Sequence organization of feline leukemis virus DNA in infected cells

A restriction site map has been deduced of unintegrated and integrated FeLV viral DNA found in human RD cells after experimental infection with the Gardner-Arnstein strain of FeLV. Restriction fragments were ordered by single and double enzyme digests followed by Southern transfer (1) and hybridization with 32P-labeled viral cDNA probes. The restriction map was oriented with respect to the 5' and 3' ends of viral RNA by using a 3' specific hybridization probe. The major form of unintegrated viral DNA found was a 8.7 kb linear DNA molecule bearing a 450 bp direct long terminal redundancy (LTR) derived from both 5' and 3' viral RNA sequences. Minor, circular forms, 8.7 kb and 8.2 kb in length were also detected, the larger one probably containing two adjacent copies of the LTR and the smaller one containing one copy of the LTR. Integrated copies of FeLV are colinear with the unintegrated linear form and contain the KpnI and SmaI sites found in each LTR

Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA·Fe(II)

In the presence of O2 and 5 mM dithiothreitol, penta-N-methylpyrrolecarboxamide-EDTA·Fe(II) [P5E·Fe(II)] at 0.5 µ M cleaves pBR322 plasmid DNA (50 µ M in base pairs) on opposite strands to afford discrete DNA fragments as analyzed by agarose gel electrophoresis. High-resolution denaturing gel electrophoresis of a 32P-end-labeled 517-base-pair restriction fragment containing a major cleavage site reveals that P5E·Fe(II) cleaves 3-5 base pairs contiguous to a 6-base-pair sequence, 5'-T-T-T-T-T-A-3' (4,323-4,328 base pairs). The major binding orientation of the pentapeptide occurs with the amino terminus at the adenine side of this sequence. In the presence of 5 mM dithiothreitol, 0.01 µ M P5E·Fe(II) converts form I pBR322 DNA at 0.22 µ M plasmid (1.0 mM in base pairs) to 40% form II, indicating the cleavage reaction is catalytic, turning over a minimum of nine times. This synthetic molecule achieves double-strand cleavage of DNA (pH 7.9, 25 degrees C) at the 6-base-pair recognition level and may provide an approach to the design of "artificial restriction enzymes.

Reconstruction of Integers from Pairwise Distances

Given a set of integers, one can easily construct the set of their pairwise distances. We consider the inverse problem: given a set of pairwise distances, find the integer set which realizes the pairwise distance set. This problem arises in a lot of fields in engineering and applied physics, and has confounded researchers for over 60 years. It is one of the few fundamental problems that are neither known to be NP-hard nor solvable by polynomial-time algorithms. Whether unique recovery is possible also remains an open question. In many practical applications where this problem occurs, the integer set is naturally sparse (i.e., the integers are sufficiently spaced), a property which has not been explored. In this work, we exploit the sparse nature of the integer set and develop a polynomial-time algorithm which provably recovers the set of integers (up to linear shift and reversal) from the set of their pairwise distances with arbitrarily high probability if the sparsity is O(n^{1/2-\eps}). Numerical simulations verify the effectiveness of the proposed algorithm.Comment: 14 pages, 4 figures, submitted to ICASSP 201

Double-digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles.

The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low-cost double-digest restriction site-associated DNA sequencing (ddRADseq) protocol to reveal among- and within-species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded adapters and incorporates universal indexes for multiplexing. We tested for reproducibility and functionality by comparing shared loci from sample replicates and assessed the effects of numbers of ambiguous sites and clustering thresholds on coverage depths, number of shared loci among samples, and phylogenetic reconstruction. Errors between technical replicates were minimal. Relaxing the quality-filtering criteria increased the mean coverage depth per locus and the number of loci recovered within a sample, but had little effect on the number of shared loci across samples. Increasing clustering threshold decreased the mean coverage depth per cluster and increased the number of loci recovered within a sample but also decreased the number of shared loci across samples, especially among distantly related species. The combination of low similarity clustering (70%) and relaxed quality-filtering (allowing up to 30 ambiguous sites per read) performed the best in phylogenetic analyses at both recent and deep genetic divergences. Hence, this method generated sufficient number of shared homologous loci to investigate the evolutionary relationships among divergent fungal lineages with small haploid genomes. The greater genetic resolution also revealed new structure within species that correlated with ecological traits, providing valuable insights into their cryptic life histories

Phase Retrieval for Sparse Signals: Uniqueness Conditions

In a variety of fields, in particular those involving imaging and optics, we often measure signals whose phase is missing or has been irremediably distorted. Phase retrieval attempts the recovery of the phase information of a signal from the magnitude of its Fourier transform to enable the reconstruction of the original signal. A fundamental question then is: "Under which conditions can we uniquely recover the signal of interest from its measured magnitudes?" In this paper, we assume the measured signal to be sparse. This is a natural assumption in many applications, such as X-ray crystallography, speckle imaging and blind channel estimation. In this work, we derive a sufficient condition for the uniqueness of the solution of the phase retrieval (PR) problem for both discrete and continuous domains, and for one and multi-dimensional domains. More precisely, we show that there is a strong connection between PR and the turnpike problem, a classic combinatorial problem. We also prove that the existence of collisions in the autocorrelation function of the signal may preclude the uniqueness of the solution of PR. Then, assuming the absence of collisions, we prove that the solution is almost surely unique on 1-dimensional domains. Finally, we extend this result to multi-dimensional signals by solving a set of 1-dimensional problems. We show that the solution of the multi-dimensional problem is unique when the autocorrelation function has no collisions, significantly improving upon a previously known result.Comment: submitted to IEEE TI

PLASMD BEARING A CDNA COPY OF THE GENOME OF BOVINE VIRAL DIARRHEA VIRUS, CHIMERIC DERIVATIVES THEREOF, AND METHOD OF PRODUCING AN INFECTIOUS BOVINE WRAL DARRHEAVIRUS USING SAD PLASMID

A plasmid bearing a cDNA copy of the genome of bovine viral diarrhea virus (BVDV), chimeric derivatives of the plasmid and a method of producing an infectious bovine viral diarrhea virus using the plasmid are disclosed. The invention relates to a plasmid DNA molecule that replicates easily in E. coli and contains a sufficient portion of the genome of BVDV, cloned as cDNA, to be a suitable template to produce RNA in vitro which, upon transfection into bovine cells, gives rise to infectious BVDV. The BVDV created by the process of the invention can be engineered for use as a vector in many advantageous applications

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-site associated DNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long

The application of artificial intelligence techniques to a sequencing problem in the biological domain

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