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PubMed2002

Altered aquaporin-4 expression in human muscular dystrophies: a common feature?

Duchenne Muscular Dystrophy (DMD) is a progressive lethal muscle disease that affects young boys. Dystrophin, absent in DMD and reduced in the milder form Becker Muscular Dystrophy (BMD), binds to several membrane-associated proteins known as dystrophin-associated proteins (DAPs). Once this critical structural link is disrupted, muscle fibers become more vulnerable to mechanical and osmotic stress. Recently, we have reported that the expression of aquaporin-4 (AQP4), a water-selective channel expressed in the sarcolemma of fast-twitch fibers and astrocyte end-feet, is drastically reduced in the muscle and brain of the mdx mouse, the animal model of DMD. In the present study, we analyzed the expression of AQP4 in several DMD/BMD patients of different ages with different mutations in the dystrophin gene. Immunofluorescence results indicate that, compared with healthy control children, AQP4 is reduced severely in all the DMD muscular biopsies analyzed and in 50% of the analyzed BMD. Western blot analysis revealed that the deficiency in sarcolemma AQP4 staining is due to a reduction in total AQP4 muscle protein content rather than to changes in immunoreactivity. Double-immunostaining experiments indicate that AQP4 reduction is independent of changes in the fiber myosin heavy chain composition. AQP4 and a-syntrophin analysis of BMD muscular biopsies revealed that the expression and stability of AQP4 in the sarcolemma does not always decrease when a-syntrophin is strongly reduced. Finally, limb-girdle muscular dystrophy biopsies and facioscapulohumeral muscular dystrophy revealed that AQP4 expression was not altered in these forms of muscular dystrophy. These experiments provide the first evidence of AQP4 reduction in a human pathology and show that this deficiency is an important feature of DMD/BMD.

Aquaporin 4↗

PubMed1988

Comparative separation of human plasma proteins on polysulphated chromatographic media.

Polysulphated chromatographic media, particularly Heparin Sepharose, are generally used to purify a variety of different plasma proteins. Heparin Sepharose, dextran sulphate Sepharose and sulphated dextran are compared with two recently available sulphated cellulose chromatographic media. The potential influence of structural features of different polysaccharides on the interaction with selected plasma proteins has been evaluated with the particular objective of developing an alternative medium for the preparation of specific therapeutic factor concentrates. The studies indicate that the degree of sulphation of the matrix is an important but not a critical determinant for resolution of factors IX and X. Despite large differences in the carbohydrate structure of the matrices, the new sulphated cellulose gel 5.2 had a total protein capacity and specific binding profile comparable to Heparin Sepharose. The sulphated cellulose which is competitively priced, and has excellent stability, is a potential alternative to Heparin Sepharose especially for larger scale industrial processing of factor IX concentrate.

Blood Proteins↗

PubMed2002

Sandia octahedral molecular sieves (SOMS): structural and property effects of charge-balancing the M(IV)-substituted (M = Ti, Zr) Niobate framework.

Sandia octahedral molecular sieves (SOMS) is an isostructural, variable composition class of ion exchangers with the general formula Na(2)Nb(2-x)M(IV)(x)O (6-x)(OH)(x).H(2)O (M(IV) = Ti, Zr; x = 0.04-0.40) where up to 20% of the framework Nb(V) can be substituted with Ti(IV) or Zr(IV). This class of molecular sieves is easily converted to perovskite through low-temperature heat treatment (500-600 degrees C). This report provides a detailed account of how the charge imbalance of this Nb(V)-M(IV) substitution is compensated. X-ray powder diffraction with Rietveld refinement, infrared spectroscopy, thermogravimetric analysis, (23)Na MAS NMR, and (1)H MAS NMR were used to determine how the framework anionic charge is cation-balanced over a range of framework compositions. All spectroscopic evidence indicated a proton addition for each M(IV) substitution. Evidences for variable proton content included (1) increasing OH observed by (1)H MAS NMR with increasing M(IV) substitution, (2) increased infrared band broadening indicating increased H-bonding with increasing M(IV) substitution, (3) increased TGA weight loss (due to increased OH content) with increasing M(IV) substitution, (4) no variance in population on the sodium sites (indicated by Rietveld refinement) with variable composition, and (5) no change in the (23)Na MAS NMR spectra with variable composition. Also observed by infrared spectroscopy and (23)Na MAS NMR was increased disorder on the Nb(V)/M(IV) framework sites with increasing M(IV) substitution, evidenced by broadening of these spectral features. These spectroscopic studies, along with ion exchange experiments, also revealed the effect of the Nb(V)/M(IV) framework substitution on materials properties. Namely, the temperature of conversion to NaNb(1-x)M(IV)(x)O(3) (M = Ti, Zr) perovskite increased with increasing Ti in the framework and decreased with increasing Zr in the framework. This suggested that Ti stabilizes the SOMS framework and Zr destabilizes the SOMS framework. Finally, comparing ion exchange properties of a SOMS material with minimal (2%) Ti to a SOMS material with maximum (20%) Ti revealed the divalent cation selectivity of these materials which was reported previously is a function of the M(IV) substitution in the framework. A thorough investigation of this class of SOMS materials has revealed the importance of understanding the influence of heterovalent substitutions in microporous frameworks on material properties.

Journal Article↗

PubMed2000

A distinctive clade B HIV type 1 is heterosexually transmitted in Trinidad and Tobago.

HIV-1 transmission worldwide is predominantly associated with heterosexual activity, and non-clade B viruses account for the most spread. The HIV-1 epidemic in Trinidad/Tobago and the Caribbean shares many features with such heterosexual epidemics, including a prominent role for coincident sexually transmitted diseases. This study evaluates the molecular epidemiology of HIV-1 in Trinidad/Tobago during a period when abrupt transition from homosexual to heterosexual transmission occurred in the absence of injecting drug use, concomitant with a rapid rise in HIV-1 prevalence in the heterosexual population. Of 31 viral isolates studied during 1987-1995, all cluster with subtype B reference strains. In the analysis of full env genes from 22 early seroconverters, the Trinidad isolates constitute a significant subcluster within the B subtype. The Trinidad V3 consensus sequence differs by a single amino acid from the prototype B V3 consensus and demonstrates stability over the decade of this study. In the majority of isolates, the V3 loop of env contains a signature threonine deletion that marks the lineage of the Trinidad HIV-1 clade B epidemic from pre-1984. No phenotypic features, including syncitium induction, neutralization profiles, and chemokine receptor usage, distinguish this virus population from other subtype B viruses. Thus, although the subtype B HIV-1 viruses being transmitted in Trinidad are genetically distinguishable from other subtype B viruses, this is probably the result of a strong founder effect in a geographically circumscribed population rather than genetic selection for heterosexual transmission. These results demonstrate that canonical clade B HIV-1 can generate a typical heterosexual epidemic.

Amino Acid Sequence↗

PubMed2001

Crystal structure at 1.5-A resolution of Pyrus pyrifolia pistil ribonuclease responsible for gametophytic self-incompatibility.

The crystal structure of the Pyrus pyrifolia pistil ribonuclease (S(3)-RNase) responsible for gametophytic self-incompatibility was determined at 1.5-A resolution. It consists of eight helices and seven beta-strands, and its folding topology is typical of RNase T(2) family enzymes. Based on a structural comparison of S(3)-RNase with RNase Rh, a fungal RNase T(2) family enzyme, the active site residues of S(3)-RNase assigned were His(33) and His(88) as catalysts and Glu(84) and Lys(87) as stabilizers of an intermediate in the transition state. Moreover, amino acid residues that constitute substrate binding sites of the two RNases could be superimposed geometrically. A hypervariable (HV) region that has an S-allele-specific sequence comprises a long loop and short alpha-helix. This region is far from the active site cleft, exposed on the molecule's surface, and positively charged. Four positively selected (PS) regions, in which the number of nonsynonymous substitutions exceeds that of synonymous ones, are located on either side of the active site cleft, and accessible to solvent. These structural features suggest that the HV or PS regions may interact with a pollen S-gene product(s) to recognize self and non-self pollen.

Amino Acid Sequence↗

PubMed1999

Continuous mixed venous (SvO2) monitoring. Too expensive or indispensible?

Based on theoretic principles and clear literature support, SvO2 (mixed venous oxyhemoglobin) monitoring offers an important advantage over traditional hemodynamic parameters. SvO2 allows more precise understanding of the adequacy of cardiac and pulmonary function than traditional parameters. SvO2 values do not replace the need to measure individual parameters of oxygen delivery or consumption but serves as the standard for assessing the impact of each parameter on tissue oxygenation. SvO2 has the ability to reflect a threat to tissue oxygenation that is unmatched by other parameters. Its ability to give a real time indication of tissue oxygenation makes it a preferred parameter for monitoring the adequacy of hemodynamics. Its use as an end point for determining the adequacy of hemodynamics (BP, CO/CI), measurement of Qs/Qt, and prediction of potential hemodynamic instability make this parameter invaluable for the knowledgeable clinician. SvO2 catheters cost more than traditional PA catheters, a factor that has limited their acceptance as the standard PA catheter. The added cost of the SvO2 catheter has not been adequately addressed in the research literature. However, research does support SvO2 allows more rapid termination of drug therapies, may improve movement out of the ICU, and reduces the incidence of mechanical ventilator manipulation. These features increase the cost-effectiveness of SvO2 catheters. The cost-effectiveness of the catheter, like any technology, is predicated on the clinician. Clinicians++ must be educated to use SvO2 as a primary end point for treatment decisions regarding hemodynamic therapy and patient stability. If used properly, every PAC should use fiberoptic SvO2 capabilities.

Adolescent↗

PubMed1990

Inheritance of species-specific behaviors in the paradise fish (Macropodus opercularis): a diallel study.

Species-specific elements of the paradise fish's ethogram were recorded in one familiar and three different unfamiliar environments, which were designed to model certain features of this species' natural habitat: (1) a densely vegetated home range, (2) a novel open field, (3) a small novel place, and (4) a small novel place with a predator. The inheritance of the behavioral elements was investigated employing a five-times-replicated diallel cross among three inbred strains. A detailed Hayman analysis of variance and a variance-covariance analysis were performed to uncover the genetic architectures of these phenotypes. Additive genetic effects and/or ambidirectional dominance was found to be characteristic of most species-specific behavioral elements studied, suggesting an evolutionary history of stabilizing selection.

Animals↗

PubMed1987

Relationships between DNA-binding kinetics and biological activity for the 9-aminoacridine-4-carboxamide class of antitumor agents.

The kinetics of dissociation of calf thymus DNA complexes of the new intercalating antitumor drug N-[2-(dimethylamino)ethyl]-9-aminoacridine-4-carboxamide (5) and selected derivatives have been investigated by using the surfactant-sequestration method. The derivatives studied include those where the position (14 and 15) and nature of attachment (20 and 21) of the cationic side chain is modified, those where the distance (16-19) and composition (22-24) of the cationic group are varied, and those in which the chromophore is further substituted (25-31). While all of the compounds dissociate by a mechanism that involves at least three intermediate bound forms, derivatives bearing a 4-CONH(CH2)2NR1R2 side chain (where R1 and R2 are groups that permit the nitrogen to be protonated at neutral pH) have access to an additional binding mode of greater kinetic stability. A positive correlation is found between in vivo antitumor activity, selectivity of binding to GC-rich DNAs, and the presence of this fourth, long-lived transient species. We have interpreted our kinetic findings in terms of a molecular model for acridinecarboxamide-DNA complexes that accounts for the appearance of the fourth component. The acridine chromophore is postulated to intercalate from the narrow groove, its major axis lying at an angle to the major axis of the base pairs so that the CH atoms of positions 5 and 6 protrude into the groove. An important feature of the model is a bifurcated hydrogen bond between the O2 oxygen atom of a cytosine base adjacent to the binding site and the NH atoms of the carboxamide and protonated terminal amino functions of the drug molecule. Since the structural features required to form this bonding interaction are necessary, although not sufficient, conditions for in vivo antitumor activity, it is suggested that the model may describe the essential characteristics of the biologically active form of the bound drug. These findings further attest to the value of investigating the kinetics of DNA-drug interaction in studies of the mode of action of antitumor intercalating agents.

Amides↗

PubMed2001

Conservation of outer membrane protein E among strains of Moraxella catarrhalis.

Outer membrane protein E (OMP E) is a 50-kDa protein of Moraxella catarrhalis which has several features that suggest that the protein may be an effective vaccine antigen. To assess the conservation of OMP E among strains of M. catarrhalis, 22 isolates were studied with eight monoclonal antibodies which recognize epitopes on different regions of the protein. Eighteen of 22 strains were reactive with all eight antibodies. The sequences of ompE from 16 strains of M. catarrhalis were determined, including the 4 strains which were nonreactive with selected monoclonal antibodies. Analysis of sequences indicate a high degree of conservation among strains, with sequence differences clustered in limited regions of the gene. To assess the stability of ompE during colonization of the human respiratory tract, the sequences of ompE of isolates collected from patients colonized with the same strain for 3 to 9 months were determined. The sequences remained unchanged. These results indicate that OMP E is highly conserved among strains of M. catarrhalis, and preliminary studies indicate that the gene which encodes OMP E remains stable during colonization of the human respiratory tract.

Adult↗

PubMed2001

Recruitment and early treatment in a multicenter study of acute spinal cord injury.

STUDY DESIGN: Post hoc secondary analysis of data from 1992 to 1998 in the trial of Sygen in Acute Spinal Cord Injury. OBJECTIVES: Quasi-epidemiologic understanding of injury and treatment patterns and of recruitment in an SCI trial. No drug efficacy results. SUMMARY OF BACKGROUND DATA: The most recent large epidemiologic study was the National SCI Database by Stover and colleagues around 1980. METHODS: Emphasis on descriptive, rather than inferential, statistics: consistent with secondary analysis. RESULTS: The study involved 760 patients at 28 centers in North America. Cervical injuries were more common than thoracic, and complete injuries were more common than incomplete injuries. Recruitment in the complete cervical stratum was 332, but the incomplete thoracic strata had only 31 patients combined. Vital signs at arrival and on randomization show fair stability. Clock times show more injuries on weekends and nights but suggest immediate attention was given. Elapsed times to treatment (especially EMT and Medevac arrival) are short. The rate of direct admission to tertiary centers, traction weight, and time to surgery vary among centers. Inpatient rehabilitation appeared driven by insurance in addition to severity. CONCLUSIONS: The imbalances in favor of cervical and of complete injuries would make it hard for studies to attain results for SCI in general. The vital signs and time patterns suggest local protocol-driven stabilization to prevent secondary physiologic injury early after SCI. Some features of care vary among centers, but the sparseness of prospective data in specific injury and treatment categories suggests that treatment guidelines have limited empirical support and should be made cautiously.

Acute Disease↗

PubMed1999

Magnetic resonance imaging features of allografts.

OBJECTIVE: To investigate the magnetic resonance imaging (MRI) features of allografts at various time intervals after surgery in patients with osteoarticular allografts. DESIGN AND PATIENTS: Sixteen patients who were treated with osteoarticular allografts and who were followed over time with MRI studies as part of their long-term follow-up were retrospectively selected for this study. T1-weighted images were obtained both before and after gadolinium administration along with T2-weighted images. All images were reviewed by an experienced musculoskeletal radiologist, with two other experienced radiologists used for consultation. Imaging studies were organized into three groups for ease of discussion: early postoperative period (2 days to 2 months), intermediate postoperative period (3 months to 2 years), and late postoperative period (greater than 2 years). RESULTS: In the early postoperative period, no gadolinium enhancement of the allograft was visible in any of the MR images. A linear, thin layer of periosteal and endosteal tissue enhancement along the margin of the allograft was visible in images obtained at 3-4 months. This enhancement appeared gradually to increase in images from later periods, and appears to have stabilized in the images obtained approximately 2-3 years after allograft placement. The endosteal enhancement diminished after several years, with examinations conducted between 6 and 8 years following surgery showing minimal endosteal enhancement. However, focal enhancement was noted adjacent to areas of pressure erosion or degenerative cysts. All the cases showed inhomogeneity in the marrow signal (scattered low signal foci on T1 with corresponding bright signal on T2), and a diffuse, inhomogeneous marrow enhancement later on. CONCLUSION: We have characterized the basic MRI features of osteoarticular allografts in 16 patients who underwent imaging studies at various time points as part of routine follow-up. We believe that the endosteal and periosteal enhancement observed on MRI during the first few months to 2 years following surgery represents vascular ingrowth and early skeletal repair. The zone of periosteal enhancement could also include the new bone laid on the surface of the allograft through which the soft tissues bind to the cortex. The exact reason for the inhomogeneity in the marrow signal, and the diffuse, inhomogeneous marrow enhancement is not clear. This may represent saponified and/or necrotic marrow fat interspersed with the fibrovascular tissue. The features noted here should provide radiologists with useful information regarding imaging characteristics they can expect to see in other allograft replacement patients.

Adolescent↗

PubMed2002

The relevance of prostatectomy findings for brachytherapy selection in patients with localized prostate carcinoma.

BACKGROUND: The efficacy of brachytherapy for patients with localized prostate carcinoma depends on adequate radiotherapeutic coverage of the primary tumor and its subclinical extraprostatic extensions. Predictive models based on pretherapy factors may be useful to estimate the likelihood for clinically relevant extraprostatic disease and may be incorporated into selection criteria for this procedure. METHODS: Multivariate logistic regression model building was performed using pretherapy factors in 2905 surgically staged patients with localized prostate carcinoma to estimate the probability of seminal vesicle and/or lymph node involvement. Bootstrap methods were employed to assess the stability of the final model parameters and to determine the sensitivity and specificity of the final model. RESULTS: Clinical tumor classification, biopsy Gleason score groupings, and serum prostate specific antigen (PSA) levels were associated with seminal vesicle and/or pelvic lymph node involvement. These factors were incorporated into a multivariate model that predicted for these adverse histopathologic features. Allowing for up to a 10% likelihood for seminal vesicle and/or pelvic lymph node involvement, patients with tumors classified as T1c-T2a, Gleason scores of 2-6, and PSA < or = 16 ng/mL; or with tumors classified as T1c-T2a, Gleason scores of 7-10, and PSA < or = 4 ng/mL; or with tumors classified as T2b-T2c, Gleason scores of 2-6, and PSA < or = 6 ng/mL would be potential candidates for brachytherapy alone. CONCLUSIONS: The predictive model presented may provide criteria whereby an adequately performed prostate brachytherapy procedure is expected to encompass the intraprostatic and adjacent extraprostatic disease. Prostate brachytherapy alone may be considered in these circumstances, whereas the addition of external beam radiotherapy may be reserved for patients with disease that is apt to extend beyond the brachytherapy target volume.

Brachytherapy↗

PubMed1996

Design, synthesis, and evaluation of nonpeptidic inhibitors of human rhinovirus 3C protease.

The design, synthesis, and biological evaluation of reversible, nonpeptidic inhibitors of human rhinovirus (HRV) 3C protease (3CP) are reported. A novel series of 2,3-dioxindoles (isatins) were designed that utilized a combination of protein structure-based drug design, molecular modeling, and structure-activity relationship (SAR). The C-2 carbonyl of isatin was envisioned to react in the active site of HRV 3CP with the cysteine responsible for catalytic proteolysis, thus forming a stabilized transition state mimic. Molecular-modeling experiments using the apo crystal structure of human rhinovirus-serotype 14 (HRV-14) 3CP and a peptide substrate model allowed us to design recognition features into the P1 and P2 subsites, respectively, from the 5- and 1-positions of isatin. Attempts to optimize recognition properties in the P1 subsite using SAR at the 5-position were performed. In addition, a series of ab initio calculations were carried out on several 5-substituted isatins to investigate the stability of sulfide adducts at C-3. The inhibitors were prepared by general synthetic methods, starting with commercially available 5-substituted isatins in nearly every case. All compounds were tested for inhibition of purified HRV-14 3CP. Compounds 8, 14, and 19 were found to have excellent selectivity for HRV-14 3CP compared to other proteolytic enzymes, including chymotrypsin and cathepsin B. Selected compounds were assayed for antiviral activity against HRV-14-infected HI-HeLa cells. A 2.8 A cocrystal structure of derivative 19 covalently bound to human rhinovirus-serotype 2 (HRV-2) 3CP was solved and revealed that the isatin was situated in essentially the same conformation as modeled.

3C Viral Proteases↗

PubMed1994

Characteristics of antitumor activity of KW-2189, a novel water-soluble derivative of duocarmycin, against murine and human tumors.

Methyl(1S)-1-bromomethyl-7-methyl-5-[(4-methylpiperazinyl)-carb onyloxy]- 3-[(5,6,7-trimethoxy-2-indolyl)-carbonyl]-1,2-dihydro-3H-pyrolo[3, 2-e] indole-8-carboxylate hydrobromide (KW-2189), a novel derivative of duocarmycin B2, was selected for extensive evaluation based on its improved antitumor activity, water solubility, and stability in the culture medium, as compared with duocarmycin B2. Although the in vitro cell growth-inhibitory activity of KW-2189 was less potent than that of duocarmycin B2, it significantly inhibited the growth of five murine solid tumors including Colon 26 adenocarcinoma, Colon 38 adenocarcinoma, and B16 melanoma in vivo. KW-2189 was also effective against murine P388 leukemia and L1210 leukemia not only by local administration (i.p.-i.p. system), but also by systemic administration (i.p.-i.v. or i.v.-i.v. system). The most remarkable feature of KW-2189 was its efficacy against various human xenografts, which was observed in 14 tumors among 16 tested tumors including drug-insensitive tumors by single i.v. administration. Tumor regression was observed in mice bearing LC-6 lung, St-4 and St-40 stomach, Li-7 liver, PAN-2 pancreas, and MX-1 breast carcinomas. In many cases, the activities of KW-2189 were more than those of clinically active agents, mitomycin C, Adriamycin, cisplatin, and cyclophosphamide. Delayed lethal toxicity, which was reported in mice treated with CC-1065 whose structure was similar to KW-2189, was not observed in mice treated with KW-2189. KW-2189 inhibited DNA synthesis more significantly than RNA or protein synthesis, although DNA strand breaks were not observed. KW-2189 was activated by porcine liver esterase, mouse liver homogenate or Hep G2 homogenate, and DU-86-DNA adducts were detected in KW-2189-treated HeLa S3 cells, suggesting that KW-2189 was converted to DU-86 in the cells. These results indicate that KW-2189 is an interesting candidate for further development as a novel antitumor agent.

Animals↗

PubMed1992

Nonlinearities in amoxycillin pharmacokinetics. I. Disposition studies in the rat.

Several features of amoxycillin pharmacokinetics in man are not well known in spite of the extensive clinical use of the antibiotic. In this paper it is demonstrated that amoxycillin disposition kinetics in rats is clearly nonlinear, and that this may be due mainly to its elimination mechanisms. At different intravenous bolus dose levels, and in steady-state perfusion studies, the most striking feature is an increased renal clearance as dose increases (from 3.5 to 7.0 mg kg-1 for intravenous bolus, and from 4.6 to 20.0 micrograms min-1 for intravenous perfusions). This phenomenon has been attributed to a saturation of the active renal tubular reabsorption of the antibiotic. When the intravenous dose is substantially increased (28.0 mg kg-1 bolus), plasma clearance tends to stabilize, probably because saturation of the active tubular secretion of amoxycillin takes place at these doses. Extrarenal clearance seems to remain linear throughout the entire dose range. On the basis of these observations and a review of selected bibliography, an interpretation of the kinetic disposition behaviour of amoxycillin in man is attempted.

Amoxicillin↗

PubMed1995

Proposed cation-pi mediated binding by factor Xa: a novel enzymatic mechanism for molecular recognition.

Factor Xa (FXa) is an important serine protease in the blood coagulation cascade. Small synthetic competitive inhibitors of FXa are under development as potential anticoagulants. To better understand FXa structural features and molecular recognition mechanisms, we have constructed three dimensional models of FXa-inhibitor complex structures via a new search approach that samples conformational space and binding space simultaneously for DABE and DX-9065a, two bis amidinoaryl derivatives that are among the most potent and selective FXa inhibitors reported to date. We find the most probable binding modes for the two inhibitors to be a folded conformation, with one distal amidino group extending into the S1 pocket, forming a salt-bridge with FXa Asp-189, and the other positively charged group fitting into the S4 subsite, and stabilized by a cation-pi interaction. We propose as a hypothesis that the cavity-like S4 subsite formed by the three pi-faces of the aromatic residues Tyr-99, Phe-174 and Trp-215 is sufficiently rich in pi electrons that it is not only a hydrophobic pocket, but also forms a cation recognition site. This proposed cation-pi binding mechanism is one of the first proposed for enzymatic molecular recognition, and for which experimental verification can be obtained without any complicating charge compensation mechanism. Our models provide plausible explanations of the structure-activity relationships observed for these inhibitors, and suggest that cation-pi interactions may provide a novel mechanism for molecular recognition.

Amino Acid Sequence↗

PubMed2001

Biocomplexity: adaptive behavior in complex stochastic dynamical systems.

Existing methods of complexity research are capable of describing certain specifics of bio systems over a given narrow range of parameters but often they cannot account for the initial emergence of complex biological systems, their evolution, state changes and sometimes-abrupt state transitions. Chaos tools have the potential of reaching to the essential driving mechanisms that organize matter into living substances. Our basic thesis is that while established chaos tools are useful in describing complexity in physical systems, they lack the power of grasping the essence of the complexity of life. This thesis illustrates sensory perception of vertebrates and the operation of the vertebrate brain. The study of complexity, at the level of biological systems, cannot be completed by the analytical tools, which have been developed for non-living systems. We propose a new approach to chaos research that has the potential of characterizing biological complexity. Our study is biologically motivated and solidly based in the biodynamics of higher brain function. Our biocomplexity model has the following features, (1) it is high-dimensional, but the dimensionality is not rigid, rather it changes dynamically; (2) it is not autonomous and continuously interacts and communicates with individual environments that are selected by the model from the infinitely complex world; (3) as a result, it is adaptive and modifies its internal organization in response to environmental factors by changing them to meet its own goals; (4) it is a distributed object that evolves both in space and time towards goals that is continually re-shaping in the light of cumulative experience stored in memory; (5) it is driven and stabilized by noise of internal origin through self-organizing dynamics. The resulting theory of stochastic dynamical systems is a mathematical field at the interface of dynamical system theory and stochastic differential equations. This paper outlines several possible avenues to analyze these systems. Of special interest are input-induced and noise-generated, or spontaneous state-transitions and related stability issues.

Adaptation, Physiological↗

PubMed1997

The foldability landscape of model proteins.

Molecular evolution may be considered as a walk in a multidimensional fitness landscape, where the fitness at each point is associated with features such as the function, stability, and survivability of these molecules. We present a simple model for the evolution of protein sequences on a landscape with a precisely defined fitness function. We use simple lattice models to represent protein structures, with the ability of a protein sequence to fold into the structure with lowest energy, quantified as the foldability, representing the fitness of the sequence. The foldability of the sequence is characterized based on the spin glass model of protein folding. We consider evolution as a walk in this foldability landscape and study the nature of the landscape and the resulting dynamics. Selective pressure is explicitly included in this model in the form of a minimum foldability requirement. We find that different native structures are not evenly distributed in interaction space, with similar structures and structures with similar optimal foldabilities clustered together. Evolving proteins marginally fulfill the selective criteria of foldability. As the selective pressure is increased, evolutionary trajectories become increasingly confined to "neutral networks," where the sequence and the interactions can be significantly changed while a constant structure is maintained.

Amino Acid Sequence↗