How was teleology eliminated in early molecular biology?

This paper approaches the issue of the status of teleological reasoning in contemporary biology through a historical examination of events of the 1930s that surrounded Niels Bohr’s efforts to introduce ‘complementarity’ into biological discussions. The paper examines responses of three theoretical physicists who engaged boundary questions between the biological and physical sciences in this period in response to Bohr—Ernst Pascual Jordan (1902–80), Erwin Schrödinger (1887–1961), and Max Delbrück (1906–81). It is claimed that none of these physicists sufficiently understood Bohr’s ‘critical’ teleological arguments, which are traced to the lineage of Kant and Harald Høffding and their respective resolutions of the Antinomy of Teleological Judgment. The positions of these four historical actors are discussed in terms of Ernst Mayr’s distinction of ‘teleological,’ ‘teleomatic,’ and ‘teleonomic’ explanations. A return to some of the views articulated by Bohr, and behind him, to Høffding and Kant, is claimed to provide a framework for reintroducing a ‘critical’ teleology into biological discussions.     

The antiapoptotic herpes simplex virus glycoprotein J localizes to multiple cellular organelles and induces reactive oxygen species formation

The Us5 gene of herpes simplex virus (HSV) encodes glycoprotein J (gJ). The only previously reported function of gJ was its ability to inhibit apoptosis. However, the mechanism by which gJ prevents apoptosis is not understood, and it is not known whether gJ mediates additional cellular effects. In this study, we evaluated the expression, localization, and cellular effects of Us5/gJ. Us5 was first expressed 4 h after infection. gJ was detectable at 6 h and was expressed in glycosylated and unglycosylated forms. Us5 was regulated as a late gene, with partial dependency on DNA replication for expression. Us5 expression was delayed in the absence of ICP22; furthermore, expression of Us5 in trans protected cells from apoptosis induced by an HSV mutant with deletion of ICP27, suggesting that the antiapoptotic effects of ICP22 and ICP27 are mediated in part through effects on gJ expression. Within HSV-infected or Us5-transfected cells, gJ was distributed widely, especially to the endoplasmic reticulum, trans-Golgi network, and early endosomes. gJ interacted with F_oF₁ ATP synthase subunit 6 by a yeast two-hybrid screen and had strong antiapoptotic effects, which were mediated by protein rather than mRNA. Antiapoptotic activity required the extracellular and transmembrane domains of gJ, but not the intracellular domain. Consistent with inhibition of F_oF₁ ATP synthase function, Us5 was required for HSV-induced reactive oxygen species (ROS) formation, and gJ was sufficient to induce ROS in Us5-transfected cells. Thus, HSV gJ is a multifunctional protein, modulating other cellular processes in addition to inhibition of apoptosis.     

Pollen morphology in <Emphasis Type="Italic">Lysipomia</Emphasis> (Campanulaceae: Lobelioideae) and interpretation of shape artifacts

The pollen of 32 species of Lysipomia was examined by light, scanning, and transmission electron microscopy. Two pollen types occur in the genus: 3-colporate and 6-colporate. The 3-colporate condition occurs in only two species, L. laciniata and L. pumila. The remaining 30 species are 6-colporate, a condition known from only one other genus in the Campanulaceae. Surface sculpturing among the species is uniformly striate. Pollen shape was highly variable within a single individual in comparisons of pollen gathered from herbarium specimens, FAA preserved material collected in the field, and fresh pollen from cultivated individuals grown from seed. Shape may change from oblate spheroidal to subprolate as a result of drying time and temperature, and should not be used as a morphological character in systematic studies if infraspecific variation is seen. When fresh or preserved pollen is not available, rehydrated pollen should be compared to reduce the possibility of inadvertent artifact production confounding the analysis of morphological data.     

Changes in quaternary structure in the signaling mechanisms of PAS domains

FixL from Bradyrhizobium japonicum is a PAS sensor protein in which two PAS domains covalently linked to a histidine kinase domain are responsible for regulating nitrogen fixation in an oxygen-dependent manner. The more C-terminal PAS domain, denoted bjFixLH, contains a heme cofactor that binds diatomic molecules such as carbon monoxide and oxygen and regulates the activity of the FixL histidine kinase as part of a two-component signaling system. We present the structures of ferric, deoxy, and carbon monoxide-bound bjFixLH in a new space group ( P1) and at resolutions (1.5-1.8 A) higher than the resolutions of those previously obtained. Interestingly, bjFixLH can form two different dimers (in P1 and R32 crystal forms) in the same crystallization solution, where the monomers in one dimer are rotated approximately 175 degrees relative to the second. This suggests that PAS monomers are plastic and that two quite distinct quaternary structures are closely similar in free energy. We use screw rotation analysis to carry out a quantitative pairwise comparison of PAS quaternary structures, which identifies five different relative orientations adopted by isolated PAS monomers. We conclude that PAS monomer arrangement is context-dependent and could differ depending on whether the PAS domains are isolated or are part of a full-length protein. Structurally homologous residues comprise a conserved dimer interface. Using network analysis, we find that the architecture of the PAS dimer interface is continuous rather than modular; the network of residues comprising the interface is strongly connected. A continuous dimer interface is consistent with the low dimer-monomer dissociation equilibrium constant. Finally, we quantitate quaternary structural changes induced by carbon monoxide binding to a bjFixLH dimer, in which monomers rotate by up to approximately 2 degrees relative to each other. We relate these changes to those in other dimeric PAS domains and discuss the role of quaternary structural changes in the signaling mechanisms of PAS sensor proteins.     

Purification and characterization of nicotinamide deamidase from yeast

Nicotinamide deamidase (YNDase) has been purified from yeast through the use of a six-step procedure that includes molecular-sieve high performance liquid chromatography. The final preparation was homogeneous by the criteria of sodium dodecyl sulfate-gel electrophoresis, and the enzyme specific activity was determined to be 175 mumol of nicotinate formed per min/mg enzyme. Gel electrophoresis and molecular-sieve high performance liquid chromatography were employed also to characterize YNDase as a monomeric protein with a molecular weight of 34,000. A Km value for nicotinamide of 33 microM was determined for the deamidase activity at pH 6, and a pH range for optimal stability of 6-8.5 was established for this enzyme. The YNDase activity was also examined over a pH range at several substrate concentrations and both the log Vmax and log Vmax/Km plots versus pH suggested that a protonated amino acid residue with an apparent pKb value of 7.8 was essential to this activity. During an in vitro assay of the YNDase-catalyzed formation of nicotinate, ammonia was generated and detected chemically. Inhibition of the YNDase activity by nicotinaldehyde suggested the presence of either an essential lysine (Schiff's base formation) or cysteine residue (thiohemiacetal intermediate) at the YNDase active site. The relatively large value of the nicotinaldehyde inhibition constant (Ki = 68 microM), the observation that this analogue is a noncompetitive inhibitor of nicotinate formation, and the fact that this inhibition can be rendered irreversible through incubation with sodium borohydride, indicates that a Schiff's base intermediate is more likely to occur upon incubation of YNDase with nicotinaldehyde. However, YNDase is inactivated completely and irreversibly by N-ethylmaleimide at pH 6, and the enzyme is protected against this modification by either nicotinamide or nicotinate. These results suggest that both nicotinate and nicotinamide bind to YNDase, even though the enzymatic reaction is essentially irreversible, and that a cysteine residue may be present at the YNDase active site.     

Denver Papillae Protocol for Objective Analysis of Fungiform Papillae

The goal of the Denver Papillae Protocol is to use a dichotomous key to define and prioritize the characteristics of fungiform papillae (FP) to ensure consistent scoring between scorers. This protocol builds off of a need that has arisen from the last two decades of taste research using FP as a proxy for taste pore density. FP density has historically been analyzed using Miller & Reedy’s 1990 characterizations of their morphology: round, stained lighter, large, and elevated. In this work, the authors forewarned that stricter definitions of FP morphology needed to be outlined. Despite this call to action, follow up literature has been scarce, with most studies continuing to cite Miller & Reedy’s original work. Consequently, FP density reports have been highly variable and, combined with small sample sizes, may contribute to the discrepant conclusions on the role of FP in taste sensitivity. The Genetics of Taste Lab explored this apparent inconsistency in counting and found that scorers were individually prioritizing the importance of these characteristics differently and had no guidance for when a papilla had some, but not all, of the reported qualities of FP. The result of this subjectivity is highly variable FP counts of the same tongue image. The Denver Papillae Protocol has been developed to remedy this consequence through use of a dichotomous key that further defines and prioritizes the importance of the characteristics put forth by Miller & Reedy. The proposed method could help create a standard way to quantify FP for researchers in the field of taste and nutritional studies.     

Sequence analysis of end-labeled DNA fragments by solvolysis in hot aqueous piperidine solutions

One-lane DNA sequencing by solvolysis in hot aqueous piperidine solutions, originally described for 5'-32P-labeled DNA (B. Ambrose and R. Pless (1985) Biochemistry 24, 6194-6200), is extended to 3'-labeled fragments. A salt-free sample for electrophoresis can be obtained by using 1 M LiCl in the solvolysis mixture and removing this salt from the dried hydrolysate by washing with ethanol. Rate and distribution of DNA cleavage in hot aqueous piperidine, containing 0.3 M NaCl, are studied in dependence of temperature, solvent, amine concentration, and reaction time. An increase in temperature strongly accelerates overall DNA degradation, but leaves the distribution of cleavage essentially unchanged. When 50% aqueous ethanol is substituted for water as the reaction solvent, the overall cleavage is slower, and scission at G-sites is enhanced relative to cleavage at the other bases. A rise in the piperidine concentration strongly accelerates the reaction, except at very high amine concentration. Cleavage at A-, G-, and C-sites increases steadily with reaction time, while the T-cleavage observed takes place primarily at the very beginning of the solvolysis.