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PubMed2006

Registration-based approach for reconstruction of high-resolution in utero fetal MR brain images.

RATIONALE AND OBJECTIVES: This paper describes a novel approach to forming high-resolution MR images of the human fetal brain. It addresses the key problem of fetal motion by proposing a registration-refined compounding of multiple sets of orthogonal fast two-dimensional MRI slices, which are currently acquired for clinical studies, into a single high-resolution MRI volume. MATERIALS AND METHODS: A robust multiresolution slice alignment is applied iteratively to the data to correct motion of the fetus that occurs between two-dimensional acquisitions. This is combined with an intensity correction step and a super-resolution reconstruction step, to form a single high isotropic resolution volume of the fetal brain. RESULTS: Experimental validation on synthetic image data with known motion types and underlying anatomy, together with retrospective application to sets of clinical acquisitions, are included. CONCLUSION: Results indicate that this method promises a unique route to acquiring high-resolution MRI of the fetal brain in vivo allowing comparable quality to that of neonatal MRI. Such data provide a highly valuable window into the process of normal and abnormal brain development, which is directly applicable in a clinical setting.

Algorithms↗

PubMed2026

DNA Methylation-Mediated Regulation of TAGLN2 Expression Promotes Pulmonary Arterial Hypertension.

BACKGROUND: Succinylation, a key post-translational modification, is implicated in the metabolic reprogramming and vascular remodeling of pulmonary arterial hypertension (PAH). While epigenetic regulation, particularly DNA methylation, potentially governs succinylation-related gene expression, its causal links to PAH remain unclear. METHODS: We performed an integrative causal analysis using two-sample Mendelian randomization (MR) and summary-data-based MR (SMR) to identify succinylation-related genes that influence PAH risk. We leveraged PAH GWAS data (FinnGen) and gene expression quantitative trait loci (eQTLGen). Subsequently, methylation-mediated effect decomposition was applied using DNA methylation data (GoDMC) to explore epigenetic regulation. Experimental validation was conducted in lung tissues from a monocrotaline (MCT)-induced PAH rat model via quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: Genetic analyses identified a significant causal effect of elevated Transgelin 2 (TAGLN2) expression on increased PAH risk. This effect was mediated by two specific DNA methylation sites, cg13892570 and cg16107628, which influenced PAH pathogenesis by regulating TAGLN2 transcription, with mediation proportions of 86.46 and 97.65%, respectively. Sensitivity analyses supported the robustness of these findings. Consistent with the genetic evidence, TAGLN2 mRNA was significantly upregulated in the lungs of MCT-induced PAH rats. CONCLUSIONS: This study establishes a clear epigenetic causal pathway in which DNA methylation regulates TAGLN2 expression to promote PAH. TAGLN2 is validated as a key disease driver and presents a promising target for diagnostic and therapeutic strategies in PAH.

Animals↗

PubMed2026

Activity of natural single nucleotide variants of human alkyladenine DNA glycosylase AAG R145H, G163S and R197C involved in DNA binding.

Alkyladenine DNA glycosylase (AAG) is a critical enzyme in the base excision repair (BER) pathway that safeguards genome integrity by removing structurally diverse alkylated and deaminated purine lesions from DNA. It serves as a primary defense against alkylation-induced mutations, which are linked to cancer development, chronic inflammation, and neurodegenerative diseases. Single nucleotide variants (SNVs) in the gene coding region have the potential to alter the enzyme's functionality, potentially modulating the repair capacity and affecting response and prognosis following chemoradiotherapy. In our study, we investigated three SNVs that lead to amino acid class changes in regions involved in DNA substrate coordination: R145H, G163S, and R197C using an in vitro approach. Using biochemical assays and molecular dynamics simulations, we evaluated the thermal stability, DNA binding affinity, and glycosylase activity of AAG variants toward hypoxanthine (Hx) and 1,N6-ethenoadenosine (εA) containing substrates. The G163S variant showed reduced thermal stability due to the conformational strain in the β-hairpin loop that intercalates in DNA, but retained εA excision activity comparable to that of wild-type AAG, while losing activity against Hx-containing DNA. The R197C variant had a four-fold reduction in DNA binding affinity for both substrates, and was catalytically inactive, unable to excise either damaged bases. This loss of function correlated with the rearrangement of the 201-210 loop and the reorientation of Arg-201 and Arg-207, which disrupts critical DNA contacts. However, the R145H variant retained near-wild-type thermal stability and activity on both substrates, despite bioinformatic predictions of deleterious effect. Molecular dynamics simulations revealed variant-specific structural disruptions. The data obtained underscore the importance of experimental validation in assessing the functional impact SNVs.

DNA Glycosylases↗

PubMed2026

Identification of molecular subtypes in clear cell renal cell carcinoma based on chromatin regulators and tumor immune microenvironment profiling.

In the histological classification of renal cell carcinoma, clear cell renal cell carcinoma (ccRCC) accounts for the highest proportion and is the most common subtype. Despite advances in management, it continues to be associated with considerable incidence and mortality. Although surgery and systemic therapies are available, their efficacy is constrained by pronounced intratumoral heterogeneity and treatment resistance. Identifying robust biomarkers and clarifying the underlying biological mechanisms are therefore essential to improving diagnosis, risk stratification and therapeutic decision-making. In this work, we identified two ccRCC molecular subtypes displaying divergent chromatin regulator (CR) profiles and different clinical prognoses. Using the genes differentially expressed between these subgroups, we constructed a CR-related score (CRS) that effectively stratified patients according to survival. More analysis concluded that the low expression of CR was more linked with the immune-activated tumors, which encompassed the immune pathway enrichment, as well as the elevation of numerous immune cell subtypes. Moreover, elevated CRS was associated with improved immunotherapy responsiveness. Drug-sensitivity analyses nominated several candidate agents, and SMARCD3 knockdown in 786-O cells inhibited proliferation and migration and reduced sensitivity to masitinib. Collectively, these findings support the prognostic and therapeutic relevance of CR-related states in ccRCC and provide a framework for future experimental validation of chromatin-regulated tumor-immune interactions.

Humans↗

PubMed2025

Integrated multi-omics analysis reveals TMEM147 as an immunosuppressive prognostic biomarker in LUAD.

TMEM147, an endoplasmic reticulum (ER) membrane protein, is implicated in lung adenocarcinoma (LUAD) progression, although its precise role remains unclear. To elucidate its function, this study integrated bioinformatics analyses with experimental validation. First, TMEM147 expression was assessed using TCGA and GEO datasets, with validation performed in LUAD cell lines. Survival analysis evaluated its prognostic significance. Subsequently, Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and single-sample gene set enrichment analysis (ssGSEA) were employed to identify associated functional pathways and interactions within the tumor immune microenvironment. Transcription factor binding predictions and in vitro functional assays (migration, invasion, proliferation) further characterized TMEM147's role. Results indicated that TMEM147 was significantly upregulated in LUAD and correlated with poor outcomes in patients. FLI1 was predicted as a key transcriptional regulator of TMEM147. Furthermore, TMEM147 expression influenced immune cell infiltration profiles and was associated with pathways involved in ribonucleoprotein biogenesis and oxidative phosphorylation (OXPHOS). Importantly, silencing TMEM147 significantly reduced cancer cell migration, invasion, and proliferation. These findings collectively suggest that TMEM147 promotes LUAD progression and holds potential as both a prognostic biomarker and a therapeutic target.

Bioinformatics analysis↗

PubMed2004

Molecular cloning and characterization of chemokine-like factor super family member 1 (CKLFSF1), a novel human gene with at least 23 alternative splicing isoforms in testis tissue.

Chemokine-like factor (CKLF) was isolated from PHA-stimulated U937 cells. It is composed of 152 amino acids and located on chromosome 16q22. Utilizing bioinformatics, based on CKLF cDNA and protein sequences, in combination with experimental validation, we identified a novel gene designated chemokine-like factor super family member 1 (CKLFSF1). CKLFSF1 maps on chromosome 16q22, and the full-length gene comprises of seven exons and six introns. Using RACE-PCR, we identified two potential alternative transcription start sites, 1A and 1B. Northern blot and RT-PCR analysis demonstrated that CKLFSF1 is predominantly expressed in human testis tissue, with only lower levels of expression in many other human tissues. RT-PCR and cDNA sequencing identified 23 alternatively spliced isoforms of CKLFSF1 in the testis tissue, which encode protein variants ranging from 36 to 169 amino acids in length. Immunohistochemistry analysis demonstrated that CKLFSF1 proteins are highly expressed in spermatocyte and in tissue fluid of human testes tissue. In light of these findings, we propose that CKLFSF1 may play an important role in spermatogenesis or testicular development.

Alternative Splicing↗

PubMed2005

Micropillar array chip for integrated white blood cell isolation and PCR.

We report the fabrication of silicon chips containing a row of 667 pillars, 10 by 20 microm in cross-section, etched to a depth of 80 microm with adjacent pillars being separated by 3.5 microm. The chips were used to separate white blood cells from whole blood in less than 2 min and for subsequent PCR of a genomic target (eNOS). Chip fluid dynamics were validated experimentally using CoventorWare microfluidic simulation software. The amplicon concentrations were determined using microchip capillary electrophoresis and were >40% of that observed in conventional PCR tubes for chips with and without pillars. Reproducible on-chip PCR was achieved using white blood cell preparations isolated from whole human blood pumped through the chip.

Cell Separation↗

PubMed2005

Number-concentration of nanoparticles in liposomal and polymeric multiparticulate preparations: empirical and calculation methods.

The actual number of particles in formulations of nanoparticles (NP) is of importance for quality assurance, comprehensive physicochemical characterization, and pharmacodynamics. Some calculation methods that have been previously employed are limited because they rely on several assumptions and are not applicable for certain preparations. Currently there are no validated experimental methods for determining the particle number-concentration (Nc) of liposomal and polymeric nanoparticulate preparations (<500 nm). This study examines a new empirical method for counting the number of particles in nanoparticulate formulations including drug-containing liposomes and polymeric NP. In the new method, suspended NP are nebulized to form aerosol droplets which are dried and counted using a scanning mobility particle sizer (SMPS). Experiments were conducted with three different preparations, empty liposomes (200 and 400 nm), drug-loaded liposomes (200 nm), and polymeric NP (150 nm). It was verified that no detrimental morphological or structural changes of the formulations have been induced by the SMPS technique, and that the obtained Nc values represent the original particles. It is concluded that nano-formulations with concentrations of up to 10(7) particles per 1 cm3 air, corresponding to approximately 10(12) particles per 1 ml solution, can be directly counted within the size range of 30-900 nm. The measured values are compared to newly developed theoretical calculations to assess the viability of these calculations.

Algorithms↗

PubMed2005

Dispersion optimization to enhance PHB production in fed-batch cultures of Ralstonia eutropha.

Despite its many useful properties, microbial production of poly-beta-hydroxybutyrate (PHB) is not yet commercially competitive with synthetic polymers. One reason is inadequate optimization of the fermentation under industrial conditions. In this study, a physiologically reasonable and experimentally validated kinetic model for PHB synthesis by Ralstonia eutropha was incorporated into a dispersion model to simulate a large fed-batch bioreactor. Solutions of the model indicated that cell growth and PHB synthesis were maximum at Peclet numbers (Pe) between 20 and 30, representing limited finite dispersion. At these Peclet numbers, the optimum feed rates also showed lower consumptions of the substrates than at Pe=0. Since complete dispersion was also difficult to achieve in production-scale bioreactors, these results pointed to the possibility of exploiting controlled dispersion for productivity enhancement.

Biopolymers↗

PubMed2004

An FET-type charge sensor for highly sensitive detection of DNA sequence.

We have fabricated an field effect transistor (FET)-type DNA charge sensor based on 0.5 microm standard complementary metal oxide semiconductor (CMOS) technology which can detect the deoxyribonucleic acid (DNA) probe's immobilization and information on hybridization by sensing the variation of drain current due to DNA charge and investigated its electrical characteristics. FET-type charge sensor for detecting DNA sequence is a semiconductor sensor measuring the change of electric charge caused by DNA probe's immobilization on the gate metal, based on the field effect mechanism of MOSFET. It was fabricated in p-channel (P) MOSFET-type because the phosphate groups present in DNA have a negative charge and this charge determines the effective gate potential of PMOSFET. Gold (Au) which has a chemical affinity with thiol was used as the gate metal in order to immobilize DNA. The gate potential is determined by the electric charge which DNA possesses. Variation of the drain current versus time was measured. The drain current increased when thiol DNA and target DNA were injected into the solution, because of the field effect due to the electrical charge of DNA molecules. The experimental validity was verified by the results of mass changes detected using quartz crystal microbalance (QCM) under the same measurement condition. Therefore it is confirmed that DNA sequence can be detected by measuring the variation of the drain current due to the variation of DNA charge and the proposed FET-type DNA charge sensor might be useful in the development for DNA chips.

Base Sequence↗

PubMed2005

Modeling conversion and transport phenomena in solid-state fermentation: a review and perspectives.

Solid-state fermentation (SSF) is accompanied inevitably by development of concentration and temperature gradients within the substrate particles and microbial biofilms. These gradients are needed for driving the transport of substrates and products. In addition, concentration gradients have been suggested to be crucial for obtaining the characteristics that define the products of SSF; nevertheless, gradients are also known to result in reduced productivity and unwanted side reactions. Solid-state fermentations are generally batch processes and this further complicates their understanding as conditions change with time. Mathematical models are therefore needed for improving the understanding of SSF processes and allowing their manipulation to achieve the desired outcomes. Existing models of SSF processes describe coupled substrate conversion and diffusion and the consequent microbial growth. Existing models disregard many of the significant phenomena that are known to influence SSF. As a result, available models cannot explain the generation of the numerous products that form during any SSF process and the outcome of the process in terms of the characteristics of the final product. This review critically evaluates the proposed models and their experimental validation. In addition, important issues that need to be resolved for improved modeling of SSF are discussed.

Algorithms↗

PubMed2006

Antidepressant-like profile of action of two 4-amine derivatives of 10,11-dihydro-5H-dibenzo [a,d] cycloheptane in mice evaluated in the forced swimming test.

This study investigated the antidepressant-like effect of 4-amine derivatives of 10,11-dihydro-5H-dibenzo-alkylamine-cycloheptane, 4-amine (3-N,N-dimethylpropylamine)-10,11-dihydro-5H-dibenzo[a,d]cycloheptane-5-one (ADDCH1) and 1,2,3,4,8,9-hexahydro-dibenzocyclohepta[4,4a,5-ef]1,4-diazepin (ADDCH2), in a validated experimental model of depression, the forced swimming test (FST) in mice. Female adult mice were sub-chronically (three doses in 24 h) or repeatedly (once a day for 10 days) treated with either of the compounds and evaluated in the FST. The sub-chronic treatment promoted a dose-dependent reduction in the immobility time in the FST with the doses of 50 mg/kg (ADDCH1) and 30 mg/kg (ADDCH2) ip being the most effective (33% and 37% of reduction, respectively). A similar profile of action was observed in the animals repeatedly treated with ADDCH1 50 mg/kg or ADDCH2 30 mg/kg ip (for 10 days) and there was no sign of motor impairment or locomotor activation as evaluated in the rota-rod and open-field tests, respectively. These findings suggest that these amine derivatives of the system dibenzocycloheptane have an antidepressant-like action which could be of clinical interest and, therefore, deserves further investigation. In addition, putative underlying mechanisms of action are discussed.

Amines↗

PubMed2006

In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells.

Inhibition of the epidermal growth factor receptor (EGFR) tyrosine kinase activity by small molecules has proved effective for the treatment of cancer. To the best of our knowledge, the crystal structure of EGFR has been used for the first time to identify novel inhibitor chemotypes by docking-based in silico screening of a large virtual chemical library followed up by experimental validation. We identified several compounds with antiproliferative effects on cancer cells. Amongst them, a C(4)-N(1)-substituted pyrazolo[3,4-d]pyrimidine MSK-039 (39) was discovered as a low-micromolar inhibitor of EGFR tyrosine kinase activity. The predicted binding mode of 39 opens a new avenue toward the optimization of novel chemical entities to develop potent and selective inhibitors of EGFR signaling.

Antineoplastic Agents↗

PubMed2006

Kinetics of bimolecular reactions in model bilayers and biological membranes. A critical review.

The quantitative study of the probability of molecular encounters giving rise to a reaction in membranes is a challenging discipline. Model systems, model in the sense that they use model bilayers and model reactants, have been widely used for this purpose, but the methodologies employed for the analysis of the results obtained in experiments, and for experimental design, are so disparate that a concerned experimentalist has difficulty in deciding about the value of each approach. This review intends to examine the several approaches that can be found in the literature showing, when feasible, the weakness, strengths and limits of application of each of them. There is not, so far, a full experimental validation of the most promising theories for the analysis of reactions in two dimensions, what leaves open a large field for new research. The major challenge resides in the time range in which the processes take place, but the possibilities of the existing techniques for these studies are far from exhausted. We review also the attempts of several authors to quantitatively analyze the kinetics of reactions in biological membranes. Especially in this field, the recently developed microspectroscopies enclose a still unexplored potential.

Animals↗

PubMed2005

A human protein-protein interaction network: a resource for annotating the proteome.

Protein-protein interaction maps provide a valuable framework for a better understanding of the functional organization of the proteome. To detect interacting pairs of human proteins systematically, a protein matrix of 4456 baits and 5632 preys was screened by automated yeast two-hybrid (Y2H) interaction mating. We identified 3186 mostly novel interactions among 1705 proteins, resulting in a large, highly connected network. Independent pull-down and co-immunoprecipitation assays validated the overall quality of the Y2H interactions. Using topological and GO criteria, a scoring system was developed to define 911 high-confidence interactions among 401 proteins. Furthermore, the network was searched for interactions linking uncharacterized gene products and human disease proteins to regulatory cellular pathways. Two novel Axin-1 interactions were validated experimentally, characterizing ANP32A and CRMP1 as modulators of Wnt signaling. Systematic human protein interaction screens can lead to a more comprehensive understanding of protein function and cellular processes.

Axin Protein↗

PubMed2026

Comparative genomic analysis of Streptococcus parasuis and Streptococcus suis reveals mobile element-associated enrichment of antimicrobial resistance and lack of detectable same-MGE colocalization with virulence-associated genes within stable species boundaries.

Streptococcus suis is a major porcine pathogen and a zoonotic agent that causes meningitis and septicemia in humans. Streptococcus parasuis, a recently recognized close relative, remains poorly characterized with regard to its clinical significance and genomic features. In this study, we generated a single-contig closed genome assembly with genome-wide DNA methylation profiles for S. parasuis strain A1, isolated from a diseased pig in Xinjiang, China, and complemented in silico genomic predictions with isolate-level experimental validation of antimicrobial resistance (AMR) genotypes, virulence genotypes, and phenotypic susceptibility for this reference strain. Using this high-quality genome as a reference anchor, we performed comparative genomic analyses across 195 streptococcal genomes, comprising 15 S. parasuis and 180 S. suis strains, to distinguish genome-level co-occurrence of resistance and virulence determinants from their physical colocalization on the same mobile genetic element (MGE).Species boundaries remained clearly delineated at the genomic level, with a median interspecies average nucleotide identity (ANI) of approximately 86.0%, compared with intraspecies ANI medians of 97.5% for S. parasuis and 96.2% for S. suis. Pangenome analysis identified 12,693 gene clusters, of which 1086 were core clusters, and functional annotation revealed significant differences in accessory gene repertoires between the two species. Within this stable genomic framework, S. parasuis genomes carried a higher AMR gene burden; strain A1 harbored 10 AMR genes, multiple virulence-associated genes, three genomic islands, and eight prophage regions. For strain A1, PCR validation confirmed six AMR genes and six virulence genes, and disk diffusion testing demonstrated a multidrug-resistant phenotype consistent with the genotypic profile.Among 235 predicted mobile elements, 19 harbored AMR genes and seven carried Virulence Factor Database (VFDB) homologs, but none carried both categories simultaneously. This finding reflects a lack of detectable same-MGE colocalization under the applied annotation and assembly framework; it should not be interpreted as evidence of biological physical decoupling. Under a random-placement model, the expected number of co-carrying regions was only 0.57, and the probability of observing zero co-carrying regions was P = 0.55. This negative result should be interpreted with caution, given the limited number of cargo-bearing regions and the predominantly draft status of most genomes. Furthermore, the A1 genome contained multiple restriction-modification systems, showed depletion of several methylation motif families in mobile regions, and had limited CRISPR spacer matching evidence, suggesting prior exposure to the relevant sequence space. None of the genomes met our predefined criteria for whole-genome convergence.Collectively, our results support a model in which S. parasuis accumulates AMR-related genes in a modular fashion via mobile elements within stable species boundaries, with no detectable same-MGE colocalization of AMR and virulence determinants under our analytical pipeline. These findings imply that AMR surveillance strategies for this species should prioritize tracking mobile genetic elements rather than inferring wholesale genomic convergence toward S. suis.

Streptococcus suis↗

PubMed2006

Buck's direct repair of lumbar spondylolysis restores disc stresses at the involved and adjacent levels.

BACKGROUND: Lumbar spondylolysis was reported to cause disc degeneration at both caudal and cranial adjacent level. However, basic disc biomechanics in the spondylolytic spine is not fully understood. Purpose of this study was to analyze the disc stresses at cranial and caudal adjacent level of lumbar spondylolysis. Also, the biomechanical effects of Buck's technique on disc stresses at these two segments were evaluated. METHODS: An experimentally validated three-dimensional non-linear finite element model of the intact ligamentous L3-S1 segment was used. Bilateral lumbar spondylolysis was simulated by creating bilateral pars defects with 1.0 mm gap at L5. Buck's direct repair model was simulated with 4.0 mm cannulated Titanium screws, placed bilaterally across the defect. Von Mises stresses in the annulus fibrosus and nucleus pulposus at L4/5 (cranial adjacent) and L5/S (caudal adjacent) disc levels were analyzed in flexion, extension, lateral bending and axial rotation in response to 400 N of axial compression and 10.6 Nm moment. The highest values were compared among the three models, intact, spondylolysis and Buck's technique. FINDINGS: After spondylolysis occurred at L5, annulus fibrosus and nucleus pulposus stresses at L4/5 increased to 111% and 120%, respectively. After the Buck's technique it recovered to 102% and 105%, correspondingly. On the other hand, at L5/S, annulus fibrosus stress increased to 168%, and nucleus pulposus, 155%, which was much higher when compared to the stresses at L4/5. After the Buck's technique the stresses were decreased to 125% and 120%, correspondingly. During rotation motion, especially, the operation normalized the disc stress completely. INTERPRETATION: Spondylolysis increases disc stresses at the affected as well as cranial adjacent level, and it may lead to disc degeneration at both levels. However, the increase in stresses is higher at the affected caudal level, when compared to the cranial level. Buck's technique may restore the disc stresses back to normal at both disc levels. Thus, this technique may be beneficial from a biomechanical perspective as well.

Bone Screws↗

PubMed2006

Individual variability, end-point effects and possible biases in electrophysiological research.

Neocortical dynamics and signals reflect spatiotemporal cortical synchronization as well as functional condition and modulation by subcortical projecting structures that determine the brain state. However, neurotransmitters interact and neuronal function and signals also reflect non-neuronal factors that should (but not necessarily are, or can) be taken into proper consideration in neuroscience. Examples in this regard are the CNS modulation by spontaneous or induced changes in metabolism (e.g. glucose, ammonia), blood flow, pO(2), pCO(2), hormones (thyroxine; sexual hormones, ATCH) and neurohormonal interaction, maturation, aging, temperature, light-dark regulation of serotonine, histamine and dopamine/melatonin/vitamin B12 secretion and interaction, etc. Hormones also regulate the (functional) maturation and differentiation between sexes both during development and in adult life. These factors interact with each other and individually or collectively can account for unexplained or underestimated individual variability; on occasions, may become critical variables in animal or human research. In specific instances, variability is the information of interest. However, physiological variability due to neuronal or non-neuronal factors can interact with the experimental setups or affect electrophysiological signals to extents that can result in biased findings in otherwise controlled studies. An "inverse problem" difficult to approach may ensue in both animal and human research; in several instances, the specificity of brain signals for the investigated function may require experimental validation.

Analgesia↗