Control region mutations and the 'common deletion' are frequent in the mitochondrial DNA of patients with esophageal squamous cell carcinoma

BACKGROUND: North central China has some of the highest rates of esophageal squamous cell carcinoma in the world with cumulative mortality surpassing 20%. Mitochondrial DNA (mtDNA) accumulates more mutations than nuclear DNA and because of its high abundance has been proposed as a early detection device for subjects with cancer at various sites. We wished to examine the prevalence of mtDNA mutation and polymorphism in subjects from this high risk area of China. METHODS: We used DNA samples isolated from tumors, adjacent normal esophageal tissue, and blood from 21 esophageal squamous cell carcinoma cases and DNA isolated from blood from 23 healthy persons. We completely sequenced the control region (D-Loop) from each of these samples and used a PCR assay to assess the presence of the 4977 bp common deletion. RESULTS: Direct DNA sequencing revealed that 7/21 (33%, 95% CI = 17–55%) tumor samples had mutations in the control region, with clustering evident in the hyper-variable segment 1 (HSV1) and the homopolymeric stretch surrounding position 309. The number of mutations per subject ranged from 1 to 16 and there were a number of instances of heteroplasmy. We detected the 4977 bp 'common deletion' in 92% of the tumor and adjacent normal esophageal tissue samples examined, whereas no evidence of the common deletion was found in corresponding peripheral blood samples. CONCLUSIONS: Control region mutations were insufficiently common to warrant attempts to develop mtDNA mutation screening as a clinical test for ESCC. The common deletion was highly prevalent in the esophageal tissue of cancer cases but absent from peripheral blood. The potential utility of the common deletion in an early detection system will be pursued in further studies

Plant-inducible virulence promoter of the Agrobacterium tumefaciens Ti plasmid

Agrobacterium tumefaciens is the causative agent of crown gall, a plant tumour that can arise on most species of dicotyledonous plants. The tumour-inducing capacity of the bacterium requires the presence of a large plasmid, designated the Ti plasmid, which itself contains two regions essential for tumour formation-the T(umour)-region and the Vir(ulence)-region. The T-region is transferred to plant cells by an unknown mechanism, and becomes stably integrated into the plant genome. The Vir-region has been identified by transposon mutagenesis, but the DNA of this region has never been detected in tumour lines. However, trans-complementation of Vir mutants indicates that genes of the Vir-region are functional in the bacterium. Moreover, the Vir- and T-regions can be physically separated in A. tumefaciens without loss of tumour-inducing capacity. Seven loci, designated virA-F and virO, have been identified in the Vir-region of the octopine Ti plasmid, but their functions are unknown. As virC mutants in the octopine-type plasmid pTiB6 are invariably avirulent in tests on various plant species, this gene seems to be essential for virulence and we are studying it in detail. We report here that the promoter of virC shows no detectable activity in A. tumefaciens and Escherichia coli K-12 grown in standard medium, but that its activity is induced by a plant product.

Predicting site index from climate and soil variables for cork oak (Quercus suber L.) stands in Portugal

Site productivity, assessed through site index, was modelled using partial least squares regression as a function of soil and climatic variables. Two alternative models were developed: a full model, considering all available explanatory variables, and a reduced model, considering only variables that can be obtained without digging a soil pit. The reduced model was used for mapping the site index distribution in Portugal, on the basis of existing digital cartography available for the whole country. The developed models indicate the importance of water availability and soil water holding capacity for site index value distribution. Site index was related to climate, namely evaporation and frost, and soil characteristics such as lithology, soil texture, soil depth, thickness of the A horizon and soil classification. The variability of the estimated values within the map (9.5–16.8 m with an average value of 13.4 m) reflects the impact of soil characteristics on the site productivity estimation. These variables should be taken into consideration during the establishment of new plantations of cork oak, and management of existing plantations. Results confirm the potential distribution of cork oak in coastal regions. They also suggest the existence of a considerable area, located both North and South of the Tagus river, where site indices values of medium (]13;15]) to high (]15;17]) productivity classes may be expected. The species is then expected to be able to have good productivity along the northern coastal areas of Portugal, where presently it is not a common species but where, according to historical records, it occurred until the middle of the sixteenth century. The present research focused on tree growth. Cork growth and cork quality distribution needs to be further researched through the establishment of long term experimental sites along the distribution area of cork oak, namely in the central and northern coastal areas of the countryinfo:eu-repo/semantics/publishedVersio

Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules

Cytoplasmic dynein is a dimeric AAA+ motor protein that performs critical roles in eukaryotic cells by moving along microtubules using ATP. Here using cryo-electron microscopy we directly observe the structure of Dictyostelium discoideum dynein dimers on microtubules at near-physiological ATP concentrations. They display remarkable flexibility at a hinge close to the microtubule binding domain (the stalkhead) producing a wide range of head positions. About half the molecules have the two heads separated from one another, with both leading and trailing motors attached to the microtubule. The other half have the two heads and stalks closely superposed in a front-to-back arrangement of the AAA+ rings, suggesting specific contact between the heads. All stalks point towards the microtubule minus end. Mean stalk angles depend on the separation between their stalkheads, which allows estimation of inter-head tension. These findings provide a structural framework for understanding dynein’s directionality and unusual stepping behaviour