Identification of ORF636 in Phage φSLT Carrying Panton-Valentine Leukocidin Genes,Acting as an Adhesion Protein for a Poly(Glycerophosphate) Chain of Lipoteichoic Acid on the Cell Surface of Staphylococcus aureus

The temperate phage φSLT of Staphylococcus aureus carries genes for Panton-Valentine leukocidin. Here, we identify ORF636, a constituent of the phage tail tip structure, as a recognition/adhesion protein for a poly(glycerophosphate) chain of lipoteichoic acid on the cell surface of S. aureus. ORF636 bound specifically to S. aureus; it did not bind to any other staphylococcal species or to several gram-positive bacteria.Staphylococcus aureus, a ubiquitous and harmful human pathogen, produces three types of bicomponent pore-forming cytotoxins, namely, γ-hemolysin (LukF and Hlg2), leukocidin (LukF and LukS), and Panton-Valentine leukocidin (PVL) (LukF-Pv and LukS-Pv) (16). Of these, PVL has been investigated as a virulence-related factor of some S. aureus infectious diseases (7, 11, 23, 24, 31, 37). PVL shows high cytolytic specificity against human polymorphonuclear leukocytes and macrophages, and it is closely associated with most cutaneous necrotic lesions, such as furuncles or primary abscesses, and severe necrotic skin infection (24, 31), as well as with severe necrotic hemorrhagic pneumonia (11, 23). LukF-Pv and LukS-Pv are expressed by the PVL locus (pvl), which is distinct from the γ-hemolysin locus (hlg) (16, 32). In previous research, we found that pvl genes are located in the genome of the lysogenic bacteriophage φPVL (17, 18). We also found another PVL-carrying temperate elongated-head Siphoviridae phage, φSLT, which has the ability to convert S. aureus to the PVL-producing strain from a clinical isolate (29). These findings indicated that at least two types of staphylococcal temperate phages are involved in the horizontal transfer of pvl genes among S. aureus strains (16, 29). Recently, the emergence of a single clonal community-acquired methicillin-resistant S. aureus (CA-MRSA), which produces PVL, was reported (7). Most CA-MRSA strains isolated in the United States and Australia carry the staphylococcal cassette chromosome mec (SCCmec) IV, and they were divided into five clonal complexes by multilocus sequence typing (30). The analysis of the CA-MRSA clones confirmed the presence of PVL genes and SCCmec IV in CA-MRSA and suggested that various CA-MRSA strains have arisen from the diverse genetic backgrounds associated with each geographic origin, rather than from the worldwide spread of a single clone (30, 37). Although there is great debate as to whether PVL is an important virulence factor, numerous studies support the hypothesis that PVL plays an important role in the pathogenesis of CA-MRSA necrotizing pneumonia (3, 6). In regard to the acquisition of PVL gene clusters and the proliferation of PVL-carrying CA-MRSA, the horizontal transfer of PVL via PVL-carrying phages, as well as that of SCCmec, has become the focus of intense research interest. To understand the horizontal transfer of PVL, the analysis of the infection ability of a PVL-carrying phage is important. If the phage has a wide host range, the PVL-carrying phage might threaten to become a source of emerging PVL-positive bacteria. Phage infection starts from an interaction between a phage virion and its host cell surface receptor. Nevertheless, little is known about phage receptors on the surface of S. aureus, and the mechanism of host cell-specific binding of staphylococcal phages has been poorly characterized. In addition, there is no information about staphylococcal phage proteins involved in host cell recognition and/or binding. Here, we identify ORF636, with a mass of 66 kDa, as a structural protein of the φSLT tail and determine that it acts as a protein for recognition/adhesion of a poly(glycerophosphate) moiety of lipoteichoic acid (LTA) on the cell surface of the host S. aureus in the first stage of infection by φSLT.     

Invasion Genetics of Ponto-Caspian Gobies in the Great Lakes: A ‘Cryptic’ Species, Absence of Founder Effects, and Comparative Risk Analysis

Genetic variability and structure of nonindigenous vs native populations are compared for the Eurasian round goby Neogobius melanostomus and the tubenose goby Proterorhinus marmoratus, which both invaded Lake St. Clair of the North American Great Lakes about 1990. The round goby spread rapidly to all of the Great Lakes and the tubenose goby largely has been restricted to Lake St. Clair, with some recent range extension into western Lake Erie. Risk analyses may indicate whether genetic variability of colonizers is predictive of their relative invasive and establishment successes. The present investigation examined DNA sequence variation across the left domain of the mitochondrial DNA cytochrome b gene in round and tubenose gobies from Eurasian and Great Lakes locations. We also sequenced six additional Neogobius species (including the monkey N.␣fluviatilis, racer N. gymnotrachelus, and bigheadN. kessleri gobies that have been ‘on the move’ in Europe) and the knout goby Mesogobius batrachocephalus from the Black Sea in order to develop diagnostic genetic characters to identify them in case of future and/or undetected invasions and to delineate their phylogenetic relationships. Results show that a diverse number of haplotypes characterize round and tubenose goby populations from both North America and Eurasian sites, fitting a risk analysis prediction of high genetic variability in their successful introductions. Phylogenetic results indicate that the current genus Neogobius is paraphyletic and that the subgenusApollonia thus should be elevated to the level of genus, containingApollonia (N.) melanostomus (the round goby) andA. (N.) fluviatilis (the monkey goby). In addition, there appear to be two separate species of Proterorhinus marmoratus, a marine P. marmoratus Pallas 1814 in the Black Sea (matching the original type locality), and a ‘cryptic’ freshwater species in the Danube and Dnieper Rivers and probably other Eurasian freshwater habitats, as well as invasive in the Great Lakes. We suggest resurrecting the name P. semilunaris Heckel 1837 for the freshwater species (a taxon that was originally described from rivers draining into the Aegean Sea and the Danube River, but was later placed in synonymy with P. marmoratus). An erratum to this article is available at .     

Effects of desertification on the C:N:P stoichiometry of soil,microbes, and extracellular enzymes in a desert grassland北大核心CSCD

Aims In order to discuss the underlying mechanism of desertification effect on the ecological stoichiometry of soil, microbes and extracellular enzymes, we studied the changes of soil, soil microbial and extracellular enzyme C:N:P stoichiometry during the desertification process in the desert grassland in Yanchi County, China. Methods The “space-for-time” method was used. Important findings The results demonstrated that: (1) Soil C, N, P contents and soil C:P, N:P significantly decreased, but soil C:N gradually increased with increasing desertification. (2) Soil microbial biomass C (MBC):soil microbial biomass P (MBP), soil microbial biomass N (MBN):MBP and soil β-1,4-glucosidase (BG):β-1,4-N-acetylglucosaminidase (NAG) gradually decreased, soil BG:alkaline phosphatase (AP) and NAG:AP basically showed an increasing trend with increasing desertification. (3) Desertification increased the soil microbial carbon use efficiency (CUE C : N and CUE C : P ) gradually, while soil microbial nitrogen use efficiency (NUE N : C ) and soil microbial phosphorus use efficiency (PUE P : C ) basically decreased. (4) Soil, soil microbial and soil extracellular enzyme C:N stoichiometry (C:N, MBC:MBN, BG:NAG) were significantly negatively correlated with the soil, soil microbial and extracellular enzyme N:P stoichiometry (N:P, MBN:MBP, NAG:AP), the soil and extracellular enzymes C:N (C:N, BG:NAG) were significantly positively correlated with the soil and extracellular enzymes C:P (C:P, BG:AP). Soil N:P was significantly positively correlated with the soil MBN:MBP, but was significantly negatively correlated with the soil NAG:AP. The analysis demonstrated that soil microbial biomass and extracellular enzyme activity changed with soil nutrient during the desertification process in the desert grassland. The co-variation relationship between soil nutrient and C:N:P stoichiometry of microbial-extracellular enzyme provides a theoretical basis for understanding the underlying mechanism of C, N, P cycling in the soil-microbial system in desert grasslands. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All Rights Reserved.     

Examining the Process of de Novo Gene Birth: An Educational Primer on “Integration of New Genes into Cellular Networks,and Their Structural Maturation”

SUMMARY New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database.     

A 370-kb Cosmid Contig of the Serpin Gene Cluster on Human Chromosome 14q32.1: Molecular Linkage of the Genes Encoding α1-Antichymotrypsin, Protein C Inhibitor, Kallistatin, α1-Antitrypsin, and Corticosteroid-Binding Globulin

The human genes encoding α1-antitrypsin (α1AT, gene symbol PI), corticosteroid-binding globulin (CBG), α1-antichymotrypsin (AACT), and protein C inhibitor (PCI) are related by descent, and they all map to human chromosome 14q32.1. This serine protease inhibitor (serpin) gene cluster also contains an antitrypsin-related sequence (ATR, gene symbol PIL), but the precise molecular organization of this region has not been defined. In this report we describe the generation and characterization of an 370-kb cosmid contig that includes all five serpin genes. Moreover, a newly described serpin, kallistatin (KAL, gene symbol PI4), was also mapped within the region. Gene order within this interval is cen–CBG–ATR–α1AT–KAL–PCI–AACT–tel. The genes occupy 320 kb of genomic DNA, and they are organized into two discrete subclusters of three genes each that are separated by 170 kb. The distal subcluster includes KAL, PCI, and AACT; it occupies 63 kb of DNA, and all three genes are transcribed in a proximal-to-distal orientation. Within the subcluster, there is 12 kb of intergenic DNA between KAL and PCI and 19 kb between PCI and AACT. The proximal subcluster includes α1AT, ATR, and CBG; it occupies 90 kb of genomic DNA, with 12 kb of DNA between α1AT and ATR and 40 kb between ATR and CBG. These genes are all transcribed in a distal-to-proximal orientation. This represents the first detailed physical map of the serpin gene cluster on 14q32.1.     

On the type species of the genus Parapodemus and late turolian Apodemus associations: Remarks on an article by P. Mein in Géobios no 11, fasc. 3, 1978

Mus (Acomys?) gaudryiDAMES, 1883 (1) is considered to be the type species of Parapodemus, because “the type of any taxon, once fixed in conformity with the provisions of the international code of zoological nomenclature, is not subject to change except by exercise of the plenary powers of the commission” (see art. 61 and 70 of the code). Parapodemus schaubiPAPP, 1947 (2) is considered to be a junior synonym of P. gaudryi. The late Turolian Apodemus primaevusHUGUENEY and MEIN, 1965 (3), and A. gudrunaeVAN DE WEERD, 1976 (4), are sufficiently different from one another and from P. gaudryi to warrant their recognition as separate species.     

Analysis of changes over 44 years in the phytoplankton of Lake Võrtsjärv (Estonia): the effect of nutrients,climate and the investigator on phytoplankton-based water quality indices

We analysed long-term changes in phytoplankton composition in relation to hydrological, meteorological and nutrient loading data in the large (270 km²) shallow (mean depth 2.8 m) Lake Võrtsjärv. Nutrient loads to the lake were heavy in the 1970s and 1980s and decreased considerably thereafter. The average nutrient concentrations for 1985–2004 (1.6 mg l^?1 of total nitrogen and 53 μg l^?1 of total phosphorus) characterize the lake as a eutrophic water body. All four calculated taxonomic indices showed a unidirectional deterioration of the lake’s ecological status, despite reduced concentrations of nutrients. We focused our analysis on the PTSI index, which revealed a stepwise change between the years 1977 and 1979 that coincided with a large increase in water level, but also with a change of investigator. After correcting input data for possible investigator-induced differences, the step change remained because it was caused by major changes in the whole phytoplankton community. The previous dominant Planktolyngbya limnetica was replaced by two species of seasonally altering Limnothrix. Among phytoplankton functional groups, there was a decrease in all groups comprising small-sized phytoplankton species, such as X1, E, F, J, N and an increase in S1 and H1, both represented by filamentous cyanobacteria. Our results suggest a non-linear response of phytoplankton to changing nutrient loadings, and that the change observed between 1977 and 1979 was a regime shift triggered by water level change. High shade tolerance of the new dominants, and their ability to create shade, obviously stabilized the new status making it resistant to restoration efforts.     

Redescription of <Emphasis Type="Italic">Parspina argentinensis</Emphasis> (Szidat, 1954) (Digenea: Cryptogonimidae) from freshwater fishes (Pimelodidae) in the basins of the Paraná and La Plata Rivers,Argentina, with comments on <Emphasis Type="Italic">P. bagre</Emphasis> Pearse, 1920

The type-specimens of Parspina argentinensis (Szidat, 1954) from Pimelodus maculatus Lacépède, and new material from Iheringichthys labrosus (Lütken), Parapimelodus valenciennis (Lütken), Pimelodella gracilis (Valenciennes), Pimelodus albicans (Valenciennes), P. argenteus Perugia and P. maculatus caught in the basins of the La Plata and Paraná Rivers, Argentina, were studied to elucidate its taxonomic status. The type-specimens of Parspina bagre Pearse, 1920 from Pimelodella metae Eigenmann in Lake Valencia, Venezuela, were also studied and new observations on its morphology recorded. The amendation of the generic diagnosis of Parspina Pearse, 1920 is proposed based on the study of both species, which revealed, among other features, the absence of a thin walled-membrane enclosing the male terminal genitalia. Parspina argentinensis is characterised by the following features: absence of a gonotyl; presence of a bipartite seminal vesicle, pars prostatica and ejaculatory duct; caeca of nearly equal length; uterus extending from the level of the ventral sucker to end of body; testes symmetrical to slightly oblique; ovary transversely elongate, compact and variable in shape; and the utilisation of a wide range of freshwater fishes as hosts. The tegumental surface of this species is covered with pectinate spines arranged quincuncially. Spines decrease in size and density from forebody to hindbody. There are two types of sensory papillae, ciliated and dome-shaped. Ciliated papillae are distributed on the surface of the oral region and on the dorsal and ventral surfaces of the body, whereas dome-shaped papillae are found on the surface of the ventral rim of the oral sucker associated with a ciliated papilla. Gland-duct openings are interspersed with the spines of the oral crown. In addition, the infection indices of P. argentinensis vary widely, not only among different hosts but also between the Paraná and La Plata River basins. Higher prevalences of P. argentinensis are recorded in the La Plata River, and Pimelodus albicans, P. maculatus and Iheringichthys labrosus are the principal final hosts in this area.