Novel Approach for Clustering Zeolite Crystal Structures.

Informatics approaches play an increasingly important role in the design of new materials. In this work we apply unsupervised statistical learning for identifying four framework-type attractors of zeolite crystals in which several of the zeolite framework types are grouped together. Zeolites belonging to these super-classes manifest important topological, chemical and physical similarities. The zeolites form clusters located around four core framework types: LTA, FAU, MFI and the combination of EDI, HEU, LTL and LAU. Clustering is performed in a 9-dimensional space of attributes that reflect topological, chemical and physical properties for each individual zeolite crystalline structure. The implemented machine learning approach relies on hierarchical top-down clustering approach and the expectation maximization method. The model is trained and tested on ten partially independent data sets from the FIZ/NIST Inorganic Crystal Structure Database.

[Epidemic security of the population of Tyrnyauz in Kabardin-Balkar Republic under the conditions of emergency situation caused by flood]. / Protivoépidemicheskoe obespechenie naseleniia g.Tyrnyauz Kabardino-Balkarskoi Respubliki v usloviiakh chrezvychainoi situatsii prirodnogo kharaktera.

Materials characterizing the consequences of emergency situation caused by natural type in Tyrnyauz, the Kabardin-Balkar Republic, are presented. As shown in these materials, mud flows from the surrounding mountains resulted in the damage inflicted to the main life-supporting systems of the town: water supply and sewage, power supply, medical institutions and, partially, housing resources. As the result of urgent measures carried out in cooperation with the departments of the Ministry of Emergency Situations, health services and state sanitary and epidemiological surveillance services epidemiological safety could be ensured in the town. In carrying out prophylactic measures the main attention was paid to the provision of the population with good-quality drinking water, foodstuffs, the active detection of patients with enteric infections, the bacteriological control of water in surface reservoirs for the pathogenic microflora.

SECOST: sequence-conformation-structure database for amino acid residues in proteins.

The sequence-conformation-structure database for amino acid residues contains information on 114 828 individual residues derived from the spatial structures of 473 high-quality non-homologous proteins. The information in the database is obtained using a variety of different methods and can be used in various protein modeling applications.

A new approach to protein fold recognition based on Delaunay tessellation of protein structure.

We propose new algorithms for sequence-structure compatibility (fold recognition) searches in multi-dimensional sequence-structure space. Individual amino acid residues in protein structures are represented by their C alpha atoms; thus each protein is described as a collection of points in three-dimensional space. Delaunay tessellation of a protein generates an aggregate of space-filling, irregular tetrahedra, or Delaunay simplices. Statistical analysis of quadruplet residue compositions of all Delaunay simplices in a representative dataset of protein structures leads to a novel four body contact residue potential expressed as log likelihood factor q. The q factors are calculated for native 20 letter amino acid alphabet and several reduced alphabets. Two sequence-structure compatibility functions are computed as (i) the sum of q factors for all Delaunay simplices in a given protein, or (ii) 3D-1D Delaunay tessellation profiles where the individual residue profile value is calculated as the sum of q factors for all simplices that share this vertex residue. Both threading functions have been implemented in structure-recognizes-sequence and sequence-recognizes-structure protocols for protein fold recognition. We find that both profile and total score based threading functions can distinguish both the native fold from incorrect folds for a sequence, and the native sequence from non-native sequences for a fold.

Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues.

Delaunay tessellation is applied for the first time in the analysis of protein structure. By representing amino acid residues in protein chains by C alpha atoms, the protein is described as a set of points in three-dimensional space. Delaunay tessellation of a protein structure generates an aggregate of space-filling irregular tetrahedra, or Delaunay simplices. The vertices of each simplex define objectively four nearest neighbor C alpha atoms, i.e., four nearest-neighbor residues. A simplex classification scheme is introduced in which simplices are divided into five classes based on the relative positions of vertex residues in protein primary sequence. Statistical analysis of the residue composition of Delaunay simplices reveals nonrandom preferences for certain quadruplets of amino acids to be clustered together. This nonrandom preference may be used to develop a four-body potential that can be used in evaluating sequence-structure compatibility for the purpose of inverted structure prediction.

Statistical geometry analysis of proteins: implications for inverted structure prediction.

The topology of folded proteins from the representative dataset of well-defined three-dimensional protein structures is studied using a statistical geometry approach. Amino acid residues in protein chains are represented by C alpha atoms, thus reducing the protein three-dimensional structure to a set of points in three dimensional space. The Delaunay tessellation of a protein structure generates an aggregate of space-filling irregular tetrahedra, or Delaunay simplices. Each simplex objectively defines four nearest neighbor C alpha atoms, i.e. four nearest neighbor residues. The statistical analysis of residue composition of Delaunay simplices reveals nonrandom preferences for certain quadruplets of amino acids. These nonrandom preferences are used to develop a fitness function that evaluates sequence-structure compatibility. Using this fitness function, several tested native proteins score the highest among 100,000 random sequences with average protein amino acid composition. The statistical geometry approach, based solely on first principles, provides a unique means for protein structure analysis and has direct implications for inverted protein structure prediction.

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer.

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

Pseudotorsional OCCO backbone angle as a single descriptor of protein secondary structure.

Protein secondary structure is conventionally identified using characteristic ranges of two backbone torsional angles phi and psi. We suggest that the secondary structure can be adequately characterized by a single descriptor, the Oi-1Ci-1CiOi (where i is the residue number) pseudotorsional backbone angle. A set of 102 structurally distinct protein chains from the Protein Data Bank was used to evaluate the adequacy of this descriptor. We find that a specific range of OCCO angles corresponds to each major secondary structure. The complete range of OCCO angles (-180 degrees to 179 degrees) was broken into 18 consecutive subranges of 20 degrees each, and each subrange was assigned a letter. Thus, the OCCO profiles for each protein in the database were "translated" into a sequence of letters. The Needleman-Wunsch primary sequence alignment algorithm was then used for secondary/tertiary structure comparison and alignment. Preliminary results indicate that this new approach has a significant potential for rapid identification of fold families in the Protein Data Bank.

[The immunochemistry of the antigenic fractions of Clostridium tetani toxin]. / Immunokhimiia antigennykh fraktsii stolbniachnogo toksina Clostridium tetani.

The localization of tetanospasmin and tetanolysin in C. tetani cells has been determined by the cytochemical method in the dynamics of the development of the microbial population. As shown in this investigation, tetanolysin, similarly to exotoxins, is released from microbial cells into the culture fluid mainly during the first 24 hours of cultivation, while tetanospasmin, similarly to endotoxins, is released only in the process of the destruction of these cells at the phase of the death of the microbial population.

[Immunocytochemistry of Clostridium novyi antigens. Electron microscopic research]. / Immunotsitokhimiia antigenov Clostridium novyi. Elektronno-mikroskopicheskoe issledovanie.

The dynamics of the synthesis, transfer and excretion of toxin in C. novyi, growing in a liquid culture medium, have been studied on the level of bacterial ultrastructure by means of immunoferritin techniques modified by the authors. As revealed in this study, the basic mechanism of toxin excretion is realized by the active transfer of toxin through the enveloping structures after its accumulation in the periplasmatic space. In ageing cultures toxin may also be released in the process of bacteriolysis with the degradation of bacterial structures.

[Cryofractographic study of intercellular junctions in the populations of agar-cultivated Bordetella pertussis]. / Kriofraktorgraficheskoe izuchenie mezhkletochnykh sviazei v populiatsiiakh agarovykh kul'tur Bordetella pertussis.

The characteristic feature of replicas obtained from the freeze-fractures of B. pertussis unfixed cultures developing on casein charcoal agar for 1-7 days is the associative growth of highly polymorphic cells, ensured by the ramified system of intercellular connections (IC) formed by the derivatives of the outer layers of the cell wall. This proves that the associative location of bacterial cells, linked by numerous IC, in the preparation is not the artefact appearing in the process of their chemical fixation. In replicas obtained from the freeze-fractures of B. pertussis cultures, previously fixed with glutaraldehyde, osmic acid and uranyl acetate, oval cells with the cytoplasm having a relatively homogeneous structure and with the smoothed-out three-layer cell wall prevail. As a rule, IC are limited to the sites of direct contacts between individual cells.

[Ultrastructural characteristics of the natural heteromorphic growth of Clostridium septicum]. / Ul'trastrukturnaia kharakteristika estestvennogo geteromorfnogo rosta Clostridium septicum.

Periodic cultures of C. septicum strain No. 59, growing in Pope's broth, have been studied by means of transmission electron microscopy on ultrathin sections. During the lagphase of growth the inoculated bacilliary cells are sequentially converted into giant filamentous multinucleate forms. These changes, reflecting the reaction of phenotypical adaptation to new environmental conditions, are followed by the restoration of the initial phenotype via the fragmentation of the giant cells. At the same time heteromorphic growth becomes, also spontaneously, atypical in some of the multinucleate cells. This atypical heteromorphic growth results in pronounced degenerative changes leading to bacteriolysis and the death of microbial cells due to disturbances in the coordination of the formation of structural and functional complexes in these cells at the period of their phenotypical adaptation. Such pathology of microbial cells leads to elimination of individual cells with developmental defects, which is finally conducive to the sanitation of the population.

[Fine morphology of the anomalies of sporulation in Clostridium tetani]. / Tonkaia morfologiia anomalii formirovaniia spor u Clostridium tetani.

The electron microscopic study of the cultures of Cl. tetani strains Nos. 154 and 741 has been carried out, starting from the late stationary phase of their development in a liquid culture medium prepared on the basis of casein hydrolysate. Under experimental conditions sporogenesis is observed in 17-33% of the organisms in the population of strain No. 154 and in 7-14% of the organisms in the population of strain No. 471. In most of the sporulating cells sporogenesis occurs in consecutive stages commonly observed in clostridia. Anomalies in the formation of pores are manifested by the ectopic initial formation of protospores, the disordered excess growth of osmiophil structures of the exosporic type, the early lysis of the cytoplasmic structures of the sporangium cell or the spore itself. Such changes resulting in the death of the cell are regarded as the pathomorphology of the bacterial cell.

[Fine structure and culture characteristics of Lactobacillus plantarum]. / Tonkoe stroenie i kul'tural'nye osobennosti Lactobacillus plantarum.

The preparations of Lactobacillus plantarum 8-PA-3 cultures growing for 6, 8 and 10 hours were taken at the phase of exponential growth in a liquid malt-containing nutrient medium, and their ultrathin sections and replicas were studied after freeze-fracturing and etching by means of electron microscopy. The authors discuss the dynamics of development of structural-functional complexes in the cells, in particular, their membranous structures. Their morphogenesis is correlated with the functional requirements of the cells due to peculiarities of the population growth. The organization of the cytoplasmic membrane is noteworthy: many vesicles appear at the periphery of the protoplast and, probably, are involved in metabolic processes via a mechanism of the exocytosis type. Membranous structures of the nucleoidosome type extend gradually in the nuclear area, most intensively by the time when the exponential growth ceases. This phenomenon may be regarded as a response to the population being crowded under these conditions.

Considerations on the value of freeze-etching technique in studying the ultrastructure of some anaerobic bacteria.

Samples from periodic cultures of Clostridium perfringens, Clostridium oedematiens, Clostridium tetani and Bifidobacterium bifidum grown in liquid nutrient media were studied after freeze-fracturing and etching without pretreatment by means of chemical agents including cryo-protectants. Subunits in the cell all of Cl. tetani and differences in the distribution of globular particles in the plasma membrane of the investigated bacteria are revealed.

[Mechanism of segregation of bacterial chromosomes following division of anaerobic clostridia]. / O mekhanizme segregatsii bakterial'nykh khromosom pri delenii anaerobnykh klostridii.

Morphological events during division in Clostridium oedematiens, strains A-277 and A-79, were studied on ultrathin sections. The bacterial cells of the species under investigation containing numerous and various intracytoplasmic membranous structures were practically devoid of the "nuclear mesosomes" type structures. In these anaerobic Clostridia the segregation of bacterial chromosomes after the replication was effected by means of direct connections between the DNA filaments and the cytoplasmic membrane of the bacterial cell. These connections were multiple, up to 250 nm in length, possibly ensuring a proper mechanical strength needed for translocation of the chromosomes into the daughter cells. It is suggested that multiple contact zones between the cytoplasmic membrane and the DNA filaments of the bacterial chromosome arose after the triggering of their DNA replication.

[Fine structure of Bifidobacterium bifidum]. / Tonkoe stroenie Bifidobacterium bifidum.

Cultures of Bifidobacterium bifidum 1 were grown in liquid and semisolid nutrient media for 14 hours to 6 days. Their preparations were then studied by electron microscopy on ultra-thin sections after a routine chemical fixation or on replicas after rapid freezing-fracturing and etching. This procedure made it possible to obtain new data about the structural organization of cells in the course of growth of cultures which were characterized by desynchronization of growth and division processes. The growth was inhibited later when populations reached the highest number of cells in the given set of conditions. The zone of nuclear vacuoles contained peculiar membrane structures which appeared and underwent certain changes related, apparently, to the mode of growth of this bacterium.