Bayesian and Maximum Likelihood Analyses of Rotifer–Acanthocephalan Relationships

Rotifera is composed of groups with unusual ultrastructural, physiological, and reproductive characters. Our ability to understand the evolution of these features is complicated by the fact that the phylogenetic relationships among the three traditional rotifer groups (Seisonidea, Monogononta, and Bdelloidea) and Acanthocephala remain unresolved. Here, I present maximum likelihood and Bayesian analyses of rotifer–acanthocephalan relationships using both the protein-coding gene hsp82 and a combined data set of hsp82 and ribosomal small subunit (SSU) DNA sequences, using nucleotide and codon based models of evolution. Statistical analysis of the phylogenetic support for any of the likely relationships among rotifer groups suggests that more than a combined hsp82 + SSU data set will be needed to resolve rotifer–acanthocephalan phylogeny with any degree of certainty.     

Spatial scale,reservoirs and nonnative species influence the homogenization and differentiation of Great Plains—Rocky Mountain fish faunas

Hydrobiologia - Reservoir construction and the introduction of nonnative species are major anthropogenic drivers of biotic change in freshwater ecosystems. To understand the influence of these...     

Temporal Proteomic Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity

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Highlights

• •Temporal proteome profiling of lipotoxicity and glucolipotoxicity in β-cells
• •Palmitate induced cholesterol metabolism earlier than fatty acid metabolism
• •Setd8 promotes palmitate + glucose-stimulated INS-1 cell proliferation
• •PA induced apoptosis partially via upregulation of Rhob in INS-1 cells

     

Distribution of Spotted Fever Group Rickettsiae in Hard Ticks (Ixodida: Ixodidae) from Panamanian Urban and Rural Environments (2007–2013)

Tick-borne rickettsiosis is an important emerging disease in Panama; to date, there have been 12 confirmed cases, including eight fatalities. To evaluate the distribution of rickettsiae in Panamanian ticks, we collected questing and on-host ticks in urban and rural towns in elevations varying between 0 and 2300 m. A total of 63 sites (13 urban and 50 rural towns) were used to develop models of spatial distributions. We found the following tick species: Rhipicephalus sanguineus s.l. (present in 54 of 63 towns and cities), Amblyomma mixtum (45/63), Dermacentor nitens (40/63), A. ovale (37/63), Rhipicephalus microplus (33/63), A. oblongoguttatum (33/63), Ixodes affinis (3/63), and Ixodes boliviensis (2/63). Rhipicephalus sanguineus s.l. was present in urban and rural towns, and other species were present only in rural towns. DNA was extracted from 408 R. sanguineus s.l., 387 A. mixtum, 103 A. ovale, and 11 A. oblongoguttatum and later tested for rickettsiae genes using PCR. Rickettsia DNA was detected in ticks from 21 of 63 localities. Rickettsia rickettsii was detected in five A. mixtum (1.29%), and Candidatus “Rickettsia amblyommii” was found in 138 A. mixtum (35%), 14 R. sanguineus (3.4%), and one A. ovale (0.9%). These results suggest that much of rural Panama is suitable for the expansion of tick populations and could favor the appearance of new tick-borne rickettsiosis outbreaks.     

Determinants and Experiences of Repeat Pregnancy among HIV-Positive Kenyan Women—A Mixed-Methods Analysis

Objective

To identify factors associated with repeat pregnancy subsequent to an index pregnancy among women living with HIV (WLWH) in western Kenya who were enrolled in a 24-month phase-II clinical trial of triple-ART prophylaxis for prevention of mother-to-child transmission, and to contextualize social and cultural influences on WLWH’s reproductive decision making.

Methods

A mixed-methods approach was used to examine repeat pregnancy within a 24 month period after birth. Counselor-administered questionnaires were collected from 500 WLWH. Forty women (22 with a repeat pregnancy; 18 with no repeat pregnancy) were purposively selected for a qualitative interview (QI). Simple and multiple logistic regression analyses were performed for quantitative data. Thematic coding and saliency analysis were undertaken for qualitative data.

Results

Eighty-eight (17.6%) women had a repeat pregnancy. Median maternal age was 23 years (range 15-43 years) and median gestational age at enrollment was 34 weeks. In multiple logistic regression analyses, living in the same compound with a husband (adjusted odds ratio (AOR): 2.33; 95% confidence interval (CI): 1.14, 4.75) was associated with increased odds of repeat pregnancy (p ≤ 0.05). Being in the 30-43 age group (AOR: 0.25; 95% CI: 0.07, 0.87), having talked to a partner about family planning (FP) use (AOR: 0.53; 95% CI: 0.29, 0.98), and prior usage of FP (AOR: 0.45; 95% CI: 0.25, 0.82) were associated with a decrease in odds of repeat pregnancy. QI findings centered on concerns about modern contraception methods (side effects and views that they ‘ruined the womb’) and a desire to have the right number of children. Religious leaders, family, and the broader community were viewed as reinforcing cultural expectations for married women to have children. Repeat pregnancy was commonly attributed to contraception failure or to lack of knowledge about post-delivery fertility.

Conclusions

In addition to cultural context, reproductive health programs for WLWH may need to address issues related to living circumstances and the possibility that reproductive-decision making may extend beyond the woman and her partner.     

Temporal effects of ocean warming and acidification on coral–algal competition

Coral Reefs - While there is an ever-expanding list of impacts on coral reefs as a result of ocean warming and acidification, there is little information on how these global changes influence...     

A Bayesian Approach to Pathway Analysis by Integrating Gene–Gene Functional Directions and Microarray Data

Many statistical methods have been developed to screen for differentially expressed genes associated with specific phenotypes in the microarray data. However, it remains a major challenge to synthesize the observed expression patterns with abundant biological knowledge for more complete understanding of the biological functions among genes. Various methods including clustering analysis on genes, neural network, Bayesian network and pathway analysis have been developed toward this goal. In most of these procedures, the activation and inhibition relationships among genes have hardly been utilized in the modeling steps. We propose two novel Bayesian models to integrate the microarray data with the putative pathway structures obtained from the KEGG database and the directional gene–gene interactions in the medical literature. We define the symmetric Kullback–Leibler divergence of a pathway, and use it to identify the pathway(s) most supported by the microarray data. Monte Carlo Markov Chain sampling algorithm is given for posterior computation in the hierarchical model. The proposed method is shown to select the most supported pathway in an illustrative example. Finally, we apply the methodology to a real microarray data set to understand the gene expression profile of osteoblast lineage at defined stages of differentiation. We observe that our method correctly identifies the pathways that are reported to play essential roles in modulating bone mass.     

Analysis of β-Subgroup Proteobacterial Ammonia Oxidizer Populations in Soil by Denaturing Gradient Gel Electrophoresis Analysis and Hierarchical Phylogenetic Probing

A combination of denaturing gradient gel electrophoresis (DGGE) and oligonucleotide probing was used to investigate the influence of soil pH on the compositions of natural populations of autotrophic β-subgroup proteobacterial ammonia oxidizers. PCR primers specific to this group were used to amplify 16S ribosomal DNA (rDNA) from soils maintained for 36 years at a range of pH values, and PCR products were analyzed by DGGE. Genus- and cluster-specific probes were designed to bind to sequences within the region amplified by these primers. A sequence specific to all β-subgroup ammonia oxidizers could not be identified, but probes specific for Nitrosospira clusters 1 to 4 and Nitrosomonas clusters 6 and 7 (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley, Appl. Environ. Microbiol. 62:4147–4154, 1996) were designed. Elution profiles of probes against target sequences and closely related nontarget sequences indicated a requirement for high-stringency hybridization conditions to distinguish between different clusters. DGGE banding patterns suggested the presence of Nitrosomonas cluster 6a and Nitrosospira clusters 2, 3, and 4 in all soil plots, but results were ambiguous because of overlapping banding patterns. Unambiguous band identification of the same clusters was achieved by combined DGGE and probing of blots with the cluster-specific radiolabelled probes. The relative intensities of hybridization signals provided information on the apparent selection of different Nitrosospira genotypes in samples of soil of different pHs. The signal from the Nitrosospira cluster 3 probe decreased significantly, relative to an internal control probe, with decreasing soil pH in the range of 6.6 to 3.9, while Nitrosospira cluster 2 hybridization signals increased with increasing soil acidity. Signals from Nitrosospira cluster 4 were greatest at pH 5.5, decreasing at lower and higher values, while Nitrosomonas cluster 6a signals did not vary significantly with pH. These findings are in agreement with a previous molecular study (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley, Appl. Environ. Microbiol 62:4147–4154, 1996) of the same sites, which demonstrated the presence of the same four clusters of ammonia oxidizers and indicated that selection might be occurring for clusters 2 and 3 at acid and neutral pHs, respectively. The two studies used different sets of PCR primers for amplification of 16S rDNA sequences from soil, and the similar findings suggest that PCR bias was unlikely to be a significant factor. The present study demonstrates the value of DGGE and probing for rapid analysis of natural soil communities of β-subgroup proteobacterial ammonia oxidizers, indicates significant pH-associated differences in Nitrosospira populations, and suggests that Nitrosospira cluster 2 may be of significance for ammonia-oxidizing activity in acid soils.Chemolithotrophic oxidation of ammonia to nitrate via nitrate (autotrophic nitrification) is of major importance in the global cycling of nitrogen in terrestrial, aquatic, and marine ecosystems (22). The first, and rate-determining, step of nitrification, ammonia oxidation, is carried out by the autotrophic ammonia-oxidizing bacteria, whose growth in liquid batch culture rarely occurs at pH values below 6.5. Nevertheless, autotrophic nitrification has been reported in acid soils at pH values as low as 3.5 (5). Nitrification in acid soils may be explained to some extent by growth on surfaces (2) or in aggregates (6), by ureolytic activity (1, 4), and by heterotrophic nitrifiers (14). An additional explanation is the existence of strains adapted to low-pH environments (7, 26), but although an acidophilic nitrite oxidizer has been isolated (9), acidophilic ammonia oxidizers have proved difficult to isolate in pure culture. Low growth rates, low biomass yield, and the limited number of distinguishing phenotypic characters for ammonia oxidizers have prevented the analysis of natural communities, in particular those in acid soils. The application of 16S ribosomal DNA (rDNA)-based techniques, however, enables the study of community structure in environmental samples, without the requirement for laboratory cultivation (8). Such studies have been particularly productive when applied to ammonia-oxidizing bacteria. With the exception of a small number of cultured marine strains belonging to the γ-proteobacteria, the phylogenetic analysis of rDNA sequences places all ammonia oxidizers in a monophyletic group within the β-proteobacteria. This group consists of two distinct monophyletic genera, Nitrosomonas and Nitrosospira (10, 28, 30, 31). An analysis of natural ammonia oxidizer populations from a variety of environments has revealed further subdivision (26), based on phylogenetic analysis of a 300-bp fragment of the 16S rDNA molecule spanning the V2 and V3 regions (20). An analysis of 1.1-kb regions (incorporating this 300-bp fragment) of representative environmental sequences has shown that Nitrosospira can be further subdivided into at least four clusters, designated 1 to 4 (26). The Nitrosomonas genus may also be subdivided, and Stephen et al. (26) recognized three clusters within this genus, designated 5 to 7 (Fig. ​(Fig.1).1). Of particular relevance to this study is a cluster containing three soil clones, here referred to as cluster 6a. These and other studies (11, 15) indicate that sequences from members of the genus Nitrosospira were more abundant than Nitrosomonas in a range of environments and suggest that the available pure cultures represent only a limited selection of the phylogenetic and, by inference, physiological diversity of natural ammonia oxidizer populations. These studies are based on the hypothesis that environmental sequences falling within the Nitrosomonas and Nitrosospira clades originate from autotrophic ammonia oxidizers (26). Evidence for this hypothesis is based on their phylogenetic positions relative to cultured taxa which uniformly possess this phenotype, including recently isolated cultures of Nitrosospira (28). In addition, no sequence from a nonautotrophic ammonia oxidizer falls within this clade. Open in a separate windowFIG. 1Schematic tree of the β-subgroup ammonia-oxidizing bacteria based on 303 bp of 16S rDNA sequence spanning E. coli positions 198 to 500 (3) and target groups for probes described in Table ​Table1.1. Ambiguous sites were removed by using the GDE 2.2 “mask” function (16) before transfer of the data to the ARB sequence analysis program (25). The tree was generated by neighbor joining (24) with the Jukes and Cantor (13) correction in ARB. Clusters of sequences are scaled vertically to represent the number of sequences and horizontally to represent the extent of variation within each cluster. Cluster designations are as described in Stephen et al. (26) with the exception of cluster 6a, which contains three soil clones (see text), and cluster 6b, which contains the remainder of cluster 6 sequences previously described (26). Soil clone pH4.2/28 and marine enrichment sequence AEM3 cannot be placed unequivocally in this scheme. The scale bar represents 0.1 estimated changes per nucleotide position. Sequence data were compiled from references 10, 15, 17, 21, 26, and 28).The available 16S rDNA sequence data for β-subgroup ammonia oxidizers can be interpreted to suggest that particular phylogenetic clusters may be associated with specific habitats (26). For example, sequences from Nitrosospira cluster 2 and Nitrosospira cluster 3 were apparently more common in acid and neutral agricultural soils, respectively (26), while sequences from Nitrosomonas cluster 6 and Nitrosospira cluster 4 were detected at similar frequencies in both soils. Biogeographic or temporal studies of community structure by determination of sequence abundance in gene libraries are severely limited by the time required for sequence acquisition and analysis, and the approach is not necessarily quantitative. Denaturing gradient gel electrophoresis (DGGE) provides a complementary tool for the analysis of complex microbial communities (19, 25). It involves the separation of DNA fragments of identical length on the basis of differences in denaturant sensitivity in an acrylamide gel matrix, resulting from differences in the primary sequence. PCR products generated from different samples can thereby be compared directly, based on their mobility, without the need for cloning or DNA sequence analysis. Specific amplification and DGGE analysis of 16S rDNA for β-subgroup ammonia-oxidizing bacteria successfully demonstrated differences between communities in dune soil samples (15). However, differences in mobility between the various sequence clusters and overlapping banding patterns prevented precise identification of the community members, which necessitated band excision and sequence determination.The recent expansion of the 16S rDNA sequence database for β-subgroup ammonia oxidizers provides the potential for the design of improved oligonucleotide probes for the analysis of natural populations (10, 15, 21, 26, 28). Published β-subgroup ammonia oxidizer probes have been based on sequence information from a limited number of cultured organisms (11, 12, 29) and would not detect much of the diversity determined by Stephen et al. (26), restricting their value for the analysis of natural communities.The first aim of this study was to design and test oligonucleotide probes capable of distinguishing the subgroups within the different clusters of β-subgroup ammonia oxidizers from each other. The second aim was then to use these probes to identify bands separated by DGGE analysis of PCR products generated from soil with ammonia oxidizer-specific primers. In particular, we aimed to investigate further the hypotheses (26) that Nitrosospira may be of significance for ammonia oxidation in acid soils and that the relative abundances of different sequence clusters are related to soil pH.     

Live Cell Analysis and Mathematical Modeling Identify Determinants of Attenuation of Dengue Virus 2’-O-Methylation Mutant

Dengue virus (DENV) is the most common mosquito-transmitted virus infecting ~390 million people worldwide. In spite of this high medical relevance, neither a vaccine nor antiviral therapy is currently available. DENV elicits a strong interferon (IFN) response in infected cells, but at the same time actively counteracts IFN production and signaling. Although the kinetics of activation of this innate antiviral defense and the timing of viral counteraction critically determine the magnitude of infection and thus disease, quantitative and kinetic analyses are lacking and it remains poorly understood how DENV spreads in IFN-competent cell systems. To dissect the dynamics of replication versus antiviral defense at the single cell level, we generated a fully viable reporter DENV and host cells with authentic reporters for IFN-stimulated antiviral genes. We find that IFN controls DENV infection in a kinetically determined manner that at the single cell level is highly heterogeneous and stochastic. Even at high-dose, IFN does not fully protect all cells in the culture and, therefore, viral spread occurs even in the face of antiviral protection of naïve cells by IFN. By contrast, a vaccine candidate DENV mutant, which lacks 2’-O-methylation of viral RNA is profoundly attenuated in IFN-competent cells. Through mathematical modeling of time-resolved data and validation experiments we show that the primary determinant for attenuation is the accelerated kinetics of IFN production. This rapid induction triggered by mutant DENV precedes establishment of IFN-resistance in infected cells, thus causing a massive reduction of virus production rate. In contrast, accelerated protection of naïve cells by paracrine IFN action has negligible impact. In conclusion, these results show that attenuation of the 2’-O-methylation DENV mutant is primarily determined by kinetics of autocrine IFN action on infected cells.     

Spatial Analysis of Hemorrhagic Fever with Renal Syndrome in Zibo City,China, 2009–2012

Background

Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in mainland China, where human cases account for 90% of the total global cases. Zibo City is one of the most serious affected areas in Shandong Province China with the HFRS incidence increasing sharply from 2009 to 2012. However, the hotspots of HFRS in Zibo remained unclear. Thus, a spatial analysis was conducted with the aim to explore the spatial, spatial-temporal and seasonal patterns of HFRS in Zibo from 2009 to 2012, and to provide guidance for formulating regional prevention and control strategies.

Methods

The study was based on the reported cases of HFRS from the National Notifiable Disease Surveillance System. Annualized incidence maps and seasonal incidence maps were produced to analyze the spatial and seasonal distribution of HFRS in Zibo City. Then spatial scan statistics and space-time scan statistics were conducted to identify clusters of HFRS.

Results

There were 200 cases reported in Zibo City during the 4-year study period. One most likely cluster and one secondary cluster for high incidence of HFRS were identified by the space-time analysis. And the most likely cluster was found to exist at Yiyuan County in October to December 2012. The human infections in the fall and winter reflected a seasonal characteristic pattern of Hantaan virus (HTNV) transmission. The secondary cluster was detected at the center of Zibo in May to June 2009, presenting a seasonal characteristic of Seoul virus (SEOV) transmission.

Conclusion

To control and prevent HFRS in Zibo city, the comprehensive preventive strategy should be implemented in the southern areas of Zibo in autumn and in the northern areas of Zibo in spring.     

Analysis and modeling of time-variant amplitude–frequency couplings of and between oscillations of EEG bursts

Low-frequency (0.5-2.5 Hz) and individually defined high-frequency (7-11 or 8-12 Hz; 11-15 or 14-18 Hz) oscillatory components of the electroencephalogram (EEG) burst activity derived from thiopental-induced burst-suppression patterns (BSP) were investigated in seven sedated patients (17-26 years old) with severe head injury. The predominant high-frequency burst oscillations (>7 Hz) were detected for each patient by means of time-variant amplitude spectrum analysis. Thereafter, the instantaneous envelope (IE) and the instantaneous frequency (IF) were computed for these low- and high-frequency bands to quantify amplitude-frequency dependencies (envelope-envelope, envelope-frequency, and frequency-frequency correlations). Time-variant phase-locking, phase synchronization, and quadratic phase couplings are associated with the observed amplitude-frequency characteristics. Additionally, these time-variant analyses were carried out for modeled burst patterns. Coupled Duffing oscillators were adapted to each EEG burst and by means of these models data-based burst simulations were generated. Results are: (1) strong envelope-envelope correlations (IE courses) can be demonstrated; (2) it can be shown that a rise of the IE is associated with an increase of the IF (only for the frequency bands 0.5-2.5 and 7-11 or 8-12 Hz); (3) the rise characteristics of all individually averaged envelope-frequency courses (IE-IF) are strongly correlated; (4) for the 7-11 or 8-12 Hz oscillation these associations are weaker and the variation between the time courses of the patients is higher; (5) for both frequency ranges a quantitative amplitude-frequency dependency can be shown because higher IE peak maxima are accompanied by stronger IF changes; (6) the time range of significant phase-locking within the 7-11 or 8-12 Hz frequency bands and of the strongest quadratic phase couplings (between 0.5-2.5 and 7-11 or 8-12 Hz) is between 0 and 1,000 ms; (7) all phase coupling characteristics of the modeled bursts accord well with the corresponding characteristics of the measured EEG burst data. All amplitude-frequency dependencies and phase locking/coupling properties described here are known from and can be discussed using coupled Duffing oscillators which are characterized by autoresonance properties.     

Temporal–spatial variation and source analysis of carbon and nitrogen in a tidal wetland of Luoyuan Bay

Carbon and nitrogen are important elements in biogeochemical studies of tidal wetlands. Three wetland zones in Luoyuan Bay in the Fujian province were chosen for this study; the Spartina alterniflora flat zone with Spartina alterniflora growing, the silt zone with no Spartina alterniflora growing and the Spartina alterniflora-silt flat zone – a transition zone between the two. The spatial and seasonal variations of total organic carbon (TOC), total nitrogen (TN), stable isotopes of organic material (δ¹³C, δ¹⁵N), C/N ratio, average particle size and sediment composition in surface and vertical sediments of different ecological zones were analyzed. Carbon and nitrogen accumulation and particle size effects in the different ecological zones were discussed and the indicators of δ¹³C and C/N ratios were also compared. TOC, TN, δ¹³C contents, C/N ratios, and average particle size varied within the ranges of 0.611–1.133%, 0.053–0.090%, ?22.60 to ?18.92‰, 12.3–15.7, and 6.4–8.7 μm, respectively. Sediments were mainly silt-sized. Besides δ¹⁵N values, the other parameters, such as TOC, TN, δ¹³C contents, C/N ratios, and average particle size showed an obvious zonal distribution in surface sediments. The distribution of TOC and TN contents reflected the distribution of Spartina alterniflora within the bay. The profile and seasonal variations of these parameters in different ecological zones indicated that variations in the Spartina alterniflora flat and transition zones were complex because of the effect of Spartina alterniflora. Vertical and seasonal variations were sampled in the silt flat area. The profile and seasonal variations of TOC, TN and δ¹³C were similar in the transition zone and the Spartina alterniflora flat zone. Seasonal concentrations of TOC, TN and δ¹³C decreased from autumn > spring > winter > summer. The seasonal variation of carbon and nitrogen in the sediments may be influenced by temperature, particle size, plankton and benthos. The particle size effect was significant in the surface sediments and profile sediments of the transition zone. However, other factors had a greater effect on the distributions of TOC and TN in the Spartina alterniflora flat and silt flat zones. C/N ratios in sediments of the Spartina alterniflora flat, transition zone and silt flat were close to or > 12, indicating that the organic material source was dominated by terrestrial inputs. However, δ¹³C values decreased from the Spartina alterniflora flat zone > transition zone > silt flat zone indicating that the organic material source was predominantly from marine inputs. Thus the indications from C/N ratios and δ¹³C were different. There was no clear relationship between C/N ratios and δ¹³C values and a better relationship between δ¹³C values and TOC concentrations suggested that δ¹³C values provided a better indication of the organic source. Limited amounts of organic material came from Spartina alterniflora. This study has provided basic data for researching biogeochemical processes of biogenic elements in tidal wetlands and vegetation restoration, and has also provided a reference for assessing and protecting the environment and ecological systems in wetlands.     

Acquisition and Evolution of Plant Pathogenesis–Associated Gene Clusters and Candidate Determinants of Tissue-Specificity in Xanthomonas

Background

Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown.

Methodology/Principal Findings

To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors) cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage.

Conclusions/Significance

Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small number of genes or in non-coding sequences, and/or differences outside the clusters, potentially among regulatory targets or secretory substrates.     

Climatic Control on Plant and Soil δ13C along an Altitudinal Transect of Lushan Mountain in Subtropical China: Characteristics and Interpretation of Soil Carbon Dynamics

Decreasing temperature and increasing precipitation along altitude gradients are typical mountain climate in subtropical China. In such a climate regime, identifying the patterns of the C stable isotope composition (δ¹³C) in plants and soils and their relations to the context of climate change is essential. In this study, the patterns of δ¹³C variation were investigated for tree leaves, litters, and soils in the natural secondary forests at four altitudes (219, 405, 780, and 1268 m a.s.l.) in Lushan Mountain, central subtropical China. For the dominant trees, both leaf and leaf-litter δ¹³C decreased as altitude increased from low to high altitude, whereas surface soil δ¹³C increased. The lower leaf δ¹³C at high altitudes was associated with the high moisture-related discrimination, while the high soil δ¹³C is attributed to the low temperature-induced decay. At each altitude, soil δ¹³C became enriched with soil depth. Soil δ¹³C increased with soil C concentrations and altitude, but decreased with soil depth. A negative relationship was also found between O-alkyl C and δ¹³C in litter and soil, whereas a positive relationship was observed between aromatic C and δ¹³C. Lower temperature and higher moisture at high altitudes are the predominant control factors of δ¹³C variation in plants and soils. These results help understand C dynamics in the context of global warming.