Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top‐Down Mass Spectrometry

Complex proteoforms contain various primary structural alterations resulting from variations in genes, RNA, and proteins. Top‐down mass spectrometry is commonly used for analyzing complex proteoforms because it provides whole sequence information of the proteoforms. Proteoform identification by top‐down mass spectral database search is a challenging computational problem because the types and/or locations of some alterations in target proteoforms are in general unknown. Although spectral alignment and mass graph alignment algorithms have been proposed for identifying proteoforms with unknown alterations, they are extremely slow to align millions of spectra against tens of thousands of protein sequences in high throughput proteome level analyses. Many software tools in this area combine efficient protein sequence filtering algorithms and spectral alignment algorithms to speed up database search. As a result, the performance of these tools heavily relies on the sensitivity and efficiency of their filtering algorithms. Here, we propose two efficient approximate spectrum‐based filtering algorithms for proteoform identification. We evaluated the performances of the proposed algorithms and four existing ones on simulated and real top‐down mass spectrometry data sets. Experiments showed that the proposed algorithms outperformed the existing ones for complex proteoform identification. In addition, combining the proposed filtering algorithms and mass graph alignment algorithms identified many proteoforms missed by ProSightPC in proteome‐level proteoform analyses.     

丝状真菌代谢工程研究进展

丝状真菌(Filamentous fungi)作为重要的工业发酵微生物,在有机酸、蛋白质及次级代谢产物等关键生物基产品生产方面发挥着重要作用.自20世纪90年代代谢工程理念提出以来,尤其是代谢工程使能技术的创新及发展,极大地促进了丝状真菌细胞工厂的构建及其在工业发酵领域的应用.文中将系统介绍近年来丝状真菌代谢工程技术的...     

中国东北地区流动沙丘生态系统丘间低地地下芽库的时空变化

中国东北地区流动沙丘生态系统丘间低地地下芽库的时空变化 地下芽库在半干旱区沙丘生态系统植被恢复中起着重要作用。然而,目前针对流动沙丘丘间低地地下芽库时空变化的研究却很少。本研究通过调查一个生长季内5个不同面积流动沙丘丘间低地地下芽库的大小和组成,确定流动沙丘丘间低地地下芽库的时空变化。研究结果显示,中等面积丘间低地的总芽库密度与分蘖芽密度最高,茎基部芽密度呈相反趋势,而根茎芽密度不随丘间低地的面积变化而变化。地下芽库大小具有明显的季节变化特征。总芽密度在8月份达到高峰,10月份最低,根茎芽密度变化趋势与总芽密度相似,而茎基芽密度变化趋势与总芽密度相反,分蘖芽密度的变化不明显。以上结果表明,地下芽库密度随丘间低地的面积和季节变化而变化。这一结果有助于认识流动沙丘生态系统中植物生长的适应策略,并可为半干旱区沙丘植被恢复和保护提供理论指导。     

Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication

A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.     

Cytologic findings in vitreous fluids. Analysis of 74 specimens

OBJECTIVE: To review the cytologic findings of vitreous specimens and propose a simplified approach to them. STUDY DESIGN: Seventy-four vitreous specimens from 60 patients obtained either during a pars plana vitrectomy or by vitreous aspiration were reviewed. Clinical correlation was obtained on all patients. RESULTS: Findings suggestive of a specific disorder were present in 30 specimens (41%); cytologic examination of the remaining 44 showed nonspecific changes. A lymphoproliferative disorder, the intraocular malignancy suspected most often in this series, was identified in eight specimens (11%). Large cell lymphomas were evident in 5 specimens, 2 specimens were suspicious for lymphoma, and 1 specimen was consistent with plasmacytoma. Twelve specimens (16%) contained hemorrhage. In rare instances, specific infectious agents, such as parasites (5%), bacteria (1%) and fungi (3%), could be identified. The diagnosis of viral infections required ancillary studies. Lens fragments were identified in four cases (5%), and a diagnosis of lens-induced endophthalmitis could be rendered in one case (1%). Changes consistent with sarcoidosis were present in 3% of cases. CONCLUSION: Based on this experience with vitreous specimens submitted for clinical reasons, we found that they could be divided into three broad diagnostic categories: inflammation/infection (54 specimens/41 patients), hemorrhage (12 specimens/12 patients) and malignancy (8 specimens/7 patients).     

Methanogen genotypes involved in methane formation during anaerobic decomposition of Microcystis blooms at different temperatures

The main goal of this work was to determine which methanogens were present during the anaerobic degradation of Microcystis biomass in the water columns of freshwater lakes. Simulation experiments were performed in which 30 ml Microcystis slurries were anaerobically incubated in 60 ml airtight bottles at three temperatures (15, 25, and 35 °C) for over 90 days. The production of CH₄ was monitored, and the methanogenic community was analyzed by cloning and sequencing the mcrA genes in samples incubated at the three different temperatures. In total, four clusters were detected at different temperatures by phylogenetic analysis of mcrA genes; these included members of Methanomicrobiales, Methanobacteriaceae, and Methanosarcina. An apparent linkage between temperature and phylogeny of the methanogenic community was observed: Methanomicrobiales and Methanobacteriaceae dominated the incubation system at the lower temperatures of 15 and 25 °C, whereas Methanosarcina prevailed at 35 °C. The dominance of these hydrogenotrophic methanogens suggested that, at least at lower temperatures, H₂ and CO₂ might be the primary substrates for CH₄ production during Microcystis anaerobic decomposition.     

云南萝芙木pnae基因全长克隆及其序列分析

根据已知的其他物种PNAE酶cDNA序列设计引物,采用RT-PCR技术从云南萝芙木叶片中扩增获得pnae基因部分cDNA序列即PNAE酶基因中间大片段,再用RACE技术获得其两端序列。序列拼接得到完整的1 004 bp的PNAE酶基因,根据获得的序列,分析得到795 bp的开放阅读框,编码264个氨基酸。序列分析显示,云南萝芙木中PNAE酶氨基酸序列与蛇根木中的该酶氨基酸序列同源性高达90%,但和其他植物物种中的PNAE酶氨基酸序列,以及其他物种间的PNAE酶氨基酸序列同源性都不高,在40%-60%之间,表明不同物种中PNAE酶氨基酸序列不具有全序列的高度同源性。进一步序列分析发现,在各植物的PNAE酶氨基酸序列中都存在两个高度保守的氨基酸区域,表明不同物种中PNAE酶存在共同的高度保守区段。     

Spectroscopic characterization and molecular weight distribution of dissolved organic matter in sediment porewaters from Lake Erhai, Southwest China

Dissolved organic matter (DOM) in sediment porewaters from Lake Erhai, Southwest China was investigated using dissolved organic carbon (DOC) concentration, UV absorbance, fluorescence and molecular weight distribution. DOC exhibited a high concentration at the sediment–water interface with a rapid decrease to the oxic–anoxic interface at approximately 7 cm, and then increased with depth. Similar trends were also found for the UV absorption coefficients at 254 and 280 nm in the porewaters. DNA in the sediment was also measured, which confirmed the high abundance of aerobic bacteria in the upper layer of the sediment. Both humic-like (peaks A and C) and protein-like (peaks B and D) fluorescence were observed in the porewater DOM, and their fluorescence intensities exhibited a similar porewater profile as DOC concentration. A strong correlation was found between the peak fluorescence intensity ratio r(A, C) and r(D, B). Both the fluorescence index and UV absorption coefficient at 254 nm suggested a dramatic increase in aromaticity of porewater DOM across the oxic–anoxic interface. Porewater DOM exhibited a multimodal distribution of molecular weight with a relatively low polydispersity. The results of this study offer significant insight into the nature and properties of DOM in freshwater ecosystems.     

运动性中枢疲劳后脊髓内主要神经递质含量的变化

目的：研究运动性中枢疲劳后脊髓内主要单胺类及氨基酸类神经递质含量的变化,探索运动性疲劳脊髓水平发生机制。方法：运用：Bedford递增负荷运动训练方案建立运动性中枢疲劳模型。将18只雄性成年Wistar大鼠随机分为对照组（C）,训练后即刻组（IT）及训练后3 h恢复组（RT）。用高效液相色谱法（HPLC）检测脊髓内单胺类和氨基酸类神经递质含量的变化。结果：大鼠脊髓内氨基酸类神经递质,在训练后即刻都出现了增高,其中谷氨酸（Glu）、γ-氨基丁酸（GABA）明显增高（P〈0.05）,甘氨酸（Gly）也出现增高但与对照组相比无显著性差异 训练后经3 h恢复后,氨基酸类神经递质含量基本恢复至对照组水平。单胺类神经递质,去甲肾上腺素（NE）,5-羟色胺（5-HT）在训练后即刻则出现降低趋势,且5-羟色胺（5-HT）含量在训练后3 h恢复组出现了明显降低（P〈0.05）。结论：运动性疲劳引起脊髓内神经递质含量的改变,可能与运动性中枢疲劳的发生过程有关。脊髓5-HT在恢复期仍明显降低,提示5-HT可能与疲劳恢复过程有较为密切的关系。