Crystal structure determination and dynamic studies of Mycobacterium tuberculosis Cytidine deaminase in complex with products

Cytidine deaminase (CDA) is a key enzyme in the pyrimidine salvage pathway. It is involved in the hydrolytic deamination of cytidine or 2′-deoxycytidine to uridine or 2′-deoxyuridine, respectively. Here we report the crystal structures of Mycobacterium tuberculosis CDA (MtCDA) in complex with uridine (2.4 Å resolution) and deoxyuridine (1.9 Å resolution). Molecular dynamics (MD) simulation was performed to analyze the physically relevant motions involved in the protein–ligand recognition process, showing that structural flexibility of some protein regions are important to product binding. In addition, MD simulations allowed the analysis of the stability of tetrameric MtCDA structure. These findings open-up the possibility to use MtCDA as a target in future studies aiming to the rational design of new inhibitor of MtCDA-catalyzed chemical reaction with potential anti-proliferative activity on cell growth of M. tuberculosis, the major causative agent of tuberculosis.     

A typical preparation of Francisella tularensis O-antigen yields a mixture of three types of saccharides

Tularemia is a severe infectious disease in humans caused by the Gram-negative bacterium Francisella tularensis (Ft). Because of its low infectious dose, high mortality rate, and the threat of its large-scale dissemination in weaponized form, development of vaccines and immunotherapeutics against Ft is essential. Ft lipopolysaccharide (LPS), which contains the linear graded-length saccharide component O-antigen (OAg) attached to a core oligosaccharide, has been reported as a protective antigen. Purification of LPS saccharides of defined length and composition is necessary to reveal the epitopes targeted by protective antibodies. In this study, we purified saccharides from LPS preparations from both the Ft subspecies holarctica live vaccine strain (LVS) and the virulent Ft subspecies tularensis SchuS4 strain using liquid chromatography. We then characterized the fractions using high-resolution mass spectrometry and tandem mass spectrometry. Three types of saccharides were observed in both the LVS and SchuS4 preparations: two consisting of OAg tetrasaccharide repeats attached to one of two core oligosaccharide variants and one consisting of tetrasaccharide repeats only (coreless). The coreless OAg oligosaccharides were shown to contain Qui4NFm (4,6-dideoxy-4-formamido-D-glucose) at the nonreducing end and QuiNAc (2-acetamido-2,6-dideoxy-O-D-glucose) at the reducing end. Purified homogeneous preparations of saccharides of each type will allow mapping of protective epitopes in Ft LPS.     

Impacts of introduced common wasps (Vespula vulgaris) on experimentally placed mealworms in a New Zealand beech forest

An introduced social wasp Vespula vulgaris may compete with native birds for honeydew and invertebrates in New Zealand forests. Experimentally hidden mealworms (Tenebrio molitor) persisted longer at two sites following wasp poisoning that at two sites where wasps were not poisoned. Mealworms persisted longer in the morning than in the afternoon within all study sites. An unusually low mealworm removal rate during a morning trial before wasp poisoning heavily influences the results of this experiment but we have no ecological reason to ignore it. Wasps may therefore be having a heavy impact on invertebrate abundance on very short time scales (within a day following dawn emergence). They may also remove cached food items that would otherwise be retrieved by the South Island robin (Petroica australis australis) during cold or dark feeding conditions.     

Using identity-by-descent information in affected sib pairs to increase the efficiency of genetic association studies.

The aim of this study was to determine whether identity-by-descent (IBD) information for affected sib pairs (ASPs) can be used to select a sample of cases for a genetic case-control study which will provide more power for detecting association with loci in a known linkage region. By modeling the expected frequency of the disease allele in ASPs showing IBD sharing of 0, 1, or 2 alleles, and considering additive, recessive, and dominant disease models, we show that cases selected from IBD 2 families are best for this purpose, followed by those selected from IBD 1 families; least useful are cases selected from IBD 0 families.     

8,000 years of climate,vegetation, fire and land-use dynamics in the thermo-mediterranean vegetation belt of northern Sardinia (Italy)

Vegetation History and Archaeobotany - Knowledge about the vegetation history of Sardinia, the second largest island of the Mediterranean, is scanty. Here, we present a new sedimentary record...     

Carbon catabolite regulation of rebeccamycin production inSaccharothrix aerocolonigenes

Summary A new antitumor antibiotic named rebeccamycin was isolated from fermentations of an actinomycete,Saccharothrix aerocolonigenes. A defined medium was developed to study the regulation of synthesis of rebeccamycin byS. aerocolonigenes. In glucose medium formation of rebeccamycin was detected only after glucose was depleted. Examination of eleven different carbon sources revealed that carbon catabolite regulation is a major control mechanism for rebeccamycin production.     

Cell division systems that account for the various arrangements and types of differentiated cells within the secondary phloem of conifers

There are two main types of arrangement of differentiated cells within the radial cell files of secondary phloem in conifer trees. In the C-type arrangement, characteristic of the Cupressaceae, fibre (F), parenchyma (P) and sieve (S) cells are arranged in recurrent groups, such as the “standard” cellular quartet (FSPS). In the P-type arrangement, characteristic of the Pinaceae, there are no fibres and one of the characteristic recurrent arrangements is the cellular sextet (PSSSSS). In addition, in both C-type and P-type arrangements, similar cell types are often organised into tangential bands. A simulation model, based on the theory of L-systems, was devised to account for the determination of these two types of regular and recurrent patterns of differentiated phloem cells. It was based on the supposition that, in the meristematic portion of the phloem domain, there are specific spatio-temporal patterns of periclinal cell division. When new cells are produced, those already present are displaced along the cell file, occupying a predictable number of cellular positions as a result of each round of cell division. Each cellular position is assumed to be associated with a specific value of a morphogen, such as the auxin, indole acetic acid, relevant for vascular differentiation. Using published quantitative data on the distribution auxin across the phloem, and assuming specific threshold values of auxin necessary for the determination of each cell type, it was found that sequences of F, S or P cells developed in accordance with the specific pattern of cell division and the related positional values of auxin experienced by the cells during their displacement through the immediately post-mitotic zone of cell determination. The model accounts not only for the typical C-type and P-type cellular arrangements, but also for certain variant arrangements. It provides a working example of the concepts of positional information and positional value for patterned differentiation within a developing plant tissue. There are similarities between the way groups of phloem cells develop and the differentiation of somites in the embryos of vertebrates.     

Imipenem and expression of multidrug efflux pump in Enterobacter aerogenes

Imipenem is often used to treat intensive care unit patients infected by Enterobacter aerogenes, but it is leading to an increasing number of antibiotic resistant strains. Clinical isolates and imipenem resistant variants presented a high level of resistance to beta-lactam antibiotic group and to chemically unrelated drugs. We report here that imipenem selects strains which contain active efflux pumps ejecting various unrelated antibiotics including quinolones, tetracycline, and chloramphenicol. An increase of AcrA, an efflux pump component, was observed in the imipenem resistant variants. The overexpression of marA, involved in the genetic control of membrane permeability via porin and efflux pump expression, indicated the activation of the resistance genetic cascade in imipenem resistant variants.     

Coral performance and bioerosion in Central Mexican Pacific reef communities

Hydrobiologia - Reef development occurs commonly under oligotrophic conditions that favor corals over competitors. In the Eastern Tropical Pacific (ETP), coral communities develop under highly...     

Prophylactic and therapeutic use of antibodies for protection against respiratory infection with Francisella tularensis

The role of Abs in protection against respiratory infection with the intracellular bacterium Francisella tularensis is not clear. To investigate the ability of Abs to clear bacteria from the lungs and prevent systemic spread, immune serum was passively administered i.p. to naive mice before intranasal F. tularensis live vaccine strain infection. It was found that immune serum treatment provided 100% protection against lethal challenge while normal serum or Ig-depleted immune serum provided no protection. Protective efficacy was correlated with increased clearance of bacteria from the lung and required expression of FcgammaR on phagocytes, including macrophages and neutrophils. However, complement was not required for protection. In vitro experiments demonstrated that macrophages were more readily infected by Ab-opsonized bacteria but became highly efficient in killing upon activation by IFN-gamma. Consistent with this finding, in vivo Ab-mediated protection was found to be dependent upon IFN-gamma. SCID mice were not protected by passive Ab transfer, suggesting that T cells but not NK cells serve as the primary source for IFN-gamma. These data suggest that a critical interaction of humoral and cellular immune responses is necessary to provide sterilizing immunity against F. tularensis. Of considerable interest was the finding that serum Abs were capable of conferring protection against lethal respiratory tularemia when given 24-48 h postexposure. Thus, this study provides the first evidence for the therapeutic use of Abs in Francisella-infected individuals.