Short adjacent repeat identification based on chemical reaction optimization

IEEE World Congress on Computational Intelligence (WCCI 2012), Brisbane, Australia, 10-15 June 2012 hosted three conferences: the 2012 International Joint Conference on Neural Networks (IJCNN 2012), the 2012 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2012), and the 2012 IEEE Congress on Evolutionary Computation (IEEE CEC 2012)The analysis of short tandem repeats (STRs) in DNA sequences has become an attractive method for determining the genetic profile of an individual. Here we focus on a more general and practical issue named short adjacent repeats identification problem (SARIP), which is extended from STR by allowing short gaps between neighboring units. Presently, the best available solution to SARIP is BASARD, which uses Markov chain Monte Carlo algorithms to determine the posterior estimate. However, the computational complexity and the tendency to get stuck in a local mode lower the efficiency of BASARD and impede its wide application. In this paper, we prove that SARIP is NP-hard, and we also solve it with Chemical Reaction Optimization (CRO), a recently developed metaheuristic approach. CRO mimics the interactions of molecules in a chemical reaction and it can explore the solution space efficiently to find the optimal or near optimal solution(s). We test the CRO algorithm with both synthetic and real data, and compare its performance in mode searching with BASARD. Simulation results show that CRO enjoys dozens of times, or even a hundred times shorter computational time compared with BASARD. It is also demonstrated that CRO can obtain the global optima most of the time. Moreover, CRO is more stable in different runs, which is of great importance in practical use. Thus, CRO is by far the best method on SARIP. © 2012 IEEE.published_or_final_versio

Rapid mapping of chromosomal breakpoints: from blood to BAC in 20 days

Structural chromosome aberrations and associated segmental or chromosomal aneusomies are major causes of reproductive failure in humans. Despite the fact that carriers of reciprocal balanced translocation often have no other clinical symptoms or disease, impaired chromosome homologue pairing in meiosis and karyokinesis errors lead to over-representation of translocations carriers in the infertile population and in recurrent pregnancy loss patients. At present, clinicians have no means to select healthy germ cells or balanced zygotes in vivo, but in vitro fertilization (IVF) followed by preimplantation genetic diagnosis (PGD) offers translocation carriers a chance to select balanced or normal embryos for transfer. Although a combination of telomeric and centromeric probes can differentiate embryos that are unbalanced from normal or unbalanced ones, a seemingly random position of breakpoints in these IVF-patients poses a serious obstacle to differentiating between normal and balanced embryos, which for most translocation couples, is desirable. Using a carrier with reciprocal translocation t(4;13) as an example, we describe our state-of-the-art approach to the preparation of patient-specific DNA probes that span or 'extent' the breakpoints. With the techniques and resources described here, most breakpoints can be accurately mapped in a matter of days using carrier lymphocytes, and a few extra days are allowed for PGD-probe optimization. The optimized probes will then be suitable for interphase cell analysis, a prerequisite for PGD since blastomeres are biopsied from normally growing day 3 – embryos regardless of their position in the mitotic cell cycle. Furthermore, routine application of these rapid methods should make PGD even more affordable for translocation carriers enrolled in IVF programs

Abundant variation in microsatellites of the parasitic nematode Trichostrongylus tenuis and linkage to a tandem repeat

An understanding of how genes move between and within populations of parasitic nematodes is important in combating the evolution and spread of anthelmintic resistance. Much has been learned by studying mitochondrial DNA markers, but autosomal markers such as microsatellites have been applied to only a few nematode species, despite their many advantages for studying gene flow in eukaryotes. Here, we describe the isolation of 307 microsatellites from Trichostrongylus tenuis, an intestinal nematode of red grouse. High levels of variation were revealed at sixteen microsatellite loci (including three sex-lined loci) in 111 male T. tenuis nematodes collected from four hosts at a single grouse estate in Scotland (average He = 0.708; mean number of alleles = 12.2). A population genetic analysis detected no deviation from panmixia either between (F(ST) = 0.00) or within hosts (F(IS) = 0.015). We discuss the feasibility of developing microsatellites in parasitic nematodes and the problem of null alleles. We also describe a novel 146-bp repeat element, TteREP1, which is linked to two-thirds of the microsatellites sequenced and is associated with marker development failure. The sequence of TteREP1 is related to the TcREP-class of repeats found in several other trichostrongyloid species including Trichostrongylus colubriformis and Haemonchus contortus

A Novel Forensic DNA Profiling Method Based On Molecular Beacons Without Dna Purification

Analysis of polymorphisms in nucleic acid sequences provides the basis for identification of individuals and their genetic deficiencies. Currently, the accepted method of analysis for profiling is Short Tandem Repeat (STR) profiling. This is a lengthy process, typically taking up to 3 days. The time necessary to generate an STR profile, along with the ever-increasing reliance on DNA to solve crimes, has led to a large DNA sample backlog, with violent crime turnaround taking an average of 103 days. The time and resource investment required for STR analysis is significant, and not all samples generate useful profiles. The current methods for use of STR technologies require an isolated template sample. This isolation typically requires hours of extractions and incubations, followed by still more time for analysis. The considerable length of time necessary for this process makes it inherently expensive, while also increasing the backlog. A universal protocol allowing amplification from various, frequently used samples would allow extremely rapid sampling and results. Further, these templates are faster and easier to amplify than standard STRs, which reduces the risk of resources and time on a sample which may not amplify. Common forensic samples include blood, hair, saliva, and buccal swabs. Using a single, universal protocol to prepare these samples for analysis without extensive isolation allows the simultaneous preparation of multiple samples. Accordingly, this work explores the development of a preparatory method for multiple forensic samples coupled with the optimization of polymerase chain reaction conditions to facilitate the real-time monitoring of the interaction of molecular beacons (MBs) with the template. These MBs can then be used to identify the presence or absence of specific nucleotide polymorphisms. This increase in throughput has extensive application in forensic and medical applications

Mol. Cell. Proteomics

Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe

Fluorescent labeling of plasmid DNA and mRNA : gains and losses of current labeling strategies

Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs