Satellite surface reflectance improves habitat distribution mapping: a case study on heath and shrub formations in the Cantabrian Mountains (NW Spain)

Aim We aim to map the distribution of four heath and shrub formations constituting habitats of high conservation priority in Europe, whose occurrence is strongly dependent on human activities. Specifically, we assess whether the use of LANDSAT data in habitat distribution modelling may account for land use management, allowing accurate mapping of real distribution patterns. In particular, we explore whether reflectance values may be a better alternative to other remote sensing data traditionally used in modelling approaches (i.e. spectral vegetation indices and classified land cover maps). Finally, we test whether modelling performance is affected by the ecological traits of the dominant species of the target formations. Location Cantabrian Mountains (NW Spain). Methods We generated maps for the four formations (two specialists vs. two generalists) using MaxEnt. First, we ran the models with environmental predictors only (topography, climate, lithology and human disturbances). Then, we compared the advantages of including, in turn, different data derived from LANDSAT imagery: reflectance values (corresponding to different wavelength channels of the multispectral image), a spectral index and a land cover map. We assessed changes in explanatory power and also in the formation’s predicted distribution patterns. Results Formations dominated by specialist species were accurately mapped on a base of environmental variables only, whereas those dominated by generalists were overpredicted. Average mean temperature, southness and distance to urban areas were the variables contributing most in predictions of environmental models. LANDSAT channels increased the accuracy of all models, but mainly those for formations dominated by generalist species. They showed advantages against other remote sensing data traditionally used in modelling approaches. Main conclusions Habitat distribution models allowed accurate mapping of heath and shrub formations. The use of reflectance values as predictors improved the accuracy of the models, particularly for formations dominated by generalist species, supplying environmental information that was otherwise unavailable.     

Evaluation of the European Union Maize Landrace Core Collection for resistance to Sesamia nonagrioides (Lepidoptera: Noctuidae) and Ostrinia nubilalis (Lepidoptera: Crambidae)

Two corn borer species are the principal maize insect pests in Europe, the European corn borer, Ostrinia nubilalis (Hübner), and the pink stem borer, Sesamia nonagrioides (Lefebvre). Hence, it would be advisable to evaluate the European maize germplasm for corn borer resistance to generate European varieties resistant to corn borer attack. The creation of the European Union Maize Landrace Core Collection (EUMLCC) allowed the screening of most of the variability for European corn borer resistance present among European maize local populations from France, Germany, Greece, Italy, Portugal, and Spain, testing a representative sample. The objective of this study was the evaluation of stem and ear resistance of the EUMLCC to European corn borer and pink stem borer attack. Trials were made at two Spanish locations that represent two very different maize-growing areas. Populations that performed relatively well under corn borer infestation for stem and ear damage were 'PRT0010008' and'GRC0010085', among very early landraces; 'PRT00100120' and 'PRT00100186', among early landraces; 'GRC0010174', among midseason landraces; and 'ESP0070441', among late landraces. Either the selection that could have happen under high insect pressure or the singular origin of determined maize populations would be possible explanations for the higher corn borer resistance of some landraces. Landraces 'PRT0010008', 'FRA0410090', 'PRT00100186', and 'ESP0090214' would be selected to constitute a composite population resistant to corn borers and adapted to short season, whereas populations 'ESP0090033', 'PRT00100530', 'GRC0010174', and 'ITA0370005' would be used to make a resistant composite adapted to longer season.     

When invasion biology meets taxonomy: <Emphasis Type="Italic">Clavelina oblonga</Emphasis> (Ascidiacea) is an old invader in the Mediterranean Sea

Taxonomic issues often confound the study of invasive species, which sometimes are unrecognized as introduced in newly colonized areas. Clavelina oblonga Herdman, 1880 is an abundant ascidian species along the southeastern coast of the United States and the Caribbean Sea. It was introduced into the eastern Atlantic and Brazil decades ago. In the Mediterranean Sea, a similar species had been described as C. phlegraea Salfi 1929 and reported from southern Italy and Corsica. In the last few years a species of Clavelina has proliferated in the embayments of the Ebro Delta (NW Mediterranean), a zone of active bivalve culture industry where it has smothered mussel spat, leading to economic loss. We here report the morphological and genetic identity of this species, synonymizing the Atlantic C. oblonga and the Mediterranean C. phlegraea (the latter therefore is a synonym of the former). Thus, C. oblonga has existed in the Mediterranean for over 80 years, but was known under a different name. We also found this species in natural habitats in the Iberian Atlantic coast close to the Strait of Gibraltar, raising concerns about an ongoing expansion. In order to obtain information relevant for management, we monitored growth, reproductive cycles and settlement patterns of this ascidian on bivalve cultures in the Ebro Delta. Its biological cycles were markedly seasonal, with peak abundance and reproduction during the warmest months, followed by regression during the cold season. The settlement period was short, mostly concentrated in a single month each year. Avoidance of mussel and oyster seeding during late summer and early autumn can readily reduce the damage caused by this species.     

Letter to the editor

Letter to the Editor

Letter to the editor     

Physiology and pathophysiology of the interstitial cells of Cajal: from bench to bedside. IV. Genetic and animal models of GI motility disorders caused by loss of interstitial cells of Cajal

Several human motility disorders have been shown to be associated with loss or defects in interstitial cells of Cajal (ICC) networks. Because tissue samples for these studies were taken from patients with well-advanced motility problems, it is difficult to determine whether the loss of ICC is a cause or a consequence of the disease process. To establish the cause-and-effect relationship of ICC loss in motility disorders, it may be feasible to use animal models in which ICC are lost as motility dysfunction develops. Several models with defects in ICC networks have been developed, and these include animals with defects in the Kit signaling pathway (e.g., white-spotting mutants that have defects in Kit receptors; steel mutants that have mutations in stem cell factor, the ligand for Kit; and animals that are chronically treated with reagents that block Kit or downstream signaling proteins). ICC do not die when Kit signaling is blocked, rather, they redifferentiate into a smooth muscle-like phenotype. Diabetic animals (NOD/LtJ mice), animals with chronic bowel obstruction, and inflammatory bowel models also have defects in ICC networks that have been associated with motility disorders. By studying these models with molecular and genomic techniques it may be possible to determine the signals that cause loss of ICC and find ways of restoring ICC to dysfunctional tissues. This article discusses recent progress in the utilization of animal models to study the consequences of losing ICC on the development of motility disorders.     

Vitamin D receptor deficiency enhances Wnt/β-catenin signaling and tumor burden in colon cancer

Aberrant activation of the Wnt/β-catenin pathway is critical for the initiation and progression of most colon cancers. This activation provokes the accumulation of nuclear β-catenin and the induction of its target genes. Apc(min/+) mice are the most commonly used model for colon cancer. They harbor a mutated Apc allele and develop intestinal adenomas and carcinomas during the first months of life. This phenotype is caused by the mutation of the second Apc allele and the consequent accumulation of nuclear β-catenin in the affected cells. Here we describe that vitamin D receptor (VDR) is a crucial modulator of nuclear β-catenin levels in colon cancer in vivo. By appropriate breeding of Apc(min/+) mice and Vdr(+/-) mice we have generated animals expressing a mutated Apc allele and two, one, or none Vdr wild type alleles. Lack of Vdr increased the number of colonic Aberrant Crypt Foci (ACF) but not that of adenomas or carcinomas in either small intestine or colon. Importantly, colon ACF and tumors of Apc(min/+)Vdr(-/-) mice had increased nuclear β-catenin and the tumors reached a larger size than those of Apc(min/+)Vdr(+/+). Both ACF and carcinomas in Apc(min/+)Vdr(-/-) mice showed higher expression of β-catenin/TCF target genes. In line with this, VDR knock-down in cultured human colon cancer cells enhanced β-catenin nuclear content and target gene expression. Consistently, VDR depletion abrogated the capacity of 1,25(OH)(2)D(3) to promote the relocation of β-catenin from the nucleus to the plasma membrane and to inhibit β-catenin/TCF target genes. In conclusion, VDR controls the level of nuclear β-catenin in colon cancer cells and can therefore attenuate the impact of oncogenic mutations that activate the Wnt/β-catenin pathway.     

EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra

Histone post-translational modifications contribute to chromatin function through their chemical properties which influence chromatin structure and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (nanoLC-MS/MS) has emerged as the most suitable technology for global histone modification analysis because of the high sensitivity and the high mass accuracy of this approach that provides confident identification. However, analysis of histones with this method is even more challenging because of the large number and variety of isobaric histone peptides and the high dynamic range of histone peptide abundances. Here, we introduce EpiProfile, a software tool that discriminates isobaric histone peptides using the distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. The accuracy of EpiProfile was evaluated by analysis of mixtures containing different ratios of synthetic histone peptides. In addition to label-free quantification of histone peptides, EpiProfile is flexible and can quantify different types of isotopically labeled histone peptides. EpiProfile is unique in generating layouts (i.e. relative retention time) of histone peptides when compared with manual quantification of the data and other programs (such as Skyline), filling the need of an automatic and freely available tool to quantify labeled and non-labeled modified histone peptides. In summary, EpiProfile is a valuable nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples.The nucleosome, the basic unit of chromatin, consists of 147 base pairs of DNA wrapped around histone proteins (H2A, H2B, H3, and H4). Histones play vital roles in chromatin, interacting with many signaling proteins and chromatin-structural proteins through various post-translational modifications (PTMs)¹ (1–3). There are numerous PTMs on histones, including methylation (mono - me1, di - me2, tri - me3), acetylation (ac), phosphorylation (ph), ubiquitination, and SUMOylation (4). Histone PTMs can affect chromatin function, and therefore influence processes such as gene accessibility, DNA repair and chromosome condensation. Moreover, histone PTMs cross-talk in a synergistic manner to fine-tune gene expression (5). Therefore, quantification of histone PTMs has become a high priority to investigate cell regulation and epigenetics (6).Traditionally, antibody-based methods (e.g. Western blot) have been used to analyze histone modifications (7), which have multiple disadvantages. First, antibodies are not available for every new PTM discovered. Second, PTMs on neighboring amino acids (e.g. H3K9me1–3 and H3S10ph) may prevent antibody binding, a phenomenon called epitope occlusion. Third, the quantification of PTMs via antibody-based methods is not sensitive to small differences (e.g. <twofold). Mass spectrometry (MS) has emerged as a sensitive and efficient technique to detect known and novel PTMs (8). The high mass accuracy and the high speed of modern mass spectrometers allow for sensitive, confident, and accurate peptide quantification when coupled with nanoflow liquid chromatography (nanoLC).NanoLC-MS/MS analysis of protein digests (i.e. bottom-up MS) is nowadays a mature and widely applied technology. Data-dependent acquisition is the most commonly adopted MS acquisition method to identify peptides via bottom-up MS (9–12), generating MS1 and MS2 spectra. Nevertheless, histone proteins are particularly challenging to analyze by using the generalized bottom-up workflow. As histones are rich with lysines and arginines, tryptic digest of histones generates short peptides that are difficult to be retained on C18 columns. To improve histone peptide retention, the unmodified and mono-methylated lysines and peptide N terminus can be selectively chemically propionylated (13–16), preventing tryptic digest after lysine to generate longer peptides. Moreover, peptide identification through traditional database searches leads to a large number of false positives, as allowing several dynamic modifications (e.g. me1/me2/me3, ac, ph) dramatically increases the number of molecular candidates and thus the possibility to achieve a false hit (12). Therefore, software tools that quantify histone peptides require additional data to correctly map a given peptide, such as previous knowledge of peptide retention time.Quantification of histone peptides is particularly challenging because of presence of isobaric peptides, near isobaric PTMs such as tri-methylation (42.047 Da) and acetylation (42.011 Da), and low abundant species. Previous knowledge about relative peptide retention time (RT) enables differentiation between species close in mass and therefore selection of the correct peak for integration of the area of the chromatographic peak (i.e. area under curve or AUC). However, determination of peptide RT might be difficult because of their low abundance though acid extraction was performed to purify histones. This problem can be solved by using isotopically labeled synthetic histone peptides (17), or data independent approaches (18). When using relative retention time information to assign peak identities, reproducible nanoLC is crucial, especially because some isobaric peptides co-elute. In this case, the MS acquisition method must perform targeted MS2 for the co-eluting isobaric peptides at the specific time that they elute. These species can be discriminated and quantified based on the intensity of fragment ions unique to each species. For instance, the peptides KacSTGGKAPR (H3K9ac) and KSTGGKacAPR (H3K14ac) have the same mass and overlap at the nanoLC elution (the full protein sequence of human canonical histone H3 and H4 are shown in Fig. 1A). Thus, the co-eluting isobaric peptides could not be quantified separately based on the MS1 signal, but the unique fragment ions present in MS2 spectra allow them to be quantified individually.Open in a separate windowFig. 1.Histones are a challenge for quantitative mass spectrometry analyses. A, Human histone H3.1 and H4 protein sequences. B, Spline fitting to calculate AUC: blue lines are the original peaks and pink lines are the fitted peaks. C, An example of isobaric PTM modified peptides. The above MS2 is matched with H3K18ac, and the same MS2 is also matched with H3K23ac below. D, The workflow of EpiProfile: inputting precursor m/z and charge state, extracting elution profiles, selecting the correct chromatographic peak, calculating AUC, and outputting quantification tables and figures.There have been few computational investigations attempting to solve the problem of quantifying co-eluting isobaric peptides. DiMaggio et al. used a mixed integer linear optimization (MILP) framework to quantify partially co-eluting isobaric histone peptides from electron transfer dissociation (ETD) spectra (19). The framework is comprised of two MILP models: (1) enumerating the entire space of the modified forms that satisfy a given peptide mass and (2) determining the relative composition of the modified forms in the spectrum. Another study by Guan et al. identified isobaric peptides by searching ETD MS/MS spectra for ions representing all possible configurations of modified peptides using a visual assistance program. The relative abundances of these species were estimated by using a nonnegative least squares procedure (20). Other quantification programs can also perform accurate peak picking, but are commonly not as suitable for heavily modified and isobaric histone peptides (e.g. Skyline) (21). These software programs are unable to provide the layouts of histone peptides (i.e. relative RTs) or discriminate all isobaric modified peptides, two tasks that are vital for full characterization of a histone sample.In this study, we developed a new quantification program named EpiProfile. EpiProfile extracts ion chromatography for known histone peptides by using previous knowledge about their elution profiles. Moreover, it discriminates and quantifies the isobaric histone peptides by resolving the linear equations listed with the peak heights of unique fragment ions between the two modification sites in the MS2 spectra (e.g. ions between H3K9ac and H3K14ac). We evaluated the accuracy of EpiProfile by mixing different ratios of synthetic histone peptides, and then tested EpiProfile by analyzing nanoLC-MS/MS data sets of the following samples: purified histones from HeLa cells, a synthetic histone peptide library, and histone peptides labeled during cell growth with ¹³C-labeled glucose media or stable isotope labeling by amino acids in cell culture (SILAC) (22). We compared EpiProfile to manual quantification of the data, and also with the openly available program Skyline. We found that manual quantification is obviously time-consuming and that Skyline cannot generate the layouts of histone peptides and cannot discriminate four or six-component isobaric peptides, a common occurrence in histone data. Moreover, EpiProfile is highly flexible, and thus it can be used to analyze various protein samples, including isotopically labeled peptides and nonhistone data sets.     

Uptake and transport of phosphorus by Agrostis capillaris seedlings from rapidly hydrolysed organic sources extracted from32 P-labelled bacterial cultures

Cultures of the soil bacterium Serratia liquifaciens grimesii were grown with³² P labelled phosphate, to produce a uniformly³² P labelled source of microbial P. Extracts of the bacteria were prepared by sonication, dialysis and filtration to provide a clear sterile solution which was characterised in terms of dissolved organic and condensed P (DOP and DCP) and molecular weight range. The extract was used as a source of P to Agrostis capillaris L. seedlings in nutrient solution from which orthophosphate was omitted. In a time course experiment, root surface phosphatase activity increased as soon as extract was added to the root medium, DOP was rapidly hydrolysed and orthophosphate concentration increased rapidly. These processes were complete within about 8 h, after which phosphatase activity fell to its original level, and the plants absorbed molybdate reactive P from the nutrient solution so that it reached its original concentration over 48 h. DCP concentrations did not change significantly throughout the experiment. This work clearly demonstrated that DOP but not DCP, as a component of a bacterial extract produced by a relatively straightforward method, was quickly hydrolysed and the P made available for plant uptake.     

Isolation of highly multidrug-resistant P388 cells from drug-sensitive P388/S cells by flow cytometric cell sorting

To investigate the spontaneous frequency of occurrence of stable multidrug-resistant cells in a population of drug-sensitive cells, we exposed drug sensitive P388/S cells to daunorubicin (dnr) for 1 h, then used fluorescence-activated cell sorting based on intracellular dnr fluorescence to isolate cells within P388/S having different intracellular content of drug. One of the sort windows chosen (low dnr content sort window) isolated only P388/S cells with intracellular drug content equal to or less than that of the known multidrug-resistant subline P388/adr. This sort window constituted approximately 3% of P388/S cells with lowest dnr content. By such a procedure we were able, on one of seven attempts, to isolate and cultivate stable, highly multidrug-resistant cells (comparable to that of P388/adr) from the P388/S cells obtained from the low dnr-content sort window. Net growth of cells in culture was observed 15-20 days after sorting, indicating that of the P388/S cells collected from the low dnr-content sort window, very few were actually highly drug-resistant. On no occasion could resistant cells be cultivated from cells sorted from P388/S with higher dnr content, as would be expected if mutation to a multidrug-resistant phenotype had occurred as a result of exposure to drug. The resistant cells isolated from P388/S by sorting (called P388/LoSort) displayed low intracellular accumulation of dnr that was enhanced by verapamil, were cross-resistant to vincristine and actinomycin-D, and distinct from P388/S, possessed a 150- to 160-kD membrane species identified by Vinca alkaloid photoaffinity labeling.(ABSTRACT TRUNCATED AT 250 WORDS)