bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grass and oak litter exert different effects on seedling emergence of herbaceous perennials from grasslands and woodlands
Authors: Donath Tobias W. , Eckstein R. Lutz 
Published: February 2008

Summary

The effects of litter on seedling emergence (e.g. during succession from grassland to woodland) may not only depend on litter amount and environmental conditions but may also be related to litter types. We tested the effect of litter types, litter cover and soil moisture on the emergence of four congeneric pairs of grassland and woodland species.
We carried out a controlled pot experiment (Experiment I) using litter and species from two habitats (grassland vs. woodland), three levels of litter cover (low, medium, high) and two levels of water‐addition (leading to constantly humid or intermittently dry substrate). Amounts of litter were adjusted to result in the same relative light reduction for both litter types. Consequently, we applied 2 g, 4 g and 8 g of grassland litter and 0.5 g, 1 g and 2 g of woodland (oak) litter per pot.
To separate the shade effect of litter from its mechanical plus chemical effects we exposed additional pots with seeds of the same species to deep shade conditions (Experiment II) corresponding to 4 g and 1 g of grass and oak litter, respectively.
Under intermittently dry conditions both litter types increased seedling emergence. In addition, we found a significant interaction between litter type and species origin: seedling emergence of woodland species was significantly lower from beneath grass litter than from beneath oak litter, whereas grassland species emerged equally well from beneath both litter types. Compared with seed germination under a shade cloth, seedling emergence of woodland species from beneath grass litter was reduced by 44%. Litter significantly affected soil humidity and the amplitude of diurnal temperature fluctuations. Differential effects of litter types on woodland and grassland species are probably related to litter structure.
Synthesis. Our experimental data present evidence that ecosystem specific litter effects slow down succession from grassland to woodland and that the effect size is controlled by the litter amount present and the environmental conditions.
Exploring climatic and biotic controls on Holocene vegetation change in Fennoscandia
Authors: Miller Paul A. , Giesecke Thomas , Hickler Thomas , Bradshaw Richard H. W. , Smith Benjamin , Seppä Heikki , Valdes Paul J. , Sykes Martin T. 
Published: February 2008

Summary

We investigated the potential drivers of Holocene vegetation changes recorded at four Scandinavian pollen sites, two in Sweden and two in Finland, at a time when they were largely free of anthropogenic influence.
We used the generalized dynamic vegetation model LPJ‐GUESS forced with climate anomaly output from an atmospheric general circulation model to simulate tree species dynamics from 10 000 years ago to the present. The model results were compared to high‐resolution pollen accumulation rates gathered at the sites.
Our results indicate that both the observed northern distributional limits of temperate trees, and the limits of Pinus sylvestris and Alnus incana at the tree line, are a result of millennial variations in summer and winter temperatures. The simulation of several distinct trends in species occurrence observed in the pollen record indicates that a time lag due to the slow spreading of species need not be invoked for most species.
Sensitivity studies indicate that competition, natural disturbance and the magnitude of interannual variability play key roles in determining the biomass, establishment and even the presence of species near their bioclimatic limits. However, neither disturbance due to fire nor limits on establishment due to drought were likely to have been major determinants of the observed trends on the timescales considered.
We were unable to limit the modelled occurrence of Picea abies at the study sites to the periods at which it was observed in the pollen records, indicating that we have still not completely understood the driving or limiting factors for Holocene changes in Picea abies abundance.
Synthesis. This study shows that by combining quantitative vegetation reconstructions with a modern, process‐based dynamic vegetation model, we may gain new insights into the potential biotic and abiotic drivers of Holocene vegetation dynamics, and their relative importance. This knowledge will be crucial in enabling us to assess more confidently the response of northern European vegetation to future climate change.
Phylogeography of a Sahelian rodent species Mastomys huberti: a Plio‐Pleistocene story of emergence and colonization of humid habitats
Authors: MOULINE KARINE , GRANJON LAURENT , GALAN MAXIME , TATARD CAROLINE , ABDOULLAYE DOUKARY , ATTEYINE SOLIMANE AG , DUPLANTIER JEAN‐MARC , COSSON JEAN‐FRANÇOIS 
Published: February 2008

AbstractThe multimammate rat Mastomys huberti is a Sahelian species restricted to West Africa. Throughout its distribution area, the species is associated with humid habitats, flood plains and ponds, which make its current distribution highly fragmented. Knowing that humid and dry climatic phases regularly alternated along the Quaternary in West Africa, it can be postulated that the evolutionary history of the species and its genetic variation largely reflect these climatic oscillations. We used mitochondrial cytochrome b sequences to investigate the phylogenetic relationships of M. huberti populations across the totality of the species’ geographical range (Mali, Senegal, Guinea and Mauritania). We found that cytochrome b sequence variation is partitioned into four divergent clades (mean Kimura 2‐parameter genetic distances varying from 0.57 to 3.08%) corresponding to distinct geographical regions. We dated the separation events of these clades between 0.93 and 0.17 million years ago, suggesting that M. huberti history was strongly influenced by the Quaternary climatic variations and related hydrographic network changes. Relationships between lineages and the partitioning of genetic diversity suggest the occurrence of two refuges along the Atlantic coast during arid periods. Moreover, the species’ current range results from a stepwise colonization from west to east. M. huberti colonized recently the Inner Delta of Niger River in Mali, probably during a humid episode some 0.6 million years ago. Demographically stable and highly diversified populations were found in South Senegal and Guinea while populations in North Senegal and in Mali experienced low numbers followed by a demographic expansion during the African Humid Period (c. 14 800–5500 bp). During the last arid period (c. 23 000–18 000 years ago), Malian populations found refuge in the northern parts of the Inner Delta of the Niger River, then expended to the southern parts of the delta and along the course of the Niger River downstream Tombouctou. More recently, M. huberti would have rapidly expanded into irrigated areas along the Senegal River and along the Canal du Sahel, Mali, reflecting the invasive and the pest character of this species.
INVITED REVIEW: Molecular analysis of predation: a review of best practice for DNA‐based approaches
Authors: KING R. A. , READ D. S. , TRAUGOTT M. , SYMONDSON W. O. C. 
Published: February 2008

AbstractMolecular analysis of predation, through polymerase chain reaction amplification of prey remains within the faeces or digestive systems of predators, is a rapidly growing field, impeded by a lack of readily accessible advice on best practice. Here, we review the techniques used to date and provide guidelines accessible to those new to this field or from a different molecular biology background. Optimization begins with field collection, sample preservation, predator dissection and DNA extraction techniques, all designed to ensure good quality, uncontaminated DNA from semidigested samples. The advantages of nuclear vs. mitochondrial DNA as primer targets are reviewed, along with choice of genes and advice on primer design to maximize specificity and detection periods following ingestion of the prey by the predators. Primer and assay optimization are discussed, including cross‐amplification tests and calibratory feeding experiments. Once primers have been made, the screening of field samples must guard against (through appropriate controls) cross contamination. Multiplex polymerase chain reactions provide a means of screening for many different species simultaneously. We discuss visualization of amplicons on gels, with and without incorporation of fluorescent primers. In more specialized areas, we examine the utility of temperature and denaturing gradient gel electrophoresis to examine responses of predators to prey diversity, and review the potential of quantitative polymerase chain reaction systems to quantify predation. Alternative routes by which prey DNA might get into the guts of a predator (scavenging, secondary predation) are highlighted. We look ahead to new technologies, including microarrays and pyrosequencing, which might one day be applied to this field.
PERSPECTIVE: A smörgåsbord of markers for avian ecology and evolution
Authors: EDWARDS SCOTT V. 
Published: February 2008

AbstractThe polymerase chain reaction has been a boon to the study of molecular ecology and population genetics of birds. But the nagging truth is that for many bird species, the number of polymerase chain reaction (PCR) primer pairs that one can pick off the shelf and expect to amplify their target loci with ease is frustratingly small. Now, studying DNA sequence variation in natural populations of birds just got a whole lot easier. This issue of Molecular Ecology reports a large‐scale bioinformatics search for exonic sequences conserved between the chicken and zebra finch genomes and flanking polymorphic introns that has generated a staggering 242 PCR primer pairs that readily amplify their single‐copy target loci in five avian species spanning ~100 million years of avian evolution (Backström et al. 2008). As proof of principle, these primers have also been used to survey the genomic landscape in over 110 kb of intronic sequence in the collared flycatcher, a model species in ecology and evolution. These resources pave the way for easy multilocus study of evolving populations and lineages of birds, and bring the goal of quickly turning nonmodel species in to ecological genomic models tantalizingly close.
Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data
Authors: BONHOMME M. , BLANCHER A. , CUARTERO S. , CHIKHI L. , CROUAU‐ROY B. 
Published: February 2008

AbstractCynomolgus macaques (Macaca fascicularis) were introduced on the island of Mauritius between 400 and 500 years ago and underwent a strong population expansion after a probable initial founding event. However, in practice, little is known of the geographical origin of the individuals that colonized the island, on how many individuals were introduced, and of whether the following demographic expansion erased any signal of this putative bottleneck. In this study, we asked whether the current nuclear genome of the Mauritius population retained a signature that would allow us to answer these questions. Altogether, 21 polymorphic autosomal and sex‐linked microsatellites were surveyed from 81 unrelated Mauritius individuals and 173 individuals from putative geographical sources in Southeast Asia: Java, the Philippines islands and the Indochinese peninsula. We found that (i) the Mauritius population was closer to different populations depending on the markers we used, which suggests a possible mixed origin with Java playing most probably a major role; and (ii) the level of diversity was lower than the other populations but there was no clear and consistent bottleneck signal using either summary statistics or full‐likelihood methods. However, summary statistics strongly suggest that Mauritius is not at mutation–drift equilibrium and favours an expansion rather than a bottleneck. This suggests that on a short time scale, population decline followed by growth can be difficult to deduce from genetic data based on mutation–drift theory. We then used a simple Bayesian rejection algorithm to estimate the number of founders under different demographic models (exponential, logistic and logistic with lag) and pure genetic drift. This new method uses current population size estimates and expected heterozygosity of Mauritius and source population(s). Our results indicate that a simple exponential growth is unlikely and that, under the logistic models, the population may have expanded from an initial effective number of individuals of 10–15. The data are also consistent with a logistic growth with different lag values, indicating that we cannot exclude past population fluctuation.
Inhibitory Properties of the Antibody Response to Plasmodium vivax Duffy Binding Protein in an Area with Unstable Malaria Transmission
Authors: Ceravolo I. P. , Souza‐Silva F. A. , Fontes C. J. F. , Braga E. M. , Madureira A. P. , Krettli A. U. , Souza J. M. , Brito C. F. A. , Adams J. H. , Carvalho L. H. 
Published: February 2008

AbstractThe function of the Plasmodium vivax Duffy binding protein (DBP) during the erythrocyte invasion process is critical for successful parasite growth and pathogenesis in human infections. Although DBP is the subject of intensive malaria vaccine research, investigations on the functional proprieties of anti‐DBP antibodies in the human population have been limited [Infect Immun68 (2000) 3164]. In the present study, we examined the ability of sera from different populations of the Brazilian Amazon – an area of markedly unstable malaria transmission – to inhibit the erythrocyte‐binding function of the DBP ligand domain (region II, DBPII). We found that long‐term exposure to malaria in the Amazon area elicits DBP‐specific antibodies that inhibit the binding of different DBPII variants to erythrocytes. Despite the great variability of inhibitory antibody responses observed among study participants, we observed a positive correlation between erythrocyte binding‐inhibitory activity and enzyme‐linked immunosorbent assay anti‐DBP antibodies. Of importance, there was a non‐significant tendency towards increased levels of anti‐DBP antibodies among individuals with asymptomatic P. vivax infections.
Evaluation of Cartilage and Bone Degradation in a Murine Collagen Antibody‐induced Arthritis Model
Authors: Oestergaard S. , Rasmussen K. E. , Doyle N. , Varela A. , Chouinard L. , Smith S. Y. , Qvist P. , Karsdal M. A. 
Published: February 2008

AbstractThe purpose of this work was to validate collagen antibody‐induced arthritis (CAIA) model in two mice strains (Balb/c and CD‐1) using clinical, biochemical, microstructural and histological techniques. We induced arthritis in mice using a cocktail of collagen type II (CII) antibodies followed by an injection with lipopolysaccharide (LPS) in different doses in Balb/c and CD‐1 mice strains. Serum CTX‐II levels were measured at study termination and correlated with microscopic severity of joint lesions as determined by a validated scoring systems. Bone involvement was assessed by microcomputer tomography (micro‐CT). Balb/c mice developed rapid (day 6) and robust (100%) arthritis, whereas CD‐1 mice showed only temporary macroscopic signs of disease. Serum CTX‐II levels in Balb/c mice showed a significant increase in cartilage degradation in diseased animals (43–64% compared with non‐diseased mice) and was decreased in animals receiving dexamethasone. Correlation of serum CTX‐II with the microscopic score was statistically significant (P < 0.01). Micro‐CT analysis demonstrated structural damage in bone in the CAIA Balb/c mice, which was prevented by dexamethasone. The CAIA‐LPS model provides a useful supplement to currently available animal models of arthritis. This is a rapid onset and robust model; however, the choice of mouse strain should be evaluated carefully.
The Impact of Substance P Signalling on the Development of Experimental Staphylococcal Sepsis and Arthritis
Authors: Verdrengh M. , Tarkowski A. 
Published: February 2008

AbstractSubstance P (SP), acting on the neurokinin‐1 receptor (NK‐1R), is a neuropeptide, involved in the inflammatory processes. It promotes vasodilatation and increases vasopermeability, thus ensuing extravasation and accumulation of leucocytes at sites of injury. The aim of this study was to assess the impact of SP signalling on the responses during staphylococcal infection and the accompanying arthritis. Three experiments were performed where NK‐1R−/− mice and controls were intravenously infected with different doses of Staphylococcus aureus. Clinical assessment of arthritis was performed as well as histological analysis of bone and cartilage destruction in the joints. In addition, the impact of NK‐1R mutation on bacterial load in the kidneys as well as the phagocytic capacity of blood leucocytes were studied. Mice lacking the NK‐1R displayed significantly higher bacterial load in the kidneys and significantly more severe synovitis and cartilage/bone destruction than the controls when inoculated with 1.4 × 107 staphylococci. Infection with 3.5 × 108 CFU/mouse induced sepsis. Thus, 11 days after bacterial inoculation 15 of 19 mice in the NK‐1R−/− group had died versus 8 of 15 in the control group. Phagocytosis test revealed that significantly fewer macrophages from NK‐1R−/− mice were able to phagocytose S. aureus when compared with macrophages from congenic control mice. Blocking the biological responses to substance P via its receptor NK‐1R results in a less efficient clearance of bacteria leading to more severe arthritic lesions in mice.
Coordinate NF‐κB and STAT1 Activation Promotes Development of Myeloid Type 1 Dendritic Cells
Authors: Vakkila J. , Demarco R. A. , Lotze M. T. 
Published: February 2008

AbstractNF‐κB and STAT1 are critically involved in the initiation of the inflammatory cascade. Using semi‐automated imaging cytometry and fluorescent antibodies, we screened several factors for their ability to induce nuclear translocation of RelA/NF‐κB and STAT1 in subsets of monocyte‐derived dendritic cells (DC). Detailed kinetics and dose–response studies are presented for IL‐1‐, LPS‐, CD40L‐, IFN‐γ‐ and IFN‐α‐stimulated responses. The results are consistent with the notion that simultaneous activation of both STAT1 and NF‐κB pathways at the initiation of differentiation culture is required for efficient priming of IL‐12 production by DC. Maturation of DC led to characteristic NF‐κB and STAT1 distribution and response patterns. During the resting stage, DC differentiated under the presence of IFN‐γ showed sustained STAT activation and remained responsive to LPS. By contrast, PGE2‐supplemented DC could be characterized by negligible responses to LPS and IFN‐γ and a remarkable NF‐κB response to CD40L. STAT1 pathway was suppressed in PGE2‐supplemented cells. We conclude that the magnitude and temporal kinetics of the nuclear shift of STAT1 and NF‐κB in myeloid DC are associated with IL‐12p70 production and are dependent on the nature of the stimulating factors and the polarization state of cells.
CD 127− and FoxP3+ Expression on CD25+CD4+ T Regulatory Cells upon Specific Diabetogeneic Stimulation in High‐risk Relatives of Type 1 Diabetes Mellitus Patients
Authors: Vrabelova Z. , Hrotekova Z. , Hladikova Z. , Bohmova K. , Stechova K. , Michalek J. 
Published: February 2008

AbstractAbnormalities in CD4+CD25+ regulatory T cells (Treg) may contribute to type 1 diabetes (T1D) development. First‐degree relatives of T1D patients are at increased risk especially when they carry certain HLA II haplotypes. Using two novel markers of CD4+CD25+ Treg (CD127− and FoxP3+ respectively), we evaluated number and function of Treg after specific stimulation with diabetogeneic autoantigens in 11 high‐risk (according to HLA‐linked risk) relatives of T1D patients and 14 age‐matched healthy controls using a cytokine secretion assay based on interferon‐γ (IFN‐γ) production. High‐risk relatives of T1D patients had significantly lower pre‐ and post‐stimulatory number of CD127− Treg than that of healthy controls (P < 0.05). Labelling Treg with FoxP3+ demonstrated similar trend but did not reach statistical significance. Although the stimulation with diabetogenic autoantigens did not lead to a significant change in number of Treg in both groups, the defective function of Treg was performed by significantly higher activation of diabetogeneic T cells in high‐risk relatives of T1D patients compared to healthy controls (P ≤ 0.02). Individuals at increased HLA‐associated genetic risk for T1D showed defects in Treg.
Immunostimulatory Oligodeoxynucleotide Containing TTTCGTTT Motif from Lactobacillus rhamnosus GG DNA Potentially Suppresses OVA‐specific IgE Production in Mice
Authors: Iliev I. D. , Tohno M. , Kurosaki D. , Shimosato T. , He F. , Hosoda M. , Saito T. , Kitazawa H. 
Published: February 2008

AbstractIn a previous study of the immunoregulatory properties of commensal bacterial DNA, we identified the strong immunostimulatory oligodeoxynucleotide (ISS‐ODN) ID35 in the genomic DNA of Lactobacillus rhamnosus GG (LGG). The observed effects of ID35 are because of the unique TTTCGTTT motif located at the 5′ end of the ODN, which is different from the previously identified ISS motifs in humans and mice. In the present study, we used an ovalbumin (OVA)‐sensitized mouse model to show that ID35 is a potent suppressor of antigen‐specific immunoglobulin E (IgE) production in vivo. This effect was toll‐like receptor 9‐dependent, as GpC negID35 failed to suppress antigen‐specific IgE production. ID35 activated the specific subset of CD11c+CD8a+ dendritic cells, which are associated with T‐helper 1 (Th1)‐type systemic responses, and effectively induced interferon‐gamma (IFN‐γ) production by CD4+ T cells in OVA‐challenged mice. These immunoregulatory effects of ID35 were comparable with those induced by the murine prototype ODN 1826. Thus, ID35 is the first ISS‐ODN with such a strong immunostimulatory and IgE suppressor activity to be found in immunobiotic bacterial DNA.
Association between PTPN22 C1858T and type 1 diabetes: a replication in continental Italy
Authors: Saccucci P. , Del Duca E. , Rapini N. , Verrotti A. , Piccinini S. , Maccari A. , Canu G. , Angelini F. , Fontana L. , Giannini C. , Chiarelli F. , Manca Bitti M. L. , Bottini N. 
Published: February 2008

AbstractThe missense PTPN22 C1858T polymorphism recently emerged as an important population‐independent risk factor for type 1 diabetes (T1D) and other autoimmune diseases. The PTPN22 gene encodes the lymphoid tyrosine phosphatase (LYP), a negative regulator of signal transduction through the T‐cell receptor. Although the frequency of the polymorphism is variable among different ethnic groups, the association between PTPN22 *T1858 and T1D has been replicated in several populations. Here, we contribute the first replication of the association between PTPN22 and T1D in populations from continental Italy, carried out in two independent samples of T1D patients (N = 216 and 82) and controls (N = 271 and 89). Our data also suggest that T1D carriers of the *T1858 allele could be at increased risk for other comorbid autoimmune disorders.