Paleodemography: “Not quite dead”

As Kim Hill¹ recently noted in Evolutionary Anthropology, humans are unique among the hominoids with regard to the length of their lives, as well as other elements in the individual life histories. The evolutionary details that modified a basic pongid life history into a hominid one remain obscure, but aspects of recent human demographic history are assailable. Study of the last 10,000 years or so is an important part of ongoing anthropological discourse, for demographic changes may be intimately linked to such major developments as agriculture and urbanization.^2-8 Whether demographic changes are antecedents for or consequences of these major developments is a matter of great contention, but at the least we should attempt to document the nature of human demographic changes in the recent past. Although this documentation can take different forms, the principal sources are archeological information on past settlement patterns and analyses of prehistoric human skeletal material.     

Various strategies for obtaining artificial hemoproteins: From “hemoabzymes” to “hemozymes”

The design of artificial hemoproteins that could lead to new biocatalysts for selective oxidation reactions of organic compounds presents a huge interest especially in pharmacology, both for a better understanding of the metabolic profile of drugs and for the synthesis of enantiomerically pure molecules that could be involved in the design of drugs.The present results show that the so-called “host-guest strategy” that involves the non-covalent incorporation of anionic water-soluble iron-porphyrins into xylanase A from Streptomyces lividans, a low cost protein, leads to such an artificial hemoprotein that is able to perform the stereoselective oxidation of sulfides.     

Evolution of Protein Targeting into “Complex” Plastids: The “Secretory Transport Hypothesis”

Abstract: In algae different types of plastids are known, which vary in pigment content and ultrastructure, providing an opportunity to study their evolutionary origin. One interesting feature is the number of envelope membranes surrounding the plastids. Red algae, green algae and glaucophytes have plastids with two membranes. They are thought to originate from a primary endocytobiosis event, a process in which a prokaryotic cyanobacterium was engulfed by a eukaryotic host cell and transformed into a plastid. Several other algal groups, like euglenophytes and heterokont algae (diatoms, brown algae, etc.), have plastids with three or four surrounding membranes, respectively, probably reflecting the evolution of these organisms by so‐called secondary endocytobiosis, which is the uptake of a eukaryotic alga by a eukaryotic host cell. A prerequisite for the successful establishment of primary or secondary endocytobiosis must be the development of suitable protein targeting machineries to allow the transport of nucleus‐encoded plastid proteins across the various plastid envelope membranes. Here, we discuss the possible evolution of such protein transport systems. We propose that the secretory system of the respective host cell might have been the essential tool to establish protein transport into primary as well as into secondary plastids.     

Gentechnik unmittelbar erleben: „BioTech mobil”︁ und „Science live”︁

The projects „BioTech mobil”︁ and „Science live”︁, initiated by the Bavarian State Government and by the German Ministry for Education and Research, espectively, inform the public about the basis, methods and applications of modern biotechnology and genetics in medicine, agriculture, food production and environmental protection. The central element of each project is a Roadshow Truck, fully equipped as modern genetic laboratory. Each truck is accompanied by three biologists with a doctor's degree. One focus group of the projects are highschool students, who have the opportunity to achieve practical skills in molecular genetics. Isolation of genomic DNA and plasmids, amplification of DNA‐stretches via polymerase chain reaction (PCR) and gel electrophoresis are taught. For most schools, the trucks offer a peculiar chance to implement practical learning possibilities for the students.     

Phylum Tardigrada: an “individual” approach

Phylum Tardigrada consists of ～1000 tiny, hardy metazoan species distributed throughout terrestrial, limno‐terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super‐families and further evidence that indicates the traditional taxonomic perspective of families in the class Eutardigrada are nonmonophyletic and require re‐working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa—specifically representatives of the nine families yet to be sampled. © The Willi Hennig Society 2008.     

“How” and “what” matters: Sampling method affects biodiversity estimates of reef fishes

Understanding changes in biodiversity requires the implementation of monitoring programs encompassing different dimensions of biodiversity through varying sampling techniques. In this work, fish assemblages associated with the “outer” and “inner” sides of four marinas, two at the Canary Islands and two at southern Portugal, were investigated using three complementary sampling techniques: underwater visual censuses (UVCs), baited cameras (BCs), and fish traps (FTs). We firstly investigated the complementarity of these sampling methods to describe species composition. Then, we investigated differences in taxonomic (TD), phylogenetic (PD) and functional diversity (FD) between sides of the marinas according to each sampling method. Finally, we explored the applicability/reproducibility of each sampling technique to characterize fish assemblages according to these metrics of diversity. UVCs and BCs provided complementary information, in terms of the number and abundances of species, while FTs sampled a particular assemblage. Patterns of TD, PD, and FD between sides of the marinas varied depending on the sampling method. UVC was the most cost‐efficient technique, in terms of personnel hours, and it is recommended for local studies. However, for large‐scale studies, BCs are recommended, as it covers greater spatio‐temporal scales by a lower cost. Our study highlights the need to implement complementary sampling techniques to monitor ecological change, at various dimensions of biodiversity. The results presented here will be useful for optimizing future monitoring programs.     

Biosynthesis “debugged”: Novel bioproduction strategies

The production of chemicals from biogenic resources is widely performed using microorganisms. These often do not meet the requirements of technical processes due to the narrow limits of microbial physiology. As a consequence, alternatives are sought. Cell‐free enzymatic reaction cascades were recently proposed as next‐generation bioproduction systems. Here, we address problems of microbial systems, show potential advantages of cell‐free concepts and give an overview over the state of the technology. Furthermore, we address current challenges of the cell‐free strategy and give an outlook on future developments.     

MorphoBank: phylophenomics in the “cloud”

A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.     

PAIRED PREFERENCE “PLACEBO” TESTS WITH “IDENTICAL” STIMULI: DOES INTRODUCING GRADED PREFERENCE RESPONSES AFFECT THE FREQUENCY OF “NO PREFERENCE” RESPONSES?

In the "placebo" control condition for paired preference testing, "identical" stimuli are presented to consumers to determine the frequency of preference and "no preference" responses induced by the hidden demand characteristics of the testing condition. As a control for bias, induced by such hidden demand characteristics, these frequencies can be compared with the actual preference frequencies of the nonidentical test stimuli to be assessed for preference. It was hypothesized that the introduction of graded preference response options might reduce the frequency of "no preference" responses in the placebo condition. Using identical yogurt stimuli with related-sample (single-group) and independent-sample (multigroup) designs, this hypothesis was not confirmed.

PRACTICAL APPLICATIONS

The "placebo" condition in paired preference testing provides a way to control the tendency of consumers to give false preference. The statistical analysis can be improved by finding a protocol that maximizes the proportion of "no preference" responses in the placebo condition. This can be done by increasing the number of response options that imply no preference. Yet, there is sometimes a desire to increase the number of preference options by using graded responses for preference strength. Does this alter the dynamics of the ever-important placebo condition by reducing the number of "no preference" responses? This project found that any effect was minimal.