Large genomes among caridean shrimp.

Recent genome size estimates for Arctic amphipods have revealed the largest genomes known in the Crustacea. Here we provide additional data for 7 species of caridean shrimp collected from the Canadian Arctic and the Gulf of St. Lawrence. Genome sizes were estimated by flow cytometry and haploid C-values ranged from 8.53 +/- 0.30 pg in Pandalus montagui (Pandalidae) to 40.89 +/- 1.23 pg in Sclerocrangon ferox (Crangonidae). The value for S. ferox represents the largest decapod genome yet recorded and indicates a 38-fold variation in genome size within this order. These data suggest that large genomes may be relatively common in Arctic crustaceans, and underline the need for further comparative studies.     

Oxidative phosphorylation differences between mitochondrial DNA haplogroups modify the risk of Leber's hereditary optic neuropathy

Leber's hereditary optic neuropathy is a maternally inherited optic atrophy caused by mitochondrial DNA point mutations. Previous epidemiological studies have shown that individuals from mitochondrial genetic backgrounds (haplogroups) J/Uk and H have a higher and a lower risk, respectively, of suffering this disorder. To analyze the bases of these associations at cellular and molecular levels, functional studies with cybrids provide high quality evidence. Cybrids from haplogroup J contain less mitochondrial deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and synthesize a smaller amount of mitochondrial DNA-encoded polypeptides than those from haplogroup H. Haplogroup J cybrids also display lower oxygen consumption, mitochondrial inner membrane potential and total adenosine-5'-triphosphate (ATP) levels. Moreover, mitochondrial DNA levels correlate with many parameters of the oxidative phosphorylation system. These results suggest that the mitochondrial DNA amount determines oxidative phosphorylation capacity and, along with other recently published observations, support the possibility that mitochondrial DNA levels may be responsible for the bias of the disorder toward males, for the incomplete penetrance of mutations causing Leber's hereditary optic neuropathy and for the association of the disease with particular mitochondrial DNA haplogroups.     

线粒体DNA与DNA甲基化的关系

线粒体DNA（mitochondrial DNA,mtDNA）遗传信息量虽小,却控制着线粒体一些最基本的性质,对细胞及其功能有着重要影响。mtDNA的损伤与衰老、肿瘤等疾病的发生有关。DNA甲基化是调节基因表达的重要方式之一。mtDNA基因的表达受核DNA（nuclear DNA,nDNA）的调控,mtDNA和nDNA协同作用参与机体代谢调节和发病。本文就近年来mtDNA与DNA甲基化的关系作一综述。     

Numerical methods in Quaternary palaeoecology. IV. Separating mixtures of morphologically similar pollen taxa

It has often been found desirable, to strengthen palaeoecological inferences, to be able to separate mixtures of pollen taxa whose morphological characteristics overlap considerably, as with the species of many circumboreal tree genera (birch and pine being much-studied examples). Statistical methods are potentially valuable in this problematic field. Previously developed numerical approaches are discussed. Methods based on the identification of single grains are shown to be less satisfactory than methods involving the fitting of frequency histograms, corresponding to possible combinations of known reference distributions, to the observed frequency histograms from fossil material, as proposed by Eneroth (1951). A solution of this type based on the maximum likelihood principle is described and applied to some of Eneroth's own data. The assumptions and limitations of the method, particularly with regard to size statistics versus other morphological data, are discussed.     

Large circular mitochondrial DNA in Crithidia luciliae

A novel circular DNA, 11.3 μm in contour length, has been found in a pure kinetoplast DNA fraction of Crithidia luciliae. The mitochondrial nature of the kinetoplast and the absence of these large circular molecules in the nuclear fraction of DNA suggest that they constitute the mitochondrial genome of this species.     

线粒体DNA与DNA甲基化

线粒体是除细胞核之外唯一携带遗传物质的细胞器,其线粒体DNA（mitochondrial DNA,mtDNA）控制着线粒体一些最基本的性质,对细胞功能有着重要影响.DNA甲基化是调节基因表达的重要方式之一.研究表明mtDNA存在CpG位点的低甲基化,并且mtDNA基因的表达受核DNA（nuclear DNA,nDNA）及线粒体自身DNA甲基化的调控,mtDNA和nDNA协同作用参与机体代谢调节和疾病发生发展过程.就近年来mtDNA与DNA甲基化的关系作一综述.     

Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA

Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus s.l. genus of marine shrimp. This phylogeny was used to test the validity of hypotheses on the species groupings, in particular the subgenus/genus subdivision, and on the species' evolutionary history. Newly derived sequences of both 16S rRNA and COI genes from 19 species of Penaeus s.l. and one outgroup were combined with previous sequences from seven additional species to allow analysis of 26 of the 28 recognised (or nominated) species. Phylogenetic analyses do not support the validity of all the previously created six subgenera (or genera) but provide evidence for division of the genus into two previously unrecognised clades (Melicertus+Marsupenaeus and Penaeus s.s.+Fenneropenaeus+Farfantepenaeus+Litopenaeus). A key conclusion from a previous molecular study, that the subgenera Farfantepenaeus and Litopenaeus are paraphyletic, was rejected. The molecular data support an Indo-West Pacific origin of the genus, with a single relatively recent colonisation of the Western Hemisphere, and subsequent subdivision into two clades prior to the emergence of the Panamanian isthmus.     

Reproductive versus floral isolation among morphologically similar Serapias L. species (Orchidaceae)

Flowers of the Mediterranean orchid genus Serapias L. form small, dark tubes that vary among taxa in diameter and depth. Visiting insects use the floral tube as shelter and act as pollinators if they touch the sticky viscidium at the rear of the tube and remove the pollinarium. It has been assumed that floral tube size and shape limit access to the flowers and thus may act as a barrier to gene flow between different Serapias species. Here we investigated floral characters and nuclear microsatellite markers in populations belonging to three morphologically similar Serapias species to test whether these species show evidence for floral or reproductive isolation. We found strong overlap of floral traits between two species, suggesting that floral isolation is nonexistent between them. Microsatellite markers applied to the same populations were highly polymorphic and revealed clear genetic differentiation among all three species. These results suggest that reproductive isolation exists, despite the lack of floral isolation between two of the species. In contrast to morphological characters, diagnostic microsatellite alleles were found for all Serapias species. The microsatellite markers could thus provide a useful tool to identify Serapias species and further investigate evolutionary relationships in this fascinating orchid lineage.     

Comparative culture and toxicity studies between the toxic dinoflagellate Pfiesteria piscicida and a morphologically similar cryptoperidiniopsoid dinoflagellate

A series of fish bioassays using cultures of the toxic dinoflagellate, Pfiesteria piscicida and a cryptoperidiniopsoid dinoflagellate indicated various degrees of toxicity for Pfiesteria piscicida and no toxicity by the cryptoperidiniopsoid. P. piscicida maintained toxicity in the presence of live fish, and this toxicity was perpetuated following a series of inoculations to other culture vessels. Differences in the onset and magnitude of the fish deaths occurred, requiring 16 days for the initial fish death when using P. piscicida from a culture that had previously been maintained on algal cells, to kills within hours when using a culture that had recently (previous day) killed fish. Autopsies of moribund fish from the test and control fish bioassays indicated a general lack of bacterial infection, which ensued following death of other autopsied fish. Moreover, bacterial comparisons of waters in the fish bioassay and control fish cultures indicated that similar bacterial concentrations were present. Neither oxygen or ammonia levels were determined to be factors in the fish death. Life stages of a cryptoperidiniopsoid dinoflagellate from Virginia estuaries were also identified, including motile zoospore, gametes, planozygote, amoebae, and cyst stages. The cryptoperidiniopsioid did not initiate fish deaths in bioassays conducted over a 14-week period at zoospore concentrations of ca. 700-800 cells ml(-1). Elemental X-ray analysis of the scales from cysts of this dinoflagellate and P. piscicida indicate that they both contain silicon. Overall, the data from this study demonstrate that the cryptoperidiniopsoid possesses several similar life stages and feeding patterns as P. piscicida, but was not toxic to fish.     

Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA.

Nucleotide sequences of the major noncoding region of human mitochondrial DNA (mtDNA) from 95 human placentas have been determined. These sequences include at least a 482-bp-long region encompassing most of the D-loop-forming region. Comparisons of these sequences with those previously determined have revealed remarkable features of nucleotide substitutions and insertion/deletion events. The nucleotide diversity among the sequences is estimated as 1.45%, which is three- to fourfold higher than the corresponding value estimated from restriction-enzyme analysis of whole mtDNA genome. A hypervariable region has also been defined. In this 14-bp region, 17 different sequences were detected. More than 97% of the base changes are transitions. A significantly nonrandom distribution of nucleotide substitutions and sequence length variations were also noted. The phylogenetic analysis indicates that diversity among the negroids is much larger than that among the caucasoids or the mongoloids. In fact, part of the negroids first diverged from other humans in the phylogenetic tree. A striking finding in the phylogenetic analysis is that the mongoloids can be separated into two distinct groups. Divergence of part of the mongoloids follows the earliest divergence of part of the negroids. The remainder of the mongoloids subsequently diverged together with the caucasoids. This observation confirmed our earlier study, which clearly demonstrated, by the restriction-enzyme analysis, existence of two distinct groups in the Japanese.     

Recent divergence between two morphologically differentiated subspecies of bluethroat (Aves: Muscicapidae: Luscinia svecica) inferred from mitochondrial DNA sequence variation

We assessed the mitochondrial DNA sequence divergence of a 718 bp fragment of the control region and 1007 bp of the cytochrome b gene between two allopatric morphologically different subspecies of bluethroat ( Luscinia svecica ). None of the 17 total haplotypes was shared between L. s. namnetum and L. s. svecica . However, the mean distances between subspecies were very low for both fragments (0.00168 ± 0.00001 (mean ± SE) for the control region; 0.00306 ± 0.00016 for the cytochrome b gene). Only one substitution made the two subspecies genetically differentiated, highlighting their recent divergence. Interestingly, the control region was not more variable than the cytochrome b gene.     

Molecular species identification of morphologically similar mussel larvae reveals unexpected discrepancy between relative abundance of adults and settlers

Understanding the relative importance of larval supply vs. post-settlement mortality underlies studies of marine invertebrate recruitment, yet is often hampered by researchers' inability to identify species among morphologically similar larvae or early juveniles. In New Zealand, two species of co-occurring intertidal mytilid mussels have morphologically indistinguishable settlers: the blue mussel Mytilus galloprovincialis, which is often numerically dominant in the mid-zone of the rocky intertidal, and the ribbed mussel Aulacomya atra maoriana which is often much less abundant. In this study, we obtained samples of newly settled mussels from 6 sample dates April-May 2005 from the rocky intertidal in Wellington Harbour, New Zealand. We used PCR-RFLP of the cytochrome c oxidase subunit I (COI) mitochondrial gene region to identify settlers to species. Of a total of 224 settlers that could be identified, 64% were identified as Mytilus galloprovincialis and 36% as Aulocomya atra maoriana. The percentage of A. atra maoriana in the samples was unexpectedly high and ranged from 22–50% among the sample dates. This study reinforces the need to quantify larval supply at the species level to understand the relative importance of pre- and post-settlement mortality, and also demonstrates the usefulness of the COI region as a species-specific marker for identifying mussel larvae and juveniles.     

The structure of Tetrahymena pyriformis mitochondrial DNA. I. Strain differences and occurrence of inverted repetitions.

We have analysed the structure of the mtDNAs of six amicronucleate Tetrahymena pyriformis strains, belonging to at least four phenosets, as defined by Borden et al. (Borden, D., Whitt, G.S. and Nanney, D.L. (1973) J. Protozool. 20, 693--700). 2. The mtDNAs of all strains are linear, but they differ in size, in their fragmentation by endonuclease EcoRI and in overall sequence; less than 20% sequence homology was found by DNA-DNA hybridization in all combinations tested, except for the mtDNAs from strains T and ST which are indistinguishable. 3. In spite of these marked sequence differences the mtDNAs of all strains share two structural peculiarities: ragged (gnawed) duplex ends and a duplication-inversion, which varies in length between 0.3 and 1.2 micrometer, depending on the strain. In four strains the duplication-inversion is terminal, allowing formation of single-stranded DNA circles with a duplex tail; in two strains it is subterminal. 4. The ragged ends and sub-terminal position of the duplication-inversion in some of the Tetrahymena mtDNAs do not fit any of the current models for the replication of linear mtDNAs.     

Rate and mode differences between nuclear and mitochondrial small-subunit rRNA genes in mushrooms.

Sequences from homologous regions of the nuclear and mitochondrial small-subunit rRNA genes from 10 members of the mushroom order Boletales were used to construct evolutionary trees and to compare the rates and modes of evolution. Trees constructed independently for each gene by parsimony and tested by bootstrap analysis have identical topologies in all statistically significant branches. Examination of base substitutions revealed that the nuclear gene is biased toward C-T transitions and that the distribution of transversions in the mitochondrial gene is strongly effected by an A-T bias. When only homologous regions of the two genes were compared, base substitutions per nucleotide were roughly 16-fold greater in the mitochondrial gene. The difference in the frequency of length mutations was at least as great but was impossible to estimate accurately because of their absence in the nuclear gene. Maximum likelihood was used to show that base-substitution rates vary dramatically among the branches. A significant part of the rate inconstancy was caused by an accelerated nuclear rate in one branch and a retarded mitochondrial rate in a different branch. A second part of the rate variability involved a consistent inconstancy: short branches exhibit ratios of mitochondrial to nuclear divergences of less than 1, while longer branches had ratios of approximately 4:1-8:1. This pattern suggests a systematic error in the branch length calculation. The error may be related to the simplicity of the divergence estimates, which assumes that all base positions have an equal probability of change.     

Striking differences in mitochondrial tRNA import between different plant species

A systematic comparison of the tRNAs imported into the mitochondria of larch, maize and potato reveals considerable differences among the three species. Larch mitochondria import at least eleven different tRNAs (more than half of those tested) corresponding to ten different amino acids. For five of these tRNAs [tRNA^Phe(GAA), tRNA^Lys(CUU), tRNA^Pro(UGG), tRNA^Ser(GCU) and tRNA^Ser(UGA)] this is the first report of import into mitochondria in any plant species. There are also differences in import between relatively closely related plants; wheat mitochondria, unlike maize mitochondria import tRNA^His, and sunflower mitochondria, unlike mitochondria from other angiosperms tested, import tRNA^Ser(GCU) and tRNA^Ser(UGA). These results suggest that the ability to import each tRNA has been acquired independently at different times during the evolution of higher plants, and that there are few apparent restrictions on which tRNAs can or cannot be imported. The implications for the mechanisms of mitochondrial tRNA Import in plants are discussed.     

线粒体DNA突变与肿瘤发生的关系

线粒体DNA（mitochondrial DNA,mtDNA）是真核细胞内的核外遗传物质。事实证明,由于线粒体特殊的生物学结构与功能,和核基因（nDNA）相比,mtDNA更容易发生突变和氧化损伤。目前研究已经发现许多肿瘤组织中mtDNA结构和拷贝量发生了变化。文章主要对mtDNA突变、整合和不稳定性与肿瘤发生的关系以及可能的机理进行了综述。     

Mason-Pfizer virus RNA genome: relationship to the RNA of morphologically similar isolates and other oncornaviruses.

The 60-70S RNA of Mason-Pfizer virus (MPV) was iodinated in vitro and used in both direct and competitive molecular hybridization studies. MPV proviral sequences are present at a frequency of approximately one to two copies per haploid genome in the DNA of experimentally infected human cells. By nucleic acid competition hybridization, MPV RNA was found to be indistinguishable from the RNA of a virus (X381) isolated from a rhesus mammary gland and from RNA isolated from the cytoplasm of AO cells (Parks et al., 1973) and HeLa cells (Gelderblom et al., 1974), both previously reported to produce MPV-related particles. No homology was observed, however, between MPV RNA and the RNA, or the DNA, from two clones of HeLa cells obtained from the American Type Culture Collection. Hybridization of MPV 60-70S RNA to the DNA of normal tissues of humans and to the DNA of 11 other species revealed that MPV is not an endogenous virus of any of these species. Competition hybridization revealed no detectable sequence homology between the RNA of MPV and the RNAs of simian sarcoma virus, murine mammary tumor virus, murine leukemia virus, BUdR-induced guinea pig virus, or avian myeloblastosis virus. These nucleic acid studies substantiate previous ultrastructural and immunological findings that MPV and morphologically similar isolates constitute a distinct group of oncornavirus.