coli O104:H4 lux; 1 × 108 CFUs) and, for the competition experime

coli O104:H4 lux; 1 × 108 CFUs) and, for the competition experiments, with a mixture of E. coli O104:H4 wild-type strain and CSS001 (E. coli O104:H4 iutA::cat; 5 × 107 CFUs per strain) in a final volume of 0.4 ml delivered by gavage (20-gauge needle), thereby using the mouse intestinal model to study enteropathogenicity of E. coli strains previously described by our group [16, 17]. Briefly, animals received streptomycin (5 g/L in drinking water) for 48 h prior to

oral inoculation with the E. coli strains and were food restricted for 12 h check details before oral inoculation. The concentration of the initial inoculum was determined by plating on selective antibiotic LB media by using the dot plate method [42]. Groups of mice (n = 10) were maintained for 7 days, and at different time points (24 h, 48 h, 96 h, and 169 h post-inoculation), groups of two or four animals were euthanized, and the cecum of each animal was collected, weighed, and homogenized for bacterial load enumeration. After homogenization, centrifugation at 3,000 xg for 30 seconds was done in order to sediment the cell debris, allowing for collection of accurate volumes

needed to make serial dilutions. Samples were plated on LB agar, LB + streptomycin (100 mg/mL), EPZ-6438 in vivo and LB + streptomycin + kanamycin (50 mg/mL) to determine total bacterial cell counts from those of E. coli O104:H4 or the iutA mutant strain. The vast majority of bacteria recovered from the cecum corresponded to the O104:H4 isogenic strains (data not shown). The replicates plated for each mouse were averaged, and competitive indices were calculated as previously described [43]. Groups were compared by using the Mann Whitney non-parametric test. Bioluminescent quantification For in-vivo imaging, mice were anesthetized with 2-3% isofluorane in an oxygen-filled induction chamber and then transferred to an isolation chamber placed inside the imaging chamber. Bioluminescent images Y-27632 2HCl were acquired by using an IVIS Spectrum (Caliper Corp., Alameda, CA) as we previously described [18]. The ex vivo images of the intestine were acquired at each time point immediately after

euthanasia. Bioluminescent signal is represented in the images with a pseudocolor scale ranging from red (most intense) to violet (least intense) indicating the intensity of the signal. Scales were manually set to the same values for every comparable image (in-vivo and ex-vivo) to facilitate comparison of intensity of the bioluminescence at each time point. Electron microscopy analysis and histopathology Segments of the mouse cecum infected with the wild-type E. coli O104:H4 strain were collected, washed gently with PBS, and fixed in a mixture of 2.5% formaldehyde, 0.1% glutaraldehyde, 0.03% trinitrophenol, and 0.03% CaCl2 in 0.05 M cacodylate buffer (pH 7.2) as previously described [16]. Samples were processed further by postfixing in 1% OsO4, stained en bloc in 2% aqueous uranyl acetate (in 0.

Taxon 53:131–143CrossRef Qiang S, Cao X (2000) Survey and analysi

Taxon 53:131–143CrossRef Qiang S, Cao X (2000) Survey and analysis of exotic weeds in China. J Plant Resour Environ 9:31–38 Rabitsch W, Essl F (2006) Biological invasions in Austria: patterns and case studies. Biol Invasion 8:295–308CrossRef Rejmánek M, Richardson DM (1996) What attributes make some plant species more invasive? Ecology 77:1655–1661CrossRef Richardson DM, Pyšek P (2006) Plant invasions: merging the concepts of species invasiveness and community Alvelestat cost invasibility. Progr Phys Geogr 30:409–431CrossRef Richardson DM, Pyšek P, Rejmánek M, Barbour MG, Panetta FD et al (2000) Naturalization

and invasion of alien plants: concepts and definitions. Divers Distrib 6:93–107CrossRef Thuiller W, Richardson DM, Pyšek P, Midgley GF, Hughes GO et al (2005) Niche-based modeling as a tool for predicting the risk of alien plant invasions at a global scale. Glob Change Biol 11:2234–2250CrossRef Vilà M, Meggaro Y, Weber E (1999) Preliminary analysis of the naturalized flora of northern Africa. Orsis 14:9–20 Villaseñor JL, Espinosa-Garcia FJ (2004) The alien flowering

plants of Mexico. Divers Distrib 10:113–123CrossRef Wang FG, Xing FW, Ye HG, Chen XY, Tang GG et al (2004) Preliminarily study on invasive alien species in Macau. Acta Sci Nat Univ Sun Yat Sen 43:105–110 Weber EF (1997) The alien flora of Europe: a taxonomic and biogeographic review. J Veg Sci 8:565–572CrossRef Weber E (2003) Invasive plant species of the world. A reference guide to environmental weeds. CABI, Wallingford Weber E, Li B (2008) Plant invasions in China: What is to be expected in the wake of economic development? Bioscience

58:437–444CrossRef Weber E, Sun SG, Li B (2008) Invasive alien plants in China: diversity and ecological insights. Biol Invasion 10:1411–1429CrossRef Wu find more SH, Hsieh CF, Chaw SM, Rejmánek M (2004a) Plant invasions in Taiwan: insights from the flora of casual and naturalized alien species. Divers Distrib 10:349–362CrossRef Wu SH, Hsieh CF, Rejmánek M (2004b) Catalogue of the naturalized flora of Taiwan. Taiwania 49:16–31 Wu T, Meng C, Dai J, Zhu Y (2006) Exotic plants in Shangdong Province. J Shangdong Norm Univ (Nat Sci Ed) 21:105–109 Wu SH, Sun HT, Teng YC, Rejmánek M, Chaw SM et al (2010a) Patterns of plant invasions in China: taxonomic, biogeographic, climatic approaches and anthropogenic effects. Biol Invasion 12:2179–2206CrossRef Wu SH, Yang TYA, Teng YC, Chang CY, Yang KC et al (2010b) Insights of the latest naturalized flora of Taiwan: change in the past eight years. Taiwania 55:139–159 Xiang YC, Peng SL, Zhou HC, Cai XA (2002) The impacts of non-native species on biodiversity and its control. Guihaia 22:425–432 Xie Y, Li ZY, Gregg WP, Dianmo L (2001) Invasive species in China—an overview.

Many gene-phenotype relations were identified: a total of 1388 OG

Many gene-phenotype relations were identified: a total of 1388 OGs or on average 565 genes per reference

strain were identified to be related to at least one of these 140 phenotypes. In the present study, we focussed on gene clusters consisting of at least two phenotype-related genes that are in close genomic proximity (e.g., in operons; see Methods). Transposases, integrases and phage proteins were also removed, because relations between these proteins and phenotypes are likely to be spurious. Discarding above-mentioned genes decreased the percentage of phenotype-related genes by about 50% on average. In analyzing gene clusters, we first selleck chemicals llc considered gene clusters of which their presence relates to a positive trait (e.g., growth) and absence relates to a negative trait (e.g., no growth). There were also many gene clusters with inverse patterns, where an absence of a gene cluster leads to a positive trait.

An inverse relationship between genes and phenotypes might indicate that in the absence of a regulator, genes previously inhibited by this particular regulator can become active, which in turn R788 mouse might lead to a positive trait (e.g., survival of a strain). In the supplementary data we provide all identified relations including inverse relations (see genotype-phenotype relations in an Additional file 2 that contains a mini-website). Genes related to carbohydrate utilization Several gene clusters related to fermentation of different sugars were identified by genotype-phenotype matching. Among them were gene clusters that were previously described to be involved in carbohydrate utilization [16]. For instance, the presence

Cell press of a gene cluster required for arabinose utilization [9] was confirmed in this study to correlate strongly with the ability to grow on arabinose (see Figure 1 for colour-coded representation of gene-phenotype relations and Figure 2 for gene-phenotype relations of KF147 genes LLKF_1616-1622, and their orthologs in query strains). Several gene clusters were found to be related to sucrose utilization; for instance a cluster of 4 genes (LLKF_0661-LLKF_0664 in strain KF147, and their orthologs in query strains) that already was annotated as being involved in sucrose utilization (Figure 2) [8]. The other three reference strains do not grow on sucrose, and this gene cluster was absent in these strains. These genes were also found to be inversely related to growth on lactose, where they were present in most of the strains that grew slowly on lactose and absent in most of the strains that can grow on lactose (Figure 2). Such a relationship suggests that most of the strains that grow well on sucrose (22 strains) cannot grow or grow slowly on lactose (17 out of 22 strains) or vice-versa (10 out of 15 lactose-degrading strains cannot grow on sucrose).

PubMedCrossRef 14 Coombs GW, Nimmo GR, Pearson JC, Christiansen

PubMedCrossRef 14. Coombs GW, Nimmo GR, Pearson JC, Christiansen KJ, Bell JM, Collignon PJ, McLaws ML: Prevalence of MRSA strains among Staphylococcus aureus isolated from outpatients, 2006. Commun Dis Intell 2009,33(1):10–20.PubMed 15.

Collignon P, Gosbell I, Vickery A, Nimmo G, Stylianopoulos T, Gottlieb T: Community-acquired meticillin-resistant Staphylococcus aureus in Australia. Australian Group on Antimicrobial Resistance. Lancet 1998,352(9122):145–146.PubMedCrossRef 16. Riley D, MacCulloch D, Morris AJ: Methicillin-resistant S. aureus in the suburbs. N Z Med J 1998,111(1060):59.PubMed 17. Ellington MJ, Ganner M, Warner M, Cookson BD, Kearns AM: Polyclonal multiply antibiotic-resistant methicillin-resistant Staphylococcus aureus with Panton-Valentine leucocidin in England. J Antimicrob Chemother 2010,65(1):46–50.PubMedCrossRef 18. Nimmo GR, Coombs GW: Community-associated methicillin-resistant Staphylococcus aureus (MRSA) in Australia. Int J Antimicrob Agents 2008,31(5):401–410.PubMedCrossRef 19. Tristan A, Bes M, Meugnier H, Lina G, Bozdogan B, Courvalin

P, Reverdy ME, Enright MC, Vandenesch F, Etienne J: Global distribution of Panton-Valentine leukocidin–positive methicillin-resistant Staphylococcus aureus , 2006. Emerg Infect Dis 2007,13(4):594–600.PubMedCrossRef ABT-263 supplier 20. Udo EE, Pearman JW, Grubb WB: Genetic analysis of community isolates of methicillin-resistant Staphylococcus aureus in Western Australia. J Hosp Infect 1993,25(2):97–108.PubMedCrossRef 21. Coombs GW,

Nimmo GR, Bell JM, Huygens F, O’Brien FG, Malkowski MJ, Pearson JC, Stephens AJ, Giffard PM: Genetic diversity among community methicillin-resistant Staphylococcus aureus strains causing outpatient infections in Australia. J Clin Microbiol 2004,42(10):4735–4743.PubMedCrossRef 22. Coombs GW, Pearson JC, O’Brien FG, Murray RJ, Grubb WB, Christiansen KJ: Methicillin-resistant Staphylococcus aureus clones, Western Australia. Emerg Infect Dis 2006,12(2):241–247.PubMed 23. Maguire GP, Arthur AD, Boustead PJ, Dwyer B, Currie BJ: Emerging epidemic of Loperamide community-acquired methicillin-resistant Staphylococcus aureus infection in the Northern Territory. Med J Aust 1996,164(12):721–723.PubMed 24. Vlack S, Cox L, Peleg AY, Canuto C, Stewart C, Conlon A, Stephens A, Giffard P, Huygens F, Mollinger A, et al.: Carriage of methicillin-resistant Staphylococcus aureus in a Queensland Indigenous community. Med J Aust 2006,184(11):556–559.PubMed 25. Stevens CL, Ralph A, McLeod JE, McDonald MI: Community-acquired methicillin-resistant Staphylococcus aureus in Central Australia. Commun Dis Intell 2006,30(4):462–466.PubMed 26. Coombs GW, Van Gessel H, Pearson JC, Godsell MR, O’Brien FG, Christiansen KJ: Controlling a multicenter outbreak involving the New York/Japan methicillin-resistant Staphylococcus aureus clone. Infect Control Hosp Epidemiol 2007,28(7):845–852.PubMedCrossRef 27.

Despite the highly significant increase of microbiota diversity w

Despite the highly significant increase of microbiota diversity with age, the diversity indeces at 18 months of age are still relatively low (~110) when compared to the approximately two-fold higher indexes (150–200) commonly observed in healthy adults [32]. It has been suggested that by the age of 1 to 2 years the microbiota resembles that of an adult [29, 43]. Our results show that microbiota succession continues at least until the age of 18 buy Ibrutinib months and most likely

even further, because the bacterial diversity has still not reached the diversity of an adult person. Thus, significant changes can be expected to occur in even after 18 months of age. Concerning the microbiota composition at 6 months of age, our results are in agreement with earlier studies [5, 29], except that we observed significant colonization by bifidobacteria in most of the children (mean relative abundances 22.9% at 6 months

and 12.6% at 18 months of age, respectively) while in the study of Palmer et al. [29] Selleckchem R428 bifidobacteria were not detected, possibly due to differences in DNA extraction, PCR primers, demographic and geographic origin, dietary patterns of the infants or other confounding factors. Primers used for PCR are often not so optimal for bifidobacteria than for other species and thus, high GC bacteria may perform less well in such PCRs. Further, in our previous studies we have shown that mechanical lysis of faecal bacteria is essential and improves the detection of especially Gram-positive bacteria including bifidobacteria [32, 44]. In the Palmer et al. study [29], mechanical lysis by bead-beating was not applied, which may have hampered the detection of bifidobacteria. Thus, we consider that the Cell press most likely explanation for the different results concerning bifidobacteria in our and Palmer et al. [29] study is the different DNA extraction methods used. When comparing healthy and eczematous

children we found statistically significant differences in microbiota composition only at 18 months of age. The total microbiota of children with eczema was found to become significantly more diverse than the microbiota of children who remained healthy by 18 months of age. Interestingly, the total microbiota and particularly Firmicutes diversity was higher in the eczema group children, although the difference with the healthy subjects was not statistically significant. Abrahamsson et al. described the infants as having atopic eczema during the first two years of life (diagnostics were done at 6, 12 and 24 months of age), but the age at the onset of symptoms was not clarified [9]. However, it can be concluded from the Abrahamsson et al.


guilliermondii JAK drugs from M. caribbica and other species of M. guilliermondii complex during in silico restriction digestion of the ITS1-5.8S-ITS2 amplicon sequences. (PDF 241 KB) Additional file

2: Figure S1: Neighbour-joining phylogenetic tree based on LSU rRNA gene D1/D2 sequences showing taxa-nonspecific segregation of M. guilliermondii strains. The tree was constructed based on the evolutionary distance calculated using Kimura-2 parameter from the representative nucleotide sequences of M. guilliermondii and M. caribbica (position 13 to 308 of LSU rRNA gene of S. cerevisiae CBS 1171, GenBank Accession No. AY048154.1). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to selleck chemicals llc the branches. The bar represents 1% sequence divergence. GenBank accession numbers are mentioned within the parentheses. S. cerevisiae was the outgroup in the analysis. T = Type strain. Figure S2. In silico identified restriction enzymes which distinctly differentiated M. guilliermondii from M. caribbica. Multiple sequence alignment of representative ITS1-5.8S-ITS2 sequences of various strains of the two species obtained from

NCBI GenBank and CBS yeast database showing position of identified ArsI (A), BfaI (B), BsrI (C), Hpy188I (D), HpyCH4III (E), and MmeI (F) restriction recognition sites (highlighted) which distinctly differentiated the two species. The nucleotide position was based on the sequence of the in silico PCR amplicon of Alanine-glyoxylate transaminase ITS1-5.8S-ITS2 of S. cerevisiae strain S288c (NC_001144) including gaps generated during multiple sequence alignment. C. fermentati is the anamorph of M. caribbica.

T = Type strain. Figure S3. In silico restriction digestion profile of M. guilliermondii and M. caribbica ITS1-5.8S-ITS2 amplicon. The theoretical restriction digestion profile was generated using NEBcutter, version 2.0 (http://​tools.​neb.​com/​NEBcutter2/​). Lane G: M. guilliermondii ATCC 6260; Lane C: M. caribbica CBS 9966; Lane M: 100 bp DNA ladder. Figure S4. Strain level diversity of M. guilliermondii revealed by PFGE karyotyping. Lane 1 − 13: Isolates A3S2Y1, Kw1S2Y1, Kw3S3Y1, A3S6Y1, A2S6Y1, A1S9Y1, A1S9Y5, A2S9Y1, A3S9Y1, A3S9Y9, A2S10Y1, A2S10Y4 and A3S11Y1. White arrow indicates the polymorphic chromosomal band. (PDF 298 KB) References 1. Dujon B: Yeast evolutionary genomics. Nat Rev Genet 2010, 11:512–524.PubMedCrossRef 2. Lachance MA, Boekhout T, Scorzetti G, Fell JW, Kurtzman CP: Candida Berkhout (1923). In The Yeasts: A Taxonomic Study, Volume 2. 5th edition. Edited by: Kurtzman CP, Fell JW, Boekhout T. San Diego: Elsevier; 2011:987–1278.CrossRef 3. Lan L, Xu J: Multiple gene genealogical analyses suggest divergence and recent clonal dispersal in the opportunistic human pathogen Candida guilliermondii . Microbiology 2006, 152:1539–1549.PubMedCrossRef 4.

On the other hand, no significant increase in CC3252 expression w

On the other hand, no significant increase in CC3252 expression was found in sigF mutant cells following dichromate exposure (Figure 1). Taken together, these results confirm the involvement of σF in C. crescentus response to chromium and cadmium stresses and suggest that the operon sigF-CC3252 is not

strongly auto-regulated under these conditions. To simplify our analyses and data presentation, we only show the expression of sigF and its target genes under dichromate stress in all subsequent experiments. Figure 1 Expression analysis of CC3255 and CC3252 under heavy metal stress. qRT-PCR experiments were performed with total RNA extracted from exponentially Proteases inhibitor growing cells immediately before and following exposure during 30 min to 55 μM potassium dichromate (K2Cr2O7), 55 μM cadmium chloride (CdCl2), 100 μM hydrogen peroxide (H2O2), 50 μM tert-butyl hydroperoxide (tBOOH), 100 μM paraquat or 50 μM diamide. Values represent the fold change in expression of CC3255 and CC3252 genes in parental strain NA1000 BAY 80-6946 manufacturer (WT) or the sigF mutant strain SG16 (ΔsigF), exposed or not to stress conditions, compared to the parental strain not exposed to stress. Results were normalized using gene CC0088 as the endogenous control, which was constitutively

expressed under the conditions analyzed. Data are mean values of two independent experiments; bars represent the standard error. Statistical analysis is shown in Additional file 1: Table S4. It is assumed that heavy metal ions cause oxidative stress inside cells [1, 12, 17]. This raises the possibility that

induction of σF-dependent genes by chromium and cadmium is a direct consequence of oxidative stress. To test this hypothesis, we stressed the parental and the sigF mutant strains with hydrogen peroxide, t-butyl hydroperoxide, paraquat (source of superoxide anion) or diamide (causes depletion of thiols). According to qRT-PCR PRKACG experiments, expression levels of CC3255 and CC3252 were not increased more than twofold in the parental strain during these stress conditions (Figure 1). In agreement, transcript levels of CC3255 and CC3252 were also not influenced by any of these stressors in cells lacking sigF. Concentrations of hydrogen peroxide and t-butyl hydroperoxide used in our analyses were previously found to be sufficient to increase expression of other genes in C. crescentus[15, 18]. Taken together, these data suggest that chromium and cadmium are able to induce the σF regulon in an oxidative stress independent manner. σF controls a small set of genes under chromium stress With the aim of identifying additional genes induced during stress conditions under the control of σF, we compared the gene expression pattern of parental cells with that of a sigF mutant under dichromate stress, using microarray chips containing up to three different probes corresponding to the beginning of the coding region of each gene from C. crescentus.

​pdf Accessed 11 Dec 2013 Figgis P (2004) Conservation on privat

​pdf. Accessed 11 Dec 2013 Figgis P (2004) Conservation on private lands: the Australian experience. IUCN, Gland and Cambridge, p i–31 Figgis P, Humann D, Looker, M (2005) Conservation on private land in Australia. Parks: protected areas programme—Private Protected Areas 15(2):19–29 Fishburn IS, Kareiva P, Gaston KJ, Armsworth PR (2009) The growth of easements as a conservation tool.

PLoS One. doi:10.​1371/​journal.​pone.​0004996 PubMedCentralPubMed George S (2002) State Government incentives for habitat conservation—a status report. Defenders of wildlife, USA. http://​www.​defenders.​org/​resources/​publications/​programs_​and_​policy/​biodiversity_​partners/​conservation_​in_​america_​state_​profiles.​pdf. Accessed 1 Dec 2013 Grodzińska-Jurczak Nutlin3 M, Cent J (2010) Udział społeczny szansą dla realizacji programu Natura 2000 w Polsce. Public participatory approach—a chance for Natura 2000 implementation in Poland. Chrońmy Przyrodę Ojczystą 66(5):341–352 Grodzińska-Jurczak M, Cent J (2011) Expansion of nature conservation areas: problems with Natura 2000 implementation in Poland? Environ Manag 47:11–27CrossRef Grodzinska-Jurczak M, Strzelecka M, Kamal S, Gutowska J (2012) Effectiveness of nature conservation—a case of Natura 2000 sites in Poland. In:

Sladonja B (ed) Protected area management. In Tech, Rijeka, pp 183–202 Joppa LN, Loarla SR, Pimm SL (2008) On the protection of protected areas. PNAS 105(18):6673–6678PubMedCentralPubMedCrossRef Kamal S, Grodzinska-Jurczak M, Brown G (2014a) Conservation on private land: a review of global strategies with a proposed classification system. J Environ Plan Manag. doi:10.​1080/​09640568.​2013.​875463 Kamal S, Kocor M, Grodzinska-Jurczak M (2014 b) Quantifying

human subjectivity: when quality meets quantity. Qual Sociol Rev 10(3) (In press) Knight AT, Cowling RM, Campbell BM (2006) An operational model for implementing conservation action. Conserv Biol 20(2):408–419PubMedCrossRef Knight AT, many Cowling RM (2007) Embracing opportunism in the selection of priority conservation areas. Conserv Biol 211:124–1126 Knight AT, Cowling RM, Difford M, Campbell BM (2010) Mapping human and social dimensions of conservation opportunity for the scheduling of conservation action on private land. Conserv Biol 24:1348–1358PubMedCrossRef Krug W (2001) Private supply of protected land in Southern Africa: A review of markets, approaches, barriers and issues. World Bank/OECD international workshop on market creation for biodiversity products and services. http://​earthmind.​net/​values/​docs/​private-protected-land-southern-africa.​pdf. Accessed 17 Dec 2013 Land Trust Alliance (2013) Total acres conserved by local and national land trusts in 2010. IOP Land Trust Alliance http://​www.​landtrustallianc​e.​org/​land-trusts/​land-trust-census/​data-tables.

This is probably due to the samples representing

a wider

This is probably due to the samples representing

a wider breadth of the population than the genomes used to calculate the core genome size in previous studies. The remaining 30% of the genome, often known as the accessory genome, is composed of many classes of genes but common themes include those that encode for functions that can mobilise DNA and those that are involved in protein transport/secretion. The former may be responsible for driving a dynamic genome in the species by permitting many mechanisms selleck for horizontal gene transfer. The latter could be involved with niche adaptation. This and other studies have shown that recombination is a significant driver of evolution of the L. pneumophila genome. However we show that the genetic signal contained in the seven loci of the SBT scheme is generally indicative of its genomic heritage. Some STs appear to have been derived from recombination between strains of two different genetic backgrounds. However by clustering STs using BAPs we can determine which STs are likely to exhibit admixture and therefore cannot be confidently assigned to a cluster. Future studies will include looking at strains within and between clusters to determine phenotypes that are shared within a cluster but differ between clusters, and subsequently to search for the genetic

differences that correlate with these phenotypes. Methods For L. pneumophila all STs up to and including ST850 (n = 838 after removing ‘withdrawn’ STs) this website were used in the study. A ST is ‘withdrawn’ when the depositor informs the database curators that the unique allelic profile was submitted in error and

is in fact not extant. As comparator data the following MLST datasets (1 representative per ST) as present in the data (July 2010 and downloaded from the links present at the URL http://​pubmlst.​org/​data/​) were included; Staphylococcus aureus (clonal), Streptococcus pneumoniae (intermediate) and Neisseria meningitidis (panmictic). Tests for recombination To examine recombination within the L. pneumophila, S. aureus, S. pneumoniae and N. meningitidis populations the following types of events were tested for: Recombination between genes (intergenic) Three methods were used to test for this a. Standardised Index of Association as Implemented Etofibrate in Start 2 [40].   b. Recombination to mutation ratio (r/m) ratio as implemented by ClonalFrame (, [41]). The exact method used was as described by Vos et al. [42]. Parameters -x 100000 -y 100000 -z 100 -M -m (where is the Watterson estimate for the scaled mutation rate theta). This is calculated as the number of segregating sites (i.e., the number of polymorphic sites as calculated by DNAsp divided by the (n-1)th harmonic number where n is the number of samples.

PubMedCrossRef 59 Hayashi Y, Jacob-Vadakot S, Dugan EA, McBride

PubMedCrossRef 59. Hayashi Y, Jacob-Vadakot S, Dugan EA, McBride S, Olexa R, Simansky K, Murray M, Shumsky JS: 5-HT precursor loading, but not 5-HT receptor agonists, increases motor function after spinal cord contusion in adult rats. Exp Neurol 2010, 221:68–78.PubMedCrossRef 60. Yamamoto T, Newsholme PLX4032 molecular weight EA: Diminished central fatigue by inhibition of the L-system transporter for the uptake of tryptophan. Brain Res Bull 2000, 52:35–38.PubMedCrossRef 61. Heckman MA, Weil J, Gonzalez de Mejia E: Caffeine (1, 3, 7-trimethylxanthine) in foods: a comprehensive review

on consumption, functionality, safety, and regulatory matters. J Food Sci 2010, 75:R77–87.PubMedCrossRef 62. Ivy JL, Kammer L, Ding Z, Wang PXD101 B, Bernard JR, Liao YH, Hwang J: Improved cycling time-trial performance after ingestion of a caffeine energy drink. Int J Sport Nutr Exerc Metab 2009, 19:61–78.PubMed 63. Goldstein E, Jacobs PL, Whitehurst M, Penhollow T, Antonio J: Caffeine enhances upper body strength in resistance-trained women. J Int Soc Sports Nutr 2010, 7:18.PubMedCrossRef 64. Del Coso J, Muñoz-Fernández VE, Muñoz G, Fernández-Elías VE, Ortega JF, Hamouti N, Barbero JC,

Muñoz-Guerra J: Effects of a Caffeine-Containing Energy Drink on Simulated Soccer Performance. PLoS One 2012, 7:e31380.PubMedCrossRef 65. Del Coso J, Salinero JJ, Gonzalez-Millan C, Abian-Vicen J, Perez-Gonzalez B: Dose response effects of a caffeine-containing energy drink on muscle performance: a repeated measures design. J Int Soc Sports Nutr 2012, 9:21.PubMedCrossRef 66. Berube-Parent S, Pelletier C, Dore J, Tremblay A: Effects of encapsulated green tea and Guarana extracts containing a mixture of epigallocatechin-3-gallate and caffeine on 24 h energy expenditure and fat oxidation in men. Br J Nutr 2005, 94:432–436.PubMedCrossRef 67. Belza A, Toubro S, Astrup A: The effect of caffeine, green tea

and tyrosine on thermogenesis and energy intake. Eur J Clin Nutr 2009, 63:57–64.PubMedCrossRef 68. Eichenberger Tideglusib P, Colombani PC, Mettler S: Effects of 3-week consumption of green tea extracts on whole-body metabolism during cycling exercise in endurance-trained men. Int J Vitam Nutr Res 2009, 79:24–33.PubMedCrossRef 69. Venables MC, Hulston CJ, Cox HR, Jeukendrup AE: Green tea extract ingestion, fat oxidation, and glucose tolerance in healthy humans. Am J Clin Nutr 2008, 87:778–784.PubMed 70. Eichenberger P, Mettler S, Arnold M, Colombani PC: No Effects of Three-week Consumption of a Green Tea Extract on Time Trial Performance in Endurance-trained Men. Int J Vitam Nutr Res 2010, 80:54–64.PubMedCrossRef 71. Chen N, Bezzina R, Hinch E, Lewandowski PA, Cameron-Smith D, Mathai ML, Jois M, Sinclair AJ, Begg DP, Wark JD, et al.: Green tea, black tea, and epigallocatechin modify body composition, improve glucose tolerance, and differentially alter metabolic gene expression in rats fed a high-fat diet. Nutr Res 2009, 29:784–793.PubMedCrossRef 72.