Role of carcinogen-modified deoxynucleotide precursors in mutagenesis

Agents which damage or modify cellular DNA will generally also modify the nucleotide precursor pools, sometimes preferentially (Topal and Baker, 1982). There are at least two different ways that incorporation of modified (possibly promutagenic) nucleotides could, theoretically, make a significant contribution to the mutations induced by these agents. Modified bases may exhibit ambiguous base pairing and produce mutations during normal replication or they may induce secondary mutations as a result of processing subsequent to incorporation. There are important precedents for such possibilities. Classical studies on mutagenesis with prototype mutagens like 2-aminopurine (2-AP) and 5-bromouracil clearly show that mutations can occur by incorporation of deoxynucleotides of tautomeric or ionized (Sowers et al., 1987) bases into newly synthesized DNA (Ronen, 1979; Lasken and Goodman, 1984, Coulondre and Miller, 1977). 5-Hydroxymethyl-2′-deoxyuridine (HMdU), a product of oxidative DNA damage, can also be (re)incorporated into cellular DNA with both toxic and mutagenic consequences (Kaufman, 1987; Shirname-More et al., 1987). Furthermore, modified nucleotides may alter the pool sizes of the normal nucleotides and indirectly produce toxic and mutagenic effects. However, these effects are generally see at high, nonphysiological, concentrations of the modified precursors and may not be relevant under physiological conditions. The relative importance of modified deoxynucleotide precursors in the production of mutations by alkylating and oxidative DNA-damaging agents is discussed.     

Efflux transporters- and cytochrome P-450-mediated interactions between drugs of abuse and antiretrovirals

Multidrug regimens and corresponding drug interactions cause many adverse reactions and treatment failures. Drug efflux transporters: P-gp, MRP, BCRP in conjunction with metabolizing enzymes (CYPs) are major factors in such interactions. Most effective combination antiretrovirals (ARV) therapy includes a PI or a NNRTI or two NRTI. Coadministration of such ARV may induce efflux transporters and/or CYP3A4 resulting in sub-therapeutic blood levels and therapeutic failure due to reduced absorption and/or increased metabolism. A similar prognosis is true for ARV-compounds and drugs of abuse combinations. Morphine and nicotine enhance CYP3A4 and MDR1 expression in vitro. A 2.5 fold rise of cortisol metabolite was evident in smokers relative to nonsmokers. Altered functions of efflux transporters and CYPs in response to ARV and drugs of abuse may result in altered drug absorption and metabolism. Appropriate in vitro models can be employed to predict such interactions. Influence of genetic polymorphism, SNP and inter-individual variation in drug response has been discussed. Complexity underlying the relationship between efflux transporters and CYP makes it difficult to predict the outcome of HAART as such, particularly when HIV patients taking drugs of abuse do not adhere to HAART regimens. HIV(+) pregnant women on HAART medications, indulging in drugs of abuse, may develop higher viral load due to such interactions and lead to increase in mother to child transmission of HIV. A multidisciplinary approach with clear understanding of mechanism of interactions may allow proper selection of regimens so that desired therapeutic outcome of HAART can be reached without any side effects.     

Novel hybrid encodes both continuous and split tRNA genes?

tRNAs are mostly transcribed from un-fragmented genes, but occasionally also from split genes, with separated 5' and 3' halves. A reanalysis of the existing data on Staphylothermus marinus and Staphylothermus hellenicus hints of a novel hybrid gene that encodes both an un-fragmented and a 5'-split-half together in one. The corresponding 3' complement-gene is located elsewhere on the genome. As un-fragmented, the hybrid gene transcribes to tRNA(lys)(TTT). But as 5'-half, it trans-splices with its 3'-complement-half to tRNA(lys)(CTT), the tRNA missed so far. This hybrid of the split and the un-fragmented in one suggests a deeper synergy between the two, and hints of co-evolution. Furthermore, in a subtle contrast to the widely held idea of conservation of 3'-half, it is precisely the 3'-half that varies in these two tRNAs; the 5'-half remains conserved.     

In silico modeling of pH-optimum of protein-protein binding

Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity (pH-optimum of binding) or pH interval at which affinity is almost pH-independent (pH-flat of binding) of the complexes made of the corresponding monomers. The analysis of interfacial properties of protein complexes demonstrates that pH-dependent properties can be roughly estimated using the interface charge alone. In addition, we introduce a parameter beta, proportional to the square root of the absolute product of the net charges of monomers, and show that protein complexes characterized with small or very large beta tend to have neutral pH-optimum. Further more, protein complexes made of monomers carrying the same polarity net charge at neutral pH have either very low or very high pH-optimum of binding. These findings are used to propose empirical rule for predicting pH-optimum of binding provided that the amino acid compositions of the corresponding monomers are available.     

Radial distance determination in the rat vibrissal system and the effects of Weber's law

Rats rhythmically tap and brush their vibrissae (whiskers) against objects to tactually explore the environment. To extract a complex feature such as the contour of an object, the rat must at least implicitly estimate radial object distance, that is, the distance from the base of the vibrissa to the point of object contact. Radial object distance cannot be directly measured, however, because there are no mechanoreceptors along the vibrissa. Instead, the mechanical signals generated by the vibrissa's interaction with the environment must be transmitted to mechanoreceptors near the vibrissa base. The first part of this paper surveys the different mechanical methods by which the rat could determine radial object distance. Two novel methods are highlighted: one based on measurement of bending moment and axial force at the vibrissa base, and a second based on measurement of how far the vibrissa rotates beyond initial contact. The second part of the paper discusses the application of Weber's law to two methods for radial distance determination. In both cases, Weber's law predicts that the rat will have greatest sensing resolution close to the vibrissa tip. These predictions could be tested with behavioural experiments that measure the perceptual acuity of the rat.     

Measuring the persistence length of MCF7 cell microtubules in vitro

The dynamic and mechanical properties of mammalian neural microtubules have been widely studied; however, similar knowledge about these properties is limited for non-neural microtubules, which, unlike neural microtubules, consist of different β-tubulin isotypes. In this study, we report, for the first time, an estimated value for the persistence length of a single non-neural microtubule polymerized from purified tubulin from human breast cancer cell lines (MCF7 tubulin). The method of measurement is based on an analysis of the local curvature of a microtubule as a result of thermal fluctuations. In parallel, we measured the persistence length of a single bovine brain microtubule under similar conditions. The results of our measurements indicate a higher value for the persistence length of MCF7 microtubules in vitro as compared to the persistence length of a neural microtubule. The difference can be associated with different β-tubulin isotypes in the structure of MCF7 microtubules.     

Sensitive single-molecule protein quantification and protein complex detection in a microarray format

Single-molecule protein analysis provides sensitive protein quantitation with a digital read-out and is promising for studying biological systems and detecting biomarkers clinically. However, current single-molecule platforms rely on the quantification of one protein at a time. Conventional antibody microarrays are scalable to detect many proteins simultaneously, but they rely on less sensitive and less quantitative quantification by the ensemble averaging of fluorescent molecules. Here, we demonstrate a single-molecule protein assay in a microarray format enabled by an ultra-low background surface and single-molecule imaging. The digital read-out provides a highly sensitive, low femtomolar limit of detection and four orders of magnitude of dynamic range through the use of hybrid digital-analog quantification. From crude cell lysate, we measured levels of p53 and MDM2 in parallel, proving the concept of a digital antibody microarray for use in proteomic profiling. We also applied the single-molecule microarray to detect the p53-MDM2 protein complex in cell lysate. Our study is promising for development and application of single-molecule protein methods because it represents a technological bridge between single-plex and highly multiplex studies.     

Attenuation of oxidative stress by allylpyrocatechol in synovial cellular infiltrate of patients with Rheumatoid Arthritis

Free radicals are involved in the pathogenesis of Rheumatoid arthritis, a systemic autoimmune disorder characterized by unchecked synovial inflammation. Allylpyrocatechol, a phytoconstituent of Piper betle leaves, has potent anti-inflammatory activity and this study evaluated its anti-oxidant effect on the synovial infiltrate of patients with Rheumatoid arthritis. The ex vivo effect of allylpyrocatechol upon generation of reactive oxygen species in neutrophils, macrophages and lymphocytes was measured by flow cytometry using dichlorodihydrofluorescein diacetate, wherein it significantly decreased basal levels as also scavenged phorbol myristate acetate generated reactive oxygen species. Furthermore, its effect on generation of superoxide and hydroxyl radicals produced within infiltrated neutrophils was measured by cytochrome c and deoxyribose assay, respectively. Allylpyrocatechol significantly scavenged superoxide and hydroxyl radicals in infiltrated neutrophils. The effect of allylpyrocatechol on nitric oxide was measured in macrophages using 4,5-diaminofluorescein diacetate by flow cytometry wherein it decreased production of nitric oxide in infiltrated macrophages, which correlated with its in vitro nitric oxide scavenging activity. Taken together, this ex vivo study has established that allylpyrocatechol has potent scavenging activity and could be considered as an add-on therapy in the treatment of inflammation-associated disorders like Rheumatoid Arthritis.