Reproductive biology of the island grouper (Mycteroperca fusca) in the Canary Islands, northwest coast of Africa

[EN]This is the first time that the reproductive characteristics of Mycteroperca fusca have been analyzed over the whole area of its distribution, using the parameter of the histological analysis of the gonads. This species is a protogynous hermaphrodite with a marked predominance of females (1:4.9). The males and females displayed marked differences in the distribution of the sizes. The females were distributed over all the size ranges analyzed (229-725 mm total length), whereas the males were observed within the larger sizes, as of 428 mm. One transitional specimen (610 mm total length) was observed. The size at which the females first reached sexual maturity was 335 mm total length whereas the size at which 95% of females reached sexual maturity was 398 mm total length. The average size at which 50% of the females had inverted to the male condition was found to be 678 mm total length. The range of sizes at which the process of sexual inversion took place was broad, between 428 and 725 mm total length. The reproductive period was long, almost covering the annual cycle, although the maximum activity was observed between April and October, with a peak in spawning in June-July.

Contribution to the biology and fishery of the deep-water red crab, Chaceon Affinis (A. Milne-Edwards & Bouvier, 1894) (Decapoda, Brachyura, Geryonidae) in deep waters of the Canary Islands (Central-East Atlantic)

[EN] This crab was captured in the whole range of depths sampled, although its highest abundance was found between 600 and 800 m, on muddy-rocky bottoms. Moreover, significant differences were observed in the average weight and length, according to depth of capture, island of origin, and date of survey. In general, the b parameter of length-weight relationship indicates a negative allometric growth pattern, although in some cases it was not statistically different from isometry, particularly in males. Males were heavier, larger, and more abundant in catches than females.

Reproductive biology of the sea cucumber Holothuria sanctori (Echinodermata: Holothuroidea)

[EN] The reproductive biology of the sea cucumber Holothuria sanctori was studied over 24 months (February 2009 to January 2011) at Gran Canaria through the gonad index and a combination of macro- and microscopic analysis of the gonads. Holothuria sanctori showed a 1:1 sex ratio and a seasonal reproductive cycle with a summer spawning: the mean gonad index showed a maximum (3.99±0.02) in summer (June-July) and a minimum (0.05±0.04) between late autumn (November) and early spring (March). Females had significantly wider gonad tubules than males. First maturity occurred at a size of 201 to 210 mm, a gutted body weight of 101 to 110 g and a total weight of 176 to 200 g. Holothuria sanctori shows a typical temperate species reproduction pattern. These results could be useful for managing current extractions of H. sanctori in the Mediterranean and in case a specific fishery is started in the eastern Atlantic region.

Reproductive biology of Boops boops (Linnaeus, 1758) off Gran Canaria (Canary Islands): a preliminary study

[EN] Preliminary data of the length-weight relationship and reproduction of the bogue Boops boops off Gran Canaria (Canary Islands, Central-east Atlantic) are provided. Two thousand and twenty-one individuals of bogue, ranging from 4 to 34 cm TL, were obtained from purse seine commercial landing. Reproduction parameters as sex determination, duration of spawning season, size at first maturity and GSI variation along time were determinated based on macroscopic evaluation of gonads. The results obtained suggest that bogue is a total spawner, with a long spawning season extending from January to May. Size at first maturity was 16.7 and 17.9 cm TL for males and females, respectively. The length-weight relationship obtained showed a positive allometry in both sexes

CMoS lab-on-a-chip devices for individual cell biology

The development of microlectronic lab-on-a-chip devices (LOACs) can now be pursued thanks to the continous advances in silicon technology. LOACs are miniaturized devices whose aim is to perform in a more efficient way specific chemical or biological analysis protocols which are usually carried out with traditional laboratory equipment. In this application area, CMOS technology has the potential to integrate LOAC functionalities for cell biology applications in single chips, e.g. sensors, actuators, signal conditioning and processing circuits. In this work, after a review of the state of the art, the development of a CMOS prototype chip for individual cell manipulation and detection based on dielectrophoresis will be presented. Issues related to the embedded optical and capacitive detection of cells will be discussed together with the main experimental results obtained in manipulation and detection of living cells and microparticles.

From "wet biology" to statistical analysis of structural features with bioinformatics tools

Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may escape detection when wild-type cells are grown under standard conditions. Here, we have taken a complementary approach where candidate outer membrane proteins have been identified by bioinformatics prediction, cloned and overexpressed, and finally localized by cell fractionation experiments. Out of eight predicted outer membrane proteins, we have confirmed the outer membrane localization for five—YftM, YaiO, YfaZ, CsgF, and YliI—and also provide preliminary data indicating that a sixth—YfaL—may be an outer membrane autotransporter.

Reconstruction and analysis of the NF-kB pathway interactome: a systems biology approach

Background. One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as “inflammaging”, negatively correlated with longevity. A prominent mediator of inflammation is the transcription factor NF-kB, that acts as key transcriptional regulator of many genes coding for pro-inflammatory cytokines. Many different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory network characterized by high complexity. NF-kB signaling has been proposed to be responsible of inflammaging. Scope of this analysis is to provide a wider, systemic picture of such intricate signaling and interaction network: the NF-kB pathway interactome. Methods. The study has been carried out following a workflow for gathering information from literature as well as from several pathway and protein interactions databases, and for integrating and analyzing existing data and the relative reconstructed representations by using the available computational tools. Strong manual intervention has been necessarily used to integrate data from multiple sources into mathematically analyzable networks. The reconstruction of the NF-kB interactome pursued with this approach provides a starting point for a general view of the architecture and for a deeper analysis and understanding of this complex regulatory system. Results. A “core” and a “wider” NF-kB pathway interactome, consisting of 140 and 3146 proteins respectively, were reconstructed and analyzed through a mathematical, graph-theoretical approach. Among other interesting features, the topological characterization of the interactomes shows that a relevant number of interacting proteins are in turn products of genes that are controlled and regulated in their expression exactly by NF-kB transcription factors. These “feedback loops”, not always well-known, deserve deeper investigation since they may have a role in tuning the response and the output consequent to NF-kB pathway initiation, in regulating the intensity of the response, or its homeostasis and balance in order to make the functioning of such critical system more robust and reliable. This integrated view allows to shed light on the functional structure and on some of the crucial nodes of thet NF-kB transcription factors interactome. Conclusion. Framing structure and dynamics of the NF-kB interactome into a wider, systemic picture would be a significant step toward a better understanding of how NF-kB globally regulates diverse gene programs and phenotypes. This study represents a step towards a more complete and integrated view of the NF-kB signaling system.

Functional Genomics and Cell Biology of the Dolphin (Tursiops runcatus): Establishment of Novel Molecular Tools to Study Marine Mammals in Changing Environments

The dolphin (Tursiops truncatus) is a mammal that is adapted to life in a totally aquatic environment. Despite the popularity and even iconic status of the dolphin, our knowledge of its physiology, its unique adaptations and the effects on it of environmental stressors are limited. One approach to improve this limited understanding is the implementation of established cellular and molecular methods to provide sensitive and insightful information for dolphin biology. We initiated our studies with the analysis of wild dolphin peripheral blood leukocytes, which have the potential to be informative of the animal’s global immune status. Transcriptomic profiles from almost 200 individual samples were analyzed using a newly developed species-specific microarray to assess its value as a prognostic and diagnostic tool. Functional genomics analyses were informative of stress-induced gene expression profiles and also of geographical location specific transcriptomic signatures, determined by the interaction of genetic, disease and environmental factors. We have developed quantitative metrics to unambiguously characterize the phenotypic properties of dolphin cells in culture. These quantitative metrics can provide identifiable characteristics and baseline data which will enable identification of changes in the cells due to time in culture. We have also developed a novel protocol to isolate primary cultures from cryopreserved tissue of stranded marine mammals, establishing a tissue (and cell) biorepository, a new approach that can provide a solution to the limited availability of samples. The work presented represents the development and application of tools for the study of the biology, health and physiology of the dolphin, and establishes their relevance for future studies of the impact on the dolphin of environmental infection and stress.

Influence of pollination and seed dispersal on the genetic population structure of two Commiphora species in Madagascar and South Africa

Pollination and seed dispersal are important ecological processes for the regeneration of plant populations and both vectors for gene exchange between plant populations. For my thesis, I studied the pollination ecology of the South African tree Commiphora harveyi (Burseraceae) and compared it with C. guillauminii from Madagascar. Both species have low visitation rates and a low number of pollinating insect species, resulting in a low fruit set. While their pollination ecology is very similar, they differ in their seed dispersal with a low seed dispersal rate in the Malagasy and a high seed dispersal rate in the South African species. This should be reflected in a stronger genetic differentiation among populations in the Malagasy than in the South African species. My results, based on AFLP markers, contradict these expectations, the overall differentiation was lower in the Malagasy (FST = 0.05) than in the South African species (FST = 0.16). However, at a smaller spatial scale (below 3 km), the Malagasy species was genetically more strongly differentiated than the South African species, which was reflected by the high inter-population variance within the sample site (C. guillauminii: 72.2 - 85.5 %; C. harveyi: 8.4 - 14.5 %). This strong differentiation could arise from limited gene flow, which was confirmed by spatial autocorrelation analyses. The shape of the autocorrelogram suggested that gene exchange between individuals occurred only up to 3 km in the Malagasy species, whereas up to 30 km in the South African species. These results on the genetic structure correspond to the expectations based on seed dispersal data. Thus, seed dispersal seems to be a key factor for the genetic structure in plant populations on a local scale.

Ornithophily in the genus Salvia L. (Lamiaceae)

This dissertation presents for the first time a survey of bird pollinated (ornithophilous) Salvia species. Within the approximately 1000 species of the worldwide distributed genus roughly 20% (186 spp.) are bird pollinated. Excepting four species in the Old World (South Africa and Madagascar), ornithophilous species are restricted to the New World where they represent about one third of the species. They occur mainly in higher altitudes (1500-3000m) and usually grow as shrubs or perennial herbs (97%). The bilabiate to tubular flowers are often red (at least 49%), averaging 35mm (7-130mm) in length and produce a large to medium volume of nectar with rather low sugar concentration. Pollination by sunbirds and white-eyes is documented in a South African species, and that by hummingbirds in 16 species of the New World (USA, Mexico, Guatemala and Bolivia). Beside pollinator observations, the functionality of the staminal levers, the process of pollen transfer and the fitting between flowers and birds are tested by inserting museum skins and metal rods into fresh flowers. The most surprising result is the finding of two different main pollen transfer mechanisms. In at least 54% of the species an active staminal lever mechanism enables pollen deposition on the birds body. This is illustrated in detail in the South African S. lanceolata at which birds were observed to release the lever mechanism and became dusted with pollen. In contrast, the lever mechanism in about 35% of the New World species is reduced in different ways. Pollen transfer by inactive ‘levers’ is demonstrated in detail in S. haenkei in Bolivia, at which four pollinating hummingbird species could be observed. The tubular corolla forced the birds in a specific position, thereby causing pollen transfer from the exserted pollen-sacs to the birds body. With respect to the floral diversity and systematic affiliation of the species, parallel evolution of ornithophily and lever reduction is likely. Considering that bird pollinated species might have derived from bee pollinated species and that the staminal levers have become secondarily inactive, it is concluded that the shift in pollinators induced phenotypic changes even disabling such a sophisticated structure as the staminal lever mechanism.

Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Evolutionary tendencies in African Marantaceae

Die Marantaceae (550 Arten) sind eine weltweit verbreitete Familie von Stauden und Lianen aus dem Unterwuchs tropischer Tieflandregenwälder. Der morphologisch-ökologische Vergleich des basal abzweigenden Sarcophrynium-Astes mit dem in abgeleiteter Position stehenden Marantochloa-Ast, soll beispielhaft evolutionäre Muster in der Familie beleuchten. So wird in der Doktorarbeit zum ersten Mal ein Überblick über die Blütenbiologie und Phylogenie von rund 30 der 40 afrikanischen Marantaceae Arten präsentiert. Die Analysen basieren auf Daten von drei mehrmonatigen Feldaufenthalten in Gabun jeweils zwischen September und Januar. Vier Blütentypen werden beschrieben, die jeweils mit einer spezifischen Bestäubergilde verbunden sind (kleine, mittlere, große Bienen bzw. Vögel). Bestäubungsexperimente belegen, dass 18 Arten selbstkompatibel, aber nur zwei Arten autogam sind, also keine Bestäubungsvermittler benötigen. Der Fruchtansatz ist generell gering (10 -30 %). Die komplexe Synorganisation der Blüte ermöglicht in den Marantaceae einen explosiven Bestäubungsmechanismus. Um dessen ökologische Funktionalität zu verstehen, werden die Blüten von 66 Arten, alle wichtigen Äste der Marantaceae abdeckend, unter einem morphologisch-funktionalen Gesichtspunkt untersucht. Es gibt große Übereinstimmungen zwischen allen untersuchten Arten im Zusammenspiel (Synorganisation) der wichtigsten Bauelemente (Griffel, Kapuzenblatt, Schwielenblatt), die eine präzise Pollenübertragung ermöglichen. Basierend auf Daten von nrDNA (ITS, 5S) und cpDNA (trnL-F) wird für ein nahezu komplettes Artenspektrum die Phylogenie der zwei afrikanischen Äste erstellt. Hierauf werden morphologische und ökologische Merkmale sowie geographischer Verbreitungsmuster nach dem Parsimonieprinzip rekonstruiert, um so deren evolutionäre Bedeutung für die Marantaceae abschätzen zu können. Die Ergebnisse weisen auf die Beteiligung einer Vielzahl verschiedener Artbildungsfaktoren hin.

"Making Sense of Figures": Statistics, Computing and Information Technologies in Agriculture and Biology in Britain, 1920s-1960s

Throughout the twentieth century statistical methods have increasingly become part of experimental research. In particular, statistics has made quantification processes meaningful in the soft sciences, which had traditionally relied on activities such as collecting and describing diversity rather than timing variation. The thesis explores this change in relation to agriculture and biology, focusing on analysis of variance and experimental design, the statistical methods developed by the mathematician and geneticist Ronald Aylmer Fisher during the 1920s. The role that Fisher’s methods acquired as tools of scientific research, side by side with the laboratory equipment and the field practices adopted by research workers, is here investigated bottom-up, beginning with the computing instruments and the information technologies that were the tools of the trade for statisticians. Four case studies show under several perspectives the interaction of statistics, computing and information technologies, giving on the one hand an overview of the main tools – mechanical calculators, statistical tables, punched and index cards, standardised forms, digital computers – adopted in the period, and on the other pointing out how these tools complemented each other and were instrumental for the development and dissemination of analysis of variance and experimental design. The period considered is the half-century from the early 1920s to the late 1960s, the institutions investigated are Rothamsted Experimental Station and the Galton Laboratory, and the statisticians examined are Ronald Fisher and Frank Yates.