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PubMed2026

3D Proteomics: Structural, Functional, Chemical and Biomarker Discovery Proteomics With LiP-MS.

Protein structural dynamics drive changes in protein function, making the capture of such dynamics essential for interrogating biological systems. Here we review limited proteolysis coupled to mass spectrometry (LiP-MS), a structural and chemical proteomics method that uses changes in susceptibility to protease cleavage to profile proteome-wide protein structural changes within complex biological samples. In the decade since its development, LiP-MS has become a broadly used structural proteomics method, with peptide-level resolution. It has identified drug targets, delineated altered cellular pathways in response to complex perturbations, revealed structural information on otherwise challenging protein targets, and demonstrated the new concept of structural biomarkers of disease. Because LiP-MS simultaneously probes numerous types of molecular events, such as molecular binding, changes in enzyme activity, chemical modifications, allosteric conformational changes, aggregation, and unfolding, it supports a new proteomics workflow which we term 3D proteomics. This workflow enables the detection of specific functional sites within proteins that are altered upon perturbation, thereby guiding the generation of molecular hypotheses. Further, by globally profiling structural in addition to protein abundance changes, LiP-MS has proven able to greatly increase the information content of functional proteomics screens. In sum, LiP-MS has supported the development of a novel conceptual framework for generating, visualizing, and interpreting structural proteomics data with peptide level resolution, thereby comprehensively probing biological systems. Here we survey the applications of LiP-MS, discuss methodological variants developed by us and others, and describe the use of this new type of omics readout for structural, functional, chemical, and biomarker discovery proteomics.

Proteomics↗
PubMed2025

Prediction of Australian wheat genotype by environment interactions and mega-environments.

Latent environmental effects of genotype by environment interactions could be predicted from observed environmental covariates. Predictions into the wider target population of environments revealed greater insights. Wheat is grown across a diverse range of environments in Australia with contrasting environmental constraints. Targeted breeding to optimise genotypes in target environments is hindered by large and ubiquitous genotype by environment interactions (GEI). Common GEI in multi-environment trial experiments, which sample the target population of environments, can be efficiently modelled using latent environmental effects from factor analytic mixed models. However, generalised prediction into the full target population of environments is difficult without a clear link to observed environmental covariates (ECs) that are defined from high-resolution weather and soil data. Here, we used a large wheat multi-environment trial dataset and demonstrated that latent environmental effects can be associated with and predicted from observed ECs. We found GEI-based environment classes could be defined by combinations of key ECs. Prediction of main and latent effects in a wider set of environments covering the full TPE across the Australian grain belt over 13 years revealed the complex trends of environmental effects and GEI over regional scales demonstrating high year-to-year variability. Regional environment types often shifted year-to-year. Cross-validation of forward genomic prediction into untested year environments demonstrated that increased accuracy is possible if estimated genetic effects are also accurate and ECs of new environments are known. These findings may guide Australian wheat breeders to better target specifically adapted material to mega-environments defined by static GEI while also considering broad adaptability and non-static GEI resulting from year-to-year variability.

Triticum↗
PubMed1978

The effect of cholesterol on the structure of phosphatidylcholine bilayers.

The effect of cholesterol on the structure of phosphatidylcholine bilayer was investigated by X-ray diffraction methods. Electron density profiles at 5 A resolution along with chain tilt and chain packing parameters were obtained and compared for phosphatidylcholine/cholesterol bilayers and for pure phosphatidylcholine bilayers in both the gel and liquid crystalline states. The cholesterol in the bilayers was localized by noting the position of discrete elevations in the electron density profiles. Cholesterol can either increase or decrease the width of the bilayer depending on the physical state and chain length of the lipid before the introduction of cholesterol. For saturated phosphatidylcholines containing 12--16 carbons per chain, cholesterol increases the width of the bilayer as it removes the chain tilt from gel state lipids or increases the trans conformations of the chains for liquid crystalline lipids. However, cholesterol reduces the width of 18 carbon chain bilayers below the phase transition temperature as the long phospholipid chains must deform or kink to accomodate the significantly shorter cholesterol molecule. Although cholesterol has a marked effect on hydrocarbon chain organization, it was found that, within the resolution limits of the data, the phosphatidylcholine head group conformation is unchanged by the addition of cholesterol to the bilayer. The head group is oriented parallel to the plane of the bilayer for phosphatidylcholine in the gel and liquid crystalline states and this orientation is not changed by the addition of cholesterol.

Cholesterol↗
PubMed1977

Instrumentation trends in nuclear medicine.

Nuclear medicine instrumentation requires use of various configurations of photon detectors for the purpose of in vivo and in vitro measurements of flow and metabolism. Computed tomography has solved a previous limitation of an ambiguous volume of interest intrinsic to projection images. Selection of instruments involves first, a definition of the medical problem to be solved; then an evaluation of the following characteristics of the candidate instruments: sensitivity, spatial resolution, saturation performance, dead time, uniformity of resolution, uniformity of sensitivity, data processing capabilities, and cost. New developments include dynamic imaging in transverse section with either single photon or positron annihilation photons, and whole-body quantitative imaging of sequential changes in radiopharmaceutical concentration.

Evaluation Studies as Topic↗
PubMed1978

Protocol for a computed tomography scanner performance repository.

An argument is presented for organization of a Computed Tomography Scanner Performance Repository. Performance data on CT scanners would be distributed in statistical form to the radiological community. A Protocol is presented for the uniform collection of data. Results of exposure, resolution and visibility measurements made by the authors are presented for the EMI 5005/U, Pfizer 0200 FS and General Electric CT/T scanners.

Humans↗
PubMed2026

Scalable, generalizable and uncertainty-aware integration of spatial multiomics across diverse modalities and platforms with SCIGMA.

Recent advances in spatial omics technologies have enabled simultaneous profiling of transcriptomic, proteomic, epigenomic, metabolomic and imaging data at high spatial resolution, offering unprecedented opportunities to dissect tissue complexity. However, integrating these diverse and large-scale spatial multimodal datasets remains a major computational challenge. We present SCIGMA, a scalable and generalizable deep learning framework for spatial multiomics integration. SCIGMA introduces an uncertainty-aware contrastive learning objective and multiview graph neural networks to preserve modality-specific signals while learning biologically meaningful joint representations. Unlike previous methods, SCIGMA provides spatially resolved uncertainty estimates, interpretably identifying regions of biological or technical heterogeneity. SCIGMA supports integration of up to five modalities, and its modular framework is extensible to future technologies with even more modalities. It also scales to more than 1 million spatial locations, enabling analysis of high-resolution datasets such as Visium HD and Xenium Prime. We evaluated SCIGMA across 19 datasets spanning 8 modalities, 10 tissues and 9 platforms. On benchmarkable datasets, SCIGMA outperformed other methods in spatial domain detection, modality preservation, feature reconstruction and reproducibility. SCIGMA identifies biologically meaningful structures, refined spatial domains and modality-specific regulatory programs, providing a robust, flexible and future-ready solution for scalable spatial multimodal integration.

Multiomics↗
PubMed1977

Crystallographic studies of bovine beta2-microglobulin.

Crystals of the bovine milk protein lactollin yield x-ray diffraction data extending to a resolution of 2.8 A. Lactollin is a bovine analogue of beta2-microglobulin, a protein that is homologous in amino acid sequence to the constant domains of immunoglobulins and is the light chain of the human and murine major histocompatability antigens. The protein crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 77.4, b = 47.9, and c = 34.3 A. The unit cell parameters and physical chemical solution studies indicate that the molecule exists in the crystal and in solution as a single polypeptide chain of 12,000 daltons.

Amino Acid Sequence↗
PubMed1978

Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA.

Refinement of the diffraction data at 2.5-A resolution from orthorhombic crystals of yeast tRNAPhe has proceeded to the point where spermine and magnesium ions can be located in the difference electron density map. Two spermine molecules are found: one is located in the major groove at one end of the anticodon stem; the other is near the variable loop and curls around phosphate 10 in a region where the polynucleotide chain takes a sharp turn. Four distinct magnesium ions have been identified: one in the anticodon loop, two in the D loop, and one coordinated with phosphates 8, 9, 11, and 12, where the polynucleotide chain is coiled. The conformation of the anticodon stem and loop is stabilized by the cations at the end of the molecule. The positions of these ions may be related to aspects of the biological activity of tRNA. The spermine and magnesium ions appear to be important in maintaining the overall folding of the tRNA molecule.

Anticodon↗
PubMed2025

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.

Predicting gene expression from DNA sequence remains challenging due to complex regulatory codes. We introduce a masked DNA language model pretrained on 165 fungal genomes closely related to budding yeast that captures conserved regulatory grammar. Fine-tuning the LM on yeast RNA-seq data-including high-resolution transcriptional regulator induction time courses generated in this study-yielded Shorkie, a model that substantially improves gene expression prediction compared to baselines trained without self-supervision. Shorkie identified canonical transcription factor (TF) binding motifs and tracked their usage across induction experiments. Furthermore, Shorkie accurately predicted variant effects, outperforming leading sequence-to-expression models in cis-eQTL classification and achieving high concordance with massively parallel reporter assays. Interpretability analyses revealed Shorkie's ability to resolve promoter dynamics, splicing signals, and temporal changes in regulatory motif usage. This framework demonstrates that evolutionary-scale pretraining combined with transfer learning substantially improves our ability to decode gene regulation from sequence, providing insights into noncoding variants and regulatory networks.

Journal Article↗
PubMedDate not supplied

Holographically stored x-ray images: gray-tone reproduction.

Storage of radiographs by holographic means is analyzed with emphasis on its gray-tone reproduction characteristics. The density range and number of gray-tone levels is found to be limited by random scattering in the holographic medium. The behavior is described quantitatively and is in satisfactory agreement with experimental data. Gray-tone resolution is shown to be reduced by speckle noise. It is shown that there exists a trade-off between speckle reduction and reproduced density range.

Holography↗
PubMed1976

Structural domains of transfer RNA molecules.

In this article, we have described various detailed features of the conformation of yeast tRNA(Phe) revealed by recent refinement analysis of x-ray diffraction data at 2.5 A resolution. The gross features of the molecule observed in the unrefined version have been largely confirmed and a number of new features found. The unique role of the ribose 2' hydroxyl groups in maintaining a series of nonhelical conformations in this RNA molecule has become apparent. Many of these features are a direct consequence of the geometry of the ribose phosphate backbone of RNA molecules, and these may also be found in structured regions of other RNA species as well. Special attention has been directed toward two conformational motifs revealed by this analysis. These include the striking similarity between the TpsiC and anticodon hairpin turns in the polynucleotide chain, which are stabilized by the participation of uridine in the U turn. In addition, there is frequent occurrence of an arch conformation in the polynucleotide chian which is stabilized by hydrogen bonds from 2' hydroxyl residues to phosphate groups across the base of the arch. The importance of the 2' hydroxyl interactions in defining tertiary structure is illustrated by the fact that, in the nonhelical regions, almost half of the ribose residues are involved in O2' hydrogen-bonding interactions which stabilize the conformation of the molecule.

Anticodon↗
PubMed1979

Selection of optimal model for the DNA histogram by analysis of error of estimated parameters.

The ability of four different mathematical models of the DNA histogram to give accurate estimates for the fractions of cells in G1, S, and G2 + M has been investigated. The models studied differ in the form and number of parameters of the function used to represent cells in S-phase. Results obtained from simulated DNA histograms suggest that the standard deviations of the model parameters increase exponentially with the width of the G1 and G2 + M peaks of the histogram. Error analysis is presented as a method to select a model of optimal complexity in relation to the resolution provided by the data in a given set of DNA histograms. Introduction of additional parameters improves the agreement between model and data but may result in a less well-posed model. A model with an optimal number of parameters can therefore be found that will yield parameter estimates with the smallest possible standard deviations.

Cell Cycle↗
PubMed2026

Aging of hair follicle stem cells and their niche: mechanisms and regenerative therapeutic strategies.

Hair follicles (HFs) are vital skin appendages that perform fundamental functions including protection, thermoregulation, and sensation. Orchestrated by hair follicle stem cells (HFSCs), HFs undergo cyclic regeneration throughout the lifespan. However, during chronological aging, this mini-organ experiences progressive physiological decline, clinically characterized by a marked reduction in hair density and hair graying due to pigmentation dysfunction. This aging process involves HFSC exhaustion accompanied by diminished regenerative potential and differentiation capacity, leading to degenerative changes in the bulge architecture. Concurrently, the niche supporting HFSC homeostasis undergoes multi-dimensional and systemic degradation. This niche deterioration disrupts the delicate balance between HFSC quiescence and activation, further impeding hair regeneration. In this review, we delineate the dynamic anatomical changes throughout the hair growth cycle and describe the alterations of HFSCs during aging. We specifically focus on the mechanisms underlying the multi-dimensional degradation of the HFSC niche at tissue, cellular, and molecular levels. Furthermore, we discuss various therapeutic strategies aimed at ameliorating HF aging, offering potential insights for future clinical translation in hair regeneration. Finally, we propose that integrating spatiotemporal high-resolution technologies with genomic data to further decipher the spatiotemporal behaviors of aging HFSCs and niche cells will facilitate the establishment of a robust mechanistic framework for HFSC and niche aging.

Hair Follicle↗
PubMedDate not supplied

Comparison of two Papanicolaou staining procedures for automated prescreening.

A "regressive" (procedure I) and a "progressive" (procedure II) modification of the Papanicolaou stain were tested for their suitability for automated screening procedures. Intermediate squamous cells and carcinoma cells were scanned with a high-resolution system, and digitized data were statistically analyzed after feature extraction. The regressive modification accentuates the textural features of intermediate squamous cell nuclei as well as the contrast ratio of nucleus and cytoplasm. The progressive modification accentuates some criteria of malignancy, such as polychromasia, hyperchromasia and shifting of nuclear to cytoplasmic ratio. Grouping of data according to patients indicates that the differences found are due to the staining procedures and not to individual variability of parameters in different patients.

Autoanalysis↗
PubMed1977

Prospects of three-dimensional high resolution electron microscopy of non-periodic structures.

In the first part of the paper the general features of three-dimensional electron microscopy of non-periodic structures at high resolution are discussed. Such an analysis requires series of 20 or more exposures of mechanically moved specimens. It is fundamentally important that the integral radiation dose, however, need not be increased--three-dimensional analysis yields extra information without additional radiation loading. It is demonstrated that the constraints characteristic for atomic resolution can in future facilitate many difficulties like restricted tilting range (conical tilting), inaccuracies in the refinement of the origin determination etc. Data collection up to atomic resolution is possible with existing image reconstruction methods if the chromatic spread of the cathodes can be partially corrected. The relatively great radiation induced changes of "stable" specimens will require additional averaging in the experiment (quasi-simultaneous registration). The advantage of a time dependent analysis of radiation sensitive structures--especially the possibility of using redundancies in the analysis (trace structure analysis)--is discussed. The experimental part (studies of radiation damage and three-dimensional work on carbon foils) presents examples of such analyses. The main experimental difficulty consists in the collection of many exposures with no extra load of the specimen in the intervals between exposures.

Carbon↗
PubMed1978

Quantitative nuclear cystogram. Aid in determining spontaneous resolution of vesicoureteral reflux.

The quantatitative data derived from serial nuclear cystograms over a five-year period in 37 children were compared with the clinical course. A direct correlation (92 per cent) between an increasing bladder volume at which reflux occurs was observed in the clinically stable group. In the clinically unstable group, there was a 75-per cent correlation of an unchanged or decreasing bladder volume at which reflux occurs. The quantitative nuclear cystogram provides an objective as opposed to subjective data base for management of patients with vesicoureteral reflux.

Child↗
PubMed1978

The quantitative nuclear cystogram: an aid in determining the spontaneous resolution of vesicoureteral reflux.

The quantitative data derived from serial nuclear cystograms during a 5-year period in 39 children were compared to the clinical course. A direct correlation (93 per cent) between an increasing bladder volume at which reflux occurs was observed in the clinically stable group. In the clinically unstable group there was a 77 per cent correlation of an unchanged or decreasing bladder volume at which reflux occurs. The quantitative nuclear cystogram provides an objective as opposed to subjective data base for management of patients with vesicoureteral reflux.

Child↗
PubMed1979

Application of ART to time-coded emission tomography.

Devices for single-photon emission tomography currently take projections either in a plane over a full angular range (0--360 degrees) or in a volume with a limited angular range. The planar, pseudo-random, time-coded aperture, in conjunction with an Anger camera, is a device of the limited angular range type. It employs multiple pinholes whose transmission varies as a function of time. Previously, image reconstruction was accomplished by simple back-projection of coefficients obtained by time-correlating pinhole transmission with detector-element count rate, resulting in a low-contrast image. Using the Algebraic Reconstruction Technique (ART) a method is introduced for division of the correlation coefficients into subsets allowing the three-dimensional reconstruction to be accomplished on a minicomputer. Results from simulations and experimental phantom data show that ART improves depth resolution compared to back-projection, that under-relaxation produces better images in the case of noisy data, and that the division of the correlation coefficients into subsets has no effect on quality. The images depict the expected resolution degradation in the direction normal to the detector plane due to the limited angular range of projections but yield quantitative results whose relative values are good, even though attenuation is neglected.

Mathematics↗