Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides the foundation for nanopore sequencing of long, complex, natural DNA strands.

Mutual information (MI) is a powerful method for detecting relationships between data sets. There are accurate methods for estimating MI that avoid problems with “binning” when both data sets are discrete or when both data sets are continuous. We present an accurate, non-binning MI estimator for the case of one discrete data set and one continuous data set. This case applies when measuring, for example, the relationship between base sequence and gene expression level, or the effect of a cancer drug on patient survival time. We also show how our method can be adapted to calculate the Jensen–Shannon divergence of two or more data sets.

An arrangement of unsaturated fine‐grained soil overlying unsaturated coarse‐grained soil along a sloping contact can, under appropriate circumstances, divert infiltrating water away from the coarser material. Such an arrangement is called a capillary barrier. The water diverted by a capillary barrier flows downdip above the contact. The volume of water moving laterally increases in the downdip direction as additional infiltration is diverted by the barrier. Sufficiently far downdip, the laterally moving water wets the contact to the point that an amount of water equal to the infiltration flows downward through the coarse soil. The lateral flow at such a point represents the diversion capacity of the capillary barrier because this flow will not increase farther downdip. If the width (measured in the direction of dip) of the system is large enough that total infiltration exceeds the diversion capacity, the downdip portion of the barrier will not be effective. The diversion capacity can be calculated exactly in the quasi‐linear approximation where the relationship between relative permeability krel and pressure potential ψ takes the form krel = eαψ. This calculation shows that an upper bound on the width of capillary barriers is Ks tan ø/qα, where Ks is the saturated hydraulic conductivity of the fine soil, ø is the dip angle of the contact, and q is the infiltration rate.

Present techniques for measuring the motion of single motor proteins, such as FRET and optical tweezers, are limited to a resolution of ~300 pm. We use ion current modulation through the protein nanopore MspA to observe translocation of helicase Hel308 on DNA with up to ~40 picometer sensitivity. This approach should be applicable to any protein that translocates on DNA or RNA, including helicases, polymerases, recombinases and DNA repair enzymes.

Recent studies of cellular networks have revealed modular organizations of genes and proteins. For example, in interactome networks, a module refers to a group of interacting proteins that form molecular complexes and/or biochemical pathways and together mediate a biological process. However, it is still poorly understood how biological information is transmitted between different modules. We have developed information flow analysis, a new computational approach that identifies proteins central to the transmission of biological information throughout the network. In the information flow analysis, we represent an interactome network as an electrical circuit, where interactions are modeled as resistors and proteins as interconnecting junctions. Construing the propagation of biological signals as flow of electrical current, our method calculates an information flow score for every protein. Unlike previous metrics of network centrality such as degree or betweenness that only consider topological features, our approach incorporates confidence scores of protein–protein interactions and automatically considers all possible paths in a network when evaluating the importance of each protein. We apply our method to the interactome networks of Saccharomyces cerevisiae and Caenorhabditis elegans. We find that the likelihood of observing lethality and pleiotropy when a protein is eliminated is positively correlated with the protein's information flow score. Even among proteins of low degree or low betweenness, high information scores serve as a strong predictor of loss-of-function lethality or pleiotropy. The correlation between information flow scores and phenotypes supports our hypothesis that the proteins of high information flow reside in central positions in interactome networks. We also show that the ranks of information flow scores are more consistent than that of betweenness when a large amount of noisy data is added to an interactome. Finally, we combine gene expression data with interaction data in C. elegans and construct an interactome network for muscle-specific genes. We find that genes that rank high in terms of information flow in the muscle interactome network but not in the entire network tend to play important roles in muscle function. This framework for studying tissue-specific networks by the information flow model can be applied to other tissues and other organisms as well.

When net recharge is less than about 0.03 mm/yr, moisture movement in deep unsaturated zones at steady state will be dominated by upward movement of vapor driven by the geothermal gradient. With zero net recharge there will be a downward flow of liquid water equal to the upward vapor flux. This will produce a profile of suction potential versus depth qualitatively similar to that expected if recharge is not negligible. Consequently, the existence of a region of uniform potential is not in itself evidence of recharge.

A landfill in Florida which received wastes in 1968 and 1969 has contaminated nearby shallow ground water. Analysis of a sample of contaminated ground water collected in 1984 from a well approximately 300 m from the landfill tentatively indicated the presence of the addictive sedative pentobarbital, among many other compounds. A well at the same location was resampled in 1991, and pentobarbital was positively identified using gas chromatography/tandem mass spectrometry. The persistence over 21 years of a supposedly unstable drug in anoxic ground water raises the possibility that other pharmacologically active compounds may be found in plumes coming from landfills that have accepted medical wastes.

Malyshev et al. showed that the four-letter genetic code within a living organism could be expanded to include the unnatural DNA bases dNaM and d5SICS. However, verification and detection of these unnatural bases in DNA requires new sequencing techniques. Here we provide proof of concept detection of dNaM and d5SICS in DNA oligomers via nanopore sequencing using the nanopore MspA. We find that both phi29 DNA polymerase and Hel308 helicase are capable of controlling the motion of DNA containing dNaM and d5SICS through the pore and that single reads are sufficient to detect the presence and location of dNaM and d5SICS within single molecules.