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At least 1,423 records · Page 79Linked to original sources
PubMed1993

Morphological changes of Candida albicans induced by BMY-28864, a highly water-soluble pradimicin derivative.

The time course of BMY-28864-dependent morphological changes in Candida albicans A9540 was studied by electron microscopy. Scanning electron microscopy revealed that BMY-28864 often induced cell surface deformations such as abnormal swelling and bulging around budding sites and bud scars. The cell membrane damage was visualized by freeze-fracturing technique as deep pit-like invaginations. Transmission electron microscopy with thin-sectioned specimens also demonstrated that BMY-28864 induced cell membrane invaginations together with cell membrane detachment from the cell wall, nuclear membrane fragmentation and mitochondrial aberration. Statistical sequence analysis of the prominent BMY-28864-dependent morphological changes of the yeast cells led to the conclusion that BMY-28864 first attacked the cell membrane and then caused disintegration of other intracytoplasmic organelles, resulting in the lethal effect.

Anthracyclines↗
PubMed2003

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins.

Features of the physical environment surrounding an ancestral organism can be inferred by reconstructing sequences of ancient proteins made by those organisms, resurrecting these proteins in the laboratory, and measuring their properties. Here, we resurrect candidate sequences for elongation factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial evolutionary tree, and measure their activities as a function of temperature. The ancient EF-Tu proteins have temperature optima of 55-65 degrees C. This value seems to be robust with respect to uncertainties in the ancestral reconstruction. This suggests that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles. This conclusion can be compared and contrasted with inferences drawn from an analysis of the lengths of branches in trees joining proteins from contemporary bacteria, the distribution of thermophily in derived bacterial lineages, the inferred G + C content of ancient ribosomal RNA, and the geological record combined with assumptions concerning molecular clocks. The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life.

Bacteria↗
PubMed2004

The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.

Thermotoga maritima invertase (beta-fructosidase) hydrolyzes sucrose to release fructose and glucose, which are major carbon and energy sources for both prokaryotes and eukaryotes. The name "invertase" was given to this enzyme over a century ago, because the 1:1 mixture of glucose and fructose that it produces was named "invert sugar." Despite its name, the enzyme operates with a mechanism leading to the retention of the anomeric configuration at the site of cleavage. The enzyme belongs to family GH32 of the sequence-based classification of glycosidases. The crystal structure, determined at 2-A resolution, reveals two modules, namely a five-bladed beta-propeller with structural similarity to the beta-propeller structures of glycosidase from families GH43 and GH68 connected to a beta-sandwich module. Three carboxylates at the bottom of a deep, negatively charged funnel-shaped depression of the beta-propeller are essential for catalysis and function as nucleophile, general acid, and transition state stabilizer, respectively. The catalytic machinery of invertase is perfectly superimposable to that of the enzymes of families GH43 and GH68. The variation in the position of the furanose ring at the site of cleavage explains the different mechanisms evident in families GH32 and GH68 (retaining) and GH43 (inverting) furanosidases.

Amino Acid Sequence↗
PubMed2006

Crystal structure of VC0702 at 2.0 A: conserved hypothetical protein from Vibrio cholerae.

VC0702, a conserved hypothetical protein of unknown function from Vibrio cholerae, resides in a three-gene operon containing the MbaA gene that encodes for a GGDEF and EAL domain-containing protein which is involved in regulating formation of the extracellular matrix of biofilms in Vibrio cholerae. The VC0702 crystal structure has been determined at 2.0 A and refined to Rwork = 22.8% and Rfree = 26.3%. VC0702 crystallized in an orthorhombic crystal lattice in the C222(1) space group with dimensions of a = 66.61 A, b = 88.118 A, and c = 118.35 A with a homodimer in the asymmetric unit. VC0702, which forms a mixed alpha + beta three-layered alphabetaalpha sandwich, belongs to the Pfam DUF84 and COG1986 families of proteins. Sequence conservation within the DUF84 and COG1986 families was used to identify a conserved patch of surface residues that define a cleft and potential substrate-binding site in VC0702. The three-dimensional structure of VC0702 is similar to that of Mj0226 from Methanococcus janeschii, which has been identified as a novel NTPase that binds NTP in a deep cleft similarly located to the conserved patch of surface residues that define an analogous cleft in VC0702. Collectively, the data suggest that VC0702 may have a biochemical function that involves NTP binding and phosphatase activity of some kind, and is likely involved in regulation of the signaling pathway that controls biofilm formation and maintenance in Vibrio cholerae.

Amino Acid Sequence↗
PubMed2005

UMD (Universal Mutation Database): 2005 update.

With the completion of the Human Genome Project, our vision of human genetic diseases has changed. The cloning of new disease-causing genes can now be performed in silico, and thousands of mutations are being identified in diagnostic and research laboratories yearly. Knowledge about these mutations and their association with clinical and biological data is essential for clinicians, geneticists, and researchers. To collect and analyze these data, we developed a generic software called Universal Mutation Databases (UMD) to create locus-specific databases. Here we report the new release (September 2004) of this freely available tool (www.umd.be), which allows the creation of LSDBs for virtually any gene and includes a large set of new analysis tools. We have implemented new features to integrate noncoding sequences, clinical data, pictures, monoclonal antibodies, and polymorphic markers (SNPs). Today the UMD retains all specifically designed tools to analyze mutations at the molecular level, as well as new sets of routines to search for genotype-phenotype correlations. We also created specific tools for infrequent mutations such as gross deletions and duplications, and deep intronic mutations. A large set of dedicated tools are now available for intronic mutations, including methods to calculate the consensus values (CVs) of potential splice sites and to search for exonic splicing enhancer (ESE) motifs. In addition, we have created specific routines to help researchers design new therapeutic strategies, such as exon skipping, aminoglycoside read-through of stop codons, or monoclonal antibody selection and epitope scanning for gene therapy.

Alternative Splicing↗
PubMed2005

Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus.

We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus. Using Bayesian, maximum-parsimony, nested clade and coalescent analyses of cytochrome b sequences, we inferred interspecific relationships, evaluated the specific distinctness of Cape (Xerus inauris) and mountain (Xerus princeps) ground squirrels, and tested hypotheses for historical patterns of gene flow within X. inauris. The inferred phylogeny supports the hypothesized existence of an 'arid corridor' from the Horn of Africa to the Cape region. Although doubts have been raised regarding the specific distinctness of X. inauris and X. princeps, our analyses show that each represents a distinct well-supported, monophyletic lineage. Xerus inauris includes three major clades, two of which are geographically restricted. The distributions of X. inauris populations are concordant with divergences within and disjunctions between other taxa, which have been interpreted as results of Plio-Pleistocene climate cycles. Nested clade analysis, coalescent analyses, and analyses of genetic structure support allopatric fragmentation as the cause of the deep divergences within this species.

Africa↗
PubMed2025

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO = 0.333-0.264) and did not reveal population differentiation within our samples (F ST = - 0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗
PubMed1992

Origin and fate of fetuin-containing neurons in the developing neocortex of the fetal sheep.

The development of the neocortex has previously been extensively studied in carnivores (cat and ferret), rodents (rat and mouse) and primates (monkey and human). In these species, it has been shown that the initial population of cells migrating from the ventricular zone forms the primordial plexiform layer. This is subsequently split into marginal zone and subplate zone by the insertion of later-migrating cells into the primordial plexiform layer, to form the cortical plate proper. Many of the cells derived from the split primordial plexiform layer are transient. The neurons of the subplate zone are found in the deeper part of layer VI, and white matter deep to layer VI in the more mature cortex; most of these neurons disappear by adulthood. [3H]-thymidine labelling in the present study has shown a similar pattern of neocortical development in Artiodactyla (sheep). In addition it has been shown that the previously described staining of subplate and cortical plate cells for the fetal protein fetuin indicates that fetuin is a useful marker for a proportion of this transient population of neurons and defines its extent in neocortical development more clearly. Dividing cells were labelled by a single intra-amniotic injection of [3H]-thymidine at E26 to E35 (birth is at E150). The brains were subsequently examined at E40 or E80 for [3H]-thymidine labelling and fetuin staining by a combination of autoradiography and immunocytochemistry. The earliest generated neocortical cells detected in this study (E26) were found in two layers by E40, the outer marginal zone and inner subplate zone. Neurons of the marginal zone were generated up to E28; those of the early subplate zone were generated up to E31. The cortical plate proper was generated by cells "born" on E32 and later. This sequence is similar to that described in other species, especially the cat. A proportion of the early-generated neurons in the marginal zone, subplate zone and early cortical plate stained for fetuin. By E80 these earliest-generated, fetuin-positive cells were found in the white matter deep to the forming neocortical layers and in layer VI. In adult brains no fetuin-positive neurons could be identified in the neocortex, and neurons had almost entirely disappeared from the white matter. The fetal glycoprotein fetuin seems to be specifically associated with a population of cells that has the same developmental history as the transient marginal zone and subplate neurons described in other species.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1999

Immunodetection and partial cDNA sequence of the proteoglycan, superficial zone protein, synthesized by cells lining synovial joints.

We have previously described a large proteoglycan named superficial zone protein that was isolated and purified from culture medium of superficial slices of bovine articular cartilage. Monoclonal antibodies were raised against superficial zone protein and used as probes in Western blot analyses for immunohistochemical studies both to determine precisely which cells within the joint synthesize the proteoglycan and to isolate a cDNA fragment from a bovine chondrocyte lambdagt11 library that encodes part of the proteoglycan. The cDNA fragment that was obtained with use of monoclonal antibody 6-A-1 encodes the 3' end of the sequence for superficial zone protein. On Western blots, monoclonal antibody 3-A-4 recognized an epitope on native, but not reduced, superficial zone protein, whereas monoclonal antibody 6-A-1 reacted with both native and denatured antigen. The proteoglycan was immunolocalized with monoclonal antibody 3-A-4 in chondrocytes predominantly within the superficial zone of fetal and adult articular cartilage and in some cells of the synovial lining. However, the proteoglycan was not detected in chondrocytes deep in articular cartilage, in nasal septal cartilage, or in synovial stromal cells. The only matrix staining positively for superficial zone protein was at the articular surface bordering the synovial cavity in adult, but not fetal, joints. Isolated chondrocytes and synovial cells showed intracellular binding of monoclonal antibody 3-A-4, and flow-cytometric analysis with the antibody gave the following percentages of immunopositive cells: 37.4, 52.5, 3.4, and 7.5 from chondrocytes from the full-thickness, superficial, and deep zones and from synovial cells, respectively. Thus, both chondrocytes and synovial cells bordering the joint cavity synthesize superficial zone protein and substantiate its usefulness as a phenotypic marker of particular cellular species lining the articular cavity.

Amino Acid Sequence↗
PubMed2000

Differential distribution of metabotropic glutamate receptors 1a, 1b, and 5 in the rat spinal cord.

Metabotropic glutamate receptors (mGluRs) modulate somatosensory, autonomic, and motor functions at spinal levels. mGluR postsynaptic actions over spinal neurons display the pharmacologic characteristics of type I mGluRs; however, the spinal distribution of type I mGluR isoforms remains poorly defined. In this study, the authors describe a differential distribution of immunoreactivity to various type I mGluR isoforms (mGluR1a, mGluR5a,b, and mGluR1b) that suggests a correlation between specific isoforms and particular aspects of spinal cord function. Two different antisera raised against mGluR5a,b detected intense immunoreactivity within nociceptive afferent terminal fields (laminae I and II) and also in autonomic regions (parasympathetic and sympathetic). In contrast, two of three anti-mGluR1a antibodies did not immunostain lamina I or II. Laminae I and II immunostaining by a third anti-mGluR1a antibody was competed by a peptide sequence obtained from a homologous region in mGluR5, suggesting possible cross reactivity in fixed tissue. Autonomic neurons did not express mGluR1a immunoreactivity. All anti-mGluR1a antibodies strongly and specifically immunolabeled dendritic and somatic membranes of neurons in the deep dorsal horn (lamina III-V) and the ventral horn (lamina VI-IX). Somatic motoneurons expressed mGluR1a immunoreactivity but little or no mGluR5 immunoreactivity. Phrenic and pudendal motoneurons expressed the highest level of mGluR1a immunoreactivity in the spinal cord. Intense mGluR1b immunoreactivity was restricted to a few scattered neurons and a prominent group of neurons in lamina X. Lamina II neurons expressed low levels of mGluR1b immunoreactivity. Ultrastructurally, type I mGluR immunoreactivity was found mostly at extrasynaptic sites on the plasma membrane, but it was also found perisynaptically, in the body of the postsynaptic regions or in relation to intracytoplasmic structures.

Animals↗
PubMed2004

Early diagnosis of cerebral involvement in Sturge-Weber syndrome using high-resolution BOLD MR venography.

Sturge-Weber syndrome (SWS) is a congenital disorder characterized by a vascular birthmark and neurological abnormalities. Typical imaging findings using MRI or CT are superficial cerebral calcification, atrophy and leptomeningeal enhancement. We present a neonate diagnosed with SWS because of a port-wine stain. In the absence of neurological symptoms the first MRI was performed when he was 4 months old, and follow-up MRI studies were performed after his first seizure at the age of 12 months. MRI was performed using standard sequences before and after administration of IV gadolinium. A high-resolution T2*-weighted, rf-spoiled 3D gradient-echo sequence with first-order flow compensation in all three directions was used for additional venographic imaging [blood-oxygen-level-dependent (BOLD) venography]. The initial conventional MRI sequences did not demonstrate any abnormality, but BOLD venography identified leptomeningeal internal veins. Follow-up MRI after the first onset of seizures demonstrated strong leptomeningeal enhancement, while BOLD venography revealed pathological medullary and subependymal veins as well as deep venous structures. At this time there were the first signs of atrophy and CT showed marginal calcifications. This report demonstrates that high-resolution BOLD MR venography allows early diagnosis of venous anomalies in SWS, making early therapeutic intervention possible.

Brain Diseases↗
PubMed1994

Localization of neuronal and glial glutamate transporters.

The cellular and subcellular distributions of the glutamate transporter subtypes EAAC1, GLT-1, and GLAST in the rat CNS were demonstrated using anti-peptide antibodies that recognize the C-terminal domains of each transporter. On immunoblots, the antibodies specifically recognize proteins of 65-73 kDa in total brain homogenates. Immunocytochemistry shows that glutamate transporter subtypes are distributed differentially within neurons and astroglia. EAAC1 is specific for certain neurons, such as large pyramidal cortical neurons and Purkinje cells, but does not appear to be selective for glutamatergic neurons. GLT-1 is localized only to astroglia. GLAST is found in both neurons and astroglia. The regional localizations are unique to each transporter subtype. EAAC1 is highly enriched in the cortex, hippocampus, and caudate-putamen and is confined to pre- and postsynaptic elements. GLT-1 is distributed in astrocytes throughout the brain and spinal cord. GLAST is most abundant in Bergmann glia in the cerebellar molecular layer brain, but is also present in the cortex, hippocampus, and deep cerebellar nuclei.

Amino Acid Sequence↗
PubMed2006

Retinal, pineal and diencephalic expression of frog arylalkylamine N-acetyltransferase-1.

The arylalkylamine N-acetyltransferase (AANAT) is a key enzyme in the rhythmic production of melatonin. Two Aanats are expressed in Teleost fish (Aanat1 in the retina and Aanat2 in the pineal organ) but only Aanat1 is found in tetrapods. This study reports the cloning of Aanat1 from R. perezi. Transcripts were mainly expressed in the retina, diencephalon, intestine and testis. In the retina and pineal organ, Aanat1 expression was in the photoreceptor cells. Expression was also seen in ependymal cells of the 3rd ventricle and discrete cells of the suprachiasmatic area. The expression of Aanat1 in both the retina and pineal organ, and the absence of Aanat2 suggests that green frog resembles more to birds and mammals than to Teleost fish, as far as Aanat is concerned. The significance of Aanat1 in extra-pineal and extra-retinal tissues remains to be elucidated; in the diencephalon, it might be associated to the so-called deep brain photoreceptor cells.

Amino Acid Sequence↗
PubMed2003

The energetics of specific binding of AT-hooks from HMGA1 to target DNA.

The interaction of the second and third AT-hooks of HMGA1 (formerly HMGI/Y), which bind selectively in the minor groove of an AT-rich DNA sequence, was studied at different temperatures and ionic strengths by spectropolarimetry, spectrofluorimetry, isothermal titration calorimetry and differential scanning calorimetry. The data show that binding of the ten amino acid core element of the two AT-hooks, which penetrates deep into the minor groove, is entropically driven: both the entropy and enthalpy of association of the peptides to the target DNA are positive up to 50 degrees C. The seven amino acid extension of the core in the second AT-hook, which extends out from the minor groove and loops over the phosphodiester backbone, adds a substantial negative enthalpic component into the binding of the 17 residue DBD2 peptide to DNA that corresponds in magnitude to the enthalpy of formation of two hydrogen bonds. The ionic strength dependence of the association constant allowed an estimation of the electrostatic component of binding and, by subtraction, the contribution of the non-electrostatic component, which results from dehydration of the contacting surfaces and makes up almost 70% of the total energy of complex formation. The exceptionally large positive entropy and enthalpy of association of the core AT-hook peptides with target DNA suggest that the water, which is removed from the minor groove of DNA upon binding, is in a highly ordered state. Acetylation of the lysine residue in the second AT-hook, which corresponds to Lys65 of HMGA1, has little effect on the DNA binding; so it appears that repression of the hIFNbeta gene, which follows this modification, is not a direct result of the abrogation of DNA binding.

Binding Sites↗
PubMed2002

Squalene-hopene cyclase: catalytic mechanism and substrate recognition.

Rapid progress on the catalytic mechanism and substrate recognition by squalene-hopene cyclase, which has occurred only in the last several years, is reported. A series of site-directed mutation experiments and some squalene analogues have provided deep insight into the polycyclization mechanism and catalytic sites in conjunction with the information from X-ray crystal data.

Amino Acid Sequence↗
PubMed2003

Streptococci and Actinomyces induce antibodies which cross react with epithelial antigens in periodontitis.

Perturbation of epithelial structure is a prominent but poorly understood feature of the immunopathological response to bacterial antigens which characterizes the destructive lesion of periodontitis. Western analysis of sera from 22 patients with periodontitis detected multiple antigens in extracts of epithelial cells whereas sera from 12 periodontally healthy subjects displayed only trace reaction with epithelial antigens. To investigate a possible relationship between the bacterial flora adjacent to diseased sites and the presence of antibodies reactive with epithelium, subgingival plaque samples were taken from deep periodontal pockets and cultured anaerobically. Gram positive bacteria containing antigens cross-reactive with epithelial cells were reproducibly isolated by probing membrane colony-lifts with affinity-isolated (epithelium-specific) antibodies and identified by 16S rDNA sequence homology as streptococci (S. mitis, S. constellatus and two S. intermedius strains) and Actinomyces (A. georgiae, and A. sp. oral clone). Conversely, when serum from patients with periodontitis was absorbed with the captured bacterial species the number of epithelial antigens recognized was specifically reduced. It was concluded that development of cross-reactive antibodies related to these organisms may contribute to perturbation of the epithelial attachment to the tooth and the progression of periodontitis. These autoreactive antibodies could also be a contributing factor in other diseases affecting epithelia.

Actinomyces↗
PubMed2000

Multiplication of antenna genes as a major adaptation to low light in a marine prokaryote.

Two ecotypes of the prokaryote Prochlorococcus adapted to distinct light niches in the ocean have been described recently. These ecotypes are characterized by their different (divinyl-) chlorophyll (Chl) a to Chl b ratios and 16S rRNA gene signatures, as well as by their significantly distinct irradiance optima for growth and photosynthesis [Moore, L. R., Rocap, G. & Chisholm, S. W. (1998) Nature (London) 393, 464-467]. However, the molecular basis of their physiological differences remained, so far, unexplained. In this paper, we show that the low-light-adapted Prochlorococcus strain SS120 possesses a gene family of seven transcribed genes encoding different Chl a/b-binding proteins (Pcbs). In contrast, Prochlorococcus sp. MED4, a high-light-adapted ecotype, possesses a single pcb gene. The presence of multiple antenna genes in another low-light ecotype (NATL2a), but not in another high-light ecotype (TAK9803-2), is demonstrated. Thus, the multiplication of pcb genes appears as a key factor in the capacity of deep Prochlorococcus populations to survive at extremely low photon fluxes.

Amino Acid Sequence↗
PubMed1997

Molecular evidence that echiurans and pogonophorans are derived annelids.

The Annelida, which includes the polychaetes and the clitellates, has long held the taxonomic rank of phylum. The unsegmented, mud-dwelling echiuran spoon worms and the gutless, deep-sea pogonophoran tube worms (including vestimentiferans) share several embryological and morphological features with annelids, but each group also has been considered as a separate metazoan phylum based on the unique characters each group displays. Phylogenetic analyses of DNA sequences from the nuclear gene elongation factor-1alpha place echiurans and pogonophorans within the Annelida. This result, indicating the derived loss of segmentation in echiurans, has profound implications for our understanding of the evolution of metazoan body plans and challenges the traditional view of the phylum-level diversity and evolutionary relationships of protostome worms.

Animals↗