Sequence alignments

Fasta files containing alignments of all sequence loci

MOESM2 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

Additional file 2. Mapping statistics of input read pairs mapped to the reference genomes. Sequencing reads derived from the Chinese strain SRA data were mapped to the Treponema pallidum subsp. pallidum (TPA) SS14 and Nichols reference genomes [6] and to the rabbit genome (Statistics was calculated from post-processed mappings; repetitive and homologous sequences and PCR duplicated reads were excluded from the statistics)

DataSheet1_Increase of intestinal bacterial sialidase activity exacerbates acute colitis in mice.PDF

The availability of endogenous and dietary carbohydrates in the gastrointestinal tract influences the composition of the gut microbiota. Carbohydrate foraging requires the action of bacterially-encoded glycoside hydrolases, which release mono- and oligosaccharides taken up as carbon sources by multiple microbial taxa. In addition to providing nutrients to the microbiota, the cleavage of host glycans by bacterial glycoside hydrolases may alter the properties of surface glycoproteins involved in cell adhesion and activation processes in the gut lumen. To investigate the impact of bacterial glycoside hydrolase activities on the gut microbial composition and on host glycans during colon inflammation, we increased local glycoside hydrolase activity by supplementing mice with recombinant E. coli expressing specific sialidase, fucosidase and rhamnosidase enzymes during acute colitis induced by dextran sulfate sodium ingestion. Whereas increased fucosidase and rhamnosidase activity did not alter the course of colitis, increased sialidase activity exacerbated disease severity. The effect of increased sialidase activity on inflammation was not caused by changes in the microbial composition given that a similar shift in gut bacteria occurred in all groups of mice supplemented with recombinant E. coli. Increased sialidase activity in the colon of treated mice however significantly altered the distribution of sialic acid on mucosal glycans. Treatment of lamina propria dendritic cells with bacterial sialidase also strongly decreased the density of sialylated ligands to anti-inflammatory siglec lectins, indicating that the remodeling of surface sialylation caused by increased sialidase activity likely accounts for the observed exacerbation of acute colitis in mice.</p

Test of the most likely period associated with orang-utan population decline.

<p>Natural logarithms of the Bayes Factors (BF) have been computed to determine during which of the important phases the populations started to decrease. a) The BF values of parameter <i>T</i> (time since the beginning of the population collapse) for all orang-utan populations were computed for each 500 year time steps and are plotted for last 50,000 years. The BF value of 3 is plotted as horizontal dash line. The vertical dash lines corresponds to the dates of forest exploitation (FE) ∼ 0.2 kya, arrival of first farmers (F) ∼ 5 kya, and arrival of hunter gatherers (HG) ∼ 40 kya. Note that LK Lot2 is Lower Kinabatangan Lot2 population. b) As 5a), and plotted for the last 5 kya. c) H1 to H4 represents four different hypotheses tested, each corresponding to one of the four factors and time periods that may have led to orang-utan population collapse (discussed in the text). Phase H4 is most ancient and corresponds to time period between 100–40 kya (before the arrival of hunter gatherers (HG) and the time when major climatic and vegetational changes associated with the Pleistocene glaciations occurred). Phase H3 corresponds to the time period after the arrival of HG. Phase H2 corresponds to the time period after the arrival of first farmers (F) and before recent forest exploitation (FE) occurred. Phase H1 is most recent and corresponds to time period of the last 200 years when major forest exploitation occurred in Borneo. Thus, the BF represents the weighted evidence in favor of each phase against the cumulative evidence of all other phases taken together. The dashed horizontal line corresponds to a BF of 3, suggesting that phase H2 has more support than H1, H3, and H4 (see results). d) H2 phase (5,000 years from present) has been divided into two periods: H2.1 and H2.2 which corresponds to the time period just before the recent forest exploitation and after the arrival of the first farmers. The dashed horizontal line corresponds to a BF of 3 and suggesting that phase H2.1 has more support than H1 and H2.2.</p

Demographic collapse detected using MSVAR 0.4.

<p>Posterior distributions of the effective population size change, log (<i>N</i>₀/<i>N</i>₁). This is shown here for one of the investigated site (Sabangau) in Central Kalimantan and pooled samples analyses from the same region. Note that for illustrative purposes only two plots are shown (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049429#pone.0049429.s001" target="_blank">Figure S1</a> for the other regions). Solid lines (multiple independent runs) correspond to the linear population size change model. Dashed lines (multiple independent runs) correspond to the exponential population size model. Log (<i>N</i>₀/<i>N</i>₁) represents the ratio of present (<i>N</i>₀) to past (<i>N</i>₁) population size. The dotted vertical line corresponds to the absence of population size change, log (<i>N</i>₀/<i>N</i>₁) = 0. The prior distribution is shown for comparison (flat dotted line). The vertical dashed line corresponds to the 95% quantile of the posterior distribution.</p

Posterior distributions for the past (<i>N</i>₁) and present (<i>N</i>₀) effective population sizes using MSVAR 1.3.

<p>This is shown here for one of the investigated site (Sabangau) in Central Kalimantan and pooled samples analyses from the same region represented on a log₁₀ scale. The solid lines correspond to the posterior distribution obtained by independent MCMC runs. Dashed lines correspond to the different priors used for <i>N</i>₀ and <i>N</i>_1.</p

Bornean orang-utan sampling sites.

<p>The sample sizes for each site are as follows: DV = Danum Valley (<i>n</i> = 20), LK = Lower Kinabatangan (<i>n</i> = 26), TU = Tuanan (<i>n</i> = 29), SL = Sungai Lading (<i>n</i> = 26), SA = Sabangau (<i>n</i> = 19), and GP = Gunung Palung (<i>n</i> = 6).</p

since the population collapse using MSVAR 1.3.

<p>The posterior distribution for the time since orang-utan populations (all) collapse started is represented on a logarithmic scale. The different coloured vertical dashed line corresponds to: forest exploitation (FE in red), arrival of farmers (F in blue), and arrival of hunter gatherers (HG in green). The most extreme 95% quantile of the posterior distribution is shown as a black vertical dashed line. The prior is shown as dashed line, its median being 100,000 y ago.</p

Molecular characterization of <i>Treponema pallidum</i> subsp. <i>pallidum</i> in Switzerland and France with a new multilocus sequence typing scheme

<div><p>Syphilis is an important public health problem and an increasing incidence has been noted in recent years. Characterization of strain diversity through molecular data plays a critical role in the epidemiological understanding of this re-emergence. We here propose a new high-resolution multilocus sequence typing (MLST) scheme for <i>Treponema pallidum</i> subsp. <i>pallidum</i> (TPA). We analyzed 30 complete and draft TPA genomes obtained directly from clinical samples or from rabbit propagated strains to identify suitable typing loci and tested the new scheme on 120 clinical samples collected in Switzerland and France. Our analyses yielded three loci with high discriminatory power: TP0136, TP0548, and TP0705. Together with analysis of the 23S rRNA gene mutations for macrolide resistance, we propose these loci as MLST for TPA. Among clinical samples, 23 allelic profiles as well as a high percentage (80% samples) of macrolide resistance were revealed. The new MLST has higher discriminatory power compared to previous typing schemes, enabling distinction of TPA from other treponemal bacteria, distinction between the two main TPA clades (Nichols and SS14), and differentiation of strains within these clades.</p></div

Orang-utan call spectrograms.

<p>Spectrograms of orang-utan calls: a) ‘nest smacks’; b) ‘raspberries’; c) ‘harmonic uuhs’; d) ‘throat scrapes’. The nest smack and raspberry are produced by orangutans during nest building. The harmonic uuh and throatscrape are produced by mothers towards infants that are separated from them and functions as a ‘come-hither’ call because infants return to the mother after these calls.</p