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At least 1,783 records · Page 99Linked to original sources
PubMed2003

Statistical approaches for estimating actinobacterial diversity in marine sediments.

Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with >/= 99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. F(ST) and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.

Actinobacteria↗
PubMed2000

[Recent knowledge allowing diagnosis and treatment of deep-seated trichosporonosis].

Deep-seated trichosporonosis is a lethal opportunistic infection in immunocompromised patients. For the rapid diagnosis of this condition, we developed a novel nested-PCR assay that detects DNA specific for clinically important strains of Trichosporon in serum of patients with disseminated trichosporonosis. In this assay, two sets of oligonucleotide primers were derived from the sequence of 26 S ribosomal RNA genes of T. asahii. The specific fragment was amplified from T. asahii and T. mucoides but not from other microorganisms. In a retrospective study using serum samples of patients with disseminated trichosporonosis, the specific fragment was detected in 64% (7 of 11). To treat this infection, we studied the efficacy of rhG-CSF alone and in combination with antifungal agents against disseminated trichosporonosis in neutropenic mice. The results suggested that rhG-CSF might be a useful immunomodulator against Trichosporon infections and the therapeutic outcome might be better when used in combination with antifungal agents.

Adjuvants, Immunologic↗
PubMedDate not supplied

[Auditory neuropathies in infants].

Auditory neuropathy is a sensorineural disorder characterized by absent or abnormal auditory evoked potentials, and normal cochlear outer hair cell function. It is believed that a variety of processes are involved in its pathophysiology and their influence on hearing can differ. We describe the diagnostic sequence and management of two new cases of auditory neuropathy in infants. The first case was a girl with no risk factors for hearing loss. Her absence of response to sounds was compared with her twin's reactions. Otoacoustic emissions were present but no auditory evoked potential response was detected. Her evolution was characteristic of deep sensorineural hearing loss without a hearing aid. At present she is awaiting a cochlear implant. The second case was a boy who underwent hearing loss screening for hyperbilirubinemia. Examinations were repeated three months later because the mother suspected hearing loss. Objective tests showed a pattern of auditory neuropathy. The boy's evolution was different: in spite of the presence of destructured auditory evoked potentials; it was evident that the boy conserved some hearing and had thresholds suggestive of moderate hearing loss.

Audiometry↗
PubMed2005

[Recombination within the human leucocyte antigen].

Understanding with greater clearness the characteristics of recombination within the human leucocyte antigen(HLA) is of deep significance to gaining an insight into the evolutionary process of shaping HLA allelic diversity and ultimately the human resistance against diverse pathogens. Family studies and statistical analysis of recombination have provided estimations of recombination fractions across the major histocompatibility complex and have identified the potential recombination hotspots. Other characteristics such as haplotype specificity and sequence motifs have been intensively studied. The recombination fractions, hotspots and other characters are reviewed in this paper.

Gene Frequency↗
PubMedDate not supplied

MR evaluation of brain iron in children with cerebral infarction.

Young children and infants normally have essentially no detectable brain iron. We evaluated brain iron patterns on 23 MR scans in 20 patients under 6 years of age with clinical and MR-documented cerebral infarctions in an attempt to further understand the neuropathologic phenomenon of increased iron deposition, which has been observed in other disease states. MR was performed at 1.5 T with spin-echo sequences from 1 day to 4 years after infarction. MR scans were interpreted without knowledge of clinical information and were assessed for (1) location and character (i.e., bland or hemorrhagic) of infarct, and (2) nonheme iron (i.e., marked hypointensity on long TR/TE images) in the basal ganglia, red nuclei, substantia nigra, thalami, dentate nuclei, and deep white matter. Sixteen of 20 infarctions were associated with increased iron. Six of seven cases with unilateral iron deposition had ipsilateral infarctions. The location (deep versus cortical) and age of the infarction had no apparent bearing on iron patterns. We conclude that increased brain iron is commonly associated with cerebral infarction and is nonspecific, rather than a marker of movement disorders. Since iron may arise from either interruption of transport pathways or directly from cell injury and, in fact, iron itself may propagate the tissue injury, this finding may have important clinical and pathophysiologic implications in ischemic brain injury.

Brain↗
PubMed1995

MFT in complex partial epilepsy: spatio-temporal estimates of interictal activity.

Magnetic field tomography (MFT) displays three dimensional estimates of the distribution of the primary current density vector, Jp, as extracted from non-invasive, non-contact, magnetoencephalographic (MEG) measurements. MFT was used to study the spatiotemporal evolution of the interictal activity during single spike events of a patient with complex partial epilepsy. The sequences of events of the interictal spikes were analysed in sagittal sections, particularly at the depth of the temporal lobe. It appeared that the left-sided interictal spikes were usually initiated at the cortical level of the left temporal lobe, the activity then propagating to the left amygdaloid and hippocampal formation. However, some focal deep activity in this region was obviously initiated in the contralateral hemisphere.

Adolescent↗
PubMed1995

A role for quaternary structure in the substrate specificity of leucine dehydrogenase.

BACKGROUND: Glutamate, phenylalanine and leucine dehydrogenases catalyze the NAD(P)(+)-linked oxidative deamination of L-amino acids to the corresponding 2-oxoacids, and sequence homology between these enzymes clearly indicates the existence of an enzyme superfamily related by divergent evolution. We have undertaken structural studies on a number of members of this family in order to investigate the molecular basis of their differential amino acid specificity. RESULTS: We have solved the X-ray structure of the leucine dehydrogenase from Bacillus sphaericus to a resolution of 2.2 A. Each subunit of this octameric enzyme contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle. CONCLUSIONS: Comparison of the structure of leucine dehydrogenase with a hexameric glutamate dehydrogenase has shown that these two enzymes share a related fold and possess a similar catalytic chemistry. A mechanism for the basis of the differential amino acid specificity between these enzymes involves point mutations in the amino acid side-chain specificity pocket and subtle changes in the shape of this pocket caused by the differences in quaternary structure.

Amino Acid Oxidoreductases↗
PubMed2003

Laparoscopic inferior vena cava and right atrial thrombectomy utilizing deep hypothermic circulatory arrest.

BACKGROUND AND PURPOSE: Surgery for renal cancer associated with a level III or IV tumor thrombus often involves cardiopulmonary bypass, deep hypothermia, and exploration of the right atrium and inferior vena cava (IVC). This major open operation necessitates a large median sternotomy incision and a midline abdominal or chevron incision. Herein, we investigate the feasibility of purely laparoscopic IVC and right atrial thrombectomy utilizing deep hypothermic circulatory arrest. MATERIALS AND METHODS: In six male calves weighing 70 to 80 kg, the right common carotid artery and right internal jugular vein were cannulated for subsequent cardiopulmonary bypass. One laparoscopic team performed right radical nephrectomy and complete mobilization of the intra-abdominal IVC by a four-port approach. Simultaneously, a second laparoscopic team obtained three-port thoracoscopic access to incise the pericardium and expose the right atrium. In sequence, cardiopulmonary bypass, complete exsanguination, cardiac arrest, and core hypothermia of 18 degrees C were achieved. A coagulum thrombus was created by needle injection into the IVC. Combined laparoscopic and thoracoscopic incision, exploration, and thrombectomy of the IVC and the right atrium were then performed in a bloodless field. An angioscope was inserted inside the heart and the IVC to confirm complete thrombus clearance visually. The IVC and right atrium were then laparoscopically suture repaired, cardiopulmonary bypass was reestablished, and the animal was gradually rewarmed. Once sinus rhythm was reestablished at normal body temperature, the animal was weaned off the pump. RESULTS: The mean total operative time was 494.5 minutes (range 355-705 minutes). The mean time needed to lower the core temperature was 63.5 minutes (range 50-120 minutes), and the mean time required to rewarm the animal was 101.8 minutes (range 70-130 minutes). The mean blood volume drained into the pump was 2633.3 mL (range 1400-3200 mL), and the mean estimated blood loss was 350 mL (range 200-750 mL). Reestablishment of sinus cardiac rhythm and weaning off the pump was successful in all animals prior to acute euthanasia. CONCLUSIONS: Laparoscopic radical nephrectomy with thrombectomy for level III or IV tumor thrombi utilizing deep hypothermic circulatory arrest is feasible in the calf model using minimally invasive techniques exclusively. The procedure is technically complex and requires the combined efforts of expert urologic and cardiac operative teams. Survival studies are planned.

Animals↗
PubMed2005

Amino acids in the pore region of Kv1 potassium channels dictate cell-surface protein levels: a possible trafficking code in the Kv1 subfamily.

Kv1.1 and Kv1.4 potassium channels have different pore region determinants that were found to affect their cell-surface levels positively and negatively [Zhu, Watanabe, Gomez and Thornhill (2001) J. Biol. Chem. 276, 39419-39427; Zhu, Watanabe, Gomez and Thornhill (2003) J. Biol. Chem. 278, 25558-25567; Zhu, Watanabe, Gomez and Thornhill (2003) Biochem. J. 375, 761-768]. In the present study, we focused on the deep pore region of Kv1 members to test whether a cell-surface trafficking code was dictated by two amino acids. Kv1 channels with a threonine/lysine amino acid pair in a non-contiguous pore region promoted high surface levels, whereas a serine/tyrosine amino acid pair inhibited high surface expression by inducing a high level of partial endoplasmic reticulum retention. Our work suggests that a possible positive trafficking amino acid pair coding here for the Kv1 subfamily is Thr/Lys>Thr/Val>Thr/Tyr>Thr/Arg approximately Thr/His>Ser/Val>Ser/Tyr>Ser/Lys. The Kv1 trafficking code was not transferable to a Kv2 family member and thus it appears that it only governs surface levels in the context of its Kv1 native pore loop region and/or its S5 and S6 regions. All members of a given Kv2, Kv3 or Kv4 potassium channel subfamily have identical amino acids at similar positions in their deep pore regions (Thr/Tyr or Thr/Val), which suggests that any difference in surface levels among members is not dictated by these amino acids. Thus a major determinant for cell-surface trafficking of Kv1 potassium channels is an amino acid pair in their deep pore regions, whereas the cell-surface levels of a given Kv2, Kv3 or Kv4 subfamily member are probably not affected by these amino acids.

Amino Acid Sequence↗
PubMed2001

Matrix metalloproteinase activity inactivates the CXC chemokine stromal cell-derived factor-1.

Chemokines provide directional cues for leukocyte migration and activation that are essential for normal leukocytic trafficking and for host responses during processes such as inflammation, infection, and cancer. Recently we reported that matrix metalloproteinases (MMPs) modulate the activity of the CC chemokine monocyte chemoattractant protein-3 by selective proteolysis to release the N-terminal tetrapeptide. Here we report the N-terminal processing, also at position 4-5, of the CXC chemokines stromal cell-derived factor (SDF)-1alpha and beta by MMP-2 (gelatinase A). Robustness of the MMP family for chemokine cleavage was revealed from identical cleavage site specificity of MMPs 1, 3, 9, 13, and 14 (MT1-MMP) toward SDF-1; selectivity was indicated by absence of cleavage by MMPs 7 and 8. Efficient cleavage of SDF-1alpha by MMP-2 is the result of a strong interaction with the MMP hemopexin C domain at an exosite that overlaps the monocyte chemoattractant protein-3 binding site. The association of SDF-1alpha with different glycosaminoglycans did not inhibit cleavage. MMP cleavage of SDF-1alpha resulted in loss of binding to its cognate receptor CXCR-4. This was reflected in a loss of chemoattractant activity for CD34(+) hematopoietic progenitor stem cells and pre-B cells, and unlike full-length SDF-1alpha, the MMP-cleaved chemokine was unable to block CXCR-4-dependent human immunodeficiency virus-1 infection of CD4(+) cells. These data suggest that MMPs may be important regulatory proteases in attenuating SDF-1 function and point to a deep convergence of two important networks, chemokines and MMPs, to regulate leukocytic activity in vivo.

Amino Acid Sequence↗
PubMed2001

Isolation and identification of pathogenic strains of Streptomyces acidiscabies from netted scab lesions of potato tubers in Hokkaido (Japan).

A relatively homogeneous group of streptomycete isolates was obtained from netted scab lesions of potato tubers collected from a potato field in Hokkaido, Japan. Based on 55 phenotypic data of 72 Streptomyces strains selected from these isolated together with spectral data on their soluble pigments and with data of a PCR analysis, using species specific primers, these netted scab causing pathogenic organisms were identified as S. acidiscabies. S. acidiscabies had previously been isolated from deep (common) scab lesions in the USA and reported as thaxtomin A producer. In contrast, our S. acidiscabies strains were not able to induce deep scab symptoms on potato minitubers in pot test, did not produce the phytotoxin thaxtomin A and did not contain the pathogenicity related gene, nec-1.

Bacterial Proteins↗
PubMed2000

Netrin-G1: a novel glycosyl phosphatidylinositol-linked mammalian netrin that is functionally divergent from classical netrins.

UNC-6/netrins compose a small phylogenetically conserved family of proteins that act as axon guidance cues. With a signal sequence trap method, we isolated a cDNA encoding a novel member of the UNC-6/netrin family, which we named netrin-G1. Unlike classical netrins, netrin-G1 consists of at least six isoforms of which five were predominantly anchored to the plasma membrane via glycosyl phosphatidyl-inositol linkages. Netrin-G1 transcripts were first detected in midbrain and hindbrain regions by embryonic day 12 and reached highest levels at perinatal stages in various brain regions, including olfactory bulb mitral cells, thalamus, and deep cerebellar nuclei. Its expression was primarily restricted to the CNS. Interestingly, netrin-G1 proteins did not show appreciable affinity to any netrin receptor examined. Unlike netrin-1, a secreted form of netrin-G1 consistently failed to attract circumferentially growing axons from the cerebellar plate. Our findings suggest that netrin-G1 and its putative receptors have coevolved independently from the classical netrins. The expression pattern of netrin-G1 and its predicted neuronal membrane localization suggest it may also have novel signaling functions in nervous system development.

Amino Acid Sequence↗
PubMed1997

Solution structure of the esperamicin A1-DNA complex.

Esperamicin A1 is an enediyne antibiotic possessing antitumor activity associated with its ability to bind and, following activation, affect strand cleavage of DNA. We report on the solution structure of the esperamicin A1-d(C-G-G-A-T-C-C-G) duplex complex based on a combined analysis of NMR and molecular dynamics calculations including intensity refinement in a water box. The refined solution structures of the complex provide a molecular explanation of the sequence specificity for binding and cleavage by this member of the enediyne family of antitumor antibiotics. Esperamicin A1 binds to the DNA minor groove with its methoxyacrylyl-anthranilate moiety intercalating into the helix at the (G2-G3)-(C6'-C7') step. The methoxyacrylyl-anthranilate intercalator and the minor groove binding A-B-C+ risaccharide moieties rigidly anchor the enediyne in the minor groove such that the pro-radical centers of the enediyne are proximal to their anticipated proton abstraction sites. Specifically, the pro-radical C-3 and C-6 atoms are aligned opposite the abstractable H-5' (pro-S) proton of C6 and the H-1' proton of C6' on partner strands, respectively, in the complex. The thiomethyl sugar B residue is buried deep in an edgewise manner in the minor groove with its two faces sandwiched between the walls of the groove. Further, the polarizable sulfur atom of the thiomethyl group of sugar B residue is positioned opposite and can hydrogen-bond to the exposed amino proton of G3' in the complex. There is little perturbation away from a right-handed Watson-Crick base-paired duplex in the complex other than unwinding of the helix at the intercalation site and widening of the minor groove centered about the enediyne-binding and anthranilate intercalation sites. Sequence-specific binding of esperamicin A1 to the d(C-G-G-A-T-C-C-G) duplex is favored by the complementarity of the fit between the drug and the floor of the minor groove, good stacking between the intercalating anthranilate ring and flanking purine bases and intermolecular hydrogen-bonding interactions.

Aminoglycosides↗
PubMed2001

Molecular systematics of the family Mormoopidae (Chiroptera) based on cytochrome b and recombination activating gene 2 sequences.

We examined 1140 bp of the mitochondrial cytochrome b gene and 1398 bp of the nuclear RAG2 gene to investigate the systematics of the eight species of bats within the family Mormoopidae. It was concluded that within the genus Pteronotus there were four valid subgenera: Phyllodia, Chilonycteris, Pteronotus, and an undescribed subgenus. Within Pteronotus, P. parnellii either was part of an unresolved tetratomy with the other three subgenera (cytochrome b data) or was basal (RAG2 and combined data). For three species, P. gymnonotus, P. macleayii, and P. quadridens, our sample revealed little geographic variation. In P. davyi and P. parnellii, the magnitude of genetic distance suggests the possibility of two biological species existing within the currently recognized taxa. Within P. personatus, there was substantial geographic variation partitioned in a step-like fashion among our specimens. Neither of the species within the genus Mormoops showed the deep distance nodes present in P. davyi, P. parnellii, and P. personatus. Cytochrome b and RAG2 data indicated that M. megalophylla evolved recently from its common ancestor. Although there was considerable agreement among the branching patterns for the nuclear and mitochondrial genes, both genes failed to provide robust data concerning the evolutionary relationships among the subgenera.

Animals↗
PubMed2002

Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction.

The melanogaster species group of Drosophila (subgenus Sophophora) has long been a favored model for evolutionary studies because of its morphological and ecological diversity and wide geographic distribution. However, phylogenetic relationships among species and subgroups within this lineage are not well understood. We reconstructed the phylogeny of 17 species representing 7 "oriental" species subgroups, which are especially closely related to D. melanogaster. We used DNA sequences of four nuclear and two mitochondrial loci in an attempt to obtain the best possible estimate of species phylogeny and to assess the extent and sources of remaining uncertainties. Comparison of trees derived from single-gene data sets allowed us to identify several strongly supported clades, which were also consistently seen in combined analyses. The relationships among these clades are less certain. The combined data set contains data partitions that are incongruent with each other. Trees reconstructed from the combined data set and from internally homogenous data sets consisting of three or four genes each differ at several deep nodes. The total data set tree is fully resolved and strongly supported at most nodes. Statistical tests indicated that this tree is compatible with all individual and combined data sets. Therefore, we accepted this tree as the most likely model of historical relationships. We compared the new molecular phylogeny to earlier estimates based on morphology and chromosome structure and discuss its taxonomic and evolutionary implications.

Animals↗
PubMed1995

Localization of the 110 kDa receptor for laminin in brains of embryonic and postnatal mice.

Laminin, a large glycoprotein of the basement membrane that promotes the growth of nerve cell processes in vitro has also been detected in the brains of developing embryos in situ where it is postulated to promote or guide neural outgrowth. We have investigated the histological and developmental patterns of a receptor to a specific pentapeptide sequence in the A chain of the laminin molecule (PA22-2 or IKVAV) that has been identified as a neuron growth-promoting sequence. Standard immunocytochemical procedures were used to localize the receptor by means of a polyclonal antibody to affinity-purified receptor (MR = 110 kDa) from mouse brains. Results for postnatal stages (P) stages (P 1,7,8,25,30,and adult) show that the 110 kDa receptor is localized in fibers in the cortex and hippocampus, in astroglial cells at the surface of the cortex, and in neuronal cell bodies in the hippocampus. In contrast, the A-chain ligand is localized in cell bodies in the same regions at P stages. For embryonic stages (E) (E 14 and E 16) the receptor is localized in bundles of fibers in the superficial and deep cortical layers, and in cell bodies in these regions at E 14 only. Staining for the A chain ligand of the receptor was first seen postnatally. We speculate that the inverse histological pattern of receptor and ligand with respect to cell bodies and fibers may reflect a role in controlling axon guidance during development or repair during regeneration.

Amino Acid Sequence↗
PubMed2006

Migratory routes and fates of cells transcribing the Wnt-1 gene in the murine hindbrain.

To investigate the origins, migrations, and fates of Wnt-1-expressing cells in the murine hindbrain, mice carrying a Wnt-1 enhancer/lacZ transgene were observed from embryonic day (E) 8 through postnatal day 18. The transgene-stained ventricular layer waxed and waned prior to and following migrations from it. Stained cells migrated first external to the hindbrain as neural crest and then within it to form typical populations of the rhombic lip, as well as others not recognized as lip derivatives. Migrations originated in a temporally defined sequence, many from discrete rhombomeres. All moved first radially, then rostrally and/or ventrally, ipsi-, or contralaterally, in the mantle or marginal layers. These movements ultimately formed elements of several nuclei, aligned in four longitudinal bands: dorsal (including the gracile, cuneate, cochlear, and vestibular nuclei, plus cerebellar granular cells), dorsal intermediate (including trigeminal sensory, parvicellular reticular, and deep cerebellar nuclei), ventral intermediate (including lateral and intermediate reticular nuclei), and ventral (including the raphe obscurus and pontine nuclei). Transgene staining often persisted long enough to identify stained cells in their definitive, adult nuclei. However, staining was transient. The strength of the staining, however, was in its ability to reveal origins and migrations in both whole-mounts and sections, in single cell detail. The present results will permit analyses of the effects of genetic manipulations on Wnt-1 lineage cells.

Animals↗
PubMed1999

[The "heme"-sequence (T2*-weighted gradient echo magnetic resonance tomography). Value in differential spontaneous intracerebral hemorrhage diagnosis].

In four patients presenting with acute non-traumatic intracerebral or intraspinal hemorrhage, T2*-weighted gradient-echo MRI showed numerous residual hemosiderin deposits due to old intracerebral hemorrhages that were missed on initial CT and spin-echo MRI. The demonstration of additional chronic bleedings and their anatomical distribution provided important diagnostic information. In a hypertensive patient, the hemosiderin deposits were most pronounced within deep brain structures suggesting hypertensive cerebral microangiopathy. In a second patient, the cortico-subcortical distribution of the hemorrhages was typical of cerebral amyloid angiopathy. In a third patient, the diffuse distribution including spinal bleeding, the marked calcification, and the characteristic appearance on spin-echo MRI were consistent with multiple cavernomas. In another patient with cerebral and spinal hemorrhage, T2*-weighted gradient-echo MRI revealed new subclinical hemorrhages during follow-up. Based on these findings, we recommend that T2*-weighted gradient-echo MRI of the brain should be performed in all patients with acute intracranial and spinal bleedings.

Aged↗