Anticipating the 1,000 dollar genome

A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diagnostics, and what will be required to achieve it.     

Anticipating the $1,000 genome

A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the $1,000 human genome is an important goal for research and clinical diagnostics, and what will be required to achieve it.     

Interactions of porphyrins with purified DNA and more highly organized structures

Studies of the solution properties of gold(III)tetrakis(4-N-methylpyridyl) porphine and its DNA binding characteristics have been conducted utilizing uv/vis absorption spectroscopy, circular dichroism (CD), Mossbauer spectroscopy, and temperature-jump relaxation techniques. These studies indicate that over the concentration range considered this water soluble gold(III) porphyrin does not aggregate, binds axial ligands only weakly with a preference for soft Lewis bases, and is capable of intercalation into nucleic acids of appropriate base pair content. The interaction of this and several other porphyrins with the synthetic polynucleotide poly(dA-dC).poly(dT-dG) has been studied. Spectroscopic signatures for intercalation were found for those derivatives not having axial ligands. Intercalation into chromatin in vitro can also occur with those porphyrins and metalloporphyrins which do not have axial ligands. Finally, studies utilizing microinjection techniques indicate that once within the cell, tetrakis(4-N-methylpyridyl)porphine tends to localize in the nucleus.     

Plant secretory structures: more than just reaction bags

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Toward more meaningful hierarchical classification of protein three-dimensional structures.

Recently, several hierarchical classifications of protein three-dimensional (3D) structures have been published. However, none of them provides any assessment of the validity of a hierarchical representation or test individual clusters contained within. In fact, testing here of published trees reveals that they vary in meaning. Protein structure similarity measures are then assessed in terms of the robustness of the resulting trees for 24 protein families. A meaningful tree is defined as one in which all the clusters are found to be reliable according to a jackknife test. With the use of this criterion, a previously published similarity measure described as a "better RMS" is shown in fact to be usually less suited to protein fold classification than normal RMS after superposition. Here the "best" protein structure similarity measure for hierarchical classification-in terms of that which after clustering produces the highest number of meaningful trees, 20, for the 24 families-is found to be a new one. This measure includes information on the relationship of a distance at a given aligned position in a pair to the rest of the unique distances at that position in a protein family. There are only 2 families of the 24 tested, the globins (3 trees) and Kazal-type serine proteinase inhibitors (21 trees), in which the topology (branching order) of the meaningful 3D structure-based trees is constant. Thus, a new view of protein family sequence-structure relationships is afforded by comparing meaningful trees for each family. More generally, there is a need for care in interpretation of the results of those molecular biology algorithms that force a tree structure on data without assessing its applicability. Proteins 1999;37:20-29.     

Answers and questions from the KvAP structures

The recent landmark structures of KvAP, a voltage-gated potassium (Kv) channel, provide the first high-resolution experimental structural models of this class of proteins. Previous extensive studies of Kv channels provide a means to evaluate and interpret the KvAP structures. In this minireview, we survey different experimental approaches to Kv channels and map these findings to KvAP, showing that the relationship between the KvAP structures and other Kv channels is uncertain.     

Amyloid structures: much more than just a cross-β fold

Solving the amyloid puzzle requires an integrated use of structural and functional approaches.

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Prediction of structures of multidomain proteins from structures of the individual domains

We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high-resolution search in which all atoms are treated explicitly and backbone and side chain degrees of freedom are simultaneously optimized. The method recapitulates, often with very high accuracy, the structures of existing multidomain proteins.     

Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years

Background

Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles.

Methodology/Principal Findings

We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a “clean- laboratory” dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the “unhandled” teeth and there was no indication of contamination, while the latter was the case with half of the “handled” teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians) supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes.

Conclusion

The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate precautions are taken and well-considered sampling is applied.     

Review of 1,000 major facial fractures and associated injuries.

The records of 1,020 major facial fractures were reviewed, and it was found that the occurrence of life-threatening associated injuries was highly predictable on the basis of the pattern of facial fractures and the circumstances of the injury. Certain groups of patients have a high probability of associated serious injuries of the central nervous system, the trunk, or the extremities. Probably these patients should be primarily under the care of a surgeon who is capable of the diagnosis and emergency therapy of these associated injuries, as well as the facial injuries, so that appropriate priorities can be established and put in effect.