Sensitivity of Patterns of Molecular Evolution to Alterations in Methodology: A Critique of Hughes and Yeager

Employing a set of 43 othologous mouse and rat genes, Hughes and Yeager (J. Mol. Evol. 45:125–130, 1997) reported (1) no correlation between synonymous and nonsynonymous rates of nucleotide substitution, (2) a positive correlation between intronic GC contents (GC _i) and intronic substitution rates (K _i), (3) that the average K _i value was very similar to the average K _s value, and (4) that the compositional correlation between the rat and the mouse genes is stronger at the third codon position (GC₃) than at the first and second codon positions (GC₁₂). We have examined the robustness of these results to alterations in substitution rate estimation protocol, alignment protocol, and statistical procedure. We find that a significant correlation between K _a and K _s is observed either if a rank correlation statistic is used instead of regression analysis, if one outlier is excluded from the analysis, or if a regression weighted by gene size is employed. The correlation between K _i and GC _i we find to be sensitive to changes in alignment protocol and disappears on the use of weighted means. The finding that K _s and K _i are approximately the same is dependent on the method for estimating K _s values. Finally, the variance around the regression line of rat GC₃ versus mouse GC₃ we find to be significantly higher than that in GC₁₂. The source of the discrepancy between this and Hughes and Yeager's result is unclear. The variance around the line for GC₄ is higher still, as might be expected. Using a methodology that may be considered preferable to that of Hughes and Yeager, we find that all four of their results are contradicted. More importantly this analysis reinforces the need for caution in assembling and analyzing data sets, as the degree of sensitivity to what many might consider minor methodological alterations is unexpected. Received: 2 February 1998 / Accepted: 23 March 1998     

Purification of a nitrate reductase kinase from Spinacea oleracea leaves, and its identification as a calmodulin-domain protein kinase

Spinach (Spinacea oleracea L.) nitrate reductase (NR) is inactivated by phosphorylation on serine-543, followed by binding of the phosphorylated enzyme to 14-3-3 proteins. We purified one of several chromatographically distinct NR_serine-543 kinases from spinach leaf extracts, and established by Edman sequencing of 80 amino acid residues that it is a calcium-dependent (calmodulin-domain) protein kinase (CDPK), with peptide sequences very similar to Arabidopsis CDPK6 (accession no. U20623; also known as CPK3). The spinach CDPK was recognized by antibodies raised against Arabidopsis CDPK. Nitrate reductase was phosphorylated at serine-543 by bacterially expressed His-tagged CDPK6, and the phosphorylated NR was inhibited by 14-3-3 proteins. However, the bacterially expressed CDPK6 had a specific activity approx. 200-fold lower than that of the purified spinach enzyme. The physiological control of NR by CDPK is discussed, and the regulatory properties of the purified CDPK are considered with reference to current models for reversible intramolecular binding of the calmodulin-like domain to the autoinhibitory junction of CDPKs. Received: 12 February 1998 / Accepted: 28 May 1998     

The auxin response of actin is altered in the rice mutantYin-Yang

Summary The rice mutantYin-Yang has been selected during a screen for resistance to cytoskeletal drugs and is characterized by alterations in epidermal cell length and a precocious onset of gravitropism. The elongation response of coleoptile segments to auxin does not reveal changes of auxin sensitivity inYin-Yang. However, in contrast to the wild type, cell elongation inYin-Yang is highly sensitive to the actin-polymerisation blocker cytochalasin D. This increased sensitivity to cytochalasin D requires optimal concentrations of auxin to become manifest. The auxin response of actin microfilaments in epidermal cells differs between wild type and mutant. In the wild type, the longitudinal microfilament bundles become loosened in response to auxin. In the mutant, these bundles disintegrate partially and are replaced by a network of short filaments surrounding the nucleus. Several aspects of the mutant phenotype can be mimicked in the wild type by treatment with cytochalasin D. The mutant phenotype is discussed in terms of signal-dependent changes of actin dynamics and the putative role of actin during cell elongation.Abbreviations CD cytochalasin D - EPC ethyl-N-phenylcarbamate     

Prebiotic chemistry: chemical evolution of organics on the primitive Earth under simulated prebiotic conditions.

A series of prebiotic mixtures of simple molecules, sources of C, H, N, and O, were examined under conditions that may have prevailed during the Hadean eon (4.6-3.8 billion years), namely an oxygen-free atmosphere and a significant UV radiation flux over a large wavelength range due to the absence of an ozone layer. Mixtures contained a C source (methanol, acetone or other ketones), a N source (ammonia or methylamine), and an O source (water) at various molar ratios of C : H : N : O. When subjected to UV light or heated for periods of 7 to 45 days under an argon atmosphere, they yielded a narrow product distribution of a few principal compounds. Different initial conditions produced different distributions. The nature of the products was ascertained by gas chromatographic-mass spectral analysis (GC-MS). UVC irradiation of an aqueous methanol-ammonia-water prebiotic mixture for 14 days under low UV dose (6 x 10(-2) Einstein) produced methylisourea, hexamethylenetetramine (HMT), methyl-HMT and hydroxy-HMT, whereas under high UV dose (45 days; 1.9 x 10(-1) Einstein) yielded only HMT. By contrast, the prebiotic mixture composed of acetone-ammonia-water produced five principal species with acetamide as the major component; thermally the same mixture produced a different product distribution of four principal species. UVC irradiation of the CH(3)CN-NH(3)-H(2)O prebiotic mixture for 7 days gave mostly trimethyl-s-triazine, whereas in the presence of two metal oxides (TiO(2) or Fe(2)O(3)) also produced some HMT; the thermal process yielded only acetamide.     

Identification of tripeptides recognized by the PDZ domain of Dishevelled

The development of inhibitors of Dishevelled (Dvl) PDZ protein–protein interactions attracts attention due to a possible application in drug discovery and development. Using nuclear magnetic resonance (NMR) spectroscopy, we found that a tripeptide VVV binds to the PDZ domain of Dvl, which is a key component involved in Wnt signaling. Using a computational approach calculating the binding free energy of the complexes of the Dvl PDZ domain and each of the tripeptides VXV (X: any amino acid residue except Pro), we found that a tripeptide VWV had the highest binding affinity. Consistent with the computational result, experimental results showed that the binding of the tripeptide VWV to the Dvl PDZ domain was stronger than that of the tripeptide VVV. The binding affinity of the tripeptide VWV was comparable to that of the organic molecule NSC668036, which was the first identified Dvl PDZ inhibitor. The three-dimensional structure of the complex Dvl1 PDZ/VWV was determined to investigate the role of the energetically favorable W(?1) residue in binding. These interactions were also explored by using molecular dynamic simulation and the molecular mechanics Poisson–Boltzmann surface area method. Taken together, these two tripeptides may be used as modulators of Wnt signaling or as a scaffold to optimize an antagonist for targeting Dvl1 PDZ protein–protein interaction.     

Association of Individual Non-Steroidal Anti-Inflammatory Drugs and Chronic Kidney Disease: A Population-Based Case Control Study

Background

Non-steroidal anti-inflammatory agents (NSAIDs) are known to be associated with renal damage. No clear evidence exists regarding differential risk of chronic kidney disease (CKD), specifically, across various NSAIDs.

Aim

The aim of this population-based case-control study was to evaluate the association between use of individual NSAIDs and risk of CKD in a general population of Southern Italy.

Methods

A nested case-control study was carried out using the general practice Arianna database, identifying incident CKD patients as cases and matched controls from 2006 to 2011. The date of first CKD diagnosis was defined as the index date (ID). Conditional logistic regressions were performed to estimate the risk of CKD associated with NSAIDs by class and individual drugs as compared to non-use during different time windows (within one year, six or three months prior to ID), with the latter being defined as current users. Among current users, the effect of cumulative exposure to these drugs was evaluated.

Results

Overall, 1,989 CKD cases and 7,906 matched controls were identified. A statistically significant increase in the risk of CKD was found for current users of oxicams (adjusted OR: 1.68; 95% CI: 1.15-2.44) and concerning individual compounds, for ketorolac (adj. OR: 2.54; 95% CI: 1.45-4.44), meloxicam (adj. OR: 1.98; 95% CI: 1.01-3.87) and piroxicam (adj. OR: 1.95; 95% CI: 1.19-3.21).

Conclusions

The risk of CKD varies across individual NSAIDs. Increased risk has been found for ketorolac, which may precipitate subclinical CKD through acute renal damage, and long-term exposure to oxicams, especially meloxicam and piroxicam.     

Current Prevalence Pattern of Hypertension in Nigeria: A Systematic Review

BackgroundThe global burden of hypertension and other non-communicable diseases (NCDs) is rapidly increasing, and the African continent seems to be the most affected region in the world. The prevalence of hypertension in Nigeria forms a substantial portion of the total burden in Africa because of the large population of the country currently estimated to be over 170 million.ObjectiveThe purpose of this systematic review is to summarise up to date data on the prevalence and distribution of hypertension in Nigeria from prevalence studies.MethodsA search of the following databases: PubMed, EMBase and WHO cardiovascular InfoBase from 1968 till date was conducted to identify studies which provide estimates of prevalence of hypertension in Nigeria.ResultsThe search yielded a total of 1748 hits from which 45 relevant studies met the inclusion criteria for the review. The overall crude prevalence of hypertension ranged from 0.1% (95%CI:-0.1 to 0.3) to 17.5% (95% CI: 13.6 to 21.4) in children and 2.1% (95%CI: 1.4 to 2.8) to 47.2% (95%CI: 43.6 to 50.8) in adults depending on the benchmark used for diagnosis of hypertension, the setting in which the study was conducted, sex and ethnic group. The crude prevalence of hypertension ranged from 6.2% (95%CI: 4.0 to 8.4) to 48.9% (95%CI: 42.3 to 55.5) for men and 10% (95%CI: 8.1 to 12) to 47.3% (95%CI: 43 to 51.6%) for women. In most studies, prevalence of hypertension was higher in males than females. In addition, prevalence across urban and rural ranged from 9.5% (95%CI: 13.6 to 21.4) to 51.6% (95%CI: 49.8 to 53.4) and 4.8% (95%CI: 2.9 to 6.7) to 43% (95%CI: 42.1 to 43.9) respectively.ConclusionsThe prevalence of hypertension is high among the Nigerian population. Appropriate interventions need to be developed and implemented to reduce the preventable burden of hypertension especially at Primary Health Care Centres which is the first point of call for over 55% of the Nigerian population.     

PTEN regulates IGF‐1R‐mediated therapy resistance in melanoma

Inhibition of the mitogen‐activated protein kinase (MAPK) pathway is a major advance in the treatment of metastatic melanoma. However, its therapeutic success is limited by the rapid emergence of drug resistance. The insulin‐like growth factor‐1 receptor (IGF‐1R) is overexpressed in melanomas developing resistance toward the BRAF^V600 inhibitor vemurafenib. Here, we show that hyperactivation of BRAF enhances IGF‐1R expression. In addition, the phosphatase activity of PTEN as well as heterocellular contact to stromal cells increases IGF‐1R expression in melanoma cells and enhances resistance to vemurafenib. Interestingly, PTEN‐negative melanoma cells escape IGF‐1R blockade by decreased expression of the receptor, implicating that only in melanoma patients with PTEN‐positive tumors treatment with IGF‐1R inhibitors would be a suitable strategy to combat therapy resistance. Our data emphasize the crosstalk and therapeutic relevance of microenvironmental and tumor cell‐autonomous mechanisms in regulating IGF‐1R expression and by this sensitivity toward targeted therapies.