Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

Population structure, recruitment, and succession of the brown alga, Padina boryana Thivy (Dictyotales, Heterokontophyta), at an exposed shore of Sirinart National Park and a sheltered area of Tang Khen Bay, Phuket Province, Thailand

The brown algal genus, Padina, has a worldwide distribution in tropical and subtropical climate zones. Padina individuals are common and sometimes dominant in both the intertidal and shallow subtidal regions associated with coral reefs. We investigated the population structure and recruitment of two populations of Padina boryana at an exposed shore in Sirinart National Park (SNP) and a sheltered shore of Tang Khen Bay (TKB), Phuket Province, Thailand. From September 2005 to August 2006, the number of released spores and the height and radius of fronds were measured monthly. New recruits were recorded and monitored on manipulated permanent plots 0.25 m². The experiment was carried out monthly over a year. We found Padina recruits 1 month after the plots were cleared at both sites. There was a significant difference in percentage cover by new individuals between the two locations (P < 0.05) and also at the shore levels within the sites. At SNP, the highest recruitment was found in the uppermost zone, while at TKB high recruitment occurred at all shore levels except at 80-100 m from the shore. The factors influencing recruitment of P. boryana include wave motion, competition with other earlier successional species and sediment. The high availability of reproductive spores throughout the year, the successful recruitment and the Dictyerpa stage promote the successful establishment of Padina populations.     

An Efficient Regression Type Estimator in Survey Sampling

For the estimation of population mean in simple random sampling, an efficient regression-type estimator is proposed which is more efficient than the conventional regression estimator and hence than mean per unit estimator, ratio and product estimators and many other estimators proposed by various authors. Some numerical examples are included for illustration.     

Genetic differentiation of Elysia timida (Risso, 1818) populations in the Southwest Mediterranean and Mar Menor coastal lagoon

Genetic variation at 10 enzyme loci was analysed in Elysia timida sacoglossan mollusc samples, originating from both coastal lagoon and marine sites. The observed heterozygosity ranged from 0.390 (Los Urrutias) to 0.277 (Tabarca). Marine and coastal lagoon populations were characterised by exclusive alleles.     

Low mtDNA Cytb diversity and shallow population structure of Eleutheronema tetradactylum in the East China Sea and the South China Sea

Eleutheronema tetradactylum is an economically important fish species in China water. To investigate the genetic diversity and describe population structure of it, an 1151 base pair (bp) fragment of the mitochondrial DNA Cytb sequence was analyzed in 120 individuals from four populations in the East China Sea and the South China Sea. A total of 16 haplotypes were defined by 24 variable nucleotide sites. High level of haplotype diversity and low nucleotide diversity were observed in all populations. The results of AMOVA detected that 89.44% of the genetic variation occurred within populations. Significant genetic differentiations were detected among populations (0.05097, P < 0.05), but no large-scale regional differences were detected. Analysis of neutral evolution and mismatch distribution suggested no recent population expansion happened. The present results provided new information for genetic assessment, fishery management and conservation of this species.     

The Effect of Leaf Age on Gas Exchange and Malate Accumulation in C3-CAM Plant Marrubium Frivaldszkyanum (Lamiaceae)

For the first time the expression of C₃ and CAM in the leaves of different age of Marrubium frivaldszkyanum Boiss, is reported. With increasing leaf age a typical C₃ photosynthesis pattern and high transpiration rate were found. In older leaves a shift to CAM occurred and the 24-h transpiration water loss decreased. A correlation was established between leaf area and accumulation of malate. Water loss at early stages of leaf expansion may be connected with the shift to CAM and the water economy of the whole plant.     

Multiple mating and sperm displacement in a natural population of Drosophila melanogaster

Summary Mother-offspring data for alcohol dehydrogenase genotypes of a vineyard cellar population of D. melanogaster are best explained by a model that allows 21% of females in the population to mate twice with an 83% level of sperm displacement. A population model with multiple mating and sperm displacement is examined theoretically. A formula for the effective population size is derived under this model. Multiple mating increases the effective population size relative to single mating.     

Interspecific competition between two species of the bean weevil

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Contributions from the Entomological Laboratory, Kyoto University, No. 110.     

Voting with your feet: Payoff biased migration and the evolution of group beneficial behavior

Human migration is nonrandom. In small scale societies of the past, and in the modern world, people tend to move to wealthier, safer, and more just societies from poorer, more violent, less just societies. If immigrants are assimilated, such nonrandom migration can increase the occurrence of culturally transmitted beliefs, values, and institutions that cause societies to be attractive to immigrants. Here we describe and analyze a simple model of this process. This model suggests that long run outcomes depend on the relative strength of migration and local adaptation. When local adaption is strong enough to preserve cultural variation among groups, cultural variants that make societies attractive always predominate, but never drive alternative variants to extinction. When migration predominates, outcomes depend both on the relative attractiveness of alternative variants and on the initial sizes of societies that provide and receive immigrants.     

Self-association of glutamic acid-rich fusion peptide analogs of influenza hemagglutinin in the membrane-mimic environments: Effects of positional difference of glutamic acids on side chain ionization constant and intra- and inter-peptide interactions deduced from NMR and gel electrophoresis measurements

Two glutamic acid-rich fusion peptide analogs of influenza hemagglutinin were synthesized to study the organization of the charged peptides in the membranous media. Fluorescence and gel electrophoresis experiments suggested a loose association between the monomers in the vesicles. A model was built which showed that a positional difference of 3, 7 and 4, 8 results in the exposure of Glu3 and Glu7 side chains to the apolar lipidic core. Supportive results include: first, pK_a values of two pH units higher than reference value in aqueous medium for Glu3 and Glu7 CγH, whereas the deviation of pK_a from the reference value for Glu4 and Glu8 CγH is substantially smaller; second, Hill coefficients of titration shift of these protons indicate anti-cooperativity for Glu3 and Glu7 side chain protons but less so for Glu4 and Glu8, implying a strong electrostatic interaction between Glu3 and Glu7 possibly resulting from their localization in an apolar environment; third, positive and larger titration shift for NH of Glu3 is observed compared to that of Glu4, suggesting stronger hydrogen bond between the NH and the carboxylic group of Glu3 than that of Glu4, consistent with higher degree of exposure to hydrophobic medium for the side chain of Glu3.