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At least 793 records · Page 44Linked to original sources
PubMed1998

MR of the normal neonatal brain: assessment of deep structures.

BACKGROUND AND PURPOSE: MR imaging is a powerful tool for studying the anatomy of and the developmental changes that occur in the brain. The purpose of this project was to determine which structures can be distinguished on standard spin-echo MR sequences of a normal neonatal brain and with what frequency they can be identified. METHODS: The T1- and T2-weighted spin-echo MR images of 12 term neonates, all of whom had normal neonatal courses and were neurologically and developmentally normal at age 12 months, were reviewed retrospectively. All structures that differed in signal intensity from unmyelinated gray matter and unmyelinated white matter were recorded. RESULTS: In general, myelinated gray matter structures, such as cranial nerve nuclei and other nuclei of the brain stem and deep cerebrum, were the structures best seen on T2-weighted images. Most of these nuclei were seen in 75% to 100% of our subjects on T2-weighted images. They were seen less well on T1-weighted images. Myelinated white matter structures, particularly axonal tracts, were the structures best seen on T1-weighted images. The medial and lateral lemnisci, median longitudinal fasciculus, optic tracts, superior and inferior cerebellar peduncles, and the posterior limbs of the internal capsules were seen in 75% to 100% of our subjects on T1-weighted images. Except for the posterior limbs of the internal capsules, these structures were seen less well on T2-weighted images. CONCLUSION: A large number of small structures, such as the nuclei of the brain stem and deep cerebral nuclei, can be routinely identified on standard spin-echo MR imaging sequences. A knowledge of these structures is essential to proper interpretation of imaging studies in neonates and infants.

Brain↗
PubMed2001

Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda:Loliginidae).

Sexually mature female squid Loligo pealei harbour dense bacterial communities in their accessory nidamental glands (ANGs) and in their egg capsules (ECs). This study describes a molecular approach using the 16S rRNA gene (rDNA) to identify bacterial populations within the ANG and the ECs of the North Atlantic squid species L. pealei. Fluorescent in situ hybridization (FISH) and 16S rDNA analysis showed that predominantly alpha- and, to a lesser extent, gamma-proteobacteria were the predominant components of the ANG and EC bacterial communities. Sequencing results showed the presence of alpha-proteobacterial populations affiliated with the Roseobacter group and additional deep-branching alpha-proteobacterial lineages. In contrast, isolates from the ANG and ECs contained only a few alpha-proteobacteria of the Roseobacter group compared with several gamma-proteobacterial isolates, mostly Shewanella and Pseudoalteromonas species. Most of the ANG-associated bacterial populations were also found within the ECs of L. pealei. The molecular approach allowed the visualization of alpha-proteobacteria as major constituents of a bacterial symbiosis within the reproductive system of the Loliginidae.

Anaerobiosis↗
PubMed1995

Ring 22 chromosomes in dermatofibrosarcoma protuberans are low-level amplifiers of chromosome 17 and 22 sequences.

Ring chromosomes have been found with some regularity as solid tumors have come increasingly under cytogenetic study. The full genetic content and significance of these rings remain unclear. Dermatofibrosarcoma protuberans, a tumor of the deep dermis, consistently has supernumerary ring chromosomes, sometimes as the sole detectable cytogenetic change. Using a modified method for comparative genomic hybridization and fluorescent in situ hybridization with a panel of various probes, we found that these ring chromosomes consistently contain the chromosome 22 centromere along with interstitial sequences from chromosomes 17 and 22, specifically from regions 17q23-24 and 22q11-12. The ring chromosomes in dermatofibrosarcoma protuberans are vehicles for a particular pattern of relatively low-level genomic amplification of selected sequences.

Adult↗
PubMed1998

Amplification of 12q13 and 12q15 sequences in a sclerosing epithelioid fibrosarcoma.

Sclerosing epithelioid fibrosarcoma (SEF) is a recently described entity. It is a low-grade sarcoma that occurs primarily in the deep soft tissues of the extremities of adults. It may histologically simulate benign lesions such as fibroma and myxoma or malignancies such as sclerosing carcinoma and lymphoma, extraskeletal myxoid chondrosarcoma, clear cell sarcoma of tendons and aponeuroses, and synovial sarcoma, depending on the lesion's cellularity, degree of fibrosis, and amount of myxoid matrix. There are no previously published cytogenetic studies of this tumor. We found the karyotype 40-45,XY,add(9)(p13),add(10)(p11),-12,-13,-18,add(18)(q11),add(20)(q11) in a SEF of a 14-year-old boy, by using chromosome banding. Fluorescence in situ hybridization showed that both the add(10) and the add(18) contained amplified sequences from 12q13 and 12q15, including the HMGIC gene. Chromosome 18 material was present in the add(9) and terminally in the add(10). The karyotype of this case indicates that SEF is unrelated to extraskeletal myxoid chondrosarcoma, clear cell sarcoma, and synovial sarcoma. When compared with the findings in other soft tissue tumors such as well-differentiated liposarcoma and low-grade malignant fibrous histiocytoma, the chromosome banding and in situ hybridization data add support to the notion that SEF is a relatively low grade variant of fibrosarcoma.

Adolescent↗
PubMed1996

Mode of insertion of the signal sequence of a bacterial precursor protein into phospholipid bilayers as revealed by cysteine-based site-directed spectroscopy.

The interactions between a bacterial precursor protein and phospholipids in bilayer-based model membrane systems is addressed in this study. The precursor-lipid interactions were assessed from the side of the lipid phase by fluorescence and electron spin resonance spectroscopy, using the precursor of the Escherichia coli outer membrane protein PhoE. The role of the signal sequence, as part of the precursor, in this interaction was investigated by using cysteine-based site-directed spectroscopy. For this purpose, purified cysteine-containing mutants of prePhoE, which were made by site-directed mutagenesis of the signal sequence part and of the mature part, and defined lipids were used. The location of the fluorescently labeled cysteine residues was established by resonance energy transfer and quenching experiments and those of the corresponding spin-labeled cysteine residues by paramagnetic relaxation enhancement. It was demonstrated that precursor-phospholipid interactions exist in model membrane systems and also that these interactions were dependent on the presence of anionic phospholipids and resulted in a deep insertion of (parts of) the precursor into the lipid bilayer. Furthermore, the results with the cysteine mutations in the signal sequence of the precursor indicate that both termini of the signal sequence are located near or at the membrane surface, with only the fluorescence of the labeled cysteines in the signal sequence part being protected against aqueous quenchers. The results demonstrate that, when part of the intact precursor, the signal sequence experiences similar lipid-protein interactions as do isolated signal peptides. They also indicate that the signal sequence inserts entirely as a looped structure into the membrane. In addition, the data also indicate that the mature part of the precursor has an affinity for the membrane.

Amino Acid Sequence↗
PubMed1999

Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand.

BACKGROUND: Lytic transglycosylases are bacterial muramidases that catalyse the cleavage of the beta- 1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of a 1,6-anhydrobond in the MurNAc residue. These muramidases play an important role in the metabolism of the bacterial cell wall and might therefore be potential targets for the rational design of antibacterial drugs. One of the lytic transglycosylases is Slt35, a naturally occurring soluble fragment of the outer membrane bound lytic transglycosylase B (MltB) from Escherichia coli. RESULTS: The crystal structure of Slt35 has been determined at 1.7 A resolution. The structure reveals an ellipsoid molecule with three domains called the alpha, beta and core domains. The core domain is sandwiched between the alpha and beta domains. Its fold resembles that of lysozyme, but it contains a single metal ion binding site in a helix-loop-helix module that is surprisingly similar to the eukaryotic EF-hand calcium-binding fold. Interestingly, the Slt35 EF-hand loop consists of 15 residues instead of the usual 12 residues. The only other prokaryotic proteins with an EF-hand motif identified so far are the D-galactose-binding proteins. Residues from the alpha and core domains form a deep groove where the substrate fragment GlcNAc can be bound. CONCLUSIONS: The three-domain structure of Slt35 is completely different from the Slt70 structure, the only other lytic transglycosylase of known structure. Nevertheless, the core domain of Slt35 closely resembles the fold of the catalytic domain of Slt70, despite the absence of any obvious sequence similarity. Residue Glu162 of Slt35 is in an equivalent position to Glu478, the catalytic acid/base of Slt70. GlcNAc binds close to Glu162 in the deep groove. Moreover, mutation of Glu162 into a glutamine residue yielded a completely inactive enzyme. These observations indicate the location of the active site and strongly support a catalytic role for Glu162.

Amino Acid Motifs↗
PubMed2025

Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC.

Despite the widespread availability of genome sequencing pipelines, many genes remain part of the genome's "dark matter," where existing inference tools cannot even begin to guess the biological function of their proteins from sequence alone. This challenge is especially pronounced in organisms that are highly evolutionarily distant from well-studied models, where homology-based methods break down. Here, we describe PHILHARMONIC, a computational method that combines deep learning-based de novo protein interaction network inference with robust unsupervised spectral clustering and remote homology to illuminate functional organization in any non-model organism. From only a sequenced proteome, we show PHILHARMONIC predicts protein functions, functional communities, and higher-order network structure with high accuracy. We validate its performance using experimental gene expression and pathway data in D. melanogaster, and we demonstrate its broad utility by analyzing temperature sensing and stress response pathways in the reef-building coral P. damicornis and its algal symbiont C. goreaui. PHILHARMONIC provides a general-purpose engine for functional discovery and biological hypothesis generation in non-model organisms, enabling systems-level insights across the full diversity of life.

Journal Article↗
PubMed2005

Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population.

Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000-160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single-origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of noncoding 17.5-kb sequence that has survived for >1 million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.

Biological Evolution↗
PubMed1996

Fidelity and predominant mutations produced by deep vent wild-type and exonuclease-deficient DNA polymerases during in vitro DNA amplification.

Denaturing gradient gel electrophoresis (DGGE) was used to examine error rates and mutations induced by native (wt) and exonuclease-deficient (exo-) Deep Vent DNA polymerases during DNA amplification by polymerase chain reaction (PCR), in the presence or absence of the T4 bacteriophage gene 32 protein (gp32).gp32 was found to decrease the error rate of the wt, but not that of the exo-, Deep Vent. The average errors per base duplication for the native form were 8.0 x 10(-5) and 6.0 x 10(-5) in the absence and presence of gp32, respectively. For the exo- form, the error rates were 2.0 x 10(-4) and 2.2 x 10(-4) errors per base duplication in the absence and presence of gp32, respectively. Examination of mutations produced by native Deep Vent showed that A/T to G/C transition predominated, consistent with the results of our earlier studies with DNA polymerases derived from other thermophilic bacteria. These results indicate that PCR with high fidelity can be achieved by using wt Deep Vent in combination with gp32.

Base Sequence↗
PubMed2005

Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments.

To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.

Archaeal Proteins↗
PubMed2000

The expression of MDM2/CDK4 gene product in the differential diagnosis of well differentiated liposarcoma and large deep-seated lipoma.

Ordinary lipomas are cytogenetically characterized by a variety of balanced rearrangements involving chromosome segment 12q13-15, whereas well differentiated liposarcomas (WDL) show supernumerary ring and giant marker chromosomes, known to contain amplified 12q sequences. The tight correlation between the presence of ring chromosomes and both amplification and overexpression of MDM2 and CDK4 genes suggests the exploration of the possibility that immunocytochemistry (ICC) might assist in the differential diagnosis of lipoma-like well differentiated liposarcomas (LL-WDL) and large deep-seated lipomas (LDSL). For this purpose, 21 cases of the former and 19 cases of the latter tumours were analysed by ICC and, according to the availability of material, by molecular and cytogenetic approaches. All lipomas displayed a null MDM2/CDK4 phenotype, whereas all LL-WDL showed MDM2/CDK4 or CDK4 phenotypes. Southern blot analysis performed on 16 suitable cases, complemented by fluorescence in situ hybridization and classical cytogenetic analysis in 11 cases, was consistent with, and further supported the immunophenotyping data. In conclusion, MDM2/CDK4 product-based immunophenotyping appears to represent a valuable method for the categorization of arguable LDSL.

Adult↗
PubMed1996

Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes.

Algal-virus-specific PCR primers were used to amplify DNA polymerase gene (pol) fragments (683 to 689 bp) from the virus-sized fraction (0.02 to 0.2 microns) concentrated from inshore and offshore water samples collected from the Gulf of Mexico. Algal-virus-like DNA pol genes were detected in five samples collected from the surface and deep chlorophyll maximum. PCR products from an offshore station were cloned, and the genetic diversity of 33 fragments was examined by restriction fragment length polymorphism and sequence analysis. The five different genotypes or operational taxonomic units (OTUs) that were identified on the basis of restriction fragment length polymorphism banding patterns were present in different relative abundances (9 to 34%). One clone from each OTU was sequenced, and phylogenetic analysis showed that all of the OTUs fell within the family Phycodnaviridae. Four of the OTUs fell within a group of viruses (MpV) which infect the photosynthetic picoplankter Micromonas pusilla. The genetic diversity among these genotypes was as large as that previously found for MpV isolates from different oceans. The remaining genotype formed its own clade between viruses which infect M. pusilla and Chrysochromulina brevifilum. These results imply that marine virus communities contain a diverse assemblage of MpV-like viruses, as well as other unknown members of the Phycodnaviridae.

Base Sequence↗
PubMed2025

Complex IV deficiency due to COX4I1 deep intronic and de novo variants results in progressive motor impairment and Leigh syndrome.

COX4I1 gene encodes cytochrome c oxidase subunit 4 isoform 1, involved in the early assembly stages of mitochondrial respiratory chain complex IV. To date, COX4I1 pathogenic variants have been reported in only a few cases, each exhibiting heterogeneous clinical phenotypes and limited functional data. Here, we describe the fourth reported case of COX4I1 deficiency associated with human disease, expanding the phenotypic and genetic spectrum of this rare mitochondrial disorder and providing novel clinical, molecular, and functional data. The herein reported individual presented with progressive deterioration of motor skills, intellectual disability and brain imaging abnormalities compatible with Leigh syndrome. Genetic studies combining short and long read next generation sequencing uncovered a peculiar genetic combination in this patient, harboring a de novo COX4I1 nonsense substitution in trans with an inherited deep intronic variant (c.[64C>T];[73+1511A>G]; p.[Arg22Ter];[Glu25ValfsTer9]). Functional studies performed in patient's tissues and transiently transfected cell lines demonstrated that the identified variants mainly exert their pathogenic effect by targeting COX4I1 protein levels, thereby impairing the proper assembly and activity of complex IV.Additionally, proteomic data in patient's fibroblasts suggested an underlying pathomechanism that involves not only the regulation of complex IV function but also the levels of mitoribosomal proteins. In summary, our findings shed light to clarify some of the main clinical features associated with COX4I1 deficiency and the molecular mechanisms involved in the pathogenesis of this disorder.

Humans↗
PubMed2004

Nuclear corroboration of DNA-DNA hybridization in deep phylogenies of hummingbirds, swifts, and passerines: the phylogenetic utility of ZENK (ii).

This paper documents the phylogenetic utility of ZENK at the avian intra-ordinal level using hummingbirds, swifts, and passerines as case studies. ZENK sequences (1.7 kb) were used to reconstruct separate gene trees containing the major lineages of each group, and the three trees were examined for congruence with existing DNA-DNA hybridization trees. The results indicate both that ZENK is an appropriate nuclear marker for resolving relationships deep in the avian tree, and that many relationships within these three particular groups are congruent among the different datasets. Specifically, within hummingbirds there was topological agreement that the major hummingbird lineages diverged in a graded manner from the "hermits," to the "mangoes," to the "coquettes," to the "emeralds," and finally to a sister relationship between the "mountain-gems" and the "bees." Concerning swifts, the deepest divergences were congruent: treeswifts (Hemiprocnidae) were sister to the typical swifts (Apodidae), and the subfamily Apodinae was monophyletic relative to Cypseloidinae. Within Apodinae, however, were short, unresolved branches among the swiftlets, spinetails, and more typical swifts; a finding which coincides with other datasets. Within passerine birds, there was congruent support for monophyly of sub-oscines and oscines, and within sub-oscines, for monophyly of New World groups relative to the Old World lineages. New World sub-oscines split into superfamilies Furnaroidea and Tyrannoidea, with the Tyrannoid relationships completely congruent among ZENK and DNA-DNA hybridization trees. Within Furnaroidea, however, there was some incongruence regarding the positions of Thamnophilidae and Formicariidae. Concerning oscine passerines, both datasets showed a split between Corvida and Passerida and confirmed the traditional membership of passerid superfamilies Muscicapoidea and Passeroidea. Monophyly of Sylvioidea, however, remained uncertain, as did the relationships among the superfamiles themselves. These results are strikingly similar to other recent findings and indicative of continuing uncertainty about the higher level relationships of oscine passerines.

Animals↗
PubMed2003

A model of desynchronizing deep brain stimulation with a demand-controlled coordinated reset of neural subpopulations.

The coordinated reset of neural subpopulations is introduced as an effectively desynchronizing stimulation technique. For this, short sequences of high-frequency pulse trains are administered at different sites in a coordinated way. Desynchronization is easily maintained by performing a coordinated reset with demand-controlled timing or by periodically administering resetting high-frequency pulse trains of demand-controlled length. Unlike previously developed methods, this novel approach is robust against variations of model parameters and does not require time-consuming calibration. The novel technique is suggested to be used for demand-controlled deep brain stimulation in patients suffering from Parkinson's disease or essential tremor. It might even be applicable to diseases with intermittently emerging synchronized neural oscillations like epilepsy.

Cortical Synchronization↗
PubMed2004

Proteomics characterization of different bran proteins between aromatic and nonaromatic rice (Oryza sativa L. ssp. indica).

Proteomic approach is applied for the analysis of seed brans of 14 rice varieties (Oryza sativa L. ssp. indica) which can classify to five aromatic rice and nine nonaromatic rice. The two-dimensional electrophoresis (2-DE) protein patterns for 14 rice varieties were similar within pH ranges of 3-10 and 4-7. To characterize aromatic group-specific proteins, we compared 2-D gels of aromatic rice to nonaromatic rice using PDQUEST image analysis. Four out of six differential spots were identified as hypothetical proteins, but one (SSP 7003) was identified by matrix assisted laser desoption/ionization-quardrupole-time of fight (MALDI-Q-TOF) as prolamin with three matching peptides based on NCBI database. Prolamin is a class of storage proteins with three different polypeptides of 10, 13, and 16 kDa. Spot SSP7003 was identified as a 13 kDa polypeptide of prolamin by combination of mass spectroscopy and N-terminal sequence analyses. In contrast, one sulfur-rich 16 kDa polypeptide of prolamin was found in extremely high intensity in brans of deep-water rice compared to nondeep-water rice. Our results suggest that proteomics is a powerful step to open the way for the identification of rice varieties.

2-Propanol↗
PubMed1995

A novel gene expressed during zebrafish gastrulation identified by differential RNA display.

Vertebrate gastrulation is a dynamic period of development characterized by extensive cell migrations. This stage of development is likely to require the expression of a new genetic repertoire to initiate and direct these dramatic changes. The differential RNA display has been used to identify genes specifically expressed during the gastrula stage of a model vertebrate, the zebrafish. One of the genes isolated by the differential display technique has been sequenced and characterized for its spatial and temporal expression. This gene, called G12, is expressed during a narrow window of time during gastrulation and is restricted to a single cell type. At this time of development the zebrafish embryo consists of three cell types: the yolk cell, EVL cells and deep cells. Interestingly, both EVL and deep cells derive early in development from common progenitor cells but G12 expression is restricted only to the EVL lineage. Comparison of the amino acid sequence from this gene with the Genbank database indicates similarity to two previously reported mammalian genes. The similarity between these three genes suggests that they may serve a common function. The G12 gene is the first example of restricted gene expression in EVL cells of the zebrafish. The G12 gene should prove to be a useful model for the study of regulated gene expression during gastrulation.

Amino Acid Sequence↗
PubMed1998

Histoplasma acquisition of calcium and expression of CBP1 during intracellular parasitism.

A highly adapted parasite of macrophages, the yeast phase of Histoplasma capsulatum, survives and proliferates within phagolysosomes, while the mycelial phase exists only as a saprophyte in the soil. We have shown previously that these two phases of Histoplasma differ in their calcium requirements for growth and in the production of a released calcium-binding protein (CBP). Cloning and sequencing the CBP1 gene revealed two introns, a putative signal peptide and potential calcium-binding sites. We also evaluated CBP1 expression by reverse transcription-polymerase chain reaction (RT-PCR) of yeasts grown in broth culture and within two host cell types, a macrophage-like cell line and respiratory epithelial cells. H. capsulatum yeasts expressed CBP1 in all of these settings. Splenocytes from mice immunized with H. capsulatum yeasts responded to purified CBP in proliferation assays, providing evidence for the production of CBP during the infection of mammalian hosts. In addition, after H. capsulatum yeasts were subjected to a calcium-free shock, exogenously added CBP allowed yeasts to incorporate more calcium than yeasts incubated without added CBP. These results suggest that CBP may function to provide yeasts with calcium when they are in a low-calcium environment, such as the phagolysosomal compartment within macrophages.

Amino Acid Sequence↗