Second Moscow Conference on Computational Molecular Biology MCCMB’05

From first principles, a simple model was derived to describe the reduplication of the molecular structure as a sequence of stages whose probabilities can be estimated using the general theory of molecular transformations. It was shown that the genetic information transfer in time (the phenomenon of life) for a long period is impossible without simultaneous “phenomenon of death” and that taking into account the features of transition states in reactions (quantum beats) leads to self-oscillations.     

The compatibiuty polymorphism in invertebrate host/trematodes interactions: research of molecular determinants

The co-evolutionary dynamics that exist in many host-parasite interactions sometimes leads to compatibility polymorphism. This phenomenon is well documented in mollusc/trematodes interactions but its molecular base is unknown. In order to identify key molecules involved in this phenomenon, we developed several molecular approaches comparing compatible or incompatible strains of mollusc or parasite. These comparisons led to the identification of numerous candidate genes listed and discussed (some of them) in the present review.     

Incomplete congruence between morphobiological characters and sex-specific molecular markers in Pacific salmons: 1. Analysis of discrepancy in five species of the genus <Emphasis Type="Italic">Oncorhynchus</Emphasis>

The congruence between molecular markers, identifying the presence of the Y chromosome, and secondary sexual characters was examined in Asian populations of five Pacific salmon species: pink salmon (Oncorhynchus gorbuscha), chum salmon (O. keta), sockeye salmon (O. nerka), chinook salmon (O. tschawytscha), and sima (O. masou). It was demonstrated that in all species examined, the presence or absence of sex-specific molecular markers was to a considerable degree congruent with secondary sexual characters, but in some cases, an incongruence was found. These findings suggested that the mechanism underlying this phenomenon was similar or identical in all species examined. Possible genetic and physiological explanations of this phenomenon are discussed.     

Stimulation of nonspecific resistance in mice with high- and low-molecular fractions of endotoxin on 2 models of Shigella infection]

The capacity of S. paratyphi B endotoxin and its high molecular (HMF) and low molecular (LMF) fractions to stimulate the resistance of mice to shigella infection in intraperitoneal and intranasal challenge was investigated. The HMF developed high activity after the intraperitoneal injection (efficiency index--EI = 2.8). All the preparations were less active on the lung model (EI = 1.6--1.7). Materials of this work lead to the conclusion that in studying the phenomenon of nonspecific resistance induction conditions providing antitoxic and antiinfectious resistance should be considered separately.     

Influence of dissolved oxygen tension and agitation speed on alginate production and its molecular weight in cultures of Azotobacter vinelandii*

The alginate production by Azotobacter vinelandii, as well as the molecular weight of the polymer, are strongly influenced by the dissolved oxygen tension (DOT) and stirring speed of the culture. Under high DOT (5% of air saturation), the bacteria produced more alginate (4.5 g/l) than that obtained at low (0.5%) oxygen tension (1.0 g/l) in cultures conducted at 300 rpm. On the other hand, under constant DOT (3%), the higher the stirring speed (from 300 to 700 rev./min), the higher the specific growth rate and the alginate production rate. However, low agitation speed (300 rev./min) lead the culture to produce a polymer of high molecular weight (680 000 g/g mol) whereas a low molecular weight (352 000 g/g mol) alginate was isolated from cultures conducted at high (700 rev./min) stirring speed. At 700 rev./min, the MMW increased to a plateau between 1 and 3% DOT and then decreased to a minimum of 0.11 x 10(6) g/g mol at 7%. Microscopic observations revealed the presence of cell aggregates (one order of magnitude larger than individual cells) when the culture was conducted at 300 rev./min. Oxygen gradients occurring within the aggregates could be responsible of this phenomenon. At high agitation rate, the MMW of the alginate dropped towards the end of the culture in all conditions evaluated. Alginase activity was detected, which would be responsible for this phenomenon.     

Anti-PD1 therapy induces lymphocyte-derived exosomal miRNA-4315 release inhibiting Bim-mediated apoptosis of tumor cells

Anti-PD1 immunotherapy, as a single agent or in combination with standard chemotherapies, has significantly improved the outcome of many patients with cancers. However, resistance to anti-PD1 antibodies often decreases the long-term therapeutic benefits. Despite this observation in clinical practice, the molecular mechanisms associated with resistance to anti-PD1 antibody therapy have not yet been elucidated. To identify the mechanisms of resistance associated with anti-PD1 antibody therapy, we developed cellular models including purified T cells and different cancer cell lines from glioblastoma, lung adenocarcinoma, breast cancer and ovarian carcinoma. A murine model of lung cancer was also used. Longitudinal blood samples of patients treated with anti-PD1 therapy were also used to perform a proof-of-concept study of our findings. We found that anti-PD1 exposure of T-cell promotes an enrichment of exosomal miRNA-4315. We also noted that exosomal miRNA-4315 induced a phenomenon of apopto-resistance to conventional chemotherapies in cancer cells receiving exosomal miRNA-4315. At molecular level, we discern that the apopto-resistance phenomenon was associated with the miRNA-4315-mediated downregulation of Bim, a proapoptotic protein. In cellular and mice models, we observed that the BH3 mimetic agent ABT263 circumvented this resistance. A longitudinal study using patient blood showed that miRNA-4315 and cytochrome c can be used to define the time period during which the addition of ABT263 therapy may effectively increase cancer cell death and bypass anti-PD1 resistance.This work provides a blood biomarker (exosomal miRNA-4315) for patient stratification developing a phenomenon of resistance to anti-PD1 antibody therapy and also identifies a therapeutic alternative (the use of a BH3 mimetic drug) to limit this resistance phenomenon.Subject terms: Cancer, miRNAs     

Nanoimaging for prion related diseases

Misfolding and aggregation of prion proteins is linked to a number of neurodegenerative disorders such as Creutzfeldt-Jacob disease (CJD) and its variants, kuru, Gerstmann-Straussler-Scheinker syndrome and fatal familial insomnia. In prion diseases, infectious particles are proteins that propagate by transmitting a misfolded state of a protein, leading to the formation of aggregates and ultimately to neurodegeneration. Prion phenomenon is not restricted to humans. There is a number of prion-related diseases in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle. All known prion diseases, collectively called transmissible spongiform encephalopathies (TSEs), are untreatable and fatal. Prion proteins were also found in some fungi where they are responsible for heritable traits. Prion proteins in fungi are easily accessible and provide a powerful model for understanding the general principles of prion phenomenon and molecular mechanisms of mammalian prion diseases. Presently, several fundamental questions related to prions remain unanswered. For example, it is not clear how prions cause the disease. Other unknowns include the nature and structure of infectious agent and how prions replicate? Generally, the phenomenon of misfolding of prion protein into infectious conformations that have the ability to propagate their properties via aggregation is of significant interest. Despite the crucial importance of misfolding and aggregation, very little is currently known about the molecular mechanisms of these processes. While there is an apparent critical need to study molecular mechanisms underlying misfolding and aggregation, the detailed characterization of these single molecule processes is hindered by the limitation of conventional methods. Although some issues remain unresolved, much progress has been recently made primarily due to the application of nanoimaging tools. The use of nanoimaging methods shows great promise for understanding the molecular mechanisms of prion phenomenon, possibly leading toward early diagnosis and effective treatment of these devastating diseases. This review article summarizes recent reports which advanced our understanding of the prion phenomenon through the use of nanoimaging methods.     

Permeability changes induced by polylysines in rat spermatids

High molecular weight (HMW, >15 kDa) but not low molecular weight (LMW, <15 kDa) polylysines (PLs) bound and induced permeability changes in rat spermatid plasma membranes, estimated by Mn2+ quenching of intracellular indo-1 fluorescence (K(1/2) = 3.3 +/- 0.5 microg/ml) and Co2+ quenching of intracellular calcein. The pharmacology of the Mn2+ entry pathway activated by HMW PL does not suggest that Ca2+ channels are involved in this phenomenon. Concentrations of HMW PL that induced divalent ion entry did not induce the entry of ethidium bromide, suggesting that HMW PL first bound and perturbed the plasma membrane structure inducing a non-specific increase in membrane permeability. High concentrations of HMW PL induced cell lysis (K(1/2) = 23 microg/ml). The binding of HMW PL, initially homogenous on the cell surface, subsequently progressed to a segregated pattern resembling a clustering phenomenon.     

A simple model based on the first principles

A simple model based on the first principles is proposed, which describes the reduplication of a molecular structure as a sequence of stages with probabilities that can be estimated on the basis of the general theory of molecular transformations. It is demonstrated that the reproduction of genetic information in time (life phenomenon) over a long period is impossible without the simultaneous "death effect". Taking into account the peculiarities of transient states (quantum beats) leads to the appearance of self-oscillations.     

Local migration of myosin in F-actin plus ATP solution on the boundary of a diffusion cell.

The diffusion phenomena of myosin (myosin A, H-meromyosin or subfragment-1) in F-actin plus ATP solutions were investigated. The upper part of the diffusion cell was filled with F-actin plus ATP, and the lower part was filled with F-actin, ATP, and myosin, then both parts were brought into contact so that a boundary of the two solutions was formed and the diffusion of myosin in F-actin plus ATP solutions started. The diffusion pattern was observed with a schlieren lens system. When almost all the ATP in the lower part of the cell had been consumed by actomyosin, a hyper-sharp schlieren pattern appeared near the boundary. On analyzing this pattern, it was found that a local fast migration of proteins was occurring. Simple Brownian motion of myosin molecules could not explain the hyper-sharp phenomenon. This phenomenon occurred in ther pesence of Mg2+ or Ca2+, but very little in the presence of EDTA. Although it is well known that the superprecipitation of myosin B suspension occurs only at physiological ionic strength, this phenomenon occurred over a relatively wide range of ionic strengths. The molecular mechanism of this phenomenon is discussed in relation to the basic mechanism of the interaction between myosin and F-actin.     

同源交叉反应发生的分子机制

具有一定同源性的蛋白之间可能存在交叉反应而使过敏现象的发生变得更为复杂。与一般的过敏反应类似,交叉反应主要通过B细胞、T细胞、肥大细胞3种途径诱导产生。而不同途径介导产生的交叉反应表现出同一抗原不同的结构特征。通过比较交叉反应在B细胞、T细胞、肥大细胞3种水平产生的不同分子机制,阐明了交叉反应发生的分子基础,为临床抗过敏疾病的治疗提供理论依据。     

Multiple Protein-immobilized Phospholipid Polymer Nanoparticles: Effect of Spacer Length on Residual Enzymatic Activity and Molecular Diagnosis

We report the development of phosphorylcholine (PC) group-covered nanoparticles for multiple immobilization reactions; the surface of these nanoparticles facilitates bioreactions such as enzymatic reactions and molecular diagnoses. The nanoparticles were covered with a bioconjugate PC group containing a polymer backbone, and their surface properties were as follows: (1) suppression of nonspecific protein adsorption and (2) stabilization of immobilized biomolecules. In this study, biomolecules were immobilized on PC-covered nanoparticles by using different spacer lengths between the polymer backbone and biomolecules. The stability of the immobilized biomolecules was evaluated using horseradish peroxidase-labeled IgG, and the bioconjugate nanoparticles were stored at 4, 25, and 40 °C. The residual enzymatic activity of the peroxidase was monitored at a particular time. On the other hand, to test the role of these nanoparticles in molecular diagnosis, we used IgG-conjugated nanoparticles and the fluorescence resonance energy transfer (FRET) phenomenon. The IgG molecules were labeled with either donor or acceptor molecules, and each labeled IgG was simultaneously immobilized on the PC-covered nanoparticles. These labeled IgG molecules induce the FRET phenomenon upon capture of the target antigen provided they are in close proximity. The resulting fluorescence was readable via the FRET phenomenon. In the present study, C-reactive protein (CRP) was used as the target antigen, and the effect of the spacer length is discussed. The bioconjugated nanoparticles covered with PC groups are promising tools for tuning bioreactions.     

The effect of TAO expression on PCD-like phenomenon development and drug resistance in Trypanosoma brucei

Drug resistance in Trypanosoma brucei causes severe problems for people and domestic animals, but molecular mechanisms of the resistance are not well known. Programmed cell death (PCD) is a fundamental process in both multicellular and unicellular organisms, and it is speculated to be one of the important factors contributing to the emergence of drug resistance. We have previously reported that the expression of TAO appears to play a role in the inhibition of the PCD-like phenomenon development in T. brucei. In this study, to ascertain the correlation between the development of the PCD-like phenomenon and the expression of TAO in T. brucei, we genetically engineered T. brucei for conditional over-expression of the TAO gene. TAO over-expressing transgenic T. brucei was refractory to the development of the PCD-like phenomenon compared to the wild-type, indicating that expression of TAO might have a regulatory role on PCD development. Furthermore, the transgenic cells showed resistance to suramin and antrycide. We postulated that intracellular reactive oxygen species (ROS) may be involved in the mechanism of resistance to antrycide because augmentation of ROS in transgenic cells was lower than that in the wild-type cells following treatment with antrycide. These results suggest a possible correlation of PCD to drug resistance in T. brucei.     

SDS-PAGE法测定His-tag融合蛋白分子量产生偏差的原因

Ｈｉｓｔａｇ／ＮｉＮＴＡ系统是新发展起来的一个亲和纯化重组蛋白的有用工具,现常用于基因编码产物的特性研究中。ＳＤＳＰＡＧＥ是实验室测定蛋白质分子量通常采用的方法,而许多实验室用此方法检测Ｈｉｓｔａｇ融合蛋白时却常发现测得的分子量偏大,产生偏差的原因尚未阐明。为弄清这一问题,本实验室在研究一个Ｈｉｓｔａｇ融合蛋白Ｐ７３Ｈｉｓ时,首先用ＳＤＳＰＡＧＥ法测得其分子量确实比理论计算值大,然后对其进行Ｃ末端氨基酸顺序测定、电喷雾质谱分析,结果证实其实际分子量与理论值一致。酶切去除包括Ｈｉｓｔａｇ在内的部分肽段使ＳＤＳＰＡＧＥ法测量蛋白分子量的偏差大大降低,证实Ｈｉｓｔａｇ确实是造成偏差的原因之一。推测由于Ｈｉｓｔａｇ中的碱性氨基酸的作用造成蛋白在ＳＤＳＰＡＧＥ中迁移变慢,而导致偏差。这一现象值得引起有关研究者的注意。     

Electrodissociation of high molecular weight complexes of interferon alpha during recycling isoelectric focusing

Natural human interferon alpha has been separated by selective ultrafiltration into low molecular weight components and the molecules exceeding 100K daltons. Interferon associated with a higher molecular weight fraction showed partial pH sensitivity and resisted dissociation after treatment with urea, mercaptoethanol, sodium chloride or significant changes in pH. However, interferon activity was released from high molecular weight components during recycling isoelectric focusing. Electrodissociation was carried out in 1% ampholytes for 574 watt-hours. The interferon activity was concentrated in a pH range of 6-6.5, whereas, the majority of proteins were generally found in a more acidic position. The dissociated interferon was neutralized by polyclonal antibody to human interferon alpha (IFN alpha) and showed no presence of pH labile form. A pH sensitivity of high molecular weight interferon (HMW-IFN) may reflect an aggregation phenomenon rather than intrinsic structural differences.     

Genetics of preneoplasia: lessons from lung cancer

From biological, histopathologic, and clinical perspectives, lung cancer is a highly complex neoplasm probably having multiple preneoplastic pathways. The sequence of histopathologic changes in the bronchial mucosa that precedes the development of squamous carcinomas of the lung has been identified. For the other major forms of lung cancer, however, such sequences have been poorly documented. This review summarizes the current knowledge regarding the molecular and histopathologic pathogenesis of lung cancer and discusses the complexity of identifying novel molecular mechanisms involved in the development of the lung premalignant disease, and their relevance to the development of new strategies for early detection and chemoprevention. Although our current knowledge of the molecular pathogenesis of lung cancer is still meager, work over the last decade has taught several important lessons about the molecular pathogenesis of this tumor, including the following: a) Better characterization of the high-risk population is needed. b) There are several histopathologic and molecular pathways associated with the development of the major types of non-small cell lung cancer. c) Although there is a field effect phenomenon for lung preneoplastic lesions, recent data suggest that there are at least two distinct lung airway compartments (central and peripheral) for lung cancer pathogenesis. d) Inflammation may play an important role in lung cancer development and could be an important component of the field effect phenomenon. e) For lung adenocarcinoma, at least two pathways (smoking-related and nonsmoking-related) have been identified. f) Finally, the identification of deregulated molecular signaling pathways in lung cancer preneoplasias may provide a rationale for designing novel strategies for early detection and targeted chemoprevention of lung cancer.     

Nanoimaging for prion related diseases

Misfolding and aggregation of prion proteins is linked to a number of neurodegenerative disorders such as Creutzfeldt-Jacob disease (CJD) and its variants: Kuru, Gerstmann-Straussler-Scheinker syndrome and fatal familial insomnia. In prion diseases, infectious particles are proteins that propagate by transmitting a misfolded state of a protein, leading to the formation of aggregates and ultimately to neurodegeneration. Prion phenomenon is not restricted to humans. There are a number of prion-related diseases in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as “mad cow disease”) in cattle. All known prion diseases, collectively called transmissible spongiform encephalopathies (TSEs), are untreatable and fatal. Prion proteins were also found in some fungi where they are responsible for heritable traits. Prion proteins in fungi are easily accessible and provide a powerful model for understanding the general principles of prion phenomenon and molecular mechanisms of mammalian prion diseases. Presently, several fundamental questions related to prions remain unanswered. For example, it is not clear how prions cause the disease. Other unknowns include the nature and structure of infectious agent and how prions replicate. Generally, the phenomenon of misfolding of the prion protein into infectious conformations that have the ability to propagate their properties via aggregation is of significant interest. Despite the crucial importance of misfolding and aggregation, very little is currently known about the molecular mechanisms of these processes. While there is an apparent critical need to study molecular mechanisms underlying misfolding and aggregation, the detailed characterization of these single molecule processes is hindered by the limitation of conventional methods. Although some issues remain unresolved, much progress has been recently made primarily due to the application of nanoimaging tools. The use of nanoimaging methods shows great promise for understanding the molecular mechanisms of prion phenomenon, possibly leading toward early diagnosis and effective treatment of these devastating diseases. This review article summarizes recent reports which advanced our understanding of the prion phenomenon through the use of nanoimaging methods.Key words: protein misfolding, prion, atomic force microscopy, nanomedicine, force spectroscopy     

Dextran-induced Agglutination of Streptococcus mutans, and Its Potential Role in the Formation of Microbial Dental Plaques

Glucose-grown washed cells of streptococci similar to Streptococcus mutans, which contain cell-bound dextransucrase, have been observed to agglutinate upon the addition of high molecular weight dextran. Low molecular weight dextran or unrelated polysaccharides were ineffective. Agglutination also occurred upon addition of sucrose, which can be converted into dextran, but not with other mono- and disaccharides. Other bacteria, including species capable of synthesizing dextrans, were not observed to exhibit this phenomenon. Cells of S. mutans agglutinated upon addition of dextran over a wide pH range, but maximal sensitivity to dextran occurred at pH 8.5. At this pH, such cells can be used for a simple, specific, and exquisitely sensitive qualitative assay for high molecular weight dextran, for addition of 6 ng of dextran with a molecular weight of 2 x 10(6) (i.e., approximately three molecules per cell) caused detectable agglutination. High concentrations of glucose, levan, and dextran of molecular weight of 2 x 10(4) inhibited the reaction. Fluorescein-labeled cells of S. mutans were observed to adhere to dextran-containing plaques and dextran-treated teeth, suggesting that this phenomenon may be of importance in the formation of streptococcal dental plaques. The mechanism responsible for dextraninduced agglutination appears to involve the affinity of a receptor site, possibly dextransucrase, on the surface of several cells for common dextran molecules.     

Mitochondrial protein alteration in active brown fat: A sodium dodecyl sulfate-polyacrylamide gel electrophoretic study

The polypeptide composition of mitochondria isolated from the brown adipose tissue of control rats (bred at 22°C) or cold-exposed animals (bred at 6°C) was compared using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A striking increase in the content of an unknown polypeptide (apparent molecular weight 32,000 daltons) was found after cold adaptation, a phenomenon which was reversed during re-adaptation to a normal temperature. This protein seems to be localized in the membrane fraction of the mitochondria.     

Testing the relationship between morphological and molecular rates of change along phylogenies

Abstract.— Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for "total-evidence" phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.