Phylogeny of the Carnivora (Mammalia): Congruence vs Incompatibility among Multiple Data Sets

The purpose of this study was to determine the higher-level phylogenetic relationships among Carnivora, using a conditional data combination (CDC) approach to analyzing multiple data sets. New nucleotide sequences (851 base pairs from intron I of the transthyretin gene) among 22 representatives of the 11 families of Carnivora were generated and analyzed in concert with, and comparison to, other mitochondrial and morphological character data. Conditional data combination analyses of the four independent data sets (transthyretin intron I, cytochromeb,partial 12S rRNA, and morphology) indicate that the phylogenetic results derived from each generally agree, with two exceptions. The first exception, signal heterogeneity in comparisons involving transthyretin and morphology, provides an example where phylogenetic conclusions drawn from total evidence analyses may differ from conclusions drawn from CDC analyses. The second exception demonstrates that while a CDC method may reject the null hypothesis of homogeneity for a particular partition, including that partition in combined analyses, may nevertheless provide an overall increase in phylogenetic signal, in terms of nodal support for most associations, without altering the topology derived from the combined homogeneous data partitions. Phylogenetic reconstruction among the feliform families supports a sister-group relationship between the hyaenas (Hyaenidae) and mongooses (Herpestidae) and places the African palm civet (Nandinia) as basal to all other living Feliformia. Among the caniform families, CDC analyses strongly support the previously enigmatic red panda (Ailurus) as a monotypic lineage that is sister to Musteloideasensu stricto(mustelids plus procyonids), in addition to pinniped monophyly and a sister-group relationship between the walrus and sea lions.     

Compound genetic ablation of nidogen 1 and 2 causes basement membrane defects and perinatal lethality in mice

Nidogen 1 and 2 are basement membrane glycoproteins, and previous biochemical and functional studies indicate that they may play a crucial role in basement membrane assembly. While they show a divergent expression pattern in certain adult tissues, both have a similar distribution during development. Gene knockout studies in mice demonstrated that the loss of either isoform has no effect on basement membrane formation and organ development, suggesting complementary functions. Here, we show that this is indeed the case. Deficiency of both nidogens in mice resulted in perinatal lethality. Nidogen 1 and 2 do not appear to be crucial in establishing tissue architecture during organ development; instead, they are essential for late stages of lung development and for maintenance and/or integrity of cardiac tissue. These organ defects are not compatible with postnatal survival. Ultrastructural analysis suggests that the phenotypes directly result from basement membrane changes. However, despite the ubiquitous presence of nidogens in basement membranes, defects do not occur in all tissues or in all basement membranes, suggesting a varying spectrum of roles for nidogens in the basement membrane.     

Photosynthesis in dynamic light: systems biology of unconventional chlorophyll fluorescence transients in Synechocystis sp. PCC 6803

Photosynthetic organisms live in a dynamic environment where light typically fluctuates around a mean level that is slowly drifting during the solar day. We show that the far-from-equilibrium photosynthesis occurring in a rapidly fluctuating light differs vastly from the stationary-flux photosynthesis attained in a constant or slowly drifting light. Photosynthetic organisms in a static or slowly drifting light can be characterized by a steady-state quantum yield of chlorophyll fluorescence emission F′ that is changing linearly with small and slow variations of the incident irradiance I+ΔI(t): F′(I+ΔI(t))≈ F_mean^′(dF)/(dI)·ΔI(t). In Synechocystis sp. PCC 6803, the linear approximation holds for an extended interval covering largely the static irradiance range experienced by the cyanobacteria in nature. The photosynthetic dynamism and, consequently, the dynamism of the chlorophyll fluorescence emission change dramatically when exposing the organism to a fluctuating irradiance. Harmonically-modulated irradiance I+ΔI · sin(2πt/T), T ≈ 1–25 s induces perpetual, far-from-equilibrium forced oscillations that are strongly non-linear, exhibiting significant hysteresis with multiple fluorescence levels corresponding to a single instantaneous level of the incident irradiance. We propose that, in nature, the far-from-equilibrium dynamic phenomena represent a significant correction to the steady-state photosynthetic activity that is typically investigated in laboratory. Analysis of the forced oscillations by the tools of systems biology suggests that the dynamism of photosynthesis observed in fluctuating light can be explained by a delayed action of regulatory agents.     

Light-dependent modification of Photosystem II in spinach leaves

In dark-adapted spinach leaves approximately one third of the Photosystem II (PS II) reaction centers are impaired in their ability to transfer electrons to Photosystem I. Although these inactive PS II centers are capable of reducing the primary quinone acceptor, Q_A, oxidation of Q_A ^– occurs approximately 1000 times more slowly than at active centers. Previous studies based on dark-adapted leaves show that minimal energy transfer occurs from inactive centers to active centers, indicating that the quantum yield of photosynthesis could be significantly impaired by the presence of inactive centers. The objective of the work described here was to determine the performance of inactive PS II centers in light-adapted leaves. Measurements of PS II activity within leaves did not indicate any increase in the concentration of active PS II centers during light treatments between 10 s and 5 min, showing that inactive centers are not converted to active centers during light treatment. Light-induced modification of inactive PS II centers did occur, however, such that 75% of these centers were unable to sustain stable charge separation. In addition, the maximum yield of chlorophyll fluorescence associated with inactive PS II centers decreased substantially, despite the lack of any overall quenching of the maximum fluorescence yield. The effect of light treatment on inactive centers was reversed in the dark within 10–20 mins. These results indicate that illumination changes inactive PS II centers into a form that quenches fluorescence, but does not allow stable charge separation across the photosynthetic membrane. One possibility is that inactive centers are converted into centers that quench fluorescence by formation of a radical, such as reduced pheophytin or oxidized P680. Alternatively, it is possible that inactive PS II centers are modified such that absorbed excitation energy is dissipated thermally, through electron cycling at the reaction center.Abbreviations A518 absorbance change at 518 nm, reflecting the formation of an electric field across the thylakoid membrane - A_FL1 amplitude of the fast (<100 ms) phase of A518 induced by the first of two saturating, single-turnover flashes spaced 30 ms apart - A_FL2 amplitude of the fast (<100 ms) phase of A518 induced by the second of two saturating, single-turnover flashes spaced 50 ms apart - DCBQ 2,6-dichloro-p-benzoquinone - Fo yield of chlorophyll fluorescence when Q_A is fully oxidized - Fm yield of chlorophyll fluorescence when Q_A is fully reduced - Fx yield of chlorophyll fluorescence when Q_A is fully reduced at inactive PS II centers, but fully oxidized at active PS II centers - Pheo pheophytin - P680 the primary donor of Photosystem II - PPFD photosynthetic photon flux density - Q_A Primary quinone acceptor of PS II - Q_B secondary quinone acceptor of PS II     

Direct Evidence of Plant-pathogenic Activity of Fungal Metabolites of Trichothecium roseum on Apple

Apples were exposed to various concentrations of roseotoxins – metabolites of Trichothecium roseum and kinetic fluorescence imaging was used to detect the area influenced by the phytotoxin. Contrast was quantified within these images between the areas exposed to roseotoxins and the untreated areas. It was proved that roseotoxin B is able to penetrate apple peel and produce chlorotic lesions. Activity of roseotoxin B is similar as the activity of destruxins, host specific phytotoxins of Alternaria brassicae parasitic on canola.     

E-photosynthesis: web-based platform for modeling of complex photosynthetic processes

E-photosynthesis framework is a web-based platform for modeling and analysis of photosynthetic processes. Compared to its earlier version, the present platform employs advanced software methods and technologies to support an effective implementation of vastly diverse kinetic models of photosynthesis. We report on the first phase implementation of the tool new version and demonstrate the functionalities of model visualization, presentation of model components, rate constants, initial conditions and of model annotation. The demonstration also includes export of a model to the Systems Biology Markup Language format and remote numerical simulation of the model.     

High resolution analysis of the chromatin landscape of the IgE switch region in human B cells

Antibodies are assembled by a highly orchestrated series of recombination events during B cell development. One of these events, class switch recombination, is required to produce the IgG, IgE and IgA antibody isotypes characteristic of a secondary immune response. The action of the enzyme activation induced cytidine deaminase is now known to be essential for the initiation of this recombination event. Previous studies have demonstrated that the immunoglobulin switch regions acquire distinct histone modifications prior to recombination. We now present a high resolution analysis of these histone modifications across the IgE switch region prior to the initiation of class switch recombination in primary human B cells and the human CL-01 B cell line. These data show that upon stimulation with IL-4 and an anti-CD40 antibody that mimics T cell help, the nucleosomes of the switch regions are highly modified on histone H3, accumulating acetylation marks and tri-methylation of lysine 4. Distinct peaks of modified histones are found across the switch region, most notably at the 5' splice donor site of the germline (I) exon, which also accumulates AID. These data suggest that acetylation and K4 tri-methylation of histone H3 may represent marks of recombinationally active chromatin and further implicates splicing in the regulation of AID action.     

Strategies of ultraviolet-B protection in microscopic algae

Different species of microalgae show a wide range of susceptibility to ultraviolet-B (UV-B) radiation. To identify factors responsible for the UV-B tolerance of some of the algae, we compared 8 species that are highly tolerant to UV-B to 8 species that are highly susceptible. The tolerant species contained substantial amounts of an acetolysis-resistant residue. The residue consists of sporopollenin, a biopolymer of variable chemical composition that occurs in the algal cell walls and absorbs UV-B radiation. The susceptible species contained little or no sporopollenin. We propose that sporopollenin provides protection to the tolerant species by screening the incident UV-B radiation. Previous studies showed that the mycosporine-like amino acids (MAA) also act as effective UV-B screens. Our data indicate that sporopollenin provides a constant protection while MAA are induced by radiation stress and occur with some delay. The tolerant species also differ from the susceptible species in their capacity to repair the reaction centers damaged by UV-B. The tolerant algae became vulnerable to UV-B when protein synthesis needed for repair was blocked by streptomycin. In the susceptible species, streptomycin had no effect during the UV-B stress. The repair deficiency in the susceptible species can be explained either by relatively less effective protein synthesis or by an inhibition of the protein synthesis by UV-B. In the tolerant species, the structures needed for protein synthesis are protected by UV-B screening of sporopollenin and MAA.     

Conventional and combinatorial chlorophyll fluorescence imaging of tobamovirus-infected plants

We compared by chlorophyll (Chl) fluorescence imaging the effects of two strains of the same virus (Italian and Spanish strains of the Pepper mild mottle virus — PMMoV-I and-S, respectively) in the host plant Nicotiana benthamiana. The infection was visualized either using conventional Chl fluorescence parameters or by an advanced statistical approach, yielding a combinatorial set of images that enhances the contrast between control and PMMoV-infected plants in the early infection steps. Among the conventional Chl fluorescence parameters, the non-photochemical quenching parameter NPQ was found to be an effective PMMoV infection reporter in asymptomatic leaves of N. benthamiana, detecting an intermediate infection phase. The combinatorial imaging revealed the infection earlier than any of the standard Chl fluorescence parameters, detecting the PMMoV-S infection as soon as 4 d post-inoculation (dpi), and PMMoV-I infection at 6 dpi; the delay correlates with the lower virulence of the last viral strain.