Land use changes, landscape ecology and their socioeconomic driving forces in the Spanish Mediterranean coast (the Maresme County, 1850-2005)

[cat] Utilitzem un conjunt de mètriques del paisatge per estudiar l'evolució a llarg termini seguida en una típica zona costanera del Mediterrani des de 1850 fins a 2005, que mostren una greu deterioració del medi ambient entre 1950 i 2005. Les principals forces motores d'aquesta degradació del paisatge han estat el creixement urbà experimentat a les antigues zones agrícoles situades a les planes litorals, juntament amb l'abandonament i la reforestació dels vessants dels pujols interceptats per àrees residencials de baixa densitat, carreteres i altres infraestructures lineals. Duem a terme una anàlisi estadística de redundància (RDA) amb la finalitat d'identificar els que considerem com alguns agents rectors socioeconòmics i polítics d'última instància d'aquests impactes ambientals. Els resultats confirmen les nostres hipòtesis interpretatives, que són que: 1) els canvis en les cobertes i usos del sòl determinen canvis en les propietats dels paisatge, tant estructurals com funcionals; 2) aquests canvis no es produeixen per atzar, sinó que estan relacionats amb factors geogràfics i forces socioeconòmiques i polítiques.

Land use changes, landscape ecology and their socioeconomic driving forces in the Spanish Mediterranean coast (the Maresme County, 1850-2005)

[cat] Utilitzem un conjunt de mètriques del paisatge per estudiar l'evolució a llarg termini seguida en una típica zona costanera del Mediterrani des de 1850 fins a 2005, que mostren una greu deterioració del medi ambient entre 1950 i 2005. Les principals forces motores d'aquesta degradació del paisatge han estat el creixement urbà experimentat a les antigues zones agrícoles situades a les planes litorals, juntament amb l'abandonament i la reforestació dels vessants dels pujols interceptats per àrees residencials de baixa densitat, carreteres i altres infraestructures lineals. Duem a terme una anàlisi estadística de redundància (RDA) amb la finalitat d'identificar els que considerem com alguns agents rectors socioeconòmics i polítics d'última instància d'aquests impactes ambientals. Els resultats confirmen les nostres hipòtesis interpretatives, que són que: 1) els canvis en les cobertes i usos del sòl determinen canvis en les propietats dels paisatge, tant estructurals com funcionals; 2) aquests canvis no es produeixen per atzar, sinó que estan relacionats amb factors geogràfics i forces socioeconòmiques i polítiques.

The Ovarian Cancer Chemokine Landscape Is Conducive to Homing of Vaccine-Primed and CD3/CD28-Costimulated T Cells Prepared for Adoptive Therapy.

PURPOSE: Chemokines are implicated in T-cell trafficking. We mapped the chemokine landscape in advanced stage ovarian cancer and characterized the expression of cognate receptors in autologous dendritic cell (DC)-vaccine primed T cells in the context of cell-based immunotherapy. EXPERIMENTAL DESIGN: The expression of all known human chemokines in patients with primary ovarian cancer was analyzed on two independent microarray datasets and validated on tissue microarray. Peripheral blood T cells from five HLA-A2 patients with recurrent ovarian cancer, who previously received autologous tumor DC vaccine, underwent CD3/CD28 costimulation and expansion ex vivo. Tumor-specific T cells were identified by HER2/neu pentamer staining and were evaluated for the expression and functionality of chemokine receptors important for homing to ovarian cancer. RESULTS: The chemokine landscape of ovarian cancer is heterogeneous with high expression of known lymphocyte-recruiting chemokines (CCL2, CCL4, and CCL5) in tumors with intraepithelial T cells, whereas CXCL10, CXCL12, and CXCL16 are expressed quasi-universally, including in tumors lacking tumor-infiltrating T cells. DC-vaccine primed T cells were found to express the cognate receptors for the above chemokines. Ex vivo CD3/CD28 costimulation and expansion of vaccine-primed Tcells upregulated CXCR3 and CXCR4, and enhanced their migration toward universally expressed chemokines in ovarian cancer. CONCLUSIONS: DC-primed tumor-specific T cells are armed with the appropriate receptors to migrate toward universal ovarian cancer chemokines, and these receptors are further upregulated by ex vivo CD3/CD28 costimulation, which render T cells more fit for migrating toward these chemokines. Clin Cancer Res; 21(12); 2840-50. ©2015 AACR.

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options.

TCF3-HLF-positive acute lymphoblastic leukemia (ALL) is currently incurable. Using an integrated approach, we uncovered distinct mutation, gene expression and drug response profiles in TCF3-HLF-positive and treatment-responsive TCF3-PBX1-positive ALL. We identified recurrent intragenic deletions of PAX5 or VPREB1 in constellation with the fusion of TCF3 and HLF. Moreover somatic mutations in the non-translocated allele of TCF3 and a reduction of PAX5 gene dosage in TCF3-HLF ALL suggest cooperation within a restricted genetic context. The enrichment for stem cell and myeloid features in the TCF3-HLF signature may reflect reprogramming by TCF3-HLF of a lymphoid-committed cell of origin toward a hybrid, drug-resistant hematopoietic state. Drug response profiling of matched patient-derived xenografts revealed a distinct profile for TCF3-HLF ALL with resistance to conventional chemotherapeutics but sensitivity to glucocorticoids, anthracyclines and agents in clinical development. Striking on-target sensitivity was achieved with the BCL2-specific inhibitor venetoclax (ABT-199). This integrated approach thus provides alternative treatment options for this deadly disease.

Comparative genomics of Hedgehog loci in chordates and the origin of Shh regulatory novelties

The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequenced and characterized the Hedgehog (Hh) loci from three invertebrate chordate amphioxus species, which share several early expression domains with Shh. Using phylogenetic footprinting within and between chordate lineages, and reporter assays in zebrafish probing >30 Kbp of amphioxus Hh, we report large sequence and functional divergence between both groups. In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications.

The political ecology of weeds : a scalar approach to landscape transformations

How do plants that move and spread across landscapes become branded as weeds and thereby objects of contention and control? We outline a political ecology approach that builds on a Lefebvrian understanding of the production of space, identifying three scalar moments that make plants into 'weeds' in different spatial contexts and landscapes. The three moments are: the operational scale, which relates to empirical phenomena in nature and society; the observational scale, which defines formal concepts of these phenomena and their implicit or explicit 'biopower' across institutional and spatial categories; and the interpretive scale, which is communicated through stories and actions expressing human feelings or concerns regarding the phenomena and processes of socio-spatial change. Together, these three scalar moments interact to produce a political ecology of landscape transformation, where biophysical and socio-cultural processes of daily life encounter formal categories and modes of control as well as emotive and normative expectations in shaping landscapes. Using three exemplar 'weeds' - acacia, lantana and ambrosia - our political ecology approach to landscape transformations shows that weeds do not act alone and that invasives are not inherently bad organisms. Humans and weeds go together; plants take advantage of spaces and opportunities that we create. Human desires for preserving certain social values in landscapes in contradiction to actual transformations is often at the heart of definitions of and conflicts over weeds or invasives.

The genomics of micronutrient requirements.

Healthy nutrition is accepted as a cornerstone of public health strategies for reducing the risk of noncommunicable conditions such as obesity, cardiovascular disease, and related morbidities. However, many research studies continue to focus on single or at most a few factors that may elicit a metabolic effect. These reductionist approaches resulted in: (1) exaggerated claims for nutrition as a cure or prevention of disease; (2) the wide use of empirically based dietary regimens, as if one fits all; and (3) frequent disappointment of consumers, patients, and healthcare providers about the real impact nutrition can make on medicine and health. Multiple factors including environment, host and microbiome genetics, social context, the chemical form of the nutrient, its (bio)availability, and chemical and metabolic interactions among nutrients all interact to result in nutrient requirement and in health outcomes. Advances in laboratory methodologies, especially in analytical and separation techniques, are making the chemical dissection of foods and their availability in physiological tissues possible in an unprecedented manner. These omics technologies have opened opportunities for extending knowledge of micronutrients and of their metabolic and endocrine roles. While these technologies are crucial, more holistic approaches to the analysis of physiology and environment, novel experimental designs, and more sophisticated computational methods are needed to advance our understanding of how nutrition influences health of individuals.

Landscape Systems and Human Land-Use Interactions in Mediterranean Highlands and Littoral Plains during the Late Holocene: Integrated Analysis from the InterAmbAr Project (North-Eastern Catalonia).

The main goal of the InterAmbAr reseach project is to analyze the relationships between landscape systems and human land-use strategies on mountains and littoral plains from a long-term perspective. The study adopts a high resolution analysis of small-scale study areas located in the Mediterranean region of north-eastern Catalonia. The study areas are distributed along an altitudinal transect from the high mountain (above 2000m a.s.l.) to the littoral plain of Empordà (Fig. 1). High resolution interdisciplinary research has been carried out from 2010, based on the integration of palaeoenvironmental and archaeological data. The micro-scale approach is used to understand human-environmental relationships. It allows better understanding of the local-regional nature of environmental changes and the synergies between catchment-based systems, hydro-sedimentary regimes, human mobility, land-uses, human environments, demography, etc.

Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.

Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure-based computer-aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand-protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state-of-the-art docking programs. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Genomics of clinal variation in Drosophila: disentangling the interactions of selection and demography.

Clines in phenotypes and genotype frequencies across environmental gradients are commonly taken as evidence for spatially varying selection. Classical examples include the latitudinal clines in various species of Drosophila, which often occur in parallel fashion on multiple continents. Today, genomewide analysis of such clinal systems provides a fantastic opportunity for unravelling the genetics of adaptation, yet major challenges remain. A well-known but often neglected problem is that demographic processes can also generate clinality, independent of or coincident with selection. A closely related issue is how to identify true genic targets of clinal selection. In this issue of Molecular Ecology, three studies illustrate these challenges and how they might be met. Bergland et al. report evidence suggesting that the well-known parallel latitudinal clines in North American and Australian D. melanogaster are confounded by admixture from Africa and Europe, highlighting the importance of distinguishing demographic from adaptive clines. In a companion study, Machado et al. provide the first genomic comparison of latitudinal differentiation in D. melanogaster and its sister species D. simulans. While D. simulans is less clinal than D. melanogaster, a significant fraction of clinal genes is shared between both species, suggesting the existence of convergent adaptation to clinaly varying selection pressures. Finally, by drawing on several independent sources of evidence, Bo?ičević et al. identify a functional network of eight clinal genes that are likely involved in cold adaptation. Together, these studies remind us that clinality does not necessarily imply selection and that separating adaptive signal from demographic noise requires great effort and care.

Ager Tarraconensis 5. Paisatge, poblament, cultura material i història = Landscape, Settlement, Material Culture and History Proceedings of the International Symposium

Aquesta obra recull 28 comunicacions presentades al Simposi internacional «L’ager Tarraconensis. Paisatge, poblament, cultura material i història», celebrat a Tarragona el 27 i 28 d’octubre del 2010, organitzat per l’Institut Català d’Arqueologia Clàssica a la seu de l’Institut i a la Diputació de Tarragona. Les aportacions al simposi se centren en l'evolució del paisatge al Camp de Tarragona i en altres regions del món romà, en la varietat de les primeres estratègies de control romà del territori, en les tipologies i evolució dels establiments, en aspectes econòmics i en la dinàmica del poblament, sense faltar-hi alguna aportació de l'epigrafia. Tot plegat fa referència molt especialment al territori de Tarraco, tot i que el simposi també va comptar amb comunicacions sobre altres territoris de l'àrea catalana i saguntina i d'altres províncies romanes, com la Lusitània, les Gàl·lies i la Transpadana; les comparacions entre diferents regions han donat una riquesa notable al debat. Entre els resultats més suggerents comptem amb la constatació de la similitud en els models de romanització del territori en les diferents àrees d'àmbit català i valencià, que contrasten significativament amb els models de territoris d'Andalusia, França i Portugal.

Molluscan radiations and landscape evolution in Miocene Amazonia

This PhD study aims to exploit the rich archive provided by the Miocene mollusc fauna of the Pebas Formation and other inland Miocene Amazonian formations to reconstruct landscape evolution and biotic development in lowland Amazonia during the Neogene. Over 160 samples from more than 70 Pebas Formation outcrops mostly collected by the author were processed for this study. Additional samples were collected in Andean areas of Colombia and Venezuela and further material from other northwestern South American basins was studied in museums. Pebas Formation samples and well log data made available by Occidental Peru from three wells in the Marañon Basin in Peru were also investigated. During this study four genera and 74 species from the Pebas Formation have been described and a further 13 species have been introduced in open nomenclature, and several species were reported for the first time. The number of mollusc species attributed to the Pebas fauna has increased from around 50 to 156. The Pebas fauna is characterised as aquatic, endemic and extinct, and is a typical representative of a long-lived lake fauna. Fluvial taxa are not common, (marginal) marine taxa are rare. An additional molluscan fauna from the Miocene Solimões Formation of Brazil, containing 13 fresh water species was also described. The newly documented fauna was used to improve biostratigraphic framework of Miocene Amazonian deposits. Twelve mollusc zones were introduced, the upper eleven of which cover a time interval of approximately seven million years covered previously by only three pollen zones. An age model calculated for the borehole data indicates that the Pebas Formation was deposited between c. 24 and 11 Ma. The areal distribution of the outcropping mollusc zones uncovered a broad dome structure, termed here the Iquitos-Araracuara anteclise in the study area. The structure appears to have influenced river courses and also contributed to edaphic heterogeneity that may have been in part responsible for the current high biodiversity in the study area. The Pebas system was a huge system (> one million km2) dominated by relatively shallow lakes, but also containing swamps and rivers. The system was fed by rivers draining the emergent Andes in the west and lowlands and cratons to the east. The Pebas system was located at sea level and was open to marine settings through a northern portal running through the Llanos Basin and East Venezuela Basin towards the Caribbean. Cyclical baselevel changes possibly related to Mylankhovitch cycles, have been documented in depositional sequences of the Pebas Formation. The composition of the Pebasian mollusc fauna implies that the system was mostly a fresh water system. Such an interpretation is matched by strontium isotope ratios as well as very negative δ18O ratios found in the shells, but is at odds with oligohaline and mesohaline ichnofacies found in the same strata. The mollusc fauna of the Pebas Formation diversified through most of the existence of the lake system. The diversification was mostly the result of in-situ cladogenesis. The success of some of the Pebasian endemic clades is explained by adaptation to fresh water, low oxygen, common unconsolidated lake bottoms (soup grounds) as well as high predation intensity. Maximum diversity was reached at the base of the late Middle to early Late Miocene Grimsdalea pollen zone, some 13 Ma. At the time some 85 species co-occurred, 67 of which are considered as Pebasian endemics. A subsequent drop in species richness coincides with indications of elevated salinities, although a causal relation still needs to be established. Apparently the Pebas fauna went (almost) entirely extinct with the replacement of the lake system into a fluvio-tidal system during the Early Late Miocene, some 11 Ma.