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At least 1,729 records · Page 96Linked to original sources
PubMed1995

NADPH-diaphorase active and calbindin D-28k-immunoreactive neurons and fibers in the olfactory bulb of the hedgehog (Erinaceus europaeus).

The hedgehog, a macrosomatic insectivore with an extraordinary development of the olfactory structures, has a crucial value for any phylogenetic or comparative study in mammals. The distribution pattern and morphology of NADPH-diaphorase-active and calbindin D-28k-immunoreactive neurons were studied in the main and accessory olfactory bulbs of the hedgehog. NADPH-diaphorase (ND) staining was carried out by a direct histochemical method, and the calbindin D-28k (CaBP) immunoreaction by using a monoclonal antibody and the avidin-biotin-immunoperoxidase method. The possible coexistence of both markers was determined by sequential histochemical-immunohistochemical double labeling of the same sections. Specific neuronal populations were positive for both ND and CaBP markers. No cell colocalized both stains in the hedgehog olfactory bulb. A subpopulation of olfactory fibers, and a subpopulation of olfactory glomeruli, located on the medial side, were positive for ND. Surrounding both the ND-positive and ND-negative glomeruli, there were ND- and CaBP-positive periglomerular cells, the latter group being much more abundant. A subpopulation of superficial short-axon cells was CaBP positive but, contrary to what is observed in rodents, this neuronal type was always ND negative. In addition, three neuronal types were observed in the GL-EPL border after CaBP immunostaining. These neuronal types have not been previously described either in the hedgehog or in the rodent olfactory bulb. Horizontal cells and vertical cells of Cajal were also observed after both ND and CaBP labeling. Distinct groups of ND- and CaBP-positive cells, differing in size, shape, dendritic branching pattern, and staining intensity, were distinguished in the granule cell layer and in the white matter. The large and medium-sized cells were identified as a very heterogeneous population of deep short-axon cells, whereas a subpopulation of granule cells was ND positive. The accessory olfactory bulb showed ND staining in all vomeronasal fibers and glomeruli, and in subpopulations of periglomerular cells, granule cells, and deep short-axon cells. The CaBP immunolabeling was more restricted and located in subpopulations of periglomerular cells and in deep short-axon cells. These results indicate different and more complex ND and CaBP staining patterns in the hedgehog olfactory bulb than those previously described in rodents, including the presence of specific, chemically and morphologically defined new neuronal types.

Amino Acid Oxidoreductases↗
PubMed2006

Spermatozoal ultrastructure in three Atlantic solenocerid shrimps (Decapoda, Dendrobranchiata).

The spermatozoal ultrastructure in three solenocerid shrimps (Solenocera membranacea, S. africana, and Pleoticus muelleri) from different Atlantic locations was examined with the aim of increasing understanding of the phylogenetic relationships in the Dendrobranchiata. A considerable structural similarity between the sperm of these species and those of penaeid shrimps supports a close affinity between the Penaeidae and Solenoceridae. However, significant differences in the sperm morphology of the previously investigated sicyoniids (namely, a greater complexity of the acrosomal complex) suggest evolutionary separation of the Sicyoniidae from the assemblage Penaeidae-Solenoceridae. Two ultrastructural features distinguish the spermatozoa of the three studied solenocerids from penaeid sperm: 1) separation of the plasma and acrosome membranes at the base of the spike and anterior region of the cap, and 2) asymmetry of the acrosomal cap, which appears to be a synapomorphy of the group. No striking ultrastructural differences were found between the spermatozoa of the closely related species S. membranacea and S. africana, whereas a great number of morphological differences separate the spermatozoa of Pleoticus from those of Solenocera (e.g., shape of the acrosomal cap, structural arrangement of the contents of the whole acrosome vesicle, thickness and distribution of the cytoplasm, and external shape of the spike).

Animals↗
PubMed1976

Excitability and functional organization of cutaneous tactile units of the bullfrog (R. catesbeiana).

Frog skin touch receptors are discrete structures which appear as dome-shaped translucent elevations of the epidermis. These domes are particularly responsive to direct touch. Tactile stimulation of adjacent skin never caused impulse activity, except when the skin distortion disturbed the domes. On stimulation at threshold intensity, the response of all units studied always consisted of a single impulse whether the stimulus energy was electrical or mechanical. While most tactile units discharged one impulse upon application of mechanical stimulation, a few also discharged one impulse upon stimulus release (on-off response). No after discharge was seen at stimulus strengths of three or four times threshold or after repetitive stimulation at 1,000 pps. The range of distribution of active domes/receptive field was 1--14. Generally the most sensitive domes appeared to be in or near center field. Twice as many of the tactile units responded more readily to cold than to warmth. The impulse frequency of units responding to thermal stimulation ranged from 3-11/sec. The conduction velocity of tactile units measured was within a range of 9--25 m/sec, with a mean of 12 m/sec. The results suggest that the following: 1) the existence of discrete structures which respond to tactile stimuli; a phylogenetic relationship might be postulated; 2) cold/touch receptors which appear to be present in greater quantity in the frog's skin than are warm/touch receptors, 3) touch units which should be considered primarily as mechanoreceptors with a possible secondary function as thermoreceptors.

Animals↗
PubMed2002

Hypophyseal development in vertebrates from amphibians to mammals.

Classically, it has been widely accepted that epithelial hypophysis develops from the stomodeal ectoderm. This notion was based on purely morphological observation of normal specimens. Recently, evidence is being accumulated that indicates another lineage for the developmental origin of adenohypophysis. This minireview focuses on several series of experimental works that have demonstrated a neuroectodermal origin of the hypophysis in vertebrates from amphibians to mammals. Phylogenetic consideration of the pituitary-like structures of prechordal animals is also presented.

Amphibians↗
PubMed1996

Genetic characterization and phylogeny of Sabiá virus, an emergent pathogen in Brazil.

Sabiá virus, one of five arenaviruses from South America known to cause hemorrhagic fever in humans, emerged in 1990 when it was isolated from a fatal case in Sao Paulo, Brazil. Subsequently, it has caused two laboratory-acquired infections. Its natural distribution and host are still unknown. Using viral RNA and multiple polymerase chain reaction products as templates, the nucleotide sequence of the small (S) RNA segment of Sabiá virus, which codes for the nucleocapsid (N) and glycoprotein precursor, was determined. This virus shares an ambisense genome in common with other arenaviruses, although it has a unique predicted three stem--loop structure in the S RNA intergenic region. Phylogenetic analysis of a portion of the N gene sequence confirmed that Sabiá virus is distinct from all other members of the Arenaviridae and shares a progenitor with Junin, Machupo, Tacaribe, and Guanarito viruses.

Amino Acid Sequence↗
PubMed2001

Zebrafish--an emerging genetic model for the study of cytokines and hematopoiesis in the era of functional genomics.

Now that whole genomes are sequenced, the identification of gene function rather than gene discovery is a major challenge. Saturation mutagenesis and screening for mutant phenotypes are methods that allow sampling of the genome for lesions in genes critical for particular physiological processes. This approach promises to provide new insights into gene function, even for molecularly well-characterized processes such as hematopoiesis and cytokine signaling. Animal models for such genetic approaches have traditionally included Drosophila and the mouse. Recently, the zebrafish (Danio rerio) has emerged as a flexible and informative vertebrate for genetic studies. Zebrafish hematopoiesis has a morphological and molecular complexity closer to that of mammals than does Drosophila, providing scope for recognizing mutant zebrafish phenotypes representing finely tuned lesions in these processes. Compared to mice, zebrafish represent an economical, flexible, and genetically tractable animal model for mutagenesis studies. The structure of the teleost genome creates several phylogenetic issues in assessing zebrafish and piscine orthologues and paralogues of known mammalian genes, here exemplified by a cytokine ligand (interleukin-1beta), kinase receptors (c-kit and c-fins), and a family of intracellular signaling molecules (JAK kinases). Several anemic zebrafish mutants are now genetically characterized, and others present hematopoietic phenotypes that promise novel insights into the regulation of hematopoiesis.

Animals↗
PubMed1998

Phylogenetic and functional classification of mitogen- and stress-activated protein kinases.

All currently sequenced stress-activated protein kinases (SAPKs), extracellular signal-regulated kinases (ERKs), and other mitogen-activated protein kinases (MAPKs) were analyzed by sequence alignment, phylogenetic tree construction, and three-dimensional structure modeling in order to classify members of the MAPK family. Based on this analysis the MAPK family was divided into three subgroups (SAPKs, ERKs, and MAPK3) that consist of at least nine subfamilies. Members of a given subfamily were exclusively from animals, plants, or yeast/fungi. A single signature sequence, [LIVM][TS]XX[LIVM]XT[RK][WY]YRXPX[LIVM] [LIVM], was identified that is characteristic for all MAPKs and sufficient to distinguish MAPKs from other members of the protein kinase superfamily. This signature sequence contains the phosphorylation site and is located on loop 12 of the three-dimensional structure of MAPKs. I also identified signature sequences that are characteristic for each of the nine subfamilies of MAPKs. By modeling the three-dimensional structure of three proteins for each MAPK subfamily based on the resolved atomic structures of rat ERK2 and murine p38, it is demonstrated that amino acids conserved in all MAPKs are located primarily in the center of the protein around the catalytic cleft. I conclude that these residues are important for maintaining proper folding into the gross structure common to all MAPKs. On the other hand, amino acids conserved in a given subfamily are located mainly in the periphery of MAPKs, indicating their possible importance for defining interactions with substrates, activators, and inhibitors. Within these subfamily-specific regions, amino acids were identified that represent unique residues occurring in only a single subfamily and their location was mapped in three-dimensional structure models. These unique residues are likely to be crucial for subfamily-specific interactions of MAPKs with substrates, inhibitors, or activators and, therefore, represent excellent targets for site-directed mutagenesis experiments.

Amino Acid Sequence↗
PubMed2006

A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms.

Nitrogen fixation is an important process in biogeochemical cycles exclusively carried out by prokaryotes, mostly by an evolutionarily conserved nitrogenase protein complex, of which one of the structural genes (nifH) is highly valuable for phylogenetic and diversity analyses. We developed a nifH-based short oligonucleotide microarray (nifH diagnostic microarray) as a rapid tool to effectively monitor nitrogen-fixing diazotrophic populations in a wide range of environments. Taking account of the overwhelming predominance of environmental nifH fragments from uncultivated microorganisms in public databases, our nifH microarray is mainly based on nifH sequences from as yet unidentified prokaryotes. Standard conditions for microarray performance were determined, and criteria for the design of specific oligonucleotides were defined. A primary set of 56 oligonucleotides was validated with fluorescence-labeled single-stranded nifH targets from five reference strains, 26 environmental clones, and artificial mixtures of reference strains. The nifH microarray was applied to analyze the diversity (based on DNA) and activity (based on mRNA) of diazotrophs in roots of wild rice samples from Namibia. Results demonstrated that only a small subset of diazotrophs being present in the sample were actually fixing nitrogen actively. Our data suggest that the developed nifH microarray is a highly reproducible and semiquantitative method for mapping the variability of diazotrophic diversity, allowing rapid comparisons of the relative abundance and activity of diazotrophic prokaryotes in the environment. A further refined nifH microarray comprising of 194 oligonucleotide probes now covers more than 90% of sequences in our nifH database.

Azoarcus↗
PubMed2005

Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein.

Recently, close relatives of class B floral homeotic genes, termed B(sister) genes, have been identified in both angiosperms and gymnosperms. In contrast to the B genes themselves, B(sister) genes are exclusively expressed in female reproductive organs, especially in the envelopes or integuments surrounding the ovules. This suggests an important ancient function in ovule or seed development for B(sister) genes, which has been conserved for about 300 million years. However, investigation of the first loss-of-function mutant for a B(sister) gene (ABS/TT16 from Arabidopsis) revealed only a weak phenotype affecting endothelium formation. Here, we present an analysis of two additional mutant alleles, which corroborates this weak phenotype. Transgenic plants that ectopically express ABS show changes in the growth and identity of floral organs, suggesting that ABS can interact with floral homeotic proteins. Yeast-two-hybrid and three-hybrid analyses indicated that ABS can form dimers with SEPALLATA (SEP) floral homeotic proteins and multimeric complexes that also include the AGAMOUS-like proteins SEEDSTICK (STK) or SHATTERPROOF1/2 (SHP1, SHP2). These data suggest that the formation of multimeric transcription factor complexes might be a general phenomenon among MIKC-type MADS-domain proteins in angiosperms. Heterodimerization of ABS with SEP3 was confirmed by gel retardation assays. Fusion proteins tagged with CFP (Cyan Fluorescent Protein) and YFP (Yellow Fluorescent Protein) in Arabidopsis protoplasts showed that ABS is localized in the nucleus. Phylogenetic analysis revealed the presence of a structurally deviant, but closely related, paralogue of ABS in the Arabidopsis genome. Thus the evolutionary developmental genetics of B(sister) genes can probably only be understood as part of a complex and redundant gene network that may govern ovule formation in a conserved manner, which has yet to be fully explored.

Alleles↗
PubMed1981

Right-sided population bias and lateralization of activity in normal rats.

Of 602 rats tested for amphetamine-induced or nocturnal rotation (circling behavior), 54.8% (P less than 0.025) had right side biases. Of 292 rats tested in two-lever operant situations, 57.5% (P less than 0.02) preferred the right lever. Right-biased rats were significantly more active and had stronger side preferences than left-biased rats. It is suggested that the increase in right-sided population bias in humans, as compared to rodents, is related to a cortical asymmetry and the phylogenetic increase in cortical modulation of subcortical structures.

Animals↗
PubMed1979

Distinctive features of cilia in metazoans and their significance for systematics.

A comparative study of epidermal cilia in the Turbellaria and Nemertea has revealed features in these organelles that are specific to certain taxonomic groups. Turbellarians of the order Acoela, in particular, have a characteristic pattern of axonemal filament termination in the distal tips of their cilia and a characteristic ciliary rootlet system that is not seen in other turbellarian orders nor in other metazoans. Each epidermal cilium in acoels has a typical 9 + 2 axonemal pattern through the main part of its length, but near its distal tip there is an abrupt shelf-life narrowing at which filaments 4-7 terminate; filaments 1, 2, 8 and 9 continue into the thinner distal-most part of the shaft along with singlet microtubules from the axonemal center. The rootlet system in acoel cilia involves an interconnecting pattern with lateral connectives. The unique structure of these cilia has systematic and phylogenetic significance for the Acoela, and it is argued that ultrastructural characters in general, including characters of organelles, can be validly applied to the phylogeny and systematics of the Metazoa.

Animals↗
PubMed1991

Structure and evolution of ribonuclease P RNA.

Eubacterial RNase P contains a catalytic RNA that cleaves 5' leader sequences from precursor tRNAs. We review the current understanding of RNase P RNA structure and evolution, from the perspective of phylogenetic comparative analysis.

Bacillus subtilis↗
PubMed1982

Comparative aspects of transferrin-reticulocyte interactions: membrane receptors and iron uptake.

1. A comparative study was made of transferrin and iron uptake by rabbit, rat and human reticulocytes and chick embryo erythrocytes from rabbit, rat, human, chicken and porcine transferrins, human lactoferrin and chicken conalbumin. 2. Three methods were used, viz. direct and competitive uptake studies of transferrin and iron by the four species of cells, and competitive studies of transferrin binding by solubilized membrane receptors (rabbit reticulocytes only). 3. Methods were devised to analyse the data so as to obtain indices of relatedness or relative affinities of each type of heterologous transferrin in rates of iron uptake found with transferrin and cells from various species are largely due to variation in the affinity of cellular receptors for different transferrins. 5. It is concluded that the procedure used in this investigation allow the assessment of phylogenetic relationships and evolutionary trends obtained by structural studies of proteins.

Animals↗
PubMed1992

Split decomposition: a new and useful approach to phylogenetic analysis of distance data.

In order to analyze the structure inherent to a matrix of dissimilarities (such as evolutionary distances) we propose to use a new technique called split decomposition. This method accurately dissects the given dissimilarity measure as a sum of elementary "split" metrics plus a (small) residue. The split summands identify related groups which are susceptible to further interpretation when casted against the available biological information. Reanalysis of previously published ribosomal RNA data sets using split decomposition illustrate the potential of this approach.

Animals↗
PubMed2026

Genome-wide identification of the HSP70 superfamily in tropical sea cucumber Stichopus monotuberculatus and their expression analysis under low-salinity stress.

Heat shock proteins (HSPs) are a group of evolutionarily conserved molecular chaperones that serve as indispensable core regulators in preserving cellular homeostasis and orchestrating organismal stress responses. The tropical sea cucumber Stichopus monotuberculatus, a high-value aquaculture species, is sensitive to fluctuations in environmental salinity-a challenge that has emerged as a critical bottleneck limiting its large-scale commercial cultivation. However, no systematic investigation has been conducted to characterize the HSP70 superfamily in S. monotuberculatus and elucidate its functional roles in salinity adaptation. In the present study, we performed a comprehensive genome-wide scan and identified 19 HSP70 superfamily genes in the S. monotuberculatus genome, with the HSP70IV subfamily showing remarkable gene expansion, containing 8 distinct copies. Phylogenetic analysis, conserved motif identification, and gene structure characterization demonstrated high evolutionary conservation within each HSP subfamily. These genes were unevenly distributed across the chromosomes of S. monotuberculatus, and prediction of cis-acting elements revealed that their upstream regulatory regions were enriched with numerous functional elements associated with stress response and immune regulation. Salinity stress experiments revealed that under severe low-salinity conditions (18‰), the expression levels of SmHSPA14L and multiple HSP70IV subfamily members were significantly elevated, while SmHYOU1D was significantly downregulated; in contrast, only subtle changes were detected in the expression of most HSP70 genes under moderate low-salinity stress (24‰). These findings strongly suggest that HSP70 genes, particularly the expanded HSP70IV subfamily, may act as key modulators in the low-salinity stress response. This work provides valuable insight into the molecular mechanisms underlying salinity adaptation in tropical sea cucumbers.

Animals↗
PubMed2006

Control of Hoxd genes' collinearity during early limb development.

Hoxd genes are essential for limb growth and patterning. They are activated following a complex transcriptional regulation, leading to expression domains that are collinear in both space and time. To understand the mechanism(s) underlying collinearity, we produced and analyzed a set of mouse strains containing systematic deletions and duplications within the HoxD cluster. We show that two waves of transcriptional activation, controlled by different mechanisms, generate the observed developmental expression patterns. The first wave is time-dependent, involves the action of opposite regulatory modules, and is essential for the growth and polarity of the limb up to the forearm. The second phase involves a different regulation and is required for the morphogenesis of digits. We propose that these two phases reflect the different phylogenetic histories of proximal versus distal limb structures and discuss the biological relevance of these collinear patterns, particularly for the origin of the anterior-to-posterior limb polarity.

Age Factors↗
PubMed2003

Construction and characterisation of a full-length infectious molecular clone from a fast replicating, X4-tropic HIV-1 CRF02.AG primary isolate.

Based on our previous analysis of HIV-1 isolates from Cameroon, we constructed a full-length infectious molecular clone from a primary isolate belonging to the CRF02.AG group of recombinant viruses which dominate the HIV-epidemic in West and Central Africa. The virus derived by transfection of the proviral clone pBD6-15 replicated with similar efficiency compared to its parental isolate and used CXCR4 as coreceptor as well. Furthermore, HIV-1 BD6-15 exhibited similar replication properties and virus yield as the reference B-type HIV-1 strain NL4-3. Sequence analysis revealed open reading frames for all structural and accessory genes apart from vpr. Phylogenetic and bootscanning analyses confirmed that BD6-15 clusters with CRF02.AG recombinant strains from West and Central Africa with similar cross-over points as described for the CRF02.AG prototype strain lbNG. Thus, pBD6-15 represents the first non-subtype B infectious molecular clone of a fast replicating, high producer, X4-tropic primary HIV-1 isolate, which had only been briefly passaged in primary cells.

Adult↗
PubMed2005

Construction of bacterial artificial chromosome libraries for use in phylogenetic studies.

Bacterial artificial chromosome (BAC) libraries are emerging as valuable tools for investigating phylogenetic relationships at the level of genome structure. To date, BAC library construction has been restricted to a fairly small number of laboratories and species that represent a not insignificant, but a fairly small, fraction of diversity in the plant kingdom. This chapter is intended to contribute to rectifying this situation by providing protocols that facilitate BAC library construction in laboratories possessing basic molecular biology skills.

Chromosomes, Artificial, Bacterial↗