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At least 91 records · Page 5Linked to original sources

PubMed2026

EPIC: multi-objective guided diffusion for epitope design in TCR-pMHC complexes.

MOTIVATION: T cell receptor (TCR) recognition of peptide-major histocompatibility complex (pMHC) complexes is central to adaptive immunity, yet rational design of immunogenic epitopes remains elusive due to complex triplet binding constraints and data scarcity. No existing method can generate epitopes satisfying simultaneous requirements for antigenicity, MHC presentation, and TCR specificity. RESULTS: We present EPIC, a multi-objective diffusion framework that decomposes TCR-pMHC binding into three biologically grounded sub-tasks, enabling training-free gradient guidance without end-to-end retraining. By integrating ESM-based classifiers with a peptide diffusion generator, EPIC leverages heterogeneous immunological interaction datasets to generate diverse, context-aware epitopes. EPIC-designed top-three epitopes achieve lower predicted interface energies compared to ground-truth epitopes in 78.31% of test cases, while maintaining 80.1% sequence novelty and comparable structural confidence. Generated epitopes exhibit 100% uniqueness, high diversity (64.05%), and high antigenicity scores (0.4723). To our knowledge, EPIC is the first computational framework capable of de novo epitope design while explicitly integrating the triplet constraints of TCR-pMHC binding. This paradigm shift from discovery to design unlocks new potential for personalized cancer vaccines, precision adoptive T cell therapy, and rapid response to emerging infectious diseases. AVAILABILITY AND IMPLEMENTATION: The source code of EPIC is available at https://github.com/Octopus125/EPIC and archived on Zenodo (DOI: 10.5281/zenodo.18537646).

Receptors, Antigen, T-Cell↗

PubMed1988

Photochemical reactions of dyes and olefins in monolayer films and supported multilayers.

The studies cited in this paper demonstrate that the unique environment provided by L. B. films and supported multilayers can produce a variety of molecular effects on photochemical reactivity that can, in turn, result in films, interfaces or surfaces having macroscopic properties which can be modulated by light. Although these investigations have been focused on molecular reactivity in films and how it can be modified (or persist unchanged), the results suggest several possible technological applications which might result from investigations directed more closely to them.

Alkenes↗

PubMed1991

Electrophoretic gel image analysis software for the molecular biology laboratory.

We present GelReader 1.0, a microcomputer program designed to make precision, digital analysis of one-dimensional electrophoretic gels accessible to the molecular biology laboratory of modest means. Images of electrophoretic gels are digitized via a desktop flatbed scanner from instant photographs, autoradiograms or chromogenically stained blotting media. GelReader is then invoked to locate lanes and bands and generate a report of molecular weights of unknowns, based on specified sets of standards. Frequently used standards can be stored in the program. Lanes and bands can be added or removed, based upon users' subjective preferences. A unique lane histogram feature facilitates precise manual addition of bands missed by the software. Image enhancement features include palette manipulation, histogram equalization, shadowing and magnification. The user interface strikes a balance between program autonomy and user intervention, in recognition of the variability in electrophoretic gel quality and users' analytical needs.

Computer Peripherals↗

PubMed1987

Further evidence of dimer-tetramer transition in hemoglobin from Liophis miliaris.

Liophis miliaris hemoglobins in the stripped form exhibit a high oxygen affinity, a small alkaline Bohr effect, a pronounced organic polyphosphate effect and a pH-dependent Hill coefficient, close to 2 below pH 7.5 and near 1 at higher pHs. Molecular weight determinations indicate 2 forms, a dimeric form of MW 32000 d. and a tetrameric form of about 64000 d. The deoxyhemoglobin is tetrameric. Ion-exchange chromatography shows two components which may bind to each other being eluted as a single component of MW 32000 d. The oxygen alkaline Bohr effect observed for the stripped hemoglobin may be explained by the transition from the tetramer to the dimer during oxygen addition experiments. The phenomenon appears to be unique among animals. beta-Chain sequencing determinations show that abnormal human hemoglobin with similar properties has a glutamic acid residue substituted at the alpha 1-beta 2 interface by valine in snake hemoglobin.

Animals↗

PubMed1989

Orthogonal arrays of particles in plasma membranes of Müller cells in the guinea pig retina.

Plasma membranes of guinea pig Müller cells were examined with a freeze-fracture technique to see how orthogonal arrays are distributed in the avascular retina. Examination of the portion approximately intermediate between the optic disc and equator of the eyeball showed that all end-feet of Müller cells were provided with arrays. Orthogonal arrays were concentrated on vitreal end-foot membranes, i.e., membranes that were covered by the basal lamina and contacted the vitreous body, called vitreal membranes here. The arrays were rarely observed in the portions of end-feet that did not contact the vitreous body, called lateral membranes. The distribution density of arrays in the vitreal membranes was 122.5 +/- 45.3/microns2, which was over 10 times higher than that (9.6 +/- 9.6/microns2) in the lateral membranes. The arrays became numerous and extended in shape at the periphery of the vitreal membrane, characteristically aligned in rows at the border where vitreal met lateral membrane, but never intruded into the domain of lateral membrane. Some arrays were composed of loosely attached particles and/or rod-like profiles. Sometimes rod-like profiles, 9-13 nm wide and 20-50 nm long, called linear structures here, were isolated, and sometimes they appeared in rows. Ordinary intramembrane particles (IMPs) were significantly smaller and less numerous in vitreal than in lateral membranes. IMPs larger than 9 nm in diameter were significantly fewer in the vitreal membranes, which suggests that they have been consumed to form the arrays. Although the distribution of orthogonal arrays is similar to that of K+ channels (Newman: J. Neurosci., 7:2423-2432, 1987), we consider the array an unlikely candidate for the ion channel, because its subunit particles do not protrude onto either the inner or outer surface of the membrane (Gotow and Hashimoto: J. Neurocytol., 17:399-413, 1988). Judging from their unique alignment in rows where the membrane is bent and vitreal and lateral membranes meet, the arrays may contribute to some membrane stability, resisting the physical tension at the interface with mesenchymal tissue.

Animals↗

PubMed1989

Urea-induced inactivation, dissociation, and unfolding of the allosteric phosphofructokinase from Escherichia coli.

The influence of urea on the allosteric phosphofructokinase from Escherichia coli has been studied by measuring the changes in enzymatic activity, protein fluorescence, circular dichroism, and retention in size-exclusion chromatography. Tetrameric, dimeric, and monomeric forms of the protein can be discriminated by their elution from a high-performance liquid chromatography gel filtration column. Three successive steps can be detected during the urea-induced denaturation of phosphofructokinase: (i) the dissociation of the native tetramer into dimers which abolishes the activity; (ii) the dissociation of dimers into monomers which exposes the unique tryptophan, Trp-311, to the aqueous solvent; (iii) the unfolding of the monomers which disrupts most of the secondary structure. This pathway involves the ordered dissociation of the interfaces between subunits and supports a previous hypothesis (Deville-Bonne et al., 1989). Phosphofructokinase can be quantitatively renatured from urea solutions, provided that precautions are taken to avoid the aggregation of one insoluble monomeric state. The renaturation of phosphofructokinase from urea implies three steps: an initial folding reaction within the monomeric state is followed by two successive association steps. The faster association step restores the native fluorescence, and the slower regenerates the active enzyme. The renaturation and denaturation of phosphofructokinase correspond to the complex pathway: tetramer in equilibrium dimer in equilibrium folded monomer in equilibrium unfolded monomer. It is found that the subunit interface which forms the regulatory site is more stable and associates 40 times more rapidly than the subunit interface which forms the active site.

Allosteric Regulation↗

PubMed1986

Spread monolayers of proteins.

The study of spread monolayers of proteins is of interest for understanding the fundamental behavior of proteins as well as the many phenomena resulting from their ubiquitous presence at interfaces in nature. Spread monolayers of proteins is a branch of the developing field of membrane mimetic chemistry. In recent times, it has been somewhat neglected in comparison to other branches (such as bilayers, liposomes and vesicles), despite the unique advantage that the arrangement and packing of molecules in monolayers may be measured and controlled. Methods for spreading proteins and techniques used for their manipulation are outlined. As well as the more traditional methods (such as surface pressure, potential and viscosity), more recent innovations, including removal of monolayers on slides for study by radiotracer techniques, electron diffraction and infrared (IR) spectroscopy, are discussed. Direct optical methods for the study of monolayers in situ are also available (e.g., multiple reflectance spectroscopy, ellipsometry). The use of measurements in the low pressure region to measure molecular weights is discussed. At higher pressures, configurational changes, surface coagulation and desorption are all observed. Experimental and theoretical work on the desorption of proteins from the air/water interface is reviewed. The introduction of multicompartment film balances has proved valuable for the study of reactions occurring in monolayers. This instrumentation has been applied to the study of enzyme reactions at the surface, of direct relevance to reactions where the enzyme is immobilized in the cell membrane. Some applications of monolayer studies are briefly illustrated with reference to biological membranes, foams and emulsions and biomedical problems.

Protein Conformation↗

PubMed2026

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases.

MOTIVATION: Epigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. RESULTS: We developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG- searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. AVAILABILITY AND IMPLEMENTATION: The eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

DNA methylation↗

PubMed1975

Community mental health and the community college.

This paper represents one solution to the present mental health dilemma facing today's colleges and universities--static or declining services in the face of increased student needs. What is unique to this solution is that it developed out of a collaborative interaction between a community college and a prototype of a community mental health center in the same geographical area. Multiple interfaces between systems and various members within these systems were established in an effort to provide improved mental health services and the training of all personnel so involved to a higher level of professional functioning.

Community Mental Health Services↗

PubMed1985

Environmental modulation of the expression of differentiation and malignancy in six human squamous cell carcinoma cell lines.

Cell lines from six human squamous cell carcinomas exhibiting different degrees of differentiation and malignancy were studied under in vitro and in vivo growth conditions. The stability of phenotypic traits of these carcinoma cells and their sensitivity to environmental influences were analyzed to further elucidate the interdependency of differentiation and malignancy expressed under experimental conditions. In conventional (submerged) cultures the cell lines exhibited unique growth patterns with an individual but generally poor expression of differentiation (stratification). In a new organotypical culture assay where the cells grew on lifted collagen gels at the air-medium interface, three-dimensional structures were formed exhibiting organizational features and degrees of differentiation similar to those of the respective tumors. Both in tumors formed after s.c. injection of cells and in transplants (performed with silicone chambers on the dorsal muscle fascia) in nude mice, an enhancement of the individually distinct pattern of differentiation was observed. While anchorage independent growth was an unreliable marker for malignancy, all six lines were tumorigenic after s.c. injection into nude mice. However, the tumor yield (20 to 100%) and latency period (2 to 12 weeks) varied considerably. In contrast all lines exhibited (within 1 to 2 weeks) invasive growth in 100% of animals after transplantation onto the dorsal muscle fascia. All tumors (squamous carcinomas) and invading cells were identified as epithelial and as human by specific antibodies. The two new test systems, the organotypical culture assay in vitro and the transplantation assay in vivo, proved to be reliable and sensitive models also for human squamous carcinoma cells to analyze their differentiative and malignant potential. In comparing the individually maintained degrees of differentiation and malignancy in the different test systems, it was apparent that, opposite to the prevailing opinion, cell lines with the highest differentiation potential were at least as malignant as were the least differentiated ones.

Animals↗

PubMed2026

Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.

MOTIVATION: The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used separate database instances and backend technologies to manage integrated phenotypic and genotypic data. RESULTS: We discuss the challenges encountered when integrating dispersed data to serve through a single interface such as the Plant Breeding Application Programming Interface, BrAPI. We examine how the consistent mappability of genebank data to the BrAPI model can enable the implementation of effective services. The advantages of BrAPI in transparently linking distributed data entities through embedded, unique identifiers are highlighted. We present a technical solution involving a BrAPI proxy, which combines and merges separate BrAPI endpoints. Finally, we demonstrate the AGENT BrAPI implementation with an illustrative example that validates a suggested SNP for a trait from the literature by linking phenotypic, genotypic and passport data. AVAILABILITY AND IMPLEMENTATION: The BrAPI proxy implementation and documentation is available at the Python Package Index (https://pypi.org/project/brapi-proxy) and archived in Zenodo (doi: 10.5281/zenodo.19436445). SUPPLEMENTARY INFORMATION: A Jupyter Notebook file for the validation example using a marker-trait relationship found in the literature.

Phenotype↗

PubMed1987

The role of secretory granules in peptide biosynthesis.

There are many events in the posttranslational processing of bioactive peptides that occur in secretory granules and not to any great extent in other cellular organelles and that do not appear as modifications of the structure of many conventional neurotransmitters. In addition, at least two very important steps are unique to peptide-containing granules: (1) the peptides must begin their trek to the secretory granule in the RER as a larger precursor, rather than being taken up as a finished or nearly finished product into a mature granule; (2) there is at least one crucial sorting step on the way from the RER to the secretory granule that must occur faithfully before the peptide correctly appears in the granule. As for small molecules such as the catecholamines, the posttranslational processing enzymes and any required cofactors must also be put into the granules if the final events of processing are to occur with fidelity. Many of the posttranslational processing enzymes are only beginning to be identified. It is clear from these studies on purified PAM and peptide alpha-amidation as it occurs in cells that correlating test tube studies with the functioning of secretory granules is a worthwhile, if difficult, pursuit. The unique milieu inside the granule is difficult to mimic in a test tube. Transfection of peptide-producing cells with cDNAs encoding precursors with specific alterations in processing sites offers perhaps the best way to interface the studies of secretory granules and the posttranslational processing enzymes that mediate those functions.

Animals↗

PubMed1991

Information retrieval using a "digital book shelf".

WALT (Washington University's Approach to Lots of Text), is a prototype interface designed to support information retrieval research. The WALT interface serves as a "front end" to a wide array of retrieval engines including those based on Boolean retrieval, latent semantic indexing, term frequency--inverse document frequency, and Bayesian inference techniques. The WALT interface is composed of seven distinct components: a document examination component known as the Document Browsing Area; four navigation components called the Book Shelf, the Book Spine, the Table of Contents, and the Path Clipboard; a term-based information retrieval component called Control Panel; and a relevance feedback component known as the Reader Feedback Panel. WALT's most unique feature may be it's use of "book shelf" and "book spine" metaphors both to facilitate navigation and to provide a histogram-based display showing documents deemed appropriate for answering user queries.

Books↗

PubMed1981

Molecular considerations relevant to the mechanism of active transport.

A small group of closely related proteins is responsible for all active transport in animal cells, and inorganic cations are the only substances transported by these enzymes. They share a common kinetic mechanism in which two fundamental conformations participate, each receiving and dispatching substrates from its unique side of the membrane. During transport, the cations must pass through their enzyme to cross the membrane and intense interest is currently focused on the possibility that the path which they follow lies within the interface between two discrete subunits in a dimeric structure. Although 'half-of-sites' behaviour, consistent with this hypothesis, has been reported, it is now known that systematic errors were responsible for this mistaken conclusion. The number of protomers which comprise a functional unit of active transport has not been determined.

Adenosine Triphosphatases↗

PubMed1970

Bilateral symmetry in morphogenesis of embryos.

It is suggested that differentiated embryonic cells have a high specificity of molecular constitution as regards the surface layers surrounding their cellular membranes. Correspondingly, specific interface energies may characterize the early contacts between different cell types. The question is raised whether the morphology of the developing embryo may be understood in terms of cellular arrangements which minimize the total interface energy. Bilateral symmetry prevalent in early embryonic development of higher animals might be understood on the basis of the adoption of such a minimum energy principle if, in addition, one assumes that embryonic development is uniquely determined for a particular species.

Embryology↗

PubMed1989

Refined atomic model of glutamine synthetase at 3.5 A resolution.

An atomic model of 43,692 non-hydrogen atoms has been determined for the 12-subunit enzyme glutamine synthetase from Salmonella typhimurium, by methods of x-ray diffraction including restrained least-squares atomic refinement against 65,223 unique reflections. At 3.5 A resolution the crystallographic R-factor (on 2 sigma data) is 25.8%. As reported earlier for the unrefined structure, the 12 subunits are arranged in two layers of six; at the interface of pairs of subunits within each layer, cylindrical active sites are formed by six anti-parallel beta strands contributed by one subunit and two strands by the neighboring subunit. This interpretation of the electron density map has now been supported by comparison with glutamine synthetase from Escherichia coli by the Fourier difference method. Each active site cylinder holds two Mn2+ ions, with each ion having as ligands three protein side chains and two water molecules (one water shared by both metals), as well as a histidyl side chain just beyond liganding distance. The protein ligands to Mn2+ 469 are Glu-131, Glu-212, and Glu-220; those to Mn2+ 470 are Glu-129, His-269, and Glu-357. The two layers of subunits are held together largely by the apolar COOH terminus, a helical thong, which inserts into a hydrophobic pocket formed by two neighboring subunits on the opposite ring. Also between layers, there is a hydrogen-bonded beta sheet interaction, as there is between subunits within a ring, but hydrophobic interactions account for most of the intersubunit stability. The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."

Binding Sites↗

PubMed1991

Ultrasonographic diagnosis of chondromalacia of the femoropatellar joint.

In 35 patients suffering from femoropatellar arthralgia, ultrasound of the cartilage at the femoral side of the FP joint and double contrast computed arthrotomography were obtained. The criteria for chondromalacia in these examination techniques are discussed. In US the sharpness of the cartilage-bone interface and the relative reflectivity of the quadriceps tendon in comparison to the cartilage appeared to be relevant. US seemed to be a very specific technique in comparison with double contrast ARCT, but those patients with unique degeneration of the cartilage of the patella were missed with US (22%). Because US is a non-invasive, cheap and widely available procedure, we believe that US is a very useful screening procedure in the approach of the patient suspected of chondromalacia.

Adolescent↗

PubMed1975

A morphological study of anaerobic bacteria from the hypolimnia of two Michigan lakes.

Dense populations of anaerobic bacteria were found sequentially layered below the thermocline in two eutrophic lakes in southwest Michigan. Phase and electron microscopy of whole cells and thin sections were used to reveal the in situ morphology of the dominant members of the community. The predominant chlorophyll-containing bacteria were identified on the basis of their morphology to be members of the genera Pelodictyon, Prosthecochloris, Clathrochloris, Chlorochromatium, Pelochromatium, Thiopedia, Thiocystis, Thiospirillum, and Chromatium. The natural morphology of these organisms is described and compared with the morphology of reported isolates, the morphology of unisolated genera was compared with previous descriptions of natural samples. Most of the organisms near the sediment-water interface and two from the upper hypolimnion have not been previously described. They have been divided into six distinct groups based on morphology; the morphological features of each group are presented. This approach, based on the morphological uniqueness of the procaryotes present, provides a satisfactory method for grouping members of the hypolimnetic community for ecological studies.

Anaerobiosis↗