Molecular archeology of L1 insertions in the human genome

Background  

As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after insertion into the human genome that are amenable to computational analysis. We carried out a detailed analysis of the anatomy and distribution of L1 elements in the human genome using a new computer program, TSDfinder, designed to identify transposon boundaries precisely.     

MOsDB: an integrated information resource for rice genomics

The MIPS Rice (Oryza sativa) database (MOsDB; http://mips.gsf.de/proj/rice) provides a comprehensive data collection dedicated to the genome information of rice. Rice (O. sativa L.) is one of the most important food crops for over half the world's population and serves as a major model system in cereal genome research. MOsDB integrates data from two publicly available rice genomic sequences, O. sativa L. ssp. indica and O. sativa L. ssp. japonica. Besides regularly updated rice genome sequence information, MOsDB provides an integrated resource for associated analysis data, e.g. internal and external annotation information as well as a complex characterization of all annotated rice genes. The MOsDB web interface supports various search options and allows browsing the database content. MOsDB is continuously expanding to include an increasing range of data type and the growing amount of information on the rice genome.     

The Shine-Dalgarno-like sequence is a negative regulatory element for translation of tobacco chloroplast rps2 mRNA: an additional mechanism for translational control in chloroplasts

Most prokaryotic mRNAs contain within the 5' untranslated region (UTR), a Shine-Dalgarno (SD) sequence, which is complementary to the 3' end of 16S rRNA and serves as a major determinant for correct translational initiation. The tobacco chloroplast rps2 mRNA possesses an SD-like sequence (GGAG) at a proper position (positions -8 to -5 from the start codon). Using an in vitro translation system from isolated tobacco chloroplasts, the role of this sequence in translation was examined. Unexpectedly, the mutation of the SD-like element resulted in a large increase in translation. Internal and external deletions within the 5' UTR revealed that the region from -20 to -5 was involved in the negative regulation of translation. Scanning mutagenesis assays confirmed the above result. Competition assays suggested the existence of a trans-acting factor(s) involved in translational regulation. In this study, we discuss a possible mechanism for the negative regulation of rps2 mRNA translation.     

A formula for correlating pKa values determined in D2O and H2O

A linear correlation between pH-meter readings in equivalent D2O and H2O solutions, determined experimentally, leads to a novel equation, which allows for a direct recalculation of pKa values measured in D2O into a H2O equivalent: pKH=0.929pKH*+0.42. The comparison of this equation with the previously used approach is discussed.     

Complexes of amylose and amylopectins with multivalent metal salts

Metal cations [Cu(II), Fe(III), Mn(II), and Ni(II)] are ligated by amylose as well as potato, and corn amylopectins as proven by electron paramagnetic resonance spectra and conductivity measurements. The hydroxyl groups of polysaccharides are the coordination sites. Isolated starch polysaccharides did not coordinate to metal ions so well as starch did. The resulting polycenter Werner complexes were mainly square planar species. The ligation of the central metal atoms resulted in a variation of the thermal stability, pathway, and rate of thermal decomposition of starch as proven by thermogravimetric (TG, DTG) and scanning differential calorimetric measurements. Frequently, amylose and potato amylopectin willingly formed clathrates in which the water molecules were caged. The mode of the coordination of the hydroxyl groups to the central metal atom controlled the clathrate formation from amylose and in the case of potato amylopectin metal atoms bound to the phosphoric acid moiety formed cage by coordination of the hydroxyl groups to them. Coordination to selected metal salts controls pathway and products of polysaccharide ligand thermolysis.     

The Fanconi anaemia gene FANCC promotes homologous recombination and error-prone DNA repair

The Fanconi anemia (FA) protein FANCC is essential for chromosome stability in vertebrate cells, a feature underscored by the extreme sensitivity of FANCC-deficient cells to agents that crosslink DNA. However, it is not known how this FA protein facilitates the repair of both endogenously acquired and mutagen-induced DNA damage. Here, we use the model vertebrate cell line DT40 to address this question. We discover that apart from functioning in homologous recombination, FANCC also promotes the mutational repair of endogenously generated abasic sites. Moreover in these vertebrate cells, the efficient repair of crosslinks requires the combined functions of FANCC, translesion synthesis, and homologous recombination. These studies reveal that the FA proteins cooperate with key mutagenesis and repair processes that enable replication of damaged DNA.     

tRNAPhe cleavage by aminoglycosides is triggered off by formation of an abasic site

This communication reports the characteristics of the mechanism of highly specific tRNA(Phe) cleavage, which occurs in the anticodon loop in the presence of aminoglycoside antibiotic-neomycin B. The data prove that the cleavage requires previous depurination of the polynucleotide chain at position 37, which is occupied by a hypermodified guanine base-wybutine. The results suggest that the phenomenon, previously considered as selective with respect to the presence of tRNA hypermodification, may concern far more RNA molecules, namely the ones carrying abasic sites.     

Gynecomasty as a first sign of adrenal carcinoma--case report

We present a case of 50 year-old man with feminizing adrenal carcinoma. He was admitted to the hospital because of weakness and one year history of gynecomastia and high blood pressure. Examinations revealed a large left adrenal mass and increased levels of estradiol. Patient underwent adrenalectomy and followed by mitotan therapy as the result of histopathological examination was adrenocortical carcinoma. One year after operation patient stays free from the recurrence of the disease and his estradiol, androstendion and DHEA levels are below the detection limits. We report this case because feminizing adrenal carcinoma is a very rare but serious disease and gynecomastia that could be its manifestation is quite frequent symptom in men's population and thus it could easily be missed. In every case of gynecomastia related to estradiol excess feminizing tumors of testis and adrenal gland should be ruled out.