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MCL1 is phosphorylated in the PEST region and stabilized upon ERK activation in viable cells, and at additional sites with cytotoxic okadaic acid or taxol.

BCL2 family members are subject to regulation at multiple levels, providing checks on their ability to contribute to tumorigenesis. However, findings on post-translational BCL2 phosphorylation in different systems have been difficult to integrate. Another antiapoptotic family member, MCL1, exhibits a difference in electrophoretic mobility upon phosphorylation induced by an activator of PKC (12-O-tetradecanoylphorbol 13-acetate; TPA) versus agents that act on microtubules or protein phosphatases 1/2A. A multiple pathway model is now presented, which demonstrates that MCL1 can undergo distinct phosphorylation events - mediated through separate signaling processes and involving different target sites - in cells that remain viable in the presence of TPA versus cells destined to die upon exposure to taxol or okadaic acid. Specifically, TPA induces phosphorylation at a conserved extracellular signal-regulated kinase (ERK) site in the PEST region (Thr 163) and slows turnover of the normally rapidly degraded MCL1 protein; however, okadaic acid and taxol induce ERK-independent MCL1 phosphorylation at additional discrete sites. These findings add a new dimension to our understanding of the complex regulation of antiapoptotic BCL2 family members by demonstrating that, in addition to transcriptional and post-transcriptional regulation, MCL1 is subject to multiple, separate, post-translational phosphorylation events, produced in living versus dying cells at ERK-inducible versus ERK-independent sites.

Amino Acid Sequence↗

Feedback dynamics and cell function: Why systems biology is called Systems Biology.

A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

Computational Biology↗

People into Employment: supporting people with disabilities and carers into work.

Carers and people with disabilities are two disadvantaged groups at risk of social exclusion. Work is an important route to social inclusion, but carers and people with disabilities are under-represented in the work force. The present paper reports key findings from a new study that evaluated People into Employment (PIE), a pilot employment project in the north-east of England designed to support people with disabilities, carers and former carers in gaining mainstream work. The study aimed to identify what clients, partner agencies and employers perceived to be PIE's most important services, its strengths and areas where there was scope for further development. The study collected quantitative and qualitative data at the mid-point and at the end of the project through two questionnaire surveys, and interviews with PIE clients, the project development officer, partner agencies and employers. Drawing on the 'pathway model', the findings show that PIE's interventions included mobilising, matching, mediating and supporting activities. Key ingredients in PIE's success include: tailor-made job-search activities and training; adjusting the pace at which people move towards sustained employment; recognising and responding to the differing needs of people with disabilities, carers and former carers; confidence boosting; accompanying clients to job interviews; good job matching; and ongoing practical and emotional support for both clients and employers. Rudimentary calculations suggest that the cost per job to the project is less than the cost per job for large national projects. Overall, these findings illustrate how access to employment via flexible job-search services geared up to the local labour market can successfully promote social inclusion for carers and people with disabilities.

Adult↗

Is there a single pathway for the folding of a polypeptide chain?

We argue that folding of the compact domains of proteins can occur with adequate rapidity in the absence of a unique directed mechanism, provided that native-like local structure dominates the folding process. We further suggest that the evolution of amino acid sequences should favor multiple paths to the folded state. Existing physicochemical and mutational data are not inconsistent with a many-pathway model. The analogy of a jigsaw puzzle, with multiple routes to a unique solution, appears to be particularly apt.

Amino Acid Sequence↗

Role of proline peptide bond isomerization in unfolding and refolding of ribonuclease.

The isomerization of the proline peptide bond between tyrosine-92 and proline-93 in bovine pancreatic ribonuclease A has been investigated in the unfolded protein as well as during the slow refolding process. This bond is in the cis state in the native protein. By comparison of various homologous ribonucleases we show that isomerization of proline-93 is associated with a change in fluorescence of tyrosine-92. This provides a spectroscopic probe to monitor this process in the disordered chain after unfolding as well as its reversal in the course of slow refolding. In unfolded ribonuclease incorrect trans isomers of proline-93 are found in both slow-folding species. trans----cis reversal of isomerization of this proline peptide bond during refolding shows kinetics that are identical with the time course of formation of native protein. Isomerization of proline-93 is slower than the formation of a native-like folded intermediate that accumulates on the major slow refolding pathway. Models to explain these results are discussed.

Animals↗

Another factor besides hydrophobicity can affect signal peptide interaction with signal recognition particle.

Translocation of alkaline extracellular protease (AEP) into the endoplasmic reticulum of Yarrowia lipolytica is cotranslational and signal recognition particle (SRP)-dependent, whereas translocation of P17M AEP (proline to methionine at position 17, second amino acid in the pro-region) is posttranslational and SRP-independent. P17M signal peptide mutations that resulted in more rapid SRP-dependent translocation of AEP precursor were isolated. Most of these mutations significantly increased hydrophobicity, but the A12P/P17M mutation did not. The switch from SRP-dependent to SRP-independent translocation without a decrease in hydrophobicity (wild type to P17M) and restoration of SRP-dependent translocation without an increase in hydrophobicity (P17M to A12P/P17M) indicate that some factor(s) in addition to hydrophobicity determines selection of targeting pathway. Models of extended forms of wild type and A12P/P17M signal peptides are kinked, whereas the P17M signal peptide is relatively straight. Possibly the conformation/orientation of signal peptides at the ribosomal surface affects SRP binding and consequently the targeting route to the endoplasmic reticulum. Kinked signal peptides might approach SRP more closely more often. Most likely, these effects were only detectable because of the short length and low average hydrophobicity of the AEP signal peptide.

Ascomycota↗

Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence.

MOTIVATION: The Open Targets Platform (https://platform.opentargets.org) is a unique, comprehensive, open-source resource supporting systematic identification and prioritisation of targets for drug discovery. The Platform combines, harmonizes and integrates data from >20 diverse sources to provide target-disease associations, covering evidence derived from genetic associations, somatic mutations, known drugs, differential expression, animal models, pathways and systems biology. An in-house target identification scoring framework weighs the evidence from each data source and type, contributing to an overall score for each of the 7.8M target-disease associations. However, the old infrastructure did not allow user-led dynamic adjustments in the contribution of different evidence types for target prioritisation, a limitation frequently raised by our user community. Furthermore, the previous Platform user interface did not support navigation and exploration of the underlying target-disease evidence on the same page, occasionally making the user journey counterintuitive. RESULTS: Here, we describe 'Associations on the Fly' (AOTF), a new Platform feature-developed with a user-centred vision-that enables the user to formulate more flexible therapeutic hypotheses through dynamic adjustment of the weight of contributing evidence from each source, altering the prioritisation of targets. AVAILABILITY AND IMPLEMENTATION: The codebases that power the Platform-including our pipelines, GraphQL API, and React UI-are all open source and licensed under the APACHE LICENSE, VERSION 2.0. You can find all of our code repositories on GitHub at https://github.com/opentargets and on Zenodo at https://zenodo.org/records/14392214. This tool was implemented using React v18 and its code is accessible here: (https://github.com/opentargets/ot-ui-apps). The tools are accessible through the Open Targets Platform web interface (https://platform.opentargets.org/) and GraphQL API (https://platform-docs.opentargets.org/data-access/graphql-api). Data is available for download here: (https://platform.opentargets.org/downloads) and from the EMBL-EBI FTP: (https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/).

Software↗

pathSCOUT: exploration and analysis of biochemical pathways.

UNLABELLED: pathSCOUT provides access, display and exploration of data relevant to biochemical pathways, and enables analysis of pathway model structure and behavior. AVAILABILITY: pathSCOUT is available as a customized solution from contact@lionbioscience.com; limited evaluation access and additional information is available from http://simpath.lionbioscience.com:8080/documents/pathscout11/.

Biochemical Phenomena↗

Socioeconomic trajectories across the life course and health outcomes in midlife: evidence for the accumulation hypothesis?

BACKGROUND: Recent research in social epidemiology has established the importance of considering the accumulation of advantage and disadvantage across the life course when examining adult health outcomes. This paper examines (1) accumulation across trichotomous categories of socioeconomic position (SEP), and (2) accumulation in analysis stratified by adult SEP. METHODS: Data are from the Whitehall II study. Each participant was categorized as having high (0), intermediate (1), or low (2) SEP at three time points in the life course, leading to 27 socioeconomic trajectories. These trajectories were summarized to yield a scale ranging from 0 (high SEP at all three time points) to 6 (low SEP at all three time points). Logistic regression was used to examine odds of incident coronary heart disease (CHD), poor mental and physical functioning, and minor psychiatric disorder. RESULTS: There was a graded linear relationship between accumulation of socioeconomic exposure and health. Men with a score of 6 had increased odds of CHD (2.53, 95% CI: 1.3, 5.1), poor physical functioning (2.19, 95% CI: 1.4, 4.1), and poor mental functioning (2.60, 95% CI: 1.4, 4.9) compared with men with a score of 0. In women there was an accumulation effect for CHD and physical functioning. No cumulative effect of SEP on minor psychiatric disorder was observed. The effects of accumulation were weaker in analyses stratified by adult SEP, with early deprivation followed by high adult SEP particularly detrimental for CHD. CONCLUSIONS: The health effects of socioeconomic disadvantage accumulate over the life course. In addition to accumulation effects, analysis stratified by adult SEP also provided support for the critical period and the pathway model.

Adult↗

Compound dual radiation action theory for 252Cf brachytherapy.

The existing dosimetry protocol that uses the concept of RBE for 252Cf brachytherapy contains large uncertainties. A new formula has been developed to correlate the biological effect (i.e. cell survival fraction) resulting from a mixed n + gamma radiation field with two physical quantities and two biological quantities. The formula is based on a pathway model evolved from that of the compound-dual-radiation-action (CDRA) theory, previously proposed by Rossi and Zaider. The new model employs the recently published data on radiation-induced DNA lesions. The new formula is capable of predicting quantitatively the synergistic effect caused by the interactions between neutron events and gamma ray events, and it is intended to be included into a new dosimetry protocol for future 252Cf brachytherapy.

Algorithms↗

Internal dose following a major nuclear war.

The PATHWAY model results were used, in conjunction with a hypothetical major nuclear attack on the U.S., to arrive at the ratio of internal to external dose for humans from early (48 h) fallout. Considered were the four nuclides (137Cs, 89Sr, 90Sr, 131I) that account for most of the reconstructed whole-body committed equivalent dose from internal radiation in people who lived downwind of the Nevada Test Site during atmospheric tests. Effects of climate perturbations (the "nuclear winter" effect) on food crops were considered. These could increase internal dose estimates, depending on the severity of the climate perturbations. Internal and external doses to humans for 10 locations within the U.S. have been calculated, with varying local conditions and varying assumption about their shelters. The estimated 50-y internal dose commitment ranged from 0.0-0.17 Sv, the 48-h external dose from 0.15-4.6 Sv. The resultant ratios of internal to external committed dose received in the first months (until food transport was restored) varied from less than 0.01 to about 0.2. In all cases examined, the total dose from early fallout was found to be dominated by the external dose.

Humans↗

Transfer of 137Cs from soil to grass--analysis of possible sources of uncertainty.

On the basis of experimental data on the fallout of 137Cs from the Chernobyl accident, a statistical analysis was made of possible values of the coefficients of transfer via the soil-grass pathway. Model calculations of the possible radionuclide concentration in milk are performed by the Monte Carlo method using the probability distribution function obtained. It is shown that not only our limited knowledge and the possible diversity of the external conditions, but also the very nature of the phenomenon under consideration, make it desirable to switch from a deterministic to a stochastic formulation of the model. The fact that the dependence of the soil-to-grass radionuclide transfer coefficients on the initial concentration in soil might be non-linear in character is an indication of the limitation of the conventional linear model.

Accidents↗

Temperature effects on a whole metabolic reaction cannot be inferred from its components.

Changes in temperature affect the kinetic energy of the constituents of a system at the molecular level and have pervasive effects on the physiology of the whole organism. A mechanistic link between these levels of organization has been assumed and made explicit through the use of values of organismal Q10 to infer control of metabolic rate. To be valid this postulate requires linearity and independence of the isolated reaction steps, assumptions not accepted by all. We address this controversy by applying dynamic systems theory and metabolic control analysis to a metabolic pathway model. It is shown that temperature effects on isolated steps cannot rigorously be extrapolated to higher levels of organization.

Computer Simulation↗

Mlh1 is unique among mismatch repair proteins in its ability to promote crossing-over during meiosis.

In eukaryotes, homologs of the bacterial MutS and MutL proteins function in DNA mismatch repair and recombination pathways. The mutL homolog MLH1 is required for nuclear mismatch repair. Previously, cytological analysis of MLH1-deficient mice has implied a role for Mlh1 in crossing-over during meiosis. Here we demonstrate that Saccharomyces cerevisiae diploids containing a deletion of MLH1 have reduced crossing-over in addition to a deficiency in the repair of mismatched DNA during meiosis. Absence of either of the meiosis-specific mutS homologs Msh4 or Msh5 results in a similar reduction in crossing-over. Analysis of an mlh1 msh4 double mutant suggests that both genes act in the same pathway to promote crossing-over. All genetic markers analyzed in mlh1 mutants display elevated frequencies of non-Mendelian segregation. Most of these events are postmeiotic segregations that represent unrepaired heteroduplex. These data suggest that either restorational repair is frequent or heteroduplex tracts are shorter in wild-type cells. Comparison of mlh1 segregation data with that of pms1, msh2, msh3, and msh6 mutants show that the ability to promote crossing-over is unique to MLH1. Taken together these observations indicate that both crossing-over and gene conversion require MutS and MutL functions and that Mlh1 represents an overlap between these two pathways. Models of Mlh1 function are discussed.

Adaptor Proteins, Signal Transducing↗

Platelet activating factor, lyso-platelet activating factor and arachidonic acid release in normal human skin and the influence of topical steroid treatment.

1. Previous, in vitro, studies have established the synthesis of platelet activating factor (PAF) by the 're-modelling' pathways in which the activation of a phospholipase A2 (PLA2) enzyme catalyses the hydrolysis of an ether-acyl-phosphocholine to give concomitant release of lyso-PAF, the immediate precursor of PAF, and arachidonic acid, the precursor of the icosanoids. The aim of this study was to investigate the relationship between PAF and eicosanoid release in human skin, and to study the effect of treatment of skin with a topical steroid, on the release of PAF, lyso-PAF and arachidonic acid. 2. A novel assay procedure was developed for the simultaneous assay of PAF and lyso-PAF in skin exudates from abrasions and suction blisters in normal human skin. In addition we assayed arachidonic acid and prostaglandin E2 (PGE2), a representative eicosanoid. 3. The mean amounts of mediator recovered in the first 30 min period following abrasion were PAF 0.43, lyso-PAF 11.9, PGE2 25.7 and arachidonic acid 760 pmol/sample. The molar ratio of PAF:lyso-PAF:arachidonic acid in skin exudates from abrasions was 1:30:1800 and in suction blister exudates was 1:90:3660. 4. Time course studies showed a decline in the recoveries of arachidonic acid and lyso-PAF, of about 50% in 2 h. In contrast, PAF was recovered in exudates at a constant rate over 2 h but PGE2 release decreased by more than 90% after the initial 30 min period. 5. Topical application under occlusion, of 0.05% clobetasol propionate, a potent corticosteroid, significantly reduced lyso-PAF by 30% in suction blister exudates but did not significantly alter the concentrations of PAF or arachidonic acid.(ABSTRACT TRUNCATED AT 250 WORDS)

Administration, Topical↗

The Pun1 gene for pungency in pepper encodes a putative acyltransferase.

Pungency in Capsicum fruits is due to the accumulation of the alkaloid capsaicin and its analogs. The biosynthesis of capsaicin is restricted to the genus Capsicum and results from the acylation of an aromatic moiety, vanillylamine, by a branched-chain fatty acid. Many of the enzymes involved in capsaicin biosynthesis are not well characterized and the regulation of the pathway is not fully understood. Based on the current pathway model, candidate genes were identified in public databases and the literature, and genetically mapped. A published EST co-localized with the Pun1 locus which is required for the presence of capsaicinoids. This gene, AT3, has been isolated and its nucleotide sequence has been determined in an array of genotypes within the genus. AT3 showed significant similarity to acyltransferases in the BAHD superfamily. The recessive allele at this locus contains a deletion spanning the promoter and first exon of the predicted coding region in every non-pungent accession tested. Transcript and protein expression of AT3 was tissue-specific and developmentally regulated. Virus-induced gene silencing of AT3 resulted in a decrease in the accumulation of capsaicinoids, a phenotype consistent with pun1. In conclusion, gene mapping, allele sequence data, expression profile and silencing analysis collectively indicate that the Pun1 locus in pepper encodes a putative acyltransferase, and the pun1 allele, used in pepper breeding for nearly 50 000 years, results from a large deletion at this locus.

Acyltransferases↗

Cost minimization analysis of antiepileptic drugs in newly diagnosed epilepsy in 12 European countries.

A recent United Kingdom cost minimization analysis (CMA) of four antiepileptic drugs (AEDs) used to treat newly diagnosed adult epilepsy demonstrated that a new drug, lamotrigine (LTG), incurred higher costs than carbamazepine (CBZ), phenytoin (PHT), and valproate (VPA), whose costs were similar. This analysis took account of each drug's side-effect and tolerability profile. The present analysis investigated the costs of treatment with LTG, CBZ, PHT, and VPA in 12 European countries. Data were derived from published sources and from a panel of locally based experts. When no published data were available, estimates were obtained using expert opinion by a consensus method. These data were incorporated into a treatment pathway model, which considered the treatment of patients during the first 12 months after diagnosis. The primary outcome considered was seizure freedom. Randomized controlled trials demonstrate that the drugs considered are equally effective in terms of their ability to achieve seizure freedom, and thus the most appropriate form of economic evaluation is a CMA. These trials provided data on the incidence of side effects, dosages, and retention rates. The economic perspective taken was that of society as a whole and the analysis was calculated on an "intent-to-treat" basis. Only direct medical costs were considered. In each country considered, LTG was twofold to threefold more expensive than the other drugs considered. A sensitivity analysis demonstrated that varying each of the assumptions (range defined by expert panels) did not significantly alter the results obtained.

Anticonvulsants↗

Computational processing and error reduction strategies for standardized quantitative data in biological networks.

High-quality quantitative data generated under standardized conditions is critical for understanding dynamic cellular processes. We report strategies for error reduction, and algorithms for automated data processing and for establishing the widely used techniques of immunoprecipitation and immunoblotting as highly precise methods for the quantification of protein levels and modifications. To determine the stoichiometry of cellular components and to ensure comparability of experiments, relative signals are converted to absolute values. A major source for errors in blotting techniques are inhomogeneities of the gel and the transfer procedure leading to correlated errors. These correlations are prevented by randomized gel loading, which significantly reduces standard deviations. Further error reduction is achieved by using housekeeping proteins as normalizers or by adding purified proteins in immunoprecipitations as calibrators in combination with criteria-based normalization. Additionally, we developed a computational tool for automated normalization, validation and integration of data derived from multiple immunoblots. In this way, large sets of quantitative data for dynamic pathway modeling can be generated, enabling the identification of systems properties and the prediction of targets for efficient intervention.

Algorithms↗