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At least 343 records · Page 19Linked to original sources
PubMed2005

OsPPR1, a pentatricopeptide repeat protein of rice is essential for the chloroplast biogenesis.

In this paper, we report a novel pentatricopeptide repeat (PPR) protein gene in rice. PPR, a characteristic repeat motif consisted of tandem 35 amino acids, has been found in various biological systems including plant. Sequence analysis revealed that the gene designated OsPPR1 consisted of an open reading frame of 2433 nucleotides encoding 810 amino acids that include 11 PPR motifs. Blast search result indicated that the gene did not align with any of the characterized PPR genes in plant. The OsPPR1 gene was found to contain a putative chloroplast transit peptide in the N-terminal region, suggesting that the gene product targets to the chloroplast. Southern blot hybridization indicated that the OsPPR1 is the member of a gene family within the rice genome. Expression analysis and immunoblot analysis suggested that the OsPPR1 was accumulated mainly in rice leaf. Antisense transgenic strategy was used to suppress the expression of OsPPR1 and the resulted transgenic rice showed the typical phenotypes of chlorophyll-deficient mutants; albinism and lethality. Cytological observation using microscopy revealed that the antisense transgenic plant contained a significant defect in the chloroplast development. Taken together, the results suggest that the OsPPR1 is a nuclear gene of rice, encoding the PPR protein that might play a role in the chloroplast biogenesis. This is the first report on the PPR protein required for the chloroplast biogenesis in rice.

Amino Acid Sequence↗
PubMed1991

Synthesis and characterization of the Kunitz protease-inhibitor domain of the beta-amyloid precursor protein.

To understand the pathological process by which amyloid is deposited in Alzheimer's disease, it is important to characterize the proteolytic processing events of the beta-amyloid precursor protein (beta-APP) from which the amyloid-forming fragment is excised. A potentially important component in beta-APP processing is the 57-amino acid (aa) Kunitz serine protease inhibitor (KPI) located within the extracellular domain of both the 751- and 770-aa isoforms of beta-APP. We have synthesized DNA encoding the 57-aa KPI domain as a necessary step in identifying the role of the protease inhibitor in beta-APP processing and amyloid formation. A bacterial secretion system directed by the alkaline phosphatase signal peptide of Escherichia coli linked to a synthetic gene encoding KPI was used to produce soluble, extracellular recombinant KPI (reKPI) protein. The reKPI protein was purified to homogeneity from bacterial supernatants and was biochemically and biologically characterized. Complete aa sequence analysis confirmed the fidelity of the reKPI, and fast-atom bombardment mass-spectral analysis was used to document that reKPI was of the predicted Mr. The reKPI is as active on a molar basis as the inhibitor-containing beta-APP when assayed for inhibition of trypsin activity. Together these data suggest that reKPI protein is properly folded and lacking in modified aa. Hence, this reKPI will be an important reagent in gaining a better understanding of the role of the KPI domain in beta-APP function and metabolism, as well as in the proteolytic events involved in beta-amyloid formation.

Alzheimer Disease↗
PubMed1993

Hybridization and DNA sequence analyses suggest an early evolutionary divergence of related biosynthetic gene sets encoding polyketide antibiotics and spore pigments in Streptomyces spp.

The whiE gene cluster of Streptomyces coelicolor, which is related to gene sets encoding the biosynthesis of polycyclic aromatic polyketide antibiotics, determines a spore pigment. Southern blotting using probes from three different parts of the whiE cluster revealed related gene sets in about half of a collection of diverse Streptomyces strains. A 5.2-kb segment of one such cluster, sch, previously shown to determine spore pigmentation in Streptomyces halstedii, was sequenced. Seven open reading frames (ORFs), two of them incomplete, were found. Six of the ORFs resemble the known part of the whiE cluster closely. The derived gene products include a ketosynthase (= condensing enzyme) pair, acyl carrier protein and cyclase, as well as two of unidentified function. The seventh ORF diverges from the main cluster and encodes a protein that resembles a dichlorophenol hydroxylase. Comparison with sequences of related gene sets for the biosynthesis of antibiotics suggests that gene clusters destined to specify pigment production diverged from those destined to specify antibiotics early in the evolution of the Streptomyces genus.

Amino Acid Sequence↗
PubMed2006

Iron metabolism in insect disease vectors: mining the Anopheles gambiae translated protein database.

All animals require iron for survival. This requirement reflects the role of this mineral as a cofactor of numerous proteins. However, under physiological conditions, Fe(2+) oxidizes to Fe(3+) encouraging the formation of toxic free radicals. In mammals, the potential for oxidative damage from iron is minimized by binding iron to proteins. Mammalian iron metabolism is complex and numerous proteins are involved in iron absorption, transport, uptake and utilization. We have analyzed the Anopheles gambiae translated protein database for candidates that show identity to proteins involved in mammalian iron metabolism (Holt et al., 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298, 129-149). Our results indicate that proteins involved in iron absorption and intracellular iron utilization are, for the most part, conserved in A. gambiae. In contrast, proteins involved in the pathways of iron export from the gut, transport in hemolymph and uptake at peripheral tissues in mosquitos differ from those for mammals.

Animals↗
PubMed2006

Phylogeny of the genus Aphis Linnaeus, 1758 (Homoptera: Aphididae) inferred from mitochondrial DNA sequences.

Aphis is the largest aphid genus in the world and contains several of the most injurious aphid pests. It is also the most reluctant aphid genus to any comprehensive taxonomic treatment: while most species are easily classified into "species groups" that form well defined entities, numerous species within these groups are difficult to tell apart morphologically and identification keys remain ambiguous and mostly rely on host plant affiliation. In this paper, we used partial sequences of COI/COII and CytB genes to reconstruct the first phylogeny of Aphis and discuss the present systematics. The monophyly of the subgenus Bursaphis and of the tree major species groups, Black aphid, Black backed aphid and frangulae-like species was recovered by all phylogenetic analyses. However our data suggested that the nominal subgenus was not monophyletic. Relationships between major species groups were often ambiguous but "Black" and "Black backed" species groups appeared as sister clades. The most striking result of this study was that our molecular data met the same limits as the morphological characters used in classifications: mitochondrial DNA did not allow the differentiation of species that are difficult to identify. Further, interspecies relationships within groups of species for which taxonomic treatment is difficult stayed unresolved. This suggests that species delineation in the genus Aphis is often ambiguous and that diversification might have been a rapid process.

Animals↗
PubMed2026

Non-reciprocal coevolution in a fungus-gardening ant.

Symbioses are often characterized by nonrandom associations between hosts and symbionts. Hosts may obtain symbionts horizontally from the environment or vertically from a parent or sometimes use both methods. Macroevolutionary examinations of fungus-gardening ants and their fungi have shown either a 1:1 coevolution model or a 'diffuse' model between ant host and fungal symbionts. However, some of these conclusions may have been based on using relatively conservative molecular markers, which could obscure cryptic variation. The use of whole genome approaches potentially offer more power in elucidating coevolutionary history. In this study, we examined patterns of coevolution in a single species (Trachymyrmex septentrionalis) using genomic and experimental approaches. We tested whether ant-fungal specificity patterns reflected either 1:1 or diffuse models of coevolution. While we report significant co-phylogenetic signal among intraspecific ant host and fungal symbiont lineages, we found evidence of 1:1 coevolution in some lineages and diffuse in others. These conclusions were supported by the results of experiments where newly mated T. septentrionalis queens were forced to grow novel fungi that suggested that not all fungi are equivalent symbionts and would require specialized hosts. Thus, within a single ant species, there is a mixed support for both models.

Animals↗
PubMed1999

Molecular biology for the pediatric surgeon.

Molecular biology is leading a revolution in our understanding, diagnosis, and treatment of disease and will continue to do so. Medicine in the future will require a greater understanding of this field and its methods by medical practitioners. This report reviews the basic aspects of the field including recombinant DNA methods. Of particular importance is how molecular biology will impact pediatric surgeons. Accordingly, the final section of this report briefly reviews the molecular biology of three diseases commonly treated by pediatric surgeons.

DNA, Recombinant↗
PubMed2000

A common motif in proparts of Cnidarian toxins and nematocyst collagens and its putative role.

In Cnidarians, cnidoblast cells contain organelles called cnidocysts, which are believed to be the product of an extremely complex regulated secretory pathway. When matured, these stinging organelles are capable of storing and delivering toxins. We hypothesized that translated nematocyst proteins might comprise specific sequences serving as signals in sorting to the organelle. A sodium channel neurotoxin from the sea anemone Actinia equina was cloned and the toxin precursor sequence was compared to those of nematocyst collagens, pore-forming toxins and ion channel neurotoxins. It was found that all the analyzed sequences possess a highly conserved stretch of nine amino acid residues ending with Lys-Arg N-terminally of the mature region.

Amino Acid Sequence↗
PubMed1996

Slow rate of phosphodiester bond formation accounts for the strong bias that Taq DNA polymerase shows against 2',3'-dideoxynucleotide terminators.

Taq and T7 DNA polymerases have become basic molecular biology "tools" for DNA sequence analysis. However, Taq, unlike T7 DNA polymerase, is strongly biased against the incorporation of 2',3'-dideoxynucleotide triphosphates (ddNTPs) indicating very different substrate selectivities. Equilibrium binding and rate constants were measured for 2',3'-ddNTPs as well as for several other 3'-substituted terminators and compared to 2'-deoxynucleotide substrates (dNTPs). In steady-state experiments, Taq Pol I was strongly biased in favor of dATP1 over ddATP incorporation by about 700 to 1, in contrast to T7 DNA polymerase which showed a preference of only about 4 to 1. Manganese reduced but did not eliminate selectivity against 2',3'-ddNTPs. Transient kinetic traces indicated different rate-limiting steps for substrate and terminator incorporation. Further mechanistic studies showed that the binding constants for substrates and terminators were equivalent. However, the rate constants for phosphodiester bond formation for 2',3'-ddNTPs were 200-3000-fold lower than for dNTPs. Alternative terminators showed only slight improvements. The data were consistent with a model in which both substrates and terminators undergo ground-state binding followed by formation of a tight-binding Enz.DNA.Nucleotide complex. Immediately after complex formation, substrates undergo a rapid nucleoside phosphoryl transfer reaction. However, the reaction rates for terminators were slower presumably due to misalignment of reactive groups in the active site. Thus, the strong bias that Taq DNA polymerase shows against terminators is due to a very slow "chemistry" step. Such a strong bias has several kinetic consequences for DNA sequence patterns. These consequences are discussed in the text.

Base Sequence↗
PubMed2001

Fish x 3.

Explore the source record for details and available documents.

Animals↗
PubMed2000

Guardian ancestry: fly p53 and damage-inducible apoptosis.

The tumor suppressor, p53, is among the most commonly mutated genes in human cancers. Recent reports describe shared and divergent properties of a Drosophila p53 homolog Dmp53. Like its mammalian counterpart, Dmp53 also functions in damage-induced cell death. In this model system, the apoptosis activator reaper has emerged as an important target gene. Together with the wealth of genomic data available in Drosophila, continued studies on Dmp53 promise new insights into the regulation and function of this important gene family.

Animals↗
PubMed2002

Locating the sources of an invasive pest, grape phylloxera, using a mitochondrial DNA gene genealogy.

Range expansions through human introductions have increased with global commerce and have led to the extinction of native species, alterations in community structure and pest status of the invasive species. Inferring the evolutionary history of invasive species can help to build a firmer footing for management tactics. This study used mitochondrial DNA (mtDNA) sequence comparisons of samples collected from the native and introduced ranges of a pest herbivore of cultivated grapes, grape phylloxera (Daktulosphaira vitifoliae Fitch, Phylloxeridae) to infer the sources and pattern of introductions into worldwide viticulture. Introductions into viticulture from its native North American range first occurred in the mid-19th century. The pattern of spread has suggested a focus of introduction into France, but independent introductions may have occurred elsewhere. The results show that the introduced population represents a limited subsample of the native genetic diversity. The data suggest that most grape phylloxera in viticulture, including all European, have originated in the northeastern USA where the grape species Vitis riparia dominates. There was evidence for independent introductions into South Africa and California. Most California haplotypes were most closely related to native grape phylloxera from the Atlantic Coast on V. vulpina. It is likely that subsequent spread from California into Australia, New Zealand and Peru has occurred.

Animals↗
PubMed2000

Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine.

Francisella tularensis is the etiological agent of tularemia, a serious disease in several Northern hemisphere countries. The organism has fastidious growth requirements and is very poorly understood at the genetic and molecular levels. Given the lack of data on this organism, we undertook the sample sequencing of its genome. A random library of DNA fragments from a highly virulent strain (Schu 4) of F. tularensis was constructed and the nucleotide sequences of 13,904 cloned fragments were determined and assembled into 353 contigs. A total of 1.83 Mb of nucleotide sequence was obtained that had a G+C content of 33.2%. Genes located on plasmids pOM1 and pNFL10, which had been previously isolated from low virulence strains of F. tularensis, were absent but all of the other known F. tularensis genes were represented in the assembled data. F. tularensis Schu4 was able to grow in the absence of aromatic amino acids and orthologues of genes which could encode enzymes in the shikimate pathway in other bacteria were identified in the assembled data. Genes that could encode all of the enzymes in the purine biosynthetic and most of the en- zymes in the purine salvage pathways were also identified. This data will be used to develop defined rationally attenuated mutants of F. tularensis, which could be used as replacements for the existing genetically undefined live vaccine strain.

Bacterial Vaccines↗
PubMed1997

Path costs in evolutionary tree reconstruction.

This paper describes a dynamic programming algorithm to solve a family of problems in the reconstruction of evolutionary trees from protein sequence data, that of constructing "minimal" colorings. This dynamic programming formulation can be modified to efficiently enumerate the number of minimal colorings and thereby be used to calculate the average cost of any given edge, where the average is taken over the entire set of minimal colorings. An extension of our dynamic programming formulation allows for the calculation of average path costs amongst all minimal colorings. our results resolve questions raised in (Hendy and penny, 1987); in particular, we develop polynomial time procedures to find the minimum, maximum, and average (expected) cost of an edge, and more generally of a path, for a minimal coloring. Our algorithm is distinguished in its flexibility to address further distribution and statistical questions relating to the minimal colorings. Furthermore, the more general concept of calculating statistics describing the set of optimal solutions may be of interest in other combinatorial problems.

Algorithms↗
PubMed1998

An efficient, automatable template preparation for high throughput sequencing.

We have developed a 96-well format for DNA template isolation that can be readily automatable. The template isolation protocol involves simple alkaline lysis chemistry and reversible capture on a silica solid phase. After the cells are lysed, no centrifugation is necessary, as lysate purification, DNA binding, washing, and release occur in 96-well filter plates. Large numbers of templates prepared using the silica purification method have been sequenced and analyzed. The quality of sequence resulting from our method has been compared with that generated from several commercial plasmid preparation protocols. We found sequence quality of the silica bead preparations to be equivalent to or, in some cases, better than those prepared by other methods. This method offers many advantages over other protocols we have used. First, the silica purifications have allowed us to more than double overall laboratory throughput while decreasing our template isolation materials cost at least five-fold. Second, because we have eliminated all centrifugation steps in the protocol, automation has been much simpler. The protocol has also been adapted to purify PCR products for use as templates in subsequent sequencing reactions.

Automation↗