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PubMed2026

Tumor-Intrinsic Blood and Imaging Correlatives in Advanced Prostate Cancer Treated with Combination Radiopharmaceutical Therapy and Immunotherapy.

The PRINCE trial showed the clinical activity for 177Lu-PSMA-617 in combination with pembrolizumab for metastatic castration-resistant prostate cancer. To refine patient selection and improve response monitoring strategies to this combination, we investigated candidate tumor-intrinsic biomarkers of treatment response and resistance. Methods: We performed circulating tumor DNA (ctDNA), circulating tumor cell (CTC), and PET imaging analyses at baseline, 12 wk on-treatment, and disease progression in participants enrolled in PRINCE (n = 37). We performed targeted sequencing for ctDNA quantification and genomic analysis of more than 70 prostate cancer genes. CTC enumeration was performed on the EpicSciences platform and was combined with selective single-cell whole-genome sequencing. PET imaging included serial PSMA PET as well as 18F-FDG PET imaging at baseline. Results: A low baseline ctDNA fraction and high PSMA avidity in metastatic lesions were linked to superior treatment responses and may have composite biomarker value. Genomic alterations in tumor suppressor genes TP53, RB1, or PTEN were associated with higher 18F-FDG avidity and metabolic tumor volume on 18F-FDG PET imaging and worse prognosis. At 12-wk on-treatment, both ctDNA detection and PSMA PET imaging were strong indicators of response depth and durability. At disease progression, PSMA expression on PET imaging was lower compared with baseline and supported by subclonal remodeling of ctDNA and CTC copy number profiles and by clonal expansions of tumor suppressor gene mutations. Conclusion: We provide the first integrated molecular and imaging insights into determinants of response and resistance to combined radiopharmaceutical therapy and immunotherapy in prostate cancer and propose biomarker strategies to inform future clinical development.

177Lu-PSMA-617↗

PubMed2026

Protocol for Duplex Sequencing of Mitochondrial DNA in Single Human Oocytes.

Oocytes are densely packed with mitochondria, the energy-producing organelles that contain their own genome, mitochondrial DNA (mtDNA). Each cell contains multiple copies of mtDNA, with copy number varying among tissue types. Oocytes possess the highest mtDNA copy number, containing hundreds of thousands of mtDNA molecules per cell. Because mitochondria are inherited exclusively through the maternal lineage, accurate detection of mtDNA variants is essential for studies of inheritance, aging, and disease. The presence of multiple mtDNA copies allows wild-type and mutant molecules to coexist within the same cell, a condition known as heteroplasmy, in which low-frequency and de novo variants may occur at frequencies below 1%. Conventional next-generation sequencing (NGS) lacks sufficient accuracy to reliably distinguish these rare variants from errors introduced during library preparation and sequencing. Here, we present a protocol for enriching mtDNA from single human oocytes using Exonuclease V to remove linear DNA, followed by duplex sequencing library preparation for highly accurate mtDNA analysis. This workflow enables error-corrected sequencing of individual oocytes, facilitating reliable detection of low-frequency mtDNA variants and analysis of heteroplasmy and de novo mutagenesis. The protocol provides a reproducible approach for investigating mitochondrial genome variation in single oocytes using Illumina-compatible sequencing platforms.

Humans↗

PubMed2005

Comparison of muscle torque, balance, and confidence in older tai chi and healthy adults.

PURPOSE: The objectives of this cross-sectional study were to examine whether older Tai Chi practitioners had better knee muscle strength, less body sway in perturbed single-leg stance, and greater balance confidence than healthy older adults. METHODS: Tai Chi and control subjects (N = 24 each, aged 69.3 +/- 5.0 and 71.6 +/- 6.1 yr, respectively) were matched with respect to age, gender, height, weight, and physical activity level. Concentric and eccentric isokinetic tests of the subjects" dominant knee extensors and flexors were conducted at an angular velocity of 30 degrees.s(-1). Control of body sway was assessed in static double-leg stance and in single-leg stance perturbed by forward or backward platform perturbations. The Activities-specific Balance Confidence (ABC) scale was used to investigate subjects" balance confidence in daily activities. RESULTS: Tai Chi practitioners had higher peak torque-to-body weight ratios in concentric and eccentric isokinetic contractions of their knee extensors and flexors (P = 0.044). They manifested less anteroposterior body sway angles in perturbed single-leg but not static double-leg stance than did control subjects (P < 0.001). Tai Chi practitioners also reported significantly higher balance confidence score ratios (P = 0.001). Older adults" knee muscle strengths showed negative correlations with body sway angles in perturbed single-leg stance and positive correlations with ABC score ratios. Moreover, their body sway angles in perturbed single-leg stance were negatively correlated with their ABC score ratios (all P < 0.05). CONCLUSION: Our results demonstrate that long-term Tai Chi practitioners had better knee muscle strength, less body sway in perturbed single-leg stance, and greater balance confidence. Significant correlations among these three measures uncover the importance of knee muscle strength and balance control during perturbed single-leg stance in older adults" balance confidence in their daily activities.

Aged↗

PubMed2003

Large-scale identification of single-feature polymorphisms in complex genomes.

We have developed a high-throughput genotyping platform by hybridizing genomic DNA from Arabidopsis thaliana accessions to an RNA expression GeneChip (AtGenome1). Using newly developed analytical tools, a large number of single-feature polymorphisms (SFPs) were identified. A comparison of two accessions, the reference strain Columbia (Col) and the strain Landsberg erecta (Ler), identified nearly 4000 SFPs, which could be reliably scored at a 5% error rate. Ler sequence was used to confirm 117 of 121 SFPs and to determine the sensitivity of array hybridization. Features containing sequence repeats, as well as those from high copy genes, showed greater polymorphism rates. A linear clustering algorithm was developed to identify clusters of SFPs representing potential deletions in 111 genes at a 5% false discovery rate (FDR). Among the potential deletions were transposons, disease resistance genes, and genes involved in secondary metabolism. The applicability of this technique was demonstrated by genotyping a recombinant inbred line. Recombination break points could be clearly defined, and in one case delimited to an interval of 29 kb. We further demonstrate that array hybridization can be combined with bulk segregant analysis to quickly map mutations. The extension of these tools to organisms with complex genomes, such as Arabidopsis, will greatly increase our ability to map and clone quantitative trait loci (QTL).

Arabidopsis↗

PubMed2004

Simultaneously monitoring gene expression kinetics and genetic noise in single cells by optical well arrays.

An optical fiber based well array platform was used for simultaneous, dynamic gene expression monitoring from hundreds of individual live Escherichia coli cells carrying promoter-fluorescent reporter gene fusions. High information content about gene expression kinetics and cell-to-cell gene expression variability can be collected from a single experiment. These data are invaluable for investigating gene regulation and gene networks as well as for systems biology applications.

Escherichia coli↗

PubMed2005

Gene mapping with pooled samples on three genotyping platforms.

We have evaluated three genotyping techniques to detect allelic association between single nucleotide polymorphisms (SNPs) and disease loci by using pooled DNA samples. The use of DNA pools instead of individual samples saves considerably time, DNA quantity, and reagent costs. The methods that were compared were PCR-restriction fragment length polymorphism (PCR-RFLP), Single nucleotide primer extension, and chip-based mass spectrometry. As a model disease we studied an autosomal recessive disorder, congenital chloride diarrhea (CLD), caused by mutations in the human gene SLC26A3 on chromosome 7q31. Patient, carrier, and control pools were genotyped with eight SNP markers located within 10 cM around the target gene. Measured allele frequencies were consistent between the three platforms and we detected disease association with a cluster of several SNPs, the most significant being the marker located closest to the target gene (p=1.56 x 10(-16)). The largest source of error in pooled genotyping was shown to be the volumetric error in preparing the pools. The PCR-RFLP method was further evaluated by applying the pooling strategy to an ongoing multicenter-study. Measured allele frequencies of six polymorphisms agreed well with those measured individually and confirmed that multiple platforms are suitable for pooled genotyping.

Chromosome Mapping↗

PubMed2026

Single-cell profiling of mitochondrial phenotyping-coupled mtDNA genotyping.

Simultaneously profiling mitochondrial DNA (mtDNA) heteroplasmy and phenotypic variability at the single-cell level remains a challenge due to the absence of integrated methods that map mitochondrial genotypes alongside their functional states. We introduce human single-cell mitochondrial phenotype-coupled mtDNA sequencing (scMPCDS), a platform that quantifies mtDNA mutations and heteroplasmy together with mitochondrial membrane potential and reactive oxygen species within individual cells. Unlike bulk sequencing or separate single-omics techniques, scMPCDS directly correlates mitochondrial genomic instability with functional outcomes. Using this approach, we demonstrate that DdCBE-mediated mtDNA editing induces cell-specific off-target mutations in the mitochondrial genome, which coincide with diverse phenotypic changes. Applying scMPCDS to HeLa cells and clear cell renal cell carcinoma tissues, we identify single-cell subpopulations exhibiting distinct mtDNA mutation burdens and altered bioenergetic profiles, implicating potential mitochondrial heterogeneity-driven tumor evolution. Overall, scMPCDS serves as a versatile tool to unravel mitochondrial genotype-phenotype relationships at the single-cell level in both normal and disease states, thereby advancing precise mitochondrial diagnostics and therapeutics.

Humans↗

PubMed2003

In situ generation of carbenes: a general and versatile platform for organocatalytic living polymerization.

A metal-free, organocatalytic approach to living polymerization using N-heterocyclic carbenes as nucleophilic catalysts generated and used in situ in a single-pot process is detailed. The N-heterocyclic carbene catalyst platform is extremely versatile, as the nature of the substituents has a pronounced effect of catalyst stability and activity toward different substrates. The generation of imidazolium- and thiazaolium-based carbenes was accomplished from the reaction of the corresponding salts with the appropriate bases. This allowed the rapid screening of libraries of catalysts that provided a basic understanding of catalyst structure (sterics, electronics, etc.) with the polymerization rate, control, substrate, and range of molecular weights. The imidazole-based catalysts were significantly more active toward ROP than the thiazolium-based analogues. No appreciable differences between imidazol-2-ylidene and imidazolin-2-ylidene catalysts were observed. Less sterically demanding carbenes were found to be more active toward ring-opening polymerization (ROP) than their sterically encumbered analogues for lactone polymerization. These data prompted the investigation of ionic liquid as a precatalyst reservoir in a phase-transfer polymerization with an immiscible THF solution of monomer and initiator. In situ activation of the ionic liquid generates carbene that migrates to the organic phase effecting living ROP. Precatalyst (ionic liquid) regeneration terminates polymerization. This simple reaction/recycle protocol readily allows repetitive ROPs from the ionic liquid using commercially available materials.

Journal Article↗

PubMed2004

Deep space environments for human exploration.

Mission scenarios outside the Earth's protective magnetic shield are being studied. Included are high usage assets in the near-Earth environment for casual trips, for research, and for commercial/operational platforms, in which career exposures will be multi-mission determined over the astronaut's lifetime. The operational platforms will serve as launching points for deep space exploration missions, characterized by a single long-duration mission during the astronaut's career. The exploration beyond these operational platforms will include missions to planets, asteroids, and planetary satellites. The interplanetary environment is evaluated using convective diffusion theory. Local environments for each celestial body are modeled by using results from the most recent targeted spacecraft, and integrated into the design environments. Design scenarios are then evaluated for these missions. The underlying assumptions in arriving at the model environments and their impact on mission exposures within various shield materials will be discussed.

Aerospace Medicine↗

PubMed2004

A tautomeric zinc sensor for ratiometric fluorescence imaging: application to nitric oxide-induced release of intracellular zinc.

Zinc is an essential metal ion for human growth and development, the disruption of cellular Zn(2+) homeostasis being implicated in several major disorders including Alzheimer's disease, diabetes, and cancer. The molecular mechanisms of Zn(2+) physiology and pathology are insufficiently understood, however, owing in part to the lack of tools for measuring changes in intracellular Zn(2+) concentrations with high spatial and temporal fidelity. To address this critical need, we have synthesized, characterized, and applied an intracellular fluorescent probe for the ratiometric imaging of Zn(2+) based on a tautomeric seminaphthofluorescein platform. Zin-naphthopyr 1 (ZNP1) affords single-excitation, dual-emission ratiometric detection of intracellular Zn(2+) through Zn(2+)-controlled switching between fluorescein and naphthofluorescein tautomeric forms. The probe features visible excitation and emission profiles, excellent selectivity responses for Zn(2+) over competing Ca(2+) and Mg(2+) ions at intracellular concentrations, a dissociation constant (K(d)) for Zn(2+) of <1 nM, and an 18-fold increase in fluorescence emission intensity ratio (lambda(624)/lambda(528)) upon zinc binding. We demonstrate the value of the ZNP1 platform for biological applications by imaging changes in intracellular [Zn(2+)] in living mammalian cells. Included is the ratiometric detection of endogenous pools of intracellular Zn(2+) after NO-induced release of Zn(2+) from cellular metalloproteins. We anticipate that ZNP1 and related probes should find utility for interrogating the biology of Zn(2+).

Animals↗

PubMed2004

Towards sorting of biolibraries using single-molecule fluorescence detection techniques.

The selection of specific binding molecules like peptides and proteins from biolibraries using, for instance, phage display methods can be quite time-consuming. It is therefore desirable to develop a strategy that is much faster in selection and sorting of potential binders out of a biolibrary. In this contribution we separately discuss the current achievements in generation of biolibraries, single-molecule detection techniques and microfluidic devices. A high-throughput microfluidic platform is then proposed that combines the propulsion of liquid containing fluorescent components of the biolibrary through microchannels, single-molecule fluorescence photon burst detection and real-time sorting of positive hits.

Fluorescence↗

PubMed2026

Molecular biomarker profiling in noninfectious uveitis: a chronological review of discovery.

PURPOSE OR REVIEW: Noninfectious uveitis (NIU) encompasses a heterogeneous group of immune-mediated intraocular inflammatory diseases whose complexity has driven systematic molecular biomarker discovery. This review presents NIU molecular biomarkers organized by biological category; autoantigens, human leukocyte antigens (HLA) and genetic markers, cellular immune subsets, cytokines, chemokines, and multiomics platforms including proteomics, microbiome metagenomics, metabolomics, and single-cell transcriptomics with each category presented in strict chronological order of landmark discovery. RECENT FINDINGS: We present a review organized along two nested timelines. Categories are presented in the order they historically emerged in the field, and within each category, landmark discoveries appear in chronological sequence. This allows the reader to trace how each biomarker category evolved: from foundational autoantigen identification in experimental uveitis models, through the genomic revolution of HLA association studies, into cellular immunophenotyping, cytokine profiling of aqueous humor, chemokine mapping of intraocular trafficking, and finally the emerging omics platforms that may potentially anchor precision medicine in NIU. Each biomarker is paired in line with its linked targeted therapeutic. SUMMARY: Biomarker research has transformed the understanding of NIU from a clinically defined syndrome into a group of molecularly distinct immune disorders. Advances spanning autoantigens, genetics, immune-cell profiling, cytokines, chemokines, and multiomics have revealed novel pathogenic mechanisms and therapeutic targets. Integration of these biomarkers with targeted therapies may accelerate the transition toward precision medicine in uveitis care.

cytokines↗

PubMed2006

An improved gel-based DNA microarray method for detecting single nucleotide mismatch.

3-D polyacrylamide gel-based DNA microarray platforms provide a high capacity for nucleic acids immobilization and a solution-mimicking environment for hybridization. However, several technological bottlenecks still remain in these platforms, such as difficult microarray preparation and high fluorescent background, which limit their application. In this study, two new approaches have been developed to improve the convenience in microarray preparation and to reduce the background after hybridization. To control the polymerization process, solutions containing acrylamide-modified oligonucleotide, acrylamide, glycerol and ammonium persulfate are spotted onto a functionalized glass slide, and then the slide is transferred to a vacuum chamber with TEMED, so that TEMED is vaporized and diffused into the spots to induce polymerization. By applying an electric field across a hybridized microarray to remove the nonspecifically bound labeled targets, this approach can solve the problem of high fluorescent background of the gel-based microarray after hybridization. Experimental results show that our immobilization method can be used to construct high quality microarrays and exhibits good reproducibility. Moreover, the polymerization is not affected by PCR medium, so that PCR products can be used for microarray construction without being treated by commercial purification cartridges. Electrophoresis can improve the signal-to-noise significantly and has the ability to differentiate single nucleotide variation between two homozygotes and a heterozygote. Our results demonstrated that this is a reliable novel method for high-throughput mutation analysis and disease diagnosis.

Base Pair Mismatch↗

PubMed2006

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.

BACKGROUND: DNA microarrays are rapidly becoming a fundamental tool in discovery-based genomic and biomedical research. However, the reliability of the microarray results is being challenged due to the existence of different technologies and non-standard methods of data analysis and interpretation. In the absence of a "gold standard"/"reference method" for the gene expression measurements, studies evaluating and comparing the performance of various microarray platforms have often yielded subjective and conflicting conclusions. To address this issue we have conducted a large scale TaqMan Gene Expression Assay based real-time PCR experiment and used this data set as the reference to evaluate the performance of two representative commercial microarray platforms. RESULTS: In this study, we analyzed the gene expression profiles of three human tissues: brain, lung, liver and one universal human reference sample (UHR) using two representative commercial long-oligonucleotide microarray platforms: (1) Applied Biosystems Human Genome Survey Microarrays (based on single-color detection); (2) Agilent Whole Human Genome Oligo Microarrays (based on two-color detection). 1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan Gene Expression Assay based real-time PCR validation. For each platform, four technical replicates were performed on the same total RNA samples according to each manufacturer's standard protocols. For Agilent arrays, comparative hybridization was performed using incorporation of Cy5 for brain/lung/liver RNA and Cy3 for UHR RNA (common reference). Using the TaqMan Gene Expression Assay based real-time PCR data set as the reference set, the performance of the two microarray platforms was evaluated focusing on the following criteria: (1) Sensitivity and accuracy in detection of expression; (2) Fold change correlation with real-time PCR data in pair-wise tissues as well as in gene expression profiles determined across all tissues; (3) Sensitivity and accuracy in detection of differential expression. CONCLUSION: Our study provides one of the largest "reference" data set of gene expression measurements using TaqMan Gene Expression Assay based real-time PCR technology. This data set allowed us to use an alternative gene expression technology to evaluate the performance of different microarray platforms. We conclude that microarrays are indeed invaluable discovery tools with acceptable reliability for genome-wide gene expression screening, though validation of putative changes in gene expression remains advisable. Our study also characterizes the limitations of microarrays; understanding these limitations will enable researchers to more effectively evaluate microarray results in a more cautious and appropriate manner.

Gene Expression Profiling↗

PubMed2000

Anticipatory postural adjustments depend on final equilibrium and task complexity in vertical high jump movements.

Anticipatory postural adjustments (APA) associated with high vertical jumping were studied in five normal men. The dependence of APA on final equilibrium and task complexity was studied by analyzing the characteristics of single versus repetitive jumps. Subjects performed series of 25 single jumps and 25 repetitive jumps on a force platform, in response to a Go signal. Surface EMG from the Soleus (SO), Tibialis anterior (TA), Vastus lateralis (VL) and Biceps femoris (BF) muscles were recorded simultaneously with the three components of the ground reaction forces. The existence of APA associated with both single and repetitive jumps was evidenced by a backward shift of the center of pressure, an SO deactivation, and a TA activation which preceded the onset of movement by hundreds of milliseconds. In repetitive jumps, SO deactivation occurred later than in single jump, whereas the center of pressure shift started earlier, lasted longer and had a greater amplitude. Moreover, repetitive jumps were initiated later with respect to the Go signal. These data show that the central nervous system anticipates not only the equilibrium disturbance caused by an initial movement but that caused by a whole sequence of movements. They also show that the corresponding APA are based heavily on a single functional ankle synergy.

Adaptation, Physiological↗

PubMed2006

Whole-genome genotyping.

We have developed an array-based whole-genome genotyping (WGG) assay (Infinium) using our BeadChip platform that effectively enables unlimited multiplexing and unconstrained single nucleotide polymorphism (SNP) selection. A single tube whole-genome amplification reaction is used to amplify the genome, and loci of interest are captured by specific hybridization of amplified gDNA to 50-mer probe arrays. After target capture, SNPs are genotyped on the array by a primer extension reaction in the presence of hapten-labeled nucleotides. The resultant signal is amplified during staining and the array is read out on a high-resolution confocal scanner. We have employed our high-density BeadChips supporting up to 288,000 bead types to create an array that can query over 100,000 SNPs using the Infinium assay. In addition, we have developed an automated BeadChip processing platform using Tecan's GenePaint slide processing system. Hybridization, washing, array-based primer extension, and staining are performed directly in Tecan's capillary gap Te-Flow chambers. This automation process increases assay robustness and throughput greatly while enabling laboratory information management system control of sample tracking.

Animals↗

PubMed2006

Kondo effect in the presence of magnetic impurities.

We measure transport through gold grain quantum dots fabricated using electromigration, with magnetic impurities in the leads. A Kondo interaction is observed between dot and leads, but the presence of magnetic impurities results in a gate-dependent zero-bias conductance peak that is split due to a RKKY interaction between the spin of the dot and the static spins of the impurities. A magnetic field restores the single Kondo peak in the case of an antiferromagnetic RKKY interaction. This system provides a new platform to study Kondo and RKKY interactions in metals at the level of a single spin.

Journal Article↗

PubMed2026

Scalable medium-density genotyping platforms for cultivar identification, pedigree authentication, marker-assisted and genomic selection, and other applications in strawberry.

A broad spectrum of high-density genotyping approaches, including single-nucleotide polymorphism (SNP) arrays, genotyping-by-sequencing, and whole-genome reduced-representation sequencing, have been shown to perform well in strawberry (Fragaria × ananassa), despite the inherent complexity of the octoploid genome. While these approaches are effective, their routine deployment in breeding programs can be constrained by cost, computational requirements, and workflow complexity. In parallel, many breeding programs continue to rely on locus-specific assays for marker-assisted selection, resulting in fragmented and inefficient genotyping strategies. Here, we describe medium-density amplicon-based genotyping platforms for strawberry designed to provide cost-effective, turnkey solutions that integrate markers used for marker-assisted selection with genome-wide markers suitable for genomic prediction in a single laboratory assay. These platforms were developed by targeting 1,650 or 4,811 target SNPs via amplicon sequencing, and are interoperable with existing high-density genotyping resources, including a widely used 50K SNP array, thereby facilitating data integration across platforms. We benchmarked their performance relative to the 50K SNP array across breeding-relevant applications, including identity and purity testing, pedigree authentication, marker-assisted selection, and genomic selection, and further evaluated the feasibility of genotype imputation to enhance genome-wide information content. Across analyses, the 1,650- and 4,811-amplicon platforms produced results comparable to higher-density platforms while substantially reducing genotyping cost and analytical overhead. This work demonstrates that targeted amplicon-based genotyping can support efficient, scalable, and integrated genome-informed breeding, enabling the routine application of both marker-assisted and genomic selection within strawberry breeding workflows. Open-source R workflows are provided to support streamlined analyses in breeding contexts.

Fragaria↗