Sexual dimorphism in the skull geometry of newt species of <Emphasis Type="Italic">Ichthyosaura,Triturus</Emphasis> and <Emphasis Type="Italic">Lissotriton</Emphasis> (Salamandridae,Caudata, Amphibia)

In this study, we applied geometric morphometrics to explore variations in the level and pattern of sexual size dimorphism (SSD) and sexual shape dimorphism (SShD) of the ventral cranium in three different Modern Eurasian newt taxa (Ichthyosaura alpestris, Triturus species group and Lissotriton vulgaris). The ventral cranium is the part of the skull that is more directly related to foraging and feeding. Our results indicate that the level and pattern of sexual dimorphism in the ventral cranium differ among Modern Eurasian newt taxa. Regarding sexual dimorphism in skull size, Ichthyosaura alpestris and Triturus species show female-biased patterns (females are larger than males), whereas Lissotriton vulgaris appears to be non-dimorphic in skull size. In I. alpestris and Triturus species, SShD is mostly absent, whereas in L. vulgaris, SShD is more pronounced. A high level of variation between populations in both SSD and SShD indicates that local conditions may have a profound effect on the magnitude and direction of sexual dimorphism. The significant sexual differences in ventral cranium size and shape indicate possible subtle intersexual differences in ecological demands due to diet specialisation, in spite of similar general ecological settings.     

Conformational evaluation of labeled C3′‐O‐P‐13CH2‐O‐C4″ phosphonate internucleotide linkage,a phosphodiester isostere

Modified internucleotide linkage featuring the C3′‐O‐P‐CH₂‐O‐C4″ phosphonate grouping as an isosteric alternative to the phosphodiester C3′‐O‐P‐O‐CH₂‐C4″ bond was studied in order to learn more on its stereochemical arrangement, which we showed earlier to be of prime importance for the properties of the respective oligonucleotide analogues. Two approaches were pursued: First, the attempt to prepare the model dinucleoside phosphonate with ¹³C‐labeled CH₂ group present in the modified internucleotide linkage that would allow for a more detailed evaluation of the linkage conformation by NMR spectroscopy. Second, the use of ab initio calculations along with molecular dynamics (MD) simulations in order to observe the most populated conformations and specify main structural elements governing the conformational preferences. To deal with the former aim, a novel synthesis of key labeled reagent (CH₃O)₂P(O)¹³CH₂OH for dimer preparation had to be elaborated using aqueous ¹³C‐formaldehyde. The results from both approaches were compared and found consistent. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 514–529, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

EPR Spin-Trapping and Spin-Probing Spectroscopy in Assessing Antioxidant Properties: Example on Extracts of Catkin, Leaves, and Spiny Burs of Castanea sativa

Electron paramagnetic resonance (EPR) spin-trapping and spin-probing techniques were applied to determine antioxidant activity of extracts of catkin, leaves, and spiny burs of Castanea sativa against physiologically relevant reactive species—superoxide and hydroxyl radical generated in simple chemical systems and hydrogen peroxide applied on erythrocytes. Efflux of K⁺ was used as a marker of membrane integrity. Chemical composition of extracts was analyzed using HPLC/DAD and LC/MS. Extracts showed high antioxidative capacity against superoxide but lower activity against hydroxyl radical. They protected fluidity and integrity of membranes of erythrocytes exposed to hydrogen peroxide. Levels of derivatives of ellagitannins showed positive correlation with the antioxidative activity of extracts. Therefore, ellagitannins from chestnut extracts could represent easily accessible natural antioxidants and beneficial component of human diet in pathophysiological conditions related to oxidative stress. In conclusion, EPR spectroscopy represents a valuable tool for evaluation of antioxidant activity in both hydrophilic and lipophilic media. This work was supported by the Federal Ministry of Education and Science of Bosnia and Herzegovina Grant No. 614300 and the Ministry of Science, Technology, and Development of Republic of Serbia Grant No. 143016. We would like to thank Ms. Ana Martinović on technical support.     

Identification of MicroRNAs controlling human ovarian cell proliferation and apoptosis

Previous studies have shown that microRNAs (miRNAs) can control steroidogenesis in cultured granulosa cells. In this study we wanted to determine if miRNAs can also affect proliferation and apoptosis in human ovarian cells. The effect of transfection of cultured primary ovarian granulosa cells with 80 different constructs encoding human pre‐miRNAs on the expression of the proliferation marker, PCNA, and the apoptosis marker, Bax was evaluated by immunocytochemistry. Eleven out of 80 tested miRNA constructs resulted in stimulation, and 53 miRNAs inhibited expression of PCNA. Furthermore, 11 of the 80 miRNAs tested promoted accumulation of Bax, while 46 miRNAs caused a reduction in Bax in human ovarian cells. In addition, two selected antisense constructs that block the corresponding miRNAs mir‐15a and mir‐188 were evaluated for their effects on expression of PCNA. An antisense construct inhibiting mir‐15a (which precursor suppressed PCNA) increased PCNA, whereas an antisense construct for mir‐188 (which precursor did not change PCNA) did not affect PCNA expression. Verification of effects of selected pre‐mir‐10a, mir‐105, and mir‐182 by using other markers of proliferation (cyclin B1) and apoptosis (TdT and caspase 3) confirmed specificity of miRNAs effects on these processes. This is the first direct demonstration of the involvement of miRNAs in controlling both proliferation and apoptosis by ovarian granulose cells, as well as the identification of miRNAs promoting and suppressing these processes utilizing a genome‐wide miRNA screen. J. Cell. Physiol. 223: 49–56, 2010. © 2009 Wiley‐Liss, Inc.     

Propagating uncertainty in microarray data analysis

Microarray technology is associated with many sources of experimentaluncertainty. In this review we discuss a number of approachesfor dealing with this uncertainty in the processing of datafrom microarray experiments. We focus here on the analysis ofhigh-density oligonucleotide arrays, such as the popular AffymetrixGeneChip® array, which contain multiple probes for eachtarget. This set of probes can be used to determine an estimatefor the target concentration and can also be used to determinethe experimental uncertainty associated with this measurement.This measurement uncertainty can then be propagated throughthe downstream analysis using probabilistic methods. We giveexamples showing how these credibility intervals can be usedto help identify differential expression, to combine informationfrom replicated experiments and to improve the performance ofprincipal component analysis.      

Open software for biologists: from famine to feast

Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits.     

Formation of peroxynitrite during thiol-mediated reduction of sodium nitroprusside

Aerobic incubations of equimolar concentrations (5-500 microM) of sodium nitroprusside (SNP) and dithiothreitol (DTT) carried out at pH 7.4 in the absence of light caused a concentration-dependent increase in the rates of oxidation of dihydrorhodamine-123. The enhancement of the rates of oxidation under such conditions was only partially sensitive to the inhibition by 100 mM dimethyl sulfoxide implying the involvement of both peroxynitrite and hydroxyl radicals in the observed effects. The oxidation of dihydrorhodamine-123 in the presence of SNP and DTT was nearly completely abolished by superoxide dismutase (20 U/ml). It was found that such an effect of the enzyme was related primarily to the stabilization of an intermediate of SNP reduction formed upstream to the liberation of nitrosonium ligand. Increased rates of oxidation of dihydrorhodamine-123 were also observed during the reduction of SNP with either L-cysteine or glutathione. It is concluded that thiol-mediated reduction of SNP under aerobic conditions is accompanied by the formation of oxygen-derived free radicals. Nitrosonium ligand liberated from the product(s) of SNP reduction is, under such conditions, converted to peroxynitrite.