Gene tree parsimony vs uninode coding for phylogenetic reconstruction

have suggested that there are important weaknesses of gene tree parsimony in reconstructing phylogeny in the face of gene duplication, weaknesses that are addressed by method of uninode coding. Here, we discuss Simmons and Freudenstein's criticisms and suggest a number of reasons why gene tree parsimony is preferable to uninode coding. During this discussion we introduce a number of recent developments of gene tree parsimony methods overlooked by Simmons and Freudenstein. Finally, we present a re-analysis of data from that produces a more reasonable phylogeny than that found by Simmons and Freudenstein, suggesting that gene tree parsimony outperforms uninode coding, at least on these data.     

Explicit Mentalizing Mechanisms and Their Adaptive Role in Memory Conformity

Memory conformity occurs when an individual endorses what other individuals remember about past events. Research on memory conformity is currently dominated by a ‘forensic’ perspective, which views the phenomenon as inherently undesirable. This is because conformity not only distorts the accuracy of an individual''s memory, but also produces false corroboration between individuals, effects that act to undermine criminal justice systems. There is growing awareness, however, that memory conformity may be interpreted more generally as an adaptive social behavior regulated by explicit mentalizing mechanisms. Here, we provide novel evidence in support of this emerging alternative theoretical perspective. We carried out a memory conformity experiment which revealed that explicit belief-simulation (i.e. using one''s own beliefs to model what other people believe) systematically biases conformity towards like-minded individuals, even when there is no objective evidence that they have a more accurate memory than dissimilar individuals. We suggest that this bias is functional, i.e. adaptive, to the extent that it fosters trust, and hence cooperation, between in-group versus out-group individuals. We conclude that memory conformity is, in more fundamental terms, a highly desirable product of explicit mentalizing mechanisms that promote adaptive forms of social learning and cooperation.     

Circadian rhythms in the electroretinogram of the cockroach

Circadian regulation of the amplitude of the electroretinogram (ERG) of the cockroach Leucophaea maderae was investigated. Two components of the ERG exhibited circadian rhythms in amplitude. Interestingly, the peak amplitudes for the two rhythms were approximately 12 hr out of phase. The dominant corneal negative potential (the "sustained component") exhibited maximum amplitude during the subjective night. A second corneal negative potential (the "off-transient") was at a maximum during the subjective day. Intensity-response curves of the sustained component were measured at both the peak and trough of the rhythm. The results showed that the circadian rhythm in amplitude reflected a sensitivity change equivalent to 0.2-0.6 log unit of intensity. An effort was also made to identify the anatomical locus of the pacemaking oscillator for the ERG rhythm in a series of lesion experiments. Neural isolation of the optic lobe from the midbrain by bisection of the optic lobe proximal to the distal edge of the lobula had no effect on the circadian rhythm of ERG amplitude. Bisection of the optic lobe distal to the lobula abolished the ERG amplitude rhythm. These results suggest that the pacemaker is located in the optic lobe near the lobula; that its motion continues in the absence of neural connections with the rest of the nervous system; and that its regulation of ERG amplitude depends on neural pathways in the optic lobe.     

P450 BM3: the very model of a modern flavocytochrome

Flavocytochrome P450 BM3 is a bacterial P450 system in which a fatty acid hydroxylase P450 is fused to a mammalian-like diflavin NADPH-P450 reductase in a single polypeptide. The enzyme is soluble (unlike mammalian P450 redox systems) and its fusion arrangement affords it the highest catalytic activity of any P450 mono-oxygenase. This article discusses the fundamental properties of P450 BM3 and how progress with this model P450 has affected our comprehension of P450 systems in general.     

Cultivation of Macrocystis integrifolia (Laminariales,Phaeophyta) in southeastern Alaskan waters

The artificial culture of Macrocystis integrifolia in southeastern Alaskan waters has been initiated as a first step in a project to augment the existing herring roe-on-kelp fishery in the state. The growing of Macrocystis in Prince William Sound has the potential of considerably enhancing this fishery by eliminating the costly importation of this kelp from southeast Alaska. In an ongoing feasibility study, Macrocystis has been cultured under laboratory conditions through the embryonic sporophyte stage and outplanted in waters near Sitka, Alaska (57° N). Growth of the outplanted kelps has been monitored as a function of the time and depth of the outplanting. Preliminary results suggest that light is limiting for growth in winter and that the optimal depth for outplanting will vary with the season.     

Identifying habitat conservation priorities and gaps for migratory shorebirds and waterfowl in California

Conservation of migratory shorebirds and waterfowl presents unique challenges due to extensive historic loss of wetland habitats, and current reliance on managed landscapes for wintering and migratory passage. We developed a spatially-explicit approach to estimate potential shorebird and waterfowl densities in California by integrating mapped habitat layers and statewide bird survey data with expert-based habitat rankings. Using these density estimates as inputs, we used the Marxan site-selection program to identify priority shorebird and waterfowl areas at the ecoregional level. We identified 3.7 million ha of habitat for shorebirds and waterfowl, of which 1.4 million ha would be required to conserve 50% of wintering populations. To achieve a conservation goal of 75%, more than twice as much habitat (3.1 million ha) would be necessary. Agricultural habitats comprised a substantial portion of priority areas, especially at the 75% level, suggesting that under current management conditions, large areas of agricultural land, much of it formerly wetland, are needed to provide the habitat availability and landscape connectivity required by shorebird and waterfowl populations. These habitats were found to be largely lacking recognized conservation status in California (96% un-conserved), with only slightly higher levels of conservation for priority shorebird and waterfowl areas. Freshwater habitats, including wetlands and ponds, were also found to have low levels of conservation (67% un-conserved), although priority shorebird and waterfowl areas had somewhat higher levels of conservation than the state as a whole. Conserving migratory waterfowl and shorebirds will require a diversity of conservation strategies executed at a variety of scales. Our modeled results are complementary with other approaches and can help prioritize areas for protection, restoration and other actions. Traditional habitat protection strategies such as conservation easements and fee acquisitions may be of limited utility for protecting and managing significant areas of agricultural lands. Instead, conservation strategies focused on incentive-based programs to support wildlife friendly management practices in agricultural settings may have greater utility and conservation effectiveness.     

Endopeptidase-24.11, a Cell-Surface Peptidace of Central Nervous System Neurons, Is Expressed by Schwann Cells in the Pig Peripheral Nervous System

Endopeptidase-24.11 is a 90-kDa surface glycoprotein with the ability to hydrolyze a variety of biologically active peptides. Interest in this enzyme is based on the consensus that it may play a role in the termination of peptide signals in the central nervous system. In the present study, we have investigated the distribution of endopeptidase-24.11 in two nerves of the peripheral nervous system of newborn pigs: the sciatic, composed of a mixture of myelinated and nonmyelinated axons, and cervical sympathetic trunk in which greater than 99% of the axons are nonmyelinated. The endopeptidase was monitored enzymatically, as well as by immunoblotting and immunocytochemistry using mono- and polyclonal anti-endopeptidase antibodies. Endopeptidase-24.11 was detected in both the sciatic nerve and the cervical sympathetic trunk. Membrane preparations from sciatic nerve hydrolyzed 125I-insulin B-chain, and more than 50% of the activity was inhibited by phosphoramidon with an IC50 concentration of 3.2 nM. Moreover, a 90-kDa polypeptide was detected by immunoblotting of sciatic nerve membranes. The type of cells expressing the endopeptidase was determined by immunohistochemistry. In teased nerve preparations, these cells were identified morphologically as myelin- and non-myelin-forming Schwann cells. Endopeptidase-24.11 was also expressed by cultured Schwann cells from sciatic nerve and cervical sympathetic trunk maintained for 3 h in vitro. The presence of endopeptidase-24.11 on the Schwann cell surface raises the possibility of a potential role for the enzyme in nerve development and/or regeneration.     

Threonine-insensitive Homoserine Dehydrogenase from Soybean: GENOMIC ORGANIZATION, KINETIC MECHANISM, AND IN VIVO ACTIVITY*

Aspartate kinase (AK) and homoserine dehydrogenase (HSD) function as key regulatory enzymes at branch points in the aspartate amino acid pathway and are feedback-inhibited by threonine. In plants the biochemical features of AK and bifunctional AK-HSD enzymes have been characterized, but the molecular properties of the monofunctional HSD remain unexamined. To investigate the role of HSD, we have cloned the cDNA and gene encoding the monofunctional HSD (GmHSD) from soybean. Using heterologously expressed and purified GmHSD, initial velocity and product inhibition studies support an ordered bi bi kinetic mechanism in which nicotinamide cofactor binds first and leaves last in the reaction sequence. Threonine inhibition of GmHSD occurs at concentrations (K_i = 160–240 mm) more than 1000-fold above physiological levels. This is in contrast to the two AK-HSD isoforms in soybean that are sensitive to threonine inhibition (K_i∼150 μm). In addition, GmHSD is not inhibited by other aspartate-derived amino acids. The ratio of threonine-resistant to threonine-sensitive HSD activity in soybean tissues varies and likely reflects different demands for amino acid biosynthesis. This is the first cloning and detailed biochemical characterization of a monofunctional feedback-insensitive HSD from any plant. Threonine-resistant HSD offers a useful biotechnology tool for manipulating the aspartate amino acid pathway to increase threonine and methionine production in plants for improved nutritional content.