The Changjiang estuary and the coastal area of the East China Sea (ECS) represent important interfaces of terrestrial and marine environments. This study included analyses of water and sediments collected during different seasons in these regions to determine the composition of microbial assemblages by means of 16S rRNA gene clone libraries. We retrieved 1946 sequences and 779 distinct operational taxonomic units from 36 clone libraries. Shannon-Weaver diversity index values and rarefaction analysis indicated that bacterial diversity in the sediment samples was much higher than in the water samples. Proteobacteria (72.9%) was the most abundant phylum, followed by Firmicutes (6.4%), Bacteroidetes (4.6%) and Actinobacteria (4.1%). In the water, clone sequences related to Alphaproteobacteria were the most abundant, whereas in the sediment samples, sequences affiliated with Gammaproteobacteria were predominant. Principal coordinate analysis showed that water samples collected from the Changjiang estuary and the ECS clustered separately. However, this spatial pattern could not be observed in sediment samples, which were mainly distinguished from one another by the season. Bacterial diversity in the Changjiang estuary was higher than that in the ECS, which may be the result of the mixing of bacterial communities from the Changjiang River, the estuary and the coastal ocean.

BackgroundDNA damage response (DDR) plays pivotal roles in maintaining genome integrity and stability. An effective DDR requires the involvement of hundreds of genes that compose a complicated network. Because DDR is highly conserved in evolution, studies in lower eukaryotes can provide valuable information to elucidate the mechanism in higher organisms. Fission yeast (Schizosaccharomyces pombe) has emerged as an excellent model for DDR research in recent years. To identify novel genes involved in DDR, we screened a genome-wide S. pombe haploid deletion library against six different DNA damage reagents. The library covered 90.5% of the nonessential genes of S. pombe.ResultsWe have identified 52 genes that were actively involved in DDR. Among the 52 genes, 20 genes were linked to DDR for the first time. Flow cytometry analysis of the repair defective mutants revealed that most of them exhibited a defect in cell cycle progression, and some caused genome instability. Microarray analysis and genetic complementation assays were carried out to characterize 6 of the novel DDR genes in more detail. Data suggested that SPBC2A9.02 and SPAC27D7.08c were required for efficient DNA replication initiation because they interacted genetically with DNA replication initiation proteins Abp1 and Abp2. In addition, deletion of sgf73+, meu29+, sec65+ or pab1+ caused improper cytokinesis and DNA re-replication, which contributed to the diploidization in the mutants.ConclusionsA genome-wide screen of genes involved in DDR emphasized the key role of cell cycle control in the DDR network. Characterization of novel genes identified in the screen helps to elucidate the mechanism of the DDR network and provides valuable clues for understanding genome stability in higher eukaryotes.

This study investigated the molecular types of the Cryptococcus neoformans species complex isolates and their clinical manifestations among human immunodeficiency virus (HIV)-positive and HIV-negative patients in southeast China in the past 15 years. The molecular types of 109 isolates from 108 patients were analyzed by the PCR fingerprinting method, sequences of internal transcribed spacers of rDNA (ITS region), and sequences of the capsule-associated gene (CAP59). In HIV-positive patients, clinical isolates were grouped into molecular types VNI (75%, 15/20), VNII (15%, 3/20), and VNIII (10%, 2/20). In HIV-negative patients, the majority of the clinical isolates were grouped into molecular types VNI (72%, 64/89), VNII (13%, 12/89), VGI (12%, 11/89), VNIII (1%, 1/89), and VGII (1%, 1/89). In reference to the mating type of the isolates, 97% (106/109) were of the MATα, 2% (2/109) were of the MATα/-and 1% (1/109) were of the MATα/a. As for the clinical manifestations of the molecular types among the patients, the average cerebrospinal fluid (CSF) pressure of the patients infected by the C. gattii was higher than that of the patients infected by the C. neoformans. These results suggest that both HIVpositive and HIV-negative cryptococcal patients in the southeast of China are mostly infected by the C. neoformans strains. No C. gattii strains were found in HIVpositive patients.

Serine/Threonine-specific calcineurin (CN) is highly conserved in eukaryotes, which plays an important role in transcriptional regulation. In Schizosaccharomyces pombe, CN exists as a heterodimer composed by catalytic subunit Ppb1 and regulatory subunit Cnb1. Deletion of cnb1+ reduced the growth rate of cells, and caused a chained phenotype, and had delay in cytokinesis. In cytokinesis, Cnb1 could form CN complex with Ppb1 and could colocalize and constrict with the contractile ring at division plane. Tubulin could cross the septum in cnb1Δ strain, suggesting that the septum is not fully matured. These results suggest Cnb1 might be involved in maturation of septum. The signals of septins in cnb1Δ strain were also analyzed. Septins include Spn1, Spn2, Spn3, and Spn4. Septins help to guide hydrolytic enzymes for septum degrada-tion. Eighty percent of cnb1Δ cells lacked the signals of Spn2 or Spn3 at septum, and twenty percent of cnb1Δ cells lacked the signals of Spn1 or Spn4 at septum. The reduction of the septin signals was not due to impaired transcription of septins, since the protein levels of septins in the cnb1Δ cells were not decreased. These results imply that Cnb1 might regulate the stability of septin ring in a transcription-independent manner. In general, our study showed that Cnb1 contributes to the maturation of septum and the stability of septin ring and is important in the cytokinesis.

Genomic integrity is crucial for normal cell replication, proliferation and differentiation. DNA lesions resulted from exogenous and endogenous factors will lead to genomic instability, and consequently the cause for various diseases. Epigenetic regulation (including DNA methylation, histone modifications and non-coding RNA) plays important roles in DNA lesion repair and cell cycle regulation as well as maintaining the genetic integrity. The yeast, a type of single cell eukaryotic organism, is an ideal model for the researches of epigenetics, especially in the area of DNA lesion repair and the formation of heterochromatin. Previous researches on epigenetics were mainly focus on histone modifications. Recent re-searches have observed that non-coding RNAs are able to direct the cytosine methylation and histone modifications that are related to gene expression regulation. This paper discuss the mechanism, research progress and future development of epi-genetics in maintaining the genomic integrity, using the yeast as a model.

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