ALBERT

Description: Based on studies of continuous waveform data recorded on broad-band seismograph stations in Africa, Europe and North America, we report evidences for two temporally persistent and spatially localized monochromatic vibrating sources (around 0.036 and 0.038 Hz, respectively) in the Gulf of Guinea, instead of just one source (0.038 Hz or 26 s) found 50 yr ago. The location of the 0.036 Hz source is close to the Sao Tome Volcano, therefore it may be related to volcano processes. However, the 0.038 Hz source cannot be explained with known mechanisms, such as tectonic or oceanic processes. The most likely mechanism is volcano processes, but there is no reported active volcano in source region. Such repetitive vibration sources may provide valuable tools for detecting temporal variation of crustal structure of the Earth.

Description: Similarity-based clustering and classification of compounds enable the search of drug leads and the structural and chemogenomic studies for facilitating chemical, biomedical, agricultural, material and other industrial applications. A database that organizes compounds into similarity-based as well as scaffold-based and property-based families is useful for facilitating these tasks. CFam Chemical Family database http://bidd2.cse.nus.edu.sg/cfam was developed to hierarchically cluster drugs, bioactive molecules, human metabolites, natural products, patented agents and other molecules into functional families, superfamilies and classes of structurally similar compounds based on the literature-reported high, intermediate and remote similarity measures. The compounds were represented by molecular fingerprint and molecular similarity was measured by Tanimoto coefficient. The functional seeds of CFam families were from hierarchically clustered drugs, bioactive molecules, human metabolites, natural products, patented agents, respectively, which were used to characterize families and cluster compounds into families, superfamilies and classes. CFam currently contains 11 643 classes, 34 880 superfamilies and 87 136 families of 490 279 compounds (1691 approved drugs, 1228 clinical trial drugs, 12 386 investigative drugs, 262 881 highly active molecules, 15 055 human metabolites, 80 255 ZINC-processed natural products and 116 783 patented agents). Efforts will be made to further expand CFam database and add more functional categories and families based on other types of molecular representations.

Description: DNA methylation of transcription units (gene bodies) occurs in the genomes of many animal and plant species. Phylogenetic persistence of gene body methylation implies biological significance; yet, the functional roles of gene body methylation remain elusive. In this study, we analyzed methylation levels of orthologs from four distantly related invertebrate species, including the honeybee, silkworm, sea squirt, and sea anemone. We demonstrate that in all four species, gene bodies distinctively cluster to two groups, which correspond to high and low methylation levels. This pattern resembles that of sequence composition arising from the mutagenetic effect of DNA methylation. In spite of this effect, our results show that protein sequences of genes targeted by high levels of methylation are conserved relative to genes lacking methylation. Our investigation identified many genes that either gained or lost methylation during the course of invertebrate evolution. Most of these genes appear to have lost methylation in the insect lineages we investigated, particularly in the honeybee. We found that genes that are methylated in all four invertebrate taxa are enriched for housekeeping functions related to transcription and translation, whereas the loss of DNA methylation occurred in genes whose functions include cellular signaling and reproductive processes. Overall, our study helps to illuminate the functional significance of gene body methylation and its impacts on genome evolution in diverse invertebrate taxa.

Description: A major barrier to the commercialization of somatic embryogenesis technology in loblolly pine ( Pinus taeda L.) is recalcitrance of some high-value crosses to initiate embryogenic tissue (ET) and continue early-stage somatic embryo growth. Developing initiation and multiplication media that resemble the seed environment has been shown to decrease this recalcitrance. Glutathione (GSH), glutathione disulfide (GSSG), ascorbic acid and dehydroascorbate analyses were performed weekly throughout the sequence of seed development for female gametophyte and zygotic embryo tissues to determine physiological concentrations. Major differences in stage-specific oxidation–reduction (redox) agents were observed. A simple bioassay was used to evaluate potential growth-promotion of natural and inorganic redox agents added to early-stage somatic embryo growth medium. Compounds showing statistically significant increases in early-stage embryo growth were then tested for the ability to increase initiation of loblolly pine. Low-cost reducing agents sodium dithionite and sodium thiosulfate increased ET initiation for loblolly pine and Douglas fir (Mirb) Franco. Germination medium supplementation with GSSG increased somatic embryo germination. Early-stage somatic embryos grown on medium with or without sodium thiosulfate did not differ in GSH or GSSG content, suggesting that sodium thiosulfate-mediated growth stimulation does not involve GSH or GSSG. We have developed information demonstrating that alteration of the redox environment in vitro can improve ET initiation, early-stage embryo development and somatic embryo germination in loblolly pine.

Description: RNA research and therapy relies primarily on synthetic RNAs. We employed recombinant RNA technology toward large-scale production of pre-miRNA agents in bacteria, but found the majority of target RNAs were not or negligibly expressed. We thus developed a novel strategy to achieve consistent high-yield biosynthesis of chimeric RNAs carrying various small RNAs (e.g. miRNAs, siRNAs and RNA aptamers), which was based upon an optimal noncoding RNA scaffold (OnRS) derived from tRNA fusion pre-miR-34a (tRNA/mir-34a). Multi-milligrams of chimeric RNAs (e.g. OnRS/miR-124, OnRS/GFP-siRNA, OnRS/Neg (scrambled RNA) and OnRS/MGA (malachite green aptamer)) were readily obtained from 1 l bacterial culture. Deep sequencing analyses revealed that mature miR-124 and target GFP-siRNA were selectively released from chimeric RNAs in human cells. Consequently, OnRS/miR-124 was active in suppressing miR-124 target gene expression and controlling cellular processes, and OnRS/GFP-siRNA was effective in knocking down GFP mRNA levels and fluorescent intensity in ES-2/GFP cells and GFP -transgenic mice. Furthermore, the OnRS/MGA sensor offered a specific strong fluorescence upon binding MG, which was utilized as label-free substrate to accurately determine serum RNase activities in pancreatic cancer patients. These results demonstrate that OnRS-based bioengineering is a common, robust and versatile strategy to assemble various types of small RNAs for broad applications.

Description: Aims Road effects from maintenance and traffic have the potential to alter plant communities, but the exact relationships between these effects and changes in plant community composition have not often been studied in diverse environments. To determine the direction and level of community composition changes in saline environment due to road effects, we conducted a study along roads of different ages and in nearby non-road (i.e. natural) areas in the Yellow River Delta, China. Additionally, to potentially elucidate the mechanisms underlying the changes in the richness and composition of plant communities along roads, we evaluated physiochemical changes in soil of roadside and non-road areas. Methods Floristic and environmental data were collected along roadside of different ages and nearby non-road areas. To evaluate plant communities at each site, six 2 m x 2 m quadrats were placed at 3-m intervals along roads and six quadrats were arranged randomly in non-road areas. To determine the difference in plant community composition between roadside and non-road areas, we measured species richness and the abundance of each species, examined species turnover and floristic dissimilarity between the two areas and positioned plant species and sites in an abstract multivariate space. Plant community (species richness, percentage of halophytes) and soil physicochemical properties (pH, salinity, moisture content, bulk density, nitrate and ammonium nitrogen concentration) were compared between roadside and non-road areas (young roadside vs. corresponding non-road areas, old roadside vs. corresponding non-road areas) by using t -tests. Classification and ordination techniques were used to examine the relationship between vegetation and related environmental variables in both roadside and non-road areas. Important Findings For both the young and old roadside areas, species richness in roadside areas was significantly higher than in non-road areas and high floristic dissimilarity values indicated that roadside and non-road areas differed greatly in community composition. In both the young and old roadside areas, the plant communities in roadside areas had lower percentages of halophytes than non-road communities. Correspondence analysis and two-way indicator species analysis showed that halophytes dominated in the non-road areas, while a number of typical non-salt-tolerant species dominated in the roadside areas. Compared to non-road areas, activities associated with roads significantly decreased soil moisture, bulk density and salinity and increased soil pH and nitrate content. Forward selection for the environmental variables in canonical correspondence analysis showed that soil salinity was the most important factor related to the variation of species composition between roadside and non-road areas. Our study demonstrates that road effects have a significant impact on the associated vegetation and soil, and these changes are consistent across roads of different ages in our system.

Description: Conditionally anonymous ring signatures are a variant of ring signatures such that the anonymity is conditional: if a user is the true signer, then he can claim this through a confirmation protocol; if he is not the signer, he can prove this through a disavowal protocol. Hence, this can preserve the anonymity of a signer while reserving the right to trace it when necessary. The security of such a signature also requires that an innocent non-signer will not be framed as a signer. In this paper, we propose a new framework for this type of signature without random oracles. Our construction can be realized under general complexity assumptions and has a simple structure. In contrast, previous works are based on non-standard assumptions or proved secure in the random oracle model.

Description: Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease that affects mainly females. What role the X chromosome plays in the disease has always been an intriguing question. In this study, we examined the genetic variants on the X chromosome through meta-analysis of two genome-wide association studies (GWAS) on SLE on Chinese Han populations. Prominent association signals from the meta-analysis were replicated in 4 additional Asian cohorts, with a total of 5373 cases and 9166 matched controls. We identified a novel variant in PRPS2 on Xp22.3 as associated with SLE with genome-wide significance (rs7062536, OR = 0.84, P = 1.00E–08). Association of the L1CAM-MECP2 region with SLE was reported previously. In this study, we identified independent contributors in this region in NAA10 (rs2071128, OR = 0.81, P = 2.19E–13) and TMEM187 (rs17422, OR = 0.75, P = 1.47E–15), in addition to replicating the association from IRAK1-MECP2 region (rs1059702, OR = 0.71, P = 2.40E–18) in Asian cohorts. The X-linked susceptibility variants showed higher effect size in males than that in females, similar to results from a genome-wide survey of associated SNPs on the autosomes. These results suggest that susceptibility genes identified on the X chromosome, while contributing to disease predisposition, might not contribute significantly to the female predominance of this prototype autoimmune disease.

Description: The relationships between above-ground stem, branch, leaf masses and stand density index (SDI) were analysed in Populus x euramericana (Dode) Guinier stands in Jiangsu Province, China. The allometric equations developed in this study accurately estimated masses of above-ground and specific above-ground tree components in stands with different SDIs. The relationship between the mean above-ground mass w and the ratio of stem to the above-ground ( w S / w ) was examined. With increasing w , the stem mass ratio w S / w increased. Mean masses of above-ground and tree components decreased significantly with increasing SDI at age 9 years, indicating the presence of competition-induced limitations to growth. The mean above-ground mass–SDI and mean component mass–SDI were strongly correlated with above-ground mass-SDI and tree component mass–SDI, respectively. An equation describing the relationship between the mean leaf area u and SDI was developed, which fitted well for the u -SDI data. Stem mass increment exponentially increased with increasing leaf area index.

Description: Systemic lupus erythematosus (SLE) has a complex etiology and is affected by both genetic and environmental factors. Although more than 40 loci have shown robust association with SLE, the details of these loci, such as the independent contributors and the genes involved, are still unclear. In this study, we performed meta-analysis of two existing genome-wide association studies (GWASs) on Chinese Han populations from Hong Kong and Anhui, China, and followed the findings by further replication on three additional Chinese and Thailand cohorts with a total of 4254 cases and 6262 controls matched geographically and ethnically. We discovered multiple susceptibility variants for SLE in the 11q23.3 region, including variants in/near PHLDB1 (rs11603023, P_ combined = 1.25E–08, OR = 1.20), DDX6 (rs638893, P_ combined = 5.19E–07, OR = 1.22) and CXCR5 (rs10892301, P_ combined = 2.51E–08, OR = 0.85). Genetic contributions from the newly identified variants were all independent of SNP rs4639966, whose association was reported from the previous GWAS. In addition, the three newly identified variants all showed independent association with the disease through modeling by both stepwise and conditional logistic regression. The presence of multiple independent variants in this region emphasizes its role in SLE susceptibility, and also hints the possibility that distinct biological mechanisms might be involved in the disease involving this genomic region.