Origins and genetic features of the Okhotsk people,revealed by ancient mitochondrial DNA analysis

In order to investigate the phylogenetic status of the Okhotsk people that were distributed in northern and eastern Hokkaido as well as southern Sakhalin during the fifth to the thirteenth centuries, DNA was carefully extracted from human bone and tooth remains excavated from archaeological sites. The hypervariable region 1 sequences of the mitochondrial DNA (mtDNA) control region were successfully amplified and 16 mtDNA haplotypes were identified from 37 individuals of the Okhotsk people. Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies.     

Codon usage,genetic code and phylogeny of Dictyostelium discoideum mitochondrial DNA as deduced from a 7.3-kb region

We have sequenced a region (7 376-bp) of the mitochondrial (mt) DNA (54 kb) of the cellular slime mold, Dictyostelium discoideum. From the DNA and amino-acid sequence comparisons with known sequences, genes for ATPase subunit 9 (ATP), cytochrome b (CYTB), NADH dehydrogenase subunits 1, 3 and 6 (ND1, ND3 and ND6), small subunit rRNA (SSU rRNA) and seven tRNAs (Arg, Asn, Cys, Lys, f-Met, Met and Pro) have been identified. The sequenced region of the mtDNA has a high average A+T-content (70.8%). The A+T-content of protein-genes (73.6%) is considerably higher than that of RNA genes (61.3%). Even with the strong AT-bias, the genetic code employed is most probably the universal one. All seven tRNAs are able to form typical clover leaf structures. The molecular phylogenetic trees of CYTB and SSU rRNA suggest that D. discoideum is closer to green plants than to animals and fungi.     

Multidisciplinary approach in study of the zoonotic Anisakis larval infection in the blue mackerel (Scomber australasicus) and the largehead hairtail (Trichiurus lepturus) in Northern Taiwan

BackgroundAnisakid larvae are the food-borne pathogen highly prevalent among numerous marine fishes. Accidental consumption of infected raw or poorly cooked fish fillets may cause anisakiasis.MethodsThis study used the multidisciplinary approach to investigate the occurrence of Anisakis nematodes in commonly consumed fish species, Scomber australasicus and Trichiurus lepturus purchased in Taipei Xinyi traditional fish market.ResultsAll the Anisakis larvae collected herein were identified morphologically as Anisakis type I or Anisakis type II. The prevalence and the mean intensity of Anisakis larvae collected from S. australasicus was 80.77%, 26.8 (10–32) and 100%, 49.0 (27–70) for T. lepturus. Using molecular analysis, 83.33% (180/216) were identified as Anisakis pegreffii, 6.05% (13/216) as Ascaris typica, 1.85% (4/216) as Ascaris physeteris and 8.80% (19/216) as hybrid genotype (A. pegreffii + Anisakis simplex) in S. australasicus. In T. lepturus, 86.31% (290/336) were identified as A. pegreffii, 2.38% (8/336) as A. typica, and 11.31% (38/336) as hybrid genotype (A. pegreffii + A. simplex [s.s]). The molecular phylogenetic analysis shows two cluster clades, one group includes A. pegreffii complex and the other include Ascaris paggiae, Ascaris brevispiculata, and A. physeteris.ConclusionThus, A. pegreffii is the most abundant species and may be the potential causes of human infection.     

Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera

PCR amplification of the highly conserved baculovirus genes late expression factor 8 (lef-8), late expression factor 9 (lef-9) and polyhedrin/granulin (polh/gran) combined with molecular phylogenetic analyses provide a powerful tool to identify lepidopteran-specific baculoviruses and to study their diversity. In the present investigation, we have improved the degenerate oligonucleotides and corroborated the approach that was recently described by Lange et al. (Lange, M., Wang, H., Zhihong, H., Jehle, J.A., 2004. Towards a molecular identification and classification system of lepidopteran-specific baculoviruses. Virology 325, 36-47.). Baculovirus DNA was isolated from 71 uncharacterized historic baculovirus samples, and partial gene sequences were amplified by using gene-specific degenerate PCR primers. The obtained PCR products were directly sequenced, and the deduced amino acid sequences were compiled and aligned with published sequences of these target genes. A phylogenetic tree of 117 baculoviruses was inferred using maximum parsimony and distance methods. Based on the comprehensive phylogenetic analysis of the partial lef-8, lef-9 and polh/gran genes, we propose a phylogenetic species criterion for lepidopteran-specific baculoviruses that uses the genetic distances of these genes for species demarcation.     

Karyology,mitochondrial DNA and the phylogeny of Australian termites

A comprehensive karyological characterization of 20 Australian and three European species of Isoptera, together with a mitochondrial gene analysis is presented. Higher termites appear karyotypically very uniform, while lower termites are highly variable. The differences in chromosome number are explained through Robertsonian changes or multiple translocation events. An ancestral acrocentric karyotype can be suggested as the most primitive one. In Kalotermitidae chromosomal repatterning has repeatedly arisen with the X0-male type possibly representing a XY-derived condition. This argues against a simple origin of termites from cockroaches. The fixed chromosome number of Rhinotermitidae and Termitidae (2n=42, XY/XX) may be explained with the non-random nature of chromosomal evolution. A sex-linked multivalent, either with a ring or a chain structure, is found in the majority of species. Phylogenetic analyses on COII sequences recognize Mastotermitidae as the basal lineage and define the Rhinotermitidae + Termitidae cluster with a good bootstrap support. Kalotermitidae fail to be joined in a single cluster in agreement with the detected chromosomal variability. On the other hand, the karyotypic conservation of the Termitidae family contrasts with the polytomy evidenced at the subfamily level. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Microbial competition, lack in macronutrients, and acidity as main obstacles to the transfer of basidiomycetous ground fungi into (organically or heavy-metal contaminated) soils

Non-symbiotic soil microorganisms which have been expensively engineered or selected to support plant nutrition, control root diseases, degrade xenobiotic hydrocarbons, and repress or stimulate heavy metal uptake of plants fail to survive in target soils. This prompted studies into the role of chemistry and microbial pre-colonization of 23 top soils in long-term growth of basidiomycetes. Fungi are seen as auxiliary agents in soil remediation. Untreated soils (1.5 L) were colonized by lignocellulose preferring ground fungi such as Agaricus aestivalis, A. bisporus, A. campestris, A. edulis, A. macrocarpus, A. porphyrizon, Agrocybe dura, A. praecox, Clitocybe sp., Coprinus comatus, Lepista nuda, L. sordida, Macrolepiota excoriata, M. procera, Stropharia coronilla, and S. rugoso-annulata. Spawn mycelia of fairy-ring-type fungi such as Agaricus arvensis, A. fissuratus, A. langei, A. lanipes, A. pilatianus, Lyophyllum sp., and Marasmius oreades died back in contact with non-sterile soils. Fungal growth correlated positively with the soils' Ct Ca K Mg content and negatively with microbial CO2 evolution. Pasteurization and autoclaving increased mycelial growth and life span in soils pH 6.6-8.2. Growth of pH-sensitive but not of pH-tolerant fungi was inhibited on the Ca-deficient soils pH 4-4.4 (-5.6) and was not improved by autoclaving. The pretended fungistasis of acid soils to pH-sensitive fungi was controlled by N P K mineral (pH not altering) or organic (pH increasing) fertilizing as well as by neutralization with NaOH or CaCO3. Although microbial competition was mortal to 33% of the fungal mycelia inserted into natural unplanted soils, further seriously antifungal effects beyond those pretended by low pH conditions and shortage in mineral macronutrients were not identified.     

Recent emergence of the Arctic rabies virus lineage

The rabies viruses that circulate in Arctic countries and in much of northern and central Asia are phylogenetically closely related and collectively referred to as the Arctic/Arctic-like (AL) lineage. The emergence and spread of this lineage is of significant interest given that rabies remains a serious zoonotic disease in many parts of Asia, especially in India where the prevalence of dog rabies leads to frequent human exposures and deaths. Previous molecular epidemiological studies of rabies viruses in India identified the AL lineage as the type circulating across much of the country. To further explore the relationship of Indian and Arctic rabies viruses, a collection of samples recovered from Rajasthan state in northern India was characterised at the N gene locus. Combination of these data with a larger collection of samples from India, central/northern Asia and the Arctic has permitted detailed phylogenetic analysis of this viral lineage and estimation of its time-frame of emergence. These analyses suggest that most current Indian viruses emerged from a common progenitor within the last 40 years and that the entire Arctic/AL lineage emerged within the last 200 years, a time-frame in accord with historical records of the invasion of Canada by the Arctic clade.     

分子伴侣基因的克隆及表达

用聚合酶链反应方法从大肠杆菌染色体ＤＮＡ中扩增得到２０００ｂｐ的ＤＮＡ片段，并克隆到ＰＧＥＭ３ｚｆ（＋）载体中，经限制性图谱分析和部分ＤＮＡ序列测定，证实２０００ｂｐ的ＰＣＲ产物为ＧｒｏＥ基因全部编序列。将ＰＣＲ产物构建在ＰＬＰＲ启动子控制下的ＰＢＶ２２０表达质粒中，转入大肠杆菌ＤＨ５ａ，经４２℃热诱导，获得ＧｒｏＥ基因的表达产物，在ＳＤＳ－ＰＡＧＥ上出现分子量约６００００（ＧｒｏＥＬ）及１５００     

Chromosomal phylogeny and evolution of the African mole-rats (Bathyergidae)

The subterranean African mole-rats (Family Bathyergidae) show considerable variation in their diploid numbers, but there is limited understanding of the events that shaped the extant karyotypes. Here we investigate chromosomal evolution in specimens representative of six genera and an outgroup species, the cane rat Thryonomys swinderianus, using flow-sorted painting probes isolated from the naked mole-rat, Heterocephalus glaber (2n = 60). A chromosomal phylogeny based on the cladistic analysis of adjacent syntenies detected by cross-species chromosome painting was not consistent with that obtained using DNA sequences due, in large part, to the conserved nature of the Bathyergus, Georychus and Cryptomys karyotypes. In marked contrast, the Fukomys and Heliophobius species showed extensive chromosome reshuffling, permitting their analysis by a computational approach that has conventionally been employed in comparative genomic studies for retrieving phylogenetic information based on DNA sequence or gene order data. Using the multiple genome rearrangements (MGR) algorithm and chromosomal rearrangement data detected among F. damarensis, F. darlingi, F. mechowi and the sister taxa B. janetta and Heliophobius argenteocinereus, cytogenetic support for the monophyly of Fukomys and a sister association for F. darlingi + F. damarensis was retrieved, mirroring the published sequence-based topology. We show that F. damarensis, a lineage adapted to arid and climatically unpredictable environments in Southern Africa, is characterized by a large number of fissions the fixation of which has probably been favoured by environmental factors and/or its particular eusocial structure.     

Effects of phylogeny and locomotor style on the allometry of body mass and pelvic dimensions in birds

The pelvic girdle provides physical support and attachment for the hind limb musculature. In birds there is variability in pelvic morphology across different orders and this has been used as evidence for various types of locomotion. However, the morphological variation of pelvic bones has yet to be studied systematically in birds. Therefore, we investigated basic allometric relationships among female body mass (as a size proxy) and various pelvic measurements in a phylogenetic context. We also examined in detail the inter‐relationships among various pelvic measurements. Also considered were the effects of broader taxonomic relationships at the level of order, with further examination of the influence of style of terrestrial locomotion on the allometric relationships. Positive relationships were initially found among all pelvic linear measurements and female body mass (FBM). The relationships among measures of pelvic width and FBM were isometric, whereas those between pelvic length and FBM showed positive allometry. Also, FBM explained more of the variance in pelvic length than in width. Similarly, the angle of the pelvis had a significant negative relationship, but FBM only explained a very low proportion of the variation in pelvic angles. In general terms, ancova showed that the effect of FBM was smaller than the effect of locomotor style in this species set. Both the synsacrum and pelvic girdle play roles in weight support and therefore scale in proportion to body weight accordingly. All three parts of the pelvis (ilium, ischium and pubis) are attached around the acetabulum and also provide muscle attachment points, so it might be expected for them to scale in a similar manner. Increased angulation of the pelvis is linked to orders which employ their hind limbs in feeding, perching and running, although FBM also explains a very low proportion of the variation in pelvic angle. Muscle attachment and the confines on morphology presented by locomotion explain much of the variation exhibited by the relationships among pelvic measurements.     

Molecular Biology and DNA Microarray Technology for Microbial Quality Monitoring of Water

Public concern over polluted water is a major environmental issue worldwide. Microbial contamination of water arguably represents the most significant risk to human health on a global scale. An important challenge in modern water microbial quality monitoring is the rapid, specific, and sensitive detection of microbial indicators and waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. Rapid microbiological analyses and detection of rare events in water systems are important challenges in water safety assessment since culture methods present serious limitations from both quantitative and qualitative points of view. To circumvent lengthy culture methods, newer enzymatic, immunological, and genetic methods are being developed as an alternative. DNA microarray technology is a new and promising tool that allows the detection of several hundred or even thousands DNA sequences simultaneously. Recent advances in sample processing and DNA microarray technologies provide new perspectives to assess microbial water quality.

The aims of this review are to (1) summarize what is currently known about microbial indicators, (2) describe the most important waterborne pathogens, (3) present molecular methods used to monitor the presence of pathogens in water, and (4) show the potential of DNA microarrays in water quality monitoring.     

Mitochondrial DNA of the filamentous ascomycete Cochliobolus heterostrophus

Summary The mitochondrial chromosome of Cochliobolus heterostrophus is a circle approximately 115 kb in circumference, among the largest known from fungi. A physical map of C. heterostrophus mtDNA was constructed using the restriction enzymes BamHI, EcoRI, and PvulI by DNA-DNA hybridizations with cloned or purified mtDNA BamHI fragments. The following sequences were located on the mtDNA map: (1) the large and small mitochondrial ribosomal RNA genes (identified by heterologous hybridization to cloned Neurospora crassa rRNA genes); (2) the sequence homologous to a mitochondrial plasmid present in one field isolate of C. heterostrophus; and (3) a 1.05 kb EcoRI fragment that functions as an autonomously replicating sequence in Saccharomyces cerevisiae. An examination of mtDNA from 23 isolates of C. heterostrophus collected worldwide revealed polymorphisms in restriction enzyme sites. One such polymorphism, coupled with data on a polymorphism in nuclear rDNA, suggests that there are two genetically distinct but geographically overlapping mating populations of C. heterostrophus in the world.     

Chromosome-wide haplotype sharing: a measure integrating recombination information to reconstruct the phylogeny of human populations

The vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships. One reason is that estimation of the recombination parameter from genotyping data is computationally challenging and practically difficult. Here we propose chromosome-wide haplotype sharing (CHS) as a measure of genetic similarity between human populations, which is an indirect approach to integrate recombination information. We showed in both empirical and simulated data that recombination differences and genetic differences between human populations are strongly correlated, indicating that recombination events in different human populations are evolutionarily related. We further demonstrated that CHS can be used to reconstruct reliable phylogenies of human populations and the majority of the variation in CHS matrix can be attributed to recombination. However, for distantly related populations, the utility of CHS to reconstruct correct phylogeny is limited, suggesting that the linear correlation of CHS and population divergence could have been disturbed by recurrent recombination events over a large time scale. The CHS we proposed in this study is a practical approach without involving computationally challenging and time-consuming estimation of recombination parameter. The advantage of CHS is rooted in its integration of both drift and recombination information, therefore providing additional resolution especially for populations separated recently.     

Plastid genomes of the Rhodophyta and Chromophyta constitute a distinct lineage which differs from that of the Chlorophyta and have a composite phylogenetic origin,perhaps like that of the Euglenophyta

Summary A phylogenetic tree has been constructed from comparisons of entire 16S rRNA gene sequences from different prokaryotes and from several algal plastids. According to this study, and to previous work on the ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) large and small subunit genes, we postulate that: (1) rhodophyte and chromophyte plastid genomes have a common, composite phylogenetic origin which implies at least two different ancestors, a cyanobacterial and a -proteobacterial ancestor; (2) chlorophyte (green algae and land plants) plastids have a cyanobacterial ancestor which probably differs from that of rhodophyte and chromophyte plastids, and in any case constitute a different lineage; (3) euglenophyte plastid genomes also seem to have a composite phylogenetic origin which involves two different lineages.     

In search of mitochondrial markers for resolving the phylogeny of cyclophyllidean tapeworms (Platyhelminthes,Cestoda) — a test study with Davaineidae

The most species rich order of tapeworms is the Cyclophyllidea and prior to wide-scale sampling of these worms for phylogenetics, we wished to develop reliable PCR primers that would capture fragments of mitochondrial (mt) DNA with phylogenetic utility across the order. Nuclear ribosomal RNA gene sequences are well-established and valuable markers for resolving flatworm interrelationships spanning a wide range of taxonomic divergences, but fail to provide resolution amongst recently diverged lineages. Entire mt genomes of selected cyclophyllidean tapeworms are available on GenBank, and we used these to design PCR primers to amplify mtDNA from cox1, rrnL and nad1 for a range of cyclophyllideans (7 davaineids, 1 hymenolepidid and 1 dilepidid) and selected outgroups (Tetrabothrius sp. and Mesocestoides sp.). A combined nuclear and mt gene data set was used to estimate a reference phylogeny and the performance of the individual genes was compared to this. Although nuclear and mt genes each contributed to the structure and stability of the phylogenetic estimate, strongest nodal support was provided by nuclear data amongst the basal lineages and by mt data amongst the most recently diverged lineages. The apparent complementarity afforded by combining nuclear and mt data was compromised by these data partitions providing conflicting signal at poorly supported nodes. Nevertheless, we argue for a combined evidence approach. PCR primers that amplify rrnL were designed and tested successfully against a diversity of cyclophyllideans; rrnL and nad1 appeared to be more informative than the fragment of cox1. The genus Raillietina was not supported by molecular evidence. The new primers will likely provide considerable resolution to estimates of cyclophyllidean interrelationships in future studies.     

A small insertion in the SSU rDNA of the lichen fungusArthonia lapidicola is a degenerate group-I intron

 Insertions of less than 100 nt occurring in highly conserved regions of the small subunit ribosomal DNA (SSU rDNA) may represent degenerate forms of the group-I introns observed at the same positions in other organisms. A 63-nt insertion at SSU rDNA position 1512 (relative to the Escherichia coli SSU rDNA) of the lichen-forming fungus Arthonia lapidicola can be folded into a secondary structure with two stem loops and a pairing of the insertion and flanking sequences. The two stem loops may correspond to the P1 and P2, and the insertion-flanking pairing to the P10, of a group-I intron. Considering these small insertions as degenerate introns provides important clues to the evolution and catalytic function of group-I introns. Received: 30 Deember 1994/1 November 1995     

青光眼分子遗传学的研究进展

青光眼 (glaucoma) 分子遗传学的研究是当前眼科学领域的重要课题,一些青光眼的致病位点和相关基因相继定位于相应的染色体上,并进行基因的克隆、测序、表达、调控及突变分析。目前报道过的与青光眼相关的基因有：TIGR/MYOC基因、OPTN基因、CYP1B1基因、WDR36基因、OPA1基因和LMX1B 基因等,相关的位点有：GLCA、GLCB、GLCC、GLCD、GLCE、GLCF、GLCG、GLC3A等,此文就相关基因的发现、定位、结构、编码产物和突变研究做一综述。