The cytoplast: A unit structure in chromatophores

We followed the translocation of identifiable pigment granules in living erythrophores through normal aggregation and dispersion and observed that they always return in dispersion to the same location relative to the whole pigment complex. This is interpreted to mean that each granule occupies a fixed position within a unit structure, the cytoplast. This position is retained even though the cytoplast undergoes dramatic reversals in form from ellipsoid to spheroid and back again with each aggregation and dispersion. The major structural components of the cytoplast, besides pigment granules, are microtubules and microtrabeculae. The latter constitute an irregular lattice that is confluent with microtubules and contains the pigment granules. In aggregation, the microtrabeculae shorten and seemingly contribute to the contraction of the entire cytoplast plus pigment. In dispersion, the microtrabeculae elongate in an apparent restructuring of the ellipsoidal cytoplast. The microtubules, however, persist in the cell cortex and appear to give radial direction to the pigment motion.     

Cytoarchitecture of Utricularia nutritive tissue

Beginning with light microscopy studies in the late 19th century, the placental "nutritive tissue" in carnivorous plants of Utricularia spp. has been well described by several authors. Based on observations of direct contact between the embryo sac and the "nutritive tissue" and the lack of vascularization of the ovule, it has been suggested that this nutritive tissue plays a key role in the nutrition of the female gametophyte. To date, however, the structure of this tissue has received only scant attention. To fill this knowledge gap, we have characterized its anatomy and histochemistry in more detail and addressed the speculations of a number of earlier researchers. Nutritive tissue during the period of flower opening in three Utricularia species, each belonging to different sections and subgenera (Polypompholyx, Bivalvaria and Utricularia), was examined by light and, in particular, electron microscopy. In all of the investigated species, nutritive tissue cells differ from placental parenchyma cells in having no huge vacuole, no large amyloplasts with starch grains, and no protein inclusions in the nucleus. The funicular nutritive tissue in U. dichotoma consists of active cells with a secretory character, while U. sandersonii has a small placental nutritive tissue consisting of colenchymatous cells accumulating lipids. The most complex nutritive tissue occurs in aquatic U. intermedia, which occupies a derived position in the genus phylogeny. In this latter species, the cells of this tissue resemble meristematic cells in having a relatively large nucleus, thin cell walls, and reduced vacuoles, but the well-developed endoplasmic reticulum (ER) in some cells is similar to that in secretory cells. The cytoplasm is rich in microtubules, some of which are in close contact with the ER cisternae. We found very thick cell walls between nutritive tissue cells and parenchyma cells, but plasmodesmata between these types of cells are rare. Similarities in both the position and structure of nutritive tissue in Polypompholyx and section Pleiochasia support their classification together in one subgenus, based on results from a molecular study. The position and structure of the nutritive tissue in Utricularia spp. are related to the position of various species in the genus phylogeny.     

Optimal setups for forced-choice staircases with fixed step sizes

Forced-choice staircases with fixed step sizes are used in a variety of formats whose relative merits have never been studied. This paper presents a comparative study aimed at determining their optimal format. Factors included in the study were the up/down rule, the length (number of reversals), and the size of the steps. The study also addressed the issue of whether a protocol involving three staircases running for N reversals each (with a subsequent average of the estimates provided by each individual staircase) has better statistical properties than an alternative protocol involving a single staircase running for 3N reversals. In all cases the size of a step up was different from that of a step down, in the appropriate ratio determined by García-Pérez (Vision Research, 1998, 38, 1861 - 1881). The results of a simulation study indicate that a) there are no conditions in which the 1-down/1-up rule is advisable; b) different combinations of up/down rule and number of reversals appear equivalent in terms of precision and cost: c) using a single long staircase with 3N reversals is more efficient than running three staircases with N reversals each: d) to avoid bias and attain sufficient accuracy, threshold estimates should be based on at least 30 reversals: and e) to avoid excessive cost and imprecision, the size of the step up should be between 2/3 and 3/3 the (known or presumed) spread of the psychometric function. An empirical study with human subjects confirmed the major characteristics revealed by the simulations.     

Evolution under reversals: parsimony and conservation of common intervals

In comparative genomics, gene order data is often modeled as signed permutations. A classical problem for genome comparison is to detect common intervals in permutations, that is, genes that are colocalized in several species, indicating that they remained grouped during evolution. A second largely studied problem related to gene order is to compute a minimum scenario of reversals that transforms a signed permutation into another. Several studies began to mix the two problems and it was observed that their results are not always compatible: Often, parsimonious scenarios of reversals break common intervals. If a scenario does not break any common interval, it is called perfect. In two recent studies, Berard et al. defined a class of permutations for which building a perfect scenario of reversals sorting a permutation was achieved in polynomial time and stated as an open question whether it is possible to decide, given a permutation, if there exists a minimum scenario of reversals that is perfect. In this paper, we give a solution to this problem and prove that this widens the class of permutations addressed by the aforementioned studies. We implemented and tested this algorithm on gene order data of chromosomes from several mammal species and we compared it to other methods. The algorithm helps to choose among several possible scenarios of reversals and indicates that the minimum scenario of reversals is not always the most plausible     

Substrate selectivity APPLies to Akt

The protein kinase Akt occupies a central position in multiple signaling pathways. Although numerous Akt substrates have been identified, less is known about the factors that regulate specific cellular responses to Akt signaling. In this issue, Schenck et al. (2008) demonstrate that the endosomal protein Appl1 modulates Akt's substrate selectivity to promote cell survival during zebrafish development.     

线粒体在神经元程序性死亡中的作用新进展

神经元的死亡是许多神经系统疾病如阿尔茨海默病、帕金森病、急性青光眼等发生发展过程中的重要事件,传统认为,细胞死亡有凋亡、自噬、坏死三种方式,凋亡和自噬为程序性的细胞死亡,坏死为非程序性的死亡途径。而近年来的研究发现了一种名为程序性坏死(necroptosis)的可调控的坏死,因此,对这些可调控的细胞死亡的研究对治疗这类神经系统疾病有重要的意义。大量研究发现,在能量代谢和自由基代谢中占据着重要地位的线粒体在细胞死亡过程中也发挥重要作用。本文对线粒体在神经元凋亡、自噬和程序性坏死中的生物学作用的最新进展做一综述。     

Sorting by reversals and block-interchanges with various weight assignments

Background  

A classical problem in studying genome rearrangements is understanding the series of rearrangement events involved in transforming one genome into another in accordance with the parsimonious principle when two genomes with the same set of genes differ in gene order. The most studied event is the reversal, but an increasing number of reports have considered reversals along with other genome rearrangement events. Some recent studies have investigated the use of reversals and block-interchanges simultaneously with a weight proportion of 1:2. However, there has been less progress towards exploring additional combinations of weights.     

Expected gene-order distances and model selection in bacteria

MOTIVATION: The evolutionary distance inferred from gene-order comparisons of related bacteria is dependent on the model. Therefore, it is highly important to establish reliable assumptions before inferring its magnitude. RESULTS: We investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene-order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetrical reversals, single gene transpositions and single gene reversals. We also derive method of moments distance estimates for some previously uncomputed cases, such as symmetrical reversals, single gene reversals and their combinations, as well as the single gene transpositions edit distance.     

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss

Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. These findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.     

Polycyclic aromatic hydrocarbon-DNA adducts in humans: relevance as biomarkers for exposure and cancer risk

The methodology applied for DNA adducts in humans has become more reliable in recent years, allowing to detect even background carcinogenic adduct levels in environmentally exposed persons. Particularly, combinations of the various methods now allow the elucidation of specific adduct structures with detection limits of 1 adduct in 10⁸ unmodified nucleotides or even lower. The quantification of polycyclic aromatic hydrocarbon-DNA (PAH-DNA) adducts in human tissues and cells has been achieved with a number of highly sensitive techniques: immunoassays and immunocytochemistry using polyclonal or monoclonal antisera specific for DNA adducts or modified DNA, the ³²P-postlabelling assay, and adduct identification using physicochemical instrumentation. The results summarized in this review show that PAH-DNA adducts have been detected in a variety of human tissues, including target organs of PAH- and tobacco-associated cancers. Although dosimetry has not always been precise, a large number of data now clearly show that lowering exposure to carcinogenic PAH results in decreasing PAH-DNA adduct levels. In most studies, however, bulk DNA of a certain tissue or cell type has been examined, and there were relatively few studies in which mutations as a consequence of DNA damage at specific genes have been investigated. Promising as these biomarker studies seem for epidemiology and health surveillance, future biomonitoring and molecular epidemiological studies should be directed to combine several endpoint measurements: i.e., adduct formation (preferably at specific sites), mutational spectra in cancer-relevant genes, and genetic markers of (cancer) susceptibility in a number of cancer-predisposing genes.     

Different roles for aspartates and glutamates for cation permeation in bacterial sodium channels

A key driving force for ion channel selectivity is represented by the negative charge of the Selectivity Filter carried by aspartate (D) and glutamate (E) residues. However, the structural effects and specific properties of D and E residues have not been extensively studied. In order to investigate this issue we studied the mutants of NaChBac channel with all possible combinations of D and E in the charged rings in position 191 and 192. Electrophysiological measurements showed significant Ca²⁺ currents only when position 191 was occupied by E. Equilibrium Molecular Dynamics simulations revealed the existence of two binding sites, corresponding to the charged rings and another one, more internal, at the level of L190. The simulations showed that the ion in the innermost site can interact with the residue in position 191 only when this is glutamate. Based on the MD simulations, we suggest that a D in position 191 leads to a high affinity Ca²⁺ block site resulting from a significant drop in the free energy of binding for an ion moving between the binding sites; in contrast, the free energy change is more gradual when an E residue occupies position 191, resulting in Ca²⁺ permeability. This scenario is consistent with the model of ion channel selectivity through stepwise changes in binding affinity proposed by Dang and McCleskey. Our study also highlights the importance of the structure of the selectivity filter which should contribute to the development of more detailed physical models for ion channel selectivity.     

Phosphorylation‐dependent localization of the response regulator FrzZ signals cell reversals in Myxococcus xanthus

The life cycle of Myxococcus xanthus includes co‐ordinated group movement and fruiting body formation, and requires directed motility and controlled cell reversals. Reversals are achieved by inverting cell polarity and re‐organizing many motility proteins. The Frz chemosensory pathway regulates the frequency of cell reversals. While it has been established that phosphotransfer from the kinase FrzE to the response regulator FrzZ is required, it is unknown how phosphorylated FrzZ, the putative output of the pathway, targets the cell polarity axis. In this study, we used Phos‐tag SDS‐PAGE to determine the cellular level of phospho‐FrzZ under different growth conditions and in Frz signalling mutants. We detected consistent FrzZ phosphorylation, albeit with a short half‐life, in cells grown on plates, but not from liquid culture. The available pool of phospho‐FrzZ correlated with reversal frequencies, with higher levels found in hyper‐reversing mutants. Phosphorylation was not detected in hypo‐reversing mutants. Fluorescence microscopy revealed that FrzZ is recruited to the leading cell pole upon phosphorylation and switches to the opposite pole during reversals. These results are consistent with the hypothesis that the Frz pathway modulates reversal frequency through a localized response regulator that targets cell polarity regulators at the leading cell pole.     

Primary cell culture from the nose of a marine organism, the banded houndshark, Triakis scyllium

Animal cells have been widely and continuously studied due to their usefulness in biological researches and production of pharmacological agents as well as food additives. Nevertheless, there are several problems such as the existence of viruses which introduce the possibility of mammalian-infection. In this reason, recently, animal cells derived from marine organisms have emerged to overcome these problems by many researches. However, marine animal-derived cells have not yet been well developed. The banded hound shark occupies an important position in an evolutionary perspective and currently a few biological substances have been used for medicines or food additives such as shark squalene and cartilage extract. In this study, primary cells were cultivated from a banded hound shark nose containing many extracellular matrix (ECM) materials. After successful isolation of one type of primary nasal cell, we optimized culture conditions including coating materials, media composition, serum concentrations and pH. Additionally, these cells demonstrated proliferation ability in vitro, generating secretions of collagen and sulfated polysaccharides. The cultivated primary cells are useful in the study of cellular biology and may be used to create a variety of ECM-originated bioactive substances.     

Systematic position and phylogenetic relationships of the family Omphalometridae (Digenea, Plagiorchiida) inferred from partial lsrDNA sequences

The phylogenetic relationships and systematic position of the digenean genus Omphalometra Looss, 1899 and several other closely related genera, have always been controversial and opinions of different authors on the systematic rank and content of this group have varied greatly. Molecular analysis based on the partial sequences of the large subunit ribosomal DNA gene of representatives of the genera Omphalometra, Rubenstrema and Neoglyphe as well as previously published sequences of members of five families of Plagiorchioidea, has demonstrated: (1) close phylogenetic relationships between these three genera, and (2) a strong support of their position within the family Plagiorchiidae as a well-defined separate clade considered here as a subfamily Omphalometrinae. Molecular data do not support the close affinities of the members of Omphalometrinae and genus Opisthioglyphe as has been suggested by majority of previous authors. Among Omphalometrinae, Omphalometra flexuosa (a parasite of moles, Talpidae) occupies a basal position in relation to Rubenstrema exasperatum and Neoglyphe locellus (both parasitic in shrews, members of the more evolutionary advanced family Soricidae). An extremely low level of lsrDNA sequence divergence between Neoglyphe and Rubenstrema suggests very close phylogenetic relationships of these two genera. Results of the molecular analysis are briefly discussed in comparison with the previously published systems.     

Oriented cell division in vertebrate embryogenesis

Tissue morphogenesis depends on the spatial arrangement of cells during development. A number of mechanisms have been described to contribute to the final shape of a tissue or organ, ranging from cell intercalation to the response of cells to chemotactic cues. One such mechanism is oriented cell division. Oriented cell division is determined by the position of the mitotic spindle. Indeed, there is increasing evidence implicating spindle misorientation in tissue and organ misshaping, which underlies disease conditions such as tumorigenesis or polycystic kidneys. Here we review recent studies addressing how the direction of tissue growth is determined by the orientation of cell division and how both extrinsic and intrinsic cues control the position of the mitotic spindle.     

DNA synthesis in the early embryo of the nematode Ascaris suum.

We have used microspectrofluorimetry to measure the rate of DNA synthesis in the first two embryonic cell cycles of the parasitic nematode Ascaris suum. The S-phase of the early Ascaris cell cycles occupies at most 1 hr; G2 phase is prominent and occupies approximately 11 hr; no G1 phase could be detected. These results contrast with our previous measurements made with embryos of the free-living nematode Caenorhabditis elegans, in which the earliest cell cycles consist of simple alternations between S and M phases.     

A Bacterial Ras-Like Small GTP-Binding Protein and Its Cognate GAP Establish a Dynamic Spatial Polarity Axis to Control Directed Motility

Regulated cell polarity is central to many cellular processes. We investigated the mechanisms that govern the rapid switching of cell polarity (reversals) during motility of the bacterium Myxococcus xanthus. Cellular reversals are mediated by pole-to-pole oscillations of motility proteins and the frequency of the oscillations is under the control of the Frz chemosensory system. However, the molecular mechanism that creates dynamic polarity remained to be characterized. In this work, we establish that polarization is regulated by the GTP cycle of a Ras-like GTPase, MglA. We initially sought an MglA regulator and purified a protein, MglB, which was found to activate GTP hydrolysis by MglA. Using live fluorescence microscopy, we show that MglA and MglB localize at opposite poles and oscillate oppositely when cells reverse. In absence of MglB, MglA-YFP accumulates at the lagging cell end, leading to a strikingly aberrant reversal cycle. Spatial control of MglA is achieved through the GAP activity of MglB because an MglA mutant that cannot hydrolyze GTP accumulates at the lagging cell end, despite the presence of MglB. Genetic and cell biological studies show that the MglA-GTP cycle controls dynamic polarity and the reversal switch. The study supports a model wherein a chemosensory signal transduction system (Frz) activates reversals by relieving a spatial inhibition at the back pole of the cells: reversals are allowed by Frz-activated switching of MglB to the opposite pole, allowing MglA-GTP to accumulate at the back of the cells and create the polarity switch. In summary, our results provide insight into how bacteria regulate their polarity dynamically, revealing unsuspected conserved regulations with eukaryots.     

The somitic level of origin of embryonic chick hindlimb muscles

Studies of avian chimeras made by transplanting groups of quail somites into chick embryos have consistently shown that the muscle cells of the hindlimb are derived from the adjacent somites, however, the pattern of cell distribution from individual somites to individual hindlimb muscles has not been characterized. I have mapped quail cell distribution in the chick hindlimb after single somite transplantation to determine if cells from an individual somite populate discrete limb muscle regions and if there is a spatial correspondence between a muscle's somitic level of origin and the known spinal cord position of its motoneuron pool. At stages 15-18 single chick somites or equivalent lengths of unsegmented somitic mesoderm adjacent to the prospective hindlimb region were replaced with the corresponding tissue from quail embryos. At stages 28-34, quail cell distribution was mapped within individual thigh muscles and shank muscle regions. A quail-specific antiserum and Feulgen staining were used to identify quail cells. Transplants from somite levels 26-33 each gave rise to consistent quail cell labeling in a unique subset of limb muscles. The anteroposterior positions of these subsets corresponded to that of the transplanted somitic tissue. For example, more anterior or anteromedial thigh muscles contained quail cells when more anterior somitic tissue had been transplanted. For the majority of thigh muscles studied and for shank muscle groups, there was also a clear correlation between somitic level of origin and motoneuron pool position. These data are compatible with the hypothesis that motoneurons and the muscle cells of their targets share axial position labels. The question of whether motoneurons from a specific spinal cord segment recognize and consequently innervate muscle cells derived from the same axial level during early axon outgrowth is addressed in the accompanying paper (C. Lance-Jones, 1988, Dev. Biol. 126, 408-419). Quail cell distribution was also mapped in chick embryos in which quail somites or unsegmented mesoderm had been placed 2-3 somites away from their position of origin. In all cases donor somitic tissues contributed to muscles in accord with their host position. These results indicate that muscle cell precursors within the somites are not specified to migrate to a predetermined target region.     

Pollen ultrastructure in anther cultures of Datura innoxia. III. Incomplete microspore division.

During the microspore division in Datura innoxia, the mitotic spindle is oriented in planes both perpendicular (PE) and oblique (OB) to the spore wall against which the nucleus is situated. However, irrespective of polarity, the usual type of hemispherical wall is laid down at cytokinesis and isolates the generative cell from the rest of the pollen grain (type A). In PE spores the vegetative nucleus initially occupies a central position in the pollen grain, whereas in OB spores the vegetative nucleus lies at the periphery of the grain close to the generative cell. In anther cultures initiated just before the microspore division is due to take place, no marked change can be observed in either orientation or symmetry of the mitotic spindle when the spores divide. In some, however, cytokinesis is disrupted and deposition of the hemispherical wall arrested. In the absence of a complete wall, differentiation of the generative cell cannot take place and binucleate pollen grains are formed having 2 vegetative-type nuclei (type B). The 2 nuclei in the B pollens are always situated against the pollen-grain wall, suggesting that the disruption phenomenon is related to the OB spores. The incomplete wall always makes contact with the intine on the intine-side of the spindle. Wall material may be represented merely as short stubs projecting out from the intine into the cytoplasm, in which event the 2 nuclei lie close to each other and are separated by only a narrow zone of cytoplasm. In other grains the wall is partially developed between the nuclei and terminates at varying distances from the tonoplast; in these, the nuclei are separated by a wider zone of cytoplasm. The significance of these binucleate grains in pollen embryogenesis is discussed.     

CHARACTERIZATION OF DEVELOPMENT IN MAIZE THROUGH THE USE OF MUTANTS. II. THE ABNORMAL GROWTH CONDITIONED BY THE KNOTTED MUTANT

The maize mutant Knotted (Kn) is characterized by hollow, finger-like outgrowths (knots) occurring mainly in the leaf blade. Portions of the ligule are displaced from the normal position to more distal locations within the blade. Knots apparently result from continued meristematic activity of isolated patches of cells surrounded by maturing tissue. Small knots appear to be centers of cell division. Epidermal cells overlying a small knot have been observed to undergo periclinal divisions. In addition to cell division, a reorientation of the axis of cell elongation is associated with knot formation. The pattern of knot distribution varies at different levels on the plant axis and within a leaf blade. From leaf 4 to leaf 10 or 11 the number of knots per leaf increases progressively, then declines in leaves initiated later. Knots always occur in association with lateral veins. The greatest number per vein occurs on the 3rd or 4th vein from the midrib. One plant developing from an X-rayed heterozygous seed possessed a sector of normal tissue bisecting the plant in a vertical plane passing through the midrib of each leaf except the top two. The normal sector was knot-free and had the ligule restored to the normal position. These observations suggest that cells with the characteristics of those from intercalary meristems occur throughout the blade in Knotted plants.