Use of Wishart Prior and Simple Extensions for Sparse Precision Matrix Estimation

A conjugate Wishart prior is used to present a simple and rapid procedure for computing the analytic posterior (mode and uncertainty) of the precision matrix elements of a Gaussian distribution. An interpretation of covariance estimates in terms of eigenvalues is presented, along with a simple decision-rule step to improve the performance of the estimation of sparse precision matrices and associated graphs. In this, elements of the estimated precision matrix that are zero or near zero can be detected and shrunk to zero. Simulated data sets are used to compare posterior estimation with decision-rule with two other Wishart-based approaches and with graphical lasso. Furthermore, an empirical Bayes procedure is used to select prior hyperparameters in high dimensional cases with extension to sparsity.     

The promoters of Arabidopsis thaliana genes AtCOX17-1 and -2, encoding a copper chaperone involved in cytochrome c oxidase biogenesis, are preferentially active in roots and anthers and induced by biotic and abiotic stress

AtCOX17 genes encode Arabidopsis thaliana homologs of the yeast metallochaperone Cox17p, involved in the delivery of copper for cytochrome c oxidase (COX) assembly. Two different AtCOX17 genes, located in chromosomes 1 and 3, are present in the Arabidopsis genome. Sequences available in data banks indicate that the presence of two genes is a common feature in monocots, but not in dicots, suggesting that Arabidopsis genes may be the result of a recent duplication. Sequences upstream from the translation start sites of AtCOX17 genes, which include an intron located in the 5' leader region, were introduced into plants in front of the gus gene. For both genes, expression was localized preferentially in young roots and anthers, but almost 10-fold higher β-glucuronidase activity levels were observed in plants transformed with AtCOX17-1 upstream regions. Both promoters were induced to different extents by wounding, treatment of leaves with the bacterial pathogen Pseudomonas syringae and incubation with agents that produce oxidative stress and metals. AtCOX17-2 showed similar responses to these factors, while AtCOX17-1 was more strongly induced by relatively low (10–100 μ M ) copper. The results indicate that both AtCOX17 genes have similar, though not identical, expression characteristics and suggest the existence in their promoters of elements involved in tissue-specific expression and in responses to factors that may produce mitochondrial or cell damage. It can be speculated that Arabidopsis COX17 accumulates under stress conditions to actively replace damaged or inactive cytochrome c oxidase to sustain cyanide-sensitive respiration in plant cells.     

Huntington disease in Finland: a molecular and genealogical study

Summary Huntington disease (HD) is found at exceptionally low frequency in the Finnish population. In this population, linkage disequilibrium was earlier established with markers from the D4S10 and D4S43 loci. We now report a continuation to the restriction fragment length polymorphism haplotype analysis, in combination with a genealogical study of all the Finnish HD families. When the HD pedigrees were systematically traced to the 18th century, only one consanguinity was found, and a high percentage (28%) of the families had foreign ancestors. The majority of the Finnish ancestors were localized to border regions or trade centers of the country following the old postal routes. The observed high risk haplotypes formed with markers from the D4S10 and D4S43 loci were evenly distributed among the HD families in different geographical locations. Consequently, the HD gene(s) has most probably arrived in Finland on several occasions via foreign immigrants during the last few centuries.     

Distribution of Chlorophyll-Protein Complexes during Chilling in the Light Compared with Heat-Induced Modifications

The effects of chilling in the light (4 days at 5°C and 100-200 micromoles of photons per square meter per second) on the distribution of chlorophyll (Chl) protein complexes between appressed and nonappressed thylakoid regions of pumpkin (Cucurbita pepo L.) chloroplasts were studied and compared with the changes occurring during in vitro heat treatment (5 minutes at 40°C) of isolated thylakoids. Both treatments induced an increase (18 and 65%, respectively) in the relative amount of the antenna Chl a protein complexes (CP47 + CP43) of photosystem II (PSII) in stroma lamellae vesicles. Freeze-fracture replicas of light-chilled material revealed an increase in the particle density on the exoplasmic fracture face of unstacked membrane regions. These two treatments differed markedly, however, in respect to comigration of the light-harvesting Chl a/b protein complex (LHCII) of PSII. The LHCII/PSII ratio in stroma lamellae vesicles remained fairly constant during chilling in the light, whereas it dropped during the heat treatment. Moreover, it was a minor light-harvesting Chl a/b protein complex of PSII, CP29, that increased most in stroma lamellae vesicles during light-chilling. Changes in the organization of LHCII during chilling were suggested by a shift to particles of smaller sizes on the protoplasmic fracture face of stacked membrane regions and a decrease in the amount of trans-Δ³-hexadecenoic acid in the phosphatidyldiacylglycerol fraction.     

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.     

Cloning and characterization of the platypus mitochondrial genome

The vertebrate mitochondrial genome is highly conserved in size and gene content. Among the chordates there appears to be one basic gene arrangement, but rearrangements in the mitochondrial gene order of the avian lineages have indicated that the mitochondrial genome may be more variable than once thought. Different gene orders in marsupials and eutherian mammals leave the ancestral mammalian order in some doubt. We have investigated the mitochondrial gene order in the platypus (Ornithorhynchus anatinus), a representative of the third major group of mammals, to determine which mitochondrial gene arrangement is ancestral in mammals. We have found that the platypus mtDNA conforms to the basic chordate gene arrangement, common to fish, amphibians, and eutherian mammals, indicating that this arrangement was the original mammalian arrangement, and that the unusual rearrangements observed in the avians and marsupials are probably lineage-specific. Correspondence to: N.J. Gemmell     

Chlorophyll-Protein Complexes in Salix sp. 'Aquatica Gigantea' under Strong and Weak Light I. Spectral Characterization of the Chlorophyll-Protein Complexes

The distribution of chlorophyll in the chlorophyll-protein complexeswas studied in Salix sp. ‘aquatica gigantea’ grownunder high and low irradiance. The chlorophyll- containing bandsthat could be separated by SDS-polyacrylamide gel electrophoresisin strong and weak light numbered 9 to 13 and 9 to 11, respectively.In strong light the following bands were separated, in the orderof the highest to the lowest molecular weight: one to two chlorophylla/b-protein complexes, three to four chlorophyll a-containingbands similar to the P700-chlorophyll a-protein complex (CPIand its oligomers), three oligomers of the light-harvestingchlorophyll a/b-protein complex (LHCP^***, LHCP^**, LHCP^*), twochlorophyll a-protein complexes (CPa₂ and CPa₁), the light-harvestingchlorophyll a/b-protein complex (LHCP) and the protein freepigment (FP). In weak light the same chlorophyll-containingbands were separated with the exception that no high molecularweight chlorophyll a/b-protein complexes could be observed.In strong light the CPI complexes were the largest structuralcomponent of the chloroplast lamellae. In weak light the LHCPcomplexes together contributed the major proportion of the totalchlorophyll. The increase in the chlorophyll associated withthe LHCP complex was possibly caused by reorganization of thelamellar structure or by increased synthesis of the LHCP^** complex,which appeared to be a labile complex in weak light. (Received February 1, 1982; Accepted May 10, 1982)