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We developed a computer program, GeneHackerTL, which predictsthe most probable translation initiation site for a given nucleotidesequence. The program requires that information be extractedfrom the nucleotide sequence data surrounding the translationinitiation sites according to the framework of the Hidden MarkovModel. Since the translation initiation sites of 72 highly abundantproteins have already been assigned on the genome of Synechocystissp. strain PCC6803 by amino-terminal analysis, we extractednecessary information for GeneHackerTL from the nucleotide sequencedata. The prediction rate of the GeneHackerTL for these proteinswas estimated to be 86.1%. We then used GeneHackerTL for predictionof the translation initiation sites of 24 other proteins, ofwhich the initiation sites were not assigned experimentally,because of the lack of a potential initiation codon at the amino-terminalposition. For 20 out of the 24 proteins, the initiation siteswere predicted in the upstream of their amino-terminal positions.According to this assignment, the processed regions representa typical feature of signal peptides. We could also predictmultiple translation initiation sites for a particular genefor which at least two initiation sites were experimentallydetected. This program would be e.ective for the predictionof translation initiationsites of other proteins, not only inthis species but also in other prokaryotes as well. 相似文献
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In this paper, we review developments in probabilistic methods of gene recognition in prokaryotic genomes with the emphasis on connections to the general theory of hidden Markov models (HMM). We show that the Bayesian method implemented in GeneMark, a frequently used gene-finding tool, can be augmented and reintroduced as a rigorous forward-backward (FB) algorithm for local posterior decoding described in the HMM theory. Another earlier developed method, prokaryotic GeneMark.hmm, uses a modification of the Viterbi algorithm for HMM with duration to identify the most likely global path through hidden functional states given the DNA sequence. GeneMark and GeneMark.hmm programs are worth using in concert for analysing prokaryotic DNA sequences that arguably do not follow any exact mathematical model. The new extension of GeneMark using the FB algorithm was implemented in the software program GeneMark.fba. Given the DNA sequence, this program determines an a posteriori probability for each nucleotide to belong to coding or non-coding region. Also, for any open reading frame (ORF), it assigns a score defined as a probabilistic measure of all paths through hidden states that traverse the ORF as a coding region. The prediction accuracy of GeneMark.fba determined in our tests was compared favourably to the accuracy of the initial (standard) GeneMark program. Comparison to the prokaryotic GeneMark.hmm has also demonstrated a certain, yet species-specific, degree of improvement in raw gene detection, ie detection of correct reading frame (and stop codon). The accuracy of exact gene prediction, which is concerned about precise prediction of gene start (which in a prokaryotic genome unambiguously defines the reading frame and stop codon, thus, the whole protein product), still remains more accurate in GeneMarkS, which uses more elaborate HMM to specifically address this task. 相似文献
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Evolution of the Group 1 late embryogenesis abundant (Lea) genes: analysis of the Lea B19 gene family in barley 总被引:2,自引:0,他引:2
Robin A. P. Stacy Mari Espelund Stein Sæbøe-Larssen Kristin Hollung Even Helliesen Kjetill S. Jakobsen 《Plant molecular biology》1995,28(6):1039-1054
The highly conserved Group 1 late embryogenesis abundant (Lea) genes are present in the genome of most plants as a gene family. Family members are conserved along the entire coding region, especially within the extremely hydrophilic internal 20 amino acid motif, which may be repeated. Cloning of Lea Group 1 genes from barley resulted in the characterization of four family members named B19.1, B19.1b, B19.3 and B19.4 after the presence of this motif 1, 1, 3 and 4 times in each gene, respectively. We present here the results of comparative and evolutionary analyses of the barley Group 1 Lea gene family (B19). The most important findings resulting from this work are (1) the tandem clustering of B19.3 and B19.4, (2) the spatial conservation of putative regulatory elements between the four B19 gene promoters, (3) the determination of the relative age of the gene family members and (4) the chimeric nature of B19.3 and B19.4, reflecting a cross-over or gene-conversion event in their common ancestor. We also show evidence for the presence of one or two additional expressed B19 genes in the barley genome. Based on our results, we present a model for the evolution of the family in barley, including the 20 amino acid motif. Comparisons of the relatedness between the barley family and all other known Group 1 Lea genes using maximum parsimony (PAUP) analysis provide evidence for the time of divergence between the barley genes containing the internal motif as a single copy and as a repeat. The PAUP analyses also provide evidence for independent duplications of Group 1 genes containing the internal motif as a repeat in both monocots and dicots. 相似文献
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Yasunari Matsuno Yoshihiro Adachi Yasushi Kondo 《The International Journal of Life Cycle Assessment》2006,11(5):354-360
- Preamble. In this series of two papers, a methodology to calculate the average number of times a material is used in a society
from cradle to grave is presented and applied to allocation of environmental impact of virgin material. Part 1 focuses on
methodology development and shows how the methodology works with hypothetical examples of material flows. Part 2 presents
case studies for steel recycling in Japan, in which the methodology is applied and allocation of environmental impact of virgin
steel is conducted.
- Abstract
Goal, Scope and Background. It has been recognized that LCA has a limitation in assessing open cycle recycling of materials
because of inevitable subjective judgments in setting system boundary. According with the enforcement of recycling laws, there
has been a rapid increase in recycling ratio of materials at the end-of-life of products in many industrialized countries.
So, materials' life cycle is getting more complicated, which makes it difficult to quantify the environmental impacts of materials
used in a product in an appropriate way. The purpose of this paper is to develop a methodology to calculate the average number
of times a material is used in a society from cradle to grave. The method developed in this paper derives the average number
of times material is used; this value could be used for allocation of environmental burdens of virgin material as well as
an indicator for assessing the state of material use in a certain year, based on material flow of material in that year.
Main Features Our methodology is based on Markov chain model using matrix-based numerical analysis. A major feature of this method is that
it creates transition probability matrices for a material from the way in which the material is produced, consumed, and recycled,
making it possible to simply elicit indicators that assess the status of material use in products in society. Our methodology
could be an alternative method to derive the average number of times material is used, which could be used for allocation
of environmental burdens of virgin material.
Results and Discussions The methodology was applied to hypothetical examples of material flows, in which a virgin material was produced and used
in products, recycled and finally landfilled. In some cases, closed loop and open loop recycling of materials existed. The
transition probability matrix was created for each material flow, and how many times a virgin material is used in products
until all of the elements are ultimately landfilled.
Conclusions This methodology is applicable to a complicated material flow if the status of residence of a material and its flow in a
society can be figured out. All the necessary data are the amount of virgin material production, amount of the material used
in products, recycling rate of the material at the end of life of each product, the amount of scrap of the material that are
used for products. In Part 2 of this paper, case studies for steel were conducted. 相似文献
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An extensive computational analysis of available sequence and crystal structure data was used to identify functionally important residue interactions within the motor domain of the kinesin molecular motor. Principal component analysis revealed that all current kinesin crystal structures reside in one of two main conformations, which differ at the active site, and in the position of a microtubule-binding sub-domain relative to a rigid central core. This sub-domain consists of secondary structure elements alpha4-loop12-alpha5-loop13 and contains a conserved hydrophilic surface patch that may be involved in strong binding to microtubules. A hinge point for the sub-domain motion lies near a conserved glycine at position 292. Statistical coupling analysis revealed a network of co-evolving positions that link this region to the nucleotide-binding site, via a highly conserved histidine in the switch I loop. The data are consistent with a model in which the nucleotide status of the active site shifts kinesin between weak and strong binding conformations via reconfiguration of the identified sub-domain. Our data provide a statistically supported framework for further examination of this and other structure-function relationships in the kinesin family. 相似文献
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Yoshihiro Adachi 《The International Journal of Life Cycle Assessment》2007,12(1):34-39
- Preamble. In this series of two papers, a methodology to calculate the average number of times a material is used in a society from cradle to grave is presented and applied to allocation of environmental impact of virgin material. Part 1 focused on methodology development and showed how the methodology works with hypothetical examples of material flows. Part 2 presents case studies for steel recycling in Japan, in which the methodology is applied and allocation of environmental impact of virgin steel is conducted. - Abstract Goal, Scope and Background. The life cycle of steel begins with the mining of iron ore from the earth. Steel is produced in steel works and used in various products. Some of the steels are recycled at the products' end of life and used as a resource for the production of new steel in electric furnaces, while the remaining steel is used just once in products before being discarded (landfilled). In this paper, case studies were conducted to analyze the average number of times the element of iron is used and its residence time in society, in which the methodology developed in Part 1 of the paper was applied. CO2 emissions caused by steel productions and recycling were allocated by the number of times the element of steel is used in a society. Results and Discussion On the basis of the material flows of steel in Japan in 2000, it was calculated that at least 70% of the BF crude iron produced in Japan in 2000 was ultimately exported. On the assumption that steel is used in other countries in the same way as it is in Japan, the average number of times of use and the residence time of elemental iron in society are 2.67 and 62.9 years, respectively. Both of these values depend significantly on the recycling ratios of steel from construction and automobiles. Our model indicated that if the recycling ratio of steel from civil engineering and construction increased from 50% to 60%, the average number of times used would increase to 3.17 and the residence time of elemental iron in society would increase to 75.8 years. If CO2 emissions caused by steel productions and recycling are allocated by the number of times the element of steel is used in a society, it was calculated that steel use of one time generates in average an environmental burden of 1.03 t-CO2/t. Conclusion A method was developed to calculate the average number of times a material is used in a society from cradle to grave. Our methodology is based on Markov chain model using matrix-based numerical analysis, and has been successfully applied to steel. The results obtained by this methodology, i.e. the average number of times the element of iron is used in society, could be used for allocation of environmental burdens of virgin material as well as an indicator for assessing the state of material use in a certain year, based on material flow of material in that year. Recommendation and Perspective It is recognized that further researches must be conducted to gather data on steel production, use, and recovery in other countries and incorporate them into the transition probability matrix to obtain more precise results. Although this paper deals only with steel, this method can also be applied to other materials. 相似文献
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The proliferation of retrotransposons within a genome can contribute to increased size and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the Western corn rootworm, using survey sequences from bacterial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation genome sequence assembly. Eleven unique D. v. virgifera BEL elements were identified that contained full-length gag–pol coding sequences, whereas 88 different partial coding regions were characterized from partially assembled elements. Estimated genome copy number for full and partial BEL-like elements ranged from ~ 8 to 1582 among individual contigs using a normalized depth of coverage (DOC) among Illumina HiSeq reads (total genome copy number ~ 8821). BEL element copy number was correlated among different D. v. virgifera populations (R2 = 0.9846), but individual element numbers varied ≤ 1.68-fold and the total number varied by ~ 527 copies. These data indicate that BEL element proliferation likely contributed to a large genome size, and suggest that differences in copy number are a source of genetic variability among D. v. virgifera. 相似文献
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The complete mitochondrial genome of the sycamore lace bug, Corythucha ciliata, was sequenced in this study. It represents the first sequenced mitogenome of family Tingidae in Heteroptera. The mitogenome of C. ciliata is 15,257 bp and contains 37 genes including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a large non-coding region. Gene arrangement, nucleotide content, codon usage, and amino acid composition and asymmetry indicate a high degree of conservation with six other species of Cimicomorpha. The 13 PCGs initiated with ATN as the start codon and terminated with TAA, TA or T as stop codon. The evolutionary rate of each PCG was different, among which ATP8 showed the highest rate while ATP6 indicated the lowest rate. The 22 tRNAs genes apparently fold into a typical cloverleaf structure; however, the anticodon (TTC) of trnSer (AGN) differs from other Heteropteran insects. Secondary structure modeling of rRNA genes revealed similarity to other insects, except for two incomplete helices (H1648 and H2735) in lrRNA. The predicted secondary structure of lrRNA indicates 45 helices in six domains, whereas srRNA has 27 helices in three domains. Three potential stem–loops and two tandem repeats (–TCTAAT–) were identified in the A+T-rich region. Phylogenetic analysis indicated that C. ciliata is a sister group to other Heteroptera species based on analysis of the 13 PCGs. 相似文献
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The complete mitochondrial genome of the oriental fruit fly Bactrocera dorsalis s.s. has been sequenced, and is here described and compared with the homologous sequences of Bactrocera oleae and Ceratitis capitata. The genome is a circular molecule of 15,915 bp, and encodes the set of 37 genes generally found in animal mitochondrial genomes. The structure and organization of the molecule is typical and similar to the two closely related species B. oleae and C. capitata, although it presents an interesting case of putative intra-molecular recombination. The relevance of the growing comparative dataset of tephritid complete mitochondrial genomes is discussed in relation to the possibility to develop robust assays for species discrimination in quarantine and agricultural monitoring practices, as well as basic phylogeography/population genetic studies. 相似文献
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The complete mitochondrial genome (mitogenome) of the Chinese pistacia looper Biston panterinaria was sequenced and annotated (15,517 bp). It contains the typical 37 genes of animal mitogenomes and a high A + T content (79.5%). All protein coding genes (PCGs) use standard ATN initiation codons except for cytochrome c oxidase 1 (COX1) with CGA. Eleven PCGs use a common stop codon of TAA or TAG, whereas COX2 and NADH dehydrogenase 4 (ND4) use a single T. All transfer RNA (tRNA) genes have the typical clover-leaf structure with the exception of tRNASer(AGN). We reconstructed a preliminary mitochondrial phylogeny of six ditrysian superfamilies and performed comparative analyses of inference methods (Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP)), dataset compositions (including and excluding 3rd codon positions), and alignment methods (Muscle, Clustal W, and MAFFT). Our analyses indicated that inference methods and dataset compositions more significantly affected the phylogenetic results than alignment methods. BI analysis consistently revealed uncontroversial relationships with all dataset compositions. By contrast, ML analysis failed to reconstruct stable phylogeny at two nodes, whereas MP analysis had more difficulties in the tree resolution and nodal support. Distinct from most previous studies, our analyses revealed that Geometroidea had a closer lineage relationship with Bombycoidea than Noctuoidea. Similar to previous molecular studies, our analyses revealed that Hesperiidae were nested in the Papilionoidea clade, providing further evidence to the previous concept that Papilionoidea was paraphyletic, and none of the butterflies were associated with the Macroheterocera. 相似文献
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The genus Ovis (Bovidae, Artiodactyla) includes six species, i.e. Ovis ammon, Ovis aries, Ovis canadensis, Ovis dalli, Ovis nivicola and Ovis vignei. Based on morphology, geographical location, habitat, etc., the species O. ammon is divided into nine subspecies. The near threatened Tibetan argali is distributed across the Tibetan Plateau and its peripheral mountains, and believed to be one of the O. ammon subspecies (O. a. hodgsoni). However, considering its morphological features and distributions, a question has been proposed by some researchers about the subspecies status of Tibetan argali. In this study, we employed complete mitochondrial DNA (mtDNA) to explore the phylogenetic relationship and population genetic structure of Tibetan argali. The results revealed that the nucleotide composition, gene arrangement and codon usage pattern of the mitochondrial genome of Tibetan argali are similar to those of other caprines. Phylogenetic analyses showed that Tibetan argali was clustered with O. ammon. Interestingly, five Tibetan argali individuals and one of the three Gansu argali (O. a. dalailamae) individuals were clustered in the same branch, which is a sister group to other two Gansu argali individuals. Together with morphological characteristics, our results suggested that Tibetan argali and Gansu argali may belong to the same subspecies (O. a. hodgsoni) of O. ammon, rather than two different subspecies. 相似文献
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We present the complete mitogenome of a stonefly, Cryptoperla stilifera Sivec (Plecoptera; Peltoperlidae). The mitogenome was a circular molecule consisting of 15,633 nucleotides, 37 genes and a A + T-rich region. C. stilifera mitogenome was similar to Pteronarcys princeps mitogenome (Plecoptera; Pteronarcyidae). All transfer RNA genes (tRNAs) had typical cloverleaf secondary structures except for trnSer (AGN), where the stem-loop structure of the dihydrouridine (DHU) arm was missing. The A + T-rich region of C. stilifera had two stem-loops and each had two interlink. Three conserved sequence blocks (CSBs) were present in the A + T-rich regions of C. stilifera, Peltoperla tarteri and Peltoperla arcuata. Moreover, many polynucleotide stretches (Poly N, N = A, T and C) in the A + T-rich region of C. stilifera Phylogenetic relationships of Polyneopteran species were constructed based on the nucleotide sequences of 13 protein coding genes (PCGs). Both maximum likelihood (ML) and Bayesian inference (BI) analyses supported Grylloblattodea as the sister group to Plecoptera + Dermaptera and Embiidina and Phasmatodea as sister groups. 相似文献
15.
Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera 总被引:1,自引:0,他引:1
We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A + T composition (79.3%–80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNAGln and ND2 (64–87 bp), conserved ATACTAA motif between tRNASer (UCN) and ND1, and characteristic features of the A + T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNAAsn/tRNASer (AGN), instead of the rearrangement tRNASer (AGN)/tRNAAsn, found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea + Noctuoidea + Geometroidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae + (Hesperiidae + (Pieridae + ((Lycaenidae + Riodinidae) + Nymphalidae)))) were strongly supported in all analyses (0.98–1 by BI and 96–100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies. 相似文献