Endogenous pain pathways: applications to pain control in dental practice.
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Acupuncture Therapy↗
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Results for “Biologic pathways”
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Coordinating ERK/MAPK signalling through scaffolds and inhibitors.
The pathway from Ras through Raf and MEK (MAPK and ERK kinase) to ERK/MAPK (extracellular signal-regulated kinase/mitogen-activated protein kinase) regulates many fundamental cellular processes. Recently, a number of scaffolding proteins and endogenous inhibitors have been identified, and their important roles in regulating signalling through this pathway are now emerging. Some scaffolds augment the signal flux, but also mediate crosstalk with other pathways; certain adaptors target MEK-ERK/MAPK complexes to subcellular localizations; others provide regulated inhibition. Computational modelling indicates that, together, these modulators can determine the dynamic biological behaviour of the pathway.
Adaptor Proteins, Signal Transducing↗
[The dynamics and its clinical significance of complement system, especially alternative pathway related to normal human pregnancy, delivery, puerperium and fetus (author's transl)].
The author studied human complement system, especially alternative pathway as a primitive biological defense system, in maternal serum during normal pregnancy, delivery and puerperium. The results obtained were as follows. 1. The mean value of hemolytic activity of alternative pathway (AlCH50) in healthy women was 18.3 +/- 1.1. This value was increased gradually in progress of gestational stages up to 26.6 +/- 2.3 of the average in the last trimester. Stochastically, significant differences about this value was noted between in the first trimester and in the last. This AlCH50 is decreased temporarily at delivery, and it was increased again rapidly, then went down to normal range about one month after delivery. 2. The average of immunochemical C3PA by SRID method during pregnancy was 22.5 +/- 0.4 mg/dl. It was significantly higher than the average 18.1 +/- 0.4 mg/dl of 59 healthy women. C3PA was noted to remain high level constantly during pregnancy. This C3PA level after delivery was observed to take a similar pattern as AlCH50. 3. beta 1C/1A globulin (C3) in 19 healthy women was 60.7 +/- 2.1 mg/dl. This C3 was also increased gradually during pregnancy up to maximum level of 87.5 +/- 2.8 mg/dl at the 3rd trimester. 4. Classical pathway (CH50, C4 and Cl INA) and fetal complement level were investigated at the same time and discussed here.
Adolescent↗
Viral immune evasion molecules attack the ER peptide-loading complex and exploit ER-associated degradation pathways.
The CD8+ cytotoxic-T-cell response is a potent mechanism that controls intracellular pathogens, including many viruses. To facilitate transmission, viruses often counter this response by inhibiting the cell surface display of virus-derived peptides on MHC class I molecules. More specifically, recent studies have demonstrated that viruses have evolved remarkable mechanisms to inhibit MHC class I expression by interfering with the function of the MHC class I assembly machinery (the peptide-loading complex) in the endoplasmic reticulum and/or by exploiting endoplasmic-reticulum-associated degradation pathways. These viral molecules are proving invaluable as research tools to illuminate the novel features of physiological pathways that are central to normal cell biology. Furthermore, the detailed characterization of such pathways has yielded significant new insights into host-pathogen interplay.
Animals↗
A sense of time: how molecular clocks organize metabolism.
The discovery of an internal temporal clockwork that coordinates behavior and metabolism according to the rising and setting of the sun was first revealed in flies and plants. However, in the past decade, a molecular transcription-translation feedback loop with similar properties has also been identified in mammals. In mammals, this transcriptional oscillator programs 24-hour cycles in sleep, activity and feeding within the master pacemaker neurons of the suprachiasmatic nucleus of the hypothalamus. More recent studies have shown that the core transcription mechanism is also present in other locations within the brain, in addition to many peripheral tissues. Processes ranging from glucose transport to gluconeogenesis, lipolysis, adipogenesis and mitochondrial oxidative phosphorylation are controlled through overlapping transcription networks that are tied to the clock and are thus time sensitive. Because disruption of tissue timing occurs when food intake, activity and sleep are altered, understanding how these many tissue clocks are synchronized to tick at the same time each day, and determining how each tissue 'senses time' set by these molecular clocks might open new insight into human disease, including disorders of sleep, circadian disruption, diabetes and obesity.
Animals↗
Representing, storing and accessing molecular interaction data: a review of models and tools.
One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.
Computational Biology↗
Distinct inflammatory gene pathways induced by particles.
The biologic response to particulate load after arthroplasty has not been fully characterized but is believed mediated by proinflammatory cytokines released from mononuclear cells in the periprosthetic region. To investigate the contribution of lymphocytes to expression of proinflammatory genes induced by metal particles, we compared gene expression of mononuclear cells in response to metal and polymethylmethacrylate particles using cDNA microarray profiling. Peripheral blood mononuclear cells and monocytes were stimulated with polymethylmethacrylate and titanium particles of clinically relevant sizes. Polymethylmethacrylate elicited a six- to 12-fold increase in gene expression of tumor necrosis factor alpha, interleukin 1alpha, interleukin 1beta, interleukin 6, and interleukin 8 in purified monocytes and unfractionated peripheral blood mononuclear cells. Although the effect of titanium on stimulation of purified monocytes was modest, stimulation of lymphocyte-containing peripheral blood mononuclear cells by titanium particles resulted in monocyte-derived proinflammatory cytokine expression. In contrast to polymethylmethacrylate, titanium particles stimulated increased expression of T lymphocyte-derived cytokines, including interleukin 2, interferon gamma, interleukin 9, and interleukin 22, in peripheral blood mononuclear cell cultures. The induction of T cell activation by titanium particles suggests lymphocytes may contribute to the inflammation that mediates osteolysis in patients with metallic particulate debris after total joint replacement.
Cell Survival↗
Making the connection: coupling of stress-activated ERK/MAPK (extracellular-signal-regulated kinase/mitogen-activated protein kinase) core signalling modules to extracellular stimuli and biological responses.
Signal-transduction pathways that employ members of the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) family of protein Ser/Thr kinases are widely conserved among eukaryotes. The multiplicity of these pathways allows the cell to respond to divergent extracellular stimuli by initiating a broad array of responses ranging from cell growth to apoptosis. ERK/MAPK pathways are comprised of a three-tiered core-signalling module wherein ERK/MAPKs are regulated by MAPK/ERK kinases (MEKs) and MEKs, in turn, are regulated by MAPK kinase kinases (MAPKKKs). The regulation of MAPKKK-->MEK-->ERK/MAPK core-signalling modules by upstream components is poorly understood. Mammalian stress-activated ERK/MAPK pathways have been implicated in numerous important physiological functions, including inflammatory responses and apoptosis. In this review, I will discuss how mammalian stress-regulated ERK/MAPK core-signalling modules couple with members of the SPS1 family of protein kinases and to other upstream elements, and how these stress-regulated pathways influence cell function.
Animals↗
[Metabolism of monocarbon compounds during biological purification of sewage waters].
Pathways and rates of metabolism of three 14C1-compounds (methanol, formaldehyde, and formic acid) were investigated by means of the heterogeneous population of activated sludge microorganisms. For the above microbial population formaldehyde was the primary or preferential substrate. During an hour aeration it was processed by activated sludge 6 times faster than by sodium formiate and 2 times faster than by methanol. The basic pathways of its transformation were oxidation via formiate to CO2 with its partial reutilization and direct incorporation into the sludge biomass via the primary formation of serine. An addition of methanol increased the incorporation of 14C-formadehyde into biomass and decreased the formation of free 14CO2. The main mechanism of the transformation of 14C-formiate in activated sludge was its oxidation to CO2. An addition of methanol and formaldehyde induced no essential changes in the rate or pattern of their metabolism.
Aerobiosis↗
Renin gene expression, biosynthesis, and cellular pathways of secretion.
The molecular biology of the human renin gene is reviewed. This 12.5 kb gene contains 10 exons and 9 introns. In its 5' flanking region, major control elements are present. These include promoters and enhancers as well as regulatory elements. The combined action of these elements would result in tissue specific expression and regulation of the gene. In addition to the control at the gene expression level, renin is also regulated at the posttranslational and secretory levels. The translational product of renin mRNA is preprorenin, which is cotranslationally cleaved to prorenin, an inactive precursor of renin. The majority of new synthesized human prorenin is constitutively secreted. However, prorenin is also processed intracellularly to the mature single chain active renin which is stored in secretory granules. Active renin is released by a regulated mechanism which can be stimulated by cAMP and other secretagogues. Studies are under way to examine the responses of renin gene expression, biosynthesis and secretion to various physiological conditions.
Animals↗
Exploring biomolecular machines: energy landscape control of biological reactions.
For almost 15 years, our Pathway model has been the most powerful model in terms of predicting the tunnelling mechanism for electron transfer (ET) in biological systems, particularly proteins. Going beyond the conventional Pathway models, we have generalized our method to understand how protein dynamics modulate not only the Franck-Condon factor, but also the tunnelling matrix element. We have demonstrated that when interference among pathways modulates the electron tunnelling interactions in proteins (particularly destructive interference), dynamical effects are of critical importance. Tunnelling can be controlled by protein conformations that lie far from equilibrium-those that minimize the effect of destructive interference during tunnelling, for example. In the opposite regime, electron tunnelling is mediated by one (or a few) constructively interfering pathway tubes and dynamical effects are modest. This new mechanism for dynamical modulation of the ET rate has been able to explain and/or predict several rates that were later confirmed by experiment. However, thermal fluctuations can also affect these molecular machines in many other ways. For example, we show how global transformations, which control protein functions such as allostery, may involve large-scale motion and possibly partial unfolding during the reaction event.
Azurin↗
Antagonism between jasmonate- and salicylate-mediated induced plant resistance: effects of concentration and timing of elicitation on defense-related proteins, herbivore, and pathogen performance in tomato.
The jasmonate (JA) and salicylate (SA) signaling pathways in plants provide resistance to herbivorous insects and pathogens. It is known that these pathways interact, sometimes resulting in antagonism between the pathways. We tested how the timing and concentration of elicitation of each pathway influenced the interaction between the jasmonate and salicylate pathways measured in terms of five biochemical responses and biological resistance to caterpillars and bacteria. The salicylate pathway had a stronger effect on the jasmonate pathway than did the reverse. The negative signal interaction was generated by two distinct paths in the plant. A negative interaction in the biochemical expression of the two pathways was most consistent in the simultaneous elicitation experiments compared to when the elicitors were temporally separated by two days. Herbivore bioassays with Spodoptera exigua also consistently reflected an interaction between the two pathways in the simultaneous elicitation experiments. The negative signal interaction reducing biological resistance to the herbivore was also demonstrated in some temporally separated treatment combinations where attenuation of the biochemical response was not evident. Concentration of the elicitors had an effect on the pathway interaction with consistent biochemical and biological antagonism in the high concentration experiments and inconsistent antagonism in the low concentration experiments. The bacterial pathogen, Pseudomonas syringae pv. tomato (Pst), consistently showed reduced lesion development on plants with SA responses activated and, in some experiments, on JA-elicited plants. Resistance to Pst was not reduced or enhanced in dual-elicited plants. Thus, signal interaction is most consistent when elicitors are applied at the same time or when applied at high doses. Signal interaction affected the herbivore S. exigua, but not the pathogen Pst.
Animals↗
Modeling the VPAC2-activated cAMP/PKA signaling pathway: from receptor to circadian clock gene induction.
Increasing evidence suggests an important role for VPAC2-activated signal transduction pathways in maintaining a synchronized biological clock in the suprachiasmatic nucleus (SCN). Activation of the VPAC2 signaling pathway induces per1 gene expression in the SCN and phase-shifts the circadian clock. Mice without the VPAC2 receptor lack an overt, coherent circadian rhythm in clock gene expression, SCN neuron firing rate, and locomotor behavior. Using a systems approach, we have developed a kinetic model integrating VPAC2 signaling mediated by the cyclic AMP (cAMP)/protein kinase A (PKA) pathway and leading to induced circadian clock gene expression. We fit the model to experimental data from the literature for cAMP accumulation, PKA activation, cAMP-response element binding protein phosphorylation, and per1 induction. By linking the VPAC2 model to a published circadian clock model, we also simulated clock phase shifts induced by vasoactive intestinal polypeptide (VIP) and matched experimental data for the VIP response. The simulated phase response curve resembled the hamster response to a related neuropeptide, GRP1-27, and light. Simulations using pulses of VIP revealed that the system response is extraordinarily robust to input signal duration, a result with physiologically relevant consequences. Lastly, simulations using varied receptor levels matched literature experimental data from animals overexpressing VPAC2 receptors.
Animals↗
Improving the delivery of therapeutic agents to CNS neoplasms: a clinical review.
Even though nearly thirty-years of clinical research has attempted to improve the outcomes for patients with central nervous system neoplasms, the survival remains limited for a majority of these patients. Diverse intracellular signaling pathways involving apoptosis, invasion, angiogenesis and relevant mechanisms of resistance associated with CNS neoplasms are continuing to be elucidated. Phase I and II studies of systemically delivered chemotherapeutic agents and biological agents targeting these pathways have largely resulted in modest outcomes. Although the functional blood brain barrier was identified nearly eighty years ago only recently has the complexity and relevance of the blood brain-tumor barrier (BTB) been recognized as an important factor that limits the effective treatment of CNS neoplasms. Several groups have focused their efforts at improving the delivery of therapeutic agents across the blood brain-tumor barrier. The purpose of the article is to review novel methods that have attempted to improve the delivery of therapeutic agents into the CNS for the treatment of CNS neoplasm.
Animals↗
Study of the biologic effects of lapatinib, a reversible inhibitor of ErbB1 and ErbB2 tyrosine kinases, on tumor growth and survival pathways in patients with advanced malignancies.
PURPOSE: This was a pilot study to assess the biologic effects of lapatinib on various tumor growth/survival pathways in patients with advanced ErbB1 and/or ErbB2-overexpressing solid malignancies. PATIENTS AND METHODS: Heavily pretreated patients with metastatic cancers overexpressing ErbB2 and/or expressing ErbB1 were randomly assigned to one of five dose cohorts of lapatinib (GW572016) administered orally once daily continuously. The biologic effects of lapatinib on tumor growth and survival pathways were assessed in tumor biopsies obtained before and after 21 days of therapy. Clinical response was determined at 8 weeks. RESULTS: Sequential tumor biopsies from 33 patients were examined. Partial responses occurred in four patients with breast cancer, and disease stabilization occurred in 11 others with various malignancies. Responders exhibited variable levels of inhibition of p-ErbB1, p-ErbB2, p-Erk1/2, p-Akt, cyclin D1, and transforming growth factor alpha. Even some nonresponders demonstrated varying degrees of biomarker inhibition. Increased tumor cell apoptosis (TUNEL) occurred in patients with evidence of tumor regression but not in nonresponders (progressive disease). Clinical response was associated with a pretreatment TUNEL score > 0 and increased pretreatment expression of ErbB2, p-ErbB2, Erk1/2, p-Erk1/2, insulin-like growth factor receptor-1, p70 S6 kinase, and transforming growth factor alpha compared with nonresponders. CONCLUSION: Lapatinib exhibited preliminary evidence of biologic and clinical activity in ErbB1 and/or ErbB2-overexpressing tumors. However, the limited sample size of this study and the variability of the biologic endpoints suggest that further work is needed to prioritize biomarkers for disease-directed studies, and underscores the need for improved trial design strategies in early clinical studies of targeted agents.
Adult↗
Raf/MAPK and rapamycin-sensitive pathways mediate the anti-apoptotic function of p21Ras in IL-3-dependent hematopoietic cells.
The Ras signal transduction pathway is activated by a number of hematopoietic cytokines and is implicated in the prevention of apoptotic death in hematopoietic cells. Recent studies have provided evidence that the downstream of Ras is highly divergent and several independent pathways appear to mediate distinct biological functions of Ras. In the present study, we investigated the downstream pathway(s) of Ras responsible for the maintenance of hematopoietic cell survival by using various mutants of signaling molecules. Activation of the Raf/MAPK pathway in interleukin (IL) 3-dependent cells by expression of an oncogenic Raf or a Ras mutant (G12V/T35S) prevented apoptosis following IL-3 deprivation. In contrast, another Ras mutant (G12V/V45E), which is apparently incapable of activating MAPK, efficiently blocked apoptosis as well. It is therefore likely that the activation of the Raf/MAPK pathway is not an absolute requirement for the prevention of apoptosis, and there appears to be a Raf/MAPK-independent pathway that contributes to hematopoietic cell survival. Since Ras(G12V/V45E) was able to cause the phosphorylation of p70/S6 kinase, we inhibited the S6 kinase pathway by rapamycin and by wortmannin, and found that the anti-apoptotic function of Ras(G12V/V45E), but not of Ras(G12V), was critically influenced by both inhibitors. These results indicate that the Raf/MAPK and a rapamycin/wortmannin-sensitive pathways mediate Ras function to prevent apoptotic death in hematopoietic cells.
Androstadienes↗
iModMix: integrative module analysis for multi-omics data.
SUMMARY: Integrative Module Analysis for Multi-omics Data (iModMix) is a biology-agnostic framework that enables the discovery of novel associations across any type of quantitative abundance data, including but not limited to transcriptomics, proteomics, and metabolomics. Instead of relying on pathway annotations or prior biological knowledge, iModMix constructs data-driven modules using graphical lasso to estimate sparse networks from omics features. These modules are summarized into eigenfeatures and correlated across datasets for horizontal integration, while preserving the distinct feature sets and interpretability of each omics type. iModMix operates directly on matrices containing expression or abundances for a wide range of features, including but not limited to genes, proteins, and metabolites. Because it does not rely on annotations (e.g., KEGG identifiers), it can seamlessly incorporate both identified and unidentified metabolites, addressing a key limitation of many existing metabolomics tools. iModMix is available as a user-friendly R Shiny application requiring no programming expertise (https://imodmix.moffitt.org), and as a Bioconductor R package for advanced users (https://bioconductor.org/packages/release/bioc/html/iModMix.html). The tool includes several public and in-house datasets to illustrate its utility in identifying novel multi-omics relationships in diverse biological contexts. AVAILABILITY AND IMPLEMENTATION: iModMix is freely available from Bioconductor (https://bioconductor.org/packages/release/bioc/html/iModMix.html), and the example dataset package (iModMixData) is also available from Bioconductor (https://bioconductor.org/packages/release/ data/experiment/html/iModMixData.html). The R package source code and Docker are available from GitHub: https://github.com/biodatalab/iModMix. Shiny application can be accessed at: https://imodmix.moffitt.org.
Multiomics↗
Turning a disulfide isomerase into an oxidase: DsbC mutants that imitate DsbA.
There are two distinct pathways for disulfide formation in prokaryotes. The DsbA-DsbB pathway introduces disulfide bonds de novo, while the DsbC-DsbD pathway functions to isomerize disulfides. One of the key questions in disulfide biology is how the isomerase pathway is kept separate from the oxidase pathway in vivo. Cross-talk between these two systems would be mutually destructive. To force communication between these two systems we have selected dsbC mutants that complement a dsbA null mutation. In these mutants, DsbC is present as a monomer as compared with dimeric wild-type DsbC. Based on these findings we rationally designed DsbC mutants in the dimerization domain. All of these mutants are able to rescue the dsbA null phenotype. Rescue depends on the presence of DsbB, the native re-oxidant of DsbA, both in vivo and in vitro. Our results suggest that dimerization acts to protect DsbC's active sites from DsbB-mediated oxidation. These results explain how oxidative and reductive pathways can co-exist in the periplasm of Escherichia coli.
Bacterial Proteins↗