Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.     

Interregional comparisons of sediment microbial respiration in streams

• 1 The rate of microbial respiration on fine‐grained stream sediments was measured at 371 first to fourth‐order streams in the Central Appalachian region (Maryland, Pennsylvania, Virginia, and West Virginia), Southern Rocky Mountains (Colorado), and California's Central Valley in 1994 and 1995.
• 2 Study streams were randomly selected from the United States Environmental Protection Agency's (USEPA) River Reach File (RF3) using the sample design developed by USEPA's Environmental Monitoring and Assessment Program (EMAP).
• 3 Respiration rate ranged from 0 to 0.621 g O₂ g^‐1 AFDM h^‐1 in Central Appalachian streams, 0‐0.254 g O₂ g^‐1 AFDM h^‐1 in Rocky Mountain streams, and 0‐0.436 g O₂ g^‐1 AFDM h^‐1 in Central Valley streams.
• 4 Respiration was significantly lower in Southern Rocky Mountain streams and in cold water streams (< 15 °C) of the Central Appalachians.
• 5 Within a defined index period, respiration was not significantly different between years, and was significantly correlated with stream temperature and chemistry (DOC, total N, total P, K, Cl, and alkalinity).
• 6 The uniformity of respiration estimates among the three study regions suggests that sediment microbial respiration may be collected at any number of scales above the site‐level for reliable prediction of respiration patterns at larger spatial scales.

     

A scanning tunnelling microscopy study of Clostridium pasteurianum rubredoxin

Scanning tunnelling microscopy (STM), which can provide 'direct' and 'non-averaged' information on molecular structure in three dimensions, has been used to achieve sub-molecular resolution in a 'single molecule' of rubredoxin, an important iron-sulphur protein, at the gold (111)/water interface. The metal-ligand site [Fe(III)-Cys4] appears distinct because of an enhancement of the tunnelling current over this region compared to the surrounding protein structure.     

Lacticin 3147, a Broad-Spectrum Bacteriocin Which Selectively Dissipates the Membrane Potential

Lacticin 3147 is a broad-spectrum bacteriocin produced by Lactococcus lactis subsp. lactis DPC3147 (M. P. Ryan, M. C. Rea, C. Hill, and R. P. Ross, Appl. Environ. Microbiol. 62:612–619, 1996). Partial purification of the bacteriocin by hydrophobic interaction chromatography and reverse-phase fast protein liquid chromatography revealed that two components are required for full activity. Lacticin 3147 is bactericidal against L. lactis, Listeria monocytogenes, and Bacillus subtilis; at low concentrations of the bacteriocin, bactericidal activity is enhanced when target cells are energized. This finding suggests that the presence of a proton motive force promotes the interaction of the bacteriocin with the cytoplasmic membrane, leading to the formation of pores at these low lacticin 3147 concentrations. These pores were shown to be selective for K⁺ ions and inorganic phosphate. The loss of these ions resulted in immediate dissipation of the membrane potential and hydrolysis of internal ATP, leading to an eventual collapse of the pH gradient at the membrane and ultimately to cell death. Our results suggest that lacticin 3147 is a pore-forming bacteriocin which acts on a broad range of gram-positive bacteria.     

Using species abundance models as indicators of habitat disturbance in tropical forests

1. In temperate communities, species abundance distributions have been used to detect ecosystem disturbance: in undisturbed habitats, distributions are claimed to generally fit log-normal models, whereas in disturbed habitats, distributions fit log-series models.
2. There is a growing literature on the effects of habitat disturbance in tropical ecosystems and several studies suggest that species abundance models may be useful in detecting disturbance, although data are lacking.
3. Nummelin (1998) claims that these models are not universal indicators of forest disturbance, but we highlight a number of problems with the data presented in Nummelin's study and conclude that it is too soon to dismiss these models. We discuss several important points arising from Nummelin's study which need to be considered if species abundance models are to be used appropriately.     

Functions Encoded by Pyrrolnitrin Biosynthetic Genes from Pseudomonas fluorescens

Pyrrolnitrin is a secondary metabolite derived from tryptophan and has strong antifungal activity. Recently we described four genes, prnABCD, from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin. In the work presented here, we describe the function of each prn gene product. The four genes encode proteins identical in size and serology to proteins present in wild-type Pseudomonas fluorescens, but absent from a mutant from which the entire prn gene region had been deleted. The prnA gene product catalyzes the chlorination of l-tryptophan to form 7-chloro-l-tryptophan. The prnB gene product catalyzes a ring rearrangement and decarboxylation to convert 7-chloro-l-tryptophan to monodechloroaminopyrrolnitrin. The prnC gene product chlorinates monodechloroaminopyrrolnitrin at the 3 position to form aminopyrrolnitrin. The prnD gene product catalyzes the oxidation of the amino group of aminopyrrolnitrin to a nitro group to form pyrrolnitrin. The organization of the prn genes in the operon is identical to the order of the reactions in the biosynthetic pathway.The antibiotic pyrrolnitrin [3-chloro-4-(2′-nitro-3′-chlorophenyl)pyrrole] (PRN) is produced by many pseudomonads and has broad-spectrum antifungal activity (1, 5, 12–14, 17). PRN has been implicated as an important mechanism of biological control of fungal plant pathogens by several Pseudomonas strains (12–14), including P. fluorescens BL915, from which the prn genes were isolated (10).Tryptophan was identified as the precursor for PRN, based on the feeding of cultures with isotopically labeled and substituted tryptophan (2, 7, 8, 17, 25). Biosynthetic pathways were proposed as early as 1967 (7) and have been refined on the basis of tracer studies and the isolation of intermediates (Fig. ​(Fig.1)1) (2, 8, 17, 19, 23, 25). Recently, Hammer et al. (9) described the cloning and characterization of a 5.8-kb DNA region which encodes the PRN biosynthetic pathway. This DNA region confers the ability to produce PRN when expressed heterologously in Escherichia coli and contains four genes, prnABCD, each of which is required for PRN production. In the research described here, we used mutants in which each of the four genes was disrupted and strains which overexpress the individual genes to elucidate the function of each gene product in PRN biosynthesis. Open in a separate windowFIG. 1Biosynthetic pathways for PRN as proposed by van Pée et al. (23) (A) and by Chang et al. (2) (B). The reactions catalyzed by the PRN biosynthetic enzymes encoded by the prnABCD genes are indicated above the appropriate reaction arrows.

Bacterial strains and plasmids.

The bacterial strains and plasmids used in this study are described in Table ​Table1.1. Pseudomonas strains were cultured in Luria-Bertani medium at 28°C. Antibiotics, when used, were added at the following concentrations: tetracycline, 30 μg/ml; and kanamycin, 50 μg/ml. The expression vector pPEH14 consists of the P_tac promoter and rrnB ribosomal terminator from pKK223-3 (Pharmacia, Uppsala, Sweden) cloned into the BglII site of the broad-host-range plasmid pRK290 (4). P_tac is a strong constitutive promoter in Pseudomonas (unpublished data). The PRN biosynthetic genes are the coding regions described by Hammer et al. (9). Each coding region was cloned from the translation initiation codon to the stop codon by PCR with restriction sites added to the ends to facilitate cloning. For prnB, the native GTG initiation codon was changed to ATG. The clones were sequenced after PCR.

TABLE 1

Bacterial strains and plasmids used in this study

The Arcanobacterium (Actinomyces) pyogenes Plasmid pAP1 Is a Member of the pIJ101/pJV1 Family of Rolling Circle Replication Plasmids

The 2.4-kb plasmid pAP1 from Arcanobacterium (Actinomyces) pyogenes had sequence similarity within the putative replication protein and double-stranded origin with the pIJ101/pJV1 family of plasmids. pJGS84, a derivative of pAP1 containing a kanamycin resistance gene, was able to replicate in Escherichia coli and Corynebacterium pseudotuberculosis, as well as in A. pyogenes. Detection of single-stranded DNA intermediates of pJGS84 replication suggested that this plasmid replicates by the rolling circle mechanism.     

Rhs Elements Comprise Three Subfamilies Which Diverged Prior to Acquisition by Escherichia coli

The Rhs elements are complex genetic composites widely spread among Escherichia coli isolates. One of their components, a 3.7-kb, GC-rich core, maintains a single open reading frame that extends the full length of the core and then 400 to 600 bp beyond into an AT-rich region. Whereas Rhs cores are homologous, core extensions from different elements are dissimilar. Two new Rhs elements from strains of the ECOR reference collection have been characterized. RhsG (from strain ECOR-11) maps to min 5.3, and RhsH (from strain ECOR-45) maps to min 32.8, where it lies in tandem with RhsE. Comparison of strain K-12 to ECOR-11 indicates that RhsG was once present in but has been largely deleted from an ancestor of K-12. Phylogenetic analysis shows that the cores from eight known elements fall into three subfamilies, RhsA-B-C-F, RhsD-E, and RhsG-H. Cores from different subfamilies diverge 22 to 29%. Analysis of substitutions that distinguish between subfamilies shows that the origin of the ancestral core as well as the process of subfamily separation occurred in a GC-rich background. Furthermore, each subfamily independently passed from the GC-rich background to a less GC-rich background such as E. coli. A new example of core-extension shuffling provides the first example of exchange between cores of different subfamilies. A novel component of RhsE and RhsG, vgr, encodes a large protein distinguished by 18 to 19 repetitions of a Val-Gly dipeptide occurring with a eight-residue periodicity.     

Influence of phosphorus on the growth and ergot alkaloid content of Neotyphodium coenophialum-infected tall fescue (Festuca arundinacea Schreb.)

Tall fescue (Festuca arundinacea Schreb.) plants infected by the fungal endophyte Neotyphodium coenophialum (Morgan-Jones & Gams) (Glenn et al., 1996) often perform better than noninfected plants, especially in marginal resource environments. There is a lack of information about endophyte related effects on the rhizosphere of grasses. In a greenhouse experiment, four endophyte-infected (E+) tall fescue clones (DN2, DN4, DN7, DN11) and their endophyte-free (E–) forms were grown in limed (pH 6.3) Porter soil (low fertility, acidic, high aluminum and low phosphorus content, coarse-loamy mixed mesic Umbric Dystrochrept) at three soil P levels (17, 50, and 96 mg P kg^-1 soil) for five months. Excluding the genotype effect, endophyte infection significantly increased cumulative herbage DM yield by 8% at 17 mg P kg^-1 soil but reduced cumulative herbage DM yield by 12% at 96 mg P kg^-1 soil. With increased P availability in the soil, shoot and root DM, and root/shoot ratio in E+ plants were significantly less when compared to E– plants. Endophyte infection increased specific root length at 17 and 50 mg P kg^-1soil. At soil P level of 17 mg P kg^-1soil, E+ plants had significantly higher P concentrations both in roots and shoots. Similar relationships were found for Mg and Ca. E+ plants had significantly higher Zn, Fe, and Al concentration in roots, and lower Mn and Al concentration in shoots when compared to E– plants. Ergot alkaloid concentration and content in shoot of E+ plants increased with increasing P availability in the soil from 17 to 50 mg P kg^-1 but declined again at 96 mg P kg^-1 soil. Ergot alkaloid accumulation in roots increased linearly with P availability in the soil. Results suggest that endophyte infection affects uptake of phosphorus and other mineral nutrients and may benefit tall fescue grown on P-deficient soils. Phosphorus seems also to be involved in ergot alkaloid accumulation in endophyte-infected tall fescue.