Simple Splicing Pattern and Pure Pattern Grammar Systems

2011 ◽  
Author(s):  
Sindhu J. Kumaar ◽  
P.J. Abisha ◽  
D.G. Thomas
Keyword(s):  
Splicing Pattern ◽  
Grammar Systems

Some Power-Decreasing Derivation Restrictions in Grammar Systems

2010 ◽  
Vol 19 (-1) ◽  
pp. 23-34
Author(s):  
Alexander Meduna ◽  
Martin Čermák ◽  
Tomáš Masopust
Keyword(s):  
Grammar Systems

scholarly journals Trans-acting Factors Required for Inclusion of Regulated Exons in the Ultrabithorax mRNAs of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1517-1529 ◽  
Author(s):  
James M Burnette ◽  
Allyson R Hatton ◽  
A Javier Lopez
Keyword(s):  
Drosophila Melanogaster ◽  
Alternative Splicing ◽  
P Element ◽  
Splicing Factors ◽  
Loss Of Function ◽  
Large Collection ◽  
Splicing Pattern ◽  
Alternatively Spliced ◽  
Hypomorphic Alleles

Abstract Alternatively spliced Ultrabithorax mRNAs differ by the presence of internal exons mI and mII. Two approaches were used to identify trans-acting factors required for inclusion of these cassette exons. First, mutations in a set of genes implicated in the control of other alternative splicing decisions were tested for dominant effects on the Ubx alternative splicing pattern. To identify additional genes involved in regulation of Ubx splicing, a large collection of deficiencies was tested first for dominant enhancement of the haploinsufficient Ubx haltere phenotype and second for effects on the splicing pattern. Inclusion of the cassette exons in Ubx mRNAs was reduced strongly in heterozygotes for hypomorphic alleles of hrp48, which encodes a member of the hnRNP A/B family and is implicated in control of P-element splicing. Significant reductions of mI and mII inclusion were also observed in heterozygotes for loss-of-function alleles of virilizer, fl(2)d, and crooked neck. The products of virilizer and fl(2)d are also required for Sxl autoregulation at the level of splicing; crooked neck encodes a protein with structural similarities to yeast-splicing factors Prp39p and Prp42p. Deletion of at least five other loci caused significant reductions in the inclusion of mI and/or mII. Possible roles of identified factors are discussed in the context of the resplicing strategy for generation of alternative Ubx mRNAs.

Identification of a novel neuronal C-SRC exon expressed in human brain

1990 ◽  
Vol 10 (5) ◽  
pp. 2035-2040
Author(s):  
J M Pyper ◽  
J B Bolen
Keyword(s):  
Amino Acids ◽  
Human Brain ◽  
Phosphorylation Site ◽  
Fetal Brain ◽  
Serine Residue ◽  
Developmentally Regulated ◽  
Site Analysis ◽  
Rna Transcripts ◽  
Splicing Pattern ◽  
Src Gene

Neuronal cells are known to express at least two different forms of the C-SRC proto-oncogene as a consequence of alternative splicing events which add an 18-nucleotide exon (the NI exon) between C-SRC exons 3 and 4. Here we report that a second neuronal exon of C-SRC is also present between C-SRC exons 3 and 4. This neuronal exon (the NII exon) of C-SRC was isolated from human adult and fetal brain-derived cDNAs and contains 33 nucleotides capable of encoding 11 amino acids (Gln-Thr-Trp-Phe-Thr-Phe-Arg-Trp-Leu-Gln-Arg). The human NI exon was located approximately 390 nucleotides from the end of C-SRC exon 3, whereas the NII exon was approximately 1,000 nucleotides from the beginning of C-SRC exon 4. Analysis of human brain RNA revealed that the NII exon is utilized primarily in conjunction with the NI exon to yield transcripts capable of encoding C-SRC products possessing 17 additional amino acids. These splicing events, which occur between the NI and NII exons, are predicted to alter the sixth amino acid encoded by the NI exon from an arginine to a serine residue, producing a potentially novel phosphorylation site. Analysis of the different C-SRC RNA transcripts revealed that the level of C-SRC RNA containing both NI and NII exons is similar in adult and fetal brain tissue, whereas the level of C-SRC RNA containing only the NI exon or the nonneuronal form of C-SRC RNAs is significantly higher in fetal brain tissues. These results indicate that the expression and splicing pattern of the C-SRC gene are developmentally regulated in the human brain.

Improved superoxide-generating ability by interferon γ due to splicing pattern change of transcripts in neutrophils from patients with a splice site mutation inCYBB gene

Blood ◽  
2001 ◽  
Vol 98 (2) ◽  
pp. 436-441 ◽  
Author(s):  
Fuminari Ishibashi ◽  
Tomoyuki Mizukami ◽  
Shiro Kanegasaki ◽  
Lena Motoda ◽  
Ryota Kakinuma ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Present Report ◽  
Interferon Γ ◽  
Silent Mutation ◽  
Site Mutation ◽  
Splicing Pattern ◽  
Cybb Gene ◽  
Gene Transcripts ◽  
Ifn Γ ◽  
Neutrophil Superoxide

Chronic granulomatous disease (CGD) is an inherited disorder of host defense against microbial infections caused by defective activity of the phagocyte NADPH oxidase. Based on an increase of neutrophil superoxide-generating ability in response to interferon γ (IFN-γ) in a single patient with CGD, multicentered group studies demonstrated a beneficial effect of prophylactic IFN-γ. However, no apparent increase of the phagocyte superoxide generation was found in patients enrolled in these studies. The present report offers an additional kindred in whom an IFN-γ–dependent increase in neutrophil superoxide production was observed in 3 affected patients. The defect in the CYBB gene for gp91-phox was identified as an otherwise silent mutation adjacent to the third intron of theCYBB gene that alters messenger RNA splicing. By molecular analysis, significant differences were found in the splicing pattern ofCYBB gene transcripts in patient neutrophils between 1 and 25 days after administration of IFN-γ. Furthermore, a complete transcript containing the missing exons could be detected in all specimens after the treatment. The changes in the splicing pattern of the transcripts and the prolonged effect on superoxide-generating ability of patient neutrophils indicate that IFN-γ induced a partial correction of the abnormal splicing of CYBB gene transcripts in myeloid progenitor cells.

scholarly journals Parallel communicating grammar systems with context-free components are Turing complete for any communication model

2016 ◽  
Vol 8 (2) ◽  
pp. 113-170
Author(s):  
Mary Sarah Ruth Wilkin ◽  
Stefan D. Bruda
Keyword(s):  
Concurrent Systems ◽  
Communication Model ◽  
Broadcast Communication ◽  
Turing Completeness ◽  
One Step ◽  
Grammar Systems ◽  
Turing Complete ◽  
Context Free ◽  
Original Construction ◽  
Parallel Communicating Grammar Systems

Abstract Parallel Communicating Grammar Systems (PCGS) were introduced as a language-theoretic treatment of concurrent systems. A PCGS extends the concept of a grammar to a structure that consists of several grammars working in parallel, communicating with each other, and so contributing to the generation of strings. PCGS are usually more powerful than a single grammar of the same type; PCGS with context-free components (CF-PCGS) in particular were shown to be Turing complete. However, this result only holds when a specific type of communication (which we call broadcast communication, as opposed to one-step communication) is used. We expand the original construction that showed Turing completeness so that broadcast communication is eliminated at the expense of introducing a significant number of additional, helper component grammars. We thus show that CF-PCGS with one-step communication are also Turing complete. We introduce in the process several techniques that may be usable in other constructions and may be capable of removing broadcast communication in general.

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