Genome-Wide Profiling of Circular RNAs in the Rapidly Growing Shoots of Moso Bamboo (Phyllostachys edulis).

Circular RNAs, including circular exonic RNAs (circRNA), circular intronic RNAs (ciRNA) and exon-intron circRNAs (EIciRNAs), are a new type of noncoding RNAs. Growing shoots of moso bamboo (Phyllostachys edulis) represent an excellent model of fast growth and their circular RNAs have not been studied yet. To understand the potential regulation of circular RNAs, we systematically characterized circular RNAs from eight different developmental stages of rapidly growing shoots. Here, we identified 895 circular RNAs including a subset of mutually inclusive circRNA. These circular RNAs were generated from 759 corresponding parental coding genes involved in cellulose, hemicellulose and lignin biosynthetic process. Gene co-expression analysis revealed that hub genes, such as DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1), MAINTENANCE OF METHYLATION (MOM), dicer-like 3 (DCL3) and ARGONAUTE 1 (AGO1), were significantly enriched giving rise to circular RNAs. The expression level of these circular RNAs presented correlation with its linear counterpart according to transcriptome sequencing. Further protoplast transformation experiments indicated that overexpressing circ-bHLH93 generating from transcription factor decreased its linear transcript. Finally, the expression profiles suggested that circular RNAs may have interplay with miRNAs to regulate their cognate linear mRNAs, which was further supported by overexpressing miRNA156 decreasing the transcript of circ-TRF-1 and linear transcripts of TRF-1. Taken together, the overall profile of circular RNAs provided new insight into an unexplored category of long noncoding RNA regulation in moso bamboo

The Survey of H5N1 Flu Virus in Wild Birds in 14 Provinces of China from 2004 to 2007

The highly pathogenic H5N1 avian influenza emerged in the year 1996 in Asia, and has spread to Europe and Africa recently. At present, effective monitoring and data analysis of H5N1 are not sufficient in Chinese mainland.)) were obviously higher than those in other 13 provinces. The results of sequence analysis indicated that the 17 strains isolated from wild birds were distributed in five clades (2.3.1, 2.2, 2.5, 6, and 7), which suggested that genetic diversity existed among H5N1 viruses isolated from wild birds. The five isolates from Qinghai came from one clade (2.2) and had a short evolutionary distance with the isolates obtained from Qinghai in the year 2005.We have measured the prevalence of H5N1 virus in 56 species of wild birds in 14 provinces of China. Continuous monitoring in the field should be carried out to know whether H5N1 virus can be maintained by wild birds

Wild Bird Migration across the Qinghai-Tibetan Plateau: A Transmission Route for Highly Pathogenic H5N1

BACKGROUND: Qinghai Lake in central China has been at the center of debate on whether wild birds play a role in circulation of highly pathogenic avian influenza virus H5N1. In 2005, an unprecedented epizootic at Qinghai Lake killed more than 6000 migratory birds including over 3000 bar-headed geese (Anser indicus). H5N1 subsequently spread to Europe and Africa, and in following years has re-emerged in wild birds along the Central Asia flyway several times. METHODOLOGY/PRINCIPAL FINDINGS: To better understand the potential involvement of wild birds in the spread of H5N1, we studied the movements of bar-headed geese marked with GPS satellite transmitters at Qinghai Lake in relation to virus outbreaks and disease risk factors. We discovered a previously undocumented migratory pathway between Qinghai Lake and the Lhasa Valley of Tibet where 93% of the 29 marked geese overwintered. From 2003-2009, sixteen outbreaks in poultry or wild birds were confirmed on the Qinghai-Tibet Plateau, and the majority were located within the migratory pathway of the geese. Spatial and temporal concordance between goose movements and three potential H5N1 virus sources (poultry farms, a captive bar-headed goose facility, and H5N1 outbreak locations) indicated ample opportunities existed for virus spillover and infection of migratory geese on the wintering grounds. Their potential as a vector of H5N1 was supported by rapid migration movements of some geese and genetic relatedness of H5N1 virus isolated from geese in Tibet and Qinghai Lake. CONCLUSIONS/SIGNIFICANCE: This is the first study to compare phylogenetics of the virus with spatial ecology of its host, and the combined results suggest that wild birds play a role in the spread of H5N1 in this region. However, the strength of the evidence would be improved with additional sequences from both poultry and wild birds on the Qinghai-Tibet Plateau where H5N1 has a clear stronghold

An Empirical Analysis of an Integrated Accounting Method to Assess the Non-Monetary and Monetary Value of Ecosystem Services

The process of ecosystem service value evaluation has developed from the use of a single economic value that only accounts for material products to an assessment of ecological value and the value of ecosystem services. However, due to the complexity of ecosystems and different understandings of ecosystem service values, different classification methods of ecosystem services and service values have been developed internationally, and this has resulted in a lack of clarity regarding the correlation between ecosystem service value and various ecosystems. The correspondence between the system and each value type is not clear; therefore, based on an analysis of the inadequacy of domestic and foreign ecosystem service classification systems and methods, this study constructed a new accounting framework for non-monetary ecosystem service functions based on emergy analysis and integrated monetary accounting methods. The practical application of the method was also researched. The research results re-classified the value of ecosystem services, established an accounting method for various ecosystem service values, clarified the principle of addition in accounting, and avoided double counting. In the empirical analysis, a large number of correlation coefficients, parameters, and index values found in the foreign literature were used, so, our method also has value for international use

Multi-objective AGV scheduling in an automatic sorting system of an unmanned (intelligent) warehouse by using two adaptive genetic algorithms and a multi-adaptive genetic algorithm.

Automated guided vehicle (AGV) is a logistics transport vehicle with high safety performance and excellent availability, which can genuinely achieve unmanned operation. The use of AGV in intelligent warehouses or unmanned warehouses for sorting can improve the efficiency of warehouses and enhance the competitiveness of enterprises. In this paper, a multi-objective mathematical model was developed and integrated with two adaptive genetic algorithms (AGA) and a multi-adaptive genetic algorithm (MAGA) to optimize the task scheduling of AGVs by taking the charging task and the changeable speed of the AGV into consideration to minimize makespan, the number of AGVs used, and the amount of electricity consumption. The numerical experiments showed that MAGA is the best of the three algorithms. The value of objectives before and after optimization changed by about 30%, which proved the rationality and validity of the model and MAGA

Expression and regulatory network of E3 ubiquitin ligase NEDD4 family in cancers

Abstract NEDD4 family represent an important group of E3 ligases, which regulate various cellular pathways of cell proliferation, cell junction and inflammation. Emerging evidence suggested that NEDD4 family members participate in the initiation and development of tumor. In this study, we systematically investigated the molecular alterations as well as the clinical relevance regarding NEDD4 family genes in 33 cancer types. Finally, we found that NEDD4 members showed increased expression in pancreas cancer and decreased expression in thyroid cancer. NEDD4 E3 ligase family genes had an average mutation frequency in the range of 0-32.1%, of which HECW1 and HECW2 demonstrated relatively high mutation rate. Breast cancer harbors large amount of NEDD4 copy number amplification. NEDD4 family members interacted proteins were enriched in various pathways including p53, Akt, apoptosis and autophagy, which were confirmed by further western blot and flow cytometric analysis in A549 and H1299 lung cancer cells. In addition, expression of NEDD4 family genes were associated with survival of cancer patients. Our findings provide novel insight into the effect of NEDD4 E3 ligase genes on cancer progression and treatment in the future

Cladophorareblooming after half a century: effect of climate change-induced increases in the water level of the largest lake in Tibetan Plateau

MassiveCladophoragrowth was reported half a century ago around Birds Island in Qinghai Lake, and in 2015,Cladophorapopulations have rebloomed and have formed green "meadows," with areas up to thousands of hectares. The present study investigated the distribution and biomass ofCladophorain Qinghai Lake and found that two key factors contribute toCladophorablooming. First, recent climate change, especially increased precipitation, has induced the expansion of the lake's area, and the submerged grassland around Birds Island has provided a plethora of grass stems on whichCladophoracan attach and twine. In addition, the submerged grasslands are covered with less than 1 m of water, which allows enough sunlight to support the growth ofCladophoraon available substrates. Second, the submerged grassland may function as a key source of nutrients, especially phosphate. A large number of migratory birds live in these area for very long times, which lead to higher phosphorus content due to the accumulated birds dropping. Thus, the high phosphate level further exacerbates the massive growth. Future studies should investigate the functions ofCladophorain the nutrient cycling of submerged areas, and the improvement of methods for removingCladophorabiomass

Single-Cell RNA Sequencing of the Testis of Ciona intestinalis Reveals the Dynamic Transcriptional Profile of Spermatogenesis in Protochordates

Spermatogenesis is a complex and continuous process of germ-cell differentiation. This complex process is regulated by many factors, of which gene regulation in spermatogenic cells plays a decisive role. Spermatogenesis has been widely studied in vertebrates, but little is known about spermatogenesis in protochordates. Here, for the first time, we performed single-cell RNA sequencing (scRNA-seq) on 6832 germ cells from the testis of adult Ciona intestinalis. We identified six germ cell populations and revealed dynamic gene expression as well as transcriptional regulation during spermatogenesis. In particular, we identified four spermatocyte subtypes and key genes involved in meiosis in C. intestinalis. There were remarkable similarities and differences in gene expression during spermatogenesis between C. intestinalis and two other vertebrates (Chinese tongue sole and human). We identified many spermatogenic-cell-specific genes with functions that need to be verified. These findings will help to further improve research on spermatogenesis in chordates

Arsenic induces functional re-expression of estrogen receptor α by demethylation of DNA in estrogen receptor-negative human breast cancer.

Estrogen receptor α (ERα) is a marker predictive for response of breast cancers to endocrine therapy. About 30% of breast cancers, however, are hormone- independent because of lack of ERα expression. New strategies are needed for re-expression of ERα and sensitization of ER-negative breast cancer cells to selective ER modulators. The present report shows that arsenic trioxide induces reactivated ERα, providing a target for therapy with ER antagonists. Exposure of ER-negative breast cancer cells to arsenic trioxide leads to re-expression of ERα mRNA and functional ERα protein in in vitro and in vivo. Luciferase reporter gene assays and 3-(4,5-dimethylthiazol-2-yl)- 5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assays show that, upon exposure to arsenic trioxide, formerly unresponsive, ER-negative MDA-MB-231 breast cancer cells become responsive to ER antagonists, 4-hydroxytamoxifen and ICI 182,780. Furthermore, methylation- specific PCR and bisulfite-sequencing PCR assays show that arsenic trioxide induces partial demethylation of the ERα promoter. A methyl donor, S-adenosylmethionine (SAM), reduces the degree of arsenic trioxide-induced re-expression of ERα and demethylation. Moreover, Western blot and ChIP assays show that arsenic trioxide represses expression of DNMT1 and DNMT3a along with partial dissociation of DNMT1 from the ERα promoter. Thus, arsenic trioxide exhibits a previously undefined function which induces re-expression ERα in ER-negative breast cancer cells through demethylation of the ERα promoter. These findings could provide important information regarding the application of therapeutic agents targeting epigenetic changes in breast cancers and potential implication of arsenic trioxide as a new drug for the treatment of ER-negative human breast cancer