Type Sequences (type + sequence)

Distribution by Scientific Domains

Selected Abstracts


EVOLUTION, Issue 7 2002
H. Allen Orr
Abstract I describe several patterns characterizing the genetics of adaptation at the DNA level. Following Gillespie (1983, 1984, 1991), I consider a population presently fixed for the ith best allele at a locus and study the sequential substitution of favorable mutations that results in fixation of the fittest DNA sequence locally available. Given a wild type sequence that is less than optimal, I derive the fitness rank of the next allele typically fixed by natural selection as well as the mean and variance of the jump in fitness that results when natural selection drives a substitution. Looking over the whole series of substitutions required to reach the best allele, I show that the mean fitness jumps occurring throughout an adaptive walk are constrained to a twofold window of values, assuming only that adaptation begins from a reasonably fit allele. I also show that the first substitution and the substitution of largest effect account for a large share of the total fitness increase during adaptation. I further show that the distribution of selection coefficients fixed throughout such an adaptive walk is exponential (ignoring mutations of small effect), a finding reminiscent of that seen in Fisher's geometric model of adaptation. Last, I show that adaptation by natural selection behaves in several respects as the average of two idealized forms of adaptation, perfect and random. [source]


M. Musso
Connexin 32 (Cx32) belongs to a protein family that forms intercellular channels mediating the exchange of ions and chemical messengers. In the peripheral nervous system (PNS) Cx32 is expressed in Schwann cells and contributes to the homeostasis and structural integrity of myelin. Mutations of this gene determine X-linked form of Charcot Marie-Tooth (CMTX) disease. Cx 32 is transcriptionally regulated in a tissue-specific manner by two different promoters termed P1 and P2. P2, active in Schwann cells, is located 5 kb downstream from the P1 promoter and at 500 bp from the exon 2 that contains the entire coding region. Previously, by Electrophoretical Mobility Shift Assay (EMSA) we have identified a sequence (-101/-93), within P2, specifically recognized by recombinant Egr2. In order to prove the direct involvement of Egr2 in the transcriptional control of the Cx32 gene, we have performed transfection experiments in HeLa cells with a luciferase driven by the P2 promoter in presence or not of a vector expressing Krox20, the mouse homologue of human Egr2. We have found that the construct in which the sequence -103/-93 is mutated is not activated as well as the wild type sequence. Moreover we have detected another upstream sequence (-236/-213) recognized by recombinant Egr2 and other transcription factors present in HeLa nuclear extract like SP1. The construct, lacking this sequence and carrying the mutated downstream Egr2 recognition sequence, is not activated at all by Krox20. Taken together these findings strongly suggest the role of Egr2 in the transcriptional control of Connexin 32 through both sequences. The laboratory is a member of the European CMT Consortium; partially granted by Ministero della Sanit, to PM, MURST and Ateneo to FA. [source]

Motor foundations of higher cognition: similarities and differences in processing regular and violated perceptual sequences of different specificity

Andreja Bubic
Abstract Processing perceptual sequences relies on the motor system, which is able to simulate the dynamics of the environment by developing internal representations of external events and using them to predict the incoming stimuli. Although it has previously been demonstrated that such models may incorporate predictions based on exact stimulus properties and single stimulus dimensions, it is not known whether they can also support abstract predictions pertaining to the level of stimulus categories. This issue was investigated within the present event-related functional magnetic resonance imaging study, which compared the processing of perceptual sequences of different specificity, namely those in which the sequential structure was based on the order of presentation of individual stimuli (token), and those in which such structure was defined by stimulus categories (type). The results obtained indicate a comparable engagement of the basic premotor,parietal network in processing both specific and categorical perceptual sequences. However, type sequences additionally elicited activations within the lateral prefrontal, occipital and posterior temporal regions that supported categorization in this task context. Introducing sequential deviants into token sequences activated parietotemporal and ventrolateral frontal cortices, whereas a less pronounced overall response, dominated by lateral prefrontal activation, was elicited by violations introduced into type sequences. Overall, the findings obtained suggest that, although forward models in perception may be able to incorporate expectations of lower specificity when compared to the motor domain, such processing is crucially dependent on additional contributions from lateral prefrontal as well as inferior occipital and temporal cortices that support categorization occurring in such a dynamic context. [source]

Tracking temporal changes of bacterial community fingerprints during the initial stages of composting

Patrick D Schloss
Abstract The initial phase of composting is the most dynamic part of the process and is characterized by rapid increases in temperature, large swings in pH, and the degradation of simple organic compounds. DNA samples were taken from an active compost system to determine the microbial 16S rRNA gene sequences that were present during this phase. We observed two significant shifts in the composition of the microbial community, one between 12 and 24 h and the other between 60 and 72 h into the process using automated 16S,23S rRNA intergenic spacer amplification (ARISA). The 16S rRNA gene sequences adjoining the most common ARISA fragments at each time point were determined. We found that sequences related to lactic acid bacteria were most common during the first 60 h and Bacillus -type sequences were most common between 72 and 96 h. While the temperature increased steadily over the first 96 h, the pH dropped after 12 h and increased after 60 h correlating with the shift from Bacillus to lactic acid sequences and the later return to Bacillus -type sequences. [source]

NS5A mutations predict biochemical but not virological response to interferon-, treatment of sporadic hepatitis C virus infection in European patients

I. Stratidaki
The NS5A region of the hepatitis C virus (HCV) genome has been reported by Japanese but not European investigators to be a significant factor in predicting interferon (IFN) response patients with HCV of genotype 1. We correlated the NS5A region with treatment outcome in patients with sporadic HCV infection. Twenty-eight patients (10 men, 18 women, mean age 60 2 years) with histologically proven HCV chronic hepatitis, genotype 1b, were treated with 6 MU IFN-, for 6 months. The 6954,7073 area of the NS5A region was directly sequenced for nucleotide and amino acids mutations and the results were related to biochemical and virological response. None of the patients had a strain with nucleotide sequence identical to the Japanese HCV-J. However, in five strains the nucleotide mutations led to synonymous amino acids and the amino acid sequences were identical to the prototype Japanese strain. Only 2/28 patients had four or more amino acid mutations (mutant strains) while 21 demonstrated an intermediate type and five belonged to the wild-type. The most frequent non-synonymous substitution was at position 6982 (A,G) corresponding to an amino acid change at codon 2218 (His,Arg). All patients with the wild-type were biochemical nonresponders while the two patients with the mutant strains had a sustained biochemical response. Twenty-three percent of the intermediate type had a sustained biochemical response. NS5A mutations predict the biochemical but not the virological response of patients. Virological response was poor and unrelated to the type of HCV strain. Biochemical responders had significantly lower amino acid mutations (1.14 0.19) compared with nonresponders (2.57 1.4, P < 0.003) as well as lower aminotransferase values (P < 0.01). Hence, mutational analysis of the NS5A region showed that our patients have a mutational profile similar to the European studies with a wild-type that is slightly different from the Japanese HCV-J sequence. The biochemical, but not the virological response to IFN-, is similar to the Japanese studies, with no response of the patients with wild-type sequence, a good response in the limited number of patients with mutant strains and 23% response rate in the patients with intermediate type sequences. [source]

Historical DNA from museum type specimens clarifies diversity of Asian leaf turtles (Cyclemys)

Species boundaries in Asian leaf turtles of the genus Cyclemys are difficult to define on the basis of morphology, primarily because many populations exhibit considerable ontogenetic variation in shell and head coloration. Two recent molecular phylogenetic hypotheses of Cyclemys species relationships, based largely on market and pet-trade samples of uncertain provenance, were highly incongruent. We used historical DNA methods to sequence fragments of the mitochondrial cytochrome b gene from eight type specimens of Cyclemys (including one collected by Alfred Russel Wallace), and phylogenetically placed these type sequences into the context of published cytochrome b variation. Our phylogenetic hypothesis supports the recognition of four named species (Cyclemys atripons, Cyclemys dentata, Cyclemys oldhamii, and C. pulchristriata), as well as a fifth species of unknown geographical provenance obtained from the Hong Kong pet trade. The type sequences show that previous molecular phylogenetic studies were hampered by misidentifications, supporting the notion that Cyclemys of unknown provenance are not reliably identified to species solely on the basis of morphology. 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 131,141. [source]