The evolution of molecular biology into systems biology

Systems analysis has historically been performed in many areas of biology, including ecology, developmental biology and immunology. More recently, the genomics revolution has catapulted molecular biology into the realm of systems biology. In unicellular organisms and well-defined cell lines of higher organisms, systems approaches are making definitive strides toward scientific understanding and biotechnological applications. We argue here that two distinct lines of inquiry in molecular biology have converged to form contemporary systems biology.     

Chlorophyll breakdown in tobacco: on the structure of two nonfluorescent chlorophyll catabolites

In extracts of senescent leaves of the tobacco plant Nicotiana rustica, two colorless compounds with UV/VIS characteristics of nonfluorescent chlorophyll catabolites (NCCs) were detected and tentatively identified as Nr-NCCs. These two polar NCCs were found in similar amounts in the fresh extracts, and their constitutions could be determined by spectroscopic analysis. The data showed both of the two Nr-NCCs to have the same tetrapyrrolic core structure, as reported previously for all other NCCs from senescent higher plants. In the less polar catabolite, named Nr-NCC-2, this core structure was conjugated with a glucopyranose unit, as similarly discovered earlier in Bn-NCC-2, an NCC from oilseed rape (Brassica napus). The more polar NCC from tobacco leaves, Nr-NCC-1, carried an additional malonyl substituent at the 6'-OH group of the glucopyranosyl moiety. Partial (enzyme-catalyzed) hydrolysis of Nr-NCC-1 gave Nr-NCC-2, while enzyme-catalyzed malonylation of Nr-NCC-2 gave Nr-NCC-1, establishing the identity of their basic tetrapyrrole structure. In earlier work (on the polar NCCs from oilseed rape), only separate glucopyranosyl and malonyl functionalities were detected. Nr-NCC-1, thus, represents a further variant of the structures of NCCs from senescent higher plants and exhibits an unprecedented peripheral refunctionalization in chlorophyll catabolites.     

The value of biodiversity experiments

Recent biodiversity experiments have investigated the relationship between diversity and ecosystem functioning by synthesizing plant communities from pools of species that have been experimentally manipulated to vary numbers and types of species present while holding abiotic factors constant. Biodiversity experiments therefore focus on a previously under-explored aspect of global change: the feedback from diversity to environment. Consequences of random manipulation of species communities may not correspond well to those of specific extinction sequences observed in the past in response to extinction drivers that cause highly non-random loss. However, random manipulation provides a good starting point given that existing communities could undergo many alternative orders of species loss in the future in response to a variety of different potential extinction drivers. Further, the effects of some extinction drivers are currently poorly understood and therefore difficult to predict (e.g. climate change) and it may be premature to dismiss the predictions of random scenarios as irrelevant to all real examples of species loss. The first generations of biodiversity experiments have provided valuable, and sometimes unexpected, discoveries about the general nature of the relationship between diversity and ecosystem functioning. These discoveries could not have been made using observational studies. We propose that different examples of extinction loss in the real or a potential future world form a continuum from situations where the results of the first-generation biodiversity experiments will be highly relevant to less relevant. At the one extreme are examples where the effects of biodiversity on ecosystem functioning will be overwhelmed by direct effects of the extinction driver on processes (e.g. chronic eutrophication). At the other extreme are situations where ecosystem processes are not strongly affected by direct effects of the extinction driver and where the effects of species loss on functioning may be more important (e.g. habitat fragmentation). Given the unprecedented uncertainty about the future of biodiversity and the functioning of ecosystems, a general approach with randomly varying species pools was the right place to start in order to provide a general foundation. The new challenge is to test for effects of biodiversity on functioning in real-world examples of species loss.

Zusammenfassung

Biodiversitätsversuche zeichnen sich dadurch aus, dass natürliche Artenpools experimentell reduziert werden und anschließend der Zusammenhang zwischen der Artenzahl und Ökosystemfunktionen unter konstanten abiotischen Umweltbedingungen untersucht wird. Dadurch unterscheiden sich Biodiversitätsexperimente grundsätzlich von anderen Versuchen, die die Biodiversität als Zielvariable behandeln und stattdessen die abiotische Umwelt manipulieren. Die Auswahl der Arten für die reduzierten Artenpools in Biodiversitätsexperimenten erfolgte bisher meist zufällig, während natürliche Aussterbefaktoren wie Eutrophierung nicht alle Arten gleichermassen gefährden. Für verschiedene Aussterbefaktoren ist aber so wenig bekannt, dass ein zufälliges Aussterbeszenario die beste gegenwärtig verfügbare Option ist. Dies trifft insbesondere für mögliche zukünftige Aussterbeprozesse zu, die durch globale Umweltveränderungen (Klima, biologische Invasionen) oder Habitatsfragmentierung ausgelöst werden könnten. Die erste Generation von Biodiversitätsexperimenten mit zufälligen Aussterbeszenarien hat wertvolle, teilweise unerwartete, generelle Zusammenhänge zwischen Artenzahl und Ökosystemfunktionen aufgedeckt. Diese Zusammenhänge ließen sich durch vergleichende Studien nicht erkennen. In Zukunft sollten Biodiversitätsexperimente dennoch vermehrt Aussterbeszenarien simulieren, die in der realen Umwelt mit größter Wahrscheinlichkeit auftreten.     

Neogenin mediates the action of repulsive guidance molecule

Repulsive guidance molecule (RGM) is a recently identified protein implicated in both axonal guidance and neural tube closure. The avoidance of chick RGM in the posterior optic tectum by growing temporal, but not nasal, retinal ganglion cell axons is thought to contribute to visual map formation. In contrast to ephrins, semaphorins, netrins and slits, no receptor mechanism for RGM action has been defined. Here, an expression cloning strategy identified neogenin as a binding site for RGM, with a sub-nanomolar affinity. Consistent with selective axonal responsiveness to RGM, neogenin is expressed in a gradient across the chick retina. Neogenin is known to be one of several netrin-binding proteins but only neogenin interacts with RGM. The avoidance of RGM by temporal retinal axons is blocked by the anti-neogenin antibody and the soluble neogenin ectodomain. Dorsal root ganglion axons are unresponsive to RGM but are converted to a responsive state by neogenin expression. Thus, neogenin functions as an RGM receptor.     

Floxed allele for conditional inactivation of the GABAB(1) gene

GABA(B) receptors are the G-protein-coupled receptors for the neurotransmitter GABA. GABA(B) receptors are broadly expressed in the nervous system. Their complete absence in mice causes premature lethality or--when mice are viable--epilepsy, impaired memory, hyperalgesia, hypothermia, and hyperactivity. A spatially and temporally restricted loss of GABA(B) function would allow addressing how the absence of GABA(B) receptors leads to these diverse phenotypes. To permit a conditional gene inactivation, we flanked critical exons of the GABA(B(1)) gene with lox511 sites. GABA(B(1)) (lox511/lox511) mice exhibit normal levels of GABA(B(1)) protein, are fertile, and do not display any behavioral phenotype. We crossed GABA(B(1)) (lox511/lox511) with Cre-deleter mice to produce mice with an unrestricted GABA(B) receptor elimination. These GABA(B(1)) (-/-) mice no longer synthesize GABA(B(1)) protein and exhibit the expected behavioral abnormalities. The conditional GABA(B(1)) allele described here is therefore suitable for generating mice with a site- and time-specific loss of GABA(B) function.     

Glucuronidation of the green tea catechins, (-)-epigallocatechin-3-gallate and (-)-epicatechin-3-gallate, by rat hepatic and intestinal microsomes

The flavonoids (-)-epigallocatechin-3-gallate (EGCg) and (-)-epicatechin-3-gallate (ECg) are major components of green tea and show numerous biological effects. We investigated the glucuronidation of these compounds and of quercetin by microsomes. Quercetin was almost fully glucuronidated by liver microsomes after 3 h, whereas ECg and ECGg were conjugated to a lesser extent ([Formula: See Text] and [Formula: See Text] respectively). The intestinal microsomes also glucuronidated quercetin much more efficiently than ECg and EGCg. Although the rates were lower than quercetin, intestinal microsomes exhibited higher activity on the galloyl group of ECg and EGCg compared to the flavonoid ring, whereas hepatic glucuronidation was higher on the flavonoid ring of EGCg and ECg compared to the galloyl groups. The low glucuronidation rates could partially explain why these flavanols are present in plasma as unconjugated forms.     

Plasticity of rat bone marrow-derived 5-hydroxytryptamine-sensitive neurons: dedifferentiation and redifferentiation

Inducing cellular dedifferentiation has been proposed as a potential method for enhancing endogenous regeneration in mammals. Here we demonstrate that phenotypic and functional neurons derived from adult rat bone marrow stromal stem cells (MSCs) can be induced to undergo dedifferentiation, then proliferation and redifferentiation. In addition to morphological changes and expression of neuronal markers, neuron-specific enolase and neurofilament H, functional differentiation was monitored by intracellular Ca2+ mobilization in response to a ubiquitous neurotransmitter, 5-hydroxytryptamine (5-HT) at different stages. The neurons derived from rMSCs were found to have increased 5-HT response. This 5-HT sensitivity could be reversed to basal level similar to that found in rMSCs when neurons, up to 3 days after neuronal induction, were induced to undergo dedifferentiation. Increase in 5-HT-induced Ca2+ mobilization was again observed when rMSCs derived from dedifferentiated neurons were induced to redifferentiate into neurons again. Variation in 5-HT1A receptor immunoreactivity was observed in stem cells, differentiated neurons, dedifferentiated neurons and redifferentiation neurons, consistent with their respective 5-HT sensitivity. These results suggest that adult bone marrow-derived 5-HT sensitive neurons are capable of dedifferentiation, then proliferation and redifferentiation, indicating their plasticity and potential use in treatment of neural degenerative diseases.     

New CMS-associated phenotypes in cybrids Nicotiana tabacum L. (+Hyoscyamus niger L.)

Morphological characteristics were studied in cytoplasmic male sterile (CMS) cybrids possessing the tobacco nuclear genome, Hyoscyamus niger plastome and recombinant mitochondria. After backcrosses with tobacco, new flower modifications were found, including: conversions of stamens into branched filamentous structures; alterations in the shape of petals and the corolla limb; and high degrees of reduction in most flower organs. Vegetative alterations (leaf elongation and stem branching) occurred in some cybrids. Results confirmed that a protoplast fusion-based alloplasmic cytoplasm transfer, followed by conventional backcrosses, is a useful tool for generating alternative CMS sources with novel nucleo-cytoplasmic compositions. These alterations in the genetic status were accompanied by modified floral and vegetative phenotypes.