Codon bias in actin multigene families and effects on the reconstruction of phylogenetic relationships

Codon usage patterns and phylogenetic relationships in the actin multigene family have been analyzed for three dipteran species—Drosophila melanogaster, Bactrocera dorsalis, and Ceratitis capitata. In certain phylogenetic tree reconstructions, using synonymous distances, some gene relationships are altered due to a homogenization phenomenon. We present evidence to show that this homogenization phenomenon is due to codon usage bias. A survey of the pattern of synonymous codon preferences for I I actin genes from these three species reveals that five out of the six Drosophila actin genes show high degrees of codon bias as indicated by scaled ² values. In contrast to this, four out of the five actin genes from the other species have low codon bias values. A Monte Carlo contingency test indicates that for those Drosophila actin genes which exhibit codon bias, the patterns of codon usage are different compared to actin genes from the other species. In addition, the genes exhibiting codon bias also appear to have reduced rates of synonymous substitution. The homogenization phenomenon seen in terms of synonymous substitutions is not observed for nonsynonymous changes. Because of this homogenization phenomenon, trees constructed based on synonymous substitutions will be affected. These effects can be overt in the case of multigene families, but similar distortions may underlie reconstructions based on single-copy genes which exhibit codon usage bias.Correspondence to: M. He     

Comparative genotypic and phenotypic characterisation of methicillin-resistant Staphylococcus aureus ST398 isolated from animals and humans

The high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) ST398 among pigs in certain European countries and North America and its occurrence in other animal species raises a question concerning the molecular mechanisms mediating the success of this lineage. In this study a panel of S. aureus strains belonging to sequence type (ST) 5 (n = 4), ST8 (n = 5), ST15 (n = 5), ST22 (n = 8), clonal complex (CC) 30 (n = 8), CC97 (n = 8), CC130 (n = 4), CC151 (n = 4) and ST398 (n = 18) were screened by DNA microarray and PCR for the carriage of virulence and antimicrobial resistance genes. Isolates belonging to the same sequence type/clonal complex (ST/CC) were found to share similar virulence gene profiles. The ST398 lineage displayed the lowest content of virulence genes, which consisted mainly of genes detected among the majority or all of the analysed lineages. All MRSA ST398 isolates lacked accessory virulence genes that were detected in other ST/CC. In contrast to virulence genotype, the antimicrobial resistance genes profiles varied between isolates belonging to the same ST/CC and profile similarities could be observed for isolates from different lineages. MRSA ST398 isolates in particular displayed significant diversity and high content of antimicrobial resistance genes. This was comparable with certain MRSA belonging to other sequence types particularly the equine MRSA ST8. The apparent lack of significant virulence genes among MRSA ST398 strains, demonstrates that the lineage features a unique genetic background but no ST398-specific virulence markers could be identified.     

ADH and phylogenetic relationships ofDrosophila lebanonensis (Scaptodrosophila)

Summary Increasing data onDrosophila alcohol dehydrogenase (ADH) sequences have made it possible to calculate the rate of amino acid replacement per year, which is 1.7×10^–9. This value makes this protein suitable for reconstructing phylogenetic relationships within the genus for those species for which no molecular data are available such asScaptodrosophila. The amino acid sequence ofDrosophila lebanonensis is compared to all of the already knownDrosophila ADHs, stressing the unique characteristic features of this protein such as the conservation of an initiating methionine at the N-terminus, the unique replacement of a glycine by an alanine at a very conserved position in the NAD domain of all dehydrogenases, the lack of a slowmigrating peptide, and the total conservation of the maximally hydrophilic peptide. The functional significance of these features is discussed.Although the percent amino acid identity of the ADH molecule inDrosophila decreases as the number of sequences compared increases, the conservation of residue type in terms of size and hydrophobocity for the ADH molecule is shown to be very high throughout the genusDrosophila. The distance matrix and parsimony methods used to establish the phylogenetic relationships ofD. lebanonensis show that the three subgenera,Scaptodrosophila, Drosophila, andSophophora separated at approximately the same time.     

Structural relationships among chloramphenicol-resistance plasmids of Staphylococcus aureus

Abstract Twelve different chloramphenicol-resistance (Cm^r) plasmids detected in Staphylococcus aureus strains isolated between 1952 and 1981 were characterized by restriction endonuclease, DNA hybridization and heteroduplex analyses. These studies revealed three families of Cm^r plasmids which were distinguished by their chloramphenicol acetyltransferase sequences; the prototype plasmids of the families were pC221, pC223 and pC194. The cat and replication ( rep ) genes of the plasmid pC221 were highly conserved in other pC221 family members and were related to their homologs in the pC223 family plasmids; however, the cat and rep genes of the pC194 family plasmids were distinct.     

Molecular phylogenetic relationships among Asiatic shrewlike moles inferred from the complete mitogenomes

Asiatic shrewlike moles are distributed almost entirely in south‐west China; four of the five species of the genus Uropsilus, Uropsilus aequodonenia, U. andersoni, U. investigator and U. soricipes are endemic to China. Excluding the five species, three cryptic species (U. sp. 1, U. sp. 2 and U. sp. 3) and two putative species, U. nivatus and U. atronates, are recognized. The phylogenetic relationships among the species remain unclear and these preclude investigations of their potential adaptations for living in high altitudes. We sequenced the complete mitochondrial DNA genomes of three species of Asiatic shrewlike moles (U. aequodonenia, U. andersoni and U. nivatus). Phylogenetic analyses of 16 published and our de novo mitogenomes yield single, robust trees with the relationships being (U. soricipes (U. sp. 1 (U. nivatus (U. andersoni, U. aequodonenia)))). Further, the tree verifies the validity of recently described U. aequodonenia. Analyses of selection pressure suggest that the 13 mtDNA‐encoding genes of species in the genus Uropsilus all have experienced strong purifying selection, although ATP8 accumulated a higher ratio of non‐synonymous substitutions than the other loci, which might reflect adaptation of the genus Uropsilus to different environments/elevations.     

Systematics of Cafius corallicola (Fairmaire) (Coleoptera: Staphylinidae) with a discussion of its phylogenetic relationships

A systematic review of the marine littoral Cafius corallicola (Fairmaire), widely distributed along the coasts from the Indian Ocean to the western Atlantic Ocean through the southern Pacific Ocean, is presented based on morphological and molecular characters (COI and 28S). Specimens of the two species [C. corallicola and C. caribeanus Bierig] are extremely similar to each other including the form of the aedeagus. The molecular analyses support the validity of C. corallicola with one synonymy based on morphological characters. Genetic divergence of COI using uncorrected p-distance among these two species ranged from 0.35% to 4.49%. Cafius caribeanus Bierig syn. nov. is synonymized under C. corallicola. Phylogenetic relationships of C. corallicola with similar congeners are resolved as (C. corallicola (C. rufescens (C. filum + C. sericeus))). Cafius corallicola is redescribed with illustrations of diagnostic characters.     

实验动物金黄色葡萄球菌LAMP检测方法的建立

目的建立一种能够应用于实验动物金黄色葡萄球菌检测及鉴定的环介导等温扩增（loop-mediatedisothermal amplification,LAMP）方法。方法本研究针对金黄色葡萄球菌特异的nuc基因设计4条引物,对反应条件进行优化。结果通过优化,该方法 60℃、40 min、Mg2＋浓度8 mmol/L、dNTP浓度2.0 mmol/L、甜菜碱浓度0.8mmol/L时,对金黄色葡萄球菌检测限为2 cfu,且与其它常见实验动物致病菌无交叉反应。反应结果可通过添加荧光染料SYBR green I直接肉眼观察。结论本研究建立的金黄色葡萄球菌LAMP方法具有快速、灵敏、操作简单、设备要求低的特点,适用于基层、大批量样本、快速检测的要求。     

Nasal carriage of methicillin-resistant Staphylococcus aureus among smokers and cigarette factory workers

Effects of smoking and tobacco on nasal carriage and colonisation rates of Staphylococcus aureus were investigated on 368 healthy males aged between 30 and 40 years old. The study group comprised 100 non-smokers (control group), 91 smokers, and 177 cigarette factory workers (42 smokers, 135 non-smokers). Quantitative cultures were done from the nasal swabs of all participants. After identification and determination of colony counts, S. aureus strains were tested for methicillin resistance using the oxacillin disk diffusion method. The rates of nasal carriage of S. aureus were found to be 30% in the control group, 33% in smokers, and 41% in cigarette factory workers. Overall, S. aureus colonisation (> or = 500 cfu/ml) was detected in 72% of the carriers (55/76). Colonisation rates were 43%, 63%, and 85% in the carriers of the study groups, respectively. An increasing colonisation rate was detected in accordance with the increasing number of cigarettes smoked per day, and smoking period. While methicillin-resistant Staphylococcus aureus was only found in 3% of the 30 S. aureus strains isolated from the control group, its isolation rate was 20% in the 30 S. aureus isolates of the smokers, and 33% in the 72 S. aureus isolates of the cigarette factory workers. These results indicate that cigarette and/or tobacco appear to have noticeable effects on the ecology of the nose.     

A preliminary study on the phylogenetic relationships of Copelatus Erichson (Coleoptera: Dytiscidae: Copelatinae) based on larval chaetotaxy and morphology

The phylogenetic relationships of the diving-beetle (Dytiscidae) subfamily Copelatinae are not well known. Some authors postulated a sister-group relationship between Copelatus Erichson and the remaining Dytiscidae, relying mainly on the absence of a mandibular channel in Copelatus. Other authors suggested a more derived position of the genus. Larval characters have been underutilized in phylogenetic studies, mainly because the larvae of many taxa within the family and, in particular, within Copelatinae are unknown. A comprehensive approach aimed to study the phylogenetic placement of a member of this subfamily based on larval characters has not been produced so far. In this study, the phylogenetic relationships of Copelatus are explored based on a cladistic analysis of 24 taxa and 120 chaetotaxic and morphological characters from larvae. For this purpose, larvae of Copelatus longicornis Sharp are described and illustrated in detail for the first time, with particular emphasis on morphometry and chaetotaxy, with the latter being unexplored until now. The results support a derived position of Copelatus within Dytiscidae, with a sister-group relationship between this genus and a clade formed by the subfamilies Lancetinae, Coptotominae, Laccophilinae, Colymbetinae, Matinae, and Dytiscinae, and part of Agabinae. No evidence was found for a sister-group relationship between Copelatus and the remaining Dytiscidae so that the absence of a mandibular channel in this genus is likely a reduction. Copelatus is supported by three apomorphies within Dytiscidae: mandibular channel absent, internal margin of the stipes with three robust spinulae, and seta MX8 inserted subapically on the galea. Handling editor: K. Martens     

Aminoacid profiles in the study of phylogenetic relationships in the genusOryza

Summary The amino acid profiles in seeds of thirteen different species ofOryza, including two cultivated rices,O. glaberrima andO. sativa and the two major geographical racesindica andjaponica were studied using an automatic amino acid analyser to assess differences in the profiles of cultivated species and their wild progenitors. The polygon graphic method was employed to envision the species relationship. Essential amino acid profiles in different species were also compared with those of the Food and Agriculture Organization (FAO) standards. The results suggest a wide range of variability amongOryza species for lysine (up to 4.4% as against 3.5% in cultivated rices) and other essential amino acids. This will be of considerable interest to rice breeders, when after overcoming genetic barriers, the possible utilization of these species in rice breeding becomes feasible.     

Isolation and molecular characterization of methicillin-resistant Staphylococcus aureus from public transport

Methicillin-resistant Staphylococcus aureus (MRSA) not only causes disease in hospitals, but also in the community. The characteristics of MRSA transmission in the environment remain uncertain. In this study, MRSA were isolated from public transport in Tokyo and Niigata, Japan. Of 349 trains examined, eight (2.3%) were positive for MRSA. The MRSA isolated belonged to sequence types (STs) 5, 8, 88, and 89, and included community infection-associated ST8 MRSA (with novel type IV staphylococcal cassette chromosome mec) and the ST5 New York/Japan hospital clone. The data indicate that public transport could contribute to the spread of community-acquired MRSA, and awareness of this mode of transmission is necessary.     

Utility of arginine kinase for resolution of phylogenetic relationships among Brachyuran genera and families

The molecular phylogenetics of decapod crustaceans has been based on sequence data from a limited number of genes. These have included rapidly evolving mitochondrial genes, which are most appropriate for studies of closely related species, and slowly evolving nuclear ribosomal RNA genes, which have been most useful for resolution of deep branches within the Decapoda. Here we examine the utility of the nuclear gene that encodes arginine kinase for phylogenetic reconstruction at intermediate levels (relationships among genera and families) within the decapod infraorder Brachyura (the true crabs). Analyses based on arginine kinase sequences were compared and combined with those for the mitochondrial cytochrome oxidase I gene. All of the genera in our taxon sample were resolved with high support with arginine kinase data alone. However, some of these genera were grouped into clades that are in conflict with recognized brachyuran families. A phylogeny based on cytochrome oxidase I was consistent with the arginine kinase phylogeny, but with weaker support. A recently proposed measure of phylogenetic informativeness indicated that arginine kinase was generally more informative than cytochrome oxidase I for relationships above the level of genus. Combined analysis of data from both genes provided strong support for clades that are in conflict with current assignments of genera to the families Epialtidae, Mithracidae, Pisidae, and Portunidae.     

Diaulota koreana,new species on Korean coasts with a discussion of its phylogenetic relationships (Coleoptera: Staphylinidae: Aleocharinae)

Diaulota koreana Yoo and Ahn new species is described in the intertidal zones of the southern part of the Korean peninsula and illustrations of diagnostic characters are presented. A cladistic analysis of the Liparocephalini based on 50 adult characters suggests that the new species belongs to the genus Diaulota Casey within the Liparocephalini. Similarities and differences among the liparocephaline genera are presented. Phylogenetic relationships of Diaulota koreana Yoo and Ahn new species among the Liparocephalini are briefly discussed.     

Catalytic mechanism and cofactor preference of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus

Given the rapid rise in antibiotic resistance, including methicillin resistance in Staphylococcus aureus (MRSA), there is an urgent need to characterize novel drug targets. Enzymes of the lysine biosynthesis pathway in bacteria are examples of such targets, including dihydrodipicolinate reductase (DHDPR, E.C. 1.3.1.26), which is the product of an essential bacterial gene. DHDPR catalyzes the NAD(P)H-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) in the lysine biosynthesis pathway. We show that MRSA–DHDPR exhibits a unique nucleotide specificity utilizing NADPH (K_m = 12 μM) as a cofactor more effectively than NADH (K_m = 26 μM). However, the enzyme is inhibited by high concentrations of DHDP when using NADPH as a cofactor, but not with NADH. Isothermal titration calorimetry (ITC) studies reveal that MRSA–DHDPR has ∼20-fold greater binding affinity for NADPH (K_d = 1.5 μM) relative to NADH (K_d = 29 μM). Kinetic investigations in tandem with ITC studies show that the enzyme follows a compulsory-order ternary complex mechanism; with inhibition by DHDP through the formation of a nonproductive ternary complex with NADP⁺. This work describes, for the first time, the catalytic mechanism and cofactor preference of MRSA–DHDPR, and provides insight into rational approaches to inhibiting this valid antimicrobial target.     

Structural and evolutionary relationships of beta-lactamase transposons from Staphylococcus aureus

A comparison of the beta-lactamase elements detected on three classes of large plasmids together with the chromosomes of penicillin-resistant Staphylococcus aureus revealed substantial physical and genetic relatedness. In most cases, beta-lactamase production could be associated with the presence of a DNA segment of approximately 6.7 kb. Analysis showed that the plasmid-borne determinants constitute nearly identical transposons or transposon-like elements. An element indistinguishable from one of these, Tn4002, which is carried by the pSK1 family of plasmids in clinical isolates from Australian hospitals, was also identified on the staphylococcal chromosome and is implicated in an evolutionary cycle of transposition between chromosomal and extrachromosomal sites in Australian strains of multiresistant S. aureus.     

Genetic diversity and phylogenetic relationships among five endemic Pinus taxa (Pinaceae) of China as revealed by SRAP markers

The genetic diversity and phylogenetic relationships among five endemic Pinus taxa of China (Pinus tabulaeformis, P. tabulaeformis var. mukdensis, P. tabulaeformis f. shekanensis, Pinus massoniana and Pinus henryi) were studied by SRAP markers. Using 10 SRAP primer pairs, 247 bands were generated. The percent of polymorphic bands (94.8%), Nei's genetic diversity (0.2134), and Shannon's information index (0.3426) revealed a high level of genetic diversity at the genus-level. At the taxon level, P. tabulaeformis f. shekanensis and P. henryi showed a higher genetic diversity than the others. The coefficient of genetic differentiation among taxa (0.3332) indicated a higher level of genetic diversity within taxon, rather than among taxa. An estimate of gene flow among taxa was 1.0004 and implied a certain amount of gene exchange among taxa. The results of neighbor-joining cluster analysis and principal co-ordinate analysis revealed that P. tabulaeformis, P. tabulaeformis var. mukdensis and P. tabulaeformis f. shekanensis were conspecific, which was in agreement with the traditional classification. Phylogenetic relationships analysis also indicated that P. henryi might be a distinct species closely related to P. tabulaeformis.     

Novel arbekacin- and amikacin-modifying enzyme of methicillin-resistant Staphylococcus aureus

An aminoglycoside-modifying enzyme in arbekacin-resistant methicillin-resistant Staphylococcus aureus (MRSA), exhibiting 4'-N-acetylation, was examined. Although the MRSA strain with AAC(4') had no AAC(6')-APH(2") activity, a DNA fragment of the AAC(6')-APH(2") gene was amplified by PCR and the purified N-terminal 30-amino acid sequence of this AAC(4') was identical to AAC(6')-APH(2"). Direct DNA sequencing of this 'silent' AAC(6')-APH(2") gene revealed a single point mutation leading to a substitution of Gly for Asp80, through which the secondary structure is affected. A change in protein conformation could lead to a cleavage and a change of the enzymatic activity. We propose a new aminoglycoside-resistance mediated by AAC(4') is caused by a mutation-modified AAC(6')-APH(2").