The fragility of a structurally diverse duplication block triggers recurrent genomic amplification

The human genome contains hundreds of large, structurally diverse blocks that are insufficiently represented in the reference genome and are thus not amenable to genomic analyses. Structural diversity in the human population suggests that these blocks are unstable in the germline; however, whether or not these blocks are also unstable in the cancer genome remains elusive. Here we report that the 500 kb block called KRTAP_region_1 (KRTAP-1) on 17q12–21 recurrently demarcates the amplicon of the ERBB2 (HER2) oncogene in breast tumors. KRTAP-1 carries numerous tandemly-duplicated segments that exhibit diversity within the human population. We evaluated the fragility of the block by cytogenetically measuring the distances between the flanking regions and found that spontaneous distance outliers (i.e DNA breaks) appear more frequently at KRTAP-1 than at the representative common fragile site (CFS) FRA16D. Unlike CFSs, KRTAP-1 is not sensitive to aphidicolin. The exonuclease activity of DNA repair protein Mre11 protects KRTAP-1 from breaks, whereas CtIP does not. Breaks at KRTAP-1 lead to the palindromic duplication of the ERBB2 locus and trigger Breakage-Fusion-Bridge cycles. Our results indicate that an insufficiently investigated area of the human genome is fragile and could play a crucial role in cancer genome evolution.     

In Vitro Amphotericin B Effects on Growth,Viability and Dimorphism of Paracoccidioides brasiliensis: Reversal of the Treatment

The in vitro effects of amphotericin B deoxycholate suspension (fungizone) on Paracoccidioides brasiliensis growth, cell viability and transformation were investigated. We also analyzed the protein synthesis patterns of both cellular forms, yeast and mycelium in the presence of AmB. This drug, at 30 μg/ml, highly inhibited yeast growth, which could be recovered depending on treatment time, where the most effective reversion was observed after 6 hr of incubation. The yeast cell viability, that had been partially affected by the drug, could also be efficiently recovered after AmB was removed. The effect of AmB on the cellular dimorphism process showed a strong reduction in the mycelium to yeast transformation (80% inhibition compared to the control without the drug). On the other hand, the transformation from yeast to mycelium in the presence of AmB was 50% affected, relative to the control. In contrast to the growth and cell viability experiments, the reversion effects on dimorphism were partial when the drug was removed, even with only 6 hr treatment. The two-dimensional gels of ³⁵S-labeled proteins revealed a strong reduction in the three species of 80, 71 and 56 kDa in yeast and mycelium when treated with AmB.     

Multiple nutritional phenotypes of fission yeast mutants defective in genes encoding essential mitochondrial proteins

Mitochondria are essential for regulation of cellular respiration, energy production, small molecule metabolism, anti-oxidation and cell ageing, among other things. While the mitochondrial genome contains a small number of protein-coding genes, the great majority of mitochondrial proteins are encoded by chromosomal genes. In the fission yeast Schizosaccharomyces pombe, 770 proteins encoded by chromosomal genes are located in mitochondria. Of these, 195 proteins, many of which are implicated in translation and transport, are absolutely essential for viability. We isolated and characterized eight temperature-sensitive (ts) strains with mutations in essential mitochondrial proteins. Interestingly, they are also sensitive to limited nutrition (glucose and/or nitrogen), producing low-glucose-sensitive and ‘super-housekeeping'' phenotypes. They fail to produce colonies under low-glucose conditions at the permissive temperature or lose cell viability under nitrogen starvation at the restrictive temperature. The majority of these ts mitochondrial mutations may cause defects of gene expression in the mitochondrial genome. mrp4 and mrp17 are defective in mitochondrial ribosomal proteins. ppr3 is defective in rRNA expression, and trz2 and vrs2 are defective in tRNA maturation. This study promises potentially large dividends because mitochondrial quiescent functions are vital for human brain and muscle, and also for longevity.     

Crystal structure of thioredoxin 1 from Cryptococcus neoformans at 1.8 Å resolution shows unexpected plasticity of the loop preceding the catalytic site

An elevated prevalence of cryptococcal infection is a tendency in low-income countries and constitutes a global public health problem due to factors such as the limited efficacy of antifungal therapy and the AIDS/transplant immunocompromised patients. The fungus Cryptococcus neoformans, implicated in this burden, has had several genes validated as drug targets. Among them, the thioredoxin system is one of the major regulators of redox homeostasis and antioxidant defense acting on protein disulfide bonds. Thioredoxin 1 from C. neoformans (CnTrx1) was cloned and expressed in E. coli and the recombinant protein was purified and crystallized. Functional assay shows that CnTrx1 catalyzes the reduction of insulin disulfide bonds using dithiothreitol, while acting as a monomer in solution. The crystal structure of oxidized CnTrx1 at 1.80 Å resolution presents a dimer in the asymmetric unit with typical Trx-fold. Differences between the monomers in the asymmetric unit are found specially in the loop leading to the Cys-Gly-Pro-Cys active-site motif, being even larger when compared to those found between reduced and oxidized states of other thioredoxins. Although the thioredoxins have been isolated and characterized from many organisms, this new structural report provides important clues for understanding the binding and specificity of CnTrx1 to its targets.     

Fibroblast growth-stimulating activity of S100A9 (MRP-14).

Fibroblasts play a critical role in chronic inflammation and wound healing. In this study, a fibroblast growth-stimulating factor was purified from the exudate of carrageenan-induced inflammation in rats. The purified protein was a disulfide-linked homodimer. Amino acid sequence analysis of the peptides generated by cleavage with cyanogen bromide and proteinase V8 resulted in identification of the protein as S100A9. Recombinant S100A9 as well as its disulfide-linked homodimer stimulated the proliferation of fibroblasts at a similar concentration of the purified protein. The concentration of S100A9 in the exudate was determined by immunoblot analysis. The total protein concentration in the exudate reached a maximum 4 days after carrageenan injection and then slightly decreased, whereas the concentration of S100A9 reached a maximum at day 3 and then decreased rapidly. These studies show that S100A9 is present at a high concentration in the exudate of carrageenan-induced inflammation in rats, and that S100A9 stimulates proliferation of fibroblasts, suggesting that it plays a role in chronic inflammation.     

Fine structure of the spermatophores and their ejaculated forms,sperm reservoirs,of the Japanese common squid,Todarodes pacificus

Spermatophores in a squid, Todarodes pacificus, were observed by light and electron microscopy and were further analyzed by X-ray microanalysis (XMA) of frozen thin sections. Each spermatophore consists of a sperm mass, a cement body, an ejaculatory apparatus, and some fluid materials, all of which are covered by an outer tunic. The outer tunic consists of about 20 membranous layers, each containing straight, parallel microgrooves. Each layer's microgroove pattern is roughly in an orthogonal arrangement with respect to the next layer's pattern. The sperm mass, which is the only cellular component, consists of a sperm rope which is coiled more than 500 times. Most of the spermatozoa in the rope are arranged regularly and are enveloped in materials which are well-stained by Alcian blue. The cement body is located between the sperm mass and ejaculatory apparatus and has a hard outer shell with an arrowhead-like structure, presumably for penetration into the tissue of the female. Calcium and phosphorus are present in the shell of the cement body, which also has an affinity for alizarin red. The ejaculatory apparatus consists of two tubes, designated as the inner tunic and the inner membrane. After the spermatophoric reaction, a sperm reservoir is formed at the anterior end of the extruded and inverted ejaculatory apparatus. The sperm reservoir, which encases the sperm mass, is composed of the cement body at the anterior end and the inner tunic of the ejaculatory apparatus at the posterior end.     

Satellite cells in the tail muscles of the urodelan larvae during development

The incidence and ultrastructure of satellite cells in the tail muscles of urodelan larvae were examined during development during which the number of satellite cells is gradually reduced. They are found more frequently in red than in the white fibres in all four stages examined (stage 53, 64, 66+ and juvenile). As development proceeds, intercellular space between satellite cell and muscle fibre is in general gradually extended and is mostly filled with basal lamina. Small muscle cells, satellite fibres, which are situated under the basal lamina of the parent fibre, are morphologically similar to satellite cells but contain a small amount of myofibrils. Three types of satellite fibres are distinguishable on the basis of differences in K2-EDTA-treated ATPase activity, width of Z line, and parent fibre type. Neuromuscular junctions are visible in satellite fibres.