The Serengeti food web: empirical quantification and analysis of topological changes under increasing human impact

1.?To address effects of land use and human overexploitation on wildlife populations, it is essential to better understand how human activities have changed species composition, diversity and functioning. Theoretical studies modelled how network properties change under human-induced, non-random species loss. However, we lack data on realistic species-loss sequences in threatened, real-world food webs to parameterize these models. 2.?Here, we present a first size-structured topological food web of one of the most pristine terrestrial ecosystems in the world, the Serengeti ecosystem (Tanzania). The food web consists of 95 grouped nodes and includes both invertebrates and vertebrates ranging from body masses between 10(-7) and 10(4) kg. 3.?We study the topological changes in this food web that result from the simulated IUCN-based species-loss sequence representing current species vulnerability to human disturbances in and around this savanna ecosystem. We then compare this realistic extinction scenario with other extinction sequences based on body size and connectance and perform an analysis of robustness of this savanna food web. 4.?We demonstrate that real-world species loss in this case starts with the biggest (mega) herbivores and top predators, causing higher predator-prey mass ratios. However, unlike theoretically modelled linear species deletion sequences, this causes poor-connected species to be lost first, while more highly connected species become lost as human impact progresses. This food web shows high robustness to decreasing body size and increasing connectance deletion sequences compared with a high sensitivity to the decreasing connectance deletion scenario. 5.?Furthermore, based on the current knowledge of the Serengeti ecosystem, we discuss how the focus on food web topology alone, disregarding nontrophic interactions, may lead to an underestimation of human impacts on wildlife communities, with the number of trophic links affected by a factor of two. 6.?This study underlines the importance of integrative efforts between the development of food web theory and basic field work approaches in the quantification of the structure of interaction networks to sustain natural ecosystems in a changing world.     

Oscillations in the lateral pressure of lipid monolayers induced by nonlinear chemical dynamics of the second messengers MARCKS and protein kinase C

The binding of the MARCKS peptide to the lipid monolayer containing PIP₂ increases the lateral pressure of the monolayer. The unbinding dynamics modulated by protein kinase C leads to oscillations in lateral pressure of lipid monolayers. These periodic dynamics can be attributed to changes in the crystalline lipid domain size. We have developed a mathematical model to explain these observations based on the changes in the physical structure of the monolayer by the translocation of MARCKS peptide. The model indicates that changes in lipid domain size drives these oscillations. The model is extended to an open system that sustains chemical oscillations.     

Characterization of heterotrophic nitrifying bacteria with respiratory ammonification and denitrification activity – Description of Paenibacillus uliginis sp. nov., an inhabitant of fen peat soil and Paenibacillus purispatii sp. nov., isolated from a spacecraft assembly clean room

In the course of studying the influence of N-fertilization on N₂ and N₂O flux rates in relation to soil bacterial community composition of a long-term fertilization experiment in fen peat grassland, a strain group was isolated that was related to a strain isolated from a spacecraft assembly clean room during diversity studies of microorganisms, which withstood cleaning and bioburden reduction strategies. Both the fen soil isolates and the clean room strain revealed versatile physiological capacities in N-transformation processes by performing heterotrophic nitrification, respiratory ammonification and denitrification activity.     

Endomyocardial biopsy derived adherent proliferating cells—A potential cell source for cardiac tissue engineering

Heart diseases are a leading cause of morbidity and mortality. Cardiac stem cells (CSC) are considered as candidates for cardiac‐directed cell therapies. However, clinical translation is hampered since their isolation and expansion is complex. We describe a population of human cardiac derived adherent proliferating (CAP) cells that can be reliably and efficiently isolated and expanded from endomyocardial biopsies (0.1 cm³). Growth kinetics revealed a mean cell doubling time of 49.9 h and a high number of 2.54 × 10⁷ cells in passage 3. Microarray analysis directed at investigating the gene expression profile of human CAP cells demonstrated the absence of the hematopoietic cell markers CD34 and CD45, and of CD90, which is expressed on mesenchymal stem cells (MSC) and fibroblasts. These data were confirmed by flow cytometry analysis. CAP cells could not be differentiated into adipocytes, osteoblasts, chondrocytes, or myoblasts, demonstrating the absence of multilineage potential. Moreover, despite the expression of heart muscle markers like α‐sarcomeric actin and cardiac myosin, CAP cells cannot be differentiated into cardiomyocytes. Regarding functionality, CAP cells were especially positive for many genes involved in angiogenesis like angiopoietin‐1, VEGF, KDR, and neuropilins. Globally, principal component and hierarchical clustering analysis and comparison with microarray data from many undifferentiated and differentiated reference cell types, revealed a unique identity of CAP cells. In conclusion, we have identified a unique cardiac tissue derived cell type that can be isolated and expanded from endomyocardial biopsies and which presents a potential cell source for cardiac repair. Results indicate that these cells rather support angiogenesis than cardiomyocyte differentiation. J. Cell. Biochem. 109: 564–575, 2010. © 2009 Wiley‐Liss, Inc.     

Structure of a GDP:AlF4 complex of the SRP GTPases Ffh and FtsY, and identification of a peripheral nucleotide interaction site

The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement. We have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the activation region. We report here the structure of a complex of the SRP GTPases formed in the presence of GDP:AlF4. This complex accommodates the putative transition-state analog without undergoing significant change from the structure of the ground-state complex formed in the presence of the GTP analog GMPPCP. However, small shifts that do occur within the shared catalytic chamber may be functionally important. Remarkably, an external nucleotide interaction site was identified at the activation region, revealed by an unexpected contaminating GMP molecule bound adjacent to the catalytic chamber. This site exhibits conserved sequence and structural features that suggest a direct interaction with RNA plays a role in regulating the activity of the SRP targeting complex.     

2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei

The variant surface glycoprotein (VSG) of Trypanosoma brucei forms a coat on the surface of the parasite; by the expression of a series of antigenically distinct VSGs in the surface coat the parasite escapes the host immune response. The 2.9 A resolution crystal structure of the N-terminal domain of one variant, MITat 1.2, has been determined. The structure was solved using data collected from two crystal forms. Initially a partial model was built into an electron density map based on multiple isomorphous replacement phases and improved by phase combination methods. Subsequently this model was used to obtain the molecular replacement solution for a second crystal form, providing starting phases which were refined using 2-fold non-crystallographic symmetry averaging. The current model includes 362 residues and has been refined using X-PLOR to an R value of 0.22 for data between 7 and 2.9 A. The molecule is a dimer, approximately 100 A long, having an asymmetrical cross section with maximum dimensions of approximately 40 A x 60 A. Two long, approximately 70 A, alpha-helices from each monomer pack together to form, with several other helices, a core helix bundle that extends nearly the full length of the molecule. The "top" of the protein, which in the surface coat may be exposed to the external environment, is formed from the ends of the two long helices, a short three-stranded beta-sheet, and a strand having irregular conformation that packs above these secondary structure elements. Two conserved disulfide bridges are in this part of the molecule. Several elements of the MITat 1.2 sequence, which contribute to the formation of the helix bundle structure, have been identified. These elements can be found in the sequences of several different VSGs, suggesting that to some extent the VSG structure is conserved in those variants.     

LAMP-1 and LAMP-2, but not LAMP-3, are reliable markers for activation-induced secretion of human mast cells.

BACKGROUND: Mast cells are resident tissue cells that induce anaphylactic reactions by rapidly releasing mediators after antigen-mediated cross-linking of immunoglobulin E receptors. In the similarly active peripheral blood basophilic leukocyte, lysosome-associated membrane protein 3 (LAMP-3; CD63) has been described as an activation marker, but LAMPs have not been investigated in normal tissue mast cells. METHODS: Intra- and extracellular expressions of LAMP-1 (CD107a), LAMP-2 (CD107b), and LAMP-3 (CD63) were analysed by flow cytometry, immunocytochemistry, and functional assays in unstimulated and stimulated leukemic human mast cell line 1 (HMC-1) and skin mast cells. RESULTS: On flow cytometry, all mast cells expressed LAMP-3 at their cell membranes, whereas LAMP-1 and LAMP-2 were barely detectable (HMC-1 cells) or expressed at low levels (<10% of skin mast cells). After fixation and permeabilisation, high intracellular levels of all three LAMPs were noted in both cell types. After stimulation, a rapid translocation of intracellular LAMPs to the cell membrane, with an associated release of histamine, leukotriene C(4) and prostaglandin D(2), was ascertained in skin mast cells only. CONCLUSION: These results show that LAMP-1 and LAMP-2 are activation markers for normal mast cells. The lack of LAMP translocation after activation of leukemic mast cells may be related to maturation or malignancy-associated defects of these cells.     

Identification and characterisation of IS1383, a new insertion sequence isolated from Pseudomonas putida strain H

A new insertion sequence (IS1383) was identified on plasmids from Pseudomonas putida strain H and its nucleotide sequence was determined. IS1383 contains perfect terminal inverted repeats of 13-bp flanking a 1.4-kb internal sequence. A single significant open reading frame was identified that can encode a 342-amino acid polypeptide which was predicted to be highly basic and to have homology to polypeptides known from several other bacterial insertion sequences. At least six copies of IS1383 are present on the plasmids pPGH1 and pPGH2, whereas no copy could be detected on the chromosome of P. putida strain H. Target duplications did not flank the inverted repeats of any of the six IS1383 copies examined. Analysis of the integration sites of IS1383 revealed hints for a target specificity. Multiple sequence alignments of the transposases, the inverted repeats and the integration sites pointed to the assignment of IS1383 into a putative new family of insertion sequences defined as the IS1111 family.     

Characterisation of the mating-type locus in the genus Xanthoria (lichen-forming ascomycetes, Lecanoromycetes)

Conserved regions of mating-type genes were amplified in four representatives of the genus Xanthoria (X. parietina, X. polycarpa, X. flammea, and X. elegans) using PCR-based methods. The complete MAT locus, containing one ORF (MAT1-2-1) coding for a truncated HMG-box protein, and two partial flanking genes, were cloned by screening a genomic lambda phage library of the homothallic X. parietina. The flanking genes, a homologue of SLA2 of Saccharomyces cerevisiae and a DNA lyase gene, served to amplify the two idiomorphs of the X. polycarpa MAT locus. Each idiomorph contains a single gene: MAT1-2-1 codes for a HMG-box protein, MAT1-1-1 encodes an alpha domain protein. The occurrence of mating-type genes in eight single spore isolates derived from one ascus was studied with a PCR assay. In the homothallic X. parietina a HMG fragment, but no alpha box fragment was found in all isolates, whereas in X. elegans, another homothallic species, all tested isolates contained a fragment of both idiomorphs. Conversely, isolates of the heterothallic X. polycarpa contained either a HMG or an alpha box fragment, but never both.