Carbon Stocks in an African Woodland Landscape: Spatial Distributions and Scales of Variation

Current knowledge of Africa’s carbon (C) pools is limited despite its importance in the global C budget. To increase the understanding of C stocks in African woodlands, we asked how C stocks in soil and vegetation vary across a miombo woodland landscape and to what degree and at what scales are these stocks linked? We sampled along a 5-km transect using a cyclic sampling scheme to allow geostatistical analyses. Soil C stocks in the top 5?cm (12.1?±?0.6?Mg?C?ha^?1 (±?SE)) and 30?cm depths (40.1?±?2.5?Mg?C?ha^?1) varied significantly at scales of a few meters (autocorrelation distance 14?m in 0–5-cm and 26?m in 0–30-cm interval), and aboveground (AG) woody C stocks (20.7?±?1.8?Mg?C?ha^?1) varied significantly at kilometer scales (1,426?m). Soil textural distributions were linked to topography (r ²?=?0.54) as were large-tree AG C stocks (r ²?=?0.70). AG C stocks were constrained to an upper boundary by soil texture with greater AG C being associated with coarser textured soils. Vegetation and soil C stocks were coupled in the landscape in the top 5?cm of soil (r ²?=?0.24) but not with deeper soil C stocks, which were coupled to soil clay content (r ²?=?0.38). This study is one of the most complete transect studies in an African miombo woodland, and suggests that C stock distributions are strongly linked to topography and soil texture. To optimize sampling strategies for C stock assessments in miombo, soil C should be sampled at more than 26?m apart, and AG C should be sampled at more than 1,426?m apart in plots larger than 0.5?ha.     

Trp-tRNA synthetase bridges DNA-PKcs to PARP-1 to link IFN-γ and p53 signaling

Interferon-γ (IFN-γ) engenders strong antiproliferative responses, in part through activation of p53. However, the long-known IFN-γ-dependent upregulation of human Trp-tRNA synthetase (TrpRS), a cytoplasmic enzyme that activates tryptophan to form Trp-AMP in the first step of protein synthesis, is unexplained. Here we report a nuclear complex of TrpRS with the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) and with poly(ADP-ribose) polymerase 1 (PARP-1), the major PARP in human cells. The IFN-γ-dependent poly(ADP-ribosyl)ation of DNA-PKcs (which activates its kinase function) and concomitant activation of the tumor suppressor p53 were specifically prevented by Trp-SA, an analog of Trp-AMP that disrupted the TrpRS-DNA-PKcs-PARP-1 complex. The connection of TrpRS to p53 signaling in vivo was confirmed in a vertebrate system. These and further results suggest an unexpected evolutionary expansion of the protein synthesis apparatus to a nuclear role that links major signaling pathways.     

Discovering implicit protein–protein interactions in the <Emphasis Type="Italic">Cell Cycle</Emphasis> using bioinformatics approaches

The cell division control protein (Cdc2) kinase is a catalytic subunit of a protein kinase complex, called the M phase promoting factor, which induces entry into mitosis and is universal among eukaryotes. This protein is believed to play a major role in cell division and control. The lives of biological cells are controlled by proteins interacting in metabolic and signaling pathways, in complexes that replicate genes and regulate gene activity, and in the assembly of the cytoskeletal infrastructure. Our knowledge of protein–protein (P–P) interactions has been accumulated from biochemical and genetic experiments, including the widely used yeast two-hybrid test. In this paper we examine if P–P interactions in regenerating tissues and cells of the anuran Xenopus laevis can be discovered from biomedical literature using computational and literature mining techniques. Using literature mining techniques, we have identified a set of implicitly interacting proteins in regenerating tissues and cells of Xenopus laevis that may interact with Cdc2 to control cell division. Genome sequence based bioinformatics tools were then applied to validate a set of proteins that appear to interact with the Cdc2 protein. Pathway analysis of these proteins suggests that Myc proteins function as the regulator of M phase initiation by controlling expression of the Akt1 molecule that ultimately inhibits the Cdc2-cyclin B complex in cells. P–P interactions that are implicitly appearing in literature can be effectively discovered using literature mining techniques. By applying evolutionary principles on the P–P interacting pairs, it is possible to quantitatively analyze the significance of the associations with biological relevance. The developed BioMap system allows discovering implicit P–P interactions from large quantity of biomedical literature data. The unique similarities and differences observed within the interacting proteins can lead to the development of the new hypotheses that can be used to design further laboratory experiments.     

Pyrrolidine dithiocarbamate restores endothelial cell membrane integrity and attenuates monocrotaline-induced pulmonary artery hypertension

Monocrotaline (MCT)-induced pulmonary artery hypertension (PAH) in rats is preceded by an inflammatory response, progressive endothelial cell membrane disruption, reduction in the expression of caveolin-1, and reciprocal activation of STAT3 (PY-STAT3). Superoxide and NF-kappaB have been implicated in PAH. To evaluate the role of caveolin-1, PY-STAT3 activation, and superoxide in PAH, MCT-injected rats were treated daily with pyrrolidine dithiocarbamate (PDTC; starting on days 1, 3, and 14 x 2 wk), an inhibitor of inflammation and NF-kappaB activation. Hemodynamic data, the expression of inhibitory (I)-kappaBalpha, caveolin-1, and Tie2 (a membrane protein), activation of PY-STAT3 and NF-kappaB, and superoxide chemiluminescence were examined. Rats developed progressive PAH at 2 wk post-MCT. There was progressive reduction in the expression of caveolin-1, Tie2, and activation of PY-STAT3 in the lungs. Reduction in I-kappaBalpha expression was present at 2 and 4 wk post-MCT. Superoxide chemiluminescence and NF-kappaB activation were observed only at 2 wk post-MCT and both decreased by 4 wk post-MCT despite progressive PAH. PDTC (starting on days 1 and 3) rescued caveolin-1 and Tie2, reversed MCT-induced PY-STAT3 activation, and attenuated PAH. In addition, PDTC restored I-kappaBalpha expression and reduced superoxide chemiluminescence at 2 wk but did not inhibit NF-kappaB activation despite attenuation of PAH. PDTC had no effect on established PAH. Increased superoxide chemiluminescence and NF-kappaB activation appear to be a transient phenomenon in the MCT model. Thus the disruption of endothelial cell membrane integrity resulting in caveolin-1 loss and reciprocal activation of PY-STAT3 plays a key role in the MCT-induced PAH.     

Analysis of genetic relatedness of Haemophilus influenzae isolates by multilocus sequence typing

The gram-negative bacterium Haemophilus influenzae is a human-restricted commensal of the nasopharynx that can also be associated with disease. The majority of H. influenzae respiratory isolates lack the genes for capsule production and are nontypeable (NTHI). Whereas encapsulated strains are known to belong to serotype-specific phylogenetic groups, the structure of the NTHI population has not been previously described. A total of 656 H. influenzae strains, including 322 NTHI strains, have been typed by multilocus sequence typing and found to have 359 sequence types (ST). We performed maximum-parsimony analysis of the 359 sequences and calculated the majority-rule consensus of 4,545 resulting equally most parsimonious trees. Eleven clades were identified, consisting of six or more ST on a branch that was present in 100% of trees. Two additional clades were defined by branches present in 91% and 82% of trees, respectively. Of these 13 clades, 8 consisted predominantly of NTHI strains, three were serotype specific, and 2 contained distinct NTHI-specific and serotype-specific clusters of strains. Sixty percent of NTHI strains have ST within one of the 13 clades, and eBURST analysis identified an additional phylogenetic group that contained 20% of NTHI strains. There was concordant clustering of certain metabolic reactions and putative virulence loci but not of disease source or geographic origin. We conclude that well-defined phylogenetic groups of NTHI strains exist and that these groups differ in genetic content. These observations will provide a framework for further study of the effect of genetic diversity on the interaction of NTHI with the host.     

Stages in follicle cell/oocyte interface during vitellogenesis in caecilians <Emphasis Type="Italic">Ichthyophis tricolor</Emphasis> and <Emphasis Type="Italic">Gegeneophis ramaswamii</Emphasis>: a transmission electron-microscopic study

We describe the ultrastructural organization of the vitellogenic follicle stages in two caecilian species. Monthly samples of slices of ovary of Ichthyophis tricolor and Gegeneophis ramaswamii from the Western Ghats of India were subjected to transmission electron-microscopic analysis, with special attention to the follicle cell/oocyte interface. In order to maintain uniformity of the stages among the amphibians, all the stages in the caecilian follicles were assigned to stages I–VI, the vitellogenic and post-vitellogenic follicles being assigned to stages III–VI. Stage III commences with the appearance of precursors of vitelline envelope material in the perivitelline space. Stages IV and V have been assigned appropriate substages. During the transition of stage III to stage VI oocytes, a sequential change occurs in the manifestations of follicle cells, perivitelline space, vitelline envelope and oocyte cortex. The vitelline envelope becomes a tough coat through the tunnels of which the macrovilli pass to interdigitate between the microvilli. The oocyte surface forms pinocytic vesicles that develop into coated pits and, later, coated vesicles. Contributions of the oocyte cortex to the vitelline envelope and of the follicle cells to yolk material via synthesis within them are indicated. The follicle cell/oocyte interface of vitellogenic follicles of these two caecilians resembles that in anurans and urodeles, with certain features being unique to caecilians. Thus, this paper throws light on the possible relationships of caecilians to anurans and urodeles with special reference to ovarian follicles. This research was supported by funds from the Kerala State Council for Science, Technology and Environment (KSCSTE), through the SARD facility, and by the FIST scheme of Department of Science and Technology, Government of India, New Delhi, to the Department of Zoology, University of Kerala, Thiruvananthapuram, and to the Department of Animal Science, Bharathidasan University, Thiruchirapalli (SR/FST/LSI-233/2002).     

C3G regulates cortical neuron migration, preplate splitting and radial glial cell attachment

Neuronal migration is integral to the development of the cerebral cortex and higher brain function. Cortical neuron migration defects lead to mental disorders such as lissencephaly and epilepsy. Interaction of neurons with their extracellular environment regulates cortical neuron migration through cell surface receptors. However, it is unclear how the signals from extracellular matrix proteins are transduced intracellularly. We report here that mouse embryos lacking the Ras family guanine nucleotide exchange factor, C3G (Rapgef1, Grf2), exhibit a cortical neuron migration defect resulting in a failure to split the preplate into marginal zone and subplate and a failure to form a cortical plate. C3G-deficient cortical neurons fail to migrate. Instead, they arrest in a multipolar state and accumulate below the preplate. The basement membrane is disrupted and radial glial processes are disorganised and lack attachment in C3G-deficient brains. C3G is activated in response to reelin in cortical neurons, which, in turn, leads to activation of the small GTPase Rap1. In C3G-deficient cells, Rap1 GTP loading in response to reelin stimulation is reduced. In conclusion, the Ras family regulator C3G is essential for two aspects of cortex development, namely radial glial attachment and neuronal migration.     

COBioSIFTER – A CORBA-Based Distributed Multi-Agent Biological Information Management System

In this paper, we describe the COBioSIFTER project that aims at constructing a framework for managing information from the biological domain. It uses a distributed multi-agent approach based on the CORBA middleware and contains an architecture made up of functionally heterogeneous agents. A series of experiments has been carried out with a prototype of COBioSIFTER to illustrate its advantages such as high performance, scalability, heterogeneity, and fault tolerance. The results of these experiments demonstrate the effectiveness of such an agent-based biological information framework.     

Evolution in metacommunities: on the relative importance of species sorting and monopolization in structuring communities

Abstract: Adaptive evolution within species and community assembly involving multiple species are both affected by dispersal and spatiotemporal environmental variation and may thus interact with each other. We examined this interaction in a simple three-patch metacommunity and found that these two processes produce very different associations between species composition and local environment. In most conditions, we find a pattern we call "species sorting," wherein local adaptation by resident species cannot prevent invasions by other preadapted species as environmental conditions change (strong association between local environmental conditions and local community composition). When dispersal rates are very low relative to the other two rates, local adaptation by resident species predominates, leading to strong priority effects that prevent successful colonization by other species that would have been well adapted, a pattern we call "local monopolization." When dispersal and evolutionary rates are both very high, we find that an evolving species outcompetes other species in all patches, a pattern we call "global monopolization." When environmental oscillations are very frequent, local monopolization predominates. Our findings indicate that there can be strong modification of community assembly by local adaptive processes and that these depend strongly on the relative rates of evolution, dispersal, and environmental change.