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At least 613 records · Page 34Linked to original sources
PubMed2003

Interrelationships of the subgenera of Coryphaenoides (Teleostei: Gadiformes: Macrouridae): synthesis of allozyme, peptide mapping, and DNA sequence data.

DNA sequences of the 12s rRNA mitochondrial gene from 12 species key to the question of the monophyly of the deep-sea fish genus Coryphaenoides (Macrouridae) were analyzed phylogenetically using maximum parsimony and maximum likelihood. The results were compared with those of three previous studies in which allozyme, peptide mapping, and DNA sequence data were similarly analyzed. The allozyme and DNA sequence data suggested that the largest subgenus (Coryphaenoides), which contained most of the species inhabiting continental slopes between approximately 600 and 2000m depth, is monophyletic. Two of the three subgenera containing the species inhabiting abyssal ocean basins below approximately 2000m together formed a sister group to subgenus Coryphaenoides. The macrourids of the abyssal basins and those of the continental slopes thus appear to have experienced separate radiations from a common ancestor.

Animals↗
PubMed2001

Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise.

The diversity associated with a microbial mat sample collected from a deep-sea hydrothermal vent on the Southern East Pacific Rise was determined using a molecular phylogenetic approach based on the comparison of sequences from the small subunit ribosomal RNA gene (16S rDNA). The DNA was extracted from the sample and the 16S rDNA was amplified by PCR. Sixteen different phylotypes were identified by restriction fragment length polymorphism analysis; four phylotypes were later identified as putative chimeras. Analysis of the 16S rDNA sequences placed all the phylotypes within the Proteobacteria. The majority of the sequences (98%) were most closely related to a new clade of epsilon-Proteobacteria that were initially identified from an in situ growth chamber deployed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge in 1995. The similarity between phylotypes identified from Atlantic and Pacific deep-sea hydrothermal vent sites indicates that this new clade of Proteobacteria may be endemic to and widely distributed among deep-sea hydrothermal vents.

Journal Article↗
PubMed2024

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.

Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We present DeepSomatic, a deep learning method for detecting somatic SNVs and insertions and deletions (indels) from both short-read and long-read data, with modes for whole-genome and exome sequencing, and able to run on tumor-normal, tumor-only, and with FFPE-prepared samples. To help address the dearth of publicly available training and benchmarking data for somatic variant detection, we generated and make openly available a dataset of five matched tumor-normal cell line pairs sequenced with Illumina, PacBio HiFi, and Oxford Nanopore Technologies, along with benchmark variant sets. Across samples and technologies (short-read and long-read), DeepSomatic consistently outperforms existing callers, particularly for indels.

Journal Article↗
PubMed2002

Experience-dependent changes in cerebellar contributions to motor sequence learning.

Studies in experimental animals and humans have stressed the role of the cerebellum in motor skill learning. Yet, the relative importance of the cerebellar cortex and deep nuclei, as well as the nature of the dynamic functional changes occurring between these and other motor-related structures during learning, remains in dispute. Using functional magnetic resonance imaging and a motor sequence learning paradigm in humans, we found evidence of an experience-dependent shift of activation from the cerebellar cortex to the dentate nucleus during early learning, and from a cerebellar-cortical to a striatal-cortical network with extended practice. The results indicate that intrinsic modulation within the cerebellum, in concert with activation of motor-related cortical regions, serves to set up a procedurally acquired sequence of movements that is then maintained elsewhere in the brain.

Adult↗
PubMed1996

Structural and mechanistic relationships between nucleic acid polymerases.

A superfamily of nucleic acid polymerases that includes the pol I and pol alpha classes of DNA-directed DNA polymerases, mitochondrial and phage DNA-directed RNA polymerases, and most RNA-directed polymerases may be defined on the basis of the occurrence of conserved sequence motifs and tertiary structure similarities between HIV-1 reverse transcriptase, DNA polymerase I and T7 RNA polymerase. Although sequence or structural similarities do not yet justify inclusion of the multi-subunit DNA-directed RNA polymerases in this superfamily, mechanistic similarities suggest a deep relationship between these and the simpler T7-like RNA polymerases.

Amino Acid Sequence↗
PubMed2003

Insights into catalysis by a knotted TrmD tRNA methyltransferase.

The crystal structure of Escherichia coli tRNA (guanosine-1) methyltransferase (TrmD) complexed with S-adenosyl homocysteine (AdoHcy) has been determined at 2.5A resolution. TrmD, which methylates G37 of tRNAs containing the sequence G36pG37, is a homo-dimer. Each monomer consists of a C-terminal domain connected by a flexible linker to an N-terminal AdoMet-binding domain. The two bound AdoHcy moieties are buried at the bottom of deep clefts. The dimer structure appears integral to the formation of the catalytic center of the enzyme and this arrangement strongly suggests that the anticodon loop of tRNA fits into one of these clefts for methyl transfer to occur. In addition, adjacent hydrophobic sites in the cleft delineate a defined pocket, which may accommodate the GpG sequence during catalysis. The dimer contains two deep trefoil peptide knots and a peptide loop extending from each knot embraces the AdoHcy adenine ring. Mutational analyses demonstrate that the knot is important for AdoMet binding and catalytic activity, and that the C-terminal domain is not only required for tRNA binding but plays a functional role in catalytic activity.

Amino Acid Sequence↗
PubMed2025

N6-methyladenine identification using deep learning and discriminative feature integration.

N6-methyladenine (6 mA) is a pivotal DNA modification that plays a crucial role in epigenetic regulation, gene expression, and various biological processes. With advancements in sequencing technologies and computational biology, there is an increasing focus on developing accurate methods for 6 mA site identification to enhance early detection and understand its biological significance. Despite the rapid progress of machine learning in bioinformatics, accurately detecting 6 mA sites remains a challenge due to the limited generalizability and efficiency of existing approaches. In this study, we present Deep-N6mA, a novel Deep Neural Network (DNN) model incorporating optimal hybrid features for precise 6 mA site identification. The proposed framework captures complex patterns from DNA sequences through a comprehensive feature extraction process, leveraging k-mer, Dinucleotide-based Cross Covariance (DCC), Trinucleotide-based Auto Covariance (TAC), Pseudo Single Nucleotide Composition (PseSNC), Pseudo Dinucleotide Composition (PseDNC), and Pseudo Trinucleotide Composition (PseTNC). To optimize computational efficiency and eliminate irrelevant or noisy features, an unsupervised Principal Component Analysis (PCA) algorithm is employed, ensuring the selection of the most informative features. A multilayer DNN serves as the classification algorithm to identify N6-methyladenine sites accurately. The robustness and generalizability of Deep-N6mA were rigorously validated using fivefold cross-validation on two benchmark datasets. Experimental results reveal that Deep-N6mA achieves an average accuracy of 97.70% on the F. vesca dataset and 95.75% on the R. chinensis dataset, outperforming existing methods by 4.12% and 4.55%, respectively. These findings underscore the effectiveness of Deep-N6mA as a reliable tool for early 6 mA site detection, contributing to epigenetic research and advancing the field of computational biology.

Deep Learning↗
PubMed1991

Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts.

A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.

Archaea↗
PubMedDate not supplied

MR imaging-related heating of deep brain stimulation electrodes: in vitro study.

BACKGROUND AND PURPOSE: Recent work has shown a potential for excessive heating of deep brain stimulation electrodes during MR imaging. This in vitro study investigates the relationship between electrode heating and the specific absorption rate (SAR) of several MR images. METHODS: In vitro testing was performed by using a 1.5-T MR imaging system and a head transmit-receive coil, with bilateral deep brain stimulation systems positioned in a gel saline-filled phantom, and temperature monitoring with a fluoroptic thermometry system. Standardized fast spin-echo sequences were performed over a range of high, medium, and low SAR values. Several additional, clinically important MR imaging techniques, including 3D magnetization prepared rapid acquisition gradient-echo imaging, echo-planar imaging, quantitative magnetization transfer imaging, and magnetization transfer-suppressed MR angiography, were also tested by using typical parameters. RESULTS: A significant, highly linear relationship between SAR and electrode heating was found, with the temperature elevation being approximately 0.9 times the local SAR value. Minor temperature elevations, <1 degrees C, were found with the fast spin-echo, magnetization prepared rapid acquisition gradient-echo, and echo-planar clinical imaging sequences. The high dB/dt echo-planar imaging sequence had no significant heating independent of SAR considerations. Sequences with magnetization transfer pulses produced temperature elevations in the 1.0 to 2.0 degrees C range, which was less than theoretically predicted for the relatively high SAR values. CONCLUSION: A potential exists for excessive MR imaging-related heating in patients with deep brain stimulation electrodes; however, the temperature increases are linearly related to SAR values. Clinical imaging sequences that are associated with tolerable temperature elevations in the <or=2.0 degrees C range at the electrode tips can be performed safely within an SAR range <2.4 W/kg local (0.9 W/kg whole body averaged).

Body Temperature↗
PubMed2003

A novel G-to-A mutation in the intron-N of the protein S gene leading to abnormal RNA splicing in a patient with protein S deficiency.

BACKGROUND AND OBJECTIVES: Hereditary protein S (PS) deficiency is a rare autosomal disorder of the coagulation pathway associated with familial thrombophilia. DESIGN AND METHODS: We investigated a young propositus with recurrent deep vein thrombosis, a positive family history for thrombotic episodes, and low plasma concentrations of free, but not total PS antigen (12% and 70%, respectively). RESULTS: Sequence analysis of the PS gene showed a heterozygous G-to-A mutation at the first nucleotide of intron N. The patient's father, who had suffered from deep vein thrombosis and had reduced total and free PS antigen (59% and 28%, respectively) was a heterozygote. The G-to-A change predicts the disappearance of a donor splice site. After transfection with a construct, containing either the wild-type or the mutated sequence, cells with the mutant construct showed an aberrant mRNA, consistent with exclusion of exon 14, but not the expected mRNA. Sequencing of the abnormal mRNA showed the complete absence of exon 14. Exclusion of exon 14 predicts the deletion of the amino acid sequence from residue 508 to residue 582, and the shift of the reading frame of the following 8 amino acids with a premature stop codon within exon 15 at position 591. Thus, the truncated PS gene product would not contain the terminal portion of the sex hormone binding globulin-like domain. INTERPRETATION AND CONCLUSIONS: We have identified a mutation in a highly conserved intronic region of PS gene. The mutation affects in vitro mRNA processing and efficiency of normal splicing.

Adult↗
PubMed2026

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstruction of transmission events, and identification of antimicrobial resistance mutations. Although many tools have been developed to identify single-nucleotide variants (SNVs) from whole-genome sequencing, they often suffer from high false-positive rates owing to the complexity of bacterial genomes and the need for different filtering cutoffs across sample types and sequencing depths. As data sets increase in size, the manual filtering required for high accuracy presents a significant obstacle. Here, we present AccuSNV, a novel deep learning-based tool for high-precision and automated bacterial SNV calling. Unlike traditional methods that process one sample at a time, AccuSNV leverages a convolutional neural network (CNN) that integrates alignment information across multiple samples, enhancing precision through learned across-sample patterns. We evaluate AccuSNV against seven popular SNV-calling tools using simulated data from six bacterial species with varied sequencing depths, numbers of isolates, mutations, and divergence levels. To further validate its real-world utility, we test AccuSNV on multiple curated bacterial data sets containing reported SNVs. In both simulated and real-world scenarios, AccuSNV consistently achieves the best performance. Moreover, AccuSNV provides comprehensive user-friendly downstream analysis modules and outputs, including mutation annotation information, phylogenetic inference, d N/d S calculations, and optional manual filtering. Together with the automated deep learning-based calling, these features make AccuSNV broadly accessible to users with different levels of computational expertise.

Deep Learning↗
PubMedDate not supplied

Detection of deep venous thrombosis by DMP 444, a platelet IIb/IIIa antagonist: a preliminary report.

BACKGROUND: We report a method for detection of deep venous thrombosis with a technetium 99m-labeled peptide (DMP 444). The N-methyl-arginine-glycine-aspartic acid sequence on DMP 444 binds the glycoprotein IIb/IIIa receptor on activated platelets (inhibition constant [IC50] for fibrinogen binding = 6 nmol/L). METHODS: DMP 444 (23 to 27 mCi) was injected into 11 patients with clinical suspicion of deep venous thrombosis, diagnostic confirmation by ultrasound, and a positive D-dimer test result. Planar images in the anterior and posterior projections were obtained at 10 to 40 minutes, 50 to 80 minutes, and 120 to 150 minutes after injection. RESULTS: No clinically significant adverse effects were noted after DMP 444 administration. One patient (excluded from the analysis) withdrew consent, so image acquisition was not complete. By 10 to 40 minutes after injection, 8 of 10 patients demonstrated an area of increased activity that was clearly related to the abnormality noted on ultrasound. Most patients were taking warfarin (Coumadin) and heparin (n = 8) or heparin (n = 1) and warfarin (n = 1) alone at the time of the imaging. The average time from onset of symptoms to injection of DMP 444 was 5 days (range 1 to 18 days). CONCLUSION: These preliminary human studies indicate that DMP 444 is safe and may be of value in the diagnosis of deep venous thrombosis.

Aged↗
PubMed2002

Plant expansins are a complex multigene family with an ancient evolutionary origin.

Expansins are a group of extracellular proteins that directly modify the mechanical properties of plant cell walls, leading to turgor-driven cell extension. Within the completely sequenced Arabidopsis genome, we identified 38 expansin sequences that fall into three discrete subfamilies. Based on phylogenetic analysis and shared intron patterns, we propose a new, systematic nomenclature of Arabidopsis expansins. Further phylogenetic analysis, including expansin sequences found here in monocots, pine (Pinus radiata, Pinus taeda), fern (Regnellidium diphyllum, Marsilea quadrifolia), and moss (Physcomitrella patens) indicate that the three plant expansin subfamilies arose and began diversifying very early in, if not before, colonization of land by plants. Closely related "expansin-like" sequences were also identified in the social amoeba, Dictyostelium discoidium, suggesting that these wall-modifying proteins have a very deep evolutionary origin.

Amino Acid Sequence↗
PubMed2002

Phylogeny of the genus Simonsiella and other members of the Neisseriaceae.

16S rDNA was sequenced from 16 strains of the oral commensal Simonsiella and was used to assess relationships between Simonsiella strains and other members of the Neisseriaceae. In all analyses, Simonsiella strains grouped according to established species designations and the mammalian hosts from which they were isolated. The commensals from cats and dogs formed a monophyletic group. The monophyly of the genus Simonsiella, however, could be neither supported nor rejected; deep nodes in the trees were unstable depending on the phylogenetic method or on the particular sequences used in the analysis. Instabilities may be attributable to frequent gene transfer between Neisseria or other members of the Neisseriaceae and Simonsiella.

Animals↗
PubMed1991

A comparison of different pre-oxygenation techniques in the elderly.

The efficacy of five different techniques of pre-oxygenation before a modified rapid intubation sequence was assessed, using oxygen saturation measurement, in patients aged over 65 years. Twenty patients in each group were pre-oxygenated using four deep breaths or normal tidal breathing for 1, 2, 3, or 4 minutes. The acceptable period of apnoea was defined as the time taken to desaturate to 93%. The mean times (SD) taken to reach this end-point were 3.7 (1.6), 4.1 (1.2), 5.4 (1.7), 5.4 (1.4) and 5.2 (1.7) minutes respectively. The apnoea times with 2, 3 and 4 minutes pre-oxygenation were not significantly different from each other but were significantly longer than after four deep breaths and 1 minute. It is concluded that a pre-oxygenation period of at least 2 minutes should be employed in the elderly before a rapid sequence induction.

Aged↗
PubMed1997

Role of MR venography in the evaluation of deep venous thrombosis.

PURPOSE: MR venography has been recommended for the evaluation of deep venous thrombosis. The purpose of our study was to determine the role of MR venography, in particular at the level of the pelvis where other diagnostic modalities show major limitations. MATERIALS AND METHODS: Forty-three patients with clinical suspicion of deep venous thrombosis were examined by means of pelvic MR venography. In all cases, a 2D-TOF sequence was used with cranial arterial presaturation. In selected cases, i.e. when a small intraluminal filling defect was present, a cine-PC sequence was used in addition in order to exclude the presence of a pulsatility artifact as causing the filling defect. In all cases, contrast venography was also performed and considered to be the standard of reference. RESULTS: MR venography showed 26 patients to be positive for deep venous thrombosis at the pelvic level. These positive results were correct in 25 cases. The analysis of the results provided values of sensitivity and specificity of respectively 100% and 94%, with an overall accuracy of 97.6%. CONCLUSIONS: Our results indicate that MR can provide highly accurate images, similar to those of contrast venography, in a noninvasive fashion. It is particularly useful in the pelvic region where the limitations of other imaging modalities are more evident.

Contrast Media↗
PubMed2004

A deep-sea slant on the molecular phylogeny of the Scleractinia.

Lophelia pertusa and Madrepora oculata are azooxanthellate corals with nearly cosmopolitan distributions. They form cold-water reefs in the upper bathyal zone on continental margins and offshore banks [A.D. Rogers, Int. Rev. Hydrobiol. 84 (1999) 315]. Lophelia is classified in the family Caryophylliidae and Madrepora in the family Oculinidae, both on the basis of skeletal morphology. Recent molecular studies of the scleractinians have given a new insight into the evolutionary history of this group. This study was aimed at clarifying the phylogenetic relationships of Lophelia and Madrepora, through the analysis of partial sequences of the mitochondrial 16S rDNA. Sequences were obtained for samples of L. pertusa collected in the northeast Atlantic and off Brazil, M. oculata, four other deep-sea and eight tropical coral species from the Réunion island in the Indian Ocean. The sequences were aligned with 69 homologous sequences of Scleractinia. Maximum parsimony and Bayesian analyses support previously published molecular topologies. The two specimens of L. pertusa grouped with two caryophylliids, confirming the existing classification of the species, but the large genetic distance between the two Lophelia samples suggests that these populations are genetically isolated from one another. M. oculata did not cluster with oculinids, but formed a monotypic clade lying between the families Pocilloporidae and Caryophyliidae. Phylogenetic analysis also suggested cryptic speciation within the tropical taxa Pocillopora meandriana and possibly Acropora humilis.

Animals↗
PubMed2026

Expanding the Genomic Spectrum of NHLRC2-Associated FINCA Disease: Integrated Bioinformatic Characterization of a Novel Deep Intronic Variant Predicted to Activate a Pseudoexon.

NHLRC2-associated FINCA disease is an ultra-rare autosomal recessive multisystem disorder caused by biallelic pathogenic variants in NHLRC2. Its mutational spectrum and genotype-phenotype correlations remain incompletely defined, and the contribution of non-coding variants is poorly understood. Here, we report a male infant with a severe FINCA-like phenotype, including early-onset hemolytic anemia, pulmonary involvement, neurodevelopmental impairment, growth failure, recurrent infections, and fatal progression at 8.5 months. Whole-genome sequencing identified a compound heterozygous NHLRC2 genotype comprising the previously reported pathogenic missense variant c.442G>T (p.Asp148Tyr) and a novel deep intronic variant, c.331+6863A>G. Segregation analysis confirmed inheritance from different parents. Integrated genomic and splicing analysis predicted that c.331+6863A>G creates a strong cryptic donor splice site and supports pseudoexon inclusion. Reconstruction of the predicted aberrant transcript indicated premature termination and potential susceptibility to nonsense-mediated mRNA decay. To our knowledge, this is the first reported deep intronic NHLRC2 variant predicted to activate pseudoexon inclusion. Although experimental validation was unavailable, convergent clinical, segregation, population, and computational evidence supports c.331+6863A>G as the most plausible second disease-associated allele. This case expands the genomic spectrum of NHLRC2-associated FINCA disease and highlights the diagnostic value of phenotype-driven whole-genome sequencing.

Humans↗