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PubMed1985

Quantitative studies of auditory hair cells and nerves in lizards.

Because the lizard cochlear duct is anatomically accessible as well as relatively simple in structure it is an excellent model in which to study auditory hair cells, nerve fibers, and innervational patterns. The objectives of this study were to determine the intra- and interspecific variations of auditory hair cell and nerve fiber numbers, nerve fiber/hair cell ratios, and nerve fiber sizes in a varied of lizard species and to relate these to auditory function and phylogeny. Hair cell numbers were determined by SEM and serial frontal sections of the papilla basilaris and nerve fiber numbers and diameters by use of a Zeiss TGZ3 particle counter. The coefficient of variation of hair cell numbers varied from 3.2 to 16.6 (171 specimens, 15 species) and of nerve fiber numbers from 1.2 to 14.4 (381 specimens, 35 species). There was no correlation between hair cell or nerve fiber number and age or sex. The nerve fiber number/hair cell number ratio was 3.5-11.1/1 in small papillae basilares of the iguanid-agamid-anguid type, 2.4-3.2/1 in the teiid type, and 0.6-1.5/1 in the larger specialized papillae of the scincid and gekkonid types. Nerve fibers varied in diameter from 0.8 to 6.0 microns (largest percentage were 2-4 microns) and were unimodally distributed. Larger nerve fibers usually supplied the unidirectionally oriented hair cells of the papilla basilaris. Variations in hair cell and nerve fiber numbers in other vertebrate classes and the functional and phylogenetic aspects of lizard papilla basilaris structure and innervation are discussed.

Animals↗
PubMed2005

Improved prediction of critical residues for protein function based on network and phylogenetic analyses.

BACKGROUND: Phylogenetic approaches are commonly used to predict which amino acid residues are critical to the function of a given protein. However, such approaches display inherent limitations, such as the requirement for identification of multiple homologues of the protein under consideration. Therefore, complementary or alternative approaches for the prediction of critical residues would be desirable. Network analyses have been used in the modelling of many complex biological systems, but only very recently have they been used to predict critical residues from a protein's three-dimensional structure. Here we compare a couple of phylogenetic approaches to several different network-based methods for the prediction of critical residues, and show that a combination of one phylogenetic method and one network-based method is superior to other methods previously employed. RESULTS: We associate a network with each member of a set of proteins for which the three-dimensional structure is known and the critical residues have been previously determined experimentally. We show that several network-based centrality measurements (connectivity, 2-connectivity, closeness centrality, betweenness and cluster coefficient) accurately detect residues critical for the protein's function. Phylogenetic approaches render predictions as reliable as the network-based measurements, although, interestingly, the two general approaches tend to predict different sets of critical residues. Hence we propose a hybrid method that is composed of one network-based calculation--the closeness centrality--and one phylogenetic approach--the Conseq server. This hybrid approach predicts critical residues more accurately than the other methods tested here. CONCLUSION: We show that network analysis can be used to improve the prediction of amino acids critical for protein function, when utilized in combination with phylogenetic approaches. It is proposed that such improvement is due to the complementary nature of these approaches: network-based methods tend to predict as critical those residues that are highly connected and internal (i.e., non-surface), although some surface residues are indeed identified as critical by network analyses; whereas residues chosen by phylogenetic approaches display a lower overall probability of being surface inaccessible.

Computational Biology↗
PubMed2000

RNA secondary structures of the bacteriophage phi6 packaging regions.

Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.

Bacteriophage phi 6↗
PubMed1996

Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA.

Comparative modeling of secondary structure is a proven approach to predicting higher order structural elements in homologous RNA molecules. Here we present the results of a comprehensive comparison of newly modeled or refined secondary structures for the cytoplasmic large subunit (23 S-like) rRNA of eukaryotes. This analysis, which covers a broad phylogenetic spectrum within the eukaryotic lineage, has defined regions that differ widely in their degree of structural conservation, ranging from a core of primary sequence and secondary structure that is virtually invariant, to highly variable regions. New comparative information allows us to propose structures for many of the variable regions that had not been modeled before, and rigorously to confirm or refine variable region structures previously proposed by us or others. The present analysis also serves to identify phylogenetically informative features of primary and secondary structure that characterize these models of eukaryotic cytoplasmic 23 S-like rRNA. Finally, the work summarized here provides a basis for experimental studies designed both to test further the validity of the proposed secondary structures and to explore structure-function relationships.

Base Sequence↗
PubMed2004

Filamentous fungi: the indeterminate lifestyle and microbial ecology.

The filamentous fungi have dynamic and variable hyphal structures within which cytoplasm can be moved, synthesized, and degraded, in response to changes in environmental conditions, resource availability, and resource distribution. Their study has gone through several phases. In the first phase, direct observation was emphasized without undue concern for interior structures or in the presence of cytoplasm. By the mid-1970s, single biochemical proxies (ergosterol, marker fatty acids, chitin derivatives, etc.) were being used increasingly. The use of these surrogate single measurements continues, in spite of their inability to provide information on the physical structure of the filamentous fungi. Molecular approaches also are being used, primarily through the use of bulk nucleic acid extraction and cloning. Because the sources of the nucleic acids used in such studies usually are not known, taxonomic and phylogenetic information derived by this approach cannot be linked to specific fungal structures. Recently, a greater emphasis has been placed on assessing physical aspects of indeterminate fungal growth, involving the assessment of cytoplasm-filled and evacuated (empty) hyphae. Both of these parameters are important for describing filamentous fungal growth and function. The use of phase contrast microscopy and varied general stains, as well as fluorogenic substrates with observation by epifluorescence microscopy, has made it possible to provide estimates of cytoplasm-filled hyphal lengths. Using this approach, it has been possible to evaluate the responses of the indeterminate fungal community to changes in environmental conditions, including soil management. It is now possible to obtain molecular information from individual bacteria and fungal structures (hyphae, spores, fruiting bodies) recovered from environments, making it possible to link individual fungal structures with their taxonomic and phylogenetic information. In addition, this information can be considered in the context of the indeterminate filamentous fungal lifestyle, involving the dynamics of resource allocation to hyphal structural development and synthesis of cytoplasm. Use of this approach should make it possible to gain a greater appreciation of the indeterminate filamentous fungal lifestyle, particularly in the context of microbial ecology.

Cytoplasm↗
PubMed1994

The muscle Z band: lessons in stress management.

Two of the most characteristic features of striated muscle are (i) its ability to contract and generate tension when activated and (ii) its ability to return to its original length and form after contraction or stretching ceases. These two properties are to a large extent the primary manifestations of separate sets of filament systems: contractile actin and myosin filaments and viscoelastic titin and intermediate filaments. Z bands function as a common link that mechanically integrates contractile and elastic elements and as such they play a fundamental role in transmission of active and passive forces. Differences in Z band structure have been described for distinct classes of muscle and fibre types. The diversity in Z band architecture has been built around its phylogenetically conserved role as an actin-anchoring structure. Novel proteins are likely to account for structural and functional differences seen across the phyla.

Animals↗
PubMed2005

Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites.

We studied genetic relationships among 5069 Mycobacterium tuberculosis strains recovered from patients enrolled in 4 population-based studies in the United States and Europe, by analysis of 36 synonymous single-nucleotide polymorphisms (SNPs). All strains were assigned to 1 of 9 major genetic clusters based on sSNP profile. The same 9 genetic clusters were revealed by analysis of 227 nonsynonymous SNPs, 121 intergenic SNPs, and concatenated profiles of 578 SNPs available for a subset of 48 representative strains. IS6110 profiles, spoligotypes, and mycobacterial interspersed repetitive unit patterns were nonrandomly associated with SNP-based phylogenetic lineages, together indicating a strongly clonal population structure. Isolates of the 9 genetic clusters were not distributed with equal frequency in all localities, reflecting geographic subdivision. The SNP-based phylogenetic framework provides new insight into the worldwide evolution of M. tuberculosis and a gateway for investigating genotype-disease phenotype relationships in large samples of strains.

Bacterial Typing Techniques↗
PubMed2001

Cardiac Na(+)-Ca(2+) exchange: molecular and pharmacological aspects.

The Na(+)-Ca(2+) exchanger (NCX) is one of the essential regulators of Ca(2+) homeostasis in cardiomyocytes and thus an important modulator of the cardiac contractile function. The purpose of this review is to survey recent advances in cardiac NCX research, with particular emphasis on molecular and pharmacological aspects. The NCX function is thought to be regulated by a variety of cellular factors. However, data obtained by use of different experimental systems often appear to be in conflict. Where possible, we endeavor to provide a rational interpretation of such data. We also provide a summary of current work relating to the structure and function of the cardiac NCX. Recent molecular studies of the NCX protein are beginning to shed light on structural features of the ion translocation pathway in the NCX membrane domain, which seems likely to be formed, at least partly, by the phylogenetically conserved alpha-1 and alpha-2 repeat structures and their neighboring membrane-spanning segments. Finally, we discuss new classes of NCX inhibitors with improved selectivity. One of these, 2-[2-[4-(4-nitrobenzyloxy)phenyl]ethyl]isothiourea methanesulfonate (KB-R7943), appears to exhibit unique selectivity for Ca(2+)-influx-mode NCX activity. Data obtained with these inhibitors should provide a basis for designing more selective and clinically useful drugs targeting NCX.

Animals↗
PubMed1999

Rainbow trout (Oncorhynchus mykiss) urotensin-I: structural differences between urotensins-I and urocortins.

In bony fishes, both corticotropin-releasing factor (CRF) and urotensin-I play a role in the regulation of interrenal glucocorticoid release. The rainbow trout, Oncorhynchus mykiss, is a useful model for understanding the mechanisms of stress and the hypothalamo-pituitary-interrenal axis because of its phylogenetic position at the base of the euteleostei and its popularity as a food fish. Urotensin-I may act as a glucocorticoid releaser in a mechanism phylogenetically older than that of CRF. The structural and functional relationships of trout urotensin-I have been investigated. The transcript was cloned from a trout brain hypothalamic cDNA library. A single positive clone was isolated and sequenced. It possesses 3218 bases and has the longest 3' untranslated region of all urotensins-I and CRF transcripts found to date. In comparison to the other fish orthologues, it has the closest sequence identity to the mammalian urocortins. The transcript appears to be differentially processed in brain and urophysis as determined by Northern blot analysis and the presence of polyadenylation signals in the 3' untranslated region. Synthetic trout urotensin-I activated both human CRF-R1 and -R2 receptor-transfected CHO cells with a potency similar to that of white sucker (Catostomus commersoni) urotensin-I. Both fish neuropeptides possessed an order of magnitude less potency than human urocortin in CRF-R2 transfected cells.

Amino Acid Sequence↗
PubMed1987

Phylogenetic receptor research: implications in studying psychiatric and neurological disease.

Phylogenetic studies will help to evaluate the structure and function of receptors. We were able to show that the regional heterogeneity of the central benzodiazepine receptor previously described in mammals also applies to avians. In addition, a systematic species comparison of the subunit patterns revealed a certain phylogenetic relationship suggesting evolution by gene duplication and subsequent divergence. In analogy to isozyme systems, these results possibly indicate that the GABA/benzodiazepine receptor is an isoreceptor complex. The implications for neuropsychiatric genetics are discussed.

Animals↗
PubMed1996

Comparative analysis of ribonuclease P RNA structure in Archaea.

Although the structure of the catalytic RNA component of ribonuclease P has been well characterized in Bacteria, it has been little studied in other organisms, such as the Archaea. We have determined the sequences encoding RNase P RNA in eight euryarchaeal species: Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacteriurn trapanicum, Methanobacterium thermoautotrophicum strains deltaH and Marburg, Methanothermus fervidus and Thermococcus celer strain AL-1. On the basis of these and previously available sequences from Sulfolobus acidocaldarius, Haloferax volcanii and Methanosarcina barkeri the secondary structure of RNase P RNA in Archaea has been analyzed by phylogenetic comparative analysis. The archaeal RNAs are similar in both primary and secondary structure to bacterial RNase P RNAs, but unlike their bacterial counterparts these archaeal RNase P RNAs are not by themselves catalytically proficient in vitro.

Archaea↗
PubMed2001

Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots.

Sequences of 191 flavivirus RNAs belonging to four sero-groups were used to predict the secondary structure of the 3' noncoding region (3' NCR) directly upstream of the conserved terminal hairpin. In mosquito-borne flavivirus RNAs (n = 164) a characteristic structure element was identified that includes a phylogenetically well-supported pseudoknot. This element is repeated in the dengue and Japanese encephalitis RNAs and centers around the conserved sequences CS2 and RCS2. In yellow fever virus RNAs that contain one CS2 motif, only one copy of this pseudoknotted structure was found. The conserved pseudoknotted element is absent from the 3' NCR of tick-borne virus RNAs, which altogether adopt a secondary structure that is very different from that of mosquito-borne virus RNAs. The strong conservation of the pseudoknot in mosquito-borne flavivirus RNAs implies a stronger relationship between these viruses than concluded from previous secondary structure analyses. The role of the (tandem) pseudoknots in flavivirus replication is discussed.

Base Sequence↗
PubMed2002

Motility proteins and the origin of the nucleus.

Hypotheses on the origin of eukaryotic cells must account for the origin of the microtubular cytoskeletal structures (including the mitotic spindle, undulipodium/cilium (so-called flagellum) and other structures underlain by the 9(2)+2 microtubular axoneme) in addition to the membrane-bounded nucleus. Whereas bacteria with membrane-bounded nucleoids have been described, no precedent for mitotic, cytoskeletal, or axonemal microtubular structures are known in prokaryotes. Molecular phylogenetic analyses indicate that the cells of the earliest-branching lineages of eukaryotes contain the karyomastigont cytoskeletal system. These protist cells divide via an extranuclear spindle and a persistent nuclear membrane. We suggest that this association between the centriole/kinetosome axoneme (undulipodium) and the nucleus existed from the earliest stage of eukaryotic cell evolution. We interpret the karyomastigont to be a legacy of the symbiosis between thermoacidophilic archaebacteria and motile eubacteria from which the first eukaryote evolved. Mutually inconsistent hypotheses for the origin of the nucleus are reviewed and sequenced proteins of cell motility are discussed because of their potential value in resolving this problem. A correlation of fossil evidence with modern cell and microbiological studies leads us to the karyomastigont theory of the origin of the nucleus.

Animals↗
PubMed2004

Primate auditory diversity and its influence on hearing performance.

The auditory region contains numerous structures that have proven useful for phylogenetic classification at various taxonomic levels. However, little work has been done in primates relating differences in morphology to variations in hearing performance. This study documents anatomical and physiological distinctions within primates and begins to address the functional and evolutionary consequences of these and other auditory features. The dimensions of the outer ear (pinna) were measured in cadaveric specimens representing nearly every primate family and used to calculate a shape ratio (height/width). It was found that nonanthropoids have a significantly higher ratio than anthropoids, although the actual height was not found to differ. This indicates that most nonanthropoids have ears that are tall and narrow, whereas monkeys and apes are characterized by ears with more equal height and width dimensions. Eardrum area, stapedial footplate area, and ossicular lever arm lengths were measured in dried specimens to calculate an impedance transformer ratio. A distinction was found between anthropoids and strepsirrhines, with the latter group having a transformer ratio indicative of a higher percentage of acoustic energy transmission through the middle ear. Audiogram data were gathered from the literature to analyze hearing sensitivity and it was found that platyrrhines illustrate more low-frequency sensitivity than like-sized lorisoids. The effects of intraspecific variation on the audiogram results were also examined and were found to produce similar results as the analysis using species mean threshold values. Lastly, correlations between morphological and audiogram variables were examined. Several measures of hearing sensitivity were found to be correlated with pinna shape but correlations with middle ear transmission properties were weaker. In addition to using traditional statistical techniques, phylogenetic corrective methods were applied to address the problem of statistical nonindependence of the data and the results of both analyses are compared. These findings are discussed with respect to how sensory adaptations and phylogenetic history may be related to the current radiation of primates.

Adaptation, Physiological↗
PubMed2005

A three-dimensional atlas of pituitary gland development in the zebrafish.

The pituitary gland is unique to Chordates, with significant variation within this group, offering an excellent opportunity to increase insight into phylogenetic relationships within this phylum. The structure of the pituitary in adult Teleosts (class: Osteichthyes) is quite different from that in other chordates and is also variable among members of the class. Therefore, a complete description of the structure and development of the pituitary in members of this class is a critical component to our overall understanding of this gland. An obvious teleost model organism is the zebrafish, Danio rerio, as a significant amount of work has been done on the molecular control of pituitary development in this fish. However, very little work has been published on the morphological development of the pituitary in the zebrafish; the present study aims to fill this void. The pituitary develops from cells on the rostrodorsal portion of the head and reaches its final position, ventral to the hypothalamus, as the cephalic flexure occurs and the jaws and mouth form. The pituitary placode is juxtaposed to cells that will form the olfactory vesicles, the stomodeum, and the hatching gland. The volume of the pituitary is greatest at 24 hours post fertilization (hpf). From 24 to 120 hpf, the pituitary decreases in height and width as it undergoes convergent extension, increasing in length with the axis. The adenohypophysis is a morphologically distinct structure by 24 hpf, whereas the neurohypophysis remains indistinct until 72 hpf. The findings of this study correlate well with the available molecular data.

Animals↗
PubMed1994

Use of human leukocyte-specific monoclonal antibodies for clinically immunophenotyping lymphocytes of rhesus monkeys.

The rhesus monkey (Macaca mulatta) is an important experimental animal frequently utilized for studies of infectious diseases, immunity, hematopoiesis, and transplantation. Since the structure of cell surface molecules is phylogenetically conserved, monoclonal antibodies raised against human leukocyte antigens can sometimes recognize the homologous determinant on monkey leukocytes. To facilitate better utilization of this animal model, we tested 89 commercially available monoclonal antibodies which define 27 human cell surface antigens for reactivity with rhesus monkey PBL. Certain antigens which delineate clinical useful lymphocyte subsets such as CD2, CD4, CD8, CD14, CD16, CD20, and MHC class II are apparently well conserved since most human cell-specific antibodies identified the homologous cell subset in monkeys. However, other antigens such as CD3, CD19, CD45, and CD56 were identified infrequently by human cell-specific antibodies. FITC-modification of antibodies which had no effect on their binding to human cells occasionally inhibited antibody binding to monkey cells. Nevertheless, an adequate number of cross-reactive monoclonal antibodies was identified to allow gating of lymphocytes for accurate flow cytometric analysis and quantitation of the major lymphocyte subsets of the rhesus monkey. The T lymphocyte subset distribution in blood and lymphoid tissue of rhesus monkeys was similar to man. However, the B subset was significantly larger in monkeys. The daily variation in absolute PBL subset size was marked and found to be due mainly to daily fluctuations in total lymphocyte number.

Animals↗
PubMed1990

The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases.

The Bacillus subtilis FI DNA methyltransferase (M.BsuFI) modifies the outer cytosine of the DNA sequence CCGG, causing resistance against R.BsuFI and R.MspI restriction. The M.BsuFI gene was cloned and expressed in B.subtilis and Escherichia coli. As derived from the nucleotide sequence, the M.BsuFI protein has 409 amino acids, corresponding to a molecular mass of 46,918 daltons. Including these data we have compared the nucleotide and amino acid sequences of different CCGG recognizing enzymes. These analyses showed that M.BsuFI is highly related to two other CCGG specific methyltransferases, M.MspI and M.HpaII, which were isolated from Gram-negative bacteria. Between M.BsuFI and M.MspI the sequence similarity is particularly significant in a region, which has been postulated to contain the target recognition domains (TRDs) of cytosine-specific DNA methyltransferases. Apparently M.BsuFI and M.MspI, derived from phylogenetic distant organisms, use highly conserved structural elements for the recognition of the CCGG target sequence. In contrast the very same region of M.HpaII is quite different from those of M.BsuFI and M.MspI. We attribute this difference to the different targeting of methylation within the sequence CCGG, where M.HpaII methylates the inner, M.BsuFI/M.MspI the outer cytosine. Also the CCGG recognizing TRD of the multispecific B.subtilis phage SPR Mtase is distinct from that of the host enzyme, possibly indicating different requirements for TRDs operative in mono- and multispecific enzymes.

Amino Acid Sequence↗
PubMed2006

Molecular epidemiology of hepatitis C virus subtype 3a in injecting drug users.

Hepatitis C virus subtype 3a (HCV-3a) originates from Asia and has spread widely among injecting drug users as well as other patient groups in industrialized countries. HCV subtype 3a infection remains highly prevalent and frequently transmitted in the population of intravenous drug users. The objective of this study was to understand better the mechanisms of the worldwide HCV-3a epidemics in drug users. Ninety-three sera from HCV-3a-infected IDUs from France, the United States, Brazil, Argentina, and Australia were studied. Phylogenetic analyses of the non-structural 5B region showed no specific clustering according to the continent of the patient's origin. Non-exclusive clusters of viral sequences from South America, Australia, and California were observed, but topologies were not supported by strong bootstrap values. The results suggest that HCV-3a has been transmitted from a common origin through a unique worldwide epidemic that rapidly spread among drug users. Regional transmission occurred in the recent past, leading to an embryonic genetic diversification of HCV-3a among local injecting drug user population.

Argentina↗