La experiencia como base en la metodología aplicada al desarrollo rural del País Vasco

[EUS] Experitentzia, Eukal Autonomi Erkideko nekazal zonaldeen garapeneko metodologiaren oinarria. Nekazal zonaldeen garapenerako legearen onarpenaren hamarkada baten ondoren, non administrazioaren artean eta Eskualde Planaren bitartez ekiteko eredua definitzen zen, programen gauzapenean hutsune haundiak antzematen dira. Planak berritzeko helburuarekin egindako akatzen inguruan gogoeta bat burutzen da eta metodologi proposamen ezberdinak planteatzen dira. Hauen artean aurreko planen zehaztapen eta konpromesuz kale egin zuten izaera partizipatibo eta irikiaren aurrean asmo induktiboak, erabilgarriak eta ejekutagarriak proposatzen dira orain.

Biometric comparison of the anchoveta, Cetengraulis mysticetus (Gunther), from ten localities of the Eastern Tropical Pacific Ocean

ENGLISH: It is important to the Inter-American Tropical Tuna Commission to know whether the anchoveta (Cetengraulis mysticetus), the principal tuna bait species in the Eastern Tropical Pacific Ocean, is composed of one or several populations. Earlier research indicated that, on the basis of significant differences in certain meristic counts, populations of this species in six of the major baiting localities between Mexico and Peru, should provisionally be considered as separate stocks. Since that time, additional collections of anchovetas have been obtained from these and other intervening localities. Purpose of the present study was to confirm the results of the earlier work, and to determine whether the differences in the meristic counts persisted from year to year, as well as to examine certain morphometric characters of the fish from these areas, and to learn whether the populations from the other localities are also separate entities. SPANISH: La Comisión Interamericana del Atún Tropical está interesada en saber si la anchoveta (Ceteugrautís mvsticetus}, la principal especie usada como cebo para la pesca del atún en el Océano Pacífico Oriental Tropical, está compuesta de una o de varias poblaciones. Investigaciones previas indicaron que, a base de diferencias significativas encontradas en ciertos caracteres numéricos, las poblaciones de esta especie en seis de las principales localidades entre México y Perú, podían ser consideradas provisionalmente como pertenecientes a "stocks'' separados. Desde entonces se han venido haciendo recolecciones adicionales de anchovetas en éstas y otras localidades intermedias. El propósito del presente trabajo ha sido confirmar los resultados obtenidos previamente, y determinar si las diferencias en los caracteres numéricos han persistido de un año a otro, así como examinar ciertos caracteres morfométricos en los peces de estas áreas, y resolver si las poblaciones de las nuevas localidades muestreadas son también entidades diferentes. (PDF contains 76 pages.)

Contributions to the biology of the engraulid Anchoa naso (Gilbert and Pierson, 1898) from Ecuadorian waters

ENGLISH: One phase of the duties of the Inter-American Tropical Tuna Commission is the gathering and interpretation of data concerning the life history of the commercially important bait species throughout the Eastern Pacific Ocean. During 1958 the Commission established a laboratory in Manta, Ecuador to study tuna. It was subsequently found that this fishery was dependent upon one species of anchovy, Anchoa naso, which was locally referred to as "colorado." During the calendar year 1959 approximately 380,000 scoops of bait were taken by the Manta tuna fleet (Schaefer, 1960), which at that time numbered about 23 vessels. Since then the fleet has increased by about 25 per cent and it is probable that the bait catch has increased also. Virtually nothing has been reported concerning the life history of this species. Hildebrand (1943) reviewed its taxonomy and reported standard lengths ranging from 32 to 135 mm. Peterson (1956) examined specimens from Central America and found them to range from 27 to 66 mm. He also indicated that the species spawned over a long period of time. The present report describes some aspects of the life history of Anchoa naso in Ecuadorian waters. The findings are based on 121 collections taken during the period March 1959 through June 1961. SPANISH: Una fase de las obligaciones de La Comisión Interamericana del Atún Tropical es la obtensión e interpretación de los datos concernientes a la historia natural de las especies de carnada comercialmente importantes en todo el Océano Pacifico Oriental. En el año de 1958 la Comisión estableció un laboratorio en Manta, Ecuador, para estudiar el atún. Se encontró subsecuentemente que esta pesquería dependía de una especie de anchoa, Anchoa naso, conocida localmente con el nombre de colorado. Durante el año calendario de 1959, la flota atunera de Manta, que en ese tiempo alcanzaba a unos 23 barcos, obtuvo aproximadamente 380,000 copas (scoops) de carnada (Schaefer, 1960). Desde entonces la flota ha aumentado en un 25 por ciento, y es probable que la captura de peces-cebo haya aumentado también. Nada se ha informado virtualmente sobre la historia natural de esta especie. Hildebrand (1943) revisó su taxonomia e informó sobre su longitud estándar, que varia entre los 32 y 135 mm. Peterson (1956) examinó especímenes de la América Central, y encontró que variaban entre los 27 y 66 mm. También indicó que la especie desova durante un largo periodo de tiempo. El presente informe describe algunos aspectos de la historia natural de la Anchoa naso en aguas ecuatorianas. Los hallazgos están basados en 121 recolecciones hechas durante el periodo de marzo de 1959 a junio de 1961. (PDF contains 30 pages.)

Distribucion del genero Anodontites (Mollusca: Bivalvia: Mycetopodidae) en Uruguay

Distribution of the genus Anodontites (Mollusca: Bivalvia: Mycetopodidae) in Uruguay. Seven species of the freshwater mussel genus Anodontites were recorded from Uruguay. The populations of these bivalves suffer the negative effects of invasive bivalves, damming, industrial and urban discharges, and agrotoxic runoff. The distribution of these species is generally characterized at the level of basin or politic divisions, and precise geographic records are scarce. In order to detail the distribution of those species, the most representative collections of Uruguay were examined, the material of Anodontites was identified (612 records) and geographic coordenates were assigned at each locality (213 localities), using Geographic Information System (GIS) to obtain a distribution map for each species. Most of the localities with Anodontites were located in the left margin of Uruguay River and southwest of Uruguay, mainly in Soriano, Artigas, Salto and Colonia departments. The Salto Grande basin presented the highest species richness. The species with a highest number of records was A. patagonicus, which was also recorded in all basins. A. trapesialis and A. tenebricosus had a wide distribution and a high number of records. A. lucidus and A. ferrarisii, had a wide distribution (more than 6 basins) but comparatively lower number of records. Finally A. trapezeus and A. trigonus showed a limited distribution. There is a critical lack of samples in Merín Lagoon, Atlantic and Upper Negro River basins. It is necessary to carry out new sampling considering many variables in order to evaluate the current distribution and the ecologic preferences for each species.

Actualización del proyecto fin de carrera: «fototriangulación aplicada a elementos patrimoniales»

[ES] Este proyecto corresponde a una actualización del siguiente proyecto fin de carrera:

Seltene Fischlarven in den Ichthyoplanktonfängen der westlichen Ostsee im Zeitraum 1993 - 1996

Distribution and abundance of fish eggs and larvae in North Sea and Baltic Sea have been objectives of fishery research for over 100 years. Most fish species produce pelagic eggs or larvae. The early developmental stages of many marine fish species important to commercial fishery are part of plankton communities, and can be sampled by a single gear. Collections of fish in their larval phase provide material for studies of many aspects of fishery research: e.g. information on plankton communities and abundance of fish species in the area of investigation.

Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

La cerámica de la Segunda Edad del Hierro en el País Vasco: Estudio tecnológico, funcional y social

670 p. Capítulos de introducción, metodología, discusión y conclusiones en castellano e inglés.

Ancylidae (Mollusca, Heterobranchia, Pulmonata, Basommatophora) do Estado do Rio de Janeiro, Brasil: morfologia, sistemática e distribuição geográfica

Os moluscos pateliformes de água doce da região Neotropical são comumente atribuídos a família Ancylidae sensu latum, abrangendo sete gêneros com pelo menos 13 espécies válidas e sete com identificação duvidosa. Os ancilídeos possuem pequenas dimensões, alcançam no máximo 15 mm de comprimento. Sua concha é frágil, composta por duas regiões, a protoconcha e a teleoconcha, as quais apresentam caracteres relevantes para a sistemática. Na parte mole as impressões musculares, a pigmentação do manto, o sistema reprodutor e a rádula são importantes para o estudo da família. Apesar de existirem vários registros de ocorrência para ancílideos no Estado do Rio de Janeiro (ERJ), existem poucos dados morfológicos. O principal objetivo deste estudo foi fornecer e ampliar as informações sobre a morfologia e distribuição geográfica das espécies de Ancylidae encontradas no ERJ. Os materiais utilizados foram procedentes de coletas próprias, material depositado em Coleções Científicas e dados de revisão bibliográfica. O estudo da morfologia comparada das conchas foi realizado com o auxílio de imagens de microscópio óptico e de varredura. Para a comparação das partes moles, os espécimes foram corados e dissecados sob lupa. Através da conquiliometria analisamos as diferenças inter e intrapopulacionais. Com este trabalho, a riqueza conhecida para Ancylidae no ERJ, aumentou de cinco para sete espécies: Burnupia sp., Ferrissia sp., Gundlachia radiata (Guilding, 1828),G. ticaga (Marcus & Marcus, 1962), Gundlachia sp., Hebetancylus moricandi (d`Orbigny, 1837) e Uncancylus concentricus (d`Orbigny, 1837). Gundlachia radiata e U. concentricus constituem novos registros para o ERJ, e G. radiata para a Região Sudeste. As três espécies com o maior número de registros de ocorrência no ERJ foram: G. ticaga (66%), Ferrissia sp. (37%) e Gundlachia sp. (18%). A ampla distribuição de G. ticaga pode ser devido à capacidade de suportar ambientes impactados. Em relação à morfologia, Burnupia sp. difere de Burnupia ingae Lanzer, 1991, única espécie deste gênero descrita para o Brasil, por apresentar diferenças na microescultura da concha e também na forma das impressões musculares. Ferrissia sp. difere de F. gentilis Lanzer, 1991, devido a diferenças na microescultura apical e número de cúspides no dente central da rádula. Gundlachia sp. é diferente de G. ticaga e G. radiata, por apresentar a abertura da concha mais arredondada, ápice mais recurvado, ultrapassando a borda da concha, pontuações irregulares em toda a protoconcha e forma dos músculos adutores anterior direito e posterior mais elíptica. A morfologia interna também mostra diferenças entre Gundlachia sp. e G. ticaga, como o apêndice terminal do útero e o número de folículos do ovoteste. Através das análises conquiliométricas, constatamos para os gêneros Burnupia, Ferrrissia e Gundlachia, que os índices morfométricos se mostraram melhores que as medidas lineares para a discriminação das espécies, provavelmente porque esses índices diminuem o efeito da amplitude de tamanho das conchas, que são fortemente influenciadas pelas variações ecofenotípicas. Contudo, os caracteres diagnósticos das conchas e das partes moles (impressões musculares) são indispensáveis para a identificação dos gêneros e espécies de Ancylidae. Palavras-chave: Mollusca. Moluscos de água doce. Morfologia. Distribuição geográfica. Estado do Rio de Janeiro.uscos.

The importance of organic detritus in lotic ecosystems: Aspects of trophic interactions

Very little research has been carried out on detrital energetics and pathways in lotic ecosystems. Most investigations have concentrated on the degradation of allochthonous plant litter by fungi, with a glance at heterotrophic bacteria associated with decaying litter. In this short review, the author describes what is known of the detrition of plant litter in lotic waters, which results from the degradative activities of colonising saprophytic fungi and bacteria, and goes on to relate this process to those invertebrates that consume coarse and/or fine particulate detritus, or dissolved organic matter that aggregates into colloidal exopolymer particles. It is clear that many of the key processes involved in the relationships between the physical, chemical, biotic and biochemical elements present in running waters are very complex and poorly understood. Those few aspects for which there are reliable models with predictive power have resulted from data collections made over periods of 20 years or more. Comprehensive research of single catchments would provide a fine opportunity to collect data over a long period.

Composição florística e estrutura da comunidade arbustivo-arbórea de um trecho de floresta submontana na vertente sudeste do Parque Estadual da Ilha Grande, Angra dos Reis / RJ

O estudo objetivou avaliar a composição florística e estrutural dos componentes arbustivo-arbóreo da Floresta Ombrófila Densa submontana em diferentes estágios de regeneração natural, na vertente sudeste do Parque Estadual da Ilha Grande/RJ. Para o inventário florístico foram realizadas coletas assistemáticas em diferentes trechos nessa vertente. A complementação da lista de espécies foi feita a partir, da consulta às exsicatas dos herbários do Rio de Janeiro (FCAB, GUA, HB, HRJ, R, RB, RBR, RFA, RFFP e RUSU) e do inventário fitossociológico. Foi verificado o status de conservação das espécies inventariadas para a Flora Brasileira. Para o inventário fitossociológico foram estabelecidas 34 parcelas amostrais, totalizando 1,02 ha de área amostrada. Todos os indivíduos arbustivo-arbóreos com DAP ≥ 5 cm foram registrados e, após identificação, foram depositados no Herbário da Universidade do Estado do Rio de Janeiro (HRJ). O pacote estatístico FITOPAC 2.1. foi utilizado para a análise dos dados. A similaridade entre o remanescente investigado neste estudo e as outras quatorze áreas distintas do Rio de Janeiro, da própria Ilha Grande ou não, foi avaliada, utilizando-se o coeficiente de Similaridade de Sorensen; pelo critério de agrupamento por ligação média não ponderada (UPGMA) e pelo método de autorreamostragem para a estrutura de grupos; utilizados os programas PAST v1.34 e Multiv 2.4. A partir do levantamento em herbários e dos inventários florístico e fitossociológico realizados neste trabalho, foram analisados 3.470 registros, sendo 1.778 do levantamento de herbários, 1.536 do levantamento fitossociológico e 156 do inventário florístico. Esses registros corresponderam a 606 espécies ou morfo-espécies de Angiospermas e uma de Pteridófita. Os resultados obtidos revelaram a existência de 22 espécies ameaçadas de extinção para a Flora do Brasil. Dentre, as quais, sete são exclusivas da amostragem fitossociológica: Abarema cochliacarpos (Gomes) Barneby & J.W. Grimes, Chrysophyllum flexuosum Mart., Ficus pulchella Schott ex Spreng., Macrotorus utriculatus Perkins, Myrceugenia myrcioides (Cambess.) O.Berg, Rudgea interrupta Benth e Urbanodendron bahiense (Meisn.) Rohwer. No estudo fitossociológico, inventariou-se 1.536 indivíduos de 217 espécies, subordinadas a 53 famílias. O índice de diversidade de Shannon (H) calculado foi de 4,702 nats/ind e equabilidade (J) de 0,874. As 10 famílias com maior riqueza foram: Myrtaceae (31 spp.), Rubiaceae (21), Fabaceae (17), Lauraceae (12), Euphorbiaceae (11), Monimiaceae (8), Melastomataceae (7), Sapindaceae (7), Sapotaceae (6) e Annonaceae (6). Os 10 maiores Valores de Importância das espécies foram para Chrysophyllum flexuosum (3,43%), Lamanonia ternata Vell. (3,40%), Hyeronima alchorneoides Allemão (2,83%), Actinostemon verticillatus (Klotzsch) Baill. (2,55%), Psychotria brasiliensis Vell. (2,55%), Eriotheca pentaphylla (Vell.) A. Robyns (2,28%), Guatteria australis A. St.-Hil. (2,12%), Mabea brasiliensis Müll. Arg. (2,04%), Miconia prasina (Sw.) DC. (1,89%) e Rustia formosa (Cham. & Schltdl. ex DC.) Klotzsch (1,82%). Amostraram-se 27% de espécies representadas por apenas um indivíduo. As análises florísticas avaliadas a partir do Índice de Similaridade de Sorensen indicaram como principais variáveis para a formação dos blocos, os diferentes valores de diversidade para as áreas e a distribuição fitogeográfica das espécies. Os resultados obtidos junto aos dados dos grupos ecológicos, para os indivíduos da fitossociologia, indicaram maior percentual de indivíduos secundários tardios amostrados. Conclui-se que a área de estudo é uma floresta secundária em estágio intermediário de regeneração, com grande riqueza de espécies, muitas das quais de relevante importância ecológica.

Cyclops singularis Einsle (1996) in Oxford, a new British record

The authors report the record of Cyclops singularis collected from Peasemoor Piece, a seasonal pond on the outskirts of Oxford. This preliminary note is to alert others to the possibility that C singularis may occur in collections from seasonal ponds in the UK. The recent record of this species in Belgium (Alekseev et al. 2002) indicates that this species is not restricted to its type locality.

On the feeding of freshwater ostracods. [Translation of: Zoologicheskij zhurnal, 27(2), 1948, 125-136]

The present work appertains to a series of investigations in the field of trophodynamics of water bodies conducted by the department of hydrobiology ”Mosrybvtuza” under the leadership of Prof. Director N.S. Gaevska. Usually with quantitative collections of benthos ostracoda are hardly taken account of. But with the employment of special methods it is possible to be convinced that they are encountered in massive numbers. The role of ostracods in the nutrition of fish is recognised as important by many authors. On the question of the feeding of ostracods, in the literature there are only the fragmentary indications about the occurrence in the gut of ostracods of algae (diatoms, desmids) and detritus. The study of the feeding of ostracods was conducted both by the method of dissecting the guts of ostracods taken from natural waters, and by the method of feeding ostracods under laboratory conditions with a variety of food objects. Moreover, with a view to revision of obtained quantitative data, for determination of food requirements of ostracods the respiration method was applied.

The influence of blue-green algae on development of the zooplankton. [Translation of: Byull.mosk.Obshch.Ispyt.Prir.(Biol.) 67, 128-131, 1962]

Many have observed the reduction of the quantity of zooplankton in the presence of water blooms. It is known that in seas zooplankton as it were avoids places of accumulation of blue-green algae. By observations on one of the tributaries of the Rybinsk reservoir - the River Shumorovka - the authors tried by simultaneous collections to trace the changes in numbers, not only of zoo- and phytoplankton but also of bacteria. The plankton was collected by quantitative nets with suitable numbers of gauze and bacteria were taken account of by the method of direct calculation on membrane filters. It can be seen that the development of blue-green algae appears as an important factor, determining not only the intensity but also the direction of the process of production of zooplankton.

Eggs, Larvae and Young of The Striped Bass, Roccus saxatilis

Detailed descriptions of the early development of the striped bass, Roccus saxitilis (Walbaum), with emphasis on variation in size and morphology, sequence of fin formation, changes in body form, and attainment of the full complement of maristic numbers, are presented and illustrated for the first time. The egg is spherical, transparent, non-adhesive and relatively large. It is pelagic and buoyant, although it sinks in quiet fresh water. When unfertilized, it averages 1.3 mm, in diameter, but is 3.4 mm. when fertilized and water-hardened. The granular yolk sac, green when alive and whitish-yellow when preserved, averages 1.2 mm., and the single amber-colored oil globule is about 0.6 mm. in diameter. Newly hatched striped bass prolarvae, which range from 2.9-3.7 mm. in total length, are relatively undeveloped and nearly transparent, with no mouth opening, unpigmented eyes, and a greatly enlarged yolk sac with the large oil globule projecting beyond the head. When 5-6 mm. long the yolk sac and oil globule are assimilated and the postlarvae I show advanced development of the internal anatomy. Although the fish is still transparent, scattered melanophores are found on the head and body and chromatophores in the eyes and the ventro-posterior edge of the body. Postlarvae transform to young between 7 and 10 mm. in length when the finfolds are lost except in the dorsal, anal and caudal regions. The largest fish in this group possess a well-formed skeleton with a full complement of 25 vertebrae. Between 10 and 20 mm. in length all fish are fully transformed, muscular tissue renders most of the internal structure obscure, and the myotomes, which generally correspond in number with the vertebrae, are no longer visible. At fish lengths of 20-30 mm. scales are found on all specimens, and with the exception of the pectoral fin-rays, a full complement of meristic structures is present in all other fins. At this stage the body is pigmented uniformly with small spots. Linear regressions between several dependent variables and the , independent variable of standard length indicate that the rate of development of head, eye. and snout to anus lengths is proportional to the length of the larvae and young. Body depth and standard length are non-linear among newly-hatched larvae. Hatchery-reared striped bass demonstrated a slow rate of growth, and were regarded as "stunted," when compared to growth rates observed in another study and field collections. Observations were also made on abnormal eggs and teratological larvae and young. Blue-sac disease is tentatively identified and described for the first time in larvae and pugnosed larvae and young are also described for the first time in striped bass.