Stability of the Plasmodium falciparum AMA1-RON2 Complex Is Governed by the Domain II (DII) Loop

Plasmodium falciparum is an obligate intracellular protozoan parasite that employs a highly sophisticated mechanism to access the protective environment of the host cells. Key to this mechanism is the formation of an electron dense ring at the parasite-host cell interface called the Moving Junction (MJ) through which the parasite invades. The MJ incorporates two key parasite components: the surface protein Apical Membrane Antigen 1 (AMA1) and its receptor, the Rhoptry Neck Protein (RON) complex, the latter one being targeted to the host cell membrane during invasion. Crystal structures of AMA1 have shown that a partially mobile loop, termed the DII loop, forms part of a deep groove in domain I and overlaps with the RON2 binding site. To investigate the mechanism by which the DII loop influences RON2 binding, we measured the kinetics of association and dissociation and binding equilibria of a PfRON2sp1 peptide with both PfAMA1 and an engineered form of PfAMA1 where the flexible region of the DII loop was replaced by a short Gly-Ser linker (ΔDII-PfAMA1). The reactions were tracked by fluorescence anisotropy as a function of temperature and concentration and globally fitted to acquire the rate constants and corresponding thermodynamic profiles. Our results indicate that both PfAMA1 constructs bound to the PfRON2sp1 peptide with the formation of one intermediate in a sequential reversible reaction: A↔B↔C. Consistent with Isothermal Titration Calorimetry measurements, final complex formation was enthalpically driven and slightly entropically unfavorable. Importantly, our experimental data shows that the DII loop lengthened the complex half-life time by 18-fold (900 s and 48 s at 25°C for Pf and ΔDII-Pf complex, respectively). The longer half-life of the Pf complex appeared to be driven by a slower dissociation process. These data highlight a new influential role for the DII loop in kinetically locking the functional binary complex to enable host cell invasion.     

Major plant communities of the Carson Desert (Nevada), North America's coldest and driest desert

This paper describes the vegetation of the Carson Desert (Nevada, USA) based on a phytosociological analysis of its major plant associations, as determined by the Braun-Blanquet method. Diagnostic tables, climatic, edaphic, and biogeographical data were used to establish floristic affinities among identified plant communities and to interpret their distributions in zonal gradients. Their syntaxonomic positions in the classes Allenrolfeetea occidentalis and Artemisio tridentatae–Juniperetea osteospermae, and in the new class Sarcobatetea vermiculati were also established. Three associations (Atriplici confertifoliae–Sarcobatetum baileyi, Atriplici canescentis–Psorothamnetum polydenii, and Suaedo moquinii–Sarcobatetum vermiculati) are described here for the first time along with the order Sarcobatetalia vermiculati and the alliance Sarcobation vermiculati.     

Pseudocrossidium replicatum (Taylor) R.H. Zander is a fully desiccation-tolerant moss that expresses an inducible molecular mechanism in response to severe abiotic stress

Plant Molecular Biology - The moss Pseudocrossidium replicatum is a desiccation-tolerant species that uses an inducible system to withstand severe abiotic stress in both protonemal and gametophore...     

Environmental and social cues can be used in combination to develop sustainable breeding techniques for goat reproduction in the subtropics

Goat breeds from subtropical latitudes show different annual reproductive cycles. Some of them display large seasonal variations in their annual breeding season, while others display a moderate seasonality or sexual activity all year round. This reproductive seasonality causes seasonality of milk, cheese and meat productions and, as a consequence, induces wide variation in producer incomes. To solve this problem and provide methods allowing producers to breed animals during the anestrous period and stabilize production all year round, it is necessary to have a deep knowledge of their annual sexual activity and to identify the environmental factors controlling the timing of the annual reproductive cycle. Then, it is possible to build on these knowledge sustainable breeding techniques adapted to the environmental, economic and social characteristics of the local breeding system. In this review, I will illustrate this strategy through the example of our experiments in subtropical goats. First, we determined the characteristics of the annual breeding season in both male and female goats. Second, we identified the photoperiod as the major environmental factor controlling the timing of this annual breeding season. Third, we used the photoperiod to stimulate indirectly the sexual behavior of does. Indeed, we used photoperiodic treatments to stimulate the sexual activity of bucks during the non-breeding season. These sexually active male goats were then used to induce and synchronize the estrous behavior and ovulatory activity of anestrous females in confined or grazing conditions by using the 'male effect'. Under subtropical conditions, these results constitute an original manner to control the reproductive activity of local goats using the photoperiod combined with the 'male effect.'     

Refractoriness to short and long days determines the end and onset of the breeding season in subtropical goats

The objective was to determine whether refractoriness to short and long days were involved in the end and onset of the breeding season, respectively, in goats adapted to subtropical latitudes. Ovariectomized does given a subcutaneous implant constantly releasing estradiol-l7 β (OVX+E) were used in two experiments. Plasma LH concentrations were determined twice weekly. In Experiment 1, the control group remained in an open-shed pen (natural day length and ambient temperature). Two experimental groups were placed in light-proof buildings (with natural temperature variations). One group was exposed to natural simulated increasing days (winter to spring), whereas the other was exposed to a winter solstice photoperiod (10 h of light) from December 21 to April 28. In Experiment 2, the control group remained under natural day length and ambient temperature. One experimental group was exposed to natural simulated decreasing days (summer to autumn), whereas the other group was exposed to a summer solstice photoperiod (14 h of light) from June 21 to October 20. In Experiment 1, the breeding season was not prolonged in does maintained in the winter solstice day length. Mean dates of decrease in LH secretion (end of the breeding season) did not differ significantly between does exposed to natural (February 3 ± 5 d) or natural simulated photoperiod (January 26 ± 14 d) and those exposed to constant short days of winter solstice (February 4 ± 10 d). In Experiment 2, the onset of the breeding season was not delayed in does maintained in the summer solstice day length. Mean dates of increase in LH secretion (onset of the breeding season) did not differ significantly between does exposed to natural (September 7 ± 8 d) or natural simulated photoperiod (September 18 ± 10 d) and those exposed to constant long days photoperiod of summer solstice (September 24 ± 4 d). In goats adapted to a subtropical environment, we concluded that: 1) the end of breeding season was due to refractoriness to short days, and not the inhibitory effect of increasing day length; and 2) the onset of the breeding season was due to refractoriness to long days, and not a stimulatory effect of decreasing day length.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

Substrata mechanical stiffness can regulate adhesion of viable bacteria

The competing mechanisms that regulate adhesion of bacteria to surfaces and subsequent biofilm formation remain unclear, though nearly all studies have focused on the role of physical and chemical properties of the material surface. Given the large monetary and health costs of medical-device colonization and hospital-acquired infections due to bacteria, there is considerable interest in better understanding of material properties that can limit bacterial adhesion and viability. Here we employ weak polyelectrolyte multilayer (PEM) thin films comprised of poly(allylamine) hydrochloride (PAH) and poly(acrylic acid) (PAA), assembled over a range of conditions, to explore the physicochemical and mechanical characteristics of material surfaces controlling adhesion of Staphylococcus epidermidis bacteria and subsequent colony growth. Although it is increasingly appreciated that eukaryotic cells possess subcellular structures and biomolecular pathways to sense and respond to local chemomechanical environments, much less is known about mechanoselective adhesion of prokaryotes such as these bacteria. We find that adhesion of viable S. epidermidis correlates positively with the stiffness of these polymeric substrata, independently of the roughness, interaction energy, and charge density of these materials. Quantitatively similar trends observed for wild-type and actin analogue mutant Escherichia coli suggest that these results are not confined to only specific bacterial strains, shapes, or cell envelope types. These results indicate the plausibility of mechanoselective adhesion mechanisms in prokaryotes and suggest that mechanical stiffness of substrata materials represents an additional parameter that can regulate adhesion of and subsequent colonization by viable bacteria.     

Host-specific effect of P1 exchange between two potyviruses

The potyviruses Plum pox virus (PPV) and Tobacco vein mottling virus (TVMV) have distinct host ranges and induce different symptoms in their common herbaceous hosts. To test the relevance of the P1 protein in host compatibility and pathogenicity, hybrid viruses were constructed in which the P1 coding sequence of PPV was completely or partially replaced by the corresponding sequences from TVMV. Infections induced by these chimeric viruses revealed that the TVMV P1 and a PPV/TVMV hybrid P1 proteins are functionally equivalent in herbaceous plants to the P1 protein of a PPV isolate adapted to these hosts, in spite of having high sequence divergence. Moreover, the presence of TVMV P1 sequences enhanced the competence of a low-infectivity PPV-D-derived chimera in Nicotiana clevelandii . Conversely, all PPV/TVMV hybrids were unable to infect Prunus persicae , a specific host for PPV, suggesting that TVMV P1 is not functionally competent in this plant. Together, these data highlight the importance of the P1 protein in defining the virus host range.