Functional profiling of the Saccharomyces cerevisiae genome

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.     

Nitric oxide as an inhibitory non-adrenergic non-cholinergic neurotransmitter

Inhibitory non-adrenergic non-cholinergic (NANC) nerves are thought to be important in the autonomic innervation of the gastrointestinal tract and other organ systems. The nature of their neurotransmitter is still debated. Speculation that nitric oxide (NO), formed from L-arginine in neuronal structures and other cells, could act as a neurotransmitter, is not yet supported by demonstration of its release upon nerve stimulation. Using a superfusion bioassay, we report the release of a vasorelaxant factor upon stimulation of the NANC nerves in the canine ileocolonic junction. Several pieces of evidence, including the selectivity of the bioassay tissues, chemical instability, inactivation by superoxide anion and haemoglobin, inhibition by NG-nitro-L-arginine (L-NNA) and potentiation by L-arginine all indicated that NO accounted for the biological activity of this transferable NANC factor.     

Constant elevation of southern Tibet over the past 15 million years

The uplift of the Tibetan plateau, an area that is 2,000 km wide, to an altitude of about 5,000 m has been shown to modify global climate and to influence monsoon intensity. Mechanical and thermal models for homogeneous thickening of the lithosphere make specific predictions about uplift rates of the Tibetan plateau, but the precise history of the uplift of the plateau has yet to be confirmed by observations. Here we present well-preserved fossil leaf assemblages from the Namling basin, southern Tibet, dated to approximately 15 Myr ago, which allow us to reconstruct the temperatures within the basin at that time. Using a numerical general circulation model to estimate moist static energy at the location of the fossil leaves, we reconstruct the elevation of the Namling basin 15 Myr ago to be 4,689 +/- 895 m or 4,638 +/- 847 m, depending on the reference data used. This is comparable to the present-day altitude of 4,600 m. We conclude that the elevation of the southern Tibetan plateau probably has remained unchanged for the past 15 Myr.     

Soil invertebrate fauna enhances grassland succession and diversity

One of the most important areas in ecology is to elucidate the factors that drive succession in ecosystems and thus influence the diversity of species in natural vegetation. Significant mechanisms in this process are known to be resource limitation and the effects of aboveground vertebrate herbivores. More recently, symbiotic and pathogenic soil microbes have been shown to exert a profound effect on the composition of vegetation and changes therein. However, the influence of invertebrate soil fauna on succession has so far received little attention. Here we report that invertebrate soil fauna might enhance both secondary succession and local plant species diversity. Soil fauna from a series of secondary grassland succession stages selectively suppress early successional dominant plant species, thereby enhancing the relative abundance of subordinate species and also that of species from later succession stages. Soil fauna from the mid-succession stage had the strongest effect. Our results clearly show that soil fauna strongly affects the composition of natural vegetation and we suggest that this knowledge might improve the restoration and conservation of plant species diversity.     

Limitation of the size of the vulval primordium of Caenorhabditis elegans by lin-15 expression in surrounding hypodermis

In the nematode Caenorhabditis elegans six hypodermal cells, the vulval precursor cells, are each competent to generate vulval cells. Normally only the three nearest precursor cells to the uterine anchor cell generate the vulva (22 nuclei), while the three others fuse with the non-specialized hypodermal syncytium (hyp7) surrounding each precursor cell and covering the body. Without an inductive signal from the anchor cell, all six vulval precursor cells fuse with hyp7 and no vulva is formed. But without activity of the vulval determination gene lin-15(+), all six cells undergo vulval divisions whether the anchor cell is present or not. Using mosaic analysis, we demonstrate here that lin-15(+) expression is necessary in cells other than the vulval precursor cells or the anchor cell, most probably in the hyp7 syncytium. We propose that lin-15(+) is active in hyp7 in order to repress an intrinsic vulval program in the precursor cells. The inductive signal from the anchor cell counteracts this repression for three precursor cells, allowing them to generate vulval cells. Such a two-signal (repressor/derepressor) mechanism may operate in other cases of tissue induction.     

Increased aggression in rats after withdrawal of long term used oxazepam

Summary The withdrawal of oxazepam (5 mg/kg i.p.) applied for 1 year in rats, increased shock-induced aggression of animals. This phenomenon is interpreted as a sign of abstinence and suggests that long-term treatment causes dependence to oxazepam in rats.Acknowledgment. Authors express their gratitude to Polfa, Warszawa, for the generous supply of oxazepam.     

A bird's eye view of global methylation

Restriction landmark genomic scanning applied to a broad variety of cancer types can disclose tumour-specific and tumour-type-specific global methylation profiles. This and other genome-scanning approaches allows the rapid analysis of methylation profiles of thousands of genes in parallel-and promises to identify new genes critical to carcinogenesis and other biological processes.     

GSK-3α/β kinases and amyloid production in vivo

Arising from C. J. Phiel, C. A. Wilson, V. M.-Y. Lee & P. S. Klein 423, 435-439 (2003)A major unresolved issue in Alzheimer's disease is identifying the mechanisms that regulate proteolytic processing of amyloid precursor protein (APP)-glycogen synthase kinase-3 (GSK-3) isozymes are thought to be important in this regulation. Phiel et al. proposed that GSK-3α, but not GSK-3β, controls production of amyloid. We analysed the proteolytic processing of mouse and human APP in mouse brain in vivo in five different genetic and viral models. Our data do not yield evidence for either GSK-3α-mediated or GSK-3β-mediated control of APP processing in brain in vivo.     

Global tests of biodiversity concordance and the importance of endemism

Understanding patterns of biodiversity distribution is essential to conservation strategies, but severe data constraints make surrogate measures necessary. For this reason, many studies have tested the performance of terrestrial vertebrates as surrogates for overall species diversity, but these tests have typically been limited to a single taxon or region. Here we show that global patterns of richness are highly correlated among amphibians, reptiles, birds and mammals, as are endemism patterns. Furthermore, we demonstrate that although the correlation between global richness and endemism is low, aggregate regions selected for high levels of endemism capture significantly more species than expected by chance. Although areas high in endemism have long been targeted for the protection of narrow-ranging species, our findings provide evidence that endemism is also a useful surrogate for the conservation of all terrestrial vertebrates.