Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Efficient Removal of Ciprofloxacin from Contaminated Water via Polystyrene Anion Exchange Resin with Nanoconfined Zero-Valent Iron

Ciprofloxacin (CIP), an important emerging contaminant, has been frequently detected in water, and its efficient removal has become an issue of great concern. In this study, a nanocomposite material nZVI/PA was synthesized by impregnating nanoscale zero-valent iron (nZVI) inside a millimeter-sized porous host (polystyrene-based anion exchange resin (PA)) for CIP removal. The nZVI/PA composite was characterized by field emission scanning electron microscopy coupled with energy-dispersive X-ray, transmission electron microscopy, X-ray diffraction, as well as X-ray photoelectron spectroscopy, and it was confirmed that nZVI was uniformly dispersed in PA with a small particle size. Furthermore, several key factors were investigated including initial solution pH, initial CIP concentration, co-existing ions, organic ligands, and dissolved oxygen. The experimental results indicated that the nZVI/PA composites exhibited a high removal efficiency for CIP under the conditions of initial pH 5.0, and initial CIP concentration 50 mg L−1 at 25 °C, with the maximum removal rate of CIP reaching 98.5%. Moreover, the nZVI/PA composites exhibited high efficiency even after five cycles. Furthermore, quenching tests and electron spin resonance (ESR) confirmed that CIP degradation was attributed to hydroxyl (·OH) and superoxide radicals (⋅O2−). Finally, the main degradation products of CIP were analyzed, and degradation pathways including the hydroxylation of the quinolone ring, the cleavage of the piperazine ring, and defluorination were proposed. These results are valuable for evaluating the practical application of nZVI/PA composites for the removal of CIP and other fluoroquinolone antibiotics

Evaluation of peripapillary choroidal distribution in children by enhanced depth imaging optical coherence tomography

Abstract Background To evaluate the peripapillary choroidal thickness (PPCT) in Chinese children aged 6 to 12 years old and to analyze correlative factors. Methods PPCT was measured with enhanced depth imaging optical coherence tomography (EDI-OCT) in 154 children (76 myopes and 78 emmetropia) aged 6 to 12 years, with spherical equivalent refractive errors between + 0.50 and − 5.50 diopters(D). Peripapillary choroidal imaging was performed using circular scans of a diameter of 3.4 mm around the optic disc. PPCT and the corresponding peripapillary retinal thickness (PPRT) were measured by EDI-OCT at nine positions: I, inferior; IN, inferonasal; IT, inferotemporal; N, nasal; T, temporal; S, superior; SN, superonasal; ST, superotemporal, and the Fovea Centralis. Results The mean global PPCT was 165.80 ± 39.86 μm.The mean global PPRT was 101.47 ± 10.74 μm. The Inferior had the thinnest PPCT but the thickest PPRT (p < 0.001), while the Nasal had thickest PPCT but the thinnest PPRT (p < 0.001). Significant differences in RT between the myopic group and the emmetropic group were found at all positions except T, TS, S and the fovea. Myopic group had thinner choroidal thickness (CT) than that of emmetropic group at all measured positions. Choroidal thickness had negative relation with the corresponding retinal thickness, age and axial length. Conclusion The peripapillary choroid was thicker nasally and thinner inferiorly, while the peripapillary retina was thickest inferiorly and thinnest nasally. Myopic group had thinner PPCT. The axial length was found to be negatively correlated to PPCT

Cryptosporidiosis in broiler chickens in Zhejiang Province, China: molecular characterization of oocysts detected in fecal samples

Cryptosporidium is one of the most important parasites in poultry, and this pathogen can infect more than 30 avian species. The present study investigated the infection rate of Cryptosporidium among broiler chicken flocks. A total of 385 fecal samples from broiler chickens in 7 regions of Zhejiang Province collected from November 2010 to January 2012 were examined by microscopy. Thirty-eight (10%) samples were positive for Cryptosporidium infection, and 3 genotypes (Cryptosporidium baileyi, Cryptosporidium meleagridis, and avian genotype II) were identified by PCR and sequencing. A phylogenetic tree of the isolates was analyzed. These results suggest that cryptosporidiosis is widespread in poultry in Zhejiang Province, and is a potential threat to public health as well as the economy. This is the first report about the infection rate and molecular characterization of Cryptosporidium in broiler chickens in Zhejiang

A general salt-resistant hydrophilic/hydrophobic nanoporous double layer design for efficient and stable solar water evaporation distillation

A novel and elegant hydrophilic/hydrophobic nanoporous double layer structure was designed and developed for efficient long-term water desalination. It contained a hydrophobic salt-resistant hierarchical layer of well-defined Cu2SnSe3 (or Cu2ZnSnSe4) nanosphere arrays for broad solar harvesting and water vapor evaporation, and a hydrophilic filter membrane for continuous water supply and vapor generation. The as-fabricated self-floatable devices achieve remarkable solar water evaporation performances (average evaporation rate: 1.657 kg m−2 h−1 and solar thermal conversion efficiency: 86.6% under one sun) with super stability for water distillation from seawater and wastewater containing organic dyes, heavy metals and bacteria.This work was supported by the National Natural Science Foundation of China (Grant No. 61774122), the Science and Technology Developing Project of Shaanxi Province under Grant No. 2015KW-001, and the 111 Project from China (B18013, B14040). Y. P. Du gratefully acknowledge the NSFC (Grant No. 21371140), the National Key R&D Program of China (2017YFA0208000), 111 Project (B18030) from China, and the China National Funds for Excellent Young Scientists (Grant No. 21522106)

A Five-Gene Signature for Recurrence Prediction of Hepatocellular Carcinoma Patients

Background. Hepatocellular carcinoma (HCC) is one of the most aggressive malignancies with poor prognosis. There are many selectable treatments with good prognosis in Barcelona Clinic Liver Cancer- (BCLC-) 0, A, and B HCC patients, but the most crucial factor affecting survival is the high recurrence rate after treatments. Therefore, it is of great significance to predict the recurrence of BCLC-0, BCLC-A, and BCLC-B HCC patients. Aim. To develop a gene signature to enhance the prediction of recurrence among HCC patients. Materials and Methods. The RNA expression data and clinical data of HCC patients were obtained from the Gene Expression Omnibus (GEO) database. Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were conducted to screen primarily prognostic biomarkers in GSE14520. Multivariate Cox regression analysis was introduced to verify the prognostic role of these genes. Ultimately, 5 genes were demonstrated to be related with the recurrence of HCC patients and a gene signature was established. GSE76427 was adopted to further verify the accuracy of gene signature. Subsequently, a nomogram based on gene signature was performed to predict recurrence. Gene functional enrichment analysis was conducted to investigate the potential biological processes and pathways. Results. We identified a five-gene signature which performs a powerful predictive ability in HCC patients. In the training set of GSE14520, area under the curve (AUC) for the five-gene predictive signature of 1, 2, and 3 years were 0.813, 0.786, and 0.766. Then, the relative operating characteristic (ROC) curves of five-gene predictive signature were verified in the GSE14520 validation set, the whole GSE14520, and GSE76427, showed good performance. A nomogram comprising the five-gene signature was built so as to show a good accuracy for predicting recurrence-free survival of HCC patients. Conclusion. The novel five-gene signature showed potential feasibility of recurrence prediction for early-stage HCC

ncRNA.gff3.tar.gz

The ncRNA annotation file of Heterodera glycines

pasa2.longest.filter.pep.tar.gz

The protein sequence file of Heterodera glycines

Data from: Chromosome-level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome-level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole-genome shotgun (WGS) sequencing, PacBio sequencing, Illumina paired-end sequencing, 10X Genomics linked reads and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques, a 141.01-Mb assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kb, respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach (CEGMA) and Benchmarking Universal Single-Copy Orthologs (BUSCO). A total of 11,882 genes were predicted using De novo, Homolog and RNAseq data generated from eggs, second-stage juveniles (J2), third-stage juveniles (J3) and fourth-stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high-quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN-plant interactions and coevolution, and also contribute to the development of technology for overall SCN management

repeat_annotation.gff.tar.gz

The repeats annotation file of Heterodera glycines