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An interview is presented with computational biologist Ewan Birney about his experience leading the ENCODE (Encyclopedia of DNA Elements) project. Topics include how 1.2 percent of bases are involved in protein-coding exons, how estimates implicate at least 9 percent of bases in regulation, and genome-wide association studies and their implications for medicine.

The article discusses the history of the genome. The author presents a DNA sequence, noting that the sequence is found in every cell of every organism on Earth and is more than a recipe for creating life, but is a living historical record of life itself. Topics include a historical overview of the role of RNA in creating the first-ever genome, a theory that at least 100 genes can be traced back to a mixture of virus-like elements that separated to become simple cells, known as the last universal common ancestor (LUCA), and the role of sex in evolution. Also discussed is the emergence of introns and exons, which resulted in genetic modularity, and the evolution of multicellularity.

Abstract: Gene finding techniques in eukaryotic cells can be divided into two categories, viz. – model-dependent and model-independent. In model-independent category, transforms are commonly used to identify exons or genes present in DNA sequences. In this work, a Post-Processing Algorithm (PPA) for enhancing gene prediction features of transforms is developed. PPA compares the spectral components of DNA signal with the corresponding spectrum of period-3 suppressed DNA signal. In the spectrum of DNA sequences, the bases for which the difference between these two spectrums is within a predefined threshold level are marked as non-coding (introns) regions. In such regions the signal values are replaced by the difference signal of the two spectrums. This substitution suppresses the noise in the intronic regions of the spectrum; while the coding region (exonic) signals are not affected, resulting in de-noised period-3 measures. PPA has been applied to process the period-3 coefficients of Discrete Fourier Transform (DFT), Paired Spectral Content (PSC), and Modified Gabor Wavelet Transform (MGWT) methods to de-noise their period-3 measures. Performance of the algorithm has been evaluated on HMR195, Burset/Guigo570, and Asp67 datasets using Receiver Operating Characteristic (ROC) and specificity versus sensitivity curves. The PPA, while preserving the model-independent characteristic of transform based methods, improves the probability of correct prediction of the exonic regions. [Copyright &y& Elsevier]

Since 2004 there has been a remarkable increment in our knowledge of the proteins and glycans that reside at, or are released from the surfaces of schistosomes in the mammalian host. Initial characterization of the soluble proteome permits distinctions to be made between the parasite secretome and its necrotome. The principal proteins secreted by the cercaria to gain access to the skin have been described as well as those released by migrating schistosomula. An inventory of transporters, enzymes and structural proteins has been shown to reside the tegument surface, but also immunoglobulins, complement factors and host CD44. The secreted membranocalyx that overlies the plasma membrane may contain a small number of proteins, not simply acting as physical barrier, but its lipid composition remains elusive. Analysis of worm vomitus has provided insights into blood feeding, increasing the number of known lysosomal hydrolases, and identifying a series of carrier proteins potentially involved in uptake of lipids and inorganic ions by the gut epithelium. The egg secretions that aid escape from the tissues include a mixture of MEG-2 and MEG-3 family variant proteins. The utility of identified proteins for the development of new diagnostics, and their potential as vaccines candidates is evaluated. [ABSTRACT FROM AUTHOR]

The article focuses on some techniques which explore how they are helping researchers in finding out effective treatment in muscular dystrophies, amyotrophic lateral sclerosis (ALS) and other diseases. According to a neurologist, exon skipping is an interesting approach for the treatment of duchenne muscular dystrophy. It discusses the benefits of using magnetic resonance imaging (MRI) in studying muscle disease. INSETS: MRI: What Is It?;MRI of DMD-Affected Thigh Muscles;MRI: How Does It Feel?;Optical Images of Mouse Legs

The article reports on the method developed by geneticists at Emory University School of Medicine in Georgia to target genetic disorders linked to X chromosome. It notes that geneticists in cooperation with RainDance Technologies Inc., have developed the sequencing method which allow the routine amplification and highly accurate sequencing and identification of all genes in X chromosome. Moreover, DNA sequencing techniques targets more than 800 exons using polymerase chain reaction (PCR).

Abstract: Base sequences of deoxyribonucleic acid (DNA) in an organism carry all the instructions regarding its growth and development. On the surface, such sequences seem irregular; yet in reality, they are symbolic sequences with an organized structure. This study investigates the characteristics of base arrangement and distribution in DNA sequences from the fractal theory viewpoint. In addition to multifractal features demonstrated by the DNA sequence, this study also compares the multifractal spectra derived from a particular family of gene among several different species. The results reveal that a considerable correlation exists between base distribution and evolutionary order. Furthermore, local scaling exponent (Hölder exponent) differences between coding segments (exon) and non-coding segments (intron) are also examined. It is suggested that such differences in the local distribution of bases can be applied to find coding segments within the DNA sequence that is to be translated into protein. This local scaling analysis is feasible and has the potential to become an effective tool for rapid location of possible coding sites in DNA sequences. The authors hope that future studies using more complicated bioinformatics methods for analyzing DNA sequences can benefit from this study. [Copyright &y& Elsevier]

This report shows the PCR-based identification of the eight known self-(in)compatibility alleles (S1 to S7 and Sc) of apricot (Prunus armeniaca L.). Two sets of consensus primers, designed from P. armeniaca S-RNase genomic sequences and sweet cherry (P. avium L.) S-RNase-cDNAs, were used to amplify fragments containing the first and the second S-RNase intron, respectively. When the results obtained from the two PCRs were combined, all S-alleles could be distinguished. The identity of the amplified S-alleles was verified by sequencing the first intron and 135 base pairs (bp) of the second exon. The deduced amino acid sequences of these fragments showed the presence of the C1 and C2 Prunus L. S-RNase conserved regions. These results allowed us to confirm S-genotypes previously assigned by stylar ribonuclease analyses and to propose one self-(in)compatibility group (I) and one universal donor group (O) containing unique S-genotypes and self-compatible cultivars (SC). This PCR-based typing system also facilitates the identification of the Sc-allele and might be a very useful tool for predicting self-compatibility in apricot breeding progenies. [ABSTRACT FROM AUTHOR]

Fractal image compression is time consuming in the encoding process. The time is essentially spent on the search for the best-match block in a large domain pool. In this paper, the spatial correlations in both the domain pool and the range pool are utilized to reduce the searching space. With this technique, the encoding speed is 2.6 times faster than that of the full search method while the quality of the retrieved image is almost the same. Moreover, since the searching space is limited to the matched blocks of the previous range blocks, fewer bits are required to represent the transform. The bit rate is thus improved by about 20%. [Copyright &y& Elsevier]

The article offers information on albumin-based half-life extension technology. It states that the technology has been developed to offer the capability to tune the drug's half-life according to specific patient needs. Albumin forms the basis of the newly developed drug delivery platform, is a natural non-immunogenic plasma protein with a safe and proven regulatory profile that allows manufacturers to tune protein or peptide half-life to specific medical requirements.

The article informs that results from the Clinical Diagnostic Exome testing conducted at Kennedy Krieger Institute in Baltimore, Maryland have been revealed by the company Ambry Genetics. It further informs that the patients undergoing the testing suffered from intellectual disability and autism. It mentions the benefits of using the Exome test for diagnosing genetic diseases which includes effective, cost saving and time saving.

Focuses on the study conducted by Steve Wilton and colleagues on the gene modification called exon skipping in treating muscular dystrophy. Relevance of antisense oligonucleotides in the strategy; Functionalism of antisense oligonucleotides; Concept of exon skipping.

The article discusses a report published in the May 8 issue of “Cell Stem Cell” regarding the discovery of a way to make adult cells revert back to their stem cell state without using the required insertion of four specific genes, one of which causes cancer. Brief details regarding how researchers achieved pluripotency in adult mice through encoding proteins are presented.

Explains that snippets of DNA called retrotransposons may have played a constructive part in evolution. Retrotransposons usual behavior involving the destruction of genes; Role of the retrotransposon L1 in copying exons; Work by Kazazian et al at the University of Pennsylvania, Philadelphia; Role of so-called exon shuffling in evolution; L1 carrying exons.

Reports that British researchers have devised a new test to detect carriers of muscular dystrophy. Screening for other genetic diseases; Duchenne and Becker muscular dystrophy; Dystrophin gene; Duplication or deletion of exons; Guy's hospital in London.

The article offers information on the extension of genetic testmenu by Courtagen Life Sciences Inc. A new genetic test, nucSEEKPDx will be released by the company for diagnosis of mitochondrial disorders. The nucSEEKPDx will help in sequencing nuclear genes of mitochondrial exome which are responsible for encoding majority of proteins.

The article informs about the First-Step Exome sequencing test performed by the company Ambry Genetics. It informs that the test analyzes the DNA sequence of the exons and intronic regions of the genes and is appropriate for a variety of whole exome sequencing. It mentions that the company expects that this will provide answers to the clinicians which they look for in many clinical scenarios without the added expense and complexity of whole exome analysis.

The article offers information related to an announcement made by Agilent Technologies Inc. regarding selection of its SureSelect XT Human All Exon target enrichment system by the Erasmus Medical Center in Rotterdam, Netherlands researchers. Wilfred van IJcken, research head, Erasmus Medical Center states that the genetically isolated population of the study is ideal for the discovery of new genetic variants associated with complex disorders. A brief account of company is also offered.

The article discusses the impact of exon skipping on Duchenne muscular dystrophy (DMD). It mentions that exon skipping allows the creation of partially functional dystrophin which is the muscle protein missing in DMD. According to the author, the strategy could potentially lessen the severe muscle weaknesses and atrophy which is considered as the hallmark of the disease. The author further highlights the effort of AVI BioPharma Inc. in developing drug that targets exon 50.

The article reports on the research conducted by Georgia State University, Northwestern University, and University of California at Berkeley regarding the DNA transcription. Topics discussed include the use of cryo-electron microscopy (cryo-EM) for gene expression, the visualisation of pre-initiation complexes (PIC) of DNA, and other aspects linked with DNA transcription such as RNA polymerase and gene encoding.

The article focuses on a study by the Functional Genomics team at the Civil Aerospace Medical Institute of the U.S. Federal Aviation Administration (FAA) which examines gene expression from exon arrays. The team uses the Affymetrix GeneChip® system, which offers hGU133 plus 2.0 array and the human Exon 1.0 ST array, in performing the gene expression research. The finding of the study reveals that exon chips are more sensitive to differential expression (DE).

This exploratory study investigated the relationship between respiratory infections and MBL serum concentrations and the presence of six SNPs in the MBL2 gene promoter region (alleles H/L, X/Y, and P/Q) and exon 1 (wild type allele A and variant alleles B, C, and D) using real-time PCR. In this study, 111 Finnish military recruits with asthma and 362 recruits without asthma were studied. Paired serum samples were obtained at the beginning and end of service (which was generally between six and 12 months duration), as well as paired samples for each infectious episode. No promoter region or exon 1 genotypes were associated with asthma. However, there was a significant association between the frequency of respiratory tract infections in subjects with MBL levels above and below the mean concentration of 1087.5 ng/mL. Thirty percent of subjects under the mean vs. 16% of subjects above the mean MBL concentration had ≥ 2 infectious episodes during their term of service, and were associated with an odds ratio (OR) of 2.5 adjusted for asthma status. Similarly, a Y/Y MBL2 promoter genotype variant was associated with an OR of 2.3 for infection. A trend toward association between exon 1 alleles associated with low levels of MBL was seen but did not reach statistical significance. [ABSTRACT FROM AUTHOR]

The article reports that a trial of a synthetic compound that coaxes muscle cells to ignore a genetic mutation in the gene for dystrophin has opened in London, England. It will test at least two and possibly three dosage levels of an antisense oligonucleotide that tells cells to ignore mutations in and around a section of the dystrophin gene known as exon 51.

The article focuses on drug approvals by the U.S. Food and Drug Administration (FDA) regarding two exon-skipping drugs. Topics discussed include accelerated approval for drug eteplirsen to treat duchenne muscular dystrophy (DMD) patients with mutations from Sarepta Therapeutics and study of the exon-skipping drug drisapersen by the Dutch biotechnology company Prosensa. Also mentions that Prosensa is seeking accelerated approval of drisapersen.

The article presents a study which examines hepatocellular adenomas. The study employs whole exome sequencing, methylome analyses and CGH-SNP analyses. Results identify the genetic determinants of the malignant transformation and key factors at stage of the transformation. It adds that the study wants to identify new biomakers that can be use for precise diagnosis and as therapeutic targets.

An introduction is presented in which the editor discusses various reports within the issue on topics including exon skipping, caregiving, and assistive technology.

The article presents a study on the GSK2402968 exon-skipping compound for the treatment of patients with Duchenne Muscular Dystrophy (DMD), which will open at the Nationwide Children's Hospital in Columbus, Ohio.

The article discusses the whole transcriptome analysis with the use of the next generation sequencing. It provides information overall transcriptome workflow including the isolation and fragmentation of RNA as well as the feature for whole transcriptome analysis involving unannotated exons. It also states that sequencing technology is ideal for whole transcriptome analysis as it offers detection of known, novel and low abundant transcripts.

The article highlights the results of a study which show that extending a gene-repair technique known as exon skipping to an additional type of gene mutation that causes Duchenne muscular dystrophy or Becker muscular dystrophy is feasible. The research was coordinated by Kevin Flanigan at the University of Utah.

The article reports on the results of the first-phase trial of an exon skipping compound in Duchenne muscular dystrophy (DMD) by Muscular Dystrophy Association (MDA) grantee Judith van Deutekom at Prosensa in Leiden, Netherlands, as published in the December 27, 2007 issue of the "New England Journal of Medicine." The injection of the exon-skipping compound induced the production of the missing dystrophin protein.

The article discusses a study which examined the use of molecular medicine in patients diagnosed with muscular dystrophy. The study included four patients with Duchenne's muscular dystrophy who were given intramuscular PRO 051 into their tibialis anterior muscle. They claim that antisense-mediated exon skipping may be effective in restoring dystrophin.

The article reports that the Leiden University Medical Center in the Netherlands is conducting the first trial to test a treatment strategy called exon skipping in boys with Duchenne muscular dystrophy. Exon skipping encourages cells to skip over faulty genetic information and builds a nearly normal protein from the remaining correct information, using antisense oligonucleotides (AONs). The AONs were developed by Dutch firm Prosensa, sponsor of the clinical trial.

The article provides updates related to international medical research . AVI BioPharma Inc. scientists including University of Western Australia professor Stephen Wilton report reliable progress in the observation of exon skipping. The group headed by researcher Graham McClorey have seen developments in the study of muscle cells from dogs with duchenne muscular dystrophy. The study involved by researcher Abbie Fall have advanced in the study of becker muscular dystrophy with the use of mice.

Reports on the collaboration of Muscular Dystrophy Association with pharmaceutical company GlaxoSmithKline and other parties to develop an exon skipping strategy as experimental treatment for Duchenne Muscular Dystrophy in the U.S. Design of exon skipping to coax cells to reinterpret genetic instructions; Treatment of genetic mutations via exon skipping; Lack of dystrophin.

The article reports that new findings from researchers at UT-Southwestern Medical Center help explain how the 20,000 to 25,000 genes in the human genome can make the hundreds of thousands of different proteins in bodies. Alternative splicing is a key mechanism for achieving a diverse range of proteins, which contributes to the complexity of higher organisms. RNA segments called exons carry the protein-making information, while the segments between exons, called introns, are snipped out of pre-mRNA by special proteins.

Discusses researches being done on the identification of specific activating mutations within the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene, which correlate with clinical responsiveness in a subgroup of patients with non-small-cell lung cancer treated with the tyrosine kinase inhibitor gefinitib. Reference to studies by Lynch TJ et al and Green MR published in the May 20, 2004 issue of the "New England Journal of Medicine"; Exons in which the researchers had studied EGFR mutations; Number of patients with a response to gefinitib who were identified with heterozygous mutations within the tyrosine kinase domain of EFGR.

Reports on the discovery of a new intron in a gene for an enzyme called TPI. Theory on introns and exons; Implications of the study.