Alexander von Humboldt and the hand-beast: A contribution to palaeontology from the last universal scholar

Despite a certain interest in the discipline, Alexander von Humboldt did not personally contribute much to the progress of palaeozoology. His most remarkable input derived from a communication about hand-like archosaur footprints from the Buntsandstein at the very acme of the important controversy that the discovery of these fossils generated (1835). Humboldt thought that the tracks were probably from a possum-like marsupial, but he did not discount that they could be from a primate. This study is characterized by its superficiality: both the anatomical comparisons and the considerations of the functional morphology of locomotion are very poor. Its effect on the scientific community proved about nil, in both the short and the long run, and Humboldt may himself have doubted his initial conclusions in later years. Nevertheless, in contrast with some contemporaneous renowned geognosts, he had no hesitation from the beginning that the footprints were genuine. He also did not hesitate to weaken the belief of the time on the timing of the succession of organised beings in geological ages, naturally without lapsing into “antiprogressionism”.     

The contribution of chicken embryology to the understanding of vertebrate limb development

The chicken is an excellent model organism for studying vertebrate limb development, mainly because of the ease of manipulating the developing limb in vivo. Classical chicken embryology has provided fate maps and elucidated the cell-cell interactions that specify limb pattern. The first defined chemical that can mimic one of these interactions was discovered by experiments on developing chick limbs and, over the last 15 years or so, the role of an increasing number of developmentally important genes has been uncovered. The principles that underlie limb development in chickens are applicable to other vertebrates and there are growing links with clinical genetics. The sequence of the chicken genome, together with other recently assembled chicken genomic resources, will present new opportunities for exploiting the ease of manipulating the limb.     

The prolonged depolarizing afterpotential and its contribution to the understanding of photoreceptor function

Comparison of flies bred on vitamine A-poor and vitamine A-rich diets show the latter to exhibit, after blue illumination, 1) slight deviation from the linear relationship between stimulus intensity and receptor sensitivity and, 2) after intense blue illumination the phenomenon of the PDA. Both these effects could result from reduced pigment distances in such membranes. Maximum PDA was produced after about 20 s of illumination with blue light, and following this the resistance of the membrane was seen to stay low, returning to the resting value at the same rate as the PDA decline. The response to test flashes, repressed during illumination, gradually returned during the decline of the PDA, similar to the way the photoreceptor would respond to the sum of two stimuli: the test flash and a decreasing background illumination. Red light immediately following blue abolished the PDA and white light produced a small PDA. All these experiments corroborate a new model (without resorting to the concept of inhibitors) which links the photopigments with receptor excitation, the assumptions for which are the following: 1) PDA is produced after abnormally high primary quantum absorption by rhodopsin molecules, 2) PDA is a retarded membrane excitation by a substance in stored form, 3) the store is built up when production of this substance is larger than its consumption, and 4) time and energy are necessary for the regeneration of excitatory rhodopsin molecules.This work was supported by the DFG (Ha 258/10) and by the SFB 114Presented at the EMBO-Workshop on Transduction Mechanism of Photoreceptors, Jülich, Germany, October 4–8, 1976     

The tumor microenvironment and its contribution to tumor evolution toward metastasis

Cancer cells acquire cell-autonomous capacities to undergo limitless proliferation and survival through the activation of oncogenes and inactivation of tumor suppressor genes. Nevertheless, the formation of a clinically relevant tumor requires support from the surrounding normal stroma, also referred to as the tumor microenvironment. Carcinoma-associated fibroblasts, leukocytes, bone marrow-derived cells, blood and lymphatic vascular endothelial cells present within the tumor microenvironment contribute to tumor progression. Recent evidence indicates that the microenvironment provides essential cues to the maintenance of cancer stem cells/cancer initiating cells and to promote the seeding of cancer cells at metastatic sites. Furthermore, inflammatory cells and immunomodulatory mediators present in the tumor microenvironment polarize host immune response toward specific phenotypes impacting tumor progression. A growing number of studies demonstrate a positive correlation between angiogenesis, carcinoma-associated fibroblasts, and inflammatory infiltrating cells and poor outcome, thereby emphasizing the clinical relevance of the tumor microenvironment to aggressive tumor progression. Thus, the dynamic and reciprocal interactions between tumor cells and cells of the tumor microenvironment orchestrate events critical to tumor evolution toward metastasis, and many cellular and molecular elements of the microenvironment are emerging as attractive targets for therapeutic strategies.     

The fish community of Loch Lomond,Scotland: its history and rapidly changing status

The fish community of Loch Lomond is of national importance. Its diversity of species and rare populations of powan (Coregonus lavaretus) and freshwater feeding river lampreys (Lampetra fluviatilis) warrant high conservation status. It is also of value for its sport fisheries for sea-trout (Salmo trutta), salmon (Salmo salar) and pike (Esox lucius). Historical records demonstrate that the species composition of the fish community has remained stable over a very long period until recently when a series of introductions of fish species new to the catchment has resulted in successful colonisation by a number of species. These have resulted in fundamental changes in the ecosystem. Here using historical records the long-term stability of the fish community is examined, recent rapid changes in the fish community are documented and some of the resultant effects of changes in the fish community are demonstrated.     

Fox-hunting in England and Wales: its contribution to the management of woodland and other habitats

Hunting foxes with hounds has been a countryside pursuit in Britain since the 17th Century, but its effect nationally on habitat management is little understood by the general public. A survey questionnaire was distributed to 163 mounted fox hunts of England and Wales to quantify their management practices in woodland and other habitat. Ninety-two hunts (56%), covering 75,514 km², returned details on woodland management motivated by the improvement of their sport. The management details were verified via on-site visits for a sample of 200 woodlands. Following verification, the area of woodlands containing the management was conservatively estimated at 24,053 (±2241) ha, comprising 5.9% of woodland area within the whole of the area hunted by the 92 hunts. Management techniques included: tree planting, coppicing, felling, ride and perimeter management. A case study in five hunt countries in southern England examined, through the use of botanical survey and butterfly counts, the consequences of the hunt management on woodland ground flora and butterflies. Managed areas had, within the last 5 years, been coppiced and rides had been cleared. Vegetation cover in managed and unmanaged sites averaged 86% and 64%, respectively, and managed areas held on average 4 more plant species and a higher plant diversity than unmanaged areas (Shannon index of diversity: 2.25 vs. 1.95). Both the average number of butterfly species (2.2 vs. 0.3) and individuals counted (4.6 vs. 0.3) were higher in the managed than unmanaged sites.     

The optical activity of D-erythro-sphingomyelin and its contribution to the circular dichroism of sphingomyelin-containing systems.

Circular dichroism studies on bovine brain sphingomyelin show the presence of a strong negative cotton effect below 200 nm, the position and magnitude of which depend on the physical state of the lipid. This cotton effect is thought to arise from the pi-pi transition of the amide group in the sphingomyelin backbone. The sphingomyelin contribution to the observed ellipticity of membranes and lipoprotein complexes depends on the mol fraction of amide groups present as sphingomyelin: this contribution is calculated to be less than 2% in the case of serum high density lipoprotein and the order of 20% below 200 nm in the case of the erythrocyte ghost membrane. Due to the similarity of the CD spectrum of sphingomyelin to that of a random coil polypeptide, use of uncorrected ellipticity data is expected to lead to an overestimate of the random coil content of proteins in systems containing a high sphingomyelin content.     

Styles of Reasoning in Early to mid-Victorian Life Research: Analysis:Synthesis and Palaetiology

To better understand the work of pre-Darwinian British life researchers in their own right, this paper discusses two different styles of reasoning. On the one hand there was analysis:synthesis, where an organism was disintegrated into its constituent parts and then reintegrated into a whole; on the other hand there was palaetiology, the historicist depiction of the progressive specialization of an organism. This paper shows how each style allowed for development, but showed it as moving in opposite directions. In analysis:synthesis, development proceeded centripetally, through the fusion of parts. Meanwhile in palaetiology, development moved centrifugally, through the ramifying specialization of an initially simple substance. I first examine a community of analytically oriented British life researchers, exemplified by Richard Owen, and certain technical questions they considered important. These involved the neurosciences, embryology, and reproduction and regeneration. The paper then looks at a new generation of British palaetiologists, exemplified by W.B. Carpenter and T.H. Huxley, who succeeded at portraying analysts’ questions as irrelevant. The link between styles of reasoning and physical sites is also explored. Analysts favored museums, which facilitated the examination and display of unchanging marine organisms while providing a power base for analysts. I suggest that palaetiologists were helped by vivaria, which included marine aquaria and Wardian cases. As they became popular in the early 1850s, vivaria provided palaetiologists with a different kind of living and changing evidence. Forms of evidence, how they were preserved and examined, and career options all reinforced each other: social and epistemic factors thus merged.     

DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies

Single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variations in numerous organisms, have emerged as important tools for the study of complex genetic traits and deciphering of genome evolution. High-throughput genome sequencing projects worldwide provide an unprecedented opportunity for whole-genome SNP analysis in a variety of species. To facilitate SNP discovery in vertebrates, we have developed a web-based, user-friendly, and fully automated application, DigiPINS, for genome-wide identification of exonic SNPs from EST data. Currently, the database can be used to the mining of exonic SNPs in six complete genomes (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus and Danio rerio). In addition to providing information on sequence conservation, DigiPINS allows compilation of comprehensive sets of polymorphisms within cancer candidate genes or identification of novel cancer markers, making it potentially useful for cancer association studies. The DigiPINS server is available via the internet at http://pbil.univ-lyon1.fr/gem/DigiPINS/query_DigiPINS.php.     

The fish community of a high mountain stream in Taiwan and its relation to dam design

Synopsis The fish community of a high mountain stream in Taiwan was studied from 1988 to 1990 in a 16 km section of Ta-chia river where a new dam is planned for construction. There were 16 species of fish belonging to 7 families; 15 genera were recorded. Six species are endemic to Taiwan. The dominant species wereZacco pachycephalus, Acrosscheileus paradoxus andRhinogobius brunneus. The composition of fish fauna was different between the eight study sites. Adjacent sites did not show a higher similarity than remote ones. AdultZ. pachycephalus andA. paradoxus showed seasonal aggregation behavior in the stream. At two distinct sites, Kukan and Tungmau, these two species had similar breeding and stock composition patterns with an intensified production period of juveniles from late autumn to early winter and a low, but continuous production period of juveniles in summer months. This information suggest that fishes in the river have special adaptations to the typhoon season in summer and benthic algal blooming in winter. The similarity of fish community and the independent breeding sites of endemic fishes in Kukan and Tungmau also suggest that these are important factors to consider for conservation when the flooding area of a high mountain dam is designed.     

Comparative genomics of Thermus thermophilus: Plasticity of the megaplasmid and its contribution to a thermophilic lifestyle

The bacterium Thermus thermophilus grows at temperatures up to 85 degrees C and is equipped with thermostable enzymes of biotechnological interest. The recently decoded genomes of two strains of T. thermophilus, HB27 and HB8, each composed of a chromosome and a megaplasmid, must certainly encode specific strategies to encounter the thermophile challenge. Here, a genome comparison was undertaken to distinguish common functions from the flexible gene pool, which gave some clues about the biological traits involved in a thermophile lifestyle. The chromosomes were highly conserved, with about 100 strain-specific genes probably reflecting adaptations to the corresponding biological niche, such as metabolic specialities and distinct cell surface determinates including type IV pili. The two megaplasmids showed an elevated plasticity. Upon comparison and re-examination of their gene content, both megaplasmids seem to be implicated in assisting thermophilic growth: a large portion of their genes are apparently involved in DNA repair functions. About 30 plasmid-encoded genes exhibit sequence and domain composition similarity to a predicted DNA repair system specific for thermophilic Archaea and bacteria. Moreover, the plasmid-encoded carotenoid biosynthesis gene cluster is interlocked with genes involved in UV-induced DNA damage repair. This illustrates the importance of DNA protection and repair at elevated growth temperatures.     

The application of gene transfer techniques to marine resource management: recent advances, problems and future directions

Recent advantages in transgenic fish research are reviewed, with special reference to the methods for gene transfer. These include microinjection, electroporation, particle bombardment, and lipofection. The success and problems associated with each of these methods, and the possible applications of transgenic fish research to aquaculture are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas

Background

Molecular phylogenetic analyses have identified Trimeniaceae, a monotypic family distributed only in Oceania, as among the earliest diverging families of extant angiosperms. Therefore, the fossils of this family are helpful to understand the earliest flowering plants. Paleobotanical information is also important to track the historical and geographical pathways to endemism of the Trimeniaceae. However, fossils of the family were previously unknown from the Early Cretaceous, the time when the angiosperm radiated. In this study, we report a seed from the late Albian (ca. 100 million years ago) of Japan representing the oldest known occurrence of Trimeniaceae and discuss the character evolution and biogeography of this family.

Results

A structurally preserved seed was collected from the early Late Albian Hikagenosawa Formation of the Yezo Group, which was deposited in palaeolatitudes of 35 to 40°N. The seed has a multilayered stony exotesta with alveolate surface, parenchymatous mesotesta, and operculate inner integument, which are characteristic to extant trimeniaceous seeds. However, the seed differs from extant seeds, i.e., in its well-developed endosperm and absence of antiraphal vascular bundle. Thus, the seed would be a new genus and species of Trimeniaceae.

Conclusion

The fossil seed indicates that seed coat characters were conserved for 100 million years or more in Trimeniaceae. It also suggests that the antiraphal vascular bundle and perispermy originated secondarily in Trimeniaceae as previously inferred from the phylogeny and character distribution in the extant basalmost angiosperms. The fossil seed provides the first evidence that Trimeniaceae was distributed in a midlatitude location of the Northern Hemisphere during the Early Cretaceous, when angiosperms radiated extensively, supporting a hypothesis that the extant austral distribution is relict.     

The synthetic theory of evolution: general problems and the German contribution to the synthesis

Summary A metatheoretical and historiographical re-analysis of the Evolutionary Synthesis (the process) and the Synthetic Theory (the result) leads to the following conclusion: The Synthetic Theory is not a reductionistic, but rather a structuralistic theory with a limited range of relevant hierarchical levels. Historically the Synthesis was not a sudden event but a rational long-term project carried out between 1930 and 1950 by a large number of biologists in several countries. In the second part of our paper the contributions of several German biologists to the Synthesis are analyzed.