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5' splice site mutations in tau associated with the inherited dementia FTDP-17 affect a stem-loop structure that regulates alternative splicing of exon 10.

Missense and splice site mutations in the microtubule-associated protein tau gene were recently found associated with fronto-temporal dementia and parkinsonism linked to chromosome 17 (Poorkaj et al. (1998) Ann. Neurol. 43, 815-825; Hutton et al. (1998) Nature 393, 702-705; Spillantini et al. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 7737-7741). The mutations in the 5' splice site of exon 10 were shown to increase the ratio of tau mRNAs containing exon 10 and thus the proportion of Tau protein isoforms with 4 microtubule binding repeat domains, although how this increase leads to neurodegeneration is presently unclear. The mechanism by which these mutations increase tau exon 10 splicing was not determined, although the mutations were predicted to disrupt a potential stem-loop structure that was likely involved in the regulation of exon 10 alternative splicing. Here we describe in vitro splicing assays and RNA structural analysis that demonstrate that the mutations do indeed act through disruption of the stem-loop structure and that the stability of this secondary structure feature at least partially determines the ratio of tau exon 10+/- transcripts. In addition, we provide evidence that the stability of the stem-loop structure underlies the alternative splicing of this exon in other species.

Alternative Splicing↗

The unusual stability of the IS10 anti-sense RNA is critical for its function and is determined by the structure of its stem-domain.

IS10 transposition is regulated by an approximately 70 nt anti-sense RNA, RNA-OUT. RNA-OUT folds into a duplex 'stem-domain' topped by a loosely paired 'loop-domain'. The loop-domain is critical for RNA-RNA pairing per se; pairing initiates by interaction of the RNA-OUT loop with the 5' end of the target mRNA. We show here that RNA-OUT is unusually stable in vivo (half-life 60 min) and that this stability is conferred by specific features of the RNA-OUT stem-domain. One critical feature is stable base-pairing: mutations that disrupt stem pairing destabilize RNA-OUT in vivo and abolish anti-sense control; combinations of mutations that restore pairing also restore both stability and control. We propose that the stem renders RNA-OUT resistant to 3' exoribonucleases. Other features of the stem-domain prevent this essential duplex from being an effective substrate for double-strand nucleases: two single base mutations disrupt antisense control by making RNA-OUT susceptible to RNase III. Mutations in the loop region have little effect on RNA-OUT stability. Implications for IS10 biology and the design of efficient anti-sense RNAs are discussed.

Bacteriophage lambda↗

Protein-protein interaction: an analysis by computer simulation.

A survey of protein-protein interactions in structures derived by X-ray crystallography of protease-inhibitor and antigen-antibody complexes shows that they form close-packed interfaces from which water is excluded. The interfaces are of almost constant size, and they contain about ten hydrogen bonds. These features account for the stability of the complexes. To test whether they also account for specificity, we designed a computer simulation that searches for complementary surfaces on two protein molecules. In all cases tested, the simulation finds a number of complexes having interfaces and hydrogen bonds equivalent to those of the native complexes. These artificial complexes might represent secondary specificities, which can be detected when normal association is prevented by mutation or other means.

Computer Simulation↗

Large-scale gene expression profiling reveals major pathogenetic pathways of cartilage degeneration in osteoarthritis.

OBJECTIVE: Despite many research efforts in recent decades, the major pathogenetic mechanisms of osteoarthritis (OA), including gene alterations occurring during OA cartilage degeneration, are poorly understood, and there is no disease-modifying treatment approach. The present study was therefore initiated in order to identify differentially expressed disease-related genes and potential therapeutic targets. METHODS: This investigation consisted of a large gene expression profiling study performed based on 78 normal and disease samples, using a custom-made complementary DNA array covering >4,000 genes. RESULTS: Many differentially expressed genes were identified, including the expected up-regulation of anabolic and catabolic matrix genes. In particular, the down-regulation of important oxidative defense genes, i.e., the genes for superoxide dismutases 2 and 3 and glutathione peroxidase 3, was prominent. This indicates that continuous oxidative stress to the cells and the matrix is one major underlying pathogenetic mechanism in OA. Also, genes that are involved in the phenotypic stability of cells, a feature that is greatly reduced in OA cartilage, appeared to be suppressed. CONCLUSION: Our findings provide a reference data set on gene alterations in OA cartilage and, importantly, indicate major mechanisms underlying central cell biologic alterations that occur during the OA disease process. These results identify molecular targets that can be further investigated in the search for therapeutic interventions.

Aged↗

Perfusion flow bioreactor for 3D in situ imaging: investigating cell/biomaterials interactions.

The capability to image real time cell/material interactions in a three-dimensional (3D) culture environment will aid in the advancement of tissue engineering. This paper describes a perfusion flow bioreactor designed to hold tissue engineering scaffolds and allow for in situ imaging using an upright microscope. The bioreactor can hold a scaffold of desirable thickness for implantation (>2 mm). Coupling 3D culture and perfusion flow leads to the creation of a more biomimetic environment. We examined the ability of the bioreactor to maintain cell viability outside of an incubator environment (temperature and pH stability), investigated the flow features of the system (flow induced shear stress), and determined the image quality in order to perform time-lapsed imaging of two-dimensional (2D) and 3D cell culture. In situ imaging was performed on 2D and 3D, culture samples and cell viability was measured under perfusion flow (2.5 mL/min, 0.016 Pa). The visualization of cell response to their environment, in real time, will help to further elucidate the influences of biomaterial surface features, scaffold architectures, and the influence of flow induced shear on cell response and growth of new tissue.

Animals↗

Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains.

The 5' region of HIV-1 RNA contains functional elements involved in key steps of the retroviral cycle, such as genomic RNA transcription, splicing, translation, dimerization or initiation of reverse transcription. In the present work, we investigated the conformation of the first 500 nucleotides covering the RNA leader and the 5' gag coding sequences of HIV-MAL, using chemical probing. We provide detailed information on almost each nucleotide at one of their Watson-Crick positions and on position N-7 of purines. Experiments were conducted on two in vitro transcribed RNA fragments (1 to 707 and 1 to 311). A secondary structure model was derived by combining the experimental data, computer predictions and sequence comparison. Under conditions favoring dimerization (high salt concentration), HIV-1 RNA folds into independent structural domains that can be related to defined functional regions. The first domain corresponds to TAR forming a stable stem-loop. Intrinsic structural features are found to stabilize the TAR hairpin loop. The second domain (nucleotides 56 to 299) contains the PBS sequence, which is located in a stable subdomain constrained by a four stem junction (nucleotides 139 to 218). Although the MAL isolate has an insertion near the PBS, probably resulting from the duplication of a 23-nucleotide sequence, the structural organization of this subdomain is conserved in all other HIV-1 isolates. The third domain (nucleotides 300 to 404) contains the splice donor site, packaging and dimerization elements and the AUG initiation codon of gag. A major result is the structural versatility of this region. Two mutually exclusive structures, both equally in agreement with probing data, could modulate the different functions involving this domain. The reduced accessibility of the gag translational initiation site possibly accounts for the low efficiency of the in vitro translation of the dimer. Finally, the 5' gag coding sequences form a metastable domain.

Animals↗

Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex.

We have solved the structure of Escherichia coli cytidine deaminase (CDA) complexed to the transition state analog, 5-fluoroprimidin-2-one riboside. The monomer of the alpha 2 CDA dimer is composed of a small N-terminal alpha-helical domain with no obvious connection to the active sites, and two, larger, core domains. The two core domains have nearly identical tertiary structures and are related by approximate 2-fold symmetry, but lack internal amino acid sequence homology. Comparison of the core domain structure with known structures by sequence homology and structural compatibility searches suggests that the CDA tertiary structure cannot be superimposed on any known protein structure. The two active sites per dimer are formed across the subunit interface. The N-terminal core domain provides a pyrimidine nucleoside and zinc-binding pocket and the structurally homologous C-terminal core domain in the other monomer covers this active-site cleft, completely sequestering the ligand from solvent. The deeply buried zinc-binding site is formed by a novel "topological switch point" at the amino termini of two alpha-helices in consecutive alpha-beta-alpha-beta segments. The transition state analog is bound as a covalent hydrate at C4. The inhibitor hydroxyl oxygen atom interacts both with the zinc atom and the Glu104 carboxylate group, affording high differential affinity for the hydroxyl group relative to a hydrogen atom, in a manner reminiscent of that observed in adenosine deaminase (ADA). Unlike the latter enzyme, the zinc atom is coordinated in a tetrahedral ligand field to two cysteine and one histidine ligands, plus the hydroxyl group. Moreover, the inhibitor stereochemistry is of the opposite hand from that of the corresponding ADA inhibitor at C4(R), but is the same at the hydroxyl group O4(S). A consequence of these stereochemical differences is that in CDA a single conserved carboxylate side-chain, Glu104, can provide all of the necessary proton transfer functions involved in generating the zinc hydroxide nucleophile, and protonating the pyrimidine ring nitrogen atom and leaving amino group. The differences in zinc ligands, ligand-binding stereochemistry, and tertiary structures of CDA and ADA strongly suggest that the common features of transition state stabilization arose by convergent evolution.

Amino Acid Sequence↗

Naturally occurring antisense RNA control--a brief review.

Biological control by naturally occurring anti-sense RNAs has been documented in a number of prokaryotic cases, and strongly suggested in several eukaryotic systems. The biological activities controlled are diverse, including transposition, phage development, chromosomal gene expression, and plasmid replication, compatibility and conjugation. Control is exerted at many different levels, by both direct and long-range effects. The stem/loop structures common to all anti-sense RNAs are important functional domains: loops are the sites of critical interactions in the initiation of pairing to the target RNA; stems determine anti-sense RNA stability in vivo. These features need to be considered in the design of artificial anti-sense RNA control. Details of RNA/RNA pairing have emerged; pairing initiates at single-stranded regions in anti-sense RNA loops, and stable complex formation involves the nearby end of one or both molecules.

Base Sequence↗

Determination of serum cholinesterase activity and dibucaine numbers by an amperometric choline sensor.

Serum cholinesterase activity and the dibucaine numbers have been determined by using a hydrogen peroxide electrode and the enzyme choline oxidase immobilized on a nylon net. The analysis procedure is extremely simple and very fast allowing 30 cholinesterase determinations per hour. Both cholinesterase activity and dibucaine number measurements could be performed in 5 min and by using serum samples of only 10 microliters. When used in sera the probe showed no interference from electroactive compounds present in blood, and also showed good stability and reproducibility. These features make this sensor appropriate for continuous extracorporeal circuit blood monitoring of succinylcholine during surgery.

Alcohol Oxidoreductases↗

Cemented posterior stabilized total knee arthroplasty.

In the development of modern cemented total knee arthroplasty, the posterior stabilized knee prosthesis was designed to substitute for the function of the posterior cruciate ligament. Implant designs include the Insall Burstein posterior stabilized knee and the Legacy posterior stabilized knee. The primary feature of these prostheses is the femoral cam and tibial spine mechanism, which prevents posterior tibial subluxation and enhances knee kinematics. Another important feature is the relatively conforming round on round articular geometry that mitigates edge loading and reduces polyethylene damage. In concert, these features have produced a lineage of implants with unsurpassed clinical results, predictable kinematics and durability, which have been reproducible and well documented.

Arthroplasty, Replacement, Knee↗

Machine learning-enabled multi-omics discovery of prognostic biomarkers and signaling targets in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains difficult to subtype using single omics layers. We conducted an exploratory investigation integrating reverse-phase protein array (RPPA) and DNA methylation data from the cancer genome atlas (TCGA)- pancreatic adenocarcinoma (PAAD) to assess the feasibility of multi-omics subtyping, alongside a supervised machine learning analysis of a small gene expression omnibus (GEO) transcriptomic cohort (n = 26) to identify candidate diagnostic genes. RPPA-based K-means clustering suggested a weak, possible two-subtype structure (silhouette ≈ 0.16) that remained unassociated with overall survival (log-rank p = 0.113) and lacked independent prognostic value. An independently performed similarity network fusion (SNF) analysis integrating RPPA and methylation data showed low concordance with RPPA-derived subtypes (Adjusted Rand Index (ARI) = 0.014), indicating limited convergence between molecular modalities. Supervised machine learning analysis of the GEO cohort using a fully nested leave-one-out cross-validation pipeline achieved a mean (area under the curve) AUC of 0.896 across four classifiers and identified four-fold-stable candidate genes (ESCO2, COL17A1, BCL2L14, and SOWAHB). However, this gene panel demonstrated limited external validity across two independent PDAC cohorts (log-rank p = 0.438 for both GSE62452 and GSE28735), indicating limited generalizability despite robust internal performance. Collectively, these findings provide limited evidence for a robust, prognostically significant multi-omics subtype or a validated diagnostic gene signature; instead, this study serves as a hypothesis-generating resource and highlights the importance of rigorous cross-validation and independent external validation in small-sample transcriptomic biomarker discovery.

Humans↗

Common motifs and topological effects in the protein folding transition state.

Through extensive experiment, simulation, and analysis of protein S6 (1RIS), we find that variations in nucleation and folding pathway between circular permutations are determined principally by the restraints of topology and specific nucleation, and affected by changes in chain entropy. Simulations also relate topological features to experimentally measured stabilities. Despite many sizable changes in phi values and the structure of the transition state ensemble that result from permutation, we observe a common theme: the critical nucleus in each of the mutants share a subset of residues that can be mapped to the critical nucleus residues of the wild-type. Circular permutations create new N and C termini, which are the location of the largest disruption of the folding nucleus, leading to a decrease in both phi values and the role in nucleation. Mutant nuclei are built around the wild-type nucleus but are biased towards different parts of the S6 structure depending on the topological and entropic changes induced by the location of the new N and C termini.

Amino Acid Motifs↗

Measuring fluid and slurry density and solids concentration non-invasively.

Staff at Pacific Northwest National Laboratory have developed a highly sensitive, non-invasive, self-calibrating, on-line sensor to measure the density, speed of sound, and attenuation of ultrasound for a liquid or slurry flowing through a pipeline; the approach can also be applied for measurements made in vessels. The sensor transducers are mounted directly upon the stainless steel wall and the pipeline wall becomes part of the measurement system. Multiple reflections within the stainless steel wall are used to determine the acoustic impedance of the liquid, where the acoustic impedance is defined as the product of the density and the speed of sound. The probe becomes self-calibrating because variations in the pulser voltage do not affect the measurements. This feature leads to the stability of the measurements and the instrument requires much less time and effort to calibrate. Further, the calibration remains constant in time, because it does not depend upon the pulser voltage remaining at a given value. By basing the measurement upon multiple reflections, the sensitivity of the measurement is significantly increased. For slurries with wt% solids concentration of 1% or less, high sensitivity is gained by analyzing attenuation measurements obtained from multiple paths through the slurry. For slurries with higher concentrations of solids, sufficient sensitivity is obtained by analyzing data from a simple transmission. Data are presented that show probe performance for each of these cases: very dilute and highly concentrated kaolin clay slurries.

Journal Article↗

Evolution of cooperation: cooperation defeats defection in the cornfield model.

"Cooperation" defines any behavior that enhances the fitness of a group (e.g. a community or species), but which, by its nature, can be exploited by selfish individuals, meaning, firstly, that selfish individuals derive an advantage from exploitation which is greater than the average advantage that accrues to unselfish individuals. Secondly, exploitation has no intrinsic fitness value except in the presence of the "cooperative behavior". The mathematics is described by the simple Prisoner's Dilemma Game (PDG). It has previously been shown that koinophilia (the avoidance of sexual mates displaying unusual or atypical phenotypic features, such as mutations) stabilizes any inherited strategy in the simple or iterated PDG, meaning that it cannot be displaced by rare forms of alternative behavior which arise through mutation or occasional migration. In the present model equal numbers of cooperators and defectors (in the simple PDG) were randomly spread in a two-dimensional "cornfield" with uniformly distributed resources. Every individual was koinophilic, and interacted (sexually and in the PDG tournaments) only with individuals from within its immediate neighborhood. This model therefore tested whether cooperation can outcompete defection or selfishness in a straight, initially equally matched, evolutionary battle. The results show that in the absence of koinophilia cooperation was rapidly driven to extinction. With koinophilia there was a very rapid loss of cooperators in the first few generations, but thereafter cooperation slowly spread, ultimately eliminating defection completely. This result was critically dependent on sampling effects of neighborhoods. Small samples (resulting from low population densities or small neighborhood sizes) increase the probability that a chance neighborhood comes to consist predominantly of cooperators. A sexual preference for the most common phenotype in the neighborhood then makes that phenotype more common still. Once this occurs cooperation's spread becomes almost inevitable.

Animals↗

Distinctive phonological features differ in relevance for both spoken and written word recognition.

This paper discusses four experiments on Dutch which show that distinctive phonological features differ in their relevance for word recognition. The relevance of a feature for word recognition depends on its phonological stability, that is, the extent to which that feature is generally realized in accordance with its lexical specification in the relevant word position. If one feature value is uninformative, all values of that feature are less relevant for word recognition, with the least informative feature being the least relevant. Features differ in their relevance both in spoken and written word recognition, though the differences are more pronounced in auditory lexical decision than in self-paced reading.

Humans↗

Exploring hyperthermophilic proteins under pressure: theoretical aspects and experimental findings.

Proteins from hyperthermophilic microorganisms are generally capable of withstanding temperatures close to, or even higher than the boiling point. As a rule, these proteins are strongly piezostable as well, although exceptions have been also reported. This observation has a theoretical relevance, as the understanding of the effects of pressure and temperature on protein stability is equally important to develop a comprehensive model for their thermodynamic stability. Nevertheless, the structural features justifying the correlation between heat resistance and pressure resistance are poorly understood. Actually, most reports do not exceed the phenomenological level. Only in the case of the small protein Sso7d from Sulfolobus solfataricus, characterisation of wild-type and some mutants showed that both properties are largely accounted for by a network of aromatic residues found in the hydrophobic core of the molecule. Current knowledge, however, does not allow to establish to what extent this finding may be generalised. In a biotechnological perspective, hyperthermophilic enzymes seem to be more suitable for bioprocesses at high pressure with respect to their mesophilic counterparts. Indeed, thanks to their higher resistance towards pressure and temperature, they may be exploited in a much broader range of working conditions for tuning activity and specificity. Furthermore, they are often activated by increasing pressure, although it cannot be established, to date, to what extent this is a common feature.

Archaeal Proteins↗

Hydrophobicity--getting into hot water.

In his famous 1959 review, Walter Kauzmann clarified important features of the thermodynamic stabilities of proteins. The hydrophobic effect is recognised as an important contributor to the stability of proteins and an important determinant of their structural patterns. As generally understood, it depends on the unusual properties of cold water and its interactions with nonpolar solutes. Here we comment on the relationship between this paradigm and the stabilities and structures of proteins from thermophilic organisms.

Archaeal Proteins↗

Revision total knee arthroplasty using the porous-coated anatomic revision prosthesis: six- to twelve-year results.

The porous-coated anatomic (PCA) revision prosthesis was one of the earliest revision total knee systems to feature more constraint for stability, stems for fixation, and thicker femoral components to address bone loss. From 1981 to 1989, 36 revision total knee arthroplasties were performed using the PCA prosthesis. Patients were evaluated by clinical examination, radiographs, and the Hospital for Special Surgery Knee Rating Scale. Six patients died and three were lost to follow-up; 27 knees remained for follow-up. The average age at surgery was 66 years. Follow-up averaged 9.8 years (range, 6-12.4 years). Range of motion averaged 4 degrees to 91 degrees before surgery and 1 degrees to 92 degrees after surgery. Knee scores averaged 48 before surgery and 86 after surgery. Three femoral and 10 tibial components showed lucent lines, with 3 tibial components showing progressive lucency. Six patients required reoperation: 3 for tibial component loosening, 1 for wound infection, 1 for deep infection, and 1 for persistent pain. These results suggest that the use of an implant specifically designed for revision can yield successful long-term results.

Adult↗