Is part of the Bibliography
"Blut ist ein ganz besonderer Saft" : zur Kultur und Biologie eines flüssigen Organs
- Mit Blut unterzeichnete Dr. Faust seinen zweifelhaften Pakt mit dem Teufel. In der Kulturgeschichte des Menschen hat Blut von jeher eine mystisch aufgeladene Rolle gehabt, die sich in religiösen Ritualen, Heilpraktiken, Liebes- und Freundschaftsbünden niederschlug. Roland Prinzinger beginnt mit einigen Schlaglichtern auf die vielfältigen Bedeutungen des Blutes, die heute noch mitschwingen, wenn wir uns dem Thema nähern. Als Biologe erklärt er dann am Beispiel der Diagnostik bei Vögeln, warum Blut auch aus naturwissenschaftlicher Sicht ein »ganz besonderer Saft« ist.
"Forschungspotenzial muss sich entfalten können" : Prof. Dr. Günther Wess im Gespräch mit Dr. Monika Mölders über Wissenschaft im internationalen Wettbewerb
- Fachliche Exzellenz und Bildungsnotstand – diese beiden Extreme beherrschen gegenwärtig die Diskussion um Schul- und Hochschulausbildung. Die Universität Frankfurt stellt sich der Elitediskussion und setzt auf Fokussierung und Schwerpunktbildung. Studiengänge werden modifiziert, die Art und Vielfalt möglicher Abschlüsse internationalen Standards angepasst. Die Universität will und wird wettbewerbsfähig sein, auch im internationalen Vergleich. Darüber sprach Dr. Monika Mölders mit Prof. Dr. Günther Wess, Honorarprofessor der Universität Frankfurt, Forschungsleiter Europa von Aventis und Mitglied der Geschäftsführung der Aventis Pharma Deutschland GmbH.
3D ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft X-ray tomography
Achilleas S. Frangakis
- The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.
40S ribosome biogenesis co-factors are essential for gametophyte and embryo development
Benjamin L. Weis
- Ribosome biogenesis is well described in Saccharomyces cerevisiae. In contrast only very little information is available on this pathway in plants. This study presents the characterization of five putative protein co-factors of ribosome biogenesis in Arabidopsis thaliana, namely Rrp5, Pwp2, Nob1, Enp1 and Noc4. The characterization of the proteins in respect to localization, enzymatic activity and association with pre-ribosomal complexes is shown. Additionally, analyses of T-DNA insertion mutants aimed to reveal an involvement of the plant co-factors in ribosome biogenesis. The investigated proteins localize mainly to the nucleolus or the nucleus, and atEnp1 and atNob1 co-migrate with 40S pre-ribosomal complexes. The analysis of T-DNA insertion lines revealed that all proteins are essential in Arabidopsis thaliana and mutant plants show alterations of rRNA intermediate abundance already in the heterozygous state. The most significant alteration was observed in the NOB1 T-DNA insertion line where the P-A3 fragment, a 23S-like rRNA precursor, accumulated. The transmission of the T-DNA through the male and female gametophyte was strongly inhibited indicating a high importance of ribosome co-factor genes in the haploid stages of plant development. Additionally impaired embryogenesis was observed in some mutant plant lines. All results support an involvement of the analyzed proteins in ribosome biogenesis but differences in rRNA processing, gametophyte and embryo development suggested an alternative regulation in plants.
A differential genome-wide transcriptome analysis: impact of cellular copper on complex biological processes like aging and development
Heinz D. Osiewacz
- The regulation of cellular copper homeostasis is crucial in biology. Impairments lead to severe dysfunctions and are known to affect aging and development. Previously, a loss-of-function mutation in the gene encoding the copper-sensing and copper-regulated transcription factor GRISEA of the filamentous fungus Podospora anserina was reported to lead to cellular copper depletion and a pleiotropic phenotype with hypopigmentation of the mycelium and the ascospores, affected fertility and increased lifespan by approximately 60% when compared to the wild type. This phenotype is linked to a switch from a copper-dependent standard to an alternative respiration leading to both a reduced generation of reactive oxygen species (ROS) and of adenosine triphosphate (ATP). We performed a genome-wide comparative transcriptome analysis of a wild-type strain and the copper-depleted grisea mutant. We unambiguously assigned 9,700 sequences of the transcriptome in both strains to the more than 10,600 predicted and annotated open reading frames of the P. anserina genome indicating 90% coverage of the transcriptome. 4,752 of the transcripts differed significantly in abundance with 1,156 transcripts differing at least 3-fold. Selected genes were investigated by qRT-PCR analyses. Apart from this general characterization we analyzed the data with special emphasis on molecular pathways related to the grisea mutation taking advantage of the available complete genomic sequence of P. anserina. This analysis verified but also corrected conclusions from earlier data obtained by single gene analysis, identified new candidates of factors as part of the cellular copper homeostasis system including target genes of transcription factor GRISEA, and provides a rich reference source of quantitative data for further in detail investigations. Overall, the present study demonstrates the importance of systems biology approaches also in cases were mutations in single genes are analyzed to explain the underlying mechanisms controlling complex biological processes like aging and development.
A fast and efficient translational control system for conditional expression of yeast genes
Julia E. Weigand
- A new artificial regulatory system for essential genes in yeast is described. It prevents translation of target mRNAs upon tetracycline (tc) binding to aptamers introduced into their 5'UTRs. Exploiting direct RNA–ligand interaction renders auxiliary protein factors unnecessary. Therefore, our approach is strain independent and not susceptible to interferences by heterologous expressed regulatory proteins. We use a simple PCR-based strategy, which allows easy tagging of any target gene and the level of gene expression can be adjusted due to various tc aptamer-regulated promoters. As proof of concept, five differently expressed genes were targeted, two of which could not be regulated previously. In all cases, adding tc completely prevented growth and, as shown for Nop14p, rapidly abolished de novo protein synthesis providing a powerful tool for conditional regulation of yeast gene expression.
A functional genomics approach to the family of heat stress transcription factors of Arabidopsis and unraveling the essential role of HsfA9 during seed development
- The experiments presented in my thesis were performed to resolve the following major questions: i. Initial experiments are based on the systematic characterization of the C-terminal domains of all 21 HSFs of Arabidopsis with respect to their transactivation potential as well as intracellular localization. This led to the identification of a signature motif for class A HSFs, that consists of an AHA motif (essential for activator potential), and a C-treminal NES (nuclear export signal). With this signature motif, we could identify homologues sequences of more than 90 HSFs in various plant species. ii. Analysis of developmental expression profiles of HSFs using AtGenExpress microarray data led to the identification of the unique expression of HsfA9 during late seed developmental stages. This was the starting point for the investigation of the regulation of HsfA9 as well as its function during seed development. iii. The seed specific transcription factor ABI3 was identified to be responsible for the regulation of HsfA9 by using knock out mutant lines and ectopically expressing transgenic lines for ABI3 gene. Furthermore, the importance of a RY/Sph motif, as binding site for ABI3 on HsfA9 promoter has been analyzed with transient GUS reporter assays. In addition, contribution of component(s) of ABA (abscisic acid) signaling cascade as a functional interacting partner of ABI3 on HsfA9 promoter has been shown and discussed. iv. The essential role of HsfA9 as master regulator for the expression of seed specific members of of HSP encoding genes and GolS1 was shown by analyzing transgenic plants ectopically expressing HsfA9 as well as, by carrying out transient GUS reporter assays. Correlating with this, transgenic plants with ectopic expression of HsfA9 showed a thermotolerent phenotype. Furthermore, a model where HsfA9 plays a key function for the regulation of seed expressed genes which might involved in providing dessication tolerance during seed maturation has been proposed.
A GPS-based system for recording the flight paths of birds
Karen von Hünerbein
- The GPS recorder consists of a GPS receiver board, a logging facility, an antenna, a power supply, a DC-DC converter and a casing. Currently, it has a weight of 33 g. The recorder works reliably with a sampling rate of 1/s and with an operation time of about 3 h, providing time-indexed data on geographic positions and ground speed. The data are downloaded when the animal is recaptured. Prototypes were tested on homing pigeons. The records of complete flight paths with surprising details illustrate the potential of this new method that can be used on a variety of medium-sized and large vertebrates.
A new method for examining hominin dietary strategy: occlusal microwear vector analysis of the Sangiran 7 Homo erectus molars
- Many hominin species are best physically represented and understood by the
sum of their dental morphologies. Generally, taxonomic affinities and evolutionary
trends in development (ontogeny) and morphology (phylogeny) can be deduced from
dental analyses. More specifically, the study of dental remains can yield a wealth of
information on many facets of hominin evolution, life history, physiology and ecological
adaptation; in short, the organisms paleobiomics. Functionally, teeth present information
about dietary preferences, that is, the dietary niche in ecological context and, in turn,
As the amount and types of information that can be gleaned from 2-dimensional
tooth measurement exhaust themselves, 3-dimensional microscopic modeling and
analysis presents a largely fertile ground for reexamination and reinterpretation of dental
characteristics (Bromage et al., 2005). As such, a novel, non-destructive approach has
been developed which combines the work of two established technologies (confocal
microscopy and 3D modeling) adapted specifically for the purpose of mineralized tissue
imaging. Through this method, 3D functional masticatory and therefore occlusal molar
microwear is able to be visualized, quantified and comparatively analyzed to assess
dietary preference in Javanese Homo erectus. This method differs from other microwear
investigative techniques (defining 'pits'- vs- 'scratches', microtexture analysis etc.) in
that it defines a molars masticatory microwear functional interactions in 3-dimensions as
its baseline dataset for further interpretations and analyses.
Due to poor specimen collection techniques employed during the first half of the
20th century, the very complex geologic nature of the Sangiran Dome and disagreements over its chronostratigraphy, only very few scientific works have
addressed the Sangiran 7 (S7) Homo erectus molar collection (n=25) (e.g. Grine and
Franzen, 1994; Kaifu, 2006). Grine and Franzen's (1994) work was a predominantly
qualitative initial assessment of the specimens and identified five specimens that might
better be ascribed to a fossil pongid rather than H. erectus. They also noted several
molars to which tooth position (M1 or M2) was unable to be ascribed (Grine and
Franzen, 1994). Kaifu (2006) comparatively examined crown sizes in several S7 molars.
The Sangiran 7 collection originates from two distinct geologic horizons: ten from
the older Sangiran Formation (S7a, ~1.7 to 1.0mya) and fifteen from the younger,
overlying Bapang Formation (S7b, ~1.0 to .7mya). During this million year period, Java
was connected to the mainland during various glacio-eustatic low-stands in sea level.
These mainland connections varied in size, extent, climatic condition and therefore in
faunal and floral composition. As the S7 sample may be representative of the earliest
Homo erectus migrants into Java and spans long durations of occupation, its
investigation yields potential to understand the various influences climatic and
ecogeographic fluctuations had on these populations. Since the sample consists only of
teeth, an ecodietary approach has been deemed the most logical and appropriate
investigative approach. Questions regarding the intra- and inter- S7 sample
relationships will also be addressed.
By comparing various aspects of the H. erectus dentition against that of hunter/
gatherer's (H/G) whose diet is known, functional dietary similarity can be directly
correlated. Thus a comparative molar sample consisting of the below historic hunter/
gather's (n=63) has been included in order to assess H. erectus's diet in ecological context: Inuit (n=9), Pacific Northwest Tribes (n=11), Fuegians (n=11), Australian
Aborigines (n=12) and Bushman (n=20).
Methodologically, this approach produces a 3D facet microwear vector (fmv)
signature for each molar which can then be compared for statistical similarity.
Microwear (and, as such, the fmv signatures) was defined by the regular, parallel
striations found on specific cusp facets known to arise from patterned, directional
masticatory movements. This differs significantly from post-mortem or taphonomic
microwear which produces striations at irregular angles on multiple, non-masticatory
surfaces (Peuch et al.1985, Teaford, 1988). A 'match value' is produced to determine
the similarity of two molars fmv's. The 'match values' are ranked (high to low) and these
rankings are used to statistically analyze and infer dietary preference: between
Sangiran 7 (as an entire sample) compared against that of the historic hunter/ gatherer
H. sapiens whose diet and ecogeography is known; within S7a and S7b and then
among the S7 sample (eg. S7a-vs-S7b); whether the purported Pongo molars actually
affiliate well with H. erectus, the hunter-gatherer's or if they demonstrate distinctly
different fmv signatures altogether; whether fmv signatures are useful in distinguishing
molars whose tooth position is in doubt (eg. M1 or M2).
When compared against individual H/G molars, the results show that Sangiran 7
H. erectus most closely correlates with Bushmen across all areas of fmv signature
analysis. However, within broader dietary categories (yearly reliant on proteinaceous
foods; seasonally reliant on proteinaceous foods; not reliant on proteinaceous foods), it
was found that H. erectus most closely allied with the two hunter/ gatherer subpopulations
associated with the 'Seasonally reliant on proteinaceous foods' (Australian Aboriginals and Pacific Northwest Tribes). There was also evidence for dietary change
or specialization over time. As the environment changed during occupation by the
earlier Sangiran to the later Bapang individuals, the dietary preference shifted from a
focus on vegetative foods to a diet much more inclusive of proteinaceous resources.
These results are considered logical within the larger ecogeographic and
chronostratigraphic context of the Sangiran Dome during the Pleistocene. However, a
larger sample would be needed to confirm this. Although general dietary preferences
can be drawn from this method, it is not possible at present to define specific foods
consumed on a daily basis (eg. tubers or tortoise meat).
Out of the five specimens possibly allied with Pongo, S7-14 matched at the 'high'
designation with a hunter/ gatherer, S7-62 matched 'moderately', S7-20 matched 'low'
while the remaining two were not able to be matched with any other teeth for various
reasons. Although designation to Pongo cannot be ruled on at this time using this
method, it does demonstrate that at least two of the teeth correlate well with various
hunter/ gatherer's who do not share dietary similarity with Pongo. This suggests their
designation as Pongo should be more closely reevaluated. As for the four specimens
whose tooth position was unsure, S7-14 matched 'highly' with 1st molars, S7-62 and S7-
78 matched 'moderately' with 2nd and 1st molars respectively while S7-20 only matched
at the 'low' designation. Although this approach is still exploratory, it adds another
analytical tool for use in defining tooth position.
In sum, this method has demonstrated its usefulness in defining and functionally
analyzing a novel 3D molar microwear dataset to interpret dietary preference. Future
work would include a pan- H. erectus molar sample in order to illuminate broader populational, taxonomic and dietary correlations within and amoung all H. erectus
specimens. A larger, more heterogenous historic H/G sample would also be included in
order to provide a wider dietary comparative population. This method can be further
extended to include and compare any and all hominins as well as any organism which
produces micro wear upon it molars. Also, the data obtained and resultant fmv signature
diagrams have the potential to be incorporated into 3D VR reconstructions of
mandibular movement thus recreating mastication in extinct organisms and leading to
more robust anatomical and physiological investigations especially when viewed in the
context of larger environmental conditions or changes.
A new type of proton coordination in an F1Fo-ATP synthase rotor ring
David B. Hicks
Terry A. Krulwich
- We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 Å, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle. Formal Correction: This article has been formally corrected to address the following errors. 1. The images for Figures S2 and S3 were incorrectly switched. The image that appears as Figure S2 should be Figure S3, and the image that appears as Figure S3 should be Figure S2. The figure legends appear in the correct order. Please view the correct... (read formal correction) 2. The images for Figures S2 and S3 were incorrectly switched. The image that appears as Figure S2 should be Figure S3, and the image that appears as Figure S3 should be Figure S2. The figure legends appear in the correct order. Please view the correct... (read formal correction)