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At least 721 records · Page 40Linked to original sources
PubMed1996

The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates.

The complete DNA sequence (16,646 bp) of the mitochondrial genome of the African lungfish, Protopterus dolloi, was determined. The evolutionary position of lungfish as possibly the closest living relative among fish of land vertebrates made its mitochondrial DNA sequence particularly interesting. Its mitochondrial gene order conforms to the consensus vertebrate gene order. Several sequence motifs and secondary structures likely involved in the regulation of the initiation of replication and transcription of the mitochondrial genome are conserved in the lungfish and are more similar to those of land vertebrates than those of ray-finned fish. A novel feature discovered is that the putative origin of L-strand replication partially overlaps the adjacent tRNA(Cys). The phylogenetic analyses of genes coding for tRNAs and proteins confirm the intermediate phylogenetic position of lungfish between ray-finned fishes and tetrapods. The complete nucleotide sequence of the African lungfish mitochondrial genome was used to estimate which mitochondrial genes are most appropriate to elucidate deep branch phylogenies. Only a combined set of either protein or tRNA mitochondrial genes (but not each gene alone) is able to confidently recover the expected phylogeny among vertebrates that have diverged up to but not over approximately 400 mya.

Amino Acid Sequence↗
PubMed2025

Improving RNA Secondary Structure Prediction Through Expanded Training Data.

In recent years, deep learning has revolutionized protein structure prediction, achieving remarkable speed and accuracy. RNA structure prediction, however, has lagged behind. Although several methods have shown some success in predicting RNA secondary and tertiary structures, none have reached the accuracy observed with contemporary protein models. The lack of success of these RNA structure prediction models has been proposed to be due to limited high-quality structural information that can be used as training data. To probe this proposed limitation, we developed a large and diverse dataset comprising paired RNA sequences and their corresponding secondary structures. We assess the utility of this enhanced dataset by retraining on a deep learning model, SincFold. We find that SincFold exhibited improved generalization to some previously unseen RNA families, enhancing its capability to predict accurate de novo RNA secondary structures. The RNASSTR dataset provides a substantial advance for RNA structure modeling, laying a strong foundation for the development of future RNA secondary structure prediction algorithms.

Journal Article↗
PubMed1999

Antiendotoxin agents share molecular homology within their lipopolysaccharide binding domains.

BACKGROUND: The purpose of this study was to determine whether antiendotoxin agents exhibit molecular homology within their lipopolysaccharide (LPS) binding domains, suggesting a common mechanism of action. We hypothesized that the presence of positively charged basic amino acids or a paucity of negatively charged acidic amino acids, or both, would be a critical characteristic of that portion of the molecule that binds to the highly negatively charged deep core/lipid A (DCLA) region of LPS. MATERIALS AND METHODS: We analyzed the amino acid sequences of the variable light (VL) and heavy (VH) chain complementarity-determining regions (CDRs) of anti-DCLA monoclonal antibodies (mAbs) 1B6, 5A5, and 7C5 and compared them with (1) the CDRs of three irrelevant control mAbs and (2) the LPS binding region of bactericidal permeability-increasing protein (BPI). We purified and amplified the specific nucleotide sequences of the variable regions using reverse transcriptase polymerase chain reaction. DNA was sequenced by dideoxy termination, and protein sequences were deduced and analyzed. The percentages of acidic, basic, polar, and hydrophobic amino acids within VH and VL chain CDRs were determined. RESULTS: We identified a paucity of negatively charged acidic amino acids exclusively within VL chain CDRs of anti-DCLA mAbs (P < 0.005). Although increased, the number of positively charged basic residues was not statistically significantly different; neither was the number of polar or hydrophobic amino acids. Conclusions. Our data suggest that the near absence of negatively charged acidic residues is critical for LPS binding. This characteristic appears to reside exclusively in the VL chain CDRs of anti-DCLA mAbs.

Amino Acid Sequence↗
PubMed1999

Functional MR with use of FLASH sequences in the evaluation of the phono-articulatory tract.

The aims of this study are to determine visualization of normal phonation structures with the use of MR fast sequences and anatomical reference indices which can be used in evaluating upper resonator pathologies. A total of 12 normal subjects were studied, a 1 T system, a volumetric receiving head and neck coil and FLASH sequences for one sagittal and two coronal scans. Each subject was instructed to take a deep breath and then to produce the vowel sounds for the entire duration of the scan. The movement of the following anatomical structures were considered: lips, tongue, soft palate, pharynx and epiglottis. For each subject sagittal scans were used to measure the minimal palate tongue distance (p-t), the minimal anterio-posterior diameter of the mesopharynx (mp), and the epiglottis excursion angle (ep) with respect to the plane determined by the false vocal cords. Our results were compared with a diagrammed representation of tongue movements (vocal trapezium). This study underlines the validity of MR imaging techniques in the study of the phono-articulatory tract, because MR provided good detail of the phono-articulatory structures enabling an overall functional evaluation. MR would appear useful in evaluating defects in the velum and palate, in staging of oropharyngeal neoplasms and in surgical reconstructions of the tongue.

Adult↗
PubMed1989

Fusion of phospholipid vesicles mediated by cytochrome c.

Fusion of phosphatidylserine/phosphatidylethanolamine (1/1) vesicles induced by cytochrome c is studied at a wide range of pH values. A pH profile for the fusion with maximum values at pH 5 and pH 8 is obtained and this is found to be similar to the profile for cytochrome c binding to the vesicles. The binding property of apocytochrome c to the same phospholipid vesicles is found to be about the same as that of the cytochrome c at low ionic strength, but very different at high salt concentrations. No appreciable fusion of vesicles by apocytochrome c is observed. Proteolytic treatment and dansyl chloride labeling of cytochrome c- and apocytochrome c-vesicle complexes show that the C-terminal segments of these proteins with molecular weights of about 3000 and 5000, respectively, penetrate the bilayer. The hydrophobic labeling studies with photoreactive phosphatidylcholine in the bilayer show that segments of both cytochrome c and apocytochrome c go deep into the bilayer.

Amino Acid Sequence↗
PubMed1982

The development of cerebellar primordia transplanted to the neocortex of the rat.

Pieces of cerebellar primordia were dissected from the developing fetus at day 18 of gestation in Sprague-Dawley rats and transplanted to the neocortex of a 10- to 12-day-old rat. The histological development of 53 such transplants was analyzed at a series of survival times ranging from 5 min to 426 days. The cerebellar cortex developed much as it does in situ. However, only migratory sequences were strictly followed, while Purkinje cell differentiation and folia formation were initially retarded. In deep parts of the transplant, and throughout transplants confined to deep layers of the neocortex, the external granule layer was associated with penetrating blood vessels. An inverted cytoarchitectural pattern developed as concentric cylindrical layers around these vessels. In contrast, normal lamination and foliation were found only in transplants growing on the neocortical surface. Axons coursing between host and transplant were seen frequently and were especially pronounced at those sites beneath the internal granule layer which appeared to contain deep cerebellar nuclei. At the longest survival time there was preliminary evidence that suggested morphological deterioration of the transplant. Surface transplants, in addition to developing a normal orientation of cells and layers, have the added benefit of being accessible for further experimental manipulations after the transplant has become established.

Animals↗
PubMed2005

New methods ring changes for the tree of life.

Relationships among prokaryotes and the origin of eukaryotes have both proven controversial, with results depending upon the gene sequences and methods used. Extensive horizontal gene transfer is one possible reason why inferring such deep phylogenetic relationships is difficult. In two recent papers, Lake and Rivera introduce new methods that can be used to reconstruct the genomic tree in the presence of horizontal gene transfers, but which suggest that a ring rather than a tree is a better representation of some parts of the history of life on Earth.

Journal Article↗
PubMed2005

Cytochrome b and Bayesian inference of whale phylogeny.

In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.

Animals↗
PubMed1999

Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A.

The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of activated Rab3A/GTP/Mg2+ bound to the effector domain of rabphilin-3A was solved to 2.6 A resolution. Rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion.

Adaptor Proteins, Signal Transducing↗
PubMed2004

[Multiplex PCR in clinical microbiology].

The introduction of molecular biology methods in clinical microbiology laboratories brings important insights to obtain sensitive and specific diagnoses as fast as possible. These methods are not intended for replacement but for complement of the already applied microbiologic methods. The integrated analyses of all of them is bringing to the most feasible and efficient results. Within the molecular techniques applied, polymerase chain reaction (PCR) has acquired a great diagnostic value, permitting the identification of etiologic agents and the fast and sensitive detection of their virulence and resistance genotypes. Since some years ago, the development of the so called multiplex PCRs has gained deep interest. Those are reactions that get the simultaneous single tube amplification of different target sequences, allowing the simultaneous detection and identification of various genes of interest. In the present article, the most relevant applications of multiplex PCR for clinical microbiology are summarized.

Bacterial Infections↗
PubMedDate not supplied

Design and synthesis of a short-chain bitistatin analogue for imaging thrombi and emboli.

Previously, we showed that labeled bitistatin analogues possessed excellent characteristics for imaging both deep-vein thrombosis and pulmonary embolism. We hypothesized that the N-terminal amino acid sequence of bitistatin, which is different from other disintegrins, likely interacts with the binding site of platelets to confer desirable properties to bitistatin for imaging. In this study, we present the design, synthesis, and initial biological testing of a short-chain analogue of the native 83-amino-acid bitistatin sequence. Our initial molecular modeling of the binding loop of bitistatin showed that the minimal sequence that represented the binding region was a cyclic 10 amino acid sequence cyclo[Cys-Arg-Ile-Ala-Arg-Gly-Asp-Trp-Asn-Cys(S)]. Systematic modeling of a truncated N-terminal sequence of bitistatin fused with the optimized binding region having a thioether sequence through a Gaba spacer ultimately yielded the 24-amino acid peptide, cyclo-[CH(2)CO-Arg-Ile-Ala-Arg-Gly-Asp-Trp-Asn-Cys(S-)]-Gaba-Gly-Asn-Glu-Ile-Leu-Glu-Gln-Gly-Glu-Asp-Ser-Asp-Ser-Lys-OH, 1. The peptide was then coupled to the hydrazino-nicotinic acid bifunctional chelating agent and the purified adduct labeled with (99m)Tc using tricine as a coligand. Binding of the unlabeled and labeled peptide to stimulated human platelets was assayed in vitro. The (99m)Tc labeling yield was > 90%. The in vitro binding assays showed that the IC(50) for inhibition of platelet aggregation was 3694 nM, while the Kd of the (99m)Tc labeled peptide was 185 nM, indicating moderate affinity for the receptor. The (99m)Tc-labeled peptide was able to identify sites of experimental thrombi and emboli in a canine model. The results suggest initial success in attempting to mimic the behavior of bitistatin for imaging thrombi and emboli.

Amino Acid Sequence↗
PubMed2024

Transcriptomic pathology of neocortical microcircuit cell types across psychiatric disorders.

Psychiatric disorders such as major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SCZ) are characterized by altered cognition and mood, brain functions that depend on information processing by cortical microcircuits. We hypothesized that psychiatric disorders would display cell type-specific transcriptional alterations in neuronal subpopulations that make up cortical microcircuits: excitatory pyramidal (PYR) neurons and vasoactive intestinal peptide- (VIP), somatostatin- (SST), and parvalbumin- (PVALB) expressing inhibitory interneurons. Using laser capture microdissection followed by RNA sequencing (LCM-seq), we performed cell type-specific molecular profiling of subgenual anterior cingulate cortex, a region implicated in mood and cognitive control. We sequenced libraries from 130 whole cells pooled per neuronal subtype (VIP, SST, PVALB, superficial and deep PYR) in 76 subjects from the University of Pittsburgh Brain Tissue Donation Program, evenly split between MDD, BD and SCZ subjects and healthy controls (totaling 380 bulk transcriptomes from ~50,000 neurons). We identified hundreds of differentially expressed (DE) genes and biological pathways across disorders and neuronal subtypes, with the vast majority in interneurons, particularly PVALB. While DE genes were unique to each cell type, there was a partial overlap across disorders for genes involved in the formation and maintenance of neuronal circuits. We observed coordinated alterations in biological pathways between select pairs of microcircuit cell types, also partially shared across disorders. Finally, DE genes coincided with known risk variants from psychiatric genome-wide association studies, suggesting cell type-specific convergence between genetic and transcriptomic risk for psychiatric disorders. Our study suggests transdiagnostic cortical microcircuit pathology in SCZ, BD, and MDD and sets the stage for larger-scale studies investigating how cell circuit-based changes contribute to shared psychiatric risk.

Humans↗
PubMed2002

Gene cluster of nitrous oxide reduction in the deep sea of mariana trench.

The gene of nitrous oxide reductase (nosZ) and entire region of nos gene cluster from Pseudomonas sp. strain MT-1, which is isolated from the sediment of Mariana Trench, was identified. Gene organization in nos gene cluster is similar to that of other bacteria, and nosZ was highly homologous to nosZ of other Pseudomonads. The remarkable property was the existence of a gap from Arg-302 to Ser-309 (numbered by NosZ of P. aeruginosa), which might be a feature of marine bacterial NosZ. It is interesting that nosZ of the strain MT-1 is not related so closely to P. stutzeri, although 16S rDNA of the strain MT-1 is highly homologous to that of P. stutzeri. The existence of nosZ gene in the strain MT-1 indicated the presence of a complete denitrification (nitrate to N(2)) in the Mariana Trench. This is the first report on genetic analysis of denitrification in the deep sea.

Amino Acid Sequence↗
PubMed2026

Mutational signatures in blood-brain barrier: mechanisms, computational insights, and clinical applications in precision oncology.

The blood - brain barrier (BBB) plays a central role in maintaining central nervous system (CNS) homeostasis, and its disruption is a defining feature of malignant brain tumors such as glioblastoma. Emerging evidence indicates that BBB dysfunction not only alters the tumor microenvironment but also shapes the mutational processes that drive genomic instability in CNS malignancies. This review synthesizes current understanding of the biological mechanisms linking BBB breakdown with distinct mutational signatures, including those arising from oxidative stress, hypoxia-induced replication stress, lipid peroxidation, inflammation, and metabolic reprogramming. Advances in next-generation sequencing, coupled with computational tools such as non-negative matrix factorization, Bayesian modeling, and deep learning, have enabled precise extraction of these signatures and their integration with multi-omics data. Clinically, BBB-associated mutational signatures offer significant promise for therapeutic stratification, prediction of treatment response, and noninvasive monitoring through cerebrospinal fluid - derived circulating tumor DNA. Despite these advances, challenges persist due to limited tissue accessibility, low-yield CSF samples, incomplete mechanistic models, and the lack of CNS-specific analytical frameworks. A deeper understanding of BBB-driven mutational processes, supported by improved computational approaches and integrative datasets, holds potential to advance precision oncology in neuro-oncology.

Humans↗
PubMed2026

shinyDeepGxP: a user-friendly R shiny app for predicting surface protein abundance from scRNA-seq expression using deep learning in blood cells.

MOTIVATION: Understanding accurate immune cell heterogeneity and function in single-cell datasets requires access to protein-level information, which is often unavailable due to experimental limitations. RESULTS: We present shinyDeepGxP, an interactive web application featuring our deep learning model, DeepGxP, for predicting surface protein abundance from single-cell RNA-sequencing (scRNA-seq) data. This platform makes DeepGxP accessible to researchers without programming skills. Users can upload scRNA-seq count matrices and use "Predict Protein" to predict the abundance of 224 biologically relevant surface proteins. shinyDeepGxP provides visualizations to help identify distinct cell populations based on predicted protein profiles. Moreover, users can choose "Explore Model" to reveal key RNA predictors and their associated biological pathways for each protein. Overall, shinyDeepGxP is a user-friendly, freely available web tool that provides protein-level detail for RNA-only single-cell datasets, enabling multimodal discovery without additional experiments. AVAILABILITY AND IMPLEMENTATION: shinyDeepGxP can be launched on https://shiny.crc.pitt.edu/deepgxp/.

Journal Article↗
PubMed2003

Idraparinux and liver enzymes: observations from the PERSIST trial.

A potential influence of idraparinux--a synthetic analogue of the pentasaccharide sequence in heparins--on plasma liver enzyme levels was analysed in 37 patients suffering from deep vein thrombosis and participating in the PERSIST trial. Plasma gamma-glutamyl-transferase, aspartate aminotransferase and alanine aminotransferase were determined prior to enoxaparin treatment (screening), prior to randomization (baseline) and once weekly during the 12-week treatment period. Patients were initially treated with weight-adjusted enoxaparin for 4-7 days and then randomized to either idraparinux (2.5, 5, 7.5 or 10 mg) or warfarin. Gamma-glutamyl-transferase was significantly increased after administration of enoxaparin at the baseline visit (P = 0.004) and in week 2 (P = 0.009) to return to screening levels in week 3 for the remaining study period (all P > 0.05). Aspartate aminotransferase (P = 0.001) and alanine aminotransferase (P < 0.001) were significantly increased at the baseline visit and returned to screening values at week 2 for the remaining study period (all P > 0.05). There was no significant difference between the mean values of plasma liver enzymes of the four idraparinux groups and the warfarin group in all 13 measurements. We concluded that idraparinux in contrast to enoxaparin does not increase plasma liver enzymes significantly.

Adult↗
PubMed1999

Treponema lecithinolyticum sp. nov., a small saccharolytic spirochaete with phospholipase A and C activities associated with periodontal diseases.

Strong phospholipase A (PLA) and phospholipase C (PLC) activities as potential virulence factors are the outstanding characteristics of eight strains of small oral spirochaetes isolated from deep periodontal lesions. By qualitative dot-blot DNA-DNA hybridization and 16S rDNA sequence comparison, these spirochaetes form a distinct phylogenetic group, with Treponema maltophilum as its closest cultivable relative. Growth of these treponemes, cells of which contain two endoflagella, one at each pole, was autoinhibited by the PLA-mediated production of lysolecithin unless medium OMIZ-Pat was prepared without lecithin. N-Acetylglucosamine was essential and D-ribose was stimulatory for growth. All isolates were growth-inhibited when 1% foetal calf serum was added to the medium. Growth on agar plates supplemented with human erythrocytes produced haemolysis. In addition to PLA and PLC, the new isolates displayed strong activities of alkaline and acid phosphatases, beta-galactosidase, beta-glucuronidase, N-acetyl-beta-glucosaminidase and sialidase, intermediate activities of C4- and C8-esterases, naphthol phosphohydrolase and alpha-fucosidase and a distinctive 30 kDa antigen detectable on Western blots. This phenotypically and genotypically homogeneous group is proposed as a novel species, Treponema lecithinolyticum sp. nov., with isolate OMZ 684T designated as the type strain. A molecular epidemiological analysis using a T. lecithinolyticum-specific probe showed this organism to be associated with affected sites when compared with unaffected sites of periodontitis patients. This association was more pronounced in patients with rapidly progressive periodontitis than in those with adult periodontitis.

Adult↗
PubMed2003

Respiratory patterns and oxygen consumption in singing zebra finches.

Song production in birds is driven by temporally complex respiratory patterns. In zebra finches (Taeniopygia guttata), song consists of repetitions of a stereotyped sequence of distinct syllables (motif). Syllables correspond to distinct expiratory pulses, which alternate with short deep inspirations. We investigated the effect of the song motor pattern on respiration using a newly developed mask system to measure oxygen consumption while simultaneously monitoring subsyringeal air sac pressure. The metabolic cost of song is closely related to song duration (mean=85.7 microl O(2) g(-1) x min(-1) over pre-song levels) and confirms earlier estimates for this species. When motif duration is controlled for, there is only small interindividual variability in oxygen consumption per motif. The oxygen measurements were also used to evaluate various methods of estimating and reporting the metabolic cost. Up to 20s before song, respiratory activity and oxygen consumption increased. Shortly before and during the introductory notes of the song bout, respiration and oxygen consumption decreased markedly. In some individuals, significant hyperventilation occurred during song, causing almost complete apnea after the song. In three different birds, we measured tracheal airflow and air sac pressure during song. Birds with higher airflow during song relative to flow during quiet respiration had a more pronounced decrease in respiratory activity after the song bout. These results suggest that gas exchange continues in the lung during the song bout and that long expiratory pressure pulses of the song motif can lead to hyperventilation but that no oxygen debt resulted from song. This research allows a first assessment of respiratory constraints that may influence the evolution of song complexity.

Animals↗