The evolutionary history of Sium sensu lato (Apiaceae): dispersal, vicariance, and domestication as inferred from ITS rDNA phylogeny

The biogeographic history of Sium sensu lato (s.l.) (including Sium sensu stricto [s.s.], Afrocarum, and Berula) was inferred using a nuclear rDNA ITS sequence phylogeny and dispersal-vicariance analysis. One hundred accessions were analyzed, including 86 specimens of Sium s.l., representing all taxa throughout their geographical range. The phylogenetic analyses showed that Afrocarum and the African and St. Helena species of Sium were nested within Berula forming the Berula s.l. clade. The remaining species of Sium constituted a weakly supported Sium s.s. clade. The cultivated S. sisarum is closely related to the western Asian S. sisaroideum. The divergence of Sium s.s. from Berula s.l., estimated under the assumption of a molecular clock and using a substitution rate of 0.61% per million years, took place around 10.4 million years ago. Dispersal-vicariance analysis suggested that the biogeographic pattern of this group resulted from simple vicariance and eventual migration to adjacent areas rather than from long-distance dispersal. The ancestral area of Sium s.l. was probably western Palearctic. The dispersal of Berula to North America occurred ca. 3 million years ago, possibly by island hopping. The migration of S. suave to North America took place ca 0.6 million years ago through Beringia.     

Expression of genes coding for GerA and GerK spore germination receptors is dependent on the protein phosphatase PrpE

The ability of Bacillus subtilis to form spores is a strategy for survival under unfavorable environmental conditions. It is equally crucial to break spore dormancy and return to vegetative growth at the appropriate time. Here we present data showing that the PrpE phosphatase is involved in the control of expression of genes coding for GerA receptors, which are necessary for L-alanine-induced spore germination. Moreover, PrpE is also involved in aspartic acid, glucose, fructose, and potassium (AGFK)-induced spore germination by controlling expression of genes coding for GerK receptors. In the absence of PrpE, the production of spores was essentially normal. However, L-alanine-induced spore germination and, to a lesser extent, the AGFK-induced pathway were abolished. In contrast, the germination pathway dependent on Ca2+-dipicolinate or dodecylamine remained intact. A protein phosphatase PrpE-green fluorescent protein fusion was localized to the prespore and to the dormant spore, consistent with a role in controlling expression of genes coding for GerA receptors. We propose that PrpE is an important element in a signal transduction pathway in Bacillus subtilis that controls the expression of genes coding for germination receptors.     

Interference between Streptococcus pneumoniae and Staphylococcus aureus: In vitro hydrogen peroxide-mediated killing by Streptococcus pneumoniae

The bactericidal activity of Streptococcus pneumoniae toward Staphylococcus aureus is mediated by hydrogen peroxide. Catalase eliminated this activity. Pneumococci grown anaerobically or genetically lacking pyruvate oxidase (SpxB) were not bactericidal, nor were nonpneumococcal streptococci. These results provide a possible mechanistic explanation for the interspecies interference observed in epidemiologic studies.     

Detecting molecular interactions that stabilize native bovine rhodopsin

Using single-molecule force spectroscopy we probed molecular interactions within native bovine rhodopsin and discovered structural segments of well-defined mechanical stability. Highly conserved residues among G protein-coupled receptors were located at the interior of individual structural segments, suggesting a dual role for these segments in rhodopsin. Firstly, structural segments stabilize secondary structure elements of the native protein, and secondly, they position and hold the highly conserved residues at functionally important environments. Two main classes of force curves were observed. One class corresponded to the unfolding of rhodopsin with the highly conserved Cys110-Cys187 disulfide bond remaining intact and the other class corresponded to the unfolding of the entire rhodopsin polypeptide chain. In the absence of the Cys110-Cys187 bond, the nature of certain molecular interactions within folded rhodopsin was altered. These changes highlight the structural importance of this disulfide bond and may form the basis of dysfunctions associated with its absence.     

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.     

Mitochondrial ion channels

Ion channels are proteins, which facilitate the ions flow throught biological membranes. In recent years the structure as well as the function of the plasma membrane ion channels have been well investigated. The knowledge of intracellular ion channels however is still poor. Up till now, the calcium channel described in endoplasmatic reticulum and mitochondrial porine are the examples of intracellular ion channels, which have been well characterized. The mitochondrial potassium channels: regulated by ATP (mitoK(ATP)) and of big conductance activated by Ca2+ (mitoBK(Ca)), which were described in inner mitochondrial membrane, play a key role in the protection of heart muscle against ischemia. In this review the last date concerning the mitochondrial ion channels as well as they function in cell metabolism have been presented.     

Interactions between Subunits in Heterodimeric Ncd Molecules

The nonprocessive minus-end-directed kinesin-14 Ncd is involved in the organization of the microtubule (MT) network during mitosis. Only one of the two motor domains is involved in the interaction with the MT. The other head is tethered to the bound one. Here we prepared, purified, and characterized mutated Ncd molecules carrying point mutations in one of the heads, thus producing heterodimeric motors. The mutations tested included substitutions in Switch I and II: R552A, E585A, and E585D; the decoupling mutant N600K; and a deletion in the motor domain in one of the subunits resulting in a single-headed molecule (NcN). These proteins were isolated by two sequential affinity chromatography steps, followed by measurements of their affinities to MT, enzymatic properties, and the velocity of the microtubule gliding test in vitro. A striking observation is a low affinity of the single-headed NcN for MT both without nucleotides and in the presence of 5′-adenylyl-β,γ-imidodiphosphate, implying that the tethered head has a profound effect on the structure of the Ncd-MT complex. Mutated homodimers had no MT-activated ATPase and no motility, whereas NcN had motility comparable with that of the wild type Ncd. Although the heterodimers had one fully active and one inactive head, the ATPase and motility of Ncd heterodimers varied dramatically, clearly demonstrating that interactions between motor domains exist in Ncd. We also show that the bulk property of dimeric proteins that interact with the filament with only one of its heads depends also on the distribution of the filament-interacting subunits.     

Intragenic complementation at the Lotus japonicus CELLULOSE SYNTHASE-LIKE D1 locus rescues root hair defects

Root hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In legumes, they are typically the first cells to become infected by nitrogen-fixing soil bacteria during root nodule symbiosis. Here, we report a role for the CELLULOSE SYNTHASE-LIKE D1 (CSLD1) gene in root hair development in the legume species Lotus japonicus. CSLD1 belongs to the cellulose synthase protein family that includes cellulose synthases and cellulose synthase-like proteins, the latter thought to be involved in the biosynthesis of hemicellulose. We describe 11 Ljcsld1 mutant alleles that impose either short (Ljcsld1-1) or variable (Ljcsld1-2 to 11) root hair length phenotypes. Examination of Ljcsld1-1 and one variable-length root hair mutant, Ljcsld1-6, revealed increased root hair cell wall thickness, which in Ljcsld1-1 was significantly more pronounced and also associated with a strong defect in root nodule symbiosis. Lotus japonicus plants heterozygous for Ljcsld1-1 exhibited intermediate root hair lengths, suggesting incomplete dominance. Intragenic complementation was observed between alleles with mutations in different CSLD1 domains, suggesting CSLD1 function is modular and that the protein may operate as a homodimer or multimer during root hair development.

Intragenic complementation reveals that Lotus japonicus CELLULOSE SYNTHASE-LIKE D1 multimers facilitate root hair development.     

Two translation products of Yersinia yscQ assemble to form a complex essential to type III secretion

The bacterial flagellar C-ring is composed of two essential proteins, FliM and FliN. The smaller protein, FliN, is similar to the C-terminus of the larger protein, FliM, both being composed of SpoA domains. While bacterial type III secretion (T3S) systems encode many proteins in common with the flagellum, they mostly have a single protein in place of FliM and FliN. This protein resembles FliM at its N-terminus and is as large as FliM but is more like FliN at its C-terminal SpoA domain. We have discovered that a FliN-sized cognate indeed exists in the Yersinia T3S system to accompany the FliM-sized cognate. The FliN-sized cognate, YscQ-C, is the product of an internal translation initiation site within the locus encoding the FliM-sized cognate YscQ. Both intact YscQ and YscQ-C were found to be required for T3S, indicating that the internal translation initiation site, which is conserved in some but not all YscQ orthologs, is crucial for function. The crystal structure of YscQ-C revealed a SpoA domain that forms a highly intertwined, domain-swapped homodimer, similar to those observed in FliN and the YscQ ortholog HrcQ(B). A single YscQ-C homodimer associated reversibly with a single molecule of intact YscQ, indicating conformational differences between the SpoA domains of intact YscQ and YscQ-C. A "snap-back" mechanism suggested by the structure can account for this. The 1:2 YscQ-YscQ-C complex is a close mimic of the 1:4 FliM-FliN complex and the likely building block of the putative Yersinia T3S system C-ring.     

Universal Algorithm for Identification of Fractional Brownian Motion. A?Case of Telomere Subdiffusion

We present a systematic statistical analysis of the recently measured individual trajectories of fluorescently labeled telomeres in the nucleus of living human cells. The experiments were performed in the U2OS cancer cell line. We propose an algorithm for identification of the telomere motion. By expanding the previously published data set, we are able to explore the dynamics in six time orders, a task not possible earlier. As a result, we establish a rigorous mathematical characterization of the stochastic process and identify the basic mathematical mechanisms behind the telomere motion. We find that the increments of the motion are stationary, Gaussian, ergodic, and even more chaotic—mixing. Moreover, the obtained memory parameter estimates, as well as the ensemble average mean square displacement reveal subdiffusive behavior at all time spans. All these findings statistically prove a fractional Brownian motion for the telomere trajectories, which is confirmed by a generalized p-variation test. Taking into account the biophysical nature of telomeres as monomers in the chromatin chain, we suggest polymer dynamics as a sufficient framework for their motion with no influence of other models. In addition, these results shed light on other studies of telomere motion and the alternative telomere lengthening mechanism. We hope that identification of these mechanisms will allow the development of a proper physical and biological model for telomere subdynamics. This array of tests can be easily implemented to other data sets to enable quick and accurate analysis of their statistical characteristics.