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[Self-stimulation of phylogenetically new and ancient hypothalamic structures when reinforcement schedules are changed].

The following two types of reaction are exhibited by self-stimulating rats following a transition from the regimen of preference (free) to that of fixed series of stimuli: I. increased frequency of pressings with simultaneous shortening of their duration, approaching the duration of fixed series; II. reduced frequency of pressings with their longer duration. Of the two studied hypothalamic areas, the former type of reaction is exhibited predominantly in the self-stimulation points located in the lateral hypothalamic area, while the latter type - in the lateral preoptic area. Different strategy of the animals' behaviour observed during the change of reinforcement routines is discussed with regard to different levels of integration of emotionally-positive mechanisms of brain structures of phylogenetically different age.

Animals↗

The postnatal growth of the temporal bone and its implications for cochlear implantation in children.

The postnatal growth of the human temporal bone was examined by direct anatomical measurements on 60 cadaver specimens of all ages. The bones were dissected as one would perform cochlear implant surgery using a posterior tympanotomy approach. Nineteen anatomical/surgical landmarks with implications for cochlear implant surgery were identified on each bone and the distance between these points measured. The temporal bone was found to be a complex structure, phylogenetically, anatomically and functionally consisting of four different parts with independent postnatal development. The inner and middle ears were adult size at birth. The external auditory canal and most parts of the temporal bone were subject to significant lateral growth. The size of the pneumatised mastoid increased in all directions. In the facial recess, however, no postnatal growth was observed. Between birth and adulthood an average of 12 mm (SD 5 mm) of growth was seen directly between the sino-dural angle and the round window, the landmarks approximating the implantation site for the receiver-stimulator and the electrode entry point into the inner ear. However, if an electrode leadwire is fixed at a cortical fixation site such as the posterosuperior point of Macewen's triangle, the leadwire would be subject to approximately 20 mm of growth. These results indicate that a paediatric cochlear implant design incorporating an expandable leadwire to accommodate this growth should allow up to 25 mm of leadwire lengthening. The fossa incudis showed no growth relative to the round window and was found to be a convenient fixation site for the electrode array close to the cochlea. From an anatomical and surgical point of view, cochlear implantation in very young children is feasible, provided the electrode array is secured and the design accommodates for controlled leadwire lengthening.

Adolescent↗

Evidence for a subclinical involvement of the central nervous system in mild or moderate chronic respiratory insufficiency.

Nineteen patients with mild or moderate chronic respiratory insufficiency, mean age, 63.3 y., have been investigated with pulmonary function tests, clinical examination and somatosensory (SEPs), visual (VEPs) and brainstem auditory (BAEPs) evoked potentials. Nineteen age and sex matched subjects acted as controls. None of the subjects had conditions known to affect the central nervous system (CNS). SEP N20 latency was significantly prolonged in 7 out of 19 patients and its mean value in the patients' group was significantly higher (21.02 vs 19.49 msec p < 0.001). VEP P100 latency was prolonged in the patients' group in 16/38 and 15/38 eyes with spatial frequencies of 30' and 15' of arc respectively. The P100 mean value was also significantly prolonged in the patients' group for both eyes and spatial frequencies (108.08 vs 101.87 msec p < 0.001 and 115.82 vs 107.63 msec p < 0.001 for spatial frequencies of 30' and 15' respectively). No significant difference was evident with BAEPs The data seem to support the hypothesis of a subclinical involvement of CNS in these cases, with preferential damage to the newer phylogenetic structures.

Aged↗

Exoribonuclease superfamilies: structural analysis and phylogenetic distribution.

Exoribonucleases play an important role in all aspects of RNA metabolism. Biochemical and genetic analyses in recent years have identified many new RNases and it is now clear that a single cell can contain multiple enzymes of this class. Here, we analyze the structure and phylogenetic distribution of the known exoribonucleases. Based on extensive sequence analysis and on their catalytic properties, all of the exoribonucleases and their homologs have been grouped into six superfamilies and various subfamilies. We identify common motifs that can be used to characterize newly-discovered exoribonucleases, and based on these motifs we correct some previously misassigned proteins. This analysis may serve as a useful first step for developing a nomenclature for this group of enzymes.

Amino Acid Sequence↗

[Difference in the postnatal development of the layer structures in the phylogenetically different cat cerebellar cortices].

Although it has long been accepted that the structure of the cerebellar cortex is the same all over its areas, some of the recent studies indicated that there are regional differences in the time course of development of the cortical layer structures as well as in its cytoarchitecture. The cerebellum consists of 3 phylogenetically different areas; archi-, paleo- and neocerebellum, which deals with vestibular, spinal cord and cerebral cortical activities respectively. The development of the structures of cerebellar cortex occurs mostly after birth in the altrical animals, and the control of the posture and movement takes place faster in the trunk than in the extremities in such animals. It could be expected that the postnatal development occurs faster in the phylogenetically older parts than in the newer ones. To elucidate the above mentioned assumption, post-natal development of the cerebellar cortical structures was studied, cytoarchitectonically and cell morphologically, using cats from birth to the adult state. The external granular layer increased in thickness from birth to 2-9th postnatal days, then decreased gradually, and almost disappeared by the 63rd postnatal day. While the molecular and the internal granular layers increased in thickness gradually after birth, and reached the adult level by the 63rd postnatal day. Cytoarchitectonically, postnatal development took place faster in the archicerebellum, next in the paleocerebellum and slowest in the neocerebellum. Silver impregnation study showed the first dendritic arborization of the Purkinje cell appeared on the 7th postnatal day in the arch- and paleocerebellum, while the same phenomenon was observed on the 14th postnatal day in the neocerebellum. The above observations confirmed our assumption that phylogenetically older parts of the cerebellar cortex have faster postnatal development than the newer ones. This is in agreement with the fact that the function of the neuronal activity in these phylogenetically older parts occurs earlier than in the newer parts.

Animals↗

Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures.

The phylogenetic diversity of sulfate-reducing prokaryotes occurring in active deep-sea hydrothermal vent chimney structures was characterized based on the deduced amino acid sequence analysis of the polymerase chain reaction-amplified dissimilatory sulfite reductase (DSR) gene. The DSR genes were successfully amplified from microbial assemblages of the chimney structures, derived from three geographically and geologically distinct deep-sea hydrothermal systems in the Central Indian Ridge (CIR), in the Izu-Bonin Arc (IBA), and the Okinawa Trough (OT), respectively. Phylogenetic analysis revealed seven major phylogenetic groups. More than half of the clones from the CIR chimney structure were related to DSR amino acid sequences of the hyperthermophilic archaeal members of the genus Archaeoglobus, and those of environmental DSR clones within the class Thermodesulfobacteria. From the OT chimney structure, a different group was obtained, which comprised a novel, deep lineage associated with the DSRs of the thermophilic sulfate-reducing bacterium Thermodesulfovibrio. Most of the DSR clones from the IBA chimney structure were phylogenetically associated with the delta-proteobacterial sulfate-reducing bacteria represented by the genus Desulfobulbus. Sequence analysis of DSR clones demonstrated a diverse sulfate-reducing prokaryotic community in the active deep-sea hydrothermal chimney structures.

Genetic Variation↗

Voltage-gated H+ channels associated with human phagocyte superoxide-generating NADPH oxidases: sequence comparisons, structural predictions, and phylogenetic analyses.

The N-terminal domain of the human phagocyte flavocytochrome b558 NADPH oxidase, gp91phox, is believed to be a heme-containing voltage-gated H+ channel. The authors have conducted structural, sequence and phylogenetic analyses of the putative transmembrane channel/heme-binding domains of all homologous proteins in the NCBI GenBank database as of May 2001, as well as of the full-length proteins. Fifty-six homologues were identified, including 26 from animals, 19 from plants, seven from yeast, one from a slime mould and three from bacteria. Six well-defined sub-families were revealed by phylogenetic tree construction, two consisting of animal proteins, two of plant proteins, and one each of yeast and bacterial homologues, with the slime mould protein clustering loosely with one of the animal clusters. Signature sequences for the entire family as well as for the sub-families were determined. Most proteins have six putative TMSs, four of which may comprise the heme-binding H+ channel. The hydrophobic and amphipathic characteristics of each of the putative alpha-helical transmembrane segments were defined, and conserved residues that may be involved in heme binding, channel formation, and/or conformational changes were identified. The analyses lead to the suggestion that the oxidase domain became associated with the channel/heme-binding domain to form a single polypeptide chain early in evolutionary history, before eukaryotes diverged from prokaryotes, and that genetic transmission to present day organisms occurred primarily by vertical descent.

Amino Acid Motifs↗

Structural characterization and phylogenetic relationships of myotoxin II from Atropoides (Bothrops) nummifer snake venom, a Lys49 phospholipase A(2) homologue.

In order to analyze its structure-function relationships, the complete amino acid sequence of myotoxin II from Atropoides (Bothrops) nummifer from Costa Rica was determined. This toxin is a Lys49-type phospholipase A(2) (PLA(2)) homologue, devoid of catalytic activity, structurally belonging to class IIA. In addition to the Asp49 --> Lys change in the (inactive) catalytic center, substitutions in the calcium-binding loop suggest that its lack of enzymatic activity is due to the loss of ability to bind Ca(2+). The toxin occurs as a homodimer of basic subunits of 121 residues. Its sequence has highest similarity to Lys49 PLA(2)s from Cerrophidion, Trimeresurus, Bothrops and Agkistrodon species, which form a subfamily of proteins that diverged early from Asp49 PLA(2)s present in the same species, as shown by phylogenetic analysis. The tertiary structure of the toxin was modeled, based on the coordinates of Cerrophidion godmani myotoxin II. Its exposed C-terminal region 115-129 shows several differences in comparison to the homologous sequences of other Lys49 PLA(2)s, i.e. from Agkistrodon p. piscivorus and Bothrops asper. Region 115-129 of the latter two proteins has been implicated in myotoxic activity, on the basis of the direct membrane-damaging of their corresponding synthetic peptides. However, peptide 115-129 of A. nummifer myotoxin II did not exert toxicity upon cultured skeletal muscle cells or mature muscle in vivo. Differences in several amino acid residues, either critical for toxicity, or influencing the conformation of free peptide 115-129 from A. nummifer myotoxin II, may account for its lack of direct membrane-damaging properties.

Amino Acid Sequence↗

[Construction, structure prediction and phylogenetic analysis of murine scFv gene against human cervical cancer].

AIM: To construct the gene of murine single-chain Fv fragment (scFv) against human cervical cancer and to predict the physical and chemical characteristics, secondary structure, tertiary structure and the molecular evolution of the scFv using computer-assisted modeling. METHODS: The variable region gene of the heavy and light chains were amplified respectively using recombinant DNA techniques from CSA125 hybridoma cells that can secret monoclonal antibodies with high activity and specificity against human cervical cancer. These two fragments were then spliced together through a flexible linker to scFv against human cervical cancer by using splicing overlap extension (SOE) PCR. The scFv gene, named CSAs-1, was cloned into the vector pMD18-T. The physical and chemical characteristics secondary and tertiary structure and the phylogenetic tree were predicted using Internet and corresponding softwares. RESULTS: The whole scFv gene was cloned successfully and encoded 278 amino acids. Theoretically, the CSAs-1 scFv was relative molecular masses 28,800, the isoelectric point (pI) was 7.215. PHDsec indicated that CSAs-1 was alpha+beta globin. There were many protein kinase C phosphorylation sites and casein kinase II phosphorylation sites in the V(H) and V(L) domains. The computer graphic modeling indicated the linker was isolated from V(H) and V(L). The V(L), as well as the V(H), was involved in composing the hydrophobic "pocket" which was beneficial to the antigen binding. Phylogenetic tree analysis indicated that V(H) genes from various vertebrate species formed three clusters that corresponded to three V(H) groups and that V(L) sequences from each species had a level of diversity similar to that of their V(H) genes. CSAs-1 V regions belong to A group. CONCLUSION: The construction and analysis of a molecular model of scFv laid the foundation for the further research into genetic engineering antibody and the mechanism of antigen-antibody interaction.

Animals↗

Phylogenetic Composition, Spatial Structure, and Dynamics of Lotic Bacterial Biofilms Investigated by Fluorescent in Situ Hybridization and Confocal Laser Scanning Microscopy.

> Abstract The phylogenetic composition, three-dimensional structure and dynamics of bacterial communities in river biofilms generated in a rotating annular reactor system were studied by fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). Biofilms grew on independently removable polycarbonate slides exposed in the reactor system with natural river water as inoculum and sole nutrient and carbon source. The microbial biofilm community developed from attached single cells and distinct microcolonies via a more confluent structure characterized by various filamentous bacteria to a mature biofilm rich in polymeric material with fewer cells on a per-area basis after 56 days. During the different stages of biofilm development, characteristic microcolonies and cell morphotypes could be identified as typical features of the investigated lotic biofilms. In situ analysis using a comprehensive suite of rRNA-targeted probes visualized individual cells within the alpha-, beta-, and gamma-Proteobacteria as well as the Cytophaga-Flavobacterium group as major parts of the attached community. The relative abundance of these major groups was determined by using digital image analysis to measure specific cell numbers as well as specific cell area after in situ probing. Within the lotic biofilm community, 87% of the whole bacterial cell area and 79% of the total cell counts hybridized with a Bacteria specific probe. During initial biofilm development, beta-Proteobacteria dominated the bacterial population. This was followed by a rapid increase of alpha-Proteobacteria and bacteria affiliated to the Cytophaga-Flavobacterium group. In mature biofilms, alpha-Proteobacteria and Cytophaga-Flavobacteria continued to be the prevalent bacterial groups. Beta-Proteobacteria constituted the morphologically most diverse group within the biofilm communities, and more narrow phylogenetic staining revealed the importance of distinct phylotypes within the beta1-Proteobacteria for the composition of the microbial community. The presence of sulfate-reducing bacteria affiliated to the Desulfovibrionaceae and Desulfobacteriaceae confirmed the range of metabolic potential within the lotic biofilms.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p225.html

Journal Article↗

A new U2 RNA secondary structure provided by phylogenetic analysis of trypanosomatid U2 RNAs.

A new model of U2 RNA secondary structure has been developed by comparing U2 RNA sequences from distantly related trypanosomatids, which process their RNAs by trans-splicing, and U2 RNAs from cis-splicing organisms. The trypanosomatid U2 RNA retains structural similarity in important functional domains of cis-splicing U2 RNAs yet differs from previous consensus models in that only two helices, rather than three, can form in the stem-loop II region. This alteration eliminates the capacity for pseudoknot formation and produces a single-stranded region 3' to stem-loop II, which may be accessible for snRNP protein binding. Trypanosomatid U2 RNAs differ in the putative branchpoint recognition sequences, which completely diverge from the conserved GUAGUA consensus of cis-splicing organisms.

Animals↗

The orbivirus genus. Diversity, structure, replication and phylogenetic relationships.

The general properties of the orbiviruses have been examined at the physical, structural and molecular level. At the structural level, the orbiviruses (with the exception of the Kemerovo serogroup) appear similar. The replicative events are also similar, however differences in the ultrastructure of virus-specific structures and their association with components of the host cell have been observed. Further research in this area may be used to differentiate between the serogroups and even some serotypes, of orbiviruses. At the molecular level the properties of the genome can be used to determine relationships between members of the orbivirus genus. These relationships are revealed using a variety of techniques including serology and gene sequence analysis. Not only are the different serological responses to gene products present in the mature virus particle used for differential diagnosis, but the gene sequences themselves can also be utilized. Understanding of the relationships between these viruses is progressing to the point that insights into orbivirus molecular epidemiology is now possible.

Animals↗

Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy.

A molecular and phylogenetic characterization on env and gag subgenomic regions has been performed in our laboratory on HIV-1 variants identified in seropositive individuals residing in Italy, infected in the 1999-2001 period, and five non-B-subtype HIV-1 isolates have been described. To confirm the phylogenetic characterization and to determine the genomic organization of three non-B HIV-1 isolates (A, G, and CRF02- AG), the complete gag, pol, and gp120 ORFs (approx. 6900 bp) have been sequenced for each of them. The phylogenetic tree analyses performed on the whole sequence or on individual genes suggested, for the A and G isolates, the identification of divergent strains that do not cluster into any of the known subsubtypes. This has been further validated by pairwise distance analysis. On the contrary, the phylogenetic classification of the CRF02-AG isolate has been confirmed and an overall typical pattern of intragenomic breakpoints has been observed by a Simplot analysis. These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates.

Genes, env↗

Sequence, structural, functional, and phylogenetic analyses of three glycosidase families.

Glycosidases, which cleave the glycosidic bond between a carbohydrate and another moiety, have been classified into over 63 families. Here, a variety of computational techniques have been employed to examine three families important in normal and abnormal pathology with the aim of developing a framework for future homology modeling, experimental and other studies. Family 1 includes bacterial and archaeal enzymes as well as lactase phlorizin-hydrolase and klotho, glycosidases implicated in disaccharide intolerance II and aging respectively. A statistical model, a hidden Markov model (HMM), for the family 1 glycosidase domain was trained and used as the basis for comparative examination of the conserved and variable sequence and structural features as well as the phylogenetic relationships between family members. Although the structures of four family 1 glycosidases have been determined, this is the first comparative examination of all these enzymes. Aspects that are unique to specific members or subfamilies (substrate binding loops) as well those common to all members (a beta/alpha)8 barrel fold) have been defined. Active site residues in some domains in klotho and lactase-phlorizin hydrolases differ from other members and in one instance may bind but not cleave substrate. The four invariant and most highly conserved residues are not residues implicated in catalysis and/or substrate binding. Of these, a histidine may be involved in transition state stabilization. Glucosylceramidase (family 30) and galactosylceramidase (family 59) are mutated in the lysosomal storage disorders Gaucher disease and Krabbe disease, respectively. HMM-based analysis, structure prediction studies and examination of disease mutations reveal a glycosidase domain common to these two families that also occurs in some bacterial glycosidases. Similarities in the reactions catalyzed by families 30 and 59 are reflected in the presence of a structurally and functionally related (beta/alpha)8 barrel fold related to that in family 1.

Amino Acid Sequence↗

Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages.

Although associated with all plants, fungal endophytes (microfungi that live within healthy plant tissues) represent an unknown proportion of fungal diversity. While there is a growing appreciation of their ecological importance and human uses, little is known about their host specificity, geographic structure, or phylogenetic relationships. We surveyed endophytic Ascomycota from healthy photosynthetic tissues of three plant species (Huperzia selago, Picea mariana, and Dryas integrifolia, representing lycophytes, conifers, and angiosperms, respectively) in northern and southern boreal forest (Québec, Canada) and arctic tundra (Nunavut, Canada). Endophytes were recovered from all plant species surveyed, and were present in <1-41% of 2 mm2 tissue segments examined per host species. Sequence data from the nuclear ribosomal internal transcribed spacer region (ITS) were obtained for 280 of 558 isolates. Species-accumulation curves based on ITS genotypes remained non-asymptotic, and bootstrap analyses indicated that a large number of genotypes remain to be found. The majority of genotypes were recovered from only a single host species, and only 6% of genotypes were shared between boreal and arctic communities. Two independent Bayesian analyses and a neighbor-joining bootstrapping analysis of combined data from the nuclear large and small ribosomal subunits (LSUrDNA, SSUrDNA; 2.4 kb) showed that boreal and arctic endophytes represent Dothideomycetes, Sordariomycetes, Chaetothyriomycetidae, Leotiomycetes, and Pezizomycetes. Many well-supported phylotypes contained only endophytes despite exhaustive sampling of available sequences of Ascomycota. Together, these data demonstrate greater than expected diversity of endophytes at high-latitude sites and provide a framework for assessing the evolution of these poorly known but ubiquitous symbionts of living plants.

Ascomycota↗

Evolution of the insulin molecule: insights into structure-activity and phylogenetic relationships.

The conformation of insulin in the crystalline state has been known for more than 30 years but there remains uncertainty regarding the biologically active conformation and the structural features that constitute the receptor-binding domain. The primary structure of insulin has been determined for at least 100 vertebrate species. In addition to the invariant cysteines, only ten amino acids (GlyA1, IleA2, ValA3, TyrA19, LeuB6, GlyB8, LeuB11, ValB12, GlyB23 and PheB24) have been fully conserved during vertebrate evolution. This observation supports the hypothesis derived from alanine-scanning mutagenesis studies that five of these invariant residues (IleA2, ValA3, TyrA19, GlyB23, and Phe24) interact directly with the receptor and five additional conserved residues (LeuB6, GlyB8, LeuB11, GluB13 and PheB25) are important in maintaining the receptor-binding conformation. With the exception of the hagfish, only conservative substitutions are found at B13 (Glu --> Asp) and B25(Phe --> Tyr). In contrast, amino acid residues that were also considered to be important in receptor binding based upon the crystal structure of insulin (GluA4, GlnA5, AsnA21, TyrB16, TyrB26) have been much less well conserved and are probably not components of the receptor-binding domain. The hypothesis that LeuA13 and LeuB17 form part of a second receptor-binding site in the insulin molecule finds some support in terms of their conservation during vertebrate evolution, although the site is probably absent in some hystricomorph insulins. In general, the amino acid sequences of insulins are not useful in cladistic analyses especially when evolutionary distant taxa are compared but, among related species in a particular order or family, the presence of unusual structural features in the insulin molecule may permit a meaningful phylogenetic inference. For example, analysis of insulin sequences supports monophyletic status for Dipnoi, Elasmobranchii, Holocephali and Petromyzontiformes.

Alanine↗

Functional classification of amino acid decarboxylases from the alanine racemase structural family by phylogenetic studies.

Arginine decarboxylase (ADC) and ornithine decarboxylase (ODC) are involved in the biosynthesis of putrescine, which is the precursor of other polyamines in animals, plants, and bacteria. These pyridoxal-5'-phosphate-dependent decarboxylases belong to the alanine racemase (AR) structural family together with diaminopimelate decarboxylase (DapDC), which catalyzes the final step of lysine biosynthesis in bacteria. We have constructed a multiple-sequence alignment of decarboxylases in the AR structural family and, based on the alignment, inferred phylogenetic trees. The phylogenetic tree consists of 3 distinct clades formed by ADC, DapDC, and ODC that diverged from an ancestral decarboxylase. The ancestral decarboxylase probably was able to recognize several substrates, and in archaea and bacteria, ODC may have retained the ability to bind other amino acids. Previously, a paralogue of ODC has been proposed to account for ADC activity detected in mammalian cells. According to our results, this appears unlikely, emphasizing the need for more caution in functional assignment made using sequence data and illustrating the continuing value of phylogenetic analysis in clarifying relationships and putative functions.

Alanine Racemase↗

Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives.

Although DNA replication is the universal process for the transmission of genetic information in all living organisms, until very recently evidence was lacking for a related structure and function in the proteins (initiators) that trigger replication in the three 'Life Domains' (Bacteria, Archaea and Eukarya). In this article new data concerning the presence of common features in the initiators of chromosomal replication in bacteria, archaea and eukaryotes are reviewed. Initiators are discussed in the light of: (i) The structure and function of their conserved ATPases Associated with various cellular Activities (AAA+) and winged-helix domains. (ii) The nature of the macromolecular assemblies that they constitute at the replication origins. (iii) Their possible phylogenetic relationship, attempting to sketch the essentials of a hypothetical DNA replication initiator in the micro-organism proposed to be the ancestor of all living cells.

Amino Acid Sequence↗