A profile for molecular biology databases and information resources

This paper examines the requirements for building database managementsystems and multi-database information resources to supportmolecular biology research. The paper profiles the most importantfeatures of 16 integrated resources and 102 databases relatedto molecular biology research. The aspects surveyed in thispaper include the nature of information in these databases,their sizes, update properties, cross-references, database managementsystem heterogeneity, geographical distribution, data quality,use of temporal information and level of interpretation. Thepaper also comments on the access patterns to these databases.Since not all these aspects were available for all databases,specific comparisons sometimes compare fewer than the full 102databases. Consequently, the same set of databases is not necessarilyalways being compared with respect to every aspect. The paperis organized primarily according to these comparison aspectsand ends with some concluding remarks.     

Anatomical ontologies: names and places in biology

Ontology has long been the preserve of philosophers and logicians. Recently, ideas from this field have been picked up by computer scientists as a basis for encoding knowledge and with the hope of achieving interoperability and intelligent system behavior. In bioinformatics, ontologies might allow hitherto impossible query and data-mining activities. We review the use of anatomy ontologies to represent space in biological organisms, specifically mouse and human.     

Roles of cell volume in molecular and cellular biology

Extracellular tonicity and volume regulation control a great number of molecular and cellular functions including: cell proliferation, apoptosis, migration, hormone and neuromediator release, gene expression, ion channel and transporter activity and metabolism. The aim of this review is to describe these effects and to determine if they are direct or are secondarily the result of the activity of second messengers.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

Firefly luciferase as a tool in molecular and cell biology

The unique properties of firefly luciferase and the cloning of the gene for this enzyme have spawned a number of novel applications of this protein. We summarize a few of these applications including its use as a reporter gene, as a model for the study of protein import into peroxisomes, and as a component of a heterologous gene expression system.     

Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names

When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.     

A package of computer programs for handling taxonomic databases

A package of programs is described which processes taxonomicdata, suitable to use when preparing monographs, handbooks,Floras or Faunas, in which species or other taxa are describedand identified. There is also an interactive program for specimenidentification, and conversion routines which prepare data fornumerical taxonomy (clustering and cladistics). The programsare equally suitable for botany or for zoology, or even fornon-biological data. Received on September 20, 1985; accepted on November 11, 1985     

Role of molecular cell biology in understanding disease.

Molecular techniques have revolutionised our knowledge of cell and tissue function in both health and disease. We already have new and powerful treatments based on an understanding of communication between cells by messenger molecules called cytokines. Furthermore, there is great therapeutic promise in defining molecules which regulate cell adhesion, motility, proliferation, survival, and death. Rational manipulation of cell and tissue function for therapeutic ends may be much closer than you think.     

Recent developments in the cell and molecular biology of root hairs

Recent results in root hair research show that these tip-growing cells are useful models in plant cell biology research. The review covers a range of topics, but there is particular emphasis on the use of mutants in molecular (genetic) analysis.     

A decade of molecular cell biology: achievements and challenges

Nature Reviews Molecular Cell Biology celebrated its 10-year anniversary during this past year with a series of specially commissioned articles. To complement this, here we have asked researchers from across the field for their insights into how molecular cell biology research has evolved during this past decade, the key concepts that have emerged and the most promising interfaces that have developed. Their comments highlight the broad impact that particular advances have had, some of the basic understanding that we still require, and the collaborative approaches that will be essential for driving the field forward.