Johns Hopkins University School of Medicine

About: Johns Hopkins University School of Medicine is a(n) healthcare organization based out in Baltimore, Maryland, United States. It is known for research contribution in the topic(s): Population & Cancer. The organization has 44277 authors who have published 79222 publication(s) receiving 4788882 citation(s).

Fast gapped-read alignment with Bowtie 2

Abstract: As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity

Abstract: A technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described. DNA fragments are purified from agarose gels directly by ethanol precipitation and are then denatured and labeled with the large fragment of DNA polymerase I, using random oligonucleotides as primers. Over 70% of the precursor triphosphate is routinely incorporated into complementary DNA, and specific activities of over 10(9) dpm/microgram of DNA can be obtained using relatively small amounts of precursor. These "oligolabeled" DNA fragments serve as efficient probes in filter hybridization experiments.

Multilineage Potential of Adult Human Mesenchymal Stem Cells

Abstract: Human mesenchymal stem cells are thought to be multipotent cells, which are present in adult marrow, that can replicate as undifferentiated cells and that have the potential to differentiate to lineages of mesenchymal tissues, including bone, cartilage, fat, tendon, muscle, and marrow stroma. Cells that have the characteristics of human mesenchymal stem cells were isolated from marrow aspirates of volunteer donors. These cells displayed a stable phenotype and remained as a monolayer in vitro. These adult stem cells could be induced to differentiate exclusively into the adipocytic, chondrocytic, or osteocytic lineages. Individual stem cells were identified that, when expanded to colonies, retained their multilineage potential.

The sequence of the human genome.

Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

A genetic model for colorectal tumorigenesis

Abstract: Tumorigenesis has long been thought to be a multistep process (Foulds, 1958); however, only recently has it become possible to identify the molecular events that underlie the initiation and progression of human tumors (Weinberg, 1989; Bishop, 1987). Colorectal tumors provide an excellent system in which to search for and study the genetic alterations involved in the development of a common human neoplasm. Abundant clinical and histopathological data suggest that most, if not all, malignant colorectal tumors (carcinomas) arise from preexisting benign tumors (adenomas) (Sugarbaker et al., 1985). Tumors of various stages of development, from very small adenomas to large metastatic carcinomas, can be obtained for study, unlike the situation in most other common human tumor types. Furthermore, both hereditary and environmental factors contribute to the development of colorectal neoplasia, allowing for the study of both inherited and somatic genetic alterations. In this review we present a model for the genetic basis of colorectal neoplasia that includes the following salient features. First, colorectal tumors appear to arise as a result of the mutational activation of oncogenes coupled with the mutational inactivation of tumor suppressor genes; the latter changes predominate. Second, mutations in at least four to five genes are required for the formation of a malignant tumor. Fewer changes suffice for benign tumorigenesis. Third, although the genetic alterations often occur according to a preferred sequence, the total accumulation of changes, rather than their order with respect to one another, is responsible for determining the tumor’s biologic properties. Fourth, in some cases, mutant tumor suppressor genes appear to exert a phenotypic effect even when present in the heterozygous state; thus, some tumor suppressor genes may not be “recessive” at the cellular level. The general features of this model may be applicable to other common epithelial neoplasms, in which tumors of varying stage are more difficult to study.