We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules (‘‘lipoplexes’’)—a promising nonviral carrier of DNA for gene therapy. We identify the resulting structures through direct visualization of the molecular arrangements and through calculations of the corresponding scattering plots. The latter approach provides...

Identification of somatic rearrangements in cancer genomes has accelerated through analysis of high-throughput sequencing data. However, characterization of complex structural alterations and their underlying mechanisms remains inadequate. Here, applying an algorithm to predict structural variations from short reads, we report a comprehensive catalog of somatic structural variations and the mec...

Genomic structural variations are known to play an important role in cancer and other diseases. Next-generation sequencing is a key technology for the identification of such variations, but current data and algorithms yield many false positives and false negative predictions. We have created a prototype tool called Seqeyes to explore and interpret predicted structural variations to help guide e...

The discovery of in vivo catalytic activity for the hammerhead RNA self-cleaving domain has led to the development of a new class of sequence-specific RNA endonucleases. Two such ribozymes have been synthesized using in vitro transcription with T7 polymerase and their structures have been studied by optical spectroscopy, nuclear magnetic resonance and nondenaturing gel electrophoresis. These da...

A majority of species B adenoviruses (Ads) use CD46 as their primary receptor; however, the precise mechanisms involved in the binding of different Ad types to CD46 have not been resolved. Although previous studies indicate close similarities between two members of species B2 Ads in their usage of CD46, our current investigations revealed a surprisingly low CD46 binding affinity of the species ...

Aneuploidy and structural variations (SVs) generate cancer genomes containing a mixture of rearranged genomic segments with extensive somatic copy number alterations. However, existing methods can identify either SVs or allele-specific copy number alterations but not both simultaneously, which provides a limited view of cancer genome structure. Here, we introduce Weaver, an algorithm for the qu...

Pediatric osteosarcoma is characterized by multiple somatic chromosomal lesions, including structural variations (SVs) and copy number alterations (CNAs). To define the landscape of somatic mutations in pediatric osteosarcoma, we performed whole-genome sequencing of DNA from 20 osteosarcoma tumor samples and matched normal tissue in a discovery cohort, as well as 14 samples in a validation coho...

The emergence of third-generation photovoltaics based on Si relies on tunable bandgap materials with embedded nanocrystalline Si. One of the most promising approaches is based on the mixed-phase Si1 - xCx. We have investigated the light absorption controllability of nanocrystalline Si-embedded Si1 - xCx produced by thermal annealing of the Si-rich Si1 - xCx and composition-modulated superlattic...

Despite the long term interest in hydroxyoximes as metal ion extractants, there is a lack of information on the possible coordination modes these ligands can assume, particularly in concert with a co-ligand. This is pertinent to the use of these extractants in synergistic systems, where a combination of extractants can achieve commercially useful results. We report here the structures of some m...

OBJECTIVE To determine the relative contributions of mutations in congenital cataract cases in an Indian population by systematic screening of genes associated with cataract. METHODS We enrolled 100 congenital cataract cases presenting at the Dr. R. P. Centre for Ophthalmic Sciences, a tertiary research and referral hospital (AIIMS, New Delhi, India). Crystallin, alpha A (CRYAA), CRYAB, CRYGs...