Short-term leaf elongation kinetics of maize in response to salinity are independent of the root

The essentiality of roots to the short-term responses of leaf elongation to salinity was tested by removing the roots of maize (Zea mays L.) from the shoots and comparing the initial short-term response of leaf elongation to that with intact plants. Eightday-old seedlings growing in solution culture were treated with 80 millimolar NaCl and their leaf elongation rate (LER) was monitored with a linear variable differential transformer connected to a computerized data aquisition system. Initially, LER of intact plants was sharply reduced by salinity, then rose rapidly to reach a new steady-state rate about 1.5 hours after salinization. The new steady-state rate of salinized intact plants was about 80% of the control rate. When the roots of nonsalinized plants were excised under the surface of the nutrient solution, excision did not disturb the steady-state LER. When these shoots were salinized, they responded in a manner nearly identical to that of intact plants, indicating that roots are not essential for the modulation of short-term LER of salt-stressed plants.     

A comparative structural analysis of the ADF/cofilin family

Actin-depolymerizing factor (ADF) and cofilin define a family of actin-binding proteins essential for the rapid turnover of filamentous actin in vivo. Here we present the 2.0 A crystal structure of Arabidopsis thaliana ADF1 (AtADF1), the first plant crystal structure from the ADF/cofilin (AC) family. Superposition of the four AC isoform structures permits an accurate sequence alignment that differs from previously reported data for the location of vertebrate-specific inserts and reveals a contiguous, vertebrate-specific surface opposite the putative actin-binding surface. Extending the structure-based sequence alignment to include 30 additional isoforms indicates three major groups: vertebrates, plants, and "other eukaryotes." Within these groups, several structurally conserved residues that are not conserved throughout the entire AC family have been identified. Residues that are highly conserved among all isoforms tend to cluster around the tryptophan at position 90 and a structurally conserved kink in alpha-helix 3. Analysis of surface character shows the presence of a hydrophobic patch and a highly conserved acidic cluster, both of which include several residues previously implicated in actin binding.     

Core formation and the acquisition of fusion competence are linked during secretory granule maturation in Tetrahymena

The formation of dense core secretory granules is a multistage process beginning in the trans Golgi network and continuing during a period of granule maturation. Direct interactions between proteins in the membrane and those in the forming dense core may be important for sorting during this process, as well as for organizing membrane proteins in mature granules. We have isolated two mutants in dense core granule formation in the ciliate Tetrahymena thermophila, an organism in which this pathway is genetically accessible. The mutants lie in two distinct genes but have similar phenotypes, marked by accumulation of a set of granule cargo markers in intracellular vesicles resembling immature secretory granules. Sorting to these vesicles appears specific, since they do not contain detectable levels of an extraneous secretory marker. The mutants were initially identified on the basis of aberrant proprotein processing, but also showed defects in the docking of the immature granules. These defects, in core assembly and docking, were similarly conditional with respect to growth conditions, and therefore are likely to be tightly linked. In starved cells, the processing defect was less severe, and the immature granules could dock but still did not undergo stimulated exocytosis. We identified a lumenal protein that localizes to the docking-competent end of wildtype granules, but which is delocalized in the mutants. Our results suggest that dense cores have functionally distinct domains that may be important for organizing membrane proteins involved in docking and fusion.     

Proposal of Xanthomonas translucens pv. pistaciae pv. nov., pathogenic to pistachio (Pistacia vera)

Strains of Xanthomonas translucens have caused dieback in the Australian pistachio industry for the last 15 years. Such pathogenicity to a dicotyledonous woody host contrasts with that of other pathovars of X. translucens, which are characterized by their pathogenicity to monocotyledonous plant families. Further investigations, using DNA-DNA hybridization, gyrB gene sequencing and integron screening, were conducted to confirm the taxonomic status of the X. translucens pathogenic to pistachio. DNA-DNA hybridization provided a clear classification, at the species level, of the pistachio pathogen as a X. translucens. In the gyrB-based phylogeny, strains of the pistachio pathogen clustered among the X. translucens pathovars as two distinct lineages. Integron screening revealed that the cassette arrays of strains of the pistachio pathogen were different from those of other Xanthomonas species, and again distinguished two groups. Together with previously reported pathogenicity data, these results confirm that the pistachio pathogen is a new pathovar of X. translucens and allow hypotheses about its origin. The proposed name is Xanthomonas translucens pv. pistaciae pv. nov.     

The Roles of Entropy and Kinetics in Structure Prediction

Background

Here we continue our efforts to use methods developed in the folding mechanism community to both better understand and improve structure prediction. Our previous work demonstrated that Rosetta''s coarse-grained potentials may actually impede accurate structure prediction at full-atom resolution. Based on this work we postulated that it may be time to work completely at full-atom resolution but that doing so may require more careful attention to the kinetics of convergence.

Methodology/Principal Findings

To explore the possibility of working entirely at full-atom resolution, we apply enhanced sampling algorithms and the free energy theory developed in the folding mechanism community to full-atom protein structure prediction with the prominent Rosetta package. We find that Rosetta''s full-atom scoring function is indeed able to recognize diverse protein native states and that there is a strong correlation between score and Cα RMSD to the native state. However, we also show that there is a huge entropic barrier to folding under this potential and the kinetics of folding are extremely slow. We then exploit this new understanding to suggest ways to improve structure prediction.

Conclusions/Significance

Based on this work we hypothesize that structure prediction may be improved by taking a more physical approach, i.e. considering the nature of the model thermodynamics and kinetics which result from structure prediction simulations.     

Vegetation,fire and soil feedbacks of dynamic boundaries between rainforest,savanna and grassland

At fine spatial scales, savanna‐rainforest‐grassland boundary dynamics are thought to be mediated by the interplay between fire, vegetation and soil feedbacks. These processes were investigated by quantifying tree species composition, the light environment, quantities and flammability of fuels, bark thickness, and soil conditions across stable and dynamic rainforest boundaries that adjoin grassland and eucalypt savanna in the highlands of the Bunya Mountains, southeast Queensland, Australia. The size class distribution of savanna and rainforest stems was indicative of the encroachment of rainforest species into savanna and grassland. Increasing dominance of rainforest trees corresponds to an increase in woody canopy cover, the dominance of litter fuels (woody debris and leaf), and decline in grass occurrence. There is marked difference in litter and grass fuel flammability and this result is largely an influence of strongly dissimilar fuel bulk densities. Relative bark thickness, a measure of stem fire resistance, was found to be generally greater in savanna species when compared to that of rainforest species, with notable exceptions being the conifers Araucaria bidwillii and Araucaria cunninghamii. A transect study of soil nutrients across one dynamic rainforest – grassland boundary indicated the mass of carbon and nitrogen, but not phosphorus, increased across the successional gradient. Soil carbon turnover time is shortest in stable rainforest, intermediate in dynamic rainforest and longest in grassland highlighting nutrient cycling differentiation. We conclude that the general absence of fire in the Bunya Mountains, due to a divergence from traditional Aboriginal burning practices, has allowed for the encroachment of fire‐sensitive rainforest species into the flammable biomes of this landscape. Rainforest invasion is likely to have reduced fire risk via changes to fuel composition and microclimatic conditions, and this feedback will be reinforced by altered nutrient cycling. The mechanics of the feedbacks here identified are discussed in terms of landscape change theory.     

Characterization of the cit-1 gene from Neurospora crassa encoding the mitochondrial form of citrate synthase

We have isolated the cDNA and corresponding genomic DNA encoding citrate synthase in Neurospora crassa. Analysis of the protein coding region of this gene, named cit-1, indicates that it specifies the mitochondrial form of citrate synthase. The predicted protein has 469 amino acids and a molecular mass of 52002 Da. The gene is interrupted by four introns. Hybridization experiments show that a cit-1 probe binds to two different fragments of genomic DNA, which are located on different chromosomes. Neurospora crassa may have two isoforms of citrate synthase, one in the mitochondria and the other in microbodies.     

PKCβ/NF-κB pathway in diabetic atrial remodeling

Journal of Physiology and Biochemistry - Atrial remodeling in diabetes is partially attributed to NF-κB/TGF-β signal transduction pathway activation. We examined whether the...     

Concentrations,Viability, and Distribution of Cryptosporidium Genotypes in Lagoons of Swine Facilities in the Southern Piedmont and in Coastal Plain Watersheds of Georgia

Waste lagoons of swine operations are a source of Cryptosporidium oocysts. Few studies, however, have reported on oocyst concentrations in swine waste lagoons; none have reported on oocyst viability status, nor has there been a systematic assessment of species/genotype distributions across different types of swine facilities. Ten swine waste lagoons associated with farrowing, nursery, finishing, and gestation operations were each sampled once a month for a year. Oocysts were extracted from triplicate 900-ml effluent samples, enumerated by microscopy, and assessed for viability by dye exclusion/vital stain assay. DNA was extracted from processed samples, and 18S ribosomal DNA (rDNA) genes were amplified by PCR and sequenced for species and genotype identification. Oocysts were observed at each sampling time at each lagoon. Annual mean concentrations of total oocysts and viable oocysts ranged between 24 and 51 and between 0.6 and 12 oocysts ml⁻¹ effluent, respectively. The species and genotype distributions were dominated (95 to 100%) by Cryptosporidium suis and Cryptosporidium pig genotype II, the latter of which was found at eight of the lagoons. The lagoon at the gestation facility was dominated by Cryptosporidium muris (90%), and one farrowing facility showed a mix of pig genotypes, Cryptosporidium muris, and various genotypes of C. parvum. The zoonotic C. parvum bovine genotype was observed five times out of 407 18S rDNA sequences analyzed. Our results indicate that pigs can have mixed Cryptosporidium infections, but infection with C. suis is likely to be dominant.Over the last few decades, pork production in North America has undergone significant growth and centralization into large concentrated swine (Sus scrofa) operations with more animals on fewer farms (18). A consequence of the increase in numbers of swine per facility is a concomitant increased concentration of swine waste. Present housing facilities for swine are designed to collect feces and urine in wastewater lagoons, in which the waste undergoes anaerobic transformations. One of several public health concerns over swine lagoons is the potential presence of infectious bacteria, viruses, and protozoa (4). Because of the notoriety given to swine waste lagoon spills in the coastal flood plain of North Carolina that were associated with a series of hurricanes in 1998 and 1999 (21), large-scale swine operations have become a focus of environmental and public health concerns.The cause of the massive outbreak of cryptosporidiosis in Milwaukee, WI, in 1993 was afterwards determined to be Cryptosporidium hominis, the human genotype of C. parvum and an obligate parasite of humans (33, 44). At the time, however, it was thought to be caused by C. parvum (22). Because of this initial misidentification of the cryptosporidial source of the outbreak, the connection between C. parvum and large-scale confined livestock operations has become a focused area of research. Although manure-associated outbreaks of C. parvum have implicated bovine sources, a Canadian study found that the prevalence of Cryptosporidium in swine lagoons was greater than that in dairy liquid manure (9). Olson et al. (24) also reported the presence of Cryptosporidium oocysts of undetermined genotype at four of six hog operations in Canada. Atwill et al. (2) observed C. parvum oocysts in feces of feral pigs. Hutchison et al. (13) observed C. parvum oocysts of undetermined genotype in 5 and 13% of fresh and stored fecal samples, respectively, from pigs of undeclared age. Guselle et al. (10) followed the course of a naturally occurring C. parvum infection in 33 weaned pigs. Following the protocol of the genetic analysis of Morgan et al. (23), Guselle et al. (10) identified this C. parvum genotype as being adapted to pigs. At the time, the zoonotic potential of this C. parvum pig-adapted genotype was considered uncertain (23).Recently, two genotypes of Cryptosporidium have been recognized as host adapted to swine: Cryptosporidium suis (formerly Cryptosporidium pig genotype I) and Cryptosporidium pig genotype II (28, 29). Xiao et al. (37) reported on an immunocompromised person who was infected with a Cryptosporidium pig genotype and thus implicated Cryptosporidium from swine as potentially zoonotic and a public health concern. Before molecular methods were developed to differentiate pig genotypes of Cryptosporidium from other species, C. parvum was thought to infect 152 species of mammals and consist of several cryptic species (6). An extensive survey of swine effluent from swine finishing operations in Ireland indicated a prevalence of both C. suis and Cryptosporidium pig genotype II (39). Hamnes et al. (11) reported prevalence of both C. suis and Cryptosporidium pig genotype II in feces of suckling pigs across Norway and thus implicated farrowing operations as sources of this parasite.Other than the prevalence of Cryptosporidium in feces of young pigs and effluent lagoons of older pigs in finishing operations, little comprehensive data on oocyst concentrations, viability of oocysts, and distributions of Cryptosporidium species and genotypes have been reported. No systematic study of swine lagoon effluents from large-scale facilities has been reported for the four separate stages of swine development, (i) breeding and gestation, (ii) farrowing (parturition), (iii) nursery (in which weaned piglets are kept until 8 to 9 weeks of age), and (iv) finishing (in which 8- to 9-week-old pigs are kept to market weight). The objective of this investigation was to determine for 1 year the frequencies, concentrations, viability statuses, and distributions of Cryptosporidium species and genotypes in lagoons associated with the four types of swine operations in the Southern Piedmont and in coastal plain watersheds of Georgia.