Stages of life: A new metaphysics of conceptionism

When a human being comes into existence is crucial in bioethics. Conceptionism is the view that a human being comes into existence at conception. The twinning argument is an influential objection to this view. All versions of the twinning argument rely on a metaphysics of material objects, namely, endurantism. Given this, a strategy for defending conceptionism against the twinning argument is to deny endurantism and adopt an alternative metaphysics of material objects. A version of this strategy which has been debated in this journal is to adopt perdurantism, or the ‘multiple occupancy view’, on which monozygotic twins share the zygote region as a temporal part. We present a novel version of this strategy: conceptionists can evade the twinning argument by adopting an exdurantist metaphysics of material objects. We suggest reasons for thinking that this is a plausible and, indeed, preferable way for conceptionists to avoid the twinning argument.     

Geometric characterization of cell membrane of mouse oocytes for ICSI

Intracytoplasmic sperm injection (ICSI) is a broadly utilized assisted reproductive technology. A number of technologies for this procedure have evolved lately, such as the most commonly utilized piezo-assisted ICSI technique (P-ICSI). An important problem with this technique, however, is that it requires a small amount of mercury to stabilize the tip of the penetration micropipette. A completely different and mercury-free injection technology, called the rotationally oscillating drill (Ros-Drill) (RD-ICSI), was recently developed. It uses microprocessor-controlled rotational oscillations of a spiked micropipette after the pipette deforms the membrane to a certain tension level. Inappropriate selection of this initiation instant typically results in cell damage, which ultimately leads to unsuccessful ICSI. During earlier manual clinical tests of Ros-Drill, the technicians' expertise determined this instant in an ad hoc fashion. In this paper, we introduce a computer-vision-based tool to mechanize this process with the objective of maintaining the repeatability and introducing potential automation. Computer images are used for monitoring the membrane deformations and curvature variations as the basis for decision making. The main contribution of this paper is in the specifics of the computer logic to perform the monitoring. These new tools are expected to provide a practicable means for automating the Ros-Drill-assisted ICSI operation.     

The fallacy of the Principle of Procreative Beneficence

The claim that we have a moral obligation, where a choice can be made, to bring to birth the 'best' child possible, has been highly controversial for a number of decades. More recently Savulescu has labelled this claim the Principle of Procreative Beneficence. It has been argued that this Principle is problematic in both its reasoning and its implications, most notably in that it places lower moral value on the disabled. Relentless criticism of this proposed moral obligation, however, has been unable, thus far, to discredit this Principle convincingly and as a result its influence shows no sign of abating. I will argue that while criticisms of the implications and detail of the reasoning behind it are well founded, they are unlikely to produce an argument that will ultimately discredit the obligation that the Principle of Procreative Beneficence represents. I believe that what is needed finally and convincingly to reveal the fallacy of this Principle is a critique of its ultimate theoretical foundation, the notion of impersonal harm. In this paper I argue that while the notion of impersonal harm is intuitively very appealing, its plausibility is based entirely on this intuitive appeal and not on sound moral reasoning. I show that there is another plausible explanation for our intuitive response and I believe that this, in conjunction with the other theoretical criticisms that I and others have levelled at this Principle, shows that the Principle of Procreative Beneficence should be rejected.     

Ultimate Use of Two-Photon Fluorescence Microscopy to Map Orientational Behavior of Fluorophores

The orientational distribution of fluorophores is an important reporter of the structure and function of their molecular environment. Although this distribution affects the fluorescence signal under polarized-light excitation, its retrieval is limited to a small number of parameters. Because of this limitation, the need for a geometrical model (cone, Gaussian, etc.) to effect such retrieval is often invoked. In this work, using a symmetry decomposition of the distribution function of the fluorescent molecules, we show that polarized two-photon fluorescence based on tunable linear dichroism allows for the retrieval of this distribution with reasonable fidelity and without invoking either an a priori knowledge of the system to be investigated or a geometrical model. We establish the optimal level of detail to which any distribution can be retrieved using this technique. As applied to artificial lipid vesicles and cell membranes, the ability of this method to identify and quantify specific structural properties that complement the more traditional molecular-order information is demonstrated. In particular, we analyze situations that give access to the sharpness of the angular constraint, and to the evidence of an isotropic population of fluorophores within the focal volume encompassing the membrane. Moreover, this technique has the potential to address complex situations such as the distribution of a tethered membrane protein label in an ordered environment.     

Quantifying the degree of self-nestedness of trees: application to the structural analysis of plants

In this paper, we are interested in the problem of approximating trees by trees with a particular self-nested structure. Self-nested trees are such that all their subtrees of a given height are isomorphic. We show that these trees present remarkable compression properties, with high compression rates. In order to measure how far a tree is from being a self-nested tree, we then study how to quantify the degree of self-nestedness of any tree. For this, we define a measure of the self-nestedness of a tree by constructing a self-nested tree that minimizes the distance of the original tree to the set of self-nested trees that embed the initial tree. We show that this measure can be computed in polynomial time and depict the corresponding algorithm. The distance to this nearest embedding self-nested tree (NEST) is then used to define compression coefficients that reflect the compressibility of a tree. To illustrate this approach, we then apply these notions to the analysis of plant branching structures. Based on a database of simulated theoretical plants in which different levels of noise have been introduced, we evaluate the method and show that the NESTs of such branching structures restore partly or completely the original, noiseless, branching structures. The whole approach is then applied to the analysis of a real plant (a rice panicle) whose topological structure was completely measured. We show that the NEST of this plant may be interpreted in biological terms and may be used to reveal important aspects of the plant growth.     

Genetic identification of hybrid camelids

North American zoos in 1984 had the first opportunity in many years to obtain South American camelids after a long embargo on imports. The Rio Grande Zoo in Albuquerque, New Mexico, purchased two alpacas and one presumptive llama during this period. The llama, however, appeared to be phenotypically intermediate between a llama and an alpaca. In an attempt to ascertain the identity of this animal, it and purebred individuals of llama and alpaca were compared at 22 presumptive genic loci using starch-gel electrophoresis. Genic differences between llama and alpaca suggest this animal to be a hybrid. If further tests prove consistent with the findings of this study, this technique will provide a simple assay using easily obtained blood for identifying llama and alpaca. The use of genetic management techniques such as this in zoos holds great potential for helping to preserve pure breeding lines of closely related interfertile animals.     

Role of a solvent-exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo-beta-lactamase

Numerous X-ray crystal structures of the metallo-beta-lactamase from Bacteroides fragilis and related organisms show a beta-hairpin loop immediately adjacent to the active-site zinc atom(s). Both crystallographic and NMR information show that the end of this beta-hairpin loop, which contains a solvent exposed tryptophan residue, Trp49, is highly flexible in the absence of substrates or other ligands, giving rise in some of the X-ray structures to a lack of observable electron density in this region. We report an investigation of the role of this mobile, solvent-exposed tryptophan using site-directed mutagenesis, steady state kinetics measurements and characterization by NMR. Trp49 appears to have a role both in substrate binding and in promotion of catalysis. Substitution of this residue with a number of different side chains indicates that the binding interaction depends on the bulky hydrophobic and aromatic nature of the indole ring, which can provide relatively non-specific interactions with a variety of antibiotic substrates. In this way, the tryptophan at this position provides a large degree of the breadth of substrate specificity for the metallo-beta-lactamase. Previous studies established that the antibiotic binding site was sufficiently plastic that the derivatization of existing antibiotics is unlikely to result in the successful treatment of bacterial infections incorporating this resistance element. Rather, a more productive approach may be to design therapeutics directed towards this solvent-exposed tryptophan residue.     

Ultimate Use of Two-Photon Fluorescence Microscopy to Map Orientational Behavior of Fluorophores

The orientational distribution of fluorophores is an important reporter of the structure and function of their molecular environment. Although this distribution affects the fluorescence signal under polarized-light excitation, its retrieval is limited to a small number of parameters. Because of this limitation, the need for a geometrical model (cone, Gaussian, etc.) to effect such retrieval is often invoked. In this work, using a symmetry decomposition of the distribution function of the fluorescent molecules, we show that polarized two-photon fluorescence based on tunable linear dichroism allows for the retrieval of this distribution with reasonable fidelity and without invoking either an a priori knowledge of the system to be investigated or a geometrical model. We establish the optimal level of detail to which any distribution can be retrieved using this technique. As applied to artificial lipid vesicles and cell membranes, the ability of this method to identify and quantify specific structural properties that complement the more traditional molecular-order information is demonstrated. In particular, we analyze situations that give access to the sharpness of the angular constraint, and to the evidence of an isotropic population of fluorophores within the focal volume encompassing the membrane. Moreover, this technique has the potential to address complex situations such as the distribution of a tethered membrane protein label in an ordered environment.     

Williams's theory of the evolution of senescence: still useful at fifty

George Williams indicated that he would not expect senescence to evolve in organisms that lack a distinction between germ line and soma. Escherichia coli--long assumed to lack even a hint of this distinction--is now known to senesce, posing what would seem to be a challenge to Williams's well-known theory of the evolution of senescence. However, in this review, I will show that cell division in E. coli produces a degree of germ-soma modularity sufficient to generate age structure and antagonistic pleiotropic effects, thereby satisfying the requirements of Williams's theory. From this perspective, senescence in E. coli is supportive and points the way to a better understanding of the pleiotropies that connect adaptive complexity and senescence. Sexual reproduction is but one of the complex adaptations illuminated by this approach.     

Calpain 1 binding capacities of the N1-line region of titin are significantly enhanced by physiological concentrations of calcium

Calpain 1, an ubiquitous well-known calcium-dependent intracellular protease, was recently shown to bind tightly to the proximal end of the I-band titin segment in a calcium-dependent manner [Raynaud et al. (2005) FEBS J. 272, 2578-2590]. In the present work we identified the titin Ig-domain of concern by this interaction and the role of calcium in this interaction using a recombinant fragment of titin spanning the I2-I6 region and its subfragments. The heterodimeric form of calpain 1 binds to this titin fragment with a very high affinity ( K d = 5.1 +/- 0.2 x 10 (-7) M) at much lower calcium levels than those saturating the high-affinity binding sites of the peptidase ( K d = 25 microM). Investigation of this interaction with I2-I6 subfragments clearly showed that the dimeric form of calpain 1 binds exclusively to the Ig-domain I4 of titin with an affinity similar to that of the whole I2-I6 segment. As for the I2-I6 fragment, this interaction is calcium regulated. Calcium was shown to bind tightly to titin ( K d = 1.9 x 10 (-7) M), causing an oligomerization of the titin segment. At physiological calcium concentration (10 (-6) to 10 (-8) M), the prevailing form of the titin fragment is a trimer, suggesting that calpain 1 binds to this titin structure. From the present findings, it was concluded that calcium binding to titin increased the amount of bound calpain 1 (up to 40% of the total calpain 1) and that this bound calpain 1 might constitute a reservoir for this peptidase. In this context, we proposed a schematic diagram of this series of calcium-dependent events with the inherent unanswered questions. These events are probably under a complex regulation involving undoubtedly different yet unidentified proteins.     

An Atg13 protein-mediated self-association of the Atg1 protein kinase is important for the induction of autophagy

Autophagy pathways in eukaryotic cells mediate the turnover of a diverse set of cytoplasmic components, including damaged organelles and abnormal protein aggregates. Autophagy-mediated degradation is highly regulated, and defects in these pathways have been linked to a number of human disorders. The Atg1 protein kinase appears to be a key site of this control and is targeted by multiple signaling pathways to ensure the appropriate autophagic response to changing environmental conditions. Despite the importance of this kinase, relatively little is known about the molecular details of Atg1 activation. In this study we show that Atg13, an evolutionarily conserved regulator of Atg1, promotes the formation of a specific Atg1 self-interaction in the budding yeast, Saccharomyces cerevisiae. The appearance of this Atg1-Atg1 complex is correlated with the induction of autophagy, and conditions that disrupt this complex result in diminished levels of both autophagy and Atg1 kinase activity. Moreover, the addition of a heterologous dimerization domain to Atg1 resulted in elevated kinase activity both in vivo and in vitro. The formation of this complex appears to be an important prerequisite for the subsequent autophosphorylation of Thr-226 in the Atg1 activation loop. Previous work indicates that this modification is necessary and perhaps sufficient for Atg1 kinase activity. Interestingly, this Atg1 self-association does not require Atg17, suggesting that this second conserved regulator might activate Atg1 in a manner mechanistically distinct from that of Atg13. In all, this work suggests a model whereby this self-association stimulates the autophosphorylation of Atg1 within its activation loop.     

一种降刺猬内源性脂蛋白(a)反义靶向连接物

通过酶联免疫法测定了刺猬体内脂蛋白（ａ）的含量,从中选出一些脂蛋白（ａ）水平较高的刺猬,研究脱唾液酸糖蛋白－多聚赖氨酸－反义载脂蛋白（ａ）ＲＮＡ连接物对刺猬内源性脂蛋白（ａ）的降低作用．结果表明,该连接物可明显降低刺猬体内脂蛋白（ａ）的水平,而脱唾液酸糖蛋白－多聚赖氨酸－正义载脂蛋白（ａ）ＲＮＡ连接物对刺猬体内脂蛋白（ａ）无降低作用,无脱唾液酸糖蛋白靶向的反义载脂蛋白（ａ）ＲＮＡ寡核苷酸对刺猬体内脂蛋白（ａ）的降低作用明显低于有脱唾液酸糖蛋白靶向的连接物．连接物几乎不影响刺猬体内的纤维蛋白溶酶原的活性,连接物对刺猬脂蛋白（ａ）的降低作用至少可持续１６ｈ．     

Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition

A theory of equilibrium denaturation of proteins is suggested. According to this theory, a cornerstone of protein denaturation is disruption of tight packing of side chains in protein core. Investigation of this disruption is the object of this paper. It is shown that this disruption is an "all-or-none" transition (independent of how compact is the denatured state of a protein and independent of the protein-solvent interactions) because expansion of a globule must exceed some threshold to release rotational isomerization of side chains. Smaller expansion cannot produce entropy compensation of nonbonded energy loss; this is the origin of a free-energy barrier (transition state) between the native and denatured states. The density of the transition state is so high that the solvent cannot penetrate into protein in this state. The results obtained in this paper make it possible to present in the following paper a general phase diagram of protein molecule in solution.     

Prospects for the involvement of cancer stem cells in the pathogenesis of osteosarcoma

Osteosarcoma (OS) is one of the most common bone tumors in children and adolescents that cause a high rate of mortality in this age group and tends to be metastatic, in spite of chemotherapy and surgery. The main reason for this can be returned to a small group of malignant cells called cancer stem cells (CSCs). OS-CSCs play a key role in the resistance to treatment and relapse and metastasis through self-renewal and differentiation abilities. In this review, we intend to go through the different aspects of this malignant disease, including the cancer stem cell-phenotype, methods for isolating CSCs, signaling pathways, and molecular markers in this disease, and drugs showing resistance in treatment efforts of OS.     

Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae

Understanding the regulation of gene expression requires the identification of cis -acting control elements that modulate gene function. The recent availability of complete genome sequences and profiles of mRNA expression has facilitated the development and utilization of computational methods to identify discrete regulatory elements. We have developed an oligomer counting method that identifies sequences that occur significantly more often in a group of interest relative to other genes in the genome. The use of a second parameter, which measures the frequency of oligomers within the group of interest, allows the detection of false positive signals caused by very infrequent oligomers that would otherwise appear as significant. Applying this method to gene groups that have a common expression pattern or shared function should identify oligomers that comprise cis -acting control elements. As a test of this method, we applied this approach to a set of intron-containing yeast genes, where we easily identified the known splicing signals as control elements. We have used this training set to examine how this method is affected by the length of the oligomer examined, as well as the size and composition of the gene group. These simulations allowed us to identify rules for selecting groups of genes to analyze. Finally, application of this method to nuclear genes encoding proteins targeted to the mitochondria identified a new putative cis -acting sequence in the 3'-untranslated region of this family of genes, which may play a role in mRNA localization or the regulation of mRNA stability or translation.     

Implication of an unfavorable residue (Thr346) in intrinsic flexibility of firefly luciferase

In order to better understand the functional role of an unusual residue (Thr346) of firefly luciferase mutagenesis at this residue was performed. Firefly luciferase, catalyzes the bioluminescence reaction and is an excellent tool as a reporter in nano-system biology studies. Nonetheless, the enzyme rapidly loses its activity at temperatures above 30°C and this leads to reduced sensitivity and precision in analytical applications. Residue Thr346 in a connecting loop (341-348) of firefly luciferase is located in a disallowed region of Ramachandran plot. In this study, we have substituted this residue (T346) with anomalous dihedral angles with Val, Gly and Pro to clarify the role of this residue in structure and function of the enzyme using site-directed mutagenesis. Substitution of this unfavorable residue (T346) with atypical dihedral angles (ψ, φ) with other residues brought about an increase of thermostability and decrease of specific activity. Structural and functional properties of the mutants were analyzed using different spectroscopic methods. It seems that this residue is a critically conserved residue to support the functional flexibility for a fast kinetic bioluminescence reaction at the expense of lower stability.     

A thermodynamic theory of evolution

As a closed thermodynamic system subject to an essentially constant free energy gradient, the biosphere must evolve toward a stationary state of maximum structuring and minimum dissipation with respect to this applied gradient. Since biological evolution occurs opportunistically through chance and selection, rather than as a direct response to the free energy gradient, the conformance of this phase of evolution with thermodynamics requires that natural selection, and the particular adaptive strategies employed by species of organisms, be related to the principles of increasing structuring and decreasing dissipation. In this paper, some general features of this relationship are proposed.     

Mechanisms of disuse muscle atrophy: role of oxidative stress

Prolonged periods of skeletal muscle inactivity lead to a loss of muscle protein and strength. Advances in cell biology have progressed our understanding of those factors that contribute to muscle atrophy. To this end, abundant evidence implicates oxidative stress as a potential regulator of proteolytic pathways leading to muscle atrophy during periods of prolonged disuse. This review will address the role of reactive oxygen species and oxidative stress as potential contributors to the process of disuse-mediated muscle atrophy. The first section of this article will discuss our current understanding of muscle proteases, sources of reactive oxygen in muscle fibers, and the evidence linking oxidative stress to disuse muscle atrophy. The second section of this review will highlight gaps in our knowledge relative to the specific role of oxidative stress in the regulation of disuse muscle atrophy. By discussing unresolved issues and suggesting topics for future research, it is hoped that this review will serve as a stimulus for the expansion of knowledge in this exciting field.     

Dynamics of spreading of cells of L-929 line after the mitosis

Using time-lapse microscopy, the changes in L-929 cells shape were analyzed during a cell cycle. During this time the cells were established to pass through three spreading stages. The highest rate of the cell spreading was observed during the first 1.5 h of mitosis. In this period, the cell area increases approximately 3-3.5 times following sigmoid dependence. After a short plateau the augmentation of the cell area starts also as a sigmoid dependence. This period is longer (up to 6 h after the beginning of cell division) with an additional 1.5-fold augmentation of the cells size. Next, the augmentation of the cells area goes linearly up to the beginning of the following mitosis. After the mother L-929 cell division, the daughter cells remained to be bridged together in the fission furrow site almost in 100% cases. The structure known as an intercellular bridge is related to a late telophase. In this connected state the L-cells are spreading and migrating up to 2.13 +/- 0.06 h where upon they are separated. Transition of the daughter cells from a round shape to the spread one occurring with the simultaneous maintenance of the intercellular bridge during a strictly determined time allows us to consider this phenomenon as independent and not relating to mitosis. We suggest naming this junction between the daughter cells as the "posttelophase intercellular bridge".     

Utility of protein electrophoretic analysis in the characterization of malignant tissues

High-resolution electrophoresis of samples from malignant tissues and tumour cells has developed from a simple analytical tool to a high-tech system requiring a lot of satellite techniques. Though this developmental history now demands additional expensive instrumentation and a detailed knowledge of protein chemistry, the usefulness of this technique in tumour biology has been dramatically enhanced. Consequently, electrophoretic techniques combined with additional high-resolution and sensitive analytical tools can now be used to elucidate a particular phenotype of a cancer cell; moreover, the chemical nature of this phenotype can be revealed. The way from the protein backwards to the gene is now open!