Functional genomics does not have to be limited to a few select organisms

A response to Whither genomics by Andrew W Murray, Genome Biology 2000, 1:comment003.1-003.6     

Functional genomics does not have to be limited to a few select organisms

A response to Whither genomics by Andrew W Murray, Genome Biology 2000, 1:comment003.1-003.6     

Why should bats be protected? A challenge for conservation

In Britain, the distribution of a few bat species appears to have declined over the past century. Generally, the documentary evidence is sparse, but improving knowledge of how bats exploit their roost and foraging habitats, combined with investigations into their prey selection suggests causes that will have affected them. Reduction in insect diversity and abundance resulting from much less grazed pasture and the loss of over 300000 km of hedgerow is considered to have had the most impact on bats. In addition, loss of, or damage to, roosts is known to have had deleterious consequences. Large scale management of landscape to create shelter and an abundance of insects is considered necessary if bat populations, especially of die rarest species, are to flourish.     

Thermally perturbed rhodanese can be protected from inactivation by self-association

A fluorescence-detected structural transition occurs in the enzyme rhodanese between 30–40°C that leads to inactivation and aggregation, which anomalously decrease with increasing protein concentration. Rhodanese at 8 µg/ml is inactivated at 40°C after 50 min of incubation, but it is protected as its concentration is raised, such that above 200 µg/ml, there is only slight inactivation for at least 70 min. Inactivation is increased by lauryl maltoside, or by low concentrations of 2-mercaptoethanol. The enzyme is protected by high concentrations of 2-mercaptoethanol or by the substrate, thiosulfate. The fluorescence of 1,8-anilinonaphthalene sulfonate reports the appearance of hydrophobic sites between 30–40°C. Light scattering kinetics at 40°C shows three phases: an initial lag, a relatively rapid increase, and then a more gradual increase. The light scattering decreases under several conditions: at increased protein concentration; at high concentrations of 2-mercaptoethanol; with lauryl maltoside; or with thiosulfate. Aggregated enzyme is inactive, although enzyme can inactivate without significant aggregation. Gluteraldehyde cross-linking shows that rhodanese can form dimers, and that higher molecular weight species are formed at 40°C but not at 23°;C. Precipitates formed at 40°C contain monomers with disulfide bonds, dimers, and multimers. We propose that thermally perturbed rhodanese has increased hydrophobic exposure, and it can either: (a) aggregate after a rate-limiting inactivation; or (b) reversibly dimerize and protect itself from inactivation and the formation of large aggregates.     

Native healing traditions must be protected and preserved for future generations.

Toronto physician Mel Borins, who has travelled extensively to developing countries to examine traditional healing practices, recently visited elders at an Ontario Indian reserve to learn more about native healing practices. He is concerned that much native knowledge about the use of herbs and plants for healing will be lost and steps should be taken to protect it. He is also worried about the possible extinction of useful medicinal plants as civilization encroaches on remote areas.     

制备动物乳腺生物反应器的问题和对策

动物乳腺是理想的用于生产复杂的生物活性蛋白的生物反应器。目前,显微注射仍然是制备大型转基因动物的主要方法,但外源基因整合效率低下和位置效应还需要解决。要解决这两个问题,人们探索了几种策略。尽管使用转染的体细胞和基因打靶的体细胞作为核移植的供体的动物克隆技术还在改善中,但是这一技术是有应用前景的转基因牲畜的方法。在转基因载体中使用LCR和MAR序列可显著提高表达水平和转基因效率。YAC、BAC作为理想的转基因载体可能因为它们能容纳基因座的所有元件。虽然这些技术和方法还存在不完善之处,但其发展将极大地提高动物乳腺生物反应器的整合率和表达水平。     

A role for the sampling effect in invaded ecosystems

Species loss and invasion of exotic species are two components of global biodiversity change that are expected to influence ecosystem functioning. Yet how they interact in natural settings remains unclear. Experiments have revealed two major mechanisms for the observed increase in primary productivity with plant species richness. Plant productivity may rise with species richness due to the increased amount of resources used by more diverse communities (niche complementarity) or through the increased probability of including a highly productive, dominant species in the community (sampling effect). Current evidence suggests that niche complementarity is the most relevant mechanism, whereas the sampling effect would only play a minor and transient role in natural systems. In turn, exotic species can invade by using untapped resources or because they possess a fitness advantage over resident species allowing them to dominate the community. We argue that the sampling effect can be a significant biodiversity mechanism in ecosystems invaded by dominant exotic species, and that the effect can be persistent even after decades of succession. We illustrate this idea by analyzing tree species richness–productivity relationships in a subtropical montane forest (NW Argentina) heavily invaded by Ligustrum lucidum, an evergreen tree from Asia. We found that the forest biomass increased along a natural gradient of tree species richness whether invaded by L. lucidum or not. Consistent with the sampling effect, L. lucidum invasion tripled total tree biomass irrespective of species richness, and monocultures of L. lucidum were more productive than any of the most species‐rich, uninvaded communities. Hence, the sampling effect may not be restricted to randomly assembled, synthetic communities. We emphasize that studying invaded ecosystems may provide novel insights on the mechanisms underlying the effect of biodiversity on ecosystem function.     

To be or not to be in the nucleolus

Compartmentalization has long been known to have a key role in regulation of cellular processes. By keeping enzymes and regulatory complexes in compartments where the delivery of substrate or exit of product is controlled, competing reactions can occur simultaneously in different parts of the cell. Moreover, spatial confinement facilitates the working of molecules participating in reaction chains and is crucial for coupling unfavourable with energetically favourable chemical reactions. Although in many cases intracellular compartmentalization relies on boundaries imposed by membranes, several non-membrane-bounded compartments exist in eukaryotic cells. One of these, the nucleolus, has recently attracted much attention. The emerging view is that molecular confinement in the nucleolus actively contributes to the control of cellular survival and proliferation.     

Generic names in the Orbiliaceae (Orbiliomycetes) and recommendations on which names should be protected or suppressed

A list of all generic names that have been connected with the Orbiliomycetes is provided. Recommendations are made as to which names should be used in accordance with the rules and the different generic concepts. There is a mismatch in the current generic concepts within Orbiliomycetes regarding the two morphs: a narrow concept is used for the asexual morphs, but a broad concept relies on the sexual morphs. As a consequence, many more generic names have been established for the asexual morphs. A number of previous generic concepts are artificial, since they were based on single characters without molecular support. In order to provide solutions for this mismatch, we present three different generic concepts within the Orbiliomycetes. A broad concept recognizes a large genus Orbilia, with which most of the listed names fall into synonymy, but could be maintained as infrageneric names. Due to the lack of data proving phylogenetic relationships, this broad concept, at present, is the most practicable and recommended one. A moderate concept subdivides Orbilia into several genera, with all nematode-trapping fungi merged in Arthrobotrys. A narrow generic concept accepts genera based on differences in trapping organs, but also subdivides the remaining groups of Orbilia into additional genera. Trapping of invertebrates (zoophagy) is not restricted to Arthrobotrys in a broad sense, but occurs also in the more distant basal genera Hyalorbilia and Lecophagus, which mainly prey on rhizopods and rotifers. Whether these predatory capabilities trace back to a common ancestor is not clear. The following new combinations are proposed: Hyalorbilia oviparasitica, Hyalorbilia quadridens, Hyalorbilia tenuifusaria, and Orbilia fissilis.     

Responses of invertebrates to herbicide in Salix cinerea invaded wetlands: Restoration implications

The use of herbicides to control weeds, particularly large invasions, has now become an essential management tool in many ecological restoration projects. The herbicide glyphosate is routinely used to control the invasive weed, Grey Willow (Salix cinerea), within New Zealand wetlands. However, little is known about the effects of glyphosate on invertebrates. We determine the short‐term effects of glyphosate on the abundance and composition of the nontarget canopy invertebrate community in wetlands invaded by Grey Willow in New Zealand. Initially, the application of glyphosate and a surfactant showed no detectable effect on the canopy invertebrates examined in this study. However, 27 days after herbicide application, significant Grey Willow canopy loss caused dramatic decreases in the abundance of invertebrates in the glyphosate‐treated plots compared with the unsprayed plots. Invertebrates appeared to be sensitive to changes in vegetation structure, such as canopy loss. These results agree with previous studies that have shown that the negative impacts of glyphosate on invertebrate communities are related to indirect effects via habitat modification as the herbicide‐treated vegetation dies. From a terrestrial invertebrate perspective, this study suggests that the use of glyphosate herbicide is suitable for the control of invasive weeds within wetland restoration projects as it appears to have negligible impact on the canopy invertebrate assemblage.     

Myocardium tolerant to an adenosine-dependent ischemic preconditioning stimulus can still be protected by stimuli that employ alternative signaling pathways

Clinical studies on cardioprotection by preinfarct angina are ambiguous, which may involve development of tolerance to repeated episodes of ischemia. Not all preconditioning stimuli use identical signaling pathways, and because patients likely experience varying numbers of episodes of preinfarct angina of different degrees and durations, it is important to know whether myocardium tolerant to a particular preconditioning stimulus can still be protected by stimuli employing alternative signaling pathways. We tested the hypothesis that development of tolerance to a particular stimulus does not affect cardioprotection by stimuli that employ different signaling pathways. Anesthetized rats underwent classical, remote or pharmacological preconditioning. Infarct size (IS), produced by a 60-min coronary artery occlusion (CAO), was determined after 120 min of reperfusion. Preconditioning by two 15-min periods of CAO (2CAO15, an adenosine-dependent stimulus) limited IS from 69 +/- 2% to 37 +/- 6%, but when 2CAO15 was preceded by 4CAO15, protection by 2CAO15 was absent (IS = 68 +/- 1%). This development of tolerance coincided with a loss of cardiac interstitial adenosine release, whereas two 15-min infusions of adenosine (200 microg/min i.v.) still elicited cardioprotection (IS = 40 +/- 4%). Furthermore, cardioprotection was produced when 4CAO15 was followed by the adenosine-independent stimulus 3CAO3 (IS = 50 +/- 8%) or the remote preconditioning stimulus of two 15-min periods of mesenteric artery occlusion (IS = 49 +/- 6%). In conclusion, development of tolerance to cardioprotection by an adenosine-dependent preconditioning stimulus still allows protection by pharmacological or ischemic stimuli intervention employing different signaling pathways.