biochemical phenomena


Summary: The chemical processes, enzymatic activities, and pathways of living things and related temporal, dimensional, qualitative, and quantitative concepts.

Top Publications

  1. Chou I, Voit E. Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math Biosci. 2009;219:57-83 pubmed publisher
    ..The article concludes with a discussion of the present state of the art and with a description of open questions. ..
  2. Daigle B, Roh M, Gillespie D, Petzold L. Automated estimation of rare event probabilities in biochemical systems. J Chem Phys. 2011;134:044110 pubmed publisher
    ..Furthermore, by incorporating information-theoretic principles, our approach provides a framework for the development of more sophisticated influencing schemes that should further improve estimation accuracy. ..
  3. Morohashi M, Winn A, Borisuk M, Bolouri H, Doyle J, Kitano H. Robustness as a measure of plausibility in models of biochemical networks. J Theor Biol. 2002;216:19-30 pubmed
    ..Our analysis successfully identifies known weaknesses in the older model and suggests areas for further investigation in the more recent, more plausible model. It also correctly highlights why the more recent model is more plausible. ..
  4. Krewski D, Wang Y, Bartlett S, Krishnan K. Uncertainty, variability, and sensitivity analysis in physiological pharmacokinetic models. J Biopharm Stat. 1995;5:245-71 pubmed
    ..Many of the model parameters are related to body weight, which is assumed to vary in accordance with a doubly truncated normal distribution. The application of the proposed methods is illustrated using a PBPK model for benzene. ..
  5. Neuman M, Briggs K, Masuda K, Sah R, Watson D. A compositional analysis of cadaveric human nasal septal cartilage. Laryngoscope. 2013;123:2120-4 pubmed publisher
    ..In addition, it may assist in defining design goals for tissue-engineered septal neocartilage constructs to meet specific reconstructive needs in the future. ..
  6. Komenda J, Barker M, Kuviková S, de Vries R, Mullineaux C, Tichy M, et al. The FtsH protease slr0228 is important for quality control of photosystem II in the thylakoid membrane of Synechocystis sp. PCC 6803. J Biol Chem. 2006;281:1145-51 pubmed
    ..Overall, our results show that FtsH (slr0228) plays an important role in controlling the removal of PSII subunits from the thylakoid membrane and is not restricted to selective D1 turnover. ..
  7. Kutz K, Drewe J, Vankan P. Pharmacokinetic properties and metabolism of idebenone. J Neurol. 2009;256 Suppl 1:31-5 pubmed publisher
    ..Idebenone showed linear pharmacokinetics after single and repeated oral dosing. Administration after a meal resulted in the highest exposure to parent idebenone. ..
  8. Covaceuszach S, Cattaneo A, Lamba D. Neutralization of NGF-TrkA receptor interaction by the novel antagonistic anti-TrkA monoclonal antibody MNAC13: a structural insight. Proteins. 2005;58:717-27 pubmed
    ..The structure of the MNAC13 Fab fragment may assist in the rational structure-based design of high affinity humanized forms of MNAC13, appropriate for therapeutic approaches in neuropathy and inflammatory pain states. ..
  9. Hidalgo Rodríguez M, Fuguet E, Rafols C, Rosés M. Estimation of biological properties by means of chromatographic systems: evaluation of the factors that contribute to the variance of biological-chromatographic correlations. Anal Chem. 2010;82:10236-45 pubmed publisher

More Information


  1. Collins C, Nelson W. Running with neighbors: coordinating cell migration and cell-cell adhesion. Curr Opin Cell Biol. 2015;36:62-70 pubmed publisher
    ..Here, we summarize recent advances made in understanding the interplay between these pathways at cadherin-based and integrin-based adhesions during collective cell migration and highlight outstanding questions that remain in the field. ..
  2. Samal A, Ghanam R, Fernandez T, Monroe E, Saad J. NMR, biophysical, and biochemical studies reveal the minimal Calmodulin binding domain of the HIV-1 matrix protein. J Biol Chem. 2011;286:33533-43 pubmed publisher
    ..The present findings provide new insights on how MA interacts with CaM that may ultimately help in identification of the functional role of CaM-Gag interactions in the HIV replication cycle. ..
  3. Pourrajab F, Forouzannia S, Tabatabaee S. Molecular characteristics of bone marrow mesenchymal stem cells, source of regenerative medicine. Int J Cardiol. 2013;163:125-31 pubmed publisher
    ..Understanding the molecular mechanisms underlying dynamic regulation of various signals, plays an important role for future treatment of heart disorders. ..
  4. Jia J, Liang C, Cao J, Li Z. Application of probabilistic neural network in bacterial identification by biochemical profiles. J Microbiol Methods. 2013;94:86-87 pubmed publisher
    ..The PNN shows the correct identification of all the taxa belonging to the training and test sets and possesses merits over the conventional methods. ..
  5. Basañez G, Sharpe J, Galanis J, Brandt T, Hardwick J, Zimmerberg J. Bax-type apoptotic proteins porate pure lipid bilayers through a mechanism sensitive to intrinsic monolayer curvature. J Biol Chem. 2002;277:49360-5 pubmed
    ..Altogether, these results are consistent with a model whereby Bax-type proteins change the bending propensity of the membrane to form pores comprised at least in part of lipids in a structure of net positive monolayer curvature. ..
  6. Kuroiwa T. [Disagreement between cytology and biochemistry/molecular biology in studies of organelle inheritance--observation]. Seikagaku. 2008;80:167-76 pubmed
  7. Turakainen M, Hartikainen H, Ekholm P, Seppänen M. Distribution of selenium in different biochemical fractions and raw darkening degree of potato (Solanum tuberosum L.) tubers supplemented with selenate. J Agric Food Chem. 2006;54:8617-22 pubmed
    ..At low levels, Se improved the processing quality of potato tubers by diminishing and retarding their raw darkening. The value of Se-enriched potato tubers as a Se source in the human diet was discussed. ..
  8. Martínez Fernández M, Rodríguez Piñeiro A, Oliveira E, Páez de la Cadena M, Rolan Alvarez E. Proteomic comparison between two marine snail ecotypes reveals details about the biochemistry of adaptation. J Proteome Res. 2008;7:4926-34 pubmed publisher
  9. Lippard S. The inorganic side of chemical biology. Nat Chem Biol. 2006;2:504-7 pubmed
    ..Metal ions function in numerous metalloenzymes, are incorporated into pharmaceuticals and imaging agents, and inspire the synthesis of catalysts used to achieve many chemical transformations. ..
  10. Alberty R. Relations between biochemical thermodynamics and biochemical kinetics. Biophys Chem. 2006;124:11-7 pubmed
    ..Several simple enzymatic mechanisms and their complete rate equations are discussed. ..
  11. Pomper M. Translational molecular imaging for cancer. Cancer Imaging. 2005;5 Spec No A:S16-26 pubmed
    ..This brief review outlines several of the more promising areas of pursuit in molecular imaging for oncology with an emphasis on those that show the most immediate likelihood for clinical translation. ..
  12. Kalay Z. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry. Crit Rev Biochem Mol Biol. 2011;46:310-26 pubmed publisher
    ..With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry. ..
  13. Kastrup C, Runyon M, Lucchetta E, Price J, Ismagilov R. Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks. Acc Chem Res. 2008;41:549-58 pubmed publisher
    ..By creating nonideal, stressful, and perturbed environments, microfluidic experiments could reveal the function of pathways thought to be nonessential under ideal conditions. ..
  15. Schoenlechner R, Drausinger J, Ottenschlaeger V, Jurackova K, Berghofer E. Functional properties of gluten-free pasta produced from amaranth, quinoa and buckwheat. Plant Foods Hum Nutr. 2010;65:339-49 pubmed publisher
    ..2% emulsifier (distilled monoglycerides) texture firmness as well as cooking quality of gluten-free pasta produced from such a flour blend reached acceptable values comparable to wheat pasta. ..
  16. Reitz M, Sacher O, Tarkhov A, Trumbach D, Gasteiger J. Enabling the exploration of biochemical pathways. Org Biomol Chem. 2004;2:3226-37 pubmed
    ..The database is accessible at and . ..
  17. Muramatsu M, Arisue Y. [New drug approvals over three decades from 1980 to 2009 in Japan--their therapeutic targets and biochemical properties]. Yakugaku Zasshi. 2011;131:603-19 pubmed
    ..The results obtained in this study indicated changes in the therapeutic targets, biochemical properties and therapeutic areas of new drugs approved over the last 30 years and suggest the aspects of the future development of new drugs. ..
  18. Parnaudeau V, Condom N, Oliver R, Cazevieille P, Recous S. Vinasse organic matter quality and mineralization potential, as influenced by raw material, fermentation and concentration processes. Bioresour Technol. 2008;99:1553-62 pubmed
    ..The concentrated vinasse had a smaller labile fraction, induced N immobilization at the beginning of incubation, and exhibited greater N concentration in the acid-insoluble fraction than the dilute vinasse. ..
  19. Buxbaum J, Ye Z, Reixach N, Friske L, Levy C, Das P, et al. Transthyretin protects Alzheimer's mice from the behavioral and biochemical effects of Abeta toxicity. Proc Natl Acad Sci U S A. 2008;105:2681-6 pubmed publisher
    ..The interaction may represent a unique normal host defense mechanism, enhancement of which could be therapeutically useful. ..
  20. Tsintavi E, Pontillo N, Dareioti M, Kornaros M. Ozone pretreatment of olive mill wastewaters (OMW) and its effect on OMW biochemical methane potential (BMP). Water Sci Technol. 2013;68:2712-7 pubmed publisher
    ..Nevertheless, the ozone-pretreated OMW exhibited lower chemical oxygen demand removal and methane production during BMP testing compared to the untreated OMW. ..
  21. Carbone M, Ayroles J, Yamamoto A, Morozova T, West S, Magwire M, et al. Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma. PLoS ONE. 2009;4:e4216 pubmed publisher
    ..This process could occur at a late age with wild-type MYOC, but might be accelerated by MYOC mutants to account for juvenile onset glaucoma. ..
  22. Mäkinen V, Forsblom C, Thorn L, Wadén J, Kaski K, Ala Korpela M, et al. Network of vascular diseases, death and biochemical characteristics in a set of 4,197 patients with type 1 diabetes (the FinnDiane Study). Cardiovasc Diabetol. 2009;8:54 pubmed publisher
  23. Tiefenbrunn T, Dawson P. Chemoselective ligation techniques: modern applications of time-honored chemistry. Biopolymers. 2010;94:95-106 pubmed publisher
    ..In this review we highlight several promising reactions that may have widespread applicability in the generation of new materials based on biological macromolecules. ..
  24. Challand G, Vasikaran S. The assessment of interpretation in clinical biochemistry: a personal view. Ann Clin Biochem. 2007;44:101-5 pubmed
  25. Jain K, Kathiravan M, Somani R, Shishoo C. The biology and chemistry of hyperlipidemia. Bioorg Med Chem. 2007;15:4674-99 pubmed
    ..The emphasis has been laid in particular on the new potential biological targets and the possible treatments as well as the current ongoing research status in the field of lipid lowering agents. ..
  26. Lu G, Broze G, Krishnaswamy S. Formation of factors IXa and Xa by the extrinsic pathway: differential regulation by tissue factor pathway inhibitor and antithrombin III. J Biol Chem. 2004;279:17241-9 pubmed
  27. Bernardo P, Chai C, Heath G, Mahon P, Smith G, Waring P, et al. Synthesis, electrochemistry, and bioactivity of the cyanobacterial calothrixins and related quinones. J Med Chem. 2004;47:4958-63 pubmed
    ..6 microM undergo reduction to their respective semiquinones readily, with their E(1/2) values being more positive than -0.5 V versus the standard hydrogen electrode (SHE). ..
  28. Daniel I, Oger P, Winter R. Origins of life and biochemistry under high-pressure conditions. Chem Soc Rev. 2006;35:858-75 pubmed
    ..After a short introduction to Earth history, the current tutorial review presents biological and physico-chemical arguments in support of high-pressure origin for life on Earth. ..
  29. Römpp A, Taban I, Mihalca R, Duursma M, Mize T, McDonnel L, et al. Examples of Fourier transform ion cyclotron resonance mass spectrometry developments: from ion physics to remote access biochemical mass spectrometry. Eur J Mass Spectrom (Chichester). 2005;11:443-56 pubmed
    ..This concept of remote experimentation opens new possibilities for scientific collaborations between expert scientists at different locations and allows the efficient use of this expensive instrumentation. ..
  30. Lloyd J, Renshaw J. Microbial transformations of radionuclides: fundamental mechanisms and biogeochemical implications. Met Ions Biol Syst. 2005;44:205-40 pubmed
  31. Yeo D, Srinivasan R, Chen G, Yao S. Expanded utility of the native chemical ligation reaction. Chemistry. 2004;10:4664-72 pubmed
  32. Field T, Diego M, Hernandez Reif M, Vera Y, Gil K, Schanberg S, et al. Prenatal maternal biochemistry predicts neonatal biochemistry. Int J Neurosci. 2004;114:933-45 pubmed
  33. Cassinelli E, Hall R, Kang J. Biochemistry of intervertebral disc degeneration and the potential for gene therapy applications. Spine J. 2001;1:205-14 pubmed
    ..Ongoing research efforts in the area of gene therapy show promise as a way to prevent, or even reverse, some of these changes. ..
  34. Axelsson S. Perspectives on handedness, life and physics. Med Hypotheses. 2003;61:267-74 pubmed
    ..Instead, decay and formation will balance each other in a continuum of matter in an intuitively cyclic Multiverse. ..
  35. Vogel T, Driemel C, Hauser A, Hansmann A, Lange S, Jonas M, et al. [Comparison of different stool tests for the detection of cancer of the colon]. Dtsch Med Wochenschr. 2005;130:872-7 pubmed
    ..Reducing incidence and mortality of colorectal cancer should be achieved by colonoscopy, a recommendation that requires specific communication to the public. ..
  36. Herbig M, Fromm U, Leuenberger J, Krauss U, Beck Sickinger A, Merkle H. Bilayer interaction and localization of cell penetrating peptides with model membranes: a comparative study of a human calcitonin (hCT)-derived peptide with pVEC and pAntp(43-58). Biochim Biophys Acta. 2005;1712:197-211 pubmed
    ..Generally, we found strong peptide-phospholipid interactions, especially when negatively charged lipids were present. ..
  37. Itoh K, Asakawa T, Hoshino K, Adachi M, Fukiya K, Watanabe N, et al. Functional analysis of aldehyde oxidase using expressed chimeric enzyme between monkey and rat. Biol Pharm Bull. 2009;32:31-5 pubmed
    ..Thus, the use of chimeric enzymes revealed that 2Fe-2S/FAD and MoCo domains affect the velocity and the quantitative profiles of AO-catalyzed (S)-RS-8359 2-oxidation, respectively. ..
  38. Coradin T, Lopez P. Biogenic silica patterning: simple chemistry or subtle biology?. Chembiochem. 2003;4:251-9 pubmed
  39. Williams N. Nervous systems. Curr Biol. 2003;13:R168 pubmed
  40. Marin Sanguino A, Torres N. Optimization of biochemical systems by linear programming and general mass action model representations. Math Biosci. 2003;184:187-200 pubmed
  41. Nancharaiah Y, Mohan S, Lens P. Biological and Bioelectrochemical Recovery of Critical and Scarce Metals. Trends Biotechnol. 2016;34:137-155 pubmed publisher
    ..In the past decade bioelectrochemical systems have emerged as a new technology platform for metal recovery coupled to the removal of organic matter. ..
  42. Ha T. Single-molecule approaches embrace molecular cohorts. Cell. 2013;154:723-6 pubmed publisher
    ..The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company. ..
  43. Gao J, Shimada N, Maruyama A. Enhancement of deoxyribozyme activity by cationic copolymers. Biomater Sci. 2015;3:308-16 pubmed publisher
    ..In contrast to the copolymer, a cationic surfactant, CTAB, strongly inhibited the DNAzyme activity under either single- or multiple-turnover conditions. ..
  44. Sarfarazi M, Stoilov I, Schenkman J. Genetics and biochemistry of primary congenital glaucoma. Ophthalmol Clin North Am. 2003;16:543-54, vi pubmed
    ..This article also discusses the molecular evidence for reduced penetrance in congenital glaucoma and the phenotypic heterogeneity of CYP1B1 mutations, mouse models of CYP1B1, and the biochemistry of CYP1B1. ..
  45. Becker K, Kitatani K, Idkowiak Baldys J, Bielawski J, Hannun Y. Selective inhibition of juxtanuclear translocation of protein kinase C betaII by a negative feedback mechanism involving ceramide formed from the salvage pathway. J Biol Chem. 2005;280:2606-12 pubmed
    ..Together, these results define a novel pathway of regulated formation of ceramide, the salvage pathway, and they define a role for this pathway in regulating juxtanuclear translocation of PKC betaII. ..
  46. Kritz M, Trindade Dos Santos M, Urrutia S, Schwartz J. Organising metabolic networks: Cycles in flux distributions. J Theor Biol. 2010;265:250-60 pubmed publisher
    ..This methodology unveils the role of cycles in driving and maintaining metabolic fluxes under perturbations in these examples, and may be used to further investigate and understand the organisational invariance of biological systems. ..
  47. Benveniste J, Guillonnet D. QED and digital biology. Riv Biol. 2004;97:169-72 pubmed
  48. Farr A, Freeman K. Quality control validation, application of sigma metrics, and performance comparison between two biochemistry analyzers in a commercial veterinary laboratory. J Vet Diagn Invest. 2008;20:536-44 pubmed
    ..The findings in the present study emphasize the need for QC specific for the analyte and the clinical decision level and the need for separate QC validation on every instrument. ..
  49. Lynch K, Macdonald T. Sphingosine 1-phosphate chemical biology. Biochim Biophys Acta. 2008;1781:508-12 pubmed publisher
    ..Neither fact was known prior to FTY720; indeed, this molecule is testament to the power of chemical biology. In this communication, we attempt to summarize progress to date in S1P chemical biology. ..
  50. Maffeis C, Banzato C, Rigotti F, Nobili V, Valandro S, Manfredi R, et al. Biochemical parameters and anthropometry predict NAFLD in obese children. J Pediatr Gastroenterol Nutr. 2011;53:590-3 pubmed publisher
    ..88 [95% confidence interval 0.79-0.97], P?<?10). In conclusion, a predictive equation combining routinely available variables may allow physicians to identify obese children at the highest risk of NAFLD. ..
  51. Zhang Y, Ju J, Peng H, Gao F, Zhou C, Zeng Y, et al. Biochemical and structural characterization of the intracellular mannanase AaManA of Alicyclobacillus acidocaldarius reveals a novel glycoside hydrolase family belonging to clan GH-A. J Biol Chem. 2008;283:31551-8 pubmed publisher
    ..Based on sequence comparisons, the enzyme was assigned to a new glycoside hydrolase family (GH113) that belongs to clan GH-A. ..
  52. Clary D. Quantum dynamics of chemical reactions. Science. 2008;321:789-91 pubmed publisher
  53. Abraham G. [Is the existence of a cellular wisdom, or lack thereof, conceivable?]. Rev Med Suisse. 2006;2:2768 pubmed