Utilization of Whole-Cell MALDI-TOF Mass Spectrometry to Differentiate Burkholderia pseudomallei Wild-Type and Constructed Mutants

Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has been widely adopted as a useful technology in the identification and typing of microorganisms. This study employed the whole-cell MALDI-TOF MS to identify and differentiate wild-type and mutants containing constructed single gene mutations of Burkholderia pseudomallei, a pathogenic bacterium causing melioidosis disease in both humans and animals. Candidate biomarkers for the B. pseudomallei mutants, including rpoS, ppk, and bpsI isolates, were determined. Taxon-specific and clinical isolate-specific biomarkers of B. pseudomallei were consistently found and conserved across all average mass spectra. Cluster analysis of MALDI spectra of all isolates exhibited separate distribution. A total of twelve potential mass peaks discriminating between wild-type and mutant isolates were identified using ClinProTools analysis. Two peaks (m/z 2721 and 2748 Da) were specific for the rpoS isolate, three (m/z 3150, 3378, and 7994 Da) for ppk, and seven (m/z 3420, 3520, 3587, 3688, 4623, 4708, and 5450 Da) for bpsI. Our findings demonstrated that the rapid, accurate, and reproducible mass profiling technology could have new implications in laboratory-based rapid differentiation of extensive libraries of genetically altered bacteria.     

Evolutionary stability and quasi-stationary strategy in stochastic evolutionary game dynamics

Stochastic evolutionary game dynamics for finite populations has recently been widely explored in the study of evolutionary game theory. It is known from the work of Traulsen et al. [2005. Phys. Rev. Lett. 95, 238701] that the stochastic evolutionary dynamics approaches the deterministic replicator dynamics in the limit of large population size. However, sometimes the limiting behavior predicted by the stochastic evolutionary dynamics is not quite in agreement with the steady-state behavior of the replicator dynamics. This paradox inspired us to give reasonable explanations of the traditional concept of evolutionarily stable strategy (ESS) in the context of finite populations. A quasi-stationary analysis of the stochastic evolutionary game dynamics is put forward in this study and we present a new concept of quasi-stationary strategy (QSS) for large but finite populations. It is shown that the consistency between the QSS and the ESS implies that the long-term behavior of the replicator dynamics can be predicted by the quasi-stationary behavior of the stochastic dynamics. We relate the paradox to the time scales and find that the contradiction occurs only when the fixation time scale is much longer than the quasi-stationary time scale. Our work may shed light on understanding the relationship between the deterministic and stochastic methods of modeling evolutionary game dynamics.     

Vibrio vulnificus quorum-sensing system operates in cirrhotic ascites, a human ex vivo experimental system

This study was conducted to experimentally determine whether a Vibrio vulnificus quorum sensing (QS) system actually operates ex vivo. The expressions of luxS encoding autoinducer-2 synthase, of smcR encoding the master regulator of QS system, and of vvpE encoding a metalloprotease, the best known target directly regulated by QS, were increased with increasing bacterial density in cirrhotic ascites used as a human ex vivo experimental system. A luxS or smcR mutation significantly decreased vvpE expression under the same conditions. Accordingly, V. vulnificus QSS is likely to operate ex vivo.     

The Burkholderia pseudomallei BpeAB-OprB efflux pump: expression and impact on quorum sensing and virulence

BpeAB-OprB is a multidrug efflux pump of the bacterial pathogen Burkholderia pseudomallei and is responsible for conferring antimicrobial resistance to aminoglycosides and macrolides. Expression of bpeAB-oprB is inducible by its substrate erythromycin and upon entry into stationary phase. BpeR, a member of the TetR family, functions as a repressor of the bpeAB-oprB operon. bpeR expression was similarly induced at stationary phase but lagged behind the induction of bpeAB-oprB expression. The induction of bpeAB-oprB expression could be advanced to the early exponential phase by exogenous addition of the B. pseudomallei autoinducers N-octanoyl-homoserine lactone (C8HSL) and N-decanoyl-homoserine lactone (C10HSL), suggesting that the bpeAB-oprB operon may be quorum regulated. On the other hand, acyl-homoserine lactone (acyl-HSL) production was undetectable in the bpeAB-null mutant and strains which overexpress bpeR. The failure of these strains to produce acyl-HSLs seemed to be at the level of synthesis of acyl-HSLs, as growth-phase-dependent expression of the autoinducer synthase BpsI was abolished in the bpeAB-null mutant. bpsI expression remained growth phase dependent in the bpeR mutant which had functional BpeAB-OprB. BpeAB-OprB function is likewise necessary for optimal production of quorum-sensing-controlled virulence factors such as siderophore and phospholipase C and for biofilm formation. Cell invasion and cytotoxicity towards human lung epithelial (A549) and human macrophage (THP-1) cells were also significantly attenuated in both the bpeAB mutant and bpeR-overexpressing strains, thus suggesting the possibility of attenuating B. pseudomallei virulence using inhibitors of the BpeAB-OprB efflux pump.     

Genome-Wide Comparative Analysis Reveals Similar Types of NBS Genes in Hybrid Citrus sinensis Genome and Original Citrus clementine Genome and Provides New Insights into Non-TIR NBS Genes

In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.     

Exploitation of host signaling pathways by microbial quorum sensing signals

Environmental and commensal microbes that live within, on and around us have an enormous impact on human health. Recent progress in studies of prokaryotic interplay as well as host-bacteria interactions suggests that secreted microbial products, including quorum sensing signals (QSS), are important mediators of these intrakingdom and interkingdom relations. Reports have assigned QSS diverse and sometimes seemingly contradictory effects on mammalian cell physiology ranging from either blunting of the immune response or exerting pro-inflammatory activities to inducing cellular stress pathways and ultimately apoptosis. Thus, it is still unclear whether microbes utilize QSS to establish and maintain infections via modulation of host signaling pathways or if the eukaryotic host uses the conserved microbial QSS structures as molecular danger beacons to detect and fight infections. Along the same lines exactly how and under what circumstances QSS are detected by host cells remains a mystery, especially considering the distinct chemical properties of the QSS classes with some being small enough to passively diffuse across membranes while others most likely require extracellular recognition mechanisms.     

Determination and Distribution of cry-Type Genes of Bacillus thuringiensis Isolates from Taiwan

Using PCR with a set of specific oligonucleotide primers to detect cryI-type genes, we were able to screen the cry-type genes of 225 Bacillus thuringiensis soil isolates from Taiwan without much cost in time or labor. Some combinations of cry genes (the cry-type profile) in a single isolate were unique. We identified five distinct profiles of crystal genes from the B. thuringiensis soil isolates from Taiwan. The cry genes included cryIA(a), cryIA(b), cryIA(c), cryIC, cryID, and cryIV. Interestingly, 501 B. thuringiensis isolates (93.5% of the total number that we identified) were isolated from areas at high altitudes. The profiles of cry-type genes were distinct in all isolation areas. The distribution of cry-type genes of our isolates therefore depended on geography. Using PCR footprinting to detect cryIC-type genes, we identified two distinct cryIC footprints from some of our isolates, indicating that these isolates may contain novel cryIC-type genes. B. thuringiensis isolates containing cryIA(a)-, cryIA(b)-, and cryIA(c)-type genes exhibited much greater activity against Plutella xylostella than did other isolates, indicating that multiple cry-type genes may be used as markers for the prediction of insecticidal activities.     

AGL6-like MADS-box genes are sister to AGL2-like MADS-box genes

AGL6-like genes form one of the major subfamilies of MADS-box genes and are closely related to the AGL2 (Eclass) and SQUA (A-class) subfamilies. In Arabidopsis, AGL6 and AGL13 have been reported from the AGL6 subfamily, and AGL6 controls lateral organ development and flowering time. However, little is known about homologs of these genes in basal angiosperms. We identified new AGL6-like genes from several taxa from gymnosperms, basal angiosperms, monocots, and eudicots. These genes were analyzed together with previously reported AGL6-like genes. Structural analyses showed 1) a one-aa (amino acid) gap in the I-domain in all AGL6-like genes relative to AGL2-like and SQUA-like genes, 2) a seven-aa insertion in the C-domain of genes from asterids, and 3) a one-aa insertion in the C-domain of genes from gymnosperms. Broad phylogenetic analyses strongly showed that AGL6-like genes are sister to AGL2-like genes, and SQUA-like genes are sister to these two groups. The phylogenetic tree of AGL6-like genes generally tracks organismal phylogeny as inferred from multigene data sets; several gene duplications were detected in angiosperms (e.g., within Magnoliales), and one duplication was detected in gymnosperms. We hypothesize that the split between AGL6-like and AGL2-like genes occurred at least 290–309.2 mya based on our phylogenetic tree and the fossil record.     

Codon Usage in Brassica Genes

We have examined codon bias in 20 Brassica gene sequences collected from the literature. A comparison with the codon usage profile derived from 207 plant genes showed that Brassica genes distinctly differ from the plant genes with respect to Gly, Asp, Arg, lie, Try, Thr, Leu and Gin. Codon preferences for various amino acids did not differ among the three Brassica species, B. napus, B. oleracea and B. campestris considered in the present analysis. G ending codons for Thr, Ala, Pro and Ser are avoided by Brassica genes as in plant genes, in general. However, the avoidance of CG and TA doublets in Brassica genes is less than that observed in plant genes.     

Function of the aux and rol genes of the Ri plasmid in plant cell division in vitro

Auxin-autonomous growth in vitro may be related to the integration and expression of the aux and rol genes from the root-inducing (Ri) plasmid in plant cells infected by agropine-type Agrobacterium rhizogenes. To elucidate the functions of the aux and rol genes in plant cell division, plant cell lines transformed with the aux1 and aux2 genes or with the rolABCD genes were established using tobacco (Nicotiana tabacum) Bright Yellow-2 (BY-2) cells. The introduction of the aux1 and aux2 genes enabled the auxin-autonomous growth of BY-2 cells, but the introduction of the rolABCD genes did not affect the auxin requirement of the BY-2 cells. The results clearly show that the aux genes are necessary for auxinautotrophic cell division, and that the rolABCD genes are irrelevant in auxin autotrophy.Key words: Agrobacterium rhizogenes, auxin-autotrophic cell, auxin biosynthesis, hairy root, plant cell division, Ri plasmid, T-DNA, aux, rol, tobacco BY-2 cells     

Application of Quasi-Steady-State Methods to Nonlinear Models of Intracellular Transport by Molecular Motors

Molecular motors such as kinesin and dynein are responsible for transporting material along microtubule networks in cells. In many contexts, motor dynamics can be modelled by a system of reaction–advection–diffusion partial differential equations (PDEs). Recently, quasi-steady-state (QSS) methods have been applied to models with linear reactions to approximate the behaviour of the full PDE system. Here, we extend this QSS reduction methodology to certain nonlinear reaction models. The QSS method relies on the assumption that the nonlinear binding and unbinding interactions of the cellular motors occur on a faster timescale than the spatial diffusion and advection processes. The full system dynamics are shown to be well approximated by the dynamics on the slow manifold. The slow manifold is parametrized by a single scalar quantity that satisfies a scalar nonlinear PDE, called the QSS PDE. We apply the QSS method to several specific nonlinear models for the binding and unbinding of molecular motors, and we use the resulting approximations to draw conclusions regarding the parameter dependence of the spatial distribution of motors for these models.     

A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: Osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)

One common goal in evolutionary biology is the identification of genes underlying adaptive traits of evolutionary interest. Recently next-generation sequencing techniques have greatly facilitated such evolutionary studies in species otherwise depauperate of genomic resources. Kangaroo rats (Dipodomys sp.) serve as exemplars of adaptation in that they inhabit extremely arid environments, yet require no drinking water because of ultra-efficient kidney function and osmoregulation. As a basis for identifying water conservation genes in kangaroo rats, we conducted a priori bioinformatics searches in model rodents (Mus musculus and Rattus norvegicus) to identify candidate genes with known or suspected osmoregulatory function. We then obtained 446,758 reads via 454 pyrosequencing to characterize genes expressed in the kidney of banner-tailed kangaroo rats (Dipodomys spectabilis). We also determined candidates a posteriori by identifying genes that were overexpressed in the kidney. The kangaroo rat sequences revealed nine different a priori candidate genes predicted from our Mus and Rattus searches, as well as 32 a posteriori candidate genes that were overexpressed in kidney. Mutations in two of these genes, Slc12a1 and Slc12a3, cause human renal diseases that result in the inability to concentrate urine. These genes are likely key determinants of physiological water conservation in desert rodents.