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PubMed2002

Stephen J Gould.

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Biological Evolution↗
PubMed1993

Interphotoreceptor retinoid-binding protein (IRBP). Molecular biology and physiological role in the visual cycle of rhodopsin.

The regeneration of visual pigment in rod photoreceptors of the vertebrate retina requires an exchange of retinoids between the neural retina and the retina pigment epithelium (RPE). It has been hypothesized that interphotoreceptor retinoid-binding protein (IRBP) functions as a two-way carrier of retinoid through the aqueous compartment (interphotoreceptor matrix) that separates the RPE and the photoreceptors. The first part of this review summarizes the cellular and molecular biology of IRBP. Work on the IRBP gene indicates that the protein contains a four-fold repeat structure that may be involved in binding multiple retinoid and fatty acid ligands. These repeats and other aspects of the gene structure indicate that the gene has had an active and complex evolutionary history. IRBP mRNA is detected only in retinal photoreceptors and in the pineal gland; expression is thus restricted to the two photosensitive tissues of vertebrate organisms. In the second part of this review, we consider the results obtained in experiments that have examined the activity of IRBP in the process of visual pigment regeneration. We also consider the results obtained on the bleaching and regeneration of rhodopsin in the acutely detached retina, as well as in experiments testing the ability of IRBP to protect its retinoid ligand from isomerization and oxidation. Taken together, the findings provide evidence that, in vivo, IRBP facilitates both the delivery of all-trans retinol to the RPE and the transfer of 11-cis retinal from the RPE to bleached rod photoreceptors, and thereby directly supports the regeneration of rhodopsin in the visual cycle.

Animals↗
PubMed1998

Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea.

A sample of 15 cultivars and 56 Pisum accessions from the JIC germplasm core collection has been studied using a modification of the SSAP (sequence-specific amplification polymorphisms) technique; the specific primer was designed to correspond to the polypurine tract (PPT) of PDR1, a Ty1-copia group retrotransposon of pea. Most of these SSAP products were shown to be PDR1 derived. The PDR1 SSAP markers are more informative than previously studied AFLP or RFLP markers and are distributed throughout the genome. Their pattern of variation makes them ideal for integrating genetic maps derived from related crosses. Data sets obtained with AFLP and PDR1 SSAP markers were used to construct neighbour-joining trees and for principal component analysis. These data sets give greater resolution than hitherto available for the characterisation of variation within Pisum, showing that the genus has three main groups: P. fulvum, P. abyssinicum and all other Pisum spp. P. abyssinicum is not a subgroup of cultivated P. sativum, as was previously thought, but has probably been domesticated independently. Modern cultivars are shown to form a single group within Pisum as a whole.

Biological Evolution↗
PubMed1997

The status of biology and the meaning of biodiversity.

During the past 40 years or so genetics and molecular biology have played a major role in the study of living systems. There is some substance to the belief of many biologists that the molecular approach supplies us with the key to an understanding of life. At the same time other biological disciplines have been unfairly neglected. More recently, however, alarmed by the loss of species around the world, many researchers have turned to ecological problems and rediscovered the importance of systematics and taxonomy. It has become apparent that the number of still unknown species is enormous, and the very dimensions of biodiversity are a great challenge to biologists. Moreover, the preservation of species has become an important task for ethical as well as economic reasons. In this contribution biodiversity research is discussed as an essential interdisciplinary enterprise of contemporary biology which compels us to critically reconsider and reflect the status of the science of life and its anthropological and ethical implications. It is also argued that recognizing biodiversity gives a fresh impetus to biology teaching.

Animals↗
PubMed2002

Sequence and phylogenetic analyses of the twin-arginine targeting (Tat) protein export system.

Twin-arginine targeting (Tat) protein secretion systems consist of two protein types, members of the TatA and TatC families. Homologues of these proteins are found in many archaea, bacteria, chloroplasts and mitochondria. Every prokaryotic organism with a fully sequenced genome exhibits either neither family member, or between one and three paralogues of these two family members. The Arabidopsis thaliana genome encodes three of each. Although many mitochondrially encoded TatC homologues have been identified, corresponding TatA homologues have not been found in this organelle. Phylogenetic analyses reveal that most prokaryotic Tat systems consist of one TatC homologue and two sequence-divergent TatA homologues (TatA and TatB). When only one TatA homologue is present, TatB is missing, and when three TatA homologues are present, the third one arose by duplication of TatA, not TatB. Further, homologues most resembling TatB are more sequence-divergent than those more closely resembling TatA. In contrast to the TatA family, the TatC family shows phylogenetic clustering in strict accordance with organismal type. These results are discussed in terms of their probable structural, functional and evolutionary significance.

Arginine↗
PubMed2003

A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily.

An ABC-type transporter in Escherichia coli that transports both L- and D-methionine, but not other natural amino acids, was identified. This system is the first functionally characterized member of a novel family of bacterial permeases within the ABC superfamily. This family was designated the methionine uptake transporter (MUT) family (TC #3.A.1.23). The proteins that comprise the transporters of this family were analyzed phylogenetically, revealing the probable existence of several sequence-divergent primordial paralogues, no more than two of which have been transmitted to any currently sequenced organism. In addition, MetJ, the pleiotropic methionine repressor protein, was shown to negatively control expression of the operon encoding the ABC-type methionine uptake system. The identification of MetJ binding sites (in gram-negative bacteria) or S-boxes (in gram-positive bacteria) in the promoter regions of several MUT transporter-encoding operons suggests that many MUT family members transport organic sulfur compounds.

ATP-Binding Cassette Transporters↗
PubMed2001

Structural changes induced by antineoplastic therapies: keys to evaluate tumor response to treatment.

The criteria to define therapeutic response in oncology are those proposed by Miller, characterized by four response categories (complete response, partial response, no change, progression of disease), and based upon both measurable and non-measurable (and otherwise assessable) morphological parameters in comparison with baseline and subsequently modified following the Response Evaluation Criteria In Solid Tumors. In addition to these classical morphological criteria, we review the predictive value of structural changes in the evaluation of response to antineoplastic therapies. The goal of the present review is to evaluate in detail structural variations (calcification, fibrosis, differentiation, necrosis, cavitation, vascularization, edema, and pseudocapsule formation) induced by therapy, and to ascertain their significance in terms of biological evolution of the neoplastic process.

Calcinosis↗
PubMed2005

Psychological altruism vs. biological altruism: narrowing the gap with the Baldwin effect.

This paper defends the position that the supposed gap between biological altruism and psychological altruism is not nearly as wide as some scholars (e.g., Elliott Sober) insist. Crucial to this defense is the use of James Mark Baldwin's concepts of "organic selection"and "social heredity" to assist in revealing that the gap between biological and psychological altruism is more of a small lacuna. Specifically, this paper argues that ontogenetic behavioral adjustments, which are crucial to individual survival and reproduction, are also crucial to species survival. In particular, it is argued that human psychological altruism is produced and maintained by various sorts of mimicry and self-reflection in the aid of both individual and species survival. The upshot of this analysis is that it is possible to offer an account of psychological altruism that is closely tethered to biological altruism without reducing entirely the former to the latter.

Altruism↗
PubMed2005

The function debate in philosophy.

This paper reviews the debate on the notion of biological function and on functional explanation as this takes place in philosophy. It describes the different perspectives, issues, intuitions, theories and arguments that have emerged. The author shows that the debate has been too heavily influenced by the concerns of a naturalistic philosophy of mind and argues that in order to improve our understanding of biology the attention should be shifted from the study of intuitions to the study of the actual practice of biological inquiry.

Animals↗
PubMed2006

Protocell-like microspheres from thermal polyaspartic acid.

One of the most prominent amino acids to appear in monomer-generating origin-of-life experiments is aspartic acid. Hugo Schiff found in 1897 that aspartic acid polymerizes when heated to form polyaspartylimide which hydrolyzes in basic aqueous solution to form thermal polyaspartic acid which is a branched polypeptide. We recently reported at the ISSOL 2005 Conference that commercially made thermal polyaspartic acid forms microspheres when heated in boiling water and allowed to cool. In a new experiment we heated aspartic acid at 180 degrees C for up to 100 h to form thermal polyaspartylimide which when heated in boiling water without addition of base hydrolyzed to form thermal polyaspartic acid which upon cooling formed microspheres. Thermal polyaspartic acid microspheres appear protocell-like in the sense of being prebiotically plausible lattices or containers that could eventually have been filled with just the right additions of primordial proteins, nucleic acids, lipids, and metabolites so as to constitute protocells capable of undergoing further chemical and biological evolution. Thermal polyaspartic acid microspheres are extremely simple models of protocells that are more amenable to precise quantitative experimental investigation than the proteinoid microspheres of Sidney W. Fox. We present here scanning electron microscope images of such thermal polyaspartic acid microspheres. Figure 1 shows thermal polyaspartic acid microspheres from L: -aspartic acid heated at 180 degrees C for 50 h, at a magnification of 3,500x. Figure 2 shows thermal polyaspartic acid microspheres from the same sample at a magnification of 7,000x. The thermal polyaspartic acid microspheres have a diameter of approximately 1 mum These images were viewed with a Hitachi S2460N scanning electron microscope at 20 kV acceleration voltage. Figure 1 Thermal polyaspartic acid microspheres from L: -aspartic acid heated at 180 degrees C for 50 h, at a magnification of 3,500x. Figure 2 Thermal polyaspartic acid microspheres from L: -aspartic acid heated at 180 degrees C for 50 h, at a magnification of 7,000x.

Evolution, Chemical↗