Upregulation of PHLDA2 in Dicer knockdown HEK293 cells

It has been reported that RNAi-dependent chromatin silencing in vertebrates is not restricted to the centromeres. To address whether RNAi machinery could regulate the chromatin structure of imprinted genes, we knocked down Dicer in HEK293 cells and found that the expression of PHLDA2, one of the several genes in the imprinted gene domain of 11p15.5, was specifically upregulated. This was accompanied by a shift towards more activated chromatin at PHLDA2 locus as indicated by change in H3K9 acetylation, however, the methylation state at this locus was not affected. Furthermore, we found that PHLDA2 was downregulated in growth-arrested HEK293 cells induced by either serum deprivation or contact inhibition. This suggests that PHLDA2 upregulation might be a direct result of Dicer depletion rather than the consequence of growth arrest induced by Dicer knockdown. Considering the reports that there is consistent placental outgrowth in PHLDA2 knockout mice and that PHLDA2 overexpression in mice causes growth inhibition, we speculate that PHLDA2 may be a candidate for contributing to the reduced growth rate of Dicer-deficient cells and the very early embryonic lethality in Dicer knockout mice.     

Transgenerational changes in the genome stability and methylation in pathogen-infected plants: (virus-induced plant genome instability)

Previously, we reported the generation of a virus-induced systemic signal that increased the somatic and meiotic recombination rates in tobacco mosaic virus (TMV)-infected tobacco plants. Here, we analyzed the progeny of plants that received the signal and found that these plants also have a higher frequency of rearrangements in the loci carrying the homology to LRR region of the gene of resistance to TMV (N-gene). Analysis of the stability of repetitive elements from Nicotiana tabacum loci and 5.8S ribosomal RNA loci did not show any changes. Further analysis of the changes in the progeny of infected plants revealed that they had substantially hypermethylated genomes. At the same time, loci-specific methylation analysis showed: (1) profound hypomethylation in several LRR-containing loci; (2) substantial hypermethylation of actin loci and (3) no change in methylation in the loci of repetitive elements from N. tabacum or 5.8S ribosomal RNA. Global genome hypermethylation of the progeny is believed to be part of a general protection mechanism against stress, whereas locus-specific hypomethylation is associated with a higher frequency of rearrangements. Increased recombination events combined with the specific methylation pattern induced by pathogen attack could be a sign of an adaptive response by plants.     

Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site

Small cytoplasmic RNA (scRNA) of Bacillus subtilis is the RNA component of the signal recognition particle. scRNA is transcribed as a 354-nt precursor, which is processed to the mature 271-nt scRNA. Previous work demonstrated the involvement of the RNase III-like endoribonuclease, Bs-RNase III, in scRNA processing. Bs-RNase III was found to cleave precursor scRNA at two sites (the 5′ and 3′ cleavage sites) located on opposite sides of the stem of a large stem-loop structure, yielding a 275-nt RNA, which was then trimmed by a 3′ exoribonuclease to the mature scRNA. Here we show that Bs-RNase III cleaves primarily at the 5′ cleavage site and inefficiently at the 3′ site. RNase J1 is responsible for much of the cleavage that releases scRNA from downstream sequences. The subsequent exonucleolytic processing is carried out largely by RNase PH.     

CAF1 plays an important role in mRNA deadenylation separate from its contact to CCR4

The CAF1 protein is a component of the CCR4–NOT deadenylase complex. While yeast CAF1 displays deadenylase activity, this activity is not required for its deadenylation function in vivo, and CCR4 is the primary deadenylase in the complex. In order to identify CAF1-specific functional regions required for deadenylation in vivo, we targeted for mutagenesis six regions of CAF1 that are specifically conserved among CAF1 orthologs. Defects in residues 213–215, found to be a site required for binding CCR4, reduced the rate of deadenylation to a lesser extent and resulted in in vivo phenotypes that were less severe than did defects in other regions of CAF1 that displayed greater contact to CCR4. These results imply that CAF1, while affecting deadenylation through its contact to CCR4, has functions in deadenylation separate from its contact to CCR4. Synthetic lethalities of caf1Δ, but not that of ccr4Δ, with defects in DHH1 or PAB1, both of which are involved in translation, further supports a role of CAF1 separate from that of CCR4. Importantly, other mutations in PAB1 that reduced translation, while not affecting deadenylation by themselves or when combined with ccr4Δ, severely blocked deadenylation when coupled with a caf1 deletion. These results indicate that both CAF1 and factors involved in translation are required for deadenylation.     

Nickel-Resistant Determinant from Leptospirillum ferriphilum

Leptospirillum ferriphilum strain UBK03 isolated from a mine in Jiangxi, China, is resistant to Ni²⁺ (30 to 40 mM). A four-gene nickel resistance cluster was identified and, when transformed into Escherichia coli, enabled growth in 6 mM nickel. Mutation experiments revealed that the genes ncrA, ncrB, and ncrC could confer nickel resistance in Escherichia coli, whereas the gene ncrY could have a negative effect on nickel resistance.     

Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.     

Environmental changes in Lake Taihu during the past century as recorded in sediment cores

The Lake Taihu drainage basin is an economically developed area with some of the highest population densities in China. The lake has deteriorated due to ecological destruction and eutrophication. Three short sediment cores from eastern, northeastern and southwestern Lake Taihu were collected. Total organic carbon (TOC), total nitrogen (TN), pigments, elements and particle size were analyzed for the purpose of understanding past trophic status and pollution levels. Sedimentation rates were based on ¹³⁷Cs or ²¹⁰Pb methods. Results indicated that sediment particle size became coarser since the 1920s, and the lake was contaminated by heavy metals, such as Cu and Zn, since the 1970s. A remarkable increase in eutrophication since the 1980s due to increased loading of untreated effluents from industry, agriculture and urbanization is reflected by total organic carbon, total nitrogen and pigments in the studied cores. However the onset times of eutrophication in different parts of Lake Taihu were not synchronous.     

Magnetic investigation of two helical frameworks derived from mixed ligands

Although the 2,2′-biphenyldicarboxylate ligand (2,2′-dpa) has been widely used to construct metal-organic frameworks (MOFs) with helical sub-structure, the effect of the helical arrangement of spin carriers on the magnetic properties remains rarely scarce. In this article, two unique magnetic metal-organic supramolecular frameworks with different structural features, [Cu₂(dpa)₂(H₂O)₂(4,4′-dpdo)_0.5]_n (1) and [Ni(H₂O)₄(dpa)] · (4,4′-dpdo)(H₂O) (2) (dpdo = 4,4′-dipyridine-N,N′-dioxide), have been isolated from the direct reaction of H₂dpa with their corresponding salts in the presence of dpdo. In complex 1, the Cu-dpa double-helical chains, which are bridged by long flexible μ₂-dpdo ligands to give rise to a regular 6³ covalent layer, exhibit strong antiferromagnetic coupling interactions. Whereas the 1D [Ni(dpa)]_n helical chains in complex 2 exhibit weak antiferromagnetic coupling interactions. Rich hydrogen bonds between perpendicular 1D [Ni(dpa)]_n helical chains and quasi-1D (dpdo)_n chains result in an intricate 3D supramolecular network.     

Ketonization of methylene of bis(benzimidazol-2-yl)methane by molecular oxygen under the catalysis of cobalt(II) ion

A cobalt(II) complex [Co((bnzim)₂CO)Cl₂] (1) (where (bnzim)₂CO; bis(benzimidazol-2-yl)methanone), was obtained by reacting cobalt(II) chloride with bis(benzimidazol-2-yl)methane ((bnzim)₂CH₂) in CH₃OH/CH₃CN and characterized using EA, IR, XRD and X-ray single crystal diffraction. The process of ketonization of methylene of (bnzim)₂CH₂ was investigated using spectroscopy and electrochemistry method. The experimental results reveal that there were new species forming in the reaction system and the formation of new species was related to the dissolving oxygen in the mixture. Oxygenation mechanism was thus proposed, in which oxygen atom transfer from a superoxo intermediate species {((bnzim)₂CH₂)Co(III)-O-O} to the methylenic carbon of (bnzim)₂CH₂, and then goes O-O hemolytic cleavage and hydrogen migration to give intermediate species [Co((bnzim)₂CHOH)]²⁺. The ketonization was achieved after [Co((bnzim)₂CHOH)]²⁺repeating the process.     

Chronic sodium hydrosulfide treatment decreases medial thickening of intramyocardial coronary arterioles, interstitial fibrosis, and ROS production in spontaneously hypertensive rats

Hydrogen sulfide (H(2)S) is a gasotransmitter that regulates cardiovascular functions. The present study aimed to examine the hypothesis that chronic treatment with sodium hydrosulfide (NaHS, an H(2)S donor) is able to prevent left-ventricular remodeling in spontaneously hypertensive rats (SHR). Four-week-old SHR were treated with NaHS (10, 30, and 90 micromol x kg(-1) x day(-1)), a combination of NaHS (30 micromol x kg(-1) x day(-1)) and glibenclamide (5 mg x kg(-1) x day(-1)), glibenclamide alone (5 mg x kg(-1) x day(-1)), hydralazine alone (10 mg x kg(-1) x day(-1)), and placebo for 3 mo. At the end of the treatment period, variables such as cardiac geometry and function, intramyocardial arterioles ranging in diameter from 25 to 100 microm, perivascular and interstitial collagen content, reactive oxygen species (ROS), thiol groups, conjugated dienes, and DNA base modification were examined. The novel finding of the present study is that chronic NaHS treatment prevented the hypertrophy of intramyocardial arterioles and ventricular fibrosis, as well as decreased myocardial ROS and conjugated diene levels. The cardioprotective effects were blunted by coadministration of glibenclamide, suggesting a role of ATP-sensitive potassium channels in mediating the action of NaHS. Hydralazine caused a comparable reduction of blood pressure compared with NaHS treatment; however, it exerted no effect on the remodeling process or on ROS and conjugated diene levels. Moreover, NaHS treatment caused an increase in myocardial thiol group levels, whereas DNA base modification was not altered by NaHS treatment. In conclusion, the superior cardioprotective effects of NaHS treatment are worthy to be further explored to develop novel therapeutic approaches for the treatment of cardiac remodeling in hypertension.