Tandemly repeated DNA families in the mouse genome

<p>Abstract</p> <p>Background</p> <p>Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.</p> <p>Results</p> <p>Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.</p> <p>To confirm our data, we next performed <it>in situ </it>hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to <it>in silico </it>predicted several extra-chromosomes were positive for TR by <it>in situ </it>analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.</p> <p>Conclusions</p> <p>Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified <it>in silico </it>and confirmed <it>in situ </it>3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.</p

Genetic characterization of Iranian grapes (Vitis vinifera L.) and their relationships with Italian ecotypes

Grapevine (Vitis vinifera L.) is one of the oldest and most important fruit crops in the world. Iran is considered as one of the regions where grapevine plants have been used and taken into cultivation. In the present study, 12 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity among Iranian grape cultivars and their relationships with Italian ones. The observed number of alleles (N) per locus varied from 6 to 20 and also the number of effective alleles (Ne) ranged from 1.34 to 2.00 among cultivars, indicating that the SSRs were highly informative. The polymorphism information content (PIC) values ranged from 0.49 to 0.87 and classified the six loci as highly informative markers (PIC &gt; 0.70). The mean observed heterozygosity (Ho) was higher (0.85) than the mean expected heterozygosity (He) (0.43), demonstrating a random union of gametes in the population. Genetic similarity among cultivars ranged from 0.14 to 0.93, indicating high genetic variation among them. UPGMA and Bayesian clustering analyses revealed high genetic variation among studied cultivars and grouped them into two main clusters. The present findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement

Unruptured intracranial aneurysms : development, rupture and preventive management

Saccular unruptured intracranial aneurysms (UIAs) have a prevalence of 3% in the adult population, and are being increasingly detected because of improved quality and higher frequency of cranial imaging. Large amounts of data, providing varying levels of evidence, have been published on aneurysm development, progression and rupture, but less information is available on the risks and efficacy of preventive treatment. When deciding how to best manage UIAs, clinicians must consider the age and life expectancy of the patient, the estimated risk of rupture, the risk of complications attributed to preventive treatment, and the level of anxiety caused by the awareness of having an aneurysm. This Review highlights the latest human data on the formation, progression and rupture of intracranial aneurysms, as well as risks associated with preventive treatment. Considering these we discuss the implication for clinical management. Furthermore, we highlight pivotal questions arising from current data on intracranial aneurysms and the implications the data have for future experimental or clinical research. We also discuss data on novel radiological surrogates for rupture for those aneurysms that do not require preventive occlusion. Finally, we provide guidance for clinicians who are confronted with patients with incidentally detected UIAs