Conformations Consistent with Charge Migration Observed in DNA and RNA X-ray Structures

Abstract

Electron holes are known to migrate along the DNA or RNA duplexes and to localize preferentially on successive guanines. The stationary point conformations of Gua pairs that can trap or let pass these holes have been characterized by quantum chemistry calculations. Here we show their recurrent occurrence in DNA and RNA X-ray structures, often in quadruplex conformations or in interaction with proteins, ligands or metal ions. These findings give support to the biological, possibly regulatory, roles of charge migration in cell functioning.     

Serum proteomic profiling for the early diagnosis of colorectal cancer

No ideal serum biomarker currently exists for the early diagnosis of colorectal cancer (CRC). Magnetic bead‐based fractionation coupled with MALDI‐TOF MS was used to screen serum samples from CRC patients, healthy controls, and other cancer patients. A diagnostic model with five proteomic features (m/z 1778.97, 1866.16, 1934.65, 2022.46, and 4588.53) was generated using Fisher algorithm with best performance. The Fisher‐based model could discriminate CRC patients from the controls with 100% (46/46) sensitivity and 100% (35/35) specificity in the training set, 95.6% (43/45) sensitivity and 83.3% (35/42) specificity in the test set. We further validated the model with 94.4% (254/269) sensitivity and 75.5% (83/110) specificity in the external independent group. In other cancers group, the Fisher‐based model classified 25 of 46 samples (54.3%) as positive and the other 21 as negative. With FT‐ICR‐MS, the proteomic features of m/z 1778.97, 1866.16, 1934.65, and 2022.46, of which intensities decreased significantly in CRC, were identified as fragments of complement C3f. Therefore, the Fisher‐based model containing five proteomic features was able to effectively differentiate CRC patients from healthy controls and other cancers with a high sensitivity and specificity, and may be CRC‐specific. Serum complement C3f, which was significantly decreased in CRC group, may be relevant to the incidence of CRC. J. Cell. Biochem. 114: 448–455, 2013. © 2012 Wiley Periodicals, Inc.     

HEF1 promotes epithelial mesenchymal transition and bone invasion in prostate cancer under the regulation of microRNA‐145

The principal problem arising from prostate cancer (PCa) is its propensity to metastasize to bones, and it's crucial to understand the mechanism of tumor progression to metastasis in order to develop therapies that may reduce the morbidity and mortality of PCa patients. Although we had identified that microRNA(miR)‐145 could repress bone metastasis of PCa via regulating epithelial–mesenchymal transition (EMT) in previous study, it is still unknown how miR‐145 regulated EMT. In the present study, we constructed a luciferase reporter system and identified HEF1 as a direct target of miR‐145. More importantly, HEF1 was shown to promote migration, invasion and EMT of PC‐3 cells, a human PCa cell line originated from a bone metastatic PCa specimen. And HEF1 was also shown to partially mediate miR‐145 suppression of EMT and invasion. Furthermore, inhibition of HEF1 repressed bone invasion of PC‐3 cells in vivo. Expression of HEF1 was negatively correlated with miR‐145 in primary PCa and bone metastatic specimens, but HEF1 was higher in samples which were more likely to commit to bone metastasis or those with higher free prostate‐specific antigen (fPSA) levels and Gleason scores. Taken together, these findings indicate that HEF1 promotes EMT and bone invasion in prostate cancer by directly targeted by miR‐145, and miR‐145 suppresses EMT and invasion, at least in part, through repressing HEF1. J. Cell. Biochem. 114: 1606–1615, 2013. © 2013 Wiley Periodicals, Inc.     

On the phylogeny and evolution of Mesozoic and extant lineages of Adephaga (Coleoptera,Insecta)

The relationships of extant and extinct lineages of Adephaga were analysed formally for the first time. Emphasis is placed on the aquatic and semiaquatic groups and their evolution in the Mesozoic. ?Triadogyrus and ?Mesodineutus belong to Gyrinidae, the sister group of the remaining families. ?Triaplidae are the sister group of the following groups (Haliplidae, Geadephaga, Dytiscoidea incl. ?Liadytidae, ?Parahygrobiidae and ?Coptoclavidae [major part]). The lack of a ventral procoxal joint and a very short prosternal process are plesiomorphies of ?Triaplidae. ?Coptoclavidae and ?Timarchopsinae are paraphyletic. ?Timarchopsis is placed in a geadephagan clade. In contrast to other coptoclavids, its metathorax is close to the condition found in Haliplidae, with a complete transverse ridge and coxae with large plates and free mesal walls. ?Coptoclavidae s.str., i.e. excl. ?Timarchopsis, is a dytiscoid subgroup. The mesal metacoxal walls are fused, the coxal plates are reduced, and the transverse ridge is absent. ?Stygeonectes belongs to this dytiscoid coptoclavid unit and is therefore misplaced in ?Timarchopsinae. ?Liadytidae belongs to a dytiscoid subgroup, which also comprises the extant families Aspidytidae, Amphizoidae, Hygrobiidae and Dytiscidae. ?Parahygrobia is the sister group of Hygrobiidae. The larvae are characterized by a broad gula, the absence of the lacinia, retractile maxillary bases and very long urogomphi set with long setae. ?Liadytiscinae is the sister group of extant Dytiscidae. There is no support for a clade ?Eodromeinae and for Trachypachidae incl. ?Eodromeinae. ?Fortiseode is nested within Carabidae. The exclusion of fossil taxa has no effect on the branching pattern. The evolution of Adephaga in the Mesozoic is discussed. Possible reasons for the extinction of ?Coptoclavidae are the rise of teleost fish and the competition of Gyrinidae and Dytiscidae, which possess efficient defensive glands and larval mandibular sucking channels.     

Milling plant and soil material in plastic tubes over-estimates carbon and under-estimates nitrogen concentrations

Background and aims

Milling of plant and soil material in plastic tubes, such as microcentrifuge tubes, over-estimates carbon (C) and under-estimates nitrogen (N) concentrations due to the introduction of polypropylene into milled samples, as identified using Fourier-transform infra-red spectroscopy.

Methods and results

This study compares C and N concentrations of roots and soil milled in microcentrifuge tubes versus stainless steel containers, demonstrating that a longer milling time, greater milling intensity, smaller sample size and inclusion of abrasive sample material all increase polypropylene contamination from plastic tubes leading to overestimation of C concentrations by up to 8 % (0.08 g?g^?1).

Conclusions

Erroneous estimations of C and N, and other analytes, must be assumed after milling in plastic tubes and milling methods should be adapted to minimise such error.