Dissident remarks on the origin of optical activity. An intrabiological explanation

The attempts to explain the origin of natural optical activity through external, extrabiological, agents, typically ionizing rays, i.e. as a purely incidental effect without deeper significance, have failed and should be abandoned. An alternative, intrabiological, Darwinian, explanation seeks to explain optical activity as a necessary phenomenon in early evolution. This explanation is based on the idea that organisms with the existing stereospecificity initially happened, by chance, to be more efficient than organisms with the opposite stereospecificity on independent grounds that have nothing to do with their stereospecificity. If cells based on L aminoacids are called L cells, it is to be assumed that cosmic bodies carrying L cells are about equally frequent as those carrying D cells.     

Chirality-independent protein-protein recognition between transmembrane domains in vivo

Stereospecificity in protein-protein recognition and docking is an unchallenged dogma. Soluble proteins provide the main source of evidence for stereospecificity. In contrast, within the membrane little is known about the role of stereospecificity in the recognition process. Here, we have reassessed the stereospecificity of protein-protein recognition by testing whether it holds true for the well-defined glycophorin A (GPA) transmembrane domain in vivo. We found that the all-D amino acid GPA transmembrane domain and two all-D mutants specifically associated with an all-L GPA transmembrane domain, within the membrane milieu of Escherichia coli. Molecular dynamics techniques reveal a possible structural explanation to the observed interaction between all-D and all-L transmembrane domains. A very strong correlation was found between amino acid residues at the interface of both the all-L homodimer structure and the mixed L/D heterodimer structure, suggesting that the original interactions are conserved. The results suggest that GPA helix-helix recognition within the membrane is chirality-independent.     

Inositol signaling and plant growth

Living organisms have evolved to contain a wide variety of receptors and signaling pathways that are essential for their survival in a changing environment. Of these, the phosphoinositide pathway is one of the best conserved. The ability of the phosphoinositides to permeate both hydrophobic and hydrophilic environments, and their diverse functions within cells have contributed to their persistence in nature. In eukaryotes, phosphoinositides are essential metabolites as well as labile messengers that regulate cellular physiology while traveling within and between cells. The stereospecificity of the six hydroxyls on the inositol ring provides the basis for the functional diversity of the phosphorylated isomers that, in turn, generate a selective means of intracellular and intercellular communication for coordinating cell growth. Although such complexity presents a difficult challenge for bench scientists, it is ideal for the regulation of cellular functions in living organisms.     

Darwin, historical biogeography, and the importance of overcoming binary opposites

It is well known that Darwin and Wallace came to discover the phenomenon of evolution through a historical approach to the geographical distribution of organisms. Before Darwin, evolution was a mere speculation that could be invoked to explain some facts. Darwin's biogeographical argument for evolution is based largely on three main explanatory hypotheses. The first is that the geographical distribution of organisms is historically informative. The second hypothesis is that long-distance dispersal over barriers is one main force (extinction is the other) that modifies the distribution of organisms. The third of Darwin's biogeographical hypotheses is that the factors that shape the distribution of organisms are mainly historical (large, often global and long temporal scales) rather than ecological (small spatial and short temporal scales). From the time of Darwin until now, a wide spectrum of biogeographical schools have provided new insights that challenge the central role of space, dispersal and history as the main explanatory hypotheses for the distribution of organisms, generating three binary opposites: (1) the spatial dimension of evolution: geographical distribution of organisms as historically informative vs. historically uninformative; (2) the processes that modify the geographical distribution of organisms: dispersal vs. vicariance; and (3) the explanation of geographical distribution: history vs. ecology. We analyse these three binary opposites to show that the components of each are complementary rather than antagonistic approaches to the study of biogeography.     

A proposal for using the ensemble approach to understand genetic regulatory networks

Understanding the genetic regulatory network comprising genes, RNA, proteins and the network connections and dynamical control rules among them, is a major task of contemporary systems biology. I focus here on the use of the ensemble approach to find one or more well-defined ensembles of model networks whose statistical features match those of real cells and organisms. Such ensembles should help explain and predict features of real cells and organisms. More precisely, an ensemble of model networks is defined by constraints on the "wiring diagram" of regulatory interactions, and the "rules" governing the dynamical behavior of regulated components of the network. The ensemble consists of all networks consistent with those constraints. Here I discuss ensembles of random Boolean networks, scale free Boolean networks, "medusa" Boolean networks, continuous variable networks, and others. For each ensemble, M statistical features, such as the size distribution of avalanches in gene activity changes unleashed by transiently altering the activity of a single gene, the distribution in distances between gene activities on different cell types, and others, are measured. This creates an M-dimensional space, where each ensemble corresponds to a cluster of points or distributions. Using current and future experimental techniques, such as gene arrays, these M properties are to be measured for real cells and organisms, again yielding a cluster of points or distributions in the M-dimensional space. The procedure then finds ensembles close to those of real cells and organisms, and hill climbs to attempt to match the observed M features. Thus obtains one or more ensembles that should predict and explain many features of the regulatory networks in cells and organisms.     

Peptide transport by germinating barley embryos: Uptake of physiological di- and oligopeptides

The uptake of a variety of physiological di- and oligopeptides by germinating barley (Hordeum vulgare L.) embryos is described. Peptides as large as pentaalanine can be absorbed. Evidence is presented suggesting the peptides are absorbed intact and subsequently undergo rapid intracellular hydrolysis. Uptake shows stereospecificity. The transport of peptides is generally faster than the transport of amino acids, making it likely that the former could play an important role in the mobilization of the protein storage reserves during germination. The peptide transport system in barley is compared with similar systems from other groups of organisms.Abbreviations Gly-sar glycylsarcosine - Gly-sar-sar glycylsarcosylsarcosine - Gly-sar-sar-sar Glycylsarcosylsarcosylsarcosine     

Detection without deflection? A hypothesis for direct sensing of sound pressure by hair cells

It is widely thought that organisms detect sound by sensing the deflection of hair-like projections, the stereocilia, at the apex of hair cells. In the case of mammals, the standard interpretation is that hair cells in the cochlea respond to deflection of stereocilia induced by motion generated by a hydrodynamic travelling wave. But in the light of persistent anomalies, an alternative hypothesis seems to have some merit: that sensing cells (in particular the outer hair cells) may, at least at low intensities, be reacting to a different stimulus — the rapid pressure wave that sweeps through the cochlear fluids at the speed of sound in water. This would explain why fast responses are sometimes seen before the peak of the travelling wave. Yet how could cells directly sense fluid pressure? Here, a model is constructed of the outer hair cell as a pressure vessel able to sense pressure variations across its cuticular pore, and this ‘fontanelle’ model, based on the sensing action of the basal body at this compliant spot, could explain the observed anomalies. Moreover, the fontanelle model can be applied to a wide range of other organisms, suggesting that direct pressure detection is a general mode of sensing complementary to stereociliar displacement.     

Natural selection and the conditions for existence: representational vs. conditional teleology in biological explanation

Human intentional action, including the design and use of artifacts, involves the prior mental representation of the goal (end) and the means to achieve that goal. This representation is part of the efficient cause of the action, and thus can be used to explain both the action and the achievement of the end. This is intentional teleological explanation. More generally, teleological explanation that depends on the real existence of a representation of the goal (and the means to achieve it) can be called representational teleological explanation. Such explanations in biology can involve both external representations (e.g., ideas in the mind of God) and internal representations (souls, vital powers, entelechies, developmental programs, etc.). However, another type of explanation of intentional action (or any other process) is possible. Given that an action achieving a result occurs, the action can be explained as fulfilling the necessary conditions (means) for that result (end), and, reciprocally, the result explained by the occurrence of those necessary conditions. This is conditional teleological explanation. For organisms, natural selection is often understood metaphorically as the designer, intentionally constructing them for certain ends. Unfortunately, this metaphor is often taken rather too literally, because it has been difficult to conceive of another way to relate natural selection to the process of evolution. I argue that combining a conditional teleological explanation of organisms and of evolution provides such an alternative. This conditional teleology can be grounded in existence or survival. Given that an organism exists, we can explain its existence by the occurrence of the necessary conditions for that existence. This principle of the 'conditions for existence' was introduced by Georges Cuvier in 1800, and provides a valid, conditional teleological method for explaining organismal structure and behavior. From an evolutionary perspective, the conditions for existence are the range of boundary conditions within which the evolutionary process must occur. Moreover, evolutionary change itself can be subjected to conditional teleological explanation, because natural selection theory is primarily a theory about the relation between the conditions for the existence of organisms and the conditions for the existence of traits in populations. I show that failure to distinguish representational from conditional teleological explanation has confused previous attempts to clarify the relation of teleology to biology.     

The stereospecificity of the reduction of nitrate by reduced nicotinamide-adenine dinucleotides catalysed by Candida utilis preparations.

The reduction of nitrate by reduced nicotinamide-adenine dinucleotides, catalysed by extract of Candida utilis, exhibits an apparent high degree of stereospecificity for the 'B' methylene hydrogen atom of NADPH and mixed stereospecificity for the methylene hydrogen atoms of NADH. Purified nitrate reductase, on the other hand, exhibits 'A' stereospecificity for NADH and NADPH. The apparent switch of stereospecificity from the 'B' to the 'A' side of NADPH, which occurs after purification of the enzyme, is partly explained by the fact that in crude extracts nitrate is reduced completely to ammonia. Nitrite does not accumulate but is reduced to ammonia by nitrite dehydrogenase, which is 'B'-specific, so that up to 75% of hydrogen removed from NADPH during the reduction of nitrate could occur from the 'B' side. A further increase in the removal of hydrogen from the 'B' side of NADPH could be the kinetic isotope effect that is observed when ['A'-3H]NADPH is the reductant, the H--C bond being cleaved 2.3 times faster than the 3H--C bond. The mixed stereospecificity observed with NADH has been traced to an uncharacterized enzyme that catalyses a 'B'-specific exchange between NAD+ and NADH. This reaction is discussed in relation to the possibility that it may explain other cases of apparent mixed stereospecificity that have been reported.     

Properties of a mini 9R-lipoxygenase from Nostoc sp. PCC 7120 and its mutant forms

Lipoxygenases (LOXs) consist of a class of enzymes that catalyze the regio- and stereospecific dioxygenation of polyunsaturated fatty acids. Current reports propose that a conserved glycine residue in the active site of R-lipoxygenases and an alanine residue at the corresponding position in S-lipoxygenases play a crucial role in determining the stereochemistry of the product. Recently, a bifunctional lipoxygenase with a linoleate diol synthase activity from Nostoc sp. PCC7120 with R stereospecificity and the so far unique feature of carrying an alanine instead of the conserved glycine in the position of the sequence determinant for chiral specificity was identified. The recombinant carboxy-terminal domain was purified after expression in Escherichia coli. The ability of the enzyme to use linoleic acid esterified to a bulky phosphatidylcholine molecule as a substrate suggested a tail-fist binding orientation of the substrate. Site directed mutagenesis of the alanine to glycine did not cause alterations in the stereospecificity of the products, while mutation of the alanine to valine or isoleucine modified both regio- and enantioselectivity of the enzyme. Kinetic measurements revealed that substitution of Ala by Gly or Val did not significantly influence the reaction characteristics, while the A162I mutant showed a reduced vmax. Based on the mutagenesis data obtained, we suggest that the existing model for stereocontrol of the lipoxygenase reaction may be expanded to include enzymes that seem to have in general a smaller amino acid in R and a bulkier one in S lipoxygenases at the position that controls stereospecificity.     

Poly(ADP-ribose) polymerase: A guardian of the genome that facilitates DNA repair by protecting against DNA recombination

We have studied the clonogenic survival response to X-rays and MNNG of V79 Chinese hamster cells and two derivative cell lines, ADPRT54 and ADPRT351, deficient in poly(ADP-ribose) polymerase (PARP) activity. Under conditions of exponential growth, both PARP-deficient cell lines are hypersensitive to X-rays and MNNG compared to their parental V79 cells. In contrast, under growth-arrested, confluent conditions, V79 and PARP-deficient cells become similarly sensitive to X-rays and MNNG suggesting that PARP may be involved in the repair of X-ray or MNNG-induced DNA damage in logarithmically growing cells but not in growth-arrested confluent cells. This suggestion, however, creates a dilemma as to how PARP can be involved in DNA repair in only selected growth phases while it is functionally active in all growth phases. To explain these paradoxical results and resolve this dilemma we propose a hypothesis based on the consistent observation that inhibition of PARP results in a significant increase in sister chromatid exchange (SCEs). Thus, we propose that PARP is a guardian of the genome that protects against DNA recombination. We have extended this theme to provide an explanation for our results and the studies done by many others.     

Organisms as natural purposes: the contemporary evolutionary perspective

Kant's conception of organisms as natural purposes raises a challenge to the adequacy of mechanistic explanation in biology. Certain features of organisms appear to be inexplicable by appeal to mechanical law alone. Some biological phenomena, it seems, can only be accounted for teleologically. Contemporary evolutionary biology has by and large ignored this challenge. It is widely held that Darwin's theory of natural selection gives us an adequate, wholly mechanical account of the nature of organisms. In contemporary biology, the category of the organism plays virtually no explanatory role. Contemporary evolutionary biology is a science of sub-organismal entities-replicators. I argue that recent advances in developmental biology demonstrate the inadequacy of sub-organismal mechanism. The category of the organism, construed as a 'natural purpose' should play an ineliminable role in explaining ontogenetic development and adaptive evolution. According to Kant the natural purposiveness of organisms cannot be demonstrated to be an objective principle in nature, nor can purposiveness figure in genuine explain. I attempt to argue, by appeal to recent work on self-organization, that the purposiveness of organisms is a natural phenomenon, and, by appeal to the apparatus of invariance explanation, that biological purposiveness provides genuine, ineliminable biological explanations.     

COEXISTENCE OF EVOLVING BACTERIA STABILIZED BY A SHARED BLACK QUEEN FUNCTION

The Black Queen Hypothesis (BQH) was originally proposed to explain the dependence of some marine bacteria on helper organisms for protection from hydrogen peroxide (HOOH). The BQH predicts that selection for the evolutionary loss of leaky functions from individuals can produce commensal or mutualistic interactions. We demonstrated the leakiness of HOOH detoxification by complementing a HOOH‐sensitive Escherichia coli mutant with a plasmid‐encoded HOOH‐detoxifying enzyme, KatG, and then evolving populations founded by this strain in two environments. When HOOH was absent, plasmid‐carrying cells were outcompeted by plasmid‐free segregants, reflecting the high cost of KatG expression. However, plasmid‐carrying and plasmid‐free cells coexisted for at least 1200 generations in three replicate populations evolved in the presence of HOOH, although their relative proportions fluctuated as beneficial mutations arose in one type or the other. Evolved plasmid‐bearing cells reduced the cost of plasmid carriage even as they increased the rate of HOOH removal relative to the ancestor. Meanwhile, plasmid‐free cells remained dependent on HOOH detoxification by the plasmid‐bearing cells. These results demonstrate that partitioning of a Black Queen function can enable the stable coexistence of very similar organisms, even in this most restrictive case where the two types are competing for a single resource.     

Do regulatory antibodies offer an alternative mechanism to explain the hygiene hypothesis?

The 'hygiene hypothesis', or lack of microbial and parasite exposure during early life, is postulated as an explanation for the recent increase in autoimmune and allergic diseases in developed countries. The favored mechanism is that microbial and parasite-derived products interact directly with pathogen recognition receptors to subvert proinflammatory signaling via T regulatory cells, thereby inducing anti-inflammatory effects and control of autoimmune disease. Parasites, such as helminths, are considered to have a major role in the induction of immune regulatory mechanisms among children living in developing countries. Invoking Occam's razor, we believe we can select an alternative mechanism to explain the hygiene hypothesis, based on antibody-mediated inhibition of immune responses that may more simply explain the available evidence.     

Structural and biochemical analyses of regio- and stereospecificities observed in a type II polyketide ketoreductase

Type II polyketides include antibiotics such as tetracycline and chemotherapeutics such as daunorubicin. Type II polyketides are biosynthesized by the type II polyketide synthase (PKS) that consists of 5-10 stand-alone domains. In many type II PKSs, the type II ketoreductase (KR) specifically reduces the C9-carbonyl group. How the type II KR achieves such a high regiospecificity and the nature of stereospecificity are not well understood. Sequence alignment of KRs led to a hypothesis that a well-conserved 94-XGG-96 motif may be involved in controlling the stereochemistry. The stereospecificity of single-, double-, and triple-mutant combinations of P94L, G95D, and G96D were analyzed in vitro and in vivo for the actinorhodin KR (actKR). The P94L mutation is sufficient to change the stereospecificity of actKR. Binary and ternary crystal structures of both wild-type and P94L actKR were determined. Together with assay results, docking simulations, and cocrystal structures, a model for stereochemical control is presented herein that elucidates how type II polyketides are introduced into the substrate pocket such that the C9-carbonyl can be reduced with high regio- and stereospecificities. The molecular features of actKR important for regio- and stereospecificities can potentially be applied in biosynthesizing new polyketides via protein engineering that rationally controls polyketide keto reduction.     

Evaluation of alternative hypotheses to explain temperature-induced life history shifts in Daphnia

Negative correlations between environmental temperature andbody size are widespread in planktonic organisms, and ectothermsgenerally, but remain poorly understood. Here we evaluate experimentallytwo alternative hypotheses suggested to explain life historyshifts induced by raised temperature using parthenogenetic clonesfrom two Daphnia species. Explanation 1 proposes that the lifehistory shifts could be adaptive if increased temperature isused as an indirect cue to indicate increased risk from size-selectivepredators. Explanation 2 proposes that at larger body size energybecomes more limiting as temperature increases because of aless favourable assimilation: metabolism balance. In a factoriallaboratory experiment we examine the effects of three rearingtemperatures on the growth and reproductive traits of Daphniaraised in water with fish kairomone, Chaoborus kairomone, orin uncontaminated water. None of the three predictions of explanation1 were met by the data. In both D. pulex and D. curvirostris,and some other published studies, data suggested that at largerbody sizes the sum of growth and reproduction was lower at hightemperature, supporting our prediction from explanation 2. However,we propose a novel third explanation based on new evidence oftemperature-dependence in both reproductive effort and costin D. pulex.     

Enzymatic synthesis of electroconductive biocomposites based on DNA and optically active polyaniline

Electroconductive interpolymer polyaniline complexes are synthesized on the DNA matrix, using the method of oxidative polymerization of aniline with two different biocatalyzers: horseradish root peroxidase and micropiroxidase-11 biomimetic. The spectral characteristics and morphology of the acquired biocomposites have been studied. The stereospecificity of the acquired samples of interpolymer complexes is shown, depending on the biocatalyzers used. The results acquired indicate the important role of a biocatalyzer in the formation of the twist direction of an electroconductive polymer spiral on the DNA matrix; i.e., the optical activity of the polymer samples acquired is apparently associated with the biocatalyzer properties.     

Enzymatic synthesis of electroconductive biocomposites based on DNA and optically active polyaniline

Electroconductive interpolymer polyaniline complexes are synthesized on the DNA matrix, using the method of oxidative polymerization of aniline with two different biocatalyzers: horseradish root peroxidase and micropiroxidase-11 biomimetic. The spectral characteristics and morphology of the acquired biocomposites have been studied. The stereospecificity of the acquired samples of interpolymer complexes is shown, depending on the biocatalyzers used. The results acquired indicate the important role of a biocatalyzer in the formation of the twist direction of an electroconductive polymer spiral on the DNA matrix; i.e., the optical activity of the polymer samples acquired is apparently associated with the biocatalyzer properties.     

Stereospecificity of NADH-ferricyanide reductase is a convenient marker for the endoplasmic reticulum of plant cells

The stereospecificity of NADH-ferricyanide reductase and NADH-cytochrome c reductase in the endoplasmic reticulum (ER) for the α-hydrogen on the nicotinamide ring is presented as a very sensitive and convenient assay to detect ER contamination in preparations of membranes lacking α-specific NADH-acceptor reductase, such as the plasma membrane and the tonoplast. The experimental details of the assay are given and the limitations explored (time-course, amount of protein, possible side reactions, speed, reproducibility, etc.). The NADH-ferricyanide reductase activity of plasma membranes from spinach and sugarbeet leaf was completely β-specific and always showed a latency (increase upon addition of Triton X-100), whereas the α-specificity in the ER was non-latent. This is consistent with the presence of mainly right-side-out vesicles in preparations of plasma membranes with the binding site for NADH and ferricyanide on the inner, cytoplasmic surface. In contrast, right-side-out ER vesicles have the binding site on the outer, cytoplasmic surface. The addition of as little as 1% of the α-specific ER (on an NADH-ferricyanide activity basis) to the spinach leaf plasma membrane could be detected with the stereospecificity assay. Wheat root plasma membrane showed some α-specificity (in addition to β-specificity) which was probably due to ER contamination since the activity was non-latent. The stereospecificity assay is also shown to be useful in monitoring the separation of tonoplast vesicles from ER vesicles by countercurrent distribution of a light microsomal fraction. It follows that the NADH-acceptor reductase activities in preparations of plasma membrane and tonoplast are due to distinct enzymes characteristic for those membranes.     

Distribution of bacterial growth activity in flow-chamber biofilms.

In microbial communities such as those found in biofilms, individual organisms most often display heterogeneous behavior with respect to their metabolic activity, growth status, gene expression pattern, etc. In that context, a novel reporter system for monitoring of cellular growth activity has been designed. It comprises a transposon cassette carrying fusions between the growth rate-regulated Escherichia coli rrnBP1 promoter and different variant gfp genes. It is shown that the P1 promoter is regulated in the same way in E. coli and Pseudomonas putida, making it useful for monitoring of growth activity in organisms outside the group of enteric bacteria. Construction of fusions to genes encoding unstable Gfp proteins opened up the possibility of the monitoring of rates of rRNA synthesis and, in this way, allowing on-line determination of the distribution of growth activity in a complex community. With the use of these reporter tools, it is demonstrated that individual cells of a toluene-degrading P. putida strain growing in a benzyl alcohol-supplemented biofilm have different levels of growth activity which develop as the biofilm gets older. Cells that eventually grow very slowly or not at all may be stimulated to restart growth if provided with a more easily metabolizable carbon source. Thus, the dynamics of biofilm growth activity has been tracked to the level of individual cells, cell clusters, and microcolonies.