Structural Analysis of Divalent Metals Binding to the <Emphasis Type="Italic">Bacillus subtilis</Emphasis> Response Regulator Spo0F: The Possibility for <Emphasis Type="Italic">In Vitro</Emphasis> Metalloregulation in the Initiation of Sporulation

The presence of a divalent metal ion in a negatively charged aspartic acid pocket is essential for phosphorylation of response regulator proteins. Here, we present metal binding studies of the Bacillus subtilis response regulator Spo0F using NMR and μESI-MS. NMR studies show that the divalent metals Ca²⁺, Mg²⁺ and Mn²⁺ primarily bind, as expected, in the Asp pocket phosphorylation site. However, identical studies with Cu²⁺ show distinct binding effects in three specific locations: (i) the Asp pocket, (ii) a grouping of charged residues at a site opposite of the Asp pocket, and (iii) on the β4-α4 loop and the β5/α5 interface, particularly around and including H101. μESI-MS studies stoichiometrically confirm the NMR studies and demonstrate that most divalent metal ions bind to Spo0F primarily in a 1:1 ratio. Again, in the case of Cu²⁺, multiple metal-bound species are observed. Subsequent experiments reveal that Mg²⁺ supports phosphotransfer between KinA and Spo0F, while Cu²⁺ fails to support KinA phosphotransfer. Additionally, the presence of Cu²⁺ at non-lethal concentrations in sporulation media for B. subtilis and the related organism Pasteuria penetrans was found to inhibit spore formation while continuing to permit vegetative growth. Depending on the type of divalent metal ion present, in vitro phosphorylation of Spo0F by its cognate kinase KinA can be inhibited.     

GRIF-1 and OIP106, members of a novel gene family of coiled-coil domain proteins: association in vivo and in vitro with kinesin

Gamma-aminobutyric acid(A) receptor-interacting factor (GRIF-1) is a 913-amino acid protein proposed to function as a GABA(A) receptor beta(2) subunit-interacting, trafficking protein. GRIF-1 shares approximately 44% amino acid sequence identity with O-linked N-acetylglucosamine transferase interacting protein 106, OIP106. Both proteins contain predicted coiled-coil domains and probably constitute a novel gene family. The Drosophila orthologue of this family of proteins may be Milton. Milton shares approximately 44% amino acid homology with GRIF-1. Milton is proposed to function in kinesin-mediated transport of mitochondria to nerve terminals. We report here that GRIF-1 and OIP106 also associate with kinesin and mitochondria. Following expression in human embryonic kidney 293 cells, both GRIF-1 and OIP106 were shown by co-immunoprecipitation to be specifically associated with an endogenous kinesin heavy chain species of 115 kDa and exogenous KIF5C. Association of GRIF-1 with kinesin was also evident in native brain and heart tissue. In the brain, anti-GRIF-1-(8-633) antibodies specifically co-immunoprecipitated two kinesin-immunoreactive species with molecular masses of 118 and 115 kDa, and in the heart, one kinesin-immunoreactive species, 115 kDa, was immunoprecipitated. Further studies revealed that GRIF-1 was predominantly associated with KIF5A in the brain and with KIF5B in both the heart and in HEK 293 cells. Yeast two-hybrid interaction assays and immunoprecipitations showed that GRIF-1 associated directly with KIF5C with the GRIF-1/KIF5C interaction domain localized to GRIF-1-(124-283). These results further support a role for GRIF-1 and OIP106 in protein and/or organelle transport in excitable cells in a manner analogous to glutamate receptor-interacting-protein 1, in the motor-dependent transport of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate glutamate excitatory neurotransmitter receptors to dendrites.     

Experience in the application of Java Technologies in telemedicine

Java language has been demonstrated to be an effective tool in supporting medical image viewing in Russia. This evaluation was completed by obtaining a maximum of 20 images, depending on the client's computer workstation from one patient using a commercially available computer tomography (CT) scanner. The images were compared against standard CT images that were viewed at the site of capture. There was no appreciable difference. The client side is a lightweight component that provides an intuitive interface for end users. Each image is loaded in its own thread and the user can begin work after the first image has been loaded. This feature is especially useful on slow connection speed, 9.6 Kbps for example. The server side, which is implemented by the Java Servlet Engine works more effective than common gateway interface (CGI) programs do. Advantages of the Java Technology place this program on the next level of application development. This paper presents a unique application of Java in telemedicine.     

Ecological characterization of a tropical myxomycete assemblage--Maquipucuna Cloud Forest Reserve, Ecuador

The assemblage of myxomycetes (plasmodial slime molds) associated with cloud forests of the Maquipucuna Cloud Forest Reserve in the western Andes was investigated. Within three study sites located along a gradient extending from 1200 to 2700 m above sea level, a clear pattern of decreasing myxomycete diversity and productivity with elevation was apparent. As such, these data conform to the pattern of "reverse diversity" for myxomycetes in the neotropics, with higher diversity for less mesic forest types than for more mesic forest types. Canonical correspondence analysis of myxomycete abundances in relation to microhabitat parameters revealed three major ecological assemblages: wood-, litter- and inflorescence-inhabiting species. All three assemblages include a number of specialized species, with the assemblage associated with litter being the most diverse and the one associated with inflorescences being the most distinctive. In addition, samples from the microhabitat represented by the cover of epiphyllic liverworts on living leaves regularly produce myxomycetes in moist chamber culture but with few sporocarps and no evidence of any specialized species. At least near ground level, bark-inhabiting (corticolous) myxomycetes are uncommon in the cloud forests sampled in the present study.     

Biotelemetry transmitter implantation in rodents: impact on growth and circadian rhythms

The implantation of a biotelemetry transmitter for core body temperature (T(c)) and motor activity (MA) measurements is hypothesized to have effects on growth and circadian rhythmicity depending on animal body-to-transmitter (B:T) size ratio. This study examined the impact of transmitter implantation (TM) on body weight, food intake (FI), water intake (WI), and circadian T(c) and MA rhythms in mice (23.8 +/- 0.04 g) and rats (311.5 +/- 5.1 g) receiving no treatment (NT), anesthesia, laparotomy (LAP), and TM. The B:T size ratio was 6:1 and 84:1 for mice and rats, respectively. In mice, body weight required 14 days to recover to presurgical levels and never attained the level of the other groups. FI recovered in 3 days, whereas WI never reached presurgical levels. Rat body weight did not decrease below presurgical levels. FI and WI recovered to presurgical levels in rats by day 2 postsurgery. Anesthesia decreased mouse body weight for 1 wk, but was without effect in rats. LAP significantly decreased body weight for 5 days in mice and 1 day in rats, showing a significant effect of the surgical procedure in the absence of TM in both species. Circadian T(c) and MA rhythms were evident within the first week in both species, indicating dissociation between circadian rhythmicity and recovery of growth variables. Cosinor analysis showed a TM effect on T(c) min, T(c) max, mesor, amplitude, and period of mice, whereas only the amplitude of the rhythm was affected in rats. These data indicate that a large B:T size ratio is associated with minimization of the adverse effects of surgical implantation. We recommend that B:T size ratio, recovery of presurgical body weight, and display of a robust circadian T(c) and MA rhythm be established before collection of biotelemetry data collection under an experimental paradigm.     

Potential for false positive identifications from large databases through tandem mass spectrometry

The biomedical research community at large is increasingly employing shotgun proteomics for large-scale identification of proteins from enzymatic digests. Typically, the approach used to identify proteins and peptides from tandem mass spectral data is based on the matching of experimentally generated tandem mass spectra to the theoretical best match from a protein database. Here, we present the potential difficulties of using such an approach without statistical consideration of the false positive rate, especially when large databases, as are encountered in eukaryotes are considered. This is illustrated by searching a dataset generated from a multidimensional separation of a eukaryotic tryptic digest against an in silico generated random protein database, which generated a significant number of positive matches, even when previously suggested score filtering criteria are used.     

Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics

Two ketoreductases, RED1 and RED2, are involved in the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2) and dihydrogranaticin in S. violaceoruber Tu22, respectively. They are responsible for the stereospecific reductions of the bicyclic intermediate to give (S)- or (R)-DNPA, although there is no similarity between their amino acid sequences. Biotransformation using synthetic analogous substrates revealed that the substrate specificities are quite different. Homology modelling studies and site directed mutagenesis showed remarkable differences in three-dimensional structures and catalytic mechanisms between RED1 and RED2.     

CgDN3: an essential pathogenicity gene of colletotrichum gloeosporioides necessary to avert a hypersensitive-like response in the host Stylosanthes guianensis

A gene of Colletotrichum gloeosporioides that is induced by nitrogen starvation in axenic culture and is expressed at the early stages of infection of the host Stylosanthes guianensis has been identified and its role in pathogenicity tested. The sequence of this gene, named CgDN3, indicated that it encodes a protein of 74 amino acids that contains a predicted 18 amino acid signal sequence for secretion of a basic 54 amino acid mature protein with weak homology to an internal region of plant wall-associated receptor kinases. Mutants of C. gloeosporioides were produced by homologous recombination in which part of the coding sequence and promoter region of the CgDN3 gene was replaced with a hygromycin-resistance gene cassette. Mutations in the CgDN3 gene were confirmed in two independent transformants and Northern (RNA) analysis demonstrated the disrupted CgDN3 gene was not expressed. The mutants had faster mycelial growth rates in vitro but produced spores that germinated to form appressoria normally on the leaf surface. However, the CgDN3 mutants were unable to infect and reproduce on intact host leaves. Microscopic analysis revealed small clusters of necrotic host cells at inoculation sites on leaves, suggesting that these mutants elicited a localized, host hypersensitive-like response. The mutants were able to grow necrotrophically and reproduce on leaves when conidia were inoculated directly onto wound sites. The putative promoter region of the CgDN3 gene was fused to a gene encoding a modified jellyfish green fluorescent protein and introduced into the fungus. Following inoculation, strong expression of green fluorescent protein was observed in primary infection vesicles in infected epidermal cells with weaker expression evident in hyphae growing within infected leaf tissue. These findings indicate that CgDN3 encodes a novel pathogenicity determinant associated with the biotrophic phase of primary infection and required to avert a hypersensitive-like response by a compatible host.     

Apparent climatically induced increase of tree mortality rates in a temperate forest

We provide a first detailed analysis of long-term, annual-resolution demographic trends in a temperate forest. After tracking the fates of 21 338 trees in a network of old-growth forest plots in the Sierra Nevada of California, we found that mortality rate, but not the recruitment rate, increased significantly over the 22 years of measurement (1983–2004). Mortality rates increased in both of two dominant taxonomic groups ( Abies and Pinus ) and in different forest types (different elevational zones). The increase in overall mortality rate resulted from an increase in tree deaths attributed to stress and biotic causes, and coincided with a temperature-driven increase in an index of drought. Our findings suggest that these forests (and by implication, other water-limited forests) may be sensitive to temperature-driven drought stress, and may be poised for die-back if future climates continue to feature rising temperatures without compensating increases in precipitation.