DNA片段拼接中的预归并重复序列屏蔽方法

针对DNA片段拼接中的重复序列识别及屏蔽问题,提出一种预归并重复序列屏蔽方法。在片段拼接前通过扫描子串标识出可能存在重叠关系的shotgun片段,利用子串归并该相关片段,标识出重复序列的位置信息,达到屏蔽的目的。计算机模拟分析表明,该方法识别重复序列的错误率低,通过预归并有效缩减了shotgun集合的规模,降低了拼接时的计算复杂度。     

The sequence of 55 kb on the left arm of yeast chromosome XVI identifies a small nuclear RNA,a new putative protein kinase and two new putative regulators

We have sequenced and analysed a 55 786 bp fragment located on the left arm of chromosome XVI of Saccharomyces cerevisiae. The sequence contains 29 non-overlapping open reading frames (ORFs) longer than 300 bp, among which 12 genes have previously been sequenced: OYE3, REV3, SVS1, BEM4, CDC60, KIP2, PEP4, SPK1, PAL1, KES1, SNR17B and RPL37A. Three new ORFs, P2591, P2594 and P2597 are highly homologous to the human phosphotyrosyl phosphatase activator PTPA, to the pleiotropic regulator PRL1 of PP1 and PP2a protein phosphatases in plants and to the protein kinase PAR-1 in Caenorhabditis elegans, respectively. Three other ORFs, P2545, P2567 and P2578 have significant homology with ORFs of unknown function located on yeast chromosomes VIII, XVI and IV respectively. The sequences in nucleotides and in amino acids have been deposited in the EMBL data library under the Accession Number X96770.     

Deciphering the Complex Molecular Pathogenesis of Myotonic Dystrophy Type 1 through Omics Studies

Omics studies are crucial to improve our understanding of myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults. Employing tissue samples and cell lines derived from patients and animal models, omics approaches have revealed the myriad alterations in gene and microRNA expression, alternative splicing, 3′ polyadenylation, CpG methylation, and proteins levels, among others, that contribute to this complex multisystem disease. In addition, omics characterization of drug candidate treatment experiments provides crucial insight into the degree of therapeutic rescue and off-target effects that can be achieved. Finally, several innovative technologies such as single-cell sequencing and artificial intelligence will have a significant impact on future DM1 research.     

利用CRISPRi技术构建乙醛酸生物合成Corynebacterium glutamicum工程菌

以谷氨酸棒状杆菌(Corynebacterium glutamicumATCC 13032)为出发菌株,敲除其支流代谢关键酶乳酸脱氢酶合成基因lldh,建立规律间隔成簇短回文重复序列干扰(clustered regularly interspaced short palindromic repeats interfer...     

The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes,Structural Characterization,Comparative Analysis,Phylogenomics and Time Divergence

The mechanism and course of Triticum plastome evolution is currently unknown; thus, it remains unclear how Triticum plastomes evolved during recent polyploidization. Here, we report the complete plastomes of two polyploid wheat species, Triticum sphaerococcum (AABBDD) and Triticum turgidum subsp. durum (AABB), and compare them with 19 available and complete Triticum plastomes to create the first map of genomic structural variation. Both T. sphaerococcum and T. turgidum subsp. durum plastomes were found to have a quadripartite structure, with plastome lengths of 134,531 bp and 134,015 bp, respectively. Furthermore, diploid (AA), tetraploid (AB, AG) and hexaploid (ABD, AGA^m) Triticum species plastomes displayed a conserved gene content and commonly harbored an identical set of annotated unique genes. Overall, there was a positive correlation between the number of repeats and plastome size. In all plastomes, the number of tandem repeats was higher than the number of palindromic and forward repeats. We constructed a Triticum phylogeny based on the complete plastomes and 42 shared genes from 71 plastomes. We estimated the divergence of Hordeum vulgare from wheat around 11.04–11.9 million years ago (mya) using a well-resolved plastome tree. Similarly, Sitopsis species diverged 2.8–2.9 mya before Triticum urartu (AA) and Triticum monococcum (AA). Aegilops speltoides was shown to be the maternal donor of polyploid wheat genomes and diverged ~0.2–0.9 mya. The phylogeny and divergence time estimates presented here can act as a reference framework for future studies of Triticum evolution.     

不同羊肚菌菌株的遗传差异性与胃黏膜保护作用的比较研究

为研究不同羊肚菌菌株之间的遗传差异性和比较不同菌株的胃黏膜保护作用。采用简单重复序列区间（inter-simple sequence repeats,ISSR）分子标记技术,对羊肚菌进行了遗传差异性分析;以菌丝体干质量为指标,比较不同菌株液体发酵的菌丝体生物量;研究不同菌株对酒精引起的小鼠急性胃黏膜损伤的保护作用。结果表明：16 株羊肚菌菌株可分为2 组,羊肚菌M1～M10生物量较高,羊肚菌M1、M2、M3的胃黏膜保护作用最好。不同羊肚菌菌株在液体发酵生物量和胃黏膜损伤的保护作用方面存在较大的差异。     

酿酒葡萄新品系‘黑珍珠’果实品质分析

为了研究‘黑珍珠’葡萄果实的酿酒特性,探究其亲本信息,分别利用高效液相色谱-质谱（high performance liquid chromatography-mass spectrometry,HPLC-MS）和气相色谱-质谱（gas chromatography-mass spectrometer,GC-MS）技术分析了‘黑珍珠’葡萄果实的花色苷和香气化合物的组成及含量。HPLC-MS分析结果表明,‘黑珍珠’葡萄果皮中花色苷总量为2 774.76 mg/kg mf,以花色素双葡萄糖苷为主（71.2%）,推测其含有非欧亚种葡萄的血缘。GC-MS分析结果表明,‘黑珍珠’葡萄果实香气化合物以游离态与糖苷结合态形式存在,共检测到123 种化合物。简单序列重复分析结果表明,在供试品种（‘贝达’、‘烟73’和‘Kolor’）中未发现‘黑珍珠’的亲本。由于‘黑珍珠’果皮花色苷的种类与含量丰富,且其单品种葡萄酒颜色深,未来可以作为酿造具有地区特色红葡萄酒的新品种或调色新品种。     

String analysis by sliding positioning strategy

Discovering frequent factors from long strings is an important problem in many applications, such as biosequence mining. In classical approaches, the algorithms process a vast database of small strings. However, in this paper we analyze a small database of long strings. The main difference resides in the high number of patterns to analyze. To tackle the problem, we have developed a new algorithm for discovering frequent factors in long strings. We present an Apriori-like solution which exploits the fact that any super-pattern of a non-frequent pattern cannot be frequent. The SANSPOS algorithm does a multiple-pass, candidate generation and test approach. Multiple length patterns can be generated in a pass. This algorithm uses a new data structure to arrange nodes in a trie. A Positioning Matrix is defined as a new positioning strategy. By using Positioning Matrices, we can apply advanced prune heuristics in a trie with a minimal computational cost. The Positioning Matrices let us process strings including Short Tandem Repeats and calculate different interestingness measures efficiently. Furthermore, in our algorithm we apply parallelism to transverse different sections of the input strings concurrently, speeding up the resulting running time. The algorithm has been successfully used in natural language and biological sequence contexts.     

Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes

The development of biophysical systems that enable an understanding of the structure and ligand‐binding properties of G‐quadruplex (GQ)‐forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ‐directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H‐Telo) DNA and RNA repeats in a cell‐like confined environment by using conformation‐sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2‐ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2′‐deoxy and ribonucleoside probes, composed of a 5‐benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H‐Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H‐Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy‐to‐handle RMs could provide new opportunities to study and devise screening‐compatible assays in a cell‐like environment to discover GQ binders of clinical potential.