VISUALIZING MULTIVARIATE SELECTION

Recent developments in quantitative-genetic theory have shown that natural selection can be viewed as the multivariate relationship between fitness and phenotype. This relationship can be described by a multidimensional surface depicting fitness as a function of phenotypic traits. We examine the connection between this surface and the coefficients of phenotypic selection that can be estimated by multiple regression and show how the interpretation of multivariate selection can be facilitated through the use of the method of canonical analysis. The results from this analysis can be used to visualize the surface implied by a set of selection coefficients. Such a visualization provides a compact summary of selection coefficients, can aid in the comparison of selection surfaces, and can help generate testable hypotheses as to the adaptive significance of the traits under study. Further, we discuss traditional definitions of directional, stabilizing, and disruptive selection and conclude that selection may be more usefully classified into two general modes, directional and nonlinear selection, with stabilizing and disruptive selection as special cases of nonlinear selection.     

Efficient generation of infectious recombinant baculoviruses by site-specific transposon-mediated insertion of foreign genes into a baculovirus genome propagated in Escherichia coli.

The construction and purification of recombinant baculovirus vectors for the expression of foreign genes in insect cells by standard transfection and plaque assay methods can take as long as 4 to 6 weeks. This period can be reduced to several days by using a novel baculovirus shuttle vector (bacmid) that can replicate in Escherichia coli as a plasmid and can infect susceptible lepidopteran insect cells. The bacmid is a recombinant virus that contains a mini-F replicon, a kanamycin resistance marker, and attTn7, the target site for the bacterial transposon Tn7. Expression cassettes comprising a baculovirus promoter driving expression of a foreign gene that is flanked by the left and right ends of Tn7 can transpose to the target bacmid in E. coli when Tn7 transposition functions are provided in trans by a helper plasmid. The foreign gene is expressed when the resulting composite bacmid is introduced into insect cells.     

Hyperphagia by self- and xeno-cannibalism: cell death by indigestion?: a reminiscence of the Phedrus Fabula "Rana Rupta et Bos"?

The occurrence of self- and xeno-cannibalism could be considered as two different aspects of the same well-regulated process. The formation of autophagosomes can represent a survival option for a cell in unfavorable conditions but it can also lead to cell demise. In fact, autophagy has been considered as an additional and clear-cut cell death pathway. We herein speculate that selfeating by autophagy could be paralleled by a cannibalistic behavior, e.g., by cell feeding of siblings, that can also become detrimental. This behavior in fact, once exacerbated, can also lead to cell death, probably bolstering intracellular oxidative imbalance. In this case, a survival option, such as self- and xeno-cannibalism, can be turned into a peculiar death option: cell death by feeding excess. Under this point of view, over-feeding cells are reminiscent of the frog in the Phedrus Fabula "Rana Rupta et Bos".     

一种实时检测剪切力引起培养的大鼠动脉内皮细胞内一氧化氮含量的新方法

建立一个稳定和实时检测在不同剪切力作用下内皮细胞内一氧化氮含量的方法。利用流动小室建立内皮细胞剪切模型 ,在内皮细胞用DAF FM染色后 ,用Zeiss荧光共聚焦显微镜和ICCD摄象头检测细胞内的荧光强度。DAF FM的荧光强度可以反映一氧化氮的胞内含量。剪切力引起内皮细胞合成一氧化氮增加 ,并且这种作用是随着剪切力的增加而增加。剪切力的作用被一氧化氮合酶抑制剂L NAME全部抑制 ,被无Ca2 缓冲液部分抑制。这个方法可以实时反映一氧化氮含量的变化 ,可以用来研究剪切力引起一氧化氮变化的机制以及用来评价内皮细胞对剪切力的反应特性     

Differentiation genes: are they primary targets for human carcinogenesis?

In spite of extensive research in molecular carcinogenesis, genes that can be considered primary targets in human carcinogenesis remain to be identified. Mutated oncogenes or cellular growth regulatory genes, when incorporated into normal human epithelial cells, failed to immortalize or transform these cells. Therefore, they may be secondary events in human carcinogenesis. Based on some experimental studies we have proposed that downregulation of a differentiation gene may be the primary event in human carcinogenesis. Such a gene could be referred to as a tumor-initiating gene. Downregulation of a differentiation gene can be accomplished by a mutation in the differentiation gene, by activation of differentiation suppressor genes, and by inactivation of tumor suppressor genes. Downregulation of a differentiation gene can lead to immortalization of normal cells. Mutations in cellular proto-oncogenes, growth regulatory genes, and tumor suppressor genes in immortalized cells can lead to transformation. Such genes could be called tumor-promoting genes. This hypothesis can be documented by experiments published on differentiation of neuroblastoma (NB) cells in culture. The fact that terminal differentiation can be induced in NB cells by adenosine 3',5'-cyclic monophosphate (cAMP) suggests that the differentiation gene in these cells is not mutated, and thus can be activated by an appropriate agent. The fact that cAMP-resistant cells exist in NB cell populations suggests that a differentiation gene is mutated in these cancer cells, or that differentiation regulatory genes have become unresponsive to cAMP. In addition to cAMP, several other differentiating agents have been identified. Our proposed hypothesis of carcinogenesis can also be applied to other human tumors such as melanoma, pheochromocytoma, medulloblastoma, glioma, sarcoma, and colon cancer.     

A single spiking neuron that can represent interval timing: analysis,plasticity and multi-stability

The ability to represent interval timing is crucial for many common behaviors, such as knowing whether to stop when the light turns from green to yellow. Neural representations of interval timing have been reported in the rat primary visual cortex and we have previously presented a computational framework describing how they can be learned by a network of neurons. Recent experimental and theoretical results in entorhinal cortex have shown that single neurons can exhibit persistent activity, previously thought to be generated by a network of neurons. Motivated by these single neuron results, we propose a single spiking neuron model that can learn to compute and represent interval timing. We show that a simple model, reduced analytically to a single dynamical equation, captures the average behavior of the complete high dimensional spiking model very well. Variants of this model can be used to produce bi-stable or multi-stable persistent activity. We also propose a plasticity rule by which this model can learn to represent different intervals and different levels of persistent activity.     

Regulation of pancreatic exocrine secretion in vitro: the action of secretagogues

Pancreatic acinar cells possess two functionally distinct mechanisms by which secretagogues can increase enzyme secretion. One mechanism is mediated by mobilization of cellular calcium and can be activated by any one of four different classes of receptors. The other mechanism is mediated by cyclic AMP and can be activated by either of two different classes of receptors. In addition to stimulating enzyme secretion, a secretagogue can cause potentiation of secretion, desensitization to the subsequent stimulation caused by the same or other secretagogues as well as residual stimulation of enzyme secretion. Although each class of secretagogue receptors can cause the same final effect, stimulation of enzyme secretion, the existence of multiple classes of receptors and the different mechanisms of action endow the acinar cell with a wide range of patterns of response depending on which of the several classes of receptors are activated.     

Percoll and Ficoll self-generated density gradients by low-speed osmocentrifugation

Percoll and Ficoll self-generated density gradients can be obtained by low-speed centrifugation of their solutions within dialysis cells. Useful Percoll density gradients can be obtained after 10-30 min centrifugation at 220-2010g, within dialysis cells. Ficoll density gradients, which are more difficult to self-generate, can be obtained by the same technique. Red cell band formation in a Percoll density gradient can be done in a single step by using dialysis cells as the centrifugation solution container.     

Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences.

A graphical method is presented for displaying how binding proteins and other macromolecules interact with individual bases of nucleotide sequences. Characters representing the sequence are either oriented normally and placed above a line indicating favorable contact, or upside-down and placed below the line indicating unfavorable contact. The positive or negative height of each letter shows the contribution of that base to the average sequence conservation of the binding site, as represented by a sequence logo. These sequence 'walkers' can be stepped along raw sequence data to visually search for binding sites. Many walkers, for the same or different proteins, can be simultaneously placed next to a sequence to create a quantitative map of a complex genetic region. One can alter the sequence to quantitatively engineer binding sites. Database anomalies can be visualized by placing a walker at the recorded positions of a binding molecule and by comparing this to locations found by scanning the nearby sequences. The sequence can also be altered to predict whether a change is a polymorphism or a mutation for the recognizer being modeled.     

Mechanism of actin-based motility: a dynamic state diagram

Cells move by a dynamical reorganization of their cytoskeleton, orchestrated by a cascade of biochemical reactions directed to the membrane. Designed objects or bacteria can hijack this machinery to undergo actin-based propulsion inside cells or in a cell-like medium. These objects can explore the dynamical regimes of actin-based propulsion, and display different regimes of motion, in a continuous or periodic fashion. We show that bead movement can switch from one regime to the other, by changing the size of the beads or the surface concentration of the protein activating actin polymerization. We experimentally obtain the state diagram of the bead dynamics, in which the transitions between the different regimes can be understood by a theoretical approach based on an elastic force opposing a friction force. Moreover, the experimental characteristics of the movement, such as the velocity and the characteristic times of the periodic movement, are predicted by our theoretical analysis.     

Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle

ABSTRACT: BACKGROUND: Low cost genotyping of individuals using high density genomic markers were recently introduced as genomic selection in genetic improvement programs in dairy cattle. Most implementations of genomic selection only use marker information, in the models used for prediction of genetic merit. However, in other species it has been shown that only a fraction of the total genetic variance can be explained by markers. Using 5217 bulls in the Nordic Holstein population that were genotyped and had genetic evaluations based on progeny, we partitioned the total additive genetic variance into a genomic component explained by markers and a remaining component explained by familial relationships. The traits analyzed were production and fitness related traits in dairy cattle. Furthermore, we estimated the genomic variance that can be attributed to individual chromosomes and we illustrate methods that can predict the amount of additive genetic variance that can be explained by sets of markers with different density. RESULTS: The amount of additive genetic variance that can be explained by markers was estimated by an analysis of the matrix of genomic relationships. For the traits in the analysis, most of the additive genetic variance can be explained by 44 K informative SNP markers. The same amount of variance can be attributed to individual chromosomes but surprisingly the relation between chromosomal variance and chromosome length was weak. In models including both genomic (marker) and familial (pedigree) effects most (on average 77.2%) of total additive genetic variance was explained by genomic effects while the remaining was explained by familial relationships. CONCLUSIONS: Most of the additive genetic variance for the traits in the Nordic Holstein population can be explained using 44 K informative SNP markers. By analyzing the genomic relationship matrix it is possible to predict the amount of additive genetic variance that can be explained by a reduced (or increased) set of markers. For the population analyzed the improvement of genomic prediction by increasing marker density beyond 44 K is limited.     

Pathological interactions of bacteria and toxins with the gastrointestinal epithelial tight junctions and/or the zonula adherens: an update.

Communication between bacteria and the gastrointestinal tight junctions (TJs) and zonula adherens is examined. Bacteial-epithelial TJs "crosstalk" can be mediated by many virulence factors, mainly secreted toxins, or can be induced by direct contact of the pathogen with epithelial membrane. Moreover, there are several mechanisms by which bacteria may act on gastrointestinal TJs. First, bacteria can act indirectely at the TJs level by inducing cell transepithelial migration. More particularly, neutrophil or dendritic cells can cross the epithelium by a paracellular pathway. Secondly, bacteria and/or toxins can trigger actin cytoskeleton reorganization (depolymerization or hyperpolymerization). Thirdly, some enteric pathogens are susceptible to act on TJs by activation of cellular signal transduction. Finally, cleavage or modification of TJs proteins can be used by bacteria. New therapeutic strategies may result from a deeper knowledge of the cellular and molecular processes induced by bacteria at the TJ level. Moreover, studies of action of the different bacterial virulence factors on the molecules comprising the TJs and zonula adherens allow us an interesting approach on our understanding of TJ complex regulation.     

Mathematical characterization of Chaos Game Representation. New algorithms for nucleotide sequence analysis.

Chaos Game Representation (CGR) can recognize patterns in the nucleotide sequences, obtained from databases, of a class of genes using the techniques of fractal structures and by considering DNA sequences as strings composed of four units, G, A, T and C. Such recognition of patterns relies only on visual identification and no mathematical characterization of CGR is known. The present report describes two algorithms that can predict the presence or absence of a stretch of nucleotides in any gene family. The first algorithm can be used to generate DNA sequences represented by any point in the CGR. The second algorithm can simulate known CGR patterns for different gene families by setting the probabilities of occurrence of different di- or trinucleotides by a trial and error process using some guidelines and approximate rules-of-thumb. The validity of the second algorithm has been tested by simulating sequences that can mimic the CGRs of vertebrate non-oncogenes, proto-oncogenes and oncogenes. These algorithms can provide a mathematical basis of the CGR patterns obtained using nucleotide sequences from databases.     

Anthramycin inhibition of restriction endonuclease cleavage and its use as a reversible blocking agent in DNA constructions.

Anthramycin can form a stable complex with DNA which does not dissociate upon repeated ethanol precipitations. The complex forms in less than one hour at pH 5.5. Bound anthramycin seems to be located in the minor groove of the DNA helix in the anthramycin DNA complex, since methylation of adenosine residues at N-3 by dimethylsulfate is reduced. The anthramycin-DNA complex is resistant to digestion by an excess of a number of restriction enzymes. Anthramycin can be removed from DNA by incubation at acid pH. The released DNA can then be cleaved by restriction enzymes. Anthramycin-DNA complexes can be acted upon by T4 polynucleotide ligase to form longer DNA molecules. The ability of anthramycin to form a stable but reversible complex which is not cleaved by restriction enzymes but can engage in joining reactions may allow a wider variety of DNA fragments to be more readily constructed in vitro.     

ESPript: analysis of multiple sequence alignments in PostScript.

MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information. RESULTS: ESPript can be run via a command file or a friendly html-based user interface. The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences. It offers a palette of markers to highlight important regions in the alignment. ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program. AVAILABILITY: ESPript can be accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file is held in the directory pub/ESPript.     

Use of bioluminescence in nucleic acid hybridization reactions

Luminescence reactions can be used to detect specific nucleic acid sequences hybridized with a nucleic probe. Different labels such as cytidine sulphone, fluorescein, and biotin can be incorporated into DNA or oligonucleotide molecules and detected by antibody or avidin conjugates coupled to glucose-6P dehydrogenase. On supports such as nitrocellulose filters, sensitivity is not greatly increased using luminescence, but detection is rapid and easy to perform using polaroid film. Moreover, hybridization can be performed with different labelled probes on the same sample. In solution, luminescence can be used to monitor sandwich reactions. The method is less sensitive than detection on filters but can easily be automated. The performance of these assays can be increased considerably by enzymatic amplification of the target catalysed by a thermostable polymerase.     

Ambiguous incorporation of N4-aminodeoxycytidine 5'-triphosphate to DNA synthesized in vitro

Molecular mechanism of the mutation induced by N4-aminocytidine was studied. The specificity of in vitro incorporation of N4-aminodeoxycytidine 5'-triphophate catalyzed by E. coli DNA polymerase large fragment was analyzed. The results have shown that this cytosine analog can be efficiently incorporated as a substitute of cytosine, and that it can also be incorporated with a low efficiency as a substitute of thymine. We have also shown that the N4-aminocytosine incorporated opposite adenine can be excised as its monophosphate at a high frequency. The N4-aminocytosine residues in the polynucleotide templates can be read by the enzyme as efficiently as cytosines, and guanines were incorporated opposite them.     

Hyperphagia by self- and xeno-cannibalism: Cell death by indigestion? A reminiscence of the Phedrus Fabula “Rana Rupta et Bos”?

The occurrence of self- and xeno-cannibalism could be considered as two different aspects of the same well-regulated process. The formation of autophagosomes can represent a survival option for a cell in unfavorable conditions but it can also lead to cell demise. In fact, autophagy has been considered as an additional and clear-cut cell death pathway. We herein speculate that self-eating by autophagy could be paralleled by a cannibalistic behavior, e.g., by cell feeding of siblings, that can also become detrimental. This behavior in fact, once exacerbated, can also lead to cell death, probably bolstering intracellular oxidative imbalance. In this case, a survival option, such as self- and xeno-cannibalism, can be turned into a peculiar death option: cell death by feeding excess. Under this point of view, over-feeding cells are reminiscent of the frog in the Phedrus Fabula “Rana Rupta et Bos”.     

Substrate-dependent control of ERK phosphorylation can lead to oscillations

The extracellular signal-regulated kinase (ERK) controls cellular processes by phosphorylating multiple substrates. The ERK protein can use the same domains to interact with phosphatases, which dephosphorylate and deactivate ERK, and with substrates, which connect ERK to its downstream effects. As a consequence, substrates can compete with phosphatases and control the level of ERK phosphorylation. We propose that this effect can qualitatively change the dynamics of a network that controls ERK activation. On its own, this network can be bistable, but in a larger system, where ERK accelerates the degradation of a substrate competing with a phosphatase, this network can oscillate. Previous studies proposed that oscillatory ERK signaling requires a negative feedback in which active ERK reduces the rate at which it is phosphorylated by upstream kinase. We argue that oscillations can also emerge even when this rate is constant, due to substrate-dependent control of ERK phosphorylation.     

Mussel disturbance dynamics: signatures of oceanographic forcing from local interactions

Local interactions, biotic and abiotic, can have a strong influence on the large-scale properties of ecosystems. However, ecological models often explore the influence of local biotic interactions where physical disturbance is included as a large-scale and imposed source of variability but is not allowed to interact with biotic processes at the local scale. In marine intertidal communities dominated by mussels, wave disturbances create gaps in the mussel bed that recover through a successional sequence. We present a lattice model of mussel disturbance dynamics that allows local interactions between wave disturbance and mussel recolonization, in which each cell of the lattice can be empty, occupied by a mussel bed element, or disturbed (which corresponds to a newly disturbed cell that has unstable edges). As in natural ecosystems, wave disturbance can also spread from disturbed to adjacent occupied cells, and recolonization can also spread from occupied to adjacent empty cells. We first validate the local rules from artificial gap experiments and from natural gap monitoring along the Oregon coast. We analyze the properties of the model system as a function of different oceanographic forcings of productivity and disturbance. We show that the mussel bed can go through phase transitions characterized by a large sensitivity of mussel cover and patterns to oceanographic forcings but also that criticality (scale invariance) is observed over wide ranges of parameters, which suggests self-organization. We also show that spatial patterns in the intertidal can provide a robust signature of local processes and can inform about oceanographic regimes. We do so by comparing the large-scale patterns of the simulation (scaling exponents) with field data, which suggest that some experimental sites are close to criticality. Our results suggest that regional patterns in disturbed populations can be explained by local biotic and abiotic processes submitted to oceanographic forcing.