Microtubule changes during the development of generative cells in Hippeastrum vittatum pollen

Summary The three-dimensional organization of microtubules in generative cells during their development in pollen grains of Hippeastrum vittatum and the dynamic changes that occur were studied by collecting large quantities of fixed and isolated generative cells for immunofluorescence microscopy. The framework configuration and the arrangement pattern of the microtubule organization was investigated. The microtubule framework changed in shape from being spherical at an early stage to being long spindle-shaped at maturity: various transitional forms were observed: ellipsoidal, pear-shaped and short spindle-shaped. The microtubule arrangement making up this framework changed correspondingly from the original network, which was random in distribution, to axially oriented long bundles via an intermediate pattern composed of a mixture of networks with long bundles. However, cells with the same framework configuration might be heterogeneous in microtubule arrangements.     

Expression of a cell surface protein during morphogenesis of the reproductive system in Manduca sexta embryos

New antibody markers have allowed more refined examinations of embryogenesis. Features are being found that were overlooked in whole and sectioned embryos stained with traditional histochemical labels. Two monoclonal antibodies that recognize two different cell surface proteins in Manduca sexta label cells of the developing reproductive system. These specific immunolabels reveal that during a brief period of Manduca embryogenesis, rudiments of both male and female genital ducts are present in a single embryo. This transient phase of genital differentiation parallels the transient indifferent stage known to occur during development of reproductive systems in many vertebrate embryos. At the end of this indifferent stage, one of the two pairs of genital ducts retracts and degenerates. The dynamic expression of the two surface proteins on cells involved in morphogenesis of both the female and male reproductive systems also suggests that these proteins are important in orchestrating the specific cellular interactions that occur between mesodermal cells of the genital ducts and the nearby ventral ectoderm.     

A Model for the Origin of Life through Rearrangements among Prebiotic Phosphodiester Polymers

This model proposes that the origin of life on Earth occurred as a result of a process of alteration of the chemical composition of prebiotic macromolecules. The stability of organic compounds assembled into polymers generally exceeded the stability of the same compounds as free monomers. This difference in stability stimulated accumulation of prebiotic macromolecules. The prebiotic circulation of matter included constant formation and decomposition of polymers. Spontaneous chemical reactions between macromolecules with phosphodiester backbones resulted in a non-Darwinian selection for chemical stability, while formation of strong structures provided an advantage in the struggle for stability. Intermolecular structures between nucleotide-containing polymers were further stabilized by occasional acquisition of complementary nucleotides. Less stable macromolecules provided the source of nucleotides. This process resulted first in the enrichment of nucleotide content in prebiotic polymers, and subsequently in the accumulation of complementary oligonucleotides. Finally, the role of complementary copy molecules changed from the stabilization of the original templates to the de novo production of template-like molecules. I associate this stage with the origin of life in the form of cell-free molecular colonies. Original life acquired ready-to-use substrates from constantly forming prebiotic polymers. Metabolism started to develop when life began to consume more substrates than the prebiotic cycling produced. The developing utilization of non-polymeric compounds stimulated the formation of the first membrane-enveloped cells that held small soluble molecules. Cells “digested” the nucleotide-containing prebiotic macromolecules to nucleotide monomers and switched the mode of replication to the polymerization of nucleotide triphosphates.     

Stable polymers of the axonal cytoskeleton: the axoplasmic ghost

We have examined the monomer-polymer equilibria which form the cytoskeletal polymers in squid axoplasm by extracting protein at low concentrations of monomer. The solution conditions inside the axon were matched as closely as possible by the extraction buffer (buffer P) to preserve the types of protein associations that occur in axoplasm. Upon extraction in buffer P, all of the neurofilament proteins in axoplasm remain polymerized as part of the stable neurofilament network. In contrast, most of the polymerized tubulin and actin in axoplasm is soluble although a fraction of these proteins also exists as a stable polymer. Thus, the axoplasmic cytoskeleton contains both stable polymers and soluble polymers. We propose that stable polymers, such as neurofilaments, conserve cytoskeletal organization because they tend to remain polymerized, whereas soluble polymers increase the plasticity of the cytoskeleton because they permit rapid and reversible changes in cytoskeletal organization.     

Templates of food–habitat resources for the organization of soil animals in temperate and tropical forests

The functioning and structure of terrestrial ecosystems are shaped and maintained by plant–decomposer interactions. The food and habitat of animal populations are biogenic and are mainly of plant origin (plant litter) in terrestrial ecosystems. Primary resources of the food-habitat template for the organization of soil animals are provided by the primary production of plants, and are then modified through decomposition processes by microbial populations. In the microbial decomposition system, the efficiency of carbon utilization by microbial decomposers characterizes the decomposition processes between tropical and temperate forest ecosystems. Tropical forests show poor development of soil reservoir systems because of the high efficiency of lignin decomposition by microbial populations. The decomposition processes of leaf litter are described briefly for the understanding of organization of soil animal communities in tropical and temperate forests. A comparison of decomposition processes shows qualitative differences in decomposition between temperate and tropical forests. The composition of functional groups of soil animals is well explained by the decomposition processes in both forests.     

Investigating the influence of extractives on the oil yield and alkane production obtained from three kinds of biomass via deoxy-liquefaction

The aim of this study is to investigate the influence of extractives on the yield and composition of oil obtained from biomass samples (Artemisia ordosica, corn stalk and wheat straw). Direct deoxy-liquefaction experiments of original and extracted biomass were performed at certain temperature in a stainless steel tubular reactor. Benzene-alcohol solvent extraction had significant effect on the product distribution of biomass, especially on the yield and composition of the product oils. The oil yield of original biomass and alkane content in the oil were in the range of 5.44-9.27% and 8.23-23.64%, while decreased to 3.83-4.45% and 1.07-6.03% for the extracted biomass. This study concludes that most of alkanes in the oil mainly derive from the decomposition of triglyceride and hydrocarbon existed in the extractives of biomass. The results might be helpful to study the origin of alkanes and benzene derivatives in the oil obtained from biomass via direct deoxy-liquefaction.     

Inversion Concept of the Origin of Life

The essence of the inversion concept of the origin of life can be narrowed down to the following theses: 1) thermodynamic inversion is the key transformation of prebiotic microsystems leading to their transition into primary forms of life; 2) this transformation might occur only in the microsystems oscillating around the bifurcation point under far-from-equilibrium conditions. The transformation consists in the inversion of the balance "free energy contribution / entropy contribution", from negative to positive values. At the inversion moment the microsystem radically reorganizes in accordance with the new negentropy (i.e. biological) way of organization. According to this approach, the origin-of-life process on the early Earth took place in the fluctuating hydrothermal medium. The process occurred in two successive stages: a) spontaneous self-assembly of initial three-dimensional prebiotic microsystems composed mainly of hydrocarbons, lipids and simple amino acids, or their precursors, within the temperature interval of 100-300°C (prebiotic stage); b) non-spontaneous synthesis of sugars, ATP and nucleic acids started at the inversion moment under the temperature 70-100°C (biotic stage). Macro- and microfluctuations of thermodynamic and physico-chemical parameters able to sustain this way of chemical conversion have been detected in several contemporary hydrothermal systems. A minimal self-sufficient unit of life on the early Earth was a community of simplest microorganisms (not a separate microorganism).     

Affinity precipitation of proteins: design criteria for an efficient polymer

Affinity precipitation is fast emerging as a successful technique for the purification of proteins which can be introduced at an early stage of downstream processing. The technique applies the use of reversibly soluble-insoluble polymers which have either natural or synthetic origin. Apart from the successful use of some natural polymers, such as chitosan and alginate, the vast application of the technique depends upon the design of efficient synthetic polymers. In this laboratory, N-isopropylacrylamide (NIPAM) copolymers have been developed for metal chelate affinity precipitation of proteins. The copolymers of 1-vinylimidazole (VI) and iminodiacetic acid (IDA) with NIPAM were synthesized. The copolymers were thoroughly characterized with a view to designing an efficient soluble-insoluble polymer for metal chelate affinity precipitation of proteins.     

Mosaic origin of the mitochondrial proteome

Although the origin of mitochondria from the endosymbiosis of an α-proteobacterium is well established, the nature of the host cell, the metabolic complexity of the endosymbiont and the subsequent evolution of the proto-mitochondrion into all its current appearances are still the subject of discovery and sometimes debate. Here we review what has been inferred about the original composition and subsequent evolution of the mitochondrial proteome and essential mitochondrial systems. The evolutionary mosaic that currently constitutes mitochondrial proteomes contains (i) endosymbiotic proteins (15-45%), (ii) proteins without detectable orthologs outside the eukaryotic lineage (40%), and (iii) proteins that are derived from non-proteobacterial Bacteria, Bacteriophages and Archaea (15%, specifically multiple tRNA-modification proteins). Protein complexes are of endosymbiotic origin, but have greatly expanded with novel eukaryotic proteins; in contrast to mitochondrial enzymes that are both of proteobacterial and non-proteobacterial origin. This disparity is consistent with the complexity hypothesis, which argues that proteins that are a part of large, multi-subunit complexes are unlikely to undergo horizontal gene transfer. We observe that they neither change their subcellular compartments in the course of evolution, even when their genes do.     

Effects of the Development of Thyroid and Sex Glands on the Synthesis of Brain Tubulin in Chick and Mouse Embryos

Using the specific affinity of tubulin for colchicine and the strong absorption of tubulin to DEAEion exchangers at neutral pH and moderate ionic strength,the amounts of tubulin in the brain fromboth mice and chicks during different developing stages were measured by ~3H-colchicine assay(expressed as colchicine binding activity).The results show that the rate oftubulin synthesis reacheda peak value during the critical period of brain development.This is exactly the period during whichthe organization and function of thyroid are being perfected.Besides,during breeding period,thedifference of tubulin contents between male and female is significant(P<0.001).The synthesis oftubulin is strictly sex dependent(this phenomenon appeared only during sex maturation stage).It issuggested that sexual hormones might exert their effect on tubulin synthesis.     

SPECIES SPECIFIC PATTERN OF CILIOGENESIS IN DEVELOPING SEA URCHIN EMBRYOS

The events of cell division and ciliogenesis in individual blastomeres of developing embryos of the sea urchins Temnopleurus toreumaticus and Hemicentrotus pulcherrimus were followed with a Nomarski differential interference microscope. The number of cell divisions before initiation of ciliogenesis was determined with respect to species. In T. toreumaticus , ciliogenesis began about 4 hr after fertilization at 25°C. The sequence of ciliogenesis was as follows: cilia appeared first on smaller micromeres, followed in order by blastomeres derived from larger micromeres, those from mesomeres and finally those derived from macromeres. Blastomeres originating from mesomeres, macromeres, larger micromeres and smaller micromeres had completed the 8th, 9th, 7th and 5th divisions respectively, before they generated cilia.
In H. pulcherrimus , embryos started to form cilia about 9 hr after fertilization at 18°C. Cilia appeared first on blastomeres of mesomere origin and, then on those of macromere origin. Before initiation of ciliogenesis, descendants of mesomeres and macromeres completed 9 and 10 rounds of cell division. Descendants of larger micromeres and the majority of cells derived from smaller micromeres did not acquired cilia even when the embryo began to rotate within the fertilization membrane. At this stage, the former had completed the 6th division and the latter the 8th division. Cell counts of blastomeres per embryo at the blastula stage also supported this observation.     

The evolution of titin and related giant muscle proteins

Titin and twitchin are giant proteins expressed in muscle. They are mainly composed of domains belonging to the fibronectin class III and immunoglobulin c2 families, repeated many times. In addition, both proteins have a protein kinase domain near the C-terminus. This paper explores the evolution of these and related muscle proteins in an attempt to determine the order of events that gave rise to the different repeat patterns and the order of appearance of the proteins. Despite their great similarity at the level of sequence organization, titin and twitchin diverged from each other at least as early as the divergence between vertebrates and nematodes. Most of the repeating units in titin and twitchin were estimated to derive from three original domains. Chicken smooth-muscle myosin light-chain kinase (smMLCK) also has a kinase domain, several immunoglobulin domains, and a fibronectin domain. From a comparison of the kinase domains, titin is predicted to have appeared first during the evolution of the family, followed by twitchin and with the vertebrate MLCKs last to appear. The so-called C-protein from chicken is also a member of this family but has no kinase domain. Its origin remains unclear but it most probably pre-dates the titin/twitchin duplication. Correspondence to: D.G. Higgins     

Characterization of two integral membrane proteins located in the protein bodies of pumpkin seeds

Two integral membrane proteins, MP28 and MP23, were found in protein bodies isolated from pumpkin (Cucurbita sp.) seeds. Molecular characterization revealed that both MP28 and MP23 belong to the seed TIP (tonoplast intrinsic protein) subfamily. The predicted 29 kDa precursor to MP23 includes six putative membrane-spanning domains, and the loop between the first and second transmembrane domains is larger than that of MP28. The N-terminal sequence of the mature MP23 starts from residue 66 in the first loop, indicating that an N-terminal 7 kDa fragment that contains one transmembrane domain is post-translationally removed. During maturation of pumpkin seeds, mRNAs for MP28 and MP23 became detectable in cotyledons at the early stage, and their levels increased slightly until a rapid decrease occurred at the late stage. This is consistent with the accumulation of the 29 kDa precursor and MP28 in the cotyledons at the early stage. By contrast, MP23 appeared at the late stage simultaneously with the disappearance of the 29 kDa precursor. Thus, it seems possible that the conversion of the 29 kDa precursor to the mature MP23 might occur in the vacuoles after the middle stage of seed maturation. Both proteins were localized immunocytochemically on the membranes of the vacuoles at the middle stage and the protein bodies at the late stage. These results suggest that both MP28 and the precursor to MP23 accumulate on vacuolar membranes before the deposition of storage proteins, and then the precursor is converted to the mature MP23 at the late stage. These two TIPs might have a specific function during the maturation of pumpkin seeds.     

Inhibitory effects of Bacillus probionts on growth and toxin production of Vibrio harveyi pathogens of shrimp

Aim:  To investigate the effects of Bacillus subtilis , Bacillus licheniformis and Bacillus megaterium in terms of toxin and growth of pathogenic Vibrio harveyi .
Methods and Results:  Three Bacillus probionts were isolated from probiotic BZT aquaculture and identified using a 16S rDNA sequence. Growth inhibition assay showed that supernatants from the 24-h culture of three Bacillus species were able to inhibit the growth of V. harveyi (LMG 4044); B. subtilis was the most effective based on the well diffusion method. Results of a liquid culture model showed that B. subtilis was also widely effective in inhibiting three strains of V. harveyi (isolated from Thailand, the Philippines and LMG 4044), and that both B. licheniformis and B. megaterium inhibit the growth of V. harveyi isolated from the Philippines. Moreover, a haemolytic activity assay demonstrated that V. harveyi (IFO 15634) was significantly decreased by the addition of B. licheniformis or B. megaterium supernatant.
Conclusions:  Bacillus subtilis inhibited Vibrio growth, and both B. licheniformis and B. megaterium suppressed haemolytic activity in Vibrio .
Significance and Impact of the Study:  The cell-free supernatants produced by Bacillus probionts inhibit Vibrio disease, and Bacillus probionts might have an influence on Vibrio cell-to-cell communications.     

Interactions of Human Skin Fibroblasts with Monomeric or Fibrillar Collagens Induce Different Organization of the Cytoskeleton

Fibrillar collagens represent the most abundant extracellular matrix components surrounding fibroblasts. Although there is a large heterogeneity in the collagen composition and in the physiological functions of different tissues, interactions between cells and native collagens monomers are mediated by only two integrins, the α1β1 and α2β1 integrins. In tissue, fibroblasts are exposed to collagen polymers, supramolecular assemblies which might play a role on the availability of the cell-binding sites at the surface of the fibrils. We have addressed this issue by investigating the patterns of adhesion structures in normal human skin fibroblasts exposed to collagen monomers or polymers. Our results showed that cell morphology, cell adhesion pattern, actin organization, and distribution of integrin subunits, talin, vinculin, and phosphotyrosine-containing proteins are dependent on the supramolecular organization of the collagens. In particular, compared to monomers, collagen polymers induced a looser organization of the actin network and a linear clustering of integrins, talin, vinculin, and phosphotyrosine-containing proteins. These results emphasize the role of the physical state of collagen on cellular interactions and underline the role of the extracellular matrix in the phenotypic modulation of fibroblasts. Furthermore, our studies suggest the existence of a local heterogeneity in the biological activity of collagen fibrils.     

Network-based pipeline for analyzing MS data: an application toward liver cancer

Current limitations in proteome analysis by high-throughput mass spectrometry (MS) approaches have sometimes led to incomplete (or inconclusive) data sets being published or unpublished. In this work, we used an iTRAQ reference data on hepatocellular carcinoma (HCC) to design a two-stage functional analysis pipeline to widen and improve the proteome coverage and, subsequently, to unveil the molecular changes that occur during HCC progression in human tumorous tissue. The first involved functional cluster analysis by incorporating an expansion step on a cleaned integrated network. The second used an in-house developed pathway database where recovery of shared neighbors was followed by pathway enrichment analysis. In the original MS data set, over 500 proteins were detected from the tumors of 12 male patients, but in this paper we reported an additional 1000 proteins after application of our bioinformatics pipeline. Through an integrative effort of network cleaning, community finding methods, and network analysis, we also uncovered several biologically interesting clusters implicated in HCC. We established that HCC transition from a moderate to poor stage involved densely connected clusters that comprised of PCNA, XRCC5, XRCC6, PARP1, PRKDC, and WRN. From our pathway enrichment analyses, it appeared that the HCC moderate stage, unlike the poor stage, is enriched in proteins involved in immune responses, thus suggesting the acquisition of immuno-evasion. Our strategy illustrates how an original oncoproteome could be expanded to one of a larger dynamic range where current technology limitations prevent/limit comprehensive proteome characterization.     

Interaction of initiator proteins with the origin of replication of an IncL/M plasmid

The origin of replication of the IncL/M plasmid pMU604 was analyzed to identify sequences important for binding of initiator proteins and origin activity. A thrice repeated sequence motif 5'-NANCYGCAA-3' was identified as the binding site (RepA box) of the initiator protein, RepA. All three copies of the RepA box were required for in vivo activity and binding of RepA to these boxes appeared to be cooperative. A DnaA R box (box 1), located immediately upstream of the RepA boxes, was not required for recruitment of DnaA during initiation of replication by RepA of pMU604 unless a DnaA R box located at the distal end of the origin (box 3) had been inactivated. However, DnaA R box 1 was important for recruitment of DnaA to the origin of replication of pMU604 when the initiator RepA was that from a distantly related plasmid, pMU720. A mutation which scrambled DnaA R boxes 1 and 3 and one which scrambled DnaA R boxes 1, 3 and 4 had much more deleterious effects on initiation by RepA of pMU720 than on initiation by RepA of pMU604. Neither Rep protein could initiate replication from the origin of pMU604 in the absence of DnaA, suggesting that the difference between them might lie in the mechanism of recruitment of DnaA to this origin. DnaA protein enhanced the binding and origin unwinding activities of RepA of pMU604, but appeared unable to bind to a linear DNA fragment bearing the origin of replication of pMU604 in the absence of other proteins.     

Procaryotic genesis and evolution of chemosignaling systems of eukaryotes

The analysis of own and literature data accumulated in the last two decades allowed to check and confirm the author's hypothesis about the prokaryotic origin and endosymbiotic genesis of chemosignalling systems of higher eukaryotes. The comparison of structural-functional organization of these information systems and their components (receptors, GTP-binding proteins, enzymes with cyclase activity, protein kinases etc.) in bacteria and eukaryotes revealed a number of similar features giving evidence for their evolutionary relationship. The conclusion was made that eukaryotic signaling systems have prokaryotic roots. The systems of signal transduction revealed in unicellular eukaryotes according to their architecture and functional properties represent a transient stage in the evolution of chemosignalling systems from prokaryotes to higher eukaryotes. The spreading of signalling systems among three super kingdoms--Bacteria, Archaea and Eukarya occurred as a result of horizontal transfer of bacterial genes and co-evolution of signalling components.