Experimental design in fluvial ichthyology: getting the most for your money

In field biology, cost efficiency is an essential element of experimental design, with ramifications extending well beyond the basic monetary considerations associated with labour and equipment acquisition. Current economic constraints often require scientists to undertake many technical, secretarial and managerial tasks in addition to those associated with data collection, analysis, interpretation and publication. Because the time spent to process material in the laboratory can rarely be shortened without compromising the integrity of the results, it is imperative that field experiments be well-organised, addressing as many aspects of the problem as possible during the same sampling excursion. The sampling strategy employed should provide a maximum of good field data with a minimum cost of time and effort.

Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.

The impact of molecular biology on assessment of water quality: advantages and limitations of current techniques

The advent of molecular biology has had a dramatic impact on all aspects of biology, not least applied microbial ecology. Microbiological testing of water has traditionally depended largely on culture techniques. Growing understanding that only a small proportion of microbial species are culturable, and that many microorganisms may attain a viable but non-culturable state, has promoted the development of novel approaches to monitoring pathogens in the environment. This has been paralleled by an increased awareness of the surprising genetic diversity of natural microbial populations. By targeting gene sequences that are specific for particular microorganisms, for example genes that encode diagnostic enzymes, or species-specific domains of conserved genes such as 16S ribosomal RNA coding sequences (rrn genes), the problems of culture can be avoided. Technical developments, notably in the area of in vitro amplification of DNA using the polymerase chain reaction (PCR), now permit routine detection and identification of specific microorganisms, even when present in very low numbers. Although the techniques of molecular biology have provided some very powerful tools for environmental microbiology, it should not be forgotten that these have their own drawbacks and biases in sampling. For example, molecular techniques are dependent on efficient lysis and recovery of nucleic acids from both vegetative forms and spores of microbial species that may differ radically when growing in the laboratory compared with the natural environment. Furthermore, PCR amplification can introduce its own bias depending on the nature of the oligonucleotide primers utilised. However, despite these potential caveats, it seems likely that a molecular biological approach, particularly with its potential for automation, will provide the mainstay of diagnostic technology for the foreseeable future.

Freshwater biology and water supply in Britain

This paper is designed to give a general account of freshwater biology as it bears on waterworks practice. Most water that is used for consumption will commonly go through a storage reservoir. Here special reference is given to the biological relations in standing waters, the biological control of water supplies, methods of plankton estimation, the biology of slow sand filtration and the use of algicides.

Proceedings of the first world meeting on bigeye tuna

The annual catches of big eye are exceeded by those of only two other species of tuna, skipjack, Katsuwonus pelamis, and yellowfin, Thunnus albacares. However, because most of the bigeye caught are consumed fresh, whereas most of the skipjack and yellowfin caught are canned, the economic value of big eye exceeds that of any other species of tuna. Despite its importance, less is known of the biology of bigeye than of the biology of any of the other principal market species of tunas. Historically, bigeye have been harvested mostly by longlines, which take only medium to large fish. During recent years, however, greater amounts of small bigeye have been caught by purse seines and other surface gear. This is a matter of concern for several reasons. First, long line fishermen are concerned that the harvesting of small bigeye will decrease the amounts of medium to large bigeye available to them. Second, since small bigeye are canned, rather than eaten fresh, consumers are concerned about the possible decrease in the supply of high-quality fresh fish. Third, economists are concerned about the possible economic loss associated with harvesting fish at less than their maximum economic value. Fourth, biologists are concerned about the possibility that harvesting of small bigeye could decrease the overall catches of that species. These concerns cannot be properly addressed until more knowledge of the biology of big eye is available. The purposes of the meeting were to review and discuss the information available and to make recommendations for further research.

Social, economic, and health impact of the respiratory syncytial virus: a systematic search

Background: Bronchiolitis caused by the respiratory syncytial virus (RSV) and its related complications are common in infants born prematurely, with severe congenital heart disease, or bronchopulmonary dysplasia, as well as in immunosuppressed infants. There is a rich literature on the different aspects of RSV infection with a focus, for the most part, on specific risk populations. However, there is a need for a systematic global analysis of the impact of RSV infection in terms of use of resources and health impact on both children and adults. With this aim, we performed a systematic search of scientific evidence on the social, economic, and health impact of RSV infection. Methods: A systematic search of the following databases was performed: MEDLINE, EMBASE, Spanish Medical Index, MEDES-MEDicina in Spanish, Cochrane Plus Library, and Google without time limits. We selected 421 abstracts based on the 6,598 articles identified. From these abstracts, 4 RSV experts selected the most relevant articles. They selected 65 articles. After reading the full articles, 23 of their references were also selected. Finally, one more article found through a literature information alert system was included. Results: The information collected was summarized and organized into the following topics: 1. Impact on health (infections and respiratory complications, mid-to long-term lung function decline, recurrent wheezing, asthma, other complications such as otitis and rhino-conjunctivitis, and mortality; 2. Impact on resources (visits to primary care and specialists offices, emergency room visits, hospital admissions, ICU admissions, diagnostic tests, and treatments); 3. Impact on costs (direct and indirect costs); 4. Impact on quality of life; and 5. Strategies to reduce the impact (interventions on social and hygienic factors and prophylactic treatments). Conclusions: We concluded that 1. The health impact of RSV infection is relevant and goes beyond the acute episode phase; 2. The health impact of RSV infection on children is much better documented than the impact on adults; 3. Further research is needed on mid-and long-term impact of RSV infection on the adult population, especially those at high-risk; 4. There is a need for interventions aimed at reducing the impact of RSV infection by targeting health education, information, and prophylaxis in high-risk populations.

Marine biology of the Sierra Leone River Estuary. 1. The physical environment

The Sierra Leone River Estuary is a relatively young drowned river valley, it is shallow except for a deep channel which passes close to the Freetown shoreline. The upper reaches merge into a network of creeks and channels fringed by large areas of mangrove swamps. It is a tidal estuary of the semi-mixed type with the saline oceanic water entering it on a diurnal cycle. The climate of Sierra Leone is marked by a very distinct change between a very wet rainy season and a dry season. The tidal range of the Estuary (spring 3.03m; neap 2.28m) does not impede normal use of the harbour. The tidal variations can be felt as far as 42 miles inland along the water courses of the Sierra Leone River and its tributaries. The volume of fresh water entering the Estuary is large during the rainy season and greatly reduced during the dry season. Consequently there is a marked fall in salinity during the rainy season and higher salinities due to the marine influence prevailing during the dry season. The nature of the shores and bottom, the hydrography and chemistry of the estuarine system have been outlined in relation to the prevailing climatic conditions.

The impact of economic crises on social inequalities in health: what do we know so far?

Since 2008, Western countries are going through a deep economic crisis whose health impacts seem to be fundamentally counter-cyclical: when economic conditions worsen, so does health, and mortality tends to rise. While a growing number of studies have presented evidence on the effect of crises on the average population health, a largely neglected aspect of research is the impact of crises and the related political responses on social inequalities in health, even if the negative consequences of the crises are primarily borne by the most disadvantaged populations. This commentary will reflect on the results of the studies that have analyzed the effect of economic crises on social inequalities in health up to 2013. With some exceptions, the studies show an increase in health inequalities during crises, especially during the Southeast Asian and Japanese crises and the Soviet Union crisis, although it is not always evident for both sexes or all health or socioeconomic variables. In the Nordic countries during the nineties, a clear worsening of health equity did not occur. Results about the impacts of the current economic recession on health equity are still inconsistent. Some of the factors that could explain this variability in results are the role of welfare state policies, the diversity of time periods used in the analyses, the heterogeneity of socioeconomic and health variables considered, the changes in the socioeconomic profile of the groups under comparison in times of crises, and the type of measures used to analyze the magnitude of social inequalities in health. Social epidemiology should further collaborate with other disciplines to help produce more accurate and useful evidence about the relationship between crises and health equity.

A biologia moral da atenção: a constituição do sujeito (des)atento

Esse trabalho analisa a constituição do indivíduo atento e do indivíduo desatento no interior do processo histórico de biologização moral da atenção. Em nossa tese, a história da biologia moral da atenção está dividida em três momentos principais: a segunda metade do século XVIII; a segunda metade do século XIX; as últimas três décadas do século XX. A investigação do terceiro momento está no centro da pesquisa. Nele, damos prioridade a análise da constituição do diagnóstico do Transtorno do Déficit de Atenção e Hiperatividade TDAH. Nos três períodos analisados, os interesses pelos estudos da atenção se intensificaram e seu controle e gestão tornaram-se objeto das tecnologias morais, sociais, econômicas, médicas e psicológicas. Neles a capacidade de controle da atenção passou a ser o que distinguia o sábio do tolo; o indivíduo senhor de si do alienado; o sujeito ativo, mestre no controle de seu corpo e de sua vontade, do impulsivo, portador de um corpo descontrolado e de uma vontade fraca. No século XVIII, a atenção era a direção ativa da mente que possibilitava o conhecimento racional do mundo e de si. Ela deveria ser treinada, incitada e estimulada. Aos que se dedicavam à sua disciplina e mestria era concedido um lugar privilegiado. A moral da atenção se constituía. Ao vinculá-la aos conceitos de inibição e de vontade, o século XIX lhe outorgou uma outra função: o controle do comportamento. Além de ser importante para a constituição do conhecimento, a atenção tornou-se responsável pela regulação da ação. Um novo valor da atenção se constituía. O século XIX também possibilitou que sua moral fosse naturalizada, atada ao corpo e, em seguida, "cerebrizada. O século XX vinculou a atenção à moral do sucesso e da produtividade e radicalizou o processo de sua cerebrização. No processo de moralização e valorização da atenção, as histórias da constituição do sujeito (des)atento são extremamente diversas. A versão analisada em nosso trabalho dialoga com a história do sujeito cerebral. A constituição do sujeito atento e do sujeito desatento é analisada nos espaços fronteiriços criados entre a moral e a biologia cerebral da atenção.

A review of IATTC research on the early life history and reproductive biology of scombrids conducted at the Achotines Laboratory from 1985 to 2005

English: For nearly a century, fisheries scientists have studied marine fish stocks in an effort to understand how the abundances of fish populations are determined. During the early lives of marine fishes, survival is variable, and the numbers of individuals surviving to transitional stages or recruitment are difficult to predict. The egg, larval, and juvenile stages of marine fishes are characterized by high rates of mortality and growth. Most marine fishes, particularly pelagic species, are highly fecund, produce small eggs and larvae, and feed and grow in complex aquatic ecosystems. The identification of environmental or biological factors that are most important in controlling survival during the early life stages of marine fishes is a potentially powerful tool in stock assessment. Because vital rates (mortality and growth) during the early life stages of marine fishes are high and variable, small changes in those rates can have profound effects on the properties of survivors and recruitment potential (Houde 1989). Understanding and predicting the factors that most strongly influence pre-recruit survival are key goals of fisheries research programs. Spanish: Desde hace casi un siglo, los científicos pesqueros han estudiado las poblaciones de peces marinos en un intento por entender cómo se determina la abundancia de las mismas. Durante la vida temprana de los peces marinos, la supervivencia es variable, y el número de individuos que sobrevive hasta las etapas transicionales o el reclutamiento es difícil de predecir. Las etapas de huevo, larval, y juvenil de los peces marinos son caracterizadas por tasas altas de mortalidad y crecimiento. La mayoría de los peces marinos, particularmente las especies pelágicas, son muy fecundos, producen huevos y larvas pequeños, y se alimentan y crecen en ecosistemas acuáticos complejos. La identificación los factores ambientales o biológicos más importantes en el control de la supervivencia durante las etapas tempranas de vida de los peces marinos es una herramienta potencialmente potente en la evaluación de las poblaciones. Ya que las tasas vitales (mortalidad y crecimiento) durante las etapas tempranas de vida de los peces marinos son altas y variables, cambios pequeños en esas tasas pueden ejercer efectos importantes sobre las propiedades de los supervivientes y el potencial de reclutamiento (Houde 1989). Comprender y predecir los factores que más afectan la supervivencia antes del reclutamiento son objetivos clave de los programas de investigación pesquera.

Penaeus indicus H. Milne Edwards, 1837: resumo das conclusões dos cruzeiros de pesca exploratória entre 1979 e 1983 no banco de Sofala em Moçambique

From 1979 to 1983, several surveys were carried out with research and fishing vessels at Sofala Bank in Mozambique. Their main objective was the assessment of shallow water prawn stocks, as this resource is of great economic importance for the country. A summary of the conclusions of these surveys regarding the species Penaeus indicus is presented. During the rainy season the species occurs closer to the shore than during the dry season. Estimates of biomass are very variable. The spawning peak seems to occur at the beginning of the rainy season (September-October). The spawning areas are located very close to the shore in the northern part of Sofala Bank and South of 17 degree 10'S in the 15-25 m depth interval.

Análisis de la desigualdad económica en los municipios del País Vasco agrupados por tamaño de la población. Economic Inequality in the municipalities of the Basque Country aggregated by population size.

This paper analyses the economic inequality in the municipalities of the Basque Country during the period 1996 and 2010. We have used dates from the Udalmap database mainly the GDP per capita. We have drawn Lorenz Curves and also we have computed Gini indexes to analyse the evolution of inequality during this period. Therefore, we have concluded that there has been an increase of the economic inequality in the municipalities of the Basque Country during this period of time.

Macrophytes aquatiques dans les eaux "continentales" ivoiriennes

Inventory and socio-economic impacts of water weed are presented. Free-floating species (Eichhornia crassipes, Pistia strationes) floating leaves plants (Nymphaea lotus, Polygonum senegalense) as well as emerged species such as Echinochloa pyramidalis and Nelumbo nucifera are the most common species in the concerned aquatic environments. These plants have been colonizing these environments for about a decade and the colonized area are equivalent to 70 % of the whole of the water surface. Besides, these plants strongly affect water quality and constitute a nuisance for water uses.

Economic analysis of the privatization of publicly-owned firms

modelo económico sobre la privatización de Telefónica