Radiotherapy Treatment Patients were treated in a breast board in the supine position with both arms extended overhead and supported by a dedicated arm rest. 3D Treatment plans (Eclipse Treatment Planning System- Varian CA) were based on CT images acquired by a Idasanutlin dedicated radiotherapy AQ Sim CT scan (Philips Medical systems, Netherlands) with a 5 mm spacing from the apex of the lungs to the diaphragm, including the whole lung and breast. The Clinical Target Volume (CTV) consisted of the whole breast parenchyma. The Planning Target Volume (PTV) was obtained by adding a 1 cm margin to the CTV except in the direction of the skin’s surface. Organs at risk (OARs) such as omolateral

lung – from the apex to the base – and the heart in the Raf inhibitor left-side breast cancer were also outlined in every slice. 3D conformal radiotherapy was delivered by two opposed 6 MV photon beams (Varian LINAC 2100 endowed with a Millenium multileaf collimator). Wedge compensation was used to ensure

a uniform dose distribution to the target volume of -5% and +7% [16]. The total dose was 34 Gy delivered in 10 daily fractions, 3.4 Gy per day, 5 days a week; the dose was normalized at the ICRU (International Commission on Radiation Units and Measurements) reference point [16]. Portal images were taken to check positioning just before the first session and then every learn more two sessions. The boost dose of 8 Gy (prescribed to the 90% reference isodose) was administered in a single fraction by a 6 to 12 MeV electron field according to the location of the tumour bed defined by metallic clips purposefully positioned at the time of the surgery and/or by computer tomography analysis. Dose on the lungs (considering only the homolateral) was kept below the limit of 15.6 Gy to no more than 12.5%

of the volume, 10.1 Gy to no more than 14.5% and 7.8 Gy to no more than 16% (Table 3, i.e equivalent to V20 Gy<12.5%, V13<14.5% and Etofibrate V10<16% respectively at 2 Gy/fr regime considering an α/β value for the lung equal to 3 Gy [17, 18]). Table 3 Volume and dosimetric parameters related to lung   Minimum Average ± sd Maximum Lung Volume (cm 3 ) 807 1403 ± 305 2050 Mean Lung Dose (Gy) 0.76 1.69 ± 0.7 4.44 V 7.8 Gy (%) 1.1 4.5 ± 2.3 13.0 V 10.1 Gy (%) 0.9 4.1 ± 2.1 12.2 V 15.6 Gy (%) 0.6 3.4 ± 1.9 10.9 Maximum lung distance (mm) 2 14 ± 4 23 Abbreviations: sd = standard deviation, Vx = the % of lung volume receiving at least the dose X in Gy. Dose-volume histograms (DVHs) analysis were calculated and registered for all OARs. Pulmonary function tests (PFTs) Pulmonary function tests were performed before the beginning of radiotherapy and then after 6, 12 and 24 months from the end of radiotherapy. Forced Vital Capacity (FVC), Forced Expiratory Volume in 1 s (FEV1) and Carbon Monoxide Diffusing Capacity (DLCO) acquired with the single breath technique have been measured with a Quark PFT Cosmed spirometer.

1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol 2005,55(4):1415–1427.Selleckchem PF-6463922 PubMedCrossRef 26. Darrasse A, Priou S, Kotoujansky A, Bertheau Y: PCR and restriction fragment length polymorphism of a pel gene as a tool

to identify Erwinia carotovora Selleck GS-9973 in relation to potato diseases. Appl Environ Microbiol 1994,60(5):1437–1443.PubMed 27. Duarte V, De Boer SH, Ward LJ, De Oliveira AMR: Characterization of atypical Erwinia carotovora strains causing blackleg of potato in Brazil. J Appl Microbiol 2004,96(3):535–545.PubMedCrossRef 28. Yap MN, Barak JD, Charkowski AO: Genomic diversity of Erwinia carotovora subsp carotovora and its correlation with virulence. Appl Environ Microbiol 2004,70(5):3013–3023.PubMedCrossRef

29. Glasner JD, Marquez-Villavicencio M, Kim HS, Jahn CE, Ma B, Biehl BS, Rissman AI, Mole B, Yi X, Yang CH, et al.: Niche-specificity and the variable fraction of the pectobacterium pan-genome. Mol Plant Microbe Interact 2008,21(12):1549–1560.PubMedCrossRef 30. Terta M, Kettani-Halabi GF120918 mouse M, Ibenyassine K, Tran D, Meimoun P, M’Hand RA, El-Maarouf-Bouteau H, Val F, Ennaji MM, Bouteau F: Arabidopsis thaliana cells: a model to evaluate the virulence of pectobacterium carotovorum. Mol Plant Microbe many Interact

2010,23(2):139–143.PubMedCrossRef 31. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al.: Clustal W and Clustal X version 2.0. Bioinformatics 2007,23(21):2947–2948.PubMedCrossRef 32. Tamura K, Nei M, Kumar S: Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004,101(30):11030–11035.PubMedCrossRef 33. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987,4(4):406–425.PubMed 34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods . Mol Biol Evol 2011,28(10):2731–2739.PubMedCrossRef Competing interests The authors declare that they have no competing interests. Authors’ contributions MK-H designed the study, performed the experiments, data analyses and wrote the paper, MT and MA participated in the sample preparation and preliminary examination, EE participated in the design of the study, FB drafted the manuscript, MME coordinated the study, designed and participated in manuscript preparation. All authors read and approved the manuscript.”
“Background When grown in spatially structured environments several Pseudomonas species are known to produce variants with altered phenotypic properties.

These models allocated units of each option based upon the benefit they provided to pollinator habitats relative to other

options Defactinib in vitro within specific categories; with the most beneficial option allocated the greatest number of units and the least beneficial allocated the least units. This method was chosen over optimisation models for the sake of methodological simplicity, particularly given the high number of variables involved, and to avoid scenarios dominated by high benefit and/or low cost options. The changes in costs and habitat benefit (measured as the sum value of PHB) were then appraised for each model. The number of units and total ELS points generated by each option as of December 2012 were obtained from Natural England databases (Cloither 2013, Pers Comm) excluding options that are no longer available (e.g. EM1-4) or those Selleck JQEZ5 that relate only GDC-0973 chemical structure to historic or built features (e.g. ED1-5) and water bodies. Mixed stocking (EK5) was also excluded to avoid double counting as this option can be combined with other grassland options. Options relating to severely disadvantaged areas (EL1-6) and ELS variants, (organic and upland ELS), were not included to reduce respondent fatigue and maintain model simplicity by only considering broadly applicable options.

The remaining options were grouped into categories based upon their management units (hedge/ditch options, managed in metres/hectares; further subdivided into grassland and arable, and plots/trees) and the area and points values of options within each category were summed to produce a baseline estimate (Table 1). For option EC4, which could be present in both grassland and cropland, the area and points were distributed proportionate to the relative area of the two groups; 24 % cropland and 76 % grassland (DEFRA 2013). Table 1 Baseline data   Units Points Total length (H) 191,556,761 m 48,503,029 Total Nabilone arable area (A) 133,123 ha 37,178,883 Total grassland area (G) 420,225 ha 45,219,223 Total trees and plots (P) 206,993

2,254,303 Total 2012   133,155,438 Key Units the number of units of each option category in the baseline mix considered. Points: The total ELS points of all units of the options considered Table 2 Weighted and unweighted mean PHB scores attributed to 2010 ELS options ELS option Description Type 2012 Pts % PHB WPHB EB1/2 Hedgerow management for landscape H 17.5 1.83 1.83 EB3 Enhanced hedgerow management H 8.8 1.94 1.96 EB6 Ditch/half ditch management H 3.2 1.33 1.38 EB7 Half ditch management H 0.5 1.33 1.40 EB8/9 Combined hedge and ditch management (inc EB1/2) H 3.6 1.83 1.88 EB10 Combined hedge and ditch management (Inc EB3) H 1.9 1.94 2.00 EB12/13 Earth bank management H 0.6 1.61 1.60 EC1 Protection of in-field trees (arable) T 0.3 0.94 1.00 EC2 Protection of in-field trees (grassland) T 1.3 1.00 1.04 EC3 Maintenance of woodland fences H 0.2 0.72 0.

We had a concrete research

question (…) and this research question was of course completely decoupled from the sustainability aspect. And this [the sustainability aspect] then played a role when interpreting the results. So when I look at these two research sites now, and interpret the results of our measurements, it becomes clear that the [one] site was obviously overgrazed. And therefore there’s the risk that—given the use is continued in the same way—a sustainable development is not ensured. (…) But sustainability per se was not our focus or object [of research]. Rather check details the results now available can be put into the context of sustainability and the project‘s results can be integrated into sustainable land use. But that’s a bigger picture EPZ015938 cost and we are only a small piece of it” (translated from CARB 1, p. 10). In such cases, the sustainability vision concerned, for example, the overall context and motivation into which the research was embedded in (POLL). This greater vision—being based on a longer-term collaborative research effort in the area—in this case served as a normative frame for the PhD project. Thus, both the contents of this vision and the single actors’ perspectives on sustainability goals were not deliberated at the level of this specific study, but

they were in the wider research program within which the Vorinostat in vitro project was embedded. Integrating various crucial local stakeholders’ visions and priorities into the project was, for instance, realized on the basis of scenarios provided by the research project, which in turn allowed exchange and discussion of different notions and priorities in participative workshops (WAT). Discussion: Implications for moving towards adequate sustainability conceptions of research projects Implications of relating research to normative concepts like sustainable development Sustainability goals and scientific research

Resminostat can be regarded as being decoupled. In this case, there is, however, still the risk of referring to specific sustainability visions and thus implicitly clearly taking a certain position in this regard. In the investigated sample, this happened notably when putting the research into the wider societal problem context, i.e., in the stages of both project development and results interpretation. Thus, outsourcing sustainability orientations apparently does not guarantee that respective value judgments do not re-enter by the back door. The findings of this article suggest that research that aims to support societal change towards sustainable development cannot avoid making an effort to clarify how normative goals can be dealt with. Trying to be value-free is thus too simplistic.

cruzi CL Brener [13] were aligned by reciprocal BLAST against each amastin coding sequences. Unique reads showing at least 99.7% of identity were mapped on the CDS and the coverage for each nucleotide was determined. Coverage values were normalized through z-score and the copy numbers were determined after determining the ratios between z-score and the whole genome coverage. Parasite culture T. cruzi strains or clones, obtained from different sources, were classified according to the nomenclature and genotyping protocols described by [32]. Epimastigote

forms of T. cruzi strains or clones Colombiana, G, Sylvio X-10, Protein Tyrosine Kinase inhibitor Dm28c, Y and CL Brener were maintained at 28°C in liver infusion tryptose (LIT) medium supplemented with 10% fetal calf serum (FCS) as previously described [3]. Tissue culture derived trypomastigotes and amastigotes were obtained after infection of LLC-MK2 or L6 cells with metacyclic trypomastigotes generated in LIT medium as previously described [3]. Pulse-field gel

electrophoresis and Southern blot analyses Genomic DNA, extracted from 107epimastigotes and included in agarose blocks were separated as chromosomal bands by pulse-field gel electrophoresis (PFGE) using the Gene Navigator System (Pharmacia) as described by Cano et al. (1995) [33], with the following modifications: separation was done in 0.8% agarose gels using a program with 5 phases of homogeneous pulses (north/south, east/west) with interpolation for 135 h at 83 V. Phase 1 had pulse time of 90 s (run time 30 h); phase 2 120 s (30 h); phase 3200 s (24 h); phase 4 350 s (25 h); phase 5 800 s (26 h). Chromosomes from Saccharomyces cerevisiae (Bio-Rad) were used as molecular mass standards. Separated BYL719 cost chromosomes were transferred to nylon filters and MM-102 cell line hybridized with 32P labelled probes prepared as described in the following section. RNA purification and

Northern blot assays Total RNA was isolated from approximately 5 × 108 epimastigote, trypomastigote and amastigote forms using the RNeasy® kit (Qiagen) following manufacturer’s recommendations. RNA samples (15 μg/lane) were separated by denaturing agarose gel electrophoresis, transferred to Hybond-N+ membranes and hybridized with the 32P labeled Thiamet G fragments corresponding to each T. cruzi amastin sequence as described [3]. The probes used were PCR amplified fragments from total genomic DNA extracted from the CL Brener strain using primers described in Table 1, in addition to a PCR fragment generated by amplification of the insert cloned in plasmid TcA21 (corresponding to δ-amastin) and the 24Sα ribosomal RNA[6]. DNA fragments were labeled using the Megaprime DNA-labeling kit (GE HealthCare) according to the manufacturer’s protocol. All membranes were hybridized in a 50% formamide buffer for 18 h at 42°C and washed twice with 2X SSC/0.1% SDS at 42°C for 30 min each, as previously described [3]. The membranes were exposed to X-ray films (Kodak) or revealed using the STORM840 PhosphoImager (GE HealthCare).

In G. metallireducens and G. sulfurreducens, however, the β2 gene trpB2 (Gmet_2493 = GSU2379, 60% identical to the T. maritima Akt targets protein [67]) is the penultimate gene of the predicted trp operon and the trpB1 (Gmet_2482 = GSU2375, 66% identical to the Acinetobacter calcoaceticus protein [68]) and trpA (Gmet_2477 = GSU2371, 47% identical to the Azospirillum brasilense protein [69]) genes are separated from the 3′ end of the operon and from each other by three or more intervening genes, most of which are not conserved between the two genomes (not shown). Next to the trpB2 gene of G. metallireducens is one of 24 pairs of a conserved nucleotide motif

(Additional file 7: Figure S3, Additional file 5: Table S4) hypothesized to bind an unidentified global regulator protein. Other, evolutionarily related paired sites where another unidentified global regulator may bind (Additional file 8: Figure S4, Additional file 5: Table S4) are found in 21 locations. Between the proBA genes of G. metallireducens, encoding the first two enzymes of proline biosynthesis (Gmet_3198-Gmet_3199 = GSU3212-GSU3211,

41% and 45% identical to the E. coli enzymes [70]), is one of eight pairs of predicted binding sites for yet another unidentified global regulator (Additional file 9: Figure S5, Additional file 5: Table S4). In G. sulfurreducens, the space between proBA is occupied by a different conserved nucleotide sequence (not shown), click here found only in four other places in the same genome. Overall, a comparison of the two genomes offers insight into unique features of amino acid biosynthesis and its regulation that deserve further study. Nucleotide metabolism Differences in nucleotide metabolism were identified in the two genomes. G. metallireducens

has acquired a possibly redundant large subunit of carbamoyl-phosphate Miconazole synthetase (Gmet_0661, 50% identical to the P. aeruginosa protein [71]) in addition to the ancestral gene (Gmet_1774 = GSU1276, 65% identity to P. aeruginosa), Both genomes encode a second putative thymidylate kinase (Gmet_3250 = GSU3301) https://www.selleckchem.com/products/MGCD0103(Mocetinostat).html distantly related to all others, in addition to the one found in other Geobacteraceae (Gmet_2318 = GSU2229, 41% identical to the E. coli enzyme [72]). G. sulfurreducens has evidently lost the purT gene product of G. metallireducens and several other Geobacteraceae (Gmet_3193, 58% identical to the E. coli enzyme [73]), which incorporates formate directly into purine nucleotides instead of using the folate-dependent purN gene product (Gmet_1845 = GSU1759, 46% identical to the E. coli enzyme [74]). Carbohydrate metabolism Comparative genomics indicates that, similar to most Geobacter species, G.

The reduced photosynthetic capacity relative to light harvesting maintains photon #Wnt inhibitor randurls[1|1|,|CHEM1|]# absorption high in the light limited shade conditions, whereas investment in a high photosynthetic capacity would not result in sufficient return as photosynthetic rates are predominantly low.

The reduced amount of photosynthetic proteins per area in shade requires a lower number of chloroplasts. This in turn requires less space in mesophyll cells (Terashima et al. 2011), which makes the shade-grown leaf thinner. Shade leaves thus have reduced costs per area in terms of nitrogen (Pons and Anten 2004) and of carbon as the leaf dry mass per area (LMA) is lower (Poorter et al. 2009). A similar shift in the balance between light harvesting and photosynthetic capacity is observed with variation in growth temperature (Hikosaka et al. 2006). The amount of Rubisco and other components that determine photosynthetic capacity expressed per unit area and per chlorophyll increases at low temperature. This compensates for the reduced activity of the photosynthetic proteins, whereas light harvesting is largely unaffected by temperature (Hikosaka 1997). Acclimation to high growth irradiance and Pitavastatin purchase low growth temperature is thus generally reflected in high Rubisco content per unit leaf area and per chlorophyll, a high chlorophyll a/b ratio and

thick leaves (Hikosaka 2005; Muller et al. 2005). An additional phenomenon associated with acclimation to low growth temperature is increased investment in the capacity of assimilate processing. Warm-grown plants measured at low temperatures typically show inhibition of photosynthesis at high [CO2] and/or low [O2] (Sage and Sharkey 1987; Atkin et al. 2006; Sage and Kubien 2007). The high rate of production of triose-phosphate by the chloroplast cannot be met by the reduced capacity of its utilization in sucrose synthesis as a result of a lower protein activity at low temperature. This leads to sequestering of phosphate in the cytosol, which limits ATP production in the chloroplast. The limitation of photosynthesis by triose-phosphate utilization (TPU) is avoided in the cold by increasing

the capacity of sucrose synthesis (Stitt and Hurry 2002). The light saturated photosynthetic rate in the Interleukin-2 receptor absence of limitation by TPU can be limited by two processes. Limitation by the carboxylation capacity of Rubisco at ribulose-bisphosphate (RuBP) saturation (V Cmax) occurs at low [CO2], whereas at higher [CO2] the regeneration of RuBP as determined by the electron transport capacity (J max) limits photosynthesis. The limitation by these two processes can be distinguished in CO2 response curves (Farquhar et al. 1980). The J max /V Cmax ratio varies little between species (Wullschleger 1993; Leuning 1997) causing the [CO2] where co-limitation by the two processes occurs to be close to the intercellular CO2 partial pressure (C i) at ambient values or somewhat above (Stitt 1991).

Antibodies used in this study were obtained from eBioscience (San Diego, CA). DNA content of cell lines derived from metastatic loci was determined by staining the cells with propidium iodide (PI, Sigma, St. Louis, MO) and analyzed on a BD FACScan cytometer as previously described [14]. Results https://www.selleckchem.com/products/NVP-AUY922.html DCs Infiltrating TRAMPC2 Tumors are Phenotypically Immature TRAMPC2 tumors grow progressively in immune competent mice suggesting that these cells induce a weak or inefficient anti-tumor immune www.selleckchem.com/products/fosbretabulin-disodium-combretastatin-a-4-phosphate-disodium-ca4p-disodium.html response. This may reflect the ability of the TRAMPC2 TME to impair DC (CD11c+ cells) function. CD11c has been

used here to identify DCs, although it can also be expressed by activated T and B cells as well as natural killer (NK) cells. However, intratumoral T cells remain quiescent in the TRAMP TME because they do not express the activation antigens CD25 or CD69 (data not shown). Furthermore, T and B cells are not a major infiltrating cell types in TRAMP tumors. NK cells are typically not detected in TRAMP TILs or are present as a trace population and therefore do not contribute significantly to CD11c expression in the TRAMP MK0683 ic50 TME. We observed that the majority of DCs infiltrating TRAMPC2 tumors failed to express normal levels of class II antigens (IAb), B7.2 and CD40 molecules compared to their counterparts isolated from either normal or tumor bearing spleens (Fig. 1-b). Most

of the infiltrating DCs appeared to be myeloid in origin because they did not express CD8α (B-g, h and i and C). Class I antigen (H2Db) expression was not suppressed by the TME as equivalent levels of expression were observed on intratumoral

and splenic Docetaxel DCs (Fig. 1-b; g, h and i). Surprisingly, CD86 expression, but not CD80, was suppressed suggesting differential regulation of B7 family members within the prostate TME (Fig. 1-c). As expected, expression of the chemokine receptor CCR7 was down-regulated relative to normal spleen (Fig. 1-c). In contrast, DC expression of PDL2 shown to inhibit the activation and cytokine production of CD4+ T cells [16] was elevated on intratumoral DCs relative to normal splenic DCs (Fig. 1-c). Thus, these data suggest that tumor-associated DCs are immature because they fail to express a number of cell surface markers associated with DC maturation. Fig. 1 Dendritic cells isolated from prostate tumors display an immature phenotype. Mice were transplanted orthotopically with TRAMPC2 tumor cells and 30 days later excised when tumor mass reached approximately 1 cm in diameter. Single cell suspension from normal and tumor bearing (TB) spleens were prepared and TILs isolated from TRAMPC2 tumors. Cells were stained with indicated mAbs and evaluated by 4-color flow cytometry. a Single color analysis (forward scatter vs. log fluorescent intensity) of CD11c+ cells of normal spleen and TILs isolated from TRAMPC2 tumors. The R1 region was set based on the appropriate isotype matched control. The background for isotype matched control was 0.

The diploid yeast-expressing proteins that interacted were finally selected in medium that contained

a chromogenic substrate (X-α-GAL) to observe the transcriptional activation of the reporter gene mel1, a GAL4-regulated gene coding for the α-galactosidase enzyme. A total of 24 clones showed the activation of the reporter gene mel1 by turning blue (data not shown), which confirmed that there was interaction between PbMLS and the gene products listed in the Additional file 4: Table S3. To identify gene products that interacted with PbMLS, the cDNAs of the clones were EPZ015666 molecular weight sequenced after PCR amplification. ESTs (Expressed Sequence Tags) were processed using the bioinformatics tool Blast2GO. The functional classification was based on the homology of each selleckchem EST against the GenBank database using the BLAST algorithm [17], with a significant homology cutoff of ≤ 1e-5 and functional annotation by MIPS [16]. Additionally, sequences were grouped into functional categories through the PEDANT 3 database [18]. The analysis indicated the presence of several NVP-HSP990 mouse functional categories of genes and cell functions related to cellular transport, protein fate, protein synthesis, nucleotide metabolism, signal transduction, cell cycle and DNA processing, and hypothetical protein (Additional file 4: Table S3). Construction of

protein interaction maps A comprehensive genetic interaction dataset has Idoxuridine been described for the model yeast S. cerevisiae[19]. Because genes that act in the same pathway display similar patterns of genetic interactions with other genes [19–22], we investigated whether Paracoccidioides Pb01 protein sequences that interacted with PbMLS and were tracked by the pull-down and two-hybrid assays (Additional file 3: Table S2 and

Additional file 4: Table S3, respectively) were found in the structural genome database of S. cerevisiae[23]. Those sequences and others from The GRID protein interaction database [24] of S. cerevisiae were used to construct protein interaction maps generated by the Osprey Network Visualization System [25] (Figure 1). Protein sequences from macrophage were not used because some of them were not found in the S. cerevisiae database. The blue lines indicate protein interactions with MLS from Paracoccidioides Pb01 experimental data. The green lines indicate protein interactions with MLS already described in The GRID interaction database [24] of S. cerevisiae. A pink line corresponds to both. The colored dots show the functional classification of proteins. Figure 1 Map of interactions between MLS and other proteins generated by the Osprey Network Visualization System [25]. (A) Protein interactions obtained by a two-hybrid assay. Protein interactions obtained by pull-down assays with protein extracts of Paracoccidioides mycelium (B), yeast (C) and yeast secretions (D).

Further details are provided in Ewers et al. (2011). We used survey points established as part of a large-scale, long-term experiment investigating the effects of Selleck EPZ015666 forest fragmentation: the “Stability of Altered Forest Ecosystems (SAFE) Project” (Ewers et al. 2011). Fifty-nine survey points were sampled in our study: 18 in old growth forest, 32 in logged forest of varying forest quality, and nine in oil

palm plantation (Online Resource, Fig. S1). A larger number of survey points were sampled in logged forest and old growth forest because we expected these habitats to be more heterogeneous SB525334 ic50 and we wanted our points to span a gradient of habitat disturbance across all the habitats. Neighbouring survey points were 178 m apart. Selection of these survey points was made with future repeat-surveys in mind once

clearance of logged forest for oil palm plantation has resulted in the creation of forest fragments. There are no areas of continuous, unfragmented old growth forest near to the SAFE project sites and hence the study design does not allow separation of the effects of location from those of habitat disturbance. We are therefore cautious in our interpretation of the results, particularly about assigning causal relationships between treatments and assemblage composition. Ant and termite collection Survey work was conducted in April and May 2010 during the dry season, Selleckchem NVP-HSP990 between 0800 h and 1700 h. This coincided with the end of an El Nino-related drought between February and April that year (see http://​www.​searrp.​org/​danum-valley/​the-conservation-area/​climate/​).

None of the sites was affected by fire during the drought period, however. At each survey point a 4 × 4 m2 quadrat was placed, with sixteen soil pits dug Idoxuridine (1,131 cm3 per pit: 12 cm diameter by 10 cm deep) centred within each square metre of the quadrat. Soil was removed from each pit and hand-searched for ants and termites using a white tray for 10 person-minutes. Large dead wood (diam > 5 cm) within the quadrat (up to a height of 2 m) was also searched for ants and termites, once per metre of dead wood (following Davies et al. 2003). Bark was removed and holes in the wood were examined. These methods only sample the fauna living within the soil and dead wood, and do not sample the leaf litter community. Ants and termites were sorted to genus using the collections of the Natural History Museum, London, and relevant literature (Ahmed and Akhtar 1981; Tho and Kirton 1992; Bolton 1994; Gathorne-Hardy 2001; Hashimoto 2003). Ant and termite reproductives were excluded from counts to avoid including vagrants, and immature termites could not be identified. Ants and termites show niche conservatism within genera (Andersen 2000; Donovan et al. 2001) and so genus-level identification of both taxa was suitable for functional group assignment.