Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA)

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples from three activated sludge wastewater treatment plants (WWTPs) with the MLE configuration were collected for both oxic and anoxic reactors, and ARDRA patterns using double enzyme digestions AluI+MspI were obtained. A matrix of Dice similarity coefficients was calculated and used to compare these restriction patterns. Differences in the community structure due to influent characteristics and temperature could be observed, but not between the oxic and anoxic reactors of each of the three MLE configurations. Other possible applications of ARDRA for detecting and monitoring changes in activated sludge systems are also discussed

Rapid Biodiversity Assessment and Monitoring Method for Highly Diverse Benthic Communities: A Case Study of Mediterranean Coralligenous Outcrops

Increasing anthropogenic pressures urge enhanced knowledge and understanding of the current state of marine biodiversity. This baseline information is pivotal to explore present trends, detect future modifications and propose adequate management actions for marine ecosystems. Coralligenous outcrops are a highly diverse and structurally complex deep-water habitat faced with major threats in the Mediterranean Sea. Despite its ecological, aesthetic and economic value, coralligenous biodiversity patterns are still poorly understood. There is currently no single sampling method that has been demonstrated to be sufficiently representative to ensure adequate community assessment and monitoring in this habitat. Therefore, we propose a rapid non-destructive protocol for biodiversity assessment and monitoring of coralligenous outcrops providing good estimates of its structure and species composition, based on photographic sampling and the determination of presence/absence of macrobenthic species. We used an extensive photographic survey, covering several spatial scales (100s of m to 100s of km) within the NW Mediterranean and including 2 different coralligenous assemblages: Paramuricea clavata (PCA) and Corallium rubrum assemblage (CRA). This approach allowed us to determine the minimal sampling area for each assemblage (5000 cm² for PCA and 2500 cm²for CRA). In addition, we conclude that 3 replicates provide an optimal sampling effort in order to maximize the species number and to assess the main biodiversity patterns of studied assemblages in variability studies requiring replicates. We contend that the proposed sampling approach provides a valuable tool for management and conservation planning, monitoring and research programs focused on coralligenous outcrops, potentially also applicable in other benthic ecosystems

Assessment of the water chemistry and the macroinvertebrate community changes produced during the creation of the new Llobregat river mouth (Barcelona, NE Spain)

In 1999, a set of coordinated projects and investments whose principal objective was to transform Barcelona into one of the main distribution points of southern Europe resulted in the relocation of the Llobregat River mouth. The mouth was relocated by draining the old river mouth and constructing a new one. The aim of this study was to characterise the physico-chemical properties and the aquatic macroinvertebrate communities of the new river mouth and to monitor the changes experienced by the estuarine environment during its creation. A sampling point was established in the river 1.8 km upstream from its connection with the new mouth, and two sampling points were established in the new mouth. Samples of water and macroinvertebrates were collected every two months from May 2004 to June 2005, covering the periods before (from May to September 2004) and after (from September 2004 to June 2005) the new mouth was connected to the river and the sea. During the period before its connection to the river and the sea, the new mouth was functionally similar to a lagoon, with clear waters, charophytes and a rich invertebrate community. After the connection was completed, seawater penetrated the river mouth and extended to the connection point with the river (approximately 3.9 km upstream). An increase in conductivity from 4-6 mS cm 1 to 24-30 mS cm 1 caused important changes in the macroinvertebrate community of the new mouth. An initial defaunation was followed by a colonisation of the new mouth by brackish-water and marine invertebrate species. Due to its design (which allows the penetration of the sea) and the decreased discharge from the lower part of the Llobregat River, the new mouth has become an arm of the sea

Understanding Flood Regime Changes in Europe: a state-of-the-art assessment

There is growing concern that flooding is becoming more frequent and severe in Europe. A better understanding of flood regime changes and their drivers is therefore needed. The paper reviews the current knowledge on flood regime changes in European rivers that has traditionally been obtained through two alternative research approaches. The first approach is the data-based detection of changes in observed flood events. Current methods are reviewed together with their challenges and opportunities. For example, observation biases, the merging of different data sources and accounting for nonlinear drivers and responses. The second approach consists of modelled scenarios of future floods. Challenges and opportunities associated with flood change scenarios are discussed such as fully accounting for uncertainties in the modelling cascade and feedbacks. To make progress in flood change research, we suggest that a synthesis of these two approaches is needed. This can be achieved by focusing on long duration records and flood-rich and flood-poor periods rather than on short duration flood trends only, by formally attributing causes of observed flood changes, by validating scenarios against observed flood regime dynamics, and by developing low-dimensional models of flood changes and feedbacks. The paper finishes with a call for a joint European flood change research network.

Socio-economic impacts and assessment biological invasions

Biological invasions have been object of ecological research for years. As one objective, natural scientists investigate the effects of invasive species on ecosystems and their functioning (Levine et al. 2003). However, impacts on ecosystems are also of relevance for society. Changes in ecosystems affect humans in so far as ecosystems provide goods and services, such as fresh water, food and fibbers or recreation, which might be altered due to invasive species. Therefore impacts of biological invasions should be an object of socio-economic interest, which is also demanded by the Convention on Biological Diversity

Conflict, Peace and Security in Africa: an Assessment and New Questions After 50 Years of African Independence

Since the independence processes in the African continent, armed conflicts, peace and security have raised concern and attention both at the domestic level and at the international scale. In recent years, all aspects have undergone significant changes which have given rise to intense debate. The end of some historical conflicts has taken place in a context of slight decrease in the number of armed conflicts and the consolidation of post-conflict reconstruction processes. Moreover, African regional organizations have staged an increasingly more active internal shift in matters related to peace and security, encouraged by the idea of promoting “African solutions to African problems”. This new scenario, has been accompanied by new uncertainties at the security level and major challenges at the operational level, especially for the African Union. This article aims to ascertain the state of affairs on all these issues and raise some key questions to consider.

On-farm animal welfare assessment in dairy cattle: improved lameness detection

Estudi realitzat a partir d’una estada a la University of British Columbia, Canada, entre 2010 i 2012. Primerament es va desenvolupar una escala per mesurar coixeses (amb valors de l’1 al 5). Aquesta escala es va utilitzar per estudiar l’associació entre factors de risc a nivell de granja (disseny de le instal.lacions i maneig) i la prevalencia de coixeses a Nord America. Les dades es van recollir en un total de 40 granges al Nord Est dels E.E.U.U (NE) i 39 a California (CA) . Totes les vaques del group mes productiu es van categoritzar segons la severitat de les coixeses: sanes, coixes i severament coixes. La prevalencia de coixeses en general fou del 55 % a NE i del 31% a CA. La prevalencia de coixeses severes fou del 8% a NE i del 4% a Ca. A NE, les coixeses en general increntaren amb la presencia de serradura als llits i disminuiren en granjes grans, amb major quantitat de llit i acces a pastura. Les coixeses mes severes incrementaren amb la falta d’higiene als llit i amb la presencia de serradura als llits, i disminuiren amb la quantitat de llit proveit, l’us de sorra als llits i amb la mida de la granja. A CA, les coixeses en general incrementaren amb la falta d’higiene al llit, i disminuiren amb la mida de la granja, la presencia de terres de goma, l’increment d’espai als cubicles , l’espai a l’abeuredor i la desinfeccio de les peulles. Les coixeses severes incrementaren amb la falta d’higiene al llit i disminuixen amb la frequencia de neteja del corral. En conclusio, canvis en el maneig i el disseny de les instal.lacions poden ajudar a disminuir la prevalencia de coixeses, tot i que les estrategies a seguir variaran segons la regio.

Biodiversity and global change in Mediterranean benthic communities: perspectives over large spatial and long temporal scales

Many terrestrial and marine systems are experiencing accelerating decline due to the effects of global change. This situation has raised concern about the consequences of biodiversity losses for ecosystem function, ecosystem service provision, and human well-being. Coastal marine habitats are a main focus of attention because they harbour a high biological diversity, are among the most productive systems of the world and present high anthropogenic interaction levels. The accelerating degradation of many terrestrial and marine systems highlights the urgent need to evaluate the consequence of biodiversity loss. Because marine biodiversity is a dynamic entity and this study was interested global change impacts, this study focused on benthic biodiversity trends over large spatial and long temporal scales. The main aim of this project was to investigate the current extent of biodiversity of the high diverse benthic coralligenous community in the Mediterranean Sea, detect its changes, and predict its future changes over broad spatial and long temporal scales. These marine communities are characterized by structural species with low growth rates and long life spans; therefore they are considered particularly sensitive to disturbances. For this purpose, this project analyzed permanent photographic plots over time at four locations in the NW Mediterranean Sea. The spatial scale of this study provided information on the level of species similarity between these locations, thus offering a solid background on the amount of large scale variability in coralligenous communities; whereas the temporal scale was fundamental to determine the natural variability in order to discriminate between changes observed due to natural factors and those related to the impact of disturbances (e.g. mass mortality events related to positive thermal temperatures, extreme catastrophic events). This study directly addressed the challenging task of analyzing quantitative biodiversity data of these high diverse marine benthic communities. Overall, the scientific knowledge gained with this research project will improve our understanding in the function of marine ecosystems and their trajectories related to global change.

Forced oscillation assessment of respiratory mechanics in ventilated patients

The forced oscillation technique (FOT) is a method for non-invasively assessing respiratory mechanics that is applicable both in paralysed and non-paralysed patients. As the FOT requires a minimal modification of the conventional ventilation setting and does not interfere with the ventilation protocol, the technique is potentially useful to monitor patient mechanics during invasive and noninvasive ventilation. FOT allows the assessment of the respiratory system linearity by measuring resistance and reactance at different lung volumes or end-expiratory pressures. Moreover, FOT allows the physician to track the changes in patient mechanics along the ventilation cycle. Applying FOT at different frequencies may allow the physician to interpret patient mechanics in terms of models with pathophysiological interest. The current methodological and technical experience make possible the implementation of portable and compact computerised FOT systems specifically addressed to its application in the mechanical ventilation setting.

Assessment of therapeutic benefit of antiviral therapy in chronic hepatitis C: is hepatic venous pressure gradient a better end point?

Chronic hepatitis C is a major healthcare problem. The response to antiviral therapy for patients with chronic hepatitis C has previously been defined biochemically and by PCR. However, changes in the hepatic venous pressure gradient (HVPG) may be considered as an adjunctive end point for the therapeutic evaluation of antiviral therapy in chronic hepatitis C. It is a validated technique which is safe, well tolerated, well established, and reproducible. Serial HVPG measurements may be the best way to evaluate response to therapy in chronic hepatitis C.

The psychosocial difficulties in brain disorders that explain short term changes in health outcomes.

BACKGROUND: This study identifies a set of psychosocial difficulties that are associated with short term changes in health outcomes across a heterogeneous set of brain disorders, neurological and psychiatric. METHODS: Longitudinal observational study over approximately 12 weeks with three time points of assessment and 741 patients with depression, bipolar disorders, multiple sclerosis, parkinson's disease, migraine, traumatic brain injury and stroke. The data on disability was collected with the checklist of the International Classification of Functioning, Disability and Health. The selected health outcomes were the Short Form 36 and the World Health Organization Disability Assessment Schedule. Multilevel models for change were applied controlling for age, gender and disease severity. RESULTS: The psychosocial difficulties that explain the variability and change over time of the selected health outcomes were energy and drive, sleep, and emotional functions, and a broad range of activities and participation domains, such as solving problems, conversation, areas of mobility and self-care, relationships, community life and recreation and leisure. CONCLUSIONS: Our findings are of interest to researchers and clinicians for interventions and health systems planning as they show that in addition to difficulties that are diagnostic criteria of these disorders, there are other difficulties that explain small changes in health outcomes over short periods of time.

Ultra-Deep Pyrosequencing Detects Conserved Genomic Sites and Quantifies Linkage of Drug-Resistant Amino Acid Changes in the Hepatitis B Virus Genome

Selection of amino acid substitutions associated with resistance to nucleos(t)ide-analog (NA) therapy in the hepatitis B virus (HBV) reverse transcriptase (RT) and their combination in a single viral genome complicates treatment of chronic HBV infection and may affect the overlapping surface coding region. In this study, the variability of an overlapping polymerase-surface region, critical for NA resistance, is investigated before treatment and under antiviral therapy, with assessment of NA-resistant amino acid changes simultaneously occurring in the same genome (linkage analysis) and their influence on the surface coding region.

Soil quality assessment through a multi-approach analysis in soils of abandoned terraced land in NE Spain

The abandonment of agricultural land in mountainous areas has been an outstanding problem along the last century and has captured the attention of scientists, technicians and administrations, for the dramatic consequences sometimes occurred due to soil instability, steep slopes, rainfall regimes and wildfires. Hidromorfological and pedological alterations causing exceptional floods and accelerated erosion processes has therefore been studied, identifying the cause in the loss of landscape heterogeneity. Through the disappearance of agricultural works and drainage maintenance, slope stability has resulted severely affected. The mechanization of agriculture has caused the displacement of vines, olives and corks trees cultivation in terraced areas along the Mediterranean catchment towards more economically suitable areas. On the one hand, land use and management changes have implicated sociological changes as well, transforming areas inhabited by agricultural communities into deserted areas where the colonization of disorganized spontaneous vegetation has buried a valuable rural patrimony. On the other hand, lacking of planning and management of the abandoned areas has produced badlands and infertile soils due to wildfire and high erosion rates strongly degrading the whole ecosystems. In other cases, after land abandonment a process of soil regeneration has been recorded. Investigations have been conducted in a part of NE Spain where extended areas of terraced soils previously cultivated have been abandoned in the last century. The selected environments were semi-abandoned vineyards, semi-abandoned olive groves, abandoned stands of cork trees, abandoned stands of pine trees, scrubland of Cistaceaea, scrubland of Ericaceaea, and pasture. The research work was focused on the study of most relevant physical, chemical and biological soil properties, as well as runoff and erosion under soils with different plant cover to establish the abandonment effect on soil quality, due to the peculiarity and vulnerability of these soils with a much reduced depth. The period of observation was carried out from autumn 2009 to autumn 2010. The sediment concentration of soil erosion under vines was recorded as 34.52 g/l while under pasture it was 4.66 g/l. In addition, the soil under vines showed the least amount of organic matter, which was 12 times lower than all other soil environments. The carbon dioxide (CO2) and total glomalin (TG) ratio to soil organic carbon (SOC) in this soil was 0.11 and 0.31 respectively. However, the soil under pasture contained a higher amount of organic matter and showed that the CO2 and TG ratio to SOC was 0.02 and 0.11 respectively indicating that the soil under pasture better preserves the soil carbon pool. A similar trend was found in the intermediate soils in the sequence of land use change and abandonment. Soil structural stability increased in the two soil fractions investigated (0.25-2.00 mm, 2.0-5.6 mm) especially in those soils that did not undergo periodical perturbations like wildfires. Soil quality indexes were obtained by using relevant physical and chemical soil parameters. Factor analysis carried out to study the relationship between all soil parameters allowed to related variables and environments and identify those areas that better contribute to soil quality towards others that may need more attention to avoid further degradation processes