“On A Piece of Chalk”-Updated1

ABSTRACT. Many advances have been made in our knowledge of the biology of foraminifera over the past several decades. Fine structural, biophysical, and molecular biological studies have shown that the most prominent components of their distinctive bidirectional granuloreliculopods are bundles of micro tubules linked by crossbridges to each other, as well as to membrane-bound organelles and the plasma membrane. the microtubules ratchet past each other as dynein transduces the free energy of ATP to produce pseudopodal movements. In spite of the fact that there are over 40,000 described species of living and fossil species of foraminifera, there have been many recent exciting discoveries of new species and groups. New casting techniques are providing us with greater understanding of the complexities and functional aspects of form in the group. Significant advances are being made in understanding the distribution and energetics of deep-sea forms. Larger and planktonic foraminifera are the hosts for a particularly diverse range of endosymbiotic algae, including dinoflagellates, chlorophytes, unicellular rhodophytes, and diatoms. Chloroplast husbandry also occurs. Significant research effort has been expended yielding us considerable insight into various aspects of the endosymbiotic phenomenon. A unified conceptual framework has been drawn to help us understand the life cycle options found in foraminifera.     

Enzymatic RNA synthesis and RNase P

TransferRNA recognition was used as leit-motiv in the illustration of possible links between a hypothetical primordial RNA world and the contemporary DNA world. In an RNA world, proto-tRNA could have functioned as replication origin and as primitive telomere. Possibly, this primitive structure is preserved in a universal substrate for modern tRNA-specific enzymes. The combination of acceptor stem and T arm (plus a linker) was finally revealed as sufficient for the recognition by prokaryotic and eukaryotic RNase P, as well as other tRNA enzymes. In modern life forms, a tRNA-like element in viral RNAs still serves as replication origin, and furthermore, the recognition of similar structures as cryptic promoters is universally conserved for template-dependent RNA polymerases. Another common property of modern polymerases is their high, but clearly limited and condition-dependent substrate specificity. Very likely, also substrate recognition by primitive polymerases was not more stringent, and this lead to the ocurrence of mixed nucleic acids as intermediates in the transition from genomic RNA to contemporary genomic DNA.Abbreviations (d)NTP (deoxy)nucleoside triphosphate - nt nucleotide(s)     

A stem-loop "kissing" model for the initiation of recombination and the origin of introns

Mutations which improve the efficiency of recombination should affect either the proteins which mediate recombination or their substrate, DNA itself. The former mutations would be localized to a few sites. The latter would be dispersed. Studies of hybridization between RNA molecules have suggested that recombination may be initiated by a homology search involving the "kissing" of the tips of stem loops. This predicts that, in the absence of other constraints, mutations which assist the formation of stem loops would be favored. From comparisons of the folding of normal and shuffled DNA sequences, I present evidence for an evolutionary selection pressure to distribute stem loops generally throughout genomes. I propose that this early pressure came into conflict with later local pressures to impose information concerning specific function. The conflict was accommodated by permitting sections of DNA concerned with a specific function to evolve in dispersed segments. Traces of the conflict seem to be present in some modern intron-containing genes. Thus, introns may have allowed the interspersing of selectively advantageous stem loops in coding regions of DNA.      

A requirement for trypsin-sensitive cell-surface components for cell-cell interactions of embryonic neural retina cells

A quantitative assay was used to measure the rate of collection of a population of embryonic neural retina cells to the surface of cell aggregates. The rate of collection of freshly trysinized cells was limited in the initial stages by the rate of replacement of trypsin-sensitive cell- surface components. When cells were preincubated, or "recovered," and then added to cell aggregates, collection occurred at a linear rate and was independent of protein and glycoprotein synthesis. The adhesion of recovered cells was temperature and energy dependent, and was reversibly inhibited by cytochalasin B. Colchicine had little effect on collection of recovered cells. Antiserum directed against recovered cell membranes was shown to bind to recovered cells by indirect immunofluorescence. The antiserum also was shown to inhibit collection of recovered cells to aggregates, suggesting that at least some of the antigens identified might be involved in the adhesion process. The inhibitory effect of the antiserum was dose dependent . Freshly trypsinized cells absorbed neither the immunofluorescence activity nor the adhesion-inhibiting activity. Recovered cells absorbed away both activities. In specificity studies, dorsal neural retina cells adhered to aggregates of ventral optic tectum in preference to aggregates of dorsal optic tectum. The adhesive specificity of the dorsal retina cells was less sensitive to trypsin than the adhesive specificity of ventral retina cells which adhered preferentially to dorsal tectal aggregates only after a period of recovery.     

A highly multiplexed quantitative phosphosite assay for biology and preclinical studies

Reliable methods to quantify dynamic signaling changes across diverse pathways are needed to better understand the effects of disease and drug treatment in cells and tissues but are presently lacking. Here, we present SigPath, a targeted mass spectrometry (MS) assay that measures 284 phosphosites in 200 phosphoproteins of biological interest. SigPath probes a broad swath of signaling biology with high throughput and quantitative precision. We applied the assay to investigate changes in phospho‐signaling in drug‐treated cancer cell lines, breast cancer preclinical models, and human medulloblastoma tumors. In addition to validating previous findings, SigPath detected and quantified a large number of differentially regulated phosphosites newly associated with disease models and human tumors at baseline or with drug perturbation. Our results highlight the potential of SigPath to monitor phosphoproteomic signaling events and to nominate mechanistic hypotheses regarding oncogenesis, response, and resistance to therapy.     

BlotBase: a northern blot database

With the availability of high-throughput gene expression analysis, multiple public expression databases emerged, mostly based on microarray expression data. Although these databases are of significant biomedical value, they do hold significant drawbacks, especially concerning the reliability of single gene expression profiles obtained by microarray data. Simultaneously, reliable data on an individual gene's expression are often published as single northern blots in individual publications. These data were not yet available for high-throughput screening. To reduce the gap between high-throughput expression data and individual highly reliable expression data, we designed a novel database "BlotBase", a freely and easily accessible database, currently containing approximately 700 published northern blots of human or mouse origin (http://www.medicalgenomics.org/Databases/BlotBase). As the database is open for public data submission, we expect this database to quickly become a large expression profiling resource, eventually providing higher reliability in high-throughput gene expression analysis. Realizing BlotBase, Pubmed was searched manually and by computer based text mining methods to obtain publications containing northern blot results. Subsequently, northern blots were extracted and expression values of different tissues calculated utilizing Image J. All data were made available through a user friendly web front end. The data may be searched by either full text search or list of available northern blots of a specific tissue. Northern blot expression profiles were displayed by three expression states as well as a bar chart, allowing for automated evaluation. Furthermore, we integrated additional features, e.g. instant access to the corresponding RNA sequence or primer design tools making further expression analysis more convenient. Finally, through a semiautomatic submission system this database was opened to the bioinformatics community.     

Diets high in selenium and isoflavones decrease androgen-regulated gene expression in healthy rat dorsolateral prostate

Background  

High dietary intake of selenium or soybean isoflavones reduces prostate cancer risk. These components each affect androgen-regulated gene expression. The objective of this work was to determine the combined effects of selenium and isoflavones on androgen-regulated gene expression in rat prostate.     

Influences of dietary soy isoflavones on metabolism but not nociception and stress hormone responses in ovariectomized female rats

Background  

Isoflavones, the most abundant phytoestrogens in soy foods, are structurally similar to 17beta-estradiol. Few studies have examined the nociception and stress hormone responses after consumption of soy isoflavones.     

CULTURING,ULTRASTRUCTURE AND COLONY FORMATION IN PECTODICTYON CUBICUM (CHLOROPHYCEAE,CHLOROCOCCALES) 12

Pectodictyon cubicum Taft collected in California develops typical eight-celled, cuboidal colonies only in alkaline media. Vegetative cell ultrastructure is similar to that in other genera of the Chlorococcales, except for an extensive endoplasmic reticulum system paralleling the plasmalemma (termed a paramural ER). Autosporogenesis proceeds inside the parent cell wall by three mitotic divisions producing eight nuclei in two tiers of four. Cleavage furrows following paths delineated by long ER segments and indistinct microtubules bisect and then radically separate the protoplast into eight pyramidal units. Walls comprised of a thick, presumably cellulose layer and a thinner trilaminar layer (not acetolysis resistant) form as cells become rounded, except where touching. A gelatinous matrix is produced around and between cells with concentration at the three sites of prior cell contact 90 degrees apart. Pulsed production of mucilage in three solid strands forces cells to separate, and the expanding colony becomes a hollow cube with a cell at each corner.