466 research outputs found
Structure of the 5' region of the human hexokinase type I (HKI) gene and identification of an additional testis-specific HKI mRNA
No full text: We previously reported the structure of the human hexokinase type I (HKI) gene and provided direct evidence of an alternative red blood cell-specific exon 1 located in the 5' flanking region of the gene. Three unique HKI mRNA species have also been described in human spermatogenic cells. These mRNAs contain a testis-specific sequence not present in somatic cell HKI, but lack the sequence for the porin-binding domain necessary for HKI to bind to porin on the outer mitochondrial membrane. The present study reports a new mRNA isoform, hHKI-td, isolated from human sperm. hHKI-td mRNA contains both a testis-specific sequence at the 5' end common to the three other mRNA isoforms and an additional unique sequence. Screening of a cosmid library and analysis of the cosmids containing the HKI gene revealed that testis-specific sequences are encoded by six different exons. Five of these exons are located upstream from the somatic exon 1 (5.6-30 kb) and one within intron 1. This study shows that a single human HKI gene spanning at least 100 kb encodes multiple transcripts that are generated by alternative splicing of different 5' exons. Testis-specific transcripts are probably produced by a separate promoter that induces the expression of the HKI gene in spermatogenic cells
Reply: KRAS status analysis and anti-EGFR therapies: is comprehensiveness a biologist's fancy or a clinical necessity?
No full textWe thank Dr Lopez-Crapez et al 2010 to have taken cue fro
<i>De Novo</i> Discovery of Structured ncRNA Motifs in Genomic Sequences
No full textDe novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.</p
[Construction of an apparatus for pulsed field electrophoresis for the analysis of high molecular weight DNA]
No full textAn inexpensive apparatus for Pulsed Field Gel Electrophoresis constructed by the Authors, is described. According to our experimental condition it was found that this apparatus is capable to resolve DNA fragments in order of 50-1500 Kb. This range of analysis is adequate for the molecular studies adjacent regions of prokaryotes, primitive eukaryotes and mammals
VEGF gene polymorphisms and susceptibility to colorectal cancer disease in italian population
No full textThe vascular endothelial growth factor (VEGF) is an endothelial cell-specific mitogen involved in the process of angiogenesis, a crucial phase in tumor growth and metastasis. We carried out a case-control study to evaluate whether polymorphisms of VEGF gene modulate the risk of developing colorectal cancer disease (CCD).
We evaluated VEGF -2578A/C, -460T/C, and +405C/G genotypes obtained from a series of 302 CCD patients and 115 controls from the Italian population using polymerase chain reaction restriction fragment length polymorphism assay.
Strong linkage disequilibrium (LD) was detected between -2578A/C and -460T/C (D'aEuro parts per thousand= 0.97; CI = 0.93-1) and between -2578A/C and +405C/G (D'aEuro parts per thousand= 0.97; CI = 0.98-1) in the case group. Complete LD was detected between -2578A/C and +405C/G and between -460T/C and +405C/G (D'aEuro parts per thousand= 1; CI = 0.84-1; CI = 0.82-1, respectively) in the control group. A reduced risk for the disease was associated with -2578C/A and -2578C/C (odds ratio (OR) = 0.34, CI = 0.162-0.676 and OR = 0.38, CI = 0.181-0.775, respectively). A direct association was found for carriers of the VEGF -460C/C polymorphism (OR = 3.55; CI = 1.659-8.469). We identified a protective haplotype -2578A, -460T, and +405G (OR = 0.04; CI = 0.009-0.19) and two different high-risk haplotypes -2578A, -460C, and +405G (OR = 1.90; CI = 1.31-2.27) and -2578C, -460C, and +405C (OR = 9.62; CI = 1.3-70.87).
The present study suggests that the VEGF gene polymorphisms may play a role in the development of colorectal cancer
Glucose-6-phosphate dehydrogenase nucleotide 1311 polymorphism in central Italy(Marche Region).
No full textAbstract
Glucose-6-phosphate dehydrogenase Mediterranean (G6PD Med) is a common G6PD variant around the Mediterranean Sea characterized by severe enzyme deficiency and B-like electrophoretic mobility. The molecular basis of G6PD Med is a single C-->T transition at nucleotide (NT) 563. A polymorphic site exists in exon 11 of G6PD gene: in the wild-type NT 1311 is a C (1311C), but in some individuals from diverse populations a T (1311T) is present instead. Recent studies suggest that this C-->T transition is in linkage disequilibrium with G6PD Med genotype. In the normal population of Southern Italy (Sicily and Calabria) who is at risk for G6PD Med the NT 1311 allelic frequency is 16.7-20%; no data are available for the other regions. We screened the population of Marche region, Central Italy, in order to know the percentage of this polymorphism in an area not at risk for G6PD Med: we found that the 1311T frequency is about one half of that found in Southern Italy
Faster Genome Annotation of Non-coding RNA Families without Loss of Accuracy
No full textRNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are slow. This paper shows how to make CMs faster while provably sacrificing none of their accuracy. Specifically, based on the CM, our software builds a profile hidden Markov model (HMM), which filters the genome database. This HMM is a rigorous filter, i.e., its filtering eliminates only sequences that provably could not be annotated as homologs. The CM is run only on what remains. Optimizing the HMM for filtering involves minimizing an exponential objective # Dept. of Computer Science & Engineering, University of Washington, Box 352350, Seattle, WA, USA, 98195, [email protected] + Depts. of Computer Science & Engineering and Genome Sciences, University of Washington, Box 352350, Seattle, WA, USA, 98195, [email protected] c ACM, 2004. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version will be published in Proc. Eighth Annual Inter. Conf. on Computational Molecular Biology (RECOMB) , 2004. See http://recomb04.sdsc.edu/
Linkage disequilibrium for DNA haplotypes near the cystic fibrosis locus in twosouth European populations
No full textShape based indexing for faster search of RNA family databases
No full textJanssen S, Reeder J, Giegerich R. Shape based indexing for faster search of RNA family databases. BMC Bioinformatics. 2008;9(1):131.Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally annotated RNA families. Unfortunately, searching for new family members using covariance models (CMs) is very time consuming. Filtering approaches that use the sequence conservation to reduce the number of CM searches, are fast, but it is unknown to which sacrifice.
Results: We present a new filtering approach, which exploits the family specific secondary structure and significantly reduces the number of CM searches. The filter eliminates approximately 85% of the queries and discards only 2.6% true positives when evaluating Rfam against itself. First results also capture previously undetected non-coding RNAs in a recent human RNAz screen.
Conclusion: The RNA shape index filter (RNAsifter) is based on the following rationale: An RNA family is characterised by structure, much more succinctly than by sequence content. Structures of individual family members, which naturally have different length and sequence composition, may exhibit structural variation in detail, but overall, they have a common shape in a more abstract sense. Given a fixed release of the Rfam data base, we can compute these abstract shapes for all families. This is called a shape index. If a query sequence belongs to a certain family, it must be able to fold into the family shape with reasonable free energy. Therefore, rather than matching the query against all families in the data base, we can first (and quickly) compute its feasible shape(s), and use the shape index to access only those families where a good match is possible due to a common shape with the query
Parallel RAMs with Owned Global Memory and Deterministic Context-Free Language Recognition
No full textWe identify and study a natural and frequently occurring subclass of Concurrent Read, Exclusive Write Parallel Random Access Machines (CREW-PRAMs). Called Concurrent Read, Owner Write, or CROW-PRAMs, these are machines in which each global memory location is assigned a unique "owner" processor, which is the only processor allowed to write into it. Considering the difficulties that would be involved in physically realizing a full CREW-PRAM model, it is interesting to observe that in fact, most known CREW-PRAM algorithms satisfy the CROW restriction or can be easily modified to do so. This paper makes three main contributions. First, we formally define the CROW-PRAM model and demonstrate its stability Department of Computer Science, York University, Toronto, Canada M3J 1P3; [email protected]. y Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350; [email protected]. z Parts of this work were done at the Department of ..
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