Mitochondrial DNA (mtDNA) occurs in cells in nucleoids containing several copies of the genome. Previous studies have identified proteins associated with these large DNA structures when they are biochemically purified by sedimentation and immunoaffinity chromatography. In this study, formaldehyde cross-linking was performed to determine which nucleoid proteins are in close contact with the mtDNA. A set of core nucleoid proteins is found in both native and cross-linked nucleoids, including 13 proteins with known roles in mtDNA transactions. Several other metabolic proteins and chaperones identified in native nucleoids, including ATAD3, were not observed to crosslink to mtDNA. Additional immunofluorescence and protease susceptibility studies showed that an N-terminal domain of ATAD3 previously proposed to bind to the mtDNA D-loop is directed away from the mitochondrial matrix, so it is unlikely to interact with mtDNA in vivo. These results are discussed in relation to a model for a layered structure of mtDNA nucleoids in which replication and transcription occur in the central core, whereas translation and complex assembly may occur in the peripheral region.Eukaryotic cells typically contain thousands of mtDNA 2 genomes assembled into hundreds of aggregates known as nucleoids (1-3). These nucleoids show considerable dynamic stability, raising the possibility that this higher order organization is very important to the inheritance and segregation of mtDNAs. Nucleoid organization is thought to contribute to the rapid segregation of mtDNA mutations during oocyte maturation, the so-called "bottleneck" (4, 5), since early primordial germ cells appear to have only a small number of segregation units (6). The degree of mtDNA heteroplasmy varies considerably during embryonic development of somatic tissues as well, reflecting an uneven distribution of mtDNA genotypes that may be influenced by the clustered organization of mtDNA. A high rate of mitochondrial fusion appears to be essential for the maintenance of mtDNA in nucleoids (7,8). One of the consequences of active cycling of mitochondrial fusion and fission may be to permit an individual nucleoid to have access to a larger pool of diffusible proteins required for replication or transcription than it would if it were trapped within a single mitochondrion.Quantitative analysis of the size and mtDNA content of nucleoids in cultured mammalian cells suggests that an average nucleoid may contain 5-7 mtDNA genomes packed in a space with a diameter of only 70 nm (9). A human mtDNA nucleoid with seven 16.6-kb mtDNA genomes is a large structure containing 70 million daltons of DNA and a comparable mass of protein. These nucleoids resemble their counterparts in eubacteria, which employ abundant basic DNA binding proteins to package their genomes in a restricted volume. The packing density of bacterial nucleoids is impressive, since 4700 kb of E. coli DNA is folded into a volume of 0.08 -0.24 m 3 (10). If 5-7 mtDNA molecules are packed in a sphere with a diameter of 70 nm, the ca...

Analyses of AREDS2 data on natural history of GA provide representative data on GA evolution and enlargement. GA enlargement, which was influenced by lesion features, was relentless, resulting in rapid central vision loss. The genetic variants associated with faster enlargement were partially distinct from those associated with risk of incident GA. These findings are relevant to further investigations of GA pathogenesis and clinical trial planning.

The clinical utility of miR-215 as a potential biomarker in colon cancer was investigated. The levels of miR-215 were quantified by real-time qRT-PCR in 34 paired normal and tumor specimens. The expression levels of miR-215 were decreased in colon tumors, and were associated with patient survival. Thus, miR-215 is a potential prognostic biomarker in colon cancer. Background We have previously shown that miR-215 suppressed the expression of key targets such as thymidylate synthase (TS), dihydrofolate reductase, and denticleless protein homolog (DTL) in colon cancer. miR-215 is a tumor suppressor candidate due to the upregulation of p53 and p21 by targeting DTL. However, high levels of miR-215 conferred chemoresistance due to cell cycle arrest and reduced cell proliferation by suppressing DTL. In this study, the clinical significance of miR-215 was further investigated as a potential prognostic biomarker in colon cancer patients. Methods Total RNAs were extracted from 34 paired normal and colon (stage II and III) tumor specimens using the Trizol-based approach. The levels of miR-215 and a closely related miR-192 were quantified using quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis. The expression of DTL mRNA and protein were quantified by real time qRT-PCR and immunohistochemistry. Results The expression levels of miR-192 (P = .0008) and miR-215 (P < .0001) were significantly decreased in colon tumors compared with normal tissues. DTL was significantly over-expressed and was inversely correlated with miR-215, further suggesting an in vivo physiologic relevance of miR-215 mediated DTL suppression. Kaplan-Meier survival analysis by Cox regression revealed that high levels of miR-215 expression (hazard ratio, 3.516; 95% confidence interval, 1.007–12.28, P = .025) are closely associated with poor patient’s overall survival. Furthermore, an elevated expression of a miR-215 target protein DTL was detected in colon cancer tissues whereas no expression was present in normal tissues. Conclusion miR-215 has a unique potential as a prognostic biomarker in stage II and III colon cancer.