• Local understandings of conservation in southeastern Mexico and their implications for community-based conservation as an alternative paradigm

      Reyes-Garcia, Victoria; Ruiz-Mallen, Isabel; Porter-Bolland, Luciana; Garcia-Frapolli, Eduardo; Ellis, Edward A.; Mendez, Maria-Elena; Pritchard, Diana J.; Sanchez-Gonzalez, Maria-Consuelo; Institucio Catalana de Recerca i Estudis Avancats; Centro de Investigaciones en Ecosistemas; et al. (Wiley, 2013-08)
      Since the 1990s national and international programs have aimed to legitimize local conservation initiatives that might provide an alternative to the formal systems of state-managed or otherwise externally driven protected areas. We used discourse analysis (130 semistructured interviews with key informants) and descriptive statistics (679 surveys) to compare local perceptions of and experiences with state-driven versus community-driven conservation initiatives. We conducted our research in 6 communities in southeastern Mexico. Formalization of local conservation initiatives did not seem to be based on local knowledge and practices. Although interviewees thought community-based initiatives generated less conflict than statemanaged conservation initiatives, the community-based initiatives conformed to the biodiversity conservation paradigm that emphasizes restricted use of and access to resources. This restrictive approach to community-based conservation in Mexico, promoted through state and international conservation organizations, increased the area of protected land and had local support but was not built on locally relevant and multifunctional landscapes, a model that community-based conservation is assumed to advance.
    • Community based biodiversity monitoring in Mexico: current status, challenges, and future strategies for collaboration with scientists

      Pritchard, Diana J. (Springer, 2013-07-18)
      An array of social and political actors, from international to local levels, increasingly demand monitoring data on biodiversity and ecosystem functions. As elsewhere, prevalent approaches in Mexico emphasize the collection of scientific data regarding biological indicators, by professionals, for conservation planning, global targets, and biological inquiry. These are complicated, expensive, and dependent on external funding. They also fail to engage with communities, many of whom practice traditional forms of monitoring to manage their local environments and livelihoods. Community-based monitoring, an approach involving collaborations between scientists and communities, has the potential to contribute to sustainable forms of resource use management and as a cost-effective method. Efforts could develop once local rights of use and traditional knowledge systems are recognized, access to information is ensured, and a broad array of relevant environmental and social indicators are included.
    • Coral reef populations in the Caribbean: is there a case for better protection against climate change?

      Crabbe, M. James C.; University of Bedfordshire (Scientific Research Publishing, 2013-06)
      Knowledge of factors that are important in coral reef growth help us to understand how reef ecosystems react following major environmental disturbances due to climate change and other anthropogenic effects. This study shows that despite a range of anthropogenic stressors, corals on the fringing reefs south of Kingston harbour, as well as corals on fringing reefs on the north coast of Jamaica near Discovery Bay can survive and grow. Skewness values for Sidastrea siderea and Porites astreoides were positive (0.85 1.64) for all sites, implying more small colonies than large colonies. Coral growth rates are part of a demographic approach to monitoring coral reef health in times of climate change, and linear extension rates (mm.yr-1) of Acropora palmata branching corals at Dairy Bull, Rio Bueno, and Pear Tree Bottom on the north coast of Jamaica were c. 50 90 mm.year-1 from 2005-2012. The range of small-scale rugosities at the Port Royal cay sites studied was lower than that at the Discovery Bay sites; for example Rio Bueno was 1.05 ± 0.15 and Dairy Bull the most rugose at 2.3 ± 0.16. Diary Bull reef has for several years been the fringing reef with the most coral cover, with a benthic community similar to that of the 1970s. We discuss whether Jamaica can learn from methods used in other Caribbean countries to better protect its coral reefs against climate change. Establishing and maintaining fully-protected marine parks in Jamaica and elsewhere in the Caribbean is one tool to help the future of the fishing industry in developing countries. Developing MPAs as part of an overall climate change policy for a country may be the best way of integrating climate change into MPA planning, management, and evaluation.
    • Complete chloroplast genome sequence of Holoparasite Cistanche Deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from Its host Haloxylon Ammodendron (Chenopodiaceae)

      Li, Xi; Zhang, Ti-Cao; Qiao, Qin; Ren, Zhumei; Zhao, Jiayuan; Yonezawa, Takahiro; Hasegawa, Masami; Crabbe, M. James C.; Li, Jianqiang; Zhong, Yang; et al. (Public Library of Science, 2013)
      The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. The authors report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae.
    • Water pollutant fingerprinting tracks recent industrial transfer from coastal to inland China: a case study

      Zheng, Weiwei; Wang, Xia; Tian, Dajun; Jiang, Songhui; Andersen, Melvin E.; He, Genhsjeng; Crabbe, M. James C.; Zheng, Yuxin; Zhong, Yang; Qu, Weidong (Nature Publishing Group, 2013)
      In recent years, China’s developed regions have transferred industries to undeveloped regions. Large numbers of unlicensed or unregistered enterprises are widespread in these undeveloped regions and they are subject to minimal regulation. Current methods for tracing industrial transfers in these areas, based on enterprise registration information or economic surveys, do not work. The authors have developed an analytical framework combining water fingerprinting and evolutionary analysis to trace the pollution transfer features between water sources. We collected samples in Eastern China (industrial export) and Central China (industrial acceptance) separately from two water systems. Based on the water pollutant fingerprints and evolutionary trees, we traced the pollution transfer associated with industrial transfer between the two areas. The results are consistent with four episodes of industrial transfers over the past decade. The results also show likely types of the transferred industries - electronics, plastics, and biomedicines - that contribute to the water pollution transfer.
    • Experimentally testing the accuracy of an extinction estimator: Solow's optimal linear estimation model

      Clements, Christopher F.; Worsfold, Nicholas T.; Warren, Philip H.; Collen, Ben; Clark, Nick; Blackburn, Tim M.; Petchey, Owen L.; Butler, Simon; University of Sheffield; University of York; et al. (Wiley Blackwell, 2013)
      Mathematical methods for inferring time to extinction have been widely applied but poorly tested. Optimal linear estimation (also called the 'Weibull' or 'Weibull extreme value' model) infers time to extinction from a temporal distribution of species sightings. Previous studies have suggested optimal linear estimation provides accurate estimates of extinction time for some species; however, an in-depth test of the technique is lacking. The use of data from wild populations to gauge the error associated with estimations is often limited by very approximate estimates of the actual extinction date and poor sighting records. Microcosms provide a system in which the accuracy of estimations can be tested against known extinction dates, whilst incorporating a variety of extinction rates created by changing environmental conditions, species identity and species richness. We present the first use of experimental microcosm data to exhaustively test the accuracy of one sighting-based method of inferring time of extinction under a range of search efforts, search regimes, sighting frequencies and extinction rates. Our results show that the accuracy of optimal linear estimation can be affected by both observer-controlled parameters, such as change in search effort, and inherent features of the system, such as species identity. Whilst optimal linear estimation provides generally accurate and precise estimates, the technique is susceptible to both overestimation and underestimation of extinction date. Microcosm experiments provide a framework within which the accuracy of extinction predictors can be clearly gauged. Variables such as search effort, search regularity and species identity can significantly affect the accuracy of estimates and should be taken into account when testing extinction predictors in the future.
    • Environmental regulation of reproductive phase change in Agaricus bisporus by 1-octen-3-ol, temperature and CO2

      Eastwood, Daniel C.; Herman, Bram; Noble, Ralph; Dobrovin-Pennington, Andreja; Sreenivasaprasad, Surapareddy; Burton, Kerry S.; University of Swansea; University of Warwick; East Malling Research; University of Bedfordshire; et al. (Elsevier, 2013)
      Reproductive phase change from vegetative mycelium to the initiation of fruiting in Agaricus bisporus is regulated in large part by the sensing of environmental conditions. A model is proposed in which three separate environmental factors exert control at different stages of the reproductive developmental process change. The eight carbon volatile 1-octen-3-ol controls the early differentiation from vegetative hyphae to multicellular knots; temperature reduction is essential for the later differentiation of primodia; and carbon dioxide level exerts quantitative control on the number of fruiting bodies developed. Analysis of transcriptomic changes during the reproductive phase change was carried out with initiation-specific microarrays, and the newly published A. bisporus genome was used to analyse the promoter regions of differentially regulated genes. Our studies have shown there to be both early and late initiation responses relating to sensing of eight carbon volatiles and temperature respectively. A subset of 45 genes was transcriptionally regulated during the reproductive phase change which exhibited a range of functions including cell structure, nitrogen and carbon metabolism, and sensing and signalling. Three gene clusters linking increased transcription with developmental stage were identified. Analysis of promoter regions revealed cluster-specific conserved motifs indicative of co-ordinated regulation of transcription
    • Effect of slope on development of pahoehoe flow fields: evidence from Mount Etna

      Guest, John E.; Duncan, Angus M.; Stofan, Ellen R.; Anderson, Steve W. (Elsevier, 2012-03-15)
    • Magnaporthe oryzae populations adapted to finger millet and rice exhibit distinctive patterns of genetic diversity, sexuality and host interaction

      Takan, J.P.; Chipili, J.; Muthumeenakshi, S.; Talbot, N.J.; Manyasa, E.O.; Bandyopadhyay, R.; Sere, Y.; Nutsugah, S.K.; Talhinhas, Pedro; Hossain, M.; et al. (Humana Press, 2012-02)
    • Effect of methanol on mitochondrial organization in zebrafish (Danio rerio) ovarian follicles.

      Spikings, Emma; Zampolla, Tiziana; Rawson, David M.; Wang, Y.; Zhang, Tiantian; University of Bedfordshire; China Agricultural University (Elsevier, 2012-01-01)
      Successful cryopreservation is usually measured in terms of cell survival. However, there may also be more subtle effects within cells that survive. Previous studies on zebrafish have produced evidence of mitochondrial DNA (mtDNA) damage in cryopreserved embryonic blastomeres and, after exposure to cryoprotectants, alterations in mtDNA replication in embryos and decreased mitochondrial membrane potential, mtDNA and ATP production in ovarian follicles. This study shows that the decreased ATP levels previously observed in stage III zebrafish ovarian follicles exposed to ≥3 M methanol persisted in those follicles that subsequently developed to stage IV. However, the decreased mtDNA levels were restored in those follicles. In order to determine whether mitochondrial distribution and/or their transport network was affected by the methanol exposure, immunocytochemistry analysis of tubulin and mitochondrial cytochrome c oxidase I (COX-I) was performed, along with phalloidin staining of polymerized actin. Neat arrangements of all proteins were observed in control follicles, with COX-I and tubulin being colocalized near granulosa cell nuclei, while actin formed hexagonal and/or polygonal structures nearer granulosa cell membranes and projected into the oocyte surface. Exposure to methanol (2 to 4 M) disrupted the COX-I and tubulin arrangements and the hexagonal and/or polygonal actin distribution and actin projections into the oocyte. These effects were still observed in those follicles that developed to stage IV, although the severity was reduced. In summary, the disruption to function and distribution of mitochondria in ovarian follicles exposed to >2 M methanol may be mediated via disruption of the mitochondrial transport system. Some recovery of this disruption may take place after methanol removal and subsequent follicle maturation.
    • Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs

      Yang, Zhen; Dong, Dong; Zhang, Zhaolei; Crabbe, M. James C.; Wang, Li; Zhong, Yang (BioMed Central, 2012)
      In this study, we comprehensively explored the stably expressed genes (SE genes) and fluctuant genes (FL genes) in the human genome by a meta-analysis of large scale microarray data. We found that these genes have distinct function distributions. miRNA targets are shown to be significantly enriched in SE genes by using propensity analysis of miRNA regulation, supporting the hypothesis that miRNAs can buffer whole genome expression fluctuation. The expression-buffering effect of miRNA is independent of the target site number within the 3'-untranslated region. In addition, we found that gene expression fluctuation is positively correlated with the number of transcription factor binding sites in the promoter region, which suggests that coordination between transcription factors and miRNAs leads to balanced responses to external perturbations.
    • The influence of extreme climate events on models of coral colony recruitment and survival in the Caribbean

      Crabbe, M. James C. (Scientific Research Publishing, 2012)
      Knowledge of coral recruitment patterns helps us understand how reefs react following major disturbances and provides us with an early warning system for predicting future reef health problems. We have reconstructed and interpreted historical and modern-day recruitment patterns, using growth modeling, in order to understand how hurricanes, storms and bleaching events have influenced coral recruitment in the Caribbean. The results indicate that regional hurricane events negatively impact coral recruitment patterns in the Caribbean, from the south in Tobago to more northerly areas in Belize and Jamaica. However, despite multiple large-scale disturbances, corals are still recruiting to marginal reef systems, and to the Mesoamerican Barrier reef off the coast of Belize. While recruitment and initial growth since the Caribbean-wide bleaching event of 2005 has been successful for Colpophylia natans at the sites studied in North Jamaica, medium and large sized colonies of this species have decreased in numbers since the bleaching event at most sites, except where the rugosity is highest, at Dairy Bull reef.
    • From citizen science to policy development on the coral reefs of Jamaica

      Crabbe, M. James C. (Hindawi Publishing Corporation, 2012)
      This paper explores the application of citizen science to help generation of scientific data and capacity-building, and so underpin scientific ideas and policy development in the area of coral reef management, on the coral reefs of Jamaica. From 2000 to 2008, ninety Earthwatch volunteers were trained in coral reef data acquisition and analysis and made over 6,000 measurements on fringing reef sites along the north coast of Jamaica. Their work showed that while recruitment of small corals is returning after the major bleaching event of 2005, larger corals are not necessarily so resilient and so need careful management if the reefs are to survive such major extreme events. These findings were used in the development of an action plan for Jamaican coral reefs, presented to the Jamaican National Environmental Protection Agency. It was agreed that a number of themes and tactics need to be implemented in order to facilitate coral reef conservation in the Caribbean. The use of volunteers and citizen scientists from both developed and developing countries can help in forging links which can assist in data collection and analysis and, ultimately, in ecosystem management and policy development.
    • Cytoskeleton proteins F-actin and tubulin distribution and interaction with mitochondria in the granulosa cells surrounding stage III zebrafish (Danio rerio) oocytes

      Zampolla, Tiziana; Spikings, Emma; Rawson, David M.; Zhang, Tiantian; University of Bedfordshire (Elsevier, 2011-10-01)
      The distributional arrangement of mitochondria in the granulosa cells surrounding stage III zebrafish oocyte has been reported as a contiguous aggregation of mitochondria at the margin of the each granulosa cell. The aim of the present study was to further investigate the mitochondrial distribution in the granulosa cell layer in stage III ovarian follicles and the interaction between mitochondria and cytoskeleton elements actin and tubulin. To determine mitochondrial distribution/transport, immunocytochemistry analysis of tubulin and mitochondrial COX-I was carried out along with phalloidin staining of polymerised F-actin. The follicles were also exposed to a range of conditions that are known to affect mitochondria and the cytoskeleton proteins actin and tubulin. The mitochondrial inhibitor FCCP, the anti-mitotic drug nocodazole, and actin polymerisation inhibitor cytochalasin B were used. Levels of ATP, mtDNA copy number, and viability assessed by Trypan blue were also studied after exposure to inhibitors in order to determine the relationship between mitochondrial distribution/activity and ATP production. F-actin showed a hexagonal-polygonal distribution surrounding the mitochondria in granulosa cells, with the F-actin network adjacent to the plasma membrane of each granulosa cell. Tubulin structure presented a less organised distribution than F-actin, it was sparse in the cytosol. Interaction between mitochondria and tubulin was found indicating that mitochondria and tubulin are colocalised in zebrafish ovarian follicles. The exposure of ovarian follicles to inhibitors induced the loss of mitochondrial structural integrity showing that mitochondria distribution in granulosa cells of stage III zebrafish ovarian follicles is determined by the microtubules network.
    • Effect of chilling on sox2, sox3 and sox19a gene expression in zebrafish (Danio rerio) embryos

      Desai, Kunjan; Spikings, Emma; Zhang, Tiantian; University of Bedfordshire (Elsevier, 2011-10)
      Zebrafish embryos have not been cryopreserved due to their structural limitations. Although embryo survival rates have been used as the measured outcome for most of the cryopreservation protocols studied, there are very limited data available at the molecular level. This study focused on the effect of chilling and subsequent warming on gene expression of sox2, sox3 and sox19a which play vital roles in the development of zebrafish embryos. A quantitative RT-PCR approach was used to investigate gene expression following chilling at 0°C for up to 180 min. The effect on gene expression was also studied during a 180 min warming period after chilling for 30 or 60 min. There were significant decreases in sox2 (up to 4-fold) and sox3 (up to 3-fold) expressions following chilling. Significant increases in gene expressions of sox2 (up to 2-fold), sox3 (up to 33-fold) and sox19a (up to 25-fold) were observed during warming in the embryos that had been chilled for 30 min. Similarly, significant increases were observed in sox2 (up to 3-fold) and sox3 (up to 2-fold) during warming in embryos that had been chilled for 60 min. These increases may be explained by compensation for the suppression observed during chilling and/or to activate repair mechanisms or maintain homeostasis.
    • Robustness of Self-Organised Systems to Changes in Behaviour: An Example from Real and Simulated Self-Organised Snail Aggregations

      Stafford, Richard; Williams, Gray A.; Davies, Mark S.; de Polavieja, Gonzalo G. (Public Library of Science, 2011-07-28)
    • Why does the giant panda eat bamboo? a comparative analysis of appetite-reward-related genes among mammals

      Jin, Ke; Xue, Chenyi; Wu, Xiaoli; Qian, Jinyi; Zhu, Yong; Yang, Zhen; Yonezawa, Takahiro; Crabbe, M. James C.; Cao, Ying; Hasegawa, Masami; et al. (2011-07-27)
    • Epidemiology, histopathology and aetiology of olive anthracnose caused by Colletotrichum acutatum and C. gloeosporioides in Portugal

      Talhinhas, Pedro; Mota-Capitão, C.; Martins, S.; Ramos, A.P.; Neves-Martins, João; Guerra-Guimarães, L.; Várzea, V.; Silva, M.C.; Sreenivasaprasad, Surapareddy; Oliveira, Helena (Wiley-Blackwell, 2011-06)
    • A framework for assessing threats and benefits to species responding to climate change

      Thomas, Chris D.; Hill, Jane K.; Anderson, Barbara J.; Bailey, Sallie; Beale, Colin M.; Bradbury, Richard B.; Bulman, Caroline R.; Crick, Humphrey Q. P.; Eigenbrod, Felix; Griffiths, Hannah M.; et al. (Wiley Blackwell, 2011-04)
      Current national and international frameworks for assessing threats to species have not been developed in the context of climate change, and are not framed in a way that recognises new opportunities that arise from climate change. The framework presented here separates the threats and benefits of climate change for individual species. Threat is assessed by the level of climate-related decline within a species’ recently occupied (e.g. pre-1970s) historical distribution, based on observed (e.g. repeat census) and/or projected changes (e.g. modelled bioclimate space). Benefits are assessed in terms of observed and/or projected increases outside the recently occupied historical range. Exacerbating factors (e.g. small population size, low dispersal capacity) that might increase levels of threat or limit expansion in response to climate change are taken into consideration within the framework. Protocols are also used to identify levels of confidence (and hence research and/or monitoring needs) in each species’ assessment.