molecular or cellular level-offer great potential to understand environmentally mediated disease and to improve the process of risk assessment. A valid biomarker could also be considered a key event linking a specific environmental exposure to a health outcome. A molecular biomarkers paradigm has its origins in the National Council's (NRC) 1983 Red Book, Risk Assessment in the Federal Government (1). In 1989, the NRC published monographs on Biologic Markers in Pulmonary Toxicology (2) and Biologic Markers in Reproductive Toxicology (3) in which biomarkers of exposure, effect, and susceptibility were discussed as they may relate to disease. In Figure 1, the exposure-todisease paradigm has been drawn to emphasize the application of biomarkers in assessing dose, mode-of-action, and disease etiology. Biomarkers of susceptibility may influence the magnitude of each sequential element in the pathway. Biomarkers useful for disease prevention and intervention may appear anywhere along the pathway. Earlier markers (to the extent that they are measurable at low exposure or dose) have the greatest potential utility to avert disease; later markers are most closely related to the disease. Over the last decade the biomarker model has resulted in considerable research enterprise and nourished and challenged the emerging field of molecular epidemiology. The National Institute of Environmental Health Sciences (NIEHS) and the U.S. Environmental Protection Agency (U.S. EPA), in both their intramural and extramural research programs, have targeted biomarkers for a greater role in human health risk assessment and have worked for their validation in the field and their extension into the clinical environment. At the same time, much of the biomarker research has remained confined to the laboratory, with the promise of successful applications to improve public health or mitigate disease largely unmet. A biomarker should allow better measurements of exposure or earlier identification of health effects. Biomarkers can provide data needed for assessing progress in improving the Nation's health, such as the Healthy People 2010 objectives (4). In summary, biomarkers may break open the black box between exposure and disease and show what individual factors make a difference. Recognizing their substantial investments in intramural and extramural research on biomarkers, the NIEHS and the U.S. EPA held Biomarkers: Taking Stock, An EPA/NIEHS In-House Workshop on Applying Biomarker Research on 30-31 August 1999 in Chapel Hill, North Carolina. Approximately 90 participants explored biomarker research through presentations by invited plenary speakers, posters on individual research projects, and breakout discussion groups. Participants focused on both scientific and organizational objectives. Scientifically, they sought to understand the state of the art and current applications of biomarkers of exposure, effect, and susceptibility; to discern research directions that are likely to make the promise of usable biomarkers a reality; and to explore the role of biomarkers in understanding environmentally-induced disease and in assessing human health risk. Organizational objectives were to increase communication among NIEHS and U.S. EPA staff, including those involved in clinical studies; to complement the ongoing environmental genome research at NIEHS and the planned NIEHS workshops on exposure assessment and environmental epidemiology; and to lay the groundwork for a possible extramural conference on biomarkers in spring 2001.

GATA-dependent recruitment of MEF2 proteins to target promoters.

The myocyte enhancer factor-2 (MEF2) proteins are MADS-box transcription factors that are essential for differentiation of all muscle lineages but their mechanisms of action remain largely undefined. In mammals, the earliest site of MEF2 expression is the heart where the MEF2C isoform is detectable as early as embryonic day 7.5. Inactivation of the MEF2C gene causes cardiac developmental arrest and severe downregulation of a number of cardiac markers including atrial natriuretic factor (ANF). However, most of these promoters contain no or low affinity MEF2 binding sites and they are not significantly activated by any MEF2 proteins in heterologous cells suggesting a dependence on a cardiac-enriched cofactor for MEF2 action. We provide evidence that MEF2 proteins are recruited to target promoters by the cell-specific GATA transcription factors, and that MEF2 potentiates the transcriptional activity of this family of tissue-restricted zinc finger proteins. Functional MEF2/GATA-4 synergy involves physical interaction between the MEF2 DNA-binding domain and the carboxy zinc finger of GATA-4 and requires the activation domains of both proteins. However, neither MEF2 binding sites nor MEF2 DNA binding capacity are required for transcriptional synergy. The results unravel a novel pathway for transcriptional regulation by MEF2 and provide a molecular paradigm for elucidating the mechanisms of action of MEF2 in muscle and non-muscle cells.

A Two-Level, Discrete-Particle Approach for Simulating Ordered Colloidal Structures

We devise a new, two-level discrete-particle model to simulate ordered colloidal structures with vastly different scales. We use the molecular dynamics paradigm with a Lennard-Jones-type potential to define colloidal particle system and dissipative particle dynamics (DPD) to model the solvent. The initially mixed, disordered particle ensemble undergoes a phase transition. We observe the spontaneous creation of spherical or rod-like micelles and their crystallization in stable hexagonal or worm-like structures, respectively. The ordered arrays obtained by using the particle model are similar to the two-dimensional colloidal crystals observed in laboratory experiments. The micelle shape depends on the ratio between the scaling factors of the colloid–colloid to colloid–solvent particle interactions. The properties of the DPD solvent, such as the strongly variable viscosity and partial pressure, determine the speed of crystallization. The intriguing features of colloidal arrays and their exotic symmetries, which persist also over two-dimensional domains, can be simulated numerically by using the two-level discrete-particle approach and are illustrated here.

Cell biology as the centuries change - about as good as it gets

Cell biology as the centuries change - about as good as it gets