Relationships between genomic dissipation and de novo SNP evolution.

Patterns of single nucleotide polymorphisms (SNPs) in eukaryotic DNA are traditionally attributed to selective pressure, drift, identity descent, or related factors-without accounting for ways in which bias during de novo SNP formation, itself, might contribute. A functional and phenotypic analysis based on evolutionary resilience of DNA points to decreased numbers of non-synonymous SNPs in human and other genomes, with a predominant component of SNP depletion in the human gene pool caused by robust preferences during de novo SNP formation (rather than selective constraint). Ramifications of these findings are broad, belie a number of concepts regarding human evolution, and point to a novel interpretation of evolving DNA across diverse species.

SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution.

In this study, we show novel DNA motifs that promote single nucleotide polymorphism (SNP) formation and are conserved among exons, introns, and intergenic DNA from mice (Sanger Mouse Genomes Project), human genes (1000 Genomes), and tumor-specific somatic mutations (data from TCGA). We further characterize SNPs likely to be very recent in origin (i.e., formed in otherwise congenic mice) and show enrichment for both synonymous and parallel DNA variants occurring under circumstances not attributable to purifying selection. The findings provide insight regarding SNP contextual bias and eukaryotic codon usage as strategies that favor long-term exonic stability. The study also furnishes new information concerning rates of murine genomic evolution and features of DNA mutagenesis (at the time of SNP formation) that should be viewed as "adaptive."

Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA.

Like many other ancient genes, the cystic fibrosis transmembrane conductance regulator (CFTR) has survived for hundreds of millions of years. In this report, we consider whether such prodigious longevity of an individual gene--as opposed to an entire genome or species--should be considered surprising in the face of eons of relentless DNA replication errors, mutagenesis, and other causes of sequence polymorphism. The conventions that modern human SNP patterns result either from purifying selection or random (neutral) drift were not well supported, since extant models account rather poorly for the known plasticity and function (or the established SNP distributions) found in a multitude of genes such as CFTR. Instead, our analysis can be taken as a polemic indicating that SNPs in CFTR and many other mammalian genes may have been generated--and continue to accrue--in a fundamentally more organized manner than would otherwise have been expected. The resulting viewpoint contradicts earlier claims of 'directional' or 'intelligent design-type' SNP formation, and has important implications regarding the pace of DNA adaptation, the genesis of conserved non-coding DNA, and the extent to which eukaryotic SNP formation should be viewed as adaptive.

Expression-based network biology identifies immune-related functional modules involved in plant defense.

BACKGROUND: Plants respond to diverse environmental cues including microbial perturbations by coordinated regulation of thousands of genes. These intricate transcriptional regulatory interactions depend on the recognition of specific promoter sequences by regulatory transcription factors. The combinatorial and cooperative action of multiple transcription factors defines a regulatory network that enables plant cells to respond to distinct biological signals. The identification of immune-related modules in large-scale transcriptional regulatory networks can reveal the mechanisms by which exposure to a pathogen elicits a precise phenotypic immune response. RESULTS: We have generated a large-scale immune co-expression network using a comprehensive set of Arabidopsis thaliana (hereafter Arabidopsis) transcriptomic data, which consists of a wide spectrum of immune responses to pathogens or pathogen-mimicking stimuli treatments. We employed both linear and non-linear models to generate Arabidopsis immune co-expression regulatory (AICR) network. We computed network topological properties and ascertained that this newly constructed immune network is densely connected, possesses hubs, exhibits high modularity, and displays hallmarks of a "real" biological network. We partitioned the network and identified 156 novel modules related to immune functions. Gene Ontology (GO) enrichment analyses provided insight into the key biological processes involved in determining finely tuned immune responses. We also developed novel software called OCCEAN (One Click Cis-regulatory Elements ANalysis) to discover statistically enriched promoter elements in the upstream regulatory regions of Arabidopsis at a whole genome level. We demonstrated that OCCEAN exhibits higher precision than the existing promoter element discovery tools. In light of known and newly discovered cis-regulatory elements, we evaluated biological significance of two key immune-related functional modules and proposed mechanism(s) to explain how large sets of diverse GO genes coherently function to mount effective immune responses. CONCLUSIONS: We used a network-based, top-down approach to discover immune-related modules from transcriptomic data in Arabidopsis. Detailed analyses of these functional modules reveal new insight into the topological properties of immune co-expression networks and a comprehensive understanding of multifaceted plant defense responses. We present evidence that our newly developed software, OCCEAN, could become a popular tool for the Arabidopsis research community as well as potentially expand to analyze other eukaryotic genomes.

Optimizing nasal potential difference analysis for CFTR modulator development: assessment of ivacaftor in CF subjects with the G551D-CFTR mutation.

Nasal potential difference (NPD) is used as a biomarker of the cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC) activity. We evaluated methods to detect changes in chloride and sodium transport by NPD based on a secondary analysis of a Phase II CFTR-modulator study. Thirty-nine subjects with CF who also had the G551D-CFTR mutation were randomized to receive ivacaftor (Kalydeco™; also known as VX-770) in four doses or placebo twice daily for at least 14 days. All data were analyzed by a single investigator who was blinded to treatment assignment. We compared three analysis methods to determine the best approach to quantify changes in chloride and sodium transport: (1) the average of both nostrils; (2) the most-polarized nostril at each visit; and (3) the most-polarized nostril at screening carried forward. Parameters of ion transport included the PD change with zero chloride plus isoproterenol (CFTR activity), the basal PD, Ringer's PD, and change in PD with amiloride (measurements of ENaC activity), and the delta NPD (measuring CFTR and ENaC activity). The average and most-polarized nostril at each visit were most sensitive to changes in chloride and sodium transport, whereas the most-polarized nostril at screening carried forward was less discriminatory. Based on our findings, NPD studies should assess both nostrils rather than a single nostril. We also found that changes in CFTR activity were more readily detected than changes in ENaC activity, and that rigorous standardization was associated with relatively good within-subject reproducibility in placebo-treated subjects (± 2.8 mV). Therefore, we have confirmed an assay of reasonable reproducibility for detecting chloride-transport improvements in response to CFTR modulation.

Massive microRNA sequence conservation and prevalence in human and chimpanzee introns.

Human and chimpanzee introns contain numerous sequences strongly related to known microRNA hairpin structures. The relative frequency is precisely maintained across all chromosomes, suggesting the possible co-evolution of gene networks dependent upon microRNA regulation and with origins corresponding to the advent of primate transposable elements (TEs). While the motifs are known to be derived from transposable elements, the most common are far more numerous than expected from the number of TEs and their paralogous sequences, and exhibit striking conservation in comparison to the surrounding TE sequence context. Several of these motifs also exhibit structural complimentarity to each other, suggesting a pairing function at the level of DNA or RNA. These "pseudomicroRNAs," in semblance to pseudogenes, include hundreds of thousands of vestigial paralogs of primate microRNAs, many of which may have functioned historically or remain active today.

An international randomized multicenter comparison of nasal potential difference techniques.

BACKGROUND: The transepithelial nasal potential difference (NPD) is used to assess cystic fibrosis transmembrane conductance regulator (CFTR) activity. Unreliability, excessive artifacts, and lack of standardization of current testing systems can compromise its use as a diagnostic test and outcome measure for clinical trials. METHODS: To determine whether a nonperfusing (agar gel) nasal catheter for NPD measurement is more reliable and less susceptible to artifacts than a continuously perfusing nasal catheter, we performed a multicenter, randomized, crossover trial comparing a standardized NPD protocol using an agar nasal catheter with the same protocol using a continuously perfusing catheter. The data capture technique was identical in both protocols. A total of 26 normal adult subjects underwent NPD testing at six different centers. RESULTS: Artifact frequency was reduced by 75% (P < .001), and duration was less pronounced using the agar catheter. The measurement of sodium conductance was similar between the two catheter methods, but the agar catheter demonstrated significantly greater CFTR-dependent hyperpolarization, because Δ zero Cl- + isoproterenol measurements were significantly more hyperpolarized with the agar catheter (224.2 ± 12.9 mV with agar vs 18.2 ± 9.1 mV with perfusion, P < .05). CONCLUSIONS: The agar nasal catheter approach demonstrates superior reliability compared with the perfusion nasal catheter method for measurement of NPD. This nonperfusion catheter method should be considered for adoption as a standardized protocol to monitor CFTR activity in clinical trials.

Evolutionary maintenance of oncogenesis.

BACKGROUND: Transformation of normal cells into cells with malignant phenotypes is often the result of loss of tumor suppressor gene (TSG) function after exposure to a carcinogen. CONCLUSIONS: We propose that TSGs susceptible to mutation and consequent loss of function are evolutionarily preserved in normal cell genomes so that the cells survive mutation-inducing insults and thereby evade apoptosis. While the mutations produced in TSGs confer cellular persistence and preclude apoptosis, oncogenesis is the untoward consequence. Proto-oncogenes might similarly be maintained and contain evolutionarily selected and fixed sequences susceptible to mutations (oncogene activation) that prevent cell death but ironically result in host death from malignancy.

The non-random distribution of intronless human genes across molecular function categories.

It has been proposed that one function of introns is to coordinate expression across/within networks of related genes. This same hypothesis also predicts that intronless genes will not be uniformly distributed among the functional categories of human genes, but will be found most frequently in those categories that have less need to communicate changes in their expression. Statistical analysis demonstrates significant clustering of single exon genes among those with binding or signal transduction/receptor activities and fewer than expected among those with catalytic function.

Micro-RNA-like effects of complete intronic sequences.

MicroRNAs (miRNAs) have been suggested as suppressors of numerous target genes in human cells. In this report, we present gene chip array data indicating that in the absence of miRNA sequences, complete human introns are similarly capable of coordinating expression of large numbers of gene products at spatially diverse sites within the genome. The expression of selected intronic sequences (6a, 14b and 23) derived from the cystic fibrosis transmembrane conductance regulator (CFTR) gene caused extensive and specific transcriptional changes in epithelial cells (HeLa) that do not normally express this gene product. Each intron initiated a distinctive pattern of gene transcription. Affected genes such as FOXF1, sucrase-isomaltase, collagen, interferon, complement and thrombospondin 1 have previously been linked to CFTR function or are known to contribute to the related processes of epithelial differentiation and repair. A possible regulatory function of this nature has not been demonstrated previously for non-coding sequences within eukaryotic DNA. The results are consistent with the observation that splicesomal introns are found only in eukaryotic organisms and that the number of introns increases with phylogenetic complexity.

Human genome -- from pieces to patterns.

A profile of exon-intron lengths in genes shows a normal distribution. This observation suggests that different genes may have portions of their total exon and/or intron lengths in common. In order to explore the common exon-intron structural patterns that may arise due to common lengths across genes, we compared the exon-intron length patterns of annotated human genes. We discovered 1762278 conserved arrangements of exon-intron length across the otherwise unrelated and diverse genomic landscape. The existence of common exon-intron length patterns across unrelated genes suggests for their role of in gene assemblage and human genome design and architecture.

Common structural patterns in human genes.

MOTIVATION: A graphical representation of the exon-intron structure of various genes, such as that presented by the National Center for Biotechnology Information Map Viewer, suggests a digital waveform or pattern that varies either in amplitude or frequency. This observation suggests that different genes may have portions of their total exon-intron structure in common. The existence of common structural patterns across unrelated genes suggests the repeated insertion of transposable elements throughout the human genome and/or a common structural function. RESULTS: We compared the exon-intron size patterns of a number of human genes and discovered numerous conserved arrangements with similarity at a high degree of stringency (>99%) across the otherwise unrelated and diverse genomic landscape. In our experimental analyses, more than 200 patterns of length 2 or greater at 99% stringency were found among the 72 genes we compared.

The UAB Proteomics Database.

SUMMARY: The University of Alabama at Birmingham (UAB) Proteomics Database (UPD) (http://www.uab.edu/proteinmenu) was created to provide a repository for the storage and linkage of two-dimensional (2D) gel images and the associated information obtained through mass spectrometry analysis of the proteins excised from the 2D gels in a manner similar to the SWISS-2DPAGE database and the Stanford Microarray Database. This was accomplished through the development of a web interface, a relational database, image maps and hyperlinks stored in the database. In addition to the internally generated data, UPD provides links to the National Center for Biotechnology Information via accession number hyperlinks. UPD currently contains information on 44 individual proteins derived from four experiments conducted by four UAB faculty members. Images of the gels from which each of these proteins was isolated are accessed by hyperlinks embedded in the database. AVAILABILITY: The UAB Proteomics Database can be accessed at http://www.uab.edu/proteinmenu.

Comparative gene expression profile analysis of GLI and c-MYC in an epithelial model of malignant transformation.

Transcription factor oncogenes such as GLI and c-MYC are central to the pathogenesis of human tumors. GLI encodes a zinc finger protein that is activated by Sonic Hedgehog signaling. Mutations in this pathway induce GLI expression in basal cell carcinoma, and expression of GLI in mice is sufficient to induce these skin tumors. We used microarrays to identify transcripts regulated by GLI or c-MYC after retroviral transduction and short-term culture of epithelial RK3E cells. Although each of these oncogenes induces malignant transformation of RK3E, two distinct sets of genes were identified. Of approximately 17,500 transcripts represented on the microarrays, GLI up-regulated the expression of 158 and repressed the expression of 52. In contrast, transcripts regulated by c-MYC were mainly repressed (424 of 682 regulated transcripts). Transcripts induced by the GLI transgene are likewise expressed in association with endogenous GLI in Ptch-deficient murine fibroblasts or in human skin tumors, but are not up-regulated in RK3E cells transformed by c-MYC, KLF4, or HRAS1. Unlike these other oncogenes, GLI induced the expression of mesenchymal cell markers including Snail, a zinc finger protein implicated in epithelial-mesenchymal transition in development and during tumor progression. A novel GLI-estrogen receptor fusion protein rapidly induced Snail mRNA expression in a manner like Ptch, a known direct transcriptional target gene. Induction of Snail expression and epithelial-mesenchymal transition by GLI may account for certain histopathological features of basal cell carcinoma, such as the absence of a well-defined, intraepithelial precursor lesion. In addition, consistent expression of the newly identified GLI-induced transcripts within GLI-expressing tumors in vivo indicates that oncogene-specific transcriptional profiles may be useful diagnostic tools for analysis of human tumors.

Synthesis of adenine from HCN tetramer and ammonium formate.

Adenine is formed in about 18% yield when HCN tetramer is heated with ammonium formate at 110 degrees C. The prebiotic significance of this reaction is discussed.