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PubMed2026

A contextual activity score (CAS) for inferring ADAR-associated transcriptional activity across RNA-seq, single-cell, and spatial transcriptomics.

BACKGROUND AND OBJECTIVE: Adenosine-to-inosine RNA editing, catalyzed by Adenosine Deaminases Acting on RNA (ADARs), is a widespread modification involved in neural function, immune regulation, and cancer. The Alu Editing Index (AEI) is the standard metric to estimate ADAR activity but requires raw sequencing reads and is poorly suited for single-cell and spatial transcriptomic data. This study aimed to develop an alternative framework for inferring ADAR-associated transcriptional activity from gene expression data across diverse transcriptomic technologies. METHODS: We developed the Contextual Activity Score (CAS), a framework based on transcriptional signatures from ADAR perturbation experiments. Context-specific signatures were generated for human neurons, mouse neurons, and cancer models to infer ADAR1 and ADAR2 activity. CAS was computed from normalized gene expression matrices using regulon-based enrichment analysis. Performance was evaluated by comparing with the Alu Editing Index across bulk RNA sequencing datasets, simulated sequencing depths, and library preparation protocols. RESULTS: CAS showed strong concordance with the Alu Editing Index across multiple datasets, while remaining robust to reduced sequencing depth and different library protocols. Unlike the Alu Editing Index, CAS can be applied to single-cell and spatial transcriptomic data and enables the independent assessment of ADAR2 activity. In cancer and neuronal contexts, CAS captured biologically meaningful variations in ADAR-associated transcriptional activity at sample, cell-type, and spatial levels. CONCLUSION: CAS provides a scalable approach applicable across multiple RNA-seq protocols for estimating ADAR-associated transcriptional activity using gene expression data. This method, implemented in an open-source R package for broad adoption, expands the ability to study ADAR-associated transcriptional activity across transcriptomic modalities where direct editing quantification is challenging, such as single-cell and spatial transcriptomics.

Adenosine Deaminase↗
PubMed2006

In vivo measurement of the apparent diffusion coefficient in normal and malignant prostatic tissue using thin-slice echo-planar imaging.

PURPOSE: Diffusion is a physical process based on the random movement of water molecules, known as Brownian movement. Diffusion-weighted imaging (DWI) is a magnetic resonance imaging (MRI) technique that provides information on such biophysical properties of tissues as density, cell organisation and microstructure, which influence the diffusion of water molecules. The aim of this study was to evaluate the ability of MRI to obtain information on the diffusion of water molecules in normal and malignant prostate tissues. MATERIALS AND METHODS: Ten volunteers and 19 patients with prostate lesions diagnosed by transrectal ultrasound (TRUS) were enrolled in our study. Morphological imaging was obtained with T2-weighted turbo spin-echo (TSE) sequences with and without fat suppression [spectral presaturation with inversion recovery (SPIR)] and an axial dynamic T1-weighted SPIR fast-field echo (FFE) sequence during intravenous administration of contrast material. DWI was obtained with a high-spatial-resolution single-shot spin-echo echo planar imaging (EPI) inversion recovery (IR) sequence. The apparent diffusion coefficient (ADC) maps were analysed by positioning an 8-pixel region of interest (ROI) over different zones of the prostate, and the focal lesion when present. The tumour was confirmed by a TRUS-guided needle biopsy taken within 1 month of the MRI examination. RESULTS: The mean ADC value of the central zones (1,512.07+/-124.85x10(-3) mm2/s) was significantly lower than the mean ADC of the peripheral zones (1,984.11+/-226.23x10(-3) mm2/s) (p<0.01). The mean ADC value of tumours (958.97+/-168.98x10(-3) mm2/s) was significantly lower than the mean values of normal peripheral zones (p<0.01). CONCLUSIONS: Our preliminary results indicate that DWI is useful for characterising tissue in the different regions of the prostate gland and in distinguishing normal from cancerous tissues, given its ability to detect early changes in the structural organisation of prostate tissue.

Adult↗
PubMedDate not supplied

The role of the RGD peptides and the gamma chain peptide of fibrinogen on fibrinogen binding to activated platelets.

The interaction of fibrinogen with platelet membrane glycoprotein (GP) IIb/IIIa complex is inhibited by the RGD peptides and the peptides corresponding to a sequence unique to fibrinogen in the carboxyl-terminal domain of the gamma chain. The present study was designed to examine the effects of these synthetic peptides on fibrinogen binding to thrombin-activated platelets. The order of potency of these peptides was as follows: RGDS = RGDF > GQQHHLGGAKQAGDV (G15). The RGES peptide had no inhibitory activity. The inhibitory effects of the peptides were synergistic when fibrinogen binding was measured in the mixture of the RGD peptide and the gamma chain peptide. By contrast, the inhibitory effect was additive when the binding was measured in the presence of the RGDS peptide and the RGDF peptide. Thrombin-induced platelet aggregation was also inhibited by these synthetic peptides. The order of potency was the same as that of the inhibition binding assay. These results provide evidence that the RGD sequences present at two different sites in the alpha chain and the gamma chain sequence inhibit fibrinogen binding to the GPIIb/IIIa complex, are mutually exclusive, and are in close spatial proximity in the folded molecule. We conclude that the presence of the RGD sequence and the gamma chain sequence involved in fibrinogen binding domains increases the affinity of fibrinogen to activated platelets.

Amino Acid Sequence↗
PubMed2005

[In silico identification and characterization of meiotic DNA: AluJb possibly participates in the attachment of chromatin loops to synaptonemal complex].

Earlier, using bioinformatic methods, we reported the identification of repeated DNA sequences (RS), presumably responsible for the attachment of chromatin loops to the lateral elements of synaptonemal complex in meiotic chromosomes. In the present study, consensus sequences for this class of RS were identified. It was demonstrated that at least part of these sequences belonged to the AluJb subfamily of Alu sequences. The Alu copies distribution along the major human histocompatibility complex (MHC) and their spatial separation from the sites of meiotic recombination was examined. It was demonstrated that simple sequences, like (GC/CA)n, were flanking meiotic recombination sites. A model of the RS organization in meiotic chromosome, most efficiently linking experimental data on the meiotic recombination in MHC and the in silico data on the RS localization (the coefficient of multiple correlation, r = 0.92) is suggested.

Alu Elements↗
PubMed2002

Isolation and characterization of cDNA clones encoding ADP-glucose pyrophosphorylase (AGPase) large and small subunits from chickpea (Cicer arietinum L.).

Four cDNA clones encoding two large subunits and two small subunits of the starch regulatory enzyme ADP-glucose pyrophosphorylase (AGPase) were isolated from a chickpea (Cicer arietinum L.) stem cDNA library. DNA sequence and Southern blot analyses of these clones, designated CagpL1, CagpL2 (large subunits) and CagpS1 and CagpS2 (small subunits), revealed that these isoforms represented different AGPase large and small subunits. RNA expression analysis indicated that CagpL1 was expressed strongly in leaves with reduced expression in the stem. No detectable expression was observed in seeds and roots. CagpL2 was expressed moderately in seeds followed by weak expression in leaves, stems and roots. Similar analysis showed that CagpS1 and CagpS2 displayed a spatial expression pattern similar to that observed for CagpL2 with the exception that CagpS1 showed a much higher expression in seeds than CagpS2. The spatial expression patterns of these different AGPase subunit sequences indicate that different AGPase isoforms are used to control starch biosynthesis in different organs during chickpea development.

Amino Acid Sequence↗
PubMed1997

Site-directed mutagenesis of the sodium pump: analysis of mutations to amino acids in the proposed nucleotide binding site by stable oxygen isotope exchange.

A model for the active site of P type ATPases has been tested by site-directed mutagenesis of amino acids in two conserved sequences of Mg(2+)-dependent and Na(+)- and K(+)-stimulated ATPase. The mutants K501R, K501E, D586E, D586N, P587A, and P588A were expressed in yeast cells and compared with wild type. In addition to previously published assays of adenosine 5'-triphosphate binding and hydrolysis, measurements of 18O exchange between Pi and water have been used to identify steps in the E2 half of the reaction cycle affected by the mutations. The study supports the prediction that K501 in the KGAP sequence interacts with adenosine 5'-triphosphate. However, quantitative comparisons of the effect of mutation K501E on the activity with the effects of mutations to an enzyme of known structure that also catalyzes phosphoryl group transfer make a direct role for the positive charge on the side chain of K501 in catalysis by stabilizing the transition state unlikely. No evidence for the predicted interaction between D586 and the hydroxyl groups of ribose was found. However, the data do indicate that the spatial organization of the loop containing the DPPR sequence is critical for phosphorylation of the enzyme. A role for D586 in coordinating the Mg2+ that is required for activity is proposed.

Adenosine Triphosphate↗
PubMed2003

Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability.

Multiple sequence alignment on 73 proteins belonging to glycosyl hydrolase family 1 reveals the occurrence of a segment (83-124) in the enzyme sequences from hyperthermophilic archaea bacteria, which is absent in all the mesophilic members of the family. The alignment of the known three-dimensional structures of hyperthermophilic glycosidases with the known ones from mesophilic organisms shows a similar spatial organizations of beta-glycosidases except for this sequence segment whose structure is located on the external surface of each of four identical subunits, where it overlaps two alpha-helices. Site-directed mutagenesis substituting N97 or S101 with a cysteine residue in the sequence of beta-glycosidase from hyperthermophilic archaeon Sulfolobus solfataricus caused some changes in the structural and dynamic properties as observed by circular dichroism in far- and near-UV light, as well as by frequency domain fluorometry, with a simultaneous loss of thermostability. The results led us to hypothesize an important role of the sequence segment present only in hyperthermophilic beta-glycosidases, in the thermal adaptation of archaea beta-glycosidases. The thermostabilization mechanism could occur as a consequence of numerous favorable ionic interactions of the 83-124 sequence with the other part of protein matrix that becomes more rigid and less accessible to the insult of thermal-activated solvent molecules.

Adaptation, Physiological↗
PubMedDate not supplied

[Initial studies of 3-dimensional imaging using ultrasound].

In the study reported here three-dimensional sonographic imaging of organs was achieved for the first time. To make this possible it was first necessary to ensure, by appropriate guidance of the probe, that the sequence of sonographic sections was coordinated in their spatial arrangement. This was accomplished by constructing a probe guide with which parallel sonographic sections could be demonstrated. The distance between these sections was known, so that with the aid of suitable computer programs three-dimensional reconstruction of a kidney examined in a water bath was possible. Since, however, due to the uneven surface of the body, it will hardly be possible to obtain parallel sonographic sections of an organ, a new solution had to be found to ensure the necessary coordinated sequence of sections. The solution lay in rotating the probe. A further device was constructed in which the probe could be rotated farther, by known angles, from section to section. The pivotal point was at the center of the probe tip. The computer knew the angular distance between these sections and reconstruction to a three-dimensional image was therefore possible. Prior the three-dimensional reconstruction the ultrasonographic sections had to be contoured, since only the surface of the organ was available for three-dimensional image construction. Three-dimensional imaging of an organ can be achieved on the one hand by binary representation and on the other with a continuous organ surface. The advantage of binary representation is that the original sonographic data are incorporated in the image-producing process without any computer manipulation; with a continuous surface the distance between the individual sections has to be interpolated.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Simulation↗
PubMed2026

Malignant epithelial states drive immune dysfunction in ampulla of Vater carcinoma.

BACKGROUND: Ampulla of Vater (AoV) carcinoma is a rare malignancy arising at the junction of intestinal and pancreatobiliary epithelium. Its heterogeneous clinical behavior and histological diversity have hindered therapeutic advances, and the cellular basis of this heterogeneity remains unclear. We aimed to construct a single-cell transcriptomic atlas of AoV carcinoma, with a focus on identifying epithelial subtypes and their interactions with the tumor microenvironment (TME). METHODS: We performed single-cell RNA sequencing on eight primary AoV tumors and four matched normal tissues. Comprehensive clustering and transcriptomic analyses identified cell-type composition, epithelial heterogeneity, and tumor-immune interactions. Findings were validated using deconvolution of bulk RNA-seq data from 62 AoV carcinoma patients. Results Malignant epithelial cells were categorized into four distinct subtypes: Int-Wnt, PB-KRAS, Int-Hypoxia, and Cycling stage. PB-KRAS cells exhibited stem-like transcriptional programs and high genomic instability. Deconvolution analysis of bulk RNA-seq data from the independent AoV cohort revealed that enrichment of the PB-KRAS subtype correlated with tumor recurrence and poor survival. Our immune profiling analysis discovered a significant association between PB-KRAS subtype and GZMK+ CD8+ T cells, which are in a pre-dysfunctional state, alongside SPP1+ macrophages exhibiting immunosuppressive traits. Spatial transcriptome data further supports the immunosuppressive natures of TME around PB-KRAS subtype malignant epithelial cells in AoV carcinoma. CONCLUSIONS: Our study presents a single-cell atlas of AoV carcinoma, highlighting the molecular diversity of malignant epithelium and its association with the immune microenvironment. The PB-KRAS subtype emerges as a stem-like, immunosuppressive tumor state associated with poor prognosis, providing insights for future therapeutic targeting.

Ampulla of Vater carcinoma↗
PubMedDate not supplied

Optimizing fast spin echo acquisitions for hepatic imaging in normal subjects.

The purpose of this study was to determine which implementations of a T2-weighted fast spin-echo sequence of the liver resulted in observer preference in normal subjects. Five volunteers were scanned with a series of fast spin-echo sequences modified to allow for flow compensation, respiratory triggering (RT), ECG triggering, randomized phase encoding (RPE), breath-holding, and echo train length (ETL). Images were compared with conventional 2500/40/80 msec spin-echo images using flow compensation and spatial presaturation by two observers blinded to the specific sequence parameters. All FSE sequences were completed in less than the 12 minutes necessary to perform a conventional spin-echo sequence. The most preferred fast spin-echo sequence employed flow compensation, RT, and used an 8 ETL. Analysis of image preference, signal to noise, and contrast to noise showed that RT was the single most important variable in determining each image response (P < .01, P < .02, P < .01, respectively). There was some evidence that images obtained with an 8 ETL were preferred over those using a 16 ETL (P = .07). No other variables approached statistical significance although one reader preferred images with flow compensation in the frequency direction to those either not flow compensated or flow compensated in the slice direction. Respiratory triggered fast spin-echo images combined with flow compensation in the frequency direction and using ETL = 8 can provide image quality equal to conventional spin-echo sequences with significant time savings.

Electrocardiography↗
PubMed2001

Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile.

Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the Actinobacteria, low-G+C gram-positive bacteria, the beta- and gamma-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in R. odorabile. High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge.

Actinobacteria↗
PubMed2000

Specific sequences outside the E-box are required for proper per expression and behavioral rescue.

A 69 bp circadian regulatory sequence (CRS) upstream of the per gene is sufficient to drive circadian transcription, mediate proper spatial expression, and rescue behavioral rhythmicity in per01 flies. Within the CRS, an E-box is required for transcriptional activation by two basic-helix-loop-helix (bHLH) PERARNT-SIM (PAS) transcription factors, dCLOCK (dCLK) and CYCLE (CYC). To define sequences within the CRS that are required for spatial expression, circadian expression, and behavioral rhythmicity, a series of mutants that alter blocks of 3 to 12 nucleotides across the entire CRS were used to drive lacZ or per expression in vivo. As expected, the E-box within the CRS is necessary for high-level expression and behavioral rhythmicity, but sequences outside the E-box are also required for transcriptional activation, proper spatial expression, and behavioral rhythmicity. These results indicate that the dCLK-CYC target site extends beyond the E-box and that factors other than dCLK and CYC modulate per transcription.

ARNTL Transcription Factors↗
PubMed1988

Structure of the von Willebrand factor domain interacting with glycoprotein Ib.

von Willebrand factor is a multifunctional adhesive protein of plasma, platelets, and endothelial cells that mediates a crucial interaction for normal hemostasis and thrombus formation by binding to platelet membrane glycoprotein Ib. We provide here evidence that this function involves two limited noncontiguous regions of the molecule, each contained within 15 amino acid residues, separated in the linear sequence by 205 residues, and maintained in close spatial proximity in the folded molecule by disulfide bonding. Definition of this chemical structure clarifies a fundamental mechanism of platelet adhesion to thrombogenic surfaces and sets the bases for obtaining synthetic replicas that may be used to modulate platelet function.

Amino Acid Sequence↗
PubMed2006

Distinct distal regulatory elements control tyrosinase expression in melanocytes and the retinal pigment epithelium.

Pigment cells of mammals are characterized by two different developmental origins: cells of the retinal pigment epithelium (RPE) originate from the optic cup of the developing forebrain, whereas melanocytes arise from the neural crest. The pigmentation gene tyrosinase is expressed in all pigment cells but differentially regulated in melanocytes and RPE. The tyrosinase promoter does not confer strong expression in pigment cells in vivo, while inclusion of a distal regulatory element at position -15 kb is necessary and sufficient to provide strong expression in melanocytes. Nevertheless, the regulatory elements responsible for correct spatial and temporal tyrosinase expression in the RPE remained unidentified so far. In this report, we show that a 186 kb BAC containing the tyrosinase gene provides transgene expression in both RPE and melanocytes indicating the presence of regulatory sequences required for expression in the RPE. A deletion analysis of the BAC was performed demonstrating that a RPE-regulatory element resides between -17 and -75 kb. Using multi-species comparative genomic analysis we identified three conserved sequences within this region. When tested in transgenic mice one of these sequences located at -47 kb targeted expression to the RPE. In addition, deletion of this regulatory element within a tyrosinase::lacZ BAC provided evidence that this sequence is not only sufficient but also required for correct spatial and temporal expression in the RPE. The identification of this novel element demonstrates that tyrosinase gene expression is controlled by separate distal regulatory sequences in melanocytes and RPE.

Albinism, Oculocutaneous↗
PubMed2006

A dynamic conditional random field model for foreground and shadow segmentation.

This paper proposes a dynamic conditional random field (DCRF) model for foreground object and moving shadow segmentation in indoor video scenes. Given an image sequence, temporal dependencies of consecutive segmentation fields and spatial dependencies within each segmentation field are unified by a dynamic probabilistic framework based on the conditional random field (CRF). An efficient approximate filtering algorithm is derived for the DCRF model to recursively estimate the segmentation field from the history of observed images. The foreground and shadow segmentation method integrates both intensity and gradient features. Moreover, models of background, shadow, and gradient information are updated adaptively for nonstationary background processes. Experimental results show that the proposed approach can accurately detect moving objects and their cast shadows even in monocular grayscale video sequences.

Algorithms↗
PubMed1985

On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities.

A 410 base-pair (bp) Sau3A restriction fragment derived from a Leishmania tarentolae kinetoplast DNA minicircle, which is known to have slower than expected electrophoretic mobilities in polyacrylamide gels, has been cloned in a plasmid and deletions from one end of the cloned segment have been constructed. Analysis of the gel electrophoretic mobility data of a large number of restriction fragments derived from the kinetoplast DNA clone and its deletion subclones has led to the conclusion that two sequences, one in the region bp 100 to 170 and the other bp 190 to 250, both numbered from one end of the 410 bp kinetoplast DNA segment, are important for the abnormal gel electrophoretic behavior of the kinetoplast DNA fragment. One common feature of these sequences is the periodic presence of short runs of A residues (3 to 6 As in each); auto-correlation analysis of these runs of A residues shows a strong harmonic component with a period around 11 bp. These results support and extend the previous analysis of Wu & Crothers (1984). The abnormal electrophoretic behavior is accentuated at low temperature and by the addition of Mg2+ to the electrophoresis buffer; addition of Na+ has the opposite effect. Insertion of sequences derived from the kinetoplast DNA fragment into nicked circular DNA causes no unexpected change in its electrophoretic mobility in agarose gel, suggesting that the 410 bp sequence, or segments of it, has no significant spatial writhe. Abnormal shifts in agarose gel mobilities are observed, however, when certain segments of the kinetoplast DNA are inserted into positively or negatively supercoiled DNA topoisomers. These results are consistent with a bent structure of the kinetoplast DNA in which the bend has zero writhe in its undistorted form but is easily distorted.

Animals↗
PubMed2002

Event-related potentials elicited by stimulus spatial discrepancy in humans.

Sixteen subjects were instructed to discriminate whether the spatial locations of two visual stimuli presented in sequence were identical and event-related potentials (ERPs) were recorded from their scalps. The first and the second stimuli were presented in the same location in condition 1, but were in different locations in condition 2. ERP components of P100, N150, late positive component (LPC) and slow negative wave (SNW) were recorded in condition 1; in condition 2, N150 was enhanced and N270 was elicited before LPC. N150, N270 and SNW were all mainly distributed bilaterally over P3, P4, Pz, O1, O2, and Oz. N270 represents the brain activity for processing spatial discrepancy. There are several specialized brain areas involved in the generation of the N270.

Adult↗