Evolutionary placement of Xanthomonadales based on conserved protein signature sequences

Xanthomonadales comprises one of the largest phytopathogenic bacterial groups, and is currently classified within the gamma-proteobacteria. However, the phylogenetic placement of this group is not clearly resolved, and the results of different studies contradict one another. In this work, the evolutionary position of Xanthomonadales was determined by analyzing the presence of shared insertions and deletions (INDELs) in highly conserved proteins. Several distinctive insertions found in most of the members of the gamma-proteobacteria are absent in Xanthomonadales and groups such as Legionelalles, Chromatiales, Methylococcales, Thiotrichales and Cardiobacteriales. These INDELs were most likely introduced after the branching of Xanthomonadales from most of the gamma-proteobacteria and provide evidence for the phylogenetic placement of the early gamma-proteobacteria. Moreover, other proteins contain insertions exclusive to the Xanthomonadales order, confirming that this is a monophyletic group and provide important specific genetic markers. Thus, the data presented clearly support the Xanthomonadales group as an independent subdivision, and constitute one of the deepest branching lineage within the gamma-proteobacteria clade.     

Nucleocytoplasmic traffic of CPEB1 and accumulation in Crm1 nucleolar bodies

The translational regulator CPEB1 plays a major role in the control of maternal mRNA in oocytes, as well as of subsynaptic mRNAs in neurons. Although mainly cytoplasmic, we found that CPEB1 protein is continuously shuttling between nucleus and cytoplasm. Its export is controlled by two redundant NES motifs dependent on the nuclear export receptor Crm1. In the nucleus, CPEB1 accumulates in a few foci most often associated with nucleoli. These foci are different from previously identified nuclear bodies. They contain Crm1 and were called Crm1 nucleolar bodies (CNoBs). CNoBs depend on RNA polymerase I activity, indicating a role in ribosome biogenesis. However, although they form in the nucleolus, they never migrate to the nuclear envelope, precluding a role as a mediator for ribosome export. They could rather constitute a platform providing factors for ribosome assembly or export. The behavior of CPEB1 in CNoBs raises the possibility that it is involved in ribosome biogenesis.     

A Thin-skull Window Technique for Chronic Two-photon In vivo Imaging of Murine Microglia in Models of Neuroinflammation

Traditionally in neuroscience, in vivo two photon imaging of the murine central nervous system has either involved the use of open-skull^1,2 or thinned-skull ³ preparations. While the open-skull technique is very versatile, it is not optimal for studying microglia because it is invasive and can cause microglial activation. Even though the thinned-skull approach is minimally invasive, the repeated re-thinning of skull required for chronic imaging increases the risks of tissue injury and microglial activation and allows for a limited number of imaging sessions. Here we present a chronic thin-skull window method for monitoring murine microglia in vivo over an extended period of time using two-photon microscopy. We demonstrate how to prepare a stable, accessible, thinned-skull cortical window (TSCW) with an apposed glass coverslip that remains translucent over the course of three weeks of intermittent observation. This TSCW preparation is far more immunologically inert with respect to microglial activation than open craniotomy or repeated skull thinning and allows an arbitrary number of imaging sessions during a time period of weeks. We prepare TSCW in CX₃CR₁ GFP/+ mice ⁴ to visualize microglia with enhanced green fluorescent protein to ≤150 μm beneath the pial surface. We also show that this preparation can be used in conjunction with stereotactic brain injections of the HIV-1 neurotoxic protein Tat, adjacent to the TSCW, which is capable of inducing durable microgliosis. Therefore, this method is extremely useful for examining changes in microglial morphology and motility over time in the living brain in models of HIV Associated Neurocognitive Disorder (HAND) and other neurodegenerative diseases with a neuroinflammatory component.     

Resolving the native provenance of invasive fireweed (Senecio madagascariensis Poir.) in the Hawaiian Islands as inferred from phylogenetic analysis

Accurate identification of weedy species is critical to the success of biological control programs seeking host-specific control agents. Phylogenetic relationships based on internal transcribed spacer region (ITS1, ITS2) DNA sequence data were used to elucidate the most likely origin and taxonomic placement of Senecio madagascariensis Poir. (fireweed; Asteraceae) in the Hawaiian archipelago. Putative S. madagascariensis populations from Madagascar, South Africa, Swaziland, and Hawaii were included in the analysis. Different phylogenetic models (maximum parsimony and maximum likelihood) were congruent in suggesting that Hawaiian fireweed is most closely related to populations from the KwaZulu-Natal region in South Africa. Phylogenetic divergence and morphological data (achene characteristics) suggest that the S. madagascariensis complex is in need of revised alpha-level taxonomy. Taxonomic identity of invasive fireweed in Hawaii is important for finding effective biological control agents as native range populations constitute different biotypic variants across a wide geographical area. Based on our phylogenetic results, research directed at biological control of Hawaiian infestations should focus on areas in the KwaZulu-Natal region in South Africa where host-specific natural enemies are most likely to be found. Our results show that phylogeographical analysis is a potential powerful and efficient tool to address questions relevant to invasion biology of plants.     

Intracranial Injection of Adeno-associated Viral Vectors

Intracranial injection of viral vectors engineered to express a fluorescent protein is a versatile labeling technique for visualization of specific subsets of cells in different brain regions both in vivo and in brain sections. Unlike the injection of fluorescent dyes, viral labeling offers targeting of individual cell types and is less expensive and time consuming than establishing transgenic mouse lines. In this technique, an adeno-associated viral (AAV) vector is injected intracranially using stereotaxic coordinates, a micropipette and an automated pump for precise delivery of AAV to the desired area with minimal damage to the surrounding tissue. Injection parameters can be tailored to individual experiments by adjusting the animal age at injection, injection location, volume of injection, rate of injection, AAV serotype and the promoter driving gene expression. Depending on the conditions chosen, virally-induced transgene expression can allow visualization of groups of cells, individual cells or fine cellular processes, down to the level of dendritic spines. The experiment shown here depicts an injection of double-stranded AAV expressing green fluorescent protein for the labeling of neurons and glia in the mouse primary visual cortex.Download video file.^{(51M, mov)}     

A Processed Multidomain Mycoplasma hyopneumoniae Adhesin Binds Fibronectin,Plasminogen, and Swine Respiratory Cilia

Porcine enzootic pneumonia is a chronic respiratory disease that affects swine. The etiological agent of the disease, Mycoplasma hyopneumoniae, is a bacterium that adheres to cilia of the swine respiratory tract, resulting in loss of cilia and epithelial cell damage. A M. hyopneumoniae protein P116, encoded by mhp108, was investigated as a potential adhesin. Examination of P116 expression using proteomic analyses observed P116 as a full-length protein and also as fragments, ranging from 17 to 70 kDa in size. A variety of pathogenic bacterial species have been shown to bind the extracellular matrix component fibronectin as an adherence mechanism. M. hyopneumoniae cells were found to bind fibronectin in a dose-dependent and saturable manner. Surface plasmon resonance was used to show that a recombinant C-terminal domain of P116 bound fibronectin at physiologically relevant concentrations (K_D 24 ± 6 nm). Plasmin(ogen)-binding proteins are also expressed by many bacterial pathogens, facilitating extracellular matrix degradation. M. hyopneumoniae cells were found to also bind plasminogen in a dose-dependent and saturable manner; the C-terminal domain of P116 binds to plasminogen (K_D 44 ± 5 nm). Plasminogen binding was abolished when the C-terminal lysine of P116 was deleted, implicating this residue as part of the plasminogen binding site. P116 fragments adhere to the PK15 porcine kidney epithelial-like cell line and swine respiratory cilia. Collectively these data suggest that P116 is an important adhesin and virulence factor of M. hyopneumoniae.     

Activation of Phenylalanine Hydroxylase Induces Positive Cooperativity toward the Natural Cofactor

Protein misfolding with loss-of-function of the enzyme phenylalanine hydroxylase (PAH) is the molecular basis of phenylketonuria in many individuals carrying missense mutations in the PAH gene. PAH is complexly regulated by its substrate l-Phenylalanine and its natural cofactor 6R-l-erythro-5,6,7,8-tetrahydrobiopterin (BH₄). Sapropterin dihydrochloride, the synthetic form of BH₄, was recently approved as the first pharmacological chaperone to correct the loss-of-function phenotype. However, current knowledge about enzyme function and regulation in the therapeutic setting is scarce. This illustrates the need for comprehensive analyses of steady state kinetics and allostery beyond single residual enzyme activity determinations to retrace the structural impact of missense mutations on the phenylalanine hydroxylating system. Current standard PAH activity assays are either indirect (NADH) or discontinuous due to substrate and product separation before detection. We developed an automated fluorescence-based continuous real-time PAH activity assay that proved to be faster and more efficient but as precise and accurate as standard methods. Wild-type PAH kinetic analyses using the new assay revealed cooperativity of activated PAH toward BH₄, a previously unknown finding. Analyses of structurally preactivated variants substantiated BH₄-dependent cooperativity of the activated enzyme that does not rely on the presence of l-Phenylalanine but is determined by activating conformational rearrangements. These findings may have implications for an individualized therapy, as they support the hypothesis that the patient''s metabolic state has a more significant effect on the interplay of the drug and the conformation and function of the target protein than currently appreciated.     

Tradicional use of medicinal plants with diuretic properties at Quemado de Güines Municipality, Cuba

Medicinal plants are highly rich in Cuba and an amount of 179 species have been reported to be used by the population for diuretic purposes, nevertheless, no experimental validation has supported this effect. This study presents the relative importance of the medicinal plant species most widely used for diuretic purposes in two communities of Quemado de Guines Municipality, Villa Clara province. The information was obtained through the application of an interview to 85 inhabitants, from which 80 were random surveys to people with a great knowledge of plants, and five to herbalists and doctors practicing natural medicine. The etnopharmacological information was registered (gathered) by means of the "Tradicional of the Medicine of the Island" (TRAMIL) methodology and the interesting species were identified by a botanist and deposited in the Herbarium of the Central University "Marta Abreu" from Villa Clara, registered in the Index Herbarium, published periodically by the International Association for Plant Taxonomy. The data was analyzed by means of the indexes of use values and significant use level after TRAMIL. From the total of 19 botanical families, 26 medicinal species were identified, and 10 plants resulted with higher significant use and higher indexes of use values. From the plants reported as diuretics, 53.8% have not been experimentally validated in Cuba, the rest of the identified species have been validated at a preclinical level in some centers in the country, but its use have not been authorized as phytochemicals by the Cuban Regulatory Agency. The documentation related to the use of medicinal plants in the studied areas reveals that the traditional knowledge continues deeply rooted in the communities, and popular wisdom is kept through the representative images of the herbalist and people with considerable knowledge about this topic.     

Targeted manipulation of leaf form via local growth repression

A classical view is that leaf shape is the result of local promotion of growth linked to cell proliferation. However, an alternative hypothesis is that leaf form is the result of local repression of growth in an otherwise growing system. Here we show that leaf form can indeed be manipulated in a directed fashion by local repression of growth. We show that targeting expression of an inhibitor of a cyclin-dependent kinase (KRP1) to the sinus area of developing leaves of Arabidopsis leads to local growth repression and the formation of organs with extreme lobing, including generation of leaflet-like organs. Directing KRP1 expression to other regions of the leaf using an miRNA target sequence tagging approach also leads to predictable novel leaf forms, and repression of growth in the leaf margin blocks the outgrowth of lobes, leading to a smoother perimeter. In addition, we show that decreased growth around the perimeter and across the leaf abaxial surface leads to a change in 3D form, as predicted by mechanical models of leaf growth. Our analysis provides experimental evidence that local repression of growth influences leaf shape, suggesting that it could be part of the mechanism of morphogenesis in plants in the context of an otherwise growing system.