The embryonic leaf identity gene FUSCA3 regulates vegetative phase transitions by negatively modulating ethylene-regulated gene expression in Arabidopsis

Background

Protein kinase CK2 is a pleiotropic serine/threonine protein kinase with hundreds of reported substrates, and plays an important role in a number of cellular processes. The cellular functions of Plasmodium falciparum CK2 (PfCK2) are unknown. The parasite's genome encodes one catalytic subunit, PfCK2??, which we have previously shown to be essential for completion of the asexual erythrocytic cycle, and two putative regulatory subunits, PfCK2??1 and PfCK2??2.

Results

We now show that the genes encoding both regulatory PfCK2 subunits (PfCK2??1 and PfCK2??2) cannot be disrupted. Using immunofluorescence and electron microscopy, we examined the intra-erythrocytic stages of transgenic parasite lines expressing hemagglutinin (HA)-tagged catalytic and regulatory subunits (HA-CK2??, HA-PfCK2??1 or HA-PfCK2??2), and localized all three subunits to both cytoplasmic and nuclear compartments of the parasite. The same transgenic parasite lines were used to purify PfCK2??1- and PfCK2??2-containing complexes, which were analyzed by mass spectrometry. The recovered proteins were unevenly distributed between various pathways, with a large proportion of components of the chromatin assembly pathway being present in both PfCK2??1 and PfCK2??2 precipitates, implicating PfCK2 in chromatin dynamics. We also found that chromatin-related substrates such as nucleosome assembly proteins (Naps), histones, and two members of the Alba family are phosphorylated by PfCK2?? in vitro.

Conclusions

Our reverse-genetics data show that each of the two regulatory PfCK2 subunits is required for completion of the asexual erythrocytic cycle. Our interactome study points to an implication of PfCK2 in many cellular pathways, with chromatin dynamics being identified as a major process regulated by PfCK2. This study paves the way for a kinome-wide interactomics-based approach to elucidate protein kinase function in malaria parasites.     

Nutrient limitation of phytoplankton communities in Subarctic lakes and ponds in Wapusk National Park, Canada

We determined the limiting nutrient of phytoplankton in 21 lakes and ponds in Wapusk National Park, Canada, using nutrient enrichment bioassays to assess the response of natural phytoplankton communities to nitrogen and phosphorus additions. The goal was to determine whether these Subarctic lakes and ponds were nutrient (N or P) limited, and to improve the ability to predict future impacts of increased nutrient loading associated with climate change. We found that 38% of lakes were not limited by nitrogen or phosphorus, 26% were co-limited by N and P, 26% were P-limited and 13% were N-limited. TN/TP, DIN/TP and NO₃ ⁻/TP ratios from each lake were compared to the Redfield ratio to predict the limiting nutrient; however, these predictors only agreed with 29% of the bioassay results, suggesting that nutrient ratios do not provide a true measure of nutrient limitation within this region. The N-limited lakes had significantly different phytoplankton community composition with more chrysophytes and Anabaena sp. compared to all other lakes. N and P limitation of phytoplankton communities within Wapusk National Park lakes and ponds suggests that increased phytoplankton biomass may result in response to increased nutrient loading associated with environmental change.     

Development of a multiplex real-time PCR assay with an internal amplification control for the detection of total and pathogenic Vibrio parahaemolyticus bacteria in oysters

Vibrio parahaemolyticus is an estuarine bacterium that is the leading cause of shellfish-associated cases of bacterial gastroenteritis in the United States. Our laboratory developed a real-time multiplex PCR assay for the simultaneous detection of the thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and thermostable-related hemolysin (trh) genes of V. parahaemolyticus. The tlh gene is a species-specific marker, while the tdh and trh genes are pathogenicity markers. An internal amplification control (IAC) was incorporated to ensure PCR integrity and eliminate false-negative reporting. The assay was tested for specificity against >150 strains representing eight bacterial species. Only V. parahaemolyticus strains possessing the appropriate target genes generated a fluorescent signal, except for a late tdh signal generated by three strains of V. hollisae. The multiplex assay detected <10 CFU/reaction of pathogenic V. parahaemolyticus in the presence of >10(4) CFU/reaction of total V. parahaemolyticus bacteria. The real-time PCR assay was utilized with a most-probable-number format, and its results were compared to standard V. parahaemolyticus isolation methodology during an environmental survey of Alaskan oysters. The IAC was occasionally inhibited by the oyster matrix, and this usually corresponded to negative results for V. parahaemolyticus targets. V. parahaemolyticus tlh, tdh, and trh were detected in 44, 44, and 52% of the oyster samples, respectively. V. parahaemolyticus was isolated from 33% of the samples, and tdh(+) and trh(+) strains were isolated from 19 and 26%, respectively. These results demonstrate the utility of the real-time PCR assay in environmental surveys and its possible application to outbreak investigations for the detection of total and pathogenic V. parahaemolyticus.     

Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage ϕ29 Capsids

The bacteriophage ϕ29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of a portal motor complex. Several mechanical models for the generation of these high forces by the motor complex predict coupling of DNA translocation to rotation of the head-tail connector dodecamer. Putative connector rotation is investigated here by combining the methods of single-molecule force spectroscopy with polarization-sensitive single-molecule fluorescence. In our experiment, we observe motor function in several packaging complexes in parallel using video microscopy of bead position in a magnetic trap. At the same time, we follow the orientation of single fluorophores attached to the portal motor connector. From our data, we can exclude connector rotation with greater than 99% probability and therefore answer a long-standing mechanistic question.     

Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli

Protoplast fusion has been used to combine genes from different organisms to create strains with desired properties. A recently developed variant on this approach, genome shuffling, involves generation of a genetically heterogeneous population of a single organism, followed by recursive protoplast fusion to allow recombination of mutations within the fused protoplasts. These are powerful techniques for engineering of microbial strains for desirable industrial properties. However, there is a prevailing opinion that it will be difficult to use these methods for engineering of Gram-negative bacteria because the outer membrane makes protoplast fusion more difficult. Here we describe the successful use of protoplast fusion in Escherichia coli. Using two auxotrophic strains of E. coli, we obtained prototrophic strains by recombination in fused protoplasts at frequencies of 0.05-0.7% based on the number of protoplasts subjected to fusion. This frequency is three-four orders of magnitude better than those previously reported for recombination in fused protoplasts of Gram-negative bacteria such as E. coli and Providencia alcalifaciens.     

Analysis of residues determining specificity of Vibrio cholerae TonB1 for its receptors

In gram-negative organisms, high-affinity transport of iron substrates requires energy transduction to specific outer membrane receptors by the TonB-ExbB-ExbD complex. Vibrio cholerae encodes two TonB proteins, one of which, TonB1, recognizes only a subset of V. cholerae TonB-dependent receptors and does not facilitate transport through Escherichia coli receptors. To investigate the receptor specificity exhibited by V. cholerae TonB1, chimeras were created between V. cholerae TonB1 and E. coli TonB. The activities of the chimeric TonB proteins in iron utilization assays demonstrated that the C-terminal one-third of either TonB confers the receptor specificities associated with the full-length TonB. Single-amino-acid substitutions near the C terminus of V. cholerae TonB1 were identified that allowed TonB1 to recognize E. coli receptors and at least one V. cholerae TonB2-dependent receptor. This indicates that the very C-terminal end of V. cholerae TonB1 determines receptor specificity. The regions of the TonB-dependent receptors involved in specificity for a particular TonB protein were investigated in experiments involving domain switching between V. cholerae and E. coli receptors exhibiting different TonB specificities. Switching the conserved TonB box heptapeptides at the N termini of these receptors did not alter their TonB specificities. However, replacing the amino acid immediately preceding the TonB box in E. coli receptors with an aromatic residue allowed these receptors to use V. cholerae TonB1. Further, site-directed mutagenesis of the TonB box -1 residue in a V. cholerae TonB2-dependent receptor demonstrated that a large hydrophobic amino acid in this position promotes recognition of V. cholerae TonB1. These data suggest that the TonB box -1 position controls productive interactions with V. cholerae TonB1.     

Association of monocyte chemoattractant protein-1 with adipocyte number, insulin resistance and liver function markers

Background  Monocyte chemoattractant protein-1 (MCP-1) is an inflammatory chemokine known to induce adipocyte dedifferentiation and insulin resistance. Inflammation, insulin resistance, and obesity have been implicated in the pathogenesis of non-alcoholic fatty liver disease (NAFLD).
Methods  Fasting plasma from 43 baboons were assayed for MCP-1, insulin, glucose, alanine aminotransferase (ALT), and aspartate aminotransferase (AST). Adipocyte number and volume were measured via biopsies of omental adipose tissue. The homeostatic model assessment method (HOMA) was used to estimate systemic insulin resistance.
Results  Sex and age adjusted correlations were significant for MCP-1 with adipocyte number (r = −0.42; P  = 0.01), adipocyte volume (r = 0.38; P  = 0.02), HOMA (r = 0.45; P  = 0.004), ALT (r = 0.46; P  = 0.03) and AST (r = 0.45; P  = 0.03).
Conclusions  These results suggest that MCP-1 is related with adipocyte dedifferentiation and systemic insulin resistance, thereby potentially contributing to the development of NAFLD.     

Bird species turnover and stochastic extinction in woodland fragments

Year-to-year turnover in bird species composition was recorded across, the whole size range (0 02-30 ha) of 146 woods studied The mean number of resident breeding species both lost and gained per wood between consecutive breeding seasons was 2 (range 0-8) No relationship was found between this absolute turnover rate and woodland area, or any other of 24 predictor variables (describing woodland structure, isolation, connectedness and surrounding land use) Extriction and colonisation rates (in terms of numbers of species lost and gained) were also unrelated to woodland area In all sizes of woods, the species most likely to show local extinctions and colonisations were those with small populations within those woods, but the identity of the species concerned changed as woodland area increased In the smallest woods, the majority of turnover involved common species, such as wren and dunnock, which occurred in only small numbers in these small woods As woodland area increased, these species attained sufficient numbers to usually avoid stochastic extinction The majority of turnover was then due to more specialist (and less numerous) woodland species, such as great-spotted woodpecker and marsh tit, which were usually lacking in small woods In Britain, much existing broadleaved woodland falls within the size range studied Thus the numbers of many bird species are liable to be small enough for yearly turnover in woodland bird communities to be appreciable, and for the long-term persistence of individual species in particular woods to depend on dispersal