Hybrid tetramers reveal elements of cooperativity in Escherichia coli D-3-phosphoglycerate dehydrogenase

d-3-Phosphoglycerate dehydrogenase from Escherichia coli is a tetramer of identical subunits that is inhibited when l-serine binds at allosteric sites between subunits. Co-expression of two genes, the native gene containing a charge difference mutation and a gene containing a mutation that eliminates serine binding, produces hybrid tetramers that can be separated by ion exchange chromatography. Activity in the hybrid tetramer with only a single intact serine binding site is inhibited by approximately 58% with a Hill coefficient of 1. Thus, interaction at a single regulatory domain interface does not, in itself, lead to the positive cooperativity of inhibition manifest in the native enzyme. Tetramers with only two intact serine binding sites purify as a mixture that displays a maximum inhibition level that is less than that of native enzyme, suggesting the presence of a population of tetramers that are unable to be fully inhibited. Differential analysis of this mixture supports the conclusion that it contains two forms of the tetramer. One form contains two intact serine binding sites at the same interface and is not fully inhibitable. The second form is a fully inhibitable population that has one serine binding site at each interface. Overall, the hybrid tetramers show that the positive cooperativity observed for serine binding is mediated across the nucleotide binding domain interface, and the negative cooperativity is mediated across the regulatory domain interface. That is, they reveal a pattern in which the binding of serine at one interface leads to negative cooperativity of binding of a subsequent serine at the same interface and positive cooperativity of binding of a subsequent serine to the opposite interface. This trend is propagated to subsequent binding sites in the tetramer such that the negative cooperativity that is originally manifest at one interface is decreased by subsequent binding of ligand at the opposite interface.     

Effects of different peptide fragments derived from proadrenomedullin on gene expression of adrenomedullin gene

Primary culture of vascular smooth muscle cells (VSMC) from rat aorta was used for the study of the effect of different peptides derived from proadrenomedullin on the expression of adrenomedullin (ADM) gene. ADM and preproADM(22-41) (PAMP) secreted by VSMC were measured by radioimmunoassay, and ADM mRNA in VSMC was determined by quantitative RT-PCR. After the incubation of VSMC in 10(-7)M ADM for 24h, PAMP in the medium and ADM mRNA in the VSMC were decreased by 34 and 41.3%, respectively, and cAMP concentration in the VSMC was increased by 385%. After the incubation of VSMC in 10(-7)M PAMP for 24h, ADM in the medium and ADM mRNA in the VSMC were decreased by 12.2 and 39.1%, respectively, and cAMP concentration in the VSMC was increased by 67%. The decreased ADM mRNA in VSMC induced by the ADM and PAMP treatment was completely reversed by the pre-treatment of the cells in 10(-7)M protein kinase inhibitor for 30 min. After the incubation of VSMC in 10(-7)M preproADM(153-185) (ADT) for 24h, however, ADM in the medium and ADM mRNA in the VSMC were increased by 21 and 35.2%. The increased ADM mRNA in VSMC induced by the ADT treatment was partially blocked by the co-incubation in ADM and ADT, and was totally blocked by the co-incubation in PAMP+ADM and ADT, but was not blocked by the co-incubation in PAMP and ADT. Our results suggest that the four peptides derived from proadrenomedullin may have different effects, possibly through a cAMP-dependent pathway, on the expression of ADM gene.     

Discovering genes responsible for silk synthesis in Bombyx mori by piggyBac‐based random insertional mutagenesis

Silkworm mutants are valuable resources for both transgenic breeding and gene discovery. PiggyBac-based random insertional mutagenesis has been widely used in gene functional studies. In order to discover genes involved in silk synthesis, a piggyBac-based random insertional library was constructed using Bombyx mori, and the mutants with abnormal cocoon were particularly screened. By this means, a “thin cocoon” mutant was identified. This mutant revealed thinner cocoon shell and shorter posterior silk gland (PSG) compared with the wild type. The messenger RNA (mRNA) levels of all the three fibroin genes, including Fib-H, Fib-L and P25, were significantly down-regulated in the PSG of mutants. Four piggyBac insertion sites were identified in Aquaporin (AQP), Longitudinals lacking protein-like {Lola), Glutamyl aminopeptidase-like (GluAP) and Loc101744460. The mRNA levels of all the four genes were significantly altered in the silk gland of mutants. In particular, the mRNA amount of AQP, a gene responsible for the regulation of osmotic pressure, decreased dramatically immediately prior to the spinning stage in the anterior silk gland of mutants. The identification of the genes disrupted in the “thin cocoon” mutant in this study provided useful information for understanding silk production and transgenic breeding of silkworms in the future.     

Chromosome‐level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies

Sarcophaga peregrina is considered to be of great ecological, medical and forensic significance, and has unusual biological characteristics such as an ovoviviparous reproductive pattern and adaptation to feed on carrion. The availability of a high‐quality genome will help to further reveal the mechanisms underlying these charcateristics. Here we present a de novo‐assembled genome at chromosome scale for S. peregrina. The final assembled genome was 560.31 Mb with contig N50 of 3.84 Mb. Hi‐C scaffolding reliably anchored six pseudochromosomes, accounting for 97.76% of the assembled genome. Moreover, 45.70% of repeat elements were identified in the genome. A total of 14,476 protein‐coding genes were functionally annotated, accounting for 92.14% of all predicted genes. Phylogenetic analysis indicated that S. peregrina and S. bullata diverged ~ 7.14 million years ago. Comparative genomic analysis revealed expanded and positively selected genes related to biological features that aid in clarifying its ovoviviparous reproduction and carrion‐feeding adaptations, such as lipid metabolism, olfactory receptor activity, antioxidant enzymes, proteolysis and serine‐type endopeptidase activity. Protein‐coding genes associated with ovoviparity, such as yolk proteins, transferrin and acid sphingomyelinase, were identified. This study provides a valuable genomic resource for S. peregrina, and sheds insight into further revealing the underlying molecular mechanisms of adaptive evolution.     

Incidence,Risk Factors,Treatment and Prognosis of Popliteal Artery Embolization in the Superficial Femoral Artery Interventions

Objective

Percutaneous transluminal angioplasty and stenting (PTA + stent) has gained acceptance as a primary treatment modality for the superficial femoral artery (SFA) diseases. Popliteal artery embolization (PAE) is a severe complication in SFA interventions. The purpose of this study was to evaluate the incidence, risk factors, treatment and prognosis of PAE in primary SFA PTA + stent.

Methods

Chronic SFA arteriosclerosis cases that underwent primary PTA + stent were reviewed from a retrospectively maintained database. Runoff vessels were evaluated in all cases before and after the interventions for PAE detection. The primary patency, secondary patency and limb salvage rates were calculated using Kaplan-Meier analysis and compared using log-rank analysis. Cox multivariate regression was performed to evaluate predictors of patency and limb salvage rates.

Results

There were 436 lesions treated in 388 patients with 10 PAE events (2.3%) in total. PAE rate was significantly higher in Transatlantic Inter-Society Consensus (TASC) C/D group compared with TASC A/B group (OR = 8.91, P = .002), in chronic total occlusion (CTO) lesions compared with stenotic lesions (P<.0001), and in group with history of cerebral ischemic stroke (OR = 6.11, P = .007). PAE rates were not significantly affected by age, sex, smoking, hypertension, diabetes, hyperlipidemia and runoff status. The binary logistic regression showed that only the TASC C/D was an independent predictor of PAE (P = .031). The 12-month and 24-month primary patency, secondary patency and limb salvage rates in PAE group showed no significant differences comparing with non-PAE group.

Conclusions

PAE is a rare event in primary SFA PTA + stent. TASC C/D lesion, CTO and cerebral ischemic stroke history are risk factors for PAE. PAE is typically reversible by comprehensive techniques. If the popliteal flow is restored in time, PAE has no significant effect on long-term patency and limb salvage rates.     

Automation of Molecular-Based Analyses: A Primer on Massively Parallel Sequencing

Recent advances in genetics have been enabled by new genetic sequencing techniques called massively parallel sequencing (MPS) or next-generation sequencing. Through the ability to sequence in parallel hundreds of thousands to millions of DNA fragments, the cost and time required for sequencing has dramatically decreased. There are a number of different MPS platforms currently available and being used in Australia. Although they differ in the underlying technology involved, their overall processes are very similar: DNA fragmentation, adaptor ligation, immobilisation, amplification, sequencing reaction and data analysis. MPS is being used in research, translational and increasingly now also in clinical settings. Common applications include sequencing of whole genomes, whole exomes or targeted genes for disease-causing gene discovery, genetic diagnosis and targeted cancer therapy. Even though the revolution that is occurring with MPS is exciting due to its increasing use, improving and emerging technologies and new applications, significant challenges still exist. Particularly challenging issues are the bioinformatics required for data analysis, interpretation of results and the ethical dilemma of ‘incidental findings’.     

大渡河上游不同林龄云杉人工林与原始林下地表苔藓层片结构与物种组成

为评估在人工林早期发育过程中地表苔藓层片物种组成和结构的演变趋势, 选择四川省金川县507林场4–30年林龄的5块云杉(Picea asperata)人工林和1块300年岷江冷杉(Abies faxoniana)原始林, 开展了地表苔藓植物调查。采用方差分析法(ANOVA)对苔藓植物特征参数进行差异性检验, 采用Sørensen群落相似性系数比较了苔藓群落β多样性差异。结果表明: (1)云杉人工林较原始林地表苔藓物种丰富度高。年轻的人工林(<16年)较中龄林(21–30年)地表有更多的苔藓种类; (2)原始林较人工林有更高的地表苔藓植物盖度、密度、平均高度和厚度, 而不同林龄的人工林之间在苔藓植物层片盖度和密度上并没有表现出统计学意义上的差异(P>0.05), 但地表苔藓优势种及次优势种组成具有较明显的差异; (3)人工林与原始林地表苔藓共有种具有明显的喜光耐旱特性, 4年生未成林地段与原始林共有种数最多, 为19种; (4)原始林下地表24种苔藓植物中, 除Rhytidium rugosum外, 23种在云杉人工林早期发育过程中存在。在人工林发育过程中地表苔藓物种替代明显, 替代率随林龄呈增加趋势(0.24–0.60), 有明显的物种替代现象发生。综合分析表明: (1) 本文所研究的4–30年的云杉人工林发育过程中地表苔藓结构与多样性并没有表现出预期的恢复趋势, 大多数土著苔藓种群还未能有效恢复; (2)要恢复重建林地后演替阶段的苔藓种群结构和多样性, 不仅需要在采伐和造林过程中减少对土壤的扰动以保护地表微生境, 还应在云杉人工林处于16–20年林龄, 地表苔藓植物丰富度发生显著衰退时进行合理疏伐。     

Recognition of the core RNA promoter for minus-strand RNA synthesis by the replicases of Brome mosaic virus and Cucumber mosaic virus

Replication of viral RNA genomes requires the specific interaction between the replicase and the RNA template. Members of the Bromovirus and Cucumovirus genera have a tRNA-like structure at the 3' end of their genomic RNAs that interacts with the replicase and is required for minus-strand synthesis. In Brome mosaic virus (BMV), a stem-loop structure named C (SLC) is present within the tRNA-like region and is required for replicase binding and initiation of RNA synthesis in vitro. We have prepared an enriched replicase fraction from tobacco plants infected with the Fny isolate of Cucumber mosaic virus (Fny-CMV) that will direct synthesis from exogenously added templates. Using this replicase, we demonstrate that the SLC-like structure in Fny-CMV plays a role similar to that of BMV SLC in interacting with the CMV replicase. While the majority of CMV isolates have SLC-like elements similar to that of Fny-CMV, a second group displays sequence or structural features that are distinct but nonetheless recognized by Fny-CMV replicase for RNA synthesis. Both motifs have a 5'CA3' dinucleotide that is invariant in the CMV isolates examined, and mutational analysis indicates that these are critical for interaction with the replicase. In the context of the entire tRNA-like element, both CMV SLC-like motifs are recognized by the BMV replicase. However, neither motif can direct synthesis by the BMV replicase in the absence of other tRNA-like elements, indicating that other features of the CMV tRNA can induce promoter recognition by a heterologous replicase.     

反义CD151基因转染对大鼠血管平滑肌细胞迁移的影响

目的观察pcDNA3.1真核表达载体介导的反义CD151基因转染对培养的大鼠动脉平滑肌细胞(VSMCs)迁移的影响。方法构建携带全长正义和反义CD151的真核表达载体pcDNA3.1-CD151和pcDNA3.1-anti-CD151重组质粒,转染体外培养的VSMCs,以RT-PCR和Western blot方法检测CD151的表达,用Boyden趋化小室方法观察细胞迁移。结果与载体对照组、脂质体对照组和空白对照组3组均值比较,转染48h后,反义CD151组mRNA表达降低58%,蛋白表达降低51%,正义CD151组的VSMCs CD151mRNA表达增加171%,蛋白表达增加133%;趋化迁移的细胞数,反义CD151组为37.9±6.3,正义CD151组为86.5±12.4;载体对照组、脂质体对照组和空白对照组分别为60.3±7.1、61.8±7.6和67.3±9.6。反义CD151组显著低于其余各组(P<0.01),正义CD151组显著高于其余各组(P<0.01)。结论pcDNA3.1真核表达载体介导的反义CD151转染,通过抑制CD151的表达,能够显著抑制大鼠VSMCs的迁移。