bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multiscale study of silty soil structure
Authors: Bartoli F. , Genevois‐Gomendy V. , Royer J. J. , Niquet S. , Vivier H. , Grayson R. 
Published: March 2005

SummaryDependency of soil properties on scale is a crucial issue in soil physics. In this paper, fractal approaches are used in two case studies in France and Australia, respectively, to study how measured physical soil properties change with the sample spacing and the scale of observation. At a scale of 10–1000 m (104 to 106 mm), fractals were applied to sample data from a linear transect, while at the 10−6 to 102 mm scale, fractals were applied in two dimensions to analyse both soil micro‐ and macrostructure, based on thin section samples. Porosity was characterized by short‐range spatial variations using sample spacings of 0.5 and 5 m (from the transect data), and a sample spacing of 1 cm (from the thin section analysis). The size of the representative elementary volume (REV) or representative elementary area (REA), required to represent statistically the elementary soil structure, was identified in three ways: (i) by the correlation length of a representative interconnected pore network, (ii) by the upper limit of the non‐linear increase with observation scale of mean porosity (upper limit of the solid mass fractal domain), and (iii) by the non‐linear decrease with observation scale of the coefficient of variation, CV, of mean porosity. Two embedded REAs were identified: the first (0.1–0.4 mm) related to the soil microstructure whereas a second (11–44 mm) related to the soil macrostructure. The solid mass fractal dimensions of the two embedded structural domains showed that hierarchical heterogeneity of soil structure was more pronounced for microstructures than for macrostructures. The mean area ratio of microstructural matrix/total surface and the CV of mean microporosity both scale similarly at observation scales smaller than the REA size. Their scaling exponents were both related to the fractal dimension of microstructural matrix. This preliminary study shows that the theory of fractals applied to soil structures at a specific scale range cannot be directly applied to predict soil physical properties at another scale range. This is because there are different interdependent structuring processes operating at different scales resulting in fractal dimensions being consistent only over particular domain limits.
Forest vegetation does recycle substantial amounts of silicon from and back to the soil solution with phytoliths as an intermediate phase, contrary to recent reports
Authors: Farmer V. C. 
Published: March 2005

SummaryRecent reports that forest vegetation takes up little Si and returns little to the soil in litter are based on the mistaken assumption that digestion of leaf and litter in hot oxidizing acids can bring phytoliths, a form of opaline silica, into solution. Phytolith formation and dissolution can explain a number of otherwise puzzling aspects of Si in soil solution.
Effects of genetic ablation of bach1 upon smooth muscle cell proliferation and atherosclerosis after cuff injury
Authors: Omura Shinji , Suzuki Hiroshi , Toyofuku Mamoru , Ozono Ryoji , Kohno Nobuoki , Igarashi Kazuhiko 
Published: March 2005

Bach1 is a transcriptional repressor of the cytoprotective enzyme heme oxygenase‐1 (HO‐1). Although HO‐1 protects against atherosclerosis, the function of Bach1 in this process is poorly understood. We isolated peritoneal macrophages and aortic smooth muscle cells (SMC) from wild‐type and bach1‐deficient mice. bach1‐deficient macrophages expressed increased levels of HO‐1 and showed elevated phagocytic activity when incubated with 0.75 µm microspheres. In SMC, bach1‐ablation resulted in increased expression of HO‐1 and decreased proliferation in bromodeoxyuridine incorporation assay as compared with wild‐type cells. The up‐regulated phagocytic activity and reduced SMC proliferation of bach1‐deficient cells were not restored by Zinc (II) protoporphyrin IX, an inhibitor of HO, suggesting that HO‐independent mechanisms are also involved in the regulation of phagocytosis of macrophages and proliferation of SMC by Bach1. In wild‐type mice, cuff placement around femoral artery caused pronounced intimal proliferation without affecting the media, thus resulting in intimal to medial (I/M) volume ratio of 65.6%. bach1‐deficient mice had less degree of intimal growth (I/M ratio of 45.6%). These results indicate that Bach1 plays a critical role in the regulation of HO‐1 expression, macrophage function, SMC proliferation and neointimal formation. Bach1 may regulate gene expression in these cells during inflammation and atherogenesis.
A new release on life: emerging concepts in proteolysis and parasite invasion
Authors: Carruthers Vern B. , Blackman Michael J. 
Published: March 2005

SummaryCell invasion by apicomplexan pathogens such as the malaria parasite and Toxoplasma is accompanied by extensive proteolysis of zoite surface proteins (ZSPs) required for attachment and penetration. Although there is still little known about the proteases involved, a conceptual framework is emerging for the roles of proteolysis in cell invasion. Primary processing of ZSPs, which includes the trimming of terminal peptides or segmentation into multiple fragments, is proposed to activate these adhesive ligands for tight binding to host receptors. Secondary processing, which occurs during penetration, results in the shedding of ZSPs by one of two mechanistically distinct ways, shaving or capping. Resident surface proteins are typically shaved from the surface whereas adhesive ligands mobilized from intracellular secretory vesicles are capped to the posterior end of the parasite before being shed during the final steps of penetration. Intriguingly, recent studies have revealed that ZSPs can be released either by being cleaved adjacent to the membrane anchor or actually within the membrane itself. Mounting evidence suggests that intramembrane cleavage is catalysed by one or more integral membrane serine proteases of the Rhomboid family and we propose that several malaria adhesive ligands may be potential substrates for these enzymes. We also discuss the evidence that the key reason for ZSP shedding during invasion is to break the connection between parasite surface ligands and host receptors. The sequential proteolytic events associated with invasion by pathogenic protozoa may represent vulnerable pathways for the future development of synergistic anti‐protozoal therapies.
Mutant forms of the Escherichia coliβ sliding clamp that distinguish between its roles in replication and DNA polymerase V‐dependent translesion DNA synthesis
Authors: Sutton Mark D. , Duzen Jill M. , Maul Robert W. 
Published: March 2005

SummaryThe Escherichia coliβ sliding clamp is proposed to play an important role in regulating DNA polymerase traffic at the replication fork. As part of an ongoing effort to understand how organisms manage the actions of their multiple DNA polymerases, we examined the ability of several mutant forms of the β clamp to function in DNA polymerase V‐ (pol V‐) dependent translesion DNA synthesis (TLS) in vivo. Our results indicate that a dnaN159 strain, which expresses a temperature sensitive form of the β clamp, was impaired for pol V‐dependent TLS at the permissive temperature of 37°C. This defect was complemented by a plasmid that expressed near‐physiological levels of the wild‐type clamp. Using a dnaN159 mutant strain, together with various plasmids expressing mutant forms of the clamp, we determined that residues H148 through R152, which comprise a portion of a solvent exposed loop, as well as position P363, which is located in the C‐terminal tail of the β clamp, are critically important for pol V‐dependent TLS in vivo. In contrast, these same residues appear to be less critical for pol III‐dependent replication. Taken together, these findings indicate that: (i) the β clamp plays an essential role in pol V‐dependent TLS in vivo and (ii) pol III and pol V interact with non‐identical surfaces of the β clamp.
Subcellular localization of a sporulation membrane protein is achieved through a network of interactions along and across the septum
Authors: Doan Thierry , Marquis Kathleen A. , Rudner David Z. 
Published: March 2005

SummaryDuring the process of spore formation in Bacillus subtilis many membrane proteins localize to the sporulation septum where they play key roles in morphogenesis and cell‐cell signalling. However, the mechanism by which these proteins are anchored at this site is not understood. In this report we have defined the localization requirements for the mother‐cell membrane protein SpoIVFA, which anchors a signalling complex in the septal membrane on the mother cell side. We have identified five proteins (SpoIID, SpoIIP, SpoIIM, BofA and SpoIIIAH) synthesized in the mother cell under the control of σE and one protein (SpoIIQ) synthesized in the forespore under the control of σF that are all required for the proper localization of SpoIVFA. Surprisingly, these proteins appear to have complementary and overlapping anchoring roles suggesting that SpoIVFA is localized in the septal membrane through a web of protein interactions. Furthermore, we demonstrate a direct biochemical interaction between the extracellular domains of two of the proteins required to anchor SpoIVFA: the forespore protein SpoIIQ and the mother‐cell protein SpoIIIAH. This result supports the idea that the web of interactions that anchors SpoIVFA is itself held in the septal membrane through a zipper‐like interaction across the sporulation septum. Importantly, our results suggest that a second mechanism independent of forespore proteins participates in anchoring SpoIVFA. Finally, we show that the dynamic localization of SpoIIQ in the forespore is impaired in the absence of SpoIVFA but not SpoIIIAH. Thus, a complex web of interactions among mother cell and forespore proteins is responsible for static and dynamic protein localization in both compartments of the sporangium. We envision that this proposed network is involved in anchoring other sporulation proteins in the septum and that protein networks with overlapping anchoring capacity is a feature of protein localization in all bacteria.
Maturation of the Escherichia coli divisome occurs in two steps
Authors: Aarsman Mirjam E. G. , Piette André , Fraipont Claudine , Vinkenvleugel Thessa M. F. , Nguyen‐Distèche Martine , den Blaauwen Tanneke 
Published: March 2005

SummaryCell division proteins FtsZ (FtsA, ZipA, ZapA), FtsE/X, FtsK, FtsQ, FtsL/B, FtsW, PBP3, FtsN and AmiC localize at mid cell in Escherichia coli in an interdependent order as listed. To investigate whether this reflects a time dependent maturation of the divisome, the average cell age at which FtsZ, FtsQ, FtsW, PBP3 and FtsN arrive at their destination was determined by immuno‐ and GFP‐fluorescence microscopy of steady state grown cells at a variety of growth rates. Consistently, a time delay of 14–21 min, depending on the growth rate, between Z‐ring formation and the mid cell recruitment of proteins down stream of FtsK was found. We suggest a two‐step model for bacterial division in which the Z‐ring is involved in the switch from cylindrical to polar peptidoglycan synthesis, whereas the much later localizing cell division proteins are responsible for the modification of the envelope shape into that of two new poles.
Characterization of Cryptococcus neoformans variety gattii SOD2 reveals distinct roles of the two superoxide dismutases in fungal biology and virulence
Authors: Narasipura Srinivas D. , Chaturvedi Vishnu , Chaturvedi Sudha 
Published: March 2005

SummaryWe studied superoxide dismutases (SODs) in the encapsulated yeast Cryptococcus neoformans (Cn) variety gattii to analyse the role of mitochondrial MnSOD (SOD2) in fungal biology and virulence. SOD2 was cloned from a Cn cosmid library, sod2 mutant and sod2 + SOD2 reconstituted strains were constructed by homologous recombination, and two sod1sod2 double mutants were constructed by replacing SOD2 in the sod1 mutant with the sod2::HYG allele. The SOD2 protein (SOD2p) encoded 225 amino acids, with 36–66% identity with other fungal SOD2ps. SOD2 deletion rendered Cn highly growth‐defective at 37°C in 19–20% oxygen (normal air), and this defect was reversed by limiting oxygen to 1.3% as well in the presence of antioxidant, ascorbic acid. The sod2 mutant accumulated significantly more reactive oxygen species (ROS) at 37°C as well at 30°C in the presence of antimycin A, suggesting that SOD2p is the primary defence of Cn against the superoxide anion (O2• −) in the mitochondria. The sod2 was also highly susceptible to redox‐cycling agents, high salt and nutrient limitations. The sod2 mutant was avirulent in intranasally infected mice and markedly attenuated in its virulence in intravenously infected mice. The virulence defect of sod2 mutant appeared related to its growth defects in high oxygen environment, but not resulting from increased sensitivity to oxidative killing by phagocytes. The sod1sod2 double mutants were avirulent in mice. Additionally, sod1sod2 double mutants showed a marked reduction in the activities of other known Cn virulence factors; and they were more susceptible to PMN killing than was the sod2 single mutant. Previously, we reported that the attenuation of sod1 mutant in mice was resulting from enhanced susceptibility to phagocyte killing, combined with a reduction in the activities of a number of virulence factors. Thus, SOD1p and SOD2p play distinct roles in the biology and virulence of Cn var. gattii via independent modes of action.
Evidence for non‐enzymatic glycosylation of Escherichia coli chromosomal DNA
Authors: Mironova Roumyana , Niwa Toshimitsu , Handzhiyski Yordan , Sredovska Angelina , Ivanov Ivan 
Published: March 2005

SummaryWe have recently shown that the process of non‐enzymatic glycosylation (glycation) takes place in Escherichia coli under physiological conditions and affects both recombinant and endogenous bacterial proteins. In this study, we further demonstrate that E. coli chromosomal DNA is also subjected to glycation under physiological growth conditions. The E. coli DNA accumulates early glycation (Amadori) products as proven by the nitroblue tetrazolium (NBT) reduction assay. It showed also immunoreactivity to a monoclonal antibody raised against N∈‐(carboxymethyl)lysine and fluorescent properties indicative of modifications with advanced glycation end‐products. Two types of fluorophores were detected in the E. coli DNA with excitation maxima at 360 nm and 380 nm and emission maxima at 440 nm and 410 nm. Using the NBT reduction assay, fluorescence spectroscopy and enzyme‐linked immunosorbent assay we revealed that glycation adducts accumulate in DNA predominantly in the stationary phase of growth, although they could be detected also in exponential‐phase cells. Besides on the growth phase, the extent of DNA glycation depends also on the nutrient broth composition being more extensive in rich media. Thiamine was found to inhibit both DNA glycation and spontaneous point mutations as judged by the decreased rate of the argE3 to Arg+ reversions in the E. coli strain AB1157.
The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus
Authors: Zago Maria A. , Dennis Patrick P. , Omer Arina D. 
Published: March 2005

SummaryArchaeal L7Ae is a multifunctional protein that binds to a distinctive K‐turn motif in RNA and is found as a component in the large subunit of the ribosome, and in ribose methylation and pseudouridylation guide RNP particles. A collection of L7Ae‐associated small RNAs were isolated from Sulfolobus solfataricus cell extracts and used to construct a cDNA library; 45 distinct cDNA sequences were characterized and divided into six groups. Group 1 contained six RNAs that exhibited the features characteristic of the canonical C/D box archaeal sRNAs, two RNAs that were atypical C/D box sRNAs and one RNA representative of archaeal H/ACA sRNA family. Group 2 contained 13 sense strand RNA sequences that were encoded either within, or overlapping annotated open reading frames (ORFs). Group 3 contained three sequences form intergenic regions. Group 4 contained antisense sequences from within or overlapping sense strand ORFs or antisense sequences to C/D box sRNAs. More than two‐thirds of these sequences possessed K‐turn motifs. Group 5 contained two sequences corresponding to internal regions of 7S RNA. Group 6 consisted of 11 sequences that were fragments from the 5′ or 3′ ends of 16S and 23S ribosomal RNA and from seven different tRNAs. Our data suggest that S. solfataricus contains a plethora of small RNAs. Most of these are bound directly by the L7Ae protein; the others may well be part of larger, transiently stable RNP complexes that contain the L7Ae protein as core component.
A magnesium‐dependent mreB null mutant: implications for the role of mreB in Bacillus subtilis
Authors: Formstone Alex , Errington Jeffery 
Published: March 2005

SummaryMreB shares a common prokaryotic ancestor with actin and is present in almost all rod‐shaped bacteria. MreB proteins have been implicated in a range of important cell processes, including cell morphogenesis, chromosome segregation and cell polarity. The mreB gene frequently lies at the beginning of a cluster of genes, immediately upstream of the conserved mreC and mreD genes. RNA analysis showed that in Bacillus subtilis mreB is co‐transcribed with mreC and that these genes form part of an operon under the control of a promoter(s) upstream of mreB. Construction of an in‐frame deletion of mreB and its complementation by mreB+ only, in trans, established that the gene is important for maintenance of cell width and cell viability under normal growth conditions, independent of polar effects on downstream genes. Remarkably, virtually normal growth was restored to the mreB null mutant in the presence of high concentrations of magnesium, especially when high concentrations of the osmoprotectant, sucrose were also present. Under these conditions, cells could be maintained in the complete absence of an mreB gene, with almost normal morphology. No detectable effect on chromosome segregation was evident in the mutant, nor was there an effect on the topology of nascent peptidoglycan insertion. A GFP–MreB fusion was used to look at the localization of MreB in live cells. The pattern of localization was similar to that previously described, but no tight linkage to nucleoid positioning was evident. Propagation of the mreB null mutant in the absence of magnesium and sucrose led to a progressive increase in cell width, culminating in cell lysis. Cell division was also perturbed but this effect may be secondary to the disturbance in cell width. These results suggest that the major role of MreB in B. subtilis lies in the control of cell diameter.
Structural and functional studies of the enteropathogenic Escherichia coli type III needle complex protein EscJ
Authors: Crepin Valérie F. , Prasannan Sunil , Shaw Rob K. , Wilson Rebecca K. , Creasey Elizabeth , Abe Cecilia M. , Knutton Stuart , Frankel Gad , Matthews Steve 
Published: March 2005

SummaryThe type III secretion system (TTSS) is a macromolecular structure that spans the cell wall of Gram‐negative bacterial pathogens, enabling delivery of virulence effector proteins directly to the membranes and cytosol of host eukaryotic cells. TTSS consists of a conserved needle complex (NC) that is composed of sets of inner and outer membranes rings connected by a periplasmic rod. Enteropathogenic Escherichia coli (EPEC) is an extracellular diarrhoeagenic pathogen that uses TTSS to induce actin polymerization and colonizes the intestinal epithelium. In EPEC, EscJ is predicted to be targeted to the periplasm, in a sec‐dependent manner, and to bridge the TTSS membrane‐associated rings. In this study we determined the global fold of EscJ using Nuclear Magnetic Resonance spectroscopy. We show that EscJ comprises two subdomains (D1 – amino acid residues 1–55 in the mature protein, and D2 – amino acid residues 90–170), each comprising a three‐stranded β‐sheet flanked by two α‐helices. A flexible region (residues 60–85) couples the structured regions D1 and D2. Periplasmic overexpression of EscJD1 and EscJD2 in a single escJ mutant bacterium failed to restore protein secretion activity, suggesting that the flexible linker is essential for the rod function. In contrast, periplasmic overexpression of EscJD1 and EscJD2 in the same wild‐type bacterium had a dominant‐negative phenotype suggesting defective assembly of the TTSS and protein translocation.
The Mycobacterium tuberculosis iniA gene is essential for activity of an efflux pump that confers drug tolerance to both isoniazid and ethambutol
Authors: Colangeli Roberto , Helb Danica , Sridharan Sudharsan , Sun Jingchuan , Varma‐Basil Mandira , Hazbón Manzour Hernando , Harbacheuski Ryhor , Megjugorac Nicholas J. , Jacobs William R. , Holzenburg Andreas , Sacchettini James C. , Alland David 
Published: March 2005

SummaryLittle is known about the intracellular events that occur following the initial inhibition of Mycobacterium tuberculosis by the first‐line antituberculosis drugs isoniazid (INH) and ethambutol (EMB). Understanding these pathways should provide significant insights into the adaptive strategies M. tuberculosis undertakes to survive antibiotics. We have discovered that the M. tuberculosis iniA gene (Rv 0342) participates in the development of tolerance to both INH and EMB. This gene is strongly induced along with iniB and iniC (Rv 0341 and Rv 0343) by treatment of Mycobacterium bovis BCG or M. tuberculosis with INH or EMB. BCG strains overexpressing M. tuberculosis iniA grew and survived longer than control strains upon exposure to inhibitory concentrations of either INH or EMB. An M. tuberculosis strain containing an iniA deletion showed increased susceptibility to INH. Additional studies showed that overexpression of M. tuberculosis iniA in BCG conferred resistance to ethidium bromide, and the deletion of iniA in M. tuberculosis resulted in increased accumulation of intracellular ethidium bromide. The pump inhibitor reserpine reversed both tolerance to INH and resistance to ethidium bromide in BCG. These results suggest that iniA functions through an MDR‐pump like mechanism, although IniA does not appear to directly transport INH from the cell. Analysis of two‐dimensional crystals of the IniA protein revealed that this predicted transmembrane protein forms multimeric structures containing a central pore, providing further evidence that iniA is a pump component. Our studies elucidate a potentially unique adaptive pathway in mycobacteria. Drugs designed to inhibit the iniA gene product may shorten the time required to treat tuberculosis and may help prevent the clinical emergence of drug resistance.