基于WorldView 2影像的矿区植被重建效果评估

植被盖度反映植被质量,是评价矿区复垦土地植被重建效果的重要指标。该文选择安太堡矿区为案例区,基于高空间分辨率World View 2(WV 2)影像新波段,使用混合像元模型和实地数据验证相结合的方法计算得到研究区的植被盖度,并对植被重建效果进行了评估,主要得到以下结论:(1)基于WV 2影像的近红外2波段和红波段,采用混合像元法得到的植被盖度反演值Fc_2与实测值最为接近,相关性最强(R~2=0.934),均方根误差最小(RMSE=0.048);(2)研究区植被重建效果整体较好,中等、较高和高植被盖度区域占研究区的60%以上,低植被盖度仅占22.09%。受植被重建年限和管理措施的影响,不同复垦区域植被重建状况之间存在着差异,内排土场、西排土场、南排土场的植被重建效果较好,而西排土场扩大区植被状况相对较差,其中等及以上植被盖度所占比例依次为75.24%、68.35%、68.20%、22.29%。(3)就植被组合模式看,乔灌草模式重建效果(按冠层盖度)最好,其次是乔草模式,其他模式如灌草、草地、自然恢复地依次降低。土壤表层水分含量随着复垦地植被盖度的增大而增大,说明植被重建状况对土壤表层的水分保持具有重要作用。     

Missense mutations in APOB within the betaalpha1 domain of human APOB-100 result in impaired secretion of ApoB and ApoB-containing lipoproteins in familial hypobetalipoproteinemia

Familial hypobetalipoproteinemia (FHBL) is associated with mutations in the APOB gene. We reported the first missense APOB mutation, R463W, in an FHBL kindred (Burnett, J. R., Shan, J., Miskie, B. A., Whitfield, A. J., Yuan, J., Tran, K., Mc-Knight, C. J., Hegele, R. A., and Yao, Z. (2003) J. Biol. Chem. 278, 13442-13452). Here we identified a second nonsynonymous APOB mutation, L343V, in another FHBL kindred. Heterozygotes for L343V (n = 10) had a mean plasma apoB at 0.31 g/liter as compared with 0.80 g/liter in unaffected family members (n = 22). The L343V mutation impaired secretion of apoB-100 and very low density lipoproteins. The secretion efficiency was 20% for B100wt and 10% for B100LV and B100RW. Decreased secretion of mutant apoB-100 was associated with increased endoplasmic reticulum retention and increased binding to microsomal triglyceride transfer protein and BiP. Reduced secretion efficiency was also observed with B48LV and B17LV. Biochemical and biophysical analyses of apoB domain constructs showed that L343V and R463W altered folding of the alpha-helical domain within the N terminus of apoB. Thus, proper folding of the alpha-helical domain of apoB-100 is essential for efficient secretion.     

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data

Clustering is a prevalent analytical means to analyze single cell RNA sequencing (scRNA-seq) data but the rapidly expanding data volume can make this process computationally challenging. New methods for both accurate and efficient clustering are of pressing need. Here we proposed Spearman subsampling-clustering-classification (SSCC),a new clustering framework based on random projection and feature construction,for large-scale scRNA-seq data. SSCC greatly improves clustering accuracy,robustness,and computational efficacy for various state-of-the-art algorithms benchmarked on multiple real datasets. On a dataset with 68,578 human blood cells,SSCC achieved 20%improvement for clustering accuracy and 50-fold acceleration,but only consumed 66%memory usage,compared to the widelyused software package SC3. Compared to k-means,the accuracy improvement of SSCC can reach 3-fold. An R implementation of SSCC is available at https://github.com/Japrin/sscClust.     

MBASED: allele-specific expression detection in cancer tissues and cell lines

Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.     

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data

We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of selection can be localized more precisely, and whether such extra evidence can lead to increased biological insights. We used two tools: simulations under neutrality or selection, and experimental investigation of two regions identified by the HapMap2 project as putatively selected in human populations. Simulations suggested that neutral and selected regions should be readily distinguished and that it should be possible to localize the selected variant to within 40 kb at least half of the time. Re-sequencing of two ~300 kb regions (chr4:158Mb and chr10:22Mb) lacking known targets of selection in HapMap CHB individuals provided strong evidence for positive selection within each and suggested the micro-RNA gene hsa-miR-548c as the best candidate target in one region, and changes in regulation of the sperm protein gene SPAG6 in the other.     

Finishing the finished human chromosome 22 sequence

Background

Although the human genome sequence was declared complete in 2004, the sequence was interrupted by 341 gaps of which 308 lay in an estimated approximately 28 Mb of euchromatin. While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences.

Results

We have used a combination of conventional chromosome walking (aided by the availability of end sequences) in fosmid and bacterial artificial chromosome (BAC) libraries, whole chromosome shotgun sequencing, comparative genome analysis and long PCR to finish 8 of the 11 gaps in the initial chromosome 22 sequence. In addition, we have patched four regions of the initial sequence where the original clones were found to be deleted, or contained a deletion allele of a known gene, with a further 126 kb of new sequence. Over 1.018 Mb of new sequence has been generated to extend into and close the gaps, and we have annotated 16 new or extended gene structures and one pseudogene.

Conclusion

Thus, we have made significant progress to completing the sequence of the euchromatic regions of human chromosome 22 using a combination of detailed approaches. Our experience suggests that substantial work remains to close the outstanding gaps in the human genome sequence.     

<Emphasis Type="Italic">Pseudoruegeria marinistellae</Emphasis> sp. nov., isolated from an unidentified starfish in Sanya,China

A taxonomic study was carried out on a Gram-stain negative, rod-shaped, non-flagellated, and facultatively anaerobic bacterial strain designated as strain SF-16^T, which was isolated from an unidentified starfish in Sanya, China. Strain SF-16^T was found to be 5.0–7.0 μm long, and oxidase and catalase positive. Cell growth was observed at pH 6.0–8.5 (optimum, 7.0–8.0), temperatures of 10–41 °C (optimum, 25–30 °C), and salinities of 0–12 % (optimum, 3.0–6.0 %). The predominant fatty acids (>20 %) were found to be C_18:1 ω7c and/or C_18:1 ω6c (summed feature 8). Ubiquinone 10 was identified as the predominant quinone for strain SF-16^T. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unidentified lipids, and three unidentified phospholipids. The DNA G+C content of the genomic DNA of strain SF-16^T was determined to be 63.0 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain SF-16^T belongs to the genus Pseudoruegeria and is closely related to Pseudoruegeria sabulilitoris GJMS-35^T (98.42 % similarity). The ANI value between strain SF-16^T and P. sabulilitoris GJMS-35^T was found to be 74.98 %, and DNA–DNA hybridization value was 21.1 ± 2.3 % in silico and 57 % in vitro. Based on the low level of the genetic relatedness, phylogenetic and phenotypic data, a novel species Pseudoruegeria marinistellae sp. nov. is proposed. The type strain is SF-16^T (=MCCC 1K01155^T = KCTC 42910^T).     

半理性改造提升细菌漆酶Lac15的催化活性

[目的]漆酶可氧化各种底物,在多个工业领域有很好的潜在应用价值.Lac15是一种微生物漆酶,已表现出可观的应用潜能,可望通过蛋白质工程改造提升和拓展其应用.[方法]通过基于结构分析的半理性改造策略,选取推测与电子/质子转移或底物结合直接或间接相关的位点进行定点突变,并测定突变酶对各种底物的活性及酶学性质.[结果]部分突...