Specific stimulation of ribosomal RNA synthesis in E. coli by a protein factor

Summary Ribosomal RNA synthesis in a purified system is stimulated by a crude protein fraction prepared from E. coli. The positive effector which is not associated with RNA polymerase, nor is the sigma factor, increases the initiation frequency on a rRNA operon. The additional rRNA synthesis is inhibited by ppGpp to the same extent as the basal one.The evidence presented points to the existence of a positive control element for rRNA synthesis, which activity depends upon the physiological state of the cell.     

The Hartnup phenotype: Mendelian transport disorder, multifactorial disease.

The Hartnup mutation affects an amino acid transport system of intestine and kidney used by a large group of neutral charge alpha-amino acids (six essential and several nonessential). We compared developmental outcomes and medical histories of 21 Hartnup subjects, identified through newborn screening, with those of 19 control sibs. We found no significant differences in means of growth percentiles and IQ scores between Hartnup and control groups (but all low academic performance scores were found in the Hartnup group, and various skin lesions occurred in five Hartnup subjects), no significant difference between means of the summed plasma values for amino acids affected by the Hartnup gene in Hartnup and control groups, two Hartnup subjects with clinical manifestations--impaired somatic growth and IQ in one, impaired growth and a "pellagrin" episode in the other--who had the lowest summed plasma amino acid values in the Hartnup group; the corresponding values for their sibs were the low outliers in the control group, and two tissue-specific forms of the Hartnup (transport) phenotype: renal and intestinal involvement (15 families) and renal involvement alone (one family), both forms having been inherited as autosomal recessives (the symptomatic probands had the usual form). Whereas deficient activity of the "Hartnup" transport system is monogenic, the associated plasma amino acid value (measured genotype) is polygenic. The latter describes the parameter of homeostasis and liability to disease. Cause of Hartnup disease is multifactorial.     

Estrogen-Induced Synthesis of Yolk Proteins in Roosters

Vitellogenin is the serum precursor of the yolk proteins -lipovitellin,rß-lipovitellin, and phosvitin. The precursor canbe dissociated to produce the yolk proteins only by proteolyticenzymatic action, to which it is very susceptible. Denaturationin sodium dodecyl sulfate, combined with reduction of disulfidebridges and blocking of thiols, yields a complex with a molecularweight of 200,000 to 250,000. -Lipovitellin contains three polypeptides,with molecular weights of about 135,000, 105,000, and 40,000,and rß-lipovitellin is composed of two polypeptidechains with molecular weights of 135,000 and 30,000. The 40,000subunit of -lipovitellin and both rß-lipovitellinsubunits are phosphopeptides We tested RNA isolated from the liver of estrogen-treated roostersfor mRNA activity in a cell-free reticulocyte system. The vitellogeninmRNA has a sedimentation coefficient greater than 28S and thuscontains enough information to code for a long polypeptide chain.Estrogen administration to roosters induces the appearance ofvitellogenin and a lowdensity lipoprotein, the syntheses ofwhich are not coordinated. The course of vitellogenin synthesiswas calculated from accumulation and turnover data, and it wasfound that from about 25 hr after estradiol-17rß administrationthe rate of vitellogenin synthesis increases linearly for severaldays, paralleling an increase in vitellogenin-synthesizing polysomes.Thus, we estimate a constant translation rate of about 8 aminoacids per ribosome per sec. A "memory" effect is observed when a second hormone dose isgiven some time after the vitellogenin induced by the firstdose has disappeared from the blood. After the second dose vitellogeninsynthesis is detected sooner, and its initial increase is morerapid, than after the first dose. Although the synthesis ofvitellogenin starts 3 to 4 hr after the second as well as afterthe first injection, the rate of synthesis after the first injectionincreases much more slowly during the first 15 hr than duringthe subsequent period of linear accumulation, whereas afterthe second injection the linear increase in the rate of synthesisbegins immediately after the lag period of 3 to 4 hr. The "memory"effect is undiminished even 50 days after the first hormonedose; thus, the causative factor either is very stable or issynthesized in great excess during the first stimulation. Whenthe second injection is given during the descending part ofthe turnover curve, an increase in vitellogenin synthesis isobserved within 3.5 hr. There are thus at least three different effects of estradiol;(i) the "memory" effect, which probably is due to commitmentor differentiation of vitellogenin-synthesizing cells; (ii)the effect that causes the committed cells to give full responseafter the 3- to 4-hr lag period; and (iii) the effect that causesthe immediate response. To explain these results we suggestthat committed cells can synthesize vitellogenin mRNA only duringa certain period of the cell cycle.     

Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain

The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer α-β sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain.     

Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes

Although a highly heritable and disabling disease, bipolar disorder''s (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,434 controls. We do not detect genome-wide significant associations for individual loci; however, across all SNPs, we show an association between the power to detect effects calculated from a previous genome-wide association study and evidence for replication (P = 1.5×10⁻⁷). To demonstrate that this result is not likely to be a false positive, we analyze replication rates in a large meta-analysis of height and show that, in a large enough study, associations replicate as a function of power, approaching a linear relationship. Within BD, SNPs near exons exhibit a greater probability of replication, supporting an enrichment of reproducible associations near functional regions of genes. These results indicate that there is likely common genetic variation associated with BD near exons (±10 kb) that could be identified in larger studies and, further, provide a framework for assessing the potential for replication when combining results from multiple studies.     

Utility of arginine kinase for resolution of phylogenetic relationships among Brachyuran genera and families

The molecular phylogenetics of decapod crustaceans has been based on sequence data from a limited number of genes. These have included rapidly evolving mitochondrial genes, which are most appropriate for studies of closely related species, and slowly evolving nuclear ribosomal RNA genes, which have been most useful for resolution of deep branches within the Decapoda. Here we examine the utility of the nuclear gene that encodes arginine kinase for phylogenetic reconstruction at intermediate levels (relationships among genera and families) within the decapod infraorder Brachyura (the true crabs). Analyses based on arginine kinase sequences were compared and combined with those for the mitochondrial cytochrome oxidase I gene. All of the genera in our taxon sample were resolved with high support with arginine kinase data alone. However, some of these genera were grouped into clades that are in conflict with recognized brachyuran families. A phylogeny based on cytochrome oxidase I was consistent with the arginine kinase phylogeny, but with weaker support. A recently proposed measure of phylogenetic informativeness indicated that arginine kinase was generally more informative than cytochrome oxidase I for relationships above the level of genus. Combined analysis of data from both genes provided strong support for clades that are in conflict with current assignments of genera to the families Epialtidae, Mithracidae, Pisidae, and Portunidae.     

The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3

Background  

SH3 domains are small protein modules of 60–85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the α-spectrin SH3 domain (Spc-SH3).     

Innate Recognition by Host Fish of their Cleaning Symbiont

Naive damselfish, Dascyllus albisella, were tested for their initial response to the Hawaiian cleaning wrasse, Labroides phthirophagus. Contrary to some current theory, some individuals, including both lab-reared and wild-caught fish, showed a full ‘pose’ response to visual stimuli from the cleaner without prior tactile stimulation, while others failed to show this response even after 4 d of exposure to visual and tactile stimuli. These individual differences could have resulted from innate differences or uncontrolled variables in their experience.     

Mean species responses predict effects of environmental change on coexistence

Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. Here, we show evidence that this is indeed possible. Using theoretical and simulation-based evidence for bi- and tritrophic communities, we show that environmental change effects on coexistence are proportional to mean species responses and depend on how trophic levels on average interact prior to environmental change. We then benchmark our findings using relevant cases of environmental change, showing that means of temperature optima and of species sensitivities to pollution predict concomitant effects on coexistence. Finally, we demonstrate how to apply our theory to the analysis of field data, finding support for effects of land use change on coexistence in natural invertebrate communities.